Source code for qcdb.interface_dftd3

# Psi4: an open-source quantum chemistry software package
# Copyright (c) 2007-2017 The Psi4 Developers.
# The copyrights for code used from other parties are included in
# the corresponding files.
# This file is part of Psi4.
# Psi4 is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, version 3.
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
# GNU Lesser General Public License for more details.
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# with Psi4; if not, write to the Free Software Foundation, Inc.,
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"""Module with functions that interface with Grimme's DFTD3 code."""
from __future__ import absolute_import, print_function
import os
import re
import sys
import math
import uuid
import shutil
import socket
import subprocess

    from psi4.driver.p4util.exceptions import *
    from psi4 import core
    isP4regime = True
except ImportError:
    from .exceptions import *
    isP4regime = False
from .dashparam import *
from .molecule import Molecule

[docs]def run_dftd3(self, func=None, dashlvl=None, dashparam=None, dertype=None, verbose=False): """Function to call Grimme's dftd3 program ( to compute the -D correction of level *dashlvl* using parameters for the functional *func*. The dictionary *dashparam* can be used to supply a full set of dispersion parameters in the absense of *func* or to supply individual overrides in the presence of *func*. Returns energy if *dertype* is 0, gradient if *dertype* is 1, else tuple of energy and gradient if *dertype* unspecified. The dftd3 executable must be independently compiled and found in :envvar:`PATH` or :envvar:`PSIPATH`. *self* may be either a qcdb.Molecule (sensibly) or a psi4.Molecule (works b/c psi4.Molecule has been extended by this method py-side and only public interface fns used) or a string that can be instantiated into a qcdb.Molecule. func - functional alias or None dashlvl - functional type d2gr/d3zero/d3bj/d3mzero/d3mbj dashparam - dictionary dertype = derivative level """ # Create (if necessary) and update qcdb.Molecule if isinstance(self, Molecule): # called on a qcdb.Molecule pass elif isinstance(self, core.Molecule): # called on a python export of a psi4.Molecule (py-side through Psi4's driver) self.create_psi4_string_from_molecule() elif isinstance(self, basestring): # called on a string representation of a psi4.Molecule (c-side through psi4.Dispersion) self = Molecule(self) else: raise ValidationError("""Argument mol must be psi4string or qcdb.Molecule""") self.update_geometry() # Validate arguments if dertype is None: dertype = -1 elif der0th.match(str(dertype)): dertype = 0 elif der1st.match(str(dertype)): dertype = 1 elif der2nd.match(str(dertype)): raise ValidationError('Requested derivative level \'dertype\' %s not valid for run_dftd3.' % (dertype)) else: raise ValidationError('Requested derivative level \'dertype\' %s not valid for run_dftd3.' % (dertype)) if dashlvl is not None: dashlvl = dashlvl.lower() dashlvl = dash_alias['-' + dashlvl][1:] if ('-' + dashlvl) in dash_alias.keys() else dashlvl if dashlvl not in dashcoeff.keys(): raise ValidationError("""-D correction level %s is not available. Choose among %s.""" % (dashlvl, dashcoeff.keys())) else: raise ValidationError("""Must specify a dashlvl""") if func is not None: dftd3_params = dash_server(func, dashlvl) else: dftd3_params = {} if dashparam is not None: dftd3_params.update(dashparam) # Move ~/.dftd3par.<hostname> out of the way so it won't interfere defaultfile = os.path.expanduser('~') + '/.dftd3par.' + socket.gethostname() defmoved = False if os.path.isfile(defaultfile): os.rename(defaultfile, defaultfile + '_hide') defmoved = True # Find environment by merging PSIPATH and PATH environment variables lenv = { 'PATH': ':'.join([os.path.abspath(x) for x in os.environ.get('PSIPATH', '').split(':') if x != '']) + \ ':' + os.environ.get('PATH'), 'LD_LIBRARY_PATH': os.environ.get('LD_LIBRARY_PATH') } # Filter out None values as subprocess will fault on them lenv = {k: v for k, v in lenv.items() if v is not None} # Find out if running from Psi4 for scratch details and such # try: # import psi4 # except ImportError as err: # isP4regime = False # else: # isP4regime = True # Setup unique scratch directory and move in current_directory = os.getcwd() if isP4regime: psioh = core.IOManager.shared_object() psio = core.IO.shared_object() os.chdir(psioh.get_default_path()) dftd3_tmpdir = 'psi.' + str(os.getpid()) + '.' + psio.get_default_namespace() + \ '.dftd3.' + str(uuid.uuid4())[:8] else: dftd3_tmpdir = os.environ['HOME'] + os.sep + 'dftd3_' + str(uuid.uuid4())[:8] if os.path.exists(dftd3_tmpdir) is False: os.mkdir(dftd3_tmpdir) os.chdir(dftd3_tmpdir) # Write dftd3_parameters file that governs dispersion calc paramcontents = dftd3_coeff_formatter(dashlvl, dftd3_params) paramfile1 = 'dftd3_parameters' # older patched name with open(paramfile1, 'w') as handle: handle.write(paramcontents) paramfile2 = '.dftd3par.local' # new mainline name with open(paramfile2, 'w') as handle: handle.write(paramcontents) # Write dftd3_geometry file that supplies geometry to dispersion calc numAtoms = self.natom() # We seem to have a problem with one atom, force the correct result if numAtoms == 1: dashd = 0.0 dashdderiv = core.Matrix(1, 3) if dertype == -1: return dashd, dashdderiv elif dertype == 0: return dashd elif dertype == 1: return dashdderiv geom = self.save_string_xyz() reals = [] for line in geom.splitlines(): lline = line.split() if len(lline) != 4: continue if lline[0] == 'Gh': numAtoms -= 1 else: reals.append(line) geomtext = str(numAtoms) + '\n\n' for line in reals: geomtext += line.strip() + '\n' geomfile = './' with open(geomfile, 'w') as handle: handle.write(geomtext) # TODO somehow the variations on save_string_xyz and # whether natom and chgmult does or doesn't get written # have gotten all tangled. I fear this doesn't work # the same btwn libmints and qcdb or for ghosts # Call dftd3 program command = ['dftd3', geomfile] if dertype != 0: command.append('-grad') try: dashout = subprocess.Popen(command, stdout=subprocess.PIPE, env=lenv) except OSError as e: raise ValidationError('Program dftd3 not found in path. %s' % e) out, err = dashout.communicate() # Parse output (could go further and break into E6, E8, E10 and Cn coeff) success = False for line in out.splitlines(): line = line.decode('utf-8') if re.match(' Edisp /kcal,au', line): sline = line.split() dashd = float(sline[3]) if re.match(' normal termination of dftd3', line): success = True if not success: os.chdir(current_directory) raise Dftd3Error("""Unsuccessful run. Possibly -D variant not available in dftd3 version.""") # Parse grad output if dertype != 0: derivfile = './dftd3_gradient' dfile = open(derivfile, 'r') dashdderiv = [] for line in geom.splitlines(): lline = line.split() if len(lline) != 4: continue if lline[0] == 'Gh': dashdderiv.append([0.0, 0.0, 0.0]) else: dashdderiv.append([float(x.replace('D', 'E')) for x in dfile.readline().split()]) dfile.close() if len(dashdderiv) != self.natom(): raise ValidationError('Program dftd3 gradient file has %d atoms- %d expected.' % \ (len(dashdderiv), self.natom())) # Prepare results for Psi4 if isP4regime and dertype != 0: core.set_variable('DISPERSION CORRECTION ENERGY', dashd) psi_dashdderiv = core.Matrix(self.natom(), 3) psi_dashdderiv.set(dashdderiv) # Print program output to file if verbose if not verbose and isP4regime: verbose = True if core.get_option('SCF', 'PRINT') >= 3 else False if verbose: text = '\n ==> DFTD3 Output <==\n' text += out.decode('utf-8') if dertype != 0: with open(derivfile, 'r') as handle: text +='D', 'E') text += '\n' if isP4regime: core.print_out(text) else: print(text) # Clean up files and remove scratch directory os.unlink(paramfile1) os.unlink(paramfile2) os.unlink(geomfile) if dertype != 0: os.unlink(derivfile) if defmoved is True: os.rename(defaultfile + '_hide', defaultfile) os.chdir('..') try: shutil.rmtree(dftd3_tmpdir) except OSError as e: ValidationError('Unable to remove dftd3 temporary directory %s' % e) os.chdir(current_directory) # return -D & d(-D)/dx if dertype == -1: return dashd, dashdderiv elif dertype == 0: return dashd elif dertype == 1: return psi_dashdderiv
try: # Attach method to libmints psi4.Molecule class core.Molecule.run_dftd3 = run_dftd3 except (NameError, AttributeError): # But don't worry if that doesn't work b/c # it'll get attached to qcdb.Molecule class pass