def printpara(para=dict()):
for key,val in para.iteritems():
s="key:"+key+" val:"
if isinstance(val, list):
s+= files.matrixToLine(val)
elif isinstance(val, dict):
for key,val in val.iteritems():
s+= key+":"+str(val)+" "
else:
s+=str(val)
print s
def poscar(self,file=__poscar, para = dict(),save=True):
"""
file: Filename of poscar
para: dictionary of parameters
"""
file=self.path+file
if self.highestFileVersion:
newfile = [file]
if not files.getHighestVersion(newfile):
return dict()
file=newfile[0]
result = dict()
readData = files.readfile(file)
if para.has_key(par.LatticeConstant):
readData[1] = files.toLine(para[par.LatticeConstant])
else:
if len(readData)>1:
s = str(readData[1])
result[par.LatticeConstant] = s.strip(' \n')
if para.has_key(par.Basisvectors):
readData[2] = files.matrixToLine(para[par.Basisvectors])
readData[3] =""
readData[4]=""
else:
if len(readData)>4:
bv = list()
for i in range(2,5):
bv.append(filter(None,str(readData[i]).strip(' \n').split(" ")))
result[par.Basisvectors] =bv
atomcount=0
if para.has_key(par.Atoms):
readData[5]=""
readData[6]=""
for atom in para[par.Atoms]:
readData[5]+=" "+atom[0]
readData[6]+=" "+str(int(float(atom[1])))
atomcount+=int(float(atom[1]))
readData[5]+='\n'
readData[6]+='\n'
else:
if len(readData)>6:
s1 = readData[5].strip(' \n').split()
s2 = readData[6].strip(' \n').split()
if (len(s1) == len(s2)):
atoms = []
for i in range(len(s1)):
atoms.append([s1[i],s2[i]])
atomcount+=int(float(s2[i]))
result[par.Atoms]=atoms
atomcount = int(atomcount)
atomlines = range(9,9+atomcount)
text=list()
for i in atomlines:
text.append("")
### atomcount has to equal #Atompos & #Atommove
atomtext=list()
if not (para.has_key(par.Atompos) and para.has_key(par.Atommove)):
for i in atomlines:
atomtext.append(filter(None,str(readData[i]).strip(' \n').split(" ")))
if para.has_key(par.Atompos):
if len(para[par.Atompos])==atomcount:
for i in range(0,atomcount):
text[i]=files.vecToLine(para[par.Atompos][i])[:-1]
else:
ap= list()
for i in range(0,atomcount):
ap.append(atomtext[i][0:3])
text[i]=" ".join(atomtext[i][0:3])
result[par.Atompos] = ap
if para.has_key(par.Atommove):
if len(para[par.Atommove])==atomcount:
for i in range(0,atomcount):
text[i]+=" "+files.vecToLine(para[par.Atommove][i])[:-1]
elif len(para[par.Atommove])==1:
for i in range(0,atomcount):
text[i]+=" "+files.vecToLine(para[par.Atommove][0])[:-1]
else:
am=list()
for i in range(0,atomcount):
am.append(atomtext[i][3:6])
text[i]+=" "+" ".join(atomtext[i][3:6])
result[par.Atommove] = am
if len(atomlines) == 0:
atomlines.append(9)
for i in range(atomlines[0],len(readData)):
readData[i]=""
while len(readData)<=atomlines[0]:
readData.append("")
readData[atomlines[0]]='\n'.join(text)
if save:
files.writefile(file,readData)
return result