def load_rho(coordinates, numbers, fn_cube, ref_ugrid, stride, chop):
'''Load densities from a file, reduce by stride, chop and check ugrid
**Arguments:**
coordinates
An array with shape (N, 3) containing atomic coordinates.
numbers
A vector with shape (N,) containing atomic numbers.
fn_cube
The cube file with the electron density.
ref_ugrid
A reference ugrid that must match the one from the density cube
file (after reduction).
stride
The reduction factor.
chop
The number of slices to chop of the grid in each direction.
'''
if fn_cube is None:
# Load the built-in database of proatoms
natom = len(numbers)
numbers = np.unique(numbers)
proatomdb = ProAtomDB.from_refatoms(numbers,
max_kation=0,
max_anion=0,
agspec='fine')
# Construct the pro-density
rho = np.zeros(ref_ugrid.shape)
for i in xrange(natom):
spline = proatomdb.get_spline(numbers[i])
ref_ugrid.eval_spline(spline, coordinates[i], rho)
else:
# Load cube
mol_rho = IOData.from_file(fn_cube)
rho = mol_rho.cube_data
ugrid = mol_rho.grid
# Reduce grid size
if stride > 1:
rho, ugrid = reduce_data(rho, ugrid, stride, chop)
# Compare with ref_ugrid (only shape)
if (ugrid.shape != ref_ugrid.shape).any():
raise ValueError(
'The densities file does not contain the same amount if information as the potential file.'
)
return rho
def test_plot_atoms():
padb = ProAtomDB.from_refatoms(numbers=[8, 1], max_cation=1, max_anion=1)
with tmpdir('horton.scripts.test.test_atomdb.test_plot_atoms') as dn:
plot_atoms(padb, dn)
fns = [
'dens_001__h.png',
'rdens_001__h.png',
'fukui_001__h.png',
'rfukui_001__h.png',
'dens_008__o.png',
'rdens_008__o.png',
'fukui_008__o.png',
'rfukui_008__o.png',
]
check_files(dn, fns)
def test_plot_atoms():
padb = ProAtomDB.from_refatoms(numbers=[8, 1], max_cation=1, max_anion=1)
with tmpdir("horton.scripts.test.test_atomdb.test_plot_atoms") as dn:
plot_atoms(padb, dn)
fns = [
"dens_001__h.png",
"rdens_001__h.png",
"fukui_001__h.png",
"rfukui_001__h.png",
"dens_008__o.png",
"rdens_008__o.png",
"fukui_008__o.png",
"rfukui_008__o.png",
]
check_files(dn, fns)
def load_rho(system, fn_cube, ref_ugrid, stride, chop):
'''Load densities from a file, reduce by stride, chop and check ugrid
**Arguments:**
system
A Horton system object for the current system. This is only used
to construct the pro-density.
fn_cube
The cube file with the electron density.
ref_ugrid
A reference ugrid that must match the one from the density cube
file (after reduction).
stride
The reduction factor.
chop
The number of slices to chop of the grid in each direction.
'''
if fn_cube is None:
# Load the built-in database of proatoms
numbers = np.unique(system.numbers)
proatomdb = ProAtomDB.from_refatoms(numbers,
max_kation=0,
max_anion=0,
agspec='fine')
# Construct the pro-density
rho = np.zeros(ref_ugrid.shape)
for i in xrange(system.natom):
spline = proatomdb.get_spline(system.numbers[i])
ref_ugrid.eval_spline(spline, system.coordinates[i], rho)
else:
# Load cube
sys = System.from_file(fn_cube)
rho = sys.extra['cube_data']
ugrid = sys.grid
# Reduce grid size
if stride > 1:
rho, ugrid = reduce_data(rho, ugrid, stride, chop)
# Compare with ref_ugrid (only shape)
if (ugrid.shape != ref_ugrid.shape).any():
raise ValueError(
'The densities file does not contain the same amount if information as the potential file.'
)
return rho
def load_rho(coordinates, numbers, fn_cube, ref_ugrid, stride, chop):
'''Load densities from a file, reduce by stride, chop and check ugrid
**Arguments:**
coordinates
An array with shape (N, 3) containing atomic coordinates.
numbers
A vector with shape (N,) containing atomic numbers.
fn_cube
The cube file with the electron density.
ref_ugrid
A reference ugrid that must match the one from the density cube
file (after reduction).
stride
The reduction factor.
chop
The number of slices to chop of the grid in each direction.
'''
if fn_cube is None:
# Load the built-in database of proatoms
natom = len(numbers)
numbers = np.unique(numbers)
proatomdb = ProAtomDB.from_refatoms(numbers, max_cation=0, max_anion=0, agspec='fine')
# Construct the pro-density
rho = np.zeros(ref_ugrid.shape)
for i in xrange(natom):
spline = proatomdb.get_spline(numbers[i])
ref_ugrid.eval_spline(spline, coordinates[i], rho)
else:
# Load cube
mol_rho = IOData.from_file(fn_cube)
rho = mol_rho.cube_data
ugrid = mol_rho.grid
# Reduce grid size
if stride > 1:
rho, ugrid = reduce_data(rho, ugrid, stride, chop)
# Compare with ref_ugrid (only shape)
if (ugrid.shape != ref_ugrid.shape).any():
raise ValueError('The densities file does not contain the same amount if information as the potential file.')
return rho
def load_rho(system, fn_cube, ref_ugrid, stride, chop):
'''Load densities from a file, reduce by stride, chop and check ugrid
**Arguments:**
system
A Horton system object for the current system. This is only used
to construct the pro-density.
fn_cube
The cube file with the electron density.
ref_ugrid
A reference ugrid that must match the one from the density cube
file (after reduction).
stride
The reduction factor.
chop
The number of slices to chop of the grid in each direction.
'''
if fn_cube is None:
# Load the built-in database of proatoms
numbers = np.unique(system.numbers)
proatomdb = ProAtomDB.from_refatoms(numbers, max_kation=0, max_anion=0, agspec='fine')
# Construct the pro-density
rho = np.zeros(ref_ugrid.shape)
for i in xrange(system.natom):
spline = proatomdb.get_spline(system.numbers[i])
ref_ugrid.eval_spline(spline, system.coordinates[i], rho)
else:
# Load cube
sys = System.from_file(fn_cube)
rho = sys.extra['cube_data']
ugrid = sys.grid
# Reduce grid size
if stride > 1:
rho, ugrid = reduce_data(rho, ugrid, stride, chop)
# Compare with ref_ugrid (only shape)
if (ugrid.shape != ref_ugrid.shape).any():
raise ValueError('The densities file does not contain the same amount if information as the potential file.')
return rho