def get_input(x, template,method='CCSD',basis='cc-pvdz'):
"""
Returns Gaussian input file text (str) based on a given template.
"""
mol = ob.get_mol(x)
mult = ob.get_multiplicity(mol)
nopen = mult - 1
charge = ob.get_charge(mol)
formula = ob.get_formula(mol)
geo = ob.get_geo(mol)
xyz = ob.get_xyz(mol)
zmat = ob.get_zmat(mol)
uniquename = ob.get_inchi_key(mol, mult)
smilesname = ob.get_smiles_filename(mol)
inp = template.replace("QTC(CHARGE)", str(charge))
inp = inp.replace("QTC(MULTIPLICITY)", str(mult))
inp = inp.replace("QTC(NOPEN)", str(nopen))
inp = inp.replace("QTC(UNIQUENAME)", uniquename)
inp = inp.replace("QTC(SMILESNAME)", smilesname)
inp = inp.replace("QTC(ZMAT)", zmat)
inp = inp.replace("QTC(GEO)", geo)
inp = inp.replace("QTC(XYZ)", xyz)
inp = inp.replace("QTC(FORMULA)", formula)
inp = inp.replace("QTC(METHOD)", method)
inp = inp.replace("QTC(BASIS)", basis)
if "QTC(" in inp:
print("Error in template file:\n" + inp)
return
return inp
def get_gaussian_input(x, template, mult=0):
"""
Returns Gaussian input file based on a given template.
"""
if type(x) is str:
mol = ob.get_mol(x)
else:
mol = x
if mult == 0:
mult = ob.get_multiplicity(mol)
charge = ob.get_charge(mol)
geo = ob.get_geo(mol)
xyz = ob.get_xyz(mol)
zmat = ob.get_zmat(mol)
uniquename = ob.get_inchi_key(mol, mult)
inp = template.replace("QTC(CHARGE)", str(charge))
inp = inp.replace("QTC(MULTIPLICITY)", str(mult))
inp = inp.replace("QTC(UNIQUENAME)", uniquename)
inp = inp.replace("QTC(ZMAT)", zmat)
inp = inp.replace("QTC(GEO)", geo)
inp = inp.replace("QTC(XYZ)", xyz)
if "QTC(" in inp:
print("Error in template file:\n" + inp)
return
return inp
def run_molpro(s, exe='molpro', template='molpro_template.txt', mult=None, overwrite=False):
"""
Runs molpro, returns a string specifying the status of the calculation.
TODO
"""
mol = ob.get_mol(s, make3D=True)
if mult is None:
mult = ob.get_multiplicity(mol)
tmp = io.read_file(template)
inptext = get_input(mol, tmp, mult)
prefix = ob.get_smiles_filename(s)
inpfile = prefix + '.nw'
outfile = prefix + '_nwchem.log'
command = [exe, inpfile]
if io.check_file(outfile, timeout=1):
if overwrite:
msg = 'Overwriting previous calculation "{0}"\n'.format(io.get_path(outfile))
run = True
else:
msg = 'Skipping calculation, found "{0}"\n'.format(io.get_path(outfile))
run = False
else:
run = True
if run:
if not io.check_file(inpfile, timeout=1) or overwrite:
io.write_file(inptext, inpfile)
if io.check_file(inpfile, timeout=1):
msg = io.execute(command,stdoutfile=outfile,merge=True)
if io.check_file(outfile, timeout=1):
msg += ' Output file: "{0}"\n'.format(io.get_path(outfile))
else:
msg = 'Failed, cannot find input file "{0}"\n'.format(io.get_path(inpfile))
return msg
def run_mopac(s, exe='mopac', template='mopac_template.txt', mult=None, overwrite=False):
"""
Runs mopac, returns a string specifying the status of the calculation.
mopac inp inp.out
Mopac always writes the log file into a file with .out extension
"""
mol = ob.get_mol(s, make3D=True)
if mult is None:
mult = ob.get_multiplicity(mol)
tmp = io.read_file(template)
inptext = get_input(mol, tmp, mult)
prefix = ob.get_smiles_filename(s)
inpfile = prefix + '.mop'
outfile = prefix + '.out'
command = [exe, inpfile]
if io.check_file(outfile, timeout=1):
if overwrite:
msg = 'Overwriting previous calculation "{0}"\n'.format(io.get_path(outfile))
run = True
else:
msg = 'Skipping calculation, found "{0}"\n'.format(io.get_path(outfile))
run = False
else:
run = True
if run:
if not io.check_file(inpfile, timeout=1) or overwrite:
io.write_file(inptext, inpfile)
if io.check_file(inpfile, timeout=1):
msg = io.execute(command)
if io.check_file(outfile, timeout=1):
msg += 'Output file: "{0}"\n'.format(io.get_path(outfile))
else:
msg = 'Failed, cannot find input file "{0}"\n'.format(io.get_path(inpfile))
return msg
def run_gaussian(s, exe='g09', template='gaussian_template.txt', mult=None, overwrite=False):
"""
Runs gaussian calculation
"""
mol = ob.get_mol(s, make3D=True)
if mult is None:
mult = ob.get_multiplicity(mol)
tmp = io.read_file(template)
inptext = get_gaussian_input(mol, tmp, mult)
prefix = ob.get_smiles_filename(s)
inpfile = prefix + '.g09'
outfile = prefix + '_gaussian.log'
command = [exe, inpfile, outfile]
if io.check_file(outfile, timeout=1):
if overwrite:
msg = 'Overwriting previous calculation "{0}"\n'.format(io.get_path(outfile))
run = True
else:
msg = 'Skipping calculation, found "{0}"\n'.format(io.get_path(outfile))
run = False
else:
run = True
if run:
if not io.check_file(inpfile, timeout=1) or overwrite:
io.write_file(inptext, inpfile)
if io.check_file(inpfile, timeout=1):
msg = io.execute(command)
if io.check_file(outfile, timeout=1):
msg += ' Output file: "{0}"\n'.format(io.get_path(outfile))
else:
msg = 'Failed, cannot find input file "{0}"\n'.format(io.get_path(inpfile))
return msg
def run(s):
"""
A driver function to run quantum chemistry and thermochemistry calculations based
on command line options:
--qcmethod
--qccode
"""
import qctools as qc
import obtools as ob
import tctools as tc
import iotools as io
mol = ob.get_mol(s)
mult = ob.get_multiplicity(mol)
dirpath = ob.get_unique_path(mol, method=_qcmethod, mult=mult)
groupsfile = 'new.groups'
io.mkdir(dirpath)
cwd = io.pwd()
if _runthermo:
if io.check_file(groupsfile):
io.cp(groupsfile, dirpath)
if not io.check_file(groupsfile, 1):
print 'Could not copy new.groups file to target directory {0}'.format(
dirpath)
return -1
else:
print 'new.groups file required in working directory'
return -1
if io.check_dir(dirpath, 1):
io.cd(dirpath)
else:
print 'I/O error, {0} directory not found'.format(dirpath)
return -1
if _runqc:
if _qccode == 'mopac':
outstr = qc.run_mopac(s,
mopacexe=_mopacexe,
method=_qcmethod,
mult=mult)
outfile = outstr.split(' : ')[0]
if _runthermo:
lines = io.read_file(outfile, aslines=True)
xyz = qc.get_mopac_xyz(lines)
freqs = qc.get_mopac_freq(lines)
zpe = qc.get_mopac_zpe(lines)
deltaH = qc.get_mopac_deltaH(lines)
get_chemkin_polynomial(mol, _qcmethod, zpe, xyz, freqs, deltaH)
io.cd(cwd)
return outstr
def run(s, template, parameters, mult=None):
"""
Runs nwchem, returns a string specifying the status of the calculation.
nwchem inp.nw > nw.log
NWChem writes output and error to stdout.
Generates .db (a binary file to restart a job) and .movecs (scf wavefunction) files in the run directory.
Generates many junk files in a scratch directory.
If scratch is not specified, these junk files are placed in the run directory.
"""
package = parameters['qcpackage']
overwrite = parameters['overwrite']
mol = ob.get_mol(s, make3D=True)
msg = ''
if mult is None:
mult = ob.get_multiplicity(mol)
else:
ob.set_mult(mol, mult)
tmp = io.read_file(template)
inptext = get_input(mol, tmp)
prefix = ob.get_smiles_filename(s) + '_' + package
inpfile = prefix + '.inp'
outfile = prefix + '.out'
if io.check_file(outfile, timeout=1):
if overwrite:
msg = 'Overwriting previous calculation "{0}"\n'.format(io.get_path(outfile))
run = True
else:
msg = 'Skipping calculation, found "{0}"\n'.format(io.get_path(outfile))
run = False
else:
run = True
if run:
if not io.check_file(inpfile, timeout=1) or overwrite:
io.write_file(inptext, inpfile)
if io.check_file(inpfile, timeout=1):
if package == 'extrapolation':
run_extrapolation(s, parameters)
elif package == 'nwchem':
command = [parameters['qcexe'], inpfile]
msg += io.execute(command,stdoutfile=outfile,merge=True)
else:
command = [parameters['qcexe'], inpfile, outfile]
msg = io.execute(command)
if io.check_file(outfile, timeout=1):
msg += ' Output file: "{0}"\n'.format(io.get_path(outfile))
else:
msg += 'Failed, cannot find input file "{0}"\n'.format(io.get_path(inpfile))
return msg
def run_nwchem(s, exe='nwchem', template='nwchem_template.txt', mult=None, overwrite=False):
"""
Runs nwchem, returns a string specifying the status of the calculation.
nwchem inp.nw > nw.log
NWChem writes output and error to stdout.
Generates .db (a binary file to restart a job) and .movecs (scf wavefunction) files in the run directory.
Generates many junk files in a scratch directory.
If scratch is not specified, these junk files are placed in the run directory.
"""
mol = ob.get_mol(s, make3D=True)
if mult is None:
mult = ob.get_multiplicity(mol)
tmp = io.read_file(template)
inptext = get_input(mol, tmp)
prefix = ob.get_smiles_filename(s)
inpfile = prefix + '.nw'
outfile = prefix + '_nwchem.log'
command = [exe, inpfile]
if io.check_file(outfile, timeout=1):
if overwrite:
msg = 'Overwriting previous calculation "{0}"\n'.format(io.get_path(outfile))
run = True
else:
msg = 'Skipping calculation, found "{0}"\n'.format(io.get_path(outfile))
run = False
else:
run = True
if run:
if not io.check_file(inpfile, timeout=1) or overwrite:
io.write_file(inptext, inpfile)
if io.check_file(inpfile, timeout=1):
msg = io.execute(command,stdoutfile=outfile,merge=True)
if io.check_file(outfile, timeout=1):
msg += ' Output file: "{0}"\n'.format(io.get_path(outfile))
else:
msg = 'Failed, cannot find input file "{0}"\n'.format(io.get_path(inpfile))
return msg