sixpack-0.68/0002755000175000017500000000000011577445410012117 5ustar segresegresixpack-0.68/setup.py0000666000175000017500000000032607617324506013636 0ustar segresegre# setup.py from distutils.core import setup import py2exe import spglobalfuncs setup(name="SixPACK", scripts=["sixpack.py"], version=spglobalfuncs.version, author="Sam Webb", ) sixpack-0.68/spglobalfuncs.py0000644000175000017500000000646410764341336015342 0ustar segresegre#common funcs to all mods from spdirvars import * from Tkinter import * import tkFileDialog import tkMessageBox import Pmw import os from math import * from string import * version='0.64' #file dialog def ask_for_file(defaults,dir,check=1): f = '' verbot=['(',')','-','#','&','$','@','!','{','}','+','='] if dir=='': f = tkFileDialog.askopenfilename(filetypes=defaults) else: f = tkFileDialog.askopenfilename(filetypes=defaults,initialdir=dir) bad=0 for char in f: if char in verbot: bad=1 if bad and check: tkMessageBox.showwarning("Open File"," WARNING!\n Filename contains characters not\n compatible with IFEFFIT ") return f def ask_save_file(fn,dir): f='' if dir=='': f = tkFileDialog.asksaveasfilename(initialfile=fn) else: f = tkFileDialog.asksaveasfilename(initialfile=fn,initialdir=dir) return f def trimdir(f): firstind=rfind(f,os.sep)+1 cf=f[firstind:] #cf=replace(cf,'.','_') return cf def trimdirext(f): firstind=rfind(f,os.sep)+1 lastind=rfind(f,'.') cf=f[firstind:lastind] return cf #entry replace def entry_replace(ent, val): ent.delete(0,len(ent.get())) ent.insert(0,val) def entry_replace_d(ent, val,dig): ent.delete(0,len(ent.get())) val=str(val) decind=rfind(val,'.') eind=rfind(val,"e") if eind==-1: val=val[:decind+dig] else: val=val[:4]+val[eind:len(val)] ent.insert(0,val) def valueclip_d(val,dig): val=str(val) decind=rfind(val,'.') eind=rfind(val,"e") if eind==-1: val=val[:decind+dig] else: val=val[:4]+val[eind:len(val)] return val #Load filename into an entry def fileget(master,ent,check=1): global lastreaddir verbot=['(',')','-','#','&','$','@','!','{','}','+','='] fn=ask_for_file([("data files","*.dat *.chi"),("edg files","*.nor *.xmu *.mu"),("all files","*")],lastreaddir) if fn!='': sdir=rfind(fn,os.sep) lastreaddir=fn[:sdir] bad=0 for char in fn: if char in verbot: bad=1 if bad and check: tkMessageBox.showwarning("Open File"," WARNING!\n Filename contains characters not\n compatible with IFEFFIT ") entry_replace(ent,fn) master.focus_set() #functions for updating status bars def setstatus(n,format): n.config(text=format) n.update_idletasks() def setstatus_d(n,val,dig): val=str(val) decind=rfind(val,'.') eind=rfind(val,"e") if eind==-1: val=val[:decind+dig] else: val=val[:4]+val[eind:len(val)] n.config(text=val) n.update_idletasks() def clearstatus(n): n.config(text=" ") n.update_idletasks() def programabout(root): Pmw.aboutversion(version) Pmw.aboutcopyright('Copyright Samuel Webb, 2006\nStanford Synchrotron Radiation Laboratory') Pmw.aboutcontact("""SixPACK is Sam's Interface for XAS Package Unifying SamView with SamXAS email: swebb@ssrl.slac.stanford.edu web: http://www.stanford.edu/~swebb Reference: Webb S.M. (2005) "Sixpack: A graphical user interface for XAS analysis using IFEFFIT." Physica Scripta, T115, 1011-1014. """) about=Pmw.AboutDialog(root,applicationname='SixPACK') sixpack-0.68/xasinput.py0000644000175000017500000017200610665326132014344 0ustar segresegre#Module for XAS input # #Main Routine returns a data structure with: # # self.type = file type: # SB = SSRL binary # SA = SSRL ASCII # DQ = DND Quick-Scan # DA = DND ASCII # DM = DND Multi-element # GC = Generic # self.rtc = clock normalizing counts # self.eV # self.i0 # self.i1 # self.i2 -- if not present, array of ones # self.iF -- will be array if multielement is used # self.ICR -- data for Ge13's, else array of ones from Numeric import * from string import * from struct import * import Pmw from Tkinter import * import tkSimpleDialog import tkMessageBox import os import xdrlib import binascii ################################### ## ## SSRL Binary ## ################################### class ssrlbin: global reloadps def __init__(self,fn,master,ieee=0): global reloadps #make dictionary for columns fid=open(fn,"rb") self.type='SB' title=fid.read(40) date=fid.read(40) if date[0] not in printable: self.rtc=array([1.0,1.0,1.0,1.0]) self.eV=array([1.0,2.0,3.0,4.0]) self.i0=array([1.0,1.0,1.0,1.0]) self.i1=array([1.0,1.0,1.0,1.0]) self.i2=array([1.0,1.0,1.0,1.0]) self.ICR=array([1.0,1.0,1.0,1.0]) self.iF=array([1.0,1.0,1.0,1.0]) self.comment='DID NOT READ - CORRUPT FILE' tkMessageBox.showwarning("Open File"," WARNING!\n SSRL binary file is corrupt!") return buf=fid.read(40) parse=split(buf) npts=int(parse[1]) ncols=int(parse[3]) scaler=fid.read(40) scaler=upper(scaler) region=fid.read(40) environ=fid.read(80) lsinfo=fid.read(40) self.comment=fid.read(80*6) offs=fromstring(fid.read(4*ncols),Float32) wts=fromstring(fid.read(4*ncols),Float32) lbs=[] i=0 while i0 and count(lower(typ),'lifetime')==0) or count(lower(typ),'clock')>0 or lower(typ[0:3])=='rtc': detind.update({'rtc':lbs.index(typ)}) if count(lower(typ),'requested energy')>0 or count(lower(typ),'requested position')>0: detind.update({'ev':lbs.index(typ)}) if lower(typ[0:3])=='i0 ': detind.update({'i0':lbs.index(typ)}) if count(lower(typ),'i1')>0: detind.update({'i1':lbs.index(typ)}) if count(lower(typ),'i2')>0: detind.update({'i2':lbs.index(typ)}) if count(lower(typ),'lytle')>0 or upper(typ)==ljust('FF',18): detind.update({'ifst':lbs.index(typ)}) detind.update({'ife':lbs.index(typ)}) ffl=lbs.index(typ) if (upper(typ[0:3])=='FF1' or count(upper(typ),'SCA')>0) and ffst==0: detind.update({'ifst':lbs.index(typ)}) ffst=1 if (upper(typ[0:2])=='FF' or count(upper(typ),'SCA')>0) and ffst==1: detind.update({'ife':lbs.index(typ)+1}) if upper(typ[0:4])=='ICR1' and ffst==1 or upper(typ[0:5])=='ICR:1' and ffst==1: detind.update({'icrst':lbs.index(typ)}) ffst=2 if upper(typ[0:3])=='ICR' and ffst==2: detind.update({'icre':lbs.index(typ)+1}) if count(upper(typ),'SCA2')>0: if ffscax[0][0]==0:ffscax[0][0]=lbs.index(typ) ffscax[0][1]=lbs.index(typ)+1 if count(upper(typ),'SCA3')>0: if ffscax[1][0]==0:ffscax[1][0]=lbs.index(typ) ffscax[1][1]=lbs.index(typ)+1 fid.seek(0,1) np=fromstring(fid.read(4*4),Int) i=0 d=zeros((npts,ncols),Float32) while i0 and count(lower(typ),'lifetime')==0) or count(lower(typ),'clock')>0 or lower(typ[0:3])=='rtc': detind.update({'rtc':lbs.index(typ)}) if count(lower(typ),'requested energy')>0 or count(lower(typ),'requested position')>0: detind.update({'ev':lbs.index(typ)}) if lower(typ[0:3])=='i0 ': detind.update({'i0':lbs.index(typ)}) if count(lower(typ),'i1')>0: detind.update({'i1':lbs.index(typ)}) if count(lower(typ),'i2')>0: detind.update({'i2':lbs.index(typ)}) if count(lower(typ),'lytle')>0 or upper(typ)==ljust('FF',18): detind.update({'ifst':lbs.index(typ)}) detind.update({'ife':lbs.index(typ)}) ffl=lbs.index(typ) if (upper(typ[0:3])=='FF1' or count(upper(typ),'SCA')>0) and ffst==0: detind.update({'ifst':lbs.index(typ)}) ffst=1 if (upper(typ[0:2])=='FF' or count(upper(typ),'SCA')>0) and ffst==1: detind.update({'ife':lbs.index(typ)+1}) if upper(typ[0:4])=='ICR1' and ffst==1 or upper(typ[0:5])=='ICR:1' and ffst==1: detind.update({'icrst':lbs.index(typ)}) ffst=2 if upper(typ[0:3])=='ICR' and ffst==2: detind.update({'icre':lbs.index(typ)+1}) if count(upper(typ),'SCA2')>0: if ffscax[0][0]==0:ffscax[0][0]=lbs.index(typ) ffscax[0][1]=lbs.index(typ)+1 if count(upper(typ),'SCA3')>0: if ffscax[1][0]==0:ffscax[1][0]=lbs.index(typ) ffscax[1][1]=lbs.index(typ)+1 buf=fid.readline() d=zeros((npts,ncols),Float32) j=range(npts) k=range(ncols) for i in j: buf=fid.readline() parse=split(buf) for m in k: ind=m+ncols*i put(d,ind,atof(parse[m])) fid.close() #assign arrays #first the ones that should always be in all files self.eV=d[:,detind['ev']] self.rtc=d[:,detind['rtc']] self.i0=d[:,detind['i0']] #now the optional ones -- fill with ones if not present try: self.i1=d[:,detind['i1']] except: self.i1=ones((len(self.i0)),Float32) try: self.i2=d[:,detind['i2']] except: self.i2=ones((len(self.i0)),Float32) #and then iF and ICR if detind.has_key('ifst'): try: if (reloadps[1]=='Lytle' or reloadps[1]==None) and reloadps[0]==self.type: detind.update({'ifst':ffl}) detind.update({'ife':ffl}) elif reloadps[1]=='Ge' and reloadps[0]==self.type: if reloadps[2]=='SCA2' and ffscax[0][0]!=0: detind.update({'ifst':ffscax[0][0]}) detind.update({'ife':ffscax[0][1]}) if reloadps[2]=='SCA3' and ffscax[1][0]!=0: detind.update({'ifst':ffscax[1][0]}) detind.update({'ife':ffscax[1][1]}) else: raise ValueError, "" except: reloadps=[] rsel='Ge' select='' if ffl!=0 and ffst!=0: #file has BOTH Lytle and Ge channels #ask which... roidialog=Pmw.Dialog(parent=master,title="Detector Selection",buttons=('OK','Apply All')) roiselbox=Pmw.RadioSelect(parent=roidialog.interior(),labelpos='n',label_text="Please select the fluo. channel to load") rbuts=('Lytle','Ge') for rb in rbuts: roiselbox.add(rb) roiselbox.pack(side=TOP,fill='both',expand=1,padx=5,pady=5) select=roidialog.activate() rsel=roiselbox.getvalue() if rsel=='Lytle' or rsel==None: detind.update({'ifst':ffl}) detind.update({'ife':ffl}) #SCA selection for Ge if rsel=='Ge' and ffscax[0][0]!=0: scadialog=Pmw.Dialog(parent=master,title="SCA Selection",buttons=('OK',)) scaselbox=Pmw.RadioSelect(parent=scadialog.interior(),labelpos='n',label_text="Please select SCA channel to load") sbuts=('SCA1','SCA2') if ffscax[1][0]!=0:sbuts=('SCA1','SCA2','SCA3') for sb in sbuts: scaselbox.add(sb) scaselbox.pack(side=TOP,fill='both',expand=1,padx=5,pady=5) scaselect=scadialog.activate() ssel=scaselbox.getvalue() if ssel=='SCA2': detind.update({'ifst':ffscax[0][0]}) detind.update({'ife':ffscax[0][1]}) if ssel=='SCA3': detind.update({'ifst':ffscax[1][0]}) detind.update({'ife':ffscax[1][1]}) if select=='Apply All': try: reloadps=[self.type,rsel,ssel] except: reloadps=[self.type,rsel,'SCA1'] if detind['ifst']==detind['ife']: #lytle/single channel self.iF=d[:,detind['ifst']] self.ICR=d[:,detind['ifst']] else: #multi-element self.iF=d[:,detind['ifst']:detind['ife']] if detind.has_key('icrst'): self.ICR=d[:,detind['icrst']:detind['icre']] else: self.ICR=self.iF else: self.iF=ones((len(self.i0)),Float32) self.ICR=ones((len(self.i0)),Float32) #check SHAPEs... if self.iF.shape!=self.ICR.shape: #presume 1 ICR and multiple FFs temp=ones(self.iF.shape,Float) for i in range(self.iF.shape[1]): temp[:,i]=self.ICR[:,0] self.ICR=temp ################################### ## ## DND-CAT Quick Scan Binary ## ################################### class dndquick: def __init__(self,fn,e,edg): fid=open(fn,"rb") self.type='DQ' size=fromstring(fid.read(4),Int)[0] memsize=size*2 headersize=1024*2 memsize=memsize-headersize size=size-1024 buf=fid.read(headersize) rawi0=fromstring(fid.read(memsize),Int16) buf=fid.read(headersize) rawiF=fromstring(fid.read(memsize),Int16) buf=fid.read(headersize) rawiT=fromstring(fid.read(memsize),Int16) #retype data rawi0=rawi0.astype(Float32) rawiT=rawiT.astype(Float32) rawiF=rawiF.astype(Float32) dspc=3.1353 chan=((0,size)) delE=0.5 delk=0.05 startk=2 #calcualte theta slope theta=array((arcsin(12398/(2*dspc*e[0])),arcsin(12398/(2*dspc*e[1]))),Float32) slope=(theta[0]-theta[1])/(chan[0]-chan[1]) b=theta[0]-slope*chan[0] #calculate starting parameters firstindex=0 firstenergy=12398/(2*dspc*sin(b)) lastenergy=firstenergy+delE lastangle=arcsin(12398/(2*dspc*lastenergy)) lastindex=int((lastangle-b)/slope) finalindex=len(rawi0) #calculate parameters from k range kst=startk-delk/2 kregstart=(kst/0.51233)**2+edg curk=startk-delk #initialize data arrays self.rtc=[] self.eV=[] self.i0=[] self.i1=[] self.iF=[] #main binning loop while lastindex3: type=lp[3] type2=lp[3][0:4] last=lp[len(lp)-1] if len(last)>2: reg=last[len(last)-2:len(last)] if reg[0]=='R' and len(reg)==2 and reg not in reglist: #rlab=lp[4]+' '+lp[5] rlab=line[rfind(line,'{'):rfind(line,'}')] rlab=rstrip(replace(rlab,'}',' ')) rlab=rstrip(replace(rlab,'{',' ')) roibuts.append(reg+':'+rlab) reglist.append(reg) if lower(type2)=='{lyt' or lower(type2)=='{mu}' or lower(type2)=='{if}': roibuts.append('Lytle') reglist.append('Lytle') if line[0:3]==';==': #line denotes data descripton section headerstate=1 if line[0:3]==';--': #line denotes data section headerstate=2 #decide which ROI if needed if roibuts!=[]: if len(roibuts)>1: try: #print reloadps[1],roibuts if reloadps[0]==self.type and reloadps[1] in roibuts: rsel=reloadps[1] reg1=rsel[0:2] else: raise ValueError, "" except: reloadps=[] roidialog=Pmw.Dialog(parent=master,title="ROI Selection",buttons=('OK','Apply All')) roiselbox=Pmw.RadioSelect(parent=roidialog.interior(),labelpos='n',label_text="Please select an ROI to load") rbuts=roibuts for rb in rbuts: roiselbox.add(rb) roiselbox.pack(side=TOP,fill='both',expand=1,padx=5,pady=5) select=roidialog.activate() rsel=roiselbox.getvalue() reg1=rsel[0:2] if select=='Apply All': reloadps=[self.type,rsel] else: rsel=roibuts[0] reg1=rsel[0:2] reloadps=[] else: reg1='Ly' reloadps=[] for line in lines: if line !='': if readstate==1: #in data description zone lp=split(line) if len(lp)>3: type=lp[3] type2=lp[3][0:4] last=lp[len(lp)-1] if len(last)>2: reg=last[len(last)-2:len(last)] if type=='{Energy}': chandef[0].append(lp[1]) if type=='{Scaler': chandef[1].append(lp[1]) if lower(type)=='{i0}': chandef[2].append(lp[1]) if lower(type)=='{i1}': chandef[3].append(lp[1]) if lower(type)=='{i2}': chandef[4].append(lp[1]) if lower(type2)=='{lyt' or type2=='{mu}' or lower(type2)=='{if}': chandef[7].append(lp[1]) if (lower(type2)=='{mca' and reg==reg1): chandef[5].append(lp[1]) elif (len(lp)>6 and rfind(lp[6],'mca') and reg==reg1): chandef[5].append(lp[1]) if readstate==3: #read data lines parsed=split(line) if colind[1]!=[]: self.rtc.append(atof(parsed[colind[1][0]])) else: self.rtc.append(1.0) if colind[0]!=[]: self.eV.append(atof(parsed[colind[0][0]])) else: self.eV.append(1.0) if colind[2]!=[]: self.i0.append(atof(parsed[colind[2][0]])) else: self.i0.append(1.0) if colind[3]!=[]: self.i1.append(atof(parsed[colind[3][0]])) else: self.i1.append(1.0) if colind[4]!=[]: self.i2.append(atof(parsed[colind[4][0]])) else: self.i2.append(1.0) if colind[7]!=[]: tempIFF.append(atof(parsed[colind[7][0]])) else: tempIFF.append(1.0) if colind[5]!=[]: spare=[] for sc in colind[5]: spare.append(atof(parsed[int(sc)])) tempiF1.append(spare) else: tempiF1.append(1.0) if readstate==2: #read data order line readstate=3 lp=split(line) lp.remove(';') colind=[] for cat in chandef: temp=cat for tac in cat: ind=0 for des in lp: if tac==des: dex=cat.index(tac) temp[dex]=ind ind=ind+1 colind.append(temp) #change state lines at the end of line parser if line[0:3]==';==': #line denotes data descripton section readstate=1 if line[0:3]==';--': #line denotes data section readstate=2 #decide which ROI if reg1=='Ly': self.iF=tempIFF else: self.iF=tempiF1 #mess with iF and ICR self.ICR=self.iF #no ICRs... #convert all to arrays self.iF=array(self.iF) self.ICR=array(self.ICR) self.rtc=array(self.rtc) self.eV=array(self.eV) self.i0=array(self.i0) self.i1=array(self.i1) self.i2=array(self.i2) ################################### ## ## ALS Line 10.3.2 Single Element Method ## ################################### class als10_3_2ascii: def __init__(self,fn): fid=open(fn,"r") self.type='ALS' lines=fid.read().split('\n') fid.close() #init data arrays self.rtc=[] self.eV=[] self.i0=[] self.i1=[] self.i2=[] self.iF=[] self.ICR=[] #read lines for line in lines: if line !='': parsed=split(line) if parsed[0][0] in digits: #then we have a data line self.rtc.append(atof(parsed[1])) self.eV.append(atof(parsed[0])) self.i0.append(atof(parsed[2])) self.i1.append(atof(parsed[3])) self.i2.append(1.0) self.iF.append(atof(parsed[4])) self.ICR.append(atof(parsed[5])) #convert all to arrays self.iF=array(self.iF) self.ICR=array(self.ICR) self.rtc=array(self.rtc) self.eV=array(self.eV) self.i0=array(self.i0) self.i1=array(self.i1) self.i2=array(self.i2) ################################### ## ## NSLS Single Fluorescence Channel Method ## ################################### class nslsascii: def __init__(self,fn): fid=open(fn,"r") self.type='NSLS' lines=fid.read().split('\n') fid.close() #init data arrays self.rtc=[] self.eV=[] self.i0=[] self.i1=[] self.i2=[] self.iF=[] self.ICR=[] #read lines readstate=0 for line in lines: if line !='': parsed=split(line) if readstate==1 and parsed[0][0] in digits: #then we have a data line self.rtc.append(1.0) self.eV.append(atof(parsed[0])) self.i0.append(atof(parsed[1])) self.i1.append(atof(parsed[2])) self.i2.append(atof(parsed[3])) self.iF.append(atof(parsed[4])) self.ICR.append(atof(parsed[4])) if parsed[0][0]=='-': readstate=1 #convert all to arrays self.iF=array(self.iF) self.ICR=array(self.ICR) self.rtc=array(self.rtc) self.eV=array(self.eV) self.i0=array(self.i0) self.i1=array(self.i1) self.i2=array(self.i2) ################################### ## ## NSLS "Recent" X-11A Formats ## ################################### class nslsnewascii: def __init__(self,fn): fid=open(fn,"r") self.type='NSLSv2' lines=fid.read().split('\n') fid.close() #init data arrays self.rtc=[] self.eV=[] self.i0=[] self.i1=[] self.i2=[] self.iF=[] self.ICR=[] #read lines readstate=0 for line in lines: if line !='': parsed=split(line) if readstate==1: #header line... #parse header info if 'Ge1' in parsed: #multielement chandef=[[],[],[],[],[],[],[],[]] i=0 for col in parsed: if col in ['Energy','ev','eV']: chandef[0].append(i) if col in ['Timer','Time','Clock']: chandef[1].append(i) if lower(col)=='i0': chandef[2].append(i) if lower(col)=='i1': chandef[3].append(i) if lower(col)=='i2': chandef[4].append(i) if lower(col)[0:2]=='ge':chandef[5].append(i) if len(col)>2 and lower(col)[0:3]=='icr':chandef[6].append(i) i+=1 readstate=3 else: readstate=2 if readstate==2 and parsed[0][0] in digits: #then we have a data line self.rtc.append(1.0) self.eV.append(atof(parsed[0])) self.i0.append(atof(parsed[1])) self.i1.append(atof(parsed[3])) self.i2.append(atof(parsed[4])) self.iF.append(atof(parsed[2])) self.ICR.append(atof(parsed[2])) if readstate==3 and parsed[0][0] in digits: #then we have a data line for Ge multielements if chandef[1]!=[]: self.rtc.append(atof(parsed[chandef[1][0]])) else: self.rtc.append(1.0) if chandef[0]!=[]: self.eV.append(atof(parsed[chandef[0][0]])) else: self.eV.append(1.0) if chandef[2]!=[]: self.i0.append(atof(parsed[chandef[2][0]])) else: self.i0.append(1.0) if chandef[3]!=[]: self.i1.append(atof(parsed[chandef[3][0]])) else: self.i1.append(1.0) if chandef[4]!=[]: self.i2.append(atof(parsed[chandef[4][0]])) else: self.i2.append(1.0) if chandef[5]!=[]: spare=[] for sc in chandef[5]: spare.append(atof(parsed[sc])) self.iF.append(spare) else: self.iF.append(1.0) if chandef[6]!=[]: spare=[] for sc in chandef[6]: spare.append(atof(parsed[sc])) self.ICR.append(spare) else: self.ICR.append(1.0) if parsed[0][0]=='-': readstate=1 #convert all to arrays self.iF=array(self.iF) self.ICR=array(self.ICR) self.rtc=array(self.rtc) self.eV=array(self.eV) self.i0=array(self.i0) self.i1=array(self.i1) self.i2=array(self.i2) ################################### ## ## SRC Soft X-ray Data Method ## ################################### class srcascii: def __init__(self,fn): fid=open(fn,"r") self.type='WiscSRC' lines=fid.read().split('\n') fid.close() #init data arrays self.rtc=[] self.eV=[] self.i0=[] self.i1=[] self.i2=[] self.iF=[] self.ICR=[] chandef=[[],[],[],[],[],[],[]] #read lines readstate=0 for line in lines: if line !='': parsed=split(line) if readstate==1 and parsed[0][0] in digits: #then we have a data line if chandef[1]!=[]: self.rtc.append(atof(parsed[chandef[1][0]])) else: self.rtc.append(1.0) if chandef[0]!=[]: self.eV.append(atof(parsed[chandef[0][0]])) else: self.eV.append(1.0) if chandef[2]!=[]: self.i0.append(atof(parsed[chandef[2][0]])) else: self.i0.append(1.0) if chandef[3]!=[]: self.i1.append(atof(parsed[chandef[3][0]])) else: self.i1.append(1.0) if chandef[4]!=[]: self.i2.append(atof(parsed[chandef[4][0]])) else: self.i2.append(1.0) if chandef[5]!=[]: temp1=[] temp2=[] i=0 for col in chandef[5]: temp1.append(atof(parsed[chandef[5][i]])) temp2.append(1.0) i=i+1 self.iF.append(temp1) self.ICR.append(temp2) else: self.iF.append(1.0) self.ICR.append(1.0) if parsed[0]=='Energy(eV)': #header line. Read to determine colums readstate=1 for title in parsed: if title=='Energy(eV)': chandef[0].append(parsed.index(title)) if title=='Time(s)': chandef[1].append(parsed.index(title)) if title=='I0': chandef[2].append(parsed.index(title)) if title=='I1': chandef[3].append(parsed.index(title)) if title=='I2': chandef[4].append(parsed.index(title)) if title[0:2]=='No': chandef[5].append(parsed.index(title)) #convert all to arrays self.iF=array(self.iF) self.ICR=array(self.ICR) self.rtc=array(self.rtc) self.eV=array(self.eV) self.i0=array(self.i0) self.i1=array(self.i1) self.i2=array(self.i2) ################################### ## ## PNC 1-D Scan Data Method ## ################################### class pncascii: def __init__(self,fn): fid=open(fn,"r") self.type='PNC' lines=fid.read().split('\n') fid.close() #init data arrays self.rtc=[] self.eV=[] self.i0=[] self.i1=[] self.i2=[] self.iF=[] self.ICR=[] chandef=[[],[],[],[],[],[],[]] #read lines readstate=0 for line in lines: if line !='': parsed=split(line) if readstate==1 and parsed[0][0] in digits: #then we have a data line if chandef[1]!=[]: self.rtc.append(atof(parsed[chandef[1][0]])) else: self.rtc.append(1.0) if chandef[0]!=[]: self.eV.append(atof(parsed[chandef[0][0]])) else: self.eV.append(1.0) if chandef[2]!=[]: self.i0.append(atof(parsed[chandef[2][0]])) else: self.i0.append(1.0) if chandef[3]!=[]: self.i1.append(atof(parsed[chandef[3][0]])) else: self.i1.append(1.0) if chandef[4]!=[]: self.i2.append(atof(parsed[chandef[4][0]])) else: self.i2.append(1.0) if chandef[5]!=[]: temp1=[] temp2=[] i=0 for col in chandef[5]: temp1.append(atof(parsed[chandef[5][i]])) temp2.append(1.0) i=i+1 self.iF.append(temp1) self.ICR.append(temp2) else: self.iF.append(1.0) self.ICR.append(1.0) if parsed[0]=='#Mono': #header line. Read to determine colums if parsed[7]=='ID': offset=7 elif parsed[8]=='ID': offset=8 else: offset=5 readstate=1 ignore=0 for title in parsed: if title=="DT-Corr": offset=offset+1 ignore=1 if title=='#Mono': chandef[0].append(parsed.index(title)) if title=='time': chandef[1].append(1) if title=='I0' and not ignore: chandef[2].append(parsed.index(title)-offset) if title=='I1': chandef[3].append(parsed.index(title)-offset) if title=='IT': chandef[3].append(parsed.index(title)-offset) if title=='I2': chandef[4].append(parsed.index(title)-offset) if title=='IR': chandef[4].append(parsed.index(title)-offset) if title=='CalDiode': chandef[4].append(parsed.index(title)-offset) if lower(title[0:3])=='dxp': chandef[5].append(parsed.index(title)-offset) if title=='IF': chandef[5].append(parsed.index(title)-offset) #convert all to arrays self.iF=array(self.iF) self.ICR=array(self.ICR) self.rtc=array(self.rtc) self.eV=array(self.eV) self.i0=array(self.i0) self.i1=array(self.i1) self.i2=array(self.i2) ################################### ## ## NSLS BL X26A BSIF binary Loader ## ################################### class bsifx26a: global reloadps def __init__(self,fn,master): global reloadps fid=open(fn,"rb") self.type='BSIF' #clear all arrays self.rtc=[] self.eV=[] self.i0=[] self.i1=[] self.i2=[] self.iF=[] self.ICR=[] data=fid.read() new=xdrlib.Unpacker(data) norows=new.unpack_int() nocols=new.unpack_int() nodata=new.unpack_int() j=0 while j<3: new.unpack_int() j=j+1 (estart,eend)=(new.unpack_float(),new.unpack_float()) (rstart,rend)=(new.unpack_float(),new.unpack_float()) colheads=[] j=0 while j0: char=new.unpack_string() if length>1:colheads.append(char) j=j+1 datatype=new.unpack_int() ublen=new.unpack_int() #user buffer -- energy positions! #datatype=5 is longarray of 4 bytes per data point imagedatabytes=4*norows*nocols*nodata image=new.unpack_fopaque(imagedatabytes) #parse headers roibuts=[] for i in range(2,9): if colheads[i] not in roibuts: roibuts.append(colheads[i]) #choose ROI if len(roibuts)>1: try: #print reloadps[1],roibuts if reloadps[0]==self.type and reloadps[1] in roibuts: rsel=reloadps[1] reg1=rsel[0:2] else: raise ValueError, "" except: reloadps=[] roidialog=Pmw.Dialog(parent=master,title="ROI Selection",buttons=('OK','Apply All')) roiselbox=Pmw.RadioSelect(parent=roidialog.interior(),labelpos='n',label_text="Please select an ROI to load") rbuts=roibuts for rb in rbuts: roiselbox.add(rb) roiselbox.pack(side=TOP,fill='both',expand=1,padx=5,pady=5) select=roidialog.activate() rsel=roiselbox.getvalue() reg1=rsel[0:2] if select=='Apply All': reloadps=[self.type,rsel] else: rsel=roibuts[0] reg1=rsel[0:2] reloadps=[] fmt='>' #change byte order to big-endian for i in range(nocols): fmt=fmt+'l' tempiF=[] for i in range(nodata): buf=image[i*nocols*4:(i+1)*nocols*4] dt=unpack(fmt,buf) if upper(colheads[i+2])=='TIME': self.rtc=array(dt,typecode=Float32) if upper(colheads[i+2])=='ION CHAMBER': self.i0=array(dt,typecode=Float32) if upper(colheads[i+2])=='PIN DIODE': self.i1=array(dt,typecode=Float32) if upper(colheads[i+2])=='RING CURRENT': self.i2=array(dt,typecode=Float32) if colheads[i+2][0:2]==reg1: tempiF.append(dt) i=0 energy=[] while i2: x=1 else: i=i+1 dr=replace(d,',',' ') dpp=split(dr) colnum=len(dpp) self.collist=['None'] for i in range(1,colnum+1): self.collist.append(str(i)) #open window to display intial lines of file ma=self.ma=Toplevel(master) ma.focus_set() ma.title("Generic File Read") f1=Frame(ma) f1.pack(side=TOP,padx=5,pady=5) #file display fwin=Pmw.ScrolledText(f1,label_text=fn,borderframe=1,text_padx=10,text_pady=10,labelpos=NW,usehullsize=1, hull_width=400,hull_height=300,vscrollmode='static',hscrollmode='static',text_wrap=NONE) fwin.importfile(fn) fwin.pack(side=TOP) f2=Frame(ma) f2.pack(side=TOP,padx=5,pady=5) #allow offset of data self.offset=Pmw.Counter(f2,labelpos=W,label_text='Offset lines from start of file:', entryfield_value=numcoms,entryfield_validate='numeric',datatype='numeric', entryfield_entry_width=5) self.offset.pack(side=LEFT,padx=2,pady=2) f4=Frame(ma) f4.pack(side=TOP,padx=5,pady=5) #action buttons bbox=Pmw.ButtonBox(f4) bbox.pack(side=TOP,padx=10,pady=2) a=bbox.add('Read',width=10) a.bind("",self.pressedabutton) a.bind("",self.doneclick) a=bbox.add('Cancel',width=10) a.bind("",self.pressedabutton) a.bind("",self.doneclick) f33=Pmw.ScrolledFrame(ma,labelpos=N,label_text='Column Assignments',vscrollmode='static',usehullsize=1,hull_width=400,hull_height=400) f33.pack(side=TOP,pady=2,padx=2) f3=f33.interior() #column assignments #add choices to assign data columns to assigned formats -- each type gets a column choice collabels=Pmw.RadioSelect(f3,orient='vertical',padx=1,pady=1,label_text=' ',labelpos=N) self.radioRTC=Pmw.RadioSelect(f3,buttontype='radiobutton',orient='vertical',labelpos=N, label_text='RTC',padx=1,pady=1) self.radioeV=Pmw.RadioSelect(f3,buttontype='radiobutton',orient='vertical',labelpos=N, label_text='eV',padx=1,pady=1) self.radioi0=Pmw.RadioSelect(f3,buttontype='radiobutton',orient='vertical',labelpos=N, label_text='i0',padx=1,pady=1) self.radioi1=Pmw.RadioSelect(f3,buttontype='radiobutton',orient='vertical',labelpos=N, label_text='i1',padx=1,pady=1) self.radioi2=Pmw.RadioSelect(f3,buttontype='radiobutton',orient='vertical',labelpos=N, label_text='i2',padx=1,pady=1) self.radioiF=Pmw.RadioSelect(f3,buttontype='checkbutton',orient='vertical',labelpos=N, label_text='iF',padx=1,pady=1) self.radioICR=Pmw.RadioSelect(f3,buttontype='checkbutton',orient='vertical',labelpos=N, label_text='ICR',padx=1,pady=1) butlist=[self.radioRTC,self.radioeV,self.radioi0,self.radioi1,self.radioi2] butclist=[self.radioiF,self.radioICR] for choice in self.collist: if choice=='None': collabels.add(choice,text='None ',relief=FLAT,state=DISABLED,disabledforeground='black') else: collabels.add(choice,text='Column '+choice,relief=FLAT,state=DISABLED,disabledforeground='black') collabels.pack(side=LEFT,pady=2) for but in butlist: i=0 #0? for choice in self.collist: but.add(choice,text=' ',value=i) i=i+1 but.pack(side=LEFT,pady=2) try: but.invoke(genericps[butlist.index(but)]) except: but.invoke('None') for but in butclist: for choice in self.collist: but.add(choice,text=' ') but.pack(side=LEFT,pady=2) try: for opt in genericps[len(butlist)+butclist.index(but)]: but.invoke(opt) except: pass #remove None from self.collist... self.collist.remove('None') ma.wait_window(ma) #after window is killed... def pressedabutton(self,event): b=event.widget.cget('text') event.widget.config(state=ACTIVE) event.widget.config(relief=SUNKEN) if b=='Read': self.readgenericdata() def doneclick(self,event): event.widget.config(state=NORMAL) event.widget.config(relief=RAISED) self.ma.destroy() def readgenericdata(self): global genericps #read and format the data print "Reading in generic file format" tempiF=[] tempICR=[] i=0 for l in self.lines: if i0 and count(lower(buf2),'region')>0: return als10_3_2ascii(fn) elif count(upper(buf),'NSLS')>0: return nslsascii(fn) elif count(upper(buf),'XDAC V1')>0: return nslsnewascii(fn) elif count(upper(buf),'DCM')>0 and count(upper(buf),'ACQUSITION')>0: return srcascii(fn) elif count(upper(buf),'SCAN')>0 and count(upper(buf),'LABVIEW')>0: return pncascii(fn) else: #try generic routine #try: return generic(fn,master) #except: # return generic(fn,master) sixpack-0.68/lsqfitter.py0000666000175000017500000015707310442036130014506 0ustar segresegre# Least Squares Routine from spdirvars import * from spglobalfuncs import * import spplotter from Numeric import * from Tkinter import * from Ifeffit import * import Pmw import Tix import tkFileDialog import tkMessageBox import tkSimpleDialog import os import math import types from string import * #root=Tix.Tk() #root.title("Least Squares Fitting Mod") #Pmw.initialise(root) if os.name=='nt':os.sep='/' filepath=os.getcwd()+os.sep pm='+/-' iffc=Ifeffit(screen_echo=1) iffc.ifeffit("load mnexafsfit.iff") ############################################################### ## ## Main Least Square Fitter Program Class ## ############################################################### def remundsc(text): return replace(text,'_','') class DefCParams: def __init__(self,master,big,fname): f=Frame(master) f.pack(side=TOP,padx=2,pady=0,fill=Y) self.fname=fname self.big=big if fname=='init': lt='' self.active=0 else: lt=fname self.active=1 self.lab=Label(f,text=lt,relief=GROOVE,bd=2,width=30,justify=CENTER,font="Arial 10") self.lab.pack(side=TOP,fill=X,padx=2,pady=4) #component parameters are frac and eshift w=10 self.frac=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='Frac: ',value=0,validate='real',modifiedcommand=self.clicktochange) self.eshift=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='EShift: ',label_fg='dark grey',entry_bg='light grey',value=0,validate='real',entry_state=DISABLED) self.frac.pack(side=TOP,padx=2,pady=10) self.eshift.pack(side=TOP,padx=2,pady=10) Pmw.alignlabels((self.frac,self.eshift),sticky=E) def clicktochange(self, *arg): #link to big=filelist if self.fname!='init': self.big.item_configure(self.fname,2,text=str(self.frac.get())) class DefFParams: def __init__(self,master,fname,flist): f=Frame(master) f.pack(side=TOP,padx=2,pady=0) funceqns=('y=Ax+B','y=Ax2+Bx+C','Amp/Xoff/FWHM/Yoff','Amp/Xoff/FWHM/Yoff','Amp/Xoff/FWHM/Yoff/fLorz','y=A atan((x-B)/C)+D','y=A erfc((x-B)/C)+D','y=A erf((x-B)/C)+D','y=A exp((x-B)/C)+D','y=A ln((x-B)/C)+D') feqn={} for i in range(10): feqn.update({flist[i]:funceqns[i]}) numparam=[2,3,4,4,5,6,6,6,6,6] if fname=='init': lt='' etext='' self.active=0 self.np=0 else: lt=fname ftype=fname[:rfind(fname,' ')] etext=feqn[ftype] self.active=1 self.np=numparam[flist.index(ftype)] self.lab=Label(f,text=lt,relief=GROOVE,bd=2,width=30,justify=CENTER,font="Arial 10") self.lab.pack(side=TOP,fill=X,padx=2,pady=2) l=Label(f,text=etext,bd=2,justify=CENTER) l.pack(side=TOP,fill=X,padx=2,pady=2) #function parameters, dependent on function! w=10 #2params=linear (AB) #3params=quad (ABC) #4params=guass,lorenz,atan,erfc,erf,exp,log (ABCW) #5params=pvoight (ABCWF) self.entlab=('A: ','B: ','C: ','D: ') if self.np==4 or self.np==5: self.entlab=('Amp: ','x0: ','FWHM: ','Off: ','F-Ltz: ') if self.np==6: self.np=4 #init wids self.entlist=['','','','',''] self.butvar=['','','','',''] widlist=[] for i in range(self.np): fsub=Frame(f) fsub.pack(side=TOP,padx=2,pady=2) self.entlist[i]=Pmw.EntryField(fsub,labelpos='w',entry_width=w,label_text=self.entlab[i],value=0,validate='real') self.entlist[i].pack(side=LEFT,padx=2,pady=1) widlist.append(self.entlist[i]) self.butvar[i]=StringVar() but=Checkbutton(fsub,text='',variable=self.butvar[i],onvalue='guess',offvalue='set') but.select() but.pack(side=LEFT,padx=3,pady=1) Pmw.alignlabels(widlist,sticky=E) class EdgeFit: global lastreaddir,lastsavedir def __init__(self,master,root): #efwin=root.efwin=Toplevel(root) #efwin.title("Least Squares Fitting Dialog") #efwin.protocol("WM_DELETE_WINDOW", self.closemod) self.root=root self.efwin=efwin=master #change focus... efwin.focus_set() #GUI for fitting window... #create menu for fitting window menubar=Pmw.MenuBar(efwin) #file menu menubar.addmenu('File','') menubar.addmenuitem('File','command',label='Open Data',command=self.menuopen) menubar.addmenuitem('File','separator') menubar.addmenuitem('File','command',label='Edit Default Directories',command=self.callchangedefdirs) menubar.addmenuitem('File','separator') menubar.addmenuitem('File','command',label='Close',command=self.closemod) menubar.addmenuitem('File','command',label='Quit',command=root.quit) menubar.addmenu('Save','') menubar.addmenuitem('Save','command',label='Fit Data',command=self.savefitdata) menubar.addmenuitem('Save','command',label='Residuals',command=self.saveresdata) menubar.addmenu('Workspace','') menubar.addmenuitem('Workspace','command',label='Save Workspace',command=self.saveallvars) menubar.addmenuitem('Workspace','command',label='Load Workspace',command=self.loadallvars) menubar.addmenu('Interpolate','') self.nointerp=IntVar() menubar.addmenuitem('Interpolate','checkbutton',label='Turn Off Interpolation',variable=self.nointerp) self.XRDinterp=IntVar() menubar.addmenuitem('Interpolate','checkbutton',label='XRD Q-Spacing',variable=self.XRDinterp) menubar.addmenu('Self Abs','') menubar.addmenuitem('Self Abs','command',label='Do 10 Cycles',command=self.repeatselfabs) menubar.addmenu('Help','',side=RIGHT) menubar.addmenuitem('Help','command',label='About SixPack',command=self.callprogramabout) menubar.addmenuitem('Help','separator') #menubar.addmenuitem('Help','command',label='IFEFFIT Command Line',command=RunIFEFFITCmdLine) menubar.grid(row=0,columnspan=20,sticky=W+E) #create toolbar space toolbar=Frame(efwin, relief=SUNKEN,borderwidth=2) b=Button(toolbar,text="Fit",width=6,command=self.fitdatcomp,bg="red", fg="white") b.pack(side=LEFT,padx=2,pady=2) b=Button(toolbar,text="Construct",width=8,command=self.makefitdat,bg="red", fg="white") b.pack(side=LEFT,padx=2,pady=2) b=Button(toolbar,text="Plot",width=6,command=self.plotcomp,bg="darkblue", fg="white") b.pack(side=LEFT,padx=2,pady=2) #display toolbar.grid(row=1,columnspan=20,sticky=W+E) #first area for data file filebar=Frame(efwin, relief=SUNKEN,bd=2) self.fileentry=Pmw.EntryField(filebar, label_text="Data File:",labelpos=W,validate=None,entry_width=80) self.fileentry.pack(side=LEFT,padx=5,pady=2,fill=X) b=Button(filebar,bitmap="@"+filepath+"xbms"+os.sep+"openfolder.xbm",command=self.fileme,height=21,width=30,bg='lightyellow') b.pack(side=LEFT,padx=2,pady=2) b=Button(filebar,text="Load",bg='darkgreen',fg='snow',width=7,command=self.load_data_file) b.pack(side=LEFT,padx=2,pady=2) filebar.grid(row=2,columnspan=15,rowspan=1,sticky=W+E+N+S) #Add fitting components frame in notebook format compwin=Frame(efwin,relief=SUNKEN,bd=2) l=Label(compwin,text="Fitting Components",relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) #add notebook compnb=Pmw.NoteBook(compwin) if sys.platform == 'win32': compnb.configure(hull_background="SystemButtonFace") else: compnb.configure(hull_background="#d4d0c8") compnb.recolorborders() compnb.pack(fill="both",expand=1) #file components page comppage=compnb.add('Components') s1=Frame(comppage) wd=20 b=Button(s1,text="Add Comp",bg='steel blue',fg='snow',width=wd,command=self.addcomp) b.pack(side=TOP,padx=2,pady=2) b=Button(s1,text="Add Many Comps",bg='dark blue',fg='snow',width=wd,command=self.addmanycomp) b.pack(side=TOP,padx=2,pady=2) b=Button(s1,text="Reload Comps",bg='darkgreen',fg='snow',width=wd,command=self.reloadallcomp) b.pack(side=TOP,padx=2,pady=2) b=Button(s1,text="Remove Comp",bg='red',fg='snow',width=wd,command=self.removecomp) b.pack(side=TOP,padx=2,pady=2) b=Button(s1,text="Clear All",bg='brown',fg='snow',width=wd,command=self.clearcomplist) b.pack(side=TOP,padx=2,pady=2) s1.pack(side=LEFT,padx=2,pady=2) #tree for component list filwin=Frame(comppage) filwin.pack(side=LEFT,padx=2,pady=2) #add btree legend l=Label(filwin,text='Component Frac. ',anchor=W) l.pack(side=TOP,padx=2,pady=2) #add btree internals to components ftree=Tix.ScrolledHList(filwin,options='hlist.columns 3') self.filelist=ftree.hlist self.filelist.config(separator='#',width=45, height=16, drawbranch=0, indent=0, itemtype=Tix.TEXT, command=self.choosecomp,browsecmd=self.selectcomp) self.filelist.column_width(2,chars=10) self.filelist.column_width(1,chars=30) self.filelist.column_width(0,chars=3) ftree.pack(side=TOP,fill=BOTH,expand=1,padx=2,pady=2) #notebook for component parameters sf=Frame(comppage) sf.pack(side=RIGHT,fill=BOTH) l=Label(sf,text="Component Parameters",relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) self.compdes=Pmw.NoteBook(sf,tabpos=None) if sys.platform == 'win32': self.compdes.configure(hull_background="SystemButtonFace") else: self.compdes.configure(hull_background="#d4d0c8") self.compdes.recolorborders() self.compwidlist=[] self.compwidref={} self.initaddcomp() self.compdes.pack(side=TOP,padx=2,pady=2,fill=BOTH,expand=1) self.compdes.setnaturalsize() #functions page funcpage=compnb.add('Functions') s0=Frame(funcpage) s1=Frame(s0) s2=Frame(s0) wd=20 b=Button(s1,text="Add Func",bg='steel blue',fg='snow',width=wd,command=self.addfunc) b.pack(side=TOP,padx=2,pady=2) self.allfuncs=['Linear','Quadratic','Gaussian','Lorentz','Voigt','atan','Erfc','Erf','exp','log'] self.funccount=[0,0,0,0,0,0,0,0,0,0] self.funcbox=Pmw.ComboBox(s2,label_text='Functions: ',labelpos=W,scrolledlist_items=self.allfuncs, listheight=120,entryfield_entry_width=10,history=0) self.funcbox.selectitem(self.allfuncs[0]) self.funcbox.pack(side=TOP,fill=X,padx=2,pady=3) b=Button(s1,text="Remove Func",bg='red',fg='snow',width=wd,command=self.removefunc) b.pack(side=TOP,padx=2,pady=2) b=Button(s1,text="Clear All",bg='brown',fg='snow',width=wd,command=self.clearfunclist) b.pack(side=TOP,padx=2,pady=2) s0.pack(side=LEFT,padx=2,pady=2) s1.pack(side=TOP,padx=2,pady=2) s2.pack(side=TOP,padx=2,pady=2) #tree for function list #add btree internals to components ftree=Tix.ScrolledHList(funcpage,options='hlist.columns 2') self.funclist=ftree.hlist self.funclist.config(separator='#',width=30, height=16, drawbranch=0, indent=0, itemtype=Tix.TEXT, command=self.choosefunc,browsecmd=self.selectfunc) self.funclist.column_width(1,chars=20) self.funclist.column_width(0,chars=3) ftree.pack(side=LEFT,fill=BOTH,expand=1,padx=2,pady=2) #notebook for component parameters sf=Frame(funcpage) sf.pack(side=RIGHT,fill=BOTH) l=Label(sf,text="Function Parameters",relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) self.funcdes=Pmw.NoteBook(sf,tabpos=None) if sys.platform == 'win32': self.funcdes.configure(hull_background="SystemButtonFace") else: self.funcdes.configure(hull_background="#d4d0c8") self.funcdes.recolorborders() self.funcwidlist=[] self.funcwidref={} self.initaddfunc() self.funcdes.pack(side=RIGHT,padx=2,pady=2,fill=BOTH,expand=1) self.funcdes.setnaturalsize() #results page respage=compnb.add('Results') self.restext=Pmw.ScrolledText(respage,hscrollmode='none',vscrollmode='static',label_text="Results of all fitted parameters", labelpos=N,borderframe=1,text_font="Courier 9", usehullsize=1,hull_height=250,hull_width=600) self.restext.pack(padx=2,pady=0) compnb.setnaturalsize() compwin.grid(row=3,rowspan=13,columnspan=15,sticky=W+E+N+S) #add special features #add fluo correction feat=Frame(efwin,relief=SUNKEN,bd=2) l=Label(feat,text="Special Features",relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) p10=Frame(feat,relief=GROOVE,bd=1) p11=Frame(p10) p12=Frame(p10) but=Button(p10,text="SA to Fit",width=8,command=self.selfabsfit,bg="goldenrod") but2=Button(p10,text="Fit to SA",width=8,command=self.fittoselfabs,bg="LemonChiffon3") lab=Label(p10,text="Fluorescence Self Abs Corr, D = (D/r) * muKa / (1 - (D/r))") but.pack(side=LEFT,padx=2,pady=2) but2.pack(side=LEFT,padx=2,pady=2) lab.pack(side=LEFT,padx=10,pady=2) self.mukent=Pmw.EntryField(p11,label_text="muKa:",labelpos=W,validate='real',entry_width=10,value="2") self.mukent.pack(side=TOP,padx=14,pady=1) self.deltamuk=Label(p11,text=pm,anchor=W,width=8) self.deltamuk.pack(side=TOP,padx=14,pady=1) self.ffent=Pmw.EntryField(p12,label_text="Ints. Ratio:",labelpos=W,validate='real',entry_width=10,value="2") self.ffent.pack(side=TOP,padx=2,pady=1) self.deltaff=Label(p12,text=pm,anchor=W,width=8) self.deltaff.pack(side=TOP,padx=1,pady=1) p10.pack(side=TOP,padx=2,pady=2,fill=X) p12.pack(side=RIGHT,padx=2,pady=2) p11.pack(side=RIGHT,padx=2,pady=2) #add Eshift slider p20=Frame(feat,relief=GROOVE,bd=1) p20.pack(side=TOP,padx=2,pady=2,fill=X) self.dateshift=DoubleVar() self.dateshift.set(0) self.slide=Scale(p20,label="Data Energy Shift (if enabled)",state=DISABLED,variable=self.dateshift,from_=-5, to=5,orient=HORIZONTAL,resolution=0.01,length=500,troughcolor='light slate grey',fg='dark grey') self.slide.pack(side=TOP,padx=2,pady=2) feat.grid(row=16,rowspan=8,columnspan=15,sticky=W+E+N+S) #Add fit parameters list fitpwin=Frame(efwin,relief=SUNKEN,bd=2) l=Label(fitpwin,text="Fit Parameters",relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) self.xmin=Pmw.EntryField(fitpwin,label_text="xmin:",labelpos=W,validate='real',entry_width=5,value='') self.xmax=Pmw.EntryField(fitpwin,label_text="xmax:",labelpos=W,validate='real',entry_width=5,value='') self.xwt=Pmw.EntryField(fitpwin,label_text="x-weight:",labelpos=W,validate='real',entry_width=5,value='0') self.xmin.pack(fill=X,expand=1,padx=15,pady=3) self.xmax.pack(fill=X,expand=1,padx=15,pady=3) self.xwt.pack(fill=X,expand=1,padx=15,pady=3) Pmw.alignlabels([self.xmin,self.xmax,self.xwt]) self.fpos=IntVar() cb=Checkbutton(fitpwin,text="Non-negative Fit?",variable=self.fpos,anchor=W) cb.pack(fill=X,padx=8,pady=4) self.sumone=IntVar() cb=Checkbutton(fitpwin,text="Sum comps to one?",variable=self.sumone,anchor=W) cb.pack(fill=X,padx=8,pady=4) self.stowt=Pmw.EntryField(fitpwin,label_text=" Chisq wt STone:",labelpos=W,validate='real',entry_width=7,value='1000') self.stowt.pack(fill=X,expand=1,padx=16,pady=3) #self.efloat=IntVar() #cb=Checkbutton(fitpwin,text="Allow Component E to float?",variable=self.efloat,anchor=W) #cb.pack(fill=X,padx=8,pady=4) self.edfloat=IntVar() cb=Checkbutton(fitpwin,text="Allow Data E to float?",variable=self.edfloat,anchor=W,command=self.changestate) cb.pack(fill=X,padx=8,pady=4) fitpwin.grid(row=2,column=16,columnspan=4,rowspan=10,sticky=W+E+N+S) #add plot options list plotpwin=Frame(efwin,relief=SUNKEN,bd=2) l=Label(plotpwin,text="Plot Options",relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) self.plottypes=Pmw.RadioSelect(plotpwin, buttontype='checkbutton',orient='vertical',labelpos=W) self.plottypes.pack(side=TOP,padx=5,pady=5) for text in ('Data','Fit','SA Corrected','E Shifted','Residuals','Waterfall'): self.plottypes.add(text) self.plottypes.invoke('Data') plotpwin.grid(row=12,column=16,columnspan=4,rowspan=12,sticky=W+E+N+S) #Fit Quality Bar bar=Frame(efwin, relief=SUNKEN,bd=2) l=Label(bar,text="Chi Sq: ",anchor=W) self.ChiSq=Label(bar,text="",width=25,anchor=W) l.pack(side=LEFT,padx=2,pady=2) self.ChiSq.pack(side=LEFT,padx=2,pady=2) m=Label(bar,text="Red Chi Sq: ",anchor=W) self.ChiSqR=Label(bar,text="",width=25,anchor=W) m.pack(side=LEFT,padx=2,pady=2) self.ChiSqR.pack(side=LEFT,padx=2,pady=2) n=Label(bar,text="Comp Sum: ",anchor=W) self.Csum=Label(bar,text="",width=25,anchor=W) n.pack(side=LEFT,padx=2,pady=2) self.Csum.pack(side=LEFT,padx=2,pady=2) bar.grid(row=24,columnspan=20,sticky=W+E) #Status Bar self.status=Label(efwin,text="",bd=2,relief=RAISED,anchor=W,fg='blue') self.status.grid(row=25,columnspan=20,sticky=W+E) setstatus(self.status,"Ready") self.mstat=0 self.abscor=0 self.fitabsc=0 self.autolimit=0 self.dataname='' #error window self.box=Pmw.MessageDialog(root,title='File Error',defaultbutton=0,message_text='Wrong type of parameter file chosen!', iconpos='n',icon_bitmap='warning') self.box.iconname('File Error') self.box.withdraw() def closemod(self): self.root.deiconify() self.efwin.destroy() def callprogramabout(self): programabout(self.root) def callchangedefdirs(self): global lastsavedir,lastreaddir s=changedefdirs(self.efwin) lastreaddir=s.newdir lastsavedir=s.newdir def changestate(self): if self.edfloat.get()==1: self.slide.config(state=NORMAL,fg='black') if self.edfloat.get()==0: self.dateshift.set(0) self.slide.config(state=DISABLED,fg='dark grey') self.slide.update() def fileme(self): fileget(self.efwin,self.fileentry) def load_data_file(self): self.dataname=trimdirext(self.fileentry.get()) dn=self.dataname if self.dataname=='': tkMessageBox.showwarning(title="File Error",message="Missing data file name",parent=self.efwin) else: if self.xmin.get()=='' or self.xmax.get()=='': if tkMessageBox.askokcancel(title="Parameter Error",message="Missing x-limits\nAuto-load limits from data file?",parent=self.efwin): self.autolimit=1 else: return iffc.ifeffit("read_data(file="+self.fileentry.get()+", group="+self.dataname+",label='xr yr')") setstatus(self.status,"Data file "+self.dataname+" loaded!") #autoload limits if requested... if self.autolimit==1: iffc.ifeffit("xa=floor("+dn+".xr)") iffc.ifeffit("xb=ceil("+dn+".xr)") entry_replace(self.xmin,str(iffc.get_scalar("xa"))) entry_replace(self.xmax,str(iffc.get_scalar("xb"))) self.xmin.checkentry() self.xmax.checkentry() self.autolimit=0 #interpolate data #0.1eV for XANES, 0.05A-1 for EXAFS if self.nointerp.get()==0: if self.XRDinterp.get()==1: #XRD iffc.ifeffit(dn+".x=range("+self.xmin.get()+","+self.xmax.get()+",0.005)") iffc.ifeffit(dn+".y=splint("+dn+".xr,"+dn+".yr,"+dn+".x)") self.egrid=0.005 else: if iffc.get_scalar("floor("+dn+".x)")>100: #XANES iffc.ifeffit(dn+".x=range("+self.xmin.get()+"-10,"+self.xmax.get()+"+10,0.1)") iffc.ifeffit(dn+".y=splint("+dn+".xr,"+dn+".yr,"+dn+".x)") self.egrid=0.1 else: #EXAFS iffc.ifeffit(dn+".x=range("+self.xmin.get()+","+self.xmax.get()+",0.05)") iffc.ifeffit(dn+".y=splint("+dn+".xr,"+dn+".yr,"+dn+".x)") self.egrid=0.05 else: iffc.ifeffit(dn+".x="+dn+".xr") iffc.ifeffit(dn+".y="+dn+".yr") #do x-weighting if necessary iffc.ifeffit("doxwt "+dn+" "+self.xwt.get()) def menuopen(self): self.fileme() self.load_data_file() def initaddcomp(self): fname="init" new=self.compdes.add(fname) new.p=DefCParams(new,self.filelist,fname) self.compwidref.update({fname:new}) self.compwidlist.append(fname) def initaddfunc(self): fname="init" new=self.funcdes.add(fname) new.p=DefFParams(new,fname,self.allfuncs) self.funcwidref.update({fname:new}) self.funcwidlist.append(fname) def addcomp(self): global lastreaddir if self.xmin.get()=='' or self.xmax.get()=='': tkMessageBox.showwarning(title="Parameter Error",message="Cannot open component file\nPlease fill in missing x-limit entries",parent=self.efwin) return #get file name infile=ask_for_file([("chi files","*.chi"),("mu files","*.mu"),("all files","*")],lastreaddir) #if valid... if infile !='': sdir=rfind(infile,os.sep) lastreaddir=infile[:sdir] self.compload(infile) def addfunc(self): #get current func name ftype=self.funcbox.get() #add appropriate number find=self.allfuncs.index(ftype) fnum=self.funccount[find]+1 self.funccount[find]=fnum fname=ftype+' '+str(fnum) #place entries in tree self.funclist.add(fname,text='X',state=NORMAL) self.funclist.item_create(fname,1,text=fname) self.funclist.selection_clear() self.funclist.selection_set(fname) #create page new=self.funcdes.add(fname) self.funcdes.selectpage(fname) new.p=DefFParams(new,fname,self.allfuncs) self.funcwidref.update({fname:new}) self.funcwidlist.append(fname) def addmanycomp(self): global lastreaddir if self.xmin.get()=='' or self.xmax.get()=='': tkMessageBox.showwarning(title="Parameter Error",message="Cannot open component files\nPlease fill in missing x-limit entries",parent=self.efwin) return self.multifd=Tix.ExFileSelectDialog(self.root) if lastreaddir!='': lastreaddir=replace(lastreaddir,'/','\\') self.multifd.fsbox.config(directory=lastreaddir) self.multifd.fsbox.filelist.listbox.configure(selectmode=MULTIPLE) #setup ok button... self.multifd.fsbox.ok.configure(command=self.getmultilist) self.multifd.popup() def getmultilist(self): global lastreaddir multfn=self.multifd.fsbox.filelist.listbox.curselection() multdlist=self.multifd.fsbox.filelist.listbox.get(0,END) curdir=self.multifd.fsbox.dir.entry.get() lastreaddir=curdir self.multifd.popdown() if multfn !=(): for sel in multfn: curfil=multdlist[int(sel)] fulpath=curdir+os.sep+curfil #get file data self.compload(fulpath) def clearcomplist(self): #kill pages for pg in self.compwidlist: #clear memory in IFEFFIT dn=replace(pg,'.','_') iffc.ifeffit('erase @group='+dn) self.compdes.delete(remundsc(pg)) #reset all self.compwidlist=[] self.compwidref={} self.filelist.delete_all() #reinit self.initaddcomp() def clearfunclist(self): #kill pages for pg in self.funcwidlist: #remove memory from IFEFFIT dn=replace(pg,' ','_') iffc.ifeffit('erase @group='+dn) wid=self.funcwidref[pg] for var in wid.p.entlist: if var!='': ind=wid.p.entlist.index(var) iffc.ifeffit('erase '+dn+str(ind)) self.funcdes.delete(pg) #reset all self.funcwidlist=[] self.funcwidref={} self.funclist.delete_all() self.funccount=[0,0,0,0,0,0,0,0,0,0] #reinit self.initaddfunc() def removecomp(self): cur=self.filelist.info_selection() if cur != (): cur=cur[0] #remove all associated vars ind=self.compwidlist.index(cur) self.compwidlist.remove(cur) self.filelist.delete_entry(cur) self.compdes.delete(remundsc(cur)) del self.compwidref[cur] #clear memory in IFEFFIT dn=replace(cur,'.','_') iffc.ifeffit('erase @group='+dn) #reselect if len(self.compwidlist)==1: self.filelist.selection_clear() self.compdes.selectpage('init') else: if ind==1:ind=2 new=self.compwidlist[ind-1] self.filelist.selection_set(new) self.selectcomp() def removefunc(self): cur=self.funclist.info_selection() if cur != (): cur=cur[0] #remove memory from IFEFFIT dn=replace(cur,' ','_') iffc.ifeffit('erase @group='+dn) wid=self.funcwidref[cur] for var in wid.p.entlist: if var!='': ind=wid.p.entlist.index(var) iffc.ifeffit('erase '+dn+str(ind)) #remove all associated vars ind=self.funcwidlist.index(cur) self.funcwidlist.remove(cur) self.funclist.delete_entry(cur) self.funcdes.delete(cur) del self.funcwidref[cur] #reselect if len(self.funcwidlist)==1: self.funclist.selection_clear() self.funcdes.selectpage('init') else: if ind==1:ind=2 new=self.funcwidlist[ind-1] self.funclist.selection_set(new) self.selectfunc() def reloadallcomp(self): #store path list in temp variable tpath=[] for np in self.compwidlist: #select new sample if np!='init': dat=self.compwidref.get(np) tpath.append(dat.path) #kill all data self.clearcomplist() #reload files for fn in tpath: self.compload(fn) def compload(self,infile): #load component into Ifeffit fname=trimdir(infile) #place entries in tree self.filelist.add(fname,text='X',state=NORMAL) self.filelist.item_create(fname,1,text=fname) self.filelist.item_create(fname,2,text='0') self.filelist.selection_clear() self.filelist.selection_set(fname) #create page new=self.compdes.add(remundsc(fname)) self.compdes.selectpage(remundsc(fname)) new.p=DefCParams(new,self.filelist,fname) new.path=infile self.compwidref.update({fname:new}) self.compwidlist.append(fname) #load into IFEFFIT dn=replace(fname,'.','_') #load file iffc.ifeffit("read_data(file="+infile+",group="+dn+",label='xr yr')") #interpolate components #0.1eV for XANES, 0.05A-1 for EXAFS if self.nointerp.get()==0: if self.XRDinterp.get()==1: #XRD iffc.ifeffit(dn+".x=range("+self.xmin.get()+","+self.xmax.get()+",0.005)") iffc.ifeffit(dn+".y=splint("+dn+".xr,"+dn+".yr,"+dn+".x)") self.egrid=0.005 else: if iffc.get_scalar("floor("+dn+".x)")>100: #XANES iffc.ifeffit(dn+".x=range("+self.xmin.get()+"-10,"+self.xmax.get()+"+10,0.1)") iffc.ifeffit(dn+".y=splint("+dn+".xr,"+dn+".yr,"+dn+".x)") else: #EXAFS iffc.ifeffit(dn+".x=range("+self.xmin.get()+","+self.xmax.get()+",0.05)") iffc.ifeffit(dn+".y=splint("+dn+".xr,"+dn+".yr,"+dn+".x)") else: iffc.ifeffit(dn+".x="+dn+".xr") iffc.ifeffit(dn+".y="+dn+".yr") #do x-weighting if necessary iffc.ifeffit("doxwt "+dn+" "+self.xwt.get()) setstatus(self.status,"Component file "+infile+" loaded") def selectcomp(self, *args): #get data cur=self.filelist.info_selection() if cur==(): return cur=cur[0] self.compdes.selectpage(remundsc(cur)) def selectfunc(self, *args): #get data cur=self.funclist.info_selection() if cur==(): return cur=cur[0] self.funcdes.selectpage(cur) def choosecomp(self, *args): cur=args[0] self.compdes.selectpage(remundsc(cur)) wid=self.compwidref[cur].p if wid.active==0: #turn on wid.active=1 self.filelist.item_configure(cur,0,text='X') blacktext=Tix.DisplayStyle(Tix.TEXT,fg='black',bg='white',selectforeground='white',refwindow=self.efwin) for i in range(3): self.filelist.item_configure(cur,i,style=blacktext) else: #turn off wid.active=0 self.filelist.item_configure(cur,0,text=' ') greytext=Tix.DisplayStyle(Tix.TEXT,fg='grey',bg='white',selectforeground='grey',refwindow=self.efwin) for i in range(3): self.filelist.item_configure(cur,i,style=greytext) def choosefunc(self, *args): cur=args[0] self.funcdes.selectpage(cur) wid=self.funcwidref[cur].p if wid.active==0: #turn on wid.active=1 self.funclist.item_configure(cur,0,text='X') blacktext=Tix.DisplayStyle(Tix.TEXT,fg='black',bg='white',selectforeground='white',refwindow=self.efwin) for i in range(2): self.funclist.item_configure(cur,i,style=blacktext) else: #turn off wid.active=0 self.funclist.item_configure(cur,0,text=' ') greytext=Tix.DisplayStyle(Tix.TEXT,fg='grey',bg='white',selectforeground='grey',refwindow=self.efwin) for i in range(2): self.funclist.item_configure(cur,i,style=greytext) def sp_plot(self,new,gx,gy,xlab,ylab,title,xmin,xmax,key): xdat=iffc.get_array(gx) ydat=iffc.get_array(gy) if new==1: spplotter.SPPlotter(self.root,cmd="new",lt=key,xd=xdat,yd=ydat,xt=xlab,yt=ylab, title=title,xmin=xmin,xmax=xmax) if new==0: spplotter.SPPlotter(self.root,cmd="stack",lt=key,xd=xdat,yd=ydat,xt=xlab,yt=ylab, title=title,xmin=xmin,xmax=xmax) def plotcomp(self): #Plot component fits -- choose plot type ptypes=self.plottypes.getcurselection() xm1=self.xmin.get() xm2=self.xmax.get() newg=1 for typ in ptypes: if typ=='Data': dn=self.dataname self.sp_plot(newg,dn+".x",dn+".y_xw","x","y",dn,xm1,xm2,"Data") newg=0 if typ=='Fit': self.sp_plot(newg,"fit.x","fit.y","x","y","Fit",xm1,xm2,"Fit") newg=0 if typ=='SA Corrected': dn=self.dataname self.sp_plot(newg,dn+".x",dn+".say","x","y",dn,xm1,xm2,"SACorr") newg=0 if typ=='E Shifted': dn=self.dataname self.sp_plot(newg,dn+".x",dn+".yes","x","y",dn,xm1,xm2,"Eshift") newg=0 if typ=='Residuals': dn=self.dataname self.sp_plot(newg,dn+".x",dn+".diff","x","y",dn,xm1,xm2,"Resid") newg=0 if typ=='Waterfall': #plot waterfall dn=self.dataname for name in self.compwidlist: #plot that component wid=self.compwidref[name] cn=replace(name,'.','_') if wid.p.active==1: iffc.ifeffit("set(temp.cf="+cn+".y_xw*"+wid.p.frac.get()+")") self.sp_plot(newg,dn+".x","temp.cf","x","y",dn,xm1,xm2,name) newg=0 #plot functions for name in self.funcwidlist: wid=self.funcwidref[name] cn=replace(name,' ','_') if wid.p.active==1: self.sp_plot(newg,dn+".x",cn+".y","x","y",dn,xm1,xm2,name) newg=0 setstatus(self.status,"Plots complete") def defallfuncs(self,setvar): #define functions in IFEFFIT dn=self.dataname iffc.ifeffit("set(const.x=ones(npts("+dn+".x)))") for name in self.funcwidlist: wid=self.funcwidref[name] ftype=name[:rfind(name,' ')] fn=replace(name,' ','_') #define variables for var in wid.p.entlist: if var!='': ind=wid.p.entlist.index(var) varcmd=wid.p.butvar[ind].get() if wid.p.active==0:varcmd='set' if setvar==1:varcmd='set' iffc.ifeffit(varcmd+'('+fn+str(ind)+'='+var.get()+')') #define function if ftype==self.allfuncs[0]: #linear iffc.ifeffit('def('+fn+'.y='+fn+'0*'+dn+'.x+'+fn+'1*const.x)') elif ftype==self.allfuncs[1]: #quadratic iffc.ifeffit('def('+fn+'.y='+fn+'0*'+dn+'.x**2+'+fn+'1*'+dn+'.x+'+fn+'2*const.x)') elif ftype==self.allfuncs[2]: #gauss iffc.ifeffit('def('+fn+'.y='+fn+'0*gauss('+dn+'.x,'+fn+'1,'+fn+'2)+'+fn+'3*const.x)') elif ftype==self.allfuncs[3]: #lorentz iffc.ifeffit('def('+fn+'.y='+fn+'0*loren('+dn+'.x,'+fn+'1,'+fn+'2)+'+fn+'3*const.x)') elif ftype==self.allfuncs[4]: #voight iffc.ifeffit('def('+fn+'.y='+fn+'0*pvoight('+dn+'.x,'+fn+'1,'+fn+'2,'+fn+'4)+'+fn+'3*const.x)') elif ftype==self.allfuncs[5]: #atan iffc.ifeffit('def('+fn+'.y='+fn+'0*atan(('+dn+'.x-'+fn+'1)/('+fn+'2))+'+fn+'3*const.x)') elif ftype==self.allfuncs[6]: #erfc iffc.ifeffit('def('+fn+'.y='+fn+'0*erfc(('+dn+'.x-'+fn+'1)/('+fn+'2))+'+fn+'3*const.x)') elif ftype==self.allfuncs[7]: #erf iffc.ifeffit('def('+fn+'.y='+fn+'0*erf(('+dn+'.x-'+fn+'1)/('+fn+'2))+'+fn+'3*const.x)') elif ftype==self.allfuncs[8]: #exp iffc.ifeffit('def('+fn+'.y='+fn+'0*exp(('+dn+'.x-'+fn+'1)/('+fn+'2))+'+fn+'3*const.x)') elif ftype==self.allfuncs[9]: #log iffc.ifeffit('def('+fn+'.y='+fn+'0*ln(('+dn+'.x-'+fn+'1)/('+fn+'2))+'+fn+'3*const.x)') def makefitdat(self): #Make fit construction from components if self.dataname=='': print 'ERROR: No Data File loaded' return dn=self.dataname #consider any eshifting of components... #construct using %ages iffc.ifeffit("set(fit.y=zeros(npts("+dn+".y)))") iffc.ifeffit("set(fit.x="+dn+".x)") for name in self.compwidlist: #add component to total wid=self.compwidref[name] if wid.p.active==1: cn=replace(name,'.','_') iffc.ifeffit("set(fit.y=fit.y+"+cn+".y_xw*"+wid.p.frac.get()+")") #redefine function defs self.defallfuncs(0) #add function terms! for name in self.funcwidlist: #add active funcs to total too wid=self.funcwidref[name] if wid.p.active==1: cn=replace(name,' ','_') iffc.ifeffit("set(fit.y=fit.y+"+cn+".y)") #calcualte residuals, e-shifting, and self absorption if needed if self.edfloat.get()==0: iffc.ifeffit("set(des=0)") iffc.ifeffit("set("+dn+".yes="+dn+".y_xw)") if self.edfloat.get()==1: #shift E and define new data... iffc.ifeffit("set(des="+str(self.dateshift.get())+")") iffc.ifeffit("set(new.x=range("+self.xmin.get()+"-des,"+self.xmax.get()+"-des,"+str(self.egrid)+"))") iffc.ifeffit("set("+dn+".yes=splint("+dn+".x,"+dn+".y_xw,new.x))") if self.abscor==0: iffc.ifeffit("set("+dn+".diff="+dn+".yes-fit.y)") if self.abscor==1: iffc.ifeffit("set(muka="+self.mukent.get()+",rat="+self.ffent.get()+")") iffc.ifeffit("set("+dn+".say=(muka*"+dn+".yes/rat)/(1-("+dn+".yes/rat)))") iffc.ifeffit("set("+dn+".diff="+dn+".say-fit.y)") if self.mstat==0: setstatus(self.status,"Fit constructed from fractions provided") self.mstat=0 def fitdatcomp(self): #Main fitting routine #consider eshift for components! dn=self.dataname #set guesses and def's for components minterm="fit.y=" sumterm="sumres=(0" for name in self.compwidlist: wid=self.compwidref[name] cn=replace(name,'.','_') if wid.p.active==1: iffc.ifeffit("guess(frac"+cn+"="+wid.p.frac.get()+")") if self.fpos.get()==0: minterm=minterm+"+frac"+cn+"*"+cn+".y_xw" sumterm=sumterm+"+frac"+cn if self.fpos.get()==1: iffc.ifeffit("def(pos"+cn+"=abs(frac"+cn+"))") minterm=minterm+"+pos"+cn+"*"+cn+".y_xw" sumterm=sumterm+"+pos"+cn if wid.p.active==0: iffc.ifeffit("def(frac"+cn+"=0)") iffc.ifeffit("def(pos"+cn+"=0)") #redefine function defs self.defallfuncs(0) #add function terms! for name in self.funcwidlist: #add active funcs to total too wid=self.funcwidref[name] fn=replace(name,' ','_') if wid.p.active==1: minterm=minterm+"+"+fn+".y" #shift energy scale of data if needed if self.edfloat.get()==0: iffc.ifeffit("set(des=0)") iffc.ifeffit("set("+dn+".yes="+dn+".y_xw)") if self.edfloat.get()==1: iffc.ifeffit("guess(des="+str(self.dateshift.get())+")") iffc.ifeffit("def(new.x=range("+self.xmin.get()+"-des,"+self.xmax.get()+"-des,"+str(self.egrid)+"))") iffc.ifeffit("def("+dn+".yes=splint("+dn+".x,"+dn+".y_xw,new.x))") #construct mimization #consider sum to one constraint -- not real, but close! sumterm=sumterm+")" iffc.ifeffit("def("+sumterm+")") sumtermres="sumtermres=(1-sumres)*"+self.stowt.get() iffc.ifeffit("def("+sumtermres+")") iffc.ifeffit("def("+minterm+")") if self.fitabsc==0: iffc.ifeffit("def(fit.resid=fit.y-"+dn+".yes)") if self.fitabsc==1: iffc.ifeffit("def(muka="+self.mukent.get()+",rat="+self.ffent.get()+")") iffc.ifeffit("def("+dn+".say=(muka*"+dn+".yes/rat)/(1-("+dn+".yes/rat)))") iffc.ifeffit("def(fit.resid=fit.y-"+dn+".say)") #call minimize if self.sumone.get()==0: iffc.ifeffit("minimize(fit.resid,x="+dn+".x,xmin="+self.xmin.get()+",xmax="+self.xmax.get()+")") if self.sumone.get()==1: iffc.ifeffit("minimize(fit.resid,x="+dn+".x,xmin="+self.xmin.get()+",xmax="+self.xmax.get()+",restraint=sumtermres)") #report fitting quality parameters in status bar setstatus_d(self.Csum,iffc.get_scalar("sumres"),5) setstatus_d(self.ChiSq,iffc.get_scalar("chi_square"),5) setstatus_d(self.ChiSqR,iffc.get_scalar("chi_reduced"),8) #report values in entryfields for name in self.compwidlist: wid=self.compwidref[name] cn=replace(name,'.','_') if wid.p.active==1: if self.fpos.get()==0: entry_replace_d(wid.p.frac,iffc.get_scalar("frac"+cn),5) #setstatus_d(name.deltapct,pm+str(iffc.get_scalar("delta_cf"+str(cnum))),5) if self.fpos.get()==1: entry_replace_d(wid.p.frac,iffc.get_scalar("pos"+cn),5) #setstatus_d(name.deltapct,pm+str(iffc.get_scalar("delta_cp"+str(cnum))),5) wid.p.big.item_configure(wid.p.fname,2,text=str(wid.p.frac.get())) for name in self.funcwidlist: wid=self.funcwidref[name] fn=replace(name,' ','_') if wid.p.active==1: for var in wid.p.entlist: if var!='': ind=wid.p.entlist.index(var) entry_replace_d(var,iffc.get_scalar(fn+str(ind)),8) if self.edfloat.get()==1: self.dateshift.set(iffc.get_scalar("des")) setstatus(self.status,"Fit completed!") self.mstat=1 if self.fitabsc==1: self.abscor=1 if self.fitabsc==0: self.abscor=0 self.makefitdat() #call result reporter self.reportresults(self.abscor) self.fitabsc=0 def reportresults(self,saval): #clear page self.restext.clear() #header self.restext.insert(END,"File: "+self.fileentry.get()+'\n\n') #print chisquare and R-value line="Chi-Sq: "+str(iffc.get_scalar('chi_square'))+"\t\tRed Chi-Sq: "+str(iffc.get_scalar('chi_reduced')) self.restext.insert(END,line+'\n') #print energyt shift if needed if self.edfloat.get()==1: line='\nData shifted in energy by: '+str(self.dateshift.get())+' eV' self.restext.insert(END,line+'\n') #print SA values if needed if saval==1: line="\nMuKa: \t\t"+str(self.clipresults(iffc.get_scalar("muka")))+" +/- "+str(self.clipresults(iffc.get_scalar("delta_muka")))+'\n' self.restext.insert(END,line) line="Ratio: \t\t"+str(self.clipresults(iffc.get_scalar("rat")))+" +/- "+str(self.clipresults(iffc.get_scalar("delta_rat")))+'\n' self.restext.insert(END,line) #print list of components self.restext.insert(END,'\nCOMPONENT COMPOSITIONS\n\n') for name in self.compwidlist: wid=self.compwidref[name] cn=replace(name,'.','_') if wid.p.active==1: line=name+'\t\t'+str(self.clipresults(abs(iffc.get_scalar("frac"+cn))))+' +/- '+str(self.clipresults(iffc.get_scalar("delta_frac"+cn)))+'\n' self.restext.insert(END,line) self.restext.insert(END,"Component Sum\t\t"+str(iffc.get_scalar("sumres"))+'\n') #print list of functions self.restext.insert(END,'\nFUNCTION VALUES\n') for name in self.funcwidlist: wid=self.funcwidref[name] fn=replace(name,' ','_') if wid.p.active==1: self.restext.insert(END,'\n'+name+'\n') for var in wid.p.entlist: if var!='': ind=wid.p.entlist.index(var) varcmd=wid.p.butvar[ind].get() if varcmd=='guess': line='\t'+wid.p.entlab[ind]+'\t\t'+str(self.clipresults(iffc.get_scalar(fn+str(ind))))+' +/- '+str(self.clipresults(iffc.get_scalar("delta_"+fn+str(ind))))+'\n' if varcmd=='set': line='\t'+wid.p.entlab[ind]+'\t\t'+str(self.clipresults(iffc.get_scalar(fn+str(ind))))+'\n' self.restext.insert(END,line) #end def clipresults(self,v): dig=8 val=str(v) decind=rfind(val,'.') eind=rfind(val,"e") if eind==-1: if decind>dig: val=val[:decind+2] else: val=val[:dig] else: val=val[:4]+val[eind:len(val)] return val def repeatselfabs(self): for r in range(1,11): self.fittoselfabs() setstatus(self.status,"Self absorpion fit "+str(r)+" completed!") self.selfabsfit() setstatus(self.status,"Fit "+str(r)+" to self abs corrections completed!") setstatus(self.status,"Self Absorption cycle fits completed.") def fittoselfabs(self): self.fitabsc=1 self.fitdatcomp() def selfabsfit(self): dn=self.dataname #set all components to set values iffc.ifeffit("set(fit.y=zeros(npts("+dn+".y)))") iffc.ifeffit("set(fit.x="+dn+".x)") for name in self.compwidlist: wid=self.compwidref[name] cn=replace(name,'.','_') #add components to total if wid.p.active==1: iffc.ifeffit("def(frac"+cn+"="+wid.p.frac.get()+")") iffc.ifeffit("set(fit.y=fit.y+frac"+cn+"*"+cn+".y_xw)") if wid.p.active==0: iffc.ifeffit("def(frac"+cn+"=0)") iffc.ifeffit("def(pos"+cn+"=0)") #redefine function defs -- using set terms self.defallfuncs(1) #add function terms to total! for name in self.funcwidlist: wid=self.funcwidref[name] fn=replace(name,' ','_') if wid.p.active==1: iffc.ifeffit("set(fit.y=fit.y+"+fn+".y)") #shift energy scale of data if needed if self.edfloat.get()==0: iffc.ifeffit("set(des=0)") iffc.ifeffit("set("+dn+".yes="+dn+".y_xw)") if self.edfloat.get()==1: #shift E and define new data... iffc.ifeffit("guess(des="+str(self.dateshift.get())+")") iffc.ifeffit("def(new.x=range("+self.xmin.get()+"-des,"+self.xmax.get()+"-des,"+str(self.egrid)+"))") iffc.ifeffit("def("+dn+".yes=splint("+dn+".x,"+dn+".y_xw,new.x))") #define new data.say=SAC factor iffc.ifeffit("guess(muka="+self.mukent.get()+",rat="+self.ffent.get()+")") iffc.ifeffit("def("+dn+".say=(muka*"+dn+".yes/rat)/(1-("+dn+".yes/rat)))") iffc.ifeffit("def(fit.resid=fit.y-"+dn+".say)") #do fit on data iffc.ifeffit("minimize(fit.resid,x="+dn+".x,xmin="+self.xmin.get()+",xmax="+self.xmax.get()+")") #report fitting quality parameters setstatus_d(self.Csum,iffc.get_scalar("sumres"),5) setstatus_d(self.ChiSq,iffc.get_scalar("chi_square"),5) setstatus_d(self.ChiSqR,iffc.get_scalar("chi_reduced"),5) #report values entry_replace_d(self.mukent,iffc.get_scalar("muka"),3) entry_replace_d(self.ffent,iffc.get_scalar("rat"),3) setstatus_d(self.deltamuk,pm+str(iffc.get_scalar("delta_muka")),4) setstatus_d(self.deltaff,pm+str(iffc.get_scalar("delta_rat")),4) if self.edfloat.get()==1: self.dateshift.set(iffc.get_scalar("des")) setstatus(self.status,"Self absorpion fit completed!") self.mstat=1 self.abscor=1 self.makefitdat() #call result reporter self.reportresults(self.abscor) def savefitdata(self): global lastsavedir dn=self.dataname nfn=ask_save_file('',lastsavedir) self.efwin.focus_set() if nfn!="": sdir=rfind(nfn,os.sep) lastsavedir=nfn[:sdir] iffc.ifeffit("write_data(file="+nfn+".fit,"+dn+".x,"+dn+".y_xw,fit.y)") setstatus(self.status,"Fit data saved to "+nfn) def saveresdata(self): global lastsavedir dn=self.dataname nfn=ask_save_file('',lastsavedir) self.efwin.focus_set() if nfn!="": sdir=rfind(nfn,os.sep) lastsavedir=nfn[:sdir] iffc.ifeffit("write_data(file="+nfn+".res,"+dn+".x,"+dn+".diff)") setstatus(self.status,"Data residuals saved to "+nfn) def saveallvars(self): global lastsavedir #place all paths and varibles into a parameter file #get file name nfn=ask_save_file('',lastsavedir) self.efwin.focus_set() if nfn=="": setstatus(self.status,"Save parameters aborted") else: sdir=rfind(nfn,os.sep) lastsavedir=nfn[:sdir] #open file #check for extension ending ext=rfind(nfn,".") if ext==-1: nfn=nfn+".prm" fid=open(nfn,"w") #save data-file parameters fid.write("EDGEPARAMS\n") #enter filename,xmin,xmax,fitting constraints fid.write(self.fileentry.get()+"\n") fid.write(self.xmin.get()+"\n") fid.write(self.xmax.get()+"\n") fid.write(self.xwt.get()+"\n") fid.write(str(self.fpos.get())+"\n") fid.write(str(self.sumone.get())+"\n") fid.write(self.stowt.get()+"\n") #fid.write(str(self.efloat.get())+"\n") fid.write(str(self.edfloat.get())+"\n") #save the number of components currently loaded fid.write(str(len(self.compwidlist)-1)+"\n") #save all parts of all components for name in self.compwidlist: if name!='init': wid=self.compwidref[name] fid.write(wid.path+"\n") fid.write(str(wid.p.active)+"\n") fid.write(str(wid.p.frac.get())+"\n") #save number of functions fid.write(str(len(self.funcwidlist)-1)+"\n") #save all parts of all functions for name in self.funcwidlist: if name!='init': wid=self.funcwidref[name] fid.write(str(name[:rfind(name,' ')])+"\n") #function type fid.write(str(wid.p.active)+"\n") for var in wid.p.entlist: if var!='': ind=wid.p.entlist.index(var) fid.write(str(wid.p.entlist[ind].get())+"\n") else: fid.write(''+"\n") #SA factors fid.write(self.mukent.get()+"\n") fid.write(self.ffent.get()+"\n") #E shifting fid.write(str(self.dateshift.get())+"\n") fid.write("END") fid.close() setstatus(self.status,"Fit parameters saved to "+nfn) def loadallvars(self): global lastreaddir #load paths and variables from files #get file name fn=ask_for_file([("parameter files","*.prm"),("all files","*")],lastreaddir,check=0) self.efwin.focus_set() if fn=="": setstatus(self.status,"Load parameters aborted") else: sdir=rfind(fn,os.sep) lastreaddir=fn[:sdir] #open file fid=open(fn,"r") param=fid.read() fid.close() #parse file... lp=split(param,'\n') ind=0 new=lp[ind] if new=='FPARAMS' or new=='BSPARAMS': #wrong parameter file self.box.deiconify() if new=='EDGEPARAMS': #read data-file parameters ind=ind+1 #read filename,xmin,xmax,fit contraints self.fileentry.setentry(lp[ind]);ind=ind+1 self.xmin.setentry(lp[ind]);ind=ind+1 self.xmax.setentry(lp[ind]);ind=ind+1 self.xwt.setentry(lp[ind]);ind=ind+1 self.fpos.set(int(lp[ind]));ind=ind+1 self.sumone.set(int(lp[ind]));ind=ind+1 self.stowt.setentry(lp[ind]);ind=ind+1 #self.efloat.set(int(lp[ind]));ind=ind+1 self.edfloat.set(int(lp[ind]));ind=ind+1 #read in number of components numcomp=int(lp[ind]);ind=ind+1 #clear data and functions self.clearcomplist() self.clearfunclist() #read all components for x in range(numcomp): path=lp[ind];ind=ind+1 cn=trimdir(path) self.compload(path) wid=self.compwidref[cn] wid.p.active=int(lp[ind]);ind=ind+1 wid.p.frac.setentry(lp[ind]);ind=ind+1 #read in number of functions numfunc=int(lp[ind]);ind=ind+1 #read all functions for x in range(numfunc): ftype=lp[ind];ind=ind+1 #function type self.funcbox.selectitem(ftype) self.addfunc() find=self.allfuncs.index(ftype) fnum=self.funccount[find] fname=ftype+' '+str(fnum) wid=self.funcwidref[fname] wid.p.active=int(lp[ind]);ind=ind+1 for var in wid.p.entlist: if var!='': ix=wid.p.entlist.index(var) wid.p.entlist[ix].setentry(lp[ind]);ind=ind+1 else: ind=ind+1 #read SA features self.mukent.setentry(lp[ind]);ind=ind+1 self.ffent.setentry(lp[ind]);ind=ind+1 #read E shifting self.dateshift.set(atof(lp[ind]));ind=ind+1 setstatus(self.status,"Parameter file read from "+fn) #start event handler #EdgeFit(root) #root.mainloop() sixpack-0.68/sixpack.py0000644000175000017500000052001010635254316014124 0ustar segresegre#MAIN SamXAS Routine GUI from Tkinter import * from spdirvars import * from spglobalfuncs import * import tkFileDialog import tkSimpleDialog import tkMessageBox import Pmw import os import Tix from math import * from string import * from Ifeffit import * import spsamview import spkpca import lsqfitter import spplotter import httplib import cbselfabs root=Tix.Tk() root.title("SixPACK") Pmw.initialise(root) pm='+/-' if os.name=='nt':os.sep='/' filepath=os.getcwd()+os.sep #if count(upper(filepath),'IFEFFIT')>0:filepath=filepath+'sixpack'+os.sep iffc=Ifeffit(screen_echo=1) iffc.ifeffit("load mnexafsfit.iff") global lastfeffdir lastfeffdir='' global lastreaddir global lastsavedir #return main menu def getmainmenu(win): root.deiconify() iffc.ifeffit("erase @arrays") iffc.ifeffit("erase @scalars") win.destroy() ########################################################### ## ## ## Periodic Table Interface for FEFF SS Maker ## ## ########################################################### class PT: def __init__(self): ptwin=root.ptwin=Toplevel(root) ptwin.title("Single Scattering FEFF Path Maker") ptwin.protocol("WM_DELETE_WINDOW", self.closemod) root.iconify() #change focus... ptwin.focus_set() #periodic table #define elements 1=noble, 2=alkali, 3=pseudo, 4=non, 5=metal, 6=lanth, 7=act self.elist={'H':(1,0,1),'He':(2,0,1), 'Li':(3,1,2),'Be':(4,1,2),'B':(5,1,3),'C':(6,1,4),'N':(7,1,4),'O':(8,1,4),'F':(9,1,4),'Ne':(10,1,1), 'Na':(11,2,2),'Mg':(12,2,2),'Al':(13,2,5),'Si':(14,2,3),'P':(15,2,4),'S':(16,2,4),'Cl':(17,2,4),'Ar':(18,2,1), 'K':(19,3,2),'Ca':(20,3,2),'Sc':(21,3,5),'Ti':(22,3,5),'V':(23,3,5),'Cr':(24,3,5),'Mn':(25,3,5),'Fe':(26,3,5), 'Co':(27,3,5),'Ni':(28,3,5),'Cu':(29,3,5),'Zn':(30,3,5),'Ga':(31,3,5),'Ge':(32,3,3),'As':(33,3,3),'Se':(34,3,4),'Br':(35,3,4),'Kr':(36,3,1), 'Rb':(37,4,2),'Sr':(38,4,2),'Y':(39,4,5),'Zr':(40,4,5),'Nb':(41,4,5),'Mo':(42,4,5),'Tc':(43,4,5),'Ru':(44,4,5),'Rh':(45,4,5), 'Pd':(46,4,5),'Ag':(47,4,5),'Cd':(48,4,5),'In':(49,4,5),'Sn':(50,4,5),'Sb':(51,4,3),'Te':(52,4,3),'I':(53,4,4),'Xe':(54,4,1), 'Cs':(55,5,2),'Ba':(56,5,2),'La':(57,8,6),'Ce':(58,8,6),'Pr':(59,8,6),'Nd':(60,8,6),'Pm':(61,8,6),'Sm':(62,8,6),'Eu':(63,8,6), 'Gd':(64,8,6),'Tb':(65,8,6),'Dy':(66,8,6),'Ho':(67,8,6),'Er':(68,8,6),'Tm':(69,8,6),'Yb':(70,8,6),'Lu':(71,5,5),'Hf':(72,5,5), 'Ta':(73,5,5),'W':(74,5,5),'Re':(75,5,5),'Os':(76,5,5),'Ir':(77,5,5),'Pt':(78,5,5),'Au':(79,5,5),'Hg':(80,5,5),'Tl':(81,5,5), 'Pb':(82,5,5),'Bi':(83,5,5),'Po':(84,5,5),'At':(85,5,3),'Rn':(86,5,1),'Fr':(87,6,2),'Ra':(88,6,2),'Ac':(89,9,7),'Th':(90,9,7), 'Pa':(91,9,7),'U':(92,9,7),'Np':(93,9,7),'Pu':(94,9,7),'Am':(95,9,7),'Cm':(96,9,7),'Bk':(97,9,7),'Cf':(98,9,7),'Es':(99,9,7), 'Fm':(100,9,7),'Md':(101,9,7),'No':(102,9,7),'Lr':(103,6,5),'Rf':(104,6,5),'Db':(105,6,5),'Sg':(106,6,5),'Bh':(107,6,5),'Hs':(108,6,5),'Mt':(109,6,5)} table=Frame(ptwin,relief=SUNKEN,bd=2,) table.pack(side=TOP) for en in self.elist.keys(): eprop=self.elist[en] cp=eprop[0] if eprop[0]==1: cp=0 elif eprop[0]==2: cp=17 elif 3<=eprop[0]<=4: cp=cp-3 elif 5<=eprop[0]<=10: cp=cp+7 elif 11<=eprop[0]<=12: cp=cp-11 elif 13<=eprop[0]<=18: cp=cp-1 elif 19<=eprop[0]<=36: cp=cp-19 elif 37<=eprop[0]<=54: cp=cp-37 elif 55<=eprop[0]<=70: cp=cp-55 elif 71<=eprop[0]<=86: cp=cp-69 elif 87<=eprop[0]<=102: cp=cp-87 elif 103<=eprop[0]<=118: cp=cp-101 self.addelement(table,en,eprop[1],cp,eprop[2]) spc=Frame(table,height=20) spc.grid(row=7) f=Frame(ptwin) f.pack(side=TOP,pady=2,fill=X) iact=Frame(f,relief=SUNKEN,bd=2) iact.pack(side=LEFT,pady=2,padx=10,fill=X) self.cbase="Absorbing atom: " self.ctext=StringVar() self.ctext.set(self.cbase) self.center=Label(iact,textvariable=self.ctext,width=50) self.center.pack(fill=X) self.sbase="Scattering atom: " self.stext=StringVar() self.stext.set(self.sbase) self.scat=Label(iact,textvariable=self.stext,width=50) self.scat.pack(fill=X) inst=Frame(f,relief=SUNKEN, bd=2) inst.pack(side=LEFT,pady=2,padx=10,fill=BOTH) insttext="Left click to select absorbing atom \n Right click to select scattering atom" instlab=Label(inst,text=insttext,fg="dark green",width=50) instlab.pack(side=TOP,fill=BOTH) fopt=Frame(ptwin,relief=SUNKEN,bd=2) l=Label(fopt,text="FEFF Options",relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) f=Frame(fopt,relief=GROOVE,bd=2) f.pack(side=TOP,padx=2,pady=2,fill=X) g=Frame(f) g.pack(side=LEFT,padx=2,pady=2) b=Button(g,text="Run FEFF",bg="steel blue",fg="ivory",command=self.runfeff, width=15) b.pack(side=TOP,padx=2,pady=15) self.feffversion=Pmw.RadioSelect(g,labelpos=N,label_text="FEFF Version",buttontype='radiobutton',command=self.changevers) self.feffversion.pack(fill=X,padx=8,pady=4) for text in ('FEFF6-7','FEFF8'): self.feffversion.add(text) self.feffcom=Pmw.EntryField(g,labelpos=W,label_text="FEFF Command:",value="feff800",entry_width=15) self.feffcom.pack(side=TOP,padx=15,pady=15) self.feffversion.invoke('FEFF8') g1=Frame(f) g1.pack(side=LEFT,padx=2,pady=2) edges=('K','L1','L2','L3','M1','M2','M3','M4','M5') self.feffedge=Pmw.ScrolledListBox(g1,items=edges,labelpos=N,label_text='Edge:',listbox_height=4,listbox_exportselection=0) self.feffedge.select_set(0) self.feffedge.pack(side=LEFT,padx=2,pady=2) g2=Frame(f) g2.pack(side=LEFT,padx=2,pady=2) #distance of scatterer and rough geometry self.scatdist=Pmw.EntryField(g2,labelpos=N,label_text="Distance to Scatterer:",entry_width=5,validate='real') self.scatdist.pack(padx=2,pady=5) gitems=('Tetrahedral','Sq Planar','Octahedral') self.feffgeom=Pmw.ScrolledListBox(g2,items=gitems,labelpos=N,label_text='Geometry:',listbox_height=4,listbox_exportselection=0) self.feffgeom.select_set(2) self.feffgeom.pack(padx=2,pady=5) g3=Frame(f) g3.pack(side=LEFT,padx=2,pady=2) #other options self.feffafolp=Pmw.EntryField(g3,labelpos=N,label_text="AFOLP:",value=1.15,entry_width=7,validate={'validator':'real','min':1,'max':1.3}) self.feffafolp.pack(padx=2,pady=2) xitems=('0 - Hedin-Lundqvist','1 - Dirac-Hara','2 - Ground State','3 - DH+HL','5 - Partially Nonlocal') self.feffxchange=Pmw.ComboBox(g3,labelpos=N,scrolledlist_items=xitems,label_text="Exchange:",listheight=100,listbox_exportselection=0,history=0) self.feffxchange.selectitem(xitems[0]) self.feffxchange.pack(padx=2,pady=2) fopt.pack(side=TOP,pady=2,fill=BOTH) def closemod(self): getmainmenu(root.ptwin) def addelement(self,master,ename,rpos,cpos,etyp): #add an element button 1=noble, 2=alkali, 3=pseudo, 4=non, 5=metal, 6=lanth, 7=act if etyp==1: bc='goldenrod' if etyp==2: bc='tan' if etyp==3: bc='orange' if etyp==4: bc='light blue' if etyp==5: bc='dark green' if etyp==6: bc='rosy brown' if etyp==7: bc='dark red' b=Button(master,text=ename,width=2,height=1,font='Arial 14 bold',bg=bc) b.grid(row=rpos,column=cpos) b.bind("",self.centerclick) b.bind("",self.scatclick) b.bind("",self.returnclick) def centerclick(self,event): atom=event.widget.cget('text') self.catom=atom self.ctext.set(self.cbase+atom) def scatclick(self,event): atom=event.widget.cget('text') event.widget.config(state=ACTIVE) event.widget.config(relief=SUNKEN) self.satom=atom self.stext.set(self.sbase+atom) def returnclick(self,event): event.widget.config(state=NORMAL) event.widget.config(relief=RAISED) def changevers(self,arg): if self.feffversion.getcurselection()=='FEFF8': self.feffcom.setentry('feff800') else: self.feffcom.setentry('feff7') def runfeff(self): #routine to run a feff script! #puts all work in the folder fefftemp os.chdir(filepath) try: os.chdir("fefftemp") except: os.chdir(filepath+'sixpack'+os.sep+'fefftemp') #clear directory! os.system("del *.bin") os.system("del *.dat") #open feff.inp fid=open("feff.inp","w") #set variable parameters exch=self.feffxchange.get()[0] rad=atof(self.scatdist.get()) mrad=str(rad+2) cnum=str(self.elist[self.catom][0]) snum=str(self.elist[self.satom][0]) #determine coordinates for geometry... if self.feffgeom.getcurselection()[0]=='Tetrahedral': d=rad/sqrt(3) d1=str(d) geotext=""" 0 0 0 0 Ct """+d1+""" """+d1+""" """+d1+""" 1 Sc -"""+d1+""" -"""+d1+""" """+d1+""" 1 Sc -"""+d1+""" """+d1+""" -"""+d1+""" 1 Sc """+d1+""" -"""+d1+""" -"""+d1+""" 1 Sc """ if self.feffgeom.getcurselection()[0]=='Sq Planar': d=self.scatdist.get() geotext=""" 0 0 0 0 Ct """+d+""" 0 0 1 Sc -"""+d+""" 0 0 1 Sc 0 """+d+""" 0 1 Sc 0 -"""+d+""" 0 1 Sc """ if self.feffgeom.getcurselection()[0]=='Octahedral': d=self.scatdist.get() geotext=""" 0 0 0 0 Ct """+d+""" 0 0 1 Sc -"""+d+""" 0 0 1 Sc 0 """+d+""" 0 1 Sc 0 -"""+d+""" 0 1 Sc 0 0 """+d+""" 1 Sc 0 0 -"""+d+""" 1 Sc """ #begin file writing if self.feffversion.getcurselection()=='FEFF8': fid.write(""" * This file created by SamXAS TITLE """+self.catom+"""-"""+self.satom+""" Single Scatering EDGE """+self.feffedge.getcurselection()[0]+""" S02 1 CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3 EXCHANGE """+exch+""" AFOLP """+self.feffafolp.get()+""" SCF 4 NLEG 2 RPATH """+mrad+""" EXAFS """+mrad+""" POTENTIALS 0 """+cnum+""" """+self.catom+""" 1 """+snum+""" """+self.satom+""" ATOMS * x y z ipot tag """+geotext+""" """) fid.close() else: holevar=int(self.feffedge.curselection()[0])+1 fid.write(""" * This file created by SamXAS TITLE """+self.catom+"""-"""+self.satom+""" Single Scatering HOLE """+str(holevar)+""" 1 CONTROL 1 1 1 1 PRINT 1 0 0 3 RMAX """+mrad+""" EXCHANGE """+exch+""" AFOLP """+self.feffafolp.get()+""" NLEG 2 POTENTIALS 0 """+cnum+""" """+self.catom+""" 1 """+snum+""" """+self.satom+""" ATOMS * x y z ipot tag """+geotext+""" """) fid.close() #run feff os.system(self.feffcom.get()) #move files to proper locations resdir=lower(self.catom+"paths") dp=str(int(rad*1000)) filnm=self.catom+self.feffedge.getcurselection()[0]+"-"+self.satom+"-"+dp+".dat" #copy results into buffer fid=open("feff0001.dat","r") feffout=fid.read() fid.close() #find directories dirs=os.listdir('..') dirpres=0 for dr in dirs: if lower(dr)==resdir: dirpres=1 if dirpres==0: os.chdir(filepath) os.mkdir(resdir) fid=open(filepath+resdir+os.sep+filnm,"w") fid.write(feffout) fid.close() os.chdir(filepath) ############################################################################## ## ## ## Advanced Fitting Routine ## ## ############################################################################## class DefPath: def __init__(self,master,pnum): f=Frame(master) f.pack(side=TOP,padx=2,pady=0) self.pon=IntVar() self.dset=IntVar() self.dset.set(0) textlab="Use "+pnum+" in fit?" cb=Checkbutton(f,text=textlab,variable=self.pon,anchor=W) cb.pack(side=LEFT,padx=10,pady=2) cb=Checkbutton(f,text="Set DEGEN = 1?",variable=self.dset,anchor=W) cb.pack(side=LEFT,padx=10,pady=2) b=Button(f,bitmap="@"+filepath+"xbms"+os.sep+"openfolder.xbm",command=self.feffpathme,height=21,width=30,bg='lightyellow') b.pack(side=LEFT,padx=2,pady=2) l=Label(f,text="Choose Path") l.pack(side=LEFT,padx=2,pady=2) g=Frame(master) g.pack(side=TOP,padx=2,pady=0) self.loc=Pmw.EntryField(g,label_text="Path Location:",labelpos=W,entry_width=55) self.loc.pack(side=TOP,padx=2,pady=2) self.descr=Pmw.EntryField(g,label_text="Path Label:",labelpos=W,entry_width=55) self.descr.pack(side=TOP,padx=2,pady=2) self.descr.setentry("label") self.s02=Pmw.EntryField(g,label_text="S02:",labelpos=W,entry_width=55) self.s02.pack(side=TOP,padx=2,pady=2) self.e0=Pmw.EntryField(g,label_text="E0:",labelpos=W,entry_width=55) self.e0.pack(side=TOP,padx=2,pady=2) self.deltaR=Pmw.EntryField(g,label_text="deltaR:",labelpos=W,entry_width=55) self.deltaR.pack(side=TOP,padx=2,pady=2) self.sig=Pmw.EntryField(g,label_text="sigma2:",labelpos=W,entry_width=55) self.sig.pack(side=TOP,padx=2,pady=2) self.third=Pmw.EntryField(g,label_text="third:",labelpos=W,entry_width=55) self.third.pack(side=TOP,padx=2,pady=2) self.fourth=Pmw.EntryField(g,label_text="fourth:",labelpos=W,entry_width=55) self.fourth.pack(side=TOP,padx=2,pady=2) Pmw.alignlabels([self.loc,self.descr,self.s02,self.e0,self.deltaR,self.sig,self.third,self.fourth]) def feffpathme(self): global lastfeffdir fn=ask_for_file([("feff files","*.dat"),("all files","*")],lastfeffdir,check=0) sdir=rfind(fn,os.sep) lastfeffdir=fn[:sdir] entry_replace(self.loc,fn) root.adwin.focus_set() class DefVar: def __init__(self,master): self.f=Frame(master) self.f.pack(side=TOP,padx=2) self.von=IntVar() self.von.set(1) self.cb=Checkbutton(self.f,variable=self.von) self.cb.pack(side=LEFT,padx=2,pady=0) self.type=Pmw.RadioSelect(self.f,buttontype='radiobutton',labelpos=None,padx=0,pady=0) for text in ('G','S','D'): self.type.add(text) self.type.pack(side=LEFT,padx=2,pady=0) self.vname=Pmw.EntryField(self.f,entry_width=15) self.vname.pack(side=LEFT,padx=2,pady=0) self.vexp=Pmw.EntryField(self.f,entry_width=45) self.vexp.pack(side=LEFT,padx=2,pady=0) self.buffer=' ' self.restraint=0 class AdvFit: def __init__(self): adwin=root.adwin=Toplevel(root) adwin.title("Advanced EXAFS Fitting Dialog") adwin.protocol("WM_DELETE_WINDOW", self.closemod) self.adwin=adwin self.root=root root.iconify() #change focus... adwin.focus_set() #GUI for fitting window... #create menu for fitting window menubar=Pmw.MenuBar(adwin) #file menu menubar.addmenu('File','') menubar.addmenuitem('File','command',label='Open Data',command=self.menuopen) menubar.addmenuitem('File','separator') menubar.addmenuitem('File','command',label='Edit Default Directories',command=self.callchangedefdirs) menubar.addmenuitem('File','separator') menubar.addmenuitem('File','command',label='Close',command=self.closemod) menubar.addmenuitem('File','command',label='Quit',command=root.quit) menubar.addmenu('Save','') menubar.addmenuitem('Save','command',label='Fit Data',command=self.savefitdata) menubar.addmenuitem('Save','command',label='Spec Data',command=self.saverawdata) menubar.addmenuitem('Save','command',label='Residuals',command=self.saveresiddata) menubar.addmenu('Workspace','') menubar.addmenuitem('Workspace','command',label='Save Workspace',command=self.saveallvars) menubar.addmenuitem('Workspace','command',label='Load Workspace',command=self.loadallvars) menubar.addmenu('Templates','') menubar.addmenuitem('Templates','command',label='Simple',command=self.pathsimple) menubar.addmenuitem('Templates','command',label='Simple-Linked',command=self.pathsimplel) menubar.addmenuitem('Templates','command',label='CNs-Unique',command=self.pathcnumu) menubar.addmenuitem('Templates','command',label='CNs-Linked',command=self.pathcnuml) menubar.addcascademenu('Templates','Debye Models') menubar.addmenuitem('Debye Models','command',label='General',command=self.pathdebye) menubar.addmenuitem('Debye Models','command',label='O shell',command=self.pathodebye) menubar.addmenuitem('Debye Models','command',label='Me Shell',command=self.pathMedebye) menubar.addmenuitem('Templates','command',label='Einstein Model',command=DISABLED,state=DISABLED) menubar.addmenuitem('Templates','command',label='Pair Potential',command=DISABLED,state=DISABLED) menubar.addmenu('Path Vars','') menubar.addmenuitem('Path Vars','command',label='Add reff',command=self.varreff) menubar.addmenuitem('Path Vars','command',label='Add abs to sigma2',command=self.abssigma) menubar.addmenuitem('Path Vars','command',label='Add P-P Vars',command=DISABLED,state=DISABLED) menubar.addmenuitem('Path Vars','separator') menubar.addmenuitem('Path Vars','command',label='Sort by Name',command=self.sortfitvarsbyname) menubar.addmenuitem('Path Vars','command',label='Sort by Letter',command=self.sortfitvarsbyletter) menubar.addmenuitem('Path Vars','command',label='Sort by Creation',command=self.sortfitvarsbycreation) menubar.addmenuitem('Path Vars','command',label='Sort by Path',command=self.sortfitvarsbypath) menubar.addmenuitem('Path Vars','separator') menubar.addmenuitem('Path Vars','command',label='Recall Last Fit Result',command=self.recallvarbuffer) menubar.addmenuitem('Path Vars','separator') menubar.addmenuitem('Path Vars','command',label='Search and Replace FEFF file Paths',command=self.activateSRFEFF) menubar.addmenu('Fit','') menubar.addcascademenu('Fit','Fit k-weight',tearoff=1) self.fitmenukweight=IntVar() menubar.addmenuitem('Fit k-weight','radiobutton',label='default',value=0,variable=self.fitmenukweight) menubar.addmenuitem('Fit k-weight','radiobutton',label='3210',value=1,variable=self.fitmenukweight) menubar.addmenuitem('Fit k-weight','radiobutton',label='321',value=2,variable=self.fitmenukweight) menubar.addmenuitem('Fit k-weight','radiobutton',label='32',value=3,variable=self.fitmenukweight) self.fitmenukweight.set(0) menubar.addcascademenu('Fit','Fit Background Spline',tearoff=1) self.fitmenuspline=IntVar() menubar.addmenuitem('Fit Background Spline','radiobutton',label='Off',value=0,variable=self.fitmenuspline) menubar.addmenuitem('Fit Background Spline','radiobutton',label='On',value=1,variable=self.fitmenuspline) self.fitmenuspline.set(0) menubar.addmenu('Help','',side=RIGHT) menubar.addmenuitem('Help','command',label='About SixPack',command=callprogramabout) menubar.addmenuitem('Help','separator') menubar.addmenuitem('Help','command',label='IFEFFIT Command Line',command=RunIFEFFITCmdLine) menubar.grid(row=0,columnspan=24,sticky=W+E) #create toolbar space toolbar=Frame(adwin, relief=SUNKEN,borderwidth=2) b=Button(toolbar,text="Fit",width=6,command=self.dofit,bg="red", fg="white") b.pack(side=LEFT,padx=2,pady=2) b=Button(toolbar,text="ff2chi",width=6,command=self.doff2chi,bg="red", fg="white") b.pack(side=LEFT,padx=2,pady=2) b=Button(toolbar,text="path ff2chi",width=8,command=self.dopathff2chi,bg="red", fg="white") b.pack(side=LEFT,padx=2,pady=2) s=Frame(toolbar,width=60) s.pack(side=LEFT,padx=2,pady=2) b=Button(toolbar,text="Plot Paths",width=10,command=self.plotpathcontributions,bg="red", fg="white") b.pack(side=RIGHT,padx=2,pady=2) b=Button(toolbar,text="Plot q",width=6,command=self.make_q_plot,bg="red", fg="white") b.pack(side=RIGHT,padx=2,pady=2) b=Button(toolbar,text="Plot R",width=6,command=self.make_R_plot,bg="red", fg="white") b.pack(side=RIGHT,padx=2,pady=2) b=Button(toolbar,text="Plot k",width=6,command=self.make_k_plot,bg="red", fg="white") b.pack(side=RIGHT,padx=2,pady=2) #display toolbar.grid(row=1,columnspan=24,sticky=W+E) #add body #first area for data file filebar=Frame(adwin, relief=SUNKEN,bd=2) self.fileentry=Pmw.EntryField(filebar, label_text="Data File:",labelpos=W,validate=None,entry_width=60) self.fileentry.pack(side=LEFT,padx=5,pady=2,fill=X) b=Button(filebar,bitmap="@"+filepath+"xbms"+os.sep+"openfolder.xbm",command=self.fileme,height=21,width=30,bg='lightyellow') b.pack(side=LEFT,padx=2,pady=2) b=Button(filebar,text="Load",bg='darkgreen',fg='snow',command=self.load_data_file) b.pack(side=LEFT,padx=2,pady=2) filebar.grid(row=2,columnspan=16,rowspan=2,sticky=W+E+N+S) s=Frame(filebar,width=55) #spacer to reduce flicker s.pack(side=LEFT,padx=2,pady=2) #FEFF Path Parameters fitwin=Frame(adwin,relief=SUNKEN,bd=2) l=Label(fitwin,text="FEFFIT Variables", relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) feffnb=Pmw.NoteBook(fitwin) if sys.platform == 'win32': feffnb.configure(hull_background="SystemButtonFace") else: feffnb.configure(hull_background='#d4d0c8') feffnb.recolorborders() feffnb.pack(fill="both",expand=1) pathpage=feffnb.add('Paths') s1=Frame(pathpage, relief=GROOVE,bd=2) s1.pack(side=LEFT,padx=2,pady=2) b=Button(s1,text="Define Path",bg='#c7dded',fg='black',command=self.deffeffpath) b.pack(side=TOP,padx=2,pady=2,fill=X) self.pathlist=[] self.pathsel=Pmw.ScrolledListBox(s1,label_text="Path List:",labelpos=NW,selectioncommand=self.changepath, items=self.pathlist,listbox_height=7,vscrollmode='static',listbox_exportselection=0) self.pathsel.pack(side=TOP,padx=2,pady=2,fill=X) b=Button(s1,text="Add Path",bg='darkseagreen4',fg='ivory',command=self.addfeffpath) b.pack(side=TOP,padx=2,pady=2,fill=X) b=Button(s1,text="Remove Path",bg='darkred',fg='ivory',command=DISABLED,state=DISABLED) b.pack(side=TOP,padx=2,pady=2,fill=X) self.pathdes=Pmw.NoteBook(pathpage,tabpos=None) if sys.platform == 'win32': self.pathdes.configure(hull_background="SystemButtonFace") else: self.pathdes.configure(hull_background='#d4d0c8') self.pathdes.recolorborders() self.pathwidlist=[] self.npath=0 self.addfeffpath() self.pathdes.pack(side=LEFT,padx=2,pady=2,fill=BOTH,expand=1) self.pathdes.setnaturalsize() #variable page varpage=feffnb.add('Variables') f=Frame(varpage) b=Button(f,text="Add Variable",command=self.addfitvar,bg='slateblue',fg='snow',width=20) b.pack(side=LEFT,padx=2,pady=2) b=Button(f,text="Add All Variables",command=self.addallfitvar,bg='darkblue',fg='snow',width=20) b.pack(side=LEFT,padx=2,pady=2) b=Button(f,text="Remove Variable",command=self.deletefitvar,bg='darkred',fg='snow',width=20) b.pack(side=LEFT,padx=2,pady=2) b=Button(f,text="Set as Restraint",command=self.restraintfitvar,bg='dark orange',fg='snow',width=20) b.pack(side=LEFT,padx=2,pady=2) f.pack(pady=0,padx=2) self.vsf=Pmw.ScrolledFrame(varpage) self.vsf.pack(padx=2,pady=2,fill=BOTH) self.vfield=self.vsf.interior() l=Label(self.vfield,text="Use Guess Set Def Variable Expression",font="Arial 9 bold",anchor=W) l.pack(padx=2,pady=0,fill=X) self.varwidlist=[] respage=feffnb.add('Results') self.respathvar=IntVar() self.respathvar.set(0) cb=Checkbutton(respage,text='Print FEFF path variables?',variable=self.respathvar,anchor=W,pady=0) cb.pack(padx=2,pady=0) self.restext=Pmw.ScrolledText(respage,hscrollmode='none',vscrollmode='static',label_text="Results of all guessed and defined variables", labelpos=N,borderframe=1,text_font="Courier 9") #,text_state=DISABLED) self.restext.pack(padx=2,pady=0) self.pathdes.setnaturalsize() fitwin.grid(row=4,columnspan=20,rowspan=23,sticky=N+E+S+W) #Add Fit params fitpwin=Frame(adwin,relief=SUNKEN,bd=2) l=Label(fitpwin,text="Fit Parameters",relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) entframe=Frame(fitpwin) entframe.pack(side=TOP) lhe=Frame(entframe) lhe.pack(side=LEFT,fill=X,padx=2,pady=2) rhe=Frame(entframe) rhe.pack(side=LEFT,fill=X,padx=2,pady=2) #define entries self.kmin=Pmw.EntryField(lhe,label_text="kmin:",labelpos=W,validate='real',entry_width=5,value='3') self.kmax=Pmw.EntryField(rhe,label_text="kmax:",labelpos=W,validate='real',entry_width=5,value='13') self.rmin=Pmw.EntryField(lhe,label_text="Rmin:",labelpos=W,validate='real',entry_width=5,value='1') self.rmax=Pmw.EntryField(rhe,label_text="Rmax:",labelpos=W,validate='real',entry_width=5,value='4') self.kweight=Pmw.EntryField(lhe,label_text="kweight:",labelpos=W,validate='integer',entry_width=5,value='3') self.dk=Pmw.EntryField(rhe,label_text="dk:",labelpos=W,validate='real',entry_width=5,value='1') self.fitplhe=[self.kmin,self.rmin,self.kweight] self.fitprhe=[self.kmax,self.rmax,self.dk] for ne in self.fitplhe: ne.pack(fill=X,expand=1,padx=2,pady=2) for ne in self.fitprhe: ne.pack(fill=X,expand=1,padx=2,pady=2) Pmw.alignlabels(self.fitplhe) Pmw.alignlabels(self.fitprhe) #Add ComboBox to options cbframe=Frame(fitpwin) windows=('Hanning','Kaiser-Bessel','Parzen','Welch','Sine') self.winparam=Pmw.ComboBox(cbframe,label_text='FT Window:',labelpos=W,scrolledlist_items=windows,listheight=100) self.winparam.selectitem(windows[1]) self.winparam.pack(side=TOP,fill=X,padx=2,pady=3) fitspc=('q','R','k') self.spcparam=Pmw.ComboBox(cbframe,label_text='Fitting Space:',labelpos=W,scrolledlist_items=fitspc,listheight=70) self.spcparam.selectitem(fitspc[1]) self.spcparam.pack(fill=X,padx=2,pady=3) Pmw.alignlabels([self.spcparam,self.winparam]) cbframe.pack(side=BOTTOM,fill=X,padx=2,pady=2) fitpwin.grid(row=2,column=20,columnspan=4,rowspan=8,sticky=W+E+N+S) #Add plot options plotoptwin=Frame(adwin,relief=SUNKEN,bd=2) l=Label(plotoptwin,text="Plot Options",relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) #add notebook plotnb=Pmw.NoteBook(plotoptwin) if sys.platform == 'win32': plotnb.configure(hull_background="SystemButtonFace") else: plotnb.configure(hull_background='#d4d0c8') plotnb.recolorborders() plotnb.pack(fill="both",expand=1) #add k-page kpage=plotnb.add('k') self.kplots=Pmw.RadioSelect(kpage, buttontype='checkbutton',orient='vertical',labelpos=W) self.kplots.pack(side=TOP,padx=5,pady=5) for text in ('Data','Fit','Residuals','FT Window'): self.kplots.add(text) self.kplots.invoke('Data') self.kplotwt=Pmw.EntryField(kpage,labelpos=W,label_text='kweight:',validate='integer',entry_width=5,value='3') self.kplotmin=Pmw.EntryField(kpage,labelpos=W,label_text='kmin:',validate='real',entry_width=5,value='3') self.kplotmax=Pmw.EntryField(kpage,labelpos=W,label_text='kmax:',validate='real',entry_width=5,value='13') self.kplotwt.pack(side=TOP,padx=5,pady=5) self.kplotmin.pack(side=LEFT,padx=5,pady=2) self.kplotmax.pack(side=LEFT,padx=5,pady=2) #add R-page rpage=plotnb.add('R') rframe=Frame(rpage) rframe.pack(side=TOP,fill=X) self.rplots=Pmw.RadioSelect(rframe, buttontype='checkbutton',orient='vertical',labelpos=W) self.rplots.pack(side=LEFT,padx=5,pady=5) for text in ('Data','Fit'): self.rplots.add(text) self.rplots.invoke('Data') self.rptype=Pmw.RadioSelect(rframe, buttontype='checkbutton',orient='vertical',labelpos=W) self.rptype.pack(side=LEFT,padx=5,pady=5) for text in ('Magnitude','Real','Imaginary'): self.rptype.add(text) self.rptype.invoke('Magnitude') self.rplotmin=Pmw.EntryField(rpage,labelpos=W,label_text='Rmin:',validate='real',entry_width=5,value='0') self.rplotmax=Pmw.EntryField(rpage,labelpos=W,label_text='Rmax:',validate='real',entry_width=5,value='6') self.rplotmin.pack(side=LEFT,padx=5,pady=5) self.rplotmax.pack(side=LEFT,padx=5,pady=5) #add q-page qpage=plotnb.add('q') qframe=Frame(qpage) qframe.pack(side=TOP,fill=X) self.qplots=Pmw.RadioSelect(qframe, buttontype='checkbutton',orient='vertical',labelpos=W) self.qplots.pack(side=LEFT,padx=5,pady=5) for text in ('Data','Fit'): self.qplots.add(text) self.qplots.invoke('Data') self.qptype=Pmw.RadioSelect(qframe, buttontype='checkbutton',orient='vertical',labelpos=W) self.qptype.pack(side=LEFT,padx=5,pady=5) for text in ('Real','Imaginary'): self.qptype.add(text) self.qptype.invoke('Real') self.qplotmin=Pmw.EntryField(qpage,labelpos=W,label_text='qmin:',validate='real',entry_width=5,value='3') self.qplotmax=Pmw.EntryField(qpage,labelpos=W,label_text='qmax:',validate='real',entry_width=5,value='13') self.qplotmin.pack(side=LEFT,padx=5,pady=5) self.qplotmax.pack(side=LEFT,padx=5,pady=5) #add Path Page ppage=plotnb.add('Path') self.cumpathsels=Pmw.RadioSelect(ppage,buttontype='checkbutton',orient='vertical',labelpos=W) self.cumpathsels.pack(side=LEFT,padx=5,pady=5) for text in ('Data','Fit'): self.cumpathsels.add(text) self.cumpathsels.invoke('Data') self.cumpathtype=Pmw.RadioSelect(ppage,buttontype='radiobutton',orient='vertical',labelpos=W) self.cumpathtype.pack(side=LEFT,padx=5,pady=5) for text in ('k','R','q'): self.cumpathtype.add(text) self.cumpathtype.invoke('R') #finis plotnb.setnaturalsize() plotoptwin.grid(row=10,column=20,columnspan=4,rowspan=17,sticky=W+E+N+S) #Fit Quality Bar bar=Frame(adwin, relief=SUNKEN,bd=2) l=Label(bar,text="Chi Sq: ",anchor=W) self.ChiSq=Label(bar,text="",width=20,anchor=W) l.pack(side=LEFT,padx=2,pady=2) self.ChiSq.pack(side=LEFT,padx=2,pady=2) l=Label(bar,text="Red Chi Sq: ",anchor=W) self.ChiSqR=Label(bar,text="",width=20,anchor=W) l.pack(side=LEFT,padx=2,pady=2) self.ChiSqR.pack(side=LEFT,padx=2,pady=2) m=Label(bar,text="R factor: ",anchor=W) self.Rvalue=Label(bar,text="",width=20,anchor=W) m.pack(side=LEFT,padx=2,pady=2) self.Rvalue.pack(side=LEFT,padx=2,pady=2) #check box for correlations self.calccorels=Pmw.RadioSelect(bar,labelpos=W,padx=1,pady=1,command=self.showcorelwin,buttontype='checkbutton') self.calccorels.pack(side=RIGHT,padx=10,pady=1) self.calccorels.add('Display Correlations?') bar.grid(row=27,columnspan=24,sticky=W+E) #add status bar to bottom of window if sys.platform=='win32': self.status=Label(adwin,text="",bd=2,relief=RAISED,anchor=W,fg='blue',bg='SystemButtonFace') else: self.status=Label(adwin,text="",bd=2,relief=RAISED,anchor=W,fg='blue',bg='#d4d0c8') self.status.grid(row=28,columnspan=24,sticky=W+E) setstatus(self.status,"Ready") self.mstat=0 #error window self.box=Pmw.MessageDialog(root,title='File Error',defaultbutton=0,message_text='Wrong type of parameter file chosen!', iconpos='n',icon_bitmap='warning') self.box.iconname('File Error') self.box.withdraw() #correlation window self.corwin=Pmw.TextDialog(root,title='Fit Correlations',command=self.killcorelwin,deactivatecommand=self.killcorelwin,scrolledtext_hscrollmode='static',scrolledtext_vscrollmode='static',text_wrap='none',scrolledtext_labelpos=N,label_text='Fit Variable Correlations',buttons=('Remove',)) self.corwin.iconname('Fit Correlations') self.corwin.tag_config('hi',foreground='red') self.corwin.withdraw() iffc.ifeffit("read_data(file="+filepath+"test.inp, group=firsttest,label='energy xmu')") self.pathdegen={} self.pathdegenf={} #define searchreplaceFEFF diaglog self.SRFEFFdialog=Pmw.Dialog(self.adwin,buttons=('OK','Cancel'),defaultbutton='OK',title='Search and Replace FEFF Paths',command=self.searchreplaceFEFF) self.SRFEFFdialog.withdraw() #add guts of dialog window self.SRFpathlist=[] self.SRFpath=Pmw.Counter(self.SRFEFFdialog.interior(),labelpos='w',label_text='Replace Path: ',entry_width=60,datatype=self.SRFdatatype) self.SRFreplace=Pmw.EntryField(self.SRFEFFdialog.interior(),labelpos='w',label_text='With Path:',entry_width=60) entries=(self.SRFpath,self.SRFreplace) Pmw.alignlabels(entries) for entry in entries: entry.pack(fill='x',expand=1,padx=5,pady=5) def callprogramabout(self): programabout(self.root) def callchangedefdirs(self): global lastsavedir,lastreaddir s=changedefdirs(self.adwin) lastreaddir=s.newdir lastsavedir=s.newdir def closemod(self): #erase paths for pth in self.pathlist: pi=self.pathlist.index(pth) pnum=str(pi+1) iffc.ifeffit("erase @path="+pnum) getmainmenu(root.adwin) def SRFdatatype(self,text,factor,increment): if self.SRFpathlist==[]: return '' #find index of current path try: i=self.SRFpathlist.index(text) except: self.SRFreplace.setentry(self.SRFpathlist[0]) return self.SRFpathlist[0] i=i+factor if i>(len(self.SRFpathlist)-1): i=0 newtext=self.SRFpathlist[i] self.SRFreplace.setentry(newtext) return newtext def searchreplaceFEFF(self,result): #search and replace FEFF paths in current workspace if result=='Cancel': self.SRFEFFdialog.deactivate() return st=self.SRFpath.getvalue() rt=self.SRFreplace.getvalue() if st==rt: self.SRFEFFdialog.deactivate() return #perform search and replace i=0 for pth in self.pathwidlist: ptext=pth.p.loc.getvalue() new=replace(ptext,st,rt,1) if new!=ptext: i=i+1 pth.p.loc.setvalue(new) self.SRFEFFdialog.deactivate() setstatus(self.status,"FEFF Path replaced in "+str(i)+" occurences") def activateSRFEFF(self): #create list of FEFF file path routes self.SRFpathlist=[] for pth in self.pathwidlist: ptext=pth.p.loc.getvalue() if ptext!='': #delete file info pdirind=rfind(ptext,os.sep) pdir=ptext[:pdirind] if pdir not in self.SRFpathlist: self.SRFpathlist.append(pdir) #activate dialog self.SRFEFFdialog.activate() def showcorelwin(self,*arg): if self.calccorels.getcurselection()!=(): #show box self.corwin.deiconify() else: #remove box self.killcorelwin() def killcorelwin(self,*arg): #empty=[] #self.calccorels.setvalue(empty) self.corwin.withdraw() if self.calccorels.getcurselection()!=(): self.calccorels.invoke(0) def printcorels(self): #print correlations in window self.corwin.clear() self.corwin.insert(END,"Correlations for fit\n") self.corwin.insert(END,"File: "+self.fileentry.get()+"\n\n") #print chisquare and R-value line="NumIDP: "+str(iffc.get_scalar('n_idp'))+"\t\tNumVars:"+str(iffc.get_scalar('n_varys')) self.corwin.insert(END,line+'\n') line="Chi-Sq: "+str(iffc.get_scalar('chi_square'))+"\t\tR-value: "+str(iffc.get_scalar('r_factor')) self.corwin.insert(END,line+'\n') line="Red Chi-Sq: "+str(iffc.get_scalar('chi_reduced')) self.corwin.insert(END,line+'\n\n') #get list of all guessed variables guessvar=[] for v in self.varwidlist: if v.type.getcurselection()=='G' and v.von.get()==1: guessvar.append(v) #get correlations gvar2=guessvar for v0 in guessvar: for v1 in gvar2: #get v0-v1 correlation xvar=v0.vname.get() yvar=v1.vname.get() if xvar!=yvar: iffc.ifeffit("correl(x="+xvar+",y="+yvar+",min=0,out=correl_last)") corel=iffc.get_scalar('correl_last') if abs(corel)>0.10: vartext=ljust(xvar+'-'+yvar+':',30) if abs(corel)>0.75: self.corwin.insert(END,vartext+'\t'+str(corel)+'\n',"hi") else: self.corwin.insert(END,vartext+'\t'+str(corel)+'\n') gvar2.remove(v0) def addfitvar(self): new=DefVar(self.vfield) self.varwidlist.append(new) def addallfitvar(self): for path in self.pathwidlist: if path.p.pon.get()==1: if path.p.s02.get()<>'': self.parsevarlist(path.p.s02) if path.p.e0.get()<>'': self.parsevarlist(path.p.e0) if path.p.deltaR.get()<>'': self.parsevarlist(path.p.deltaR) if path.p.sig.get()<>'': self.parsevarlist(path.p.sig) if path.p.third.get()<>'': self.parsevarlist(path.p.third) if path.p.fourth.get()<>'': self.parsevarlist(path.p.fourth) def parsevarlist(self,vf): vtotal=vf.get() parsed=['-','+','*','/','(',')',',','abs','sqrt','exp','log','erf','erfc','sign','debye','eins','min','max','cos','sin','tan','reff'] for x in parsed: vtotal=replace(vtotal,x,' ') vtotal=split(vtotal) for y in vtotal: self.addtovarlist(y) def addtovarlist(self,vw): #check to see if variable is already there! pres=0 for var in self.varwidlist: if var.vname.get()==vw: pres=1 if pres==0: self.addfitvar() newvar=self.varwidlist[len(self.varwidlist)-1] newvar.vname.setentry(vw) def restraintfitvar(self): curfoc=self.adwin.focus_get() curname=curfoc.master curframe=curname.master focvar=0 focwid='' for v in self.varwidlist: if str(v.vname)==str(curfoc.master): focvar=1 focwid=v if str(v.vexp)==str(curfoc.master): focvar=1 focwid=v if focvar==0: #not a variable tkMessageBox.showwarning("Variable Restraint","No variable selected") return #toggle restraint status focwid.restraint=focwid.restraint+1 if int(focwid.restraint)==1: #change layout to mark variable focwid.f.configure(bg='red') focwid.cb.configure(bg='red') focwid.type.configure(Button_bg='red') if int(focwid.restraint)==2: focwid.restraint=0 #undo frame if sys.platform == 'win32': focwid.f.configure(bg='SystemButtonFace') focwid.cb.configure(bg='SystemButtonFace') focwid.type.configure(Button_bg='SystemButtonFace') else: focwid.f.configure(bg='#d4d0c8') focwid.cb.configure(bg='#d4d0c8') focwid.type.configure(Button_bg='#d4d0c8') def deletefitvar(self): curfoc=self.adwin.focus_get() curname=curfoc.master curframe=curname.master focvar=0 focwid='' for v in self.varwidlist: if str(v.vname)==str(curfoc.master): focvar=1 focwid=v if str(v.vexp)==str(curfoc.master): focvar=1 focwid=v if focvar==0: #not a variable tkMessageBox.showwarning("Remove Variable","No variable selected") return #make sure name=focwid.vname.getvalue() suretext="Remove variable named "+name ask=tkMessageBox.askyesno("Remove Variable",suretext) if ask==0: return #kill variable in IFEFFIT if name!='': iffc.ifeffit("erase "+name) #remove from varlist self.varwidlist.remove(focwid) #kill widget curframe.destroy() def sortfitvarsbyname(self): #create dictionary vard={} for v in self.varwidlist: #frame name, var frame vard.update({v.vname.getvalue():v.f}) #unpack all v.f.pack_forget() #sort keys=vard.keys() keys.sort() sortlist=[vard[key] for key in keys] #repack for i in sortlist: i.pack(side=TOP,padx=2) def sortfitvarsbyletter(self): #create dictionary vard={} for v in self.varwidlist: #frame name, var frame vard.update({upper(v.vname.getvalue()):v.f}) #unpack all v.f.pack_forget() #sort keys=vard.keys() keys.sort() sortlist=[vard[key] for key in keys] #repack for i in sortlist: i.pack(side=TOP,padx=2) def sortfitvarsbycreation(self): for v in self.varwidlist: #unpack all v.f.pack_forget() #repack for v in self.varwidlist: v.f.pack(side=TOP,padx=2) def sortfitvarsbypath(self): lefttogo=self.varwidlist for v in self.varwidlist: #unpack all v.f.pack_forget() for path in self.pathwidlist: if path.p.pon.get()==1: wids=[path.p.s02,path.p.e0,path.p.deltaR,path.p.sig,path.p.third,path.p.fourth] for w in wids: for v in lefttogo: if rfind(w.get(),v.vname.getvalue())!=-1: v.f.pack(side=TOP,padx=2) lefttogo.remove(v) #do the rest by letter if len(lefttogo)!=0: vard={} for v in lefttogo: vard.update({upper(v.vname.getvalue()):v.f}) #sort keys=vard.keys() keys.sort() sortlist=[vard[key] for key in keys] #repack for i in sortlist: i.pack(side=TOP,padx=2) def addfeffpath(self): self.npath=self.npath+1 pname="Path "+str(self.npath) new=self.pathdes.add(pname) new.p=DefPath(new,pname) self.pathwidlist.append(new) self.pathlist.append(pname) #str(self.npath)+":") c=self.pathsel.curselection() self.pathsel.setlist(self.pathlist) if c==(): self.pathsel.select_set(0) else: self.pathsel.select_set(c) def changepath(self): #cursel=self.pathsel.getcurselection()[0] #ind=find(cursel,':') #curnum=cursel[0:ind] #page='Path '+curnum self.pathdes.selectpage(self.pathsel.getcurselection()[0]) def varreff(self): #get current path cptuple=self.pathsel.getcurselection() cp=cptuple[0] #get index of Path with pathlist #refer to correct widgets in pathwidlist.p.XXXX pi=self.pathlist.index(cp) ap=self.pathwidlist[pi] pnum=str(pi+1) #set entries ap.p.deltaR.setentry("R"+pnum+"-reff") def abssigma(self): #get current path cptuple=self.pathsel.getcurselection() cp=cptuple[0] #get index of Path with pathlist #refer to correct widgets in pathwidlist.p.XXXX pi=self.pathlist.index(cp) ap=self.pathwidlist[pi] pnum=str(pi+1) #set entries ap.p.sig.setentry("abs(sig"+pnum+")") def pathsimple(self): #get current path cptuple=self.pathsel.getcurselection() cp=cptuple[0] #get index of Path with pathlist #refer to correct widgets in pathwidlist.p.XXXX pi=self.pathlist.index(cp) ap=self.pathwidlist[pi] pnum=str(pi+1) #set entries ap.p.s02.setentry("s02_"+pnum) ap.p.e0.setentry("e0_"+pnum) ap.p.deltaR.setentry("delR_"+pnum) ap.p.sig.setentry("sig_"+pnum) def pathsimplel(self): #get current path cptuple=self.pathsel.getcurselection() cp=cptuple[0] #get index of Path with pathlist #refer to correct widgets in pathwidlist.p.XXXX pi=self.pathlist.index(cp) ap=self.pathwidlist[pi] pnum=str(pi+1) #set entries ap.p.s02.setentry("s02") ap.p.e0.setentry("e0") ap.p.deltaR.setentry("delR_"+pnum) ap.p.sig.setentry("sig_"+pnum) def pathcnumu(self): #get current path cptuple=self.pathsel.getcurselection() cp=cptuple[0] #get index of Path with pathlist #refer to correct widgets in pathwidlist.p.XXXX pi=self.pathlist.index(cp) ap=self.pathwidlist[pi] pnum=str(pi+1) #set entries ap.p.s02.setentry("N"+pnum+"*s02") ap.p.e0.setentry("e0_"+pnum) ap.p.deltaR.setentry("delR_"+pnum) ap.p.sig.setentry("sig_"+pnum) def pathcnuml(self): #get current path cptuple=self.pathsel.getcurselection() cp=cptuple[0] #get index of Path with pathlist #refer to correct widgets in pathwidlist.p.XXXX pi=self.pathlist.index(cp) ap=self.pathwidlist[pi] pnum=str(pi+1) #set entries ap.p.s02.setentry("N"+pnum+"*s02") ap.p.e0.setentry("e0") ap.p.deltaR.setentry("delR_"+pnum) ap.p.sig.setentry("sig_"+pnum) def pathdebye(self): #get current path cptuple=self.pathsel.getcurselection() cp=cptuple[0] #get index of Path with pathlist #refer to correct widgets in pathwidlist.p.XXXX pi=self.pathlist.index(cp) ap=self.pathwidlist[pi] pnum=str(pi+1) #set entries ap.p.s02.setentry("amp_"+pnum) ap.p.e0.setentry("e0_"+pnum) ap.p.deltaR.setentry("delR_"+pnum) ap.p.sig.setentry("debye(temp,theta_"+pnum+")") def pathMedebye(self): #get current path cptuple=self.pathsel.getcurselection() cp=cptuple[0] #get index of Path with pathlist #refer to correct widgets in pathwidlist.p.XXXX pi=self.pathlist.index(cp) ap=self.pathwidlist[pi] pnum=str(pi+1) #set entries ap.p.s02.setentry("amp_Me") ap.p.e0.setentry("e0_Me") ap.p.deltaR.setentry("delR_"+pnum+"-reff") ap.p.sig.setentry("debye(temp,thetaMe)") def pathodebye(self): #get current path cptuple=self.pathsel.getcurselection() cp=cptuple[0] #get index of Path with pathlist #refer to correct widgets in pathwidlist.p.XXXX pi=self.pathlist.index(cp) ap=self.pathwidlist[pi] pnum=str(pi+1) #set entries ap.p.s02.setentry("amp_O") ap.p.e0.setentry("e0_O") ap.p.deltaR.setentry("delR_"+pnum+"-reff") ap.p.sig.setentry("debye(temp,thetaO)") def fileme(self): fileget(root.adwin,self.fileentry) def load_data_file(self): self.dataname=trimdirext(self.fileentry.get()) if self.dataname=='': print " ERROR: Empty file name" else: iffc.ifeffit("read_data(file="+self.fileentry.get()+", group="+self.dataname+",label='k chi')") setstatus(self.status,"Data file "+self.dataname+" loaded!") def menuopen(self): self.fileme() self.load_data_file() def sp_plot(self,new,gx,gy,xlab,ylab,title,xmin,xmax,key): keytext="" if key==1: keytext="""k"""+self.kplotwt.get()+""" chi(k)-data""" elif key==2: keytext="""k"""+self.kplotwt.get()+""" chi(k)-fit""" elif key==3: keytext="""|chi(R)|-data""" elif key==4: keytext="""Re[chi(R)]-data""" elif key==5: keytext="""Im[chi(R)]-data""" elif key==6: keytext="""|chi(R)|-fit""" elif key==7: keytext="""Re[chi(R)]-fit""" elif key==8: keytext="""Im[chi(R)]-fit""" elif key==9: keytext="""Re[chi(q)]-data""" elif key==10: keytext="""Im[chi(q)]-data""" elif key==11: keytext="""Re[chi(q)]-fit""" elif key==12: keytext="""Im[chi(q)]-fit""" elif key==13: keytext="""FT Window""" elif key==14: keytext="""Residuals""" elif key==15: keytext="""Background Spline""" else: pathnum=key-15 keytext="""Path """+str(pathnum) xdat=iffc.get_array(gx) ydat=iffc.get_array(gy) if new==1: spplotter.SPPlotter(self.root,cmd="new",lt=keytext,xd=xdat,yd=ydat,xt=xlab,yt=ylab, title=title,xmin=xmin,xmax=xmax) if new==0: spplotter.SPPlotter(self.root,cmd="stack",lt=keytext,xd=xdat,yd=ydat,xt=xlab,yt=ylab, title=title,xmin=xmin,xmax=xmax) def make_k_plot(self): plotme=self.kplots.getcurselection() newg=1 km1=self.kplotmin.get() km2=self.kplotmax.get() for pt in plotme: if pt=='Data': dn=self.dataname iffc.ifeffit("dokwt "+dn+" "+self.kplotwt.get()) self.sp_plot(newg,dn+".k",dn+".chi_kw","k","chi",dn,km1,km2,1) newg=0 if pt=='Fit': iffc.ifeffit("dokwt fit "+self.kplotwt.get()) self.sp_plot(newg,"fit.k","fit.chi_kw","k","chi","FEFF Data",km1,km2,2) newg=0 if pt=='Residuals': dn=self.dataname iffc.ifeffit("dokwt "+dn+" "+self.kplotwt.get()) iffc.ifeffit("dokwt fit "+self.kplotwt.get()) iffc.ifeffit("fit.kwres="+dn+".chi_kw-fit.chi_kw") self.sp_plot(newg,"fit.k","fit.kwres","k","chi","FEFF Data",km1,km2,14) newg=0 if pt=='FT Window': dn=self.dataname iffc.ifeffit("window(k="+dn+".k,group=win,kweight="+self.kweight.get()+",kmin="+\ self.kmin.get()+",kmax="+self.kmax.get()+""",kwindow='"""+\ self.winparam.get()+"""',dk="""+self.dk.get()+")") iffc.ifeffit("win.mwin=win.win*ceil(abs("+dn+".chi_kw))") wdat=iffc.get_array("win.mwin") self.sp_plot(newg,dn+".k","win.mwin","k","chi","FEFF Data",km1,km2,13) if self.fitmenuspline.get()==1: self.sp_plot(newg,"fit.k","fit.kbkg","k","chi","FEFF Data",km1,km2,15) setstatus(self.status,"k plot complete") def make_R_plot(self): plotme=self.rplots.getcurselection() plottpy=self.rptype.getcurselection() win=self.winparam.get(ACTIVE) kw=self.kweight.get() dk=self.dk.get() rm1=self.rplotmin.get() rm2=self.rplotmax.get() newg=1 for pt in plotme: if pt=='Data': dn=self.dataname iffc.ifeffit("fftf(real="+dn+".chi,kweight="+kw+",kmin="+self.kmin.get()+\ ",kmax="+self.kmax.get()+""",kwindow='"""+win+"""',dk="""+dk+")") for pt2 in plottpy: if pt2=='Magnitude': self.sp_plot(newg,dn+".r",dn+".chir_mag","R","Amp",dn,rm1,rm2,3) newg=0 if pt2=='Real': self.sp_plot(newg,dn+".r",dn+".chir_re","R","Amp",dn,rm1,rm2,4) newg=0 if pt2=='Imaginary': self.sp_plot(newg,dn+".r",dn+".chir_im","R","Amp",dn,rm1,rm2,5) newg=0 if pt=='Fit': iffc.ifeffit("fftf(real=fit.chi,kweight="+kw+",kmin="+self.kmin.get()+\ ",kmax="+self.kmax.get()+""",kwindow='"""+win+"""',dk="""+dk+")") for pt2 in plottpy: if pt2=='Magnitude': self.sp_plot(newg,"fit.r","fit.chir_mag","R","Amp","FEFF Data",rm1,rm2,6) newg=0 if pt2=='Real': self.sp_plot(newg,"fit.r","fit.chir_re","R","Amp","FEFF Data",rm1,rm2,7) newg=0 if pt2=='Imaginary': self.sp_plot(newg,"fit.r","fit.chir_im","R","Amp","FEFF Data",rm1,rm2,8) newg=0 setstatus(self.status,"R plot complete") def make_q_plot(self): plotme=self.qplots.getcurselection() plottpy=self.qptype.getcurselection() qm1=self.qplotmin.get() qm2=self.qplotmax.get() newg=1 for pt in plotme: if pt=='Data': dn=self.dataname iffc.ifeffit("fftr(real="+dn+".chir_re,imag="+dn+".chir_im,rmin="+self.rmin.get()+\ ",rmax="+self.rmax.get()+",dr=0.2)") for pt2 in plottpy: if pt2=='Real': self.sp_plot(newg,dn+".q",dn+".chiq_re","q","chi",dn,qm1,qm2,9) newg=0 if pt2=='Imaginary': self.sp_plot(newg,dn+".q",dn+".chiq_im","q","chi",dn,qm1,qm2,10) newg=0 if pt=='Fit': iffc.ifeffit("fftr(real=fit.chir_re,imag=fit.chir_im,rmin="+self.rmin.get()+\ ",rmax="+self.kmax.get()+",dr=0.2)") for pt2 in plottpy: if pt2=='Real': self.sp_plot(newg,"fit.q","fit.chiq_re","q","chi","FEFF Data",qm1,qm2,11) newg=0 if pt2=='Imaginary': self.sp_plot(newg,"fit.q","fit.chiq_im","q","chi","FEFF Data",qm1,qm2,12) newg=0 setstatus(self.status,"q plot complete") def deffeffpath(self): #get current path cp=self.pathsel.getcurselection()[0] #get index of Path with pathlist #refer to correct widgets in pathwidlist.p.XXXX pi=self.pathlist.index(cp) ap=self.pathwidlist[pi] pnum=str(pi+1) self.deffeffpathfin(pnum,ap.p) setstatus(self.status,"FEFF Path "+pnum+" defined!") def deffeffpathfin(self,pnum,path): #tell ifeffit to define path... iffc.ifeffit("path("+pnum+",feff="+path.loc.get()+")") iffc.ifeffit("path("+pnum+",label="+path.descr.get()+")") iffc.ifeffit("path("+pnum+",s02="+path.s02.get()+",e0="+path.e0.get()+",delr="+path.deltaR.get()+",sigma2="+path.sig.get()+")") iffc.ifeffit("get_path("+pnum+")") pzn=zfill(pnum,3) #fill default degen if needed if not self.pathdegenf.has_key(pnum): self.pathdegenf.update({pnum:path.loc.get()}) self.pathdegen.update({pnum:iffc.get_scalar("path"+pzn+"_degen")}) if self.pathdegenf[pnum]!=path.loc.get(): self.pathdegenf.update({pnum:path.loc.get()}) self.pathdegen.update({pnum:iffc.get_scalar("path"+pzn+"_degen")}) if path.dset.get()==1: iffc.ifeffit("path("+pnum+",degen=1)") if path.dset.get()==0: iffc.ifeffit("path("+pnum+",degen="+str(self.pathdegen[pnum])+")") if path.third.get()<>"": iffc.ifeffit("path("+pnum+",third="+path.third.get()+")") if path.fourth.get()<>"": iffc.ifeffit("path("+pnum+",fourth="+path.fourth.get()+")") def doff2chi(self): iffc.ifeffit("set_fit_params "+self.kmin.get()+" "+self.kmax.get()+" "+self.rmin.get()+" "+\ self.rmax.get()+" "+self.kweight.get()+" "+self.dk.get()+" "+self.winparam.get(ACTIVE)+" "+self.spcparam.get(ACTIVE)) #update all variables with def for var in self.varwidlist: if var.von.get()==1: iffc.ifeffit("def("+var.vname.get()+"="+var.vexp.get()+")") if var.von.get()==0: iffc.ifeffit("def("+var.vname.get()+"=0)") #get active paths aps=[] for path in self.pathwidlist: if path.p.pon.get()==1: pi=self.pathwidlist.index(path) pnam=self.pathlist[pi] pnum=atoi(pnam[5:]) aps.append(pnum) self.deffeffpathfin(str(pnum),path.p) straps=str(aps) straps=straps[1:len(straps)-1] #call ff2chi iffc.ifeffit("ff2chi("+straps+",group=fit,do_all)") ##calculate the residuals ##dn=self.dataname ##iffc.ifeffit("fit.kwres="+dn+".chi_kw-fit.chi_kw") if self.mstat==0: setstatus(self.status,"ff2chi calculated on checked paths.") self.mstat=0 def dopathff2chi(self): iffc.ifeffit("set_fit_params "+self.kmin.get()+" "+self.kmax.get()+" "+self.rmin.get()+" "+\ self.rmax.get()+" "+self.kweight.get()+" "+self.dk.get()+" "+self.winparam.get(ACTIVE)+" "+self.spcparam.get(ACTIVE)) #update all variables with def for var in self.varwidlist: if var.von.get()==1: iffc.ifeffit("def("+var.vname.get()+"="+var.vexp.get()+")") if var.von.get()==0: iffc.ifeffit("def("+var.vname.get()+"=0)") #get current path pind=int(self.pathsel.curselection()[0]) pnam=self.pathlist[pind] pnum=atoi(pnam[5:]) self.deffeffpathfin(str(pnum),self.pathwidlist[pind].p) iffc.ifeffit("ff2chi("+str(pnum)+",group=fit,do_all)") if self.mstat==0: setstatus(self.status,"ff2chi calculated on active path.") self.mstat=0 def plotpathfittype(self,index,newg): #determine plottype if index==0: key=[2,6,11] else: key=[index+15,index+15,index+15] if self.cumpathtype.getvalue()=='k': #plot k km1=self.kplotmin.get() km2=self.kplotmax.get() iffc.ifeffit("dokwt fit "+self.kplotwt.get()) self.sp_plot(newg,"fit.k","fit.chi_kw","k","chi","FEFF Data",km1,km2,key[0]) newg=0 if self.cumpathtype.getvalue()=='R': #plot R win=self.winparam.get(ACTIVE) kw=self.kweight.get() dk=self.dk.get() rm1=self.rplotmin.get() rm2=self.rplotmax.get() iffc.ifeffit("fftf(real=fit.chi,kweight="+kw+",kmin="+self.kmin.get()+\ ",kmax="+self.kmax.get()+""",kwindow='"""+win+"""',dk="""+dk+")") self.sp_plot(newg,"fit.r","fit.chir_mag","R","Amp","FEFF Data",rm1,rm2,key[1]) newg=0 if self.cumpathtype.getvalue()=='q': #plot q win=self.winparam.get(ACTIVE) kw=self.kweight.get() dk=self.dk.get() qm1=self.qplotmin.get() qm2=self.qplotmax.get() iffc.ifeffit("fftf(real=fit.chi,kweight="+kw+",kmin="+self.kmin.get()+\ ",kmax="+self.kmax.get()+""",kwindow='"""+win+"""',dk="""+dk+")") iffc.ifeffit("fftr(real=fit.chir_re,imag=fit.chir_im,rmin="+self.rmin.get()+\ ",rmax="+self.kmax.get()+",dr=0.2)") self.sp_plot(newg,"fit.q","fit.chiq_re","q","chi","FEFF Data",qm1,qm2,key[2]) newg=0 def plotpathcontributions(self): #recalculate w/ current settings newg=1 self.doff2chi() #plot data if needed if 'Data' in self.cumpathsels.getvalue(): self.load_data_file() dn=self.dataname #determine plottype if self.cumpathtype.getvalue()=='k': #plot k km1=self.kplotmin.get() km2=self.kplotmax.get() iffc.ifeffit("dokwt "+dn+" "+self.kplotwt.get()) self.sp_plot(newg,dn+".k",dn+".chi_kw","k","chi",dn,km1,km2,1) newg=0 if self.cumpathtype.getvalue()=='R': #plot R win=self.winparam.get(ACTIVE) kw=self.kweight.get() dk=self.dk.get() rm1=self.rplotmin.get() rm2=self.rplotmax.get() iffc.ifeffit("fftf(real="+dn+".chi,kweight="+kw+",kmin="+self.kmin.get()+\ ",kmax="+self.kmax.get()+""",kwindow='"""+win+"""',dk="""+dk+")") self.sp_plot(newg,dn+".r",dn+".chir_mag","R","Amp",dn,rm1,rm2,3) newg=0 if self.cumpathtype.getvalue()=='q': #plot q qm1=self.qplotmin.get() qm2=self.qplotmax.get() iffc.ifeffit("fftr(real="+dn+".chir_re,imag="+dn+".chir_im,rmin="+self.rmin.get()+\ ",rmax="+self.rmax.get()+",dr=0.2)") self.sp_plot(newg,dn+".q",dn+".chiq_re","q","chi",dn,qm1,qm2,9) newg=0 #plot entire fit if desired if 'Fit' in self.cumpathsels.getvalue(): self.plotpathfittype(0,newg) newg=0 pinit=int(self.pathsel.curselection()[0]) self.pathsel.select_clear(pinit) #iterate through dopathff2chi adding plots for path in self.pathwidlist: if path.p.pon.get()==1: pi=self.pathwidlist.index(path) self.pathsel.select_set(pi) self.dopathff2chi() self.pathsel.select_clear(pi) #add path plot pnam=self.pathlist[pi] pnum=atoi(pnam[5:]) self.plotpathfittype(pnum,newg) newg=0 #reset current path self.pathsel.select_set(pinit) setstatus(self.status,"Path contributions calculated on active paths and plotted.") def recallvarbuffer(self): for var in self.varwidlist: temp=var.vexp.get() var.vexp.setentry(var.buffer) var.buffer=temp def dofit(self): #reload data self.load_data_file() dn=self.dataname #set fit parameters fitparamcmd=",rmin="+self.rmin.get()+",rmax="+self.rmax.get()+",kmin="+self.kmin.get()+\ ",kmax="+self.kmax.get()+",kweight="+self.kweight.get()+",dk="+self.dk.get()+\ ",kwindow="+self.winparam.get(ACTIVE)+",fit_space="+self.spcparam.get(ACTIVE) kwmenu=self.fitmenukweight.get() if kwmenu!=0: fitparamcmd=",rmin="+self.rmin.get()+",rmax="+self.rmax.get()+",kmin="+self.kmin.get()+\ ",kmax="+self.kmax.get()+",dk="+self.dk.get()+\ ",kwindow="+self.winparam.get(ACTIVE)+",fit_space="+self.spcparam.get(ACTIVE) if kwmenu==1: fitparamcmd=fitparamcmd+",kweight=3,kweight=2,kweight=1,kweight=0" if kwmenu==2: fitparamcmd=fitparamcmd+",kweight=3,kweight=2,kweight=1" if kwmenu==3: fitparamcmd=fitparamcmd+",kweight=3,kweight=2" if self.fitmenuspline.get()==1: fitparamcmd=fitparamcmd+",do_bkg=true" #update guess, set and defs... for var in self.varwidlist: var.buffer=var.vexp.get() if var.von.get()==1: if var.type.getcurselection()=='D': iffc.ifeffit("def("+var.vname.get()+"="+var.vexp.get()+")") if var.type.getcurselection()=='S': iffc.ifeffit("set("+var.vname.get()+"="+var.vexp.get()+")") if var.type.getcurselection()=='G': iffc.ifeffit("guess("+var.vname.get()+"="+var.vexp.get()+")") if var.restraint==1: fitparamcmd=fitparamcmd+",restraint="+var.vname.get() if var.von.get()==0: iffc.ifeffit("def("+var.vname.get()+"=0)") aps=[] for path in self.pathwidlist: if path.p.pon.get()==1: pi=self.pathwidlist.index(path) pnam=self.pathlist[pi] pnum=atoi(pnam[5:]) aps.append(pnum) self.deffeffpathfin(str(pnum),path.p) straps=str(aps) straps=straps[1:len(straps)-1] setstatus(self.status,"FEFF fit in progress") self.status.configure(bg='red') self.status.update_idletasks() #call ifeffit iffc.ifeffit("feffit("+straps+",chi="+dn+".chi,group=fit"+fitparamcmd+")") #set fitting statistics setstatus_d(self.Rvalue,iffc.get_scalar("r_factor"),5) setstatus_d(self.ChiSq,iffc.get_scalar("chi_square"),3) setstatus_d(self.ChiSqR,iffc.get_scalar("chi_reduced"),3) iffc.ifeffit("show n_idp,n_varys") #replace guesses for var in self.varwidlist: if var.von.get()==1: if var.type.getcurselection()=='G': var.vexp.setentry(str(iffc.get_scalar(var.vname.get()))) #print in results window... allow 15 spaces per field fwd=15 #self.restext.config(state=NORMAL) self.restext.clear() if self.respathvar.get()==1: self.restext.insert(END,'PATH VARIABLE VALUES... \n') for path in self.pathwidlist: if path.p.pon.get()==1: pi=self.pathwidlist.index(path) pnam=self.pathlist[pi] pnum=pnam[5:] pzn=zfill(pnum,3) iffc.ifeffit("get_path("+pnum+")") self.restext.insert(END,'\n '+pnam+' '+path.p.descr.get()+' \n') #evaluate all path vars... pxso2=self.clipresults(iffc.get_scalar("path"+pzn+"_s02")) pxeo=self.clipresults(iffc.get_scalar("path"+pzn+"_e0")) pxr=self.clipresults(iffc.get_scalar("path"+pzn+"_reff")+iffc.get_scalar("path"+pzn+"_delr")) pxss=self.clipresults(iffc.get_scalar("path"+pzn+"_sigma2")) pxth=self.clipresults(iffc.get_scalar("path"+pzn+"_third")) pxft=self.clipresults(iffc.get_scalar("path"+pzn+"_fourth")) newline=ljust("Amplitude",fwd)+ljust(pxso2,fwd)+"\n" self.restext.insert(END,newline) newline=ljust("e0",fwd)+ljust(pxeo,fwd)+"\n" self.restext.insert(END,newline) newline=ljust("R",fwd)+ljust(pxr,fwd)+"\n" self.restext.insert(END,newline) newline=ljust("Sigma2",fwd)+ljust(pxss,fwd)+"\n" self.restext.insert(END,newline) newline=ljust("Third",fwd)+ljust(pxth,fwd)+"\n" self.restext.insert(END,newline) newline=ljust("Fourth",fwd)+ljust(pxft,fwd)+"\n" self.restext.insert(END,newline) self.restext.insert(END,'\nALL VARIABLE VALUES... \n \n') for var in self.varwidlist: if var.von.get()==1: #print var,exp, and error if guessed varval=self.clipresults(iffc.get_scalar(var.vname.get())) newline=ljust(var.vname.get(),fwd)+ljust(varval,fwd) if var.type.getcurselection()=='G': varer=self.clipresults(iffc.get_scalar("delta_"+var.vname.get())) newline=newline+ljust(pm+varer,fwd) newline=newline+" \n" self.restext.insert(END,newline) ####calculate the residuals ###iffc.ifeffit("fit.kwres="+dn+".chi_kw-fit.chi_kw") #print correlations if needed self.printcorels() #self.restext.config(state=DISABLED) if sys.platform=='win32': self.status.configure(bg='SystemButtonFace') else: self.status.configure(bg='#d4d0c8') setstatus(self.status,"FEFF fit completed!") self.mstat=1 self.doff2chi() def clipresults(self,v): dig=8 val=str(v) decind=rfind(val,'.') eind=rfind(val,"e") if eind==-1: if decind>dig: val=val[:decind+2] else: val=val[:dig] else: val=val[:4]+val[eind:len(val)] return val def savefitdata(self): global lastsavedir nfn=ask_save_file('',lastsavedir) root.adwin.focus_set() if nfn<>"": sdir=rfind(nfn,os.sep) lastsavedir=nfn[:sdir] iffc.ifeffit("write_data(file="+nfn+"_chi.dat, fit.k,fit.chi)") iffc.ifeffit("write_data(file="+nfn+"_r.dat, fit.r,fit.chir_mag,fit.chir_re,fit.chir_im)") setstatus(self.status,"Fit data saved to "+nfn) def saverawdata(self): global lastsavedir dn=self.dataname nfn=ask_save_file('',lastsavedir) root.adwin.focus_set() if nfn<>"": sdir=rfind(nfn,os.sep) lastsavedir=nfn[:sdir] iffc.ifeffit("write_data(file="+nfn+"_chi.dat, "+dn+".k,"+dn+".chi)") iffc.ifeffit("write_data(file="+nfn+"_r.dat, "+dn+".r,"+dn+".chir_mag,"+dn+".chir_re,"+dn+".chir_im)") setstatus(self.status,"File spectral data saved to "+nfn) def saveresiddata(self): global lastsavedir dn=self.dataname nfn=ask_save_file('',lastsavedir) root.adwin.focus_set() if nfn<>"": sdir=rfind(nfn,os.sep) lastsavedir=nfn[:sdir] #iffc.ifeffit("fit.kwres="+dn+".chi_kw-fit.chi_kw") #iffc.ifeffit("fit.knz=fit.k+0.0001") #iffc.ifeffit("fit.res=fit.kwres/(fit.knz^"+self.kweight.get()+")") iffc.ifeffit("fit.res="+dn+".chi-fit.chi") iffc.ifeffit("write_data(file="+nfn+"_res_chi.dat, "+dn+".k,fit.res)") setstatus(self.status,"Residual spectral data saved to "+nfn) def saveallvars(self): global lastsavedir #place all paths and varibles into a parameter file #get file name nfn=ask_save_file('',lastsavedir) root.adwin.focus_set() if nfn=="": setstatus(self.status,"Save parameters aborted") else: sdir=rfind(nfn,os.sep) lastsavedir=nfn[:sdir] #open file #check for extension ending ext=rfind(nfn,".") if ext==-1: nfn=nfn+".prm" fid=open(nfn,"w") #save data-file parameters fid.write("FPARAMS\n") #enter filename,kmin,kmax,rmin,rmax,kw,dk fid.write(self.fileentry.get()+"\n") fid.write(self.kmin.get()+"\n") fid.write(self.kmax.get()+"\n") fid.write(self.rmin.get()+"\n") fid.write(self.rmax.get()+"\n") fid.write(self.kweight.get()+"\n") fid.write(self.dk.get()+"\n") #save all parts of all ACTIVE paths for sp in self.pathwidlist: if sp.p.pon.get()==1: pi=self.pathwidlist.index(sp) pnam=self.pathlist[pi] pnum=pnam[5:] fid.write(pnam+"\n") fid.write(str(sp.p.pon.get())+"\n") fid.write(str(sp.p.dset.get())+"\n") fid.write(sp.p.loc.get()+"\n") fid.write(sp.p.descr.get()+"\n") fid.write(sp.p.s02.get()+"\n") fid.write(sp.p.e0.get()+"\n") fid.write(sp.p.deltaR.get()+"\n") fid.write(sp.p.sig.get()+"\n") fid.write(sp.p.third.get()+"\n") fid.write(sp.p.fourth.get()+"\n") #save all ACTIVE variables fid.write("VARS\n") for var in self.varwidlist: if var.von.get()==1: fid.write(var.vname.get()+"\n") fid.write(str(var.von.get())+"\n") fid.write(var.type.getcurselection()+"\n") fid.write(var.vexp.get()+"\n") fid.write("END") fid.close() setstatus(self.status,"Fit parameters saved to "+nfn) def loadallvars(self): global lastreaddir #load paths and variables from files #get file name fn=ask_for_file([("parameter files","*.prm"),("all files","*")],lastreaddir,check=0) root.adwin.focus_set() if fn=="": setstatus(self.status,"Load parameters aborted") else: sdir=rfind(fn,os.sep) lastreaddir=fn[:sdir] #clear all paths and variables for dp in self.pathlist: self.pathdes.delete(dp) self.pathwidlist=[] self.pathlist=[] self.npath=0 for dv in self.varwidlist: dv.f.destroy() self.varwidlist=[] #open file fid=open(fn,"r") param=fid.read() fid.close() #parse file... lp=split(param,'\n') ind=0 for new in lp: if new=='EDGEPARAMS' or new=='BSPARAMS': #wrong parameter file self.box.deiconify() if new=='FPARAMS': #read data-file parameters #read filename,kmin,kmax,rmin,rmax,kw,dk self.fileentry.setentry(lp[ind+1]) self.kmin.setentry(lp[ind+2]) self.kmax.setentry(lp[ind+3]) self.rmin.setentry(lp[ind+4]) self.rmax.setentry(lp[ind+5]) self.kweight.setentry(lp[ind+6]) self.dk.setentry(lp[ind+7]) if new[0:5]=='Path ': #do paths self.addfeffpath() ep=self.pathwidlist[len(self.pathwidlist)-1] ep.p.pon.set(int(lp[ind+1])) ep.p.dset.set(int(lp[ind+2])) ep.p.loc.setentry(lp[ind+3]) ep.p.descr.setentry(lp[ind+4]) ep.p.s02.setentry(lp[ind+5]) ep.p.e0.setentry(lp[ind+6]) ep.p.deltaR.setentry(lp[ind+7]) ep.p.sig.setentry(lp[ind+8]) ep.p.third.setentry(lp[ind+9]) ep.p.fourth.setentry(lp[ind+10]) if new=='VARS': #do all variables varread=lp[ind+1:] vind=0 for nv in varread: vind=vind+1 if nv<>'END': if vind==1: self.addfitvar() newvar=self.varwidlist[len(self.varwidlist)-1] newvar.vname.setentry(nv) if vind==2: newvar.von.set(int(nv)) if vind==3: newvar.type.invoke(nv) if vind==4: newvar.vexp.setentry(nv) vind=0 ind=ind+1 setstatus(self.status,"Parameter file read from "+fn) ################################################################ ## ## ## Background Subtraction Routine ## ## ################################################################ def ktoE(k): k=float(k) e=k**2/0.262468292 return e def Etok(e): e=float(e) k=sqrt(e*0.262468292) return k def remundsc(text): return replace(text,'_','') class DefFParams: def __init__(self,master,fname): f=Frame(master) f.pack(side=TOP,padx=2,pady=0) if fname=='firsttest': lt='' else: lt=fname self.active=0 self.calc=1 self.splknot=0 self.stepheight=0 self.lab=Label(f,text=lt,relief=GROOVE,bd=2,width=50,justify=CENTER,font="Arial 10") #l.pack(side=TOP,fill=X,padx=2,pady=4) w=10 self.enot=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='E0: ',validate='real',modifiedcommand=self.clicktochange) self.rbkg=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='Rbkg: ',value=1,validate='real',modifiedcommand=self.clicktochange) self.kwt=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='k-weight: ',value=3,validate='real',modifiedcommand=self.clicktochange) self.dk=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='dk: ',value=1,validate='real',modifiedcommand=self.clicktochange) self.prea=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='PreEdg: ',validate='real',modifiedcommand=self.clicktochange) self.preb=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='to E: ',validate='real',modifiedcommand=self.clicktochange) self.norma=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='Norm: ',validate='real',modifiedcommand=self.clicktochange) self.normb=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='to E: ',validate='real',modifiedcommand=self.clicktochange) self.splka=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='k: ',validate='real',command=self.enterka,modifiedcommand=self.clicktochange) self.splkb=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='to k: ',validate='real',command=self.enterkb,modifiedcommand=self.clicktochange) self.splea=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='E: ',validate='real',command=self.enterea,modifiedcommand=self.clicktochange) self.spleb=Pmw.EntryField(f,labelpos='w',entry_width=w,label_text='to E: ',validate='real',command=self.entereb,modifiedcommand=self.clicktochange) l2=Label(f,text='Pre-Edge Normalization') l2b=Label(f,text='Post-Edge Normalization') l3=Label(f,text='Spline Region') self.pretype=Pmw.RadioSelect(f,buttontype='radiobutton',orient='horizontal',labelpos=W,pady=0,command=self.clicktochange) for text in ('Linear','Gauss'): self.pretype.add(text) self.pretype.invoke('Linear') self.posttype=Pmw.RadioSelect(f,buttontype='radiobutton',orient='horizontal',labelpos=W,pady=0,command=self.clicktochange) for text in ('Linear','Quad'): self.posttype.add(text) self.posttype.invoke('Quad') windows=('Hanning','Kaiser-Bessel','Parzen','Welch','Sine') self.winparam=Pmw.ComboBox(f,label_text='FT Window: ',labelpos=W,scrolledlist_items=windows,listheight=100,entryfield_entry_width=15,history=0, selectioncommand=self.clicktochange) self.winparam.selectitem(windows[1]) clamps=('None','Slight','Weak','Medium','Strong','Rigid') self.clamp1=Pmw.ComboBox(f,label_text='Low Clamp: ',labelpos=W,scrolledlist_items=clamps,listheight=120,entryfield_entry_width=10,history=0, selectioncommand=self.clicktochange) self.clamp1.selectitem(clamps[0]) self.clamp2=Pmw.ComboBox(f,label_text='Hi Clamp: ',labelpos=W,scrolledlist_items=clamps,listheight=120,entryfield_entry_width=10,history=0, selectioncommand=self.clicktochange) self.clamp2.selectitem(clamps[0]) #define copyable entries self.copyable=[self.enot,self.rbkg,self.kwt,self.dk,self.prea,self.preb,self.norma,self.normb,\ self.splka,self.splkb,self.splea,self.spleb] for a in self.copyable: a.bind(sequence="", func=self.clicktochange) #place all entries i=0 d=2 self.lab.grid(row=i,column=0,columnspan=2,pady=2*d);i=i+1 self.enot.grid(row=i,column=0,pady=d) self.rbkg.grid(row=i,column=1,pady=d);i=i+1 self.kwt.grid(row=i,column=0,pady=d) self.dk.grid(row=i,column=1,pady=d);i=i+1 self.clamp1.grid(row=i,column=0,pady=2*d) self.clamp2.grid(row=i,column=1,pady=2*d);i=i+1 self.winparam.grid(row=i,column=0,columnspan=2,pady=2*d);i=i+1 l2.grid(row=i,column=0,columnspan=1,pady=2*d); l2b.grid(row=i,column=1,columnspan=1,pady=2*d);i=i+1 self.pretype.grid(row=i,column=0,columnspan=1,pady=1); self.posttype.grid(row=i,column=1,columnspan=1,pady=1);i=i+1 self.prea.grid(row=i,column=0,pady=d) self.preb.grid(row=i,column=1,pady=d);i=i+1 self.norma.grid(row=i,column=0,pady=d) self.normb.grid(row=i,column=1,pady=d);i=i+1 l3.grid(row=i,column=0,columnspan=2,pady=2*d);i=i+1 self.splka.grid(row=i,column=0,pady=d) self.splkb.grid(row=i,column=1,pady=d);i=i+1 self.splea.grid(row=i,column=0,pady=d) self.spleb.grid(row=i,column=1,pady=d);i=i+1 Pmw.alignlabels((self.enot,self.kwt,self.prea,self.norma,self.splka,self.splea),sticky=E) Pmw.alignlabels((self.rbkg,self.dk,self.preb,self.normb,self.splkb,self.spleb),sticky=E) def clicktochange(self, *arg): self.calc=1 def enterea(self): enew=self.splea.get() k=Etok(enew) entry_replace_d(self.splka,k,4) self.splka.checkentry() def entereb(self): enew=self.spleb.get() k=Etok(enew) entry_replace_d(self.splkb,k,4) self.splkb.checkentry() def enterka(self): knew=self.splka.get() e=ktoE(knew) entry_replace_d(self.splea,e,3) self.splea.checkentry() def enterkb(self): knew=self.splkb.get() e=ktoE(knew) entry_replace_d(self.spleb,e,3) self.spleb.checkentry() class BSFit: def __init__(self): bswin=root.bswin=Toplevel(root) bswin.title("Background Subtraction Dialog") bswin.protocol("WM_DELETE_WINDOW", self.closemod) self.root=root self.bswin=bswin root.iconify() #change focus... bswin.focus_set() #GUI for fitting window... #create menu for fitting window menubar=Pmw.MenuBar(bswin) #file menu menubar.addmenu('File','') menubar.addmenuitem('File','command',label='Open File',command=self.loaddatafile) menubar.addmenuitem('File','command',label='Open Multiple Files',command=self.loadmultdatafile) menubar.addmenuitem('File','separator') menubar.addmenuitem('File','command',label='Clear All',command=self.clearfilelist) menubar.addmenuitem('File','separator') menubar.addmenuitem('File','command',label='Edit Default Directories',command=self.callchangedefdirs) menubar.addmenuitem('File','separator') menubar.addmenuitem('File','command',label='Close',command=self.closemod) menubar.addmenuitem('File','command',label='Quit',command=root.quit) menubar.addmenu('Save','') menubar.addmenuitem('Save','command',label='Edge Data',command=self.savemudata) menubar.addmenuitem('Save','command',label='EXAFS Data',command=self.savechidata) menubar.addmenuitem('Save','command',label='FT Data',command=self.saveRdata) menubar.addmenu('Parameters','') menubar.addmenuitem('Parameters','command',label='Mark Current Sample',command=self.menuchoosedata) menubar.addmenuitem('Parameters','separator') menubar.addmenuitem('Parameters','command',label='Restore Defaults',command=self.defaultps) menubar.addmenuitem('Parameters','command',label='Set All to Current',command=self.setallparam) menubar.addmenuitem('Parameters','command',label='Set Marked to Current',command=self.setmarkparam) menubar.addmenuitem('Parameters','separator') menubar.addmenuitem('Parameters','command',label='Save Parameter file',command=self.savecurparams) menubar.addmenuitem('Parameters','command',label='Load Parameter file',command=self.loadsavedparams) menubar.addmenuitem('Parameters','separator') menubar.addcascademenu('Parameters','Spline Knots',tearoff=1) self.splineknots=IntVar() menubar.addmenuitem('Spline Knots','radiobutton',label='default',value=0,variable=self.splineknots,command=self.clickedme) menubar.addmenuitem('Spline Knots','separator') for k in range(5,13): menubar.addmenuitem('Spline Knots','radiobutton',label=str(k),value=k,variable=self.splineknots,command=self.clickedme) self.splineknots.set(0) menubar.addmenuitem('Parameters','separator') menubar.addmenuitem('Parameters','command',label='Run Fitting',command=self.doallanalysis) menubar.addmenuitem('Parameters','separator') menubar.addmenuitem('Parameters','command',label='Show Parameter Summary',command=self.showresultsum) menubar.addmenu('Mu Options','') menubar.addmenuitem('Mu Options','command',label='Adjust Energy Scale',command=self.shiftenergy) self.optmuderiv=IntVar() menubar.addmenuitem('Mu Options','checkbutton',label='Use 1st Derivative',variable=self.optmuderiv) self.optmusmooth=IntVar() menubar.addmenuitem('Mu Options','checkbutton',label='Apply Smoothing',variable=self.optmusmooth) menubar.addmenuitem('Mu Options','command',label='Defined Self Abs. Correction',command=self.selfabscor) menubar.addmenu('Deglitching','') menubar.addmenuitem('Deglitching','command',label='Edit Data',command=self.deglitchpanel) menubar.addmenu('Help','',side=RIGHT) menubar.addmenuitem('Help','command',label='About SixPack',command=callprogramabout) menubar.addmenuitem('Help','separator') menubar.addmenuitem('Help','command',label='IFEFFIT Command Line',command=RunIFEFFITCmdLine) menubar.grid(row=0,columnspan=24,sticky=W+E) #Add project manager window pmwin=Frame(bswin,relief=SUNKEN,bd=2) l=Label(pmwin,text='Project Files',relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) act=Frame(pmwin) w=16 b=Button(act,text="Add File",width=w,command=self.loaddatafile,bg='steel blue',fg='white') b.pack(side=LEFT,padx=2,pady=2) b=Button(act,text="Add Many Files",width=w,command=self.loadmultdatafile,bg='darkblue',fg='white') b.pack(side=LEFT,padx=2,pady=2) act.pack(side=TOP,fill=X,padx=2) act=Frame(pmwin) b=Button(act,text="Remove File",width=w,command=self.removefile,bg='red',fg='white') b.pack(side=LEFT,padx=2,pady=2) b=Button(act,text="Clear All",width=w,command=self.clearfilelist,bg='brown',fg='white') b.pack(side=LEFT,padx=2,pady=2) act.pack(side=TOP,fill=X,padx=2) #Add btree tree=Tix.ScrolledHList(pmwin,options='hlist.columns 2') self.phlist=tree.hlist self.phlist.config(separator='-',width=25, drawbranch=0, indent=10,itemtype=Tix.TEXT,browsecmd=self.selectfile,command=self.choosedata) self.phlist.column_width(1,chars=50) self.phlist.column_width(0,chars=3) tree.pack(side=TOP,fill=BOTH,expand=1,padx=2,pady=2) self.datfiles=[] pmwin.grid(row=1,column=0,columnspan=6,rowspan=12,sticky=W+E+N+S) #main parameter entry fp=Frame(bswin,relief=SUNKEN,bd=2) l=Label(fp,text='File Parameters',relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) #notebook of params for each file self.filparam=Pmw.NoteBook(fp,tabpos=None) if sys.platform == 'win32': self.filparam.configure(hull_background="SystemButtonFace") else: self.filparam.configure(hull_background='#d4d0c8') self.filparam.recolorborders() self.fpwids={} self.fplist=[] self.initaddfile() self.filparam.pack(side=TOP,padx=2,pady=2,fill=BOTH,expand=1) self.filparam.setnaturalsize() #action buttons box=Frame(fp) b=Button(box,text='Save mu(E)',width=15,command=self.savemudata,bg='darkgreen',fg='snow') b.pack(side=LEFT,fill=X,padx=10,pady=1) b=Button(box,text='Save chi(k)',width=15,command=self.savechidata,bg='brown',fg='snow') b.pack(side=LEFT,fill=X,padx=10,pady=1) b=Button(box,text='Save R',width=15,command=self.saveRdata,bg='royalblue4',fg='snow') b.pack(side=LEFT,fill=X,padx=5,pady=1) box.pack(side=BOTTOM,fill=X,padx=2,pady=4) fp.grid(row=1,column=6,columnspan=12,rowspan=12,sticky=W+E+N+S) #plot parameters plp=Frame(bswin,relief=SUNKEN,bd=2) l=Label(plp,text='Plot Type',relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) l=Label(plp,text='Left click, single plot\nRight click, selected plots') l.pack(side=TOP,fill=X,padx=2,pady=4) box=Frame(plp) box2=Frame(plp) b=Button(box,text='Raw',width=5,bg='darkblue',fg='snow') self.bindplotbutton(b) b=Button(box,text='PreEdg',width=5,bg='darkblue',fg='snow') self.bindplotbutton(b) b=Button(box,text='Spline',width=5,bg='darkblue',fg='snow') self.bindplotbutton(b) b=Button(box2,text='mu(E)',width=5,bg='darkblue',fg='snow') self.bindplotbutton(b) b=Button(box2,text='chi(k)',width=5,bg='darkblue',fg='snow') self.bindplotbutton(b) b=Button(box2,text='R',width=5,bg='darkblue',fg='snow') self.bindplotbutton(b) box.pack(side=TOP,fill=X,padx=2,pady=4) box2.pack(side=TOP,fill=X,padx=2,pady=4) l=Label(plp,text='Plot Options',relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) #k-params kp=Frame(plp,relief=RIDGE,bd=2) kp.pack(side=TOP,fill=X,padx=2,pady=2) w=8 self.plotkw=Pmw.EntryField(kp,labelpos='w',entry_width=w,label_text='k-weight: ',value='3',validate='real') self.plotkmin=Pmw.EntryField(kp,labelpos='w',entry_width=w,label_text='kmin: ',value='2',validate='real') self.plotkmax=Pmw.EntryField(kp,labelpos='w',entry_width=w,label_text='kmax: ',value='15',validate='real') kfields=(self.plotkw,self.plotkmin,self.plotkmax) for fld in kfields: fld.pack(side=TOP,padx=5,pady=2) Pmw.alignlabels(kfields) #R-params rp=Frame(plp,relief=RIDGE,bd=2) rp.pack(side=TOP,fill=X,padx=2,pady=2) windows=('Hanning','Kaiser-Bessel','Parzen','Welch','Sine') self.plotwinparam=Pmw.ComboBox(rp,label_text='FT Window: ',labelpos=N,scrolledlist_items=windows,listheight=100,entryfield_entry_width=15) self.plotwinparam.selectitem(windows[1]) self.plotwinparam.pack(side=TOP,padx=2,pady=3) self.plotdk=Pmw.EntryField(rp,labelpos='w',entry_width=w,label_text='dk: ',value='3',validate='real') self.plotrmin=Pmw.EntryField(rp,labelpos='w',entry_width=w,label_text='Rmin: ',value='0',validate='real') self.plotrmax=Pmw.EntryField(rp,labelpos='w',entry_width=w,label_text='Rmax: ',value='6',validate='real') rfields=(self.plotdk,self.plotrmin,self.plotrmax) for fld in rfields: fld.pack(side=TOP,padx=5,pady=2) Pmw.alignlabels(rfields) self.plotftwin=Pmw.RadioSelect(rp,labelpos='w',buttontype='checkbutton') self.plotftwin.add('yes',text='Plot FT Win?') self.plotftwin.pack(side=TOP,padx=5,pady=1) plp.grid(row=1,column=18,columnspan=6,rowspan=12,sticky=W+E+N+S) #Status Bar self.status=Label(bswin,text="",bd=2,relief=RAISED,anchor=W,fg='blue') self.status.grid(row=13,columnspan=24,sticky=W+E) setstatus(self.status,"Ready") self.lastsel='' #correlation window self.rsumwin=Pmw.TextDialog(root,title='Parameter Summary',command=self.killrsumwin,deactivatecommand=self.killrsumwin,scrolledtext_hscrollmode='static',scrolledtext_vscrollmode='static',text_wrap='none',scrolledtext_labelpos=N,label_text='Parameter Summary',buttons=('Remove',)) self.rsumwin.iconname('Parameter Summary') self.rsumwin.tag_config('hi',foreground='red') self.rsumwin.withdraw() #error window self.box=Pmw.MessageDialog(root,title='File Error',defaultbutton=0,message_text='Wrong type of parameter file chosen!', iconpos='n',icon_bitmap='warning') self.box.iconname('File Error') self.box.withdraw() def clickedme(self): #get data cur=self.phlist.info_selection() if cur==(): return cur=cur[0] self.filparam.selectpage(remundsc(cur)) wid=self.fpwids[cur].p wid.calc=1 def callprogramabout(self): programabout(self.root) def callchangedefdirs(self): global lastsavedir,lastreaddir s=changedefdirs(root.bswin) lastreaddir=s.newdir lastsavedir=s.newdir def closemod(self): getmainmenu(root.bswin) def showresultsum(self): self.rsumwin.deiconify() def killrsumwin(self,*args): self.rsumwin.withdraw() def printressum(self): #get current data cur=self.phlist.info_selection() if cur==(): return cur=cur[0] wid=self.fpwids[cur].p #print results in text window self.rsumwin.clear() self.rsumwin.insert(END,"Summary of Background Parameters\n") self.rsumwin.insert(END,"File: "+cur+"\n\n") self.rsumwin.insert(END,'Number of spline knots: '+str(wid.splknot)+' \n') self.rsumwin.insert(END,'Step Height: '+wid.stepheight+' \n\n') self.rsumwin.insert(END,'E0: '+wid.enot.get()+' \n') self.rsumwin.insert(END,'Rbkg: '+wid.rbkg.get()+' \n') self.rsumwin.insert(END,'k-weight: '+wid.kwt.get()+' \n') self.rsumwin.insert(END,'FT Window: '+wid.winparam.get()+' \n') self.rsumwin.insert(END,'dk: '+wid.dk.get()+' \n') self.rsumwin.insert(END,'Low Clamp: '+wid.clamp1.get()+' \n') self.rsumwin.insert(END,'Hi Clamp: '+wid.clamp2.get()+' \n\n') self.rsumwin.insert(END,'Pre-edge: '+wid.pretype.getcurselection()+' \n') self.rsumwin.insert(END,'From: '+wid.prea.get()+' to '+wid.preb.get()+' \n') self.rsumwin.insert(END,'Post-Edge: '+wid.posttype.getcurselection()+' \n') self.rsumwin.insert(END,'From: '+wid.norma.get()+' to '+wid.normb.get()+' \n') self.rsumwin.insert(END,'Spline Regions: \n') self.rsumwin.insert(END,'From: '+wid.splka.get()+' to '+wid.splkb.get()+' \n') def bindplotbutton(self,b): b.bind("",self.singleplot) b.bind("",self.multiplot) b.bind("",self.returnclick) b.pack(side=LEFT,fill=X,padx=3,pady=1) def initaddfile(self): self.nfs=0 fname="firsttest" iffc.ifeffit("read_data(file="+filepath+"test.inp, group=firsttest,label='energy xmu')") new=self.filparam.add(fname) new.p=DefFParams(new,fname) self.fpwids.update({fname:new}) self.fplist.append(fname) self.SKIP=1 self.defaultps() self.SKIP=0 def clearfilelist(self): #reset all self.datfiles=[] for page in self.fplist: #destroy the page self.filparam.delete(page) self.fplist=[] self.fpwids={} iffc.ifeffit("erase @arrays") self.phlist.delete_all() self.initaddfile() def removefile(self): #get current selection cur=self.phlist.info_selection() if cur != (): cur=cur[0] #remove all associated vars iffc.ifeffit("erase @group= "+cur) ind=self.datfiles.index(cur) self.datfiles.remove(cur) self.phlist.delete_entry(cur) self.filparam.delete(remundsc(cur)) self.fplist.remove(remundsc(cur)) del self.fpwids[cur] #reselect if len(self.datfiles)==0: self.phlist.selection_clear() self.filparam.selectpage('firsttest') elif ind != 0: new=self.datfiles[ind-1] self.phlist.selection_set(new) self.selectfile() else: new=self.datfiles[0] self.phlist.selection_set(new) self.selectfile() def loadmultdatafile(self): global lastreaddir self.multifd=Tix.ExFileSelectDialog(root) if lastreaddir!='': lastreaddir=replace(lastreaddir,'/','\\') self.multifd.fsbox.configure(directory=lastreaddir) self.multifd.fsbox.filelist.listbox.configure(selectmode=MULTIPLE) #setup ok button... self.multifd.fsbox.ok.configure(command=self.getmultilist) self.multifd.popup() def getmultilist(self): global lastreaddir verbot=['(',')','-','#','&','$','@','!','{','}','+','='] multfn=self.multifd.fsbox.filelist.listbox.curselection() multdlist=self.multifd.fsbox.filelist.listbox.get(0,END) curdir=self.multifd.fsbox.dir.entry.get() lastreaddir=curdir self.multifd.popdown() if multfn !=(): for sel in multfn: curfile=multdlist[int(sel)] bad=0 for char in curfile: if char in verbot: bad=1 if bad: tkMessageBox.showwarning("Open File"," WARNING!\n Filename contains characters not\n compatible with IFEFFIT ") fulpath=curdir+os.sep+curfile #set up parmas curfil=trimdirext(curfile) #load data here iffc.ifeffit("read_data(file="+fulpath+", group="+curfil+",label='energy xmu')") new=self.filparam.add(remundsc(curfil)) new.p=DefFParams(new,curfil) self.fpwids.update({curfil:new}) self.fplist.append(remundsc(curfil)) self.datfiles.append(curfil) self.phlist.add(curfil,text=' ',state=NORMAL) self.phlist.item_create(curfil,1,text=curfil) self.phlist.selection_clear() self.phlist.selection_set(curfil) #get file data self.defaultps() #call analysis routine self.lastsel=curfil #self.doallanalysis() def loaddatafile(self): global lastreaddir infile=ask_for_file([("avg files","*.avg"),("mu files","*.mu"),("all files","*")],lastreaddir) root.bswin.focus_set() if infile !='': sdir=rfind(infile,os.sep) lastreaddir=infile[:sdir] #append lists/update tree treefile=trimdirext(infile) #load data here iffc.ifeffit("read_data(file="+infile+", group="+treefile+",label='energy xmu')") new=self.filparam.add(remundsc(treefile)) new.p=DefFParams(new,treefile) self.fpwids.update({treefile:new}) self.fplist.append(remundsc(treefile)) self.datfiles.append(treefile) self.phlist.add(treefile,text=' ',state=NORMAL) self.phlist.item_create(treefile,1,text=treefile) self.phlist.selection_clear() self.phlist.selection_set(treefile) #get file data self.defaultps() #call analysis routine self.lastsel=treefile #self.doallanalysis() def defaultps(self): #emplace default values cur=self.phlist.info_selection() if self.SKIP: iffc.ifeffit("pre_edge(firsttest.energy,firsttest.xmu,find_e0=T)") return if cur==(): return cur=cur[0] self.filparam.selectpage(remundsc(cur)) #begin placing defaults wid=self.fpwids[cur].p setstatus(wid.lab,cur) #find e0 iffc.ifeffit("pre_edge("+cur+".energy,"+cur+".xmu,find_e0=T)") entry_replace_d(wid.enot,iffc.get_scalar("e0"),3) wid.enot.checkentry() entry_replace_d(wid.prea,iffc.get_scalar("pre1"),3) wid.prea.checkentry() entry_replace_d(wid.preb,iffc.get_scalar("pre2"),3) wid.preb.checkentry() entry_replace_d(wid.norma,150.,3) wid.norma.checkentry() iffc.ifeffit("maxdelta=ceil("+cur+".energy)-e0") entry_replace_d(wid.normb,iffc.get_scalar("maxdelta"),3) wid.normb.checkentry() entry_replace_d(wid.splka,1.0,3) wid.splka.checkentry() wid.splka.invoke() entry_replace_d(wid.spleb,iffc.get_scalar("maxdelta"),3) wid.spleb.checkentry() wid.spleb.invoke() def selectfile(self, *arg): #get data cur=self.phlist.info_selection() if cur==(): return cur=cur[0] self.filparam.selectpage(remundsc(cur)) if cur!=self.lastsel: #update status self.lastsel=cur wid=self.fpwids[cur].p if wid.splknot==0: setstatus(self.status,"File "+cur+" selected") else: setstatus(self.status,"File "+cur+" selected, spline contains "+str(wid.splknot)+" knots, edge step height="+wid.stepheight) self.printressum() #do analysis #self.doallanalysis() def menuchoosedata(self): cur=self.phlist.info_selection() if cur==(): return self.choosedata(cur[0]) def choosedata(self, *arg): cur=arg[0] print cur self.filparam.selectpage(remundsc(cur)) wid=self.fpwids[cur].p if wid.active==0: #turn on wid.active=1 wid.lab.configure(font=("Arial",10,"bold")) self.phlist.item_configure(cur,0,text='X') else: #turn off wid.active=0 wid.lab.configure(font=("Arial",10)) self.phlist.item_configure(cur,0,text=' ') def doallanalysis(self): #get data cur=self.phlist.info_selection() if cur==(): return cur=cur[0] self.filparam.selectpage(remundsc(cur)) wid=self.fpwids[cur].p if wid.calc==0: return wid.calc=0 #do background fit #get absolute regions pre1=str(float(wid.enot.get())+float(wid.prea.get())) pre2=str(float(wid.enot.get())+float(wid.preb.get())) norm1=str(float(wid.enot.get())+float(wid.norma.get())) norm2=str(float(wid.enot.get())+float(wid.normb.get())) btype=wid.pretype.getcurselection() ctype=wid.posttype.getcurselection() xate0=wid.enot.get() iffc.put_scalar('xate0',float(xate0)) if btype=='Linear': #do a linear fit to the preedge region iffc.ifeffit("guess("+cur+"a=0.0001,"+cur+"b=0.001)") iffc.ifeffit(cur+".fitlin="+cur+"a*"+cur+".energy+"+cur+"b") iffc.ifeffit(cur+".misfit="+cur+".xmu-"+cur+".fitlin") iffc.ifeffit("minimize("+cur+".misfit,x="+cur+".energy,xmin="+pre1+",xmax="+pre2+")") iffc.ifeffit("set("+cur+".redxmu="+cur+".xmu-"+cur+".fitlin)") iffc.ifeffit("set("+cur+"a="+cur+"a,"+cur+"b="+cur+"b)") iffc.ifeffit("set("+cur+"shp="+cur+"a*xate0+"+cur+"b)") #and linear/polynomial to the EXAFS iffc.ifeffit("guess("+cur+"bb=0.01,"+cur+"cc=0)") if ctype=='Linear': iffc.ifeffit("set("+cur+"aa=0.0000)") iffc.ifeffit(cur+".fitpoly="+cur+"bb*"+cur+".energy+"+cur+"cc") if ctype=='Quad': iffc.ifeffit("guess("+cur+"aa=0.0001)") iffc.ifeffit(cur+".fitpoly="+cur+"aa*("+cur+".energy)**2+"+cur+"bb*"+cur+".energy+"+cur+"cc") iffc.ifeffit(cur+".misfitp="+cur+".redxmu-"+cur+".fitpoly") iffc.ifeffit("minimize("+cur+".misfitp,x="+cur+".energy,xmin="+norm1+",xmax="+norm2+")") #calculate step normalized iffc.ifeffit("set("+cur+"aa="+cur+"aa,"+cur+"bb="+cur+"bb,"+cur+"cc="+cur+"cc)") iffc.ifeffit(cur+".samnorm=("+cur+".xmu-"+cur+".fitlin)/"+cur+".fitpoly") iffc.ifeffit(cur+".polyplot="+cur+".fitlin+"+cur+".fitpoly") iffc.ifeffit("set("+cur+"shq="+cur+"aa*(xate0)**2+"+cur+"bb*xate0+"+cur+"cc+"+cur+"shp)") #calcualte step jump height iffc.ifeffit("set("+cur+"sh="+cur+"shq-"+cur+"shp)") wid.stepheight=str(iffc.get_scalar(cur+'sh')) if btype=='Gauss': #fit a gaussian type profile to the preedge region #good for multi-element detectors with signficant scatternig contributions iffc.ifeffit("guess("+cur+"yof=0,"+cur+"amp=1,"+cur+"xc=e0-400,"+cur+"w=250)") iffc.ifeffit(cur+".fitgaus="+cur+"yof+"+cur+"amp*exp(-(("+cur+".energy-"+cur+"xc)**2)/(2*"+cur+"w**2))") iffc.ifeffit(cur+".misfitg="+cur+".xmu-"+cur+".fitgaus") iffc.ifeffit("minimize("+cur+".misfitg,x="+cur+".energy,xmin="+pre1+",xmax="+pre2+")") iffc.ifeffit("set("+cur+".redxmu="+cur+".xmu-"+cur+".fitgaus)") iffc.ifeffit("set("+cur+"yof="+cur+"yof,"+cur+"amp="+cur+"amp,"+cur+"xc="+cur+"xc,"+cur+"w="+cur+"w)") iffc.ifeffit("print "+cur+"yof,"+cur+"amp,"+cur+"xc,"+cur+"w") iffc.ifeffit("set("+cur+"shp="+cur+"yof+"+cur+"amp*exp(-((xate0-"+cur+"xc)**2)/(2*"+cur+"w**2)))") #and linear/polynomial to the EXAFS iffc.ifeffit("guess("+cur+"bb=0.01,"+cur+"cc=0)") if ctype=='Linear': iffc.ifeffit("set("+cur+"aa=0.0000)") iffc.ifeffit(cur+".fitpoly="+cur+"bb*"+cur+".energy+"+cur+"cc") if ctype=='Quad': iffc.ifeffit("guess("+cur+"aa=0.0001)") iffc.ifeffit(cur+".fitpoly="+cur+"aa*("+cur+".energy)**2+"+cur+"bb*"+cur+".energy+"+cur+"cc") iffc.ifeffit(cur+".misfitp="+cur+".redxmu-"+cur+".fitpoly") iffc.ifeffit("minimize("+cur+".misfitp,x="+cur+".energy,xmin="+norm1+",xmax="+norm2+")") iffc.ifeffit("set("+cur+"aa="+cur+"aa,"+cur+"bb="+cur+"bb,"+cur+"cc="+cur+"cc)") #calculate step normalized iffc.ifeffit(cur+".samnorm=("+cur+".xmu-"+cur+".fitgaus)/"+cur+".fitpoly") iffc.ifeffit(cur+".polyplot="+cur+".fitgaus+"+cur+".fitpoly") iffc.ifeffit("set("+cur+"shq="+cur+"aa*(xate0)**2+"+cur+"bb*xate0+"+cur+"cc+"+cur+"shp)") #calcualte step jump height iffc.ifeffit("set("+cur+"sh="+cur+"shq-"+cur+"shp)") wid.stepheight=str(iffc.get_scalar(cur+'sh')) #do spline fit clampdict={'None':'','Slight':'3','Weak':'6','Medium':'12','Strong':'24','Rigid':'96'} lowclampcmd=clampdict.get(wid.clamp1.get()) if lowclampcmd!='':lowclampcmd=',clamp1='+lowclampcmd hiclampcmd=clampdict.get(wid.clamp2.get()) if hiclampcmd!='':hiclampcmd=',clamp2='+hiclampcmd nclampcmd='' if hiclampcmd!='' or lowclampcmd!='':nclampcmd=',nclamp=5' knotcmd='' if self.splineknots.get()!=0:knotcmd=',nknots='+str(self.splineknots.get()) iffc.ifeffit("spline("+cur+".energy,"+cur+".xmu,e0="+wid.enot.get()+",rbkg="+ wid.rbkg.get()+",kmin="+wid.splka.get()+",kmax="+wid.splkb.get()+ ",pre1="+wid.prea.get()+",pre2="+wid.preb.get()+",norm1="+wid.norma.get()+",norm2="+wid.normb.get()+ ",kweight="+wid.kwt.get()+",dk1="+wid.dk.get()+",dk2="+wid.dk.get()+ ",kwindow="+wid.winparam.get()+lowclampcmd+hiclampcmd+nclampcmd+knotcmd+")") #get spline knots and report in status bar wid.splknot=int(iffc.get_scalar("nknots")) setstatus(self.status,"File "+cur+" selected, spline contains "+str(wid.splknot)+" knots, edge step height="+wid.stepheight) #put parameter summary text together self.printressum() #calculate kwt chi iffc.ifeffit("dokwt "+cur+" "+self.plotkw.get()) #calcualte FT iffc.ifeffit("fftf(real="+cur+".chi,kweight="+self.plotkw.get()+",kmin="+\ self.plotkmin.get()+",kmax="+self.plotkmax.get()+""",kwindow='"""+\ self.plotwinparam.get()+"""',dk="""+self.plotdk.get()+")") #enots iffc.ifeffit("set("+cur+".enotx=ones(2)*e0)") iffc.ifeffit(cur+".enoty=linterp("+cur+".energy,"+cur+".xmu,"+cur+".enotx)") def shiftenergy(self): #get data cur=self.phlist.info_selection() if cur==(): return cur=cur[0] self.filparam.selectpage(remundsc(cur)) #dialog to get energy shift val=tkSimpleDialog.askfloat('Energy Shift','eV to shift mu',parent=self.bswin) if val==None: return #apply shift iffc.ifeffit("set("+cur+".energy="+cur+".energy+"+str(val)+")") def spmulti_plot(self,new,gx,gy,xlab,ylab,title,xmin,xmax,key): xdat=iffc.get_array(gx) ydat=iffc.get_array(gy) if new==1: spplotter.SPPlotter(self.root,cmd="new",lt=key,xd=xdat,yd=ydat,xt=xlab,yt=ylab, title=title,xmin=xmin,xmax=xmax) if new==0: spplotter.SPPlotter(self.root,cmd="stack",lt=key,xd=xdat,yd=ydat,xt=xlab,yt=ylab, title=title,xmin=xmin,xmax=xmax) def singleplot(self,event): type=event.widget.cget('text') #get data cur=self.phlist.info_selection() if cur==(): return cur=cur[0] self.doallanalysis() self.filparam.selectpage(remundsc(cur)) wid=self.fpwids[cur].p new=1 if type=='Raw': xdat=iffc.get_array(cur+".energy") ydat=iffc.get_array(cur+".xmu") spplotter.SPPlotter(self.root,cmd='new',lt=cur,xd=xdat,yd=ydat,xt='eV',yt='Raw mu',title=type,SAMEz=wid.enot.get()) if type=='PreEdg': xdat=iffc.get_array(cur+".energy") ydat=iffc.get_array(cur+".xmu") spplotter.SPPlotter(self.root,cmd='new',lt=cur,xd=xdat,yd=ydat,xt='eV',yt='Raw mu',title=type) if wid.pretype.getcurselection()=='Linear': ydat=iffc.get_array(cur+".fitlin") spplotter.SPPlotter(self.root,cmd='stack',lt="Pre",xd=xdat,yd=ydat,xt='eV',yt='Raw mu',title=type) if wid.pretype.getcurselection()=='Gauss': ydat=iffc.get_array(cur+".fitgaus") spplotter.SPPlotter(self.root,cmd='stack',lt="Pre",xd=xdat,yd=ydat,xt='eV',yt='Raw mu',title=type) ydat=iffc.get_array(cur+".polyplot") spplotter.SPPlotter(self.root,cmd='stack',lt="Post",xd=xdat,yd=ydat,xt='eV',yt='Raw mu',title=type) xdat=iffc.get_array(cur+".enotx") ydat=iffc.get_array(cur+".enoty") spplotter.SPPlotter(self.root,cmd='stack',lt="enot0",xd=xdat,yd=ydat,color='orange', symbol='circle',pixels=10,hideleg=1,xt='eV',yt='Raw mu',title=type,SAMEz=wid.enot.get()) if type=='Spline': xdat=iffc.get_array(cur+".energy") ydat=iffc.get_array(cur+".xmu") spplotter.SPPlotter(self.root,cmd='new',lt=cur,xd=xdat,yd=ydat,xt='eV',yt='Raw mu',title=type) ydat=iffc.get_array(cur+".bkg") spplotter.SPPlotter(self.root,cmd='stack',lt="Spline",xd=xdat,yd=ydat,xt='eV',yt='Raw mu',title=type) xdat=iffc.get_array(cur+".enotx") ydat=iffc.get_array(cur+".enoty") spplotter.SPPlotter(self.root,cmd='stack',lt="enot0",xd=xdat,yd=ydat,color='orange', xt='eV',yt='Raw mu',title=type,symbol='circle',pixels=10,hideleg=1,SAMEz=wid.enot.get()) if type=='mu(E)': xdat=iffc.get_array(cur+".energy") ydat=iffc.get_array(cur+".samnorm") if self.optmuderiv.get(): #take derivative of mu iffc.ifeffit("del.x=deriv("+cur+".energy)") iffc.ifeffit("del.y=deriv("+cur+".samnorm)") iffc.ifeffit("del.d=del.y/del.x") ydat=iffc.get_array("del.d") if self.optmusmooth.get(): if self.optmuderiv.get(): #smooth mu deriv iffc.ifeffit("del.ds=smooth(del.d)") ydat=iffc.get_array("del.ds") else: #smooth mu only iffc.ifeffit("del.ds=smooth("+cur+".samnorm)") ydat=iffc.get_array("del.ds") spplotter.SPPlotter(self.root,cmd='new',lt=cur,xd=xdat,yd=ydat,xt='eV',yt='Norm mu',title=type,SAMEz=wid.enot.get()) if type=='chi(k)': #calculate kwt chi iffc.ifeffit("dokwt "+cur+" "+self.plotkw.get()) xdat=iffc.get_array(cur+".k") ydat=iffc.get_array(cur+".chi_kw") spplotter.SPPlotter(self.root,cmd='new',lt=cur,xd=xdat,yd=ydat,xt='k',yt='k'+self.plotkw.get()+' chi(k)',title=type,xmin=self.plotkmin.get(),xmax=self.plotkmax.get()) if 'yes' in self.plotftwin.getvalue(): iffc.ifeffit("window(k="+cur+".k,group=win,kweight="+self.plotkw.get()+",kmin="+\ self.plotkmin.get()+",kmax="+self.plotkmax.get()+""",kwindow='"""+\ self.plotwinparam.get()+"""',dk="""+self.plotdk.get()+")") iffc.ifeffit("win.mwin=win.win*ceil(abs("+cur+".chi_kw))") wdat=iffc.get_array("win.mwin") spplotter.SPPlotter(self.root,cmd='stack',lt='FT Win',xd=xdat,yd=wdat,color='red',xt='k',yt='k'+self.plotkw.get()+' chi(k)',title=type,xmin=self.plotkmin.get(),xmax=self.plotkmax.get()) if type=='R': #calcualte FT iffc.ifeffit("fftf(real="+cur+".chi,kweight="+self.plotkw.get()+",kmin="+\ self.plotkmin.get()+",kmax="+self.plotkmax.get()+""",kwindow='"""+\ self.plotwinparam.get()+"""',dk="""+self.plotdk.get()+")") xdat=iffc.get_array(cur+".r") ydat=iffc.get_array(cur+".chir_mag") spplotter.SPPlotter(self.root,cmd='new',lt=cur,xd=xdat,yd=ydat,xt='R',yt='|chi(R)|',title=type,xmin=self.plotrmin.get(),xmax=self.plotrmax.get()) def multiplot(self,event): event.widget.config(state=ACTIVE) event.widget.config(relief=SUNKEN) type=event.widget.cget('text') if type=='PreEdg' or type=='Spline': self.singleplot(event) else: #get current data latest=self.phlist.info_selection() if latest==(): return latest=latest[0] new=1 #go through file list for cur in self.datfiles: #select latest self.phlist.selection_clear() self.phlist.selection_set(cur) self.filparam.selectpage(remundsc(cur)) wid=self.fpwids[cur].p if wid.active==1: self.doallanalysis() iffc.ifeffit("gmin=floor("+cur+".energy)") iffc.ifeffit("gmax=ceil("+cur+".energy)") xmin=str(iffc.get_scalar("gmin")) xmax=str(iffc.get_scalar("gmax")) if type=='Raw': self.spmulti_plot(new,cur+".energy",cur+".xmu","eV","Raw mu",type,xmin,xmax,cur) new=0 if type=='mu(E)': opt=0 if self.optmuderiv.get(): #take derivative of mu iffc.ifeffit("del.x=deriv("+cur+".energy)") iffc.ifeffit("del.y=deriv("+cur+".samnorm)") iffc.ifeffit("del.d=del.y/del.x") iffc.ifeffit("del.ds=del.d") opt=1 if self.optmusmooth.get(): opt=1 if self.optmuderiv.get(): #smooth mu deriv iffc.ifeffit("del.ds=smooth(del.d)") else: #smooth mu only iffc.ifeffit("del.ds=smooth("+cur+".samnorm)") if opt: self.spmulti_plot(new,cur+".energy","del.ds","eV","Norm mu",type,xmin,xmax,cur) else: self.spmulti_plot(new,cur+".energy",cur+".samnorm","eV","Norm mu",type,xmin,xmax,cur) new=0 if type=='chi(k)': #calculate kwt chi iffc.ifeffit("dokwt "+cur+" "+self.plotkw.get()) self.spmulti_plot(new,cur+".k",cur+".chi_kw","k","k"+self.plotkw.get()+" chi(k)",type,self.plotkmin.get(),self.plotkmax.get(),cur) new=0 if type=='R': #calcualte FT iffc.ifeffit("fftf(real="+cur+".chi,kweight="+self.plotkw.get()+",kmin="+\ self.plotkmin.get()+",kmax="+self.plotkmax.get()+""",kwindow='"""+\ self.plotwinparam.get()+"""',dk="""+self.plotdk.get()+")") self.spmulti_plot(new,cur+".r",cur+".chir_mag","R","|chi(R)|",type,self.plotrmin.get(),self.plotrmax.get(),cur) new=0 #restore old selection self.phlist.selection_clear() self.phlist.selection_set(latest) self.selectfile() def returnclick(self,event): event.widget.config(state=NORMAL) event.widget.config(relief=RAISED) def savemudata(self): global lastsavedir #get data cur=self.phlist.info_selection() if cur==(): return cur=cur[0] exten=".mu" if self.optmuderiv.get(): exten="_d.mu" nfn=ask_save_file(cur+exten,lastsavedir) root.bswin.focus_set() if nfn<>"": sdir=rfind(nfn,os.sep) lastsavedir=nfn[:sdir] self.doallanalysis() if rfind(nfn,'.')==-1: nfn=nfn+".mu" opt=0 if self.optmuderiv.get(): #take derivative of mu iffc.ifeffit("del.x=deriv("+cur+".energy)") iffc.ifeffit("del.y=deriv("+cur+".samnorm)") iffc.ifeffit("del.d=del.y/del.x") iffc.ifeffit("del.ds=del.d") opt=1 if self.optmusmooth.get(): opt=1 if self.optmuderiv.get(): #smooth mu deriv iffc.ifeffit("del.ds=smooth(del.d)") else: #smooth mu only iffc.ifeffit("del.ds=smooth("+cur+".samnorm)") if opt: iffc.ifeffit("write_data(file="+nfn+","+cur+".energy,del.ds)") setstatus(self.status,"mu(E) derivative data saved to "+nfn) else: iffc.ifeffit("write_data(file="+nfn+","+cur+".energy,"+cur+".samnorm)") setstatus(self.status,"mu(E) data saved to "+nfn) def savechidata(self): global lastsavedir #get data cur=self.phlist.info_selection() if cur==(): return cur=cur[0] nfn=ask_save_file(cur+".chi",lastsavedir) root.bswin.focus_set() if nfn!="": sdir=rfind(nfn,os.sep) lastsavedir=nfn[:sdir] self.doallanalysis() if rfind(nfn,'.')==-1: nfn=nfn+".chi" iffc.ifeffit("write_data(file="+nfn+","+cur+".k,"+cur+".chi)") setstatus(self.status,"chi(k) data saved to "+nfn) def saveRdata(self): global lastsavedir #get data cur=self.phlist.info_selection() if cur==(): return cur=cur[0] nfn=ask_save_file(cur+".rsp",lastsavedir) root.bswin.focus_set() if nfn<>"": sdir=rfind(nfn,os.sep) lastsavedir=nfn[:sdir] self.doallanalysis() if rfind(nfn,'.')==-1: nfn=nfn+".rsp" iffc.ifeffit("write_data(file="+nfn+","+cur+".r,"+cur+".chir_mag,"+cur+".chir_re,"+cur+".chir_im,"+cur+".chir_phase)") setstatus(self.status,"=FT data saved to "+nfn) def setallparam(self): #get data latest=self.phlist.info_selection() if latest==(): return latest=latest[0] self.filparam.selectpage(remundsc(latest)) newwid=self.fpwids[latest].p for cur in self.datfiles: #select latest self.phlist.selection_clear() self.phlist.selection_set(cur) self.filparam.selectpage(remundsc(cur)) wid=self.fpwids[cur].p #create database relate=[] for i in range(0,len(wid.copyable)): relate.append((newwid.copyable[i],wid.copyable[i])) for delta,gamma in relate: gamma.setentry(delta.get()) wid.clamp1.selectitem(newwid.clamp1.get()) wid.clamp2.selectitem(newwid.clamp2.get()) wid.pretype.setvalue(newwid.pretype.getcurselection()) wid.posttype.setvalue(newwid.posttype.getcurselection()) #restore old selection self.phlist.selection_clear() self.phlist.selection_set(latest) self.filparam.selectpage(remundsc(latest)) def setmarkparam(self): #get data latest=self.phlist.info_selection() if latest==(): return latest=latest[0] self.filparam.selectpage(remundsc(latest)) newwid=self.fpwids[latest].p for cur in self.datfiles: #select latest self.phlist.selection_clear() self.phlist.selection_set(cur) self.filparam.selectpage(remundsc(cur)) wid=self.fpwids[cur].p if wid.active==1: #create database relate=[] for i in range(0,len(wid.copyable)): relate.append((newwid.copyable[i],wid.copyable[i])) for delta,gamma in relate: gamma.setentry(delta.get()) wid.clamp1.selectitem(newwid.clamp1.get()) wid.clamp2.selectitem(newwid.clamp2.get()) wid.pretype.setvalue(newwid.pretype.getcurselection()) wid.posttype.setvalue(newwid.posttype.getcurselection()) #restore old selection self.phlist.selection_clear() self.phlist.selection_set(latest) self.filparam.selectpage(remundsc(latest)) def savecurparams(self): global lastsavedir #place all paths and varibles into a parameter file #get file name nfn=ask_save_file('',lastsavedir) root.bswin.focus_set() if nfn=="": setstatus(self.status,"Save parameters aborted") return sdir=rfind(nfn,os.sep) lastsavedir=nfn[:sdir] #open file #check for extension ending ext=rfind(nfn,".") if ext==-1: nfn=nfn+".prm" fid=open(nfn,"w") #get current widget cur=self.phlist.info_selection() if cur==(): return cur=cur[0] wid=self.fpwids[cur].p #save data-file parameters fid.write("BSPARAMS\n") fid.write(wid.enot.get()+'\n') fid.write(wid.rbkg.get()+'\n') fid.write(wid.kwt.get()+'\n') fid.write(wid.winparam.get()+'\n') fid.write(wid.dk.get()+'\n') fid.write(wid.clamp1.get()+'\n') fid.write(wid.clamp2.get()+'\n') fid.write(wid.pretype.getcurselection()+'\n') fid.write(wid.prea.get()+'\n') fid.write(wid.preb.get()+'\n') fid.write(wid.posttype.getcurselection()+'\n') fid.write(wid.norma.get()+'\n') fid.write(wid.normb.get()+'\n') fid.write(wid.splka.get()+'\n') fid.write(wid.splkb.get()+'\n') fid.write("END") fid.close() setstatus(self.status,"Background parameters saved to "+nfn) def loadsavedparams(self): global lastreaddir #load paths and variables from files #get file name fn=ask_for_file([("parameter files","*.prm"),("all files","*")],lastreaddir,check=0) root.bswin.focus_set() if fn=="": setstatus(self.status,"Load parameters aborted") return sdir=rfind(fn,os.sep) lastreaddir=fn[:sdir] #open file fid=open(fn,"r") param=fid.read() fid.close() #get current widget cur=self.phlist.info_selection() if cur==(): return cur=cur[0] wid=self.fpwids[cur].p #parse file... lp=split(param,'\n') ind=0 for new in lp: if new=='EDGEPARAMS' or new=='FPARAMS': #wrong parameter file self.box.deiconify() return if new=='BSPARAMS': #read data-file parameters #read BSub params wid.enot.setentry(lp[ind+1]) wid.rbkg.setentry(lp[ind+2]) wid.kwt.setentry(lp[ind+3]) wid.winparam.setentry(lp[ind+4]) wid.dk.setentry(lp[ind+5]) wid.clamp1.setentry(lp[ind+6]) wid.clamp2.setentry(lp[ind+7]) wid.pretype.invoke(lp[ind+8]) wid.prea.setentry(lp[ind+9]) wid.preb.setentry(lp[ind+10]) wid.posttype.invoke(lp[ind+11]) wid.norma.setentry(lp[ind+12]) wid.normb.setentry(lp[ind+13]) wid.splka.setentry(lp[ind+14]) wid.splkb.setentry(lp[ind+15]) wid.calc=1 setstatus(self.status,"Parameter file read from "+fn) ind=ind+1 def deglitchpanel(self): #get data cur=self.phlist.info_selection() if cur==(): return cur=cur[0] wid=self.fpwids[cur].p #make list of forwarding parameters #kwt,e0,Rbkg,splkwt,kmin,kmax,clamp1,clamp2,dk,Ftwin fwdps=[] fwdps.append(self.plotkw.get()) fwdps.append(wid.enot.get()) fwdps.append(wid.rbkg.get()) fwdps.append(wid.kwt.get()) fwdps.append(wid.splka.get()) fwdps.append(wid.splkb.get()) fwdps.append(wid.clamp1.get()) fwdps.append(wid.clamp2.get()) fwdps.append(wid.dk.get()) fwdps.append(wid.winparam.get()) print 'Entering deglitching panel for '+cur DeglitchPanel(cur,fwdps,self.root) def selfabscor(self): #get data cur=self.phlist.info_selection() if cur==(): return self.cur=cur[0] #element list self.esym=[ "H" , "He", "Li", "Be", "B" , "C" , "N" , "O" , "F" , "Ne", "Na", "Mg", "Al", "Si", "P" , "S" , "Cl", "Ar", "K" , "Ca", "Sc", "Ti", "V" , "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y" , "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I" , "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W" , "Re", "Os", "Ir", "Pt", "Au", "Hd", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U" ] #start new window sacwin=self.root.sacwin=Toplevel(self.root) self.sacwin=sacwin self.sacwin.title("Self Absorption Correction Panel") self.sacwin.protocol("WM_DELETE_WINDOW", self.closeselfabspanel) self.sacwin.focus_set() #help menu menubar=Pmw.MenuBar(sacwin) menubar.addmenu('File','',side=LEFT) menubar.addmenuitem('File','command',label='Open new CHI',command=self.getnewSACfile) menubar.addmenu('Help','',side=RIGHT) menubar.addmenuitem('Help','command',label='Parameters',command=self.getabshelp) menubar.pack(side=TOP,fill=X) #add current file self.saccurfile=Label(sacwin,text=self.cur,relief=GROOVE,bd=2,width=25,justify=CENTER,font="Arial 10") self.saccurfile.pack(side=TOP,pady=2,fill=X) #add entryfields entfr=Frame(sacwin) entfr.pack(side=TOP) w=15 self.sacform=Pmw.EntryField(entfr,labelpos='w',label_text='Formula: ',value='',entry_width=w) self.sacthick=Pmw.EntryField(entfr,labelpos='w',label_text='Thick (microns): ',value='0',validate='real',entry_width=w) self.sacvol=Pmw.EntryField(entfr,labelpos='w',label_text='Unit Vol. (A**3): ',value='0',validate='real',entry_width=w) self.sacphi=Pmw.EntryField(entfr,labelpos='w',label_text='Phi Angle (deg): ',value='45',validate='real',entry_width=w) self.sacfields=(self.sacform,self.sacthick,self.sacvol,self.sacphi) for fld in self.sacfields: fld.pack(side=TOP,fill=X,padx=10,pady=2) Pmw.alignlabels(self.sacfields) #add edge pulldowns self.edgepos=['K','LI','LII','LIII'] pdfr=Frame(sacwin) pdfr.pack(side=TOP) self.sacelement=Pmw.ComboBox(pdfr,labelpos='nw',label_text='Absorber',entry_width=5,scrolledlist_items=self.esym,history=0,fliparrow=1) self.sacedge=Pmw.ComboBox(pdfr,labelpos='nw',label_text='Edge',entry_width=7,listheight=100,scrolledlist_items=self.edgepos,history=0,fliparrow=1) self.sacelement.pack(side=LEFT,padx=5,pady=2) self.sacedge.pack(side=RIGHT,padx=5,pady=2) #return button controls b=Pmw.ButtonBox(sacwin,orient='vertical') b.pack(side=TOP,padx=2,pady=5,fill=X) w=30 b.add('Do SA Correction',command=self.doSAcorrection,width=w,bg='darkgreen',fg='snow') b.add('Plot Chis',command=self.doSAchiplot,width=w,bg='darkblue',fg='snow') b.add('Plot R-space',command=self.doSArspaceplot,width=w,bg='darkblue',fg='snow') b.add('Save Correction',command=self.saveSAcorr,width=w,bg='darkorange',fg='snow') b.add('Return',command=self.closeselfabspanel,width=w,bg='red',fg='snow') #add status bar self.sacstatus=Label(sacwin,text="",bd=2,relief=RAISED,anchor=W,fg='blue') self.sacstatus.pack(side=TOP,padx=0,pady=0,fill=X) setstatus(self.sacstatus,"Ready") self.doneSAcor=0 def doSAcorrection(self): setstatus(self.sacstatus,"Starting correction...") #get parameters d=float(self.sacthick.getvalue()) phi=float(self.sacphi.getvalue()) vol=float(self.sacvol.getvalue()) form=self.sacform.getvalue() elem=self.sacelement.get(None) ed=self.sacedge.get(None) #make sure thickness is converted to angstroms d=d*10000 #error check parameters if d<=0: setstatus(self.sacstatus,"ABORT: Bad Thickness") return if phi<0 or phi>90: setstatus(self.sacstatus,"ABORT: Bad Phi") return if vol<=0: setstatus(self.sacstatus,"ABORT: Bad Volume") return if form=='': setstatus(self.sacstatus,"ABORT: Bad Formula") return if elem not in self.esym: setstatus(self.sacstatus,"ABORT: Bad Absorber") return if ed not in self.edgepos: setstatus(self.sacstatus,"ABORT: Bad Edge") return #form edge edge=elem+' '+ed #get array from IFEFFIT k=iffc.get_array(self.cur+".k") chi=iffc.get_array(self.cur+".chi") #do correction self.sacnewchi=cbselfabs.fluor_corr(k,chi,d,phi,vol,form,edge,-1,'p','x') iffc.put_array(self.cur+".SACchi",self.sacnewchi) iffc.ifeffit("set SAC.chi="+self.cur+".SACchi") iffc.ifeffit("set SAC.k="+self.cur+".k") self.doneSAcor=1 setstatus(self.sacstatus,"Correction completed") def saveSAcorr(self): global lastsavedir if self.doneSAcor==0: setstatus(self.sacstatus,"Do correction first!") return #get data nfn=ask_save_file(self.cur+"_SAC.chi",lastsavedir) root.sacwin.focus_set() if nfn!="": sdir=rfind(nfn,os.sep) lastsavedir=nfn[:sdir] if rfind(nfn,'.')==-1: nfn=nfn+".chi" iffc.ifeffit("write_data(file="+nfn+",SAC.k,SAC.chi)") setstatus(self.sacstatus,"SAC chi(k) data saved") def getnewSACfile(self): #get new file for SA corrections global lastreaddir if self.doneSAcor==0: setstatus(self.sacstatus,"Do correction first!") return #get new name infile=ask_for_file([("chi files","*.chi"),("all files","*")],lastreaddir) root.sacwin.focus_set() if infile =='': setstatus(self.sacstatus,"Need Filename!") return sdir=rfind(infile,os.sep) lastreaddir=infile[:sdir] #update cur variable self.cur=trimdirext(infile) #load data here iffc.ifeffit("read_data(file="+infile+", group="+self.cur+",label='k chi')") #clear SAC group in IFEFFIT iffc.ifeffit("erase @group=SAC") self.doneSAcor=0 #update NAME and status setstatus(self.sacstatus,"New file loaded") setstatus(self.saccurfile,self.cur) def doSAchiplot(self): if self.doneSAcor==0: setstatus(self.sacstatus,"Do correction first!") return #plot corrected and uncorrected chis with whatever k-weighting is in the BackSub screen #make k-weighted array for new and old chis iffc.ifeffit("dokwt "+self.cur+" "+self.plotkw.get()) iffc.ifeffit("dokwt SAC "+self.plotkw.get()) #get data from IFEFFIT #old=iffc.get_array(self.cur+".chi_kw") #new=iffc.get_array("SAC.chi_kw") #kd=iffc.get_array("SAC.k") #pass data to plotter new=1 type="chi(k)" self.spmulti_plot(new,self.cur+".k",self.cur+".chi_kw","k","k"+self.plotkw.get()+" chi(k)",type,self.plotkmin.get(),self.plotkmax.get(),"Old") new=0 self.spmulti_plot(new,"SAC.k","SAC.chi_kw","k","k"+self.plotkw.get()+" chi(k)",type,self.plotkmin.get(),self.plotkmax.get(),"Corrected") setstatus(self.sacstatus,"Chis plotted") def doSArspaceplot(self): if self.doneSAcor==0: setstatus(self.sacstatus,"Do correction first!") return #plot corrected and uncorrected RDFs with whatever k-weighting is in the BackSub screen #make k-weighted array for new and old chis #take FTs iffc.ifeffit("fftf(real="+self.cur+".chi,kweight="+self.plotkw.get()+",kmin="+\ self.plotkmin.get()+",kmax="+self.plotkmax.get()+""",kwindow='"""+\ self.plotwinparam.get()+"""',dk="""+self.plotdk.get()+")") iffc.ifeffit("fftf(real=SAC.chi,kweight="+self.plotkw.get()+",kmin="+\ self.plotkmin.get()+",kmax="+self.plotkmax.get()+""",kwindow='"""+\ self.plotwinparam.get()+"""',dk="""+self.plotdk.get()+")") #pass data to plotter type='R' new=1 self.spmulti_plot(new,self.cur+".r",self.cur+".chir_mag","R","|chi(R)|",type,self.plotrmin.get(),self.plotrmax.get(),"Old") new=0 self.spmulti_plot(new,"SAC.r","SAC.chir_mag","R","|chi(R)|",type,self.plotrmin.get(),self.plotrmax.get(),"Corrected") setstatus(self.sacstatus,"RDFs plotted") #in changing files... #setstatus(self.saccurfile,cur) def closeselfabspanel(self): #clear ifeffit memory temp vars #iffc.ifeffit("erase @group=glitchtemp") #iffc.ifeffit("erase @group=temp") #kill panel self.sacwin.destroy() def getabshelp(self): #display a text box with instructions text="""This option performs fluorescence self-absorption corrections of EXAFS on samples of KNOWN compositions. The algorithm is based on the method of Booth and Bridges, http://xxx.lanl.gov/cond-mat/0306252. This article is also soon to be in print in Physica Scripta in the proceedings of the XAFS XII conference. The following parameters are required in order to perform the calculation. FORMULA: Chemical formula of compound, i.e. 'MnO2' or 'YBa2Fe0.31Cu2.69O7'. This should be the formula PER UNIT CELL. That is Cu metal is 'Cu4' not 'Cu'. THICKNESS: Thickness of sample, in microns. VOLUME: Volume of the unit cell in cubic angstroms. PHI: Angle of the incident beam w.r.t. the surface of the sample, in degrees. ABSORBER: The element which is the absorbing edge in the experiment. EDGE: The X-ray edge the measurement is performed at.""" tkMessageBox.showinfo('SA Correction Help',text) class DeglitchPanel: def __init__(self,active,fwdps,root): self.root=root self.fwdps=fwdps self.active=active #start new deglitching procedure dg=self.root.dg=Toplevel(self.root) self.dg=dg dg.title("Deglitching Panel for "+active) dg.protocol("WM_DELETE_WINDOW", self.closeglitch) dg.focus_set() #help menu menubar=Pmw.MenuBar(dg) menubar.addmenu('Help','',side=RIGHT) menubar.addmenuitem('Help','command',label='Deglitching',command=self.gethelp) menubar.pack(side=TOP,fill=X) #setup buttons and Tix graph panels mainfr=Frame(dg) mainfr.pack(side=TOP) bfr=Frame(mainfr) bfr.pack(side=LEFT,fill='both') gfr=Frame(mainfr,relief=SUNKEN,bd=2) gfr.pack(side=RIGHT,fill='both') #add button controls #edit buttons f1=Frame(bfr,relief=SUNKEN,bd=2) f1.pack(side=TOP,padx=1,pady=1,fill=X) l=Label(f1,text='Editing Control',relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=2) self.mubut=Button(f1,text="Edit Mu",width=20,command=self.editmu,bg='darkblue',fg='snow') self.chibut=Button(f1,text="Edit Chi",width=20,command=self.editchi,bg='brown',fg='snow') self.mubut.pack(side=TOP,padx=2,pady=5) self.chibut.pack(side=TOP,padx=2,pady=5) #spline controls f2=Frame(bfr,relief=SUNKEN,bd=2) f2.pack(side=TOP,padx=1,pady=1,fill=X) l=Label(f2,text='Spline Control',relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=2) w=10 self.plkwt=Pmw.EntryField(f2,labelpos='w',label_text='Plot k-wt: ',value='0',validate='real',entry_width=w) self.enot=Pmw.EntryField(f2,labelpos='w',label_text='e0: ',value='0',validate='real',entry_width=w) self.rbkg=Pmw.EntryField(f2,labelpos='w',label_text='Rbkg: ',value='0',validate='real',entry_width=w) self.kwt=Pmw.EntryField(f2,labelpos='w',label_text='k-wt: ',value='0',validate='real',entry_width=w) self.kmin=Pmw.EntryField(f2,labelpos='w',label_text='kmin: ',value='0',validate='real',entry_width=w) self.kmax=Pmw.EntryField(f2,labelpos='w',label_text='kmax: ',value='0',validate='real',entry_width=w) self.splfields=(self.plkwt,self.enot,self.rbkg,self.kwt,self.kmin,self.kmax) for fld in self.splfields: fld.pack(side=TOP,fill=X,padx=10,pady=2) Pmw.alignlabels(self.splfields) #return controls b=Pmw.ButtonBox(bfr,orient='vertical') b.pack(side=TOP,padx=2,pady=5,fill=X) b.add('Accept',command=self.acceptchanges,width=20,bg='darkgreen',fg='snow') b.add('Revert',command=self.getfwddata,width=20,bg='darkorange',fg='snow') b.add('Cancel',command=self.closeglitch,width=20,bg='red',fg='snow') #graph cursor positions fpb=Frame(bfr) fpb.pack(side=BOTTOM,padx=2,pady=1,fill=X) fpaa=Frame(bfr) fpaa.pack(side=BOTTOM,padx=2,pady=1,fill=X) fpa=Frame(bfr) fpa.pack(side=BOTTOM,padx=2,pady=1,fill=X) self.xlabmu=Label(fpa,text="X= ",width=11,bd=2,relief=RIDGE,anchor=W,fg='red') self.ylabmu=Label(fpa,text="Y= ",width=11,bd=2,relief=RIDGE,anchor=W,fg='red') self.xklabmu=Label(fpaa,text="Xk= ",width=11,bd=2,relief=RIDGE,anchor=W,fg='red') self.yklabmu=Label(fpaa,text="Y= ",width=11,bd=2,relief=RIDGE,anchor=W,fg='red') self.xlabchi=Label(fpb,text="X= ",width=11,bd=2,relief=RIDGE,anchor=W,fg='blue') self.ylabchi=Label(fpb,text="Y= ",width=11,bd=2,relief=RIDGE,anchor=W,fg='blue') self.xlabmu.pack(side=LEFT,fill=X) self.ylabmu.pack(side=LEFT,fill=X) self.xklabmu.pack(side=LEFT,fill=X) self.yklabmu.pack(side=LEFT,fill=X) self.xlabchi.pack(side=LEFT,fill=X) self.ylabchi.pack(side=LEFT,fill=X) #Add graph windows self.graphmu=Pmw.Blt.Graph(gfr,plotbackground='white',height=200) self.graphmu.bind(sequence="", func=self.mouseDown) self.graphmu.bind(sequence="", func=self.mouseUp ) self.graphmu.bind(sequence="", func=self.coordreport) self.graphmu.legend_configure(hide=1) self.graphmu.pack(side=TOP,expand=1,fill='both') self.graphchi=Pmw.Blt.Graph(gfr,plotbackground='white',height=200) self.graphchi.bind(sequence="", func=self.mouseDown) self.graphchi.bind(sequence="", func=self.mouseUp ) self.graphchi.bind(sequence="", func=self.coordreport) self.graphchi.legend_configure(hide=1) self.graphchi.pack(side=TOP,expand=1,fill='both') #set up plot dictionaries self.xgrlabref={} self.xgrlabref.update({self.graphmu:(self.xlabmu,self.xklabmu)}) self.xgrlabref.update({self.graphchi:(self.xlabchi,)}) self.ygrlabref={} self.ygrlabref.update({self.graphmu:(self.ylabmu,self.yklabmu)}) self.ygrlabref.update({self.graphchi:(self.ylabchi,)}) #zoom stack self.zoomstackref={} self.zoomstackref.update({self.graphmu:[]}) self.zoomstackref.update({self.graphchi:[]}) #initialize data self.muxd=[] self.muyd=[] self.chixd=[] self.chiyd=[] self.yarrays={} self.updaterefs() #get data and set parameters self.getfwddata() def coordreport(self,event): (x,y)=event.widget.invtransform(event.x,event.y) xref=self.xgrlabref.get(event.widget) yref=self.ygrlabref.get(event.widget) xlab=xref[0] ylab=yref[0] xtext="X="+str(x) ytext="Y="+str(y) xtext=xtext[:12] ytext=ytext[:12] setstatus(xlab,xtext) setstatus(ylab,ytext) if len(xref)==2: xlab=xref[1] ylab=yref[1] dele=x-float(self.enot.get()) if dele>=0: s=Etok(dele) else: s='N/A' xtext="Xk="+str(s) ytext="Y="+str(y) xtext=xtext[:12] ytext=ytext[:12] setstatus(xlab,xtext) setstatus(ylab,ytext) def updaterefs(self): self.yarrays.update({self.graphmu:self.muyd}) self.yarrays.update({self.graphchi:self.chiyd}) def zoom(self, x0, y0, x1, y1, gtype): #add last to zoomstack stack=self.zoomstackref[gtype] a0=gtype.xaxis_cget("min") a1=gtype.xaxis_cget("max") b0=gtype.yaxis_cget("min") b1=gtype.yaxis_cget("max") stack.append((a0,a1,b0,b1)) self.zoomstackref.update({gtype:stack}) #configure gtype.xaxis_configure(min=x0, max=x1) gtype.yaxis_configure(min=y0, max=y1) def mouseDrag(self,event): global x0, y0, x1, y1, gtype (x1, y1) = gtype.invtransform(event.x, event.y) gtype.marker_configure("marking rectangle", coords = (x0, y0, x1, y0, x1, y1, x0, y1, x0, y0)) self.coordreport(event) def mouseUp(self,event): global dragging,gtype global x0, y0, x1, y1 if dragging: gtype.unbind(sequence="") gtype.bind(sequence="", func=self.coordreport) gtype.marker_delete("marking rectangle") if event.num==1: if x0 <> x1 and y0 <> y1: # make sure the coordinates are sorted if x0 > x1: x0, x1 = x1, x0 if y0 > y1: y0, y1 = y1, y0 self.zoom(x0, y0, x1, y1, gtype) # zoom in else: self.rescaleplot(gtype) # zoom out def mouseDown(self,event): global dragging, x0, y0, gtype dragging = 0 gtype=event.widget if gtype.inside(event.x, event.y): dragging = 1 (x0, y0) = gtype.invtransform(event.x, event.y) gtype.marker_create("line", name="marking rectangle", dashes=(2, 2)) gtype.bind(sequence="", func=self.mouseDrag) def rescaleplot(self,gtype): #get last off stack stack=self.zoomstackref[gtype] if stack==[]: return limit=stack.pop() gtype.xaxis_configure(min=limit[0],max=limit[1]) gtype.yaxis_configure(min=limit[2],max=limit[3]) self.zoomstackref.update({gtype:stack}) def closeglitch(self): #clear ifeffit memory temp vars iffc.ifeffit("erase @group=glitchtemp") iffc.ifeffit("erase @group=temp") #kill panel self.dg.destroy() def acceptchanges(self): #tranfer data back to real arrays iffc.ifeffit("set "+self.active+".xmu=glitchtemp.xmu") #do spline on active clampdict={'None':'','Slight':'3','Weak':'6','Medium':'12','Strong':'24','Rigid':'96'} lowclampcmd=clampdict.get(self.fwdps[6]) if lowclampcmd!='':lowclampcmd=',clamp1='+lowclampcmd hiclampcmd=clampdict.get(self.fwdps[7]) if hiclampcmd!='':hiclampcmd=',clamp2='+hiclampcmd nclampcmd='' if hiclampcmd!='' or lowclampcmd!='':nclampcmd=',nclamp=5' iffc.ifeffit("spline("+self.active+".energy,"+self.active+".xmu,e0="+self.enot.get()+",rbkg="+ self.rbkg.get()+",kmin="+self.kmin.get()+",kmax="+self.kmax.get()+ ",kweight="+self.kwt.get()+",dk1="+self.fwdps[8]+",dk2="+self.fwdps[8]+ ",kwindow="+self.fwdps[9]+lowclampcmd+hiclampcmd+nclampcmd+")") #see ya self.closeglitch() def getfwddata(self): #retrieve list of forwarding parameters #kwt,e0,Rbkg,kwt,kmin,kmax....clamp1,clamp2,dk,Ftwin i=0 for ent in self.splfields: ent.setentry(self.fwdps[i]) i=i+1 #move data to temp deglitching data in ifeffit iffc.ifeffit("set glitchtemp.energy="+self.active+".energy") iffc.ifeffit("set glitchtemp.xmu="+self.active+".xmu") #do splining self.dospline() #clear plot self.clearplots([1,1]) #plot data self.plotmu('line') self.plotchi('line') def dospline(self): #do spline in ifeffit clampdict={'None':'','Slight':'3','Weak':'6','Medium':'12','Strong':'24','Rigid':'96'} lowclampcmd=clampdict.get(self.fwdps[6]) if lowclampcmd!='':lowclampcmd=',clamp1='+lowclampcmd hiclampcmd=clampdict.get(self.fwdps[7]) if hiclampcmd!='':hiclampcmd=',clamp2='+hiclampcmd nclampcmd='' if hiclampcmd!='' or lowclampcmd!='':nclampcmd=',nclamp=5' iffc.ifeffit("spline(glitchtemp.energy,glitchtemp.xmu,e0="+self.enot.get()+",rbkg="+ self.rbkg.get()+",kmin="+self.kmin.get()+",kmax="+self.kmax.get()+ ",kweight="+self.kwt.get()+",dk1="+self.fwdps[8]+",dk2="+self.fwdps[8]+ ",kwindow="+self.fwdps[9]+lowclampcmd+hiclampcmd+nclampcmd+")") def clearplots(self,select): if select[0]==1: glist=self.graphmu.element_names() if glist != (): for g in glist: self.graphmu.element_delete(g) if select[1]==1: glist=self.graphchi.element_names() if glist != (): for g in glist: self.graphchi.element_delete(g) def plotmu(self,type): #get data from ifeffit self.muxd=iffc.get_array("glitchtemp.energy") self.muyd=iffc.get_array("glitchtemp.xmu") self.updaterefs() #plot characteristics sym='' lt='mu' px=0 if type=='point': sym='circle' lt='data' px=2 self.graphmu.line_create(lt,xdata=tuple(self.muxd),ydata=tuple(self.muyd),symbol=sym,pixels=px) def plotchi(self,type): #get data from ifeffit self.chixd=iffc.get_array("glitchtemp.k") iffc.ifeffit("dokwt glitchtemp "+self.plkwt.get()) self.chiyd=iffc.get_array("glitchtemp.chi_kw") self.updaterefs() #plot characteristics sym='' lt='chi' px=0 if type=='point': sym='circle' lt='data' px=2 self.graphchi.line_create(lt,xdata=tuple(self.chixd),ydata=tuple(self.chiyd),symbol=sym,pixels=px) def GEmouseDrag(self,event): global idx, gtype u=self.yarrays[gtype] u[idx] = gtype.yaxis_invtransform(event.y) self.yarrays.update({gtype:u}) gtype.element_configure("data", ydata=tuple(u)) def GEmouseUp(self,event): global gtype gtype.element_unbind("data", "") def GEmouseDown(self,event): global idx, gtype gtype=event.widget gtype.element_bind("data", "", self.GEmouseDrag) el = gtype.element_closest(event.x, event.y) idx = el["index"] def editmu(self): #turn off chi button and switch mu function self.chibut.configure(state=DISABLED) self.mubut.configure(command=self.doneeditmu,text='Done Editing') #clear mu self.clearplots([1,0]) #replot points self.plotmu('point') #set up graphing-mouse properties self.graphmu.unbind(sequence="") self.graphmu.unbind(sequence="") self.graphmu.element_bind("data",sequence="", func=self.GEmouseDown) self.graphmu.element_bind("data",sequence="", func=self.GEmouseUp ) def doneeditmu(self): #restore buttons self.chibut.configure(state=NORMAL) self.mubut.configure(command=self.editmu,text='Edit Mu') #restore graph-mouse props self.graphmu.element_unbind("data",sequence="") self.graphmu.element_unbind("data",sequence="") self.graphmu.bind(sequence="", func=self.mouseDown) self.graphmu.bind(sequence="", func=self.mouseUp ) #update and move mu data to ifeffit self.muyd=self.yarrays[self.graphmu] iffc.ifeffit("erase glitchtemp.xmu") iffc.put_array("glitchtemp.xmu",self.muyd) #spline new data self.dospline() #clear plots self.clearplots([1,1]) #replot self.plotmu('line') self.plotchi('line') def editchi(self): #turn off mu button and switch chi function self.mubut.configure(state=DISABLED) self.chibut.configure(command=self.doneeditchi,text='Done Editing') #clear chi self.clearplots([0,1]) #replot points self.plotchi('point') #set up graphing-mouse properties self.graphchi.unbind(sequence="") self.graphchi.unbind(sequence="") self.graphchi.element_bind("data",sequence="", func=self.GEmouseDown) self.graphchi.element_bind("data",sequence="", func=self.GEmouseUp ) def doneeditchi(self): #restore buttons self.mubut.configure(state=NORMAL) self.chibut.configure(command=self.editchi,text='Edit Chi') #restore graph-mouse props self.graphchi.element_unbind("data",sequence="") self.graphchi.element_unbind("data",sequence="") self.graphchi.bind(sequence="", func=self.mouseDown) self.graphchi.bind(sequence="", func=self.mouseUp ) #update chi array self.chiyd=self.yarrays[self.graphchi] #unweight chi data and create energy scale from k inwt=float(self.plkwt.get()) kwts=[] enot=float(self.enot.get()) escale=[] ydunwt=[] ind=0 for k in self.chixd: kwts=k**inwt escale.append(ktoE(k)+enot) if k!=0: ydunwt.append(self.chiyd[ind]/kwts) else: ydunwt.append(0) ind=ind+1 #put chi data to ifeffit iffc.ifeffit("erase glitchtemp.chi_new") iffc.put_array("glitchtemp.chi_new",ydunwt) #now ifeffit chi_new has kw 0 altered data #need to shift energy scales for chi to energy #find nearest mu data point just after e0 pivot=() ind=0 for e in self.muxd: if pivot==() and e>enot: pivot=(e,ind) ind=ind+1 #interpolate edited data over range from e0 to end on same grid as mu newescale=self.muxd[pivot[1]:len(self.muxd)] iffc.ifeffit("erase temp.x,temp.oldx,temp.y") iffc.put_array("temp.x",newescale) iffc.put_array("temp.oldx",escale) iffc.ifeffit("temp.y=splint(temp.oldx,glitchtemp.chi_new,temp.x)") #now we have new edited data on same grid as mu from e0 to end stored in temp.y back=iffc.get_array("glitchtemp.bkg") newd=iffc.get_array("temp.y") #before adding... use edge_step edwt=iffc.get_scalar("edge_step") ind=pivot[1] for d in newd: self.muyd[ind]=back[ind]+d*edwt ind=ind+1 #put new mu to ifeffit iffc.ifeffit("erase glitchtemp.xmu") iffc.put_array("glitchtemp.xmu",self.muyd) #spline new data self.dospline() #clear plots self.clearplots([1,1]) #replot self.plotmu('line') self.plotchi('line') def gethelp(self): #display a text box with instructions text="""Deglitching can be performed by editing mu or chi. It is recomended to edit mu if possible -- otherwise some of the edge structure will be compromised. This will not affect the EXAFS however. Once the desired level of zoom is achieved, press the edit button and move the desired data points. Zooming cannot be performed once the editing has begun. Once editing is finished, the data will be resplined and displayed. To go back to the original data, click the revert button. Changes can be ignored by clicking cancel or loaded back to the background subtraction module by clicking accept. It is best to only deglitch one file at a time.""" tkMessageBox.showinfo('Deglitching Help',text) ############################################################ ## ## ## Run SamView ## ## ############################################################ class RunSV: def __init__(self): svwin=root.svwin=Toplevel(root) svwin.title("SamView") svwin.protocol("WM_DELETE_WINDOW", self.closemod) root.iconify() #change focus... svwin.focus_set() spsamview.Main(svwin,root) def closemod(self): getmainmenu(root.svwin) ############################################################ ## ## ## Run Least Squares Routine ## ## ############################################################ class RunLSF: def __init__(self): efwin=root.efwin=Toplevel(root) efwin.title("Least Squares Fitting") efwin.protocol("WM_DELETE_WINDOW", self.closemod) root.iconify() #change focus... efwin.focus_set() lsqfitter.EdgeFit(efwin,root) def closemod(self): getmainmenu(root.efwin) ############################################################ ## ## ## Run SixPack PCA ## ## ############################################################ class RunPCA: def __init__(self): pcawin=root.pcawin=Toplevel(root) pcawin.title("SixPack PCA") pcawin.protocol("WM_DELETE_WINDOW", self.closemod) root.iconify() #change focus... pcawin.focus_set() spkpca.PCAMain(pcawin,root) def closemod(self): getmainmenu(root.pcawin) ########################################################### ## ## ## IFEFFIT Command Line Window ## ## ########################################################### class RunIFEFFITCmdLine: def __init__(self): ifcl=root.ifcl=Toplevel(root) ifcl.title("IFEFFIT Command Line") ifcl.protocol("WM_DELETE_WINDOW", self.closemod) self.ifcl=ifcl self.root=root root.iconify() #change focus... ifcl.focus_set() #main widgets self.iftext=Pmw.ScrolledText(ifcl,hull_width=600,hull_height=300,text_wrap='none',usehullsize=1,vscrollmode='static',hscrollmode='static',text_state=DISABLED,text_bg='grey85') self.iftext.pack(side=TOP,expand=1,fill='both') self.iftext.tag_configure('input',foreground='black') self.iftext.tag_configure('output',foreground='blue') self.input=Pmw.EntryField(ifcl,labelpos='w',label_text='IFEFFIT>',label_fg='blue',command=self.sendinput) self.input.pack(side=TOP,expand=1,fill='both') iffc.ifeffit("set &screen_echo=0") def sendinput(self): #add input to text self.iftext.configure(text_state=NORMAL) self.iftext.insert(END,self.input.get()+'\n','input') #send command iffc.ifeffit(self.input.get()) #get and print return result=iffc.get_echo_buffer() if result!=[]: for r in result: self.iftext.insert(END,str(r)+'\n','output') self.iftext.see(END) self.iftext.configure(text_state=DISABLED) #clear input self.input.clear() def closemod(self): #reset screen echo iffc.ifeffit("set &screen_echo=1") self.ifcl.destroy() ########################################################### ## ## ## About SIXPACK Screen ## ## ########################################################### class callprogramabout: def __init__(self): programabout(root) ########################################################### ## ## ## SamXAS Main Menu Screen ## ## ########################################################### class SamXAS: #main window #Logo image logo=PhotoImage(file=filepath+"splogo.gif") px=logo.width() py=logo.height() samlogo=Canvas(root,borderwidth=2, relief=GROOVE, height=py, width=px) samlogo.create_image(5,5,anchor=NW, image=logo) iversion="""SIXPack (Sam's Interface for XAS analysis Package)\nPowered by IFEFFIT """+iffc.get_string('$&build') #check for update try: http=httplib.HTTP('www-ssrl.slac.stanford.edu') http.putrequest('GET','/~swebb/version.htm') http.putheader('Accept', 'text/html') http.putheader('Accept', 'text/plain') http.endheaders() errcode, errmsg, headers = http.getreply() htcontent=http.getfile().read() #ping counter ## host = "fastcounter.bcentral.com" ## url='/fastcounter?3170508+6341023' ## try: ## http2=httplib.HTTP("fastcounter.bcentral.com") ## http2.putrequest('GET','/fastcounter?3170508+6341023') ## http2.putheader('Accept', 'text/html') ## http2.putheader('Accept', 'text/plain') ## http2.endheaders() ## errcode, errmsg, headers = http2.getreply() ## htcontent2=http2.getfile().read() ## except: ## print "no counter" ## pass #ping map counter try: http2=httplib.HTTP("clustrmaps.com") http2.putrequest('GET','/counter/index2.php?url=http://www-ssrl.slac.stanford.edu/~swebb/version.htm') http2.putheader('Accept', 'text/html') http2.putheader('Accept', 'text/plain') http2.endheaders() errcode, errmsg, headers = http2.getreply() htcontent2=http2.getfile().read() except: print "no map" pass #parse content for version number parse=htcontent.split('\n') line=parse[12] #strip... stripline='' for a in range(len(line)): if line[a] not in ['<','>','p','/']: stripline=stripline+line[a] if float(stripline)<=float(version): spversion='You have the latest version of SixPack' else: spversion='Version '+stripline+' of SixPack now available!' except: spversion='Cannot check current version' #Program Buttons defbutwdth=20 butfont=("Arial 16 bold") butfont=("Comic Sans MS", 16, "bold") lab=Label(root, text="Menu Options", font="Arial 20 bold", width=defbutwdth) but1=Button(root, text="SamView", font=butfont,command=RunSV, width=defbutwdth) but2=Button(root, text="Background Removal", font=butfont,command=BSFit, width=defbutwdth) but5=Button(root, text="FEFF EXAFS Fitting", font=butfont,command=AdvFit, width=defbutwdth) but3=Button(root, text="Least Sq. Fitting", font=butfont,command=RunLSF, width=defbutwdth) but4=Button(root, text="PC Analysis", font=butfont,command=RunPCA, width=defbutwdth) but6=Button(root, text="Make FEFF SS Paths", font=butfont,command=PT, width=defbutwdth) but7=Button(root, text="About SixPACK/SamXAS", font=butfont,command=callprogramabout, width=defbutwdth) butf=Button(root, text="Quit", font=butfont,command=root.quit, width=defbutwdth) #grid these in main window i=0 lab.grid(row=i,column=1,sticky=W+E+N+S);i=i+1 but1.grid(row=i,column=1,sticky=W+E+N+S);i=i+1 but2.grid(row=i,column=1,sticky=W+E+N+S);i=i+1 but3.grid(row=i,column=1,sticky=W+E+N+S);i=i+1 but4.grid(row=i,column=1,sticky=W+E+N+S);i=i+1 but5.grid(row=i,column=1,sticky=W+E+N+S);i=i+1 but6.grid(row=i,column=1,sticky=W+E+N+S);i=i+1 but7.grid(row=i,column=1,sticky=W+E+N+S);i=i+1 butf.grid(row=i,column=1,sticky=W+E+N+S);i=i+1 versstatus=Label(root,text=iversion,bd=2,relief=RAISED,anchor=W,fg='blue',justify=LEFT) versstatus.grid(row=i,columnspan=2,sticky=W+E);i=i+1 versstatus2=Label(root,text=spversion,bd=2,relief=RAISED,anchor=W,fg='red') versstatus2.grid(row=i,columnspan=2,sticky=W+E) samlogo.grid(row=0,column=0,rowspan=i-1, sticky=W+E+N+S, padx=5, pady=5) #start main event handler root.mainloop() sixpack-0.68/spplotter.py0000666000175000017500000002752110435341310014520 0ustar segresegre# Data Plotter from Tkinter import * import Pmw from spglobalfuncs import * import tkFileDialogDir import os if os.name=='nt':os.sep='/' ############################################################### ## ## Plotter Widget ## ############################################################### class SPPlotter: def __init__(self,parent,**args): #determine if plotter open already self.root=parent wmname="SIXPack Plotter" wids=parent.winfo_children() self.bswin=0 for w in wids: try: t=w.title() except: t='' if t==wmname: pwin=w #for BS routine if t=="Background Subtraction Dialog": self.bswin=w try: #raise window pwin.focus_set() ex=1 except: #make plotter window dialog = Pmw.Dialog(parent, buttons = (), command = self.killgraph, title = wmname) self.dlog=dialog self.dint=dialog.interior() self.makewidgets() ex=0 if ex: #map widgets! ugh! t=pwin.winfo_children() self.dlog=t s0=t[1] #frame 2 in dialog t=s0.winfo_children() sg=t[1] #graph frame ss=t[2] #status frame t=sg.winfo_children() self.graph=t[0] t=ss.winfo_children() self.status=t[0] self.xcoord=t[2] self.ycoord=t[1] self.makegraph(args) def killgraph(self,event): #delete widget self.dlog.destroy() def makegraph(self,args): global sampleenot #required options: #cmd=new/stack #lt=string #xd,yd=data tuple #optional: #title=string #xt,yt=string, axes text #xmin,xmax, float, x-axis limits #symbol=''=line,'circle'=points #pixels=number -- size of data points #color=color string #hideleg=1/0 for hiding legend display if args=={}: return #required options try: cmd=args['cmd'] lt=args['lt'] xd=args['xd'] if type(xd)!=type(()):xd=tuple(xd) yd=args['yd'] if type(yd)!=type(()):yd=tuple(yd) except: print 'Need required plot commands' return #optional options try: tt=args['title'] except: tt='' try: xt=args['xt'] except: xt='' try: yt=args['yt'] except: yt='' try: xmin=args['xmin'] xmin=float(xmin) except: xmin='' try: xmax=args['xmax'] xmax=float(xmax) except: xmax='' try: sym=args['symbol'] except: sym='' try: px=args['pixels'] except: px=0 try: pc=args['color'] except: pc='' try: hideleg=args['hideleg'] except: hideleg=0 try: sampleenot=args['SAMEz'] except: self.sampleenot=0 if upper(cmd) not in ('NEW','STACK'): print 'invalid plot command' return if upper(cmd)=='NEW': #clear graphs glist=self.graph.element_names() if glist != (): for g in glist: self.graph.element_delete(g) self.graph.xaxis_configure(min='',max='') self.graph.yaxis_configure(min='',max='') self.zoomstack=[] #default color scheme order colors=['blue','red','midnightblue','darkgreen','firebrick4','orange','black','green','purple4','cyan','steel blue','yellow4','peru'] cnum=len(colors) #determine color if not given if pc=='': #determine number of elements gnum=len(self.graph.element_names()) pc=colors[int(fmod(gnum,cnum))] #plot self.graph.line_create(lt,xdata=xd,ydata=yd,symbol=sym,color=pc,pixels=px) #xlimits self.graph.xaxis_configure(min=xmin,max=xmax) #legend deactivate? if hideleg: self.graph.element_configure(lt,label='') #add axes text if opted self.graph.xaxis_configure(title=xt) self.graph.yaxis_configure(title=yt) #add title text if opted self.graph.configure(title=tt) setstatus(self.status,"Graph constructed") def makewidgets(self): #Menu bar pw=self.dint menubar=Pmw.MenuBar(pw) #file menu menubar.addmenu('Copy','') menubar.addmenuitem('Copy','command',label='Set Dump Directory',command=self.setdir) menubar.addmenuitem('Copy','command',label='Graph to File',command=self.clipgraph) menubar.addmenuitem('Copy','separator') menubar.addmenuitem('Copy','command',label='Copy Data to Clipboard',command=self.graphtextport) menubar.addmenu('Help','',side=RIGHT) menubar.addmenuitem('Help','command',label='About SixPack',command=self.callprogramabout) menubar.pack(side=TOP,fill=X) #Container frames gfr=Frame(pw,relief=SUNKEN,bd=2) gfr.pack(side=TOP,fill='both',expand=1) sfr=Frame(pw) sfr.pack(side=TOP,fill=X) #Graph Window self.graph=Pmw.Blt.Graph(gfr,plotbackground='white') self.graph.bind(sequence="", func=self.mouseDown) self.graph.bind(sequence="", func=self.mouseUp ) self.graph.bind(sequence="", func=self.coordreport) self.graph.grid_toggle() self.graph.pack(expand=1,fill='both') #Status Bar self.status=Label(sfr,text="",bd=2,relief=RAISED,anchor=W,fg='blue') self.status.pack(side=LEFT,fill=X,expand=1) setstatus(self.status,"Ready") self.xcoord=Label(sfr,text="X= ",width=15,bd=2,relief=RIDGE,anchor=W,fg='red') self.ycoord=Label(sfr,text="Y= ",width=15,bd=2,relief=RIDGE,anchor=W,fg='red') self.ycoord.pack(side=RIGHT,fill=X) self.xcoord.pack(side=RIGHT,fill=X) #init stack self.zoomstack=[] self.dumpdir='' def callprogramabout(self): programabout(self.root) def setdir(self): #set graph-dump directory self.dumpdir=tkFileDialogDir.choose_directory() def clipgraph(self): if self.dumpdir=='':self.setdir() img = PhotoImage() self.graph.snap(img) fn=self.dumpdir+os.sep+"graph_dump.gif" img.write(fn,format='gif') setstatus(self.status,"Graph copied to dump_graph.gif") def coordreport(self,event): (x,y)=self.graph.invtransform(event.x,event.y) xtext="X="+str(x) ytext="Y="+str(y) xtext=xtext[:12] ytext=ytext[:12] setstatus(self.xcoord,xtext) setstatus(self.ycoord,ytext) def zoom(self, x0, y0, x1, y1): #add last to zoomstack a0=self.graph.xaxis_cget("min") a1=self.graph.xaxis_cget("max") b0=self.graph.yaxis_cget("min") b1=self.graph.yaxis_cget("max") self.zoomstack.append((a0,a1,b0,b1)) #configure self.graph.xaxis_configure(min=x0, max=x1) self.graph.yaxis_configure(min=y0, max=y1) def unzoom(self): #get last off stack if self.zoomstack==[]: return limit=self.zoomstack.pop() self.graph.xaxis_configure(min=limit[0],max=limit[1]) self.graph.yaxis_configure(min=limit[2],max=limit[3]) def mouseDrag(self,event): global x0, y0, x1, y1, druged druged = 1 (x1, y1) = self.graph.invtransform(event.x, event.y) self.graph.marker_configure("marking rectangle", coords = (x0, y0, x1, y0, x1, y1, x0, y1, x0, y0)) self.coordreport(event) def mouseUp(self,event): global dragging, druged global x0, y0, x1, y1 global sampleenot if dragging: self.graph.unbind(sequence="") self.graph.bind(sequence="", func=self.coordreport) self.graph.marker_delete("marking rectangle") if event.num==1 and druged: if x0 <> x1 and y0 <> y1: # make sure the coordinates are sorted if x0 > x1: x0, x1 = x1, x0 if y0 > y1: y0, y1 = y1, y0 self.zoom(x0, y0, x1, y1) # zoom in if event.num==3: self.unzoom() # zoom out if event.num==2 and self.bswin!=0: try: wid=self.bswin.focus_lastfor() widend=wid.winfo_name() mk=wid.master.children.keys() for w in mk: if w!=widend: lab=w labtxt=wid.master.children[lab].cget('text') status=0 if labtxt=='E0: ' and x0>500: status=1 if labtxt=='Rbkg: ' and x0<10: status=1 if labtxt=='k: ' and x0<20: status=1 if labtxt=='to k: ' and x0<20: status=1 if labtxt=='PreEdg: ' or labtxt=='Norm: ' or labtxt=='E: ' or labtxt=="to E: ": status=2 if status==1: entry_replace_d(wid,x0,4) if status==2 and x0>500: #recalc x0 newX=x0-float(sampleenot) entry_replace_d(wid,newX,4) except: return def mouseDown(self,event): global dragging, druged, x0, y0 dragging = 0 druged = 0 if self.graph.inside(event.x, event.y): dragging = 1 (x0, y0) = self.graph.invtransform(event.x, event.y) self.graph.marker_create("line", name="marking rectangle", dashes=(2, 2)) self.graph.bind(sequence="", func=self.mouseDrag) def graphtextport(self): #export all data in tab delimited text to clipboard text='' datay=[] datax=[] allnames=self.graph.element_names() print allnames for name in allnames: temp=self.graph.element_configure(name,'xdata') datax.append(temp[4]) temp=self.graph.element_configure(name,'ydata') datay.append(temp[4]) text=text+name+'\t\t\t' text=text+'\n' #parse list now pdatax=[] pdatay=[] alllen=[] maxlen=0 for i in range(len(datax)): temp=datax[i] pdatax.append(split(temp)) temp=datay[i] temp2=split(temp) if maxlen",self.plotclick) b=Button(plotwin,text="Variance",width=w,bg='firebrick4',fg='white') b.grid(row=1,column=1,columnspan=1,padx=5,pady=2,sticky=E+W) b.bind("",self.plotclick) b=Button(plotwin,text="Component",width=w,bg='chocolate3',fg='white') b.grid(row=2,column=0,columnspan=1,padx=5,pady=2,sticky=E+W) b.bind("",self.plotclick) b=Button(plotwin,text="All Components",width=w,bg='darkorange',fg='white') b.grid(row=2,column=1,columnspan=1,padx=5,pady=2,sticky=E+W) b.bind("",self.plotclick) b=Button(plotwin,text="Sample",width=w,bg='palegreen4',fg='white') b.grid(row=3,column=0,columnspan=1,padx=5,pady=2,sticky=E+W) b.bind("",self.plotclick) b=Button(plotwin,text="All Samples",width=w,bg='darkgreen',fg='white') b.grid(row=3,column=1,columnspan=1,padx=5,pady=2,sticky=E+W) b.bind("",self.plotclick) b=Button(plotwin,text="Reconstruction/Sample Pair",width=2*w+3,bg='royalblue3',fg='white') b.grid(row=4,column=0,columnspan=2,padx=5,pady=2,sticky=E+W) b.bind("",self.plotclick) b=Button(plotwin,text="Target Transform",width=2*w+3,bg='midnightblue',fg='white') b.grid(row=5,column=0,columnspan=2,padx=5,pady=2,sticky=E+W) b.bind("",self.plotclick) #file control fitpwin=Frame(pca,relief=SUNKEN,bd=2) fitpwin.grid(row=16,column=3,columnspan=1,rowspan=10,sticky=W+E+N+S) l=Label(fitpwin,text='File Parameters',relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) self.xmin=Pmw.EntryField(fitpwin,label_text="xmin:",labelpos=W,validate='real',entry_width=7,value='') self.xmax=Pmw.EntryField(fitpwin,label_text="xmax:",labelpos=W,validate='real',entry_width=7,value='') self.xwt=Pmw.EntryField(fitpwin,label_text="x-weight:",labelpos=W,validate='real',entry_width=7,value='0') self.xmin.pack(fill=X,expand=1,padx=15,pady=3) self.xmax.pack(fill=X,expand=1,padx=15,pady=3) self.xwt.pack(fill=X,expand=1,padx=15,pady=3) Pmw.alignlabels([self.xmin,self.xmax,self.xwt]) b=Button(fitpwin,text="Reload All",bg='goldenrod',fg='white',command=self.reloadallsamps) b.pack(side=TOP,fill=X,padx=5,pady=5) #add target transform control tarwin=Frame(pca,relief=SUNKEN,bd=2) tarwin.grid(row=16,column=4,columnspan=2,rowspan=10,sticky=W+E+N+S) l=Label(tarwin,text='Target Transform',relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) self.targetfile=Tix.FileEntry(tarwin,label="Target File: ",dialogtype="tk_getOpenFile") self.targetfile.pack(side=TOP,padx=2,pady=7) b=Button(tarwin,text="Do Target Transform",command=self.dotargettrans,bg='red',fg='white') b.pack(side=TOP,fill=X,padx=15,pady=10) self.chisq=Label(tarwin,text='Chi Sq: ',anchor=W) self.chisq.pack(side=TOP,fill=X,padx=5,pady=7) self.rval=Label(tarwin,text='Rvalue: ',anchor=W) self.rval.pack(side=TOP,fill=X,padx=5,pady=7) self.spoil=Label(tarwin,text='SPOIL: ',anchor=W) self.spoil.pack(side=TOP,fill=X,padx=5,pady=7) #add results text box resbox=Frame(pca,relief=SUNKEN,bd=2) resbox.grid(row=26,column=2,columnspan=4,rowspan=5,sticky=W+E+N+S) self.restext=Pmw.ScrolledText(resbox,hscrollmode='static',vscrollmode='static',label_text='PCA Results', columnheader=1,rowheader=1,rowcolumnheader=1,rowheader_width=4,rowcolumnheader_width=3, usehullsize=1,hull_width=650,hull_height=200,text_wrap='none',Header_font="Courier 9", text_height=10,labelpos=N,borderframe=1,text_font="Courier 9") self.restext.component('rowcolumnheader').insert('end', 'Comp') self.restext.configure(text_state = 'disabled',Header_state = 'disabled') self.restext.pack(padx=2,pady=0) #add status bar d=Label(pca,text=" ",width=15) d.grid(row=31,column=1,sticky=W+E) self.status=Label(pca,text="",bd=2,relief=RAISED,anchor=W,fg='blue') self.status.grid(row=31,columnspan=4,sticky=W+E) setstatus(self.status,"Ready") self.xcoord=Label(pca,text="X= ",bd=2,width=15,relief=RIDGE,anchor=W,fg='red') self.ycoord=Label(pca,text="Y= ",bd=2,width=15,relief=RIDGE,anchor=W,fg='red') self.xcoord.grid(row=31,column=4,columnspan=1,sticky=W+E) self.ycoord.grid(row=31,column=5,columnspan=1,sticky=W+E) #init vars self.plotstk=0 self.samfiles=[] self.samvars={} self.compfiles=[] self.compvars={} self.prop=[] self.targetdat=pcasampobj() self.ttransdat=pcasampobj() self.zoomstack=[] def callprogramabout(self): programabout(self.root) def callchangedefdirs(self): global lastsavedir,lastreaddir s=changedefdirs(self.pca) lastreaddir=s.newdir lastsavedir=s.newdir def closemod(self): self.root.deiconify() self.pca.destroy() def rescaleplot(self): #get last off stack if self.zoomstack==[]: return limit=self.zoomstack.pop() self.graph.xaxis_configure(min=limit[0],max=limit[1]) self.graph.yaxis_configure(min=limit[2],max=limit[3]) def coordreport(self,event): (x,y)=self.graph.invtransform(event.x,event.y) xtext="X="+str(x) ytext="Y="+str(y) xtext=xtext[:12] ytext=ytext[:12] setstatus(self.xcoord,xtext) setstatus(self.ycoord,ytext) def zoom(self, x0, y0, x1, y1): #add last to zoomstack a0=self.graph.xaxis_cget("min") a1=self.graph.xaxis_cget("max") b0=self.graph.yaxis_cget("min") b1=self.graph.yaxis_cget("max") self.zoomstack.append((a0,a1,b0,b1)) #configure self.graph.xaxis_configure(min=x0, max=x1) self.graph.yaxis_configure(min=y0, max=y1) def mouseDrag(self,event): global x0, y0, x1, y1, druged druged = 1 (x1, y1) = self.graph.invtransform(event.x, event.y) self.graph.marker_configure("marking rectangle", coords = (x0, y0, x1, y0, x1, y1, x0, y1, x0, y0)) self.coordreport(event) def mouseUp(self,event): global dragging, druged global x0, y0, x1, y1 if dragging: self.graph.unbind(sequence="") self.graph.bind(sequence="", func=self.coordreport) self.graph.marker_delete("marking rectangle") if event.num==1 and druged: if x0 <> x1 and y0 <> y1: # make sure the coordinates are sorted if x0 > x1: x0, x1 = x1, x0 if y0 > y1: y0, y1 = y1, y0 self.zoom(x0, y0, x1, y1) # zoom in else: self.rescaleplot() # zoom out def mouseDown(self,event): global dragging, x0, y0, druged dragging = 0 druged = 0 if self.graph.inside(event.x, event.y): dragging = 1 (x0, y0) = self.graph.invtransform(event.x, event.y) self.graph.marker_create("line", name="marking rectangle", dashes=(2, 2)) self.graph.bind(sequence="", func=self.mouseDrag) def loaddatafile(self): global lastsavedir,lastreaddir if self.xmin.get()=='' or self.xmax.get()=='': tkMessageBox.showwarning(title="Parameter Error",message="Cannot load file\nPlease fill in missing x-limit entries",parent=self.pca) return infile=ask_for_file([("chi files","*.chi"),("mu files","*.mu"),("all files","*")],lastreaddir) if infile !='': indir=rfind(infile,os.sep) lastreaddir=infile[:indir] #get file data self.dataread(infile) def loadmultdatafile(self): global lastsavedir,lastreaddir if self.xmin.get()=='' or self.xmax.get()=='': tkMessageBox.showwarning(title="Parameter Error",message="Cannot load file\nPlease fill in missing x-limit entries",parent=self.pca) return self.multifd=Tix.ExFileSelectDialog(self.root) if lastreaddir!='': lastreaddir=replace(lastreaddir,'/','\\') self.multifd.fsbox.configure(directory=lastreaddir) self.multifd.fsbox.filelist.listbox.configure(selectmode=MULTIPLE) #setup ok button... self.multifd.fsbox.ok.configure(command=self.getmultilist) self.multifd.popup() def getmultilist(self): global lastsavedir,lastreaddir multfn=self.multifd.fsbox.filelist.listbox.curselection() multdlist=self.multifd.fsbox.filelist.listbox.get(0,END) curdir=self.multifd.fsbox.dir.entry.get() lastreaddir=curdir self.multifd.popdown() if multfn !=(): for sel in multfn: curfil=multdlist[int(sel)] fulpath=curdir+os.sep+curfil #get file data self.dataread(fulpath) def reloadallsamps(self): #store path list in temp variable tpath=[] for np in self.samfiles: #select new sample dat=self.samvars.get(np) tpath.append(dat.path) #reload target if needed tp=0 if self.targetdat.path != '': self.targetread() tartemp=self.targetdat.path tp=1 #kill all data self.clearfilelist() #reload files for fn in tpath: self.dataread(fn) if tp==1: self.targetfile.entry.insert(END,tartemp) def dataread(self,fn): comchars=['#','!','%','*'] #initialize info widget wid=pcasampobj() #read file fid=open(fn,"r") lines=fid.read().split('\n') for line in lines: if line !='' and line[0] not in comchars: dr=replace(line,',',' ') parsed=split(dr) if atof(self.xmin.get())<=atof(parsed[0]) and atof(parsed[0])<=atof(self.xmax.get()): wid.xdat.append(atof(parsed[0])) wid.ydat.append(atof(parsed[1])) fid.close() wid.path=fn #turn into arrays wid.xdat=array(wid.xdat) wid.ydat=array(wid.ydat) #interpolate? 0.1 for XANES, 0.05 for EXAFS if self.nointerp.get()==0: if atof(self.xmin.get())<1000: newstep=0.05 #EXAFS else: newstep=0.1 #XANES try: interp=spline.Spline(wid.xdat,wid.ydat) except: tkMessageBox.showwarning(title="Parameter Error",message="x-limits of of data range",parent=self.pca) return wid.xdat=arange(atof(self.xmin.get()),atof(self.xmax.get()),newstep) wid.ydat=interp(wid.xdat) #apply k-weighting? temp=wid.ydat*(wid.xdat**int(self.xwt.get())) wid.ydat=temp #append lists/update tree treefile=trimdir(fn) self.samfiles.append(treefile) self.samvars.update({treefile:wid}) self.samlist.add(treefile,text=treefile,state=NORMAL) self.samlist.selection_clear() self.samlist.selection_set(treefile) #update status bar self.selectsamp() def removefile(self): cur=self.samlist.info_selection() if cur != (): cur=cur[0] #remove all associated vars ind=self.samfiles.index(cur) self.samfiles.remove(cur) self.samlist.delete_entry(cur) del self.samvars[cur] #reselect if len(self.samfiles)==0: self.complist.delete_all() elif ind != 0: new=self.samfiles[ind-1] self.samlist.selection_set(new) else: new=self.samfiles[0] self.samlist.selection_set(new) def clearfilelist(self): #reset all self.samfiles=[] self.samvars={} self.compfiles=[] self.compvars={} self.samlist.delete_all() self.complist.delete_all() self.prop=[] self.targetdat=pcasampobj() self.ttransdat=pcasampobj() #clear graph glist=self.graph.element_names() if glist != (): for g in glist: self.graph.element_delete(g) #clear results self.restext.configure(text_state = 'normal',Header_state = 'normal') self.restext.clear() self.restext.component('columnheader').delete(1.0,END) self.restext.component('rowheader').delete(1.0,END) self.restext.configure(Header_state = 'disabled') self.targetfile.entry.delete(0,END) def selectsamp(self, *arg): #get data cur=self.samlist.info_selection()[0] dat=self.samvars.get(cur) #update status npts=len(dat.xdat) setstatus(self.status,"File "+cur+" contains "+str(npts)+" data points") def choosecomp(self, *arg): cur=arg[0] wid=self.compvars.get(cur) if wid.active==0: if cur=='Comp 1': wid.active=0.5 self.updatevariance() return #turn on wid.active=1 self.complist.item_configure(cur,0,text='X') elif wid.active==0.5: #turn on wid.active=1 self.complist.item_configure(cur,0,text='X') else: #turn off wid.active=0 self.complist.item_configure(cur,0,text=' ') self.updatevariance() def plotclick(self,event): #determine plot type if type(event)==types.StringType: pt=event else: pt=event.widget.cget('text') #define data based on type and plot if pt=='Scree': self.plotstk=0 xd=[] yd=[] i=0 for np in self.compfiles: i=i+1 dat=self.compvars.get(np) if dat.active!=0.5: xd.append(i) yd.append(dat.eigen) #make plot self.makeplot(tuple(xd),tuple(yd),'Eigens','Scree Plot','c') if pt=='Variance': self.plotstk=0 xd=[0] yd=[0] i=0 for np in self.compfiles: i=i+1 dat=self.compvars.get(np) if dat.active != 0.5: xd.append(i) yd.append(dat.vartot) #make plot self.makeplot(tuple(xd),tuple(yd),'Var','Variance Plot','c') if pt=='Component': self.plotstk=0 cur=self.complist.info_selection() if cur != (): cur=cur[0] dat=self.compvars.get(cur) xd=tuple(dat.xdat) yd=tuple(dat.ydat) #make plot self.makeplot(xd,yd,cur,'Component Plot','l') if pt=='All Components': self.plotstk=0 for np in self.compfiles: #select new sample dat=self.compvars.get(np) if dat.active==1: xd=tuple(dat.xdat) yd=tuple(dat.ydat) #make plot self.makeplot(xd,yd,np,pt,'l') self.plotstk=self.plotstk+1 if pt=='Sample': self.plotstk=0 #get data cur=self.samlist.info_selection() if cur != (): cur=cur[0] dat=self.samvars.get(cur) xd=tuple(dat.xdat) yd=tuple(dat.ydat) #make plot self.makeplot(xd,yd,cur,'Sample Plot','l') if pt=='All Samples': self.plotstk=0 for np in self.samfiles: #select new sample dat=self.samvars.get(np) xd=tuple(dat.xdat) yd=tuple(dat.ydat) #make plot self.makeplot(xd,yd,np,pt,'l') self.plotstk=self.plotstk+1 if pt=='Reconstruction/Sample Pair': self.plotstk=0 #get data cur=self.samlist.info_selection() if self.compfiles==[]: return if cur != (): cur=cur[0] #first calculate reconstruction #make prop and eigenvector matrices rows=len(self.compvars[self.compfiles[0]].xdat) cols=len(self.compfiles) ueig=zeros((cols,rows),Float) i=0 for np in self.compfiles: dat=self.compvars.get(np) if dat.active==1: #use this one newe=dat.ydat a=i*rows b=a+rows put(ueig,range(a,b),newe) i=i+1 ueig=transpose(ueig) newmat=matrixmultiply(ueig,self.prop) #take slice for actual data to compare... ind=self.samfiles.index(cur) ytemp=take(newmat,(ind,),1) ytemp=transpose(ytemp) ytemp=ytemp[0] yd=tuple(ytemp) xd=tuple(dat.xdat) self.makeplot(xd,yd,'Recon.','Pair Plot','l') self.plotstk=1 #then plot sample dat=self.samvars.get(cur) xd=tuple(dat.xdat) yd=tuple(dat.ydat) #make plot self.makeplot(xd,yd,cur,'Pair Plot','l') if pt=='Target Transform': self.plotstk=0 #plot target xd=tuple(self.targetdat.xdat) yd=tuple(self.targetdat.ydat) #make plot self.makeplot(xd,yd,'target','Target Transform','l') self.plotstk=1 #plot transform xd=tuple(self.ttransdat.xdat) yd=tuple(self.ttransdat.ydat) #make plot self.makeplot(xd,yd,'transform','Target Transform','l') def makeplot(self,xd,yd,lt,tt,ltyp): #update graph #first remove current plot(s) if not stacking if self.plotstk==0: glist=self.graph.element_names() if glist != (): for g in glist: self.graph.element_delete(g) #def colors colors=['blue','red','midnightblue','darkgreen','firebrick4','steel blue','orange','purple4'] if self.plotstk==0: pc='blue' else: pc=colors[int(fmod(self.plotstk,len(colors)))] if ltyp=='l': sym='' else: sym='circle' #make plot try: self.graph.line_create(lt,xdata=xd,ydata=yd,symbol=sym,color=pc) except: lt=str(self.plotstk)+lt self.graph.line_create(lt,xdata=xd,ydata=yd,symbol=sym,color=pc) self.graph.configure(title=tt) def graphtextport(self): #export all data in tab delimited text to clipboard text='' datay=[] datax=[] allnames=self.graph.element_names() print allnames for name in allnames: temp=self.graph.element_configure(name,'xdata') datax.append(temp[4]) temp=self.graph.element_configure(name,'ydata') datay.append(temp[4]) text=text+name+'\t\t\t' text=text+'\n' #parse list now pdatax=[] pdatay=[] alllen=[] maxlen=0 for i in range(len(datax)): temp=datax[i] pdatax.append(split(temp)) temp=datay[i] temp2=split(temp) if maxlen0: spoil=sqrt(spoilrad) else: spoil=0 spoil=valueclip_d(spoil,5) setstatus(self.spoil,"SPOIL: "+spoil) #run plotter self.plotclick('Target Transform') def targetread(self): #read target data comchars=['#','!','%','*'] #read file fn=self.targetdat.path self.targetdat.xdat=[] self.targetdat.ydat=[] fid=open(fn,"r") lines=fid.read().split('\n') for line in lines: if line !='' and line[0] not in comchars: dr=replace(line,',',' ') parsed=split(dr) if atof(self.xmin.get())<=atof(parsed[0]) and atof(parsed[0])<=atof(self.xmax.get()): self.targetdat.xdat.append(atof(parsed[0])) self.targetdat.ydat.append(atof(parsed[1])) fid.close() #turn into arrays self.targetdat.xdat=array(self.targetdat.xdat) self.targetdat.ydat=array(self.targetdat.ydat) #interpolate? 0.1 for XANES, 0.05 for EXAFS if self.nointerp.get()==0: if atof(self.xmin.get())<1000: newstep=0.05 #EXAFS else: newstep=0.1 #XANES try: interp=spline.Spline(self.targetdat.xdat,self.targetdat.ydat) except: tkMessageBox.showwarning(title="Parameter Error",message="x-limits out of data range",parent=self.pca) return self.targetdat.xdat=arange(atof(self.xmin.get()),atof(self.xmax.get()),newstep) self.targetdat.ydat=interp(self.targetdat.xdat) #apply k-weighting? temp=self.targetdat.ydat*(self.targetdat.xdat**int(self.xwt.get())) self.targetdat.ydat=temp #update status bar npts=len(self.targetdat.xdat) cur=trimdir(fn) setstatus(self.status,"Target File "+cur+" contains "+str(npts)+" data points") def savePCAcomponents(self): global lastreaddir,lastsavedir default="pcacomponents.txt" fname=ask_save_file(default,lastsavedir) if fname != '': sdir=rfind(fname,os.sep) lastsavedir=fname[:sdir] #assemble data cmpdat=[] flag=0 arlen=0 totcols=0 for np in self.compfiles: #select new sample dat=self.compvars.get(np) if dat.active==1: if flag==0: cmpdat.append(list(dat.xdat)) flag=1 arlen=len(dat.xdat) totcols=totcols+1 cmpdat.append(list(dat.ydat)) totcols=totcols+1 if arlen==0: print "Need selected components" return #save two column ascii w/ brief header fid=open(fname,"w") fid.write("# PCA Components "+fname+" created by SIXPack\n") for pt in range(arlen): for col in range(totcols): fid.write(str(cmpdat[col][pt])+"\t") fid.write("\n") fid.close() #start event handler #PCAMain(root) #root.mainloop() sixpack-0.68/spsamview.py0000644000175000017500000017034010764340054014505 0ustar segresegre# Data Viewer import xasinput from spdirvars import * from spglobalfuncs import * from Numeric import * from Tkinter import * import Pmw import Tix import tkFileDialog import tkMessageBox import tkSimpleDialog import os import math from string import * import MLab from Scientific.Functions.LeastSquares import leastSquaresFit #root=Tix.Tk() #root.title("SamView") #Pmw.initialise(root) if os.name=='nt':os.sep='/' filepath=os.getcwd()+os.sep #global lastsavedir,lastreaddir #lastsavedir='' #lastreaddir='' #deatime model SCA=kappa*ICR*exp(-ICR*tau) tau in usecs def dteqn(pars,point): #return pars[0]*point*exp(-pars[1]/point) return pars[2]+pars[0]*point*exp(-pars[1]*point*1e-6) ############################################################### ## ## Main Program Class ## ############################################################### class Main: global starte,ende global edge global lastsavedir,lastreaddir def __init__(self,master,root): self.vwww=vwww=master self.root=root #define scrollable frame if root.winfo_screenheight()<860: self.sf=Pmw.ScrolledFrame(vwww,usehullsize=1,hull_width=800,hull_height=720) self.vw=vw=self.sf.interior() self.sf.pack(side=TOP) else: self.vw=vw=vwww #GUI for data viewer window menubar=Pmw.MenuBar(vw) #file menu menubar.addmenu('File','') menubar.addmenuitem('File','command',label='Open Dataset',command=self.loaddatafile) menubar.addmenuitem('File','command',label='Open Multiple Datasets',command=self.loadmultdatafile) menubar.addmenuitem('File','separator') menubar.addmenuitem('File','command',label='Clear Datasets',command=self.clearfilelist) menubar.addmenuitem('File','separator') menubar.addmenuitem('File','command',label='Edit Default Directories',command=self.callchangedefdirs) menubar.addmenuitem('File','separator') menubar.addmenuitem('File','command',label='Close',command=self.closemod) menubar.addmenuitem('File','command',label='Quit',command=self.root.quit) menubar.addmenu('Copy','') menubar.addmenuitem('Copy','command',label='Copy Plot Data to Clipboard',command=self.graphtextport) menubar.addmenu('Save','') menubar.addmenuitem('Save','command',label='Averaged Spectra',command=self.averagescans) menubar.addmenu('CSXAS','') menubar.addmenuitem('CSXAS','command',label='Change Data Spacing',command=self.changespacing) menubar.addmenu('Comments','') menubar.addmenuitem('Comments','command',label='View File Comments',command=self.viewcomments) menubar.addmenu('FluoChans','') menubar.addmenuitem('FluoChans','command',label='Set all fluo channels to current',command=self.setallfluochannels) menubar.addmenuitem('FluoChans','command',label='Reset all fluo channels',command=self.resetallfluochannels) menubar.addmenu('Gains','') menubar.addmenuitem('Gains','command',label='Change I0 Gain',command=self.editi0gain) menubar.addmenu('Help','',side=RIGHT) menubar.addmenuitem('Help','command',label='About SixPack',command=self.callprogramabout) menubar.grid(row=0,columnspan=25,sticky=W+E) #Add project manager window pmwin=Frame(vw,relief=SUNKEN,bd=2) l=Label(pmwin,text='Project Files',relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=4) act=Frame(pmwin) w=16 b=Button(act,text="Add File",width=w,command=self.loaddatafile,bg='steel blue',fg='white') b.pack(side=LEFT,padx=2,pady=2) b=Button(act,text="Add Many Files",width=w,command=self.loadmultdatafile,bg='darkblue',fg='white') b.pack(side=LEFT,padx=2,pady=2) act.pack(side=TOP,fill=X,padx=2) act=Frame(pmwin) b=Button(act,text="Remove File",width=w,command=self.removefile,bg='red',fg='white') b.pack(side=LEFT,padx=2,pady=2) b=Button(act,text="Clear All",width=w,command=self.clearfilelist,bg='brown',fg='white') b.pack(side=LEFT,padx=2,pady=2) act.pack(side=TOP,fill=X,padx=2) #Add btree tree=Tix.ScrolledHList(pmwin) self.phlist=tree.hlist self.phlist.config(separator='-',width=25, drawbranch=0, indent=10,itemtype=Tix.TEXT,browsecmd=self.selectfile) tree.pack(side=TOP,fill=BOTH,expand=1,padx=2,pady=2) #Add average button b=Button(pmwin,text="Average Scans",command=self.averagescans,bg='darkgreen',fg='snow') b.pack(side=BOTTOM,fill=X,padx=2,pady=2) pmwin.grid(row=1,column=0,columnspan=5,rowspan=15,sticky=W+E+N+S) #Add graph window grwin=Frame(vw,relief=SUNKEN,bd=2) self.graph=Pmw.Blt.Graph(grwin,plotbackground='white') self.graph.bind(sequence="", func=self.mouseDown) self.graph.bind(sequence="", func=self.mouseUp ) self.graph.bind(sequence="", func=self.coordreport) self.graph.pack(expand=1,fill='both') grwin.grid(row=1,column=5,columnspan=20,rowspan=15,sticky=W+E+N+S) #Add E0 Calibration Window e0win=Frame(vw,relief=SUNKEN,bd=2) l=Label(e0win,text='E0 Calibration',relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=2) f1=Frame(e0win) f1.pack(side=TOP,padx=5,pady=2) b=Button(f1,text='prev',bitmap="@"+filepath+"xbms"+os.sep+"previous.xbm") b.bind("",self.e0moveline) b.pack(side=LEFT,padx=2,pady=5) b=Button(f1,text="Find Data E0",width=20,command=self.findenot,bg='darkblue',fg='snow') b.pack(side=LEFT,padx=5,pady=5) b=Button(f1,text='next',bitmap="@"+filepath+"xbms"+os.sep+"next.xbm") b.bind("",self.e0moveline) b.pack(side=LEFT,padx=2,pady=5) self.e0app=Pmw.EntryField(e0win,labelpos='w',label_text='Apparent: ',value='0',validate='real') self.e0act=Pmw.EntryField(e0win,labelpos='w',label_text='Actual: ',value='0',validate='real',command=self.enotcalcshift) self.e0shift=Pmw.EntryField(e0win,labelpos='w',label_text='Shift: ',value='0',validate='real') e0fields=(self.e0app,self.e0act,self.e0shift) for fld in e0fields: fld.pack(side=TOP,fill=X,padx=10,pady=2) Pmw.alignlabels(e0fields) b=Button(e0win,text="Apply Shift to Data",width=20,command=self.enotapplyshift,bg='brown',fg='snow') b.pack(side=TOP,padx=2,pady=5) e0win.grid(row=16,column=0,columnspan=5,rowspan=6,sticky=W+E+N+S) #Add Deatime Correction Window dtwin=Frame(vw,relief=SUNKEN,bd=2) l=Label(dtwin,text='Deadtime Corrections',relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=2) self.dodt=IntVar() cb=Checkbutton(dtwin,text="Do the deatime correction?",variable=self.dodt,anchor=W,command=self.dodeadtime) cb.pack(side=TOP,padx=2,pady=2) self.dtfile=Tix.FileEntry(dtwin,label="Deadtime File: ",dialogtype="tk_getOpenFile") self.dtfile.pack(side=TOP,padx=2,pady=2) b=Button(dtwin,text="New DT file",width=20,command=self.getnewdtfile,bg='darkseagreen4',fg='ivory') b.pack(side=TOP,padx=2,pady=5) dtwin.grid(row=22,column=0,columnspan=5,rowspan=6,sticky=W+E+N+S) #Add Plot control window plotwin=Frame(vw,relief=SUNKEN,bd=2) l=Label(plotwin,text='Plot Control',relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=2) lhs=Frame(plotwin) rhs=Frame(plotwin) lhs.pack(side=LEFT,fill=BOTH,padx=1,pady=1) rhs.pack(side=LEFT,fill=BOTH,padx=1,pady=1) self.plotlist=('muF','muT1','muT2','Column') self.plottype=Pmw.ScrolledListBox(lhs,items=self.plotlist,labelpos=N,label_text='Plot Type', listbox_height=4,selectioncommand=self.selectnewplot, vscrollmode='static',listbox_exportselection=0) self.plottype.select_set(0) self.plottype.pack(side=TOP,fill=X,padx=2,pady=5) b=Button(lhs,text="Stack All Plots?",width=15,command=self.stackplot,bg='darkblue',fg='snow') b.pack(side=TOP,padx=2,pady=3) self.derivlist=('None','First','Second') self.deriv=Pmw.RadioSelect(lhs,labelpos=N,label_text='Derivative',buttontype='radiobutton',orient='vertical',pady=1) for but in self.derivlist: self.deriv.add(but) self.deriv.invoke('None') self.deriv.pack(side=TOP,fill=X,padx=2,pady=30) self.collist=('i0','i1','i2','iFsum','iFind','iFall','ICRind','ICRall') self.plotcol=Pmw.ScrolledListBox(rhs,items=self.collist,labelpos=N,label_text='Column Selection', listbox_height=6,selectioncommand=self.selectnewcolumn, vscrollmode='static',listbox_exportselection=0, listbox_selectbackground='grey',listbox_fg='grey') self.plotcol.select_set(0) self.plotcol.pack(side=TOP,fill=X,padx=2,pady=5) bb=Pmw.ButtonBox(rhs,orient='vertical',pady=5) bb.pack(side=TOP,padx=2,pady=20) bb.add("Replot",width=15,command=self.makeplot,bg='darkgreen',fg='ivory') bb.add("Rescale",width=15,command=self.rescaleplot,bg='brown',fg='ivory') self.smoothpts=Pmw.Counter(rhs,labelpos=N,label_text='# Pts to Smooth',entryfield_value=0, entryfield_validate={'validator':'integer','min':0},datatype='integer', entryfield_entry_width=2) self.smoothpts.pack(side=TOP,padx=2,pady=2) plotwin.grid(row=16,column=5,columnspan=10,rowspan=12,sticky=W+E+N+S) #Add Fluorescence control window flwin=Frame(vw,relief=SUNKEN,bd=2) l=Label(flwin,text='Fluorescence Channels',relief=RAISED,bd=2) l.pack(side=TOP,fill=X,padx=2,pady=2) tree=Tix.ScrolledHList(flwin) self.fhlist=tree.hlist self.fhlist.config(separator='-',width=25, drawbranch=1, indent=30,itemtype=Tix.TEXT,browsecmd=self.makeplot) tree.pack(side=TOP,fill=BOTH,expand=1,padx=2,pady=2) bb=Pmw.ButtonBox(flwin,orient='horizontal',pady=5) bb.pack(side=TOP,padx=2,pady=5) bb.add("Zero Sel. Chan.",width=15,command=self.deleteffchan,bg='darkorange4',fg='snow') bb.add("Reload Channels",width=15,command=self.restoreffchan,bg='goldenrod',fg='snow') flwin.grid(row=16,column=15,columnspan=5,rowspan=12,sticky=W+E+N+S) #Status Bar self.status=Label(vw,text="",bd=2,relief=RAISED,anchor=W,fg='blue') self.status.grid(row=30,columnspan=15,sticky=W+E) setstatus(self.status,"Ready") self.xcoord=Label(vw,text="X= ",bd=2,relief=RIDGE,anchor=W,fg='red') self.ycoord=Label(vw,text="Y= ",bd=2,relief=RIDGE,anchor=W,fg='red') self.xcoord.bind("",self.opencoordwin) self.ycoord.bind("",self.opencoordwin) self.xcoord.grid(row=30,column=15,columnspan=2,sticky=W+E) self.ycoord.grid(row=30,column=17,columnspan=2,sticky=W+E) #Coordinates window self.coordwin=Pmw.Dialog(vw,title='SV Coord') self.winxcoord=Label(self.coordwin.interior(),text="X= ",bd=2,relief=RIDGE,anchor=W,fg='red') self.winycoord=Label(self.coordwin.interior(),text="Y= ",bd=2,relief=RIDGE,anchor=W,fg='red') self.winxcoord.pack(side=LEFT,fill=X,padx=2,pady=2) self.winycoord.pack(side=LEFT,fill=X,padx=2,pady=2) self.coordwin.iconname('SV Coord') self.coordwin.withdraw() #init new vars self.datfiles=[] self.datvars={} self.ffchan={} self.icrchan={} self.dtcvar={} self.plotstk=0 self.curmax=0 self.maxima=[] self.zoomstack=[] self.fluochannelsremoved={} def opencoordwin(self,args): self.coordwin.deiconify() def closemod(self): self.root.deiconify() self.vw.destroy() def viewcomments(self): #get data cur=self.phlist.info_selection() if len(cur)!=0: #show box self.dialog.activate() def selectnewplot(self): cur=self.plottype.getcurselection()[0] if cur=='Column': #return defaults self.plotcol.configure(listbox_selectbackground='midnight blue',listbox_fg='black') else: #turn colors to "off" self.plotcol.configure(listbox_selectbackground='grey',listbox_fg='grey') self.rescaleplot() def selectnewcolumn(self): cur=self.plottype.getcurselection()[0] if cur=='Column': self.rescaleplot() def clearfilelist(self): #reset all xasinput.PsCLEAR() self.datfiles=[] self.fflist=[] self.datvars={} self.ffchan={} self.fluochannelsremoved={} self.phlist.delete_all() self.fhlist.delete_all() #clear graph glist=self.graph.element_names() if glist != (): for g in glist: self.graph.element_delete(g) def removefile(self): #clear graph glist=self.graph.element_names() if glist != (): for g in glist: self.graph.element_delete(g) #get current selection cur=self.phlist.info_selection() if cur != (): cur=cur[0] #remove all associated vars ind=self.datfiles.index(cur) self.datfiles.remove(cur) self.phlist.delete_entry(cur) del self.datvars[cur] del self.fluochannelsremoved[cur] #reselect if len(self.datfiles)==0: self.fhlist.delete_all() elif ind != 0: new=self.datfiles[ind-1] self.phlist.selection_set(new) self.selectfile() else: new=self.datfiles[0] self.phlist.selection_set(new) self.selectfile() def loadmultdatafile(self): global lastsavedir,lastreaddir self.multifd=Tix.ExFileSelectDialog(self.root) if lastreaddir!='': lastreaddir=replace(lastreaddir,'/','\\') self.multifd.fsbox.configure(directory=lastreaddir) self.multifd.fsbox.filelist.listbox.configure(selectmode=MULTIPLE) #setup ok button... self.multifd.fsbox.ok.configure(command=self.getmultilist) self.multifd.popup() def getmultilist(self): global lastsavedir,lastreaddir multfn=self.multifd.fsbox.filelist.listbox.curselection() multdlist=self.multifd.fsbox.filelist.listbox.get(0,END) curdir=self.multifd.fsbox.dir.entry.get() lastreaddir=curdir self.multifd.popdown() if multfn !=(): for sel in multfn: curfil=multdlist[int(sel)] fulpath=curdir+os.sep+curfil #get file data f=xasinput.XASget(fulpath,self.vw) if len(f.eV)==0:return f.restore=tuple(reshape(f.iF,(-1,))) f.restoreshape=shape(f.iF) self.datfiles.append(curfil) self.datvars.update({curfil:f}) self.fluochannelsremoved.update({curfil:[]}) self.phlist.add(curfil,text=curfil,state=NORMAL) self.phlist.selection_clear() self.phlist.selection_set(curfil) #call selection routine self.selectfile() def loaddatafile(self): global lastsavedir,lastreaddir infile=ask_for_file([("all files","*"),("data files","*.dat")],lastreaddir) if infile !='': indir=rfind(infile,os.sep) lastreaddir=infile[:indir] #get file data f=xasinput.XASget(infile,self.vw) if len(f.eV)==0:return f.restore=tuple(reshape(f.iF,(-1,))) f.restoreshape=shape(f.iF) #append lists/update tree treefile=trimdir(infile) self.datfiles.append(treefile) self.datvars.update({treefile:f}) self.fluochannelsremoved.update({treefile:[]}) self.phlist.add(treefile,text=treefile,state=NORMAL) self.phlist.selection_clear() self.phlist.selection_set(treefile) #call selection routine self.selectfile() def selectfile(self, *arg): #get data cur=self.phlist.info_selection()[0] dat=self.datvars.get(cur) #update status npts=len(dat.i0) setstatus(self.status,"File "+cur+" contains "+str(npts)+" data points") #comment box self.dialog=Pmw.TextDialog(self.vw,title='File Comments',defaultbutton=0,scrolledtext_usehullsize=1, scrolledtext_hull_width=500,scrolledtext_hull_height=100) self.dialog.withdraw() self.dialog.clear() if dat.type[0]=='S': if len(dat.comment)==6: for j in dat.comment: self.dialog.insert('end',j) else: self.dialog.insert('end',dat.comment) else: self.dialog.insert('end','No comments available') #update fluobox #delete all children self.fhlist.delete_all() self.ffchan.clear() self.icrchan.clear() #add rootlevel self.fhlist.add(cur,text=cur+" SUM",state=NORMAL) #add children self.fflist=[] nfc=shape(dat.iF) if shape(nfc)[0]==1: #only one FF channel self.fhlist.add(cur+'-FF0',text='FF1',state=NORMAL) self.ffchan.update({cur+'-FF0':dat.iF}) self.ffchan.update({cur:dat.iF}) self.icrchan.update({cur:dat.ICR}) self.icrchan.update({cur+'-FF0':dat.ICR}) self.fflist.append('FF0') else: #multiple FF channels ncols=nfc[1] i=0 while ilen(x)-numpts-1: sr=range(i-numpts,len(x),1) else: sr=range(i-numpts,i+numpts+1,1) temp=0 for ind in sr: temp=temp+x[ind] smoo.append(temp/len(sr)) i=i+1 return smoo def coordreport(self,event): (x,y)=self.graph.invtransform(event.x,event.y) xtext="X="+str(x) ytext="Y="+str(y) xtext=xtext[:12] ytext=ytext[:12] setstatus(self.xcoord,xtext) setstatus(self.ycoord,ytext) setstatus(self.winxcoord,xtext) setstatus(self.winycoord,ytext) def zoom(self, x0, y0, x1, y1): #add last to zoomstack a0=self.graph.xaxis_cget("min") a1=self.graph.xaxis_cget("max") b0=self.graph.yaxis_cget("min") b1=self.graph.yaxis_cget("max") self.zoomstack.append((a0,a1,b0,b1)) #configure self.graph.xaxis_configure(min=x0, max=x1) self.graph.yaxis_configure(min=y0, max=y1) def unzoom(self): #get last off stack if self.zoomstack==[]: return limit=self.zoomstack.pop() self.graph.xaxis_configure(min=limit[0],max=limit[1]) self.graph.yaxis_configure(min=limit[2],max=limit[3]) def mouseDrag(self,event): global x0, y0, x1, y1, druged druged = 1 (x1, y1) = self.graph.invtransform(event.x, event.y) self.graph.marker_configure("marking rectangle", coords = (x0, y0, x1, y0, x1, y1, x0, y1, x0, y0)) self.coordreport(event) def mouseUp(self,event): global dragging, druged global x0, y0, x1, y1 if dragging: self.graph.unbind(sequence="") self.graph.bind(sequence="", func=self.coordreport) self.graph.marker_delete("marking rectangle") if event.num==1 and druged: if x0 <> x1 and y0 <> y1: # make sure the coordinates are sorted if x0 > x1: x0, x1 = x1, x0 if y0 > y1: y0, y1 = y1, y0 self.zoom(x0, y0, x1, y1) # zoom in else: self.unzoom() # zoom out def mouseDown(self,event): global dragging, druged, x0, y0 dragging = 0 druged = 0 if self.graph.inside(event.x, event.y): dragging = 1 (x0, y0) = self.graph.invtransform(event.x, event.y) self.graph.marker_create("line", name="marking rectangle", dashes=(2, 2)) self.graph.bind(sequence="", func=self.mouseDrag) def averagescans(self): global lastsavedir,lastreaddir #average all active scans allscans=list(self.phlist.info_children()) nscans=len(allscans) #check lengths for each file lenlist=[] for d in allscans: lenlist.append(len(self.datvars[d].i0)) match=1 maxlen=max(lenlist) maxlenind=lenlist.index(maxlen) for m in lenlist: if m != lenlist[0]:match=0 if match==0: #ask if truncation, full averaging, or cancel of averaging is desired... mtext="Files not of equal length! \nTruncate, Continue or Cancel? \n" lengtherror=Pmw.MessageDialog(self.vw,message_text=mtext,buttonboxpos='s',iconpos='w',icon_bitmap='warning', buttons=('Truncate','Continue','Cancel'),defaultbutton='Cancel') lengtherror.iconname=('Averaging Error') lengthtype=lengtherror.activate() if lengthtype=='Cancel':return mtext="WARNING: All files MUST have same intial energy spacings! \n Continue?" lengthwarning=Pmw.MessageDialog(self.vw,message_text=mtext,buttonboxpos='s',iconpos='w',icon_bitmap='warning', buttons=('Continue','Cancel'),defaultbutton='Cancel') lengthwarning.iconname=('Averaging Error') lengthwtype=lengthwarning.activate() if lengthwtype=='Cancel':return #tkMessageBox.showwarning(title="Averaging Error",parent=self.vw, # message='Not implemented yet') #return if self.plottype.getcurselection()[0]=='Column': #trap for no selection of average type tkMessageBox.showwarning(title="Averaging Error",parent=self.vw, message='Please select mu type to average') return #do averaging all files same length if match==1: total=[] if self.plottype.getcurselection()[0]=='muF': atype='_fl' #put all data in a list... fchnlist=[] for d in allscans: #calcualte sum fdat=self.datvars[d].iF nfc=shape(fdat) if shape(nfc)[0]==1: #only one FF channel fchnlist.append(fdat) else: #multiple FF channels fchnlist.append(self.sumFFdata(fdat,self.datvars[d].ICR,self.datvars[d].rtc)) for pt in range(lenlist[0]): temp=0 for d in allscans: ind=allscans.index(d) tiFsum=fchnlist[ind] temp=temp+(tiFsum[pt]/self.datvars[d].i0[pt]) total.append(temp/nscans) if self.plottype.getcurselection()[0]=='muT1': atype='_tr' for pt in range(lenlist[0]): temp=0 for d in allscans: temp=temp+log(self.datvars[d].i0[pt]/self.datvars[d].i1[pt]) total.append(temp/nscans) if self.plottype.getcurselection()[0]=='muT2': atype='_t2' for pt in range(lenlist[0]): temp=0 for d in allscans: temp=temp+log(self.datvars[d].i1[pt]/self.datvars[d].i2[pt]) total.append(temp/nscans) energy=self.datvars[allscans[0]].eV total=array(total,Float32) else: #average scans for unequal lengths -- didn't want to mess with what worked above. #choose eV from longest scan energy=self.datvars[allscans[maxlenind]].eV temp=zeros((len(energy),len(allscans)),Float32) if self.plottype.getcurselection()[0]=='muF': atype='_fl' #put all data in a list... fchnlist=[] for d in allscans: #calcualte sum fdat=self.datvars[d].iF nfc=shape(fdat) if shape(nfc)[0]==1: #only one FF channel fchnlist.append(fdat) else: #multiple FF channels fchnlist.append(self.sumFFdata(fdat,self.datvars[d].ICR,self.datvars[d].rtc)) #for pt in range(lenlist[0]): for d in allscans: for pt in range(len(self.datvars[d].i0)): ind=allscans.index(d) tiFsum=fchnlist[ind] temp[pt,ind]=(tiFsum[pt]/self.datvars[d].i0[pt]) if self.plottype.getcurselection()[0]=='muT1': atype='_tr' for d in allscans: for pt in range(len(self.datvars[d].i0)): temp[pt,allscans.index(d)]=log(self.datvars[d].i0[pt]/self.datvars[d].i1[pt]) if self.plottype.getcurselection()[0]=='muT2': atype='_t2' for d in allscans: for pt in range(len(self.datvars[d].i0)): temp[pt,allscans.index(d)]=log(self.datvars[d].i0[pt]/self.datvars[d].i1[pt]) #compile array noelems=[] for pt in range(len(energy)): i=0 for d in allscans: if temp[pt,allscans.index(d)]!=0:i=i+1 noelems.append(i) #add columns temp=sum(temp,1) #divide by noelems total=temp/noelems #deal with truncation/averaging if lengthtype=='Truncate': minlen=min(lenlist) tlen=tkSimpleDialog.askinteger('Averaging','Truncate to which point?',parent=self.vw,initialvalue=minlen) if tlen==None:return energy=energy[0:tlen] total=total[0:tlen] #now plot the average #first remove current plot(s) glist=self.graph.element_names() if glist != (): for g in glist: self.graph.element_delete(g) self.graph.line_create('avg',xdata=tuple(energy),ydata=tuple(total),symbol='',color='blue') #ask to save file... sf=tkMessageBox.askyesno(title='Continue',parent=self.vw,message='Save this average?') if sf: default=trimdirext(allscans[0])+atype+".avg" fname=ask_save_file(default,lastsavedir) if fname != '': sdir=rfind(fname,os.sep) lastsavedir=fname[:sdir] #save two column ascii w/ brief header fid=open(fname,"w") fid.write("# Averaged Data "+fname+" created by SamView\n") try: for pt in range(tlen): #lenlist[0]): fid.write(str(energy[pt])+"\t"+str(total[pt])+"\n") except: for pt in range(lenlist[0]): fid.write(str(energy[pt])+"\t"+str(total[pt])+"\n") fid.close() def findenot(self): #find all local maxima of data at current derivative level dsel=self.deriv.getcurselection() #get data cur=self.phlist.info_selection()[0] dat=self.datvars.get(cur) #determine plot type pt=self.plottype.getcurselection()[0] xd=tuple(dat.eV) if pt=='muF': #mu fluo-sum yd=tuple(self.ffchan.get(cur)/dat.i0) if pt=='muT1': #mu I1/I0 yd=tuple(log(dat.i0/dat.i1)) if pt=='muT2': #mu I2/I1 yd=tuple(log(dat.i1/dat.i2)) if dsel=='None': #take first deriv new=self.getderiv(xd,yd) pyd=tuple(new[1]) pxd=tuple(new[0]) if dsel=='First': #take second deriv new1=self.getderiv(xd,yd) new=self.getderiv(new1[0],new1[1]) pyd=tuple(new[1]) pxd=tuple(new[0]) if dsel=='Second': #take yet another deriv new2=self.getderiv(xd,yd) new1=self.getderiv(new2[0],new2[1]) new=self.getderiv(new1[0],new1[1]) pyd=tuple(new[1]) pxd=tuple(new[0]) numsmpts=int(self.smoothpts.get()) pyd=tuple(self.datasmooth(pyd,numsmpts)) #find all zeros in pyd self.curmax=self.getalllocalmax(pxd,pyd) #add lines to plot self.drawe0lines() def e0moveline(self,event): dir=event.widget.cget('text') if self.maxima != []: if dir=='prev':self.curmax=self.curmax-1 if dir=='next':self.curmax=self.curmax+1 if self.curmax<0:self.curmax=len(self.maxima)-1 if self.curmax>len(self.maxima)-1:self.curmax=0 self.drawe0lines() def drawe0lines(self): enot=self.maxima[self.curmax] entry_replace_d(self.e0app,enot,5) if float(self.e0act.get()) != 0:self.enotcalcshift() #add lines to plot self.makeplot() (dmin,dmax)=self.graph.yaxis_limits() ind=0 for ex in self.maxima: ind=ind+1 if ex==self.maxima[self.curmax]: self.graph.line_create('e0',xdata=(ex,ex),ydata=(dmin,dmax),symbol='',color='red') else: self.graph.line_create('max'+str(ind),xdata=(ex,ex),ydata=(dmin,dmax),symbol='',color='green') def getalllocalmax(self,xd,yd): self.maxima=[] maxin=0 maxdel=0 s=1 #positive ind=0 for p in yd: if ind>1 and ind0 and yd[ind+1]<0: #cross a zero as a maxima #calculate average of last two points xcross=(xd[ind]+xd[ind-1])/2 #only collect first 10... if len(self.maxima)<10: self.maxima.append(xcross) #save the index of the biggest... delta=yd[ind-1]-yd[ind] if delta>maxdel: maxdel=delta maxin=len(self.maxima)-1 s=sn ind=ind+1 return maxin def enotcalcshift(self): #calculate shift on entry app=float(self.e0app.get()) act=float(self.e0act.get()) shift=act-app entry_replace_d(self.e0shift,shift,4) def enotapplyshift(self): #apply energy shift #get data cur=self.phlist.info_selection()[0] dat=self.datvars.get(cur) dat.eV=dat.eV+float(self.e0shift.get()) self.makeplot() def changespacing(self): global chespcing,chkstart,chkspcing,chedge #routine to average CSXAS data points... chespcing=1 chkstart=2 chkspcing=0.05 chedge=float(self.e0act.get()) #ask to do all data sets same? #get data cur=self.phlist.info_selection()[0] dat=self.datvars.get(cur) #need to know... e spacing, begin k, k spacing, edge chespcing=tkSimpleDialog.askfloat('Input for CS-XAS Change','Enter energy spacing (eV)',initialvalue=chespcing,parent=self.vw) chkstart=tkSimpleDialog.askfloat('Input for CS-XAS Change','Enter start of k range',initialvalue=chkstart,parent=self.vw) chkspcing=tkSimpleDialog.askfloat('Input for CS-XAS Change','Enter k-spacing',initialvalue=chkspcing,parent=self.vw) chedge=tkSimpleDialog.askfloat('Input for CS-XAS Change','Enter edge (eV)',initialvalue=chedge,parent=self.vw) #if edge is 0 or not valid, then exit if chedge==0 or None in (chespcing,chkstart,chkspcing,chedge): tkMessageBox.showerror(title='CSXAS Operation Cancelled',parent=self.vw,message='Invalid Entries') return #start at first E... datadelE=dat.eV[1]-dat.eV[0] #if spacing is wrong... if chespcingint(self.icrbotoff.get()) and cutoff==0: tempf.append(dat.iF[i]) tempi.append(dat.ICR[i]) if dat.ICR[i]>int(self.icrcutoff.get()): cutoff=1 dat.iF=array(tempf) dat.ICR=array(tempi) self.dffchan.update({cur+'-FF0':dat.iF}) self.dicrchan.update({cur+'-FF0':dat.ICR}) self.dfflist.append('FF0') else: #multiple FF channels ncols=nfc[1] i=0 while iint(self.icrbotoff.get()) and cutoff==0: tempf.append(a[j]) tempi.append(b[j]) if b[j]>int(self.icrcutoff.get()): cutoff=1 a=array(tempf) b=array(tempi) self.dfhlist.add(cur+'-'+ch,text=ch,state=NORMAL) self.dffchan.update({cur+'-'+ch:a}) self.dicrchan.update({cur+'-'+ch:b}) i=i+1 self.dfhlist.selection_set(cur) self.plotdt() def plotdt(self, *arg): #plot dt SCA vs ICR and fits if present #first remove all plot elements glist=self.dgraph.element_names() if glist != (): for g in glist: self.dgraph.element_delete(g) #now get currently chosen element chan=self.dfhlist.info_selection()[0] #make plot of data if chan != self.datfile: flt=chan[rfind(chan,'-')+1:] self.dgraph.line_create(flt,xdata=tuple(self.dicrchan[chan]),ydata=tuple(self.dffchan[chan]),symbol='circle',color='blue',pixels=".05i",linewidth=0) #make plot of fit if it exists try: self.dgraph.line_create('Fit',xdata=tuple(self.dicrchan[chan]),ydata=tuple(self.dtfits[chan]),symbol='',color='red') except: pass def fitdt(self): #fit the deadtime curves! use SCA=kappa*ICR*exp(-ICR*tau) taus in usec self.dtfits={} #clear data fits self.dtfitvars={} #clear fit params cur=self.datfile self.restext.configure(text_state=NORMAL) self.restext.clear() self.restext.insert(END,'FF\ttau\t\toffset\t\tkappa\n') self.restext.configure(text_state=DISABLED) for ch in self.dfflist: #construct fitting parameters initguess=(0.5,1,0) #kappa,tau(usec) passdata=[] for i in range(len(self.dffchan[cur+'-'+ch])): passdata.append((self.dicrchan[cur+'-'+ch][i],self.dffchan[cur+'-'+ch][i])) try: result=leastSquaresFit(dteqn,initguess,passdata) fp=result[0] except: fp=(0,0,0) self.dtfitvars.update({cur+'-'+ch:fp}) f=dteqn(fp,self.dicrchan[cur+'-'+ch]) self.dtfits.update({cur+'-'+ch:f}) self.restext.configure(text_state=NORMAL) sca=ch[2:] self.restext.insert(END,sca+'\t'+str(fp[1])+'\t'+str(fp[2])+'\t'+str(fp[0])+'\n') self.restext.configure(text_state=DISABLED) self.restext.update_idletasks() self.plotdt() def savefitresults(self): global lastsavedir,lastreaddir #save fit window default="deadtime.dat" savedname=ask_save_file(default,lastsavedir) self.root.dt.focus_set() if savedname != '': sdir=rfind(savedname,os.sep) lastsavedir=savedname[:sdir] self.restext.exportfile(savedname) self.plc.delete(0,END) self.plc.insert(END,savedname) #start event handler #Main(root) #root.mainloop()sixpack-0.68/spdirvars.py0000666000175000017500000000353707703111160014504 0ustar segresegre global lastreaddir,lastsavedir import os from Tkinter import * import tkSimpleDialog import tkFileDialogDir import Pmw from string import * #check for directory prefs file in working path def loaddefdirprefs(): global lastreaddir,lastsavedir try: #open file fid=open(filepath+'defdir.spk',"r") except: return #file structure: single path path=fid.readline() fid.close() lastreaddir=path lastsavedir=path class changedefdirs: global lastreaddir,lastsavedir def __init__(self,master): global lastreaddir,lastsavedir self.newdir='' self.dialog=Pmw.PromptDialog(master,title='Default Directory',label_text='New Default Directory? ', entryfield_labelpos='n',buttons=('OK','Browse','Cancel'),command=self.click, entry_width=50) self.dialog.clear() self.dialog.insertentry(0,lastreaddir) self.dialog.withdraw() self.dialog.activate() def click(self,result): global lastreaddir,lastsavedir if result is None or result=='Cancel': self.dialog.deactivate() if result=='OK': #reset dirfile self.newdir=self.dialog.get() self.dialog.deactivate() fid=open(filepath+'defdir.spk',"w") fid.write(self.newdir) fid.close() if result=='Browse': ndir=tkFileDialogDir.choose_directory(initialdir=self.dialog.get()) if ndir!='': self.dialog.clear() self.dialog.insertentry(0,ndir) #directory info startup if os.name=='nt':os.sep='/' filepath=os.getcwd()+os.sep lastreaddir=filepath lastsavedir=filepath loaddefdirprefs() sixpack-0.68/func.py0000666000175000017500000001661007553106262013430 0ustar segresegreimport Numeric from Numeric import * import operator import math from types import * ArrayType = type(asarray(1.0)) UfuncType = type(Numeric.add) # unary function objects (maybe rename to UN_FUNC?) class FuncOps: """ Common mix-in operations for function objects. Normal function classes are assumed to implement a call routine, which will be chained to in the __call__ method. """ def compose(self, f): return UnCompose(self, f) def __add__(self, f): return BinCompose(Numeric.add, self, f) def __sub__(self, f): return BinCompose(Numeric.subtract, self, f) def __mul__(self, f): return BinCompose(Numeric.multiply, self, f) def __div__(self, f): return BinCompose(Numeric.divide, self, f) def __neg__(self): return UnCompose(Numeric.negative, self) def __pow__(self, f): return BinCompose(Numeric.power, self, f) def __coerce__(self, x): if type(x) in [IntType, FloatType, LongType, ComplexType]: return (self, UnConstant(x)) else: return (self, x) def __call__(self, arg): "Default call routine, used for ordinary functions." if type(arg) == ArrayType: return array_map(self.call, arg) else: return self.call(arg) def exp(self): return UnCompose(Numeric.exp, self) def log(self): return UnCompose(Numeric.log, self) # Bind a normal function # Should check if the argument is a function. class FuncBinder(FuncOps): def __init__(self, a_f): if ((type(a_f) == UfuncType) or (type(a_f) == InstanceType and FuncOps in a_f.__class__.__bases__)): self.__call__ = a_f # overwrite the existing call method self.call = a_f # wrap a constant in a Function class class UnConstant(FuncOps): def __init__(self, x): self.constant = x def __call__(self, x): return self.constant # just return the argument: f(x) = x # This is used to build up more complex expressions. class Identity(FuncOps): def __init__(self): pass def __call__(self, arg): return arg # compose two unary functions class UnCompose(FuncOps): def __init__(self, a_f, a_g): self.f = a_f self.g = a_g def __call__(self, arg): return self.f(self.g(arg)) # ------------------------------------------------- # binary function objects # classes of composition: # a,b,c,d: binary functions m,n,o: unary functions # d=c.compose(a,b) - c(a(x,y),b(x,y)) - used for a/b, a*b, etc. # m=c.compose(n,o) - c(n(x), o(x)) # d=c.compose(n,o) - c(n(x), o(y)) # d=m.compose(c) - m(c(x,y)) class BinFuncOps: # returns self(f(x), g(x)), a unary function def compose(self, f, g): return BinCompose(self, f, g) # returns self(f(x), g(y)), a binary function def compose2(self, f, g): return BinUnCompose(self, f, g) # returns f(self(x,y)), a binary function def compose_by(self, f): return UnBinCompose(f, self) def __add__(self, f): return BinBinCompose(operator.add, self, f) def __sub__(self, f): return BinBinCompose(operator.sub, self, f) def __mul__(self, f): return BinBinCompose(operator.mul, self, f) def __div__(self, f): return BinBinCompose(operator.div, self, f) def __pow__(self, f): return BinBinCompose(pow, self, f) def __neg__(self): return UnBinCompose(operator.neg, self) def reduce(self, a, axis=0): result = take(a, [0], axis) for i in range(1, a.shape[axis]): result = self(result, take(a, [i], axis)) return result def accumulate(self, a, axis=0): n = len(a.shape) sum = take(a, [0], axis) out = zeros(a.shape, a.typecode()) for i in range(1, a.shape[axis]): out[all_but_axis(i, axis, n)] = self(sum, take(a, [i], axis)) return out def outer(self, a, b): n_a = len(a.shape) n_b = len(b.shape) a2 = reshape(a, a.shape + (1,)*n_b) b2 = reshape(b, (1,)*n_a + b.shape) # duplicate each array in the appropriate directions a3 = a2 for i in range(n_b): a3 = repeat(a3, (b.shape[i],), n_a+i) b3 = b2 for i in range(n_a): b3 = repeat(b3, (a.shape[i],), i) answer = array_map_2(self, a3, b3) return answer def all_but_axis(i, axis, num_axes): """ Return a slice covering all combinations with coordinate i along axis. (Effectively the hyperplane perpendicular to axis at i.) """ the_slice = () for j in range(num_axes): if j == axis: the_slice = the_slice + (i,) else: the_slice = the_slice + (slice(None),) return the_slice # bind a binary function class BinFuncBinder(BinFuncOps): def __init__(self, a_f): self.f = a_f def __call__(self, arg1, arg2): return self.f(arg1, arg2) # bind single variables class BinVar1(BinFuncOps): def __init__(self): pass def __call__(self, arg1, arg2): return arg1 class BinVar2(BinFuncOps): def __init__(self): pass def __call__(self, arg1, arg2): return arg2 # bind individual variables within a binary function class Bind1st(FuncOps): def __init__(self, a_f, an_arg1): self.f = a_f self.arg1 = an_arg1 def __call__(self, x): return self.f(self.arg1, x) class Bind2nd(FuncOps): def __init__(self, a_f, an_arg2): self.f = a_f self.arg2 = an_arg2 def __call__(self, x): return self.f(x, self.arg2) # compose binary function with two unary functions (=> unary fcn) # i.e. given a(x,y), b(x), c(x), : d(x) = a(b(x),c(x)) # (what about e(x,y) = a(b(x), c(y)?) class BinCompose(FuncOps): def __init__(self, a_binop, a_f, a_g): self.binop = a_binop self.f = a_f self.g = a_g self.temp = lambda x, op=a_binop, f=a_f, g=a_g: op(f(x),g(x)) def __call__(self, arg): # return self.binop(self.f(arg), self.g(arg)) return self.temp(arg) # compose a unary function with a binary function to get a binary # function: f(g(x,y)) class UnBinCompose(BinFuncOps): def __init__(self, a_f, a_g): self.f = a_f self.g = a_g def __call__(self, arg1, arg2): return self.f(self.g(arg1, arg2)) # compose a two unary functions with a binary function to get a binary # function: f(g(x), h(y)) class BinUnCompose(BinFuncOps): def __init__(self, a_f, a_g, a_h): self.f = a_f self.g = a_g self.h = a_h def __call__(self, arg1, arg2): return self.f(self.g(arg1), self.h(arg2)) # compose two binary functions together, using a third binary function # to make the composition: h(f(x,y), g(x,y)) class BinBinCompose(BinFuncOps): def __init__(self, a_h, a_f, a_g): self.f = a_f self.g = a_g self.h = a_h def __call__(self, arg1, arg2): return self.h(self.f(arg1, arg2), self.g(arg1, arg2)) # ---------------------------------------------------- # Array mapping routines def array_map(f, ar): "Apply an ordinary function to all values in an array." flat_ar = ravel(ar) out = zeros(len(flat_ar), flat_ar.typecode()) for i in xrange(len(flat_ar)): out[i] = f(flat_ar[i]) out.shape = ar.shape return out def array_map_2(f, a, b): if a.shape != b.shape: raise ShapeError flat_a = ravel(a) flat_b = ravel(b) out = zeros(len(flat_a), a.typecode()) for i in xrange(len(flat_a)): out[i] = f(flat_a[i], flat_b[i]) return reshape(out, a.shape) sixpack-0.68/spline.py0000666000175000017500000000776407553106204013775 0ustar segresegreimport func from Numeric import * BadInput = "Bad xa input to routine splint." class Spline(func.FuncOps): def __init__(self, x_array, y_array, low_slope=None, high_slope=None): self.x_vals = x_array self.y_vals = y_array self.low_slope = low_slope self.high_slope = high_slope # must be careful, so that a slope of 0 still works... if low_slope is not None: self.use_low_slope = 1 else: self.use_low_slope = 0 # i.e. false if high_slope is not None: self.use_high_slope = 1 else: self.use_high_slope = 0 self.calc_ypp() def calc_ypp(self): x_vals = self.x_vals y_vals = self.y_vals n = len(x_vals) y2_vals = zeros(n, Float) u = zeros(n-1, Float) if self.use_low_slope: u[0] = (3.0/(x_vals[1]-x_vals[0])) * \ ((y_vals[1]-y_vals[0])/ (x_vals[1]-x_vals[0])-self.low_slope) y2_vals[0] = -0.5 else: u[0] = 0.0 y2_vals[0] = 0.0 # natural spline for i in range(1, n-1): sig = (x_vals[i]-x_vals[i-1]) / \ (x_vals[i+1]-x_vals[i-1]) p = sig*y2_vals[i-1]+2.0 y2_vals[i] = (sig-1.0)/p u[i] = (y_vals[i+1]-y_vals[i]) / \ (x_vals[i+1]-x_vals[i]) - \ (y_vals[i]-y_vals[i-1])/ \ (x_vals[i]-x_vals[i-1]) u[i] = (6.0*u[i]/(x_vals[i+1]-x_vals[i-1]) - sig*u[i-1]) / p if self.use_high_slope: qn = 0.5 un = (3.0/(x_vals[n-1]-x_vals[n-2])) * \ (self.high_slope - (y_vals[n-1]-y_vals[n-2]) / (x_vals[n-1]-x_vals[n-2])) else: qn = 0.0 un = 0.0 # natural spline y2_vals[n-1] = (un-qn*u[n-2])/(qn*y2_vals[n-1]+1.0) rng = range(n-1) rng.reverse() for k in rng: # backsubstitution step y2_vals[k] = y2_vals[k]*y2_vals[k+1]+u[k] self.y2_vals = y2_vals # compute approximation def __call__(self, arg): "Simulate a ufunc; handle being called on an array." if type(arg) == func.ArrayType: return func.array_map(self.call, arg) else: return self.call(arg) def call(self, x): "Evaluate the spline, assuming x is a scalar." # if out of range, return endpoint if x <= self.x_vals[0]: return self.y_vals[0] if x >= self.x_vals[-1]: return self.y_vals[-1] pos = searchsorted(self.x_vals, x) h = self.x_vals[pos]-self.x_vals[pos-1] if h == 0.0: raise BadInput a = (self.x_vals[pos] - x) / h b = (x - self.x_vals[pos-1]) / h return (a*self.y_vals[pos-1] + b*self.y_vals[pos] + \ ((a*a*a - a)*self.y2_vals[pos-1] + \ (b*b*b - b)*self.y2_vals[pos]) * h*h/6.0) class LinInt(func.FuncOps): def __init__(self, x_array, y_array): self.x_vals = x_array self.y_vals = y_array # compute approximation def __call__(self, arg): "Simulate a ufunc; handle being called on an array." if type(arg) == func.ArrayType: return func.array_map(self.call, arg) else: return self.call(arg) def call(self, x): "Evaluate the interpolant, assuming x is a scalar." # if out of range, return endpoint if x <= self.x_vals[0]: return self.y_vals[0] if x >= self.x_vals[-1]: return self.y_vals[-1] pos = searchsorted(self.x_vals, x) h = self.x_vals[pos]-self.x_vals[pos-1] if h == 0.0: raise BadInput a = (self.x_vals[pos] - x) / h b = (x - self.x_vals[pos-1]) / h return a*self.y_vals[pos-1] + b*self.y_vals[pos] def spline_interpolate(x1, y1, x2): """ Given a function at a set of points (x1, y1), interpolate to evaluate it at points x2. """ sp = Spline(x1, y1) return sp(x2) def logspline_interpolate(x1, y1, x2): """ Given a function at a set of points (x1, y1), interpolate to evaluate it at points x2. """ sp = Spline(log(x1), log(y1)) return exp(sp(log(x2))) def linear_interpolate(x1, y1, x2): """ Given a function at a set of points (x1, y1), interpolate to evaluate it at points x2. """ li = LinInt(x1, y1) return li(x2) sixpack-0.68/mnexafsfit.iff0000666000175000017500000000441107432343062014746 0ustar segresegre macro loadfeff c:\sam\common\code\mnpaths "macro to load feff paths for MnOx scattering" path(1, feff=$1\X1.dat) path(1, label="Mn-O short") path(1, s02=myso1, e0=mye0, delr=mydr1, sigma2=mysig1, third=myth1, degen=1) path(2, feff=$1\X2.dat) path(2, label="Mn-O long") path(2, s02=myso2, e0=mye0, delr=mydr2, sigma2=mysig2, third=myth2, degen=1) path(3, feff=$1\X3.dat) path(3, label="Mn-Mn face") path(3, s02=myso3, e0=mye0, delr=mydr3, sigma2=mysig3, third=myth3, degen=1) path(4, feff=$1\X4.dat) path(4, label="Mn-Mn edge") path(4, s02=myso4, e0=mye0, delr=mydr4, sigma2=mysig4, third=myth4, degen=1) path(5, feff=$1\X5.dat) path(5, label="Mn-Mn dbl corner") path(5, s02=myso5, e0=mye0, delr=mydr5, sigma2=mysig5, third=myth5, degen=1) path(6, feff=$1\X6.dat) path(6, label="Mn-Mn sing corner") path(6, s02=myso6, e0=mye0, delr=mydr6, sigma2=mysig6, third=myth6, degen=1) end macro macro init_guess 1 1 0.002 0 0 "initialize guesses for FEFF paths" guess(myso$1=$2, mysig$1=$3, mydr$1=$4) guess(mye0=$5) end macro macro set_fit_params 3 13 1 3 3 1 Kaiser Q "set basic fit limits and parameters" set (kmin=$1,kmax=$2) set (rmin=$3,rmax=$4) set (kweight=$5, dk=$6, $kwindow=$7) set ($fit_space=$8) end macro #may want this macro to be part of code for display purposes... macro print_fit_var 1 "print the final fit variables for results of path X" show mye0 show myso$1 show mysig$1 show mydr$1 end macro #need to do a fft on data first! # fftf(real=chi2.chi,kweight=3.0,kmin=3.0,kmax=13.0,dk=1.0,kwindow="kais") # set chi2.chi_kw = chi2.chi * chi2.k^kweight macro plotfitresults "plot fit results in r-space" newplot($1.r, $1.chir_re, xlabel='r',ylabel='chir_re', title='$1', xmin=0, xmax=4,key="Re[\gx(data)]") plot(fit.r, fit.chir_re,key="Re[\gx(fit)]") plot($1.r, $1.chir_mag,key="|\gx(data)|") plot(fit.r, fit.chir_mag,key="|\gx(fit)|") end macro macro dokwt "k-weight the data" $1.chi_kw=$1.chi*($1.k)^$2 end macro macro doxwt "x-weight the data" $1.y_xw=$1.y*($1.x)^$2 end macro macro plotk3chi "plot the k-weighted chi and fit" newplot($1.k, $1.chi_kw, xlabel='k',ylabel='kwchi', title='$1') plot(fit.k, fit.chi_kw) end macro sixpack-0.68/xbms/0002755000175000017500000000000011577445410013070 5ustar segresegresixpack-0.68/xbms/caution.xbm0000666000175000017500000000136107345225110015234 0ustar segresegre#define caution_width 32 #define caution_height 32 static char caution_bits[] = { 0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0x00,0xe0,0x00,0x00,0x00,0x10,0x01, 0x00,0x00,0x08,0x07,0x00,0x00,0x08,0x0e,0x00,0x00,0x04,0x0e,0x00,0x00,0x04, 0x1c,0x00,0x00,0x02,0x1c,0x00,0x00,0xe2,0x38,0x00,0x00,0xf1,0x39,0x00,0x00, 0xf1,0x71,0x00,0x80,0xf0,0x71,0x00,0x80,0xf0,0xe1,0x00,0x40,0xf0,0xe1,0x00, 0x40,0xf0,0xc1,0x01,0x20,0xf0,0xc1,0x01,0x20,0xf0,0x81,0x03,0x10,0xe0,0x80, 0x03,0x10,0xe0,0x00,0x07,0x08,0xe0,0x00,0x07,0x08,0xe0,0x00,0x0e,0x04,0x00, 0x00,0x0e,0x04,0xe0,0x00,0x1c,0x02,0xf0,0x01,0x1c,0x02,0xf0,0x01,0x38,0x01, 0xe0,0x00,0x38,0x01,0x00,0x00,0x70,0x01,0x00,0x00,0x70,0xff,0xff,0xff,0x7f, 0xf8,0xff,0xff,0x3f,0x00,0x00,0x00,0x00}; sixpack-0.68/xbms/file.xbm0000666000175000017500000000035607106373320014516 0ustar segresegre#define file_width 12 #define file_height 12 static unsigned char file_bits[] = { 0xfe, 0x00, 0x02, 0x03, 0x02, 0x02, 0x02, 0x02, 0x02, 0x02, 0x02, 0x02, 0x02, 0x02, 0x02, 0x02, 0x02, 0x02, 0x02, 0x02, 0x02, 0x02, 0xfe, 0x03}; sixpack-0.68/xbms/folder.xbm0000666000175000017500000000033407106373320015046 0ustar segresegre#define folder_width 16 #define folder_height 10 static unsigned char folder_bits[] = { 0xfc, 0x00, 0x02, 0x07, 0x01, 0x08, 0x01, 0x08, 0x01, 0x08, 0x01, 0x08, 0x01, 0x08, 0x01, 0x08, 0x01, 0x08, 0xff, 0x07}; sixpack-0.68/xbms/next.xbm0000666000175000017500000000036007522244742014557 0ustar segresegre#define next_width 16 #define next_height 16 static char next_bits[] = { 0x00,0x00,0x00,0x00,0x02,0x03,0x06,0x07,0x0e,0x0f,0x1e,0x1f,0x3e,0x3f,0xfe, 0x7f,0xfe,0x7f,0x3e,0x3f,0x1e,0x1f,0x0e,0x0f,0x06,0x07,0x02,0x03,0x00,0x00, 0x00,0x00}; sixpack-0.68/xbms/openfile.bmp0000666000175000017500000000177007420421422015365 0ustar segresegreBM6( c`c`c`c`c`c`c`c`c`c`c`:c`c`c`c`c`c`c`c`c`c`c`::c`c`c`c`c`c`c`c`c`c`c`:::c`c`c`c`c`c`c`c`c`c`c`::::c`c`c`c`c`c`c`c`c`c`c`:::::c`c`c`c`c`c`c`c`c`c`c`::::::c`c`c`c`c`c`c`c`c`c`c`:::::::c`c`c`c`c`c`c`c`c`c`::::::::::::::::::::::::::::::::::::::::sixpack-0.68/xbms/openfile.gif0000666000175000017500000000045507420421500015350 0ustar segresegreGIF89a:`c!3Created with BMPToGIF - 1.5 (C) DevelCor 1997, 1998! ,@#:WAul6WfF6ýۛ[з__֯mK+1? _w?X!_֯mIwR@Ob_{f'_A/_ǯWޤqp?u{f'_A/?د p?rCwRއoP?>ۗM5elٹ߼3b*Ģz+YSƗ.k^1jGgKQrBbI$dRI$~n^+0/7?椒IJ)$IJXy]~d[~f˩{ñڋ~Q\zgBf&]WeA-\[_k3FOR496Vגk kۿkhS@e2//Oߪ;H?~ "lwKlwQ?t6܏׾W'Rvms=Aun,$q-;t@7 2~n^+0/7?椒IJ)`qٝ UQ,o5/Vs/ƵKmmC^u3K9ևևZ^^r$ݿr$}qK*rè*vݭ($[;~BM,[[Cm~z?P[wnvZkDJ8A,J@ I$5$I)I$Ja}cvvj<#Ag2;TV9M59u~tWާO_m}&;+ozίI-UgOs~^?Gbs6t9~W;XK+V=#Ql2kY譮CgөI%q~n^ǯft.V^#+/mDZ[?wבdcZ}72v[$mvײJK%usik ^CkCkC-/nKu;(2fyqJ\פֿGUoA"Y\Zie- 6TKvd>>4:~q$EbI$I%)s_XsiɺCKu+&6[M@}{Gկ_W2~tuauc,{ cw=QN}hΤ$4Wըyvdco_Yaͮ-$I%?I%)$IJI$RI$I%>%?+8ʩ$ꤗʩ$ꤗʩ$8BIM'File written by Adobe Photoshop 4.0Adobed@     !"#D%&6(8  !1Q"2#aRb3% ?g0Ů'njgD'V]tD7mf%[8%['W1Q3ۤU ,]x &w뵦0$ŭ tsgv%A2pҤO5)PbU 6ٵ5~U`y>Kh%vB[ dYu24<>``!Ef\0wpg>wcXڲw{}V=CVS]릺|TT"NMTFD&]Т, |:A;HRcV$ieıK4)գ qN^"VnM .Ա?zOnnnSK̛fLp7ǘ^u6Aԗc*F5 K9AHbcmqԥQA !?tjh(]IlN0^\!2L*(xԤ:̍" kA * Q8m@`$65 q hCO=1nuVwປ sl⟸5O'?;ip?tľzSpz4XԽz^?sixpack-0.68/xbms/openfile.xbm0000666000175000017500000000037207106373320015376 0ustar segresegre#define openfile_width 16 #define openfile_height 12 static unsigned char openfile_bits[] = { 0x00, 0x00, 0xfc, 0x00, 0x02, 0x07, 0x01, 0x08, 0xc1, 0xff, 0xa1, 0xaa, 0x51, 0x55, 0xa9, 0x2a, 0x55, 0x15, 0xab, 0x0a, 0xff, 0x07, 0x00, 0x00}; sixpack-0.68/xbms/openfolder.xbm0000666000175000017500000000035007106373320015726 0ustar segresegre#define openfolder_width 16 #define openfolder_height 10 static unsigned char openfolder_bits[] = { 0xfc, 0x00, 0x02, 0x07, 0x01, 0x08, 0xc1, 0xff, 0x21, 0x80, 0x11, 0x40, 0x09, 0x20, 0x05, 0x10, 0x03, 0x08, 0xff, 0x07}; sixpack-0.68/xbms/previous.xbm0000666000175000017500000000037407522244742015462 0ustar segresegre#define previous_width 16 #define previous_height 16 static char previous_bits[] = { 0x00,0x00,0x00,0x00,0xc0,0x40,0xe0,0x60,0xf0,0x70,0xf8,0x78,0xfc,0x7c,0xfe, 0x7f,0xfe,0x7f,0xfc,0x7c,0xf8,0x78,0xf0,0x70,0xe0,0x60,0xc0,0x40,0x00,0x00, 0x00,0x00}; sixpack-0.68/fefftemp/0002755000175000017500000000000011577445410013713 5ustar segresegresixpack-0.68/fefftemp/chi.dat0000666000175000017500000007063107521011012015136 0ustar segresegre As-O Single Scatering Feff X7 7.00 Abs Z=33 Rmt= 1.346 Rnm= 1.458 K shell Pot 1 Z= 8 Rmt= 1.132 Rnm= 1.226 Gam_ch=2.574E+00 H-L exch Mu=-7.290E-01 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6.060237E+01 6.060237E+01 19.6500 -8.206961E-04 9.327289E-04 6.076588E+01 6.076588E+01 19.7000 -8.721625E-04 9.224298E-04 6.092940E+01 6.092940E+01 19.7500 -8.992686E-04 9.121307E-04 6.109292E+01 6.109292E+01 19.8000 -9.018220E-04 9.018316E-04 6.125644E+01 6.125644E+01 19.8500 -8.803002E-04 8.915325E-04 6.141996E+01 6.141996E+01 19.9000 -8.358235E-04 8.812334E-04 6.158348E+01 6.158348E+01 19.9500 -7.701103E-04 8.709343E-04 6.174700E+01 6.174700E+01 20.0000 -6.854175E-04 8.606351E-04 6.191052E+01 6.191052E+01 sixpack-0.68/fefftemp/feff.bin0000666000175000017500000000621207521011012015273 0ustar segresegreNfeff.bin file, written by feff version Feff X7 7.00 NMPAs-O Single Scatering Feff X7 7.00 P(PAbs Z=33 Rmt= 1.346 Rnm= 1.458 K shell P PPot 1 Z= 8 Rmt= 1.132 Rnm= 1.226 PPGam_ch=2.574E+00 H-L exch P8PMu=-7.290E-01 kf=1.817E+00 Vint=-1.330E+01 Rs_int= 1.996 P(;@s[s[( As O !?؜?vpl}?YGz?v?`@r?&al?Ae?[^?_/V?!RM?V놽YC?39? /?x#?|rB?  ?>lOx>l>шw#>dAL>md=yMYx=D&r<(1&#ս!*k.[廾 5ྦtٽw?߄Ľ`w)<HOr(EbRRÅt &5#ݹVȋM~iꁼlƿ,;? C<ަ?ChO<?<g?i<o?#<6?#<?D=A>|=1>==1?&<=?_;= ?)@:=+d?f9=6?9=ז?Ch:=?;=AI?T==?4@=?SC=ѭ?cF=.?H=Ҹ?gK=r?dL=%?=}?=?2/=z?}=:?)={@=@= @=}@}=f@&=eh@T=a$@'=*@;=0@@=*7@=[=@ݙ=C@B=GJ@5=9P@RɈ=`@x=Qq@ b=@SO=A+@q?=y@L0=$Ι@T=#='@b=@R =uJ@<@C<@ѥ<@.BX>)x>1>9>B>J>)x?-?1"?50?9=?>4K?BX?FLf?Js?'?)x?-?1?5?9?>4?B?FL?J?'@)x@+>@-@/@1"@3V)@50@76@9=@;nD@>4K@C#\@Hm@M~@)x@@.g@ޠ@3V@8E@>4@C#@H@M@)xAA.gA A3V)A@q@B   @I@I@I@Aq@q@=p?W9=e?pt=,?,=)?B=8>p=:)_&==G3A=-= e=οT= F <^s ; ;Y;9;3$i^;/+=;h1;I37~;m<0!:AR۲:=K:TV:t]ck-: distance to most distant atom. Some paths may be missing. rmax, ratx 4.00000E+00 2.00000E+00 Rmax 4.0000 keep and heap limits 0.0000000 0.0000000 Preparing neighbor table Paths found 4 (maxheap, maxscatt 1 1) Eliminating path degeneracies... Plane wave chi amplitude filter 2.50% Unique paths 1, total paths 4 Calculating EXAFS parameters... Curved wave chi amplitude ratio 4.00% Discard feff.dat for paths with cw ratio < 2.67% path cw ratio deg nleg reff 1 100.000 4.000 2 2.0000 1 paths kept, 1 examined. Calculating chi... feffdt, feff.bin to feff.dat conversion Feff X7 7.00 feff.bin header As-O Single Scatering Feff X7 7.00 Abs Z=33 Rmt= 1.346 Rnm= 1.458 K shell Pot 1 Z= 8 Rmt= 1.132 Rnm= 1.226 Gam_ch=2.574E+00 H-L exch Mu=-7.290E-01 kf=1.817E+00 Vint=-1.330E+01 Rs_int= 1.996 1 paths to process path filename 1 feff0001.dat Use all paths with cw amplitude ratio 4.00% S02 1.000 Global sig2 0.00000 Feff done. Have a nice day. sixpack-0.68/fefftemp/misc.dat0000666000175000017500000000036507521011012015323 0ustar segresegre As-O Single Scatering Feff X7 7.00 Abs Z=33 Rmt= 1.346 Rnm= 1.458 K shell Pot 1 Z= 8 Rmt= 1.132 Rnm= 1.226 Gam_ch=2.574E+00 H-L exch Mu=-7.290E-01 kf=1.817E+00 Vint=-1.330E+01 Rs_int= 1.996 sixpack-0.68/fefftemp/paths.dat0000666000175000017500000000076007521011012015506 0ustar segresegre As-O Single Scatering Rmax 4.0000, keep limit 0.000, heap limit 0.000 Plane wave chi amplitude filter 2.50% ----------------------------------------------------------------------- 1 2 4.000 index, nleg, degeneracy, r= 2.0000 x y z ipot label rleg beta eta -1.154701 -1.154701 1.154701 1 'O ' 2.0000 180.0000 0.0000 0.000000 0.000000 0.000000 0 'As ' 2.0000 180.0000 0.0000 sixpack-0.68/fefftemp/phase.bin0000666000175000017500000013627007521011012015475 0ustar segresegrePAs-O Single Scatering Feff X7 7.00 PMPAbs Z=33 Rmt= 1.346 Rnm= 1.458 K shell P(PPot 1 Z= 8 Rmt= 1.132 Rnm= 1.226 P PGam_ch=2.574E+00 H-L exch PPMu=-7.290E-01 kf=1.817E+00 Vint=-1.330E+01 Rs_int= 1.996 P8,;7X@ewnewn,ewnhumxON t;,`H{Ӑ?t.?8i?[? 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Ϊ?f?U(~K?Ge?y$`ԡ?ЁU'?n ԙ?Oв8?ЏBlFÐ?5b?x ??u-ax?3 If?8*%M?E 댶:A?LɊ.L#eO{jMְp5  r 1)dQ澇׾T_?߳y9;5x-#Ŋppe7bmE?Ɠ?g[U?%?g?I j?Z)>e?Bvn|UbϾj G ['6ppBNrM|鿉4]?q$03?8(?z5?a?`5?Y;#'?be?\6?bn3ڪ?bޏYa?;G?+͝|?qTB>??P?3z?Ced~?ԥ?i?R3 ?,S+?CFl?7L(8p?sys?ȑC~V?VX?M`IQ0?G9?Lmٙ.lpG?l.fSiQY> KQ/>W/⾒]۲>)a39¾oyМ>?5ܶ{ppE@6\?` E?Y?rO/?@?X&L?S9:vҤ?ОD?ɗt?5?-\6٠?4S?3v?Z5 ?@苗?Ra?>he??kd?dL?JԦ?OY˃?DBPHs?XT҃o>Ϟľ_+ >tJ>{zwby6pM>`{ppEF￀-\?`?#r?Qx?((P??B]?6zDb?;١?lɷA;?9fb?N>e?i ??rNkk??X[}D?H1)E?Ix? 2j?5 @J? u؞?]&~=PǾ(l >MO9 SV;>Pm,ppɓStb]W?:? E^?I*6?='K?>)̞j4?L?!w?$ ?[Ѫ? M{?%wII?:w%?Àq?w (I?ګe?M#k?Pp?!h%'؏?Pu?1Qހ?15I?pXpp?Ծ0?6%+C{?0Ks?T2q?׻ ? 2b?jz?*0^K?*Ll?*_!ĸ#?tS[?(A ̢G?jg5 ZU1?+AyVmܩ?GEsh=/'>٧ڊȾښ>f"ZppɪV Ξ?%}?`?jY&?B5 7?6'A?~O?&?/1E?t&?J3?^?2?F"m?/z? dw?~?C?eM>?w}F? 4a? eJ?? Cs?E+]E?(~?YU?Nuv?s|?hjLn?,͇??_??!(G?2=r?i82!?a3ic?G\ mh?d*?חز?b?+9L?iJ?0@`?A ?z#wޝ?-vB?n?:?|25Z ?aM1?{6?.B?v?5抔?[ofo?=cuvX7?2h?9A?Ze?cdѦ?Z U?)? 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Dt?e?cnt?aV?՛@%é?)TW?`>;/[?FRy??:Q$Fs?cO"?԰23l?EA,?8״c?k$݅Ύ?NȉU?Pe?]7A?1Zا?S]<?]u?9`WŐ/yg?~kpsixpack-0.68/fefftemp/potph.dat0000666000175000017500000000163407521011012015522 0ustar segresegre As-O Single Scatering ----------------------------------------------------------------------- 1 1.891812E-01 1 1 0 ihole, gamach, iprint, iafolp, intclc 0 0.000000E+00 0.000000E+00 0.000000E+00 ixc, vr0, vi0, rs0 0 100 0.000000E+00 1.058354E+01 ixanes, nemax, xkmin, xkmax (inv bohr) 0 0 0 0 methat, methfs, jumprm, mbconv 1 nfr 0 33 0.000 ifr, iz, ion 1 8 0.000 ifr, iz, ion 5 nat. iat, iph, x, y, z 1 0 0.000000 0.000000 0.000000 2 1 2.182068 2.182068 2.182068 3 1 -2.182068 -2.182068 2.182068 4 1 -2.182068 2.182068 -2.182068 5 1 2.182068 -2.182068 -2.182068 1 nph 0 1 0 1.000000 1.000000 0 iph, iat, ifr, xnat, folp, novr 'As ' potlbl 1 2 1 4.000000 1.000000 0 iph, iat, ifr, xnat, folp, novr 'O ' potlbl sixpack-0.68/fefftemp/pq.dat0000666000175000017500000000774707521011012015023 0ustar segresegre 1 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-?;;c}v//?͑wM͊:7?w>¥23HZh?+NJd?Afj{ݓ?wp2˽?;{WhEָZ?u1vZM)vh?o\>?"z)Ӽk3?j‰QnD{? 6<"?)M${8Ha?GhB*?B=1g?]:Qc7t?cWJY4ԥ?r?m?~_? fPR?ؑ(#?3?cAX??CPr?aF ?%M^o?;?G#a?›[im ޲?X%ֿu_]k?uKK ?­v'JL4p?yUU?.+5?5N3Wqoq?p3PQ?vupUퟫ?kMn,`X?] ?]e/e>1e?Sq>"[?+2_H$?8 S2.?h.즀ۂ?ڿC_n?zvbݹB?_ ^C?pںx+?b?/Y,<쿨#k?$W6?%HuA?>.鿮][?il&u?GvWN+?Tc #,Lg?0x?lTCE ?&0LV݂?X޿ˁ`?lnڿqH(?PtPe׿hȢ?oEӿ%u?QɅqп,_?xAɿ+<_?D'i¿e ?ILg%rd?S̸V!Z?Dc?#g?F?g*?"-?-?6+>?}b?W$? X?pOr?K?qS2?KgŴ'? w??8o?pM@Z?{?طT?õ? rC?OQ?OQ? 2ٷ?#Vr ?< ɿ!?Kؿ[j?A6 Ӂjyh?+#:t?Ӟ"΢)[?Fm0zg]sixpack-0.68/examples/0002755000175000017500000000000011577445410013735 5ustar segresegresixpack-0.68/examples/cumetal.prm0000666000175000017500000000341607470247220016111 0ustar segresegreFPARAMS C:/Sam/Common/samxas2/examples/data/cu_chi.dat 2 17 1.5 4.4 2 1 Path 1 1 0 C:/Sam/Common/samxas2/examples/feff/feffcu01.dat Cu-Cu s02 e0 delR_1 sig_1 Path 2 1 0 C:/Sam/Common/samxas2/examples/feff/feffcu02.dat Cu-Cu s02 e0 delR_2 sig_2 Path 3 1 0 C:/Sam/Common/samxas2/examples/feff/feffcu03.dat Cu-Cu s02 e0 delR_3 sig_3 Path 4 1 0 C:/Sam/Common/samxas2/examples/feff/feff0004.dat Cu-Cu s02 e0 delR_4 sig_4 Path 5 1 0 C:/Sam/Common/samxas2/examples/feff/feff0005.dat Cu-Cu s02 e0 delR_5 sig_5 Path 6 1 0 C:/Sam/Common/samxas2/examples/feff/feff0006.dat Cu-Cu s02 e0 delR_6 sig_6 Path 7 1 0 C:/Sam/Common/samxas2/examples/feff/feff0007.dat Cu-Cu s02 e0 delR_5 sig_5 Path 8 1 0 C:/Sam/Common/samxas2/examples/feff/feff0008.dat Cu-Cu s02 e0 delR_5 sig_5 Path 9 1 0 C:/Sam/Common/samxas2/examples/feff/feff0009.dat Cu-Cu s02 e0 delR_5 sig_5 Path 10 1 0 C:/Sam/Common/samxas2/examples/feff/feff0010.dat Cu-Cu s02 e0 delR_5 sig_5 Path 11 1 0 C:/Sam/Common/samxas2/examples/feff/feff0011.dat Cu-Cu s02 e0 delR_5 sig_5 Path 12 1 0 C:/Sam/Common/samxas2/examples/feff/feff0012.dat Cu-Cu s02 e0 delR_5 sig_5 Path 13 1 0 C:/Sam/Common/samxas2/examples/feff/feff0013.dat Cu-Cu s02 e0 delR_5 sig_5 VARS s02 1 G 0.978154247244 e0 1 G -0.54760159289 delR_1 1 G 0.0093975657757 sig_1 1 G 0.00377988315329 delR_2 1 G 0.0176923702369 sig_2 1 G 0.00559448849302 delR_3 1 G 0.0241695359042 sig_3 1 G 0.00610205179864 delR_4 1 G 0.0048880402033 sig_4 1 G 0.00560835351408 delR_5 1 G 0.0288137462689 sig_5 1 G 0.00402942975484 delR_6 1 G 0.0508044172623 sig_6 1 G 0.000491715072597 ENDsixpack-0.68/examples/data/0002777000175000017500000000000007513143236014646 5ustar segresegresixpack-0.68/examples/data/cu.xmu0000666000175000017500000004756107242621362016023 0ustar segresegre# Cu foil at 10K ## cu10k.dat : this file is part of the uwxafs 3.0 distribution # data taken at NSLS beamline X-11A Sept 1992 # by M Newville, B Ravel, and Y Zhang # foil of 99.999% Cu rolled and annealled to ~12 microns # sample prepared by M Newville # From X-11A : # 2-SI111 HC/2D= 1977.260 STPDEG=6400. STPMMZ= 40. # FOCUS=F TRANSLT=F E0= 8980.0 NREG= 3 NPTS= 611 NSCLRS= 3 EF= .0 # SRB= -193.7 -43.5 30.0 2381.3 # DEL= 10.020 .483 .050K # SEC= 1.000 1.000 1.000 # DETECTORSI0 I If # GAINS 8 7 10 # OFFSETS 51284 50016 48319 #--------------------------------------------------------------------- # energy xmu .8786204E+04 .1013661E+01 .8796258E+04 .9949864E+00 .8806253E+04 .9900679E+00 .8816270E+04 .9850345E+00 .8826270E+04 .9801005E+00 .8836292E+04 .9751812E+00 .8846337E+04 .9703809E+00 .8856322E+04 .9656931E+00 .8866372E+04 .9609839E+00 .8876361E+04 .9562312E+00 .8886416E+04 .9515597E+00 .8896409E+04 .9472797E+00 .8906425E+04 .9427789E+00 .8916464E+04 .9387816E+00 .8926483E+04 .9347627E+00 .8936483E+04 .9319326E+00 .8936998E+04 .9318979E+00 .8937471E+04 .9319605E+00 .8937944E+04 .9317057E+00 .8938417E+04 .9314675E+00 .8938976E+04 .9315093E+00 .8939406E+04 .9315045E+00 .8939878E+04 .9313901E+00 .8940352E+04 .9313291E+00 .8940824E+04 .9312409E+00 .8941384E+04 .9311222E+00 .8941814E+04 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.1129624E+05 .1376596E+01 .1130560E+05 .1371654E+01 .1131505E+05 .1367242E+01 .1132452E+05 .1362544E+01 .1133393E+05 .1358360E+01 .1134343E+05 .1353479E+01 .1135294E+05 .1349326E+01 .1136247E+05 .1344309E+01 sixpack-0.68/examples/data/Cu2S.xmu0000666000175000017500000004612707242621362016165 0ustar segresegre# Cu2S ; 1.5 mm teflon sample cell # Cu exafs to K=13, Cu foil in i2 # detuned at 9500; 50% # gains 6,7,7; I0=N2; I1=Ar; I2=Ar # T = 13K # SSRL - EXAFS Data Collector 1.1 AD.RGN # Sat Jul 27 16:01:27 1996 # PTS: 454 COLS: 6 # TRANS.DET # CUK15.RGN # 4-3 unfocused 0.000 -2 si(222) 1.292013 8000 # 4 2000 25 RST 0 0 # MVIEW Version 1.1 # CU_036.001 # >> /usr/people/newville/bin/XMU -e4 -05 -t6 -r7 cu036_001.dat #--------------- # energy log(i0/it) log(it/ir) i0 8759.99 -1.535827 2.9033981 40068.3 8769.98 -1.546806 2.8977250 39665.3 8780.00 -1.559545 2.8927689 39231.3 8789.99 -1.570996 2.8860354 38796.3 8800.00 -1.581097 2.8784871 38432.3 8809.99 -1.589505 2.8686704 38029.3 8820.01 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-1.662549 3.3071200 25343.0 9844.17 -1.665933 3.3038170 25298.6 9848.19 -1.669401 3.3022272 25274.3 9852.28 -1.673047 3.2986827 25200.9 sixpack-0.68/examples/data/cu_chi.dat0000666000175000017500000004137707261204352016601 0ustar segresegre# data : cu 10k, e0=8980, with standard # chi: skey ASCII of cu_010k.dat using skey ASCII of chi.dat # e0 = 8982.61; pre-edge range =[ -50.0 -200.0]; edge step = 2.257 # k range=[ .05 24.95]; k weight= 1.00; sills: dk1, dk2=[ .00 .00] # bkg r =[ .00 .98]; 1st shell r =[ .98 3.93]; 15 knots in spline # Cu foil, 10K, foil rolled and annealled by matt # 2-SI111 HC/2D= 1977.260 STPDEG=6400. STPMMZ= 40. FOCUS=F TRANSLT=F # E0= 8980.0 NREG= 3 NPTS= 611 NSCLRS= 3 EF= .0 # SRB= -193.7 -43.5 30.0 2381.3 # DEL= 10.020 .483 .050K # SEC= 1.000 1.000 1.000 # DETECTORSI0 I If # GAINS 8 7 10 # OFFSETS 51284 50016 48319 #--------------------------------------------------------------------- # k chi(k) .5000000E-01 -.1383775E+00 .1000000E+00 -.1397935E+00 .1500000E+00 -.1412636E+00 .2000000E+00 -.1427878E+00 .2500000E+00 -.1443661E+00 .3000000E+00 -.1457561E+00 .3500000E+00 -.1469721E+00 .4000000E+00 -.1487659E+00 .4500000E+00 -.1511373E+00 .5000000E+00 -.1540712E+00 .5500000E+00 -.1576023E+00 .6000000E+00 -.1621443E+00 .6500000E+00 -.1669036E+00 .7000000E+00 -.1723104E+00 .7500000E+00 -.1756163E+00 .8000000E+00 -.1719365E+00 .8500000E+00 -.1712734E+00 .9000000E+00 -.1738329E+00 .9500000E+00 -.1679564E+00 .1000000E+01 -.1598812E+00 .1050000E+01 -.1456769E+00 .1100000E+01 -.1196842E+00 .1150000E+01 -.1022159E+00 .1200000E+01 -.7008255E-01 .1250000E+01 -.3362218E-01 .1300000E+01 -.6600451E-02 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9.9761925862E-001 7.2084170000E+003 9.9825884764E-001 7.2134100000E+003 9.9841456923E-001 7.2184190000E+003 9.9752751061E-001 7.2234500000E+003 9.9823497558E-001 7.2284980000E+003 9.9751488199E-001 7.2335660000E+003 9.9836517055E-001 7.2386530000E+003 9.9839872925E-001 7.2437580000E+003 9.9824527523E-001 7.2488840000E+003 9.9792445936E-001 7.2540290000E+003 9.9865289750E-001 7.2591910000E+003 9.9823278553E-001 7.2643720000E+003 9.9843818144E-001 7.2695750000E+003 9.9810523347E-001 7.2747960000E+003 9.9899089389E-001 7.2800350000E+003 9.9879442329E-001 7.2852930000E+003 9.9868546820E-001 7.2905730000E+003 9.9891666618E-001 7.2958690000E+003 9.9922670432E-001 7.3011880000E+003 9.9933488885E-001 7.3065210000E+003 9.9969978363E-001 7.3118770000E+003 1.0002556151E+000 7.3172490000E+003 9.9981229558E-001 7.3226440000E+003 9.9971665491E-001 7.3280550000E+003 9.9960522487E-001 7.3334850000E+003 1.0000690568E+000 7.3389380000E+003 1.0005171544E+000 7.3444070000E+003 9.9976924766E-001 7.3498940000E+003 1.0009542570E+000 7.3554020000E+003 1.0010347241E+000 7.3609290000E+003 1.0010582566E+000 7.3664740000E+003 1.0012112583E+000 7.3720400000E+003 1.0009121882E+000 7.3776260000E+003 1.0015038997E+000 7.3832290000E+003 1.0020964404E+000 7.3888500000E+003 1.0016126526E+000 7.3944930000E+003 1.0034323385E+000 7.4001540000E+003 1.0018105964E+000 7.4058330000E+003 1.0023219817E+000 7.4115330000E+003 1.0020206683E+000 7.4172500000E+003 1.0022846000E+000 sixpack-0.68/examples/feff/0002777000175000017500000000000007513143236014643 5ustar segresegresixpack-0.68/examples/feff/feff0001.dat0000666000175000017500000001227307242621362016547 0ustar segresegre#Cu metal fcc a=3.603 Feff XX 6.10 #Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell #Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 #Gam_ch=1.761E+00 H-L exch #Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 #Path 1 icalc 2 #----------------------------------------------------------------------- # 2 12.000 2.5478 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge # x y z pot at# # .0000 .0000 .0000 0 29 Cu absorbing atom # .0000 -1.8016 1.8016 1 29 Cu # k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -5.1320E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 3.3976E-02 -5.6318E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 6.7038E-02 -6.1121E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 9.8421E-02 -6.5731E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 1.2760E-01 -7.0153E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 1.5432E-01 -7.4387E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 1.7856E-01 -7.8435E+00 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 2.0044E-01 -8.2297E+00 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 2.2014E-01 -8.5973E+00 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 2.3782E-01 -8.9459E+00 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 2.5358E-01 -9.2756E+00 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 2.6742E-01 -9.5864E+00 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 2.7930E-01 -9.8781E+00 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 2.8908E-01 -1.0151E+01 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 2.9658E-01 -1.0405E+01 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 3.0158E-01 -1.0639E+01 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 3.0387E-01 -1.0855E+01 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 3.0324E-01 -1.1051E+01 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 2.9952E-01 -1.1226E+01 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 2.9262E-01 -1.1381E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 2.8254E-01 -1.1513E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 2.5343E-01 -1.1702E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 2.2097E-01 -1.1853E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 2.0024E-01 -1.2187E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 1.6820E-01 -1.2400E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 1.3806E-01 -1.2407E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 1.2236E-01 -1.2189E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 1.4499E-01 -1.1933E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 1.9428E-01 -1.1822E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 2.5740E-01 -1.1838E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 3.2303E-01 -1.1902E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 3.8574E-01 -1.1985E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 4.4624E-01 -1.2073E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 5.0095E-01 -1.2161E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 5.5041E-01 -1.2241E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 5.9187E-01 -1.2322E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 6.3037E-01 -1.2396E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 6.6383E-01 -1.2463E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 6.9100E-01 -1.2531E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 7.1670E-01 -1.2591E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 7.3666E-01 -1.2649E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 7.6643E-01 -1.2784E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 7.6974E-01 -1.2906E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 7.5036E-01 -1.3022E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 7.1645E-01 -1.3130E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 6.7486E-01 -1.3230E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 6.2811E-01 -1.3331E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 5.7859E-01 -1.3435E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 5.2908E-01 -1.3544E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 4.3980E-01 -1.3760E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 3.6492E-01 -1.3977E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 3.0439E-01 -1.4200E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 2.5553E-01 -1.4407E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 2.1646E-01 -1.4623E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 1.8503E-01 -1.4821E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 1.5883E-01 -1.5018E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 1.3866E-01 -1.5217E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 1.1937E-01 -1.5388E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 1.0466E-01 -1.5591E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feff0002.dat0000666000175000017500000001227707242621362016554 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 2 icalc 2 ----------------------------------------------------------------------- 2 6.000 3.6032 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom -3.6032 .0000 .0000 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -1.9368E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 4.4009E-02 -2.6394E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 8.6894E-02 -3.3061E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 1.2768E-01 -3.9377E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 1.6565E-01 -4.5354E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 2.0037E-01 -5.1005E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 2.3172E-01 -5.6342E+00 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 2.5974E-01 -6.1379E+00 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 2.8462E-01 -6.6126E+00 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 3.0656E-01 -7.0593E+00 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 3.2577E-01 -7.4789E+00 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 3.4238E-01 -7.8721E+00 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 3.5648E-01 -8.2394E+00 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 3.6805E-01 -8.5812E+00 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 3.7703E-01 -8.8978E+00 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 3.8333E-01 -9.1894E+00 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 3.8679E-01 -9.4557E+00 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 3.8727E-01 -9.6966E+00 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 3.8462E-01 -9.9115E+00 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 3.7875E-01 -1.0100E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 3.6961E-01 -1.0260E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 3.4179E-01 -1.0490E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 3.2322E-01 -1.0664E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 3.1411E-01 -1.1143E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 2.8725E-01 -1.1528E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 2.5588E-01 -1.1788E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 2.2122E-01 -1.1928E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 2.0330E-01 -1.1932E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 2.0843E-01 -1.1850E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 2.4172E-01 -1.1788E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 2.9080E-01 -1.1783E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 3.4555E-01 -1.1825E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 4.0431E-01 -1.1893E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 4.6028E-01 -1.1975E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 5.1294E-01 -1.2055E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 5.5809E-01 -1.2140E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 6.0085E-01 -1.2222E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 6.3867E-01 -1.2297E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 6.6986E-01 -1.2373E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 6.9963E-01 -1.2443E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 7.2338E-01 -1.2508E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 7.6169E-01 -1.2661E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 7.7231E-01 -1.2797E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 7.5858E-01 -1.2924E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 7.2858E-01 -1.3042E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 6.8936E-01 -1.3151E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 6.4353E-01 -1.3258E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 5.9395E-01 -1.3367E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 5.4390E-01 -1.3480E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 4.5305E-01 -1.3702E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 3.7567E-01 -1.3922E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 3.1296E-01 -1.4149E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 2.6253E-01 -1.4359E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 2.2160E-01 -1.4577E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 1.8953E-01 -1.4778E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 1.6208E-01 -1.4977E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 1.4153E-01 -1.5177E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 1.2296E-01 -1.5346E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 1.1112E-01 -1.5554E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feff0003.dat0000666000175000017500000001235507242621362016552 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 3 icalc 2 ----------------------------------------------------------------------- 3 48.000 3.8218 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom 1.8016 -1.8016 .0000 1 29 Cu 1.8016 .0000 -1.8016 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -1.2678E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 7.5323E-03 -2.0135E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 1.4465E-02 -2.7224E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 2.0316E-02 -3.3956E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 2.4802E-02 -4.0347E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 2.7845E-02 -4.6414E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 2.9533E-02 -5.2169E+00 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 3.0057E-02 -5.7618E+00 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 2.9641E-02 -6.2760E+00 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 2.8504E-02 -6.7584E+00 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 2.6838E-02 -7.2068E+00 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 2.4809E-02 -7.6175E+00 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 2.2568E-02 -7.9849E+00 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 2.0281E-02 -8.3010E+00 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 1.8160E-02 -8.5559E+00 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 1.6487E-02 -8.7410E+00 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 1.5606E-02 -8.8598E+00 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 1.5787E-02 -8.9391E+00 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 1.7049E-02 -9.0199E+00 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 1.9133E-02 -9.1286E+00 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 2.1672E-02 -9.2686E+00 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 2.6807E-02 -9.6068E+00 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 4.7746E-02 -9.9257E+00 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 6.3102E-02 -1.0391E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 7.2888E-02 -1.0917E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 8.0560E-02 -1.1422E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 8.5362E-02 -1.1938E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 8.8480E-02 -1.2432E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 9.1415E-02 -1.2896E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 9.3018E-02 -1.3324E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 9.4162E-02 -1.3713E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 9.3341E-02 -1.4085E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 9.1584E-02 -1.4399E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 8.8501E-02 -1.4686E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 8.3407E-02 -1.4941E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 7.7451E-02 -1.5189E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 7.1005E-02 -1.5401E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 6.3853E-02 -1.5592E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 5.6736E-02 -1.5780E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 4.9805E-02 -1.5941E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 4.3070E-02 -1.6096E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 2.8587E-02 -1.6480E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 1.7707E-02 -1.6929E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 1.0833E-02 -1.7594E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 8.1835E-03 -1.8476E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 7.8310E-03 -1.9231E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 7.2695E-03 -1.9762E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 5.8733E-03 -2.0152E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 4.0262E-03 -2.0423E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 1.3315E-03 -2.0381E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 3.0702E-04 -1.8302E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 2.3913E-03 -1.8147E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 3.6319E-03 -1.8668E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 3.5305E-03 -1.9051E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 3.6558E-03 -1.9245E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 3.7914E-03 -1.9583E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 3.3486E-03 -1.9983E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 2.8699E-03 -2.0149E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 2.8370E-03 -2.0407E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feff0004.dat0000666000175000017500000001235507242621362016553 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 4 icalc 2 ----------------------------------------------------------------------- 3 48.000 4.3494 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom .0000 .0000 -3.6032 1 29 Cu .0000 1.8016 -1.8016 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -4.4874E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 6.0894E-03 -5.3316E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 1.1799E-02 -6.1250E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 1.6822E-02 -6.8693E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 2.0976E-02 -7.5667E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 2.4209E-02 -8.2200E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 2.6581E-02 -8.8316E+00 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 2.8221E-02 -9.4041E+00 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 2.9291E-02 -9.9395E+00 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 2.9952E-02 -1.0439E+01 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 3.0348E-02 -1.0905E+01 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 3.0597E-02 -1.1339E+01 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 3.0790E-02 -1.1741E+01 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 3.0992E-02 -1.2115E+01 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 3.1240E-02 -1.2461E+01 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 3.1546E-02 -1.2782E+01 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 3.1892E-02 -1.3080E+01 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 3.2233E-02 -1.3357E+01 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 3.2495E-02 -1.3616E+01 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 3.2584E-02 -1.3859E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 3.2390E-02 -1.4087E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 3.0747E-02 -1.4506E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 3.5902E-02 -1.4837E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 3.5215E-02 -1.5478E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 3.1800E-02 -1.6200E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 2.7535E-02 -1.6997E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 2.8275E-02 -1.7936E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 3.5218E-02 -1.8761E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 4.7247E-02 -1.9383E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 6.0477E-02 -1.9864E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 7.3802E-02 -2.0248E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 8.5219E-02 -2.0581E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 9.4534E-02 -2.0862E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 1.0127E-01 -2.1115E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 1.0499E-01 -2.1341E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 1.0600E-01 -2.1560E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 1.0511E-01 -2.1756E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 1.0204E-01 -2.1936E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 9.7311E-02 -2.2116E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 9.1559E-02 -2.2280E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 8.4669E-02 -2.2438E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 6.5499E-02 -2.2826E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 4.6707E-02 -2.3206E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 3.1189E-02 -2.3603E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 2.0195E-02 -2.4035E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 1.3589E-02 -2.4496E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 1.0563E-02 -2.4904E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 9.6292E-03 -2.5178E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 9.8478E-03 -2.5366E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 1.1129E-02 -2.5721E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 1.0938E-02 -2.6096E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 8.8742E-03 -2.6387E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 7.1754E-03 -2.6474E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 6.8406E-03 -2.6551E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 6.5818E-03 -2.6779E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 5.8112E-03 -2.7028E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 4.8646E-03 -2.7241E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 4.1940E-03 -2.7353E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 4.1983E-03 -2.7586E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feff0005.dat0000666000175000017500000001227707242621362016557 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 5 icalc 2 ----------------------------------------------------------------------- 2 24.000 4.4130 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom -3.6032 1.8016 1.8016 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -5.5180E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 4.7332E-02 -6.3775E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 9.3454E-02 -7.1913E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 1.3731E-01 -7.9602E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 1.7812E-01 -8.6858E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 2.1542E-01 -9.3697E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 2.4904E-01 -1.0014E+01 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 2.7903E-01 -1.0620E+01 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 3.0559E-01 -1.1189E+01 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 3.2895E-01 -1.1724E+01 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 3.4937E-01 -1.2224E+01 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 3.6701E-01 -1.2692E+01 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 3.8200E-01 -1.3128E+01 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 3.9436E-01 -1.3533E+01 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 4.0408E-01 -1.3907E+01 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 4.1108E-01 -1.4250E+01 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 4.1523E-01 -1.4563E+01 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 4.1640E-01 -1.4845E+01 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 4.1446E-01 -1.5096E+01 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 4.0930E-01 -1.5314E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 4.0084E-01 -1.5500E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 3.7420E-01 -1.5765E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 3.6107E-01 -1.5952E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 3.5653E-01 -1.6542E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 3.3217E-01 -1.7035E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 3.0183E-01 -1.7406E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 2.6475E-01 -1.7667E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 2.3884E-01 -1.7800E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 2.2997E-01 -1.7821E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 2.4812E-01 -1.7800E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 2.8581E-01 -1.7804E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 3.3345E-01 -1.7847E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 3.8891E-01 -1.7919E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 4.4371E-01 -1.8010E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 4.9658E-01 -1.8101E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 5.4253E-01 -1.8198E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 5.8663E-01 -1.8292E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 6.2601E-01 -1.8378E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 6.5876E-01 -1.8466E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 6.9021E-01 -1.8546E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 7.1562E-01 -1.8621E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 7.5785E-01 -1.8796E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 7.7197E-01 -1.8950E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 7.6099E-01 -1.9091E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 7.3295E-01 -1.9220E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 6.9500E-01 -1.9339E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 6.4982E-01 -1.9454E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 6.0041E-01 -1.9570E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 5.5025E-01 -1.9688E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 4.5882E-01 -1.9920E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 3.8046E-01 -2.0147E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 3.1677E-01 -2.0379E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 2.6568E-01 -2.0594E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 2.2392E-01 -2.0815E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 1.9155E-01 -2.1020E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 1.6357E-01 -2.1221E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 1.4261E-01 -2.1426E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 1.2309E-01 -2.1603E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 1.0770E-01 -2.1826E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feff0006.dat0000666000175000017500000001235507242621362016555 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 6 icalc 2 ----------------------------------------------------------------------- 3 48.000 4.7543 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom 1.8016 -1.8016 .0000 1 29 Cu .0000 1.8016 1.8016 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -4.3839E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 8.5093E-03 -5.3106E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 1.6738E-02 -6.1893E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 2.4451E-02 -7.0213E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 3.1486E-02 -7.8083E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 3.7764E-02 -8.5522E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 4.3278E-02 -9.2552E+00 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 4.8068E-02 -9.9192E+00 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 5.2198E-02 -1.0546E+01 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 5.5732E-02 -1.1138E+01 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 5.8722E-02 -1.1696E+01 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 6.1199E-02 -1.2222E+01 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 6.3174E-02 -1.2717E+01 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 6.4636E-02 -1.3183E+01 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 6.5560E-02 -1.3620E+01 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 6.5905E-02 -1.4029E+01 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 6.5629E-02 -1.4411E+01 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 6.4689E-02 -1.4767E+01 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 6.3054E-02 -1.5096E+01 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 6.0709E-02 -1.5400E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 5.7667E-02 -1.5679E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 4.9724E-02 -1.6159E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 5.2263E-02 -1.6693E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 5.6137E-02 -1.7450E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 5.3448E-02 -1.8151E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 4.8619E-02 -1.8782E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 4.2552E-02 -1.9392E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 3.7165E-02 -1.9942E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 3.3059E-02 -2.0427E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 3.0058E-02 -2.0818E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 2.8319E-02 -2.1114E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 2.7550E-02 -2.1334E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 2.8694E-02 -2.1478E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 3.1286E-02 -2.1603E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 3.5117E-02 -2.1718E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 3.9534E-02 -2.1852E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 4.4693E-02 -2.1988E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 5.0051E-02 -2.2121E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 5.5140E-02 -2.2261E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 6.0369E-02 -2.2395E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 6.5133E-02 -2.2523E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 7.4721E-02 -2.2837E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 8.0583E-02 -2.3129E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 8.2225E-02 -2.3408E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 8.0234E-02 -2.3671E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 7.5746E-02 -2.3916E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 6.9804E-02 -2.4149E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 6.3261E-02 -2.4377E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 5.6560E-02 -2.4607E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 4.3954E-02 -2.5060E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 3.3491E-02 -2.5490E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 2.5387E-02 -2.5909E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 1.9229E-02 -2.6320E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 1.4570E-02 -2.6704E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 1.1161E-02 -2.7093E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 8.6189E-03 -2.7461E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 6.6525E-03 -2.7809E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 5.3108E-03 -2.8172E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 4.1658E-03 -2.8477E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feff0007.dat0000666000175000017500000001235507242621362016556 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 7 icalc 2 ----------------------------------------------------------------------- 3 96.000 4.7543 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom 1.8016 3.6032 -1.8016 1 29 Cu 1.8016 1.8016 .0000 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -1.8125E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 1.4331E-02 -2.7372E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 2.7880E-02 -3.6102E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 4.0009E-02 -4.4333E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 5.0315E-02 -5.2086E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 5.8657E-02 -5.9389E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 6.5112E-02 -6.6268E+00 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 6.9907E-02 -7.2748E+00 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 7.3331E-02 -7.8846E+00 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 7.5679E-02 -8.4579E+00 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 7.7212E-02 -8.9957E+00 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 7.8143E-02 -9.4988E+00 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 7.8632E-02 -9.9679E+00 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 7.8794E-02 -1.0403E+01 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 7.8706E-02 -1.0805E+01 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 7.8414E-02 -1.1174E+01 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 7.7943E-02 -1.1510E+01 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 7.7295E-02 -1.1813E+01 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 7.6459E-02 -1.2084E+01 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 7.5404E-02 -1.2323E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 7.4088E-02 -1.2529E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 7.0460E-02 -1.2846E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 7.3011E-02 -1.2888E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 6.1728E-02 -1.3391E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 4.9840E-02 -1.3869E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 3.7170E-02 -1.4225E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 2.5188E-02 -1.4539E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 1.4730E-02 -1.4717E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 5.7665E-03 -1.4466E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 6.7265E-03 -1.3022E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 1.4551E-02 -1.2815E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 2.2098E-02 -1.2886E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 2.9714E-02 -1.2989E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 3.7047E-02 -1.3112E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 4.3732E-02 -1.3230E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 4.9608E-02 -1.3367E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 5.5512E-02 -1.3495E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 6.0440E-02 -1.3614E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 6.4515E-02 -1.3744E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 6.8275E-02 -1.3861E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 7.0772E-02 -1.3973E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 7.3261E-02 -1.4249E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 7.0644E-02 -1.4502E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 6.3968E-02 -1.4739E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 5.4643E-02 -1.4961E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 4.3841E-02 -1.5158E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 3.2787E-02 -1.5319E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 2.2589E-02 -1.5396E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 1.4611E-02 -1.5288E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 1.2558E-02 -1.4516E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 1.9242E-02 -1.4489E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 2.2992E-02 -1.4776E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 2.2955E-02 -1.5133E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 2.0330E-02 -1.5497E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 1.6638E-02 -1.5833E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 1.2525E-02 -1.6120E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 8.7669E-03 -1.6271E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 6.9705E-03 -1.6318E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 7.0175E-03 -1.6359E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feff0008.dat0000666000175000017500000001227707242621362016562 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 8 icalc 2 ----------------------------------------------------------------------- 2 12.000 5.0957 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom .0000 3.6032 -3.6032 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -3.1774E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 4.8935E-02 -4.1695E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 9.6620E-02 -5.1079E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 1.4196E-01 -5.9937E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 1.8416E-01 -6.8286E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 2.2272E-01 -7.6145E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 2.5746E-01 -8.3537E+00 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 2.8843E-01 -9.0482E+00 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 3.1585E-01 -9.7000E+00 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 3.3997E-01 -1.0311E+01 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 3.6103E-01 -1.0882E+01 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 3.7925E-01 -1.1415E+01 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 3.9475E-01 -1.1911E+01 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 4.0759E-01 -1.2371E+01 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 4.1777E-01 -1.2795E+01 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 4.2522E-01 -1.3184E+01 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 4.2983E-01 -1.3538E+01 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 4.3148E-01 -1.3856E+01 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 4.3002E-01 -1.4138E+01 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 4.2534E-01 -1.4383E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 4.1738E-01 -1.4591E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 3.9162E-01 -1.4886E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 3.8161E-01 -1.5084E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 3.7967E-01 -1.5768E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 3.5687E-01 -1.6348E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 3.2738E-01 -1.6802E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 2.8961E-01 -1.7148E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 2.6047E-01 -1.7364E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 2.4518E-01 -1.7463E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 2.5504E-01 -1.7492E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 2.8545E-01 -1.7520E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 3.2799E-01 -1.7576E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 3.8077E-01 -1.7661E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 4.3435E-01 -1.7764E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 4.8695E-01 -1.7868E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 5.3313E-01 -1.7978E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 5.7785E-01 -1.8084E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 6.1805E-01 -1.8183E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 6.5167E-01 -1.8281E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 6.8408E-01 -1.8372E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 7.1045E-01 -1.8457E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 7.5505E-01 -1.8652E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 7.7133E-01 -1.8823E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 7.6206E-01 -1.8978E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 7.3525E-01 -1.9119E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 6.9813E-01 -1.9248E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 6.5341E-01 -1.9370E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 6.0416E-01 -1.9492E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 5.5396E-01 -1.9617E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 4.6223E-01 -1.9857E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 3.8332E-01 -2.0091E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 3.1905E-01 -2.0329E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 2.6757E-01 -2.0548E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 2.2532E-01 -2.0773E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 1.9275E-01 -2.0982E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 1.6443E-01 -2.1185E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 1.4314E-01 -2.1393E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 1.2302E-01 -2.1567E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 1.0597E-01 -2.1776E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feff0009.dat0000666000175000017500000001235507242621362016560 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 9 icalc 2 ----------------------------------------------------------------------- 3 12.000 5.0957 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom .0000 -1.8016 1.8016 1 29 Cu .0000 1.8016 -1.8016 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -2.0976E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 3.5177E-02 -3.0915E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 6.8577E-02 -4.0355E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 9.8747E-02 -4.9311E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 1.2477E-01 -5.7800E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 1.4630E-01 -6.5846E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 1.6348E-01 -7.3469E+00 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 1.7679E-01 -8.0688E+00 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 1.8678E-01 -8.7517E+00 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 1.9404E-01 -9.3970E+00 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 1.9903E-01 -1.0005E+01 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 2.0209E-01 -1.0578E+01 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 2.0341E-01 -1.1115E+01 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 2.0309E-01 -1.1616E+01 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 2.0114E-01 -1.2082E+01 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 1.9751E-01 -1.2514E+01 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 1.9216E-01 -1.2909E+01 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 1.8502E-01 -1.3269E+01 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 1.7610E-01 -1.3592E+01 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 1.6545E-01 -1.3876E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 1.5322E-01 -1.4120E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 1.2507E-01 -1.4477E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 1.0739E-01 -1.4765E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 9.6432E-02 -1.5421E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 7.7058E-02 -1.5931E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 5.8087E-02 -1.6222E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 4.0299E-02 -1.6283E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 3.2183E-02 -1.6016E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 3.6706E-02 -1.5595E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 5.4747E-02 -1.5369E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 8.1501E-02 -1.5313E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 1.1394E-01 -1.5346E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 1.5246E-01 -1.5424E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 1.9320E-01 -1.5526E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 2.3516E-01 -1.5627E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 2.7380E-01 -1.5741E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 3.1294E-01 -1.5851E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 3.4940E-01 -1.5952E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 3.8057E-01 -1.6060E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 4.1159E-01 -1.6158E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 4.3677E-01 -1.6250E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 4.7717E-01 -1.6476E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 4.8519E-01 -1.6684E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 4.6421E-01 -1.6884E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 4.2551E-01 -1.7075E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 3.7904E-01 -1.7255E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 3.2904E-01 -1.7437E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 2.7942E-01 -1.7627E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 2.3373E-01 -1.7830E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 1.6156E-01 -1.8236E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 1.1083E-01 -1.8647E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 7.6808E-02 -1.9076E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 5.3988E-02 -1.9477E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 3.8459E-02 -1.9897E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 2.8110E-02 -2.0286E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 2.0556E-02 -2.0671E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 1.5663E-02 -2.1061E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 1.1815E-02 -2.1383E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 9.6635E-03 -2.1772E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feff0010.dat0000666000175000017500000001235507242621362016550 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 10 icalc 2 ----------------------------------------------------------------------- 3 24.000 5.0957 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom 3.6032 3.6032 .0000 1 29 Cu 1.8016 1.8016 .0000 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -4.9291E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 2.4675E-02 -5.9252E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 4.8042E-02 -6.8757E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 6.9064E-02 -7.7820E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 8.7141E-02 -8.6458E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 1.0215E-01 -9.4688E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 1.1434E-01 -1.0253E+01 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 1.2419E-01 -1.0999E+01 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 1.3225E-01 -1.1708E+01 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 1.3903E-01 -1.2381E+01 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 1.4494E-01 -1.3017E+01 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 1.5029E-01 -1.3617E+01 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 1.5525E-01 -1.4181E+01 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 1.5990E-01 -1.4709E+01 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 1.6425E-01 -1.5201E+01 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 1.6825E-01 -1.5658E+01 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 1.7178E-01 -1.6078E+01 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 1.7473E-01 -1.6462E+01 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 1.7694E-01 -1.6809E+01 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 1.7825E-01 -1.7119E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 1.7851E-01 -1.7390E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 1.7535E-01 -1.7808E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 1.6994E-01 -1.7987E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 1.4292E-01 -1.8754E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 1.1906E-01 -1.9461E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 9.8817E-02 -2.0046E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 8.7011E-02 -2.0430E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 9.0573E-02 -2.0594E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 1.1680E-01 -2.0675E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 1.6793E-01 -2.0827E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 2.3693E-01 -2.1019E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 3.1701E-01 -2.1225E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 4.0715E-01 -2.1427E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 5.0055E-01 -2.1617E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 5.9630E-01 -2.1787E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 6.8546E-01 -2.1949E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 7.7499E-01 -2.2095E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 8.6036E-01 -2.2225E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 9.3560E-01 -2.2351E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 1.0100E+00 -2.2463E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 1.0753E+00 -2.2566E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 1.1984E+00 -2.2798E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 1.2675E+00 -2.2995E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 1.2832E+00 -2.3170E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 1.2592E+00 -2.3328E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 1.2096E+00 -2.3470E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 1.1411E+00 -2.3605E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 1.0613E+00 -2.3739E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 9.7755E-01 -2.3874E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 8.1972E-01 -2.4133E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 6.8234E-01 -2.4383E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 5.6948E-01 -2.4634E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 4.7810E-01 -2.4866E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 4.0407E-01 -2.5102E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 3.4572E-01 -2.5319E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 2.9599E-01 -2.5529E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 2.5792E-01 -2.5743E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 2.2167E-01 -2.5933E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 1.9189E-01 -2.6176E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feff0011.dat0000666000175000017500000001243307242621362016546 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 11 icalc 2 ----------------------------------------------------------------------- 4 12.000 5.0957 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom -1.8016 1.8016 .0000 1 29 Cu .0000 .0000 .0000 0 29 Cu 1.8016 -1.8016 .0000 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -1.6264E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 3.0644E-03 -2.6212E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 5.8047E-03 -3.5676E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 7.9581E-03 -4.4665E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 9.3620E-03 -5.3185E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 9.9614E-03 -6.1244E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 9.7898E-03 -6.8834E+00 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 8.9380E-03 -7.5925E+00 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 7.5263E-03 -8.2434E+00 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 5.6947E-03 -8.8119E+00 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 3.6479E-03 -9.2108E+00 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 2.0869E-03 -9.0489E+00 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 3.0437E-03 -8.5360E+00 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 5.4840E-03 -8.7046E+00 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 8.1816E-03 -9.0608E+00 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 1.0860E-02 -9.4472E+00 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 1.3383E-02 -9.8244E+00 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 1.5636E-02 -1.0178E+01 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 1.7520E-02 -1.0501E+01 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 1.8945E-02 -1.0787E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 1.9844E-02 -1.1033E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 1.9963E-02 -1.1382E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 1.3851E-02 -1.1333E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 7.9496E-03 -1.2044E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 5.6820E-03 -1.2583E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 7.0976E-03 -1.2765E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 9.4710E-03 -1.2883E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 1.1872E-02 -1.2818E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 1.8500E-02 -1.2513E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 3.6570E-02 -1.2407E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 6.7215E-02 -1.2484E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 1.0871E-01 -1.2642E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 1.6036E-01 -1.2816E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 2.1878E-01 -1.2995E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 2.8283E-01 -1.3159E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 3.4565E-01 -1.3323E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 4.1086E-01 -1.3474E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 4.7603E-01 -1.3608E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 5.3438E-01 -1.3745E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 5.9324E-01 -1.3866E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 6.4546E-01 -1.3980E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 7.3902E-01 -1.4250E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 7.7840E-01 -1.4493E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 7.6376E-01 -1.4722E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 7.1236E-01 -1.4937E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 6.4215E-01 -1.5136E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 5.6283E-01 -1.5335E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 4.8199E-01 -1.5542E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 4.0572E-01 -1.5759E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 2.8214E-01 -1.6190E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 1.9482E-01 -1.6621E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 1.3565E-01 -1.7066E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 9.5496E-02 -1.7481E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 6.8454E-02 -1.7910E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 4.9930E-02 -1.8307E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 3.6619E-02 -1.8695E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 2.7679E-02 -1.9084E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 2.0414E-02 -1.9385E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 1.6060E-02 -1.9660E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feff0012.dat0000666000175000017500000001243307242621362016547 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 12 icalc 2 ----------------------------------------------------------------------- 4 12.000 5.0957 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom 1.8016 1.8016 .0000 1 29 Cu .0000 .0000 .0000 0 29 Cu 1.8016 1.8016 .0000 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -7.8986E-01 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 1.2267E-02 -1.7869E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 2.3969E-02 -2.7401E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 3.4637E-02 -3.6507E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 4.3958E-02 -4.5202E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 5.1797E-02 -5.3504E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 5.8164E-02 -6.1429E+00 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 6.3164E-02 -6.8989E+00 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 6.6941E-02 -7.6194E+00 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 6.9634E-02 -8.3051E+00 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 7.1345E-02 -8.9564E+00 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 7.2136E-02 -9.5736E+00 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 7.2029E-02 -1.0157E+01 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 7.1026E-02 -1.0706E+01 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 6.9111E-02 -1.1222E+01 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 6.6281E-02 -1.1703E+01 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 6.2558E-02 -1.2150E+01 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 5.8004E-02 -1.2562E+01 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 5.2729E-02 -1.2938E+01 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 4.6898E-02 -1.3277E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 4.0719E-02 -1.3575E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 2.8301E-02 -1.4042E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 2.0801E-02 -1.4514E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 1.7014E-02 -1.5231E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 1.1793E-02 -1.5771E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 7.7715E-03 -1.6064E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 5.7045E-03 -1.6216E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 6.2393E-03 -1.6523E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 9.3794E-03 -1.7088E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 1.6451E-02 -1.7612E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 2.8284E-02 -1.8016E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 4.4340E-02 -1.8327E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 6.4571E-02 -1.8586E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 8.7303E-02 -1.8815E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 1.1310E-01 -1.9003E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 1.3796E-01 -1.9190E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 1.6447E-01 -1.9357E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 1.9148E-01 -1.9501E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 2.1513E-01 -1.9653E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 2.3923E-01 -1.9786E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 2.5942E-01 -1.9913E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 2.9118E-01 -2.0220E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 2.9364E-01 -2.0506E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 2.7166E-01 -2.0782E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 2.3725E-01 -2.1043E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 1.9925E-01 -2.1290E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 1.6126E-01 -2.1543E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 1.2635E-01 -2.1811E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 9.6726E-02 -2.2101E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 5.5691E-02 -2.2677E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 3.1665E-02 -2.3274E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 1.8310E-02 -2.3901E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 1.0760E-02 -2.4481E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 6.5042E-03 -2.5106E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 4.0410E-03 -2.5671E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 2.5370E-03 -2.6249E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 1.6812E-03 -2.6828E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 1.0469E-03 -2.7345E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 4.8400E-04 -2.8273E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feff0013.dat0000666000175000017500000001243307242621362016550 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 13 icalc 2 ----------------------------------------------------------------------- 4 12.000 5.0957 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom -1.8016 .0000 1.8016 1 29 Cu -3.6032 .0000 3.6032 1 29 Cu -1.8016 .0000 1.8016 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -8.5281E-01 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 1.1361E-02 -1.8493E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 2.1987E-02 -2.8014E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 3.1302E-02 -3.7109E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 3.8981E-02 -4.5804E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 4.4977E-02 -5.4126E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 4.9456E-02 -6.2102E+00 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 5.2717E-02 -6.9751E+00 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 5.5098E-02 -7.7087E+00 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 5.6915E-02 -8.4115E+00 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 5.8427E-02 -9.0836E+00 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 5.9827E-02 -9.7246E+00 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 6.1241E-02 -1.0334E+01 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 6.2738E-02 -1.0911E+01 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 6.4341E-02 -1.1456E+01 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 6.6035E-02 -1.1967E+01 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 6.7775E-02 -1.2444E+01 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 6.9492E-02 -1.2886E+01 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 7.1103E-02 -1.3292E+01 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 7.2507E-02 -1.3662E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 7.3602E-02 -1.3993E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 7.4460E-02 -1.4528E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 6.7430E-02 -1.4671E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 4.3083E-02 -1.5526E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 2.6571E-02 -1.6331E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 1.4507E-02 -1.6784E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 1.7884E-02 -1.6591E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 4.0514E-02 -1.6947E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 8.0493E-02 -1.7449E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 1.4073E-01 -1.7940E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 2.2366E-01 -1.8349E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 3.2665E-01 -1.8699E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 4.5015E-01 -1.9001E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 5.8777E-01 -1.9261E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 7.3845E-01 -1.9485E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 8.8761E-01 -1.9688E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 1.0446E+00 -1.9866E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 1.2023E+00 -2.0021E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 1.3475E+00 -2.0169E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 1.4956E+00 -2.0299E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 1.6322E+00 -2.0415E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 1.9084E+00 -2.0677E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 2.0907E+00 -2.0897E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 2.1695E+00 -2.1090E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 2.1649E+00 -2.1262E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 2.1029E+00 -2.1415E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 1.9989E+00 -2.1561E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 1.8699E+00 -2.1705E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 1.7297E+00 -2.1850E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 1.4568E+00 -2.2127E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 1.2165E+00 -2.2392E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 1.0179E+00 -2.2657E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 8.5513E-01 -2.2901E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 7.2515E-01 -2.3147E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 6.2065E-01 -2.3374E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 5.3331E-01 -2.3589E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 4.6823E-01 -2.3805E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 4.1147E-01 -2.4006E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 3.8149E-01 -2.4271E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feffcu01.dat0000666000175000017500000001227707242621362016743 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 1 icalc 2 ----------------------------------------------------------------------- 2 12.000 2.5478 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom .0000 -1.8016 1.8016 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -5.1320E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 3.3976E-02 -5.6318E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 6.7038E-02 -6.1121E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 9.8421E-02 -6.5731E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 1.2760E-01 -7.0153E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 1.5432E-01 -7.4387E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 1.7856E-01 -7.8435E+00 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 2.0044E-01 -8.2297E+00 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 2.2014E-01 -8.5973E+00 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 2.3782E-01 -8.9459E+00 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 2.5358E-01 -9.2756E+00 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 2.6742E-01 -9.5864E+00 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 2.7930E-01 -9.8781E+00 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 2.8908E-01 -1.0151E+01 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 2.9658E-01 -1.0405E+01 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 3.0158E-01 -1.0639E+01 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 3.0387E-01 -1.0855E+01 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 3.0324E-01 -1.1051E+01 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 2.9952E-01 -1.1226E+01 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 2.9262E-01 -1.1381E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 2.8254E-01 -1.1513E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 2.5343E-01 -1.1702E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 2.2097E-01 -1.1853E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 2.0024E-01 -1.2187E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 1.6820E-01 -1.2400E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 1.3806E-01 -1.2407E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 1.2236E-01 -1.2189E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 1.4499E-01 -1.1933E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 1.9428E-01 -1.1822E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 2.5740E-01 -1.1838E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 3.2303E-01 -1.1902E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 3.8574E-01 -1.1985E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 4.4624E-01 -1.2073E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 5.0095E-01 -1.2161E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 5.5041E-01 -1.2241E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 5.9187E-01 -1.2322E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 6.3037E-01 -1.2396E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 6.6383E-01 -1.2463E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 6.9100E-01 -1.2531E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 7.1670E-01 -1.2591E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 7.3666E-01 -1.2649E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 7.6643E-01 -1.2784E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 7.6974E-01 -1.2906E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 7.5036E-01 -1.3022E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 7.1645E-01 -1.3130E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 6.7486E-01 -1.3230E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 6.2811E-01 -1.3331E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 5.7859E-01 -1.3435E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 5.2908E-01 -1.3544E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 4.3980E-01 -1.3760E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 3.6492E-01 -1.3977E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 3.0439E-01 -1.4200E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 2.5553E-01 -1.4407E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 2.1646E-01 -1.4623E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 1.8503E-01 -1.4821E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 1.5883E-01 -1.5018E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 1.3866E-01 -1.5217E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 1.1937E-01 -1.5388E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 1.0466E-01 -1.5591E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feffcu02.dat0000666000175000017500000001227707242621362016744 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 2 icalc 2 ----------------------------------------------------------------------- 2 6.000 3.6032 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom -3.6032 .0000 .0000 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -1.9368E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 4.4009E-02 -2.6394E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 8.6894E-02 -3.3061E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 1.2768E-01 -3.9377E+00 9.882E-01 1.5831E+01 1.8309E+00 .400 3.5093E+00 1.6565E-01 -4.5354E+00 9.890E-01 1.5963E+01 1.8491E+00 .500 3.5132E+00 2.0037E-01 -5.1005E+00 9.901E-01 1.6111E+01 1.8724E+00 .600 3.5175E+00 2.3172E-01 -5.6342E+00 9.915E-01 1.6258E+01 1.9005E+00 .700 3.5218E+00 2.5974E-01 -6.1379E+00 9.932E-01 1.6388E+01 1.9332E+00 .800 3.5258E+00 2.8462E-01 -6.6126E+00 9.953E-01 1.6481E+01 1.9704E+00 .900 3.5291E+00 3.0656E-01 -7.0593E+00 9.978E-01 1.6522E+01 2.0119E+00 1.000 3.5311E+00 3.2577E-01 -7.4789E+00 1.001E+00 1.6496E+01 2.0575E+00 1.100 3.5315E+00 3.4238E-01 -7.8721E+00 1.004E+00 1.6396E+01 2.1070E+00 1.200 3.5296E+00 3.5648E-01 -8.2394E+00 1.008E+00 1.6217E+01 2.1605E+00 1.300 3.5247E+00 3.6805E-01 -8.5812E+00 1.013E+00 1.5965E+01 2.2177E+00 1.400 3.5164E+00 3.7703E-01 -8.8978E+00 1.018E+00 1.5649E+01 2.2786E+00 1.500 3.5039E+00 3.8333E-01 -9.1894E+00 1.024E+00 1.5286E+01 2.3431E+00 1.600 3.4866E+00 3.8679E-01 -9.4557E+00 1.030E+00 1.4895E+01 2.4113E+00 1.700 3.4640E+00 3.8727E-01 -9.6966E+00 1.036E+00 1.4497E+01 2.4830E+00 1.800 3.4354E+00 3.8462E-01 -9.9115E+00 1.043E+00 1.4117E+01 2.5584E+00 1.900 3.4002E+00 3.7875E-01 -1.0100E+01 1.048E+00 1.3776E+01 2.6374E+00 2.000 3.3581E+00 3.6961E-01 -1.0260E+01 1.053E+00 1.3497E+01 2.7201E+00 2.200 3.2511E+00 3.4179E-01 -1.0490E+01 1.059E+00 1.3207E+01 2.8970E+00 2.400 3.1362E+00 3.2322E-01 -1.0664E+01 1.230E+00 7.5606E+00 3.0883E+00 2.600 3.1585E+00 3.1411E-01 -1.1143E+01 1.303E+00 6.1535E+00 3.2191E+00 2.800 3.1545E+00 2.8725E-01 -1.1528E+01 1.326E+00 5.6163E+00 3.3579E+00 3.000 3.1151E+00 2.5588E-01 -1.1788E+01 1.321E+00 5.3982E+00 3.5040E+00 3.200 3.0550E+00 2.2122E-01 -1.1928E+01 1.304E+00 5.3389E+00 3.6566E+00 3.400 2.9887E+00 2.0330E-01 -1.1932E+01 1.281E+00 5.3735E+00 3.8150E+00 3.600 2.9054E+00 2.0843E-01 -1.1850E+01 1.256E+00 5.4705E+00 3.9784E+00 3.800 2.8228E+00 2.4172E-01 -1.1788E+01 1.229E+00 5.6121E+00 4.1461E+00 4.000 2.7282E+00 2.9080E-01 -1.1783E+01 1.206E+00 5.7879E+00 4.3177E+00 4.200 2.6390E+00 3.4555E-01 -1.1825E+01 1.179E+00 5.9908E+00 4.4926E+00 4.400 2.5352E+00 4.0431E-01 -1.1893E+01 1.157E+00 6.2162E+00 4.6704E+00 4.600 2.4376E+00 4.6028E-01 -1.1975E+01 1.135E+00 6.4607E+00 4.8506E+00 4.800 2.3422E+00 5.1294E-01 -1.2055E+01 1.115E+00 6.7219E+00 5.0329E+00 5.000 2.2460E+00 5.5809E-01 -1.2140E+01 1.096E+00 6.9979E+00 5.2171E+00 5.200 2.1454E+00 6.0085E-01 -1.2222E+01 1.079E+00 7.2872E+00 5.4030E+00 5.400 2.0492E+00 6.3867E-01 -1.2297E+01 1.064E+00 7.5888E+00 5.5902E+00 5.600 1.9507E+00 6.6986E-01 -1.2373E+01 1.050E+00 7.9017E+00 5.7787E+00 5.800 1.8576E+00 6.9963E-01 -1.2443E+01 1.038E+00 8.2251E+00 5.9682E+00 6.000 1.7615E+00 7.2338E-01 -1.2508E+01 1.027E+00 8.5584E+00 6.1587E+00 6.500 1.5272E+00 7.6169E-01 -1.2661E+01 1.004E+00 9.4317E+00 6.6385E+00 7.000 1.2998E+00 7.7231E-01 -1.2797E+01 9.857E-01 1.0357E+01 7.1222E+00 7.500 1.0824E+00 7.5858E-01 -1.2924E+01 9.708E-01 1.1331E+01 7.6088E+00 8.000 8.7724E-01 7.2858E-01 -1.3042E+01 9.579E-01 1.2348E+01 8.0978E+00 8.500 6.8313E-01 6.8936E-01 -1.3151E+01 9.470E-01 1.3407E+01 8.5885E+00 9.000 4.9775E-01 6.4353E-01 -1.3258E+01 9.381E-01 1.4505E+01 9.0807E+00 9.500 3.2222E-01 5.9395E-01 -1.3367E+01 9.304E-01 1.5641E+01 9.5740E+00 10.000 1.4825E-01 5.4390E-01 -1.3480E+01 9.222E-01 1.6812E+01 1.0068E+01 11.000 -1.7917E-01 4.5305E-01 -1.3702E+01 9.056E-01 1.9258E+01 1.1059E+01 12.000 -4.8336E-01 3.7567E-01 -1.3922E+01 8.938E-01 2.1832E+01 1.2051E+01 13.000 -7.6646E-01 3.1296E-01 -1.4149E+01 8.879E-01 2.4527E+01 1.3045E+01 14.000 -1.0250E+00 2.6253E-01 -1.4359E+01 8.831E-01 2.7338E+01 1.4041E+01 15.000 -1.2653E+00 2.2160E-01 -1.4577E+01 8.801E-01 3.0257E+01 1.5037E+01 16.000 -1.4894E+00 1.8953E-01 -1.4778E+01 8.793E-01 3.3281E+01 1.6034E+01 17.000 -1.6950E+00 1.6208E-01 -1.4977E+01 8.776E-01 3.6404E+01 1.7031E+01 18.000 -1.8893E+00 1.4153E-01 -1.5177E+01 8.772E-01 3.9623E+01 1.8028E+01 19.000 -2.0688E+00 1.2296E-01 -1.5346E+01 8.769E-01 4.2933E+01 1.9026E+01 20.000 -2.2337E+00 1.1112E-01 -1.5554E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/feff/feffcu03.dat0000666000175000017500000001235507242621362016742 0ustar segresegre Cu metal fcc a=3.603 Feff XX 6.10 Abs Z=29 Rmt= 1.289 Rnm= 1.424 K shell Pot 1 Z=29 Rmt= 1.272 Rnm= 1.392 Gam_ch=1.761E+00 H-L exch Mu=-5.535E+00 kf=1.806E+00 Vint=-1.796E+01 Rs_int= 2.008 Path 3 icalc 2 ----------------------------------------------------------------------- 3 48.000 3.8218 2.6300 -5.53502 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# .0000 .0000 .0000 0 29 Cu absorbing atom 1.8016 -1.8016 .0000 1 29 Cu 1.8016 .0000 -1.8016 1 29 Cu k real[2*phc] mag[feff] phase[feff] red factor lambda real[p]@# .000 3.5015E+00 0.0000E+00 -1.2678E+00 9.872E-01 1.5637E+01 1.8071E+00 .100 3.5020E+00 7.5323E-03 -2.0135E+00 9.873E-01 1.5660E+01 1.8098E+00 .200 3.5035E+00 1.4465E-02 -2.7224E+00 9.877E-01 1.5726E+01 1.8177E+00 .300 3.5060E+00 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2.8370E-03 -2.0407E+01 8.754E-01 4.6332E+01 2.0025E+01 sixpack-0.68/examples/mncalib.prm0000666000175000017500000000046707470473762016103 0ustar segresegreEDGEPARAMS C:/Sam/Common/samxas2/examples/data/mn234_401050.xmu 6530 6600 0 0 0 1000 0 0 1 C:/Sam/Common/samxas2/examples/data/mn2.xmu 0.3538 1 C:/Sam/Common/samxas2/examples/data/mn3.xmu 0.1338 1 C:/Sam/Common/samxas2/examples/data/mn4.xmu 0.5088 0 0 0 0 0 0 2 2 0.0 ENDsixpack-0.68/examples/selfabsex1.prm0000666000175000017500000000033607470474346016525 0ustar segresegreEDGEPARAMS C:/Sam/Common/samxas2/examples/data/mnsg1a_fl.xmu 6530 6600 0 0 1 1000 0 0 1 C:/Sam/Common/samxas2/examples/data/mnsg1a_tr.xmu 1.0000 0 0 0 0 0 0 0 0 4.29 5.29 0.0 ENDsixpack-0.68/examples/selfabsex2.prm0000666000175000017500000000050407470474656016527 0ustar segresegreEDGEPARAMS C:/Sam/Common/samxas2/examples/data/mnsg1a_fl.xmu 6530 6600 0 0 1 1000 0 0 1 C:/Sam/Common/samxas2/examples/data/mnso4_soln.xmu 0.0702 1 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1.40579307079 7773.24707031 1.40346884727 7778.23925781 1.40112113953 7783.25097656 1.39870977402 7788.28173828 1.39640033245 7793.33203125 1.39410114288 7798.40185547 1.39170181751 7803.49072266 1.38936150074 7808.59863281 1.38697469234 7813.72607422 1.3845770359 7818.87304688 1.38225793839 7824.0390625 1.37986767292 7829.22412109 1.37749755383 7834.42871094 1.37507629395 7839.65283203 1.37266480923 7844.89599609 1.37024962902 7850.15869141 1.3678882122 7855.44042969 1.36547255516 7860.74121094 1.36309421062 7866.06201172 1.36063027382 7871.40136719 1.35818207264 7876.76074219 1.35575509071 sixpack-0.68/varimax.py0000666000175000017500000000503007704626020014133 0ustar segresegre #Varimax matrix rotation #Coded in Python by Sam Webb in 2003 #Adapted from MATLAB code modified by Tevor Park in 2002 from original code by J.O. Ramsay # from Numeric import * from math import * import MLab import LinearAlgebra def angle(z): a=z.real b=z.imag return arctan2(b,a) def var(z): s=MLab.std(z) return s**2 def vcomplex(a,b): return a+b*1j def varimax(amat,target_basis=0): MAX_ITER=50 EPSILON=1e-10 amatd=amat.shape #make sure the problem is 2D if len(amatd)!=2: raise ValueError, 'AMAT must be 2-dimensional' n=amatd[0] k=amatd[1] rotm=identity(k)*1.0 #if singular if k==1: return #error check target_basis if target_basis!=0: if len(target_basis.shape)!=2: raise ValueError, 'TARGET_BASIS must be 2-dimensional' if alltrue(target_basis.shape==(n,n)): amat=LinearAlgebra.solve_linear_equations(target_basis,amat) else: raise ValueError, 'TARGET_BASIS must be a basis for the column space' else: target_basis=identity(n)*1.0 #on to the guts varnow=sum(var(amat**2)) not_converged=1 iter=0 while not_converged and iter EPSILON) iter=iter+1 if iter>=MAX_ITER: print 'WARNING: Maximum number of iterations exceeded in varimax rotation' opt_amat=matrixmultiply(target_basis,amat) print "Total varimax iterations: "+str(iter) return rotm,opt_amat sixpack-0.68/mucal.py0000644000175000017500000027115410641476740013603 0ustar segresegre ## MUCAL ported to Python from C by Sam Webb ## Modified ala Corwin Booth to add xsec(11)=total crossection not including current edge ## This is thus a mutilation of a mutilation... ## contact: samwebb@slac.stanford.edu ## * Documentation (adapted from MUCAL.F and MUCAL.C): ## * ## * This is a program to calculate x-sections using McMaster ## * data in May 1969 edition. ## * ## * NOTE: this program has data for all the elements from 1 to 94 ## * with the following exceptions: ## * 84 po \ ## * 85 at | ## * 87 fr | ## * 88 ra > Mc Master did not have any data for these ## * 89 ac | ## * 91 pa | ## * 93 np / ## * ## * Python Usage: ## * ## * import mucal ## * [err,energy,xsec,fl_yield,errmsg] = mucal(element, Z, e_phot, unit) ## * ## * where: ## * ## * element - the name of the element of interest. If Z is given ## * (see below) element may be left blank. If both Z ## * and element are given they must agree. ## * Z - the Z for the element of interest (0 if unknown). If ## * element is given, Z may be 0. If both element and Z ## * are given they must agree. Z may not be < 0. ## * e_phot - photon energy for calculation, in kev. May not ## * be <0. if e_phot=0 no calculations for the scattering ## * crossection is done. Instead, only the various energy- ## * independent physical constants for the element of interest ## * are returned. ## * unit - units for the scattering crossections. If 'c' or 'C' ## * crossections are calculated in cm^2/g. In all other ## * cases, the crossections are in barns/atom. ## * ## * Returned values: ## * ## * energy - x-ray energies for the element, in keV ## * energy[0]=k-edge energy ## * energy[1]=l1-edge energy ## * energy[2]=l2-edge energy ## * energy[3]=l3-edge energy ## * energy[4]=m-edge energy ## * energy[5]=k-alpha1 ## * energy[6]=k-beta1 ## * energy[7]=l-alpha1 ## * energy[8]=l-beta1 ## * ## * xsec - various crossections and material constants for the element. ## * xsec[0]=photoelectric x-section ## * xsec[1]=coherent x-section ## * xsec[2]=incoherent x-section ## * xsec[3]=total x-section ## * xsec[4]=conversion factor (cm^2/g to barns/atom) ## * xsec[5]=absorption coefficient (cm^-1) ## * xsec[6]=atomic weight (g/mole) ## * xsec[7]=density (g/cm^3) ## * xsec[8]=l1-edge jump (fractional) ## * xsec[9]=l2-edge jump (fractional) ## * xsec[10]=l3-edge jump (fractional) ## * xsec[11]=total x-section not including current edge ## ## * fl_yield - fluorescent yield for the element ## * fl_yield[0]= k fluorescence yield ## * fl_yeild[1]= l1 fluorescence yield ## * fl_yield[2]= l2 fluorescence yield ## * fl_yield[3]= l3 fluorescence yield ## * ## * err_msg - text of error message (if any). contains a ## * description of any error conditions that may occur. ## * must be at least 100 chars long. when print_flag is ## * set, the text of this buffer is printed to the terminal ## * ## * Return codes (defined in mucal.h): ## * no_error - no error ## * no_input - no name, no Z, no service ## * no_zmatch - Z does not match name ## * no_data - data not avaialble for requested material ## * bad_z - bad (negative) Z ## * bad_name - invalid element name ## * bad_energy - bad (negative) photon energy ## * within_edge - photon energy within 1 eV of an edge (warning) ## * m_edge_warn - M-edge data requested for a Z<30 element (warning) ## * satan_rules - internal error of dubious origin :-) ## * ## * Remarks: ## * If e_phot = 0 the program returns data for everything but xsec[0-3] ## * ## * Acknowledgment: ## * The C port of MUCAL was made possible in part by a funds provided ## * by the Industrial Macromeollecular Crystallography Association (IMCA). ## * ## Original comments follow ## * Original credits and version history follow: ## ## * MUCAL is written by Pathikrit Bandyopadhyay and has been ## * hereby mutilated by Boyan Boyanov (boyanov@eos.ncsu.edu). ## * Ported to C from version 1.7 of MUCAL.F, as distributed ## * on xafsdb.iit.edu. Some of the input parameters have been ## * renamed and moved around to more logical positions, at ## * least IMHO. ## * ## * ## *c written by pathikrit bandyopadhyay | ## *c at the university of notre dame.i am thankful to | ## *c dr. b. a. bunker and mr. q. t. islam for their helpful | ## *c suggestions. special thanks goes to mr. m. zanabria | ## *c for helping to get all the data in. | ## * ## *c put all returned values in array xsec/jul,28 _pat | ## *c can call it either by element name or z/jul,31 _pat | ## *c data input completed on sept 1,1985 ______pat | ## *c change call format,include energy array,includ density | ## *c in xsec,add error # & error flag/sep,6 _pat | ## *c correct l-edge calculation using step jump | ## *c and warning for z<30/sep,9 _pat | ## *c return l-edges /sep 10,_ pat | ## *c return l-edge jumps,error 6 /sep 12,_ pat | ## *c check for no name & z,error 7 /sep 13,_ pat | ## *c thanks to quazi ljump can not be calculated for z<30 -pat | ## *c revision date dec 9,1985 _____________ pat | ## *c l-edges for elements z=12-26 supplied from nsls handbook | ## *c & corrections as noted by kim of nrl, april6,1991 ______anne | ## *c add if statement so accept energy e=1. kev, and | ## *c print ljump for z=27 and 28,april10,1991______________anne | ## *c corrected l2 l3 edge calculation (thanks to boyan) | ## *c using l-edge coefficianets instead of m-edge ones.____3/15/95 pat| ## *c correct AK(1,57) coefficient (for La) | ## *c----------------------------------------------------------------------+ ## *c $Log: mucal.f,v $ ## *c Revision 1.9 7/7/95 14:48:38 pat ## * ## * ## * Additions to the C version: ## * version 1.0: ## * converted everything to double precision,march 4,95_____boyan ## * checks for photon energies within 1 eV of l2 and l3 ## * edges march 4, 95_________boyan ## * issues Z<30 warning for M edges only if Z<30 march 4, 95___boyan ## * version 1.1: ## * fix bug in L1 and higher edge calculations april 23, 96___boyan ## * (thanks to L.Tavora@surrey.ac.uk for finding the bug) ## * version 1.2: ## * yet another bug fix in L-edge calculations may 29, 96___boyan ## * (thanks to N.Kawada (xnori@osk.threewebnet.or.jp) for ## * finding the bug) ## * version 1.3: ## * correct densitties for several gaceous light elements ## * april 25, 98___boyan ## */ ############################################################################# ## ## START DATA SECTION ## ############################################################################# Zmax=94 NELEM=103 #element chemical symbols esym=[ "H" , "He", "Li", "Be", "B" , "C" , "N" , "O" , "F" , "Ne", "Na", "Mg", "Al", "Si", "P" , "S" , "Cl", "Ar", "K" , "Ca", "Sc", "Ti", "V" , "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y" , "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I" , "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W" , "Re", "Os", "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U" , "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lw"] #K-edges (keV) kedge={ 1: 0.140000E-01, 2: 0.250000E-01, 3: 0.550000E-01, 4: 0.112000E+00, 5: 0.188000E+00, 6: 0.284000E+00, 7: 0.402000E+00, 8: 0.537000E+00, 9: 0.686000E+00, 10: 0.867000E+00, 11: 0.107200E+01, 12: 0.130500E+01, 13: 0.156000E+01, 14: 0.183900E+01, 15: 0.214900E+01, 16: 0.247200E+01, 17: 0.282200E+01, 18: 0.320200E+01, 19: 0.360700E+01, 20: 0.403800E+01, 21: 0.449300E+01, 22: 0.496500E+01, 23: 0.546500E+01, 24: 0.598900E+01, 25: 0.654000E+01, 26: 0.711200E+01, 27: 0.770900E+01, 28: 0.833300E+01, 29: 0.897900E+01, 30: 0.965900E+01, 31: 0.103670E+02, 32: 0.111040E+02, 33: 0.118680E+02, 34: 0.126580E+02, 35: 0.134740E+02, 36: 0.143220E+02, 37: 0.152000E+02, 38: 0.161050E+02, 39: 0.170380E+02, 40: 0.179980E+02, 41: 0.189860E+02, 42: 0.199990E+02, 43: 0.210450E+02, 44: 0.221170E+02, 45: 0.232200E+02, 46: 0.243500E+02, 47: 0.255140E+02, 48: 0.267110E+02, 49: 0.279400E+02, 50: 0.292000E+02, 51: 0.304910E+02, 52: 0.318130E+02, 53: 0.331690E+02, 54: 0.345820E+02, 55: 0.359850E+02, 56: 0.374410E+02, 57: 0.389250E+02, 58: 0.404440E+02, 59: 0.419910E+02, 60: 0.435690E+02, 61: 0.451840E+02, 62: 0.468350E+02, 63: 0.485200E+02, 64: 0.502400E+02, 65: 0.519960E+02, 66: 0.537890E+02, 67: 0.556180E+02, 68: 0.574860E+02, 69: 0.593900E+02, 70: 0.613320E+02, 71: 0.633140E+02, 72: 0.653510E+02, 73: 0.674140E+02, 74: 0.695240E+02, 75: 0.716760E+02, 76: 0.738720E+02, 77: 0.761120E+02, 78: 0.783950E+02, 79: 0.807230E+02, 80: 0.831030E+02, 81: 0.855280E+02, 82: 0.880060E+02, 83: 0.905270E+02, 84: 0.000000E+00, 85: 0.000000E+00, 86: 0.984170E+02, 87: 0.000000E+00, 88: 0.000000E+00, 89: 0.000000E+00, 90: 0.109649E+03, 91: 0.000000E+00, 92: 0.115603E+03, 93: 0.000000E+00, 94: 0.121760E+03} #L1-edges (keV) l1edge={ 1: 0.000000E+00, 2: 0.000000E+00, 3: 0.000000E+00, 4: 0.000000E+00, 5: 0.000000E+00, 6: 0.000000E+00, 7: 0.000000E+00, 8: 0.000000E+00, 9: 0.000000E+00, 10: 0.000000E+00, 11: 0.000000E+00, 12: 0.630000E-01, 13: 0.870000E-01, 14: 0.118000E+00, 15: 0.153000E+00, 16: 0.193000E+00, 17: 0.238000E+00, 18: 0.287000E+00, 19: 0.341000E+00, 20: 0.400000E+00, 21: 0.463000E+00, 22: 0.531000E+00, 23: 0.604000E+00, 24: 0.682000E+00, 25: 0.754000E+00, 26: 0.842000E+00, 27: 0.929000E+00, 28: 0.101200E+01, 29: 0.110000E+01, 30: 0.119600E+01, 31: 0.130200E+01, 32: 0.141400E+01, 33: 0.153000E+01, 34: 0.165300E+01, 35: 0.178200E+01, 36: 0.192000E+01, 37: 0.206500E+01, 38: 0.221600E+01, 39: 0.237300E+01, 40: 0.253200E+01, 41: 0.269800E+01, 42: 0.286600E+01, 43: 0.304300E+01, 44: 0.322400E+01, 45: 0.341200E+01, 46: 0.360500E+01, 47: 0.380600E+01, 48: 0.401800E+01, 49: 0.423800E+01, 50: 0.446500E+01, 51: 0.469800E+01, 52: 0.493900E+01, 53: 0.518800E+01, 54: 0.545200E+01, 55: 0.571300E+01, 56: 0.598700E+01, 57: 0.626700E+01, 58: 0.654900E+01, 59: 0.683500E+01, 60: 0.712600E+01, 61: 0.742800E+01, 62: 0.773700E+01, 63: 0.805200E+01, 64: 0.837600E+01, 65: 0.870800E+01, 66: 0.904700E+01, 67: 0.939500E+01, 68: 0.975200E+01, 69: 0.101160E+02, 70: 0.104880E+02, 71: 0.108700E+02, 72: 0.112720E+02, 73: 0.116800E+02, 74: 0.120980E+02, 75: 0.125250E+02, 76: 0.129640E+02, 77: 0.134240E+02, 78: 0.138920E+02, 79: 0.143530E+02, 80: 0.148460E+02, 81: 0.153440E+02, 82: 0.158600E+02, 83: 0.163850E+02, 84: 0.000000E+00, 85: 0.000000E+00, 86: 0.180550E+02, 87: 0.000000E+00, 88: 0.000000E+00, 89: 0.000000E+00, 90: 0.204700E+02, 91: 0.000000E+00, 92: 0.217560E+02, 93: 0.000000E+00, 94: 0.230950E+02} #L2-edges (keV) l2edge={ 1: 0.000000E+00, 2: 0.000000E+00, 3: 0.000000E+00, 4: 0.000000E+00, 5: 0.000000E+00, 6: 0.000000E+00, 7: 0.000000E+00, 8: 0.000000E+00, 9: 0.000000E+00, 10: 0.000000E+00, 11: 0.000000E+00, 12: 0.496000E-01, 13: 0.729000E-01, 14: 0.998000E-01, 15: 0.136000E+00, 16: 0.163600E+00, 17: 0.202000E+00, 18: 0.250600E+00, 19: 0.297300E+00, 20: 0.349700E+00, 21: 0.403600E+00, 22: 0.461200E+00, 23: 0.519800E+00, 24: 0.583800E+00, 25: 0.649900E+00, 26: 0.719900E+00, 27: 0.793300E+00, 28: 0.872000E+00, 29: 0.952000E+00, 30: 0.104400E+01, 31: 0.114200E+01, 32: 0.124900E+01, 33: 0.136000E+01, 34: 0.147700E+01, 35: 0.159600E+01, 36: 0.172600E+01, 37: 0.186300E+01, 38: 0.200700E+01, 39: 0.215600E+01, 40: 0.230700E+01, 41: 0.246500E+01, 42: 0.262500E+01, 43: 0.279300E+01, 44: 0.296700E+01, 45: 0.314600E+01, 46: 0.333000E+01, 47: 0.352400E+01, 48: 0.372700E+01, 49: 0.393800E+01, 50: 0.415600E+01, 51: 0.438100E+01, 52: 0.461200E+01, 53: 0.485200E+01, 54: 0.510000E+01, 55: 0.535900E+01, 56: 0.562400E+01, 57: 0.589100E+01, 58: 0.616500E+01, 59: 0.644100E+01, 60: 0.672200E+01, 61: 0.701300E+01, 62: 0.731200E+01, 63: 0.761800E+01, 64: 0.793100E+01, 65: 0.825200E+01, 66: 0.858100E+01, 67: 0.891900E+01, 68: 0.926500E+01, 69: 0.961800E+01, 70: 0.997800E+01, 71: 0.103490E+02, 72: 0.107390E+02, 73: 0.111360E+02, 74: 0.115420E+02, 75: 0.119570E+02, 76: 0.123840E+02, 77: 0.128240E+02, 78: 0.132730E+02, 79: 0.137330E+02, 80: 0.142090E+02, 81: 0.146980E+02, 82: 0.151980E+02, 83: 0.157080E+02, 84: 0.000000E+00, 85: 0.000000E+00, 86: 0.173340E+02, 87: 0.000000E+00, 88: 0.000000E+00, 89: 0.000000E+00, 90: 0.196920E+02, 91: 0.000000E+00, 92: 0.209470E+02, 93: 0.000000E+00, 94: 0.222630E+02} #L3-edges (keV) l3edge={ 1: 0.000000E+00, 2: 0.000000E+00, 3: 0.000000E+00, 4: 0.000000E+00, 5: 0.000000E+00, 6: 0.000000E+00, 7: 0.000000E+00, 8: 0.000000E+00, 9: 0.000000E+00, 10: 0.000000E+00, 11: 0.000000E+00, 12: 0.492000E-01, 13: 0.725000E-01, 14: 0.992000E-01, 15: 0.135000E+00, 16: 0.162500E+00, 17: 0.200000E+00, 18: 0.248400E+00, 19: 0.294600E+00, 20: 0.346200E+00, 21: 0.398700E+00, 22: 0.453800E+00, 23: 0.512100E+00, 24: 0.574100E+00, 25: 0.638700E+00, 26: 0.706800E+00, 27: 0.778100E+00, 28: 0.855000E+00, 29: 0.932000E+00, 30: 0.102100E+01, 31: 0.111500E+01, 32: 0.121800E+01, 33: 0.132500E+01, 34: 0.143600E+01, 35: 0.155000E+01, 36: 0.167500E+01, 37: 0.180500E+01, 38: 0.194000E+01, 39: 0.208000E+01, 40: 0.222300E+01, 41: 0.237100E+01, 42: 0.252000E+01, 43: 0.267700E+01, 44: 0.283800E+01, 45: 0.300300E+01, 46: 0.317300E+01, 47: 0.335100E+01, 48: 0.353700E+01, 49: 0.373000E+01, 50: 0.392900E+01, 51: 0.413200E+01, 52: 0.434100E+01, 53: 0.455700E+01, 54: 0.478100E+01, 55: 0.501200E+01, 56: 0.524700E+01, 57: 0.548300E+01, 58: 0.572400E+01, 59: 0.596500E+01, 60: 0.620800E+01, 61: 0.646000E+01, 62: 0.671700E+01, 63: 0.697700E+01, 64: 0.724300E+01, 65: 0.751500E+01, 66: 0.779000E+01, 67: 0.807100E+01, 68: 0.835800E+01, 69: 0.864800E+01, 70: 0.894300E+01, 71: 0.924400E+01, 72: 0.956100E+01, 73: 0.988100E+01, 74: 0.102040E+02, 75: 0.105340E+02, 76: 0.108710E+02, 77: 0.112150E+02, 78: 0.115640E+02, 79: 0.119180E+02, 80: 0.122840E+02, 81: 0.126570E+02, 82: 0.130350E+02, 83: 0.134180E+02, 84: 0.000000E+00, 85: 0.000000E+00, 86: 0.146120E+02, 87: 0.000000E+00, 88: 0.000000E+00, 89: 0.000000E+00, 90: 0.163000E+02, 91: 0.000000E+00, 92: 0.171670E+02, 93: 0.000000E+00, 94: 0.180530E+02} #M-edges (keV) medge={ 1: 0.000000E+00, 2: 0.000000E+00, 3: 0.000000E+00, 4: 0.000000E+00, 5: 0.000000E+00, 6: 0.000000E+00, 7: 0.000000E+00, 8: 0.000000E+00, 9: 0.000000E+00, 10: 0.000000E+00, 11: 0.000000E+00, 12: 0.000000E+00, 13: 0.000000E+00, 14: 0.000000E+00, 15: 0.000000E+00, 16: 0.170000E-01, 17: 0.170000E-01, 18: 0.270000E-01, 19: 0.340000E-01, 20: 0.440000E-01, 21: 0.540000E-01, 22: 0.590000E-01, 23: 0.670000E-01, 24: 0.740000E-01, 25: 0.840000E-01, 26: 0.940000E-01, 27: 0.101000E+00, 28: 0.113000E+00, 29: 0.120000E+00, 30: 0.139000E+00, 31: 0.158000E+00, 32: 0.181000E+00, 33: 0.206000E+00, 34: 0.232000E+00, 35: 0.257000E+00, 36: 0.288000E+00, 37: 0.322000E+00, 38: 0.358000E+00, 39: 0.395000E+00, 40: 0.431000E+00, 41: 0.468000E+00, 42: 0.505000E+00, 43: 0.544000E+00, 44: 0.585000E+00, 45: 0.627000E+00, 46: 0.670000E+00, 47: 0.717000E+00, 48: 0.770000E+00, 49: 0.825000E+00, 50: 0.884000E+00, 51: 0.944000E+00, 52: 0.100600E+01, 53: 0.107200E+01, 54: 0.114300E+01, 55: 0.121800E+01, 56: 0.129300E+01, 57: 0.136300E+01, 58: 0.143400E+01, 59: 0.150800E+01, 60: 0.157500E+01, 61: 0.165100E+01, 62: 0.172900E+01, 63: 0.180000E+01, 64: 0.188200E+01, 65: 0.196700E+01, 66: 0.204600E+01, 67: 0.212700E+01, 68: 0.221200E+01, 69: 0.230700E+01, 70: 0.239800E+01, 71: 0.249200E+01, 72: 0.260200E+01, 73: 0.270300E+01, 74: 0.281800E+01, 75: 0.293100E+01, 76: 0.305000E+01, 77: 0.317200E+01, 78: 0.329700E+01, 79: 0.342500E+01, 80: 0.356200E+01, 81: 0.370000E+01, 82: 0.385000E+01, 83: 0.399900E+01, 84: 0.000000E+00, 85: 0.000000E+00, 86: 0.447800E+01, 87: 0.000000E+00, 88: 0.000000E+00, 89: 0.000000E+00, 90: 0.518200E+01, 91: 0.000000E+00, 92: 0.554900E+01, 93: 0.000000E+00, 94: 0.591400E+01} #K alpha1 energies (keV) kalpha1={ 1: 0.000000E+00, 2: 0.000000E+00, 3: 0.000000E+00, 4: 0.000000E+00, 5: 0.000000E+00, 6: 0.000000E+00, 7: 0.000000E+00, 8: 0.000000E+00, 9: 0.000000E+00, 10: 0.000000E+00, 11: 0.104100E+01, 12: 0.125400E+01, 13: 0.148700E+01, 14: 0.174000E+01, 15: 0.201500E+01, 16: 0.230800E+01, 17: 0.262200E+01, 18: 0.295700E+01, 19: 0.331300E+01, 20: 0.369100E+01, 21: 0.409000E+01, 22: 0.451000E+01, 23: 0.495200E+01, 24: 0.541400E+01, 25: 0.589800E+01, 26: 0.640300E+01, 27: 0.693000E+01, 28: 0.747700E+01, 29: 0.804700E+01, 30: 0.863800E+01, 31: 0.925100E+01, 32: 0.988500E+01, 33: 0.105430E+02, 34: 0.112210E+02, 35: 0.119230E+02, 36: 0.126480E+02, 37: 0.133940E+02, 38: 0.141640E+02, 39: 0.149570E+02, 40: 0.157740E+02, 41: 0.166140E+02, 42: 0.174780E+02, 43: 0.184100E+02, 44: 0.192780E+02, 45: 0.202140E+02, 46: 0.211750E+02, 47: 0.221620E+02, 48: 0.231720E+02, 49: 0.242070E+02, 50: 0.252700E+02, 51: 0.263570E+02, 52: 0.274710E+02, 53: 0.286100E+02, 54: 0.298020E+02, 55: 0.309700E+02, 56: 0.321910E+02, 57: 0.334400E+02, 58: 0.347170E+02, 59: 0.360230E+02, 60: 0.373590E+02, 61: 0.386490E+02, 62: 0.401240E+02, 63: 0.415290E+02, 64: 0.429830E+02, 65: 0.444700E+02, 66: 0.459850E+02, 67: 0.475280E+02, 68: 0.490990E+02, 69: 0.507300E+02, 70: 0.523600E+02, 71: 0.540630E+02, 72: 0.557570E+02, 73: 0.575240E+02, 74: 0.593100E+02, 75: 0.611310E+02, 76: 0.629910E+02, 77: 0.648860E+02, 78: 0.668200E+02, 79: 0.687790E+02, 80: 0.708210E+02, 81: 0.728600E+02, 82: 0.749570E+02, 83: 0.770970E+02, 84: 0.000000E+00, 85: 0.000000E+00, 86: 0.838000E+02, 87: 0.000000E+00, 88: 0.000000E+00, 89: 0.000000E+00, 90: 0.933340E+02, 91: 0.000000E+00, 92: 0.984280E+02, 93: 0.000000E+00, 94: 0.103653E+03} #K beta1 energies (keV) kbeta1={ 1: 0.000000E+00, 2: 0.000000E+00, 3: 0.000000E+00, 4: 0.000000E+00, 5: 0.000000E+00, 6: 0.000000E+00, 7: 0.000000E+00, 8: 0.000000E+00, 9: 0.000000E+00, 10: 0.000000E+00, 11: 0.106700E+01, 12: 0.129700E+01, 13: 0.155300E+01, 14: 0.183200E+01, 15: 0.213600E+01, 16: 0.246400E+01, 17: 0.281500E+01, 18: 0.319200E+01, 19: 0.358900E+01, 20: 0.401200E+01, 21: 0.446000E+01, 22: 0.493100E+01, 23: 0.542700E+01, 24: 0.594600E+01, 25: 0.649000E+01, 26: 0.705700E+01, 27: 0.764900E+01, 28: 0.826400E+01, 29: 0.890400E+01, 30: 0.957100E+01, 31: 0.102630E+02, 32: 0.109810E+02, 33: 0.117250E+02, 34: 0.124950E+02, 35: 0.132900E+02, 36: 0.141120E+02, 37: 0.149600E+02, 38: 0.158340E+02, 39: 0.167360E+02, 40: 0.176660E+02, 41: 0.186210E+02, 42: 0.196070E+02, 43: 0.205850E+02, 44: 0.216550E+02, 45: 0.227210E+02, 46: 0.238160E+02, 47: 0.249420E+02, 48: 0.260930E+02, 49: 0.272740E+02, 50: 0.284830E+02, 51: 0.297230E+02, 52: 0.309930E+02, 53: 0.322920E+02, 54: 0.336440E+02, 55: 0.349840E+02, 56: 0.363760E+02, 57: 0.377990E+02, 58: 0.392550E+02, 59: 0.407460E+02, 60: 0.422690E+02, 61: 0.439450E+02, 62: 0.454000E+02, 63: 0.470270E+02, 64: 0.487180E+02, 65: 0.503910E+02, 66: 0.521780E+02, 67: 0.539340E+02, 68: 0.556900E+02, 69: 0.575760E+02, 70: 0.593520E+02, 71: 0.612820E+02, 72: 0.632090E+02, 73: 0.652100E+02, 74: 0.672330E+02, 75: 0.692980E+02, 76: 0.714040E+02, 77: 0.735490E+02, 78: 0.757360E+02, 79: 0.779680E+02, 80: 0.802580E+02, 81: 0.825580E+02, 82: 0.849220E+02, 83: 0.873350E+02, 84: 0.000000E+00, 85: 0.000000E+00, 86: 0.948770E+02, 87: 0.000000E+00, 88: 0.000000E+00, 89: 0.000000E+00, 90: 0.105592E+03, 91: 0.000000E+00, 92: 0.111289E+03, 93: 0.000000E+00, 94: 0.117146E+03} #L alpha1 energies (keV) lalpha1={ 1: 0.000000E+00, 2: 0.000000E+00, 3: 0.000000E+00, 4: 0.000000E+00, 5: 0.000000E+00, 6: 0.000000E+00, 7: 0.000000E+00, 8: 0.000000E+00, 9: 0.000000E+00, 10: 0.000000E+00, 11: 0.000000E+00, 12: 0.000000E+00, 13: 0.000000E+00, 14: 0.000000E+00, 15: 0.000000E+00, 16: 0.000000E+00, 17: 0.000000E+00, 18: 0.000000E+00, 19: 0.000000E+00, 20: 0.000000E+00, 21: 0.000000E+00, 22: 0.000000E+00, 23: 0.000000E+00, 24: 0.000000E+00, 25: 0.000000E+00, 26: 0.000000E+00, 27: 0.000000E+00, 28: 0.000000E+00, 29: 0.000000E+00, 30: 0.100900E+01, 31: 0.109600E+01, 32: 0.118600E+01, 33: 0.128200E+01, 34: 0.141900E+01, 35: 0.148000E+01, 36: 0.158700E+01, 37: 0.169400E+01, 38: 0.180600E+01, 39: 0.192200E+01, 40: 0.204200E+01, 41: 0.216600E+01, 42: 0.229300E+01, 43: 0.242400E+01, 44: 0.255800E+01, 45: 0.269600E+01, 46: 0.283800E+01, 47: 0.298400E+01, 48: 0.313300E+01, 49: 0.328700E+01, 50: 0.344400E+01, 51: 0.360500E+01, 52: 0.376900E+01, 53: 0.393700E+01, 54: 0.411100E+01, 55: 0.428600E+01, 56: 0.446700E+01, 57: 0.465100E+01, 58: 0.484000E+01, 59: 0.503400E+01, 60: 0.543100E+01, 61: 0.563600E+01, 62: 0.584600E+01, 63: 0.605900E+01, 64: 0.627500E+01, 65: 0.649500E+01, 66: 0.672000E+01, 67: 0.694800E+01, 68: 0.718100E+01, 69: 0.718100E+01, 70: 0.741400E+01, 71: 0.765400E+01, 72: 0.789800E+01, 73: 0.814500E+01, 74: 0.839600E+01, 75: 0.865100E+01, 76: 0.891000E+01, 77: 0.917300E+01, 78: 0.944100E+01, 79: 0.971100E+01, 80: 0.998700E+01, 81: 0.102660E+02, 82: 0.105490E+02, 83: 0.108360E+02, 84: 0.000000E+00, 85: 0.000000E+00, 86: 0.117240E+02, 87: 0.000000E+00, 88: 0.000000E+00, 89: 0.000000E+00, 90: 0.129660E+02, 91: 0.000000E+00, 92: 0.136130E+02, 93: 0.000000E+00, 94: 0.142790E+02} #L beta1 energies (keV) lbeta1={ 1: 0.000000E+00, 2: 0.000000E+00, 3: 0.000000E+00, 4: 0.000000E+00, 5: 0.000000E+00, 6: 0.000000E+00, 7: 0.000000E+00, 8: 0.000000E+00, 9: 0.000000E+00, 10: 0.000000E+00, 11: 0.000000E+00, 12: 0.000000E+00, 13: 0.000000E+00, 14: 0.000000E+00, 15: 0.000000E+00, 16: 0.000000E+00, 17: 0.000000E+00, 18: 0.000000E+00, 19: 0.000000E+00, 20: 0.000000E+00, 21: 0.000000E+00, 22: 0.000000E+00, 23: 0.000000E+00, 24: 0.000000E+00, 25: 0.000000E+00, 26: 0.000000E+00, 27: 0.000000E+00, 28: 0.000000E+00, 29: 0.000000E+00, 30: 0.103200E+01, 31: 0.112200E+01, 32: 0.121600E+01, 33: 0.131700E+01, 34: 0.137900E+01, 35: 0.152600E+01, 36: 0.163800E+01, 37: 0.175200E+01, 38: 0.187200E+01, 39: 0.199600E+01, 40: 0.212400E+01, 41: 0.225700E+01, 42: 0.239500E+01, 43: 0.253800E+01, 44: 0.268300E+01, 45: 0.283400E+01, 46: 0.299000E+01, 47: 0.315100E+01, 48: 0.331600E+01, 49: 0.348700E+01, 50: 0.366200E+01, 51: 0.384300E+01, 52: 0.402900E+01, 53: 0.422000E+01, 54: 0.442200E+01, 55: 0.462000E+01, 56: 0.482800E+01, 57: 0.504300E+01, 58: 0.526200E+01, 59: 0.548900E+01, 60: 0.595600E+01, 61: 0.620600E+01, 62: 0.645600E+01, 63: 0.671400E+01, 64: 0.697900E+01, 65: 0.724900E+01, 66: 0.752800E+01, 67: 0.781000E+01, 68: 0.810300E+01, 69: 0.810300E+01, 70: 0.840100E+01, 71: 0.870800E+01, 72: 0.902100E+01, 73: 0.934100E+01, 74: 0.967000E+01, 75: 0.100080E+02, 76: 0.103540E+02, 77: 0.107060E+02, 78: 0.110690E+02, 79: 0.114390E+02, 80: 0.118230E+02, 81: 0.122100E+02, 82: 0.126110E+02, 83: 0.130210E+02, 84: 0.000000E+00, 85: 0.000000E+00, 86: 0.143160E+02, 87: 0.000000E+00, 88: 0.000000E+00, 89: 0.000000E+00, 90: 0.162000E+02, 91: 0.000000E+00, 92: 0.172180E+02, 93: 0.000000E+00, 94: 0.182780E+02} #atomic weights (g/mole) atwt={ 1: 0.100800E+01, 2: 0.400300E+01, 3: 0.694000E+01, 4: 0.901200E+01, 5: 0.108110E+02, 6: 0.120100E+02, 7: 0.140080E+02, 8: 0.160000E+02, 9: 0.190000E+02, 10: 0.201830E+02, 11: 0.229970E+02, 12: 0.243200E+02, 13: 0.269700E+02, 14: 0.280860E+02, 15: 0.309750E+02, 16: 0.320660E+02, 17: 0.354570E+02, 18: 0.399440E+02, 19: 0.391020E+02, 20: 0.400800E+02, 21: 0.449600E+02, 22: 0.479000E+02, 23: 0.509420E+02, 24: 0.519960E+02, 25: 0.549400E+02, 26: 0.558500E+02, 27: 0.589330E+02, 28: 0.586900E+02, 29: 0.635400E+02, 30: 0.653800E+02, 31: 0.697200E+02, 32: 0.725900E+02, 33: 0.749200E+02, 34: 0.789600E+02, 35: 0.799200E+02, 36: 0.838000E+02, 37: 0.854800E+02, 38: 0.876200E+02, 39: 0.889050E+02, 40: 0.912200E+02, 41: 0.929060E+02, 42: 0.959500E+02, 43: 0.990000E+02, 44: 0.101070E+03, 45: 0.102910E+03, 46: 0.106400E+03, 47: 0.107880E+03, 48: 0.112410E+03, 49: 0.114820E+03, 50: 0.118690E+03, 51: 0.121760E+03, 52: 0.127600E+03, 53: 0.126910E+03, 54: 0.131300E+03, 55: 0.132910E+03, 56: 0.137360E+03, 57: 0.138920E+03, 58: 0.140130E+03, 59: 0.140920E+03, 60: 0.144270E+03, 61: 0.147000E+03, 62: 0.150350E+03, 63: 0.152000E+03, 64: 0.157260E+03, 65: 0.158930E+03, 66: 0.162510E+03, 67: 0.164940E+03, 68: 0.167270E+03, 69: 0.168940E+03, 70: 0.173040E+03, 71: 0.174990E+03, 72: 0.178500E+03, 73: 0.180950E+03, 74: 0.183920E+03, 75: 0.186200E+03, 76: 0.190200E+03, 77: 0.192200E+03, 78: 0.195090E+03, 79: 0.197200E+03, 80: 0.200610E+03, 81: 0.204390E+03, 82: 0.207210E+03, 83: 0.209000E+03, 84: 0.000000E+00, 85: 0.000000E+00, 86: 0.222000E+03, 87: 0.000000E+00, 88: 0.000000E+00, 89: 0.000000E+00, 90: 0.232000E+03, 91: 0.000000E+00, 92: 0.238070E+03, 93: 0.000000E+00, 94: 0.239100E+03} #density (g/cc) density={ 1: 0.000089E+00, 2: 0.000179E+00, 3: 0.534000E+00, 4: 0.184800E+01, 5: 0.234000E+01, 6: 0.226000E+01, 7: 0.125000E-02, 8: 0.142900E-02, 9: 0.110800E+01, 10: 0.900000E-03, 11: 0.970000E+00, 12: 0.174000E+01, 13: 0.272000E+01, 14: 0.233000E+01, 15: 0.182000E+01, 16: 0.200000E+01, 17: 0.156000E+01, 18: 0.178400E-02, 19: 0.862000E+00, 20: 0.155000E+01, 21: 0.299200E+01, 22: 0.454000E+01, 23: 0.611000E+01, 24: 0.719000E+01, 25: 0.742000E+01, 26: 0.786000E+01, 27: 0.890000E+01, 28: 0.890000E+01, 29: 0.894000E+01, 30: 0.714000E+01, 31: 0.590300E+01, 32: 0.532300E+01, 33: 0.573000E+01, 34: 0.479000E+01, 35: 0.312000E+01, 36: 0.374000E-02, 37: 0.153200E+01, 38: 0.254000E+01, 39: 0.440500E+01, 40: 0.653000E+01, 41: 0.857000E+01, 42: 0.102200E+02, 43: 0.115000E+02, 44: 0.124100E+02, 45: 0.124400E+02, 46: 0.121600E+02, 47: 0.105000E+02, 48: 0.865000E+01, 49: 0.728000E+01, 50: 0.531000E+01, 51: 0.669100E+01, 52: 0.624000E+01, 53: 0.494000E+01, 54: 0.590000E-02, 55: 0.187300E+01, 56: 0.350000E+01, 57: 0.615000E+01, 58: 0.667000E+01, 59: 0.676900E+01, 60: 0.696000E+01, 61: 0.678200E+01, 62: 0.753600E+01, 63: 0.525900E+01, 64: 0.795000E+01, 65: 0.827200E+01, 66: 0.853600E+01, 67: 0.880300E+01, 68: 0.905100E+01, 69: 0.933200E+01, 70: 0.697700E+01, 71: 0.984200E+01, 72: 0.133000E+02, 73: 0.166000E+02, 74: 0.193000E+02, 75: 0.210200E+02, 76: 0.225000E+02, 77: 0.224200E+02, 78: 0.213700E+02, 79: 0.193700E+02, 80: 0.135460E+02, 81: 0.118600E+02, 82: 0.113400E+02, 83: 0.980000E+01, 84: 0.000000E+00, 85: 0.000000E+00, 86: 0.973000E-02, 87: 0.000000E+00, 88: 0.000000E+00, 89: 0.000000E+00, 90: 0.117000E+02, 91: 0.000000E+00, 92: 0.190500E+02, 93: 0.000000E+00, 94: 0.197000E+02} #L1-edge jump (Z>27) l1jump=0.116000E+01 #L2-edge jump (Z>27) l2jump=0.141000E+01 #L3-edge jump l3jump={ 1: 0.000000E+00, 2: 0.000000E+00, 3: 0.000000E+00, 4: 0.000000E+00, 5: 0.000000E+00, 6: 0.000000E+00, 7: 0.000000E+00, 8: 0.000000E+00, 9: 0.000000E+00, 10: 0.000000E+00, 11: 0.000000E+00, 12: 0.000000E+00, 13: 0.000000E+00, 14: 0.000000E+00, 15: 0.000000E+00, 16: 0.000000E+00, 17: 0.000000E+00, 18: 0.000000E+00, 19: 0.000000E+00, 20: 0.000000E+00, 21: 0.000000E+00, 22: 0.000000E+00, 23: 0.000000E+00, 24: 0.000000E+00, 25: 0.000000E+00, 26: 0.000000E+00, 27: 0.000000E+00, 28: 0.277200E+01, 29: 0.287400E+01, 30: 0.568400E+01, 31: 0.567100E+01, 32: 0.570400E+01, 33: 0.487500E+01, 34: 0.458700E+01, 35: 0.455700E+01, 36: 0.417000E+01, 37: 0.422300E+01, 38: 0.390600E+01, 39: 0.403600E+01, 40: 0.397600E+01, 41: 0.377400E+01, 42: 0.367500E+01, 43: 0.359100E+01, 44: 0.343100E+01, 45: 0.372100E+01, 46: 0.340200E+01, 47: 0.322300E+01, 48: 0.324900E+01, 49: 0.325500E+01, 50: 0.306000E+01, 51: 0.293900E+01, 52: 0.297900E+01, 53: 0.285600E+01, 54: 0.287900E+01, 55: 0.284700E+01, 56: 0.283900E+01, 57: 0.271700E+01, 58: 0.273700E+01, 59: 0.269500E+01, 60: 0.266200E+01, 61: 0.270200E+01, 62: 0.268000E+01, 63: 0.272300E+01, 64: 0.270100E+01, 65: 0.271300E+01, 66: 0.904700E+01, 67: 0.286300E+01, 68: 0.293300E+01, 69: 0.275800E+01, 70: 0.257300E+01, 71: 0.262000E+01, 72: 0.241500E+01, 73: 0.260000E+01, 74: 0.261700E+01, 75: 0.267500E+01, 76: 0.252900E+01, 77: 0.238700E+01, 78: 0.263200E+01, 79: 0.243900E+01, 80: 0.240000E+01, 81: 0.249800E+01, 82: 0.246600E+01, 83: 0.233800E+01, 84: 0.000000E+00, 85: 0.000000E+00, 86: 0.234400E+01, 87: 0.000000E+00, 88: 0.000000E+00, 89: 0.000000E+00, 90: 0.238800E+01, 91: 0.000000E+00, 92: 0.229200E+01, 93: 0.000000E+00, 94: 0.225100E+01} #conversion factor (cm2/g) to (barnes/atom) convfac={ 1: 0.167400E+01, 2: 0.664700E+01, 3: 0.115200E+02, 4: 0.149600E+02, 5: 0.179500E+02, 6: 0.199400E+02, 7: 0.232600E+02, 8: 0.265700E+02, 9: 0.315500E+02, 10: 0.335100E+02, 11: 0.381900E+02, 12: 0.403800E+02, 13: 0.447800E+02, 14: 0.466300E+02, 15: 0.514300E+02, 16: 0.532400E+02, 17: 0.588700E+02, 18: 0.663200E+02, 19: 0.649300E+02, 20: 0.665500E+02, 21: 0.746500E+02, 22: 0.795300E+02, 23: 0.845900E+02, 24: 0.863400E+02, 25: 0.912200E+02, 26: 0.927400E+02, 27: 0.978500E+02, 28: 0.974500E+02, 29: 0.105500E+03, 30: 0.108600E+03, 31: 0.115800E+03, 32: 0.120500E+03, 33: 0.124400E+03, 34: 0.131100E+03, 35: 0.132700E+03, 36: 0.139100E+03, 37: 0.141900E+03, 38: 0.145500E+03, 39: 0.147600E+03, 40: 0.151500E+03, 41: 0.154300E+03, 42: 0.159300E+03, 43: 0.164400E+03, 44: 0.167800E+03, 45: 0.170900E+03, 46: 0.176700E+03, 47: 0.179100E+03, 48: 0.186600E+03, 49: 0.190700E+03, 50: 0.197100E+03, 51: 0.202200E+03, 52: 0.211900E+03, 53: 0.210700E+03, 54: 0.218000E+03, 55: 0.220700E+03, 56: 0.228100E+03, 57: 0.230700E+03, 58: 0.232700E+03, 59: 0.234000E+03, 60: 0.239600E+03, 61: 0.244100E+03, 62: 0.249600E+03, 63: 0.252400E+03, 64: 0.261100E+03, 65: 0.263900E+03, 66: 0.269800E+03, 67: 0.273900E+03, 68: 0.277700E+03, 69: 0.280500E+03, 70: 0.287300E+03, 71: 0.290600E+03, 72: 0.296400E+03, 73: 0.300500E+03, 74: 0.305400E+03, 75: 0.309200E+03, 76: 0.315800E+03, 77: 0.319100E+03, 78: 0.323900E+03, 79: 0.327400E+03, 80: 0.333100E+03, 81: 0.339400E+03, 82: 0.344100E+03, 83: 0.347000E+03, 84: 0.000000E+00, 85: 0.000000E+00, 86: 0.368600E+03, 87: 0.000000E+00, 88: 0.000000E+00, 89: 0.000000E+00, 90: 0.385200E+03, 91: 0.000000E+00, 92: 0.395300E+03, 93: 0.000000E+00, 94: 0.397000E+03} #K-edge fluo yield kyield={ 1: 0.000000E+00, 2: 0.000000E+00, 3: 0.000000E+00, 4: 0.000000E+00, 5: 0.170000E-02, 6: 0.280000E-02, 7: 0.520000E-02, 8: 0.830000E-02, 9: 0.130000E-01, 10: 0.180000E-01, 11: 0.230000E-01, 12: 0.300000E-01, 13: 0.390000E-01, 14: 0.500000E-01, 15: 0.630000E-01, 16: 0.780000E-01, 17: 0.970000E-01, 18: 0.118000E+00, 19: 0.140000E+00, 20: 0.163000E+00, 21: 0.188000E+00, 22: 0.214000E+00, 23: 0.243000E+00, 24: 0.275000E+00, 25: 0.308000E+00, 26: 0.340000E+00, 27: 0.373000E+00, 28: 0.406000E+00, 29: 0.440000E+00, 30: 0.474000E+00, 31: 0.507000E+00, 32: 0.535000E+00, 33: 0.562000E+00, 34: 0.589000E+00, 35: 0.618000E+00, 36: 0.643000E+00, 37: 0.667000E+00, 38: 0.690000E+00, 39: 0.710000E+00, 40: 0.730000E+00, 41: 0.747000E+00, 42: 0.765000E+00, 43: 0.780000E+00, 44: 0.794000E+00, 45: 0.808000E+00, 46: 0.820000E+00, 47: 0.831000E+00, 48: 0.843000E+00, 49: 0.853000E+00, 50: 0.862000E+00, 51: 0.870000E+00, 52: 0.877000E+00, 53: 0.884000E+00, 54: 0.891000E+00, 55: 0.897000E+00, 56: 0.902000E+00, 57: 0.907000E+00, 58: 0.912000E+00, 59: 0.917000E+00, 60: 0.921000E+00, 61: 0.925000E+00, 62: 0.929000E+00, 63: 0.932000E+00, 64: 0.935000E+00, 65: 0.938000E+00, 66: 0.941000E+00, 67: 0.944000E+00, 68: 0.947000E+00, 69: 0.949000E+00, 70: 0.951000E+00, 71: 0.953000E+00, 72: 0.955000E+00, 73: 0.957000E+00, 74: 0.958000E+00, 75: 0.959000E+00, 76: 0.961000E+00, 77: 0.962000E+00, 78: 0.963000E+00, 79: 0.964000E+00, 80: 0.965000E+00, 81: 0.966000E+00, 82: 0.967000E+00, 83: 0.968000E+00, 84: 0.968000E+00, 85: 0.969000E+00, 86: 0.969000E+00, 87: 0.970000E+00, 88: 0.970000E+00, 89: 0.971000E+00, 90: 0.971000E+00, 91: 0.972000E+00, 92: 0.972000E+00, 93: 0.973000E+00, 94: 0.973000E+00} #L1,L2,L3 fluo yields lyield={ 1 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00], 2 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00], 3 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00], 4 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00], 5 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00], 6 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00], 7 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00], 8 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00], 9 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00], 10 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00], 11 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00], 12 : [ 0.290000E-04, 0.120000E-02, 0.120000E-02], 13 : [ 0.260000E-04, 0.750000E-03, 0.750000E-03], 14 : [ 0.300000E-04, 0.370000E-03, 0.380000E-03], 15 : [ 0.390000E-04, 0.310000E-03, 0.310000E-03], 16 : [ 0.740000E-04, 0.260000E-03, 0.260000E-03], 17 : [ 0.120000E-03, 0.240000E-03, 0.240000E-03], 18 : [ 0.180000E-03, 0.220000E-03, 0.220000E-03], 19 : [ 0.240000E-03, 0.270000E-03, 0.270000E-03], 20 : [ 0.310000E-03, 0.330000E-03, 0.330000E-03], 21 : [ 0.390000E-03, 0.840000E-03, 0.840000E-03], 22 : [ 0.470000E-03, 0.150000E-02, 0.150000E-02], 23 : [ 0.580000E-03, 0.260000E-02, 0.260000E-02], 24 : [ 0.710000E-03, 0.370000E-02, 0.370000E-02], 25 : [ 0.840000E-03, 0.500000E-02, 0.500000E-02], 26 : [ 0.100000E-02, 0.630000E-02, 0.630000E-02], 27 : [ 0.120000E-02, 0.770000E-02, 0.770000E-02], 28 : [ 0.140000E-02, 0.860000E-02, 0.930000E-02], 29 : [ 0.160000E-02, 0.100000E-01, 0.110000E-01], 30 : [ 0.180000E-02, 0.110000E-01, 0.120000E-01], 31 : [ 0.210000E-02, 0.120000E-01, 0.130000E-01], 32 : [ 0.240000E-02, 0.130000E-01, 0.150000E-01], 33 : [ 0.280000E-02, 0.140000E-01, 0.160000E-01], 34 : [ 0.320000E-02, 0.160000E-01, 0.180000E-01], 35 : [ 0.360000E-02, 0.180000E-01, 0.200000E-01], 36 : [ 0.410000E-02, 0.200000E-01, 0.220000E-01], 37 : [ 0.460000E-02, 0.220000E-01, 0.240000E-01], 38 : [ 0.510000E-02, 0.240000E-01, 0.260000E-01], 39 : [ 0.590000E-02, 0.260000E-01, 0.280000E-01], 40 : [ 0.680000E-02, 0.280000E-01, 0.310000E-01], 41 : [ 0.940000E-02, 0.310000E-01, 0.340000E-01], 42 : [ 0.100000E-01, 0.340000E-01, 0.370000E-01], 43 : [ 0.110000E-01, 0.370000E-01, 0.400000E-01], 44 : [ 0.120000E-01, 0.400000E-01, 0.430000E-01], 45 : [ 0.130000E-01, 0.430000E-01, 0.460000E-01], 46 : [ 0.140000E-01, 0.470000E-01, 0.490000E-01], 47 : [ 0.160000E-01, 0.510000E-01, 0.520000E-01], 48 : [ 0.180000E-01, 0.560000E-01, 0.560000E-01], 49 : [ 0.200000E-01, 0.610000E-01, 0.600000E-01], 50 : [ 0.370000E-01, 0.650000E-01, 0.640000E-01], 51 : [ 0.390000E-01, 0.690000E-01, 0.690000E-01], 52 : [ 0.410000E-01, 0.740000E-01, 0.740000E-01], 53 : [ 0.440000E-01, 0.790000E-01, 0.790000E-01], 54 : [ 0.460000E-01, 0.830000E-01, 0.850000E-01], 55 : [ 0.490000E-01, 0.900000E-01, 0.910000E-01], 56 : [ 0.520000E-01, 0.960000E-01, 0.970000E-01], 57 : [ 0.550000E-01, 0.103000E+00, 0.104000E+00], 58 : [ 0.580000E-01, 0.110000E+00, 0.111000E+00], 59 : [ 0.610000E-01, 0.117000E+00, 0.118000E+00], 60 : [ 0.640000E-01, 0.124000E+00, 0.125000E+00], 61 : [ 0.660000E-01, 0.132000E+00, 0.132000E+00], 62 : [ 0.710000E-01, 0.140000E+00, 0.139000E+00], 63 : [ 0.750000E-01, 0.149000E+00, 0.147000E+00], 64 : [ 0.790000E-01, 0.158000E+00, 0.155000E+00], 65 : [ 0.830000E-01, 0.167000E+00, 0.164000E+00], 66 : [ 0.890000E-01, 0.178000E+00, 0.174000E+00], 67 : [ 0.940000E-01, 0.189000E+00, 0.182000E+00], 68 : [ 0.100000E+00, 0.200000E+00, 0.192000E+00], 69 : [ 0.106000E+00, 0.211000E+00, 0.201000E+00], 70 : [ 0.112000E+00, 0.222000E+00, 0.210000E+00], 71 : [ 0.120000E+00, 0.234000E+00, 0.220000E+00], 72 : [ 0.128000E+00, 0.246000E+00, 0.231000E+00], 73 : [ 0.137000E+00, 0.258000E+00, 0.243000E+00], 74 : [ 0.147000E+00, 0.270000E+00, 0.255000E+00], 75 : [ 0.144000E+00, 0.283000E+00, 0.268000E+00], 76 : [ 0.130000E+00, 0.295000E+00, 0.281000E+00], 77 : [ 0.120000E+00, 0.308000E+00, 0.294000E+00], 78 : [ 0.114000E+00, 0.321000E+00, 0.306000E+00], 79 : [ 0.107000E+00, 0.334000E+00, 0.320000E+00], 80 : [ 0.107000E+00, 0.347000E+00, 0.333000E+00], 81 : [ 0.107000E+00, 0.360000E+00, 0.347000E+00], 82 : [ 0.112000E+00, 0.373000E+00, 0.360000E+00], 83 : [ 0.117000E+00, 0.387000E+00, 0.373000E+00], 84 : [ 0.122000E+00, 0.401000E+00, 0.386000E+00], 85 : [ 0.128000E+00, 0.415000E+00, 0.399000E+00], 86 : [ 0.134000E+00, 0.429000E+00, 0.411000E+00], 87 : [ 0.139000E+00, 0.443000E+00, 0.424000E+00], 88 : [ 0.146000E+00, 0.456000E+00, 0.437000E+00], 89 : [ 0.153000E+00, 0.468000E+00, 0.450000E+00], 90 : [ 0.161000E+00, 0.479000E+00, 0.463000E+00], 91 : [ 0.162000E+00, 0.472000E+00, 0.476000E+00], 92 : [ 0.176000E+00, 0.467000E+00, 0.489000E+00], 93 : [ 0.187000E+00, 0.466000E+00, 0.502000E+00], 94 : [ 0.205000E+00, 0.464000E+00, 0.514000E+00]} #coherent scattering x-section coeff (barns/atom) xseccoh={ 1 : [-0.119075E+00, -0.937086E+00, -0.200538E+00, 0.106587E-01], 2 : [ 0.104768E+01, -0.851805E-01, -0.403527E+00, 0.269398E-01], 3 : [ 0.134366E+01, 0.181557E+00, -0.423981E+00, 0.266190E-01], 4 : [ 0.200860E+01, -0.461920E-01, -0.337018E+00, 0.186939E-01], 5 : [ 0.262862E+01, -0.207916E+00, -0.286283E+00, 0.144966E-01], 6 : [ 0.310861E+01, -0.260580E+00, -0.271974E+00, 0.135181E-01], 7 : [ 0.347760E+01, -0.215762E+00, -0.288874E+00, 0.115131E-01], 8 : [ 0.377239E+01, -0.148539E+00, -0.307124E+00, 0.167303E-01], 9 : [ 0.400716E+01, -0.560908E-01, -0.332017E+00, 0.187934E-01], 10 : [ 0.420151E+01, 0.416247E-01, -0.356754E+00, 0.207585E-01], 11 : [ 0.426374E+01, 0.134662E+00, -0.370080E+00, 0.214467E-01], 12 : [ 0.439404E+01, 0.137858E+00, -0.359540E+00, 0.202380E-01], 13 : [ 0.415995E+01, 0.140549E+00, -0.352441E+00, 0.193692E-01], 14 : [ 0.464678E+01, 0.162780E+00, -0.358563E+00, 0.196926E-01], 15 : [ 0.478525E+01, 0.168708E+00, -0.360383E+00, 0.197155E-01], 16 : [ 0.492707E+01, 0.165746E+00, -0.359424E+00, 0.195505E-01], 17 : [ 0.507222E+01, 0.149127E+00, -0.352858E+00, 0.189439E-01], 18 : [ 0.521079E+01, 0.135618E+00, -0.347214E+00, 0.184333E-01], 19 : [ 0.525587E+01, 0.188040E+00, -0.359623E+00, 0.193085E-01], 20 : [ 0.532375E+01, 0.206685E+00, -0.361664E+00, 0.193328E-01], 21 : [ 0.543942E+01, 0.200174E+00, -0.359064E+00, 0.191027E-01], 22 : [ 0.555039E+01, 0.197697E+00, -0.357694E+00, 0.189866E-01], 23 : [ 0.565514E+01, 0.199533E+00, -0.357487E+00, 0.189691E-01], 24 : [ 0.577399E+01, 0.203858E+00, -0.359699E+00, 0.192225E-01], 25 : [ 0.584604E+01, 0.213814E+00, -0.359718E+00, 0.191459E-01], 26 : [ 0.593292E+01, 0.225038E+00, -0.361748E+00, 0.193024E-01], 27 : [ 0.601478E+01, 0.237959E+00, -0.364056E+00, 0.194754E-01], 28 : [ 0.609024E+01, 0.222770E+00, -0.366568E+00, 0.196586E-01], 29 : [ 0.617739E+01, 0.273123E+00, -0.372360E+00, 0.201638E-01], 30 : [ 0.623402E+01, 0.284312E+00, -0.372143E+00, 0.200525E-01], 31 : [ 0.628298E+01, 0.291334E+00, -0.369391E+00, 0.197029E-01], 32 : [ 0.633896E+01, 0.291512E+00, -0.365643E+00, 0.192896E-01], 33 : [ 0.639750E+01, 0.288866E+00, -0.361747E+00, 0.188788E-01], 34 : [ 0.645637E+01, 0.286737E+00, -0.358794E+00, 0.185618E-01], 35 : [ 0.651444E+01, 0.286324E+00, -0.357027E+00, 0.183557E-01], 36 : [ 0.657113E+01, 0.287711E+00, -0.356311E+00, 0.182470E-01], 37 : [ 0.659750E+01, 0.302389E+00, -0.356755E+00, 0.181706E-01], 38 : [ 0.662203E+01, 0.324559E+00, -0.361651E+00, 0.184800E-01], 39 : [ 0.667096E+01, 0.325070E+00, -0.360613E+00, 0.183326E-01], 40 : [ 0.672275E+01, 0.323964E+00, -0.359463E+00, 0.181890E-01], 41 : [ 0.679013E+01, 0.311282E+00, -0.355233E+00, 0.178231E-01], 42 : [ 0.684600E+01, 0.302790E+00, -0.351131E+00, 0.174403E-01], 43 : [ 0.687599E+01, 0.326165E+00, -0.358969E+00, 0.180482E-01], 44 : [ 0.693136E+01, 0.334794E+00, -0.363497E+00, 0.184429E-01], 45 : [ 0.697547E+01, 0.346394E+00, -0.367794E+00, 0.187885E-01], 46 : [ 0.703216E+01, 0.349838E+00, -0.370099E+00, 0.189983E-01], 47 : [ 0.706446E+01, 0.363456E+00, -0.373597E+00, 0.192478E-01], 48 : [ 0.709856E+01, 0.372199E+00, -0.375345E+00, 0.193481E-01], 49 : [ 0.712708E+01, 0.382082E+00, -0.376855E+00, 0.194151E-01], 50 : [ 0.716085E+01, 0.385512E+00, -0.376481E+00, 0.193305E-01], 51 : [ 0.719665E+01, 0.385543E+00, -0.375054E+00, 0.191608E-01], 52 : [ 0.723460E+01, 0.382493E+00, -0.372715E+00, 0.189194E-01], 53 : [ 0.727415E+01, 0.377223E+00, -0.369728E+00, 0.186280E-01], 54 : [ 0.731469E+01, 0.370315E+00, -0.366280E+00, 0.183025E-01], 55 : [ 0.733490E+01, 0.376825E+00, -0.365713E+00, 0.181843E-01], 56 : [ 0.735812E+01, 0.379361E+00, -0.364099E+00, 0.179817E-01], 57 : [ 0.739532E+01, 0.369895E+00, -0.359376E+00, 0.175406E-01], 58 : [ 0.744255E+01, 0.371328E+00, -0.359642E+00, 0.175852E-01], 59 : [ 0.748347E+01, 0.368431E+00, -0.357689E+00, 0.174099E-01], 60 : [ 0.752334E+01, 0.366462E+00, -0.356048E+00, 0.172620E-01], 61 : [ 0.756222E+01, 0.365055E+00, -0.354511E+00, 0.171214E-01], 62 : [ 0.760020E+01, 0.364134E+00, -0.353086E+00, 0.169894E-01], 63 : [ 0.763711E+01, 0.363957E+00, -0.351900E+00, 0.168783E-01], 64 : [ 0.766938E+01, 0.359752E+00, -0.348899E+00, 0.165890E-01], 65 : [ 0.770798E+01, 0.365345E+00, -0.350031E+00, 0.166927E-01], 66 : [ 0.774188E+01, 0.367107E+00, -0.349433E+00, 0.166273E-01], 67 : [ 0.777470E+01, 0.369722E+00, -0.349132E+00, 0.165862E-01], 68 : [ 0.780643E+01, 0.373226E+00, -0.349147E+00, 0.165710E-01], 69 : [ 0.783711E+01, 0.377547E+00, -0.349441E+00, 0.165780E-01], 70 : [ 0.786662E+01, 0.382933E+00, -0.350126E+00, 0.166173E-01], 71 : [ 0.789137E+01, 0.386034E+00, -0.349756E+00, 0.165480E-01], 72 : [ 0.791803E+01, 0.387021E+00, -0.348881E+00, 0.164406E-01], 73 : [ 0.794534E+01, 0.387299E+00, -0.347926E+00, 0.163230E-01], 74 : [ 0.797266E+01, 0.387704E+00, -0.347155E+00, 0.162372E-01], 75 : [ 0.799940E+01, 0.388739E+00, -0.346726E+00, 0.161751E-01], 76 : [ 0.802574E+01, 0.390458E+00, -0.346658E+00, 0.161455E-01], 77 : [ 0.805150E+01, 0.393143E+00, -0.347052E+00, 0.161570E-01], 78 : [ 0.808084E+01, 0.395790E+00, -0.348032E+00, 0.162345E-01], 79 : [ 0.810524E+01, 0.400576E+00, -0.349340E+00, 0.163264E-01], 80 : [ 0.812542E+01, 0.405858E+00, -0.350329E+00, 0.163772E-01], 81 : [ 0.814399E+01, 0.408692E+00, -0.349802E+00, 0.162880E-01], 82 : [ 0.815996E+01, 0.418031E+00, -0.352330E+00, 0.164660E-01], 83 : [ 0.817489E+01, 0.427916E+00, -0.355068E+00, 0.166601E-01], 84 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 85 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 86 : [ 0.822553E+01, 0.451478E+00, -0.362056E+00, 0.171556E-01], 87 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 88 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 89 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 90 : [ 0.827843E+01, 0.479056E+00, -0.367657E+00, 0.174621E-01], 91 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 92 : [ 0.833010E+01, 0.478314E+00, -0.367250E+00, 0.174129E-01], 93 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 94 : [ 0.838174E+01, 0.477085E+00, -0.366556E+00, 0.173422E-01]} #incoherent scattering x-section coeff (barns/atom) xsecncoh={ 1 : [-0.215772E+01, 0.132685E+01, -0.305620E+00, 0.185025E-01], 2 : [-0.256357E+01, 0.202536E+01, -0.448710E+00, 0.279691E-01], 3 : [-0.108740E+01, 0.103368E+01, -0.190377E+00, 0.779955E-02], 4 : [-0.690079E+00, 0.946448E+00, -0.171142E+00, 0.651413E-02], 5 : [-0.791177E+00, 0.121611E+01, -0.239087E+00, 0.117686E-01], 6 : [-0.982878E+00, 0.146693E+01, -0.293743E+00, 0.156005E-01], 7 : [-0.123693E+01, 0.174510E+01, -0.354660E+00, 0.198705E-01], 8 : [-0.173679E+01, 0.217686E+01, -0.449050E+00, 0.264733E-01], 9 : [-0.187570E+01, 0.232016E+01, -0.475412E+00, 0.280680E-01], 10 : [-0.175510E+01, 0.224226E+01, -0.447640E+00, 0.255801E-01], 11 : [-0.967717E+00, 0.161794E+01, -0.287191E+00, 0.131526E-01], 12 : [-0.571611E+00, 0.135498E+01, -0.222491E+00, 0.830141E-02], 13 : [-0.439322E+00, 0.130867E+01, -0.211648E+00, 0.754210E-02], 14 : [-0.414971E+00, 0.134868E+01, -0.222315E+00, 0.841959E-02], 15 : [-0.476903E+00, 0.146032E+01, -0.251331E+00, 0.107202E-01], 16 : [-0.656419E+00, 0.165408E+01, -0.298623E+00, 0.142979E-01], 17 : [-0.718627E+00, 0.174294E+01, -0.319429E+00, 0.158429E-01], 18 : [-0.682105E+00, 0.174279E+01, -0.317646E+00, 0.156467E-01], 19 : [-0.344007E+00, 0.149236E+01, -0.254135E+00, 0.107684E-01], 20 : [-0.982420E-01, 0.132829E+01, -0.213747E+00, 0.773065E-02], 21 : [-0.159831E+00, 0.139055E+01, -0.225849E+00, 0.851954E-02], 22 : [-0.230573E+00, 0.145848E+01, -0.239160E+00, 0.938528E-02], 23 : [-0.308103E+00, 0.152879E+01, -0.252768E+00, 0.102571E-01], 24 : [-0.387641E+00, 0.159727E+01, -0.266240E+00, 0.111523E-01], 25 : [-0.247059E+00, 0.149722E+01, -0.238781E+00, 0.893208E-02], 26 : [-0.342379E+00, 0.157245E+01, -0.253198E+00, 0.985822E-02], 27 : [-0.428804E+00, 0.164129E+01, -0.266013E+00, 0.106512E-01], 28 : [-0.504360E+00, 0.170040E+01, -0.276443E+00, 0.112628E-01], 29 : [-0.570210E+00, 0.175042E+01, -0.284555E+00, 0.116930E-01], 30 : [-0.420535E+00, 0.163400E+01, -0.253646E+00, 0.927233E-02], 31 : [-0.358218E+00, 0.160050E+01, -0.244908E+00, 0.861898E-02], 32 : [-0.334383E+00, 0.160327E+01, -0.245555E+00, 0.871239E-02], 33 : [-0.339189E+00, 0.162535E+01, -0.250783E+00, 0.909103E-02], 34 : [-0.432927E+00, 0.172833E+01, -0.277138E+00, 0.111735E-01], 35 : [-0.448001E+00, 0.176082E+01, -0.285099E+00, 0.117865E-01], 36 : [-0.391810E+00, 0.173010E+01, -0.276824E+00, 0.111280E-01], 37 : [-0.128039E+00, 0.153044E+01, -0.227403E+00, 0.739033E-02], 38 : [ 0.799161E-01, 0.138397E+01, -0.192225E+00, 0.478611E-02], 39 : [ 0.629057E-01, 0.141577E+01, -0.199713E+00, 0.533312E-02], 40 : [ 0.366697E-01, 0.145207E+01, -0.208122E+00, 0.595139E-02], 41 : [ 0.202289E-03, 0.149347E+01, -0.217419E+00, 0.662245E-02], 42 : [-0.562860E-01, 0.155778E+01, -0.233341E+00, 0.785506E-02], 43 : [ 0.757616E-01, 0.144950E+01, -0.204890E+00, 0.564745E-02], 44 : [-0.424981E-01, 0.154639E+01, -0.226470E+00, 0.718375E-02], 45 : [-0.160399E+00, 0.164861E+01, -0.250238E+00, 0.893818E-02], 46 : [-0.267564E+00, 0.173740E+01, -0.269883E+00, 0.103248E-01], 47 : [-0.166475E+00, 0.165794E+01, -0.248740E+00, 0.866218E-02], 48 : [-0.516701E-01, 0.157426E+01, -0.227646E+00, 0.705650E-02], 49 : [-0.817283E-02, 0.155865E+01, -0.224492E+00, 0.685776E-02], 50 : [ 0.142151E-01, 0.155754E+01, -0.224736E+00, 0.691395E-02], 51 : [ 0.156362E-01, 0.157175E+01, -0.228753E+00, 0.726386E-02], 52 : [-0.407579E-01, 0.164267E+01, -0.247890E+00, 0.880567E-02], 53 : [-0.404420E-01, 0.165596E+01, -0.251067E+00, 0.904874E-02], 54 : [-0.282407E-02, 0.164039E+01, -0.247642E+00, 0.882144E-02], 55 : [ 0.184861E+00, 0.150030E+01, -0.213333E+00, 0.624264E-02], 56 : [ 0.344376E+00, 0.138742E+01, -0.186356E+00, 0.424917E-02], 57 : [ 0.409104E+00, 0.133075E+01, -0.170883E+00, 0.304111E-02], 58 : [ 0.439881E+00, 0.130925E+01, -0.164548E+00, 0.252641E-02], 59 : [ 0.449124E+00, 0.130351E+01, -0.161841E+00, 0.227394E-02], 60 : [ 0.437283E+00, 0.131370E+01, -0.162866E+00, 0.229377E-02], 61 : [ 0.405823E+00, 0.133837E+01, -0.167229E+00, 0.255570E-02], 62 : [ 0.355383E+00, 0.137733E+01, -0.174941E+00, 0.306213E-02], 63 : [ 0.280316E+00, 0.144016E+01, -0.188641E+00, 0.401226E-02], 64 : [ 0.273133E+00, 0.143842E+01, -0.186137E+00, 0.375240E-02], 65 : [ 0.257539E+00, 0.145064E+01, -0.187591E+00, 0.379932E-02], 66 : [ 0.242685E+00, 0.146266E+01, -0.189102E+00, 0.385628E-02], 67 : [ 0.228493E+00, 0.147438E+01, -0.190559E+00, 0.390903E-02], 68 : [ 0.225233E+00, 0.148545E+01, -0.191908E+00, 0.395645E-02], 69 : [ 0.202656E+00, 0.149625E+01, -0.193234E+00, 0.400233E-02], 70 : [ 0.202248E+00, 0.148804E+01, -0.189143E+00, 0.362264E-02], 71 : [ 0.197176E+00, 0.150264E+01, -0.192474E+00, 0.385751E-02], 72 : [ 0.199469E+00, 0.150233E+01, -0.191385E+00, 0.374011E-02], 73 : [ 0.196871E+00, 0.150623E+01, -0.191396E+00, 0.370889E-02], 74 : [ 0.191015E+00, 0.151240E+01, -0.191220E+00, 0.371450E-02], 75 : [ 0.189644E+00, 0.150867E+01, -0.189570E+00, 0.349584E-02], 76 : [ 0.116448E+00, 0.157615E+01, -0.205332E+00, 0.466731E-02], 77 : [ 0.719908E-01, 0.161204E+01, -0.213186E+00, 0.520497E-02], 78 : [ 0.420186E-01, 0.163611E+01, -0.217964E+00, 0.552670E-02], 79 : [ 0.156916E-01, 0.165406E+01, -0.220982E+00, 0.570751E-02], 80 : [ 0.114587E+00, 0.158076E+01, -0.202968E+00, 0.435692E-02], 81 : [ 0.147052E+00, 0.156695E+01, -0.200347E+00, 0.420901E-02], 82 : [ 0.182167E+00, 0.154661E+01, -0.195973E+00, 0.390772E-02], 83 : [ 0.189860E+00, 0.156125E+01, -0.200932E+00, 0.436768E-02], 84 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 85 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 86 : [ 0.196619E+00, 0.160080E+01, -0.213800E+00, 0.551717E-02], 87 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 88 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 89 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 90 : [ 0.170890E+00, 0.165561E+01, -0.229702E+00, 0.692516E-02], 91 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 92 : [ 0.108277E+00, 0.174158E+01, -0.254104E+00, 0.895056E-02], 93 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 94 : [ 0.388791E-01, 0.182229E+01, -0.276099E+00, 0.107392E-01]} #K post-edge fit coeffs (barns/atom) kfit={ 1 : [ 0.244964E+01, -0.334953E+01, -0.471370E-01, 0.709962E-02], 2 : [ 0.606488E+01, -0.329055E+01, -0.107256E+00, 0.144465E-01], 3 : [ 0.775370E+01, -0.281801E+01, -0.241378E+00, 0.262542E-01], 4 : [ 0.904511E+01, -0.283487E+01, -0.210021E+00, 0.229526E-01], 5 : [ 0.995057E+01, -0.274174E+01, -0.215138E+00, 0.227845E-01], 6 : [ 0.106879E+02, -0.271400E+01, -0.200530E+00, 0.207248E-01], 7 : [ 0.112765E+02, -0.265400E+01, -0.200445E+00, 0.200765E-01], 8 : [ 0.117130E+02, -0.257229E+01, -0.205893E+00, 0.199244E-01], 9 : [ 0.120963E+02, -0.244148E+01, -0.234461E+00, 0.219954E-01], 10 : [ 0.124485E+02, -0.245819E+01, -0.212591E+00, 0.196489E-01], 11 : [ 0.126777E+02, -0.224521E+01, -0.274873E+00, 0.250270E-01], 12 : [ 0.128793E+02, -0.212574E+01, -0.299392E+00, 0.267643E-01], 13 : [ 0.131738E+02, -0.218203E+01, -0.258960E+00, 0.222840E-01], 14 : [ 0.132682E+02, -0.198174E+01, -0.316950E+00, 0.273928E-01], 15 : [ 0.133735E+02, -0.186342E+01, -0.339440E+00, 0.288858E-01], 16 : [ 0.137394E+02, -0.204786E+01, -0.273259E+00, 0.229976E-01], 17 : [ 0.136188E+02, -0.171937E+01, -0.354154E+00, 0.290841E-01], 18 : [ 0.139491E+02, -0.182276E+01, -0.328827E+00, 0.274382E-01], 19 : [ 0.137976E+02, -0.154015E+01, -0.394528E+00, 0.323561E-01], 20 : [ 0.142950E+02, -0.188644E+01, -0.283647E+00, 0.226263E-01], 21 : [ 0.139664E+02, -0.140872E+01, -0.414365E+00, 0.334355E-01], 22 : [ 0.143506E+02, -0.166322E+01, -0.331539E+00, 0.262065E-01], 23 : [ 0.147601E+02, -0.188867E+01, -0.271861E+00, 0.215792E-01], 24 : [ 0.148019E+02, -0.182430E+01, -0.279116E+00, 0.217324E-01], 25 : [ 0.148965E+02, -0.179872E+01, -0.283664E+00, 0.222095E-01], 26 : [ 0.143456E+02, -0.123491E+01, -0.423491E+00, 0.321661E-01], 27 : [ 0.147047E+02, -0.138933E+01, -0.386631E+00, 0.303286E-01], 28 : [ 0.142388E+02, -0.967736E+00, -0.478070E+00, 0.366138E-01], 29 : [ 0.145808E+02, -0.118375E+01, -0.413850E+00, 0.312088E-01], 30 : [ 0.144118E+02, -0.933083E+00, -0.477357E+00, 0.362829E-01], 31 : [ 0.136182E+02, -0.318459E+00, -0.611348E+00, 0.458138E-01], 32 : [ 0.139288E+02, -0.479613E+00, -0.572897E+00, 0.431277E-01], 33 : [ 0.134722E+02, -0.773513E-01, -0.660456E+00, 0.492177E-01], 34 : [ 0.130756E+02, 0.183235E+00, -0.694264E+00, 0.502280E-01], 35 : [ 0.132273E+02, 0.137130E+00, -0.683203E+00, 0.495424E-01], 36 : [ 0.135927E+02, -0.305214E-01, -0.651340E+00, 0.477616E-01], 37 : [ 0.130204E+02, 0.382736E+00, -0.732427E+00, 0.529874E-01], 38 : [ 0.135888E+02, 0.220194E-02, -0.638940E+00, 0.460070E-01], 39 : [ 0.134674E+02, 0.191023E+00, -0.686616E+00, 0.497356E-01], 40 : [ 0.127538E+02, 0.697409E+00, -0.789307E+00, 0.564531E-01], 41 : [ 0.133843E+02, 0.281028E+00, -0.686607E+00, 0.486607E-01], 42 : [ 0.139853E+02, -0.117426E+00, -0.591094E+00, 0.417843E-01], 43 : [ 0.128214E+02, 0.751993E+00, -0.787006E+00, 0.558668E-01], 44 : [ 0.126658E+02, 0.885020E+00, -0.811144E+00, 0.573759E-01], 45 : [ 0.121760E+02, 0.119682E+01, -0.866697E+00, 0.606931E-01], 46 : [ 0.139389E+02, 0.164528E+00, -0.662117E+00, 0.476289E-01], 47 : [ 0.133926E+02, 0.441380E+00, -0.693711E+00, 0.482085E-01], 48 : [ 0.125254E+02, 0.107714E+01, -0.831424E+00, 0.579120E-01], 49 : [ 0.118198E+02, 0.145768E+01, -0.888529E+00, 0.605982E-01], 50 : [ 0.130323E+02, 0.790788E+00, -0.762349E+00, 0.527872E-01], 51 : [ 0.906990E+01, 0.328791E+01, -0.126203E+01, 0.853470E-01], 52 : [ 0.116656E+02, 0.171052E+01, -0.948281E+00, 0.653213E-01], 53 : [ 0.121075E+02, 0.143635E+01, -0.882038E+00, 0.603575E-01], 54 : [ 0.110857E+02, 0.208357E+01, -0.101209E+01, 0.690310E-01], 55 : [ 0.113750E+02, 0.194161E+01, -0.983232E+00, 0.671986E-01], 56 : [ 0.102250E+02, 0.267835E+01, -0.112648E+01, 0.762669E-01], 57 : [ 0.109780E+02, 0.223814E+01, -0.103549E+01, 0.702339E-01], 58 : [ 0.102725E+02, 0.274562E+01, -0.114174E+01, 0.774162E-01], 59 : [ 0.110156E+02, 0.222056E+01, -0.102216E+01, 0.690465E-01], 60 : [ 0.117632E+02, 0.179481E+01, -0.936661E+00, 0.635332E-01], 61 : [ 0.113864E+02, 0.205593E+01, -0.988180E+00, 0.669106E-01], 62 : [ 0.119223E+02, 0.179546E+01, -0.942902E+00, 0.644202E-01], 63 : [ 0.116168E+02, 0.197533E+01, -0.970901E+00, 0.658459E-01], 64 : [ 0.991968E+01, 0.303111E+01, -0.117520E+01, 0.786750E-01], 65 : [ 0.113818E+02, 0.214447E+01, -0.999222E+00, 0.675569E-01], 66 : [ 0.114845E+02, 0.210451E+01, -0.989870E+00, 0.669382E-01], 67 : [ 0.875203E+01, 0.371822E+01, -0.129273E+01, 0.855026E-01], 68 : [ 0.120195E+02, 0.184815E+01, -0.939582E+00, 0.638106E-01], 69 : [ 0.125613E+02, 0.157523E+01, -0.890467E+00, 0.609779E-01], 70 : [ 0.742791E+01, 0.428955E+01, -0.135167E+01, 0.866136E-01], 71 : [ 0.126387E+02, 0.155476E+01, -0.881094E+00, 0.602036E-01], 72 : [ 0.758160E+01, 0.447037E+01, -0.142808E+01, 0.939044E-01], 73 : [ 0.865271E+01, 0.373117E+01, -0.126359E+01, 0.823539E-01], 74 : [ 0.757541E+01, 0.428874E+01, -0.134998E+01, 0.865200E-01], 75 : [ 0.136944E+01, 0.779444E+01, -0.199822E+01, 0.126225E+00], 76 : [ 0.137534E+02, 0.102122E+01, -0.777126E+00, 0.538811E-01], 77 : [ 0.125506E+02, 0.163090E+01, -0.875676E+00, 0.592011E-01], 78 : [ 0.127882E+02, 0.163605E+01, -0.898523E+00, 0.618550E-01], 79 : [ 0.496352E+01, 0.579212E+01, -0.161842E+01, 0.102911E+00], 80 : [ 0.197594E+02, -0.197990E+01, -0.276981E+00, 0.268856E-01], 81 : [ 0.152879E+02, 0.273664E+00, -0.638890E+00, 0.457495E-01], 82 : [ 0.863374E+01, 0.369400E+01, -0.121312E+01, 0.774601E-01], 83 : [ 0.944293E+01, 0.344965E+01, -0.119886E+01, 0.783484E-01], 84 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 85 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 86 : [ 0.151782E+02, 0.349020E+00, -0.637638E+00, 0.451377E-01], 87 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 88 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 89 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 90 : [ 0.134336E+02, 0.134805E+01, -0.813280E+00, 0.555664E-01], 91 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 92 : [ 0.137951E+02, 0.123983E+01, -0.801545E+00, 0.553596E-01], 93 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 94 : [ 0.182787E+02, -0.117371E+01, -0.368344E+00, 0.298738E-01]} #L post-edge fit coeffs (barns/atom) lfit={ 1 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 2 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 3 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 4 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 5 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 6 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 7 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 8 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 9 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 10 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 11 : [ 0.102355E+02, -0.255905E+01, -0.119524E+00, 0.000000E+00], 12 : [ 0.105973E+02, -0.289818E+01, 0.234506E+00, 0.000000E+00], 13 : [ 0.108711E+02, -0.277860E+01, 0.175853E+00, 0.000000E+00], 14 : [ 0.112237E+02, -0.273694E+01, 0.127557E+00, 0.000000E+00], 15 : [ 0.115508E+02, -0.292200E+01, 0.254262E+00, 0.000000E+00], 16 : [ 0.118181E+02, -0.264618E+01, -0.968049E-01, 0.000000E+00], 17 : [ 0.120031E+02, -0.241694E+01, -0.240897E+00, 0.000000E+00], 18 : [ 0.122960E+02, -0.263279E+01, -0.736600E-01, 0.000000E+00], 19 : [ 0.124878E+02, -0.253656E+01, -0.104892E+00, 0.000000E+00], 20 : [ 0.127044E+02, -0.255011E+01, -0.943195E-01, 0.000000E+00], 21 : [ 0.128949E+02, -0.240609E+01, -0.177791E+00, 0.000000E+00], 22 : [ 0.131075E+02, -0.253576E+01, -0.957177E-01, 0.000000E+00], 23 : [ 0.132514E+02, -0.249765E+01, -0.106383E+00, 0.000000E+00], 24 : [ 0.134236E+02, -0.251532E+01, -0.101999E+00, 0.000000E+00], 25 : [ 0.135761E+02, -0.249761E+01, -0.105493E+00, 0.000000E+00], 26 : [ 0.136696E+02, -0.239195E+01, -0.137680E+00, 0.000000E+00], 27 : [ 0.138699E+02, -0.250669E+01, -0.869945E-01, 0.000000E+00], 28 : [ 0.139848E+02, -0.248080E+01, -0.888115E-01, 0.000000E+00], 29 : [ 0.142439E+02, -0.258677E+01, -0.667398E-01, 0.000000E+00], 30 : [ 0.143221E+02, -0.262384E+01, -0.264926E-01, 0.000000E+00], 31 : [ 0.144792E+02, -0.254469E+01, -0.757204E-01, 0.000000E+00], 32 : [ 0.146813E+02, -0.269285E+01, -0.208355E-01, 0.000000E+00], 33 : [ 0.146431E+02, -0.248397E+01, -0.796180E-01, 0.000000E+00], 34 : [ 0.147048E+02, -0.238853E+01, -0.105877E+00, 0.000000E+00], 35 : [ 0.148136E+02, -0.242347E+01, -0.914590E-01, 0.000000E+00], 36 : [ 0.149190E+02, -0.242418E+01, -0.876447E-01, 0.000000E+00], 37 : [ 0.149985E+02, -0.239108E+01, -0.959473E-01, 0.000000E+00], 38 : [ 0.150114E+02, -0.228169E+01, -0.126485E+00, 0.000000E+00], 39 : [ 0.151822E+02, -0.238946E+01, -0.881174E-01, 0.000000E+00], 40 : [ 0.152906E+02, -0.238703E+01, -0.912292E-01, 0.000000E+00], 41 : [ 0.152088E+02, -0.220278E+01, -0.136759E+00, 0.000000E+00], 42 : [ 0.153494E+02, -0.226640E+01, -0.116881E+00, 0.000000E+00], 43 : [ 0.155086E+02, -0.233733E+01, -0.987857E-01, 0.000000E+00], 44 : [ 0.154734E+02, -0.223080E+01, -0.119454E+00, 0.000000E+00], 45 : [ 0.155757E+02, -0.224976E+01, -0.113377E+00, 0.000000E+00], 46 : [ 0.155649E+02, -0.217229E+01, -0.127652E+00, 0.000000E+00], 47 : [ 0.156869E+02, -0.222636E+01, -0.112223E+00, 0.000000E+00], 48 : [ 0.159668E+02, -0.238363E+01, -0.801104E-01, 0.000000E+00], 49 : [ 0.162101E+02, -0.251838E+01, -0.540061E-01, 0.000000E+00], 50 : [ 0.158638E+02, -0.219019E+01, -0.113539E+00, 0.000000E+00], 51 : [ 0.157557E+02, -0.204460E+01, -0.140745E+00, 0.000000E+00], 52 : [ 0.161087E+02, -0.227876E+01, -0.929405E-01, 0.000000E+00], 53 : [ 0.164086E+02, -0.248214E+01, -0.507179E-01, 0.000000E+00], 54 : [ 0.163098E+02, -0.231679E+01, -0.854498E-01, 0.000000E+00], 55 : [ 0.165418E+02, -0.246363E+01, -0.542849E-01, 0.000000E+00], 56 : [ 0.166217E+02, -0.248972E+01, -0.449623E-01, 0.000000E+00], 57 : [ 0.163134E+02, -0.220156E+01, -0.980569E-01, 0.000000E+00], 58 : [ 0.165862E+02, -0.236288E+01, -0.654708E-01, 0.000000E+00], 59 : [ 0.167118E+02, -0.240326E+01, -0.612619E-01, 0.000000E+00], 60 : [ 0.165964E+02, -0.226007E+01, -0.872426E-01, 0.000000E+00], 61 : [ 0.168337E+02, -0.238810E+01, -0.645041E-01, 0.000000E+00], 62 : [ 0.168725E+02, -0.239051E+01, -0.601080E-01, 0.000000E+00], 63 : [ 0.170692E+02, -0.248046E+01, -0.447055E-01, 0.000000E+00], 64 : [ 0.171159E+02, -0.247838E+01, -0.437107E-01, 0.000000E+00], 65 : [ 0.171499E+02, -0.245507E+01, -0.471370E-01, 0.000000E+00], 66 : [ 0.173446E+02, -0.254821E+01, -0.317606E-01, 0.000000E+00], 67 : [ 0.176583E+02, -0.272523E+01, -0.819409E-03, 0.000000E+00], 68 : [ 0.177988E+02, -0.274671E+01, -0.287580E-02, 0.000000E+00], 69 : [ 0.174250E+02, -0.251103E+01, -0.329450E-01, 0.000000E+00], 70 : [ 0.169795E+02, -0.222577E+01, -0.732557E-01, 0.000000E+00], 71 : [ 0.172638E+02, -0.237189E+01, -0.495994E-01, 0.000000E+00], 72 : [ 0.164329E+02, -0.182851E+01, -0.132268E+00, 0.000000E+00], 73 : [ 0.172411E+02, -0.230313E+01, -0.591006E-01, 0.000000E+00], 74 : [ 0.172533E+02, -0.223874E+01, -0.727338E-01, 0.000000E+00], 75 : [ 0.178750E+02, -0.261051E+01, -0.136093E-01, 0.000000E+00], 76 : [ 0.173525E+02, -0.228550E+01, -0.588047E-01, 0.000000E+00], 77 : [ 0.165270E+02, -0.176315E+01, -0.135232E+00, 0.000000E+00], 78 : [ 0.173636E+02, -0.221120E+01, -0.730934E-01, 0.000000E+00], 79 : [ 0.174240E+02, -0.223911E+01, -0.663720E-01, 0.000000E+00], 80 : [ 0.171857E+02, -0.208470E+01, -0.853294E-01, 0.000000E+00], 81 : [ 0.177379E+02, -0.237745E+01, -0.433223E-01, 0.000000E+00], 82 : [ 0.177963E+02, -0.237691E+01, -0.455883E-01, 0.000000E+00], 83 : [ 0.175348E+02, -0.223353E+01, -0.596161E-01, 0.000000E+00], 84 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 85 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 86 : [ 0.175028E+02, -0.214876E+01, -0.724638E-01, 0.000000E+00], 87 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 88 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 89 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 90 : [ 0.185481E+02, -0.261281E+01, -0.790574E-02, 0.000000E+00], 91 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 92 : [ 0.175258E+02, -0.207237E+06, -0.723932E-01, 0.000000E+00], 93 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 94 : [ 0.175519E+02, -0.202162E+01, -0.822940E-01, 0.000000E+00]} #M post-edge fit coeffs (barns/atom) mfit={ 1 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 2 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 3 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 4 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 5 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 6 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 7 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 8 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 9 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 10 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 11 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 12 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 13 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 14 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 15 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 16 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 17 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 18 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 19 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 20 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 21 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 22 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 23 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 24 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 25 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 26 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 27 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 28 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 29 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 30 : [ 0.120597E+02, -0.110258E+01, 0.000000E+00, 0.000000E+00], 31 : [ 0.122646E+02, -0.268965E+01, 0.000000E+00, 0.000000E+00], 32 : [ 0.124133E+02, -0.253085E+01, 0.000000E+00, 0.000000E+00], 33 : [ 0.125392E+02, -0.241380E+01, 0.000000E+00, 0.000000E+00], 34 : [ 0.126773E+02, -0.239750E+01, 0.000000E+00, 0.000000E+00], 35 : [ 0.127612E+02, -0.237730E+01, 0.000000E+00, 0.000000E+00], 36 : [ 0.128898E+02, -0.226021E+01, 0.000000E+00, 0.000000E+00], 37 : [ 0.130286E+02, -0.238693E+01, 0.000000E+00, 0.000000E+00], 38 : [ 0.131565E+02, -0.236655E+01, 0.000000E+00, 0.000000E+00], 39 : [ 0.132775E+02, -0.243174E+01, 0.000000E+00, 0.000000E+00], 40 : [ 0.134508E+02, -0.250201E+01, 0.000000E+00, 0.000000E+00], 41 : [ 0.135434E+02, -0.250135E+01, 0.000000E+00, 0.000000E+00], 42 : [ 0.136568E+02, -0.248480E+01, 0.000000E+00, 0.000000E+00], 43 : [ 0.137498E+02, -0.244730E+01, 0.000000E+00, 0.000000E+00], 44 : [ 0.138782E+02, -0.248066E+01, 0.000000E+00, 0.000000E+00], 45 : [ 0.140312E+02, -0.261303E+01, 0.000000E+00, 0.000000E+00], 46 : [ 0.141392E+02, -0.257206E+01, 0.000000E+00, 0.000000E+00], 47 : [ 0.141673E+02, -0.248078E+01, 0.000000E+00, 0.000000E+00], 48 : [ 0.143497E+02, -0.252756E+01, 0.000000E+00, 0.000000E+00], 49 : [ 0.144115E+02, -0.249401E+01, 0.000000E+00, 0.000000E+00], 50 : [ 0.145572E+02, -0.256792E+01, 0.000000E+00, 0.000000E+00], 51 : [ 0.146268E+02, -0.255562E+01, 0.000000E+00, 0.000000E+00], 52 : [ 0.147125E+02, -0.254324E+01, 0.000000E+00, 0.000000E+00], 53 : [ 0.147496E+02, -0.248179E+01, 0.000000E+00, 0.000000E+00], 54 : [ 0.147603E+02, -0.245068E+01, 0.000000E+00, 0.000000E+00], 55 : [ 0.149713E+02, -0.253145E+01, 0.000000E+00, 0.000000E+00], 56 : [ 0.150844E+02, -0.256341E+01, 0.000000E+00, 0.000000E+00], 57 : [ 0.151863E+02, -0.258287E+01, 0.000000E+00, 0.000000E+00], 58 : [ 0.152693E+02, -0.258174E+01, 0.000000E+00, 0.000000E+00], 59 : [ 0.153379E+02, -0.257086E+01, 0.000000E+00, 0.000000E+00], 60 : [ 0.154335E+02, -0.259006E+01, 0.000000E+00, 0.000000E+00], 61 : [ 0.155131E+02, -0.259623E+01, 0.000000E+00, 0.000000E+00], 62 : [ 0.156000E+02, -0.261328E+01, 0.000000E+00, 0.000000E+00], 63 : [ 0.157063E+02, -0.263481E+01, 0.000000E+00, 0.000000E+00], 64 : [ 0.157159E+02, -0.260843E+01, 0.000000E+00, 0.000000E+00], 65 : [ 0.158412E+02, -0.264040E+01, 0.000000E+00, 0.000000E+00], 66 : [ 0.159225E+02, -0.265289E+01, 0.000000E+00, 0.000000E+00], 67 : [ 0.160140E+02, -0.267903E+01, 0.000000E+00, 0.000000E+00], 68 : [ 0.160672E+02, -0.267580E+01, 0.000000E+00, 0.000000E+00], 69 : [ 0.161269E+02, -0.267886E+01, 0.000000E+00, 0.000000E+00], 70 : [ 0.161794E+02, -0.267715E+01, 0.000000E+00, 0.000000E+00], 71 : [ 0.162289E+02, -0.267128E+01, 0.000000E+00, 0.000000E+00], 72 : [ 0.162758E+02, -0.266220E+01, 0.000000E+00, 0.000000E+00], 73 : [ 0.163038E+02, -0.266148E+01, 0.000000E+00, 0.000000E+00], 74 : [ 0.162613E+02, -0.260672E+01, 0.000000E+00, 0.000000E+00], 75 : [ 0.163564E+02, -0.262453E+01, 0.000000E+00, 0.000000E+00], 76 : [ 0.164233E+02, -0.263163E+01, 0.000000E+00, 0.000000E+00], 77 : [ 0.165144E+02, -0.264832E+01, 0.000000E+00, 0.000000E+00], 78 : [ 0.167024E+02, -0.271631E+01, 0.000000E+00, 0.000000E+00], 79 : [ 0.164734E+02, -0.257834E+01, 0.000000E+00, 0.000000E+00], 80 : [ 0.165903E+02, -0.260670E+01, 0.000000E+00, 0.000000E+00], 81 : [ 0.166564E+02, -0.261593E+01, 0.000000E+00, 0.000000E+00], 82 : [ 0.167131E+02, -0.261538E+01, 0.000000E+00, 0.000000E+00], 83 : [ 0.167078E+02, -0.258648E+01, 0.000000E+00, 0.000000E+00], 84 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 85 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 86 : [ 0.169000E+02, -0.260945E+01, 0.000000E+00, 0.000000E+00], 87 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 88 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 89 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 90 : [ 0.170483E+02, -0.258569E+01, 0.000000E+00, 0.000000E+00], 91 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 92 : [ 0.170353E+02, -0.256903E+01, 0.000000E+00, 0.000000E+00], 93 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 94 : [ 0.172953E+02, -0.262164E+01, 0.000000E+00, 0.000000E+00]} #N post-edge fit coeffs (barns/atom) nfit={ 1 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 2 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 3 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 4 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 5 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 6 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 7 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 8 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 9 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 10 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 11 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 12 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 13 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 14 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 15 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 16 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 17 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 18 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 19 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 20 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 21 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 22 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 23 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 24 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 25 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 26 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 27 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 28 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 29 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 30 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 31 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 32 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 33 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 34 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 35 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 36 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 37 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 38 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 39 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 40 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 41 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 42 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 43 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 44 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 45 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 46 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 47 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 48 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 49 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 50 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 51 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 52 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 53 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 54 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 55 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 56 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 57 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 58 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 59 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 60 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 61 : [ 0.155131E+02, -0.259623E+01, 0.000000E+00, 0.000000E+00], 62 : [ 0.156006E+02, -0.261328E+01, 0.000000E+00, 0.000000E+00], 63 : [ 0.157063E+02, -0.263481E+01, 0.000000E+00, 0.000000E+00], 64 : [ 0.157159E+02, -0.260843E+01, 0.000000E+00, 0.000000E+00], 65 : [ 0.158415E+02, -0.264040E+01, 0.000000E+00, 0.000000E+00], 66 : [ 0.159225E+02, -0.265289E+01, 0.000000E+00, 0.000000E+00], 67 : [ 0.160140E+02, -0.267903E+01, 0.000000E+00, 0.000000E+00], 68 : [ 0.160672E+02, -0.267580E+01, 0.000000E+00, 0.000000E+00], 69 : [ 0.161269E+02, -0.267886E+01, 0.000000E+00, 0.000000E+00], 70 : [ 0.139111E+02, -0.240380E+01, 0.000000E+00, 0.000000E+00], 71 : [ 0.139813E+02, -0.240841E+01, 0.000000E+00, 0.000000E+00], 72 : [ 0.140548E+02, -0.242829E+01, 0.000000E+00, 0.000000E+00], 73 : [ 0.141313E+02, -0.247214E+01, 0.000000E+00, 0.000000E+00], 74 : [ 0.141536E+02, -0.232580E+01, 0.000000E+00, 0.000000E+00], 75 : [ 0.142392E+02, -0.235326E+01, 0.000000E+00, 0.000000E+00], 76 : [ 0.142795E+02, -0.221971E+01, 0.000000E+00, 0.000000E+00], 77 : [ 0.143422E+02, -0.240183E+01, 0.000000E+00, 0.000000E+00], 78 : [ 0.143785E+02, -0.234834E+01, 0.000000E+00, 0.000000E+00], 79 : [ 0.144398E+02, -0.232838E+01, 0.000000E+00, 0.000000E+00], 80 : [ 0.145195E+02, -0.233016E+01, 0.000000E+00, 0.000000E+00], 81 : [ 0.145473E+02, -0.226773E+01, 0.000000E+00, 0.000000E+00], 82 : [ 0.145771E+02, -0.225279E+01, 0.000000E+00, 0.000000E+00], 83 : [ 0.146832E+02, -0.230940E+01, 0.000000E+00, 0.000000E+00], 84 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 85 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 86 : [ 0.147243E+02, -0.212905E+01, 0.000000E+00, 0.000000E+00], 87 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 88 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 89 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 90 : [ 0.147730E+02, -0.191192E+01, 0.000000E+00, 0.000000E+00], 91 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 92 : [ 0.149036E+02, -0.212148E+01, 0.000000E+00, 0.000000E+00], 93 : [ 0.000000E+00, 0.000000E+00, 0.000000E+00, 0.000000E+00], 94 : [ 0.148535E+02, -0.187733E+01, 0.000000E+00, 0.000000E+00]} ############################################################################# ## ## END OF DATA SECTION ## ############################################################################# from string import * from math import * def name_z(name): #given an element name, return the atomic number #chop to first two characters and proper capitalization if len(name)==1: name=upper(name) else: name=upper(name[0])+lower(name[1]) try: z=esym.index(name) return z+1 except: return 0 def mcmaster(ephot,fit): #given a photon energy and the fit coefficients, calculaate the McMaster x-section xsec=0 #need special handling for ephot=1 if float(ephot)==1.0: log_e=1 else: log_e=log(ephot) i=0 for c in fit: xsec=xsec+c*pow(log_e,i) i=i+1 xsec=exp(xsec) return xsec def mucal(name='ZZ',Z=200,ephot=0,unit='b'): #given an element name and photon energy, calculate the x-ray data #see top of file for full documentation # [err,energy,xsec,fl_yield,errmsg] = mucal(element, Z, e_phot, unit) errmsg='0' err=0 ZZ=Z Z=0 shell=0 #init returns energy=[0,0,0,0,0,0,0,0,0] xsec=[0,0,0,0,0,0,0,0,0,0,0,0] fl_yield=[0,0,0,0] #check to make sure name or Z given as inputs if name=='ZZ' and ZZ==200: errmsg='ERROR mucal: no shirt/name, no shoes/Z, no service' print errmsg return [1,energy,xsec,fl_yield,errmsg] #make sure ZZ is non-negative if ZZ<0: errmsg='ERROR mucal: Z must be non-negative' print errmsg return [1,energy,xsec,fl_yield,errmsg] #determine material Z, if needed if name!='ZZ': Z=name_z(name) #name and ZZ must be consistent if both given! if ZZ!=200 and Z!=ZZ: errmsg='ERROR mucal: Z and element name are not consistent' print errmsg return [1,energy,xsec,fl_yield,errmsg] ZZ=Z Z=ZZ #make sure material is available if (Z==85 or Z==85 or Z==87 or Z==88 or Z==89 or Z==91 or Z==93): errmsg='ERROR mucal: no data is avaialble for Po, At, Fr, Ra, Ac, Pa, Np' print errmsg return [1,energy,xsec,fl_yield,errmsg] #Z must be less than Zmax if Z>Zmax: errmsg='ERROR mucal: no data for Z>'+str(Zmax) print errmsg return [1,energy,xsec,fl_yield,errmsg] #must be a valid element symbol if not Z: errmsg='ERROR mucal: invalid element name '+name print errmsg return [1,energy,xsec,fl_yield,errmsg] #OK, inout is all good... #get name if needed if name=='ZZ': name=esym[Z-1] #make sure energy is positive if ephot<0: errmsg='ERROR mucal: photon energy must be non-negative' print errmsg return [1,energy,xsec,fl_yield,errmsg] #put the energy independent parts of the return arrays together energy[0] = kedge[Z] energy[1] = l1edge[Z] energy[2] = l2edge[Z] energy[3] = l3edge[Z] energy[4] = medge[Z] energy[5] = kalpha1[Z] energy[6] = kbeta1[Z] energy[7] = lalpha1[Z] energy[8] = lbeta1[Z] xsec[0] = 0.0 #/* photo */ xsec[1] = 0.0 #/* coherent */ xsec[2] = 0.0 #/* incoherent */ xsec[3] = 0.0 #/* total */ xsec[4] = 0.0 #/* conversion factor */ xsec[5] = 0.0 #/* absorption coef */ xsec[11]= 0.0 # total xsec not including current edge ala Booth xsec[6] = atwt[Z] xsec[7] = density[Z] if (Z>27): xsec[8] = l1jump xsec[9] = l2jump else: xsec[8] = 0.0 xsec[9] = 0.0 xsec[10]=l3jump[Z] fl_yield[0] = kyield[Z] fl_yield[1] = lyield[Z][0] fl_yield[2] = lyield[Z][1] fl_yield[3] = lyield[Z][2] #if ephot=0, return physical constants only if ephot==0: return [0,energy,xsec,fl_yield,errmsg] #energy dependent section #check for middle of edge input if ((abs(kedge[Z]-ephot)<=0.001) or (abs(l1edge[Z]-ephot)<=0.001) or (abs(l2edge[Z]-ephot)<=0.001) or (abs(l3edge[Z]-ephot)<=0.001) or (abs(medge[Z]-ephot)<=0.001)): errmsg='ERROR mucal: photon energy is within 1 eV of edge \nfit results may be inaccurate\n\n' print errmsg err=2 #determine shell being ionized if ephot>=kedge[Z]: #K-edge shell=1 elif ephot>=l3edge[Z]: #L-edge shell=2 elif ephot>=medge[Z]: #M1-subshell shell=3 else: #all the rest shell=4 #calculate photo-absorption barns/atom x-section if shell==1: barn_photo=mcmaster(ephot,kfit[Z]) if shell==2: barn_photo=mcmaster(ephot,lfit[Z]) if ephot>=l1edge[Z]: #above L1, no correction pass elif ephot>=l2edge[Z]: #between L1 and L2 barn_photo=barn_photo/l1jump elif ephot>=l3edge[Z]: #between L2 and L3 barn_photo=barn_photo/(l1jump+l2jump) if shell==3: barn_photo=mcmaster(ephot,mfit[Z]) if shell==4: barn_photo=mcmaster(ephot,nfit[Z]) xshell=shell+1 #calculate photo-absorption for all but current edge if xshell==2: barn_pnox=mcmaster(ephot,lfit[Z]) if xshell==3: barn_pnox=mcmaster(ephot,mfit[Z]) if xshell==4: barn_pnox=mcmaster(ephot,nfit[Z]) if xshell==5: barn_pnox=mcmaster(ephot,nfit[Z]) #print shell,barn_pnox,barn_photo #M edges for Z<30 are unreliable if shell>2 and Z<30: errmsg2='ERROR mucal: McMaster et al. use L-edge fits for the M edges for Z<30\nWARNING: results may be inaccurate\n\n' print errmsg2 errmsg=errmsg+errmsg2 err=err+4 #calculate coherent, incoherent x-sections and total barn_coh = mcmaster(ephot, xseccoh[Z]) barn_ncoh = mcmaster(ephot, xsecncoh[Z]) barn_tot = barn_photo + barn_coh + barn_ncoh barn_11 = barn_pnox + barn_coh + barn_ncoh # #stuff xsec array with the barnes/atom data xsec[0] = barn_photo xsec[1] = barn_coh xsec[2] = barn_ncoh xsec[3] = barn_tot xsec[11]= barn_11 xsec[4] = convfac[Z] #/* conversion factor */ xsec[5] = barn_tot * density[Z] / convfac[Z] #/* absorption coef */ #convert to cm**2/g if needed if upper(unit)=='C': for i in range(4): xsec[i]=xsec[i]/xsec[4] xsec[11]=xsec[11]/xsec[4] #ALL DONE! WOO-HOO return [err,energy,xsec,fl_yield,errmsg] #tests #[a,b,c,d,e]=mucal(name='S',ephot=3.0,unit='C') #print a #print b #print c #print d sixpack-0.68/atomic_sub.py0000666000175000017500000002462107750541010014614 0ustar segresegrefrom string import * from math import * ####################################### ## ## Subroutines for Corwin's Self Abs Corrections ## ###################################### ## these routines correspond to the atomic_sub.F routines ## FUNCTION sym2Z ## USAGE: ## Z=sym2Z(sym) ## ## given two chacacter sym, returns Z (atomic number). ## Only has first 103 elements of periodic table. ## Returns -1 if element not found ## ## def sym2Z(sym): esym=[ "H" , "He", "Li", "Be", "B" , "C" , "N" , "O" , "F" , "Ne", "Na", "Mg", "Al", "Si", "P" , "S" , "Cl", "Ar", "K" , "Ca", "Sc", "Ti", "V" , "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y" , "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I" , "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W" , "Re", "Os", "Ir", "Pt", "Au", "Hd", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U" , "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lw"] if len(sym)>1 and sym[1]==' ': sym=sym[0] try: i=esym.index(sym) i=i+1 except: i=-1 return i ## FUNCTION Z2sym ## USAGE: ## sym=Z2sym(Z) ## ## given two chacacter sym, returns Z (atomic number). ## Only has first 103 elements of periodic table. ## Returns -1 if element not found def Z2sym(Z): esym=[ "H" , "He", "Li", "Be", "B" , "C" , "N" , "O" , "F" , "Ne", "Na", "Mg", "Al", "Si", "P" , "S" , "Cl", "Ar", "K" , "Ca", "Sc", "Ti", "V" , "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y" , "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I" , "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W" , "Re", "Os", "Ir", "Pt", "Au", "Hd", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U" , "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lw"] if 1<=Z<104: Z=int(Z) i=esym[Z-1] else: i=-1 return i ## FUNCTION get_enot ## USAGE: ## e_not=get_e_not(Z,edge_code) ## Given Z and edge, returns Eo. Values for K-edge are from ## Teo's "EXAFS: Basic Principles and Data Analysis." Other ## edges are from the X-Ray Data Book. ## oxygen edge adjusted a la Corwin Booth def get_e_not(Z,edge_code): K_e_not=[13.6,25,55,112,192,283,399,533.4,687,867,1072, 1305,1559,1838,2142,2472,2822,3202,3607,4038, 4496,4965,5465,5989,6540,7112,7709,8333,8979, 9659,10368,11104,11868,12658,13474,14322,15201, 16105,17037,17998,18986,20002,21054,22118,23224, 24350,25514,26711,27940,29200,30491,31813,33169, 34582,35959,37441,38925,40449,41998,43571,45207, 46835,48515,50240,51996,53789,55615,57483,59390, 61332,63304,65351,67414,69524,71662,73860,76112, 78395,80723,83103,85528,88006,90527,93112,95740, 98418,191147,103927,106759,109649,112581,115603, 118619,121760,124876,128088,131357,134683] LI_e_not=[0,0,0,0,0,0,37.3,41.6,0,48.5,63.5,88.6,117.8, 149.7,189,2309,270,326.3,378.6,438.4,498.0, 560.9,626.7,695.7,769.1,844.6,925.1,1008.6, 1096.7,1196.2,1299.0,1414.6,1527.0,1652.0, 1782,1921,2065,2216,2373,2532,2698,2866,3043, 3224,3412,3604,3806,4018,4238,4465,4698,4939, 5188,5453,5714,5989,6266,6548,6835,7126,7428, 7737,8052,7376,7808,9046,9394,9751,10116, 10486,10870,11271,11682,12100,12527,12968,13419, 13880,14353,14839,15347,15861,16388,16939,17493, 18049,18639,19237,19840,20472,21105,21757,0,0,0, 0,0,0] LII_e_not=[0,0,0,0,0,0,0,0,0,21.7,30.4,49.6,72.9,99.8,136, 163.6,202,250.6,297.6,349.7,403.6,461.2,519.8, 583.8,649.9,719.9,793.3,870.0,952.3,1044.9,1143.2, 1248.1,1359.1,1474.3,1596,1730.9,1864,2007,2156, 2307,2465,2625,2793,2967,3146,3330,3524,3727,3938, 4156,4380,4612,4852,5104,5359,5624,5891,6164,6440, 6722,7013,7312,7617,7930,8252,8581,8918,9264,9617, 9978,10349,10739,11136,11544,11959,12385,12824, 13273,13734,14209,14698,15200,15711,16244,16785, 17337,17907,18484,19083,19693,20314,20948,21625,22263.,0,0, 0,0] LIII_e_not=[0,0,0,0,0,0,0,0,0,21.6,30.5,49.2,72.5,99.2,135, 162.5,200,248.4,294.6,346.2,398.7,453.8,512.1, 574.1,628.7,706.8,778.1,852.7,932.5,1021.8,1116.4, 1217.0,1323.6,1433.9,1550,1678.4,1804,1940,2080, 2223,2371,2520,2677,2838,3004,3173,3351,3538,3730, 3929,4132,4341,4557,4782,5012,5247,5483,5723,5964, 6208,6459,6716,6977,7243,7514,7790,8071,8358,8648, 8944,9244,9561,9881,10207,10535,10871,11215,11564, 11919,12284,12658,13055,13419,13814,14214,14619, 15031,15444,15871,16300,16733,17166,17700,18053,0,0,0,0] if(Z<=98): if(edge_code==0): e_not=K_e_not[Z-1] if(edge_code==1): e_not=LI_e_not[Z-1] if(edge_code==2): e_not=LII_e_not[Z-1] if(edge_code==3): e_not=LIII_e_not[Z-1] return e_not ## FUNCTION get_fl ## USAGE: ## energy=get_fl(Z,edge_code) ## Given Z and edge, returns fluorescent energy. def get_fl(Z,edge_code): #data in keV from mucal K_e=[0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00, 0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00, 0.104100E+01,0.125400E+01,0.148700E+01,0.174000E+01,0.201500E+01, 0.230800E+01,0.262200E+01,0.295700E+01,0.331300E+01,0.369100E+01, 0.409000E+01,0.451000E+01,0.495200E+01,0.541400E+01,0.589800E+01, 0.640300E+01,0.693000E+01,0.747700E+01,0.804700E+01,0.863800E+01, 0.925100E+01,0.988500E+01,0.105430E+02,0.112210E+02,0.119230E+02, 0.126480E+02,0.133940E+02,0.141640E+02,0.149570E+02,0.157740E+02, 0.166140E+02,0.174780E+02,0.184100E+02,0.192780E+02,0.202140E+02, 0.211750E+02,0.221620E+02,0.231720E+02,0.242070E+02,0.252700E+02, 0.263570E+02,0.274710E+02,0.286100E+02,0.298020E+02,0.309700E+02, 0.321910E+02,0.334400E+02,0.347170E+02,0.360230E+02,0.373590E+02, 0.386490E+02,0.401240E+02,0.415290E+02,0.429830E+02,0.444700E+02, 0.459850E+02,0.475280E+02,0.490990E+02,0.507300E+02,0.523600E+02, 0.540630E+02,0.557570E+02,0.575240E+02,0.593100E+02,0.611310E+02, 0.629910E+02,0.648860E+02,0.668200E+02,0.687790E+02,0.708210E+02, 0.728600E+02,0.749570E+02,0.770970E+02,0.000000E+00,0.000000E+00, 0.838000E+02,0.000000E+00,0.000000E+00,0.000000E+00,0.933340E+02, 0.000000E+00,0.984280E+02,0.000000E+00,0.103653E+03] L_e=[0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00, 0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00, 0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00, 0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00, 0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00, 0.000000E+00,0.000000E+00,0.000000E+00,0.000000E+00,0.100900E+01, 0.109600E+01,0.118600E+01,0.128200E+01,0.141900E+01,0.148000E+01, 0.158700E+01,0.169400E+01,0.180600E+01,0.192200E+01,0.204200E+01, 0.216600E+01,0.229300E+01,0.242400E+01,0.255800E+01,0.269600E+01, 0.283800E+01,0.298400E+01,0.313300E+01,0.328700E+01,0.344400E+01, 0.360500E+01,0.376900E+01,0.393700E+01,0.411100E+01,0.428600E+01, 0.446700E+01,0.465100E+01,0.484000E+01,0.503400E+01,0.543100E+01, 0.563600E+01,0.584600E+01,0.605900E+01,0.627500E+01,0.649500E+01, 0.672000E+01,0.694800E+01,0.718100E+01,0.718100E+01,0.741400E+01, 0.765400E+01,0.789800E+01,0.814500E+01,0.839600E+01,0.865100E+01, 0.891000E+01,0.917300E+01,0.944100E+01,0.971100E+01,0.998700E+01, 0.102660E+02,0.105490E+02,0.108360E+02,0.000000E+00,0.000000E+00, 0.117240E+02,0.000000E+00,0.000000E+00,0.000000E+00,0.129660E+02, 0.000000E+00,0.136130E+02,0.000000E+00,0.142790E+02] if(Z<=98): if(edge_code==0): energy=K_e[Z-1]*1000 if(edge_code==1): energy=L_e[Z-1]*1000 if(edge_code==2): energy=L_e[Z-1]*1000 if(edge_code==3): energy=L_e[Z-1]*1000 return energy ## FUNCTION get_atomic ## USAGE: ## [Z,edge_code,e_not]=get_atomic(in_string) ## given in_string, returns Z, e_not, and edge_code. ## in_string should be in the format 'SS EEEE' ## where SS is symbol and EEEE is edge ## for example 'Mn K' or 'U LIII' def get_atomic(in_string): Zsym=in_string[0:2] if(in_string[2:3]==' '): edge_sym=in_string[3:] else: edge_sym=in_string[2:] Z=sym2Z(Zsym) edge_sym=rstrip(edge_sym) edge_sym=ljust(edge_sym,4) edge_code=-1 if(edge_sym=='K '): edge_code=0 if(edge_sym=='LI '): edge_code=1 if(edge_sym=='LII '): edge_code=2 if(edge_sym=='LIII'): edge_code=3 e_not=get_e_not(Z,edge_code) return [Z,edge_code,e_not] ## FUNCTION get_fluo_energy ## USAGE: ## energy=get_fluo_energy(in_string) ## given in_string, returns Z, e_not, and edge_code. ## in_string should be in the format 'SS EEEE' ## where SS is symbol and EEEE is edge ## for example 'Mn K' or 'U LIII' def get_fluo_energy(in_string): Zsym=in_string[0:2] if(in_string[2:3]==' '): edge_sym=in_string[3:] else: edge_sym=in_string[2:] Z=sym2Z(Zsym) edge_sym=rstrip(edge_sym) edge_sym=ljust(edge_sym,4) edge_code=-1 if(edge_sym=='K '): edge_code=0 if(edge_sym=='LI '): edge_code=1 if(edge_sym=='LII '): edge_code=2 if(edge_sym=='LIII'): edge_code=3 energy=get_fl(Z,edge_code) return energy sixpack-0.68/cbselfabs.py0000666000175000017500000003176507750545736014445 0ustar segresegrefrom string import * from math import * import atomic_sub import mucal ## Correction uses formulae from Booth & Bridges, ## http://xxx.lanl.gov/cond-mat/0306252 ## YOU MUST cite this article, or its in-print version from ## XAFS XII (in press) if you use this correction. ## FUNCTION form2sym ## USAGE: ## [symbol,num_sym,tot_syms]=form2sym(formula) ## ## convert formula into a pair of arrays ## given: ## formula - a character string such as ## Ni2O4 ## YBa2Fe0.31Cu2.69O7 ## returns: ## symbol - sequence with the atoms in the formula ## num_sym - sequence of reals with number of symbols ## tot_syms - number of symbols in formula (an integer) def form2sym(formula): #initialize form_len=len(formula) symbol=[] num_sym=[] i=0 isym=0 numbers='0123456789.' #parse formula and build symbol for c in formula: if c in uppercase: isym=isym+1 elen=1 if (i+10.01: d=0.01 else: d=d_given alpha=mu_t+mu_f*g beta=alpha*mu_a*d*exp(-alpha*d/sin(phi))/sin(phi) gamma=1.0-exp(-alpha*d/sin(phi)) #thick limit is more accurate as it includes the XAFS oscillations if lower(option)=='u': thick=chi_exp*(alpha-mu_a)/(alpha+chi_exp*mu_a) else: thick=chi_exp/(1.0-mu_a*(1.0+chi_exp)/alpha) #criteria for checking if roundoff error is starting to be a problem crit1=(4.0*beta*alpha*gamma*chi_exp)/(gamma*(alpha-mu_a*(chi_exp+1.0))+beta) crit2=beta if (abs(crit1)>1e-7 and abs(crit2)>1e-7 and d<=0.01): #otherwise use the "nearly exact" expression if lower(option)=='u': #this is exact... #chi=(1.0-dexp(-(alpha+chi_exp*mu_a)*d/sin(phi))) #chi=chi*(chi_exp+1)*alpha/(gamma*(alpha+chi_exp*mu_a)) #chi=chi-1.0 #this is from the same approx used in the else F=gamma*mu_a/(2*beta) E=-(gamma*(alpha-mu_a)+beta)/(2*beta) H=alpha*gamma/beta chi=(chi_exp*(chi_exp-2*E))/(2*F*chi_exp+H) else: chi=-(gamma*(alpha-mu_a*(chi_exp+1))+beta) chi=chi+sqrt(chi*chi+4*beta*alpha*gamma*chi_exp) chi=chi/(2*beta) else: #if roundoff potentially bad, do the thick limit chi=thick print """WARNING: Using 'thick limit' equation at k="""+str(k) #check main approximation reality=1.0-exp(-(alpha+chi*mu_a)*d/sin(phi)) approx=1.0-exp(-alpha*d/sin(phi))*(1.0-chi*mu_a*d/sin(phi)) error=abs((approx-reality)/reality) if (error>0.02 and k>1.5): if error>1.0: error=1.0 print 'WARNING: integrand approx. only good to '+str(error*100)+' percent at k='+str(k) return chi ## GET MUS HERE ## USAGE: ## [tot_abs,fluor_abs,atomic_abs]=get_mus(formula,edge,energy, ## fluor_energy,concentration,formvol) ## Returns mus for corrections def get_mus(formula,edge,energy,fluor_energy,concentration,formvol): numbers='0123456789.' #ignoring CB "first" structure... k=0 if concentration<0: atomic_sym=' ' #isolate the atom from the kind of edge i=find(edge,' ') #find position of edge in formula j=find(formula,edge[0:i]) #make sure number of atoms stay in atomic_sym x=0 for m in formula[j+i:]: if m in numbers and x==0: k=k+1 else: x=1 atomic_sym=formula[j:j+i+k] else: atomic_sym=edge[0:2] #clean up end of atomic_sym with blanks... not needed? #atomic_sym=rstrip(atomic_sym) #atomic_sym=ljust(atomic_sym,2) fluor_abs=get_tot_abs(formula,fluor_energy,formvol) #correction needs the total absorption tot_abs=get_tot_abs(formula,energy,formvol) r1=get_tot_abs(atomic_sym,energy,formvol) r2=get_noedge_abs(atomic_sym,energy,formvol) if concentration<0: atomic_abs=r1-r2 else: atomic_abs=concentration*(r1-r2) #diagnostic check r3=get_tot_abs(atomic_sym,fluor_energy,formvol) if ((r3-r1)/r1>0.03): print 'BIG TROUBLE' print 'DIAG: energy='+str(energy) print 'DIAG: r1='+str(r1) print 'DIAG: r2='+str(r2) print 'DIAG: r3='+str(r3) return [tot_abs,fluor_abs,atomic_abs] ## FLUOR CORRECTION ## USAGE: ## corr_chi=fluor_corr(k,chi,d,phi,formvol,formula,edge,concentration,io,option) ## returns fluo corrected chi array given k,chi and other params ## k: Sequence of k wavevectors ## chi: Sequence of fluo impacted chi meaurements ## d: Thickness of sample, in ANGSTROMS ## phi: Angle of incident beam wrt sample in degrees ## formvol: Volume of formula cell ## formula: Formula of compound of interest ## edge: Element and edge, eg. 'Mn K' or 'U LIII' ## fluor_energy: energy of fluo line -- taken from edge! ## concentration: concentration (-1 by default) ## io: output option- ## 'p' or 'P' for printout to stdoutput ## other for maximum verbosity ## option: if 'U' or 'u', will undo a correction, otherwise it'll do it def fluor_corr(k,chi,d,phi,formvol,formula,edge,concentration,io,option): #initialize new array sabcor_chi=[] EV2INVANG=0.512393 #need E0 for calculating edge energy [Z,edge_code,e_not]=atomic_sub.get_atomic(edge) fluor_energy=atomic_sub.get_fluo_energy(edge) #convert angles to radians phi_rad=2*pi*phi/360 theta_rad=pi/2-phi_rad g=sin(phi_rad)/sin(theta_rad) #begin correction loop for idat in range(len(chi)): #k is the wavevector #need it in terms of eV, since that is what the Vict. Coeffs are in terms of... if k[idat]>=0.0: energy=e_not+(k[idat]/EV2INVANG)**2 else: print 'Trouble in fluo corr, k='+str(k[idat]) #correction needs the total absorption [tot_abs,fluor_abs,atomic_abs]=get_mus(formula,edge,energy,fluor_energy,concentration,formvol) #separate out chi # difference from CB version -- input is chi, NOT k-weighted chi new_chi=corr_chi(k[idat],chi[idat],tot_abs,atomic_abs,fluor_abs,d*1e-8,phi_rad,g,option) try: correction=new_chi/chi[idat] except: correction=1 sabcor_chi.append(new_chi) temp=1e8*info_depth(tot_abs,fluor_abs,phi_rad,g) if k[idat]<=5.0: corr_at_5=correction info_at_5=temp #make sure new corr_chi is same length as old one if len(sabcor_chi)!=len(chi): print 'SERIOUS ERROR -- CORRECTED CHI NOT SAME LENGTH' #stat report? if lower(io)=='p': print print 'Self-Absorption correction statistics:' print print 'info depth at 5 inv ang: '+str(info_at_5) print 'correction chi_true/chi_exp at 5 inv ang: '+str(corr_at_5) print #return final corrected chi return sabcor_chi #tests #get_mus('ZnS','Zn K',10000,8500,-1,10) #get_mus('ZnS','Zn K',10000,8500,1,10) #get_mus('ZnS','S K',2500,2308,-1,10) #get_mus('YBa2Fe0.31Cu2.69O7','Fe K',7800,6500,-1,10) #print get_tot_abs('ZnS',10000,1) #print tot_weight('NaCl') #print atomic_sub.get_atomic('Mn K') #form2sym('ZnS') #form2sym('Ni2O4') #print form2sym('YBa2Fe0.31Cu2.69O7') #print atomic_weight(1) #print atomic_sub.sym2Z('U') #print atomic_weight(atomic_sub.sym2Z('U ')) #print fluor_corr([1,2,3,4,5],[1,1,1,1,1],45000,45,50,'MnO2','Mn K',-1,'v','x') sixpack-0.68/sixpack.ico0000666000175000017500000000627610110675642014264 0ustar segresegre  ( @        m_uhhhh (,lfffffhhhhhf hp` dfhhhfff ffhfhhffifhhhhff mfffihhhhhhhhhffffff ! feffhhhhhhfffffffmekhhfffff hdfkgc hhhfffff lifccilh fffff\S eojff"ff!gh]o]gfnh dfke]Zdf fnifff]fopfeahh}g  nhb]affVNfeX X lggpe  )B X ^ffd\flegZhmfedgk]m]ffflr  HfgmP'  yl L[      ps    sixpack-0.68/splogo.gif0000666000175000017500000006016310112210214014071 0ustar segresegreGIF89a_ ^ ] \ [ Z Y X W V U T S R Q P O  ~ } ~ } | { z y x w | vvw vutsrw vuqpvvuonmlkwijhgfed c c eb a dd ` u                                                , H*\ȰÇ#JHŋ3jȱǏ CIɓ(S\ɲ˗0cʜI͛8sɳϟ@ JѣH*]ʴӧPJJիXjʵׯ`ÊKٳhӪ]˶۷pʝKݻx˷߿ LÈ+^̸ǐ#KL˘3k̹ϠCMӨS^ͺװc˞MJsͻwy>k'güM7oNH"F9I%C&9G|9nKS:%L0фNSPQV\^L7aG?Wf Iѡͅ&,"h%1J]^[peKhmqV&Cb'I* b~MgbNiWve[zh^|FԨBPZ^d}K9ݔ-\\:bI*Ǯf,z徙a&~>gK"2ڪ~!k܎AFeH IInpg0~J/OFJWX lFL@A$] fFV3U릷9}}콥xQeYXpfE7l+Eld1ȣ:"U^9#]wK1S5l5lDMGmgnp]$G$1%[h'4ѭfA;q9ڛݩJlwQJծg}82]#P :ǏӍkK=ꩲ^ఇ5!kLp)P,>r}q:q')ױݩz8l[ܚ8-x`] RqC3?pЃHvԮ.1aDM/P*вI@v< /;| `CTC|ю:l:j橤yL 7ZXC4Pi\c dF#SI;z"aᘆ&#I'dU(-n)pzawq3U :ِK-yfRA Cg7٫R+JrA`048 w9.T[6(k]:8|gd;) OeN!JhJdC,ARj2,iErTg/9Iz:'B" rNJWJURL?T֋{b%ԸY-ɲ`^#wtBl0J5SIZNA9~jUU fj꤄i^:N2,9?t'<隃>R*vys@mn` [?3CP- ^vtAy'(y +߶I-X!~ۺK3%iQ;`@kKXwD1wސJ %$PDU݂(0nfxNwũͮ l7`+@d1O$dN]5&ŨQNL8̰-`gk;yEP3'f݈OQ wZ_nPag2 PCu4!mIS֖ [h֫3"V 8[b*r=0v[XdzmnWD6 #d:2\ٺ4h@k?.݉mosi◁}+:fvm{# d~< E?ы^[sjUsoQy?O@2KwRT725sގ4qU|,ݍe63I%EӝNeEם] P@#]zxN視k.G]j 8߸+>"P으;^y[ÍZJ+?jze/}P^`;2%/5WMo<|/ ro5ve;|҇{U}E Ahgx7~ wg|Fnztʇ |l}{"jv|x~ Ѐe'jgT·sz2ׁzgro{e."+Ȃ:o˦qX Ȁ ȃ=)'I(6Zbv?||L؄G'-)h%VZj(vdwh8hh}Wj\'3xdx͗PUMH~wqGa47h;ȃjh+wxdzQT4*%C='Fqys؈GzKx(AqEH|HcH |{h)"CF=]0#׈}C/lʨ؋8щ^g8v7fHRXH%WCQ3#nZn5|Ljff|ɋ(9`6ɐ9؀臨(HH3%S))@w~~u((8y(7aE逨7W (B=R7Jf9lKN7'HesaHz(oeѕƖx(EɃ/%9RHҗ~8&n_'x蘔HɓHH#*ݔ2YЛ)qng&ƉE٘Mi薹=x9Pɜ\E yeI1fLjk Iމ樞=fLyNIyc_TC3T5eIǕII NIvɏ&2tK 4dkuu9? |ZS})yn9FbG H\SC gW韯Y[/J qe *a*#z)*f(+_m slbMJOzl`_)㘥^Z$ُ Z5b\5p:Q?uQ5nZȪ y *?9U(hʫjjE+ªJ_ZCueC,N鉨eGf™:@BD:Z1nR'QjQ!uwb9zJJ NU8ݢ {Hs#&Z6``Cz-iz5,c0d/ KkcD,9vjSq>K"Ss WtYc2fQ;QVkzLi'`B|:0g1BKni+kմd0 3Y\:Ux殡z[j گ'kd) ,k/3rk,Tde=i҅ձț䜻J˴IETiiJ[1D{C*9K]A@sԼ˶p;N%33s_#Ƶ۩K 4«kjK[3;֋cgkwK8<C7~_*뽒{8ӫHl^53\MéԹrFa2-4Ǿ@+TjƈVNV>=&%uۻp+#i!K&0!,F  P:|-J̊ڛǵ콉JLҘol7=9dhѮ KHVsHV_1cM}hԔq=նs'*jZ-·7͒Bilzl3i}؈ҒMֹlӫIWM;FB|mMCV.'Tp Q@m+4pC:}BZmJTS_Yx5 qMi0r-βѕnpws7Gw/xٿ;h mȍܖWWVQp^O^vMҕ#1=Vj.lpXq#> SdyO~A4'~쉾nGl! 6cE*rNoIL.UG]I5cR2@to0^8Z O_[` ?&)[OtJv7L`O73W0nN=]8fRIT5B{r/UnMmI]|s]?mCB/͒Ԗ_Ⓩ9 1>zE?Yzr?MU_:H >N O?8_aQ "XAaC9NXE5nG!E)TrKldi͛7ptYD :ѣ.eӏP6MZ*ՠBf`8CG`?HFsqGA/Ac1g'Z9 Q,J,& ,hKѭYt ɒjTM8̑? rA oC*@SP)=P(KޫM>X ?$?s5;sTRKS;|nHsB–P:Jp%Q'u-O14fE=9PtTj"TS3=Os@Ǒe`WLHcˠ _:VԼ'K|K@!xa`RBmЈ: #9trb!,nc! 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