def test_scf_grad(self):
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol0)).run()
# solvent only
de_cosmo = ddcosmo_grad.kernel(mf.with_solvent, mf.make_rdm1())
self.assertAlmostEqual(lib.fp(de_cosmo), 0.000770107393352652, 6)
# solvent + solute
de = mf.nuc_grad_method().kernel()
self.assertAlmostEqual(lib.fp(de), -0.1920179073822721, 6)
dm1 = mf.make_rdm1()
mf1 = ddcosmo.ddcosmo_for_scf(scf.RHF(mol1)).run()
e1 = mf1.e_tot
e1_cosmo = mf1.with_solvent.energy(dm1)
mf2 = ddcosmo.ddcosmo_for_scf(scf.RHF(mol2)).run()
e2 = mf2.e_tot
e2_cosmo = mf2.with_solvent.energy(dm1)
self.assertAlmostEqual(abs((e2 - e1) / dx - de[0, 2]).max(), 0, 7)
self.assertAlmostEqual(
abs((e2_cosmo - e1_cosmo) / dx - de_cosmo[0, 2]).max(), 0, 7)
sc = mf.nuc_grad_method().as_scanner()
e, g = sc('H 0 1 0; H 0 1 1.2; H 1. 0 0; H .5 .5 0')
self.assertAlmostEqual(e, -0.8317337703056022, 8)
self.assertAlmostEqual(lib.fp(g), 0.06804297145388238, 6)
mol3 = gto.M(atom='H 0 1 0; H 0 1 1.2; H 1. 0 0; H .5 .5 0', unit='B')
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol3)).run()
de = mf.nuc_grad_method().kernel()
self.assertAlmostEqual(lib.fp(de), 0.06804297145388238, 6)
def test_ddcosmo_scf(self):
mol = gto.M(atom=''' H 0 0 0 ''',
charge=1,
basis='sto3g',
verbose=7,
output='/dev/null')
pcm = ddcosmo.DDCOSMO(mol)
pcm.lmax = 10
pcm.lebedev_order = 29
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol), pcm)
mf.init_guess = '1e'
mf.run()
self.assertAlmostEqual(mf.e_tot, -0.1645636146393864, 9)
mol = gto.M(atom='''
6 0.000000 0.000000 -0.542500
8 0.000000 0.000000 0.677500
1 0.000000 0.935307 -1.082500
1 0.000000 -0.935307 -1.082500
''',
basis='sto3g',
verbose=7,
output='/dev/null')
pcm = ddcosmo.DDCOSMO(mol)
pcm.lmax = 6
pcm.lebedev_order = 17
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol), pcm).run()
self.assertAlmostEqual(mf.e_tot, -112.35450855007909, 9)
def test_scf_grad(self):
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol0)).run()
de_cosmo = ddcosmo_grad.kernel(mf._solvent, mf.make_rdm1())
de = mf.nuc_grad_method().kernel()
dm1 = mf.make_rdm1()
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol1)).run()
e1 = mf.e_tot
e1_cosmo = mf._solvent.energy(dm1)
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol2)).run()
e2 = mf.e_tot
e2_cosmo = mf._solvent.energy(dm1)
self.assertAlmostEqual(abs((e2-e1)/dx - de[0,2]).max(), 0, 7)
self.assertAlmostEqual(abs((e2_cosmo-e1_cosmo)/dx - de_cosmo[0,2]).max(), 0, 7)
def test_scf_grad(self):
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol0)).run()
de_cosmo = ddcosmo_grad.kernel(mf.with_solvent, mf.make_rdm1())
de = mf.nuc_grad_method().kernel()
dm1 = mf.make_rdm1()
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol1)).run()
e1 = mf.e_tot
e1_cosmo = mf.with_solvent.energy(dm1)
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol2)).run()
e2 = mf.e_tot
e2_cosmo = mf.with_solvent.energy(dm1)
self.assertAlmostEqual(abs((e2-e1)/dx - de[0,2]).max(), 0, 7)
self.assertAlmostEqual(abs((e2_cosmo-e1_cosmo)/dx - de_cosmo[0,2]).max(), 0, 7)
def ddCOSMO(method_or_mol, solvent_obj=None, dm=None):
'''Initialize ddCOSMO model.
Examples:
>>> mf = ddCOSMO(scf.RHF(mol))
>>> mf.kernel()
>>> sol = ddCOSMO(mol)
>>> mc = ddCOSMO(CASCI(mf, 6, 6), sol)
>>> mc.kernel()
'''
from pyscf import gto
from pyscf import scf, mcscf
from pyscf import tdscf
if isinstance(method_or_mol, gto.mole.Mole):
return ddcosmo.DDCOSMO(method_or_mol)
elif isinstance(method_or_mol, scf.hf.SCF):
return ddcosmo.ddcosmo_for_scf(method_or_mol, solvent_obj, dm)
elif isinstance(method_or_mol, mcscf.mc1step.CASSCF):
return ddcosmo.ddcosmo_for_casscf(method_or_mol, solvent_obj, dm)
elif isinstance(method_or_mol, mcscf.casci.CASCI):
return ddcosmo.ddcosmo_for_casci(method_or_mol, solvent_obj, dm)
elif isinstance(method_or_mol, (tdscf.rhf.TDA, tdscf.rhf.TDHF)):
return ddcosmo.ddcosmo_for_tdscf(method_or_mol, solvent_obj, dm)
else:
return ddcosmo.ddcosmo_for_post_scf(method_or_mol, solvent_obj, dm)
def ddCOSMO(method_or_mol, solvent_obj=None, dm=None):
'''Initialize ddCOSMO model.
Examples::
>>> mf = ddCOSMO(scf.RHF(mol))
>>> mf.kernel()
>>> sol = ddCOSMO(mol)
>>> mc = ddCOSMO(CASCI(mf, 6, 6), sol)
>>> mc.kernel()
'''
from pyscf import gto
from pyscf import scf, mcscf
from pyscf import tdscf
if isinstance(method_or_mol, gto.mole.Mole):
return DDCOSMO(mol)
elif isinstance(method_or_mol, scf.hf.SCF):
return ddcosmo.ddcosmo_for_scf(method_or_mol, solvent_obj, dm)
elif isinstance(method_or_mol, mcscf.mc1step.CASSCF):
return ddcosmo.ddcosmo_for_casscf(method_or_mol, solvent_obj, dm)
elif isinstance(method_or_mol, mcscf.casci.CASCI):
return ddcosmo.ddcosmo_for_casci(method_or_mol, solvent_obj, dm)
elif isinstance(method_or_mol, (tdscf.rhf.TDA, tdscf.rhf.TDHF)):
raise NotImplementedError('Solvent model for %s' % method_or_mol)
else:
return ddcosmo.ddcosmo_for_post_scf(method_or_mol, solvent_obj, dm)
def test_as_scanner(self):
mol = gto.M(atom='''
6 0.000000 0.000000 -0.542500
8 0.000000 0.000000 0.677500
1 0.000000 0.935307 -1.082500
1 0.000000 -0.935307 -1.082500
''', basis='sto3g', verbose=7,
output='/dev/null')
mf_scanner = ddcosmo.ddcosmo_for_scf(scf.RHF(mol)).as_scanner()
mf_scanner(mol)
self.assertEqual(mf_scanner.with_solvent.grids.coords.shape, (48212, 3))
mf_scanner('H 0. 0. 0.; H 0. 0. .9')
self.assertEqual(mf_scanner.with_solvent.grids.coords.shape, (20048, 3))
h2 = gto.M(atom='H 0. 0. 0.; H 0. 0. .9', basis='sto3g', verbose=7,
output='/dev/null')
mf_h2 = ddcosmo.ddcosmo_for_scf(scf.RHF(h2)).run()
self.assertAlmostEqual(mf_h2.e_tot, mf_scanner.e_tot, 9)
def test_ddcosmo_scf(self):
mol = gto.M(atom=''' H 0 0 0 ''', charge=1, basis='sto3g', verbose=7,
output='/dev/null')
pcm = ddcosmo.DDCOSMO(mol)
pcm.lmax = 10
pcm.lebedev_order = 29
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol), pcm)
mf.init_guess = '1e'
mf.run()
self.assertAlmostEqual(mf.e_tot, -0.1645636146393864, 9)
mol = gto.M(atom='''
6 0.000000 0.000000 -0.542500
8 0.000000 0.000000 0.677500
1 0.000000 0.935307 -1.082500
1 0.000000 -0.935307 -1.082500
''', basis='sto3g', verbose=7,
output='/dev/null')
pcm = ddcosmo.DDCOSMO(mol)
pcm.lmax = 6
pcm.lebedev_order = 17
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol), pcm).run()
self.assertAlmostEqual(mf.e_tot, -112.35450855007909, 9)
def test_as_scanner(self):
mol = gto.M(atom='''
6 0.000000 0.000000 -0.542500
8 0.000000 0.000000 0.677500
1 0.000000 0.935307 -1.082500
1 0.000000 -0.935307 -1.082500
''',
basis='sto3g',
verbose=7,
output='/dev/null')
mf_scanner = ddcosmo.ddcosmo_for_scf(scf.RHF(mol)).as_scanner()
mf_scanner(mol)
self.assertEqual(mf_scanner.with_solvent.grids.coords.shape,
(48212, 3))
mf_scanner('H 0. 0. 0.; H 0. 0. .9')
self.assertEqual(mf_scanner.with_solvent.grids.coords.shape,
(20048, 3))
h2 = gto.M(atom='H 0. 0. 0.; H 0. 0. .9',
basis='sto3g',
verbose=7,
output='/dev/null')
mf_h2 = ddcosmo.ddcosmo_for_scf(scf.RHF(h2)).run()
self.assertAlmostEqual(mf_h2.e_tot, mf_scanner.e_tot, 9)
def test_ddcosmo_scf_with_overwritten_attributes(self):
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol))
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -75.57036436805902, 9)
mf.with_solvent.lebedev_order = 15
mf.with_solvent.lmax = 5
mf.with_solvent.eps = .5
mf.with_solvent.conv_tol = 1e-8
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -75.55326109712902, 9)
mf.with_solvent.grids.radi_method = dft.mura_knowles
mf.with_solvent.grids.atom_grid = {"H": (8, 50), "O": (8, 50),}
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -75.55216799624262, 9)
def test_ddcosmo_scf_with_overwritten_attributes(self):
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol))
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -75.57036436805902, 9)
mf.with_solvent.lebedev_order = 15
mf.with_solvent.lmax = 5
mf.with_solvent.eps = .5
mf.with_solvent.conv_tol = 1e-8
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -75.55326109712902, 9)
mf.with_solvent.grids.radi_method = dft.mura_knowles
mf.with_solvent.grids.atom_grid = {
"H": (8, 50),
"O": (8, 50),
}
mf.kernel()
self.assertAlmostEqual(mf.e_tot, -75.55216799624262, 9)
def ddCOSMO(method):
return ddcosmo.ddcosmo_for_scf(method)
vtmp = numpy.zeros((3,nao,nao))
aow = numpy.einsum('pi,p->pi', ao[0], weight*eta_nj)
rks_grad._d1_dot_(vtmp, mol, ao[1:4], aow, mask, ao_loc, True)
vmat += vtmp
aoslices = mol.aoslice_by_atom()
for ia in range(natm):
shl0, shl1, p0, p1 = aoslices[ia]
psi1[ia] += numpy.einsum('xij,ij->x', vmat[:,p0:p1], dm[p0:p1]) * 2
return psi1
if __name__ == '__main__':
from pyscf import scf
mol = gto.M(atom='H 0 0 0; H 0 1 1.2; H 1. .1 0; H .5 .5 1', unit='B')
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol))
mf.kernel()
de = mf.nuc_grad_method().kernel()
de_cosmo = kernel(mf.with_solvent, mf.make_rdm1())
dm1 = mf.make_rdm1()
mol = gto.M(atom='H 0 0 -0.001; H 0 1 1.2; H 1. .1 0; H .5 .5 1', unit='B')
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol))
e1 = mf.kernel()
e1_cosmo = mf.with_solvent.energy(dm1)
mol = gto.M(atom='H 0 0 0.001; H 0 1 1.2; H 1. .1 0; H .5 .5 1', unit='B')
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol))
e2 = mf.kernel()
e2_cosmo = mf.with_solvent.energy(dm1)
print(abs((e2-e1)/0.002 - de[0,2]).max())
#!/usr/bin/env python
#
# Author: Qiming Sun <*****@*****.**>
#
'''
A simple example of using solvent model in the mean-field calculations.
'''
from pyscf import gto, scf
from pyscf.solvent import ddcosmo, ddpcm
mol = gto.M(atom='''
C 0.000000 0.000000 -0.542500
O 0.000000 0.000000 0.677500
H 0.000000 0.9353074360871938 -1.082500
H 0.000000 -0.9353074360871938 -1.082500
''', )
mf = scf.RHF(mol)
ddcosmo.ddcosmo_for_scf(mf).run()
ddpcm.ddpcm_for_scf(mf).run()
def ddpcm_for_scf(mf, pcmobj=None):
if pcmobj is None:
pcmobj = DDPCM(mf.mol)
return ddcosmo.ddcosmo_for_scf(mf, pcmobj)
def ddpcm_for_scf(mf, solvent_obj=None, dm=None):
if solvent_obj is None:
solvent_obj = DDPCM(mf.mol)
return ddcosmo.ddcosmo_for_scf(mf, solvent_obj, dm)
vtmp = numpy.zeros((3,nao,nao))
aow = numpy.einsum('pi,p->pi', ao[0], weight*eta_nj)
rks_grad._d1_dot_(vtmp, mol, ao[1:4], aow, mask, ao_loc, True)
vmat += vtmp
aoslices = mol.aoslice_by_atom()
for ia in range(natm):
shl0, shl1, p0, p1 = aoslices[ia]
psi1[ia] += numpy.einsum('xij,ij->x', vmat[:,p0:p1], dm[p0:p1]) * 2
return psi1
if __name__ == '__main__':
from pyscf import scf
mol = gto.M(atom='H 0 0 0; H 0 1 1.2; H 1. .1 0; H .5 .5 1', unit='B')
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol))
mf.kernel()
de = mf.nuc_grad_method().kernel()
de_cosmo = kernel(mf.with_solvent, mf.make_rdm1())
dm1 = mf.make_rdm1()
mol = gto.M(atom='H 0 0 -0.001; H 0 1 1.2; H 1. .1 0; H .5 .5 1', unit='B')
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol))
e1 = mf.kernel()
e1_cosmo = mf.with_solvent.energy(dm1)
mol = gto.M(atom='H 0 0 0.001; H 0 1 1.2; H 1. .1 0; H .5 .5 1', unit='B')
mf = ddcosmo.ddcosmo_for_scf(scf.RHF(mol))
e2 = mf.kernel()
e2_cosmo = mf.with_solvent.energy(dm1)
print(abs((e2-e1)/0.002 - de[0,2]).max())
def ddpcm_for_scf(mf, solvent_obj=None, dm=None):
if solvent_obj is None:
solvent_obj = DDPCM(mf.mol)
return ddcosmo.ddcosmo_for_scf(mf, solvent_obj, dm)
