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
def userfile_to_gtsfile(filename, gtsfile):
'''
Read a file given by the user and generate gts file
if possible
'''
gtsfile = gtsname(gtsfile, "full")
read_methods = []
read_methods.append(read_gtsfile) #(a) a gts file
read_methods.append(read_fchk) #(b) a fchk file
read_methods.append(read_gauout_v1) #(c.1) a Gaussian output file (ramos)
read_methods.append(read_gauout_v2) #(c.2) a Gaussian output file (ferro)
read_methods.append(read_orca) #(d) an Orca output file
for read_method in read_methods:
try:
xcc, atonums, ch, mtp, E, gcc, Fcc, masses, clevel = read_method(
filename)[0:9]
if read_method == read_gtsfile: clevel = ""
# in case no data in masses
if masses is None or len(masses) == 0 or sum(masses) == 0.0:
masses = atonums2masses(atonums)
# Some checking
if len(atonums) != 1 and Fcc in ([], None):
#raise Exc.FccNotFound
return -1, None
# Generate Molecule instance
molecule = Molecule()
molecule.setvar(xcc=xcc, gcc=gcc, Fcc=Fcc)
molecule.setvar(atonums=atonums, masses=masses)
molecule.setvar(ch=ch, mtp=mtp, V0=E)
molecule.prepare()
# Deal with frozen atoms
ffrozen = gtsfile + ".frozen"
frozen_xcc, frozen_symbols = molecule.remove_frozen()
RW.write_frozen(ffrozen, frozen_xcc, frozen_symbols)
# write gts
molecule.calc_pgroup(force=True)
molecule.genfile_gts(gtsfile, level=clevel)
return 1, E
except Exc.FileType:
continue
except:
continue
return 0, None