def test_water_631ppgss():
mol = Molecule(geometry=water, basis='6-31ppgss')
mol.RHF()
#p 6D int=acc2e=14 scf(conver=12) rhf/6-31++G** symmetry=none
assert_allclose(mol.energy.real, -75.9924381487, atol=1e-12)
ref_dipole = np.array([0.0, 2.4046, 0.0])
assert_allclose(mol.mu, ref_dipole, atol=1e-4)
def test_mp2_spinorbital():
helium_dimer = """
0 1
He 0.0 0.0 0.0
He 0.0 0.0 0.75
"""
# init molecule and build integrals
mol = Molecule(geometry=helium_dimer,basis='cc-pvDZ')
# do the SCF
mol.RHF()
# do MP2
PostSCF(mol).MP2()
emp2_spatial = mol.emp2.real
PostSCF(mol).MP2(spin_orbital=True)
emp2_spin = mol.emp2.real
# consistency check
assert np.allclose(emp2_spatial,emp2_spin)
# G16 reference SCF energy
assert np.allclose(-5.29648041091,mol.energy.real)
# G16 reference MP2 energy
assert np.allclose(-5.3545864180140,emp2_spatial)
def test_formaldehyde_sto3g():
mol = Molecule(geometry=formaldehyde, basis='sto-3g')
mol.RHF()
#p 6D int=acc2e=14 scf(conver=12) rhf/6-31++G** symmetry=none
assert_allclose(mol.energy.real, -112.351590112, atol=1e-12)
ref_dipole = np.array([0.0, 0.0, -1.4821])
assert_allclose(mol.mu, ref_dipole, atol=1e-4)
def test_hydrogen_sto3g():
mol = Molecule(geometry=hydrogen, basis='sto-3g')
mol.RHF()
assert_allclose(mol.energy.real, -1.11675930740, atol=1e-12)
mol.forces()
ref_forces = np.array([[0.000000000, -0.000000000, -0.027679601],
[-0.000000000, 0.000000000, 0.027679601]])
assert_allclose(mol._forces, ref_forces, atol=1e-12)
def test_tdhf():
water = """
0 1
O 0.000000 -0.075791844 0.000000
H 0.866811829 0.601435779 0.000000
H -0.866811829 0.601435779 0.000000
"""
# init molecule and build integrals
mol = Molecule(geometry=water, basis='sto-3g')
# do the SCF
mol.RHF()
# now do TDHF
PostSCF(mol).TDHF()
# G16 reference UTDHF excitation energies (full; no FC, 50-50, nosym)
# note I have manually expanded triplets in G16 to the full degeneracy
# because at this moment we don't handle spin conserved excitations
'''
# td(nstates=100,50-50,full) nosymm uhf/sto-3g int=acc2e=14
test
0 1
O 0.000000 -0.075791844 0.000000
H 0.866811829 0.601435779 0.000000
H -0.866811829 0.601435779 0.000000
'''
gau_ref = [7.7597,7.7597,7.7597,8.1564,8.1564,8.1564,9.5955,9.5955,9.5955,\
9.6540]
assert np.allclose(np.asarray(gau_ref), mol.tdhf_omega[:10])
ref_omega = mol.tdhf_omega
# check consistency in solution algorithms for TDHF
PostSCF(mol).TDHF(alg='reduced')
assert np.allclose(mol.tdhf_omega, ref_omega)
PostSCF(mol).TDHF(alg='full')
assert np.allclose(mol.tdhf_omega, ref_omega)
def test_Mag4_trivial(self):
mol = Molecule(geometry=hydrogen, basis='sto-3g')
rt = RealTime(mol,
numsteps=100,
stepsize=0.2,
field=0.0001,
pulse=None)
initial_energy = rt.mol.energy.real
rt.Magnus4(direction='z')
np.testing.assert_allclose(initial_energy * np.ones_like(rt.Energy),
rt.Energy)
def test_fci():
water = """
0 1
O 0.000000 -0.075791844 0.000000
H 0.866811829 0.601435779 0.000000
H -0.866811829 0.601435779 0.000000
"""
# init molecule and build integrals
mol = Molecule(geometry=water, basis='sto-3g')
# do the SCF
mol.RHF()
# now do FCI
PostSCF(mol).FCI()
# Psi4 reference SCF energy
assert np.allclose(-74.9420798986, mol.energy.real)
# Psi4 reference FCI energy
assert np.allclose(-75.0129801827, mol.efci.real)
def test_cisd():
water = """
0 1
O 0.000000 -0.075791844 0.000000
H 0.866811829 0.601435779 0.000000
H -0.866811829 0.601435779 0.000000
"""
# init molecule and build integrals
mol = Molecule(geometry=water, basis='sto-3g')
# do the SCF
mol.RHF()
# now do FCI
PostSCF(mol).CISD()
# G16 reference SCF energy
assert np.allclose(-74.9420799245, mol.energy.real)
# G16 reference CISD energy
assert np.allclose(-75.011223006, mol.ecisd.real)
def test_cis():
water = """
0 1
O 0.000000 -0.075791844 0.000000
H 0.866811829 0.601435779 0.000000
H -0.866811829 0.601435779 0.000000
"""
# init molecule and build integrals
mol = Molecule(geometry=water, basis='3-21G')
# do the SCF
mol.RHF()
# now do FCI
PostSCF(mol).CIS()
# G16 reference UCIS excitation energies (full; no FC, 50-50, nosym)
# note I have manually expanded triplets in G16 to the full degeneracy
# because at this moment we don't handle spin conserved excitations
'''
#p cis(nstate=40,full) uhf/3-21G int=acc2e=14 nosymm
water
0 1
O 0.000000 -0.075791844 0.000000
H 0.866811829 0.601435779 0.000000
H -0.866811829 0.601435779 0.000000
'''
gau_ref = [6.5822,6.5822,6.5822,7.7597,7.8156,7.8156,7.8156,8.4377,8.4377, \
8.4377, 9.0903,9.0903,9.0903,9.3334,10.5493]
assert np.allclose(np.asarray(gau_ref), mol.cis_omega[:15])
def test_methane_sto3g():
mol = Molecule(geometry=methane, basis='sto-3g')
mol.RHF(direct=True)
assert_allclose(mol.energy.real, -39.726850324347, atol=1e-12)
# Simple example of Born-Oppenheimer Molecular Dynamics # using minimal basis H2. Shows how you can chain together # routines to create more complex programs. This runs about # a a half of a femtosecond of molecular dynamics and plots # energy as a function of time # Molecular geometry input h2 = """ 0 1 H 0.0 0.0 0.74 H 0.0 0.0 0.00 """ # init molecule and build integrals mol = Molecule(geometry=h2,basis='sto-3g') mol.build() # do the SCF, compute initial forces on the atoms mol.RHF() mol.forces() # BOMD parameters dt = 5 # time step steps = 100 # number steps # saved lists for plotting data X = [] Y = [] Z = [] E = []
def test_water_321g():
mol = Molecule(geometry=water, basis='3-21g')
mol.RHF()
assert_allclose(mol.energy.real, -75.5613125965, atol=1e-12)
import numpy as np
from mmd.molecule import Molecule
from mmd.realtime import RealTime
from mmd.utils.spectrum import genSpectra
hydrogen = """
0 1
H 0.0 0.0 0.0
H 0.0 0.0 0.74
"""
# init molecule and build integrals
mol = Molecule(geometry=hydrogen, basis='3-21G')
# do the SCF
mol.RHF()
# define the applied field envelope as a function of time
# here, is is a narrow gaussian envelope centered at t = 0.
def gaussian(t):
return np.exp(-50 * (t**2))
# create realtime object, setting parameters and pulse envelopes
rt = RealTime(mol, numsteps=1000, stepsize=0.05, field=0.0001, pulse=gaussian)
# propagate with Magnus2
rt.Magnus2(direction='z')
m2 = rt.dipole
def test_helium_ccpvtz():
mol = Molecule(geometry=helium, basis='cc-pvtz')
mol.RHF()
assert_allclose(mol.energy.real, -2.86115357403, atol=1e-12)
from mmd.molecule import Molecule from mmd.postscf import PostSCF water = """ 0 1 O 0.000000 -0.075791844 0.000000 H 0.866811829 0.601435779 0.000000 H -0.866811829 0.601435779 0.000000 """ # init molecule and build integrals mol = Molecule(geometry=water, basis='sto-3g') # do the SCF mol.RHF() # do MP2 PostSCF(mol).MP2()
def test_water_DZ():
mol = Molecule(geometry=water, basis='DZ')
mol.RHF()
assert_allclose(mol.energy.real, -75.977878975377, atol=1e-12)
ref_dipole = np.array([0.0, 2.7222, 0.0])
assert_allclose(mol.mu, ref_dipole, atol=1e-4)
from mmd.molecule import Molecule
from mmd.realtime import RealTime
hydrogen = """
0 1
H 0.0 0.0 0.0
H 0.0 0.0 0.74
"""
# init molecule and build integrals
mol = Molecule(geometry=hydrogen, basis='sto-3g')
# do the SCF
mol.RHF()
# define the applied field envelope as a function of time
# here, is is a gaussian entered at t = 0.
def envelope(t):
gaussian = np.exp(-(t**2))
return gaussian
# create realtime object, setting parameters and pulse envelopes
rt = RealTime(mol, numsteps=100, stepsize=0.2, field=0.0001, pulse=None)
# propagate with Magnus2
rt.Magnus2(direction='z')
m2 = rt.dipole
# propagate with Magnus4
rt.Magnus4(direction='z')
def test_methane_321g():
mol = Molecule(geometry=methane, basis='3-21G')
mol.RHF(direct=False) # we need the two-electron integrals
PostSCF(mol).MP2()
assert_allclose(mol.energy.real, -39.9768654272)
assert_allclose(mol.emp2.real, -40.076963354817)
from mmd.molecule import Molecule
from mmd.postscf import PostSCF
import numpy as np
h2 = """
0 1
H 0.000000000 0.000000000 -0.368652
H 0.000000000 0.000000000 0.368652
"""
# init molecule and build integrals
mol = Molecule(geometry=h2,basis='6-311G**')
# do the SCF
mol.RHF()
# do MP2
PostSCF(mol).MP2()
#print(mol.CAP)
np.savetxt("cap_h2.dat",mol.CAP,'%10.6f',delimiter=" ")
#P_MO = np.real(np.dot(np.transpose(mol.CO),np.dot(mol.P,mol.CO)))
#DEN = np.real(np.dot(np.transpose(mol.CO),np.dot(mol.CAP,mol.CO)))
#print(DEN)
#new = np.real(np.dot(mol.CAP,mol.P))
from mmd.molecule import Molecule from mmd.postscf import PostSCF water = """ 0 1 O 0.000000 -0.075791844 0.000000 H 0.866811829 0.601435779 0.000000 H -0.866811829 0.601435779 0.000000 """ # init molecule and build integrals mol = Molecule(geometry=water, basis='aug-cc-pvdz') # do the SCF mol.RHF() # do MP2 PostSCF(mol).MP2() print(mol.CAP)
def test_water_sto3g():
mol = Molecule(geometry=water, basis='sto-3g')
mol.RHF(conver=1e-14)
assert_allclose(mol.energy.real, -74.942079928192, atol=1e-12)
ref_dipole = np.array([0.0, 1.5340, 0.0])
assert_allclose(mol.mu, ref_dipole, atol=1e-4)
