def test_fs_save_orbitals(self):
t_file = tempfile.NamedTemporaryFile()
sub1 = ClusterHLSubSystem(self.mol1,
'lda',
'rhf',
init_guess='supmol',
save_orbs=True)
sub2 = ClusterEnvSubSystem(self.mol2,
'lda',
init_guess='supmol',
save_orbs=True)
subsystems = [sub1, sub2]
sup_kwargs = [{
'env_order': 1,
'env_method': 'lda',
'fs_env_settings': {
'save_orbs': True
}
}]
mediator = InteractionMediator(subsystems,
sup_kwargs,
filename=t_file.name)
mediator.do_embedding()
for sup in mediator.supersystems:
self.assertTrue(
os.path.exists(t_file.name + '_' + str(sup.chkfile_index) +
'_fs.molden'))
def test_save_orbitals(self):
sub1 = ClusterHLSubSystem(self.mol1,
'lda',
'rhf',
init_guess='supmol',
hl_save_orbs=True)
sub2 = ClusterEnvSubSystem(self.mol2, 'lda', init_guess='supmol')
subsystems = [sub1, sub2]
t_file = tempfile.NamedTemporaryFile()
mediator = InteractionMediator(subsystems, filename=t_file.name)
mediator.do_embedding()
test_emb_energy = mediator.get_emb_energy()
def test_read_chkfile(self):
t_file = tempfile.NamedTemporaryFile()
sub1 = ClusterHLSubSystem(self.mol1, 'lda', 'rhf')
sub2 = ClusterEnvSubSystem(self.mol2, 'lda')
subsystems = [sub1, sub2]
sub3 = ClusterHLSubSystem(self.mol1.copy(), 'lda', 'rhf')
sub4 = ClusterEnvSubSystem(self.mol2.copy(), 'lda')
subsystems2 = [sub3, sub4]
mediator = InteractionMediator(subsystems, filename=t_file.name)
mediator.do_embedding()
emb_dict = {'init_guess': 'chk'}
sup_kwargs_test = [{'env_order': 1, 'embed_settings': emb_dict}]
mediator2 = InteractionMediator(subsystems2,
supersystem_kwargs=sup_kwargs_test,
filename=t_file.name)
for i in range(len(mediator.supersystems)):
test = mediator.supersystems[i]
test2 = mediator2.supersystems[i]
self.assertTrue(
np.allclose(test.get_emb_dmat(), test2.get_emb_dmat()))
def test_simple_subsystems(self):
sub1 = ClusterHLSubSystem(self.mol1, 'lda', 'rhf')
sub2 = ClusterEnvSubSystem(self.mol2, 'lda')
subsystems = [sub1, sub2]
mediator = InteractionMediator(subsystems)
mediator.do_embedding()
#True Values
sub1 = ClusterHLSubSystem(self.mol1, 'lda', 'rhf')
sub2 = ClusterEnvSubSystem(self.mol2, 'lda')
subsystems = [sub1, sub2]
mol12 = helpers.concat_mols([sub1.mol, sub2.mol])
fs_scf_obj = helpers.gen_scf_obj(mol12, 'lda')
supersystem = ClusterSuperSystem(subsystems, 'lda', fs_scf_obj)
supersystem.init_density()
sup_e = supersystem.get_supersystem_energy()
supersystem.freeze_and_thaw()
self.assertTrue(
np.allclose(supersystem.get_emb_dmat(),
mediator.supersystems[0].get_emb_dmat()))
self.assertTrue(
np.allclose(supersystem.fs_dmat, mediator.supersystems[0].fs_dmat))
def test_sub_save_density(self):
t_file = tempfile.NamedTemporaryFile()
sub1 = ClusterHLSubSystem(self.mol1,
'lda',
'rhf',
init_guess='supmol',
save_density=True)
sub2 = ClusterEnvSubSystem(self.mol2,
'lda',
init_guess='supmol',
save_density=True)
subsystems = [sub1, sub2]
sup_kwargs = [{
'env_order': 1,
'env_method': 'lda',
'embed_settings': {
'save_density': True
}
}]
mediator = InteractionMediator(subsystems,
sup_kwargs,
filename=t_file.name)
mediator.do_embedding()
def test_simple_subsystems(self):
sub1 = ClusterHLSubSystem(self.mol1, 'lda', 'rhf')
sub2 = ClusterEnvSubSystem(self.mol2, 'lda')
subsystems = [sub1, sub2]
mediator = InteractionMediator(subsystems)
mediator.do_embedding()
test_emb_energy = mediator.get_emb_energy()
#True Values
sub1 = ClusterHLSubSystem(self.mol1, 'lda', 'rhf')
sub2 = ClusterEnvSubSystem(self.mol2, 'lda')
subsystems = [sub1, sub2]
mol12 = helpers.concat_mols([sub1.mol, sub2.mol])
fs_scf_obj = helpers.gen_scf_obj(mol12, 'lda')
supersystem = ClusterSuperSystem(subsystems, 'lda', fs_scf_obj)
supersystem.init_density()
sup_e = supersystem.get_supersystem_energy()
supersystem.freeze_and_thaw()
supersystem.get_env_energy()
supersystem.get_hl_energy()
env_e = supersystem.subsystems[0].env_energy
hl_e = supersystem.subsystems[0].hl_energy
true_emb_energy = sup_e - env_e + hl_e
self.assertAlmostEqual(true_emb_energy, test_emb_energy, delta=1e-9)
def test_fs_save_density(self):
t_file = tempfile.NamedTemporaryFile()
sub1 = ClusterHLSubSystem(self.mol1, 'lda', 'rhf')
sub2 = ClusterEnvSubSystem(self.mol2, 'lda')
subsystems = [sub1, sub2]
sup_kwargs = [{
'env_order': 1,
'env_method': 'lda',
'fs_env_settings': {
'save_density': True
}
}]
mediator = InteractionMediator(subsystems,
sup_kwargs,
filename=t_file.name)
mediator.do_embedding()
mediator.get_emb_energy()
#Assert that the density file exists.
for sup in mediator.supersystems:
self.assertTrue(
os.path.exists(t_file.name + '_' + str(sup.chkfile_index) +
'_fs.cube'))
def test_density_multiple_subsystems(self):
mol1 = gto.Mole()
mol1.verbose = 3
mol1.atom = '''
H 0.758602 0.000000 0.504284
H 0.758602 0.000000 -0.504284
O 0.0 0.0 0.0'''
mol1.basis = '3-21g'
mol1.build()
mol2 = gto.Mole()
mol2.verbose = 3
mol2.atom = '''
H 0.758602 2.000000 0.504284
H 0.758602 2.000000 -0.504284
O 0.0 2.0 0.0'''
mol2.basis = '3-21g'
mol2.build()
mol3 = gto.Mole()
mol3.verbose = 3
mol3.atom = '''
H 0.758602 4.000000 0.504284
H 0.758602 4.000000 -0.504284
O 0.0 4.0 0.0'''
mol3.basis = '6-31g'
mol3.build()
mol4 = gto.Mole()
mol4.verbose = 3
mol4.atom = '''
H 0.758602 6.000000 0.504284
H 0.758602 6.000000 -0.504284
O 0.0 6.0 0.0'''
mol4.basis = 'cc-pVDZ'
mol4.build()
mol5 = gto.Mole()
mol5.verbose = 3
mol5.atom = '''
H 0.758602 8.000000 0.504284
H 0.758602 8.000000 -0.504284
O 0.0 8.0 0.0'''
mol5.basis = '3-21g'
mol5.build()
sub1 = ClusterEnvSubSystem(mol1, 'lda', env_order=1)
sub2 = ClusterEnvSubSystem(mol2, 'lda', env_order=1)
sub3 = ClusterEnvSubSystem(mol3, 'pbe', env_order=2)
sub4 = ClusterEnvSubSystem(mol4, 'm06', env_order=3)
sub5 = ClusterHLSubSystem(mol5, 'm06', 'rhf', env_order=3)
subsystems = [sub1, sub2, sub3, sub4, sub5]
sup1_alt_sub_mol = gto.Mole()
sup1_alt_sub_mol.verbose = 3
sup1_alt_sub_mol.atom = '''
H-0 0.758602 4.000000 0.504284
H-0 0.758602 4.000000 -0.504284
O-0 0.0 4.0 0.0
H-1 0.758602 6.000000 0.504284
H-1 0.758602 6.000000 -0.504284
O-1 0.0 6.0 0.0
H-2 0.758602 8.000000 0.504284
H-2 0.758602 8.000000 -0.504284
O-2 0.0 8.0 0.0'''
sup1_alt_sub_mol.basis = {
'O-0': '6-31g',
'H-0': '6-31g',
'O-1': 'cc-pVDZ',
'H-1': 'cc-pVDZ',
'O-2': '3-21g',
'H-2': '3-21g'
}
sup1_alt_sub_mol.build()
sup1_alt_sub = ClusterEnvSubSystem(sup1_alt_sub_mol,
'pbe',
env_order=2)
mol123 = helpers.concat_mols([sub1.mol, sub2.mol, sup1_alt_sub.mol])
fs_scf_obj = helpers.gen_scf_obj(mol123, 'lda')
supersystem_1 = ClusterSuperSystem([sub1, sub2, sup1_alt_sub], 'lda',
fs_scf_obj)
supersystem_1.init_density()
sup2_alt_sub_mol = gto.Mole()
sup2_alt_sub_mol.verbose = 3
sup2_alt_sub_mol.atom = '''
H-0 0.758602 6.000000 0.504284
H-0 0.758602 6.000000 -0.504284
O-0 0.0 6.0 0.0
H-1 0.758602 8.000000 0.504284
H-1 0.758602 8.000000 -0.504284
O-1 0.0 8.0 0.0'''
sup2_alt_sub_mol.basis = {
'O-0': 'cc-pVDZ',
'H-0': 'cc-pVDZ',
'O-1': '3-21g',
'H-1': '3-21g'
}
sup2_alt_sub_mol.build()
sup2_alt_sub = ClusterEnvSubSystem(sup2_alt_sub_mol,
'm06',
env_order=3)
mol123 = helpers.concat_mols([sub3.mol, sup2_alt_sub.mol])
fs_scf_obj = helpers.gen_scf_obj(mol123, 'pbe')
supersystem_2 = ClusterSuperSystem([sub3, sup2_alt_sub],
'pbe',
fs_scf_obj,
env_order=2)
supersystem_2.init_density()
mol123 = helpers.concat_mols([sub4.mol, sub5.mol])
fs_scf_obj = helpers.gen_scf_obj(mol123, 'm06')
supersystem_3 = ClusterSuperSystem([sub4, sub5],
'm06',
fs_scf_obj,
env_order=3)
supersystem_3.init_density()
supersystem_list = [supersystem_1, supersystem_2, supersystem_3]
mediator = InteractionMediator(subsystems)
#Ensure the densities are the same and the methods are correct should be enough.
self.assertEqual(len(mediator.supersystems), 3)
for i in range(len(mediator.supersystems)):
test = mediator.supersystems[i]
self.assertEqual(test.env_method, supersystem_list[i].env_method)
def test_explicit_subsystems(self):
#Use the fs settings for the smaller system for the subsystem settings.
mol1 = gto.Mole()
mol1.verbose = 3
mol1.atom = '''
O 0.0 0.0 0.0
H 0. -2.757 2.857
H 0. 2.757 2.857'''
mol1.basis = 'sto-3g'
mol1.build()
mol2 = gto.Mole()
mol2.verbose = 3
mol2.atom = '''
O 1.0 0.0 0.0
H 1. -2.757 2.857
H 1. 2.757 2.857'''
mol2.basis = '3-21g'
mol2.build()
mol3 = gto.Mole()
mol3.verbose = 3
mol3.atom = '''
O 2.0 0.0 0.0
H 2. -2.757 2.857
H 2. 2.757 2.857'''
mol3.basis = '6-31g'
mol3.build()
mol4 = gto.Mole()
mol4.verbose = 3
mol4.atom = '''
O 3.0 0.0 0.0
H 3. -2.757 2.857
H 3. 2.757 2.857'''
mol4.basis = 'aug-cc-pVTZ'
mol4.build()
mol5 = gto.Mole()
mol5.verbose = 3
mol5.atom = '''
O 4.0 0.0 0.0
H 4. -2.757 2.857
H 4. 2.757 2.857'''
mol5.basis = '3-21g'
mol5.build()
sub1 = ClusterEnvSubSystem(mol1, 'lda', env_order=1)
sub2 = ClusterEnvSubSystem(mol2, 'lda', env_order=1)
sub3 = ClusterEnvSubSystem(mol3, 'pbe', env_order=2)
sub4 = ClusterEnvSubSystem(mol4, 'm06', env_order=3)
sub5 = ClusterHLSubSystem(mol5, 'm06', 'rhf', env_order=3)
subsystems = [sub1, sub2, sub3, sub4, sub5]
sup1_alt_sub_mol = gto.Mole()
sup1_alt_sub_mol.verbose = 3
sup1_alt_sub_mol.atom = '''
O-0 2.0 0.0 0.0
H-0 2. -2.757 2.857
H-0 2. 2.757 2.857
O-1 3.0 0.0 0.0
H-1 3. -2.757 2.857
H-1 3. 2.757 2.857
O-2 4.0 0.0 0.0
H-2 4. -2.757 2.857
H-2 4. 2.757 2.857'''
sup1_alt_sub_mol.basis = {
'O-0': '6-31g',
'H-0': '6-31g',
'O-1': 'aug-cc-pVTZ',
'H-1': 'aug-cc-pVTZ',
'O-2': '3-21g',
'H-2': '3-21g'
}
sup1_alt_sub_mol.build()
sup1_alt_sub = ClusterEnvSubSystem(sup1_alt_sub_mol,
'pbe',
env_order=2)
mol123 = helpers.concat_mols([sub1.mol, sub2.mol, sup1_alt_sub.mol])
fs_scf_obj = helpers.gen_scf_obj(mol123, 'lda', conv_tol=1e-9)
supersystem_1 = ClusterSuperSystem([sub1, sub2, sup1_alt_sub], 'lda',
fs_scf_obj)
sup2_alt_sub_mol = gto.Mole()
sup2_alt_sub_mol.verbose = 3
sup2_alt_sub_mol.atom = '''
O-0 3.0 0.0 0.0
H-0 3. -2.757 2.857
H-0 3. 2.757 2.857
O-1 4.0 0.0 0.0
H-1 4. -2.757 2.857
H-1 4. 2.757 2.857'''
sup2_alt_sub_mol.basis = {
'O-0': 'aug-cc-pVTZ',
'H-0': 'aug-cc-pVTZ',
'O-1': '3-21g',
'H-1': '3-21g'
}
sup2_alt_sub_mol.build()
sup2_alt_sub = ClusterEnvSubSystem(sup2_alt_sub_mol,
'm06',
env_order=3)
mol123 = helpers.concat_mols([sub3.mol, sup2_alt_sub.mol])
fs_scf_obj = helpers.gen_scf_obj(mol123, 'pbe', unrestricted=True)
supersystem_2 = ClusterSuperSystem([sub3, sup2_alt_sub],
'pbe',
fs_scf_obj,
env_order=2,
unrestricted=True)
mol123 = helpers.concat_mols([sub4.mol, sub5.mol])
fs_scf_obj = helpers.gen_scf_obj(mol123, 'm06', max_cycle=10)
supersystem_3 = ClusterSuperSystem([sub4, sub5],
'm06',
fs_scf_obj,
env_order=3)
supersystem_list = [supersystem_1, supersystem_2, supersystem_3]
supersystem_dicts = [{
'env_order': 1,
'fs_env_settings': {
'conv_tol': 1e-9,
'env_method': 'lda'
}
}, {
'env_order': 2,
'fs_env_settings': {
'unrestricted': True,
'env_method': 'pbe'
}
}, {
'env_order': 3,
'fs_env_settings': {
'env_method': 'm06',
'max_cycle': 10
}
}]
mediator = InteractionMediator(subsystems, supersystem_dicts)
#Ensure the densities are the same and the methods are correct should be enough.
self.assertEqual(len(mediator.supersystems), 3)
for i in range(len(mediator.supersystems)):
test = mediator.supersystems[i]
self.assertEqual(test.env_method, supersystem_list[i].env_method)
self.assertEqual(test.fs_scf_obj.conv_tol,
supersystem_list[i].fs_scf_obj.conv_tol)
if hasattr(test.fs_scf_obj, 'unrestricted'):
self.assertEqual(test.fs_scf_obj.unrestricted,
supersystem_list[i].fs_scf_obj.unrestricted)
self.assertEqual(test.fs_scf_obj.max_cycle,
supersystem_list[i].fs_scf_obj.max_cycle)