import numpy as np
import ase.units
from ase.calculators.calculator import FileIOCalculator, SCFError
[docs]
class QChem(FileIOCalculator):
"""
QChem calculator
"""
name = 'QChem'
implemented_properties = ['energy', 'forces']
_legacy_default_command = 'qchem PREFIX.inp PREFIX.out'
# Following the minimal requirements given in
# http://www.q-chem.com/qchem-website/manual/qchem43_manual/sect-METHOD.html
default_parameters = {'method': 'hf',
'basis': '6-31G*',
'jobtype': None,
'charge': 0}
def __init__(self, restart=None,
ignore_bad_restart_file=FileIOCalculator._deprecated,
label='qchem', scratch=None, np=1, nt=1, pbs=False,
basisfile=None, ecpfile=None, atoms=None, **kwargs):
"""
The scratch directory, number of processor and threads as well as a few
other command line options can be set using the arguments explained
below. The remaining kwargs are copied as options to the input file.
The calculator will convert these options to upper case
(Q-Chem standard) when writing the input file.
scratch: str
path of the scratch directory
np: int
number of processors for the -np command line flag
nt: int
number of threads for the -nt command line flag
pbs: boolean
command line flag for pbs scheduler (see Q-Chem manual)
basisfile: str
path to file containing the basis. Use in combination with
basis='gen' keyword argument.
ecpfile: str
path to file containing the effective core potential. Use in
combination with ecp='gen' keyword argument.
"""
FileIOCalculator.__init__(self, restart, ignore_bad_restart_file,
label, atoms, **kwargs)
# Augment the command by various flags
if pbs:
self.command = 'qchem -pbs '
else:
self.command = 'qchem '
if np != 1:
self.command += '-np %d ' % np
if nt != 1:
self.command += '-nt %d ' % nt
self.command += 'PREFIX.inp PREFIX.out'
if scratch is not None:
self.command += f' {scratch}'
self.basisfile = basisfile
self.ecpfile = ecpfile
def read(self, label):
raise NotImplementedError
def read_results(self):
filename = self.label + '.out'
with open(filename) as fileobj:
lineiter = iter(fileobj)
for line in lineiter:
if 'SCF failed to converge' in line:
raise SCFError()
elif 'ERROR: alpha_min' in line:
# Even though it is not technically a SCFError:
raise SCFError()
elif ' Total energy in the final basis set =' in line:
convert = ase.units.Hartree
self.results['energy'] = float(line.split()[8]) * convert
elif ' Gradient of SCF Energy' in line:
# Read gradient as 3 by N array and transpose at the end
gradient = [[] for _ in range(3)]
# Skip first line containing atom numbering
next(lineiter)
while True:
# Loop over the three Cartesian coordinates
for i in range(3):
# Cut off the component numbering and remove
# trailing characters ('\n' and stuff)
line = next(lineiter)[5:].rstrip()
# Cut in chunks of 12 symbols and convert into
# strings. This is preferred over string.split() as
# the fields may overlap for large gradients
gradient[i].extend(list(map(
float, [line[i:i + 12]
for i in range(0, len(line), 12)])))
# After three force components we expect either a
# separator line, which we want to skip, or the end of
# the gradient matrix which is characterized by the
# line ' Max gradient component'.
# Maybe change stopping criterion to be independent of
# next line. Eg. if not lineiter.next().startswith(' ')
if ' Max gradient component' in next(lineiter):
# Minus to convert from gradient to force
self.results['forces'] = np.array(gradient).T * (
-ase.units.Hartree / ase.units.Bohr)
break
def write_input(self, atoms, properties=None, system_changes=None):
FileIOCalculator.write_input(self, atoms, properties, system_changes)
filename = self.label + '.inp'
with open(filename, 'w') as fileobj:
fileobj.write('$comment\n ASE generated input file\n$end\n\n')
fileobj.write('$rem\n')
if self.parameters['jobtype'] is None:
if 'forces' in properties:
fileobj.write(' %-25s %s\n' % ('JOBTYPE', 'FORCE'))
else:
fileobj.write(' %-25s %s\n' % ('JOBTYPE', 'SP'))
for prm in self.parameters:
if prm not in ['charge', 'multiplicity']:
if self.parameters[prm] is not None:
fileobj.write(' %-25s %s\n' % (
prm.upper(), self.parameters[prm].upper()))
# Not even a parameters as this is an absolute necessity
fileobj.write(' %-25s %s\n' % ('SYM_IGNORE', 'TRUE'))
fileobj.write('$end\n\n')
fileobj.write('$molecule\n')
# Following the example set by the gaussian calculator
if ('multiplicity' not in self.parameters):
tot_magmom = atoms.get_initial_magnetic_moments().sum()
mult = tot_magmom + 1
else:
mult = self.parameters['multiplicity']
# Default charge of 0 is defined in default_parameters
fileobj.write(' %d %d\n' % (self.parameters['charge'], mult))
for a in atoms:
fileobj.write(' {} {:f} {:f} {:f}\n'.format(a.symbol,
a.x, a.y, a.z))
fileobj.write('$end\n\n')
if self.basisfile is not None:
with open(self.basisfile) as f_in:
basis = f_in.readlines()
fileobj.write('$basis\n')
fileobj.writelines(basis)
fileobj.write('$end\n\n')
if self.ecpfile is not None:
with open(self.ecpfile) as f_in:
ecp = f_in.readlines()
fileobj.write('$ecp\n')
fileobj.writelines(ecp)
fileobj.write('$end\n\n')