def run_v2rdm_casscf(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
v2rdm_casscf can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('v2rdm_casscf')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
optstash = p4util.OptionsState(
['SCF', 'DF_INTS_IO'])
psi4.set_local_option('SCF', 'DF_INTS_IO', 'SAVE')
# Your plugin's psi4 run sequence goes here
scf_wfn = scf_helper(name, **kwargs)
# if restarting from a checkpoint file, this file
# needs to be in scratch with the correct name
filename = psi4.get_option("V2RDM_CASSCF","RESTART_FROM_CHECKPOINT_FILE")
# todo PSIF_V2RDM_CHECKPOINT should be definied in psifiles.h
if ( filename != "" ):
molname = psi4.wavefunction().molecule().name()
p4util.copy_file_to_scratch(filename,'psi',molname,269,False)
returnvalue = psi4.plugin('v2rdm_casscf.so',scf_wfn)
#psi4.set_variable('CURRENT ENERGY', returnvalue)
return psi4.get_variable('CURRENT ENERGY')
def run_plugin_mp2(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
mollerplesset2 can be called via :py:func:`~driver.energy`.
>>> energy('mollerplesset2')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# Your plugin's psi4 run sequence goes here
psi4.set_local_option('MOLLERPLESSET2', 'PRINT', 1)
scf_wfn = scf_helper(lowername)
# Need to semicanonicalize the ROHF orbitals
if psi4.get_global_option('REFERENCE') == 'ROHF':
scf_wfn.semicanonicalize()
# Ensure IWL files have been written when not using DF/CD
proc_util.check_iwl_file_from_scf_type(psi4.get_option('SCF', 'SCF_TYPE'),
scf_wfn)
#psi4.set_legacy_wavefunction(scf_wfn)
returnvalue = psi4.plugin('mollerplesset2.so', scf_wfn)
return returnvalue
def run_plugin_mp2(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
mollerplesset2 can be called via :py:func:`~driver.energy`.
>>> energy('mollerplesset2')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# Your plugin's psi4 run sequence goes here
psi4.set_local_option('MOLLERPLESSET2', 'PRINT', 1)
scf_wfn = scf_helper(lowername)
# Need to semicanonicalize the ROHF orbitals
if psi4.get_global_option('REFERENCE') == 'ROHF':
scf_wfn.semicanonicalize()
# Ensure IWL files have been written when not using DF/CD
proc_util.check_iwl_file_from_scf_type(psi4.get_option('SCF', 'SCF_TYPE'), scf_wfn)
#psi4.set_legacy_wavefunction(scf_wfn)
returnvalue = psi4.plugin('mollerplesset2.so', scf_wfn)
return returnvalue
def run_paralleldf(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
paralleldf can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('paralleldf')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# Your plugin's psi4 run sequence goes here
#psi4.set_global_option('BASIS', 'sto-3g')
psi4.set_local_option('MYPLUGIN', 'PRINT', 1)
# Compute a SCF reference, a wavefunction is return which holds the molecule used, orbitals
# Fock matrices, and more
ref_wfn = kwargs.get('ref_wfn', None)
if ref_wfn is None:
ref_wfn = driver.scf_helper(name, **kwargs)
# Call the Psi4 plugin
# Please note that setting the reference wavefunction in this way is ONLY for plugins
paralleldf_wfn = psi4.plugin('paralleldf.so', ref_wfn)
return paralleldf_wfn
def run_v2rdm_casscf(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
v2rdm_casscf can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('v2rdm_casscf')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
optstash = p4util.OptionsState(['SCF', 'DF_INTS_IO'])
psi4.set_local_option('SCF', 'DF_INTS_IO', 'SAVE')
# Your plugin's psi4 run sequence goes here
scf_wfn = scf_helper(name, **kwargs)
# if restarting from a checkpoint file, this file
# needs to be in scratch with the correct name
filename = psi4.get_option("V2RDM_CASSCF", "RESTART_FROM_CHECKPOINT_FILE")
# todo PSIF_V2RDM_CHECKPOINT should be definied in psifiles.h
if (filename != ""):
molname = psi4.wavefunction().molecule().name()
p4util.copy_file_to_scratch(filename, 'psi', molname, 269, False)
returnvalue = psi4.plugin('v2rdm_casscf.so', scf_wfn)
#psi4.set_variable('CURRENT ENERGY', returnvalue)
return psi4.get_variable('CURRENT ENERGY')
def run_plugin_fragment(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
plugin_fragment can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('plugin_fragment')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# Your plugin's psi4 run sequence goes here
psi4.plugin('plugin_fragment.so')
def run_plugin_fragment(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
plugin_fragment can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('plugin_fragment')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# Your plugin's psi4 run sequence goes here
psi4.plugin('plugin_fragment.so')
def run_cis(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
cis can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('cis')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# Your plugin's psi4 run sequence goes here
psi4.set_local_option('CIS', 'PRINT', 1)
scf_helper(name, **kwargs)
returnvalue = psi4.plugin('cis.so')
psi4.set_variable('CURRENT ENERGY', returnvalue)
def run_fasnocis(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
OCDFT can be called via :py:func:`~driver.energy`.
>>> energy('fasnocis')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# Run OCDFT
psi4.set_local_option('CDFT','METHOD','FASNOCIS')
returnvalue = psi4.plugin('cdft.so')
return returnvalue
def run_plugin_mp2(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
mollerplesset2 can be called via :py:func:`~driver.energy`.
>>> energy('mollerplesset2')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# Your plugin's psi4 run sequence goes here
psi4.set_local_option('MOLLERPLESSET2', 'PRINT', 1)
psi4.scf()
returnvalue = psi4.plugin('mollerplesset2.so')
return returnvalue
def run_dpd_unit_test(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
dpd_unit_test can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('dpd_unit_test')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# Your plugin's psi4 run sequence goes here
psi4.set_global_option('BASIS', 'sto-3g')
psi4.set_local_option('DPD_UNIT_TEST', 'PRINT', 1)
scf_helper(name, **kwargs)
returnvalue = psi4.plugin('dpd_unit_test.so')
psi4.set_variable('CURRENT ENERGY', returnvalue)
def run_main(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
main can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('main')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# Your plugin's psi4 run sequence goes here
# psi4.set_global_option('BASIS', 'sto-3g')
# psi4.set_local_option('MAIN', 'PRINT', 1)
scf_helper(name, **kwargs)
returnvalue = psi4.plugin('main.so')
psi4.set_variable('CURRENT ENERGY', returnvalue)
def sherrill_gold_standard(name='mp2', **kwargs):
r"""Function to call the quantum chemical method known as 'Gold Standard'
in the Sherrill group. Uses :py:func:`~wrappers.complete_basis_set` to evaluate
the following expression. Two-point extrapolation of the correlation energy
performed according to :py:func:`~wrappers.corl_xtpl_helgaker_2`.
.. math:: E_{total}^{\text{Au\_std}} = E_{total,\; \text{SCF}}^{\text{aug-cc-pVQZ}} \; + E_{corl,\; \text{MP2}}^{\text{aug-cc-pV[TQ]Z}} \; + \delta_{\text{MP2}}^{\text{CCSD(T)}}\big\vert_{\text{aug-cc-pVTZ}}
>>> # [1] single-point energy by this composite method
>>> energy('sherrill_gold_standard')
>>> # [2] finite-difference geometry optimization
>>> optimize('sherrill_gold_standard')
>>> # [3] finite-difference geometry optimization, overwriting some pre-defined sherrill_gold_standard options
>>> optimize('sherrill_gold_standard', corl_basis='cc-pV[DT]Z', delta_basis='3-21g')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
if not ('func_cbs' in kwargs):
kwargs['func_cbs'] = energy
if not ('scf_basis' in kwargs):
kwargs['scf_basis'] = 'aug-cc-pVQZ'
if not ('scf_scheme' in kwargs):
kwargs['scf_scheme'] = highest_1
if not ('corl_wfn' in kwargs):
kwargs['corl_wfn'] = 'mp2'
name = 'mp2'
if not ('corl_basis' in kwargs):
kwargs['corl_basis'] = 'aug-cc-pV[TQ]Z'
if not ('corl_scheme' in kwargs):
kwargs['corl_scheme'] = corl_xtpl_helgaker_2
if not ('delta_wfn' in kwargs):
kwargs['delta_wfn'] = 'ccsd(t)'
if not ('delta_wfn_lesser' in kwargs):
kwargs['delta_wfn_lesser'] = 'mp2'
if not ('delta_basis' in kwargs):
kwargs['delta_basis'] = 'aug-cc-pVTZ'
if not ('delta_scheme' in kwargs):
kwargs['delta_scheme'] = highest_1
return cbs(name, **kwargs)
def sherrill_gold_standard(name='mp2', **kwargs):
r"""Function to call the quantum chemical method known as 'Gold Standard'
in the Sherrill group. Uses :py:func:`~wrappers.complete_basis_set` to evaluate
the following expression. Two-point extrapolation of the correlation energy
performed according to :py:func:`~wrappers.corl_xtpl_helgaker_2`.
.. math:: E_{total}^{\text{Au\_std}} = E_{total,\; \text{SCF}}^{\text{aug-cc-pVQZ}} \; + E_{corl,\; \text{MP2}}^{\text{aug-cc-pV[TQ]Z}} \; + \delta_{\text{MP2}}^{\text{CCSD(T)}}\big\vert_{\text{aug-cc-pVTZ}}
>>> # [1] single-point energy by this composite method
>>> energy('sherrill_gold_standard')
>>> # [2] finite-difference geometry optimization
>>> optimize('sherrill_gold_standard')
>>> # [3] finite-difference geometry optimization, overwriting some pre-defined sherrill_gold_standard options
>>> optimize('sherrill_gold_standard', corl_basis='cc-pV[DT]Z', delta_basis='3-21g')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
if not ('func_cbs' in kwargs):
kwargs['func_cbs'] = energy
if not ('scf_basis' in kwargs):
kwargs['scf_basis'] = 'aug-cc-pVQZ'
if not ('scf_scheme' in kwargs):
kwargs['scf_scheme'] = highest_1
if not ('corl_wfn' in kwargs):
kwargs['corl_wfn'] = 'mp2'
name = 'mp2'
if not ('corl_basis' in kwargs):
kwargs['corl_basis'] = 'aug-cc-pV[TQ]Z'
if not ('corl_scheme' in kwargs):
kwargs['corl_scheme'] = corl_xtpl_helgaker_2
if not ('delta_wfn' in kwargs):
kwargs['delta_wfn'] = 'ccsd(t)'
if not ('delta_wfn_lesser' in kwargs):
kwargs['delta_wfn_lesser'] = 'mp2'
if not ('delta_basis' in kwargs):
kwargs['delta_basis'] = 'aug-cc-pVTZ'
if not ('delta_scheme' in kwargs):
kwargs['delta_scheme'] = highest_1
return cbs(name, **kwargs)
def run_dfdcft(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
dfdcft can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('dfdcft')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# psi4.set_local_option('SCF', 'REFERENCE', 'UHF')
# psi4.set_local_option('DFDCFT', 'REFERENCE', 'UHF')
# Your plugin's psi4 run sequence goes here
scf_helper(name, **kwargs)
returnvalue = psi4.plugin('dfdcft.so')
psi4.set_variable('CURRENT ENERGY', returnvalue)
def run_fvno(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
fvno can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('fvno')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# Your plugin's psi4 run sequence goes here
if ('wfn' in kwargs):
if (kwargs['wfn'] == 'ccsd'):
psi4.set_global_option('WFN', 'CCSD')
elif (kwargs['wfn'] == 'ccsd(t)'):
psi4.set_global_option('WFN', 'CCSD_T')
scf_helper(name, **kwargs)
psi4.transqt2()
returnvalue = psi4.plugin('fvno.so')
def run_fvno(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
fvno can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('fvno')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# Your plugin's psi4 run sequence goes here
if ('wfn' in kwargs):
if (kwargs['wfn'] == 'ccsd'):
psi4.set_global_option('WFN', 'CCSD')
elif (kwargs['wfn'] == 'ccsd(t)'):
psi4.set_global_option('WFN', 'CCSD_T')
scf_helper(name, **kwargs)
psi4.transqt2()
returnvalue = psi4.plugin('fvno.so')
def run_v2rdm_casscf(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
v2rdm_casscf can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('v2rdm_casscf')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
optstash = p4util.OptionsState(
['SCF', 'DF_INTS_IO'])
psi4.set_local_option('SCF', 'DF_INTS_IO', 'SAVE')
# Your plugin's psi4 run sequence goes here
ref_wfn = kwargs.get('ref_wfn', None)
if ref_wfn is None:
ref_wfn = driver.scf_helper(name, **kwargs)
# if restarting from a checkpoint file, this file
# needs to be in scratch with the correct name
filename = psi4.get_option("V2RDM_CASSCF","RESTART_FROM_CHECKPOINT_FILE")
# todo PSIF_V2RDM_CHECKPOINT should be definied in psifiles.h
if ( filename != "" ):
molname = ref_wfn.molecule().name()
p4util.copy_file_to_scratch(filename,'psi',molname,269,False)
# Ensure IWL files have been written when not using DF/CD
scf_type = psi4.get_option('SCF', 'SCF_TYPE')
if ( scf_type == 'PK' or scf_type == 'DIRECT' ):
proc_util.check_iwl_file_from_scf_type(psi4.get_option('SCF', 'SCF_TYPE'), ref_wfn)
returnvalue = psi4.plugin('v2rdm_casscf.so', ref_wfn)
#psi4.set_variable('CURRENT ENERGY', returnvalue)
#return psi4.get_variable('CURRENT ENERGY')
return returnvalue
def run_aomp2(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
aomp2 can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('aomp2')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
ref_wfn = kwargs.get('ref_wfn', None)
if ref_wfn is None:
ref_wfn = driver.scf_helper(name, **kwargs)
# Your plugin's psi4 run sequence goes here
#psi4.set_local_option('AOMP2', 'PRINT', 1)
#scf_helper(name, **kwargs)
returnvalue = psi4.plugin("aomp2.so", ref_wfn)
#psi4.set_variable('CURRENT ENERGY', returnvalue)
return returnvalue
def run_ccambit(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
ccambit can be called via :py:func:`~driver.energy`. For post-scf plugins.
>>> energy('ccambit')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
# Your plugin's psi4 run sequence goes here
if ('wfn' in kwargs):
if (kwargs['wfn'] == 'ccsd'):
psi4.set_global_option('WFN', 'CCSD')
elif (kwargs['wfn'] == 'ccsd(t)'):
psi4.set_global_option('WFN', 'CCSD_T')
scf_wfn = kwargs.get('ref_wfn', None)
if scf_wfn is None:
scf_wfn = driver.scf_helper(name, **kwargs)
check_iwl_file_from_scf_type(psi4.get_option('SCF', 'SCF_TYPE'), scf_wfn)
return psi4.plugin('ccambit.so', scf_wfn)
def allen_focal_point(name='mp2', **kwargs):
r"""Function to call Wes Allen-style Focal
Point Analysis. JCP 127 014306. Uses
:py:func:`~wrappers.complete_basis_set` to evaluate the following
expression. SCF employs a three-point extrapolation according
to :py:func:`~wrappers.scf_xtpl_helgaker_3`. MP2, CCSD, and
CCSD(T) employ two-point extrapolation performed according to
:py:func:`~wrappers.corl_xtpl_helgaker_2`. CCSDT and CCSDT(Q)
are plain deltas. This wrapper requires :ref:`Kallay's MRCC code <sec:mrcc>`.
.. math:: E_{total}^{\text{FPA}} = E_{total,\; \text{SCF}}^{\text{cc-pV[Q56]Z}} \; + E_{corl,\; \text{MP2}}^{\text{cc-pV[56]Z}} \; + \delta_{\text{MP2}}^{\text{CCSD}}\big\vert_{\text{cc-pV[56]Z}} \; + \delta_{\text{CCSD}}^{\text{CCSD(T)}}\big\vert_{\text{cc-pV[56]Z}} \; + \delta_{\text{CCSD(T)}}^{\text{CCSDT}}\big\vert_{\text{cc-pVTZ}} \; + \delta_{\text{CCSDT}}^{\text{CCSDT(Q)}}\big\vert_{\text{cc-pVDZ}}
>>> # [1] single-point energy by this composite method
>>> energy('allen_focal_point')
>>> # [2] finite-difference geometry optimization embarrasingly parallel
>>> optimize('allen_focal_point', mode='sow')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
if not ('func_cbs' in kwargs):
kwargs['func_cbs'] = energy
# SCF
if not ('scf_basis' in kwargs):
kwargs['scf_basis'] = 'cc-pV[Q56]Z'
if not ('scf_scheme' in kwargs):
kwargs['scf_scheme'] = scf_xtpl_helgaker_3
# delta MP2 - SCF
if not ('corl_wfn' in kwargs):
kwargs['corl_wfn'] = 'mp2'
name = 'mp2'
if not ('corl_basis' in kwargs):
kwargs['corl_basis'] = 'cc-pV[56]Z'
if not ('corl_scheme' in kwargs):
kwargs['corl_scheme'] = corl_xtpl_helgaker_2
# delta CCSD - MP2
if not ('delta_wfn' in kwargs):
kwargs['delta_wfn'] = 'mrccsd'
if not ('delta_wfn_lesser' in kwargs):
kwargs['delta_wfn_lesser'] = 'mp2'
if not ('delta_basis' in kwargs):
kwargs['delta_basis'] = 'cc-pV[56]Z'
if not ('delta_scheme' in kwargs):
kwargs['delta_scheme'] = corl_xtpl_helgaker_2
# delta CCSD(T) - CCSD
if not ('delta2_wfn' in kwargs):
kwargs['delta2_wfn'] = 'mrccsd(t)'
if not ('delta2_wfn_lesser' in kwargs):
kwargs['delta2_wfn_lesser'] = 'mrccsd'
if not ('delta2_basis' in kwargs):
kwargs['delta2_basis'] = 'cc-pV[56]Z'
if not ('delta2_scheme' in kwargs):
kwargs['delta2_scheme'] = corl_xtpl_helgaker_2
# delta CCSDT - CCSD(T)
if not ('delta3_wfn' in kwargs):
kwargs['delta3_wfn'] = 'mrccsdt'
if not ('delta3_wfn_lesser' in kwargs):
kwargs['delta3_wfn_lesser'] = 'mrccsd(t)'
if not ('delta3_basis' in kwargs):
kwargs['delta3_basis'] = 'cc-pVTZ'
if not ('delta3_scheme' in kwargs):
kwargs['delta3_scheme'] = highest_1
# delta CCSDT(Q) - CCSDT
if not ('delta4_wfn' in kwargs):
kwargs['delta4_wfn'] = 'mrccsdt(q)'
if not ('delta4_wfn_lesser' in kwargs):
kwargs['delta4_wfn_lesser'] = 'mrccsdt'
if not ('delta4_basis' in kwargs):
kwargs['delta4_basis'] = 'cc-pVDZ'
if not ('delta4_scheme' in kwargs):
kwargs['delta4_scheme'] = highest_1
return cbs(name, **kwargs)
def _nbody_gufunc(func, method_string, **kwargs):
"""
Computes the nbody interaction energy, gradient, or Hessian depending on input.
Parameters
----------
func : python function
Python function that accepts method_string and a molecule and returns a energy, gradient, or Hessian.
method_string : str
Lowername to be passed to function
molecule : psi4.Molecule (default: Global Molecule)
Molecule to use in all computations
return_wfn : bool (default: False)
Return a wavefunction or not
bsse_type : str or list (default: None, this function is not called)
Type of BSSE correction to compute: CP, NoCP, or VMFC. The first in this list is returned by this function.
max_nbody : int
Maximum n-body to compute, cannot exceede the number of fragments in the moleucle
ptype : str
Type of the procedure passed in
return_total_data : bool (default: False)
If True returns the total data (energy/gradient/etc) of the system otherwise returns interaction data
Returns
-------
data : return type of func
The interaction data
wfn : psi4.Wavefunction (optional)
A wavefunction with energy/gradient/hessian set appropriotely. This wavefunction also contains
Notes
-----
This is a generalized univeral function for compute interaction quantities.
Examples
--------
"""
### ==> Parse some kwargs <==
kwargs = p4util.kwargs_lower(kwargs)
return_wfn = kwargs.pop('return_wfn', False)
ptype = kwargs.pop('ptype', None)
return_total_data = kwargs.pop('return_total_data', False)
molecule = kwargs.pop('molecule', psi4.get_active_molecule())
molecule.update_geometry()
psi4.clean_variables()
if ptype not in ['energy', 'gradient', 'hessian']:
raise ValidationError(
"""N-Body driver: The ptype '%s' is not regonized.""" % ptype)
# Figure out BSSE types
do_cp = False
do_nocp = False
do_vmfc = False
return_method = False
# Must be passed bsse_type
bsse_type_list = kwargs.pop('bsse_type')
if bsse_type_list is None:
raise ValidationError("N-Body GUFunc: Must pass a bsse_type")
if not isinstance(bsse_type_list, list):
bsse_type_list = [bsse_type_list]
for num, btype in enumerate(bsse_type_list):
if btype.lower() == 'cp':
do_cp = True
if (num == 0): return_method = 'cp'
elif btype.lower() == 'nocp':
do_nocp = True
if (num == 0): return_method = 'nocp'
elif btype.lower() == 'vmfc':
do_vmfc = True
if (num == 0): return_method = 'vmfc'
else:
raise ValidationError(
"N-Body GUFunc: bsse_type '%s' is not recognized" %
btype.lower())
max_nbody = kwargs.get('max_nbody', -1)
max_frag = molecule.nfragments()
if max_nbody == -1:
max_nbody = molecule.nfragments()
else:
max_nbody = min(max_nbody, max_frag)
# What levels do we need?
nbody_range = range(1, max_nbody + 1)
fragment_range = range(1, max_frag + 1)
# Flip this off for now, needs more testing
# If we are doing CP lets save them integrals
#if 'cp' in bsse_type_list and (len(bsse_type_list) == 1):
# # Set to save RI integrals for repeated full-basis computations
# ri_ints_io = psi4.get_global_option('DF_INTS_IO')
# # inquire if above at all applies to dfmp2 or just scf
# psi4.set_global_option('DF_INTS_IO', 'SAVE')
# psioh = psi4.IOManager.shared_object()
# psioh.set_specific_retention(97, True)
bsse_str = bsse_type_list[0]
if len(bsse_type_list) > 1:
bsse_str = str(bsse_type_list)
psi4.print_out("\n\n")
psi4.print_out(" ===> N-Body Interaction Abacus <===\n")
psi4.print_out(" BSSE Treatment: %s\n" %
bsse_str)
cp_compute_list = {x: set() for x in nbody_range}
nocp_compute_list = {x: set() for x in nbody_range}
vmfc_compute_list = {x: set() for x in nbody_range}
vmfc_level_list = {x: set()
for x in nbody_range
} # Need to sum something slightly different
# Build up compute sets
if do_cp:
# Everything is in dimer basis
basis_tuple = tuple(fragment_range)
for nbody in nbody_range:
for x in it.combinations(fragment_range, nbody):
cp_compute_list[nbody].add((x, basis_tuple))
if do_nocp:
# Everything in monomer basis
for nbody in nbody_range:
for x in it.combinations(fragment_range, nbody):
nocp_compute_list[nbody].add((x, x))
if do_vmfc:
# Like a CP for all combinations of pairs or greater
for nbody in nbody_range:
for cp_combos in it.combinations(fragment_range, nbody):
basis_tuple = tuple(cp_combos)
for interior_nbody in nbody_range:
for x in it.combinations(cp_combos, interior_nbody):
combo_tuple = (x, basis_tuple)
vmfc_compute_list[interior_nbody].add(combo_tuple)
vmfc_level_list[len(basis_tuple)].add(combo_tuple)
# Build a comprehensive compute_range
compute_list = {x: set() for x in nbody_range}
for n in nbody_range:
compute_list[n] |= cp_compute_list[n]
compute_list[n] |= nocp_compute_list[n]
compute_list[n] |= vmfc_compute_list[n]
psi4.print_out(" Number of %d-body computations: %d\n" %
(n, len(compute_list[n])))
# Build size and slices dictionaries
fragment_size_dict = {
frag: molecule.extract_subsets(frag).natom()
for frag in range(1, max_frag + 1)
}
start = 0
fragment_slice_dict = {}
for k, v in fragment_size_dict.items():
fragment_slice_dict[k] = slice(start, start + v)
start += v
molecule_total_atoms = sum(fragment_size_dict.values())
# Now compute the energies
energies_dict = {}
ptype_dict = {}
for n in compute_list.keys():
psi4.print_out(
"\n ==> N-Body: Now computing %d-body complexes <==\n\n" % n)
print("\n ==> N-Body: Now computing %d-body complexes <==\n" % n)
total = len(compute_list[n])
for num, pair in enumerate(compute_list[n]):
psi4.print_out(
"\n N-Body: Computing complex (%d/%d) with fragments %s in the basis of fragments %s.\n\n"
% (num + 1, total, str(pair[0]), str(pair[1])))
ghost = list(set(pair[1]) - set(pair[0]))
current_mol = molecule.extract_subsets(list(pair[0]), ghost)
ptype_dict[pair] = func(method_string,
molecule=current_mol,
**kwargs)
energies_dict[pair] = psi4.get_variable("CURRENT ENERGY")
psi4.print_out(
"\n N-Body: Complex Energy (fragments = %s, basis = %s: %20.14f)\n"
% (str(pair[0]), str(pair[1]), energies_dict[pair]))
# Flip this off for now, needs more testing
#if 'cp' in bsse_type_list and (len(bsse_type_list) == 1):
# psi4.set_global_option('DF_INTS_IO', 'LOAD')
psi4.clean()
# Final dictionaries
cp_energy_by_level = {n: 0.0 for n in nbody_range}
nocp_energy_by_level = {n: 0.0 for n in nbody_range}
cp_energy_body_dict = {n: 0.0 for n in nbody_range}
nocp_energy_body_dict = {n: 0.0 for n in nbody_range}
vmfc_energy_body_dict = {n: 0.0 for n in nbody_range}
# Build out ptype dictionaries if needed
if ptype != 'energy':
if ptype == 'gradient':
arr_shape = (molecule_total_atoms, 3)
elif ptype == 'hessian':
arr_shape = (molecule_total_atoms * 3, molecule_total_atoms * 3)
else:
raise KeyError("N-Body: ptype '%s' not recognized" % ptype)
cp_ptype_by_level = {n: np.zeros(arr_shape) for n in nbody_range}
nocp_ptype_by_level = {n: np.zeros(arr_shape) for n in nbody_range}
cp_ptype_body_dict = {n: np.zeros(arr_shape) for n in nbody_range}
nocp_ptype_body_dict = {n: np.zeros(arr_shape) for n in nbody_range}
vmfc_ptype_body_dict = {n: np.zeros(arr_shape) for n in nbody_range}
else:
cp_ptype_by_level, cp_ptype_body_dict = None, None
nocp_ptype_by_level, nocp_ptype_body_dict = None, None
vmfc_ptype_body_dict = None
# Sum up all of the levels
for n in nbody_range:
# Energy
cp_energy_by_level[n] = sum(energies_dict[v]
for v in cp_compute_list[n])
nocp_energy_by_level[n] = sum(energies_dict[v]
for v in nocp_compute_list[n])
# Special vmfc case
if n > 1:
vmfc_energy_body_dict[n] = vmfc_energy_body_dict[n - 1]
for tup in vmfc_level_list[n]:
vmfc_energy_body_dict[n] += (
(-1)**(n - len(tup[0]))) * energies_dict[tup]
# Do ptype
if ptype != 'energy':
_sum_cluster_ptype_data(ptype, ptype_dict, cp_compute_list[n],
fragment_slice_dict, fragment_size_dict,
cp_ptype_by_level[n])
_sum_cluster_ptype_data(ptype, ptype_dict, nocp_compute_list[n],
fragment_slice_dict, fragment_size_dict,
nocp_ptype_by_level[n])
_sum_cluster_ptype_data(ptype,
ptype_dict,
vmfc_level_list[n],
fragment_slice_dict,
fragment_size_dict,
vmfc_ptype_by_level[n],
vmfc=True)
# Compute cp energy and ptype
if do_cp:
for n in nbody_range:
if n == max_frag:
cp_energy_body_dict[n] = cp_energy_by_level[n]
if ptype != 'energy':
cp_ptype_body_dict[n][:] = cp_ptype_by_level[n]
continue
for k in range(1, n + 1):
take_nk = nCr(max_frag - k - 1, n - k)
sign = ((-1)**(n - k))
value = cp_energy_by_level[k]
cp_energy_body_dict[n] += take_nk * sign * value
if ptype != 'energy':
value = cp_ptype_by_level[k]
cp_ptype_body_dict[n] += take_nk * sign * value
_print_nbody_energy(cp_energy_body_dict, "Counterpoise Corrected (CP)")
cp_interaction_energy = cp_energy_body_dict[
max_nbody] - cp_energy_body_dict[1]
psi4.set_variable('Counterpoise Corrected Total Energy',
cp_energy_body_dict[max_nbody])
psi4.set_variable('Counterpoise Corrected Interaction Energy',
cp_interaction_energy)
for n in nbody_range[1:]:
var_key = 'CP-CORRECTED %d-BODY INTERACTION ENERGY' % n
psi4.set_variable(var_key,
cp_energy_body_dict[n] - cp_energy_body_dict[1])
# Compute nocp energy and ptype
if do_nocp:
for n in nbody_range:
if n == max_frag:
nocp_energy_body_dict[n] = nocp_energy_by_level[n]
if ptype != 'energy':
nocp_ptype_body_dict[n][:] = nocp_ptype_by_level[n]
continue
for k in range(1, n + 1):
take_nk = nCr(max_frag - k - 1, n - k)
sign = ((-1)**(n - k))
value = nocp_energy_by_level[k]
nocp_energy_body_dict[n] += take_nk * sign * value
if ptype != 'energy':
value = nocp_ptype_by_level[k]
nocp_ptype_body_dict[n] += take_nk * sign * value
_print_nbody_energy(nocp_energy_body_dict,
"Non-Counterpoise Corrected (NoCP)")
nocp_interaction_energy = nocp_energy_body_dict[
max_nbody] - nocp_energy_body_dict[1]
psi4.set_variable('Non-Counterpoise Corrected Total Energy',
nocp_energy_body_dict[max_nbody])
psi4.set_variable('Non-Counterpoise Corrected Interaction Energy',
nocp_interaction_energy)
for n in nbody_range[1:]:
var_key = 'NOCP-CORRECTED %d-BODY INTERACTION ENERGY' % n
psi4.set_variable(
var_key, nocp_energy_body_dict[n] - nocp_energy_body_dict[1])
# Compute vmfc energy and ptype
if do_vmfc:
_print_nbody_energy(vmfc_energy_body_dict,
"Valiron-Mayer Function Couterpoise (VMFC)")
vmfc_interaction_energy = vmfc_energy_body_dict[
max_nbody] - vmfc_energy_body_dict[1]
psi4.set_variable('Valiron-Mayer Function Couterpoise Total Energy',
vmfc_energy_body_dict[max_nbody])
psi4.set_variable(
'Valiron-Mayer Function Couterpoise Interaction Energy',
vmfc_interaction_energy)
for n in nbody_range[1:]:
var_key = 'VMFC-CORRECTED %d-BODY INTERACTION ENERGY' % n
psi4.set_variable(
var_key, vmfc_energy_body_dict[n] - vmfc_energy_body_dict[1])
if return_method == 'cp':
ptype_body_dict = cp_ptype_body_dict
energy_body_dict = cp_energy_body_dict
elif return_method == 'nocp':
ptype_body_dict = nocp_ptype_body_dict
energy_body_dict = nocp_energy_body_dict
elif return_method == 'vmfc':
ptype_body_dict = vmfc_ptype_body_dict
energy_body_dict = vmfc_energy_body_dict
else:
raise ValidationError(
"N-Body Wrapper: Invalid return type. Should never be here, please post this error on github."
)
# Figure out and build return types
if return_total_data:
ret_energy = energy_body_dict[max_nbody]
else:
ret_energy = energy_body_dict[max_nbody]
ret_energy -= energy_body_dict[1]
if ptype != 'energy':
if return_total_data:
np_final_ptype = ptype_body_dict[max_nbody].copy()
else:
np_final_ptype = ptype_body_dict[max_nbody].copy()
np_final_ptype -= ptype_body_dict[1]
ret_ptype = psi4.Matrix(*np_cp_final_ptype.shape)
ret_ptype_view = np.asarray(final_ptype)
ret_ptype_view[:] = np_final_ptype
else:
ret_ptype = ret_energy
# Build and set a wavefunction
wfn = psi4.new_wavefunction(molecule, 'sto-3g')
wfn.nbody_energy = energies_dict
wfn.nbody_ptype = ptype_dict
wfn.nbody_body_energy = energy_body_dict
wfn.nbody_body_ptype = ptype_body_dict
if ptype == 'gradient':
wfn.set_gradient(ret_ptype)
elif ptype == 'hessian':
wfn.set_hessian(ret_ptype)
psi4.set_variable("CURRENT ENERGY", ret_energy)
if return_wfn:
return (ret_ptype, wfn)
else:
return ret_ptype
def _nbody_gufunc(func, method_string, **kwargs):
"""
Computes the nbody interaction energy, gradient, or Hessian depending on input.
Parameters
----------
func : python function
Python function that accepts method_string and a molecule and returns a energy, gradient, or Hessian.
method_string : str
Lowername to be passed to function
molecule : psi4.Molecule (default: Global Molecule)
Molecule to use in all computations
return_wfn : bool (default: False)
Return a wavefunction or not
bsse_type : str or list (default: None, this function is not called)
Type of BSSE correction to compute: CP, NoCP, or VMFC. The first in this list is returned by this function.
max_nbody : int
Maximum n-body to compute, cannot exceede the number of fragments in the moleucle
ptype : str
Type of the procedure passed in
return_total_data : bool (default: False)
If True returns the total data (energy/gradient/etc) of the system otherwise returns interaction data
Returns
-------
data : return type of func
The interaction data
wfn : psi4.Wavefunction (optional)
A wavefunction with energy/gradient/hessian set appropriotely. This wavefunction also contains
Notes
-----
This is a generalized univeral function for compute interaction quantities.
Examples
--------
"""
### ==> Parse some kwargs <==
kwargs = p4util.kwargs_lower(kwargs)
return_wfn = kwargs.pop('return_wfn', False)
ptype = kwargs.pop('ptype', None)
return_total_data = kwargs.pop('return_total_data', False)
molecule = kwargs.pop('molecule', psi4.get_active_molecule())
molecule.update_geometry()
psi4.clean_variables()
if ptype not in ['energy', 'gradient', 'hessian']:
raise ValidationError("""N-Body driver: The ptype '%s' is not regonized.""" % ptype)
# Figure out BSSE types
do_cp = False
do_nocp = False
do_vmfc = False
return_method = False
# Must be passed bsse_type
bsse_type_list = kwargs.pop('bsse_type')
if bsse_type_list is None:
raise ValidationError("N-Body GUFunc: Must pass a bsse_type")
if not isinstance(bsse_type_list, list):
bsse_type_list = [bsse_type_list]
for num, btype in enumerate(bsse_type_list):
if btype.lower() == 'cp':
do_cp = True
if (num == 0): return_method = 'cp'
elif btype.lower() == 'nocp':
do_nocp = True
if (num == 0): return_method = 'nocp'
elif btype.lower() == 'vmfc':
do_vmfc = True
if (num == 0): return_method = 'vmfc'
else:
raise ValidationError("N-Body GUFunc: bsse_type '%s' is not recognized" % btype.lower())
max_nbody = kwargs.get('max_nbody', -1)
max_frag = molecule.nfragments()
if max_nbody == -1:
max_nbody = molecule.nfragments()
else:
max_nbody = min(max_nbody, max_frag)
# What levels do we need?
nbody_range = range(1, max_nbody + 1)
fragment_range = range(1, max_frag + 1)
# If we are doing CP lets save them integrals
if 'cp' in bsse_type_list and (len(bsse_type_list) == 1):
# Set to save RI integrals for repeated full-basis computations
ri_ints_io = psi4.get_global_option('DF_INTS_IO')
# inquire if above at all applies to dfmp2 or just scf
psi4.set_global_option('DF_INTS_IO', 'SAVE')
psioh = psi4.IOManager.shared_object()
psioh.set_specific_retention(97, True)
bsse_str = bsse_type_list[0]
if len(bsse_type_list) >1:
bsse_str = str(bsse_type_list)
psi4.print_out("\n\n")
psi4.print_out(" ===> N-Body Interaction Abacus <===\n")
psi4.print_out(" BSSE Treatment: %s\n" % bsse_str)
cp_compute_list = {x:set() for x in nbody_range}
nocp_compute_list = {x:set() for x in nbody_range}
vmfc_compute_list = {x:set() for x in nbody_range}
vmfc_level_list = {x:set() for x in nbody_range} # Need to sum something slightly different
# Build up compute sets
if do_cp:
# Everything is in dimer basis
basis_tuple = tuple(fragment_range)
for nbody in nbody_range:
for x in it.combinations(fragment_range, nbody):
cp_compute_list[nbody].add( (x, basis_tuple) )
if do_nocp:
# Everything in monomer basis
for nbody in nbody_range:
for x in it.combinations(fragment_range, nbody):
nocp_compute_list[nbody].add( (x, x) )
if do_vmfc:
# Like a CP for all combinations of pairs or greater
for nbody in nbody_range:
for cp_combos in it.combinations(fragment_range, nbody):
basis_tuple = tuple(cp_combos)
for interior_nbody in nbody_range:
for x in it.combinations(cp_combos, interior_nbody):
combo_tuple = (x, basis_tuple)
vmfc_compute_list[interior_nbody].add( combo_tuple )
vmfc_level_list[len(basis_tuple)].add( combo_tuple )
# Build a comprehensive compute_range
compute_list = {x:set() for x in nbody_range}
for n in nbody_range:
compute_list[n] |= cp_compute_list[n]
compute_list[n] |= nocp_compute_list[n]
compute_list[n] |= vmfc_compute_list[n]
psi4.print_out(" Number of %d-body computations: %d\n" % (n, len(compute_list[n])))
# Build size and slices dictionaries
fragment_size_dict = {frag: molecule.extract_subsets(frag).natom() for
frag in range(1, max_frag+1)}
start = 0
fragment_slice_dict = {}
for k, v in fragment_size_dict.items():
fragment_slice_dict[k] = slice(start, start + v)
start += v
molecule_total_atoms = sum(fragment_size_dict.values())
# Now compute the energies
energies_dict = {}
ptype_dict = {}
for n in compute_list.keys():
psi4.print_out("\n ==> N-Body: Now computing %d-body complexes <==\n\n" % n)
print("\n ==> N-Body: Now computing %d-body complexes <==\n" % n)
total = len(compute_list[n])
for num, pair in enumerate(compute_list[n]):
psi4.print_out("\n N-Body: Computing complex (%d/%d) with fragments %s in the basis of fragments %s.\n\n" %
(num + 1, total, str(pair[0]), str(pair[1])))
ghost = list(set(pair[1]) - set(pair[0]))
current_mol = molecule.extract_subsets(list(pair[0]), ghost)
ptype_dict[pair] = func(method_string, molecule=current_mol, **kwargs)
energies_dict[pair] = psi4.get_variable("CURRENT ENERGY")
psi4.print_out("\n N-Body: Complex Energy (fragments = %s, basis = %s: %20.14f)\n" %
(str(pair[0]), str(pair[1]), energies_dict[pair]))
if 'cp' in bsse_type_list and (len(bsse_type_list) == 1):
psi4.set_global_option('DF_INTS_IO', 'LOAD')
psi4.clean()
# Final dictionaries
cp_energy_by_level = {n: 0.0 for n in nbody_range}
nocp_energy_by_level = {n: 0.0 for n in nbody_range}
cp_energy_body_dict = {n: 0.0 for n in nbody_range}
nocp_energy_body_dict = {n: 0.0 for n in nbody_range}
vmfc_energy_body_dict = {n: 0.0 for n in nbody_range}
# Build out ptype dictionaries if needed
if ptype != 'energy':
if ptype == 'gradient':
arr_shape = (molecule_total_atoms, 3)
elif ptype == 'hessian':
arr_shape = (molecule_total_atoms * 3, molecule_total_atoms * 3)
else:
raise KeyError("N-Body: ptype '%s' not recognized" % ptype)
cp_ptype_by_level = {n: np.zeros(arr_shape) for n in nbody_range}
nocp_ptype_by_level = {n: np.zeros(arr_shape) for n in nbody_range}
cp_ptype_body_dict = {n: np.zeros(arr_shape) for n in nbody_range}
nocp_ptype_body_dict = {n: np.zeros(arr_shape) for n in nbody_range}
vmfc_ptype_body_dict = {n: np.zeros(arr_shape) for n in nbody_range}
else:
cp_ptype_by_level, cp_ptype_body_dict = None, None
nocp_ptype_by_level, nocp_ptype_body_dict = None, None
vmfc_ptype_by_level= None
# Sum up all of the levels
for n in nbody_range:
# Energy
cp_energy_by_level[n] = sum(energies_dict[v] for v in cp_compute_list[n])
nocp_energy_by_level[n] = sum(energies_dict[v] for v in nocp_compute_list[n])
# Special vmfc case
if n > 1:
vmfc_energy_body_dict[n] = vmfc_energy_body_dict[n - 1]
for tup in vmfc_level_list[n]:
vmfc_energy_body_dict[n] += ((-1) ** (n - len(tup[0]))) * energies_dict[tup]
# Do ptype
if ptype != 'energy':
_sum_cluster_ptype_data(ptype, ptype_dict, cp_compute_list[n],
fragment_slice_dict, fragment_size_dict,
cp_ptype_by_level[n])
_sum_cluster_ptype_data(ptype, ptype_dict, nocp_compute_list[n],
fragment_slice_dict, fragment_size_dict,
nocp_ptype_by_level[n])
_sum_cluster_ptype_data(ptype, ptype_dict, vmfc_level_list[n],
fragment_slice_dict, fragment_size_dict,
vmfc_ptype_by_level[n], vmfc=True)
# Compute cp energy and ptype
if do_cp:
for n in nbody_range:
if n == max_frag:
cp_energy_body_dict[n] = cp_energy_by_level[n]
if ptype != 'energy':
cp_ptype_body_dict[n][:] = cp_ptype_by_level[n]
continue
for k in range(1, n + 1):
take_nk = nCr(max_frag - k - 1, n - k)
sign = ((-1) ** (n - k))
value = cp_energy_by_level[k]
cp_energy_body_dict[n] += take_nk * sign * value
if ptype != 'energy':
value = cp_ptype_by_level[k]
cp_ptype_body_dict[n] += take_nk * sign * value
_print_nbody_energy(cp_energy_body_dict, "Counterpoise Corrected (CP)")
cp_interaction_energy = cp_energy_body_dict[max_nbody] - cp_energy_body_dict[1]
psi4.set_variable('Counterpoise Corrected Total Energy', cp_energy_body_dict[max_nbody])
psi4.set_variable('Counterpoise Corrected Interaction Energy', cp_interaction_energy)
for n in nbody_range[1:]:
var_key = 'CP-CORRECTED %d-BODY INTERACTION ENERGY' % n
psi4.set_variable(var_key, cp_energy_body_dict[n] - cp_energy_body_dict[1])
# Compute nocp energy and ptype
if do_nocp:
for n in nbody_range:
if n == max_frag:
nocp_energy_body_dict[n] = nocp_energy_by_level[n]
if ptype != 'energy':
nocp_ptype_body_dict[n][:] = nocp_ptype_by_level[n]
continue
for k in range(1, n + 1):
take_nk = nCr(max_frag - k - 1, n - k)
sign = ((-1) ** (n - k))
value = nocp_energy_by_level[k]
nocp_energy_body_dict[n] += take_nk * sign * value
if ptype != 'energy':
value = nocp_ptype_by_level[k]
nocp_ptype_body_dict[n] += take_nk * sign * value
_print_nbody_energy(nocp_energy_body_dict, "Non-Counterpoise Corrected (NoCP)")
nocp_interaction_energy = nocp_energy_body_dict[max_nbody] - nocp_energy_body_dict[1]
psi4.set_variable('Non-Counterpoise Corrected Total Energy', nocp_energy_body_dict[max_nbody])
psi4.set_variable('Non-Counterpoise Corrected Interaction Energy', nocp_interaction_energy)
for n in nbody_range[1:]:
var_key = 'NOCP-CORRECTED %d-BODY INTERACTION ENERGY' % n
psi4.set_variable(var_key, nocp_energy_body_dict[n] - nocp_energy_body_dict[1])
# Compute vmfc energy and ptype
if do_vmfc:
_print_nbody_energy(vmfc_energy_body_dict, "Valiron-Mayer Function Couterpoise (VMFC)")
vmfc_interaction_energy = vmfc_energy_body_dict[max_nbody] - vmfc_energy_body_dict[1]
psi4.set_variable('Valiron-Mayer Function Couterpoise Total Energy', vmfc_energy_body_dict[max_nbody])
psi4.set_variable('Valiron-Mayer Function Couterpoise Interaction Energy', vmfc_interaction_energy)
for n in nbody_range[1:]:
var_key = 'VMFC-CORRECTED %d-BODY INTERACTION ENERGY' % n
psi4.set_variable(var_key, vmfc_energy_body_dict[n] - vmfc_energy_body_dict[1])
if return_method == 'cp':
ptype_body_dict = cp_ptype_body_dict
energy_body_dict = cp_energy_body_dict
elif return_method == 'nocp':
ptype_body_dict = nocp_ptype_body_dict
energy_body_dict = nocp_energy_body_dict
elif return_method == 'vmfc':
ptype_body_dict = vmfc_ptype_body_dict
energy_body_dict = vmfc_energy_body_dict
else:
raise ValidationError("N-Body Wrapper: Invalid return type. Should never be here, please post this error on github.")
# Figure out and build return types
if return_total_data:
ret_energy = energy_body_dict[max_nbody]
else:
ret_energy = energy_body_dict[max_nbody]
ret_energy -= energy_body_dict[1]
if ptype != 'energy':
if return_total_data:
np_final_ptype = ptype_body_dict[max_nbody].copy()
else:
np_final_ptype = ptype_body_dict[max_nbody].copy()
np_final_ptype -= ptype_body_dict[1]
ret_ptype = psi4.Matrix(*np_cp_final_ptype.shape)
ret_ptype_view = np.asarray(final_ptype)
ret_ptype_view[:] = np_final_ptype
else:
ret_ptype = ret_energy
# Build and set a wavefunction
wfn = psi4.new_wavefunction(molecule, 'sto-3g')
wfn.nbody_energy = energies_dict
wfn.nbody_ptype = ptype_dict
wfn.nbody_body_energy = energy_body_dict
wfn.nbody_body_ptype = ptype_body_dict
if ptype == 'gradient':
wfn.set_gradient(ret_ptype)
elif ptype == 'hessian':
wfn.set_hessian(ret_ptype)
psi4.set_variable("CURRENT ENERGY", ret_energy)
if return_wfn:
return (ret_ptype, wfn)
else:
return ret_ptype
def ip_fitting(molecule, omega_l, omega_r, **kwargs):
kwargs = p4util.kwargs_lower(kwargs)
# By default, zero the omega to 3 digits
omega_tol = kwargs.get('omega_tolerance', 1.0E-3)
# By default, do up to twenty iterations
maxiter = kwargs.get('maxiter', 20)
# By default, do not read previous 180 orbitals file
read = False
read180 = ''
if 'read' in kwargs:
read = True
read180 = kwargs['read']
# The molecule is required, and should be the neutral species
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
# How many electrons are there?
N = 0
for A in range(molecule.natom()):
N += molecule.Z(A)
N -= charge0
N = int(N)
Nb = int((N - mult0 + 1) / 2)
Na = int(N - Nb)
# Work in the ot namespace for this procedure
psi4.IO.set_default_namespace("ot")
# Burn in to determine orbital eigenvalues
if read:
psi4.set_global_option("GUESS", "READ")
copy_file_to_scratch(read180, 'psi', 'ot', 180)
old_guess = psi4.get_global_option("GUESS")
psi4.set_global_option("DF_INTS_IO", "SAVE")
psi4.print_out("""\n\t==> IP Fitting SCF: Burn-in <==\n""")
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
psi4.set_global_option("DF_INTS_IO", "LOAD")
# Determine H**O, to determine mult1
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Na == Nb:
H**O = -Nb
elif Nb == 0:
H**O = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
Na1 = Na
Nb1 = Nb
if H**O > 0:
Na1 = Na1 - 1
else:
Nb1 = Nb1 - 1
charge1 = charge0 + 1
mult1 = Na1 - Nb1 + 1
omegas = []
E0s = []
E1s = []
kIPs = []
IPs = []
types = []
# Right endpoint
psi4.set_global_option('DFT_OMEGA', omega_r)
# Neutral
if read:
psi4.set_global_option("GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
psi4.print_out("""\n\t==> IP Fitting SCF: Neutral, Right Endpoint <==\n""")
E0r, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
E_HOMO = 0.0
if Nb == 0:
E_HOMO = eps_a[int(Na - 1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
E_HOMO = E_a
else:
E_HOMO = E_b
E_HOMOr = E_HOMO
psi4.IO.change_file_namespace(180, "ot", "neutral")
# Cation
if read:
psi4.set_global_option("GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
psi4.print_out("""\n\t==> IP Fitting SCF: Cation, Right Endpoint <==\n""")
E1r = energy('scf', molecule=molecule, **kwargs)
psi4.IO.change_file_namespace(180, "ot", "cation")
IPr = E1r - E0r
kIPr = -E_HOMOr
delta_r = IPr - kIPr
if IPr > kIPr:
message = (
"""\n***IP Fitting Error: Right Omega limit should have kIP > IP"""
)
raise ValidationError(message)
omegas.append(omega_r)
types.append('Right Limit')
E0s.append(E0r)
E1s.append(E1r)
IPs.append(IPr)
kIPs.append(kIPr)
# Use previous orbitals from here out
psi4.set_global_option("GUESS", "READ")
# Left endpoint
psi4.set_global_option('DFT_OMEGA', omega_l)
# Neutral
psi4.IO.change_file_namespace(180, "neutral", "ot")
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
psi4.print_out("""\n\t==> IP Fitting SCF: Neutral, Left Endpoint <==\n""")
E0l, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
E_HOMO = 0.0
if Nb == 0:
E_HOMO = eps_a[int(Na - 1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
E_HOMO = E_a
else:
E_HOMO = E_b
E_HOMOl = E_HOMO
psi4.IO.change_file_namespace(180, "ot", "neutral")
# Cation
psi4.IO.change_file_namespace(180, "cation", "ot")
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
psi4.print_out("""\n\t==> IP Fitting SCF: Cation, Left Endpoint <==\n""")
E1l = energy('scf', molecule=molecule, **kwargs)
psi4.IO.change_file_namespace(180, "ot", "cation")
IPl = E1l - E0l
kIPl = -E_HOMOl
delta_l = IPl - kIPl
if IPl < kIPl:
message = (
"""\n***IP Fitting Error: Left Omega limit should have kIP < IP""")
raise ValidationError(message)
omegas.append(omega_l)
types.append('Left Limit')
E0s.append(E0l)
E1s.append(E1l)
IPs.append(IPl)
kIPs.append(kIPl)
converged = False
repeat_l = 0
repeat_r = 0
step = 0
while True:
step = step + 1
# Regula Falsi (modified)
if repeat_l > 1:
delta_l = delta_l / 2.0
if repeat_r > 1:
delta_r = delta_r / 2.0
omega = -(omega_r - omega_l) / (delta_r - delta_l) * delta_l + omega_l
psi4.set_global_option('DFT_OMEGA', omega)
# Neutral
psi4.IO.change_file_namespace(180, "neutral", "ot")
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
psi4.print_out(
"""\n\t==> IP Fitting SCF: Neutral, Omega = %11.3E <==\n""" %
omega)
E0, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
E_HOMO = 0.0
if Nb == 0:
E_HOMO = eps_a[int(Na - 1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
E_HOMO = E_a
else:
E_HOMO = E_b
psi4.IO.change_file_namespace(180, "ot", "neutral")
# Cation
psi4.IO.change_file_namespace(180, "cation", "ot")
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
psi4.print_out(
"""\n\t==> IP Fitting SCF: Cation, Omega = %11.3E <==\n""" % omega)
E1 = energy('scf', molecule=molecule, **kwargs)
psi4.IO.change_file_namespace(180, "ot", "cation")
IP = E1 - E0
kIP = -E_HOMO
delta = IP - kIP
if kIP > IP:
omega_r = omega
E0r = E0
E1r = E1
IPr = IP
kIPr = kIP
delta_r = delta
repeat_r = 0
repeat_l = repeat_l + 1
else:
omega_l = omega
E0l = E0
E1l = E1
IPl = IP
kIPl = kIP
delta_l = delta
repeat_l = 0
repeat_r = repeat_r + 1
omegas.append(omega)
types.append('Regula-Falsi')
E0s.append(E0)
E1s.append(E1)
IPs.append(IP)
kIPs.append(kIP)
# Termination
if (abs(omega_l - omega_r) < omega_tol or step > maxiter):
converged = True
break
# Properly, should clone molecule but since not returned and easy to unblemish,
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
psi4.IO.set_default_namespace("")
psi4.print_out("""\n\t==> IP Fitting Results <==\n\n""")
psi4.print_out("""\t => Occupation Determination <= \n\n""")
psi4.print_out("""\t %6s %6s %6s %6s %6s %6s\n""" %
('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
psi4.print_out("""\t Neutral: %6d %6d %6d %6d %6d %6d\n""" %
(N, Na, Nb, charge0, mult0, H**O))
psi4.print_out("""\t Cation: %6d %6d %6d %6d %6d\n\n""" %
(N - 1, Na1, Nb1, charge1, mult1))
psi4.print_out("""\t => Regula Falsi Iterations <=\n\n""")
psi4.print_out("""\t%3s %11s %14s %14s %14s %s\n""" %
('N', 'Omega', 'IP', 'kIP', 'Delta', 'Type'))
for k in range(len(omegas)):
psi4.print_out(
"""\t%3d %11.3E %14.6E %14.6E %14.6E %s\n""" %
(k + 1, omegas[k], IPs[k], kIPs[k], IPs[k] - kIPs[k], types[k]))
if converged:
psi4.print_out("""\n\tIP Fitting Converged\n""")
psi4.print_out("""\tFinal omega = %14.6E\n""" %
((omega_l + omega_r) / 2))
psi4.print_out(
"""\n\t"M,I. does the dying. Fleet just does the flying."\n""")
psi4.print_out("""\t\t\t-Starship Troopers\n""")
else:
psi4.print_out("""\n\tIP Fitting did not converge!\n""")
psi4.set_global_option("DF_INTS_IO", "NONE")
psi4.set_global_option("GUESS", old_guess)
def frac_traverse(molecule, **kwargs):
kwargs = p4util.kwargs_lower(kwargs)
# The molecule is required, and should be the neutral species
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
chargep = charge0 + 1
chargem = charge0 - 1
# By default, the multiplicity of the cation/anion are mult0 + 1
# These are overridden with the cation_mult and anion_mult kwargs
multp = kwargs.get('cation_mult', mult0 + 1)
multm = kwargs.get('anion_mult', mult0 + 1)
# By default, we start the frac procedure on the 25th iteration
# when not reading a previous guess
frac_start = kwargs.get('frac_start', 25)
# By default, we occupy by tenths of electrons
HOMO_occs = kwargs.get(
'HOMO_occs', [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0])
LUMO_occs = kwargs.get(
'LUMO_occs', [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0])
# By default, H**O and LUMO are both in alpha
Z = 0
for A in range(molecule.natom()):
Z += molecule.Z(A)
Z -= charge0
H**O = kwargs.get('H**O', (Z / 2 + 1 if (Z % 2) else Z / 2))
LUMO = kwargs.get('LUMO', H**O + 1)
# By default, DIIS in FRAC (1.0 occupation is always DIIS'd)
frac_diis = kwargs.get('frac_diis', True)
# By default, use the neutral orbitals as a guess for the anion
neutral_guess = kwargs.get('neutral_guess', True)
# By default, burn-in with UHF first, if UKS
hf_guess = False
if psi4.get_global_option('REFERENCE') == 'UKS':
hf_guess = kwargs.get('hf_guess', True)
# By default, re-guess at each N
continuous_guess = kwargs.get('continuous_guess', False)
# By default, drop the files to the molecule's name
root = kwargs.get('filename', molecule.name())
traverse_filename = root + '.traverse.dat'
# => Traverse <= #
occs = []
energies = []
potentials = []
convs = []
# => Run the neutral for its orbitals, if requested <= #
old_df_ints_io = psi4.get_global_option("DF_INTS_IO")
psi4.set_global_option("DF_INTS_IO", "SAVE")
old_guess = psi4.get_global_option("GUESS")
if (neutral_guess):
if (hf_guess):
psi4.set_global_option("REFERENCE", "UHF")
energy('scf')
psi4.set_global_option("GUESS", "READ")
psi4.set_global_option("DF_INTS_IO", "LOAD")
# => Run the anion first <= #
molecule.set_molecular_charge(chargem)
molecule.set_multiplicity(multm)
# => Burn the anion in with hf, if requested <= #
if hf_guess:
psi4.set_global_option("REFERENCE", "UHF")
energy('scf', molecule=molecule, **kwargs)
psi4.set_global_option("REFERENCE", "UKS")
psi4.set_global_option("GUESS", "READ")
psi4.set_global_option("DF_INTS_IO", "SAVE")
psi4.set_global_option("FRAC_START", frac_start)
psi4.set_global_option("FRAC_RENORMALIZE", True)
psi4.set_global_option("FRAC_LOAD", False)
for occ in LUMO_occs:
psi4.set_global_option("FRAC_OCC", [LUMO])
psi4.set_global_option("FRAC_VAL", [occ])
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
C = 1
if E == 0.0:
E = psi4.get_variable('SCF ITERATION ENERGY')
C = 0
if LUMO > 0:
eps = wfn.epsilon_a()
potentials.append(eps[int(LUMO) - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps[-int(LUMO) - 1])
occs.append(occ)
energies.append(E)
convs.append(C)
psi4.set_global_option("FRAC_START", 2)
psi4.set_global_option("FRAC_LOAD", True)
psi4.set_global_option("GUESS", "READ")
psi4.set_global_option("FRAC_DIIS", frac_diis)
psi4.set_global_option("DF_INTS_IO", "LOAD")
# => Run the neutral next <= #
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
# Burn the neutral in with hf, if requested <= #
if not continuous_guess:
psi4.set_global_option("GUESS", old_guess)
if hf_guess:
psi4.set_global_option("FRAC_START", 0)
psi4.set_global_option("REFERENCE", "UHF")
energy('scf', molecule=molecule, **kwargs)
psi4.set_global_option("REFERENCE", "UKS")
psi4.set_global_option("GUESS", "READ")
psi4.set_global_option("FRAC_LOAD", False)
psi4.set_global_option("FRAC_START", frac_start)
psi4.set_global_option("FRAC_RENORMALIZE", True)
for occ in HOMO_occs:
psi4.set_global_option("FRAC_OCC", [H**O])
psi4.set_global_option("FRAC_VAL", [occ])
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
C = 1
if E == 0.0:
E = psi4.get_variable('SCF ITERATION ENERGY')
C = 0
if LUMO > 0:
eps = wfn.epsilon_a()
potentials.append(eps[int(H**O) - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps[-int(H**O) - 1])
occs.append(occ - 1.0)
energies.append(E)
convs.append(C)
psi4.set_global_option("FRAC_START", 2)
psi4.set_global_option("FRAC_LOAD", True)
psi4.set_global_option("GUESS", "READ")
psi4.set_global_option("FRAC_DIIS", frac_diis)
psi4.set_global_option("DF_INTS_IO", "LOAD")
psi4.set_global_option("DF_INTS_IO", old_df_ints_io)
# => Print the results out <= #
E = {}
psi4.print_out(
"""\n ==> Fractional Occupation Traverse Results <==\n\n""")
psi4.print_out("""\t%-11s %-24s %-24s %11s\n""" %
('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(occs)):
psi4.print_out("""\t%11.3E %24.16E %24.16E %11d\n""" %
(occs[k], energies[k], potentials[k], convs[k]))
E[occs[k]] = energies[k]
psi4.print_out('\n\t"You trying to be a hero Watkins?"\n')
psi4.print_out('\t"Just trying to kill some bugs sir!"\n')
psi4.print_out('\t\t\t-Starship Troopers\n')
# Drop the files out
fh = open(traverse_filename, 'w')
fh.write("""\t%-11s %-24s %-24s %11s\n""" %
('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(occs)):
fh.write("""\t%11.3E %24.16E %24.16E %11d\n""" %
(occs[k], energies[k], potentials[k], convs[k]))
fh.close()
# Properly, should clone molecule but since not returned and easy to unblemish,
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
return E
def frac_nuke(molecule, **kwargs):
kwargs = p4util.kwargs_lower(kwargs)
# The molecule is required, and should be the neutral species
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
# By default, we start the frac procedure on the 25th iteration
# when not reading a previous guess
frac_start = kwargs.get('frac_start', 25)
# By default, we occupy by tenths of electrons
foccs = kwargs.get('foccs',
[1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0])
# By default, H**O and LUMO are both in alpha
N = 0
for A in range(molecule.natom()):
N += molecule.Z(A)
N -= charge0
N = int(N)
Nb = int((N - mult0 + 1) / 2)
Na = int(N - Nb)
charge = charge0
mult = mult0
# By default, nuke all the electrons
Nmin = 0
if ('nmax' in kwargs):
Nmin = N - int(kwargs['nmax'])
# By default, DIIS in FRAC (1.0 occupation is always DIIS'd)
frac_diis = kwargs.get('frac_diis', True)
# By default, drop the files to the molecule's name
root = kwargs.get('filename', molecule.name())
traverse_filename = root + '.traverse.dat'
stats_filename = root + '.stats.dat'
# => Traverse <= #
psi4.set_global_option("DF_INTS_IO", "SAVE")
Ns = []
energies = []
potentials = []
convs = []
stats = []
# Run one SCF to burn things in
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
# Determine H**O
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Na == Nb:
H**O = -Nb
elif Nb == 0:
H**O = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
stats.append("""\t%6d %6d %6d %6d %6d %6d\n""" %
(N, Na, Nb, charge, mult, H**O))
if H**O > 0:
Na = Na - 1
else:
Nb = Nb - 1
charge = charge + 1
mult = Na - Nb + 1
psi4.set_global_option("DF_INTS_IO", "LOAD")
psi4.set_global_option("FRAC_START", frac_start)
psi4.set_global_option("FRAC_RENORMALIZE", True)
# Nuke 'em Rico!
for Nintegral in range(N, Nmin, -1):
# Nuke the current H**O
for occ in foccs:
psi4.set_global_option("FRAC_OCC", [H**O])
psi4.set_global_option("FRAC_VAL", [occ])
E, wfn = energy('scf',
return_wfn=True,
molecule=molecule,
**kwargs)
C = 1
if E == 0.0:
E = psi4.get_variable('SCF ITERATION ENERGY')
C = 0
if H**O > 0:
eps = wfn.epsilon_a()
potentials.append(eps[H**O - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps[-H**O - 1])
Ns.append(Nintegral + occ - 1.0)
energies.append(E)
convs.append(C)
psi4.set_global_option("FRAC_START", 2)
psi4.set_global_option("FRAC_LOAD", True)
psi4.set_global_option("FRAC_DIIS", frac_diis)
psi4.set_global_option("GUESS", "READ")
# Set the next charge/mult
molecule.set_molecular_charge(charge)
molecule.set_multiplicity(mult)
# Determine H**O
print('DGAS: What ref should this point to?')
#ref = psi4.legacy_wavefunction()
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Na == Nb:
H**O = -Nb
elif Nb == 0:
H**O = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
stats.append("""\t%6d %6d %6d %6d %6d %6d\n""" %
(Nintegral - 1, Na, Nb, charge, mult, H**O))
if H**O > 0:
Na = Na - 1
else:
Nb = Nb - 1
charge = charge + 1
mult = Na - Nb + 1
psi4.set_global_option("DF_INTS_IO", "NONE")
# => Print the results out <= #
E = {}
psi4.print_out("""\n ==> Fractional Occupation Nuke Results <==\n\n""")
psi4.print_out("""\t%-11s %-24s %-24s %11s\n""" %
('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(Ns)):
psi4.print_out("""\t%11.3E %24.16E %24.16E %11d\n""" %
(Ns[k], energies[k], potentials[k], convs[k]))
E[Ns[k]] = energies[k]
psi4.print_out('\n')
psi4.print_out("""\t%6s %6s %6s %6s %6s %6s\n""" %
('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
for line in stats:
psi4.print_out(line)
psi4.print_out(
'\n\t"You shoot a nuke down a bug hole, you got a lot of dead bugs"\n')
psi4.print_out('\t\t\t-Starship Troopers\n')
# Drop the files out
fh = open(traverse_filename, 'w')
fh.write("""\t%-11s %-24s %-24s %11s\n""" %
('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(Ns)):
fh.write("""\t%11.3E %24.16E %24.16E %11d\n""" %
(Ns[k], energies[k], potentials[k], convs[k]))
fh.close()
fh = open(stats_filename, 'w')
fh.write("""\t%6s %6s %6s %6s %6s %6s\n""" %
('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
for line in stats:
fh.write(line)
fh.close()
# Properly, should clone molecule but since not returned and easy to unblemish,
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
return E
def ip_fitting(molecule, omega_l, omega_r, **kwargs):
kwargs = p4util.kwargs_lower(kwargs)
# By default, zero the omega to 3 digits
omega_tol = kwargs.get('omega_tolerance', 1.0E-3)
# By default, do up to twenty iterations
maxiter = kwargs.get('maxiter', 20)
# By default, do not read previous 180 orbitals file
read = False
read180 = ''
if 'read' in kwargs:
read = True
read180 = kwargs['read']
# The molecule is required, and should be the neutral species
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
# How many electrons are there?
N = 0
for A in range(molecule.natom()):
N += molecule.Z(A)
N -= charge0
N = int(N)
Nb = int((N - mult0 + 1) / 2)
Na = int(N - Nb)
# Work in the ot namespace for this procedure
psi4.IO.set_default_namespace("ot")
# Burn in to determine orbital eigenvalues
if read:
psi4.set_global_option("GUESS", "READ")
copy_file_to_scratch(read180, 'psi', 'ot', 180)
old_guess = psi4.get_global_option("GUESS")
psi4.set_global_option("DF_INTS_IO", "SAVE")
psi4.print_out("""\n\t==> IP Fitting SCF: Burn-in <==\n""")
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
psi4.set_global_option("DF_INTS_IO", "LOAD")
# Determine H**O, to determine mult1
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Na == Nb:
H**O = -Nb
elif Nb == 0:
H**O = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
Na1 = Na;
Nb1 = Nb;
if H**O > 0:
Na1 = Na1 - 1;
else:
Nb1 = Nb1 - 1;
charge1 = charge0 + 1;
mult1 = Na1 - Nb1 + 1
omegas = []
E0s = []
E1s = []
kIPs = []
IPs = []
types = []
# Right endpoint
psi4.set_global_option('DFT_OMEGA', omega_r)
# Neutral
if read:
psi4.set_global_option("GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
psi4.print_out("""\n\t==> IP Fitting SCF: Neutral, Right Endpoint <==\n""")
E0r, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
E_HOMO = 0.0;
if Nb == 0:
E_HOMO = eps_a[int(Na - 1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
E_HOMO = E_a
else:
E_HOMO = E_b
E_HOMOr = E_HOMO
psi4.IO.change_file_namespace(180, "ot", "neutral")
# Cation
if read:
psi4.set_global_option("GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
psi4.print_out("""\n\t==> IP Fitting SCF: Cation, Right Endpoint <==\n""")
E1r = energy('scf', molecule=molecule, **kwargs)
psi4.IO.change_file_namespace(180, "ot", "cation")
IPr = E1r - E0r;
kIPr = -E_HOMOr;
delta_r = IPr - kIPr;
if IPr > kIPr:
message = ("""\n***IP Fitting Error: Right Omega limit should have kIP > IP""")
raise ValidationError(message)
omegas.append(omega_r)
types.append('Right Limit')
E0s.append(E0r)
E1s.append(E1r)
IPs.append(IPr)
kIPs.append(kIPr)
# Use previous orbitals from here out
psi4.set_global_option("GUESS", "READ")
# Left endpoint
psi4.set_global_option('DFT_OMEGA', omega_l)
# Neutral
psi4.IO.change_file_namespace(180, "neutral", "ot")
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
psi4.print_out("""\n\t==> IP Fitting SCF: Neutral, Left Endpoint <==\n""")
E0l, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
E_HOMO = 0.0
if Nb == 0:
E_HOMO = eps_a[int(Na - 1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
E_HOMO = E_a
else:
E_HOMO = E_b
E_HOMOl = E_HOMO
psi4.IO.change_file_namespace(180, "ot", "neutral")
# Cation
psi4.IO.change_file_namespace(180, "cation", "ot")
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
psi4.print_out("""\n\t==> IP Fitting SCF: Cation, Left Endpoint <==\n""")
E1l = energy('scf', molecule=molecule, **kwargs)
psi4.IO.change_file_namespace(180, "ot", "cation")
IPl = E1l - E0l
kIPl = -E_HOMOl
delta_l = IPl - kIPl
if IPl < kIPl:
message = ("""\n***IP Fitting Error: Left Omega limit should have kIP < IP""")
raise ValidationError(message)
omegas.append(omega_l)
types.append('Left Limit')
E0s.append(E0l)
E1s.append(E1l)
IPs.append(IPl)
kIPs.append(kIPl)
converged = False
repeat_l = 0
repeat_r = 0
step = 0
while True:
step = step + 1
# Regula Falsi (modified)
if repeat_l > 1:
delta_l = delta_l / 2.0
if repeat_r > 1:
delta_r = delta_r / 2.0
omega = - (omega_r - omega_l) / (delta_r - delta_l) * delta_l + omega_l
psi4.set_global_option('DFT_OMEGA', omega)
# Neutral
psi4.IO.change_file_namespace(180, "neutral", "ot")
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
psi4.print_out("""\n\t==> IP Fitting SCF: Neutral, Omega = %11.3E <==\n""" % omega)
E0, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
E_HOMO = 0.0
if Nb == 0:
E_HOMO = eps_a[int(Na - 1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
E_HOMO = E_a
else:
E_HOMO = E_b
psi4.IO.change_file_namespace(180, "ot", "neutral")
# Cation
psi4.IO.change_file_namespace(180, "cation", "ot")
molecule.set_molecular_charge(charge1)
molecule.set_multiplicity(mult1)
psi4.print_out("""\n\t==> IP Fitting SCF: Cation, Omega = %11.3E <==\n""" % omega)
E1 = energy('scf', molecule=molecule, **kwargs)
psi4.IO.change_file_namespace(180, "ot", "cation")
IP = E1 - E0
kIP = -E_HOMO
delta = IP - kIP
if kIP > IP:
omega_r = omega
E0r = E0
E1r = E1
IPr = IP
kIPr = kIP
delta_r = delta
repeat_r = 0
repeat_l = repeat_l + 1
else:
omega_l = omega
E0l = E0
E1l = E1
IPl = IP
kIPl = kIP
delta_l = delta
repeat_l = 0;
repeat_r = repeat_r + 1
omegas.append(omega)
types.append('Regula-Falsi')
E0s.append(E0)
E1s.append(E1)
IPs.append(IP)
kIPs.append(kIP)
# Termination
if (abs(omega_l - omega_r) < omega_tol or step > maxiter):
converged = True
break
# Properly, should clone molecule but since not returned and easy to unblemish,
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
psi4.IO.set_default_namespace("")
psi4.print_out("""\n\t==> IP Fitting Results <==\n\n""")
psi4.print_out("""\t => Occupation Determination <= \n\n""")
psi4.print_out("""\t %6s %6s %6s %6s %6s %6s\n""" % ('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
psi4.print_out("""\t Neutral: %6d %6d %6d %6d %6d %6d\n""" % (N, Na, Nb, charge0, mult0, H**O))
psi4.print_out("""\t Cation: %6d %6d %6d %6d %6d\n\n""" % (N - 1, Na1, Nb1, charge1, mult1))
psi4.print_out("""\t => Regula Falsi Iterations <=\n\n""")
psi4.print_out("""\t%3s %11s %14s %14s %14s %s\n""" % ('N','Omega','IP','kIP','Delta','Type'))
for k in range(len(omegas)):
psi4.print_out("""\t%3d %11.3E %14.6E %14.6E %14.6E %s\n""" %
(k + 1, omegas[k], IPs[k], kIPs[k], IPs[k] - kIPs[k], types[k]))
if converged:
psi4.print_out("""\n\tIP Fitting Converged\n""")
psi4.print_out("""\tFinal omega = %14.6E\n""" % ((omega_l + omega_r) / 2))
psi4.print_out("""\n\t"M,I. does the dying. Fleet just does the flying."\n""")
psi4.print_out("""\t\t\t-Starship Troopers\n""")
else:
psi4.print_out("""\n\tIP Fitting did not converge!\n""")
psi4.set_global_option("DF_INTS_IO", "NONE")
psi4.set_global_option("GUESS", old_guess)
def frac_traverse(molecule, **kwargs):
kwargs = p4util.kwargs_lower(kwargs)
# The molecule is required, and should be the neutral species
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
chargep = charge0 + 1
chargem = charge0 - 1
# By default, the multiplicity of the cation/anion are mult0 + 1
# These are overridden with the cation_mult and anion_mult kwargs
multp = kwargs.get('cation_mult', mult0 + 1)
multm = kwargs.get('anion_mult', mult0 + 1)
# By default, we start the frac procedure on the 25th iteration
# when not reading a previous guess
frac_start = kwargs.get('frac_start', 25)
# By default, we occupy by tenths of electrons
HOMO_occs = kwargs.get('HOMO_occs', [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0])
LUMO_occs = kwargs.get('LUMO_occs', [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0])
# By default, H**O and LUMO are both in alpha
Z = 0;
for A in range(molecule.natom()):
Z += molecule.Z(A)
Z -= charge0
H**O = kwargs.get('H**O', (Z / 2 + 1 if (Z % 2) else Z / 2))
LUMO = kwargs.get('LUMO', H**O + 1)
# By default, DIIS in FRAC (1.0 occupation is always DIIS'd)
frac_diis = kwargs.get('frac_diis', True)
# By default, use the neutral orbitals as a guess for the anion
neutral_guess = kwargs.get('neutral_guess', True)
# By default, burn-in with UHF first, if UKS
hf_guess = False
if psi4.get_global_option('REFERENCE') == 'UKS':
hf_guess = kwargs.get('hf_guess', True)
# By default, re-guess at each N
continuous_guess = kwargs.get('continuous_guess', False)
# By default, drop the files to the molecule's name
root = kwargs.get('filename', molecule.name())
traverse_filename = root + '.traverse.dat'
# => Traverse <= #
occs = []
energies = []
potentials = []
convs = []
# => Run the neutral for its orbitals, if requested <= #
old_df_ints_io = psi4.get_global_option("DF_INTS_IO")
psi4.set_global_option("DF_INTS_IO", "SAVE")
old_guess = psi4.get_global_option("GUESS")
if (neutral_guess):
if (hf_guess):
psi4.set_global_option("REFERENCE","UHF")
energy('scf')
psi4.set_global_option("GUESS", "READ")
psi4.set_global_option("DF_INTS_IO", "LOAD")
# => Run the anion first <= #
molecule.set_molecular_charge(chargem)
molecule.set_multiplicity(multm)
# => Burn the anion in with hf, if requested <= #
if hf_guess:
psi4.set_global_option("REFERENCE","UHF")
energy('scf', molecule=molecule, **kwargs)
psi4.set_global_option("REFERENCE","UKS")
psi4.set_global_option("GUESS", "READ")
psi4.set_global_option("DF_INTS_IO", "SAVE")
psi4.set_global_option("FRAC_START", frac_start)
psi4.set_global_option("FRAC_RENORMALIZE", True)
psi4.set_global_option("FRAC_LOAD", False)
for occ in LUMO_occs:
psi4.set_global_option("FRAC_OCC", [LUMO])
psi4.set_global_option("FRAC_VAL", [occ])
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
C = 1
if E == 0.0:
E = psi4.get_variable('SCF ITERATION ENERGY')
C = 0
if LUMO > 0:
eps = wfn.epsilon_a()
potentials.append(eps[int(LUMO) - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps[-int(LUMO) - 1])
occs.append(occ)
energies.append(E)
convs.append(C)
psi4.set_global_option("FRAC_START", 2)
psi4.set_global_option("FRAC_LOAD", True)
psi4.set_global_option("GUESS", "READ")
psi4.set_global_option("FRAC_DIIS", frac_diis)
psi4.set_global_option("DF_INTS_IO", "LOAD")
# => Run the neutral next <= #
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
# Burn the neutral in with hf, if requested <= #
if not continuous_guess:
psi4.set_global_option("GUESS", old_guess)
if hf_guess:
psi4.set_global_option("FRAC_START", 0)
psi4.set_global_option("REFERENCE", "UHF")
energy('scf', molecule=molecule, **kwargs)
psi4.set_global_option("REFERENCE", "UKS")
psi4.set_global_option("GUESS", "READ")
psi4.set_global_option("FRAC_LOAD", False)
psi4.set_global_option("FRAC_START", frac_start)
psi4.set_global_option("FRAC_RENORMALIZE", True)
for occ in HOMO_occs:
psi4.set_global_option("FRAC_OCC", [H**O])
psi4.set_global_option("FRAC_VAL", [occ])
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
C = 1
if E == 0.0:
E = psi4.get_variable('SCF ITERATION ENERGY')
C = 0
if LUMO > 0:
eps = wfn.epsilon_a()
potentials.append(eps[int(H**O) - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps[-int(H**O) - 1])
occs.append(occ - 1.0)
energies.append(E)
convs.append(C)
psi4.set_global_option("FRAC_START", 2)
psi4.set_global_option("FRAC_LOAD", True)
psi4.set_global_option("GUESS", "READ")
psi4.set_global_option("FRAC_DIIS", frac_diis)
psi4.set_global_option("DF_INTS_IO", "LOAD")
psi4.set_global_option("DF_INTS_IO", old_df_ints_io)
# => Print the results out <= #
E = {}
psi4.print_out("""\n ==> Fractional Occupation Traverse Results <==\n\n""")
psi4.print_out("""\t%-11s %-24s %-24s %11s\n""" % ('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(occs)):
psi4.print_out("""\t%11.3E %24.16E %24.16E %11d\n""" % (occs[k], energies[k], potentials[k], convs[k]))
E[occs[k]] = energies[k]
psi4.print_out('\n\t"You trying to be a hero Watkins?"\n')
psi4.print_out('\t"Just trying to kill some bugs sir!"\n')
psi4.print_out('\t\t\t-Starship Troopers\n')
# Drop the files out
fh = open(traverse_filename, 'w')
fh.write("""\t%-11s %-24s %-24s %11s\n""" % ('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(occs)):
fh.write("""\t%11.3E %24.16E %24.16E %11d\n""" % (occs[k], energies[k], potentials[k], convs[k]))
fh.close()
# Properly, should clone molecule but since not returned and easy to unblemish,
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
return E
def frac_nuke(molecule, **kwargs):
kwargs = p4util.kwargs_lower(kwargs)
# The molecule is required, and should be the neutral species
molecule.update_geometry()
charge0 = molecule.molecular_charge()
mult0 = molecule.multiplicity()
# By default, we start the frac procedure on the 25th iteration
# when not reading a previous guess
frac_start = kwargs.get('frac_start', 25)
# By default, we occupy by tenths of electrons
foccs = kwargs.get('foccs', [1.0, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.0])
# By default, H**O and LUMO are both in alpha
N = 0;
for A in range(molecule.natom()):
N += molecule.Z(A)
N -= charge0
N = int(N)
Nb = int((N - mult0 + 1) / 2)
Na = int(N - Nb)
charge = charge0
mult = mult0
# By default, nuke all the electrons
Nmin = 0;
if ('nmax' in kwargs):
Nmin = N - int(kwargs['nmax'])
# By default, DIIS in FRAC (1.0 occupation is always DIIS'd)
frac_diis = kwargs.get('frac_diis', True)
# By default, drop the files to the molecule's name
root = kwargs.get('filename', molecule.name())
traverse_filename = root + '.traverse.dat'
stats_filename = root + '.stats.dat'
# => Traverse <= #
psi4.set_global_option("DF_INTS_IO", "SAVE")
Ns = []
energies = []
potentials = []
convs = []
stats = []
# Run one SCF to burn things in
E, wfn= energy('scf', return_wfn=True, molecule=molecule, **kwargs)
# Determine H**O
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Na == Nb:
H**O = -Nb
elif Nb == 0:
H**O = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
stats.append("""\t%6d %6d %6d %6d %6d %6d\n""" % (N, Na, Nb, charge, mult, H**O))
if H**O > 0:
Na = Na - 1
else:
Nb = Nb - 1
charge = charge + 1
mult = Na - Nb + 1
psi4.set_global_option("DF_INTS_IO", "LOAD")
psi4.set_global_option("FRAC_START", frac_start)
psi4.set_global_option("FRAC_RENORMALIZE", True)
# Nuke 'em Rico!
for Nintegral in range(N, Nmin, -1):
# Nuke the current H**O
for occ in foccs:
psi4.set_global_option("FRAC_OCC", [H**O])
psi4.set_global_option("FRAC_VAL", [occ])
E, wfn = energy('scf', return_wfn=True, molecule=molecule, **kwargs)
C = 1
if E == 0.0:
E = psi4.get_variable('SCF ITERATION ENERGY')
C = 0
if H**O > 0:
eps = wfn.epsilon_a()
potentials.append(eps[H**O - 1])
else:
eps = wfn.epsilon_b()
potentials.append(eps[-H**O - 1])
Ns.append(Nintegral + occ - 1.0)
energies.append(E)
convs.append(C)
psi4.set_global_option("FRAC_START", 2)
psi4.set_global_option("FRAC_LOAD", True)
psi4.set_global_option("FRAC_DIIS", frac_diis)
psi4.set_global_option("GUESS", "READ")
# Set the next charge/mult
molecule.set_molecular_charge(charge)
molecule.set_multiplicity(mult)
# Determine H**O
print('DGAS: What ref should this point to?')
#ref = psi4.legacy_wavefunction()
eps_a = wfn.epsilon_a()
eps_b = wfn.epsilon_b()
if Na == Nb:
H**O = -Nb
elif Nb == 0:
H**O = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if E_a >= E_b:
H**O = Na
else:
H**O = -Nb
stats.append("""\t%6d %6d %6d %6d %6d %6d\n""" % (Nintegral-1, Na, Nb, charge, mult, H**O))
if H**O > 0:
Na = Na - 1
else:
Nb = Nb - 1
charge = charge + 1
mult = Na - Nb + 1
psi4.set_global_option("DF_INTS_IO", "NONE")
# => Print the results out <= #
E = {}
psi4.print_out("""\n ==> Fractional Occupation Nuke Results <==\n\n""")
psi4.print_out("""\t%-11s %-24s %-24s %11s\n""" % ('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(Ns)):
psi4.print_out("""\t%11.3E %24.16E %24.16E %11d\n""" % (Ns[k], energies[k], potentials[k], convs[k]))
E[Ns[k]] = energies[k]
psi4.print_out('\n')
psi4.print_out("""\t%6s %6s %6s %6s %6s %6s\n""" % ('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
for line in stats:
psi4.print_out(line)
psi4.print_out('\n\t"You shoot a nuke down a bug hole, you got a lot of dead bugs"\n')
psi4.print_out('\t\t\t-Starship Troopers\n')
# Drop the files out
fh = open(traverse_filename, 'w')
fh.write("""\t%-11s %-24s %-24s %11s\n""" % ('N', 'Energy', 'H**O Energy', 'Converged'))
for k in range(len(Ns)):
fh.write("""\t%11.3E %24.16E %24.16E %11d\n""" % (Ns[k], energies[k], potentials[k], convs[k]))
fh.close()
fh = open(stats_filename, 'w')
fh.write("""\t%6s %6s %6s %6s %6s %6s\n""" % ('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
for line in stats:
fh.write(line)
fh.close()
# Properly, should clone molecule but since not returned and easy to unblemish,
molecule.set_molecular_charge(charge0)
molecule.set_multiplicity(mult0)
return E
def allen_focal_point(name='mp2', **kwargs):
r"""Function to call Wes Allen-style Focal
Point Analysis. JCP 127 014306. Uses
:py:func:`~wrappers.complete_basis_set` to evaluate the following
expression. SCF employs a three-point extrapolation according
to :py:func:`~wrappers.scf_xtpl_helgaker_3`. MP2, CCSD, and
CCSD(T) employ two-point extrapolation performed according to
:py:func:`~wrappers.corl_xtpl_helgaker_2`. CCSDT and CCSDT(Q)
are plain deltas. This wrapper requires :ref:`Kallay's MRCC code <sec:mrcc>`.
.. math:: E_{total}^{\text{FPA}} = E_{total,\; \text{SCF}}^{\text{cc-pV[Q56]Z}} \; + E_{corl,\; \text{MP2}}^{\text{cc-pV[56]Z}} \; + \delta_{\text{MP2}}^{\text{CCSD}}\big\vert_{\text{cc-pV[56]Z}} \; + \delta_{\text{CCSD}}^{\text{CCSD(T)}}\big\vert_{\text{cc-pV[56]Z}} \; + \delta_{\text{CCSD(T)}}^{\text{CCSDT}}\big\vert_{\text{cc-pVTZ}} \; + \delta_{\text{CCSDT}}^{\text{CCSDT(Q)}}\big\vert_{\text{cc-pVDZ}}
>>> # [1] single-point energy by this composite method
>>> energy('allen_focal_point')
>>> # [2] finite-difference geometry optimization embarrasingly parallel
>>> optimize('allen_focal_point', mode='sow')
"""
lowername = name.lower()
kwargs = p4util.kwargs_lower(kwargs)
if not ('func_cbs' in kwargs):
kwargs['func_cbs'] = energy
# SCF
if not ('scf_basis' in kwargs):
kwargs['scf_basis'] = 'cc-pV[Q56]Z'
if not ('scf_scheme' in kwargs):
kwargs['scf_scheme'] = scf_xtpl_helgaker_3
# delta MP2 - SCF
if not ('corl_wfn' in kwargs):
kwargs['corl_wfn'] = 'mp2'
name = 'mp2'
if not ('corl_basis' in kwargs):
kwargs['corl_basis'] = 'cc-pV[56]Z'
if not ('corl_scheme' in kwargs):
kwargs['corl_scheme'] = corl_xtpl_helgaker_2
# delta CCSD - MP2
if not ('delta_wfn' in kwargs):
kwargs['delta_wfn'] = 'mrccsd'
if not ('delta_wfn_lesser' in kwargs):
kwargs['delta_wfn_lesser'] = 'mp2'
if not ('delta_basis' in kwargs):
kwargs['delta_basis'] = 'cc-pV[56]Z'
if not ('delta_scheme' in kwargs):
kwargs['delta_scheme'] = corl_xtpl_helgaker_2
# delta CCSD(T) - CCSD
if not ('delta2_wfn' in kwargs):
kwargs['delta2_wfn'] = 'mrccsd(t)'
if not ('delta2_wfn_lesser' in kwargs):
kwargs['delta2_wfn_lesser'] = 'mrccsd'
if not ('delta2_basis' in kwargs):
kwargs['delta2_basis'] = 'cc-pV[56]Z'
if not ('delta2_scheme' in kwargs):
kwargs['delta2_scheme'] = corl_xtpl_helgaker_2
# delta CCSDT - CCSD(T)
if not ('delta3_wfn' in kwargs):
kwargs['delta3_wfn'] = 'mrccsdt'
if not ('delta3_wfn_lesser' in kwargs):
kwargs['delta3_wfn_lesser'] = 'mrccsd(t)'
if not ('delta3_basis' in kwargs):
kwargs['delta3_basis'] = 'cc-pVTZ'
if not ('delta3_scheme' in kwargs):
kwargs['delta3_scheme'] = highest_1
# delta CCSDT(Q) - CCSDT
if not ('delta4_wfn' in kwargs):
kwargs['delta4_wfn'] = 'mrccsdt(q)'
if not ('delta4_wfn_lesser' in kwargs):
kwargs['delta4_wfn_lesser'] = 'mrccsdt'
if not ('delta4_basis' in kwargs):
kwargs['delta4_basis'] = 'cc-pVDZ'
if not ('delta4_scheme' in kwargs):
kwargs['delta4_scheme'] = highest_1
return cbs(name, **kwargs)
def ip_fitting(mol, omega_l, omega_r, **kwargs):
kwargs = p4util.kwargs_lower(kwargs)
# By default, zero the omega to 3 digits
omega_tol = 1.0E-3;
if (kwargs.has_key('omega_tolerance')):
omega_tol = kwargs['omega_tolerance']
# By default, do up to twenty iterations
maxiter = 20;
if (kwargs.has_key('maxiter')):
maxiter = kwargs['maxiter']
# By default, do not read previous 180 orbitals file
read = False;
read180 = ''
if (kwargs.has_key('read')):
read = True;
read180 = kwargs['read']
# The molecule is required, and should be the neutral species
mol.update_geometry()
activate(mol)
charge0 = mol.molecular_charge()
mult0 = mol.multiplicity()
# How many electrons are there?
N = 0;
for A in range(mol.natom()):
N += mol.Z(A)
N -= charge0
N = int(N)
Nb = int((N - mult0 + 1)/2)
Na = int(N - Nb)
# Work in the ot namespace for this procedure
psi4.IO.set_default_namespace("ot")
# Burn in to determine orbital eigenvalues
if (read):
psi4.set_global_option("GUESS", "READ")
copy_file_to_scratch(read180, 'psi', 'ot', 180)
old_guess = psi4.get_global_option("GUESS")
psi4.set_global_option("DF_INTS_IO", "SAVE")
psi4.print_out('\n\t==> IP Fitting SCF: Burn-in <==\n')
energy('scf')
psi4.set_global_option("DF_INTS_IO", "LOAD")
# Determine H**O, to determine mult1
ref = psi4.wavefunction()
eps_a = ref.epsilon_a()
eps_b = ref.epsilon_b()
if (Na == Nb):
H**O = -Nb
elif (Nb == 0):
H**O = Na
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if (E_a >= E_b):
H**O = Na
else:
H**O = -Nb
Na1 = Na;
Nb1 = Nb;
if (H**O > 0):
Na1 = Na1-1;
else:
Nb1 = Nb1-1;
charge1 = charge0 + 1;
mult1 = Na1 - Nb1 + 1
omegas = [];
E0s = [];
E1s = [];
kIPs = [];
IPs = [];
types = [];
# Right endpoint
psi4.set_global_option('DFT_OMEGA',omega_r)
# Neutral
if (read):
psi4.set_global_option("GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
mol.set_molecular_charge(charge0)
mol.set_multiplicity(mult0)
psi4.print_out('\n\t==> IP Fitting SCF: Neutral, Right Endpoint <==\n')
E0r = energy('scf')
ref = psi4.wavefunction()
eps_a = ref.epsilon_a()
eps_b = ref.epsilon_b()
E_HOMO = 0.0;
if (Nb == 0):
E_HOMO = eps_a[int(Na-1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if (E_a >= E_b):
E_HOMO = E_a;
else:
E_HOMO = E_b;
E_HOMOr = E_HOMO;
psi4.IO.change_file_namespace(180,"ot","neutral")
# Cation
if (read):
psi4.set_global_option("GUESS", "READ")
p4util.copy_file_to_scratch(read180, 'psi', 'ot', 180)
mol.set_molecular_charge(charge1)
mol.set_multiplicity(mult1)
psi4.print_out('\n\t==> IP Fitting SCF: Cation, Right Endpoint <==\n')
E1r = energy('scf')
psi4.IO.change_file_namespace(180,"ot","cation")
IPr = E1r - E0r;
kIPr = -E_HOMOr;
delta_r = IPr - kIPr;
if (IPr > kIPr):
psi4.print_out('\n***IP Fitting Error: Right Omega limit should have kIP > IP')
sys.exit(1)
omegas.append(omega_r)
types.append('Right Limit')
E0s.append(E0r)
E1s.append(E1r)
IPs.append(IPr)
kIPs.append(kIPr)
# Use previous orbitals from here out
psi4.set_global_option("GUESS","READ")
# Left endpoint
psi4.set_global_option('DFT_OMEGA',omega_l)
# Neutral
psi4.IO.change_file_namespace(180,"neutral","ot")
mol.set_molecular_charge(charge0)
mol.set_multiplicity(mult0)
psi4.print_out('\n\t==> IP Fitting SCF: Neutral, Left Endpoint <==\n')
E0l = energy('scf')
ref = psi4.wavefunction()
eps_a = ref.epsilon_a()
eps_b = ref.epsilon_b()
E_HOMO = 0.0;
if (Nb == 0):
E_HOMO = eps_a[int(Na-1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if (E_a >= E_b):
E_HOMO = E_a;
else:
E_HOMO = E_b;
E_HOMOl = E_HOMO;
psi4.IO.change_file_namespace(180,"ot","neutral")
# Cation
psi4.IO.change_file_namespace(180,"cation","ot")
mol.set_molecular_charge(charge1)
mol.set_multiplicity(mult1)
psi4.print_out('\n\t==> IP Fitting SCF: Cation, Left Endpoint <==\n')
E1l = energy('scf')
psi4.IO.change_file_namespace(180,"ot","cation")
IPl = E1l - E0l;
kIPl = -E_HOMOl;
delta_l = IPl - kIPl;
if (IPl < kIPl):
psi4.print_out('\n***IP Fitting Error: Left Omega limit should have kIP < IP')
sys.exit(1)
omegas.append(omega_l)
types.append('Left Limit')
E0s.append(E0l)
E1s.append(E1l)
IPs.append(IPl)
kIPs.append(kIPl)
converged = False
repeat_l = 0;
repeat_r = 0;
step = 0;
while True:
step = step + 1;
# Regula Falsi (modified)
if (repeat_l > 1):
delta_l = delta_l / 2.0;
if (repeat_r > 1):
delta_r = delta_r / 2.0;
omega = - (omega_r - omega_l) / (delta_r - delta_l) * delta_l + omega_l;
psi4.set_global_option('DFT_OMEGA',omega)
# Neutral
psi4.IO.change_file_namespace(180,"neutral","ot")
mol.set_molecular_charge(charge0)
mol.set_multiplicity(mult0)
psi4.print_out('\n\t==> IP Fitting SCF: Neutral, Omega = %11.3E <==\n' % omega)
E0 = energy('scf')
ref = psi4.wavefunction()
eps_a = ref.epsilon_a()
eps_b = ref.epsilon_b()
E_HOMO = 0.0;
if (Nb == 0):
E_HOMO = eps_a[int(Na-1)]
else:
E_a = eps_a[int(Na - 1)]
E_b = eps_b[int(Nb - 1)]
if (E_a >= E_b):
E_HOMO = E_a;
else:
E_HOMO = E_b;
psi4.IO.change_file_namespace(180,"ot","neutral")
# Cation
psi4.IO.change_file_namespace(180,"cation","ot")
mol.set_molecular_charge(charge1)
mol.set_multiplicity(mult1)
psi4.print_out('\n\t==> IP Fitting SCF: Cation, Omega = %11.3E <==\n' % omega)
E1 = energy('scf')
psi4.IO.change_file_namespace(180,"ot","cation")
IP = E1 - E0;
kIP = -E_HOMO;
delta = IP - kIP;
if (kIP > IP):
omega_r = omega
E0r = E0
E1r = E1
IPr = IP
kIPr = kIP
delta_r = delta
repeat_r = 0;
repeat_l = repeat_l + 1;
else:
omega_l = omega
E0l = E0
E1l = E1
IPl = IP
kIPl = kIP
delta_l = delta
repeat_l = 0;
repeat_r = repeat_r + 1;
omegas.append(omega)
types.append('Regula-Falsi')
E0s.append(E0)
E1s.append(E1)
IPs.append(IP)
kIPs.append(kIP)
# Termination
if (abs(omega_l - omega_r) < omega_tol or step > maxiter):
converged = True;
break
psi4.IO.set_default_namespace("")
psi4.print_out('\n\t==> IP Fitting Results <==\n\n')
psi4.print_out('\t => Occupation Determination <= \n\n')
psi4.print_out('\t %6s %6s %6s %6s %6s %6s\n' %('N', 'Na', 'Nb', 'Charge', 'Mult', 'H**O'))
psi4.print_out('\t Neutral: %6d %6d %6d %6d %6d %6d\n' %(N, Na, Nb, charge0, mult0, H**O))
psi4.print_out('\t Cation: %6d %6d %6d %6d %6d\n\n' %(N-1, Na1, Nb1, charge1, mult1))
psi4.print_out('\t => Regula Falsi Iterations <=\n\n')
psi4.print_out('\t%3s %11s %14s %14s %14s %s\n' % ('N','Omega','IP','kIP','Delta','Type'))
for k in range(len(omegas)):
psi4.print_out('\t%3d %11.3E %14.6E %14.6E %14.6E %s\n' % (k+1,omegas[k],IPs[k],kIPs[k],IPs[k] - kIPs[k], types[k]))
if (converged):
psi4.print_out('\n\tIP Fitting Converged\n')
psi4.print_out('\tFinal omega = %14.6E\n' % ((omega_l + omega_r) / 2))
psi4.print_out('\n\t"M,I. does the dying. Fleet just does the flying."\n')
psi4.print_out('\t\t\t-Starship Troopers\n')
else:
psi4.print_out('\n\tIP Fitting did not converge!\n')
psi4.set_global_option("DF_INTS_IO", "NONE")
psi4.set_global_option("GUESS", old_guess)
