def test_nonstationary_hessian_hooh():
mol = psi4.geometry("""
0 1
H 0.90 0.77 0.46
O 0.10 0.68 -0.02
O -0.10 -0.68 -0.02
H -0.90 -0.77 0.46
""")
mol.update_geometry()
Natom = mol.natom()
psi4_options = {"basis": "cc-pvdz", "scf_type": "pk"}
psi4.set_options(psi4_options)
xyz = mol.geometry().to_array()
coords = [
stre.Stre(0, 1),
stre.Stre(2, 3),
bend.Bend(0, 1, 2),
bend.Bend(1, 2, 3),
tors.Tors(0, 1, 2, 3)
]
Z = [mol.Z(i) for i in range(0, Natom)]
masses = [mol.mass(i) for i in range(0, Natom)]
f1 = optking.frag.Frag(Z, xyz, masses, intcos=coords, frozen=False)
OptMol = optking.molsys.Molsys([f1])
grad_x = psi4.gradient("hf").to_array().flatten()
H_xy = psi4.hessian("hf").to_array()
grad_q = OptMol.gradient_to_internals(grad_x)
H_q = OptMol.hessian_to_internals(H_xy, grad_x)
H_xy2 = OptMol.hessian_to_cartesians(H_q, grad_q)
H_q2 = OptMol.hessian_to_internals(H_xy2, grad_x)
assert psi4.compare_values(H_q, H_q2, 7,
"Diff hessian cart->INT->cart->INT")
def test_stationary_hessian_hooh():
mol = psi4.geometry("""
0 1
H 0.9047154509 0.7748902860 0.4679224940
O 0.1020360382 0.6887430144 -0.0294829672
O -0.1020360382 -0.6887430144 -0.0294829672
H -0.9047154509 -0.7748902860 0.4679224940
""")
mol.update_geometry()
Natom = mol.natom()
psi4_options = {"basis": "cc-pvdz", "scf_type": "pk"}
psi4.set_options(psi4_options)
xyz = mol.geometry().to_array()
coords = [
stre.Stre(0, 1),
stre.Stre(2, 3),
bend.Bend(0, 1, 2),
bend.Bend(1, 2, 3),
tors.Tors(0, 1, 2, 3)
]
Z = [mol.Z(i) for i in range(0, Natom)]
masses = [mol.mass(i) for i in range(0, Natom)]
f1 = optking.frag.Frag(Z, xyz, masses, intcos=coords, frozen=False)
OptMol = optking.molsys.Molsys([f1])
H_xy = psi4.hessian("hf").to_array()
H_q = OptMol.hessian_to_internals(H_xy, useMasses=False)
H_xy2 = OptMol.hessian_to_cartesians(H_q)
H_q2 = OptMol.hessian_to_internals(H_xy2, useMasses=False)
assert psi4.compare_values(H_q, H_q2, 7,
"Diff hessian cart->INT->cart->INT")
def test_nonstationary_forces_h2o():
mol = psi4.geometry("""
0 1
O 0.0 -0.00 0.00
H 0.0 -0.75 0.58
H 0.0 0.75 0.58
unit Angstrom
""")
psi4_options = {"basis": "cc-pvdz", "scf_type": "pk"}
psi4.set_options(psi4_options)
mol.update_geometry()
Natom = mol.natom()
xyz = mol.geometry().to_array()
coords = [stre.Stre(0, 1), stre.Stre(0, 2), bend.Bend(0, 1, 2)]
Z = [mol.Z(i) for i in range(0, Natom)]
masses = [mol.mass(i) for i in range(0, Natom)]
f1 = optking.frag.Frag(Z, xyz, masses, intcos=coords, frozen=False)
OptMol = optking.molsys.Molsys([f1])
grad_x = psi4.gradient("hf").to_array()
grad_q = OptMol.gradient_to_internals(grad_x.flatten(), useMasses=False)
grad_x2 = OptMol.gradient_to_cartesians(grad_q).reshape(Natom, 3)
grad_x2 = psi4.core.Matrix.from_array(grad_x2)
assert psi4.compare_values(grad_x, grad_x2, 10,
"Diff grad. CART->int->CART")
grad_q = OptMol.gradient_to_internals(grad_x.flatten(), useMasses=True)
grad_x2 = OptMol.gradient_to_cartesians(grad_q).reshape(Natom, 3)
grad_x2 = psi4.core.Matrix.from_array(grad_x2)
assert psi4.compare_values(grad_x, grad_x2, 10,
"Diff grad. CART->int->CART with u=1/mass")
def test_stationary_forces_h2o():
mol = psi4.geometry("""
0 1
O 0.0000000000 -0.0000000000 0.0025968676
H 0.0000000000 -0.7487897072 0.5811909492
H -0.0000000000 0.7487897072 0.5811909492
unit Angstrom
""")
psi4_options = {"basis": "cc-pvdz", "scf_type": "pk"}
psi4.set_options(psi4_options)
mol.update_geometry()
Natom = mol.natom()
xyz = mol.geometry().to_array()
# Make an optking molecule manually, and you can choose your specific
# desired internal coordinates.
coords = [
stre.Stre(0, 1), # from-zero indexed atoms in geometry
stre.Stre(0, 2),
bend.Bend(0, 1, 2),
]
Z = [mol.Z(i) for i in range(0, Natom)]
masses = [mol.mass(i) for i in range(0, Natom)]
f1 = optking.frag.Frag(Z, xyz, masses, intcos=coords, frozen=False)
OptMol = optking.molsys.Molsys([f1])
#psi4.core.print_out(str(OptMol))
grad_x = psi4.gradient("hf") # returns an (N,3) psi4 matrix
#rms = grad_x.rms()
# Print gradient as psi4 matrix.
#psi4.core.print_out(f"Cartesian Gradient (RMS={rms:.3e})\n")
#grad_x.print_out()
# Print gradient as numpy array.
#print(f"Cartesian Gradient (RMS={rms:.3e})")
#print(grad_x.to_array())
grad_x = grad_x.to_array()
grad_q = OptMol.gradient_to_internals(grad_x.flatten(),
useMasses=False) # returns ndarray
grad_x2 = OptMol.gradient_to_cartesians(grad_q).reshape(Natom, 3)
grad_x2 = psi4.core.Matrix.from_array(grad_x2)
#psi4.core.print_out("Internal Coordinate Gradient:\n"+str(grad_q)+"\n")
#rms = grad_x2.rms()
#psi4.core.print_out(f"Cartesian Gradient (RMS={rms:.3e})\n")
#grad_x2.print_out()
#print(f"Cartesian Gradient (RMS={rms:.3e})")
#print(grad_x2.to_array())
#rms_diff = np.sqrt(np.mean((grad_x - grad_x2)**2))
#print(f"RMS diff gradient, cart->int->cart: {rms_diff:8.4e}")
assert psi4.compare_values(grad_x, grad_x2, 10,
"Diff grad. CART->int->CART")
grad_q = OptMol.gradient_to_internals(grad_x.flatten(), useMasses=True)
grad_x2 = OptMol.gradient_to_cartesians(grad_q).reshape(Natom, 3)
grad_x2 = psi4.core.Matrix.from_array(grad_x2)
assert psi4.compare_values(grad_x, grad_x2, 10,
"Diff grad. CART->int->CART with u=1/mass")
def test_stationary_forces_hooh():
mol = psi4.geometry("""
0 1
H 0.9047154509 0.7748902860 0.4679224940
O 0.1020360382 0.6887430144 -0.0294829672
O -0.1020360382 -0.6887430144 -0.0294829672
H -0.9047154509 -0.7748902860 0.4679224940
""")
mol.update_geometry()
psi4_options = {"basis": "cc-pvdz", "scf_type": "pk"}
psi4.set_options(psi4_options)
xyz = mol.geometry().to_array()
Natom = mol.natom()
coords = [
stre.Stre(0, 1),
stre.Stre(2, 3),
bend.Bend(0, 1, 2),
bend.Bend(1, 2, 3),
tors.Tors(0, 1, 2, 3)
]
Z = [mol.Z(i) for i in range(0, Natom)]
masses = [mol.mass(i) for i in range(0, Natom)]
f1 = optking.frag.Frag(Z, xyz, masses, intcos=coords, frozen=False)
OptMol = optking.molsys.Molsys([f1])
grad_x = psi4.gradient("hf").to_array()
grad_q = OptMol.gradient_to_internals(grad_x.flatten(), useMasses=False)
grad_x2 = OptMol.gradient_to_cartesians(grad_q).reshape(Natom, 3)
assert psi4.compare_values(grad_x, grad_x2, 8,
"Diff grad. CART->int->CART")
grad_q = OptMol.gradient_to_internals(grad_x.flatten(), useMasses=True)
grad_x2 = OptMol.gradient_to_cartesians(grad_q).reshape(Natom, 3)
assert psi4.compare_values(grad_x, grad_x2, 8,
"Diff grad. CART->int->CART with u=1/mass")
def test_stationary_hessian_h2o():
mol = psi4.geometry("""
0 1
O 0.0000000000 -0.0000000000 0.0025968676
H 0.0000000000 -0.7487897072 0.5811909492
H -0.0000000000 0.7487897072 0.5811909492
unit Angstrom
""")
psi4_options = {"basis": "cc-pvdz", "scf_type": "pk"}
psi4.set_options(psi4_options)
mol.update_geometry()
Natom = mol.natom()
xyz = mol.geometry().to_array()
coords = [
stre.Stre(0, 1),
stre.Stre(0, 2),
bend.Bend(0, 1, 2),
]
Z = [mol.Z(i) for i in range(0, Natom)]
masses = [mol.mass(i) for i in range(0, Natom)]
f1 = optking.frag.Frag(Z, xyz, masses, intcos=coords, frozen=False)
OptMol = optking.molsys.Molsys([f1])
# Compute the Cartesian Hessian with psi4
H_xy = psi4.hessian("hf") # returns a (3N,3N) psi4 matrix
#psi4.core.print_out("Calculated Cartesian hessian\n")
#H_xy.print_out()
# Transform hessian to internals with optking
H_q = OptMol.hessian_to_internals(H_xy.to_array()) #returns ndarray
#psi4.core.print_out(f"Hessian transformed into internal coordinates\n")
#psi4.core.Matrix.from_array(H_q).print_out()
## Transform hessian to Cartesians with optking
H_xy2 = OptMol.hessian_to_cartesians(H_q) # returns ndarray
#print("Hessian transformed back into Cartesian coordinates")
#print(H_xy2)
assert psi4.compare_values(H_xy, H_xy2, 7, "Diff hessian CART->int->CART")
H_q = OptMol.hessian_to_internals(H_xy.to_array(), useMasses=True)
H_xy2 = OptMol.hessian_to_cartesians(H_q)
assert psi4.compare_values(H_xy, H_xy2, 7,
"Diff hessian CART->int->CART with u=1/mass")
psi4.set_options(psi4_options)
# Optimize and extract information, inc. final geometry
json_output = optking.optimize_psi4('MP2')
E = json_output['energies'][-1]
print(f"Optimized Energy: {E}")
xyz_array = np.array(json_output['final_molecule']['geometry'])
xyz = xyz_array.reshape(mol.natom(), 3)
mol.set_geometry(psi4.core.Matrix.from_array(xyz))
optking.optparams.Params = optking.optparams.OptParams({})
from optking import stre, bend, tors
bonds = [stre.Stre(*bond) for bond in bonds]
angles = [bend.Bend(*angle) for angle in angles]
dihedrals = [tors.Tors(*dihedral) for dihedral in dihedrals]
coords = bonds + angles + dihedrals
psi4.set_options(psi4_options)
Z = [mol.Z(i) for i in range(0, mol.natom())]
masses = [mol.mass(i) for i in range(0, mol.natom())]
f1 = optking.frag.Frag(Z, xyz, masses, intcos=coords, frozen=False)
OptMol = optking.molsys.Molsys([f1])
print(OptMol)
# Compute the Cartesian Hessian with psi4
Hxyz = psi4.hessian('MP2') # returns a psi4 matrix
print("Cartesian hessian")
print(Hxyz.to_array())