def convertors(b):
#toGeo(b, b.name+'.geo')
toGeo(b, 'geo')
toXyz(b, b.name+'.xyz')
toGjf(b, b.name+'.gjf')
toPdb(b, b.name+'.pdb')
toReaxLammps(b)
def main():
"""get qm info
"""
if len(sys.argv) < 2:
print("g03.py logfile")
else:
for i in sys.argv[1:]:
geo = i.split(".")[0]
# get configuration
a = G03LogConf(i)
# get charge and energy (HF and Zero)
b = G03tools(i)
# parse the configuration to standard format
c = a.parser()
hf, zpe = b.getEnergy()
o = open("qm_ener.dat", "w")
o.write("%-15s HF %.8f\n" % (geo, hf))
o.write("%-15s ZPE %.8f\n" % (geo, zpe))
o.close()
charges = b.getMullikenCharge()
o = open("qm_mulliken_charge.dat", "w")
for j in charges:
o.write("%-15s%6s%6s%12s # %s\n" %
(geo, "1", j[0], j[2], j[1]))
o.close()
charges = b.getESPCharge()
o = open("qm_esp_charge.dat", "w")
for j in charges:
o.write("%-15s%6s%6s%12s # %s\n" %
(geo, "1", j[0], j[2], j[1]))
o.close()
# freq calculation if quit normally
if a.stat == 1:
method = " ".join([j.strip() for j in c.methods])
tokens = method.strip().split()
for n in range(len(tokens)):
if "opt" in tokens[n]:
tokens[n] = "freq"
elif "geo" in tokens[n]:
tokens[n] = ''
c.methods = [" ".join(tokens)]
c.options = ["%mem=800MB"]
toGjf(c, "freq.gjf")
else:
runfile = os.path.join(os.getcwd(), i)
print("Warning: unfinished calculation!: %s" % runfile)
method = " ".join([j.strip() for j in c.methods])
tokens = method.strip().split()
for n in range(len(tokens)):
if "geo" in tokens[n]:
tokens[n] = ''
c.methods = [" ".join(tokens)]
toGjf(c, "conti.gjf")
def main():
"""get qm info
"""
if len(sys.argv) < 2:
print "g03.py logfile"
else:
for i in sys.argv[1:]:
geo = i.split(".")[0]
# get configuration
a = G03LogConf(i)
# get charge and energy (HF and Zero)
b = G03tools(i)
# parse the configuration to standard format
c = a.parser()
hf, zpe = b.getEnergy()
o = open("qm_ener.dat", "w")
o.write("%-15s HF %.8f\n"%(geo, hf))
o.write("%-15s ZPE %.8f\n"%(geo, zpe))
o.close()
charges = b.getCharge()
o = open("qm_charge.dat", "w")
for j in charges:
o.write("%-15s%6s%6s%12s # %s\n"%( geo, "1", j[0], j[2], j[1]))
o.close()
# freq calculation if quit normally
if a.stat == 1:
method = " ".join([j.strip() for j in c.methods])
tokens = method.strip().split()
for n in range(len(tokens)):
if "opt" in tokens[n]:
tokens[n] = "freq"
elif "geo" in tokens[n]:
tokens[n] = ''
c.methods = [" ".join(tokens)]
c.options = ["%mem=800MB"]
toGjf(c, "freq.gjf")
else:
runfile = os.path.join(os.getcwd(), i)
print "Warning: unfinished calculation!: %s"%runfile
method = " ".join([j.strip() for j in c.methods])
tokens = method.strip().split()
for n in range(len(tokens)):
if "geo" in tokens[n]:
tokens[n] = ''
c.methods = [" ".join(tokens)]
toGjf(c, "conti.gjf")
""" read the geo file and output to data (LAMMPS), geo and xyz file.
"""
import sys, os
from mytype import System, Molecule, Atom
from g03 import G03Gjf
from output_conf import toXyz, toGeo, toGjf
usage = """gau2xyz g03logfiles"""
if len(sys.argv) < 2:
print usage
else:
for i in sys.argv[1:]:
outfile = i.split(".")[0]
if os.path.exists(i):
a = G03Gjf(i)
b = a.parser()
b.geotag = "BIOGRF 200"
toXyz(b, outfile + ".xyz")
toGeo(b, outfile + ".geo")
toGjf(b, outfile + ".gjf.bak")
else:
print "missing file %s" % i
""" read the geo file and output to data (LAMMPS), geo and xyz file.
"""
import sys, os
from mytype import System, Molecule, Atom
from g03 import G03Gjf
from output_conf import toXyz, toGeo, toGjf
usage = """gau2xyz g03logfiles"""
if len(sys.argv) < 2:
print usage
else:
for i in sys.argv[1:]:
outfile = i.split(".")[0]
if os.path.exists(i):
a = G03Gjf(i)
b = a.parser()
b.geotag = "BIOGRF 200"
toXyz(b, outfile+".xyz")
toGeo(b, outfile+".geo")
toGjf(b, outfile+".gjf.bak")
else:
print "missing file %s"%i
