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# Psi4: an open-source quantum chemistry software package
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"""Module with functions for Psi4/Cfour interface. Portions that require
calls to Boost Python psi4 module are here, otherwise in qcdb module.
Also calls to qcdb module are here and not elsewhere in driver.
Organizationally, this module isolates qcdb code from psi4 code.
"""
import os
import re
import sys
import uuid
import shutil
import inspect
import subprocess
from psi4.driver import qcdb
from psi4.driver import p4util
from psi4.driver.molutil import *
from psi4.driver.p4util.exceptions import *
# never import driver, wrappers, or aliases into this file
P4C4_INFO = {}
[docs]def run_cfour(name, **kwargs):
"""Function that prepares environment and input files
for a calculation calling Stanton and Gauss's CFOUR code.
Also processes results back into Psi4 format.
This function is not called directly but is instead called by
:py:func:`~psi4.energy` or :py:func:`~psi4.optimize` when a Cfour
method is requested (through *name* argument). In order to function
correctly, the Cfour executable ``xcfour`` must be present in
:envvar:`PATH` or :envvar:`PSIPATH`.
.. hlist::
:columns: 1
* Many :ref:`PSI Variables <apdx:cfour_psivar>` extracted from the Cfour output
* Python dictionary of associated file constants accessible as ``P4C4_INFO['zmat']``, ``P4C4_INFO['output']``, ``P4C4_INFO['grd']``, *etc.*
:type name: str
:param name: ``'c4-scf'`` || ``'c4-ccsd(t)'`` || ``'cfour'`` || etc.
First argument, usually unlabeled. Indicates the computational
method to be applied to the system.
:type keep: :ref:`boolean <op_py_boolean>`
:param keep: ``'on'`` || |dl| ``'off'`` |dr|
Indicates whether to delete the Cfour scratch directory upon
completion of the Cfour job.
:type path: str
:param path:
Indicates path to Cfour scratch directory (with respect to Psi4
scratch directory). Otherwise, the default is a subdirectory
within the Psi4 scratch directory.
If specified, GENBAS and/or ZMAT within will be used.
:type genbas: str
:param genbas:
Indicates that contents should be used for GENBAS file.
GENBAS is a complicated topic. It is quite unnecessary if the
molecule is from a molecule {...} block and basis is set through
|Psifours| BASIS keyword. In that case, a GENBAS is written from
LibMints and all is well. Otherwise, a GENBAS is looked for in
the usual places: PSIPATH, PATH, PSIDATADIR/basis. If path kwarg is
specified, also looks there preferentially for a GENBAS. Can
also specify GENBAS within an input file through a string and
setting the genbas kwarg. Note that due to the input parser's
aggression, blank lines need to be replaced by the text blankline.
"""
lowername = name.lower()
internal_p4c4_info = {}
return_wfn = kwargs.pop('return_wfn', False)
# Make sure the molecule the user provided is the active one
molecule = kwargs.pop('molecule', core.get_active_molecule())
molecule.update_geometry()
optstash = p4util.OptionsState(
['CFOUR', 'TRANSLATE_PSI4'])
# Determine calling function and hence dertype
calledby = inspect.stack()[1][3]
dertype = ['energy', 'gradient', 'hessian'].index(calledby)
#print('I am %s called by %s called by %s.\n' %
# (inspect.stack()[0][3], inspect.stack()[1][3], inspect.stack()[2][3]))
# Save submission directory
current_directory = os.getcwd()
# Move into job scratch directory
psioh = core.IOManager.shared_object()
psio = core.IO.shared_object()
os.chdir(psioh.get_default_path())
# Construct and move into cfour subdirectory of job scratch directory
cfour_tmpdir = kwargs['path'] if 'path' in kwargs else \
'psi.' + str(os.getpid()) + '.' + psio.get_default_namespace() + \
'.cfour.' + str(uuid.uuid4())[:8]
if not os.path.exists(cfour_tmpdir):
os.mkdir(cfour_tmpdir)
os.chdir(cfour_tmpdir)
# 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') + \
':' + core.get_datadir() + '/basis',
'GENBAS_PATH': core.get_datadir() + '/basis',
'CFOUR_NUM_CORES': os.environ.get('CFOUR_NUM_CORES'),
'MKL_NUM_THREADS': os.environ.get('MKL_NUM_THREADS'),
'OMP_NUM_THREADS': os.environ.get('OMP_NUM_THREADS'),
'LD_LIBRARY_PATH': os.environ.get('LD_LIBRARY_PATH')
}
if 'path' in kwargs:
lenv['PATH'] = kwargs['path'] + ':' + lenv['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}
# Load the GENBAS file
genbas_path = qcdb.search_file('GENBAS', lenv['GENBAS_PATH'])
if genbas_path:
try:
shutil.copy2(genbas_path, psioh.get_default_path() + cfour_tmpdir)
except shutil.Error: # should only fail if src and dest equivalent
pass
core.print_out("\n GENBAS loaded from %s\n" % (genbas_path))
core.print_out(" CFOUR to be run from %s\n" % (psioh.get_default_path() + cfour_tmpdir))
else:
message = """
GENBAS file for CFOUR interface not found. Either:
[1] Supply a GENBAS by placing it in PATH or PSIPATH
[1a] Use cfour {} block with molecule and basis directives.
[1b] Use molecule {} block and CFOUR_BASIS keyword.
[2] Allow Psi4's internal basis sets to convert to GENBAS
[2a] Use molecule {} block and BASIS keyword.
"""
core.print_out(message)
core.print_out(' Search path that was tried:\n')
core.print_out(lenv['PATH'].replace(':', ', '))
# Generate the ZMAT input file in scratch
if 'path' in kwargs and os.path.isfile('ZMAT'):
core.print_out(" ZMAT loaded from %s\n" % (psioh.get_default_path() + kwargs['path'] + '/ZMAT'))
else:
with open('ZMAT', 'w') as cfour_infile:
cfour_infile.write(write_zmat(lowername, dertype, molecule))
internal_p4c4_info['zmat'] = open('ZMAT', 'r').read()
#core.print_out('\n====== Begin ZMAT input for CFOUR ======\n')
#core.print_out(open('ZMAT', 'r').read())
#core.print_out('======= End ZMAT input for CFOUR =======\n\n')
#print('\n====== Begin ZMAT input for CFOUR ======')
#print(open('ZMAT', 'r').read())
#print('======= End ZMAT input for CFOUR =======\n')
if 'genbas' in kwargs:
with open('GENBAS', 'w') as cfour_basfile:
cfour_basfile.write(kwargs['genbas'].replace('\nblankline\n', '\n\n'))
core.print_out(' GENBAS loaded from kwargs string\n')
# Close psi4 output file and reopen with filehandle
print('output in', current_directory + '/' + core.outfile_name())
pathfill = '' if os.path.isabs(core.outfile_name()) else current_directory + os.path.sep
# Handle threading
# OMP_NUM_THREADS from env is in lenv from above
# threads from psi4 -n (core.get_num_threads()) is ignored
# CFOUR_OMP_NUM_THREADS psi4 option takes precedence, handled below
if core.has_option_changed('CFOUR', 'CFOUR_OMP_NUM_THREADS') == True:
lenv['OMP_NUM_THREADS'] = str(core.get_option('CFOUR', 'CFOUR_OMP_NUM_THREADS'))
#print("""\n\n<<<<< RUNNING CFOUR ... >>>>>\n\n""")
# Call executable xcfour, directing cfour output to the psi4 output file
cfour_executable = kwargs['c4exec'] if 'c4exec' in kwargs else 'xcfour'
try:
retcode = subprocess.Popen([cfour_executable], bufsize=0, stdout=subprocess.PIPE, env=lenv)
except OSError as e:
sys.stderr.write('Program %s not found in path or execution failed: %s\n' % (cfour_executable, e.strerror))
message = ('Program %s not found in path or execution failed: %s\n' % (cfour_executable, e.strerror))
raise ValidationError(message)
c4out = ''
while True:
data = retcode.stdout.readline()
data = data.decode('utf-8')
if not data:
break
core.print_out(data)
c4out += data
internal_p4c4_info['output'] = c4out
c4files = {}
core.print_out('\n')
for item in ['GRD', 'FCMFINAL', 'DIPOL']:
try:
with open(psioh.get_default_path() + cfour_tmpdir + '/' + item, 'r') as handle:
c4files[item] = handle.read()
core.print_out(' CFOUR scratch file %s has been read\n' % (item))
core.print_out('%s\n' % c4files[item])
internal_p4c4_info[item.lower()] = c4files[item]
except IOError:
pass
core.print_out('\n')
if molecule.name() == 'blank_molecule_psi4_yo':
qcdbmolecule = None
else:
molecule.update_geometry()
qcdbmolecule = qcdb.Molecule(molecule.create_psi4_string_from_molecule())
qcdbmolecule.update_geometry()
# c4mol, if it exists, is dinky, just a clue to geometry of cfour results
psivar, c4grad, c4mol = qcdb.cfour.harvest(qcdbmolecule, c4out, **c4files)
# Absorb results into psi4 data structures
for key in psivar.keys():
core.set_variable(key.upper(), float(psivar[key]))
if qcdbmolecule is None and c4mol is not None:
molecule = geometry(c4mol.create_psi4_string_from_molecule(), name='blank_molecule_psi4_yo')
molecule.update_geometry()
# This case arises when no Molecule going into calc (cfour {} block) but want
# to know the orientation at which grad, properties, etc. are returned (c4mol).
# c4mol is dinky, w/o chg, mult, dummies and retains name
# blank_molecule_psi4_yo so as to not interfere with future cfour {} blocks
if c4grad is not None:
mat = core.Matrix.from_list(c4grad)
core.set_gradient(mat)
#print ' <<< [3] C4-GRD-GRAD >>>'
#mat.print()
# exit(1)
# # Things needed core.so module to do
# collect c4out string
# read GRD
# read FCMFINAL
# see if theres an active molecule
# # Things delegatable to qcdb
# parsing c4out
# reading GRD and FCMFINAL strings
# reconciling p4 and c4 molecules (orient)
# reconciling c4out and GRD and FCMFINAL results
# transforming frame of results back to p4
# # Things run_cfour needs to have back
# psivar
# qcdb.Molecule of c4?
# coordinates?
# gradient in p4 frame
# # Process the cfour output
# psivar, c4coord, c4grad = qcdb.cfour.cfour_harvest(c4out)
# for key in psivar.keys():
# core.set_variable(key.upper(), float(psivar[key]))
#
# # Awful Hack - Go Away TODO
# if c4grad:
# molecule = core.get_active_molecule()
# molecule.update_geometry()
#
# if molecule.name() == 'blank_molecule_psi4_yo':
# p4grad = c4grad
# p4coord = c4coord
# else:
# qcdbmolecule = qcdb.Molecule(molecule.create_psi4_string_from_molecule())
# #p4grad = qcdbmolecule.deorient_array_from_cfour(c4coord, c4grad)
# #p4coord = qcdbmolecule.deorient_array_from_cfour(c4coord, c4coord)
#
# with open(psioh.get_default_path() + cfour_tmpdir + '/GRD', 'r') as cfour_grdfile:
# c4outgrd = cfour_grdfile.read()
# print('GRD\n',c4outgrd)
# c4coordGRD, c4gradGRD = qcdb.cfour.cfour_harvest_files(qcdbmolecule, grd=c4outgrd)
#
# p4mat = core.Matrix.from_list(p4grad)
# core.set_gradient(p4mat)
# print(' <<< P4 PSIVAR >>>')
# for item in psivar:
# print(' %30s %16.8f' % (item, psivar[item]))
#print(' <<< P4 COORD >>>')
#for item in p4coord:
# print(' %16.8f %16.8f %16.8f' % (item[0], item[1], item[2]))
# print(' <<< P4 GRAD >>>')
# for item in c4grad:
# print(' %16.8f %16.8f %16.8f' % (item[0], item[1], item[2]))
# Clean up cfour scratch directory unless user instructs otherwise
keep = yes.match(str(kwargs['keep'])) if 'keep' in kwargs else False
os.chdir('..')
try:
if keep or ('path' in kwargs):
core.print_out('\n CFOUR scratch files have been kept in %s\n' % (psioh.get_default_path() + cfour_tmpdir))
else:
shutil.rmtree(cfour_tmpdir)
except OSError as e:
print('Unable to remove CFOUR temporary directory %s' % e, file=sys.stderr)
exit(1)
# Return to submission directory and reopen output file
os.chdir(current_directory)
core.print_out('\n')
p4util.banner(' Cfour %s %s Results ' % (name.lower(), calledby.capitalize()))
core.print_variables()
if c4grad is not None:
core.get_gradient().print_out()
core.print_out('\n')
p4util.banner(' Cfour %s %s Results ' % (name.lower(), calledby.capitalize()))
core.print_variables()
if c4grad is not None:
core.get_gradient().print_out()
# Quit if Cfour threw error
if 'CFOUR ERROR CODE' in core.variables():
raise ValidationError("""Cfour exited abnormally.""")
P4C4_INFO.clear()
P4C4_INFO.update(internal_p4c4_info)
optstash.restore()
# new skeleton wavefunction w/mol, highest-SCF basis (just to choose one), & not energy
# Feb 2017 hack. Could get proper basis in skel wfn even if not through p4 basis kw
gobas = core.get_global_option('BASIS') if core.get_global_option('BASIS') else 'sto-3g'
basis = core.BasisSet.build(molecule, "ORBITAL", gobas)
if basis.has_ECP():
raise ValidationError("""ECPs not hooked up for Cfour""")
wfn = core.Wavefunction(molecule, basis)
optstash.restore()
if dertype == 0:
finalquantity = psivar['CURRENT ENERGY']
elif dertype == 1:
finalquantity = core.get_gradient()
wfn.set_gradient(finalquantity)
if finalquantity.rows(0) < 20:
core.print_out('CURRENT GRADIENT')
finalquantity.print_out()
elif dertype == 2:
pass
#finalquantity = finalhessian
#wfn.set_hessian(finalquantity)
#if finalquantity.rows(0) < 20:
# core.print_out('CURRENT HESSIAN')
# finalquantity.print_out()
return wfn
def cfour_list():
"""Form list of Cfour :py:func:`~driver.energy` arguments."""
return qcdb.cfour.cfour_list()
def cfour_gradient_list():
"""Form list of Cfour analytic :py:func:`~driver.gradient` arguments."""
return qcdb.cfour.cfour_gradient_list()
def cfour_hessian_list():
"""Form list of Cfour analytic :py:func:`~driver.gradient` arguments."""
return qcdb.cfour.cfour_hessian_list()
def cfour_psivar_list():
"""Form dictionary of :ref:`PSI Variables <apdx:cfour_psivar>` set by Cfour methods."""
return qcdb.cfour.cfour_psivar_list()
def write_zmat(name, dertype, molecule):
"""Returns string with contents of Cfour ZMAT file as gathered from
active molecule, current keyword settings, and cfour {...} block.
"""
# Handle memory
mem = int(0.000001 * core.get_memory())
if mem == 524:
memcmd, memkw = '', {}
else:
memcmd, memkw = qcdb.cfour.muster_memory(mem)
# Handle molecule and basis set
if molecule.name() == 'blank_molecule_psi4_yo':
molcmd, molkw = '', {}
bascmd, baskw = '', {}
core.set_local_option('CFOUR', 'TRANSLATE_PSI4', False)
else:
molecule.update_geometry()
#print(molecule.create_psi4_string_from_molecule())
qcdbmolecule = qcdb.Molecule(molecule.create_psi4_string_from_molecule())
qcdbmolecule.tagline = molecule.name()
molcmd, molkw = qcdbmolecule.format_molecule_for_cfour()
if core.get_global_option('BASIS') == '':
bascmd, baskw = '', {}
else:
user_pg = molecule.schoenflies_symbol()
molecule.reset_point_group('c1') # need basis printed for *every* atom
qbs = core.BasisSet.build(molecule, "BASIS", core.get_global_option('BASIS'))
if qbs.has_ECP():
raise ValidationError("""ECPs not hooked up for Cfour""")
with open('GENBAS', 'w') as cfour_basfile:
cfour_basfile.write(qbs.genbas())
core.print_out(' GENBAS loaded from Psi4 LibMints for basis %s\n' % (core.get_global_option('BASIS')))
molecule.reset_point_group(user_pg)
molecule.update_geometry()
bascmd, baskw = qcdbmolecule.format_basis_for_cfour(qbs.has_puream())
# Handle psi4 keywords implying cfour keyword values
if core.get_option('CFOUR', 'TRANSLATE_PSI4'):
psicmd, psikw = qcdb.cfour.muster_psi4options(p4util.prepare_options_for_modules(changedOnly=True))
else:
psicmd, psikw = '', {}
# Handle calc type and quantum chemical method
mdccmd, mdckw = qcdb.cfour.muster_modelchem(name, dertype)
# Handle calc type and quantum chemical method
mdccmd, mdckw = qcdb.cfour.muster_modelchem(name, dertype)
# Handle driver vs input/default keyword reconciliation
userkw = p4util.prepare_options_for_modules()
userkw = qcdb.options.reconcile_options(userkw, memkw)
userkw = qcdb.options.reconcile_options(userkw, molkw)
userkw = qcdb.options.reconcile_options(userkw, baskw)
userkw = qcdb.options.reconcile_options(userkw, psikw)
userkw = qcdb.options.reconcile_options(userkw, mdckw)
# Handle conversion of psi4 keyword structure into cfour format
optcmd = qcdb.options.prepare_options_for_cfour(userkw)
# Handle text to be passed untouched to cfour
litcmd = core.get_global_option('LITERAL_CFOUR')
# Assemble ZMAT pieces
zmat = memcmd + molcmd + optcmd + mdccmd + psicmd + bascmd + litcmd
if len(re.findall(r'^\*(ACES2|CFOUR|CRAPS)\(', zmat, re.MULTILINE)) != 1:
core.print_out('\n Faulty ZMAT constructed:\n%s' % (zmat))
raise ValidationError("""
Multiple *CFOUR(...) blocks in input. This usually arises
because molecule or options are specified both the psi4 way through
molecule {...} and set ... and the cfour way through cfour {...}.""")
return zmat
