def test_pcmsolver():
"""pcmsolver/scf"""
#! pcm
nucenergy = 12.0367196636183458
polenergy = -0.0053060443528559
totalenergy = -55.4559426361734040
NH3 = psi4.geometry("""
symmetry c1
N -0.0000000001 -0.1040380466 0.0000000000
H -0.9015844116 0.4818470201 -1.5615900098
H -0.9015844116 0.4818470201 1.5615900098
H 1.8031688251 0.4818470204 0.0000000000
units bohr
no_reorient
no_com
""")
psi4.set_options({
'basis': 'STO-3G',
'scf_type': 'pk',
'pcm': True,
'pcm_scf_type': 'total',
})
psi4.pcm_helper("""
Units = Angstrom
Medium {
SolverType = IEFPCM
Solvent = Water
}
Cavity {
RadiiSet = UFF
Type = GePol
Scaling = False
Area = 0.3
Mode = Implicit
}
""")
print('RHF-PCM, total algorithm')
energy_scf1, wfn1 = psi4.energy('scf', return_wfn=True)
assert psi4.compare_values(nucenergy, NH3.nuclear_repulsion_energy(), 10, "Nuclear repulsion energy (PCM, total algorithm)") #TEST
assert psi4.compare_values(totalenergy, energy_scf1, 10, "Total energy (PCM, total algorithm)") #TEST
assert psi4.compare_values(polenergy, wfn1.get_variable("PCM POLARIZATION ENERGY"), 6, "Polarization energy (PCM, total algorithm)") #TEST
psi4.set_options({'pcm_scf_type': 'separate'})
print('RHF-PCM, separate algorithm')
energy_scf2 = psi4.energy('scf')
assert psi4.compare_values(totalenergy, energy_scf2, 10, "Total energy (PCM, separate algorithm)")
assert psi4.compare_values(polenergy, psi4.get_variable("PCM POLARIZATION ENERGY"), 6, "Polarization energy (PCM, separate algorithm)")
# Now force use of UHF on NH3 to check sanity of the algorithm with PCM
psi4.set_options({'pcm_scf_type': 'total', 'reference': 'uhf'})
print('UHF-PCM, total algorithm')
energy_scf3 = psi4.energy('scf')
assert psi4.compare_values(totalenergy, energy_scf3, 10, "Total energy (PCM, separate algorithm)")
assert psi4.compare_values(polenergy, psi4.get_variable("PCM POLARIZATION ENERGY"), 6, "Polarization energy (PCM, separate algorithm)")
def test_mrcc():
"""mrcc/ccsdt"""
#! CCSDT cc-pVDZ energy for the H2O molecule using MRCC
h2o = psi4.geometry("""
o
h 1 1.0
h 1 1.0 2 104.5
""")
psi4.set_options({'basis': 'cc-pvdz', 'freeze_core': 'true'})
psi4.energy('mrccsdt')
assert psi4.compare_values(8.801465529972,
psi4.get_variable("NUCLEAR REPULSION ENERGY"),
6, 'NRE')
assert psi4.compare_values(-76.021418445155,
psi4.get_variable("SCF TOTAL ENERGY"), 6, 'SCF')
assert psi4.compare_values(-0.204692406830,
psi4.get_variable("MP2 CORRELATION ENERGY"), 6,
'MP2 correlation')
assert psi4.compare_values(-0.217715210258,
psi4.get_variable("CCSDT CORRELATION ENERGY"),
6, 'CCSDT correlation')
assert psi4.compare_values(-76.239133655413,
psi4.get_variable("CURRENT ENERGY"), 6, 'CCSDT')
def test_psi4_cc():
"""cc1"""
#! RHF-CCSD 6-31G** all-electron optimization of the H2O molecule
psi4.core.clean()
h2o = psi4.geometry("""
O
H 1 0.97
H 1 0.97 2 103.0
""")
psi4.set_options({"basis": '6-31G**'})
psi4.optimize('ccsd')
refnuc = 9.1654609427539
refscf = -76.0229427274435
refccsd = -0.20823570806196
reftotal = -76.2311784355056
assert psi4.compare_values(refnuc, h2o.nuclear_repulsion_energy(), 3,
"Nuclear repulsion energy")
assert psi4.compare_values(refscf, psi4.get_variable("SCF total energy"),
5, "SCF energy")
assert psi4.compare_values(refccsd,
psi4.get_variable("CCSD correlation energy"), 4,
"CCSD contribution")
assert psi4.compare_values(reftotal, psi4.get_variable("Current energy"),
7, "Total energy")
def run_vibronic(state1,state2,method1='ccsd',method2='eom-ccsd'):
"""
Performs the different steps needed to compute the spectrum
"""
lowermethod1 = method1.lower()
lowermethod2 = method2.lower()
# Perform optimizations and save states
psi4.set_active_molecule(state1)
print "Optimizing Ground State..."
optimize(lowermethod1)
E1=psi4.get_variable("CURRENT ENERGY")
psi4.set_active_molecule(state2)
print "Optimizing Excited State..."
optimize(lowermethod2)
E2=psi4.get_variable("CURRENT ENERGY")
# Compute Hessian on first state (for AS model)
psi4.set_active_molecule(state1)
frequencies(lowermethod1)
# Select states for vibronic:
# active molecule is initial state
# secondary molecule is final state
psi4.set_active_molecule(state1)
psi4.set_secondary_molecule(state2)
# Compute adiavatic energy
DE = (E2-E1)
psi4.set_variable("CURRENT ENERGY",DE)
# Call the plugin
psi4.plugin('vibronic.so')
def disabled_test_forte():
"""aci-10: Perform aci on benzyne"""
import forte
refscf = -229.20378006852584
refaci = -229.359450812283
refacipt2 = -229.360444943286
mbenzyne = psi4.geometry("""
0 1
C 0.0000000000 -2.5451795941 0.0000000000
C 0.0000000000 2.5451795941 0.0000000000
C -2.2828001669 -1.3508352528 0.0000000000
C 2.2828001669 -1.3508352528 0.0000000000
C 2.2828001669 1.3508352528 0.0000000000
C -2.2828001669 1.3508352528 0.0000000000
H -4.0782187459 -2.3208602146 0.0000000000
H 4.0782187459 -2.3208602146 0.0000000000
H 4.0782187459 2.3208602146 0.0000000000
H -4.0782187459 2.3208602146 0.0000000000
units bohr
""")
psi4.set_options({
'basis': 'DZ',
'df_basis_mp2': 'cc-pvdz-ri',
'reference': 'uhf',
'scf_type': 'pk',
'd_convergence': 10,
'e_convergence': 12,
'guess': 'gwh',
})
psi4.set_module_options("FORTE", {
'root_sym': 0,
'frozen_docc': [2,1,0,0,0,0,2,1],
'restricted_docc': [3,2,0,0,0,0,2,3],
'active': [1,0,1,2,1,2,1,0],
'multiplicity': 1,
'aci_nroot': 1,
'job_type': 'aci',
'sigma': 0.001,
'aci_select_type': 'aimed_energy',
'aci_spin_projection': 1,
'aci_enforce_spin_complete': True,
'aci_add_aimed_degenerate': False,
'aci_project_out_spin_contaminants': False,
'diag_algorithm': 'full',
'aci_quiet_mode': True,
})
scf = psi4.energy('scf')
assert psi4.compare_values(refscf, scf,10,"SCF Energy")
psi4.energy('forte')
assert psi4.compare_values(refaci, psi4.get_variable("ACI ENERGY"),10,"ACI energy")
assert psi4.compare_values(refacipt2, psi4.get_variable("ACI+PT2 ENERGY"),8,"ACI+PT2 energy")
def disabled_test_forte():
"""aci-10: Perform aci on benzyne"""
import forte
refscf = -229.20378006852584
refaci = -229.359450812283
refacipt2 = -229.360444943286
mbenzyne = psi4.geometry("""
0 1
C 0.0000000000 -2.5451795941 0.0000000000
C 0.0000000000 2.5451795941 0.0000000000
C -2.2828001669 -1.3508352528 0.0000000000
C 2.2828001669 -1.3508352528 0.0000000000
C 2.2828001669 1.3508352528 0.0000000000
C -2.2828001669 1.3508352528 0.0000000000
H -4.0782187459 -2.3208602146 0.0000000000
H 4.0782187459 -2.3208602146 0.0000000000
H 4.0782187459 2.3208602146 0.0000000000
H -4.0782187459 2.3208602146 0.0000000000
units bohr
""")
psi4.set_options({
'basis': 'DZ',
'df_basis_mp2': 'cc-pvdz-ri',
'reference': 'uhf',
'scf_type': 'pk',
'd_convergence': 10,
'e_convergence': 12,
'guess': 'gwh',
})
psi4.set_module_options("FORTE", {
'root_sym': 0,
'frozen_docc': [2,1,0,0,0,0,2,1],
'restricted_docc': [3,2,0,0,0,0,2,3],
'active': [1,0,1,2,1,2,1,0],
'multiplicity': 1,
'aci_nroot': 1,
'job_type': 'aci',
'sigma': 0.001,
'aci_select_type': 'aimed_energy',
'aci_spin_projection': 1,
'aci_enforce_spin_complete': True,
'aci_add_aimed_degenerate': False,
'aci_project_out_spin_contaminants': False,
'diag_algorithm': 'full',
'aci_quiet_mode': True,
})
scf = psi4.energy('scf')
assert psi4.compare_values(refscf, scf,10,"SCF Energy")
psi4.energy('forte')
assert psi4.compare_values(refaci, psi4.get_variable("ACI ENERGY"),10,"ACI energy")
assert psi4.compare_values(refacipt2, psi4.get_variable("ACI+PT2 ENERGY"),8,"ACI+PT2 energy")
def test_psi4_sapt():
"""sapt1"""
#! SAPT0 cc-pVDZ computation of the ethene-ethyne interaction energy, using the cc-pVDZ-JKFIT RI basis for SCF
#! and cc-pVDZ-RI for SAPT. Monomer geometries are specified using Cartesian coordinates.
Eref = [
85.1890645313, -0.00359915058, 0.00362911158, -0.00083137117,
-0.00150542374, -0.00230683391
]
ethene_ethyne = psi4.geometry("""
0 1
C 0.000000 -0.667578 -2.124659
C 0.000000 0.667578 -2.124659
H 0.923621 -1.232253 -2.126185
H -0.923621 -1.232253 -2.126185
H -0.923621 1.232253 -2.126185
H 0.923621 1.232253 -2.126185
--
0 1
C 0.000000 0.000000 2.900503
C 0.000000 0.000000 1.693240
H 0.000000 0.000000 0.627352
H 0.000000 0.000000 3.963929
units angstrom
""")
# this molecule will crash test if molecule passing broken
barrier = psi4.geometry("""
0 1
He
""")
psi4.set_options({
"basis": "cc-pvdz",
"guess": "sad",
"scf_type": "df",
"sad_print": 2,
"d_convergence": 11,
"puream": True,
"print": 1
})
psi4.energy('sapt0', molecule=ethene_ethyne)
Eelst = psi4.get_variable("SAPT ELST ENERGY")
Eexch = psi4.get_variable("SAPT EXCH ENERGY")
Eind = psi4.get_variable("SAPT IND ENERGY")
Edisp = psi4.get_variable("SAPT DISP ENERGY")
ET = psi4.get_variable("SAPT0 TOTAL ENERGY")
assert psi4.compare_values(Eref[0],
ethene_ethyne.nuclear_repulsion_energy(), 9,
"Nuclear Repulsion Energy")
assert psi4.compare_values(Eref[1], Eelst, 6, "SAPT0 Eelst")
assert psi4.compare_values(Eref[2], Eexch, 6, "SAPT0 Eexch")
assert psi4.compare_values(Eref[3], Eind, 6, "SAPT0 Eind")
assert psi4.compare_values(Eref[4], Edisp, 6, "SAPT0 Edisp")
assert psi4.compare_values(Eref[5], ET, 6, "SAPT0 Etotal")
def test_v2rdm_casscf():
"""v2rdm_casscf/tests/v2rdm1"""
#! cc-pvdz N2 (6,6) active space Test DQG
print(
' N2 / cc-pVDZ / DQG(6,6), scf_type = CD / 1e-12, rNN = 0.5 A')
import v2rdm_casscf
n2 = psi4.geometry("""
0 1
n
n 1 r
""")
interloper = psi4.geometry("""
0 1
O
H 1 1.0
H 1 1.0 2 90.0
""")
psi4.set_options({
'basis': 'cc-pvdz',
'scf_type': 'cd',
'cholesky_tolerance': 1e-12,
'd_convergence': 1e-10,
'maxiter': 500,
'restricted_docc': [2, 0, 0, 0, 0, 2, 0, 0],
'active': [1, 0, 1, 1, 0, 1, 1, 1],
})
psi4.set_module_options(
'v2rdm_casscf',
{
'positivity': 'dqg',
'r_convergence': 1e-5,
'e_convergence': 1e-6,
'maxiter': 20000,
#'orbopt_frequency': 1000,
#'mu_update_frequency': 1000,
})
psi4.activate(n2)
n2.r = 0.5
refscf = -103.04337420425350
refv2rdm = -103.086205379481
psi4.energy('v2rdm-casscf', molecule=n2)
assert psi4.compare_values(refscf, psi4.get_variable("SCF TOTAL ENERGY"),
8, "SCF total energy")
assert psi4.compare_values(refv2rdm, psi4.get_variable("CURRENT ENERGY"),
5, "v2RDM-CASSCF total energy")
def test_psi4_sapt():
"""sapt1"""
#! SAPT0 cc-pVDZ computation of the ethene-ethyne interaction energy, using the cc-pVDZ-JKFIT RI basis for SCF
#! and cc-pVDZ-RI for SAPT. Monomer geometries are specified using Cartesian coordinates.
Eref = [ 85.189064196429101, -0.00359915058, 0.00362911158,
-0.00083137117, -0.00150542374, -0.00230683391 ]
ethene_ethyne = psi4.geometry("""
0 1
C 0.000000 -0.667578 -2.124659
C 0.000000 0.667578 -2.124659
H 0.923621 -1.232253 -2.126185
H -0.923621 -1.232253 -2.126185
H -0.923621 1.232253 -2.126185
H 0.923621 1.232253 -2.126185
--
0 1
C 0.000000 0.000000 2.900503
C 0.000000 0.000000 1.693240
H 0.000000 0.000000 0.627352
H 0.000000 0.000000 3.963929
units angstrom
""")
# this molecule will crash test if molecule passing broken
barrier = psi4.geometry("""
0 1
He
""")
psi4.set_options({
"basis": "cc-pvdz",
"guess": "sad",
"scf_type": "df",
"sad_print": 2,
"d_convergence": 11,
"puream": True,
"print": 1})
psi4.energy('sapt0', molecule=ethene_ethyne)
Eelst = psi4.get_variable("SAPT ELST ENERGY")
Eexch = psi4.get_variable("SAPT EXCH ENERGY")
Eind = psi4.get_variable("SAPT IND ENERGY")
Edisp = psi4.get_variable("SAPT DISP ENERGY")
ET = psi4.get_variable("SAPT0 TOTAL ENERGY")
assert psi4.compare_values(Eref[0], ethene_ethyne.nuclear_repulsion_energy(), 9, "Nuclear Repulsion Energy")
assert psi4.compare_values(Eref[1], Eelst, 6, "SAPT0 Eelst")
assert psi4.compare_values(Eref[2], Eexch, 6, "SAPT0 Eexch")
assert psi4.compare_values(Eref[3], Eind, 6, "SAPT0 Eind")
assert psi4.compare_values(Eref[4], Edisp, 6, "SAPT0 Edisp")
assert psi4.compare_values(Eref[5], ET, 6, "SAPT0 Etotal")
def test_v2rdm_casscf():
"""v2rdm_casscf/tests/v2rdm1"""
#! cc-pvdz N2 (6,6) active space Test DQG
print(' N2 / cc-pVDZ / DQG(6,6), scf_type = CD / 1e-12, rNN = 0.5 A')
import v2rdm_casscf
n2 = psi4.geometry("""
0 1
n
n 1 r
""")
interloper = psi4.geometry("""
0 1
O
H 1 1.0
H 1 1.0 2 90.0
""")
psi4.set_options({
'basis': 'cc-pvdz',
'scf_type': 'cd',
'cholesky_tolerance': 1e-12,
'd_convergence': 1e-10,
'maxiter': 500,
'restricted_docc': [ 2, 0, 0, 0, 0, 2, 0, 0 ],
'active': [ 1, 0, 1, 1, 0, 1, 1, 1 ],
})
##psi4.set_module_options('v2rdm_casscf', {
psi4.set_options({
# 'positivity': 'dqg',
'r_convergence': 1e-5,
'e_convergence': 1e-6,
'maxiter': 20000,
# #'orbopt_frequency': 1000,
# #'mu_update_frequency': 1000,
})
psi4.activate(n2)
n2.r = 0.5
refscf = -103.04337420425350
refv2rdm = -103.086205379481
psi4.energy('v2rdm-casscf', molecule=n2)
assert psi4.compare_values(refscf, psi4.get_variable("SCF TOTAL ENERGY"), 8, "SCF total energy")
assert psi4.compare_values(refv2rdm, psi4.get_variable("CURRENT ENERGY"), 5, "v2RDM-CASSCF total energy")
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_gpu_dfcc(name, **kwargs):
"""Function encoding sequence of PSI module calls for
a GPU-accelerated DF-CCSD(T) computation.
>>> energy('df-ccsd(t)')
"""
lowername = name.lower()
kwargs = kwargs_lower(kwargs)
# stash user options
optstash = OptionsState(
['GPU_DFCC','COMPUTE_TRIPLES'],
['GPU_DFCC','DFCC'],
['GPU_DFCC','NAT_ORBS'],
['SCF','DF_INTS_IO'],
['SCF','SCF_TYPE'])
psi4.set_local_option('SCF','DF_INTS_IO', 'SAVE')
psi4.set_local_option('GPU_DFCC','DFCC', True)
# throw an exception for open-shells
if (psi4.get_option('SCF','REFERENCE') != 'RHF' ):
raise ValidationError("Error: %s requires \"reference rhf\"." % lowername)
# override symmetry:
molecule = psi4.get_active_molecule()
molecule.update_geometry()
molecule.reset_point_group('c1')
molecule.fix_orientation(1)
molecule.update_geometry()
# triples?
if (lowername == 'gpu-df-ccsd'):
psi4.set_local_option('GPU_DFCC','COMPUTE_TRIPLES', False)
if (lowername == 'gpu-df-ccsd(t)'):
psi4.set_local_option('GPU_DFCC','COMPUTE_TRIPLES', True)
#if (lowername == 'fno-df-ccsd'):
# psi4.set_local_option('GPU_DFCC','COMPUTE_TRIPLES', False)
# psi4.set_local_option('GPU_DFCC','NAT_ORBS', True)
#if (lowername == 'fno-df-ccsd(t)'):
# psi4.set_local_option('GPU_DFCC','COMPUTE_TRIPLES', True)
# psi4.set_local_option('GPU_DFCC','NAT_ORBS', True)
# set scf-type to df unless the user wants something else
if psi4.has_option_changed('SCF','SCF_TYPE') == False:
psi4.set_local_option('SCF','SCF_TYPE', 'DF')
if psi4.get_option('GPU_DFCC','DF_BASIS_CC') == '':
basis = psi4.get_global_option('BASIS')
dfbasis = corresponding_rifit(basis)
psi4.set_local_option('GPU_DFCC','DF_BASIS_CC',dfbasis)
scf_helper(name,**kwargs)
psi4.plugin('gpu_dfcc.so')
# restore options
optstash.restore()
return psi4.get_variable("CURRENT ENERGY")
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 test_mp2():
"""
test for energies
"""
ao_ints, test_scf_param, e_ZZ_repulsion = scf.init(\
os.path.dirname(__file__) + "/test_mp2.yml")
eps, C, D, F = scf.scf(ao_ints, test_scf_param, e_ZZ_repulsion)
energy = scf.get_SCF_energy(ao_ints['H'], F, D, False) + e_ZZ_repulsion
# psi4 setup
import psi4
mol = psi4.geometry("""
O
H 1 1.1
H 1 1.1 2 104
""")
mol.update_geometry()
bas = psi4.core.BasisSet.build(mol, target="cc-pVDZ")
mints = psi4.core.MintsHelper(bas)
# DF-MP2
psi4.set_options({"scf_type": "df"})
psi4.set_options({"MP2_type": "CONV"})
psi4_energy = psi4.energy("MP2/cc-pVDZ", molecule = mol)
psi4_energy_MP2 = psi4.get_variable('SCS-MP2 TOTAL ENERGY')
test_scf_param.update({"method": "MP2"})
test_scf_param.update({"is_fitted": "True"})
eps, C, D, F = scf.scf(ao_ints, test_scf_param, e_ZZ_repulsion)
H = ao_ints['T'] + ao_ints['V']
energy = np.sum((F+H)*D) + e_ZZ_repulsion
energy_corr = mp2.get_mp2_energy(\
eps, C, ao_ints['g4'], test_scf_param['nel_alpha'])
assert(np.allclose(energy + energy_corr, psi4_energy_MP2) == True)
def test_v2rdm6():
#! cc-pvdz N2 (6,6) active space Test DQG
print(' N2 / cc-pVDZ / DQG(6,6), geometry optimization')
import psi4
n2 = psi4.geometry("""
0 1
n
n 1 1.1
""")
psi4.set_options({
'basis': 'cc-pvdz',
'scf_type': 'pk',
'd_convergence': 1e-10,
'maxiter': 500,
'restricted_docc': [2, 0, 0, 0, 0, 2, 0, 0],
'active': [1, 0, 1, 1, 0, 1, 1, 1],
})
psi4.set_module_options(
'v2rdm_casscf',
{
'positivity': 'dqg',
#'r_convergence': 1e-7,
'r_convergence': 1e-6,
'e_convergence': 1e-5,
'orbopt_gradient_convergence': 1e-8,
'maxiter': 20000,
})
psi4.activate(n2)
psi4.optimize('v2rdm-casscf')
refnuc = 23.1968666562054260
refscf = -108.95016246035139
refv2rdm = -109.095505119442
assert psi4.compare_values(refnuc, n2.nuclear_repulsion_energy(), 4,
"Nuclear repulsion energy")
assert psi4.compare_values(refscf, psi4.get_variable("SCF TOTAL ENERGY"),
5, "SCF total energy")
assert psi4.compare_values(refv2rdm, psi4.get_variable("CURRENT ENERGY"),
4, "v2RDM-CASSCF total energy")
def test_v2rdm2():
#! cc-pvdz N2 (6,6) active space Test DQG
print(' N2 / cc-pVDZ / DQG(6,6), scf_type = DF, rNN = 1.1 A')
import psi4
n2 = psi4.geometry("""
0 1
n
n 1 r
""")
psi4.set_options({
'basis': 'cc-pvdz',
'scf_type': 'df',
'd_convergence': 1e-10,
'maxiter': 500,
'restricted_docc': [2, 0, 0, 0, 0, 2, 0, 0],
'active': [1, 0, 1, 1, 0, 1, 1, 1],
})
psi4.set_module_options(
'v2rdm_casscf', {
'positivity': 'dqg',
'r_convergence': 1e-5,
'e_convergence': 1e-6,
'maxiter': 20000,
})
psi4.activate(n2)
n2.r = 1.1
refscf = -108.95348837831371
refv2rdm = -109.094404909477
psi4.energy('v2rdm-casscf')
assert psi4.compare_values(refscf, psi4.get_variable("SCF TOTAL ENERGY"),
8, "SCF total energy")
assert psi4.compare_values(refv2rdm, psi4.get_variable("CURRENT ENERGY"),
5, "v2RDM-CASSCF total energy")
def test_mrcc():
"""mrcc/ccsdt"""
#! CCSDT cc-pVDZ energy for the H2O molecule using MRCC
h2o = psi4.geometry("""
o
h 1 1.0
h 1 1.0 2 104.5
""")
psi4.set_options({
'basis': 'cc-pvdz',
'freeze_core': 'true'})
psi4.energy('mrccsdt')
assert psi4.compare_values( 8.801465529972, psi4.get_variable("NUCLEAR REPULSION ENERGY"), 6, 'NRE')
assert psi4.compare_values(-76.021418445155, psi4.get_variable("SCF TOTAL ENERGY"), 6, 'SCF')
assert psi4.compare_values( -0.204692406830, psi4.get_variable("MP2 CORRELATION ENERGY") , 6, 'MP2 correlation')
assert psi4.compare_values( -0.217715210258, psi4.get_variable("CCSDT CORRELATION ENERGY"), 6, 'CCSDT correlation')
assert psi4.compare_values(-76.239133655413, psi4.get_variable("CURRENT ENERGY"), 6, 'CCSDT')
def test_cfour():
"""cfour/sp-rhf-ccsd_t_"""
#! single-point CCSD(T)/qz2p on water
print(' <<< Translation of ZMAT to Psi4 format to Cfour >>>')
psi4.geometry("""
O
H 1 R
H 1 R 2 A
R=0.958
A=104.5
""")
psi4.set_options({
'cfour_CALC_level': 'CCSD(T)',
'cfour_BASIS': 'qz2p',
'cfour_SCF_CONV': 12,
'cfour_CC_CONV': 12,
})
psi4.energy('cfour')
assert psi4.compare_values(-76.062748460117, psi4.get_variable('scf total energy'), 6, 'SCF')
assert psi4.compare_values(-76.332940127333, psi4.get_variable('mp2 total energy'), 6, 'MP2')
assert psi4.compare_values(-76.338453951890, psi4.get_variable('ccsd total energy'), 6, 'CCSD')
assert psi4.compare_values(-0.275705491773, psi4.get_variable('ccsd correlation energy'), 6, 'CCSD corl')
assert psi4.compare_values(-76.345717549886, psi4.get_variable('ccsd(t) total energy'), 6, 'CCSD(T)')
assert psi4.compare_values(-0.282969089769, psi4.get_variable('ccsd(t) correlation energy'), 6, 'CCSD(T) corl')
def test_cfour():
"""cfour/sp-rhf-ccsd_t_"""
#! single-point CCSD(T)/qz2p on water
print(' <<< Translation of ZMAT to Psi4 format to Cfour >>>')
psi4.geometry("""
O
H 1 R
H 1 R 2 A
R=0.958
A=104.5
""")
psi4.set_options({
'cfour_CALC_level': 'CCSD(T)',
'cfour_BASIS': 'qz2p',
'cfour_SCF_CONV': 12,
'cfour_CC_CONV': 12,
})
psi4.energy('cfour')
assert psi4.compare_values(-76.062748460117, psi4.get_variable('scf total energy'), 6, 'SCF')
assert psi4.compare_values(-76.332940127333, psi4.get_variable('mp2 total energy'), 6, 'MP2')
assert psi4.compare_values(-76.338453951890, psi4.get_variable('ccsd total energy'), 6, 'CCSD')
assert psi4.compare_values(-0.275705491773, psi4.get_variable('ccsd correlation energy'), 6, 'CCSD corl')
assert psi4.compare_values(-76.345717549886, psi4.get_variable('ccsd(t) total energy'), 6, 'CCSD(T)')
assert psi4.compare_values(-0.282969089769, psi4.get_variable('ccsd(t) correlation energy'), 6, 'CCSD(T) corl')
def test_snsmp2():
"""snsmp2/he-he"""
HeHe = psi4.geometry("""
0 1
He 0 0 0
--
He 2 0 0
""")
e = psi4.energy('sns-mp2')
assert psi4.compare_values(0.00176708227, psi4.get_variable('SNS-MP2 TOTAL ENERGY'), 5, "SNS-MP2 IE [Eh]")
def test_snsmp2():
"""snsmp2/he-he"""
HeHe = psi4.geometry("""
0 1
He 0 0 0
--
He 2 0 0
""")
e = psi4.energy('sns-mp2')
assert psi4.compare_values(0.00176708227, psi4.get_variable('SNS-MP2 TOTAL ENERGY'), 5, "SNS-MP2 IE [Eh]")
def test_psi4_basic():
"""tu1-h2o-energy"""
#! Sample HF/cc-pVDZ H2O computation
h2o = psi4.geometry("""
O
H 1 0.96
H 1 0.96 2 104.5
""")
psi4.set_options({'basis': "cc-pVDZ"})
psi4.energy('scf')
assert psi4.compare_values(-76.0266327341067125, psi4.get_variable('SCF TOTAL ENERGY'), 6, 'SCF energy')
def test_psi4_basic():
"""tu1-h2o-energy"""
#! Sample HF/cc-pVDZ H2O computation
h2o = psi4.geometry("""
O
H 1 0.96
H 1 0.96 2 104.5
""")
psi4.set_options({'basis': "cc-pVDZ"})
psi4.energy('scf')
assert psi4.compare_values(-76.0266327341067125, psi4.get_variable('SCF TOTAL ENERGY'), 6, 'SCF energy')
def test_psi4_cc():
"""cc1"""
#! RHF-CCSD 6-31G** all-electron optimization of the H2O molecule
psi4.core.clean()
h2o = psi4.geometry("""
O
H 1 0.97
H 1 0.97 2 103.0
""")
psi4.set_options({"basis": '6-31G**'})
psi4.optimize('ccsd')
refnuc = 9.1654609427539
refscf = -76.0229427274435
refccsd = -0.20823570806196
reftotal = -76.2311784355056
assert psi4.compare_values(refnuc, h2o.nuclear_repulsion_energy(), 3, "Nuclear repulsion energy")
assert psi4.compare_values(refscf, psi4.get_variable("SCF total energy"), 5, "SCF energy")
assert psi4.compare_values(refccsd, psi4.get_variable("CCSD correlation energy"), 4, "CCSD contribution")
assert psi4.compare_values(reftotal, psi4.get_variable("Current energy"), 7, "Total energy")
def test_chemps2():
"""chemps2/scf-n2"""
#! dmrg-scf on N2
N2 = psi4.geometry("""
N 0.0000 0.0000 0.0000
N 0.0000 0.0000 2.1180
units au
""")
psi4.set_options({
'basis': 'cc-pVDZ',
'reference': 'rhf',
'e_convergence': 1e-12,
'd_convergence': 1e-12,
'dmrg_irrep': 0,
'dmrg_multiplicity': 1,
'restricted_docc': [ 1 , 0 , 0 , 0 , 0 , 1 , 0 , 0 ],
'active': [ 2 , 0 , 1 , 1 , 0 , 2 , 1 , 1 ],
'dmrg_sweep_states': [ 500, 1000, 1000 ],
'dmrg_sweep_energy_conv': [ 1e-10, 1e-10, 1e-10 ],
'dmrg_sweep_dvdson_rtol': [ 1e-4, 1e-6, 1e-8 ],
'dmrg_sweep_max_sweeps': [ 5, 5, 10 ],
'dmrg_sweep_noise_prefac': [ 0.05, 0.05, 0.0 ],
'dmrg_print_corr': True,
'dmrg_mps_write': False,
'dmrg_unitary_write': True,
'dmrg_diis': True,
'dmrg_scf_diis_thr': 1e-2,
'dmrg_diis_write': True,
'dmrg_excitation': 0, # Ground state
'dmrg_scf_state_avg': False,
'dmrg_scf_active_space': 'NO', # INPUT; NO; LOC
'dmrg_local_init': False,
})
psi4.energy("dmrg-scf")
ref_energy = -109.1035023353
assert psi4.compare_values(ref_energy, psi4.get_variable("CURRENT ENERGY"), 6, "DMRG Energy")
def test_chemps2():
"""chemps2/scf-n2"""
#! dmrg-scf on N2
N2 = psi4.geometry("""
N 0.0000 0.0000 0.0000
N 0.0000 0.0000 2.1180
units au
""")
psi4.set_options({
'basis': 'cc-pVDZ',
'reference': 'rhf',
'e_convergence': 1e-12,
'd_convergence': 1e-12,
'dmrg_irrep': 0,
'dmrg_multiplicity': 1,
'restricted_docc': [ 1 , 0 , 0 , 0 , 0 , 1 , 0 , 0 ],
'active': [ 2 , 0 , 1 , 1 , 0 , 2 , 1 , 1 ],
'dmrg_sweep_states': [ 500, 1000, 1000 ],
'dmrg_sweep_energy_conv': [ 1e-10, 1e-10, 1e-10 ],
'dmrg_sweep_dvdson_rtol': [ 1e-4, 1e-6, 1e-8 ],
'dmrg_sweep_max_sweeps': [ 5, 5, 10 ],
'dmrg_sweep_noise_prefac': [ 0.05, 0.05, 0.0 ],
'dmrg_print_corr': True,
'dmrg_mps_write': False,
'dmrg_unitary_write': True,
'dmrg_diis': True,
'dmrg_scf_diis_thr': 1e-2,
'dmrg_diis_write': True,
'dmrg_excitation': 0, # Ground state
'dmrg_scf_state_avg': False,
'dmrg_scf_active_space': 'NO', # INPUT; NO; LOC
'dmrg_local_init': False,
})
psi4.energy("dmrg-scf")
ref_energy = -109.1035023353
assert psi4.compare_values(ref_energy, psi4.get_variable("CURRENT ENERGY"), 6, "DMRG Energy")
def test_libefp():
"""libefp/qchem-qmefp-sp"""
#! EFP on mixed QM (water) and EFP (water + 2 * ammonia) system.
#! An EFP-only calc performed first to test vales against q-chem.
qmefp = psi4.geometry("""
# QM fragment
0 1
units bohr
O1 0.000000000000 0.000000000000 0.224348285559
H2 -1.423528800232 0.000000000000 -0.897393142237
H3 1.423528800232 0.000000000000 -0.897393142237
# EFP as EFP fragments
--
efp h2o -4.014110144291 2.316749370493 -1.801514729931 -2.902133 1.734999 -1.953647
--
efp NH3,1.972094713645,,3.599497221584 , 5.447701074734 -1.105309 2.033306 -1.488582
--
efp NH3 -7.876296399270 -1.854372164887 -2.414804197762 2.526442 1.658262 -2.742084
""")
# <<< EFP calc >>>
psi4.set_options({
'basis': '6-31g*',
'scf_type': 'pk',
'guess': 'core',
'df_scf_guess': False})
psi4.energy('efp')
assert psi4.compare_values( 9.1793879214, qmefp.nuclear_repulsion_energy(), 6, 'QM NRE')
assert psi4.compare_values(-0.0004901368, psi4.get_variable('efp elst energy'), 6, 'EFP-EFP Elst') # from q-chem
assert psi4.compare_values(-0.0003168768, psi4.get_variable('efp ind energy'), 6, 'EFP-EFP Indc')
assert psi4.compare_values(-0.0021985285, psi4.get_variable('efp disp energy'), 6, 'EFP-EFP Disp') # from q-chem
assert psi4.compare_values( 0.0056859871, psi4.get_variable('efp exch energy'), 6, 'EFP-EFP Exch') # from q-chem
assert psi4.compare_values( 0.0026804450, psi4.get_variable('efp total energy'), 6, 'EFP-EFP Totl')
assert psi4.compare_values( 0.0026804450, psi4.get_variable('current energy'), 6, 'Current')
psi4.core.print_variables()
psi4.core.clean()
psi4.core.clean_variables()
# <<< QM + EFP calc >>>
psi4.set_options({
'e_convergence': 12,
'd_convergence': 12})
psi4.energy('scf')
assert psi4.compare_values( 9.1793879214, qmefp.nuclear_repulsion_energy(), 6, 'QM NRE')
assert psi4.compare_values( 0.2622598847, psi4.get_variable('efp total energy') - psi4.get_variable('efp ind energy'), 6, 'EFP corr to SCF') # from q-chem
assert psi4.compare_values(-0.0117694790, psi4.get_variable('efp ind energy'), 6, 'QM-EFP Indc') # from q-chem
assert psi4.compare_values(-0.0021985285, psi4.get_variable('efp disp energy'), 6, 'EFP-EFP Disp') # from q-chem
assert psi4.compare_values( 0.0056859871, psi4.get_variable('efp exch energy'), 6, 'EFP-EFP Exch') # from q-chem
assert psi4.compare_values( 0.2504904057, psi4.get_variable('efp total energy'), 6, 'EFP-EFP Totl') # from q-chem
assert psi4.compare_values(-76.0139362744, psi4.get_variable('scf total energy'), 6, 'SCF') # from q-chem
psi4.core.print_variables()
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 test_psi4_scfproperty():
"""scf-property"""
#! UFH and B3LYP cc-pVQZ properties for the CH2 molecule.
with open('grid.dat', 'w') as handle:
handle.write("""\
0.0 0.0 0.0
1.1 1.3 1.4
""")
ch2 = psi4.geometry("""
0 3
c
h 1 b1
h 1 b1 2 a1
b1 = 1.0
a1 = 125.0
""")
# Get a reasonable guess, to save some iterations
psi4.set_options({
"scf_type": "pk",
"basis": "6-31G**",
"e_convergence": 8,
"docc": [2, 0, 0, 1],
"socc": [1, 0, 1, 0],
"reference": "uhf"})
ch2.update_geometry()
assert psi4.compare_values(6.648418918908746, ch2.nuclear_repulsion_energy(), 9, "Nuclear repulsion energy")
props = ['DIPOLE', 'QUADRUPOLE', 'MULLIKEN_CHARGES', 'LOWDIN_CHARGES',
'WIBERG_LOWDIN_INDICES', 'MAYER_INDICES', 'MAYER_INDICES',
'MO_EXTENTS', 'GRID_FIELD', 'GRID_ESP', 'ESP_AT_NUCLEI',
'MULTIPOLE(5)', 'NO_OCCUPATIONS']
psi4.properties('scf', properties=props)
assert psi4.compare_values(psi4.get_variable("CURRENT ENERGY"), -38.91591819679808, 6, "SCF energy")
assert psi4.compare_values(psi4.get_variable('SCF DIPOLE X'), 0.000000000000, 4, "SCF DIPOLE X")
assert psi4.compare_values(psi4.get_variable('SCF DIPOLE Y'), 0.000000000000, 4, "SCF DIPOLE Y")
assert psi4.compare_values(psi4.get_variable('SCF DIPOLE Z'), 0.572697798348, 4, "SCF DIPOLE Z")
assert psi4.compare_values(psi4.get_variable('SCF QUADRUPOLE XX'), -7.664066833060, 4, "SCF QUADRUPOLE XX")
assert psi4.compare_values(psi4.get_variable('SCF QUADRUPOLE YY'), -6.097755074075, 4, "SCF QUADRUPOLE YY")
assert psi4.compare_values(psi4.get_variable('SCF QUADRUPOLE ZZ'), -7.074596012050, 4, "SCF QUADRUPOLE ZZ")
assert psi4.compare_values(psi4.get_variable('SCF QUADRUPOLE XY'), 0.000000000000, 4, "SCF QUADRUPOLE XY")
assert psi4.compare_values(psi4.get_variable('SCF QUADRUPOLE XZ'), 0.000000000000, 4, "SCF QUADRUPOLE XZ")
assert psi4.compare_values(psi4.get_variable('SCF QUADRUPOLE YZ'), 0.000000000000, 4, "SCF QUADRUPOLE YZ")
psi4.properties('B3LYP', properties=props)
assert psi4.compare_values(psi4.get_variable('CURRENT ENERGY'), -39.14134740550916, 6, "B3LYP energy")
assert psi4.compare_values(psi4.get_variable('B3LYP DIPOLE X'), 0.000000000000, 4, "B3LYP DIPOLE X")
assert psi4.compare_values(psi4.get_variable('B3LYP DIPOLE Y'), -0.000000000000, 4, "B3LYP DIPOLE Y")
assert psi4.compare_values(psi4.get_variable('B3LYP DIPOLE Z'), 0.641741521158, 4, "B3LYP DIPOLE Z")
assert psi4.compare_values(psi4.get_variable('B3LYP QUADRUPOLE XX'), -7.616483183211, 4, "B3LYP QUADRUPOLE XX")
assert psi4.compare_values(psi4.get_variable('B3LYP QUADRUPOLE YY'), -6.005896804551, 4, "B3LYP QUADRUPOLE YY")
assert psi4.compare_values(psi4.get_variable('B3LYP QUADRUPOLE ZZ'), -7.021817489904, 4, "B3LYP QUADRUPOLE ZZ")
assert psi4.compare_values(psi4.get_variable('B3LYP QUADRUPOLE XY'), 0.000000000000, 4, "B3LYP QUADRUPOLE XY")
assert psi4.compare_values(psi4.get_variable('B3LYP QUADRUPOLE XZ'), 0.000000000000, 4, "B3LYP QUADRUPOLE XZ")
assert psi4.compare_values(psi4.get_variable('B3LYP QUADRUPOLE YZ'), -0.000000000000, 4, "B3LYP QUADRUPOLE YZ")
P 1 1.00
0.2148820000 1.0000000000
P 1 1.00
0.0638500000 1.0000000000
D 2 1.00
2.3062000000 0.2027000000
0.7232000000 0.5791000000
D 2 1.00
0.2149000000 0.7854500000
0.0639000000 0.5338700000
****
""")
ccsd_e, wfn = psi4.properties('ccsd', properties=['dipole'], return_wfn=True)
psi4.oeprop(wfn, "DIPOLE", "QUADRUPOLE", title="(OEPROP)CC")
psi4.compare_values(psi4.get_variable("(OEPROP)CC DIPOLE X"), 0.000000000000,
6, "CC DIPOLE X") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC DIPOLE Y"), 0.000000000000,
6, "CC DIPOLE Y") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC DIPOLE Z"), -1.840334899884,
6, "CC DIPOLE Z") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC QUADRUPOLE XX"),
-7.864006962064, 6, "CC QUADRUPOLE XX") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC QUADRUPOLE XY"),
0.000000000000, 6, "CC QUADRUPOLE XY") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC QUADRUPOLE XZ"),
0.000000000000, 6, "CC QUADRUPOLE XZ") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC QUADRUPOLE YY"),
-4.537386915305, 6, "CC QUADRUPOLE YY") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC QUADRUPOLE YZ"),
0.000000000000, 6, "CC QUADRUPOLE YZ") #TEST
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 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 run_gaussian_2(name, **kwargs):
# throw an exception for open-shells
if (psi4.get_option('SCF','REFERENCE') != 'RHF' ):
raise ValidationError("""g2 computations require "reference rhf".""")
# stash user options:
optstash = p4util.OptionsState(
['FNOCC','COMPUTE_TRIPLES'],
['FNOCC','COMPUTE_MP4_TRIPLES'],
['FREEZE_CORE'],
['MP2_TYPE'],
['SCF','SCF_TYPE'])
# override default scf_type
psi4.set_local_option('SCF','SCF_TYPE','PK')
# optimize geometry at scf level
psi4.clean()
psi4.set_global_option('BASIS',"6-31G(D)")
driver.optimize('scf')
psi4.clean()
# scf frequencies for zpe
# NOTE This line should not be needed, but without it there's a seg fault
scf_e, ref = driver.frequency('scf', return_wfn=True)
# thermodynamic properties
du = psi4.get_variable('INTERNAL ENERGY CORRECTION')
dh = psi4.get_variable('ENTHALPY CORRECTION')
dg = psi4.get_variable('GIBBS FREE ENERGY CORRECTION')
freqs = ref.frequencies()
nfreq = freqs.dim(0)
freqsum = 0.0
for i in range(0, nfreq):
freqsum += freqs.get(i)
zpe = freqsum / p4const.psi_hartree2wavenumbers * 0.8929 * 0.5
psi4.clean()
# optimize geometry at mp2 (no frozen core) level
# note: freeze_core isn't an option in MP2
psi4.set_global_option('FREEZE_CORE',"FALSE")
psi4.set_global_option('MP2_TYPE', 'CONV')
driver.optimize('mp2')
psi4.clean()
# qcisd(t)
psi4.set_local_option('FNOCC','COMPUTE_MP4_TRIPLES',"TRUE")
psi4.set_global_option('FREEZE_CORE',"TRUE")
psi4.set_global_option('BASIS',"6-311G(D_P)")
ref = driver.proc.run_fnocc('qcisd(t)', return_wfn=True, **kwargs)
# HLC: high-level correction based on number of valence electrons
nirrep = ref.nirrep()
frzcpi = ref.frzcpi()
nfzc = 0
for i in range (0,nirrep):
nfzc += frzcpi[i]
nalpha = ref.nalpha() - nfzc
nbeta = ref.nbeta() - nfzc
# hlc of gaussian-2
hlc = -0.00481 * nalpha -0.00019 * nbeta
# hlc of gaussian-1
hlc1 = -0.00614 * nalpha
eqci_6311gdp = psi4.get_variable("QCISD(T) TOTAL ENERGY")
emp4_6311gd = psi4.get_variable("MP4 TOTAL ENERGY")
emp2_6311gd = psi4.get_variable("MP2 TOTAL ENERGY")
psi4.clean()
# correction for diffuse functions
psi4.set_global_option('BASIS',"6-311+G(D_P)")
driver.energy('mp4')
emp4_6311pg_dp = psi4.get_variable("MP4 TOTAL ENERGY")
emp2_6311pg_dp = psi4.get_variable("MP2 TOTAL ENERGY")
psi4.clean()
# correction for polarization functions
psi4.set_global_option('BASIS',"6-311G(2DF_P)")
driver.energy('mp4')
emp4_6311g2dfp = psi4.get_variable("MP4 TOTAL ENERGY")
emp2_6311g2dfp = psi4.get_variable("MP2 TOTAL ENERGY")
psi4.clean()
# big basis mp2
psi4.set_global_option('BASIS',"6-311+G(3DF_2P)")
#run_fnocc('_mp2',**kwargs)
driver.energy('mp2')
emp2_big = psi4.get_variable("MP2 TOTAL ENERGY")
psi4.clean()
eqci = eqci_6311gdp
e_delta_g2 = emp2_big + emp2_6311gd - emp2_6311g2dfp - emp2_6311pg_dp
e_plus = emp4_6311pg_dp - emp4_6311gd
e_2df = emp4_6311g2dfp - emp4_6311gd
eg2 = eqci + e_delta_g2 + e_plus + e_2df
eg2_mp2_0k = eqci + (emp2_big - emp2_6311gd) + hlc + zpe
psi4.print_out('\n')
psi4.print_out(' ==> G1/G2 Energy Components <==\n')
psi4.print_out('\n')
psi4.print_out(' QCISD(T): %20.12lf\n' % eqci)
psi4.print_out(' E(Delta): %20.12lf\n' % e_delta_g2)
psi4.print_out(' E(2DF): %20.12lf\n' % e_2df)
psi4.print_out(' E(+): %20.12lf\n' % e_plus)
psi4.print_out(' E(G1 HLC): %20.12lf\n' % hlc1)
psi4.print_out(' E(G2 HLC): %20.12lf\n' % hlc)
psi4.print_out(' E(ZPE): %20.12lf\n' % zpe)
psi4.print_out('\n')
psi4.print_out(' ==> 0 Kelvin Results <==\n')
psi4.print_out('\n')
eg2_0k = eg2 + zpe + hlc
psi4.print_out(' G1: %20.12lf\n' % (eqci + e_plus + e_2df + hlc1 + zpe))
psi4.print_out(' G2(MP2): %20.12lf\n' % eg2_mp2_0k)
psi4.print_out(' G2: %20.12lf\n' % eg2_0k)
psi4.set_variable("G1 TOTAL ENERGY",eqci + e_plus + e_2df + hlc1 + zpe)
psi4.set_variable("G2 TOTAL ENERGY",eg2_0k)
psi4.set_variable("G2(MP2) TOTAL ENERGY",eg2_mp2_0k)
psi4.print_out('\n')
T = psi4.get_global_option('T')
psi4.print_out(' ==> %3.0lf Kelvin Results <==\n'% T)
psi4.print_out('\n')
internal_energy = eg2_mp2_0k + du - zpe / 0.8929
enthalpy = eg2_mp2_0k + dh - zpe / 0.8929
gibbs = eg2_mp2_0k + dg - zpe / 0.8929
psi4.print_out(' G2(MP2) energy: %20.12lf\n' % internal_energy )
psi4.print_out(' G2(MP2) enthalpy: %20.12lf\n' % enthalpy)
psi4.print_out(' G2(MP2) free energy: %20.12lf\n' % gibbs)
psi4.print_out('\n')
psi4.set_variable("G2(MP2) INTERNAL ENERGY",internal_energy)
psi4.set_variable("G2(MP2) ENTHALPY",enthalpy)
psi4.set_variable("G2(MP2) FREE ENERGY",gibbs)
internal_energy = eg2_0k + du - zpe / 0.8929
enthalpy = eg2_0k + dh - zpe / 0.8929
gibbs = eg2_0k + dg - zpe / 0.8929
psi4.print_out(' G2 energy: %20.12lf\n' % internal_energy )
psi4.print_out(' G2 enthalpy: %20.12lf\n' % enthalpy)
psi4.print_out(' G2 free energy: %20.12lf\n' % gibbs)
psi4.set_variable("CURRENT ENERGY",eg2_0k)
psi4.set_variable("G2 INTERNAL ENERGY",internal_energy)
psi4.set_variable("G2 ENTHALPY",enthalpy)
psi4.set_variable("G2 FREE ENERGY",gibbs)
psi4.clean()
optstash.restore()
# return 0K g2 results
return eg2_0k
def test_libefp():
"""libefp/qchem-qmefp-sp"""
#! EFP on mixed QM (water) and EFP (water + 2 * ammonia) system.
#! An EFP-only calc performed first to test vales against q-chem.
qmefp = psi4.geometry("""
# QM fragment
0 1
units bohr
O1 0.000000000000 0.000000000000 0.224348285559
H2 -1.423528800232 0.000000000000 -0.897393142237
H3 1.423528800232 0.000000000000 -0.897393142237
# EFP as EFP fragments
--
efp h2o -4.014110144291 2.316749370493 -1.801514729931 -2.902133 1.734999 -1.953647
--
efp NH3,1.972094713645,,3.599497221584 , 5.447701074734 -1.105309 2.033306 -1.488582
--
efp NH3 -7.876296399270 -1.854372164887 -2.414804197762 2.526442 1.658262 -2.742084
""")
# <<< EFP calc >>>
psi4.set_options({
'basis': '6-31g*',
'scf_type': 'pk',
'guess': 'core',
'df_scf_guess': False
})
psi4.energy('efp')
assert psi4.compare_values(9.1793879214, qmefp.nuclear_repulsion_energy(),
6, 'QM NRE')
assert psi4.compare_values(-0.0004901368,
psi4.get_variable('efp elst energy'), 6,
'EFP-EFP Elst') # from q-chem
assert psi4.compare_values(-0.0003168768,
psi4.get_variable('efp ind energy'), 6,
'EFP-EFP Indc')
assert psi4.compare_values(-0.0021985285,
psi4.get_variable('efp disp energy'), 6,
'EFP-EFP Disp') # from q-chem
assert psi4.compare_values(0.0056859871,
psi4.get_variable('efp exch energy'), 6,
'EFP-EFP Exch') # from q-chem
assert psi4.compare_values(0.0026804450,
psi4.get_variable('efp total energy'), 6,
'EFP-EFP Totl')
assert psi4.compare_values(0.0026804450,
psi4.get_variable('current energy'), 6,
'Current')
psi4.core.print_variables()
psi4.core.clean()
psi4.core.clean_variables()
# <<< QM + EFP calc >>>
psi4.set_options({'e_convergence': 12, 'd_convergence': 12})
psi4.energy('scf')
assert psi4.compare_values(9.1793879214, qmefp.nuclear_repulsion_energy(),
6, 'QM NRE')
assert psi4.compare_values(0.2622598847,
psi4.get_variable('efp total energy') -
psi4.get_variable('efp ind energy'), 6,
'EFP corr to SCF') # from q-chem
assert psi4.compare_values(-0.0117694790,
psi4.get_variable('efp ind energy'), 6,
'QM-EFP Indc') # from q-chem
assert psi4.compare_values(-0.0021985285,
psi4.get_variable('efp disp energy'), 6,
'EFP-EFP Disp') # from q-chem
assert psi4.compare_values(0.0056859871,
psi4.get_variable('efp exch energy'), 6,
'EFP-EFP Exch') # from q-chem
assert psi4.compare_values(0.2504904057,
psi4.get_variable('efp total energy'), 6,
'EFP-EFP Totl') # from q-chem
assert psi4.compare_values(-76.0139362744,
psi4.get_variable('scf total energy'), 6,
'SCF') # from q-chem
psi4.core.print_variables()
def run_gaussian_2(name, **kwargs):
# throw an exception for open-shells
if (psi4.get_option('SCF', 'REFERENCE') != 'RHF'):
raise ValidationError("""g2 computations require "reference rhf".""")
# stash user options:
optstash = p4util.OptionsState(['FNOCC', 'COMPUTE_TRIPLES'],
['FNOCC', 'COMPUTE_MP4_TRIPLES'],
['FREEZE_CORE'], ['MP2_TYPE'],
['SCF', 'SCF_TYPE'])
# override default scf_type
psi4.set_local_option('SCF', 'SCF_TYPE', 'PK')
# optimize geometry at scf level
psi4.clean()
psi4.set_global_option('BASIS', "6-31G(D)")
driver.optimize('scf')
psi4.clean()
# scf frequencies for zpe
# NOTE This line should not be needed, but without it there's a seg fault
scf_e, ref = driver.frequency('scf', return_wfn=True)
# thermodynamic properties
du = psi4.get_variable('INTERNAL ENERGY CORRECTION')
dh = psi4.get_variable('ENTHALPY CORRECTION')
dg = psi4.get_variable('GIBBS FREE ENERGY CORRECTION')
freqs = ref.frequencies()
nfreq = freqs.dim(0)
freqsum = 0.0
for i in range(0, nfreq):
freqsum += freqs.get(i)
zpe = freqsum / p4const.psi_hartree2wavenumbers * 0.8929 * 0.5
psi4.clean()
# optimize geometry at mp2 (no frozen core) level
# note: freeze_core isn't an option in MP2
psi4.set_global_option('FREEZE_CORE', "FALSE")
psi4.set_global_option('MP2_TYPE', 'CONV')
driver.optimize('mp2')
psi4.clean()
# qcisd(t)
psi4.set_local_option('FNOCC', 'COMPUTE_MP4_TRIPLES', "TRUE")
psi4.set_global_option('FREEZE_CORE', "TRUE")
psi4.set_global_option('BASIS', "6-311G(D_P)")
ref = driver.proc.run_fnocc('qcisd(t)', return_wfn=True, **kwargs)
# HLC: high-level correction based on number of valence electrons
nirrep = ref.nirrep()
frzcpi = ref.frzcpi()
nfzc = 0
for i in range(0, nirrep):
nfzc += frzcpi[i]
nalpha = ref.nalpha() - nfzc
nbeta = ref.nbeta() - nfzc
# hlc of gaussian-2
hlc = -0.00481 * nalpha - 0.00019 * nbeta
# hlc of gaussian-1
hlc1 = -0.00614 * nalpha
eqci_6311gdp = psi4.get_variable("QCISD(T) TOTAL ENERGY")
emp4_6311gd = psi4.get_variable("MP4 TOTAL ENERGY")
emp2_6311gd = psi4.get_variable("MP2 TOTAL ENERGY")
psi4.clean()
# correction for diffuse functions
psi4.set_global_option('BASIS', "6-311+G(D_P)")
driver.energy('mp4')
emp4_6311pg_dp = psi4.get_variable("MP4 TOTAL ENERGY")
emp2_6311pg_dp = psi4.get_variable("MP2 TOTAL ENERGY")
psi4.clean()
# correction for polarization functions
psi4.set_global_option('BASIS', "6-311G(2DF_P)")
driver.energy('mp4')
emp4_6311g2dfp = psi4.get_variable("MP4 TOTAL ENERGY")
emp2_6311g2dfp = psi4.get_variable("MP2 TOTAL ENERGY")
psi4.clean()
# big basis mp2
psi4.set_global_option('BASIS', "6-311+G(3DF_2P)")
#run_fnocc('_mp2',**kwargs)
driver.energy('mp2')
emp2_big = psi4.get_variable("MP2 TOTAL ENERGY")
psi4.clean()
eqci = eqci_6311gdp
e_delta_g2 = emp2_big + emp2_6311gd - emp2_6311g2dfp - emp2_6311pg_dp
e_plus = emp4_6311pg_dp - emp4_6311gd
e_2df = emp4_6311g2dfp - emp4_6311gd
eg2 = eqci + e_delta_g2 + e_plus + e_2df
eg2_mp2_0k = eqci + (emp2_big - emp2_6311gd) + hlc + zpe
psi4.print_out('\n')
psi4.print_out(' ==> G1/G2 Energy Components <==\n')
psi4.print_out('\n')
psi4.print_out(' QCISD(T): %20.12lf\n' % eqci)
psi4.print_out(' E(Delta): %20.12lf\n' % e_delta_g2)
psi4.print_out(' E(2DF): %20.12lf\n' % e_2df)
psi4.print_out(' E(+): %20.12lf\n' % e_plus)
psi4.print_out(' E(G1 HLC): %20.12lf\n' % hlc1)
psi4.print_out(' E(G2 HLC): %20.12lf\n' % hlc)
psi4.print_out(' E(ZPE): %20.12lf\n' % zpe)
psi4.print_out('\n')
psi4.print_out(' ==> 0 Kelvin Results <==\n')
psi4.print_out('\n')
eg2_0k = eg2 + zpe + hlc
psi4.print_out(' G1: %20.12lf\n' %
(eqci + e_plus + e_2df + hlc1 + zpe))
psi4.print_out(' G2(MP2): %20.12lf\n' % eg2_mp2_0k)
psi4.print_out(' G2: %20.12lf\n' % eg2_0k)
psi4.set_variable("G1 TOTAL ENERGY", eqci + e_plus + e_2df + hlc1 + zpe)
psi4.set_variable("G2 TOTAL ENERGY", eg2_0k)
psi4.set_variable("G2(MP2) TOTAL ENERGY", eg2_mp2_0k)
psi4.print_out('\n')
T = psi4.get_global_option('T')
psi4.print_out(' ==> %3.0lf Kelvin Results <==\n' % T)
psi4.print_out('\n')
internal_energy = eg2_mp2_0k + du - zpe / 0.8929
enthalpy = eg2_mp2_0k + dh - zpe / 0.8929
gibbs = eg2_mp2_0k + dg - zpe / 0.8929
psi4.print_out(' G2(MP2) energy: %20.12lf\n' % internal_energy)
psi4.print_out(' G2(MP2) enthalpy: %20.12lf\n' % enthalpy)
psi4.print_out(' G2(MP2) free energy: %20.12lf\n' % gibbs)
psi4.print_out('\n')
psi4.set_variable("G2(MP2) INTERNAL ENERGY", internal_energy)
psi4.set_variable("G2(MP2) ENTHALPY", enthalpy)
psi4.set_variable("G2(MP2) FREE ENERGY", gibbs)
internal_energy = eg2_0k + du - zpe / 0.8929
enthalpy = eg2_0k + dh - zpe / 0.8929
gibbs = eg2_0k + dg - zpe / 0.8929
psi4.print_out(' G2 energy: %20.12lf\n' % internal_energy)
psi4.print_out(' G2 enthalpy: %20.12lf\n' % enthalpy)
psi4.print_out(' G2 free energy: %20.12lf\n' % gibbs)
psi4.set_variable("CURRENT ENERGY", eg2_0k)
psi4.set_variable("G2 INTERNAL ENERGY", internal_energy)
psi4.set_variable("G2 ENTHALPY", enthalpy)
psi4.set_variable("G2 FREE ENERGY", gibbs)
psi4.clean()
optstash.restore()
# return 0K g2 results
return eg2_0k
# Build a new vector that is orthornormal to all previous vectors
dvecs.copy(svecs, n, swork_vec)
norm = dvecs.norm(n)
dvecs.symnormalize(1 / norm, n)
total_proj = 0
for i in range(num_vecs):
proj = svecs.vdot(cvecs, swork_vec, i)
total_proj += proj
dvecs.axpy(-proj, cvecs, n, i)
norm = dvecs.norm(n)
dvecs.symnormalize(1 / norm, n)
# This *should* screen out contributions that are projected out by above
if True:
cvecs.write(num_vecs, 0)
cvecs.copy(dvecs, num_vecs, n)
num_vecs += 1
print( 'SCF energy: % 16.10f' % (scf_energy))
for n in range(nroot):
print('State %d Total Energy: % 16.10f' % (n,CI_E[n] + mol.nuclear_repulsion_energy()))
E = psi4.energy('detci')
psi4.driver.p4util.compare_values(psi4.get_variable('CI ROOT 0 TOTAL ENERGY'), CI_E[0]+ mol.nuclear_repulsion_energy(), 6, 'CI Root 0 Total Energy')
if(nroot > 1):
psi4.driver.p4util.compare_values(psi4.get_variable('CI ROOT 1 TOTAL ENERGY'), CI_E[1]+ mol.nuclear_repulsion_energy(), 6, 'CI Root 1 Total Energy')
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 test_dftd3():
"""dftd3/energy"""
#! Exercises the various DFT-D corrections, both through python directly and through c++
ref_d2 = [-0.00390110, -0.00165271, -0.00058118]
ref_d3zero = [-0.00285088, -0.00084340, -0.00031923]
ref_d3bj = [-0.00784595, -0.00394347, -0.00226683]
ref_pbe_d2 = [-0.00278650, -0.00118051, -0.00041513]
ref_pbe_d3zero = [-0.00175474, -0.00045421, -0.00016839]
ref_pbe_d3bj = [-0.00475937, -0.00235265, -0.00131239]
eneyne = psi4.geometry("""
C 0.000000 -0.667578 -2.124659
C 0.000000 0.667578 -2.124659
H 0.923621 -1.232253 -2.126185
H -0.923621 -1.232253 -2.126185
H -0.923621 1.232253 -2.126185
H 0.923621 1.232253 -2.126185
--
C 0.000000 0.000000 2.900503
C 0.000000 0.000000 1.693240
H 0.000000 0.000000 0.627352
H 0.000000 0.000000 3.963929
""")
psi4.print_stdout(' -D correction from Py-side')
eneyne.update_geometry()
E, G = eneyne.run_dftd3('b3lyp', 'd2gr')
assert psi4.compare_values(ref_d2[0], E, 7, 'Ethene-Ethyne -D2')
mA = eneyne.extract_subsets(1)
E, G = mA.run_dftd3('b3lyp', 'd2gr')
assert psi4.compare_values(ref_d2[1], E, 7, 'Ethene -D2')
mB = eneyne.extract_subsets(2)
E, G = mB.run_dftd3('b3lyp', 'd2gr')
assert psi4.compare_values(ref_d2[2], E, 7, 'Ethyne -D2')
#mBcp = eneyne.extract_subsets(2,1)
#E, G = mBcp.run_dftd3('b3lyp', 'd2gr')
#compare_values(ref_d2[2], E, 7, 'Ethyne(CP) -D2')
E, G = eneyne.run_dftd3('b3lyp', 'd3zero')
assert psi4.compare_values(ref_d3zero[0], E, 7, 'Ethene-Ethyne -D3 (zero)')
mA = eneyne.extract_subsets(1)
E, G = mA.run_dftd3('b3lyp', 'd3zero')
assert psi4.compare_values(ref_d3zero[1], E, 7, 'Ethene -D3 (zero)')
mB = eneyne.extract_subsets(2)
E, G = mB.run_dftd3('b3lyp', 'd3zero')
assert psi4.compare_values(ref_d3zero[2], E, 7, 'Ethyne -D3 (zero)')
E, G = eneyne.run_dftd3('b3lyp', 'd3bj')
assert psi4.compare_values(ref_d3bj[0], E, 7, 'Ethene-Ethyne -D3 (bj)')
mA = eneyne.extract_subsets(1)
E, G = mA.run_dftd3('b3lyp', 'd3bj')
assert psi4.compare_values(ref_d3bj[1], E, 7, 'Ethene -D3 (bj)')
mB = eneyne.extract_subsets(2)
E, G = mB.run_dftd3('b3lyp', 'd3bj')
assert psi4.compare_values(ref_d3bj[2], E, 7, 'Ethyne -D3 (bj)')
E, G = eneyne.run_dftd3('b3lyp', 'd3')
assert psi4.compare_values(ref_d3zero[0], E, 7, 'Ethene-Ethyne -D3 (alias)')
E, G = eneyne.run_dftd3('b3lyp', 'd')
assert psi4.compare_values(ref_d2[0], E, 7, 'Ethene-Ethyne -D (alias)')
E, G = eneyne.run_dftd3('b3lyp', 'd2')
assert psi4.compare_values(ref_d2[0], E, 7, 'Ethene-Ethyne -D2 (alias)')
psi4.set_options({'basis': 'sto-3g',
'scf_type': 'df',
'dft_radial_points': 50, # use really bad grid for speed since all we want is the -D value
'dft_spherical_points': 110,
#'scf print': 3, # will print dftd3 program output to psi4 output file
})
psi4.print_stdout(' -D correction from C-side')
psi4.activate(mA)
#psi4.energy('b3lyp-d2p4')
#assert psi4.compare_values(ref_d2[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling psi4 Disp class)')
#psi4.energy('b3lyp-d2gr')
#assert psi4.compare_values(ref_d2[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling dftd3 -old)')
#psi4.energy('b3lyp-d3zero')
#assert psi4.compare_values(ref_d3zero[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (calling dftd3 -zero)')
psi4.energy('b3lyp-d3bj')
assert psi4.compare_values(ref_d3bj[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (calling dftd3 -bj)')
psi4.energy('b3lyp-d2')
assert psi4.compare_values(ref_d2[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (alias)')
#psi4.energy('b3lyp-d3')
#assert psi4.compare_values(ref_d3zero[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (alias)')
#psi4.energy('b3lyp-d')
#assert psi4.compare_values(ref_d2[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D (alias)')
psi4.energy('wb97x-d')
assert psi4.compare_values(-0.000834247063, psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene wb97x-d (chg)')
psi4.print_stdout(' non-default -D correction from C-side')
psi4.activate(mB)
#psi4.set_options({'dft_dispersion_parameters': [0.75]})
#psi4.energy('b3lyp-d2p4')
#assert psi4.compare_values(ref_pbe_d2[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling psi4 Disp class)')
#psi4.set_options({'dft_dispersion_parameters': [0.75, 20.0]})
#psi4.energy('b3lyp-d2gr')
#assert psi4.compare_values(ref_pbe_d2[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling dftd3 -old)')
#psi4.set_options({'dft_dispersion_parameters': [1.0, 0.722, 1.217, 14.0]})
#psi4.energy('b3lyp-d3zero')
#assert psi4.compare_values(ref_pbe_d3zero[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (calling dftd3 -zero)')
psi4.set_options({'dft_dispersion_parameters': [1.000, 0.7875, 0.4289, 4.4407]})
psi4.energy('b3lyp-d3bj')
assert psi4.compare_values(ref_pbe_d3bj[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (calling dftd3 -bj)')
psi4.set_options({'dft_dispersion_parameters': [0.75]})
psi4.energy('b3lyp-d2')
assert psi4.compare_values(ref_pbe_d2[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (alias)')
psi4.set_options({'dft_dispersion_parameters': [1.0, 0.722, 1.217, 14.0]})
psi4.energy('b3lyp-d3')
assert psi4.compare_values(ref_pbe_d3zero[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (alias)')
psi4.set_options({'dft_dispersion_parameters': [0.75]})
psi4.energy('b3lyp-d')
assert psi4.compare_values(ref_pbe_d2[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D (alias)')
psi4.activate(mA)
psi4.set_options({'dft_dispersion_parameters': [1.0]})
psi4.energy('wb97x-d')
assert psi4.compare_values(-0.000834247063, psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene wb97x-d (chg)')
psi4.print_stdout(' non-default -D correction from Py-side')
eneyne.update_geometry()
eneyne.run_dftd3('b3lyp', 'd2gr', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[0], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene-Ethyne -D2')
mA = eneyne.extract_subsets(1)
mA.run_dftd3('b3lyp', 'd2gr', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2')
mB = eneyne.extract_subsets(2)
mB.run_dftd3('b3lyp', 'd2gr', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethyne -D2')
eneyne.run_dftd3('b3lyp', 'd3zero', {'s6': 1.0, 's8': 0.722, 'sr6': 1.217, 'alpha6': 14.0})
assert psi4.compare_values(ref_pbe_d3zero[0], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene-Ethyne -D3 (zero)')
mA = eneyne.extract_subsets(1)
mA.run_dftd3('b3lyp', 'd3zero', {'s6': 1.0, 's8': 0.722, 'sr6': 1.217, 'alpha6': 14.0})
assert psi4.compare_values(ref_pbe_d3zero[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (zero)')
mB = eneyne.extract_subsets(2)
mB.run_dftd3('b3lyp', 'd3zero', {'s6': 1.0, 's8': 0.722, 'sr6': 1.217, 'alpha6': 14.0})
assert psi4.compare_values(ref_pbe_d3zero[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethyne -D3 (zero)')
eneyne.run_dftd3('b3lyp', 'd3bj', {'s6': 1.000, 's8': 0.7875, 'a1': 0.4289, 'a2': 4.4407})
assert psi4.compare_values(ref_pbe_d3bj[0], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene-Ethyne -D3 (bj)')
mA = eneyne.extract_subsets(1)
mA.run_dftd3('b3lyp', 'd3bj', {'s6': 1.000, 's8': 0.7875, 'a1': 0.4289, 'a2': 4.4407})
assert psi4.compare_values(ref_pbe_d3bj[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (bj)')
mB = eneyne.extract_subsets(2)
mB.run_dftd3('b3lyp', 'd3bj', {'s6': 1.000, 's8': 0.7875, 'a1': 0.4289, 'a2': 4.4407})
assert psi4.compare_values(ref_pbe_d3bj[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethyne -D3 (bj)')
eneyne.run_dftd3('b3lyp', 'd3', {'s6': 1.0, 's8': 0.722, 'sr6': 1.217, 'alpha6': 14.0})
assert psi4.compare_values(ref_pbe_d3zero[0], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene-Ethyne -D3 (alias)')
eneyne.run_dftd3('b3lyp', 'd', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[0], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene-Ethyne -D (alias)')
eneyne.run_dftd3('b3lyp', 'd2', {'s6': 0.75})
assert psi4.compare_values(ref_pbe_d2[0], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene-Ethyne -D2 (alias)')
sapt_printer('Elst10', Elst10)
sapt_printer('Exch10', Exch10)
sapt_printer('Disp20', Disp20)
sapt_printer('Exch-Disp20', ExchDisp20)
sapt_printer('Ind20,r', Ind20r)
sapt_printer('Exch-Ind20,r', ExchInd20r)
print('-' * 70)
sapt0_no_S2 = Exch10 + Elst10 + Disp20 + ExchDisp20 + Ind20r + ExchInd20r
sapt_printer('Total SAPT0', sapt0_no_S2)
print('')
# Print Psi4 Results
psi4.set_options({'df_basis_sapt': 'aug-cc-pvtz-ri'})
psi4.energy('sapt0')
Eelst = psi4.get_variable('SAPT ELST ENERGY')
Eexch = psi4.get_variable('SAPT EXCH10 ENERGY')
Eexch_S2 = psi4.get_variable('SAPT EXCH10(S^2) ENERGY')
Eind = psi4.get_variable('SAPT IND20,R ENERGY')
Eexind = psi4.get_variable('SAPT EXCH-IND20,R ENERGY')
Edisp = psi4.get_variable('SAPT DISP20 ENERGY')
Eexdisp = psi4.get_variable('SAPT EXCH-DISP20 ENERGY')
print('Psi4 SAPT0 Results')
print('-' * 70)
sapt_printer('Elst10', Eelst)
sapt_printer('Exch10', Eexch)
sapt_printer('Exch10(S^2)', Eexch_S2)
sapt_printer('Disp20', Edisp)
sapt_printer('Exch-Disp20(S^2)', Eexdisp)
sapt_printer('Ind20,r', Eind)
sapt_printer('Elst10', Elst10)
sapt_printer('Exch10', Exch10)
sapt_printer('Disp20', Disp20)
sapt_printer('Exch-Disp20', ExchDisp20)
sapt_printer('Ind20,r', Ind20r)
sapt_printer('Exch-Ind20,r', ExchInd20r)
print('-' * 70)
sapt0_no_S2 = Exch10 + Elst10 + Disp20 + ExchDisp20 + Ind20r + ExchInd20r
sapt_printer('Total SAPT0', sapt0_no_S2)
print('')
# Print Psi4 Results
psi4.set_options({'df_basis_sapt': 'aug-cc-pvtz-ri'})
psi4.energy('sapt0')
Eelst = psi4.get_variable('SAPT ELST ENERGY')
Eexch = psi4.get_variable('SAPT EXCH10 ENERGY')
Eexch_S2 = psi4.get_variable('SAPT EXCH10(S^2) ENERGY')
Eind = psi4.get_variable('SAPT IND20,R ENERGY')
Eexind = psi4.get_variable('SAPT EXCH-IND20,R ENERGY')
Edisp = psi4.get_variable('SAPT DISP20 ENERGY')
Eexdisp = psi4.get_variable('SAPT EXCH-DISP20 ENERGY')
print('Psi4 SAPT0 Results')
print('-' * 70)
sapt_printer('Elst10', Eelst)
sapt_printer('Exch10', Eexch)
sapt_printer('Exch10(S^2)', Eexch_S2)
sapt_printer('Disp20', Edisp)
sapt_printer('Exch-Disp20(S^2)', Eexdisp)
sapt_printer('Ind20,r', Eind)
def test_psi4_scfproperty():
"""scf-property"""
#! UFH and B3LYP cc-pVQZ properties for the CH2 molecule.
with open('grid.dat', 'w') as handle:
handle.write("""\
0.0 0.0 0.0
1.1 1.3 1.4
""")
ch2 = psi4.geometry("""
0 3
c
h 1 b1
h 1 b1 2 a1
b1 = 1.0
a1 = 125.0
""")
# Get a reasonable guess, to save some iterations
psi4.set_options({
"scf_type": "pk",
"basis": "6-31G**",
"e_convergence": 8,
"docc": [2, 0, 0, 1],
"socc": [1, 0, 1, 0],
"reference": "uhf"
})
ch2.update_geometry()
assert psi4.compare_values(6.6484189450, ch2.nuclear_repulsion_energy(), 9,
"Nuclear repulsion energy")
props = [
'DIPOLE', 'QUADRUPOLE', 'MULLIKEN_CHARGES', 'LOWDIN_CHARGES',
'WIBERG_LOWDIN_INDICES', 'MAYER_INDICES', 'MAYER_INDICES',
'MO_EXTENTS', 'GRID_FIELD', 'GRID_ESP', 'ESP_AT_NUCLEI',
'MULTIPOLE(5)', 'NO_OCCUPATIONS'
]
psi4.properties('scf', properties=props)
assert psi4.compare_values(psi4.get_variable("CURRENT ENERGY"),
-38.91591819679808, 6, "SCF energy")
assert psi4.compare_values(psi4.get_variable('SCF DIPOLE X'),
0.000000000000, 4, "SCF DIPOLE X")
assert psi4.compare_values(psi4.get_variable('SCF DIPOLE Y'),
0.000000000000, 4, "SCF DIPOLE Y")
assert psi4.compare_values(psi4.get_variable('SCF DIPOLE Z'),
0.572697798348, 4, "SCF DIPOLE Z")
assert psi4.compare_values(psi4.get_variable('SCF QUADRUPOLE XX'),
-7.664066833060, 4, "SCF QUADRUPOLE XX")
assert psi4.compare_values(psi4.get_variable('SCF QUADRUPOLE YY'),
-6.097755074075, 4, "SCF QUADRUPOLE YY")
assert psi4.compare_values(psi4.get_variable('SCF QUADRUPOLE ZZ'),
-7.074596012050, 4, "SCF QUADRUPOLE ZZ")
assert psi4.compare_values(psi4.get_variable('SCF QUADRUPOLE XY'),
0.000000000000, 4, "SCF QUADRUPOLE XY")
assert psi4.compare_values(psi4.get_variable('SCF QUADRUPOLE XZ'),
0.000000000000, 4, "SCF QUADRUPOLE XZ")
assert psi4.compare_values(psi4.get_variable('SCF QUADRUPOLE YZ'),
0.000000000000, 4, "SCF QUADRUPOLE YZ")
psi4.properties('B3LYP', properties=props)
assert psi4.compare_values(psi4.get_variable('CURRENT ENERGY'),
-39.14134740550916, 6, "B3LYP energy")
assert psi4.compare_values(psi4.get_variable('B3LYP DIPOLE X'),
0.000000000000, 4, "B3LYP DIPOLE X")
assert psi4.compare_values(psi4.get_variable('B3LYP DIPOLE Y'),
-0.000000000000, 4, "B3LYP DIPOLE Y")
assert psi4.compare_values(psi4.get_variable('B3LYP DIPOLE Z'),
0.641741521158, 4, "B3LYP DIPOLE Z")
assert psi4.compare_values(psi4.get_variable('B3LYP QUADRUPOLE XX'),
-7.616483183211, 4, "B3LYP QUADRUPOLE XX")
assert psi4.compare_values(psi4.get_variable('B3LYP QUADRUPOLE YY'),
-6.005896804551, 4, "B3LYP QUADRUPOLE YY")
assert psi4.compare_values(psi4.get_variable('B3LYP QUADRUPOLE ZZ'),
-7.021817489904, 4, "B3LYP QUADRUPOLE ZZ")
assert psi4.compare_values(psi4.get_variable('B3LYP QUADRUPOLE XY'),
0.000000000000, 4, "B3LYP QUADRUPOLE XY")
assert psi4.compare_values(psi4.get_variable('B3LYP QUADRUPOLE XZ'),
0.000000000000, 4, "B3LYP QUADRUPOLE XZ")
assert psi4.compare_values(psi4.get_variable('B3LYP QUADRUPOLE YZ'),
-0.000000000000, 4, "B3LYP QUADRUPOLE YZ")
def test_dftd3():
"""dftd3/energy"""
#! Exercises the various DFT-D corrections, both through python directly and through c++
ref_d2 = [-0.00390110, -0.00165271, -0.00058118]
ref_d3zero = [-0.00285088, -0.00084340, -0.00031923]
ref_d3bj = [-0.00784595, -0.00394347, -0.00226683]
ref_pbe_d2 = [-0.00278650, -0.00118051, -0.00041513]
ref_pbe_d3zero = [-0.00175474, -0.00045421, -0.00016839]
ref_pbe_d3bj = [-0.00475937, -0.00235265, -0.00131239]
eneyne = psi4.geometry("""
C 0.000000 -0.667578 -2.124659
C 0.000000 0.667578 -2.124659
H 0.923621 -1.232253 -2.126185
H -0.923621 -1.232253 -2.126185
H -0.923621 1.232253 -2.126185
H 0.923621 1.232253 -2.126185
--
C 0.000000 0.000000 2.900503
C 0.000000 0.000000 1.693240
H 0.000000 0.000000 0.627352
H 0.000000 0.000000 3.963929
""")
psi4.print_stdout(' -D correction from Py-side')
eneyne.update_geometry()
E, G = eneyne.run_dftd3('b3lyp', 'd2gr')
assert psi4.compare_values(ref_d2[0], E, 7, 'Ethene-Ethyne -D2')
mA = eneyne.extract_subsets(1)
E, G = mA.run_dftd3('b3lyp', 'd2gr')
assert psi4.compare_values(ref_d2[1], E, 7, 'Ethene -D2')
mB = eneyne.extract_subsets(2)
E, G = mB.run_dftd3('b3lyp', 'd2gr')
assert psi4.compare_values(ref_d2[2], E, 7, 'Ethyne -D2')
#mBcp = eneyne.extract_subsets(2,1)
#E, G = mBcp.run_dftd3('b3lyp', 'd2gr')
#compare_values(ref_d2[2], E, 7, 'Ethyne(CP) -D2')
E, G = eneyne.run_dftd3('b3lyp', 'd3zero')
assert psi4.compare_values(ref_d3zero[0], E, 7, 'Ethene-Ethyne -D3 (zero)')
mA = eneyne.extract_subsets(1)
E, G = mA.run_dftd3('b3lyp', 'd3zero')
assert psi4.compare_values(ref_d3zero[1], E, 7, 'Ethene -D3 (zero)')
mB = eneyne.extract_subsets(2)
E, G = mB.run_dftd3('b3lyp', 'd3zero')
assert psi4.compare_values(ref_d3zero[2], E, 7, 'Ethyne -D3 (zero)')
E, G = eneyne.run_dftd3('b3lyp', 'd3bj')
assert psi4.compare_values(ref_d3bj[0], E, 7, 'Ethene-Ethyne -D3 (bj)')
mA = eneyne.extract_subsets(1)
E, G = mA.run_dftd3('b3lyp', 'd3bj')
assert psi4.compare_values(ref_d3bj[1], E, 7, 'Ethene -D3 (bj)')
mB = eneyne.extract_subsets(2)
E, G = mB.run_dftd3('b3lyp', 'd3bj')
assert psi4.compare_values(ref_d3bj[2], E, 7, 'Ethyne -D3 (bj)')
E, G = eneyne.run_dftd3('b3lyp', 'd3')
assert psi4.compare_values(ref_d3zero[0], E, 7,
'Ethene-Ethyne -D3 (alias)')
E, G = eneyne.run_dftd3('b3lyp', 'd')
assert psi4.compare_values(ref_d2[0], E, 7, 'Ethene-Ethyne -D (alias)')
E, G = eneyne.run_dftd3('b3lyp', 'd2')
assert psi4.compare_values(ref_d2[0], E, 7, 'Ethene-Ethyne -D2 (alias)')
psi4.set_options({
'basis': 'sto-3g',
'scf_type': 'df',
'dft_radial_points':
50, # use really bad grid for speed since all we want is the -D value
'dft_spherical_points': 110,
#'scf print': 3, # will print dftd3 program output to psi4 output file
})
psi4.print_stdout(' -D correction from C-side')
psi4.activate(mA)
#psi4.energy('b3lyp-d2p4')
#assert psi4.compare_values(ref_d2[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling psi4 Disp class)')
#psi4.energy('b3lyp-d2gr')
#assert psi4.compare_values(ref_d2[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling dftd3 -old)')
#psi4.energy('b3lyp-d3zero')
#assert psi4.compare_values(ref_d3zero[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (calling dftd3 -zero)')
psi4.energy('b3lyp-d3bj')
assert psi4.compare_values(
ref_d3bj[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethene -D3 (calling dftd3 -bj)')
psi4.energy('b3lyp-d2')
assert psi4.compare_values(
ref_d2[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethene -D2 (alias)')
#psi4.energy('b3lyp-d3')
#assert psi4.compare_values(ref_d3zero[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (alias)')
#psi4.energy('b3lyp-d')
#assert psi4.compare_values(ref_d2[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D (alias)')
psi4.energy('wb97x-d')
assert psi4.compare_values(
-0.000834247063, psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethene wb97x-d (chg)')
psi4.print_stdout(' non-default -D correction from C-side')
psi4.activate(mB)
#psi4.set_options({'dft_dispersion_parameters': [0.75]})
#psi4.energy('b3lyp-d2p4')
#assert psi4.compare_values(ref_pbe_d2[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling psi4 Disp class)')
#psi4.set_options({'dft_dispersion_parameters': [0.75, 20.0]})
#psi4.energy('b3lyp-d2gr')
#assert psi4.compare_values(ref_pbe_d2[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D2 (calling dftd3 -old)')
#psi4.set_options({'dft_dispersion_parameters': [1.0, 0.722, 1.217, 14.0]})
#psi4.energy('b3lyp-d3zero')
#assert psi4.compare_values(ref_pbe_d3zero[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7, 'Ethene -D3 (calling dftd3 -zero)')
psi4.set_options(
{'dft_dispersion_parameters': [1.000, 0.7875, 0.4289, 4.4407]})
psi4.energy('b3lyp-d3bj')
assert psi4.compare_values(
ref_pbe_d3bj[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethene -D3 (calling dftd3 -bj)')
psi4.set_options({'dft_dispersion_parameters': [0.75]})
psi4.energy('b3lyp-d2')
assert psi4.compare_values(
ref_pbe_d2[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethene -D2 (alias)')
psi4.set_options({'dft_dispersion_parameters': [1.0, 0.722, 1.217, 14.0]})
psi4.energy('b3lyp-d3')
assert psi4.compare_values(
ref_pbe_d3zero[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene -D3 (alias)')
psi4.set_options({'dft_dispersion_parameters': [0.75]})
psi4.energy('b3lyp-d')
assert psi4.compare_values(
ref_pbe_d2[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethene -D (alias)')
psi4.activate(mA)
psi4.set_options({'dft_dispersion_parameters': [1.0]})
psi4.energy('wb97x-d')
assert psi4.compare_values(
-0.000834247063, psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethene wb97x-d (chg)')
psi4.print_stdout(' non-default -D correction from Py-side')
eneyne.update_geometry()
eneyne.run_dftd3('b3lyp', 'd2gr', {'s6': 0.75})
assert psi4.compare_values(
ref_pbe_d2[0], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethene-Ethyne -D2')
mA = eneyne.extract_subsets(1)
mA.run_dftd3('b3lyp', 'd2gr', {'s6': 0.75})
assert psi4.compare_values(
ref_pbe_d2[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethene -D2')
mB = eneyne.extract_subsets(2)
mB.run_dftd3('b3lyp', 'd2gr', {'s6': 0.75})
assert psi4.compare_values(
ref_pbe_d2[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethyne -D2')
eneyne.run_dftd3('b3lyp', 'd3zero', {
's6': 1.0,
's8': 0.722,
'sr6': 1.217,
'alpha6': 14.0
})
assert psi4.compare_values(
ref_pbe_d3zero[0], psi4.get_variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene-Ethyne -D3 (zero)')
mA = eneyne.extract_subsets(1)
mA.run_dftd3('b3lyp', 'd3zero', {
's6': 1.0,
's8': 0.722,
'sr6': 1.217,
'alpha6': 14.0
})
assert psi4.compare_values(
ref_pbe_d3zero[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene -D3 (zero)')
mB = eneyne.extract_subsets(2)
mB.run_dftd3('b3lyp', 'd3zero', {
's6': 1.0,
's8': 0.722,
'sr6': 1.217,
'alpha6': 14.0
})
assert psi4.compare_values(
ref_pbe_d3zero[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethyne -D3 (zero)')
eneyne.run_dftd3('b3lyp', 'd3bj', {
's6': 1.000,
's8': 0.7875,
'a1': 0.4289,
'a2': 4.4407
})
assert psi4.compare_values(
ref_pbe_d3bj[0], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethene-Ethyne -D3 (bj)')
mA = eneyne.extract_subsets(1)
mA.run_dftd3('b3lyp', 'd3bj', {
's6': 1.000,
's8': 0.7875,
'a1': 0.4289,
'a2': 4.4407
})
assert psi4.compare_values(
ref_pbe_d3bj[1], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethene -D3 (bj)')
mB = eneyne.extract_subsets(2)
mB.run_dftd3('b3lyp', 'd3bj', {
's6': 1.000,
's8': 0.7875,
'a1': 0.4289,
'a2': 4.4407
})
assert psi4.compare_values(
ref_pbe_d3bj[2], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethyne -D3 (bj)')
eneyne.run_dftd3('b3lyp', 'd3', {
's6': 1.0,
's8': 0.722,
'sr6': 1.217,
'alpha6': 14.0
})
assert psi4.compare_values(
ref_pbe_d3zero[0], psi4.get_variable('DISPERSION CORRECTION ENERGY'),
7, 'Ethene-Ethyne -D3 (alias)')
eneyne.run_dftd3('b3lyp', 'd', {'s6': 0.75})
assert psi4.compare_values(
ref_pbe_d2[0], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethene-Ethyne -D (alias)')
eneyne.run_dftd3('b3lyp', 'd2', {'s6': 0.75})
assert psi4.compare_values(
ref_pbe_d2[0], psi4.get_variable('DISPERSION CORRECTION ENERGY'), 7,
'Ethene-Ethyne -D2 (alias)')
dvecs.copy(svecs, n, swork_vec)
norm = dvecs.norm(n)
dvecs.symnormalize(1 / norm, n)
total_proj = 0
for i in range(num_vecs):
proj = svecs.vdot(cvecs, swork_vec, i)
total_proj += proj
dvecs.axpy(-proj, cvecs, n, i)
norm = dvecs.norm(n)
dvecs.symnormalize(1 / norm, n)
# This *should* screen out contributions that are projected out by above
if True:
cvecs.write(num_vecs, 0)
cvecs.copy(dvecs, num_vecs, n)
num_vecs += 1
print('SCF energy: % 16.10f' % (scf_energy))
for n in range(nroot):
print('State %d Total Energy: % 16.10f' % (n, CI_E[n] + mol.nuclear_repulsion_energy()))
print("")
E = psi4.energy('detci')
for n in range(nroot):
ci_ref = psi4.get_variable('CI ROOT %d TOTAL ENERGY' % n)
ci_compute = CI_E[n] + mol.nuclear_repulsion_energy()
psi4.compare_values(ci_ref, ci_compute, 6, 'CI Root %d Total Energy' % n)
# ==> Build Stochastic Integral Matrices <==
# Create two random vector
vec = np.random.choice([-1, 1], size=(Qia.shape[0]))
vecp = np.random.choice([-1, 1], size=(Qia.shape[0]))
# Generate first R matrices
ia = np.einsum("Q,Qia->ia", vec, Qia)
iap = np.einsum("Q,Qia->ia", vecp, Qia)
# ==> Calculate a single stochastic RI-MP2 (sRI-MP2) sample <==
# Caculate sRI-MP2 correlation energy
e_srimp2 += 2.0 * np.einsum('ijab,ia,ia,jb,jb->', denom, ia, iap, ia, iap)
e_srimp2 -= np.einsum('ijab,ia,ib,jb,ja->', denom, ia, iap, ia, iap)
e_srimp2 /= float(nsample)
total_time = time.time() - t
time_per_sample = total_time / float(nsample)
# Print sample energy to output
print("\nNumber of samples: % 16d" % nsample)
print("Total time (s): % 16.2f" % total_time)
print("Time per sample (us): % 16.2f" % (time_per_sample * 1.e6))
print("sRI-MP2 correlation sample energy: % 16.10f" % e_srimp2)
psi_mp2_energy = psi4.energy("MP2")
mp2_correlation_energy = psi4.get_variable("MP2 CORRELATION ENERGY")
print("\nRI-MP2 energy: % 16.10f" % mp2_correlation_energy)
print("Sample error % 16.10f" % (e_srimp2 - mp2_correlation_energy))
def writeCSX(name, **kwargs):
"""function to write the CSX file
"""
if not psi4.get_global_option('WRITE_CSX'):
return
# import csx_api for csx writing
import os
import math
import inspect
#import openbabel
import qcdb
import qcdb.periodictable
import csx2_api as api
lowername = name.lower()
# Make sure the molecule the user provided is the active one
if ('molecule' in kwargs):
activate(kwargs['molecule'])
del kwargs['molecule']
molecule = psi4.get_active_molecule()
molecule.update_geometry()
# Determine the derivative type
calledby = inspect.stack()[1][3]
derdict = {
'energy': 0,
'property': 0,
'gradient': 1,
'optimize': 1,
'frequency': 2,
'frequencies': 2,
'hessian': 2,
}
dertype = derdict[calledby]
hasFreq = False
# Start to write the CSX file
# First grab molecular information and energies from psi4
geom = molecule.save_string_xyz() # OB
atomLine = geom.split('\n') # OB
# general molecular information
atomNum = molecule.natom()
molSym = molecule.schoenflies_symbol()
molCharge = molecule.molecular_charge()
molMulti = molecule.multiplicity()
# energy information
molBasis = psi4.get_global_option('BASIS')
molSpin = psi4.get_global_option('REFERENCE')
molMethod = psi4.get_global_option('WFN')
mol1E = psi4.get_variable('ONE-ELECTRON ENERGY')
mol2E = psi4.get_variable('TWO-ELECTRON ENERGY')
molNE = psi4.get_variable('NUCLEAR REPULSION ENERGY')
molPE = mol1E + mol2E
molEE = psi4.get_variable('CURRENT ENERGY')
# wavefunction information
try:
wfn = kwargs['wfn']
except AttributeError:
pass
if wfn:
molOrbE = wfn.epsilon_a()
molOrbEb = wfn.epsilon_b()
orbNmopi = wfn.nmopi()
orbNsopi = wfn.nsopi()
orbNum = wfn.nmo() if molOrbE else 0
orbSNum = wfn.nso()
molOrb = wfn.Ca()
orbNirrep = wfn.nirrep()
orbAotoso = wfn.aotoso()
orbDoccpi = wfn.doccpi()
orbSoccpi = wfn.soccpi()
basisNbf = wfn.basisset().nbf()
basisDim = psi4.Dimension(1, 'basisDim')
basisDim.__setitem__(0, basisNbf)
wfnRestricted = True
orbE = []
hlist = []
orblist = []
orbOcc = []
molOrbmo = psi4.Matrix('molOrbmo', basisDim, orbNmopi)
molOrbmo.gemm(False, False, 1.0, orbAotoso, molOrb, 0.0)
if molSpin == 'UHF':
wfnRestricted = False
orbEb = []
hlistCb = []
orblistCb = []
orbOccCb = []
molOrbCb = wfn.Cb()
molOrbmoCb = psi4.Matrix('molOrbmoCb', basisDim, orbNmopi)
molOrbmoCb.gemm(False, False, 1.0, orbAotoso, molOrbCb, 0.0)
count = 0
eleExtra = 1 if wfnRestricted else 0
for ih in range(orbNirrep):
for iorb in range(orbNmopi.__getitem__(ih)):
hlist.append(ih)
orblist.append(iorb)
if molOrbE:
orbE.append(molOrbE.get(count))
eleNum = 1 if iorb < (orbDoccpi.__getitem__(ih) + orbSoccpi.__getitem__(ih)) else 0
eleNum += eleExtra if iorb < orbDoccpi.__getitem__(ih) else 0
orbOcc.append(eleNum)
count += 1
orbMos = sorted(zip(orbE, zip(hlist, orblist)))
orbOccString = ' '.join(str(x) for x in sorted(orbOcc, reverse=True))
orbCaString = []
for imos in range(orbNum):
(h, s) = orbMos[imos][1]
orbCa = []
for iso in range(orbSNum):
orbEle = molOrbmo.get(h, iso, s)
orbCa.append(orbEle)
orbCaString.append(' '.join(str(x) for x in orbCa))
orbEString = ' '.join(str(x) for x in sorted(orbE))
# now for beta spin
if not wfnRestricted:
count = 0
for ih in range(orbNirrep):
for iorb in range(orbNmopi.__getitem__(ih)):
hlistCb.append(ih)
orblist.append(iorb)
if molOrbEb:
orbEb.append(molOrbEb.get(count))
eleNum = 1 if iorb < (orbDoccpi.__getitem__(ih) + orbSoccpi.__getitem__(ih)) else 0
if iorb < orbDoccpi.__getitem__(ih):
eleNum += eleExtra
orbOccCb.append(eleNum)
count += 1
orbMosCb = sorted(zip(orbEb, zip(hlist, orblist)))
orbOccCbString = ' '.join(str(x) for x in sorted(orbOccCb, reverse=True))
orbCbString = []
for imos in range(orbNum):
(h, s) = orbMosCb[imos][1]
orbCb = []
for iso in range(orbSNum):
orbEle = molOrbmoCb.get(h, iso, s)
orbCb.append(orbEle)
orbCbString.append(' '.join(str(x) for x in orbCb))
orbEbString = ' '.join(str(x) for x in sorted(orbEb))
# orbColString = ' '.join(str(x) for x in orbCol)
if wfnRestricted:
wfn1 = api.waveFunctionType(
orbitalCount=orbNum,
orbitalOccupancies=orbOccString)
orbe1 = api.stringArrayType(unit='gc:hartree')
orbe1.set_valueOf_(orbEString)
orbs1 = api.orbitalsType()
for iorb in range(orbNum):
orb1 = api.stringArrayType(id=iorb+1)
orb1.set_valueOf_(orbCaString[iorb])
orbs1.add_orbital(orb1)
wfn1.set_orbitals(orbs1)
wfn1.set_orbitalEnergies(orbe1)
else:
wfn1 = api.waveFunctionType(orbitalCount=orbNum)
# alpha electron: 1.5
orbe1 = api.stringArrayType(unit='gc:hartree')
orbe1.set_valueOf_(orbEString)
wfn1.set_alphaOrbitalEnergies(orbe1)
wfn1.set_alphaOrbitalOccupancies(orbOccString)
aorbs1 = api.orbitalsType()
for iorb in range(orbNum):
orb1 = api.stringArrayType(id=iorb+1)
orb1.set_valueOf_(orbCaString[iorb])
aorbs1.add_orbital(orb1)
wfn1.set_alphaOrbitals(aorbs1)
# beta electron: 1.5
orbeb1 = api.stringArrayType(unit='gc:hartree')
orbeb1.set_valueOf_(orbEbString)
wfn1.set_betaOrbitalEnergies(orbeb1)
wfn1.set_betaOrbitalOccupancies(orbOccCbString)
borbs1 = api.orbitalsType()
for iorb in range(orbNum):
orb1 = api.stringArrayType(id=iorb+1)
orb1.set_valueOf_(orbCbString[iorb])
borbs1.add_orbital(orb1)
wfn1.set_betaOrbitals(borbs1)
# frequency information
if dertype == 2:
hasFreq = True
molFreq = psi4.get_frequencies()
molFreqNum = molFreq.dim(0)
frq = []
irInt = []
for ifrq in range(molFreqNum):
frq.append(molFreq.get(ifrq))
irInt.append(0.0)
frqString = ' '.join(str(x) for x in frq)
intString = ' '.join(str(x) for x in irInt)
normMod = psi4.get_normalmodes()
normMdString = []
count = 0
for ifrq in range(molFreqNum):
normM = []
for iatm in range(atomNum):
for ixyz in range(3):
normM.append(normMod.get(count))
count += 1
normMdString.append(' '.join(str(x) for x in normM))
vib1 = api.vibAnalysisType(vibrationCount=molFreqNum)
freq1 = api.stringArrayType(unit="gc:cm-1")
freq1.set_valueOf_(frqString)
vib1.set_frequencies(freq1)
irint1 = api.stringArrayType()
irint1.set_valueOf_(intString)
vib1.set_irIntensities(irint1)
norms1 = api.normalModesType()
for ifrq in range(molFreqNum):
norm1 = api.normalModeType(id=ifrq+1)
norm1.set_valueOf_(normMdString[ifrq])
norms1.add_normalMode(norm1)
vib1.set_normalModes(norms1)
# dipole moment information
molDipoleX = psi4.get_variable('CURRENT DIPOLE X')
molDipoleY = psi4.get_variable('CURRENT DIPOLE Y')
molDipoleZ = psi4.get_variable('CURRENT DIPOLE Z')
molDipoleTot = math.sqrt(
molDipoleX * molDipoleX +
molDipoleY * molDipoleY +
molDipoleZ * molDipoleZ)
prop1 = api.propertiesType()
sprop1 = api.propertyType(
name='dipoleMomentX',
unit='gc:debye')
sprop1.set_valueOf_(molDipoleX)
sprop2 = api.propertyType(
name='dipoleMomentY',
unit='gc:debye')
sprop2.set_valueOf_(molDipoleY)
sprop3 = api.propertyType(
name='dipoleMomentZ',
unit='gc:debye')
sprop3.set_valueOf_(molDipoleZ)
sprop4 = api.propertyType(
name='dipoleMomentAverage',
unit='gc:debye')
sprop4.set_valueOf_(molDipoleTot)
prop1.add_systemProperty(sprop1)
prop1.add_systemProperty(sprop2)
prop1.add_systemProperty(sprop3)
prop1.add_systemProperty(sprop4)
# get the basename for the CSX file
psio = psi4.IO.shared_object()
namespace = psio.get_default_namespace()
#csxfilename = '.'.join([namespace, str(os.getpid()), 'csx'])
csxfilename = os.path.splitext(psi4.outfile_name())[0] + '.csx'
csxfile = open(csxfilename, 'w')
csxVer = psi4.get_global_option('CSX_VERSION')
# Both CSX versions 0 and 1 depended on the procedures table, which in
# turn required the writeCSX function to be in the driver.py file
# itself. Starting with 1.5 (1, to run), this dependence is broken and
# CSX has been shifted into a plugin.
# Start to generate CSX elements
# CSX version 1.5
if csxVer == 2.0:
# import csx1_api as api
cs1 = api.csType(version='2.0') #5')
# molPublication section: 1.5
mp1 = api.mpubType(
title=psi4.get_global_option('PUBLICATIONTITLE'),
abstract=psi4.get_global_option('PUBLICATIONABSTRACT'),
publisher=psi4.get_global_option('PUBLICATIONPUBLISHER'),
status=['PRELIMINARY', 'DRAFT', 'FINAL'].index(psi4.get_global_option('PUBLICATIONSTATUS')),
category=psi4.get_global_option('PUBLICATIONCATEGORY'),
visibility=['PRIVATE', 'PROTECTED', 'PUBLIC'].index(psi4.get_global_option('PUBLICATIONVISIBILITY')),
tags=psi4.get_global_option('PUBLICATIONTAGS'),
key=psi4.get_global_option('PUBLICATIONKEY'))
email = psi4.get_global_option('EMAIL').replace('__', '@')
mp1.add_author(api.authorType(
creator=psi4.get_global_option('CORRESPONDINGAUTHOR'),
type_='gc:CorrespondingAuthor',
organization=psi4.get_global_option('ORGANIZATION'),
email=None if email == '' else email))
#mp1 = api.mpType(
# title='', abstract='', publisher='', status=0, category=2, visibility=0, tags='', key='')
mp1.set_sourcePackage(api.sourcePackageType(name='Psi4', version=psi4.version()))
#mp1.add_author(api.authorType(creator='', type_='cs:corresponding', organization='', email=''))
cs1.set_molecularPublication(mp1)
# molSystem section: 1.5
ms1 = api.msysType(
systemCharge=molCharge,
systemMultiplicity=molMulti, id='s1')
temp1 = api.dataWithUnitsType(unit='gc:kelvin')
temp1.set_valueOf_(0.0) # LAB dispute
ms1.set_systemTemperature(temp1)
mol1 = api.moleculeType(id='m1', atomCount=molecule.natom())
#OBmol1 = api.moleculeType(id='m1', atomCount=atomNum)
#OBobmol1 = openbabel.OBMol()
#OBfor iatm in range(atomNum):
#OB atomField = atomLine[iatm + 1].split()
#OB atmSymbol = atomField[0]
#OB xCoord = float(atomField[1])
#OB yCoord = float(atomField[2])
#OB zCoord = float(atomField[3])
#OB obatm = obmol1.NewAtom()
#OB obatm.SetAtomicNum(qcdb.periodictable.el2z[atmSymbol.upper()])
#OB obatm.SetVector(xCoord, yCoord, zCoord)
#OBobmol1.ConnectTheDots()
#OBobmol1.PerceiveBondOrders()
#OBobmol1.SetTotalSpinMultiplicity(molMulti)
#OBobmol1.SetTotalCharge(molCharge)
#OBconv1 = openbabel.OBConversion()
#OBconv1.SetInAndOutFormats('mol', 'inchi')
#OBconv1.SetOptions('K', conv1.OUTOPTIONS)
#OBinchikey = conv1.WriteString(obmol1)
#OBmol1.set_inchiKey(inchikey.rstrip())
#OBiatm = 0
for at in range(molecule.natom()):
#xCoord1 = api.dataWithUnitsType(unit='cs:angstrom')
#yCoord1 = api.dataWithUnitsType(unit='cs:angstrom')
#zCoord1 = api.dataWithUnitsType(unit='cs:angstrom')
#xCoord1.set_valueOf_(molecule.x(at) * p4const.psi_bohr2angstroms)
#yCoord1.set_valueOf_(molecule.y(at) * p4const.psi_bohr2angstroms)
#zCoord1.set_valueOf_(molecule.z(at) * p4const.psi_bohr2angstroms)
xCoord1 = api.dataWithUnitsType(unit='gc:bohr')
yCoord1 = api.dataWithUnitsType(unit='gc:bohr')
zCoord1 = api.dataWithUnitsType(unit='gc:bohr')
xCoord1.set_valueOf_(molecule.x(at))
yCoord1.set_valueOf_(molecule.y(at))
zCoord1.set_valueOf_(molecule.z(at))
# LAB 8jun2015: not getting masses from OB anymore so now dependent on qc programs
# current proposition is changing API so masses only go into CSX if relevant (e.g., vib)
# same situation as temperature
atm = api.atomType(
id='a' + str(at + 1),
elementSymbol=molecule.symbol(at),
atomMass=molecule.mass(at), # psi4 uses mass of most common isotope; OB uses natural distribution mass
xCoord3D=xCoord1,
yCoord3D=yCoord1,
zCoord3D=zCoord1,
basisSet='bse:' + molBasis,
calculatedAtomCharge=0,
formalAtomCharge=0)
#OBiatm += 1
#OBcoord1 = api.coordinationType()
#OBibond = 0
#OBfor nb_atom in openbabel.OBAtomAtomIter(obatom):
#OB bond = obatom.GetBond(nb_atom)
#OB bond1 = api.bondType(
#OB id1='a' + str(obatom.GetId() + 1),
#OB id2='a' + str(nb_atom.GetId() + 1))
#OB if bond.GetBondOrder() == 1:
#OB bond1.set_valueOf_('single')
#OB elif bond.GetBondOrder() == 2:
#OB bond1.set_valueOf_('double')
#OB elif bond.GetBondOrder() == 3:
#OB bond1.set_valueOf_('triple')
#OB elif bond.GetBondOrder() == 5:
#OB bond1.set_valueOf_('aromatic')
#OB else:
#OB print('wrong bond order')
#OB coord1.add_bond(bond1)
#OB ibond += 1
#OBcoord1.set_bondCount(ibond)
#OBatm.set_coordination(coord1)
mol1.add_atom(atm)
ms1.add_molecule(mol1)
cs1.set_molecularSystem(ms1)
# molCalculation section: 1.5
mc1 = api.mcalType(id='c1')
qm1 = api.qmCalcType()
srs1 = api.srsMethodType()
psivars = psi4.get_variables()
def form_ene(mandatoryPsivars, optionalPsivars={}, excessPsivars={}):
"""
"""
ene = api.energiesType(unit='gc:hartree')
for pv, csx in mandatoryPsivars.iteritems():
term = api.energyType(type_=csx)
term.set_valueOf_(psivars.pop(pv))
ene.add_energy(term)
for pv, csx in optionalPsivars.iteritems():
if pv in psivars:
term = api.energyType(type_=csx)
term.set_valueOf_(psivars.pop(pv))
ene.add_energy(term)
for pv in excessPsivars:
if pv in psivars:
psivars.pop(pv)
return ene
# Reference stage- every calc has one
if 'CCSD TOTAL ENERGY' in psivars or 'CCSD(T) TOTAL ENERGY' in psivars \
or 'CISD TOTAL ENERGY' in psivars or 'FCI TOTAL ENERGY' in psivars \
or 'QCISD TOTAL ENERGY' in psivars or 'QCISD(T) TOTAL ENERGY' in psivars:
mdm1 = api.srsmdMethodType()
# CCSD(T): 1.5
if 'CCSD(T) TOTAL ENERGY' in psivars:
mandatoryPsivars = {
'CCSD(T) CORRELATION ENERGY': 'gc:correlation',
'CCSD(T) TOTAL ENERGY': 'gc:electronic'}
if not all([pv in psivars for pv in mandatoryPsivars.keys()]):
raise CSXError("""Malformed CCSD(T) computation""")
block = api.resultType( # TODO should be pointing to HF for correlation, maybe to MP2 for guess
methodology='gc:normal', # TODO handle dfcc
spinType='gc:' + molSpin, # TODO could have a closed-shell corl mtd atop open-shell scf?
basisSet='bse:' + molBasis)
block.set_energies(form_ene(mandatoryPsivars))
if hasFreq:
block.set_vibrationalAnalysis(vib1)
mdm1.set_ccsd_t(block)
# CCSD: 1.5
elif 'CCSD TOTAL ENERGY' in psivars:
mandatoryPsivars = {
'CCSD CORRELATION ENERGY': 'gc:correlation',
'CCSD TOTAL ENERGY': 'gc:electronic'}
if not all([pv in psivars for pv in mandatoryPsivars.keys()]):
raise CSXError("""Malformed CCSD computation""")
block = api.resultType( # TODO should be pointing to HF for correlation, maybe to MP2 for guess
methodology='gc:normal', # TODO handle dfcc
spinType='gc:' + molSpin, # TODO could have a closed-shell corl mtd atop open-shell scf?
basisSet='bse:' + molBasis)
block.set_energies(form_ene(mandatoryPsivars))
if hasFreq:
block.set_vibrationalAnalysis(vib1)
mdm1.set_ccsd(block)
# CISD: 1.5
elif 'CISD TOTAL ENERGY' in psivars:
mandatoryPsivars = {
'CISD CORRELATION ENERGY': 'gc:correlation',
'CISD TOTAL ENERGY': 'gc:electronic'}
if not all([pv in psivars for pv in mandatoryPsivars.keys()]):
raise CSXError("""Malformed CISD computation""")
block = api.resultType( # TODO should be pointing to HF for correlation, maybe to MP2 for guess
methodology='gc:normal', # TODO handle dfcc
spinType='gc:' + molSpin, # TODO could have a closed-shell corl mtd atop open-shell scf?
basisSet='bse:' + molBasis)
block.set_energies(form_ene(mandatoryPsivars))
if hasFreq:
block.set_vibrationalAnalysis(vib1)
mdm1.set_cisd(block)
# FCI: 1.5
elif 'FCI TOTAL ENERGY' in psivars:
mandatoryPsivars = {
'FCI CORRELATION ENERGY': 'gc:correlation',
'FCI TOTAL ENERGY': 'gc:electronic'}
if not all([pv in psivars for pv in mandatoryPsivars.keys()]):
raise CSXError("""Malformed FCI computation""")
block = api.resultType( # TODO should be pointing to HF for correlation, maybe to MP2 for guess
methodology='gc:normal', # TODO handle dfcc
spinType='gc:' + molSpin, # TODO could have a closed-shell corl mtd atop open-shell scf?
basisSet='bse:' + molBasis)
block.set_energies(form_ene(mandatoryPsivars))
mdm1.set_fci(block)
# QCISD(T): 1.5
elif 'QCISD(T) TOTAL ENERGY' in psivars:
mandatoryPsivars = {
'QCISD(T) CORRELATION ENERGY': 'gc:correlation',
'QCISD(T) TOTAL ENERGY': 'gc:electronic'}
if not all([pv in psivars for pv in mandatoryPsivars.keys()]):
raise CSXError("""Malformed QCISD(T) computation""")
block = api.resultType( # TODO should be pointing to HF for correlation, maybe to MP2 for guess
methodology='gc:normal', # TODO handle dfcc
spinType='gc:' + molSpin, # TODO could have a closed-shell corl mtd atop open-shell scf?
basisSet='bse:' + molBasis)
block.set_energies(form_ene(mandatoryPsivars))
if hasFreq:
block.set_vibrationalAnalysis(vib1)
mdm1.set_qcisd_t(block)
# QCISD: 1.5
elif 'QCISD TOTAL ENERGY' in psivars:
mandatoryPsivars = {
'QCISD CORRELATION ENERGY': 'gc:correlation',
'QCISD TOTAL ENERGY': 'gc:electronic'}
if not all([pv in psivars for pv in mandatoryPsivars.keys()]):
raise CSXError("""Malformed QCISD computation""")
block = api.resultType( # TODO should be pointing to HF for correlation, maybe to MP2 for guess
methodology='gc:normal', # TODO handle dfcc
spinType='gc:' + molSpin, # TODO could have a closed-shell corl mtd atop open-shell scf?
basisSet='bse:' + molBasis)
block.set_energies(form_ene(mandatoryPsivars))
if hasFreq:
block.set_vibrationalAnalysis(vib1)
mdm1.set_qcisd(block)
srs1.set_multipleDeterminant(mdm1)
elif 'DFT TOTAL ENERGY' in psivars or 'HF TOTAL ENERGY' in psivars \
or 'MP2 TOTAL ENERGY' in psivars or 'MP3 TOTAL ENERGY' in psivars \
or 'MP4 TOTAL ENERGY' in psivars:
sdm1 = api.srssdMethodType()
# DFT 1.5
if 'DFT TOTAL ENERGY' in psivars: # TODO robust enough to avoid MP2C, etc.?
mandatoryPsivars = {
'NUCLEAR REPULSION ENERGY': 'gc:nuclearRepulsion',
'DFT FUNCTIONAL TOTAL ENERGY': 'gc:dftFunctional',
'DFT TOTAL ENERGY': 'gc:electronic'}
optionalPsivars = {
'DOUBLE-HYBRID CORRECTION ENERGY': 'gc:doubleHybrid correction',
'DISPERSION CORRECTION ENERGY': 'gc:dispersion correction'}
excessPsivars = [
'MP2 TOTAL ENERGY',
'MP2 CORRELATION ENERGY',
'MP2 SAME-SPIN CORRELATION ENERGY']
if not all([pv in psivars for pv in mandatoryPsivars.keys()]):
raise CSXError("""Malformed DFT computation""")
block = api.resultType(
methodology='gc:normal', # TODO handle dfhf, dfmp
spinType='gc:' + molSpin,
basisSet='bse:' + molBasis,
dftFunctional=name) # TODO this'll need to be exported
block.set_energies(form_ene(mandatoryPsivars, optionalPsivars, excessPsivars))
if wfn:
block.set_waveFunction(wfn1)
if hasFreq:
block.set_vibrationalAnalysis(vib1)
block.set_properties(prop1)
sdm1.set_dft(block)
# post-reference block
# MP4: 1.5
elif 'MP4 TOTAL ENERGY' in psivars:
mandatoryPsivars = {
'MP4 CORRELATION ENERGY': 'gc:correlation',
'MP4 TOTAL ENERGY': 'gc:electronic'}
optionalPsivars = {
'MP4 SAME-SPIN CORRELATION ENERGY': 'gc:sameSpin correlation'}
if not all([pv in psivars for pv in mandatoryPsivars.keys()]):
raise CSXError("""Malformed MP4 computation""")
block = api.resultType( # TODO should be pointing to HF for correlation
methodology='gc:normal', # TODO handle dfmp
spinType='gc:' + molSpin, # TODO could have a closed-shell corl mtd atop open-shell scf?
basisSet='bse:' + molBasis)
block.set_energies(form_ene(mandatoryPsivars, optionalPsivars))
if wfn:
block.set_waveFunction(wfn1)
if hasFreq:
block.set_vibrationalAnalysis(vib1)
block.set_properties(prop1)
sdm1.set_mp4(block)
# MP3: 1.5
elif 'MP3 TOTAL ENERGY' in psivars:
mandatoryPsivars = {
'MP3 CORRELATION ENERGY': 'gc:correlation',
'MP3 TOTAL ENERGY': 'gc:electronic'}
optionalPsivars = {
'MP3 SAME-SPIN CORRELATION ENERGY': 'gc:sameSpin correlation'}
if not all([pv in psivars for pv in mandatoryPsivars.keys()]):
raise CSXError("""Malformed MP3 computation""")
block = api.resultType( # TODO should be pointing to HF for correlation
methodology='gc:normal', # TODO handle dfmp
spinType='gc:' + molSpin, # TODO could have a closed-shell corl mtd atop open-shell scf?
basisSet='bse:' + molBasis)
block.set_energies(form_ene(mandatoryPsivars, optionalPsivars))
if wfn:
block.set_waveFunction(wfn1)
if hasFreq:
block.set_vibrationalAnalysis(vib1)
block.set_properties(prop1)
sdm1.set_mp3(block)
# MP2: 1.5
elif 'MP2 TOTAL ENERGY' in psivars:
mandatoryPsivars = {
'MP2 CORRELATION ENERGY': 'gc:correlation',
'MP2 TOTAL ENERGY': 'gc:electronic'}
optionalPsivars = {
'MP2 SAME-SPIN CORRELATION ENERGY': 'gc:sameSpin correlation'}
if not all([pv in psivars for pv in mandatoryPsivars.keys()]):
raise CSXError("""Malformed MP2 computation""")
block = api.resultType( # TODO should be pointing to HF for correlation
methodology='gc:normal', # TODO handle dfmp
spinType='gc:' + molSpin, # TODO could have a closed-shell corl mtd atop open-shell scf?
basisSet='bse:' + molBasis)
block.set_energies(form_ene(mandatoryPsivars, optionalPsivars))
if wfn:
block.set_waveFunction(wfn1)
if hasFreq:
block.set_vibrationalAnalysis(vib1)
block.set_properties(prop1)
sdm1.set_mp2(block)
# SCF: 1.5
elif 'HF TOTAL ENERGY' in psivars:
mandatoryPsivars = {
'NUCLEAR REPULSION ENERGY': 'gc:nuclearRepulsion',
'HF TOTAL ENERGY': 'gc:electronic'}
if not all([pv in psivars for pv in mandatoryPsivars.keys()]):
raise CSXError("""Malformed HF computation""")
block = api.resultType(
methodology='gc:normal', # TODO handle dfhf, dfmp
spinType='gc:' + molSpin,
basisSet='bse:' + molBasis)
block.set_energies(form_ene(mandatoryPsivars))
if wfn:
block.set_waveFunction(wfn1)
if hasFreq:
block.set_vibrationalAnalysis(vib1)
block.set_properties(prop1)
sdm1.set_abinitioScf(block)
else:
psi4.print_out("""\nCSX version {0} does not support """
"""method {1} for {2}\n""".format(
csxVer, lowername, 'energies'))
srs1.set_singleDeterminant(sdm1)
#print('CSX not harvesting: ', ', '.join(psivars))
qm1.set_singleReferenceState(srs1)
mc1.set_quantumMechanics(qm1)
cs1.set_molecularCalculation(mc1)
else:
print('The future CSX file is here')
csxfile.write('<?xml version="1.0" encoding="UTF-8"?>\n')
cs1.export(csxfile, 0)
csxfile.close()
P 4 1.00
34.8564630000 0.0156480000
7.8431310000 0.0981970000
2.3062490000 0.3077680000
0.7231640000 0.4924700000
P 1 1.00
0.2148820000 1.0000000000
P 1 1.00
0.0638500000 1.0000000000
D 2 1.00
2.3062000000 0.2027000000
0.7232000000 0.5791000000
D 2 1.00
0.2149000000 0.7854500000
0.0639000000 0.5338700000
****
""")
ccsd_e, wfn = psi4.properties('ccsd',properties=['dipole'],return_wfn=True)
psi4.oeprop(wfn,"DIPOLE", "QUADRUPOLE", title="(OEPROP)CC")
psi4.compare_values(psi4.get_variable("(OEPROP)CC DIPOLE X"), 0.000000000000,6,"CC DIPOLE X") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC DIPOLE Y"), 0.000000000000,6,"CC DIPOLE Y") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC DIPOLE Z"),-1.840334899884,6,"CC DIPOLE Z") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC QUADRUPOLE XX"),-7.864006962064,6,"CC QUADRUPOLE XX") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC QUADRUPOLE XY"), 0.000000000000,6,"CC QUADRUPOLE XY") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC QUADRUPOLE XZ"), 0.000000000000,6,"CC QUADRUPOLE XZ") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC QUADRUPOLE YY"),-4.537386915305,6,"CC QUADRUPOLE YY") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC QUADRUPOLE YZ"), 0.000000000000,6,"CC QUADRUPOLE YZ") #TEST
psi4.compare_values(psi4.get_variable("(OEPROP)CC QUADRUPOLE ZZ"),-6.325836255265,6,"CC QUADRUPOLE ZZ") #TEST
psi4.core.print_variables()