"""
authors: Ben Comer (Georgia Tech), Xiangyun (Ray) Lei (Georgia Tech)
"""
import json
import multiprocessing
import os
import warnings
from io import StringIO
import numpy as np
from ase import io
from ase.calculators.calculator import (Calculator, CalculatorSetupError,
InputError, ReadError, all_changes)
from ase.config import cfg
from ase.units import Bohr, Hartree
[docs]class Psi4(Calculator):
"""
An ase calculator for the popular open source Q-chem code
psi4.
method is the generic input for whatever method you wish to use, thus
and quantum chemistry method implemented in psi4 can be input
(i.e. ccsd(t))
also note that you can always use the in-built psi4 module through:
calc.psi4
"""
implemented_properties = ['energy', 'forces']
discard_results_on_any_change = True
default_parameters = {
"basis": "aug-cc-pvtz",
"method": "hf",
'symmetry': 'c1'}
def __init__(self, restart=None, ignore_bad_restart=False,
label='psi4-calc', atoms=None, command=None,
**kwargs):
Calculator.__init__(self, restart=restart,
ignore_bad_restart=ignore_bad_restart, label=label,
atoms=atoms, command=command, **kwargs)
import psi4
self.psi4 = psi4
# perform initial setup of psi4 python API
self.set_psi4(atoms=atoms)
def set_psi4(self, atoms=None):
"""
This function sets the imported psi4 module to the settings the user
defines
"""
# Set the scrath directory for electronic structure files.
# The default is /tmp
if 'PSI_SCRATCH' in cfg:
pass
elif self.parameters.get('PSI_SCRATCH'):
# XXX We should probably not be setting envvars except
# if we are creating new processes.
os.environ['PSI_SCRATCH'] = self.parameters['PSI_SCRATCH']
# Input spin settings
if self.parameters.get('reference') is not None:
self.psi4.set_options({'reference':
self.parameters['reference']})
# Memory
if self.parameters.get('memory') is not None:
self.psi4.set_memory(self.parameters['memory'])
# Threads
nthreads = self.parameters.get('num_threads', 1)
if nthreads == 'max':
nthreads = multiprocessing.cpu_count()
self.psi4.set_num_threads(nthreads)
# deal with some ASE specific inputs
if 'kpts' in self.parameters:
raise InputError('psi4 is a non-periodic code, and thus does not'
' require k-points. Please remove this '
'argument.')
if self.parameters['method'] == 'LDA':
# svwn is equivalent to LDA
self.parameters['method'] = 'svwn'
if 'nbands' in self.parameters:
raise InputError('psi4 does not support the keyword "nbands"')
if 'smearing' in self.parameters:
raise InputError('Finite temperature DFT is not implemented in'
' psi4 currently, thus a smearing argument '
'cannot be utilized. please remove this '
'argument')
if 'xc' in self.parameters:
raise InputError('psi4 does not accept the `xc` argument please'
' use the `method` argument instead')
if atoms is None:
if self.atoms is None:
return
else:
atoms = self.atoms
if self.atoms is None:
self.atoms = atoms
# Generate the atomic input
geomline = '{}\t{:.15f}\t{:.15f}\t{:.15f}'
geom = [geomline.format(atom.symbol, *atom.position) for atom in atoms]
geom.append('symmetry {}'.format(self.parameters['symmetry']))
geom.append('units angstrom')
charge = self.parameters.get('charge')
mult = self.parameters.get('multiplicity')
if mult is None:
mult = 1
if charge is not None:
warnings.warn('A charge was provided without a spin '
'multiplicity. A multiplicity of 1 is assumed')
if charge is None:
charge = 0
geom.append(f'{charge} {mult}')
geom.append('no_reorient')
if not os.path.isdir(self.directory):
os.mkdir(self.directory)
self.molecule = self.psi4.geometry('\n'.join(geom))
def read(self, label):
"""Read psi4 outputs made from this ASE calculator
"""
filename = label + '.dat'
if not os.path.isfile(filename):
raise ReadError('Could not find the psi4 output file: ' + filename)
with open(filename) as fd:
txt = fd.read()
if '!ASE Information\n' not in txt:
raise Exception('The output file {} could not be read because '
'the file does not contain the "!ASE Information"'
' lines inserted by this calculator. This likely'
' means the output file was not made using this '
'ASE calculator or has since been modified and '
'thus cannot be read.'.format(filename))
info = txt.split('!ASE Information\n')[1]
info = info.split('!')[0]
saved_dict = json.loads(info)
# use io read to recode atoms
with StringIO(str(saved_dict['atoms'])) as g:
self.atoms = io.read(g, format='json')
self.parameters = saved_dict['parameters']
self.results = saved_dict['results']
# convert forces to numpy array
if 'forces' in self.results:
self.results['forces'] = np.array(self.results['forces'])
def calculate(self, atoms=None, properties=['energy'],
system_changes=all_changes, symmetry='c1'):
Calculator.calculate(self, atoms=atoms)
if self.atoms is None:
raise CalculatorSetupError('An Atoms object must be provided to '
'perform a calculation')
atoms = self.atoms
if atoms.get_initial_magnetic_moments().any():
self.parameters['reference'] = 'uhf'
self.parameters['multiplicity'] = None
# this inputs all the settings into psi4
self.set_psi4(atoms=atoms)
self.psi4.core.set_output_file(self.label + '.dat',
False)
# Set up the method
method = self.parameters['method']
basis = self.parameters['basis']
# Do the calculations
if 'forces' in properties:
grad, wf = self.psi4.driver.gradient(f'{method}/{basis}',
return_wfn=True)
# energy comes for free
energy = wf.energy()
self.results['energy'] = energy * Hartree
# convert to eV/A
# also note that the gradient is -1 * forces
self.results['forces'] = -1 * np.array(grad) * Hartree / Bohr
elif 'energy' in properties:
energy = self.psi4.energy(f'{method}/{basis}',
molecule=self.molecule)
# convert to eV
self.results['energy'] = energy * Hartree
# dump the calculator info to the psi4 file
save_atoms = self.atoms.copy()
# use io.write to encode atoms
with StringIO() as fd:
io.write(fd, save_atoms, format='json')
json_atoms = fd.getvalue()
# convert forces to list for json storage
save_results = self.results.copy()
if 'forces' in save_results:
save_results['forces'] = save_results['forces'].tolist()
save_dict = {'parameters': self.parameters,
'results': save_results,
'atoms': json_atoms}
self.psi4.core.print_out('!ASE Information\n')
self.psi4.core.print_out(json.dumps(save_dict))
self.psi4.core.print_out('!')