#
# @BEGIN LICENSE
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# Psi4: an open-source quantum chemistry software package
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# Copyright (c) 2007-2018 The Psi4 Developers.
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# The copyrights for code used from other parties are included in
# the corresponding files.
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# This file is part of Psi4.
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# 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
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# Psi4 is distributed in the hope that it will be useful,
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# GNU Lesser General Public License for more details.
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"""Module with functions that interface with Grimme's DFTD3 code."""
from __future__ import absolute_import
from __future__ import print_function
import os
import re
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(mol, func=None, dashlvl=None, dashparam=None, dertype=None, verbose=False):
"""Compute dispersion correction using Grimme's DFTD3 executable.
Function to call Grimme's dftd3 program to compute the -D correction
of level `dashlvl` using parameters for the functional `func`.
`dashparam` can supply a full set of dispersion parameters in the
absence of `func` or individual overrides in the presence of `func`.
The DFTD3 executable must be independently compiled and found in
:envvar:`PATH` or :envvar:`PSIPATH`.
Parameters
----------
mol : qcdb.Molecule or psi4.core.Molecule or str
Molecule on which to run dispersion calculation. Both qcdb and
psi4.core Molecule classes have been extended by this method, so
either allowed. Alternately, a string that can be instantiated
into a qcdb.Molecule.
func : str or None
Density functional (Psi4, not Turbomole, names) for which to
load parameters from dashcoeff[dashlvl][func]. This is not
passed to DFTD3 and thus may be a dummy or `None`. Any or all
parameters initialized can be overwritten via `dashparam`.
dashlvl : {'d2p4', 'd2gr', 'd3zero', 'd3bj', 'd3mzero', d3mbj', 'd', 'd2', 'd3', 'd3m'}
Flavor of a posteriori dispersion correction for which to load
parameters and call procedure in DFTD3. Must be a keys in
dashcoeff dict (or a key in dashalias that resolves to one).
dashparam : dict, optional
Dictionary of the same keys as dashcoeff[dashlvl] used to
override any or all values initialized by
dashcoeff[dashlvl][func].
dertype : {None, 0, 'none', 'energy', 1, 'first', 'gradient'}, optional
Maximum derivative level at which to run DFTD3. For large
`mol`, energy-only calculations can be significantly more
efficient. Also controls return values, see below.
verbose : bool, optional
When `True`, additionally include DFTD3 output in output.
Returns
-------
energy : float, optional
When `dertype` is 0, energy [Eh].
gradient : list of lists of floats or psi4.core.Matrix, optional
When `dertype` is 1, (nat, 3) gradient [Eh/a0].
(energy, gradient) : float and list of lists of floats or psi4.core.Matrix, optional
When `dertype` is unspecified, both energy [Eh] and (nat, 3) gradient [Eh/a0].
Notes
-----
research site: https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3
Psi4 mode: When `psi4` the python module is importable at `import qcdb`
time, Psi4 mode is activated, with the following alterations:
* output goes to output file
* gradient returned as psi4.core.Matrix, not list o'lists
* scratch is written to randomly named subdirectory of psi scratch
* psivar "DISPERSION CORRECTION ENERGY" is set
* `verbose` triggered when PRINT keywork of SCF module >=3
"""
# Create (if necessary) and update qcdb.Molecule
if isinstance(mol, (Molecule, core.Molecule)):
# 1st: called on a qcdb.Molecule
# 2nd: called on a python export of a psi4.Molecule (py-side through Psi4's driver)
pass
elif isinstance(mol, basestring):
# called on a string representation of a psi4.Molecule (c-side through psi4.Dispersion)
mol = Molecule(mol)
else:
raise ValidationError("""Argument mol must be psi4string or qcdb.Molecule""")
mol.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 = get_dispersion_aliases()[dashlvl] if dashlvl in get_dispersion_aliases() 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 = mol.natom()
# We seem to have a problem with one atom, force the correct result
if numAtoms == 1:
os.chdir(current_directory)
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 = mol.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) != mol.natom():
raise ValidationError('Program dftd3 gradient file has %d atoms- %d expected.' % \
(len(dashdderiv), mol.natom()))
# Prepare results for Psi4
if isP4regime and dertype != 0:
core.set_variable('DISPERSION CORRECTION ENERGY', dashd)
psi_dashdderiv = core.Matrix.from_list(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
