#
# @BEGIN LICENSE
#
# 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.
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# 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.
#
# Psi4 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
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# You should have received a copy of the GNU Lesser General Public License along
# with Psi4; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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# @END LICENSE
#
"""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
try:
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 (http://toc.uni-muenster.de/DFTD3/)
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 = './dftd3_geometry.xyz'
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 += handle.read().replace('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
