def kpoints(self,para=dict(),save=True):
file = self.path+self.__kpoints
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.Kcount):
readData[1] = para[par.Kcount]
else:
s=readData[1].split()[0]
result[par.Kcount] = str(s)+'\n'
ktype =""
if para.has_key(par.Ktype):
readData[2] = para[par.Ktype]
ktype=para[par.Ktype]
else:
result[par.Ktype] = readData[2]
ktype=readData[2]
if ktype[0].lower()=="l":
if para.has_key(par.Klinetype):
readData[3] = para[par.Klinetype]
else:
result[par.Klinetype] = readData[3]
if para.has_key(par.Kline):
for i in range(4,len(readData)):
readData[i]=""
data =[]
i = 0
for ks in para[par.Kline]:
d=[]
for k in ks:
d.append(str(k))
data.append(" ".join(d))
if i%2 == 1:
data.append("")
i+=1
readData[4]='\n'.join(data)
else:
klinedata =[]
for i in range(4,len(readData)):
if readData[i]!="\n":
klinedata.append(readData[i].split())
result[par.Kline]=klinedata
else:
if para.has_key(par.Kmesh):
if len(para[par.Kmesh])==1:
val = para[par.Kmesh][0]
para[par.Kmesh] = [val,val,val]
readData[3] =files.vecToLine(para[par.Kmesh],Int=True)
else:
if len(readData)>3:
s = str(readData[3])
result[par.Kmesh]=s.split()
if save:
files.writefile(file,readData)
return result
def setTempdirstart(self,count):
if self.sequential:
count=1
file =self.temppath+self.tempdirstartFilename
if os.path.isfile(file):
self.tempdirstart = int(files.readfile(file)[0])
else:
self.tempdirstart=1
files.writefile(file,"%.0d"%(self.tempdirstart+count+1))
def startjob(self,jobnr):
print "starte job"
runfile="test.sh"
if not self.testrun:
runfile=self.runLine
scriptname="run.sh"
path =self.gettemppath(jobnr)
self.startedcalcs +=1
decimalcount = int(math.floor(math.log10(self.calculations)))
fullname = self.name+("_%"+str(decimalcount+1)+"d/%d")%(self.startedcalcs,self.calculations)
fullname = fullname.replace(" ","0")
print "Name: "+fullname+" in folder: "+path
script = pbs.makescript(path,runfile,self.nodes,self.ppn,self.queue,fullname,self.email,self.outpath,self.memorymultiplikator,self.hours,self.pbsparameters)
scriptfile =path+scriptname
files.writefile(scriptfile,script)
jobid =pbs.qsub(scriptfile)
open(self.jobidfile,"a").write(jobid+"\n")
return jobid
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