def setUp(self):
mol1 = gto.Mole()
mol1.atom = '''
O 10.0 0.0 0.0
H 10. 0.7586 0.5043
H 10. 0.7586 -0.5043'''
mol1.basis = 'sto-3g'
mol1.build()
self.sub1 = cluster_subsystem.ClusterEnvSubSystem(mol1, 'lda', env_order=1)
mol2 = gto.Mole()
mol2.atom = '''
O 20.0 0.0 0.0
H 20. 0.7586 0.5043
H 20. 0.7586 -0.5043'''
mol2.basis = 'sto-3g'
mol2.build()
self.sub2 = cluster_subsystem.ClusterEnvSubSystem(mol2, 'm06', env_order=2)
mol3 = gto.Mole()
mol3.atom = '''
O 0.0 0.0 0.0
H 0. 0.7586 0.5043
H 0. 0.7586 -0.5043'''
mol3.basis = 'sto-3g'
mol3.build()
self.sub3 = cluster_subsystem.ClusterHLSubSystem(mol3, 'm06', 'rhf', env_order=2)
mol4 = gto.Mole()
mol4.verbose=3
mol4.atom = '''
O 30.0 0.0 0.0
H 30. 0.7586 0.5043
H 30. 0.7586 -0.5043'''
mol4.basis = 'sto-3g'
mol4.build()
self.sub4 = cluster_subsystem.ClusterEnvSubSystem(mol4, 'lda', env_order=2)
sup1_alt_sub_mol = gto.Mole()
sup1_alt_sub_mol.verbose = 3
sup1_alt_sub_mol.atom = '''
O 0.0 0.0 0.0
H 0. 0.7586 0.5043
H 0. 0.7586 -0.5043
O 20.0 0.0 0.0
H 20. 0.7586 0.5043
H 20. 0.7586 -0.5043'''
sup1_alt_sub_mol.basis = 'sto-3g'
sup1_alt_sub_mol.build()
self.sup1_alt_sub = cluster_subsystem.ClusterEnvSubSystem(sup1_alt_sub_mol, 'lda', env_order=2)
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 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_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_custom_subsystem(self):
t_file = tempfile.NamedTemporaryFile()
subsys = cluster_subsystem.ClusterEnvSubSystem(self.cs_mol, self.env_method,
env_order=2, env_smearsigma=0.5, damp=1, shift=1, subcycles=10,
diis=2, unrestricted=False, density_fitting=True, freeze=True,
verbose=2, nproc=4, pmem=300, scrdir='/path/to/scratch/',
save_orbs=True, save_density=True, filename=t_file.name)
self.assertEqual(subsys.mol, self.cs_mol)
self.assertEqual(subsys.env_method, self.env_method)
self.assertEqual(subsys.filename, t_file.name)
self.assertEqual(subsys.env_smearsigma, 0.5)
self.assertEqual(subsys.env_damp, 1)
self.assertEqual(subsys.env_shift, 1)
self.assertEqual(subsys.env_subcycles, 10)
self.assertEqual(subsys.freeze, True)
self.assertEqual(subsys.env_initguess, None)
self.assertEqual(subsys.verbose, 2)
self.assertEqual(subsys.save_orbs, True)
self.assertEqual(subsys.save_density, True)
#Check SCF object
scf_obj = subsys.env_scf
comp_scf_obj = dft.RKS(self.cs_mol).density_fit()
from pyscf.df.df_jk import _DFHF
self.assertTrue(isinstance(scf_obj, _DFHF))
self.assertEqual(scf_obj.xc, self.env_method)
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 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_density_fitting_subsystem(self):
subsys = cluster_subsystem.ClusterEnvSubSystem(self.cs_mol, self.env_method2, density_fitting=True)
#Check SCF object
scf_obj = subsys.env_scf
comp_scf_obj = dft.RKS(self.cs_mol).density_fit()
from pyscf.df.df_jk import _DFHF
self.assertTrue(isinstance(scf_obj, _DFHF))
def test_unrestricted_subsystem(self):
subsys = cluster_subsystem.ClusterEnvSubSystem(self.cs_mol, self.env_method, unrestricted=True)
subsys.init_density()
#Check SCF object
scf_obj = subsys.env_scf
comp_scf_obj = dft.UKS(self.cs_mol)
self.assertEqual(type(scf_obj), type(comp_scf_obj))
self.assertEqual(scf_obj.xc, 'm06')
self.assertEqual(subsys.env_method, self.env_method)
def test_restrictedos_subsystem(self):
mol = self.cs_mol.copy()
mol.spin = 2
mol.build()
subsys = cluster_subsystem.ClusterEnvSubSystem(mol, self.env_method)
subsys.init_density()
#Check SCF object
scf_obj = subsys.env_scf
comp_scf_obj = dft.ROKS(mol)
self.assertEqual(type(scf_obj), type(comp_scf_obj))
self.assertEqual(scf_obj.xc, 'm06')
def test_ovlpghost_supersystem(self):
mol = gto.Mole()
mol.verbose = 3
mol.atom = '''
H 0. -2.757 2.857
H 0. 2.757 2.857
ghost:He 1.0 20.0 0.0
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 = '''
ghost:H 0. 2.757 2.857
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)
supersystem = cluster_supersystem.ClusterSuperSystem([subsys, subsys2], 'b3lyp', ft_initguess='minao')
self.assertEqual(supersystem.fs_method, 'b3lyp')
self.assertEqual(supersystem.proj_oper, 'huz')
self.assertEqual(supersystem.ft_cycles, 100)
self.assertEqual(supersystem.ft_conv, 1e-8)
self.assertEqual(supersystem.ft_grad, None)
self.assertEqual(supersystem.ft_initguess, 'minao')
self.assertEqual(supersystem.ft_updatefock, 0)
self.assertEqual(supersystem.fs_cycles, None)
self.assertEqual(supersystem.fs_conv, None)
self.assertEqual(supersystem.fs_grad, None)
self.assertEqual(supersystem.fs_damp, 0)
self.assertEqual(supersystem.fs_shift, 0)
self.assertEqual(supersystem.fs_smearsigma, 0)
self.assertEqual(supersystem.fs_initguess, None)
self.assertEqual(supersystem.grid_level, None)
self.assertEqual(supersystem.rho_cutoff, None)
self.assertEqual(supersystem.fs_verbose, None)
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_basic_subsystem(self):
subsys = cluster_subsystem.ClusterEnvSubSystem(self.cs_mol, self.env_method)
self.assertEqual(subsys.mol, self.cs_mol)
self.assertEqual(subsys.env_method, self.env_method)
self.assertEqual(subsys.env_order, 1)
self.assertEqual(subsys.env_smearsigma, 0.)
self.assertEqual(subsys.env_damp, 0.)
self.assertEqual(subsys.env_shift, 0.)
self.assertEqual(subsys.env_subcycles, 1)
self.assertEqual(subsys.freeze, False)
self.assertEqual(subsys.env_initguess, None)
self.assertEqual(subsys.verbose, 3)
#Check SCF object
scf_obj = subsys.env_scf
comp_scf_obj = dft.RKS(self.cs_mol)
self.assertEqual(type(scf_obj), type(comp_scf_obj))
self.assertEqual(scf_obj.xc, 'm06')
def test_ghost_subsystem(self):
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
ghost.H 0. 0.0 2.857'''
mol.basis = 'aug-cc-pVDZ'
mol.build()
env_method = 'm06'
subsys = cluster_subsystem.ClusterEnvSubSystem(mol, env_method)
self.assertEqual(subsys.mol.atom_coords()[3][0],0.)
self.assertEqual(subsys.mol.atom_coords()[3][1],0.)
self.assertAlmostEqual(subsys.mol.atom_coords()[3][2],5.39894754, delta=1e-8)
self.assertEqual(subsys.mol.atom_charges()[0],8)
self.assertEqual(subsys.mol.atom_charges()[1],1)
self.assertEqual(subsys.mol.atom_charges()[2],1)
self.assertEqual(subsys.mol.atom_charges()[3],0)
self.assertEqual(subsys.mol._basis['GHOST-H'],subsys.mol._basis['H'])
def optimal_density_damping():
output_filename = 'optimal_density_damping_results.out'
molO = MolObjects()
moliter = iter(molO)
x = next(moliter)
num = 0
while x is not None:
for gp in grid_points:
for ig in init_guess:
for xc in xc_fun:
for fud in range(2):
for pud in range(fud, 2):
header_string = f"molnum: {num}\nbasis: {x[0].basis}\ncharge: {x[0].charge}\ngridsize: {gp}\ninitguess: {ig}\nxc_fun: {xc}\nfock_update: {fud}\nproj_update: {pud}\n"
with open(output_filename, 'a') as fout:
fout.write(header_string)
sub1 = cluster_subsystem.ClusterEnvSubSystem(
x[0], xc, damp=-1)
sub2 = cluster_subsystem.ClusterEnvSubSystem(
x[1], xc, damp=-1)
sup = cluster_supersystem.ClusterSuperSystem(
[sub1, sub2],
xc,
fs_grid_level=gp,
ft_cycles=100,
ft_initguess=ig,
ft_updatefock=fud,
ft_updateproj=pud,
ft_diis=None)
sup.init_density()
start_time = time.time()
sup.freeze_and_thaw()
end_time = time.time()
elapsed_time = end_time - start_time
cycles = sup.ft_iter
write_string = f" FT cycles: {cycles}\n Elapsed Time: {elapsed_time}\n Average time per cycle: {elapsed_time/float(cycles)}\n Sub1 E: {sub1.get_env_energy()}\n Sub2 E: {sub2.get_env_energy()}\n\n"
with open(output_filename, 'a') as fout:
fout.write(write_string)
if x[0].spin != 0 or x[1].spin != 0:
sub1 = cluster_subsystem.ClusterEnvSubSystem(
x[0], xc, unrestricted=True, damp=-1)
sub2 = cluster_subsystem.ClusterEnvSubSystem(
x[1], xc, unrestricted=True, damp=-1)
sup = cluster_supersystem.ClusterSuperSystem(
[sub1, sub2],
xc,
fs_grid_level=gp,
ft_cycles=100,
ft_initguess=ig,
ft_updatefock=fud,
ft_updateproj=pud,
fs_unrestricted=True,
ft_unrestricted=True,
ft_diis=None)
sup.init_density()
start_time = time.time()
sup.freeze_and_thaw()
end_time = time.time()
elapsed_time = end_time - start_time
cycles = sup.ft_iter
write_string = f"Unrestricted\n FT cycles: {cycles}\n Elapsed Time: {elapsed_time}\n Average time per cycle: {elapsed_time/float(cycles)}\n Sub1 E: {sub1.get_env_energy()}\n Sub2 E: {sub2.get_env_energy()}\n\n"
num += 2
x = next(moliter)
print("Progress")
print(f"{num/2} Done Total")
react_total_energy += react_cc.kernel()[0]
react_total_energy += ccsd_t.kernel(react_cc, react_cc.ao2mo())
trans_mf = scf.RHF(trans_mol)
trans_total_energy = trans_mf.kernel()
trans_cc = cc.CCSD(trans_mf)
trans_total_energy += trans_cc.kernel()[0]
trans_total_energy += ccsd_t.kernel(trans_cc, trans_cc.ao2mo())
print("Canonical Difference")
print(trans_total_energy - react_total_energy)
sub1_react = cluster_subsystem.ClusterActiveSubSystem(sub1_react_mol,
dft_method,
active_method)
sub2_react = cluster_subsystem.ClusterEnvSubSystem(sub2_react_mol, dft_method)
sup_react = cluster_supersystem.ClusterSuperSystem([sub1_react, sub2_react],
dft_method)
sup_react.freeze_and_thaw()
sup_react.get_active_energy()
sup_react_energy = sup_react.get_supersystem_energy()
react_energy = sup_react_energy - sup_react.subsystems[
0].env_energy + sup_react.subsystems[0].active_energy
sub1_trans = cluster_subsystem.ClusterActiveSubSystem(sub1_trans_mol,
dft_method,
active_method)
sub2_trans = cluster_subsystem.ClusterEnvSubSystem(sub2_trans_mol, dft_method)
sup_trans = cluster_supersystem.ClusterSuperSystem([sub1_trans, sub2_trans],
dft_method)
sup_trans.freeze_and_thaw()
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)