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h4iku
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coconut_python2010_preprocessed

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self.aoresults[spin][i] = Numeric.divide(tempcoeffs, scale)
tempvec = tempcoeffs/scale self.aoresults[spin][i] = Numeric.divide(tempcoeffs, scale).astype("f")
def calculate(self, indices=None, fupdate=0.05): """Perform a C^2 population analysis given the results of a parser""" if not self.parser.parsed: self.parser.parse()
self.logger.info("Creating attribute HOMO[]")
self.logger.info("Creating attribute homos[]")
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.logger.info("Creating attribute evalue[[]]") self.evalue = [[]]
self.logger.info("Creating attribute moenergies[[]]") self.moenergies = [[]]
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
HOMO = len(self.evalue[0])-1
HOMO = len(self.moenergies[0])-1
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.evalue[0].append(self.float(x)*27.2114)
self.moenergies[0].append(self.float(x)*27.2114)
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.evalue.append([])
self.moenergies.append([])
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
HOMO = len(self.evalue[1])-1
HOMO = len(self.moenergies[1])-1
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.evalue[1].append(self.float(x)*27.2114)
self.moenergies[1].append(self.float(x)*27.2114)
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.vibfreq = []
self.vibfreqs = []
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.vibfreq.extend(map(self.float,line[15:].split()))
self.vibfreqs.extend(map(self.float,line[15:].split()))
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
if not hasattr(self,"raman"):
if not hasattr(self,"vibramans"):
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.logger.info("Creating attribute raman[]")
self.logger.info("Creating attribute vibramans[]")
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.etenergy = [] self.etwavelen = [] self.etosc = [] self.etsym = [] self.etcis = [] self.logger.info("Creating attributes etenergy[], etwavelen[], etosc[], etsym[], etcis[]")
self.etenergies = [] self.etoscs = [] self.etsyms = [] self.etsecs = [] self.logger.info("Creating attributes etenergies[], etoscs[], etsyms[], etsecs[]")
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.logger.debug(parts) self.etenergy.append(convertor(self.float(parts[0]),"eV","cm-1")) self.etwavelen.append(self.float(parts[2])) self.etosc.append(self.float(parts[4].split("=")[1])) self.etsym.append(line[21:36].split())
self.etenergies.append(convertor(self.float(parts[0]),"eV","cm-1")) self.etoscs.append(self.float(parts[4].split("=")[1])) self.etsyms.append(line[21:36].split())
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.etcis.append(CIScontrib)
self.etsecs.append(CIScontrib)
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.rotatory = [] self.logger.info("Creating attribute rotatory[]")
self.etrotats = [] self.logger.info("Creating attribute etrotats[]")
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.rotatory.append(R)
self.etrotats.append(R)
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
NBasis = int(line.split('=')[1].split()[0])
nbasis = int(line.split('=')[1].split()[0])
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
if hasattr(self,"NBasis"): assert NBasis==self.NBasis else: self.NBasis = NBasis self.logger.info("Creating attribute NBasis: %d" % self.NBasis)
if hasattr(self,"nbasis"): assert nbasis==self.nbasis else: self.nbasis= nbasis self.logger.info("Creating attribute nbasis: %d" % self.nbasis)
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
NBsUse = int(line.split('=')[1].split()[0]) if hasattr(self,"NBsUse"): assert NBsUse==self.NBsUse else: self.NBsUse = NBsUse self.logger.info("Creating attribute NBsUse: %d" % self.NBsUse)
nindep = int(line.split('=')[1].split()[0]) if hasattr(self,"nindep"): assert nindep==self.nindep else: self.nindep = nindep self.logger.info("Creating attribute nindep: %d" % self.nindep)
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
NBasis = int(line.split()[0]) if hasattr(self,"NBasis"): assert NBasis==self.NBasis
nbasis = int(line.split()[0]) if hasattr(self,"nbasis"): assert nbasis==self.nbasis
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.NBasis = NBasis self.logger.info("Creating attribute NBasis: %d" % self.NBasis)
self.nbasis = nbasis self.logger.info("Creating attribute nbasis: %d" % self.nbasis)
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.logger.info("Creating attribute overlap[x,y]")
self.logger.info("Creating attribute aooverlaps[x,y]")
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.overlap = Numeric.zeros( (self.NBasis,self.NBasis), "float")
self.aooverlaps = Numeric.zeros( (self.nbasis,self.nbasis), "float")
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
while base<self.NBasis: for i in range(self.NBasis-base):
while base<self.nbasis: for i in range(self.nbasis-base):
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.overlap[base+j,i+base] = k self.overlap[i+base,base+j] = k
self.aooverlaps[base+j,i+base] = k self.aooverlaps[i+base,base+j] = k
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.mocoeff = Numeric.resize(self.mocoeff,(2,NBsUse,NBasis))
self.mocoeffs = Numeric.resize(self.mocoeffs,(2,nindep,nbasis))
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.logger.info("Creating attributes orbitals[], mocoeff[][]") self.orbitals = [] self.mocoeff = Numeric.zeros((NBsUse,NBasis),"float")
self.logger.info("Creating attributes aonames[], mocoeffs[][]") self.aonames = [] self.mocoeffs = Numeric.zeros((nindep,nbasis),"float")
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
for base in range(0,NBsUse,5):
for base in range(0,nindep,5):
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
for i in range(NBasis):
for i in range(nbasis):
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.orbitals.append("%s_%s" % (atomname,orbital))
self.aonames.append("%s_%s" % (atomname,orbital))
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.mocoeff[1,base:base+len(part)/10,i] = temp
self.mocoeffs[1,base:base+len(part)/10,i] = temp
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.mocoeff[base:base+len(part)/10,i] = temp
self.mocoeffs[base:base+len(part)/10,i] = temp
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") for line in inputfile: if line[1:8]=="NAtoms=":
self.scftargets = Numeric.array([5E-5,5E-6],"f") if not geoopt: values = [[],[]] else: values = [[]]
self.scftargets = [[5E-5,5E-6]] values = []
def parse(self,fupdate=0.05,cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename,"r") if self.progress: inputfile.seek(0,2) #go to end of file nstep=inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep=0
values[0].append(denergy) values[1].append(ddensity)
values.append([denergy,ddensity])
def parse(self,fupdate=0.05,cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename,"r") if self.progress: inputfile.seek(0,2) #go to end of file nstep=inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep=0
values[0].append(ddensity)
values.append([ddensity])
def parse(self,fupdate=0.05,cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename,"r") if self.progress: inputfile.seek(0,2) #go to end of file nstep=inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep=0
if not geoopt and line[2:24]=="start of program geopt": geoopt = True if hasattr(self,"scfvalues"):
if line[2:24]=="start of program geopt": if not geoopt:
def parse(self,fupdate=0.05,cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename,"r") if self.progress: inputfile.seek(0,2) #go to end of file nstep=inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep=0
self.scfvalues[0] = [self.scfvalues[0][1]] self.scftargets = self.scftargets[0]
self.scftargets = [[self.scftargets[0][0]]] if hasattr(self,"scfvalues"): self.scfvalues[0] = [[x[0]] for x in self.scfvalues[0]] geoopt = True else: self.scftargets.append([5E-5])
def parse(self,fupdate=0.05,cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename,"r") if self.progress: inputfile.seek(0,2) #go to end of file nstep=inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep=0
elif hasattr(self.parser,"foonames"):
elif hasattr(self.parser,"fonames"):
def partition(self,indices=None):
data[i, j, k] = bfs[bs].amp(x[i], y[j], z[k])
data[i, j, k] = bfs[bs].amp(x[i], y[j], z[k])**2
def electrondensity(coords, mocoeffs, gbasis, volume): """Calculate the magnitude of the electron density at every point in a volume. Attributes: coords -- the coordinates of the atoms mocoeffs -- mocoeffs for all of the occupied eigenvalues gbasis -- gbasis from a parser object volume -- a template Volume object (wil...
self.etsyms.append(line[21:36].split())
self.etsyms.append(line[21:36].strip())
def parse(self,fupdate=0.05,cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename,"r") if self.progress: inputfile.seek(0,2) #go to end of file nstep=inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep=0 optfinished = False # Flag that indicates whether it ...
density = electrondensity(b.atomcoords[0], b.mocoeffs[0,0:b.homos[0]]*2, a.gbasis, vol)
density = electrondensity(b.atomcoords[0], b.mocoeffs[0,0:b.homos[0]], a.gbasis, vol)
def electrondensity(coords, mocoeffs, gbasis, volume): """Calculate the magnitude of the electron density at every point in a volume. Attributes: coords -- the coordinates of the atoms mocoeffs -- mocoeffs for all of the occupied eigenvalues gbasis -- gbasis from a parser object volume -- a template Volume object (wil...
multiple = {'E':2, 'T':3}
multiple = {'E':2, 'T':3, 'P':3, 'D':5}
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
sym += ":%i"%(repeat+1)
sym = self.normalisedegenerates(info[0],repeat)
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
elif line.find("Gaussian") >= 0:
elif line.find("Gaussian System") >= 0:
def ccopen(filename,progress=None,loglevel=logging.INFO,logname="Log"): """Guess the identity of a particular log file and return an instance of it. Returns: one of ADF, GAMESS, GAMESS UK, Gaussian, Jaguar, or None (if it cannot figure it out). """ filetype = None inputfile = open(filename, "r") for line in inputfile:...
' 100 C 2 S ' ]
' 100 C 2 S ', ' 1 SI 1 S ' ]
def normalise_aonames(self,listoflines): """Normalise the aonames attribute to agree with the other parsers.
['C1_1S', 'C1_2S', 'C1_3S', 'C1_4XXXX', 'C2_1S']
['C1_S', 'C1_S', 'C1_S', 'C1_XXXX', 'C2_S', 'Si1_S']
def normalise_aonames(self,listoflines): """Normalise the aonames attribute to agree with the other parsers.
p = re.compile("(\d+)\s*([A-Z][a-z]?)\s*(\d+)\s*([A-Z]+)")
p = re.compile("(\d+)\s*([A-Z][A-Z]?)\s*(\d+)\s*([A-Z]+)")
def normalise_aonames(self,listoflines): """Normalise the aonames attribute to agree with the other parsers.
i = 0 oldatom = "0"
oldatom = "0"
def normalise_aonames(self,listoflines): """Normalise the aonames attribute to agree with the other parsers.
if g[3] in ['S','X','XX','XXX','XXXX']: i += 1 if g[2]!=oldatom: i = 1 aoname = "%s%s_%d%s" % (g[1],g[2],i,g[3])
aoname = "%s%s_%s" % (g[1].capitalize(),g[2],g[3])
def normalise_aonames(self,listoflines): """Normalise the aonames attribute to agree with the other parsers.
atomnos.append(self.table.number[temp[0]])
atomnos.append(int(round(float(temp[1]))))
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") if self.progress: inputfile.seek(0,2) #go to end of file nstep=inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep=0
if line2.find("Create") < 0:
else: line2 = None if line2 and line2.find("Create") < 0:
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
if line[1:37] == 'Orbital Energies, per Irrep and Spin' and not hasattr(self, "mosyms") and nosymflag and not unrestrictedflag:
if line.find('Orbital Energies, per Irrep and Spin') > 0 and not hasattr(self, "mosyms") and nosymflag and not unrestrictedflag:
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
while len(line) > 3:
while len(line) > 10:
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
homoa = None
homoa = 0
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
if info[3] == '0.00' and not homoa: homoa = len(self.moenergies[0]) - 2
if info[3] != '0.00': homoa = len(self.moenergies[0]) - 1
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
if info[3] == '0.00' and not homob: homob = len(self.moenergies[0]) - 2
if info[3] != '0.00': homob = len(self.moenergies[1]) - 1
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
self.logger.error("MO info up to else: self.logger.info("Creating attribute mosyms[[]]") self.mosyms = [[]] self.logger.info("Creating attribute moenergies[[]]") self.moenergies = [[]] homoA = None while len(line) > 10: info = line.split() self.mosyms[0].append('A') self.moenergies[0].append(utils.convertor(float(i...
self.logger.warning("MO info up to while int(info[0]) != len(self.moenergies[0]): self.moenergies[0].append(99999) self.mosyms[0].append('A') homoA = None while len(line) > 10: info = line.split() self.mosyms[0].append('A') self.moenergies[0].append(utils.convertor(float(info[2]), 'hartree', 'eV')) if info[1] == '0...
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
title = inputfile.next() title = inputfile.next() equals = inputfile.next()
line = inputfile.next() while line != equals: line = inputfile.next()
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0
blank = inputfile.next() blank = inputfile.next() evalues = inputfile.next()
line = inputfile.next() while line==blank: line = inputfile.next() evalues = line
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0
if line[2:12] == "m.o. irrep":
if line[7:12] == "irrep":
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0
title = inputfile.next()
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0
while line != equals:
if not line.strip(): line = inputfile.next() while line.strip() and line != equals:
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0
moenergies.append(float(temp[3]))
moenergies.append(utils.convertor(float(temp[2]), "hartree", "eV"))
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0
if coeff**2 < 1.0:
sum = coeff**2 while sum < 1.0:
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
if line[42] == ' ':
if line[42] == ' ' and len(info) > 4:
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
else:
sum += coeff**2 if sum == coeff**2:
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
def __init__(self,*args):
def __init__(self,parser,progress=None, \ loglevel=logging.INFO,logname="Log"):
def __init__(self,*args):
super(Population, self).__init__(logname="Population",*args)
super(Population, self).__init__(parser,progress,loglevel,logname)
def __init__(self,*args):
atomcoords.append(map(float, line.split()[5:]))
atomcoords.append(map(float, line.split()[5:8]))
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
break
continue
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 optfinished = False # Flag that indicates whe...
aolist = symlist[sym][spin]
if nosymflag: aolist = range(len(self.moenergies[spin])) else: aolist = symlist[sym][spin]
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
symlist = {}
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
for repeat in range(multiple.get(info[0][0], 1)):
count = multiple.get(info[0][0],1) for repeat in range(count):
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
for repeat in range(multiple.get(info[0][0], 1)):
for repeat in range(count):
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
sym = inputfile.next()
line = inputfile.next() sym = line.split()[1]
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
for i in range(8): line = inputfile.next()
for i in range(4): inputfile.next() line = inputfile.next() sym = line.split()[1] for i in range(3): inputfile.next()
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
if len(info) > 1:
if info[0] == "occup:":
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
self.mocoeffs[spin, i + symoffset + base, row + symoffset] = float(cols[i + 1])
self.mocoeffs[spin, aolist[i+base], row + symoffset] = float(cols[i + 1])
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
self.homos = [len(self.moenergies[0]) - 2]
self.homos = [len(self.moenergies[0]) - (count + 1)]
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
homoa = len(self.moenergies[0]) - 2
homoa = len(self.moenergies[0]) - (count + 1)
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
homob = len(self.moenergies[1]) - 2
homob = len(self.moenergies[1]) - (count + 1)
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
glob(os.path.join(data, "Gaussian", "Gaussian98", "*.bz2")),
glob(os.path.join(data, "Gaussian", "Gaussian98", "*.bz2")) + glob(os.path.join(data, "Gaussian", "Gaussian98", "*.gz")),
def testADF_ADF2004_01_Fe_ox3_final_out_gz(logfile): """ Make sure HOMOS are correct """ assert logfile.homos[0]==59 and logfile.homos[1]==54
print "got inside"
def parse(self,fupdate=0.05,cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename,"r") if self.progress: inputfile.seek(0,2) #go to end of file nstep=inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep=0 # Used to avoid extracting the final geometry twice i...
self.scfenergies.append(temp[temp.index("IS")+1])
self.scfenergies.append(float(temp[temp.index("IS")+1]))
def parse(self): """Extract information from the logfile.""" inputfile = open(self.filename,"r") if self.progress: inputfile.seek(0,2) #go to end of file nstep=inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep=0
assert type in ['rhf', 'uhf']
assert type in ['rhf', 'uhf'], "%s not one of 'rhf', 'uhf'" % type
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0
temp = line.split() scfvalues.append([float(temp[5])])
if line[2:6]!="****": scfvalues.append([float(line[tester-5:tester+6])])
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0
self.vibcarts.append(p[0:len(broken)/3])
self.vibcarts.extend(p[0:len(broken)/3])
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = utils.openlogfile(self.filename) if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 optfinished = False # Flag that indic...
sym = temp[1][1:] assert sym in ['s', 'p', 'd', 'f', 'sp']
sym = basisregexp.match(temp[1]).groups()[0] assert sym in ['s', 'p', 'd', 'f', 'sp'], "'%s' not a recognized symmetry" % sym
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0
if line.find("Input orientation") > -1:
if line.find("Input orientation") > -1 or line.find("Z-Matrix orientation") > -1:
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 optfinished = False # Flag that indicates whe...
if len(self.moenergies) == 0:
if len(self.moenergies) == 1:
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = utils.openlogfile(self.filename) if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final ...
while len(line) == 77:
while line.strip():
def parse(self, fupdate=0.05, cupdate=0.002): """Extract information from the logfile.""" inputfile = open(self.filename, "r") if self.progress: inputfile.seek(0, 2) #go to end of file nstep = inputfile.tell() inputfile.seek(0) self.progress.initialize(nstep) oldstep = 0 # Used to avoid extracting the final geometry...
index = self.indexPage() self.putChild('', index) self.putChild('index.html', index) self.putChild('moduleIndex.html', nevowhtml.ModuleIndexPage(self.system)) self.putChild('classIndex.html', nevowhtml.ClassIndexPage(self.system)) self.putChild('nameIndex.html', nevowhtml.NameIndexPage(self.system))
self.index = WrapperPage(self.indexPage()) self.putChild('', self.index) self.putChild('index.html', self.index) self.putChild('moduleIndex.html', WrapperPage(nevowhtml.ModuleIndexPage(self.system))) self.putChild('classIndex.html', WrapperPage(nevowhtml.ClassIndexPage(self.system))) self.putChild('nameIndex.html', Wra...
def __init__(self, system): self.system = system self.putChild('apidocs.css', File(nevowhtml.sibpath(__file__, 'templates/apidocs.css'))) self.putChild('sorttable.js', File(nevowhtml.sibpath(__file__, 'templates/sorttable.js'))) index = self.indexPage() self.putChild('', index) self.putChild('index.html', index) self.p...
return self.pageClassForObject(obj)(obj)
return WrapperPage(self.pageClassForObject(obj)(obj))
def childFactory(self, ctx, name): if not name.endswith('.html'): return None name = name[0:-5] if name not in self.system.allobjects: return None obj = self.system.allobjects[name] return self.pageClassForObject(obj)(obj)
return nevowhtml.IndexPage(self.system).renderHTTP(ctx)
return self.index.renderHTTP(ctx)
def renderHTTP(self, ctx): return nevowhtml.IndexPage(self.system).renderHTTP(ctx)
def render_recentChanges(self, context, data): return context.tag
@page.renderer def recentChanges(self, request, tag): return tag
def render_recentChanges(self, context, data): return context.tag
def __init__(self, root):
def __init__(self, root, url):
def __init__(self, root): self.root = root
def render_changes(self, context, data): item = context.tag.patternGenerator('item') tag = context.tag
self.url = url @page.renderer def changes(self, request, tag): item = tag.patternGenerator('item')
def __init__(self, root): self.root = root
tag[item(data=d)]
tag[nevowhtml.fillSlots(item, diff=self.diff(d), hist=self.hist(d), object=self.object(d), time=self.time(d), user=self.user(d))]
def render_changes(self, context, data): item = context.tag.patternGenerator('item') tag = context.tag for d in reversed(self.root.edits): tag[item(data=d)] return tag
def render_diff(self, context, data): return tags.a(href=url.URL.fromContext(context).sibling(
def diff(self, data): return tags.a(href=self.url.sibling(
def render_diff(self, context, data): return tags.a(href=url.URL.fromContext(context).sibling( 'diff').add( 'ob', data.obj.fullName()).add( 'revA', data.rev-1).add( 'revB', data.rev))["(diff)"]