def prepare_options_for_modules(changedOnly=False, commandsInsteadDict=False):
"""Function to return a string of commands to replicate the
current state of user-modified options. Used to capture C++
options information for distributed (sow/reap) input files.
.. caution:: Some features are not yet implemented. Buy a developer a coffee.
- Need some option to get either all or changed
- Need some option to either get dict or set string or psimod command list
- command return doesn't revoke has_changed setting for unchanged with changedOnly=False
"""
options = collections.defaultdict(dict)
commands = ''
for opt in core.get_global_option_list():
if core.has_global_option_changed(opt) or not changedOnly:
if opt in ['DFT_CUSTOM_FUNCTIONAL', 'EXTERN']: # Feb 2017 hack
continue
val = core.get_global_option(opt)
options['GLOBALS'][opt] = {'value': val,
'has_changed': core.has_global_option_changed(opt)}
if isinstance(val, basestring):
commands += """core.set_global_option('%s', '%s')\n""" % (opt, val)
else:
commands += """core.set_global_option('%s', %s)\n""" % (opt, val)
#if changedOnly:
# print('Appending module %s option %s value %s has_changed %s.' % \
# ('GLOBALS', opt, core.get_global_option(opt), core.has_global_option_changed(opt)))
for module in _modules:
if core.option_exists_in_module(module, opt):
hoc = core.has_option_changed(module, opt)
if hoc or not changedOnly:
val = core.get_option(module, opt)
options[module][opt] = {'value': val, 'has_changed': hoc}
if isinstance(val, str):
commands += """core.set_local_option('%s', '%s', '%s')\n""" % (module, opt, val)
else:
commands += """core.set_local_option('%s', '%s', %s)\n""" % (module, opt, val)
#if changedOnly:
# print('Appending module %s option %s value %s has_changed %s.' % \
# (module, opt, core.get_option(module, opt), hoc))
if commandsInsteadDict:
return commands
else:
return options
def cubeprop(wfn, **kwargs):
"""Evaluate properties on a grid and generate cube files.
.. versionadded:: 0.5
*wfn* parameter passed explicitly
:returns: None
:type wfn: :py:class:`~psi4.core.Wavefunction`
:param wfn: set of molecule, basis, orbitals from which to generate cube files
:examples:
>>> # [1] Cube files for all orbitals
>>> E, wfn = energy('b3lyp', return_wfn=True)
>>> cubeprop(wfn)
>>> # [2] Cube files for density (alpha, beta, total, spin) and four orbitals
>>> # (two alpha, two beta)
>>> set cubeprop_tasks ['orbitals', 'density']
>>> set cubeprop_orbitals [5, 6, -5, -6]
>>> E, wfn = energy('scf', return_wfn=True)
>>> cubeprop(wfn)
"""
# By default compute the orbitals
if not core.has_global_option_changed('CUBEPROP_TASKS'):
core.set_global_option('CUBEPROP_TASKS', ['ORBITALS'])
if ((core.get_global_option('INTEGRAL_PACKAGE') == 'ERD') and ('ESP' in core.get_global_option('CUBEPROP_TASKS'))):
raise ValidationError('INTEGRAL_PACKAGE ERD does not play nicely with electrostatic potential, so stopping.')
cp = core.CubeProperties(wfn)
cp.compute_properties()
def format_options_for_input(molecule=None, **kwargs):
"""Function to return a string of commands to replicate the
current state of user-modified options. Used to capture C++
options information for distributed (sow/reap) input files.
.. caution:: Some features are not yet implemented. Buy a developer a coffee.
- Does not cover local (as opposed to global) options.
"""
if molecule is not None:
symmetry = molecule.find_point_group(0.00001).symbol()
commands = ''
commands += """\ncore.set_memory_bytes(%s)\n\n""" % (core.get_memory())
for chgdopt in core.get_global_option_list():
if core.has_global_option_changed(chgdopt):
chgdoptval = core.get_global_option(chgdopt)
if molecule is not None:
if chgdopt.lower() in kwargs:
if symmetry in kwargs[chgdopt.lower()]:
chgdoptval = kwargs[chgdopt.lower()][symmetry]
if isinstance(chgdoptval, str):
commands += """core.set_global_option('%s', '%s')\n""" % (chgdopt, chgdoptval)
# Next four lines were conflict between master and roa branches (TDC, 10/29/2014)
elif isinstance(chgdoptval, int) or isinstance(chgdoptval, float):
commands += """core.set_global_option('%s', %s)\n""" % (chgdopt, chgdoptval)
elif isinstance(chgdoptval, list):
commands += """core.set_global_option('%s', %s)\n""" % (chgdopt, chgdoptval)
else:
commands += """core.set_global_option('%s', %s)\n""" % (chgdopt, chgdoptval)
return commands
def scf_set_reference_local(name, is_dft=False):
"""
Figures out the correct SCF reference to set locally
"""
optstash = p4util.OptionsState(
['SCF_TYPE'],
['SCF', 'REFERENCE'])
# Alter default algorithm
if not core.has_global_option_changed('SCF_TYPE'):
core.set_global_option('SCF_TYPE', 'DF')
# Alter reference name if needed
user_ref = core.get_option('SCF', 'REFERENCE')
sup = build_superfunctional_from_dictionary(functionals[name], 1, 1, True)[0]
if sup.needs_xc() or is_dft:
if (user_ref == 'RHF'):
core.set_local_option('SCF', 'REFERENCE', 'RKS')
elif (user_ref == 'UHF'):
core.set_local_option('SCF', 'REFERENCE', 'UKS')
elif (user_ref == 'ROHF'):
raise ValidationError('ROHF reference for DFT is not available.')
elif (user_ref == 'CUHF'):
raise ValidationError('CUHF reference for DFT is not available.')
# else we are doing HF and nothing needs to be overloaded
return optstash
def check_disk_df(name, optstash):
optstash.add_option(['SCF_TYPE'])
# Alter default algorithm
if not core.has_global_option_changed('SCF_TYPE'):
core.set_global_option('SCF_TYPE', 'DISK_DF')
core.print_out(""" Method '%s' requires SCF_TYPE = DISK_DF, setting.\n""" % name)
elif core.get_global_option('SCF_TYPE') == "DF":
core.set_global_option('SCF_TYPE', 'DISK_DF')
core.print_out(""" Method '%s' requires SCF_TYPE = DISK_DF, setting.\n""" % name)
else:
if core.get_global_option('SCF_TYPE') != "DISK_DF":
raise ValidationError(" %s requires SCF_TYPE = DISK_DF, please use SCF_TYPE = DF to automatically choose the correct DFJK implementation." % name)
def set_cholesky_from(mtd_type):
type_val = core.get_global_option(mtd_type)
if type_val == 'CD':
core.set_local_option('GPU_DFCC', 'DF_BASIS_CC', 'CHOLESKY')
# Alter default algorithm
if not core.has_global_option_changed('SCF_TYPE'):
optstash.add_option(['SCF_TYPE'])
core.set_global_option('SCF_TYPE', 'CD')
core.print_out(""" SCF Algorithm Type (re)set to CD.\n""")
elif type_val in ['DF', 'DISK_DF']:
if core.get_option('GPU_DFCC', 'DF_BASIS_CC') == 'CHOLESKY':
core.set_local_option('GPU_DFCC', 'DF_BASIS_CC', '')
proc_util.check_disk_df(name.upper(), optstash)
else:
raise ValidationError("""Invalid type '%s' for DFCC""" % type_val)
def __init__(self, option, module=None):
self.option = option.upper()
if module:
self.module = module.upper()
else:
self.module = None
self.value_global = core.get_global_option(option)
self.haschanged_global = core.has_global_option_changed(option)
if self.module:
self.value_local = core.get_local_option(self.module, option)
self.haschanged_local = core.has_local_option_changed(self.module, option)
self.value_used = core.get_option(self.module, option)
self.haschanged_used = core.has_option_changed(self.module, option)
else:
self.value_local = None
self.haschanged_local = None
self.value_used = None
self.haschanged_used = None
def __init__(self, option, module=None):
self.option = option.upper()
if module:
self.module = module.upper()
else:
self.module = None
self.value_global = core.get_global_option(option)
self.haschanged_global = core.has_global_option_changed(option)
if self.module:
self.value_local = core.get_local_option(self.module, option)
self.haschanged_local = core.has_local_option_changed(
self.module, option)
self.value_used = core.get_option(self.module, option)
self.haschanged_used = core.has_option_changed(self.module, option)
else:
self.value_local = None
self.haschanged_local = None
self.value_used = None
self.haschanged_used = None
def check_disk_df(name, optstash):
optstash.add_option(['SCF_TYPE'])
# Alter default algorithm
if not core.has_global_option_changed('SCF_TYPE'):
core.set_global_option('SCF_TYPE', 'DISK_DF')
core.print_out(
""" Method '%s' requires SCF_TYPE = DISK_DF, setting.\n""" %
name)
elif core.get_global_option('SCF_TYPE') == "DF":
core.set_global_option('SCF_TYPE', 'DISK_DF')
core.print_out(
""" Method '%s' requires SCF_TYPE = DISK_DF, setting.\n""" %
name)
else:
if core.get_global_option('SCF_TYPE') != "DISK_DF":
raise ValidationError(
" %s requires SCF_TYPE = DISK_DF, please use SCF_TYPE = DF to automatically choose the correct DFJK implementation."
% name)
def prepare_options_for_set_options():
"""Capture current state of C++ psi4.core.Options information for reloading by `psi4.set_options()`.
Returns
-------
dict
Dictionary where keys are option names to be set globally or module__option
mangled names to be set locally. Values are option values.
"""
flat_options = {}
has_changed_snapshot = {
module: core.options_to_python(module)
for module in _modules
}
for opt in core.get_global_option_list():
handled_locally = False
ghoc = core.has_global_option_changed(opt)
opt_snapshot = {
k: v[opt]
for k, v in has_changed_snapshot.items() if opt in v
}
for module, (lhoc, ohoc) in opt_snapshot.items():
if ohoc:
if lhoc:
key = module + '__' + opt
val = core.get_local_option(module, opt)
else:
key = opt
val = core.get_global_option(opt)
handled_locally = True
flat_options[key] = val
if ghoc and not handled_locally:
# some options are globals section (not level) so not in any module
flat_options[opt] = core.get_global_option(opt)
return flat_options
def format_options_for_input(molecule=None, **kwargs):
"""Function to return a string of commands to replicate the
current state of user-modified options. Used to capture C++
options information for distributed (sow/reap) input files.
.. caution:: Some features are not yet implemented. Buy a developer a coffee.
- Does not cover local (as opposed to global) options.
"""
if molecule is not None:
symmetry = molecule.find_point_group(0.00001).symbol()
commands = ''
commands += """\ncore.set_memory_bytes(%s)\n\n""" % (core.get_memory())
for chgdopt in core.get_global_option_list():
if core.has_global_option_changed(chgdopt):
chgdoptval = core.get_global_option(chgdopt)
if molecule is not None:
if chgdopt.lower() in kwargs:
if symmetry in kwargs[chgdopt.lower()]:
chgdoptval = kwargs[chgdopt.lower()][symmetry]
if isinstance(chgdoptval, str):
commands += """core.set_global_option('%s', '%s')\n""" % (
chgdopt, chgdoptval)
# Next four lines were conflict between master and roa branches (TDC, 10/29/2014)
elif isinstance(chgdoptval, int) or isinstance(chgdoptval, float):
commands += """core.set_global_option('%s', %s)\n""" % (
chgdopt, chgdoptval)
elif isinstance(chgdoptval, list):
commands += """core.set_global_option('%s', %s)\n""" % (
chgdopt, chgdoptval)
else:
commands += """core.set_global_option('%s', %s)\n""" % (
chgdopt, chgdoptval)
return commands
def cubeprop(wfn, **kwargs):
"""Evaluate properties on a grid and generate cube files.
.. versionadded:: 0.5
*wfn* parameter passed explicitly
:returns: None
:type wfn: :py:class:`~psi4.core.Wavefunction`
:param wfn: set of molecule, basis, orbitals from which to generate cube files
:examples:
>>> # [1] Cube files for all orbitals
>>> E, wfn = energy('b3lyp', return_wfn=True)
>>> cubeprop(wfn)
>>> # [2] Cube files for density (alpha, beta, total, spin) and four orbitals
>>> # (two alpha, two beta)
>>> set cubeprop_tasks ['orbitals', 'density']
>>> set cubeprop_orbitals [5, 6, -5, -6]
>>> E, wfn = energy('scf', return_wfn=True)
>>> cubeprop(wfn)
"""
# By default compute the orbitals
if not core.has_global_option_changed('CUBEPROP_TASKS'):
core.set_global_option('CUBEPROP_TASKS', ['ORBITALS'])
if ((core.get_global_option('INTEGRAL_PACKAGE') == 'ERD')
and ('ESP' in core.get_global_option('CUBEPROP_TASKS'))):
raise ValidationError(
'INTEGRAL_PACKAGE ERD does not play nicely with electrostatic potential, so stopping.'
)
cp = core.CubeProperties(wfn)
cp.compute_properties()
def run_sapt_dft(name, **kwargs):
optstash = p4util.OptionsState(['SCF_TYPE'], ['SCF', 'REFERENCE'], ['SCF', 'DFT_GRAC_SHIFT'],
['SCF', 'SAVE_JK'])
core.tstart()
# Alter default algorithm
if not core.has_global_option_changed('SCF_TYPE'):
core.set_global_option('SCF_TYPE', 'DF')
core.prepare_options_for_module("SAPT")
# Get the molecule of interest
ref_wfn = kwargs.get('ref_wfn', None)
if ref_wfn is None:
sapt_dimer = kwargs.pop('molecule', core.get_active_molecule())
else:
core.print_out('Warning! SAPT argument "ref_wfn" is only able to use molecule information.')
sapt_dimer = ref_wfn.molecule()
sapt_dimer, monomerA, monomerB = proc_util.prepare_sapt_molecule(sapt_dimer, "dimer")
# Grab overall settings
mon_a_shift = core.get_option("SAPT", "SAPT_DFT_GRAC_SHIFT_A")
mon_b_shift = core.get_option("SAPT", "SAPT_DFT_GRAC_SHIFT_B")
do_delta_hf = core.get_option("SAPT", "SAPT_DFT_DO_DHF")
sapt_dft_functional = core.get_option("SAPT", "SAPT_DFT_FUNCTIONAL")
# Print out the title and some information
core.print_out("\n")
core.print_out(" ---------------------------------------------------------\n")
core.print_out(" " + "SAPT(DFT) Procedure".center(58) + "\n")
core.print_out("\n")
core.print_out(" " + "by Daniel G. A. Smith".center(58) + "\n")
core.print_out(" ---------------------------------------------------------\n")
core.print_out("\n")
core.print_out(" !!! WARNING: SAPT(DFT) capability is in beta. Please use with caution. !!!\n\n")
core.print_out(" ==> Algorithm <==\n\n")
core.print_out(" SAPT DFT Functional %12s\n" % str(sapt_dft_functional))
core.print_out(" Monomer A GRAC Shift %12.6f\n" % mon_a_shift)
core.print_out(" Monomer B GRAC Shift %12.6f\n" % mon_b_shift)
core.print_out(" Delta HF %12s\n" % ("True" if do_delta_hf else "False"))
core.print_out(" JK Algorithm %12s\n" % core.get_global_option("SCF_TYPE"))
core.print_out("\n")
core.print_out(" Required computations:\n")
if (do_delta_hf):
core.print_out(" HF (Dimer)\n")
core.print_out(" HF (Monomer A)\n")
core.print_out(" HF (Monomer B)\n")
core.print_out(" DFT (Monomer A)\n")
core.print_out(" DFT (Monomer B)\n")
core.print_out("\n")
if (sapt_dft_functional != "HF") and ((mon_a_shift == 0.0) or (mon_b_shift == 0.0)):
raise ValidationError('SAPT(DFT): must set both "SAPT_DFT_GRAC_SHIFT_A" and "B".')
if (core.get_option('SCF', 'REFERENCE') != 'RHF'):
raise ValidationError('SAPT(DFT) currently only supports restricted references.')
core.IO.set_default_namespace('dimer')
data = {}
if (core.get_global_option('SCF_TYPE') == 'DF'):
# core.set_global_option('DF_INTS_IO', 'LOAD')
core.set_global_option('DF_INTS_IO', 'SAVE')
# # Compute dimer wavefunction
hf_wfn_dimer = None
if do_delta_hf:
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.set_global_option('DF_INTS_IO', 'SAVE')
hf_data = {}
hf_wfn_dimer = scf_helper("SCF", molecule=sapt_dimer, banner="SAPT(DFT): delta HF Dimer", **kwargs)
hf_data["HF DIMER"] = core.get_variable("CURRENT ENERGY")
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.IO.change_file_namespace(97, 'dimer', 'monomerA')
hf_wfn_A = scf_helper("SCF", molecule=monomerA, banner="SAPT(DFT): delta HF Monomer A", **kwargs)
hf_data["HF MONOMER A"] = core.get_variable("CURRENT ENERGY")
core.set_global_option("SAVE_JK", True)
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.IO.change_file_namespace(97, 'monomerA', 'monomerB')
hf_wfn_B = scf_helper("SCF", molecule=monomerB, banner="SAPT(DFT): delta HF Monomer B", **kwargs)
hf_data["HF MONOMER B"] = core.get_variable("CURRENT ENERGY")
core.set_global_option("SAVE_JK", False)
# Grab JK object and set to A (so we do not save many JK objects)
sapt_jk = hf_wfn_B.jk()
hf_wfn_A.set_jk(sapt_jk)
core.set_global_option("SAVE_JK", False)
# Move it back to monomer A
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.IO.change_file_namespace(97, 'monomerB', 'dimer')
core.print_out("\n")
core.print_out(" ---------------------------------------------------------\n")
core.print_out(" " + "SAPT(DFT): delta HF Segement".center(58) + "\n")
core.print_out("\n")
core.print_out(" " + "by Daniel G. A. Smith and Rob Parrish".center(58) + "\n")
core.print_out(" ---------------------------------------------------------\n")
core.print_out("\n")
# Build cache
hf_cache = sapt_jk_terms.build_sapt_jk_cache(hf_wfn_A, hf_wfn_B, sapt_jk, True)
# Electostatics
elst = sapt_jk_terms.electrostatics(hf_cache, True)
hf_data.update(elst)
# Exchange
exch = sapt_jk_terms.exchange(hf_cache, sapt_jk, True)
hf_data.update(exch)
# Induction
ind = sapt_jk_terms.induction(
hf_cache,
sapt_jk,
True,
maxiter=core.get_option("SAPT", "MAXITER"),
conv=core.get_option("SAPT", "D_CONVERGENCE"),
Sinf=core.get_option("SAPT", "DO_IND_EXCH_SINF"))
hf_data.update(ind)
dhf_value = hf_data["HF DIMER"] - hf_data["HF MONOMER A"] - hf_data["HF MONOMER B"]
core.print_out("\n")
core.print_out(print_sapt_hf_summary(hf_data, "SAPT(HF)", delta_hf=dhf_value))
data["Delta HF Correction"] = core.get_variable("SAPT(DFT) Delta HF")
sapt_jk.finalize()
del hf_wfn_A, hf_wfn_B, sapt_jk
if hf_wfn_dimer is None:
dimer_wfn = core.Wavefunction.build(sapt_dimer, core.get_global_option("BASIS"))
else:
dimer_wfn = hf_wfn_dimer
# Set the primary functional
core.set_local_option('SCF', 'REFERENCE', 'RKS')
# Compute Monomer A wavefunction
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.IO.change_file_namespace(97, 'dimer', 'monomerA')
if mon_a_shift:
core.set_global_option("DFT_GRAC_SHIFT", mon_a_shift)
# Save the JK object
core.IO.set_default_namespace('monomerA')
wfn_A = scf_helper(
sapt_dft_functional, post_scf=False, molecule=monomerA, banner="SAPT(DFT): DFT Monomer A", **kwargs)
data["DFT MONOMERA"] = core.get_variable("CURRENT ENERGY")
core.set_global_option("DFT_GRAC_SHIFT", 0.0)
# Compute Monomer B wavefunction
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.IO.change_file_namespace(97, 'monomerA', 'monomerB')
if mon_b_shift:
core.set_global_option("DFT_GRAC_SHIFT", mon_b_shift)
core.set_global_option("SAVE_JK", True)
core.IO.set_default_namespace('monomerB')
wfn_B = scf_helper(
sapt_dft_functional, post_scf=False, molecule=monomerB, banner="SAPT(DFT): DFT Monomer B", **kwargs)
data["DFT MONOMERB"] = core.get_variable("CURRENT ENERGY")
# Save JK object
sapt_jk = wfn_B.jk()
wfn_A.set_jk(sapt_jk)
core.set_global_option("SAVE_JK", False)
core.set_global_option("DFT_GRAC_SHIFT", 0.0)
# Write out header
scf_alg = core.get_global_option("SCF_TYPE")
sapt_dft_header(sapt_dft_functional, mon_a_shift, mon_b_shift, bool(do_delta_hf), scf_alg)
# Call SAPT(DFT)
sapt_jk = wfn_B.jk()
sapt_dft(dimer_wfn, wfn_A, wfn_B, sapt_jk=sapt_jk, data=data, print_header=False)
# Copy data back into globals
for k, v in data.items():
core.set_variable(k, v)
core.tstop()
return dimer_wfn
def run_sf_sapt(name, **kwargs):
optstash = p4util.OptionsState(['SCF_TYPE'], ['SCF', 'REFERENCE'],
['SCF', 'DFT_GRAC_SHIFT'],
['SCF', 'SAVE_JK'])
core.tstart()
# Alter default algorithm
if not core.has_global_option_changed('SCF_TYPE'):
core.set_global_option('SCF_TYPE', 'DF')
core.prepare_options_for_module("SAPT")
# Get the molecule of interest
ref_wfn = kwargs.get('ref_wfn', None)
if ref_wfn is None:
sapt_dimer = kwargs.pop('molecule', core.get_active_molecule())
else:
core.print_out(
'Warning! SAPT argument "ref_wfn" is only able to use molecule information.'
)
sapt_dimer = ref_wfn.molecule()
sapt_dimer, monomerA, monomerB = proc_util.prepare_sapt_molecule(
sapt_dimer, "dimer")
# Print out the title and some information
core.print_out("\n")
core.print_out(
" ---------------------------------------------------------\n")
core.print_out(" " + "Spin-Flip SAPT Procedure".center(58) + "\n")
core.print_out("\n")
core.print_out(" " +
"by Daniel G. A. Smith and Konrad Patkowski".center(58) +
"\n")
core.print_out(
" ---------------------------------------------------------\n")
core.print_out("\n")
core.print_out(" ==> Algorithm <==\n\n")
core.print_out(" JK Algorithm %12s\n" %
core.get_option("SCF", "SCF_TYPE"))
core.print_out("\n")
core.print_out(" Required computations:\n")
core.print_out(" HF (Monomer A)\n")
core.print_out(" HF (Monomer B)\n")
core.print_out("\n")
if (core.get_option('SCF', 'REFERENCE') != 'ROHF'):
raise ValidationError(
'Spin-Flip SAPT currently only supports restricted open-shell references.'
)
# Run the two monomer computations
core.IO.set_default_namespace('dimer')
data = {}
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.set_global_option('DF_INTS_IO', 'SAVE')
# Compute dimer wavefunction
wfn_A = scf_helper("SCF",
molecule=monomerA,
banner="SF-SAPT: HF Monomer A",
**kwargs)
core.set_global_option("SAVE_JK", True)
wfn_B = scf_helper("SCF",
molecule=monomerB,
banner="SF-SAPT: HF Monomer B",
**kwargs)
sapt_jk = wfn_B.jk()
core.set_global_option("SAVE_JK", False)
core.print_out("\n")
core.print_out(
" ---------------------------------------------------------\n")
core.print_out(" " +
"Spin-Flip SAPT Exchange and Electrostatics".center(58) +
"\n")
core.print_out("\n")
core.print_out(" " +
"by Daniel G. A. Smith and Konrad Patkowski".center(58) +
"\n")
core.print_out(
" ---------------------------------------------------------\n")
core.print_out("\n")
sf_data = sapt_sf_terms.compute_sapt_sf(sapt_dimer, sapt_jk, wfn_A, wfn_B)
# Print the results
core.print_out(" Spin-Flip SAPT Results\n")
core.print_out(" " + "-" * 103 + "\n")
for key, value in sf_data.items():
value = sf_data[key]
print_vals = (key, value * 1000, value * constants.hartree2kcalmol,
value * constants.hartree2kJmol)
string = " %-26s % 15.8f [mEh] % 15.8f [kcal/mol] % 15.8f [kJ/mol]\n" % print_vals
core.print_out(string)
core.print_out(" " + "-" * 103 + "\n\n")
dimer_wfn = core.Wavefunction.build(sapt_dimer, wfn_A.basisset())
# Set variables
psivar_tanslator = {
"Elst10": "SAPT ELST ENERGY",
"Exch10(S^2) [diagonal]": "SAPT EXCH10(S^2),DIAGONAL ENERGY",
"Exch10(S^2) [off-diagonal]": "SAPT EXCH10(S^2),OFF-DIAGONAL ENERGY",
"Exch10(S^2) [highspin]": "SAPT EXCH10(S^2),HIGHSPIN ENERGY",
}
for k, v in sf_data.items():
psi_k = psivar_tanslator[k]
dimer_wfn.set_variable(psi_k, v)
core.set_variable(psi_k, v)
# Copy over highspin
core.set_variable("SAPT EXCH ENERGY", sf_data["Exch10(S^2) [highspin]"])
core.tstop()
return dimer_wfn
def run_sapt_dft(name, **kwargs):
optstash = p4util.OptionsState(['SCF_TYPE'], ['SCF', 'REFERENCE'],
['SCF', 'DFT_GRAC_SHIFT'],
['SCF', 'SAVE_JK'])
core.tstart()
# Alter default algorithm
if not core.has_global_option_changed('SCF_TYPE'):
core.set_global_option('SCF_TYPE', 'DF')
core.prepare_options_for_module("SAPT")
# Get the molecule of interest
ref_wfn = kwargs.get('ref_wfn', None)
if ref_wfn is None:
sapt_dimer = kwargs.pop('molecule', core.get_active_molecule())
else:
core.print_out(
'Warning! SAPT argument "ref_wfn" is only able to use molecule information.'
)
sapt_dimer = ref_wfn.molecule()
sapt_dimer, monomerA, monomerB = proc_util.prepare_sapt_molecule(
sapt_dimer, "dimer")
# Grab overall settings
mon_a_shift = core.get_option("SAPT", "SAPT_DFT_GRAC_SHIFT_A")
mon_b_shift = core.get_option("SAPT", "SAPT_DFT_GRAC_SHIFT_B")
do_delta_hf = core.get_option("SAPT", "SAPT_DFT_DO_DHF")
sapt_dft_functional = core.get_option("SAPT", "SAPT_DFT_FUNCTIONAL")
# Print out the title and some information
core.print_out("\n")
core.print_out(
" ---------------------------------------------------------\n")
core.print_out(" " + "SAPT(DFT) Procedure".center(58) + "\n")
core.print_out("\n")
core.print_out(" " + "by Daniel G. A. Smith".center(58) + "\n")
core.print_out(
" ---------------------------------------------------------\n")
core.print_out("\n")
core.print_out(
" !!! WARNING: SAPT(DFT) capability is in beta. Please use with caution. !!!\n\n"
)
core.print_out(" ==> Algorithm <==\n\n")
core.print_out(" SAPT DFT Functional %12s\n" %
str(sapt_dft_functional))
core.print_out(" Monomer A GRAC Shift %12.6f\n" % mon_a_shift)
core.print_out(" Monomer B GRAC Shift %12.6f\n" % mon_b_shift)
core.print_out(" Delta HF %12s\n" %
("True" if do_delta_hf else "False"))
core.print_out(" JK Algorithm %12s\n" %
core.get_global_option("SCF_TYPE"))
core.print_out("\n")
core.print_out(" Required computations:\n")
if (do_delta_hf):
core.print_out(" HF (Dimer)\n")
core.print_out(" HF (Monomer A)\n")
core.print_out(" HF (Monomer B)\n")
core.print_out(" DFT (Monomer A)\n")
core.print_out(" DFT (Monomer B)\n")
core.print_out("\n")
if (sapt_dft_functional != "HF") and ((mon_a_shift == 0.0) or
(mon_b_shift == 0.0)):
raise ValidationError(
'SAPT(DFT): must set both "SAPT_DFT_GRAC_SHIFT_A" and "B".')
if (core.get_option('SCF', 'REFERENCE') != 'RHF'):
raise ValidationError(
'SAPT(DFT) currently only supports restricted references.')
core.IO.set_default_namespace('dimer')
data = {}
if (core.get_global_option('SCF_TYPE') == 'DF'):
# core.set_global_option('DF_INTS_IO', 'LOAD')
core.set_global_option('DF_INTS_IO', 'SAVE')
# # Compute dimer wavefunction
hf_wfn_dimer = None
if do_delta_hf:
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.set_global_option('DF_INTS_IO', 'SAVE')
core.timer_on("SAPT(DFT): Dimer SCF")
hf_data = {}
hf_wfn_dimer = scf_helper("SCF",
molecule=sapt_dimer,
banner="SAPT(DFT): delta HF Dimer",
**kwargs)
hf_data["HF DIMER"] = core.variable("CURRENT ENERGY")
core.timer_off("SAPT(DFT): Dimer SCF")
core.timer_on("SAPT(DFT): Monomer A SCF")
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.IO.change_file_namespace(97, 'dimer', 'monomerA')
hf_wfn_A = scf_helper("SCF",
molecule=monomerA,
banner="SAPT(DFT): delta HF Monomer A",
**kwargs)
hf_data["HF MONOMER A"] = core.variable("CURRENT ENERGY")
core.timer_off("SAPT(DFT): Monomer A SCF")
core.timer_on("SAPT(DFT): Monomer B SCF")
core.set_global_option("SAVE_JK", True)
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.IO.change_file_namespace(97, 'monomerA', 'monomerB')
hf_wfn_B = scf_helper("SCF",
molecule=monomerB,
banner="SAPT(DFT): delta HF Monomer B",
**kwargs)
hf_data["HF MONOMER B"] = core.variable("CURRENT ENERGY")
core.set_global_option("SAVE_JK", False)
core.timer_off("SAPT(DFT): Monomer B SCF")
# Grab JK object and set to A (so we do not save many JK objects)
sapt_jk = hf_wfn_B.jk()
hf_wfn_A.set_jk(sapt_jk)
core.set_global_option("SAVE_JK", False)
# Move it back to monomer A
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.IO.change_file_namespace(97, 'monomerB', 'dimer')
core.print_out("\n")
core.print_out(
" ---------------------------------------------------------\n"
)
core.print_out(" " + "SAPT(DFT): delta HF Segment".center(58) +
"\n")
core.print_out("\n")
core.print_out(" " +
"by Daniel G. A. Smith and Rob Parrish".center(58) +
"\n")
core.print_out(
" ---------------------------------------------------------\n"
)
core.print_out("\n")
# Build cache
hf_cache = sapt_jk_terms.build_sapt_jk_cache(hf_wfn_A, hf_wfn_B,
sapt_jk, True)
# Electrostatics
core.timer_on("SAPT(DFT):SAPT:elst")
elst = sapt_jk_terms.electrostatics(hf_cache, True)
hf_data.update(elst)
core.timer_off("SAPT(DFT):SAPT:elst")
# Exchange
core.timer_on("SAPT(DFT):SAPT:exch")
exch = sapt_jk_terms.exchange(hf_cache, sapt_jk, True)
hf_data.update(exch)
core.timer_off("SAPT(DFT):SAPT:exch")
# Induction
core.timer_on("SAPT(DFT):SAPT:ind")
ind = sapt_jk_terms.induction(
hf_cache,
sapt_jk,
True,
maxiter=core.get_option("SAPT", "MAXITER"),
conv=core.get_option("SAPT", "D_CONVERGENCE"),
Sinf=core.get_option("SAPT", "DO_IND_EXCH_SINF"))
hf_data.update(ind)
core.timer_off("SAPT(DFT):SAPT:ind")
dhf_value = hf_data["HF DIMER"] - hf_data["HF MONOMER A"] - hf_data[
"HF MONOMER B"]
core.print_out("\n")
core.print_out(
print_sapt_hf_summary(hf_data, "SAPT(HF)", delta_hf=dhf_value))
data["Delta HF Correction"] = core.variable("SAPT(DFT) Delta HF")
sapt_jk.finalize()
del hf_wfn_A, hf_wfn_B, sapt_jk
if hf_wfn_dimer is None:
dimer_wfn = core.Wavefunction.build(sapt_dimer,
core.get_global_option("BASIS"))
else:
dimer_wfn = hf_wfn_dimer
# Set the primary functional
core.set_local_option('SCF', 'REFERENCE', 'RKS')
# Compute Monomer A wavefunction
core.timer_on("SAPT(DFT): Monomer A DFT")
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.IO.change_file_namespace(97, 'dimer', 'monomerA')
if mon_a_shift:
core.set_global_option("DFT_GRAC_SHIFT", mon_a_shift)
core.IO.set_default_namespace('monomerA')
wfn_A = scf_helper(sapt_dft_functional,
post_scf=False,
molecule=monomerA,
banner="SAPT(DFT): DFT Monomer A",
**kwargs)
data["DFT MONOMERA"] = core.variable("CURRENT ENERGY")
core.set_global_option("DFT_GRAC_SHIFT", 0.0)
core.timer_off("SAPT(DFT): Monomer A DFT")
# Compute Monomer B wavefunction
core.timer_on("SAPT(DFT): Monomer B DFT")
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.IO.change_file_namespace(97, 'monomerA', 'monomerB')
if mon_b_shift:
core.set_global_option("DFT_GRAC_SHIFT", mon_b_shift)
core.set_global_option("SAVE_JK", True)
core.IO.set_default_namespace('monomerB')
wfn_B = scf_helper(sapt_dft_functional,
post_scf=False,
molecule=monomerB,
banner="SAPT(DFT): DFT Monomer B",
**kwargs)
data["DFT MONOMERB"] = core.variable("CURRENT ENERGY")
# Save JK object
sapt_jk = wfn_B.jk()
wfn_A.set_jk(sapt_jk)
core.set_global_option("SAVE_JK", False)
core.set_global_option("DFT_GRAC_SHIFT", 0.0)
core.timer_off("SAPT(DFT): Monomer B DFT")
# Write out header
scf_alg = core.get_global_option("SCF_TYPE")
sapt_dft_header(sapt_dft_functional, mon_a_shift, mon_b_shift,
bool(do_delta_hf), scf_alg)
# Call SAPT(DFT)
sapt_jk = wfn_B.jk()
sapt_dft(dimer_wfn,
wfn_A,
wfn_B,
sapt_jk=sapt_jk,
data=data,
print_header=False)
# Copy data back into globals
for k, v in data.items():
core.set_variable(k, v)
core.tstop()
return dimer_wfn
def _set_convergence_criterion(ptype, method_name, scf_Ec, pscf_Ec, scf_Dc, pscf_Dc, gen_Ec, verbose=1):
r"""
This function will set local SCF and global energy convergence criterion
to the defaults listed at:
http://www.psicode.org/psi4manual/master/scf.html#convergence-and-
algorithm-defaults. SCF will be converged more tightly if a post-SCF
method is select (pscf_Ec, and pscf_Dc) else the looser (scf_Ec, and
scf_Dc convergence criterion will be used).
ptype - Procedure type (energy, gradient, etc). Nearly always test on
procedures['energy'] since that's guaranteed to exist for a method.
method_name - Name of the method
scf_Ec - E convergence criterion for scf target method
pscf_Ec - E convergence criterion for scf of post-scf target method
scf_Dc - D convergence criterion for scf target method
pscf_Dc - D convergence criterion for scf of post-scf target method
gen_Ec - E convergence criterion for post-scf target method
"""
optstash = p4util.OptionsState(
['SCF', 'E_CONVERGENCE'],
['SCF', 'D_CONVERGENCE'],
['E_CONVERGENCE'])
# Kind of want to move this out of here
_method_exists(ptype, method_name)
if verbose >= 2:
print(' Setting convergence', end=' ')
# Set method-dependent scf convergence criteria, check against energy routines
if not core.has_option_changed('SCF', 'E_CONVERGENCE'):
if procedures['energy'][method_name] == proc.run_scf:
core.set_local_option('SCF', 'E_CONVERGENCE', scf_Ec)
if verbose >= 2:
print(scf_Ec, end=' ')
else:
core.set_local_option('SCF', 'E_CONVERGENCE', pscf_Ec)
if verbose >= 2:
print(pscf_Ec, end=' ')
else:
if verbose >= 2:
print('CUSTOM', core.get_option('SCF', 'E_CONVERGENCE'), end=' ')
if not core.has_option_changed('SCF', 'D_CONVERGENCE'):
if procedures['energy'][method_name] == proc.run_scf:
core.set_local_option('SCF', 'D_CONVERGENCE', scf_Dc)
if verbose >= 2:
print(scf_Dc, end=' ')
else:
core.set_local_option('SCF', 'D_CONVERGENCE', pscf_Dc)
if verbose >= 2:
print(pscf_Dc, end=' ')
else:
if verbose >= 2:
print('CUSTOM', core.get_option('SCF', 'D_CONVERGENCE'), end=' ')
# Set post-scf convergence criteria (global will cover all correlated modules)
if not core.has_global_option_changed('E_CONVERGENCE'):
if procedures['energy'][method_name] != proc.run_scf:
core.set_global_option('E_CONVERGENCE', gen_Ec)
if verbose >= 2:
print(gen_Ec, end=' ')
else:
if procedures['energy'][method_name] != proc.run_scf:
if verbose >= 2:
print('CUSTOM', core.get_global_option('E_CONVERGENCE'), end=' ')
if verbose >= 2:
print('')
return optstash
def _set_convergence_criterion(ptype,
method_name,
scf_Ec,
pscf_Ec,
scf_Dc,
pscf_Dc,
gen_Ec,
verbose=1):
r"""
This function will set local SCF and global energy convergence criterion
to the defaults listed at:
http://www.psicode.org/psi4manual/master/scf.html#convergence-and-
algorithm-defaults. SCF will be converged more tightly if a post-SCF
method is select (pscf_Ec, and pscf_Dc) else the looser (scf_Ec, and
scf_Dc convergence criterion will be used).
ptype - Procedure type (energy, gradient, etc). Nearly always test on
procedures['energy'] since that's guaranteed to exist for a method.
method_name - Name of the method
scf_Ec - E convergence criterion for scf target method
pscf_Ec - E convergence criterion for scf of post-scf target method
scf_Dc - D convergence criterion for scf target method
pscf_Dc - D convergence criterion for scf of post-scf target method
gen_Ec - E convergence criterion for post-scf target method
"""
optstash = p4util.OptionsState(['SCF', 'E_CONVERGENCE'],
['SCF', 'D_CONVERGENCE'], ['E_CONVERGENCE'])
# Kind of want to move this out of here
_method_exists(ptype, method_name)
if verbose >= 2:
print(' Setting convergence', end=' ')
# Set method-dependent scf convergence criteria, check against energy routines
if not core.has_option_changed('SCF', 'E_CONVERGENCE'):
if procedures['energy'][method_name] == proc.run_scf:
core.set_local_option('SCF', 'E_CONVERGENCE', scf_Ec)
if verbose >= 2:
print(scf_Ec, end=' ')
else:
core.set_local_option('SCF', 'E_CONVERGENCE', pscf_Ec)
if verbose >= 2:
print(pscf_Ec, end=' ')
else:
if verbose >= 2:
print('CUSTOM', core.get_option('SCF', 'E_CONVERGENCE'), end=' ')
if not core.has_option_changed('SCF', 'D_CONVERGENCE'):
if procedures['energy'][method_name] == proc.run_scf:
core.set_local_option('SCF', 'D_CONVERGENCE', scf_Dc)
if verbose >= 2:
print(scf_Dc, end=' ')
else:
core.set_local_option('SCF', 'D_CONVERGENCE', pscf_Dc)
if verbose >= 2:
print(pscf_Dc, end=' ')
else:
if verbose >= 2:
print('CUSTOM', core.get_option('SCF', 'D_CONVERGENCE'), end=' ')
# Set post-scf convergence criteria (global will cover all correlated modules)
if not core.has_global_option_changed('E_CONVERGENCE'):
if procedures['energy'][method_name] != proc.run_scf:
core.set_global_option('E_CONVERGENCE', gen_Ec)
if verbose >= 2:
print(gen_Ec, end=' ')
else:
if procedures['energy'][method_name] != proc.run_scf:
if verbose >= 2:
print('CUSTOM',
core.get_global_option('E_CONVERGENCE'),
end=' ')
if verbose >= 2:
print('')
return optstash
def prepare_options_for_modules(
changedOnly: bool = False,
commandsInsteadDict: bool = False,
globalsOnly: bool = False,
stateInsteadMediated: bool = False,
) -> Union[Dict, str]:
"""Capture current state of C++ psi4.core.Options information.
Parameters
----------
changedOnly
Record info only for options that have been set (may still be default).
When False, records values for every option.
commandsInsteadDict
Return string of commands to exec to reset options in current form.
When False, return nested dictionary with globals in 'GLOBALS' subdictionary
and locals in subdictionaries by module.
globalsOnly
Record only global options to save time querying the psi4.core.Options object.
When False, record module-level options, too.
stateInsteadMediated
When ``True``, querying this function for options to be later *reset* into the same
state -- the raw values and has_changed status at the global and local levels.
When ``False``, querying this function for mediated options to be *used* -- the results
of the globals/locals handshake as computed by the Options object itself. Here,
``dict[module][option][value]`` is the value to be used by module.
Returns
-------
dict
When ``commandsInsteadDict=False``.
str
When ``commandsInsteadDict=True``.
.. caution:: Some features are not yet implemented. Buy a developer a coffee.
- command return doesn't revoke has_changed setting for unchanged with changedOnly=False
- not all kwargs are independent
"""
has_changed_snapshot = {module: core.options_to_python(module) for module in _modules}
options = collections.defaultdict(dict)
commands = ''
for opt in core.get_global_option_list():
hoc = core.has_global_option_changed(opt)
if hoc or not changedOnly:
if opt in ['DFT_CUSTOM_FUNCTIONAL', 'EXTERN']: # Feb 2017 hack
continue
val = core.get_global_option(opt)
options['GLOBALS'][opt] = {'value': val, 'has_changed': hoc}
if isinstance(val, str):
commands += """core.set_global_option('%s', '%s')\n""" % (opt, val)
else:
commands += """core.set_global_option('%s', %s)\n""" % (opt, val)
if globalsOnly:
continue
opt_snapshot = {k: v[opt] for k, v in has_changed_snapshot.items() if opt in v}
for module, (lhoc, ohoc) in opt_snapshot.items():
if stateInsteadMediated:
hoc = lhoc
else:
hoc = ohoc
if hoc or not changedOnly:
if stateInsteadMediated:
val = core.get_local_option(module, opt)
else:
val = core.get_option(module, opt)
options[module][opt] = {'value': val, 'has_changed': hoc}
if isinstance(val, str):
commands += """core.set_local_option('%s', '%s', '%s')\n""" % (module, opt, val)
else:
commands += """core.set_local_option('%s', '%s', %s)\n""" % (module, opt, val)
if commandsInsteadDict:
return commands
else:
return options
def run_sf_sapt(name, **kwargs):
optstash = p4util.OptionsState(['SCF_TYPE'],
['SCF', 'REFERENCE'],
['SCF', 'DFT_GRAC_SHIFT'],
['SCF', 'SAVE_JK'])
core.tstart()
# Alter default algorithm
if not core.has_global_option_changed('SCF_TYPE'):
core.set_global_option('SCF_TYPE', 'DF')
core.prepare_options_for_module("SAPT")
# Get the molecule of interest
ref_wfn = kwargs.get('ref_wfn', None)
if ref_wfn is None:
sapt_dimer = kwargs.pop('molecule', core.get_active_molecule())
else:
core.print_out('Warning! SAPT argument "ref_wfn" is only able to use molecule information.')
sapt_dimer = ref_wfn.molecule()
sapt_dimer, monomerA, monomerB = proc_util.prepare_sapt_molecule(sapt_dimer, "dimer")
# Print out the title and some information
core.print_out("\n")
core.print_out(" ---------------------------------------------------------\n")
core.print_out(" " + "Spin-Flip SAPT Procedure".center(58) + "\n")
core.print_out("\n")
core.print_out(" " + "by Daniel G. A. Smith and Konrad Patkowski".center(58) + "\n")
core.print_out(" ---------------------------------------------------------\n")
core.print_out("\n")
core.print_out(" ==> Algorithm <==\n\n")
core.print_out(" JK Algorithm %12s\n" % core.get_option("SCF", "SCF_TYPE"))
core.print_out("\n")
core.print_out(" Required computations:\n")
core.print_out(" HF (Monomer A)\n")
core.print_out(" HF (Monomer B)\n")
core.print_out("\n")
if (core.get_option('SCF', 'REFERENCE') != 'ROHF'):
raise ValidationError('Spin-Flip SAPT currently only supports restricted open-shell references.')
# Run the two monomer computations
core.IO.set_default_namespace('dimer')
data = {}
if (core.get_global_option('SCF_TYPE') == 'DF'):
core.set_global_option('DF_INTS_IO', 'SAVE')
# Compute dimer wavefunction
wfn_A = scf_helper("SCF", molecule=monomerA, banner="SF-SAPT: HF Monomer A", **kwargs)
core.set_global_option("SAVE_JK", True)
wfn_B = scf_helper("SCF", molecule=monomerB, banner="SF-SAPT: HF Monomer B", **kwargs)
sapt_jk = wfn_B.jk()
core.set_global_option("SAVE_JK", False)
core.print_out("\n")
core.print_out(" ---------------------------------------------------------\n")
core.print_out(" " + "Spin-Flip SAPT Exchange and Electrostatics".center(58) + "\n")
core.print_out("\n")
core.print_out(" " + "by Daniel G. A. Smith and Konrad Patkowski".center(58) + "\n")
core.print_out(" ---------------------------------------------------------\n")
core.print_out("\n")
sf_data = sapt_sf_terms.compute_sapt_sf(sapt_dimer, sapt_jk, wfn_A, wfn_B)
# Print the results
core.print_out(" Spin-Flip SAPT Results\n")
core.print_out(" " + "-" * 103 + "\n")
for key, value in sf_data.items():
value = sf_data[key]
print_vals = (key, value * 1000, value * constants.hartree2kcalmol, value * constants.hartree2kJmol)
string = " %-26s % 15.8f [mEh] % 15.8f [kcal/mol] % 15.8f [kJ/mol]\n" % print_vals
core.print_out(string)
core.print_out(" " + "-" * 103 + "\n\n")
dimer_wfn = core.Wavefunction.build(sapt_dimer, wfn_A.basisset())
# Set variables
psivar_tanslator = {
"Elst10": "SAPT ELST ENERGY",
"Exch10(S^2) [diagonal]": "SAPT EXCH10(S^2),DIAGONAL ENERGY",
"Exch10(S^2) [off-diagonal]": "SAPT EXCH10(S^2),OFF-DIAGONAL ENERGY",
"Exch10(S^2) [highspin]": "SAPT EXCH10(S^2),HIGHSPIN ENERGY",
}
for k, v in sf_data.items():
psi_k = psivar_tanslator[k]
dimer_wfn.set_variable(psi_k, v)
core.set_variable(psi_k, v)
# Copy over highspin
core.set_variable("SAPT EXCH ENERGY", sf_data["Exch10(S^2) [highspin]"])
core.tstop()
return dimer_wfn
