def genfile_gts(self,filename,level=""):
write_gtsfile(self._xcc,self._atnums,self._ch,self._mtp,\
self._V0,self._pgroup,self._rotsigma,self._gcc,\
self._Fcc,filename,level=level)
try : write_gtsfile(self._xcc,self._atnums,self._ch,self._mtp,\
self._V0,self._pgroup,self._rotsigma,self._gcc,\
self._Fcc,filename,level=level)
except: return 0
return 1
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) #(c) a Gaussian output file
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)
# get point group
pgroup, rotsigma = get_pgs(atonums, masses, xcc)
# write gts
write_gtsfile(xcc,
atonums,
ch,
mtp,
E,
pgroup,
rotsigma,
gcc,
Fcc,
gtsfile,
level=clevel)
return 1, E
except Exc.FileType:
continue
except:
continue
return 0, None
def analyze_filefolder(ff, dtrack):
global sthwrong
global wrong1
global wrong2
iblank = " "
# Is ff a folder or a file?
if os.path.isdir(PN.UFOLDER + ff):
# Get CTC name & list of files
ctc_name = ff[:-1]
files = sorted(
[ff + filename for filename in os.listdir(PN.UFOLDER + ff)])
print " |--> %s" % ff
iblank += " "
else:
# Get CTC name & list of files
ctc_name = ff.split(".")[0]
files = [ff]
# valid name??
if not is_string_valid(ctc_name, extra="_"):
print iblank + "|--> %s (invalid name!)" % ff
sthwrong = True
wrong1 = True
return None
# only files with known extension
files = known_files(files)
# Convert to gts (provisional name)
count = 1
gtslist = []
for ifile in files:
# read file
data = data_from_file(PN.UFOLDER + ifile)
# print info
if ifile in dtrack.keys():
print iblank + "|--> %s (in %s)" % (ifile.split("/")[-1],
PN.IFILE0)
continue
elif data is None:
print iblank + "|--> %s (reading fails!)" % (ifile.split("/")[-1])
sthwrong = True
wrong2 = True
continue
else:
print iblank + "|--> %s (new)" % (ifile.split("/")[-1])
while True:
prov_gts = PN.DIR1 + "%s.gts_%i" % (ctc_name, count)
count += 1
if not os.path.exists(prov_gts): break
# expand data
xcc, atonums, ch, mtp, E, gcc, Fcc, masses, clevel = data
# get point group
pgroup, rotsigma = get_pgs(atonums, masses, xcc)
# write gts (provisional)
if not os.path.exists(PN.DIR1): os.mkdir(PN.DIR1)
write_gtsfile(xcc,
atonums,
ch,
mtp,
E,
pgroup,
rotsigma,
gcc,
Fcc,
prov_gts,
level=clevel)
gtslist.append((E, ifile, prov_gts))
# sort by energy (only those created)
gtslist.sort()
# Rename gts files
info, idx = [], 1
for E, ifile, prov_gts in gtslist:
while True:
ofile = ctc_name + ".%003i.gts" % (idx)
idx += 1
if ofile in dtrack.values(): continue
if not os.path.exists(PN.DIR1 + ofile): break
os.rename(prov_gts, PN.DIR1 + ofile)
info.append((E, ifile, ofile))
return info