Source code for ase.calculators.psi4

"""
authors: Ben Comer (Georgia Tech), Xiangyun (Ray) Lei (Georgia Tech)

"""
from io import StringIO
from ase.calculators.calculator import Calculator, all_changes
from ase.calculators.calculator import InputError, ReadError
from ase.calculators.calculator import CalculatorSetupError
import multiprocessing
from ase import io
import numpy as np
import json
from ase.units import Bohr, Hartree
import warnings
import os


[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'] 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 os.environ: pass elif self.parameters.get('PSI_SCRATCH'): 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 None 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('{} {}'.format(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 set(self, **kwargs): changed_parameters = Calculator.set(self, **kwargs) if changed_parameters: self.reset() 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, 'r') as f: txt = f.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('{}/{}'.format(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('{}/{}'.format(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 f: io.write(f, save_atoms, format='json') json_atoms = f.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('!')