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_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.variable('scf total energy'), 6, 'SCF')
assert psi4.compare_values(-76.332940127333, psi4.variable('mp2 total energy'), 6, 'MP2')
assert psi4.compare_values(-76.338453951890, psi4.variable('ccsd total energy'), 6, 'CCSD')
assert psi4.compare_values(-0.275705491773, psi4.variable('ccsd correlation energy'), 6, 'CCSD corl')
assert psi4.compare_values(-76.345717549886, psi4.variable('ccsd(t) total energy'), 6, 'CCSD(T)')
assert psi4.compare_values(-0.282969089769, psi4.variable('ccsd(t) correlation energy'), 6, 'CCSD(T) corl')
def test_psi4_cas():
"""casscf-sp"""
#! CASSCF/6-31G** energy point
geom = psi4.geometry("""
O
H 1 1.00
H 1 1.00 2 103.1
""")
psi4.set_options({
"basis" : '6-31G**',
"reference" : 'rhf',
"scf_type" : 'pk',
"mcscf_algorithm" : 'ah',
"qc_module" : 'detci',
"nat_orbs" : True})
cisd_energy, cisd_wfn = psi4.energy("CISD", return_wfn=True)
assert psi4.compare_values(-76.2198474477531, cisd_energy, 6, 'CISD Energy')
psi4.set_options({
"restricted_docc": [1, 0, 0, 0],
"active": [3, 0, 1, 2]})
casscf_energy = psi4.energy('casscf', ref_wfn=cisd_wfn)
assert psi4.compare_values(-76.073865006902, casscf_energy, 6, 'CASSCF Energy')
def test_gpu_dfcc():
"""gpu_dfcc/tests/gpu_dfcc1"""
#! cc-pvdz (H2O)2 Test DF-CCSD vs GPU-DF-CCSD
import gpu_dfcc
H20 = psi4.geometry("""
O 0.000000000000 0.000000000000 -0.068516219310
H 0.000000000000 -0.790689573744 0.543701060724
H 0.000000000000 0.790689573744 0.543701060724
""")
psi4.set_memory(32000000000)
psi4.set_options({
'cc_timings': False,
'num_gpus': 1,
'cc_type': 'df',
'df_basis_cc': 'aug-cc-pvdz-ri',
'df_basis_scf': 'aug-cc-pvdz-jkfit',
'basis': 'aug-cc-pvdz',
'freeze_core': 'true',
'e_convergence': 1e-8,
'd_convergence': 1e-8,
'r_convergence': 1e-8,
'scf_type': 'df',
'maxiter': 30})
psi4.set_num_threads(2)
en_dfcc = psi4.energy('ccsd', molecule=H20)
en_gpu_dfcc = psi4.energy('gpu-df-ccsd', molecule=H20)
assert psi4.compare_values(en_gpu_dfcc, en_dfcc, 8, "CCSD total energy")
def hide_test_xtpl_fn_fn_error():
psi4.geometry('He')
with pytest.raises(psi4.UpgradeHelper) as e:
psi4.energy('cbs', scf_basis='cc-pvdz', scf_scheme=psi4.driver_cbs.xtpl_highest_1)
assert 'Replace extrapolation function with function name' in str(e)
def test_gpudfcc2():
"""gpu_dfcc/tests/gpu_dfcc2"""
#! aug-cc-pvdz (H2O) Test DF-CCSD(T) vs GPU-DF-CCSD(T)
import psi4
H20 = psi4.geometry("""
O 0.000000000000 0.000000000000 -0.068516219310
H 0.000000000000 -0.790689573744 0.543701060724
H 0.000000000000 0.790689573744 0.543701060724
""")
psi4.set_memory(32000000000)
psi4.set_options({
'cc_type': 'df',
'basis': 'aug-cc-pvdz',
'freeze_core': 'true',
'e_convergence': 1e-8,
'd_convergence': 1e-8,
'r_convergence': 1e-8,
'scf_type': 'df',
'maxiter': 30})
psi4.set_num_threads(2)
en_dfcc = psi4.energy('ccsd(t)')
en_gpu_dfcc = psi4.energy('gpu-df-ccsd(t)')
assert psi4.compare_values(en_gpu_dfcc, en_dfcc, 8, "CCSD total 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.variable("ACI ENERGY"),10,"ACI energy")
assert psi4.compare_values(refacipt2, psi4.variable("ACI+PT2 ENERGY"),8,"ACI+PT2 energy")
def hide_test_xtpl_cbs_fn_error():
psi4.geometry('He')
with pytest.raises(psi4.UpgradeHelper) as e:
psi4.energy(psi4.cbs, scf_basis='cc-pvdz')
#psi4.energy(psi4.driver.driver_cbs.complete_basis_set, scf_basis='cc-pvdz')
assert 'Replace cbs or complete_basis_set function with cbs string' in str(e)
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.variable('efp elst energy'), 6, 'EFP-EFP Elst') # from q-chem
assert psi4.compare_values(-0.0003168768, psi4.variable('efp ind energy'), 6, 'EFP-EFP Indc')
assert psi4.compare_values(-0.0021985285, psi4.variable('efp disp energy'), 6, 'EFP-EFP Disp') # from q-chem
assert psi4.compare_values( 0.0056859871, psi4.variable('efp exch energy'), 6, 'EFP-EFP Exch') # from q-chem
assert psi4.compare_values( 0.0026804450, psi4.variable('efp total energy'), 6, 'EFP-EFP Totl')
assert psi4.compare_values( 0.0026804450, psi4.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.variable('efp total energy') - psi4.variable('efp ind energy'), 6, 'EFP corr to SCF') # from q-chem
assert psi4.compare_values(-0.0117694790, psi4.variable('efp ind energy'), 6, 'QM-EFP Indc') # from q-chem
assert psi4.compare_values(-0.0021985285, psi4.variable('efp disp energy'), 6, 'EFP-EFP Disp') # from q-chem
assert psi4.compare_values( 0.0056859871, psi4.variable('efp exch energy'), 6, 'EFP-EFP Exch') # from q-chem
assert psi4.compare_values( 0.2504904057, psi4.variable('efp total energy'), 6, 'EFP-EFP Totl') # from q-chem
assert psi4.compare_values(-76.0139362744, psi4.variable('scf total energy'), 6, 'SCF') # from q-chem
psi4.core.print_variables()
def test_dft_bench_ionization(func, expected, basis, dft_bench_systems, request):
"""functionals ionization energies vs. Q-Chem"""
if func.lower() in psi4.driver.procedures['energy']:
mols = dft_bench_systems
psi4.set_options({'basis': basis, 'reference': 'uks'})
cation = psi4.energy(func, molecule=mols['h2o_plus'])
psi4.set_options({'reference': 'rks'})
neutral = psi4.energy(func, molecule=mols['h2o'])
assert compare_values(expected, cation - neutral, 4, request.node.name)
else:
pytest.skip("{0:s} not in Psi4.".format(func))
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 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_uhf():
"""
test for uhf using (H2O)^+
"""
print("!!! %s" % os.path.dirname(__file__))
ao_ints, test_scf_param, e_ZZ_repulsion = scf.init(\
os.path.dirname(__file__) + "/test_uhf.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, True) + e_ZZ_repulsion
print("energy: %f" % energy)
# psi4 setup
import psi4
mol = psi4.geometry("""
1 2
O
H 1 1.1
H 1 1.1 2 104
""")
mol.update_geometry()
bas = psi4.core.BasisSet.build(mol, target=test_scf_param['basis'])
mints = psi4.core.MintsHelper(bas)
# DENSITY FITTED
psi4.set_options({"scf_type": "pk", "reference": "uhf"})
psi4_energy = psi4.energy("SCF/cc-pVDZ", molecule = mol)
print("psi4 energy: %f" % psi4_energy)
assert(np.allclose(energy, psi4_energy) == True)
def test_rhf():
"""
test for rhf
"""
ao_ints, test_scf_param, e_ZZ_repulsion = scf.init(\
os.path.dirname(__file__) + "/test_rhf.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)
# DENSITY FITTED
psi4.set_options({"scf_type": "df"})
psi4_energy = psi4.energy("SCF/cc-pVDZ", molecule = mol)
assert(np.allclose(energy, psi4_energy) == True)
def test_restricted_RPA_triplet_c1():
"Build out the full CIS/TDA hamiltonian (A) col by col with the product engine"
h2o = psi4.geometry("""
O
H 1 0.96
H 1 0.96 2 104.5
symmetry c1
""")
psi4.set_options({"scf_type": "pk", 'save_jk': True})
e, wfn = psi4.energy("hf/cc-pvdz", molecule=h2o, return_wfn=True)
A_ref, B_ref = build_RHF_AB_C1_triplet(wfn)
ni, na, _, _ = A_ref.shape
nia = ni * na
A_ref = A_ref.reshape((nia, nia))
B_ref = B_ref.reshape((nia, nia))
P_ref = A_ref + B_ref
M_ref = A_ref - B_ref
# Build engine
eng = TDRSCFEngine(wfn, ptype='rpa', triplet=True)
# our "guess"" vectors
ID = [psi4.core.Matrix.from_array(v.reshape((ni, na))) for v in tuple(np.eye(nia).T)]
Px, Mx = eng.compute_products(ID)[:-1]
P_test = np.column_stack([x.to_array().flatten() for x in Px])
assert compare_arrays(P_ref, P_test, 8, "RHF (A+B)x C1 products")
M_test = np.column_stack([x.to_array().flatten() for x in Mx])
assert compare_arrays(M_ref, M_test, 8, "RHF (A-B)x C1 products")
def test_unrestricted_RPA_C1():
ch2 = psi4.geometry("""
0 3
c
h 1 1.0
h 1 1.0 2 125.0
symmetry c1
""")
psi4.set_options({"scf_type": "pk", 'reference': 'UHF', 'save_jk': True})
e, wfn = psi4.energy("hf/cc-pvdz", molecule=ch2, return_wfn=True)
A_ref, B_ref = build_UHF_AB_C1(wfn)
nI, nA, _, _ = A_ref['IAJB'].shape
nIA = nI * nA
ni, na, _, _ = A_ref['iajb'].shape
nia = ni * na
P_ref = {k: A_ref[k] + B_ref[k] for k in A_ref.keys()}
M_ref = {k: A_ref[k] - B_ref[k] for k in A_ref.keys()}
eng = TDUSCFEngine(wfn, ptype='rpa')
X_jb = [psi4.core.Matrix.from_array(v.reshape((ni, na))) for v in tuple(np.eye(nia).T)]
zero_jb = [psi4.core.Matrix(ni, na) for x in range(nIA)]
X_JB = [psi4.core.Matrix.from_array(v.reshape((nI, nA))) for v in tuple(np.eye(nIA).T)]
zero_JB = [psi4.core.Matrix(nI, nA) for x in range(nia)]
# Guess Identity:
# X_I0 X_0I = X_I0 X_0I
# [ I{nOV x nOV} | 0{nOV x nov}] = [ X{KC,JB} | 0{KC, jb}]
# [ 0{nov x nOV} | I{nov x nov}] [ 0{kc,JB} | X{kc, jb}]
# Products:
# [ A+/-B{IA, KC} A+/-B{IA, kc}] [ I{KC, JB} | 0{KC,jb}] = [A+/-B x X_I0] = [ (A+/-B)_IAJB, (A+/-B)_iaJB]
# [ A+/-B{ia, KC} A+/-B{ia, kc}] [ O{kc, JB} | X{kc,jb}] [A+/-B x X_0I] = [ (A+/-B)_IAjb, (A+/-B)_iajb]
X_I0 = [[x, zero] for x, zero in zip(X_JB, zero_jb)]
X_0I = [[zero, x] for zero, x in zip(zero_JB, X_jb)]
Px_I0, Mx_I0 = eng.compute_products(X_I0)[:-1]
Px_0I, Mx_0I = eng.compute_products(X_0I)[:-1]
P_IAJB_test = np.column_stack([x[0].to_array().flatten() for x in Px_I0])
assert compare_arrays(P_ref['IAJB'].reshape(nIA, nIA), P_IAJB_test, 8, "A_IAJB")
M_IAJB_test = np.column_stack([x[0].to_array().flatten() for x in Mx_I0])
assert compare_arrays(M_ref['IAJB'].reshape(nIA, nIA), M_IAJB_test, 8, "A_IAJB")
P_iaJB_test = np.column_stack([x[1].to_array().flatten() for x in Px_I0])
assert compare_arrays(P_ref['iaJB'].reshape(nia, nIA), P_iaJB_test, 8, "P_iaJB")
M_iaJB_test = np.column_stack([x[1].to_array().flatten() for x in Mx_I0])
assert compare_arrays(M_ref['iaJB'].reshape(nia, nIA), M_iaJB_test, 8, "M_iaJB")
P_IAjb_test = np.column_stack([x[0].to_array().flatten() for x in Px_0I])
assert compare_arrays(P_ref['IAjb'].reshape(nIA, nia), P_IAjb_test, 8, "P_IAjb")
M_IAjb_test = np.column_stack([x[0].to_array().flatten() for x in Mx_0I])
assert compare_arrays(M_ref['IAjb'].reshape(nIA, nia), M_IAjb_test, 8, "M_IAjb")
P_iajb_test = np.column_stack([x[1].to_array().flatten() for x in Px_0I])
assert compare_arrays(P_ref['iajb'].reshape(nia, nia), P_iajb_test, 8, "P_iajb")
M_iajb_test = np.column_stack([x[1].to_array().flatten() for x in Mx_0I])
assert compare_arrays(M_ref['iajb'].reshape(nia, nia), M_iajb_test, 8, "M_iajb")
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_dft_bench_interaction(func, expected, basis, dft_bench_systems, request):
"""functionals interaction energies vs. Q-Chem & Orca"""
if func.lower() in psi4.driver.procedures['energy']:
mols = dft_bench_systems
psi4.set_options({'basis': basis})
psi4_ie = psi4.energy(func, molecule=mols['h2o_dimer'], bsse_type='nocp')
assert compare_values(expected, psi4_ie, 4, request.node.name)
else:
pytest.skip("{0:s} not in Psi4.".format(func))
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.variable("CURRENT ENERGY"), 6, "DMRG Energy")
def psiSCF(self):
psi4.core.set_output_file("output.dat",False)
psi4.set_options({'basis': self.options['DEFAULT']['basis'],
'scf_type': 'pk',
'reference': 'rhf',
'puream': 0,
'print': 0 })
return psi4.energy('scf')
def _build_wfn(ref, func, basis, nosym):
if ref.startswith('RHF'):
mol = tddft_systems['RHF']
else:
mol = tddft_systems['UHF']
psi4.set_options({'reference': 'UHF'})
if nosym:
mol.reset_point_group('c1')
psi4.set_options({'scf_type': 'pk', 'e_convergence': 8, 'd_convergence': 8, 'save_jk': True})
e, wfn = psi4.energy("{}/{}".format(func, basis), return_wfn=True, molecule=mol)
return wfn
def test_gdma():
"""gdma1"""
#! Water RHF/cc-pVTZ distributed multipole analysis
ref_energy = -76.0571685433842219
ref_dma_mat = psi4.core.Matrix(3, 9)
ref_dma_mat.name = 'Reference DMA values'
ref_dma_arr = [
[ -0.43406697290168, -0.18762673939633, 0.00000000000000, 0.00000000000000, 0.03206686487531,
0.00000000000000, -0.00000000000000, -0.53123477172696, 0.00000000000000 ],
[ 0.21703348903257, -0.06422316619952, 0.00000000000000, -0.11648289410022, 0.01844320206227,
0.00000000000000, 0.07409226544133, -0.07115302332866, 0.00000000000000 ],
[ 0.21703348903257, -0.06422316619952, 0.00000000000000, 0.11648289410022, 0.01844320206227,
0.00000000000000, -0.07409226544133, -0.07115302332866, 0.00000000000000 ]
]
for i in range(3):
for j in range(9):
ref_dma_mat.set(i, j, ref_dma_arr[i][j])
ref_tot_mat = psi4.core.Matrix(1, 9)
ref_tot_mat.name = "Reference total values"
ref_tot_arr = [
0.00000000516346, -0.79665315928128, 0.00000000000000, 0.00000000000000, 0.10813259329390,
0.00000000000000, 0.00000000000000, -2.01989585894142, 0.00000000000000
]
for i in range(9):
ref_tot_mat.set(0, i, ref_tot_arr[i])
# noreorient/nocom are not needed, but are used here to guarantee that the
# GDMA origin placement defined below is at the O atom.
water = psi4.geometry("""
O 0.000000 0.000000 0.117176
H -0.000000 -0.756950 -0.468706
H -0.000000 0.756950 -0.468706
noreorient
nocom
""")
psi4.set_options({"scf_type": "pk",
"basis": "cc-pvtz",
"d_convergence": 10,
"gdma_switch": 0,
"gdma_radius": [ "H", 0.65 ],
"gdma_limit": 2,
"gdma_origin": [ 0.000000, 0.000000, 0.117176 ]})
energy, wfn = psi4.energy('scf', return_wfn=True)
psi4.gdma(wfn)
dmavals = psi4.core.variable("DMA DISTRIBUTED MULTIPOLES")
totvals = psi4.core.variable("DMA TOTAL MULTIPOLES")
assert psi4.compare_values(ref_energy, energy, 8, "SCF Energy")
assert psi4.compare_matrices(dmavals, ref_dma_mat, 6, "DMA Distributed Multipoles")
assert psi4.compare_matrices(totvals, ref_tot_mat, 6, "DMA Total Multipoles")
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.variable("NUCLEAR REPULSION ENERGY"), 6, 'NRE')
assert psi4.compare_values(-76.021418445155, psi4.variable("SCF TOTAL ENERGY"), 6, 'SCF')
assert psi4.compare_values( -0.204692406830, psi4.variable("MP2 CORRELATION ENERGY") , 6, 'MP2 correlation')
assert psi4.compare_values( -0.217715210258, psi4.variable("CCSDT CORRELATION ENERGY"), 6, 'CCSDT correlation')
assert psi4.compare_values(-76.239133655413, psi4.variable("CURRENT ENERGY"), 6, 'CCSDT')
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.variable('SNS-MP2 TOTAL ENERGY'), 5, "SNS-MP2 IE [Eh]")
def test_mp2_module(inp, clsd_open_pmols, request):
tnm = request.node.name
subject = clsd_open_pmols[inp['subject']]
ref_block = _ref_module[inp['options']['scf_type']][inp['options']['reference']]
ref_ref = ref_block['HF TOTAL ENERGY']
ref_block = ref_block[inp['options']['freeze_core']][inp['options']['mp2_type']]
ref_corl = ref_block['MP2 CORRELATION ENERGY']
ref_tot = ref_block['MP2 TOTAL ENERGY']
psi4.set_options({
'basis': 'cc-pvdz',
'guess': 'sad',
'e_convergence': 8,
'd_convergence': 7,
})
psi4.set_options(inp['options'])
if inp['driver'] == 'energy':
ene, wfn = psi4.energy('mp2', molecule=subject, return_wfn=True)
elif inp['driver'] == 'gradient':
grad, wfn = psi4.gradient('mp2', molecule=subject, return_wfn=True)
ref_tot_grad = ref_block['MP2 TOTAL GRADIENT']
for obj in [psi4.core, wfn]:
for pv in ['HF TOTAL ENERGY', 'SCF TOTAL ENERGY', 'CURRENT REFERENCE ENERGY']:
assert compare_values(ref_ref, obj.variable(pv), 6, tnm + ' ' + pv)
for pv in [
'MP2 CORRELATION ENERGY',
'CURRENT CORRELATION ENERGY',
]:
assert compare_values(ref_corl, obj.variable(pv), 6, tnm + ' ' + pv)
for pv in [
'MP2 TOTAL ENERGY',
'CURRENT ENERGY',
]:
assert compare_values(ref_tot, obj.variable(pv), 6, tnm + ' ' + pv)
assert compare_values(ref_tot, wfn.energy(), 6, tnm + ' wfn')
if inp['driver'] == 'energy':
assert compare_values(ref_tot, ene, 6, tnm + ' return')
elif inp['driver'] == 'gradient':
assert compare_matrices(ref_tot_grad, wfn.gradient(), 6, tnm + ' grad wfn')
assert compare_matrices(ref_tot_grad, grad, 6, tnm + ' grad return')
def test_grimme_3c():
s16di = 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
symmetry c1
""")
ene = psi4.energy('pbeh3c', bsse_type='nocp')
assert psi4.compare_values(-2.153, ene * psi4.constants.hartree2kcalmol, 0.03, 'S22-16 PBEh-3c/def2-mSVP')
psi4.set_options({'basis': 'cc-pvdz'}) # try to confuse method
psi4.set_options({'scf_type': 'pk'})
ene = psi4.energy('hf3c/', bsse_type='nocp')
assert psi4.compare_values(-0.00240232, ene, 6, 'S22-16 HF-3c/minix')
def test_opt():
"""
We pick the physicist's water molecule in a relatively large
basis set (aug-cc-pVDZ), whose uhf and rhf solutions are the
same. And we test that energies of the following four cases
are identical:
RHF + DIIS
RHF + ODA
UHF + DIIS
UHF + ODA
Note for DIIS, we in addition require the convergence is achieved
in 30 iterations.
"""
# get integrals from psi4
ao_ints, scf_params, e_ZZ_repul = \
scf.init(os.path.dirname(__file__) + '/test_opt.yml')
# RHF, DIIS
scf_params['max_iter'] = 30
eps, C, D, F = scf.scf(ao_ints, scf_params, e_ZZ_repul)
E_rhf_diis = scf.get_SCF_energy(ao_ints['H'], F, D, False) + e_ZZ_repul
# RHF, ODA
scf_params['max_iter'] = 300
scf_params['opt'] = "oda"
eps, C, D, F = scf.scf(ao_ints, scf_params, e_ZZ_repul)
E_rhf_oda = scf.get_SCF_energy(ao_ints['H'], F, D, False) + e_ZZ_repul
# UHF, DIIS
scf_params['max_iter'] = 30
scf_params['opt'] = "diis"
scf_params['unrestricted'] = True
eps, C, D, F = scf.scf(ao_ints, scf_params, e_ZZ_repul)
E_uhf_diis = scf.get_SCF_energy(ao_ints['H'], F, D, True) + e_ZZ_repul
# UHF, ODA
scf_params['max_iter'] = 300
scf_params['opt'] = "oda"
eps, C, D, F = scf.scf(ao_ints, scf_params, e_ZZ_repul)
E_uhf_oda = scf.get_SCF_energy(ao_ints['H'], F, D, True) + e_ZZ_repul
# RHF, psi4
import psi4
mol = psi4.geometry(scf_params['geometry'])
mol.update_geometry()
ctrl_string = "SCF/" + scf_params['basis']
psi4.set_options({"scf_type": "pk"})
psi4_E_rhf = psi4.energy(ctrl_string, molecule = mol)
# check
assert(np.allclose(E_rhf_diis, E_rhf_oda) == True)
assert(np.allclose(E_rhf_diis, E_uhf_diis) == True)
assert(np.allclose(E_rhf_diis, E_uhf_oda) == True)
assert(np.allclose(E_rhf_diis, psi4_E_rhf) == True)
def psiMP2(self,options):
psi4.core.set_output_file("output.dat",False)
psi4.set_options({'basis': options['DEFAULT']['basis'],
'scf_type': 'pk',
'reference': 'uhf',
'e_convergence': 12,
'df_basis_mp2' : self.dfBasisName,
'puream': 0,
'print': 0 })
if not self.df:
psi4.set_options( {'mp2_type': 'conv'} )
return psi4.energy('mp2')
def test_RU_TDA_C1():
h2o = psi4.geometry("""0 1
O 0.000000 0.000000 0.135446
H -0.000000 0.866812 -0.541782
H -0.000000 -0.866812 -0.541782
symmetry c1
no_reorient
no_com
""")
psi4.set_options({"scf_type": "pk", 'save_jk': True})
e, wfn = psi4.energy("hf/sto-3g", molecule=h2o, return_wfn=True)
A_ref, _ = build_UHF_AB_C1(wfn)
ni, na, _, _ = A_ref['IAJB'].shape
nia = ni * na
A_sing_ref = A_ref['IAJB'] + A_ref['IAjb']
A_sing_ref = A_sing_ref.reshape(nia, nia)
A_trip_ref = A_ref['IAJB'] - A_ref['IAjb']
A_trip_ref = A_trip_ref.reshape(nia, nia)
sing_vals, _ = np.linalg.eigh(A_sing_ref)
trip_vals, _ = np.linalg.eigh(A_trip_ref)
trip_eng = TDRSCFEngine(wfn, ptype='tda', triplet=True)
sing_eng = TDRSCFEngine(wfn, ptype='tda', triplet=False)
ID = [psi4.core.Matrix.from_array(v.reshape((ni, na))) for v in tuple(np.eye(nia).T)]
psi4.core.print_out("\nA sing:\n" + str(A_sing_ref) + "\n\n")
psi4.core.print_out("\nA trip:\n" + str(A_trip_ref) + "\n\n")
A_trip_test = np.column_stack([x.to_array().flatten() for x in trip_eng.compute_products(ID)[0]])
assert compare_arrays(A_trip_ref, A_trip_test, 8, "Triplet Ax C1 products")
A_sing_test = np.column_stack([x.to_array().flatten() for x in sing_eng.compute_products(ID)[0]])
assert compare_arrays(A_sing_ref, A_sing_test, 8, "Singlet Ax C1 products")
sing_vals_2, _ = np.linalg.eigh(A_sing_test)
trip_vals_2, _ = np.linalg.eigh(A_trip_test)
psi4.core.print_out("\n\n SINGLET EIGENVALUES\n")
for x, y in zip(sing_vals, sing_vals_2):
psi4.core.print_out("{:10.6f} {:10.6f}\n".format(x, y))
# assert compare_values(x, y, 4, "Singlet ROOT")
psi4.core.print_out("\n\n Triplet EIGENVALUES\n")
for x, y in zip(trip_vals, trip_vals_2):
psi4.core.print_out("{:10.6f} {:10.6f}\n".format(x, y))
# assert compare_values(x, y, 4, "Triplet Root")
for x, y in zip(sing_vals, sing_vals_2):
assert compare_values(x, y, 4, "Singlet ROOT")
for x, y in zip(trip_vals, trip_vals_2):
assert compare_values(x, y, 4, "Triplet Root")
def plot_density(self,
which_density,
iso=0.020,
slices=1,
delete_cubefile=True):
psi4.set_options({'cubeprop_tasks': ['density']})
energy, wfn = psi4.energy(self.method,
molecule=self.geometry,
return_wfn=True)
psi4.cubeprop(wfn)
if which_density == 'Da':
D, D_info = read_cube('Da.cube')
elif which_density == 'Db':
D, D_info = read_cube('Db.cube')
elif which_density == 'Ds':
D, D_info = read_cube('Ds.cube')
elif which_density == 'Dt':
D, D_info = read_cube('Dt.cube')
if delete_cubefile == True:
os.remove('Da.cube')
os.remove('Db.cube')
os.remove('Ds.cube')
os.remove('Dt.cube')
fig, ax = plt.subplots(ncols=1, nrows=1, figsize=(10, 10))
print(D.shape)
# for i in range(0):
# for j in range(0):
ax.imshow(D[60, :, :], interpolation="nearest")
for i in range(D.shape[1]):
for j in range(D.shape[2]):
if np.isclose(D[60, i, j], iso, 0.3e-1) == True:
# if (i+j) % 0 == 0:
ax.scatter(j, i, color="white")
return D
def _build_wfn(ref, func, basis, nosym):
if ref.startswith('RHF'):
mol = tddft_systems['RHF']
else:
mol = tddft_systems['UHF']
psi4.set_options({'reference': 'UHF'})
if nosym:
mol.reset_point_group('c1')
psi4.set_options({
'scf_type': 'pk',
'e_convergence': 8,
'd_convergence': 8,
'save_jk': True
})
e, wfn = psi4.energy("{}/{}".format(func, basis),
return_wfn=True,
molecule=mol)
return wfn
def test_df_mp2(mol_str):
geometry = psi4.geometry(quest.mollib[mol_str])
basis = "STO-3G"
rhf_options = \
{
'e_conv': 1.e-8,
'd_conv': 1.e-8,
'diis': True,
'max_diis': 7,
'max_iter': 100,
}
mol = quest.Molecule(geometry, basis)
wafu = quest.Wavefunction(mol, rhf_options)
scf_energy = quest.scf_module.compute_rhf(wafu)
mp2_energy = quest.mp2.df_mp2(wafu)
psi4.set_options({"scf_type": "df"})
psi4_mp2_energy = psi4.energy('mp2/' + basis, molecule=geometry)
def psiMP2(self, options):
psi4.core.set_output_file("output.dat", False)
psi4.set_options({
'basis': options['DEFAULT']['basis'],
'scf_type': 'pk',
'reference': 'uhf',
'e_convergence': 12,
'df_basis_mp2': self.dfBasisName,
'puream': 0,
'print': 0
})
if not self.df:
psi4.set_options({'mp2_type': 'conv'})
return psi4.energy('mp2')
def _base_tdscf_test(molecule, ref_scf_energy, ref_pe_energy, exc_energies,
osc_strengths):
scf_energy, wfn = psi4.energy("TD-SCF", return_wfn=True, molecule=molecule)
assert compare_values(ref_pe_energy, wfn.variable("PE ENERGY"), 6,
"PE Energy contribution")
assert compare_values(ref_scf_energy, scf_energy, 6, "Total PE-SCF Energy")
e_calc = []
r_calc = []
for i in range(len(exc_energies)):
e_calc.append(
wfn.variable(
f'TD-HF ROOT 0 -> ROOT {i+1} EXCITATION ENERGY - A SYMMETRY'))
r_calc.append(
wfn.variable(
f'TD-HF ROOT 0 -> ROOT {i+1} OSCILLATOR STRENGTH (LEN) - A SYMMETRY'
))
assert compare_arrays(exc_energies, e_calc, 4, f'PE EXCITATION ENERGY')
assert compare_arrays(osc_strengths, r_calc, 4, f'PE OSCILLATOR STRENGTH')
def test_GGA_unrestricted_one_shell(hydrogen):
psi4.core.clean()
psi4.core.be_quiet()
psi4.set_options({
"DFT_SPHERICAL_POINTS": 6,
"DFT_RADIAL_POINTS": 12,
})
psi4.set_options({"reference": "uks"})
psi4_energy = psi4.energy("pbe/cc-pVDZ", molecule=hydrogen)
h = pdft.UMolecule(hydrogen, "cc-pvdz", "pbe")
h.scf()
pdft_energy = h.energy
assert np.isclose(psi4_energy, pdft_energy, rtol=1e-2)
def test_OH_molden(inp_oh, datadir):
mol = psi4.geometry("""
0 2
O
H 1 0.970369
symmetry c1
""")
psi4.set_options({
'basis': 'dz',
'scf_type': 'pk',
'd_convergence': 8,
'reference': inp_oh['ref']
})
molden_file = f"{inp_oh['name']}.molden"
ref = datadir.join(f"{inp_oh['name']}.ref")
e, wfn = psi4.energy('scf', return_wfn=True, molecule=mol)
wfn.write_molden(molden_file, do_virtual=True, use_natural=False)
assert compare_moldenfiles(ref, molden_file)
def execute_job():
job_id = {job_id}
molecule = "{molecule}"
method = "{method}"
basis = "{basis}"
number_of_threads = {num_threads}
memory = "{memory}"
try:
max_threads = int(subprocess.check_output(["grep", "-c", "cores", "/proc/cpuinfo"]))
print("Maximum threads: {format}".format(max_threads))
except:
print("Error detecting number of cores. \n Maxium threads: 1")
max_threads = 1
if number_of_threads > max_threads:
print("Input number of threads ({format}) greater than max threads ({format}), limiting number of threads to max threads".format(number_of_threads, max_threads))
number_of_threads = max_threads
print("Running Job")
print("Molcule: {format}".format(molecule))
print("Method: {format}".format(method))
print("Basis: {format}".format(basis))
print("Threads {format}".format(number_of_threads))
print("Memory: {format}".format(memory))
psi4.core.set_output_file("job_{format}.log".format(job_id), False)
psi4.set_memory(memory)
psi4.geometry(molecule)
psi4.set_num_threads(number_of_threads)
try:
energy = psi4.energy("{format}/{format}".format(method, basis))
print("Energy: {format}".format(energy))
success = True
except ValueError:
success = False
print("Iterations failed to Converge")
with open("job_{format}.out".format(job_id), "w") as out_file:
out_file.write("Job: {format}\n".format(job_id))
if success:
out_file.write("Energy: {format}".format(energy))
else:
out_file.write("Failure")
def test_dkh():
"""dkh/molpro-2order"""
Ne = psi4.geometry("""
0 1
Ne
""")
psi4.set_options({
'reference': 'rhf',
'basis': 'cc-pvtz-dk',
'relativistic': 'dkh',
'dkh_order': 2,
'print': 2,
'scf_type': 'pk'})
e = psi4.energy('scf')
assert psi4.compare_values(-128.66891610, e, 6, '2nd order vs Molpro')
def test_H2O_molden(inp_h2o, datadir):
mol = psi4.geometry("""
0 1
O
H 1 0.951342
H 1 0.951342 2 112.505645
""")
psi4.set_options({
'basis': 'dz',
'scf_type': 'pk',
})
psi4.set_options(inp_h2o['options'])
molden_file = f"{inp_h2o['name']}.molden"
ref = datadir.join(f"{inp_h2o['name']}.ref")
e, wfn = psi4.energy(inp_h2o['energy'], return_wfn=True, molecule=mol)
wfn.write_molden(molden_file,
do_virtual=inp_h2o['do_virtual'],
use_natural=inp_h2o['use_natural'])
assert compare_moldenfiles(ref, molden_file)
def HFenergy(row):
psi4.set_memory('500 MB')
#charge = +1, spin multipicity = 2
h2o = psi4.geometry("""
1 2
O {} {} {}
C {} {} {}
H {} {} {}
H {} {} {}
""".format(*row))
psi4.set_options({'reference': 'uhf'})
#Energy calculated using UHF/cc-pVDZ
try:
return psi4.energy('scf/cc-pvdz')
except: #In case there's a convergence error or alike
return 0.0
def test_dft_grid_threaded_raise():
dimer = psi4.geometry("""
1 1
K -4.067042 -1.894214 0.002270
""")
psi4.set_options({
"dft_grid_name": "SG1",
"dft_vv10_radial_points": 50,
"dft_vv10_spherical_points": 194,
"dft_nuclear_scheme": "treutler",
"dft_radial_scheme": "EM",
"basis": "def2-TZVPPD",
})
with pytest.raises(RuntimeError) as e:
ene = psi4.energy("wB97M-V")
assert "There is no SG-1 grid defined for the requested atomic number" in str(e.value)
def test_psi4_dfmp2():
"""dfmp2-1"""
#! Density fitted MP2 cc-PVDZ/cc-pVDZ-RI computation of formic acid dimer binding energy
#! using automatic counterpoise correction. Monomers are specified using Cartesian coordinates.
Enuc = 235.94662124
Ecp = -0.0224119246
formic_dim = psi4.geometry("""
0 1
C -1.888896 -0.179692 0.000000
O -1.493280 1.073689 0.000000
O -1.170435 -1.166590 0.000000
H -2.979488 -0.258829 0.000000
H -0.498833 1.107195 0.000000
--
0 1
C 1.888896 0.179692 0.000000
O 1.493280 -1.073689 0.000000
O 1.170435 1.166590 0.000000
H 2.979488 0.258829 0.000000
H 0.498833 -1.107195 0.000000
units angstrom
no_reorient
""")
psi4.set_options({
'basis': 'cc-pvdz',
'df_basis_scf': 'cc-pvdz-jkfit',
'df_basis_mp2': 'cc-pvdz-ri',
# not necessary to specify df_basis* for most basis sets
'scf_type': 'df',
'guess': 'sad',
'd_convergence': 11,
})
e_cp = psi4.energy('mp2', bsse_type='cp')
assert psi4.compare_values(Enuc, formic_dim.nuclear_repulsion_energy(), 7,
"Nuclear Repulsion Energy")
assert psi4.compare_values(Ecp, e_cp, 5,
"CP Corrected cc-pVDZ/cc-pVDZ-RI DFMP2")
def test_pao_H8():
"""PAO-CCSD Test"""
# Psi4 Setup
psi4.set_memory('1 GB')
psi4.core.set_output_file('output.dat', False)
psi4.set_options({'basis': 'DZ',
'scf_type': 'pk',
'guess': 'core',
'mp2_type': 'conv',
'freeze_core': 'False',
'e_convergence': 1e-12,
'd_convergence': 1e-12,
'r_convergence': 1e-12,
'diis': 8})
mol = psi4.geometry("""
H 0.000000 0.000000 0.000000
H 0.750000 0.000000 0.000000
H 0.000000 1.500000 0.000000
H 0.375000 1.500000 -0.649520
H 0.000000 3.000000 0.000000
H -0.375000 3.000000 -0.649520
H 0.000000 4.500000 -0.000000
H -0.750000 4.500000 -0.000000
symmetry c1
noreorient
nocom
""")
rhf_e, rhf_wfn = psi4.energy('SCF', return_wfn=True)
maxiter = 75
e_conv = 1e-12
r_conv = 1e-12
max_diis = 8
ccsd = pycc.ccwfn(rhf_wfn, local='PAO', local_cutoff=2e-2)
eccsd = ccsd.solve_cc(e_conv, r_conv, maxiter, max_diis)
# (H2)_4 REFERENCE:
psi3_ref = -0.108914240219735
assert (abs(psi3_ref - eccsd) < 1e-7)
def _run_init(self):
"Solve unperturbed SCF equations"
for frag in self._frags:
frag.set_point_group(psi4.core.PointGroup('c1'))
frag.reset_point_group('c1')
frag.fix_orientation(True)
frag.print_out()
en, wfn = psi4.energy('scf', return_wfn=True, molecule=frag)
bfs = wfn.basisset()
assert bfs.nbf() <= MAX_NBF, " Maximum number of basis functions %d exceeded!" % MAX_NBF
mints = psi4.core.MintsHelper(bfs)
jk = psi4.core.JK.build(bfs, jk_type="Direct")
jk.set_memory(int(5e8)) # 4GB
jk.initialize()
X = self._orthogonalizer(numpy.asarray(wfn.S()))
eps = numpy.asarray(wfn.epsilon_a())
C = numpy.asarray(wfn.Ca())
Co = numpy.asarray(wfn.Ca_subset("AO","OCC"))
H = numpy.asarray(wfn.H())
F = numpy.asarray(wfn.Fa())
D = numpy.asarray(wfn.Da())
#
self._ens .append(en) # Total energy of a fragment
self._ndocc.append(wfn.nalpha()) # number of doubly-occupied MO's
self._nbfs .append(bfs.nbf()) # number of basis functions
self._bfs .append(bfs) # basis set
self._mints.append(mints) # Integral calculator
self._jks .append(jk) # JK calculator
self._Xs .append(X) # AO orthogonalizer (S^-1/2)
self._eps .append(eps) # Eigenvalues of Fock matrix
self._Cs .append(Co) # LCAO-MO coefficients (occ)
self._Csall.append(C) # LCAO-MO coefficients (occ+vir)
self._H .append(H) # Hcore matrix in original basis
self._Hs .append(H) # Effective Hcore matrix in original basis
self._Fs .append(F) # Fock matrix in original basis
self._Ds .append(D) # One-particle density matrix in original basis
self._wfn .append(wfn) # SCF wavefunction object
# compute interfragment nuclear repulsion energy
self.enuc = self._interfragmentNuclearRepulsionEnergy()
#
self.en_0 = None
return
def test_restricted_TDA_triplet_c1():
"Build out the full CIS/TDA hamiltonian (A) col by col with the product engine"
h2o = psi4.geometry("""
O
H 1 0.96
H 1 0.96 2 104.5
symmetry c1
""")
psi4.set_options({"scf_type": "pk", 'save_jk': True})
e, wfn = psi4.energy("hf/cc-pvdz", molecule=h2o, return_wfn=True)
A_ref, _ = build_RHF_AB_C1_triplet(wfn)
ni, na, _, _ = A_ref.shape
nia = ni * na
A_ref = A_ref.reshape((nia, nia))
# Build engine
eng = TDRSCFEngine(wfn, ptype='tda', triplet=True)
# our "guess"" vectors
ID = [psi4.core.Matrix.from_array(v.reshape((ni, na))) for v in tuple(np.eye(nia).T)]
A_test = np.column_stack([x.to_array().flatten() for x in eng.compute_products(ID)[0]])
assert compare_arrays(A_ref, A_test, 8, "RHF Ax C1 products")
def psi4_scf(params, geometries):
"""
Function to run SCF along IRC using PSI4, returns array of energies at each geometry.
"""
print_header(params.outfile)
energies = []
wavefunctions = []
count = 0
start = time.time()
level_of_theory = "%s/%s" % (params.method, params.basis)
if (params.do_solvent):
set_solvent_parameters(params)
for geometry in geometries:
output = open(params.outfile, "a")
psi4.core.set_output_file("psi4_output/irc_%d.out" % count, False)
geom = geometry
geom += "\nsymmetry c1"
mol = psi4.geometry(geom)
psi4.set_options(params.keywords)
#print("pyREX:Single Point Calculation on IRC Point %d" %(count))
psi4.set_num_threads(params.nthreads)
if (params.set_memory):
psi4.set_memory(params.memory_allocation)
energy, wfn = psi4.energy(level_of_theory, return_wfn=True)
#wfn = psi4.core.Wavefunction.build(mol, self.basis)
ndocc = wfn.doccpi()[0]
#print(ndocc)
eps = np.array(wfn.epsilon_a())
#print(eps)
homo_energy = eps[ndocc - 1]
lumo_energy = eps[ndocc]
energies.append(energy)
wavefunctions.append(wfn)
output.write('{:>20.2f} {:>20.4f} {:>20.4f} {:>20.4f}\n'.format(
params.coordinates[count], energy, homo_energy, lumo_energy))
count = count + 1
output.close()
print_footer(params.outfile)
end = time.time()
print("psi4 Time = %f" % (end - start))
return energies, wavefunctions
def test_unrestricted_TDA_C1():
ch2 = psi4.geometry("""
0 3
c
h 1 1.0
h 1 1.0 2 125.0
symmetry c1
""")
psi4.set_options({"scf_type": "pk", 'reference': 'UHF', 'save_jk': True})
e, wfn = psi4.energy("hf/cc-pvdz", molecule=ch2, return_wfn=True)
A_ref, B_ref = build_UHF_AB_C1(wfn)
nI, nA, _, _ = A_ref['IAJB'].shape
nIA = nI * nA
ni, na, _, _ = A_ref['iajb'].shape
nia = ni * na
eng = TDUSCFEngine(wfn, ptype='tda')
X_jb = [psi4.core.Matrix.from_array(v.reshape((ni, na))) for v in tuple(np.eye(nia).T)]
zero_jb = [psi4.core.Matrix(ni, na) for x in range(nIA)]
X_JB = [psi4.core.Matrix.from_array(v.reshape((nI, nA))) for v in tuple(np.eye(nIA).T)]
zero_JB = [psi4.core.Matrix(nI, nA) for x in range(nia)]
# Guess Identity:
# X_I0 X_0I = X_I0 X_0I
# [ I{nOV x nOV} | 0{nOV x nov}] = [ X{KC,JB} | 0{KC, jb}]
# [ 0{nov x nOV} | I{nov x nov}] [ 0{kc,JB} | X{kc, jb}]
# Products:
# [ A{IA, KC} A{IA, kc}] [ I{KC, JB} | 0{KC,jb}] = [A x X_I0] = [ A_IAJB, A_iaJB]
# [ A{ia, KC} A{ia, kc}] [ O{kc, JB} | X{kc,jb}] [A x X_0I] = [ A_IAjb, A_iajb]
X_I0 = [[x, zero] for x, zero in zip(X_JB, zero_jb)]
X_0I = [[zero, x] for zero, x in zip(zero_JB, X_jb)]
Ax_I0 = eng.compute_products(X_I0)[0]
Ax_0I = eng.compute_products(X_0I)[0]
A_IAJB_test = np.column_stack([x[0].to_array().flatten() for x in Ax_I0])
assert compare_arrays(A_ref['IAJB'].reshape(nIA, nIA), A_IAJB_test, 8, "A_IAJB")
A_iaJB_test = np.column_stack([x[1].to_array().flatten() for x in Ax_I0])
assert compare_arrays(A_ref['iaJB'].reshape(nia, nIA), A_iaJB_test, 8, "A_iaJB")
A_IAjb_test = np.column_stack([x[0].to_array().flatten() for x in Ax_0I])
assert compare_arrays(A_ref['IAjb'].reshape(nIA, nia), A_IAjb_test, 8, "A_IAjb")
A_iajb_test = np.column_stack([x[1].to_array().flatten() for x in Ax_0I])
assert compare_arrays(A_ref['iajb'].reshape(nia, nia), A_iajb_test, 8, "A_iajb")
def FMO1iter(fragList, rmsd):
# create the new wfn objects in the 3rd array posiiton
rmsd = createChargefield(fragList, list(range(len(fragList))), new=True)
for count, i in enumerate(fragList):
fragnums = list(range(len(fragList)))
fragnums.remove(count)
createChargefield(fragList, fragnums)
E, wfn = psi4.energy(theory, return_wfn=True, molecule=fragList[i][0])
fragList[i] += [wfn]
# delete the old wfn objects
for i in fragList:
del fragList[i][1]
# calculate the FMO cluster energy
fragEnergies = []
for i in fragList:
fragEnergies += [fragList[i][1].energy()]
FMOEnergy = np.sum(fragEnergies)
return (FMOEnergy, fragEnergies, rmsd)
def energy(geom, confId, method='HF-3C', **kwargs):
"""
Finds the energy of a given molecule
:param geom: an RDKit.Mol or a string
:param confId: the ID of the conformer to optimize
:param method: the PSI4 method to calculate the H**O and LUMO
:return: wavefunction (energy is available under wavefunction.energy)
"""
try:
geom = make_psi4_geometry(geom, confId)
psi4.activate(geom)
psi4.core.IO.set_default_namespace(str(id(geom)))
psi4.core.set_global_option("MAXITER", 1000)
return psi4.energy(method, return_wfn=True, **kwargs)[1]
except Exception as e:
print(e)
return np.nan
def test_export_ao_elec_dip_deriv():
h2o = psi4.geometry("""
O
H 1 1.0
H 1 1.0 2 101.5
symmetry c1
""")
rhf_e, wfn = psi4.energy('SCF/cc-pVDZ', molecule=h2o, return_wfn=True)
mints = psi4.core.MintsHelper(wfn.basisset())
natoms = h2o.natom()
cart = ['_X', '_Y', '_Z']
D = wfn.Da()
D.add(wfn.Db())
D_np = np.asarray(D)
deriv1_mat = {}
deriv1_np = {}
MU_Gradient = np.zeros((3 * natoms, 3))
for atom in range(natoms):
deriv1_mat["MU_" + str(atom)] = mints.ao_elec_dip_deriv1(atom)
for mu_cart in range(3):
for atom_cart in range(3):
map_key = "MU" + cart[mu_cart] + "_" + str(
atom) + cart[atom_cart]
deriv1_np[map_key] = np.asarray(
deriv1_mat["MU_" + str(atom)][3 * mu_cart + atom_cart])
MU_Gradient[3 * atom + atom_cart,
mu_cart] += np.einsum("uv,uv->",
deriv1_np[map_key], D_np)
PSI4_MU_Grad = mints.dipole_grad(D)
G_python_MU_mat = psi4.core.Matrix.from_array(MU_Gradient)
assert psi4.compare_matrices(PSI4_MU_Grad, G_python_MU_mat, 10,
"DIPOLE_GRADIENT_TEST") # TEST
def test_scsmp2(inp):
"""Formerly known as dfmp2-4"""
h2o = psi4.geometry("""
O
H 1 1.0
H 1 1.0 2 90.0
""")
psi4.set_options({'basis': 'cc-pvdz'})
psi4.set_options(inp['options'])
ene, wfn = psi4.energy(inp['name'], return_wfn=True)
ref_block = _ref_h2o_ccpvdz[inp['options']['mp2_type']]
#ref_corl = ref_block[inp['pv'] + ' CORRELATION ENERGY']
#ref_tot = ref_block[inp['pv'] + ' TOTAL ENERGY']
ref_corl = ref_block['MP2 CORRELATION ENERGY']
ref_tot = ref_block['MP2 TOTAL ENERGY']
ref_custom_corl = ref_block[inp['custom'] + ' CORRELATION ENERGY']
ref_custom_tot = ref_block[inp['custom'] + ' TOTAL ENERGY']
for obj in [psi4.core, wfn]:
for pv in [
'HF TOTAL ENERGY', 'SCF TOTAL ENERGY', 'MP2 SAME-SPIN CORRELATION ENERGY',
'MP2 OPPOSITE-SPIN CORRELATION ENERGY', 'MP2 CORRELATION ENERGY', 'MP2 TOTAL ENERGY',
'SCS-MP2 CORRELATION ENERGY', 'SCS-MP2 TOTAL ENERGY', 'CURRENT REFERENCE ENERGY'
]:
assert compare_values(ref_block[pv], obj.variable(pv), 5, pv)
assert compare_values(ref_custom_corl, obj.variable('CUSTOM SCS-MP2 CORRELATION ENERGY'), 5,
'custom scsmp2 corl')
assert compare_values(ref_custom_tot, obj.variable('CUSTOM SCS-MP2 TOTAL ENERGY'), 5, 'custom scsmp2 ')
assert compare_values(ref_corl, obj.variable('CURRENT CORRELATION ENERGY'), 5, 'current corl')
assert compare_values(ref_tot, obj.variable('CURRENT ENERGY'), 5, 'current')
assert compare_values(ref_tot, ene, 5, 'return')
assert compare_values(ref_tot, wfn.energy(), 5, 'wfn')
def test_aci1():
import math
import psi4
import forte
from forte import forte_options
ref_aci = -75.010199198896
rel_tol = 1e-9
abs_tol = 1e-8
h2o = psi4.geometry("""
O
H 1 0.96
H 1 0.96 2 104.5
""")
psi4.set_options({'basis': "sto-3g"})
E_scf, wfn = psi4.energy('scf', return_wfn=True)
state = forte.StateInfo(na=5, nb=5, multiplicity=1, twice_ms=0, irrep=0)
dim = psi4.core.Dimension([4, 0, 1, 2])
options = psi4.core.get_options()
options.set_current_module('FORTE')
forte_options.update_psi_options(options)
forte.startup()
forte.banner()
mo_space_info = forte.make_mo_space_info(wfn, forte_options)
ints = forte.make_forte_integrals(wfn, options, mo_space_info)
scf_info = forte.SCFInfo(wfn)
solver = forte.make_active_space_solver('ACI', state, scf_info,
mo_space_info, ints, forte_options)
energy = solver.compute_energy()
assert math.isclose(energy, ref_aci, abs_tol=abs_tol, rel_tol=rel_tol)
print("\n\nACI Energy = {}".format(energy))
forte.cleanup()
def test_weird_basis(subject, bas, ans, mols, request):
"""non-consecutive angular momentum basis set patterns"""
mol = mols[subject]
ref = "rhf" if mol.multiplicity() == 1 else "uhf"
psi4.set_options({
"reference": ref,
"guess": "core",
"scf_type": "pk",
"df_scf_guess": "false",
"basis": "anonymous1234",
})
def basisspec_psi4_yo__anonymous1234(mol, role):
mol.set_basis_all_atoms("test", role=role)
return {"test": bas}
psi4.driver.qcdb.libmintsbasisset.basishorde[
"ANONYMOUS1234"] = basisspec_psi4_yo__anonymous1234
ene = psi4.energy("scf", molecule=mol)
assert compare_values(ans, ene, 6, request.node.name)
def CISD(ISE=False):
print('\n --------- CASCI STARTED --------- \n')
# Number of molecular orbitals is determined from the size of One-electron integral
scf_e, wfn = psi4.energy('scf', return_wfn=True)
nelec = wfn.nalpha() + wfn.nbeta()
C = wfn.Ca()
ndocc = wfn.doccpi()[0]
nmo = wfn.nmo()
nvir = nmo - ndocc
eps = np.asarray(wfn.epsilon_a())
nbf = C.shape[0]
Vnuc = wfn.molecule().nuclear_repulsion_energy()
print("Number of Electrons: {}".format(nelec))
print("Number of Basis Functions: {}".format(nbf))
print("Number of Molecular Orbitals: {}".format(nmo))
print("Number of Doubly ocuppied MOs: {}\n".format(ndocc))
# Build integrals from Psi4 MINTS
print("Converting atomic integrals to MO integrals...")
t = time.time()
mints = psi4.core.MintsHelper(wfn.basisset())
ERI = np.asarray(mints.mo_eri(C, C, C, C))
OEI = np.asarray(mints.ao_kinetic()) + np.asarray(mints.ao_potential())
OEI = np.einsum('up,vq,uv->pq', C, C, OEI)
print("Completed in {} seconds!".format(time.time() - t))
Ecas, Ccas, ref, determinants = compute(OEI,
ERI,
nelec,
ndocc,
nvir,
verb=True,
ISE=ISE)
print('Final CISD energy: {:<15.10f}'.format(Ecas + Vnuc))
def test_fcidump_scf_energy():
"""Compare FCIDUMP computed SCF energy against call to energy()"""
Ne = psi4.geometry("""
Ne 0 0 0
""")
psi4.set_options({
'basis': 'cc-pVDZ',
'scf_type': 'pk',
'reference': 'uhf',
'd_convergence': 1e-8,
'e_convergence': 1e-8
})
scf_e, scf_wfn = psi4.energy('scf', return_wfn=True)
psi4.fcidump(scf_wfn, fname='FCIDUMP_SCF', oe_ints=['EIGENVALUES'])
intdump = psi4.fcidump_from_file('FCIDUMP_SCF')
e_dict = psi4.energies_from_fcidump(intdump)
fcidump_e = e_dict['SCF TOTAL ENERGY']
assert psi4.compare_values(scf_e, fcidump_e, 5, 'SCF energy') #TEST
def test_mcmurchie_davidson_multipoles_gradient(mol_h2o):
psi4.set_options({'basis': 'cc-pvdz'})
_, wfn = psi4.energy('HF', molecule=mol_h2o, return_wfn=True)
order = 8
ints_grad = fdiff_multipole_integral(mol_h2o,
'cc-pvdz', [1.0, 2.0, 3.0],
order=order)
nmul = cumulative_cart_dim(order) - 1
grad_fdiff = np.einsum('ncmij,ij->ncm', ints_grad,
wfn.Da().np).reshape(-1, nmul)
mints = psi4.core.MintsHelper(wfn.basisset())
# test against finite differences
grad = mints.multipole_grad(D=wfn.Da(),
order=order,
origin=[1.0, 2.0, 3.0])
np.testing.assert_allclose(grad_fdiff, grad.np, atol=1e-8)
# test that we get the same result from the 'hard-wired' dipole_grad
grad_dip = mints.dipole_grad(wfn.Da())
grad = mints.multipole_grad(D=wfn.Da(), order=1, origin=[0.0, 0.0, 0.0])
np.testing.assert_allclose(grad_dip.np, grad.np, atol=1e-14)
def test_scf(mol_str):
basis = 'sto-3g'
molecule = quest.Molecule(quest.mollib[mol_str], basis)
rhf_options = \
{
'e_conv': 1.e-8,
'd_conv': 1.e-8,
'diis': True,
'max_diis': 7,
'max_iter': 100,
}
wfn = quest.Wavefunction(molecule, rhf_options)
# Compute RHF
scf_energy = quest.scf_module.compute_rhf(wfn)
psi4.set_options({"scf_type": "pk"})
ref_energy = psi4.energy("SCF" + "/" + basis, molecule=molecule.mol)
assert np.allclose(ref_energy, scf_energy)
def test_pe_adc1():
"""LR-PE-ADC(1)/sto-3g formaldehyde in presence of 6 water molecules
cross-reference against PE-CIS from Psi4 itself"""
mol = psi4.geometry(__geoms['formaldehyde'])
potfile = _dump_potential('pna_6w')
psi4.set_options({
'basis': 'sto-3g',
'pe': True,
'scf_type': 'pk',
'pe__potfile': potfile,
'roots_per_irrep': [5],
'qc_module': 'adcc',
'tdscf_states': 5,
'tdscf_tda': True,
})
_, wfn_tdhf = psi4.energy('td-hf', return_wfn=True)
_, wfn_adc = psi4.properties('adc(1)', properties=["oscillator_strength", "dipole"], environment='linear_response', return_wfn=True)
for i in range(5):
assert compare_values(wfn_tdhf.variable(f'TD-HF ROOT 0 -> ROOT {i+1} EXCITATION ENERGY'),
wfn_adc.variable(f'ADC ROOT 0 -> ROOT {i+1} EXCITATION ENERGY'),
5, f"PE-ADC(1) Excitation Energy Root {i+1}")
def test_mp2(mol_str):
mol_str = quest.mollib[mol_str]
basis = "sto-3g"
rhf_options = \
{
'e_conv': 1.e-8,
'd_conv': 1.e-8,
'diis': True,
'max_diis': 7,
'max_iter': 100,
}
molecule = quest.Molecule(mol_str, basis)
wfn = quest.Wavefunction(molecule, rhf_options)
scf_energy = quest.scf_module.compute_rhf(wfn)
mp2_energy = quest.mp2.mp2(wfn)
psi4.set_options({"scf_type": "pk", "mp2_type": "conv"})
ref_energy = psi4.energy("MP2" + "/" + basis, molecule=molecule.mol)
assert np.allclose(mp2_energy, ref_energy)