def genfile_molden(self, filename):
try:
write_molden(filename, self._xcc, self._symbols, self._ccfreqs,
self._ccFevecs)
except:
return 0
return 1
def gts_data_and_molden(gtsfile):
# read gts and prepare Molecule
molecule = Molecule()
molecule.set_from_gts(gtsfile)
molecule.setup()
# type of PES stationary point?
nimag = numimag(molecule._ccfreqs)
mformu = molecule._mform
# Get ctc and itc
ctc, itc, ext = gtsfile.split("/")[-1].split(".")
# tuple
gts_tuple = (itc, molecule._ch, molecule._mtp, molecule._V0, nimag, mformu,
molecule._pgroup)
# molden file
if not os.path.exists(PN.DIR5): os.mkdir(PN.DIR5)
if is_string_valid(ctc, extra="_"):
molden = PN.get_gtsmolden(ctc, itc)
if not os.path.exists(molden):
print " creating %s" % molden
bmolden = True
write_molden(molden,molecule._xcc,molecule._symbols,\
molecule._ccfreqs,molecule._ccFevecs)
else:
bmolden = False
else:
molden = None
bmolden = False
return ctc, gts_tuple, molden, bmolden
def molecule2molden(molecule, ctc, itc):
# gn t name for molden file
molden = PN.get_gtsmolden(ctc, itc)
## does molden file exist?
#if os.path.exists(molden): return
# create molden file
idata = (molden, molecule._xcc, molecule._symbols, molecule._ccfreqs,
molecule._ccFevecs)
write_molden(*idata)
def generate_gts_file(esfile, gtsfile, read_method):
'''
Generate gts file (and molden & frozen files)
from given electronic structure (ES) file;
The ES file is read using read_method
'''
# Extra files that (maybe) will be generated
file_frozen = gtsfile + ".frozen" # only if any frozen atom
file_molden = gtsfile + ".molden" # molden file
# read file
xcc, atonums, ch, mtp, E, gcc, Fcc, masses, clevel = read_method(
PN.UFOLDER + esfile)[0:9]
# clevel is not really clevel when using read_gtsfile as read_method
if read_method == read_gtsfile: clevel = ""
# symbols and atonums
symbols, atonums = fncs.symbols_and_atonums(atonums)
# is masses available?
if masses is None or len(masses) == 0 or sum(masses) == 0.0:
masses = atonums2masses(atonums)
# is Fcc available?
if len(atonums) != 1 and (Fcc is None or len(Fcc) == 0):
status = -1
cache = None
molec = None
else:
# Generate Molecule instance
molec = Molecule()
molec.setvar(xcc=xcc, gcc=gcc, Fcc=Fcc)
molec.setvar(atonums=atonums, masses=masses)
molec.setvar(ch=ch, mtp=mtp, V0=E)
molec.prepare()
# Deal with frozen atoms [atom i is frozen if Fij=0 forall j)
frozen_xcc, frozen_symbols = molec.remove_frozen()
# Calculate point group (must be done after remove frozen)
molec.calc_pgroup(force=True)
# Deal with Hessian
molec.setup()
# write gts file
molec.genfile_gts(PN.DIR1 + gtsfile, level=clevel)
status = 1
# write frozen (if there are frozen atoms)
RW.write_frozen(PN.DIR1 + file_frozen, frozen_xcc, frozen_symbols)
# write molden file
idata = (PN.DIR1 + file_molden, molec._xcc, molec._symbols,
molec._ccfreqs, molec._ccFevecs)
write_molden(*idata)
# save to cache
nimag = int(fncs.numimag(molec._ccfreqs))
pgroup = str(molec._pgroup)
mform = str(molec._mform)
cache = [esfile, gtsfile, E, ch, mtp, nimag, mform, pgroup]
# delete variable, just in case
del xcc, gcc, Fcc
del symbols, atonums, masses
del molec
# return
return status, cache