def check_water_hf_sto3g(scheme, expecting, needs_padb=True, **kwargs):
if needs_padb:
proatomdb = get_proatomdb_hf_sto3g()
kwargs['proatomdb'] = proatomdb
# Get the IOData
fn_fchk = context.get_fn('test/water_sto3g_hf_g03.fchk')
mol = IOData.from_file(fn_fchk)
dm_full = mol.get_dm_full()
# Create a grid for the partitioning
rtf = ExpRTransform(5e-4, 2e1, 120)
rgrid = RadialGrid(rtf)
# Do the partitioning
mode = 'only' if kwargs.get('local', True) else 'discard'
grid = BeckeMolGrid(mol.coordinates,
mol.numbers,
mol.pseudo_numbers, (rgrid, 110),
random_rotate=False,
mode=mode)
moldens = mol.obasis.compute_grid_density_dm(dm_full, grid.points)
WPartClass = wpart_schemes[scheme]
wpart = WPartClass(mol.coordinates, mol.numbers, mol.pseudo_numbers, grid,
moldens, **kwargs)
names = wpart.do_all()
check_names(names, wpart)
assert abs(wpart['charges'] - expecting).max() < 2e-3
assert abs(wpart['charges'] -
wpart['cartesian_multipoles'][:, 0]).max() < 1e-3
assert abs(wpart['charges'] - wpart['pure_multipoles'][:, 0]).max() < 1e-3
check_proatom_splines(wpart)
return wpart
def write_atomdb_sto3g(dn, do_deriv=True):
padb = get_proatomdb_hf_sto3g()
if not do_deriv:
# remove the derivatives of the pro-atoms (ugly hack to test backward compatibility).
for record in padb._records:
record._deriv = None
padb.to_file(os.path.join(dn, 'atoms.h5'))
def check_water_hf_sto3g(scheme, expecting, needs_padb=True, **kwargs):
if needs_padb:
proatomdb = get_proatomdb_hf_sto3g()
kwargs['proatomdb'] = proatomdb
# Get the IOData
fn_fchk = context.get_fn('test/water_sto3g_hf_g03.fchk')
mol = IOData.from_file(fn_fchk)
dm_full = mol.get_dm_full()
# Create a grid for the partitioning
rtf = ExpRTransform(5e-4, 2e1, 120)
rgrid = RadialGrid(rtf)
# Do the partitioning
mode = 'only' if kwargs.get('local', True) else 'discard'
grid = BeckeMolGrid(mol.coordinates, mol.numbers, mol.pseudo_numbers, (rgrid, 110), random_rotate=False, mode=mode)
moldens = mol.obasis.compute_grid_density_dm(dm_full, grid.points)
WPartClass = wpart_schemes[scheme]
wpart = WPartClass(mol.coordinates, mol.numbers, mol.pseudo_numbers, grid, moldens, **kwargs)
names = wpart.do_all()
check_names(names, wpart)
assert abs(wpart['charges'] - expecting).max() < 2e-3
assert abs(wpart['charges'] - wpart['cartesian_multipoles'][:,0]).max() < 1e-3
assert abs(wpart['charges'] - wpart['pure_multipoles'][:,0]).max() < 1e-3
if kwargs.get('greedy', False):
check_proatom_splines(wpart)
return wpart
def write_atomdb_sto3g(dn, do_deriv=True):
padb = get_proatomdb_hf_sto3g()
if not do_deriv:
# remove the derivatives of the pro-atoms (ugly hack to test backward compatibility).
for record in padb._records:
record._deriv = None
padb.to_file(os.path.join(dn, 'atoms.h5'))
def check_water_hf_sto3g(scheme, expecting, needs_padb=True, **kwargs):
if needs_padb:
proatomdb = get_proatomdb_hf_sto3g()
kwargs['proatomdb'] = proatomdb
# Get the molecule
fn_fchk = context.get_fn('test/water_sto3g_hf_g03.fchk')
sys = System.from_file(fn_fchk)
sys.wfn.update_dm('alpha')
# Create a grid for the partitioning
rtf = ExpRTransform(5e-4, 2e1, 120)
rgrid = RadialGrid(rtf)
# Do the partitioning
mode = 'only' if kwargs.get('local', True) else 'discard'
grid = BeckeMolGrid(sys, (rgrid, 110), random_rotate=False, mode=mode)
WPartClass = wpart_schemes[scheme]
wpart = WPartClass(sys, grid, **kwargs)
names = wpart.do_all()
check_names(names, wpart)
assert abs(wpart['charges'] - expecting).max() < 2e-3
assert abs(wpart['charges'] - wpart['cartesian_multipoles'][:,0]).max() < 1e-3
assert abs(wpart['charges'] - wpart['pure_multipoles'][:,0]).max() < 1e-3
if kwargs.get('greedy', False):
check_proatom_splines(wpart)
