def test_excited_supersystem(self):
mol = gto.Mole()
mol.verbose = 3
mol.atom = '''
H 0. -2.757 2.857
H 0. 2.757 2.857
'''
mol.basis = '3-21g'
mol.build()
env_method = 'm06'
hl_method = 'ccsd'
subsys = cluster_subsystem.ClusterHLSubSystem(mol, env_method, hl_method)
mol2 = gto.Mole()
mol2.verbose = 3
mol2.atom = '''
He 1.0 20.0 0.0
He 3.0 20.0 0.0'''
mol2.basis = '3-21g'
mol2.build()
env_method = 'm06'
subsys2 = cluster_subsystem.ClusterEnvSubSystem(mol2, env_method)
mol12 = helpers.concat_mols([mol, mol2])
fs_scf_obj = helpers.gen_scf_obj(mol12, 'm06')
supersystem = cluster_supersystem.ClusterSuperSystem([subsys, subsys2], 'm06', fs_scf_obj, init_guess='minao',
fs_excited=True, fs_excited_dict={'nroots':4}, ft_excited_relax=True, ft_excited_dict={'nroots':2})
self.assertTrue(supersystem.fs_excited)
self.assertTrue(supersystem.ft_excited_relax)
self.assertDictEqual(supersystem.fs_excited_dict, {'nroots':4})
self.assertDictEqual(supersystem.ft_excited_dict, {'nroots':2})
self.assertEqual(supersystem.fs_excited_nroots, 4)
self.assertEqual(supersystem.ft_excited_nroots, 2)
def combine_subsystems(subsystems, env_method, fs_kwargs=None):
"""Combines multiple subsystems into one larger subsystem object.
Parameters
__________
subsystems : array
A list of subsystem objects to combine
env_method : str
The name of the environment method to use for the combined subsystem
fs_kwargs : dict
Settings for the full system. Determines if subsystem is unrestricted
(default is None)
Returns
-------
ClusterEnvSubSystem
The combined subsystem object.
"""
mol_list = [x.mol for x in subsystems]
mol = helpers.concat_mols(mol_list)
sub_order = subsystems[0].env_order
sub_unrestricted = False
if fs_kwargs is not None:
if 'fs_unrestricted' in fs_kwargs.keys():
sub_unrestricted = fs_kwargs['fs_unrestricted']
#Need a way of specifying the settings of the implied subsystem somehow.
return cluster_subsystem.ClusterEnvSubSystem(mol,
env_method,
env_order=sub_order,
unrestricted=sub_unrestricted)
def test_basic_interaction_mediator(self):
subsystems = [self.sub2, self.sub3]
mediator = interaction_mediator.InteractionMediator(subsystems)
self.assertEqual(len(mediator.supersystems), 1)
mol12 = helpers.concat_mols([self.sub2.mol, self.sub3.mol])
fs_scf_obj = helpers.gen_scf_obj(mol12, 'm06')
supersystem_1 = cluster_supersystem.ClusterSuperSystem(subsystems, 'm06', fs_scf_obj)
for i in range(len(mediator.supersystems)):
test = mediator.supersystems[i]
self.assertEqual(test.env_method, supersystem_1.env_method)
self.assertEqual(test.proj_oper, supersystem_1.proj_oper)
self.assertEqual(test.max_cycle, supersystem_1.max_cycle)
self.assertEqual(test.conv_tol, supersystem_1.conv_tol)
self.assertEqual(test.damp, supersystem_1.damp)
self.assertEqual(test.init_guess, supersystem_1.init_guess)
self.assertEqual(test.fock_subcycles, supersystem_1.fock_subcycles)
test_fs_scf = test.fs_scf_obj
sup_fs_scf = supersystem_1.fs_scf_obj
self.assertEqual(test_fs_scf.max_cycle, sup_fs_scf.max_cycle)
self.assertEqual(test_fs_scf.conv_tol, sup_fs_scf.conv_tol)
self.assertEqual(test_fs_scf.damp, sup_fs_scf.damp)
self.assertEqual(test_fs_scf.level_shift_factor, sup_fs_scf.level_shift_factor)
self.assertEqual(test_fs_scf.init_guess, sup_fs_scf.init_guess)
self.assertEqual(test_fs_scf.grids.level, sup_fs_scf.grids.level)
self.assertEqual(test_fs_scf.small_rho_cutoff, sup_fs_scf.small_rho_cutoff)
def test_hsros_supersystem(self):
mol = gto.Mole()
mol.verbose = 3
mol.atom = '''
H 0. -2.757 2.857
H 0. 2.757 2.857
'''
mol.basis = '3-21g'
mol.spin = 2
mol.build()
env_method = 'm06'
hl_method = 'ccsd'
subsys = cluster_subsystem.ClusterHLSubSystem(mol, env_method, hl_method)
mol2 = gto.Mole()
mol2.verbose = 3
mol2.atom = '''
He 1.0 20.0 0.0
He 3.0 20.0 0.0'''
mol2.basis = '3-21g'
mol2.build()
env_method = 'm06'
subsys2 = cluster_subsystem.ClusterEnvSubSystem(mol2, env_method)
mol12 = helpers.concat_mols([mol, mol2])
fs_scf_obj = helpers.gen_scf_obj(mol12, 'm06')
supersystem = cluster_supersystem.ClusterSuperSystem([subsys, subsys2], 'm06', fs_scf_obj, init_guess='minao')
#Check SCF object
scf_obj = supersystem.fs_scf_obj
comp_scf_obj = dft.ROKS(gto.mole.conc_mol(mol, mol2))
self.assertEqual(type(scf_obj), type(comp_scf_obj))
self.assertEqual(scf_obj.xc, 'm06')
def test_partialghost_supersystem(self):
mol = gto.Mole()
mol.verbose = 3
mol.atom = '''
H 0. -2.757 2.857
H 0. 2.757 2.857
ghost:H 0. 0. 2.857
'''
mol.basis = '3-21g'
mol.build()
env_method = 'm06'
hl_method = 'ccsd'
subsys = cluster_subsystem.ClusterHLSubSystem(mol, env_method, hl_method)
mol2 = gto.Mole()
mol2.verbose = 3
mol2.atom = '''
He 1.0 20.0 0.0
He 3.0 20.0 0.0'''
mol2.basis = '3-21g'
mol2.build()
env_method = 'm06'
subsys2 = cluster_subsystem.ClusterEnvSubSystem(mol2, env_method)
mol12 = helpers.concat_mols([mol, mol2])
fs_scf_obj = helpers.gen_scf_obj(mol12, 'b3lyp')
supersystem = cluster_supersystem.ClusterSuperSystem([subsys, subsys2], 'b3lyp', fs_scf_obj, init_guess='minao')
self.assertEqual(supersystem.env_method, 'b3lyp')
self.assertEqual(supersystem.proj_oper, 'huz')
self.assertEqual(supersystem.init_guess, 'minao')
def test_density_fitting_supersystem(self):
mol = gto.Mole()
mol.verbose = 3
mol.atom = '''
H 0. -2.757 2.857
H 0. 2.757 2.857
'''
mol.basis = '3-21g'
mol.build()
env_method = 'm06'
hl_method = 'ccsd'
subsys = cluster_subsystem.ClusterHLSubSystem(mol, env_method, hl_method)
mol2 = gto.Mole()
mol2.verbose = 3
mol2.atom = '''
He 1.0 20.0 0.0
He 3.0 20.0 0.0'''
mol2.basis = '3-21g'
mol2.build()
env_method = 'm06'
subsys2 = cluster_subsystem.ClusterEnvSubSystem(mol2, env_method)
mol12 = helpers.concat_mols([mol, mol2])
fs_scf_obj = helpers.gen_scf_obj(mol12, 'm06', density_fitting=True)
supersystem = cluster_supersystem.ClusterSuperSystem([subsys, subsys2], 'm06', fs_scf_obj, init_guess='minao')
#Check SCF object
scf_obj = supersystem.fs_scf_obj
from pyscf.df.df_jk import _DFHF
self.assertTrue(isinstance(scf_obj, _DFHF))
self.assertEqual(scf_obj.xc, 'm06')
self.assertEqual(scf_obj.density_fitting, True)
def test_remove_ovlp(self):
test_mol_16 = helpers.concat_mols([self.mol1, self.mol6])
corr_mol16 = gto.M()
corr_mol16.atom = """
H-0 -1.06 0.0 0.0
C-0 0.0 0.0 0.0
C-1 1.2 0.0 0.0
H-1 2.26 0.0 0.0
"""
corr_mol16.basis = {
'C-0': 'sto-3g',
'H-0': 'sto-3g',
'C-1': '6-311g',
'H-1': '6-311g'
}
with self.assertRaises(AssertionError):
test_mol_166 = helpers.concat_mols([test_mol_16, self.mol6])
test_mol_378 = helpers.concat_mols([self.mol3, self.mol7, self.mol8])
corr_mol378 = gto.M()
corr_mol378.atom = """
O-0 -1.16 0.0 0.0
GHOST-C-1 2.0 0.0 0.0
O-1 0.0 1.16 0.0
C-2 0.0 0.0 0.0
"""
corr_mol378.basis = {
'O-0': 'sto-3g',
'O-1': 'cc-pVTZ',
'GHOST-C-1': 'aug-cc-pVDZ',
'C-2': 'cc-pVDZ'
}
corr_mol378.build()
self.assertTrue(gto.same_basis_set(test_mol_378, corr_mol378))
self.assertTrue(gto.same_mol(test_mol_378, corr_mol378))
def test_basic(self):
test_mol_12 = helpers.concat_mols([self.mol1, self.mol2])
corr_mol12 = gto.M()
corr_mol12.atom = """
H-0 -1.06 0.0 0.0
C-0 0.0 0.0 0.0
C-1 1.2 0.0 0.0
H-1 2.26 0.0 0.0
"""
corr_mol12.spin = 0
corr_mol12.basis = {
'C-0': 'sto-3g',
'H-0': 'sto-3g',
'C-1': '6-311g',
'H-1': '6-311g'
}
corr_mol12.build()
self.assertEqual(test_mol_12.spin, corr_mol12.spin)
self.assertTrue(gto.same_mol(test_mol_12, corr_mol12))
self.assertTrue(gto.same_mol(test_mol_12, corr_mol12))
test_mol_345 = helpers.concat_mols([self.mol3, self.mol4, self.mol5])
corr_mol345 = gto.M()
corr_mol345.atom = """
O-0 -1.16 0.0 0.0
C-1 0.0 0.0 0.0
O-2 1.16 0.0 0.0
"""
corr_mol345.basis = {'O-0': 'sto-3g', 'C-1': '6-311g', 'O-2': 'sto-3g'}
corr_mol345.build()
self.assertTrue(gto.same_basis_set(test_mol_345, corr_mol345))
self.assertTrue(gto.same_mol(test_mol_345, corr_mol345))
def test_basic_supersystem(self):
mol = gto.Mole()
mol.verbose = 3
mol.atom = '''
H 0. -2.757 2.857
H 0. 2.757 2.857
'''
mol.basis = '3-21g'
mol.build()
env_method = 'm06'
hl_method = 'ccsd'
subsys = cluster_subsystem.ClusterHLSubSystem(mol, env_method, hl_method)
mol2 = gto.Mole()
mol2.verbose = 3
mol2.atom = '''
He 1.0 20.0 0.0
He 3.0 20.0 0.0'''
mol2.basis = '3-21g'
mol2.build()
env_method = 'm06'
subsys2 = cluster_subsystem.ClusterEnvSubSystem(mol2, env_method)
mol12 = helpers.concat_mols([mol, mol2])
fs_scf_obj = helpers.gen_scf_obj(mol12, 'm06')
supersystem = cluster_supersystem.ClusterSuperSystem([subsys, subsys2], 'm06', fs_scf_obj, init_guess='minao')
self.assertEqual(supersystem.env_method, 'm06')
self.assertEqual(supersystem.proj_oper, 'huz')
self.assertEqual(supersystem.max_cycle, 200)
self.assertEqual(supersystem.conv_tol, 1e-9)
self.assertEqual(supersystem.damp, 0)
self.assertEqual(supersystem.init_guess, 'minao')
self.assertEqual(supersystem.fock_subcycles, 1)
#Check SCF object
scf_obj = supersystem.fs_scf_obj
comp_scf_obj = dft.RKS(gto.mole.conc_mol(mol, mol2))
self.assertEqual(type(scf_obj), type(comp_scf_obj))
print (comp_scf_obj.mol._basis)
print (supersystem.mol._basis)
self.assertTrue(gto.same_mol(comp_scf_obj.mol, supersystem.mol, cmp_basis=False))
self.assertEqual(scf_obj.xc, 'm06')
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_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 gen_supersystems(sup_kwargs, subsystems, filename, scrdir):
"""Generates the list of supersystems made from all subsystems.
Parameters
__________
sup_kwargs : array
An array of supersystem kwarg dictionaries.
subsystems : array
An array of subsystem objects.
filename : str
The name of the input file.
scrdir : str
The path to the scratch directory
Returns
_______
Array
A list of supersystem objects.
"""
supersystems = []
sorted_subs = sorted(subsystems, key=lambda x: x.env_order)
while len(sorted_subs) > 0:
curr_order = sorted_subs[0].env_order
curr_method = sorted_subs[0].env_method
curr_sup_kwargs = {}
sub_sup_kwargs = {}
if sup_kwargs is not None:
match_sup_kwargs = [
x for x in sup_kwargs if x['env_order'] == curr_order
]
sub_sup_kwargs = [
x for x in sup_kwargs if x['env_order'] == (curr_order + 1)
]
assert len(match_sup_kwargs) < 2, 'Ambigious supersystem settings'
curr_sup_kwargs = match_sup_kwargs[0]
higher_order_subs = [
x for x in sorted_subs if x.env_order > curr_order
]
sub_list = []
while len(sorted_subs) > 0 and sorted_subs[0].env_order == curr_order:
sub_list.append(sorted_subs.pop(0))
if len(higher_order_subs) > 0:
if len(sub_sup_kwargs) > 0:
combined_subs = combine_subsystems(higher_order_subs,
curr_method,
fs_kwargs=sub_sup_kwargs[0])
else:
combined_subs = combine_subsystems(higher_order_subs,
curr_method)
sub_list.append(combined_subs)
mol_list = [x.mol for x in sub_list]
full_mol = helpers.concat_mols(mol_list)
fs_env_settings = curr_sup_kwargs.pop('fs_env_settings', None)
if fs_env_settings:
env_method = fs_env_settings.pop('env_method', None)
if not env_method:
env_method = sub_list[0].env_method
fs_scf_obj = helpers.gen_scf_obj(full_mol, env_method,
**fs_env_settings)
else:
env_method = sub_list[0].env_method
fs_scf_obj = helpers.gen_scf_obj(full_mol, env_method)
embed_dict = curr_sup_kwargs.get('embed_settings', None)
if embed_dict:
embed_dict['filename'] = filename
supersystem = cluster_supersystem.ClusterSuperSystem(
sub_list,
env_method,
fs_scf_obj,
env_order=curr_order,
**embed_dict)
else:
supersystem = cluster_supersystem.ClusterSuperSystem(
sub_list,
env_method,
fs_scf_obj,
env_order=curr_order,
filename=filename)
supersystems.append(supersystem)
return supersystems
def test_custom_supersystem(self):
t_file = tempfile.NamedTemporaryFile()
mol = gto.Mole()
mol.verbose = 3
mol.atom = '''
O 0.0 0.0 0.0
H 0. -2.757 2.857
H 0. 2.757 2.857'''
mol.basis = 'aug-cc-pVDZ'
mol.build()
env_method = 'm06'
hl_method = 'ccsd'
hl_dict = {'froz_orbs': 10}
subsys = cluster_subsystem.ClusterHLSubSystem(mol, env_method, hl_method, filename=t_file.name, hl_dict=hl_dict)
mol2 = gto.Mole()
mol2.verbose = 3
mol2.atom = '''
O 1.0 0.0 0.0
O 3.0 0.0 0.0'''
mol2.basis = 'aug-cc-pVDZ'
mol2.verbose = 1
mol2.build()
env_method = 'm06'
subsys2 = cluster_subsystem.ClusterEnvSubSystem(mol2, env_method, filename=t_file.name)
mol12 = helpers.concat_mols([mol, mol2])
fs_scf_obj = helpers.gen_scf_obj(mol12, 'b3lyp', max_cycle=3, conv_tol=2,
damp=1, level_shift_factor=2.1,
init_guess='atom', grid_level=2,
small_rho_cutoff=1e-2, save_orbs=True,
save_density=True,
stability_analysis='internal')
supersystem = cluster_supersystem.ClusterSuperSystem([subsys, subsys2],
'b3lyp', fs_scf_obj, proj_oper='huzfermi', max_cycle=2,
conv_tol=1e-1, diis_num=3, init_guess='1e',
fock_subcycles=1, set_fermi=-0.1, damp=0.5,
compare_density=True, save_density=True,
save_orbs=True, filename=t_file.name)
self.assertEqual(supersystem.env_method, 'b3lyp')
self.assertEqual(supersystem.proj_oper, 'huzfermi')
self.assertEqual(supersystem.filename, t_file.name)
self.assertEqual(supersystem.max_cycle, 2)
self.assertEqual(supersystem.conv_tol, 1e-1)
self.assertEqual(supersystem.damp, 0.5)
self.assertIsInstance(supersystem.emb_diis, lib.diis.DIIS)
self.assertIsInstance(supersystem.emb_diis_2, lib.diis.DIIS)
self.assertEqual(supersystem.set_fermi, -0.1)
self.assertEqual(supersystem.init_guess, '1e')
self.assertEqual(supersystem.fock_subcycles, 1)
self.assertEqual(supersystem.compare_density, True)
self.assertEqual(supersystem.save_orbs, True)
self.assertEqual(supersystem.save_density, True)
fs_scf_obj = supersystem.fs_scf_obj
self.assertEqual(fs_scf_obj.max_cycle, 3)
self.assertEqual(fs_scf_obj.conv_tol, 2)
self.assertEqual(fs_scf_obj.damp, 1)
self.assertEqual(fs_scf_obj.level_shift_factor, 2.1)
self.assertEqual(fs_scf_obj.init_guess, 'atom')
self.assertEqual(fs_scf_obj.grids.level, 2)
self.assertEqual(fs_scf_obj.small_rho_cutoff, 1e-2)
self.assertEqual(fs_scf_obj.verbose, 1)
self.assertEqual(fs_scf_obj.stability_analysis, 'internal')
self.assertEqual(fs_scf_obj.save_orbs, True)
self.assertEqual(fs_scf_obj.save_density, True)
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)