def test_uniformgrid_from_molecule_o2_uhf():
with path('chemtools.data', 'o2_uhf.fchk') as fpath:
mol = Molecule.from_file(str(fpath))
# create cube file from molecule:
cube = UniformGrid.from_molecule(mol)
# test the cube gives the right result:
origin_result = [-5.0, -5.0, -6.1]
axes_result = [[0.0, 0.0, 0.2], [0.0, 0.2, 0.0], [0.2, 0.0, 0.0]]
shape_result = [61, 50, 50]
weight_result = np.full(cube.npoints, 0.0080)
np.testing.assert_array_almost_equal(cube.origin, origin_result, decimal=7)
np.testing.assert_array_almost_equal(cube.axes, axes_result, decimal=7)
np.testing.assert_array_equal(cube.shape, shape_result)
np.testing.assert_array_almost_equal(cube.weights(), weight_result, decimal=7)
np.testing.assert_array_almost_equal(cube.weights(method='R0'), weight_result, decimal=7)
np.testing.assert_array_almost_equal(cube.weights(method='R'), weight_result, decimal=7)
# test integration of Fukui functions:
tool = LocalConceptualDFT.from_file(str(fpath), model='linear', points=cube.points)
ffm_default = cube.integrate(tool.ff_minus)
ffm_r = cube.integrate(tool.ff_minus, method='R')
ffm_r0 = cube.integrate(tool.ff_minus, method='R0')
np.testing.assert_almost_equal(ffm_default, ffm_r, decimal=7)
np.testing.assert_almost_equal(ffm_r, ffm_r0, decimal=7)
np.testing.assert_almost_equal(ffm_default, 1.000, decimal=2)
np.testing.assert_almost_equal(ffm_default, 1.000, decimal=2)
np.testing.assert_almost_equal(ffm_default, 1.000, decimal=2)
def test_critical_point_h2o():
# test against multiwfn 3.6 dev src
with path("chemtools.data",
"data_multiwfn36_fchk_h2o_q+0_ub3lyp_ccpvtz.npz") as fname:
data = np.load(str(fname))
nna, bcp = data["nna_coords"], data["bcp_coords"]
# find critical points
with path("chemtools.data", "h2o_q+0_ub3lyp_ccpvtz.fchk") as fpath:
mol = Molecule.from_file(fpath)
cub = UniformGrid.from_molecule(mol,
spacing=0.15,
extension=0.1,
rotate=False)
top = TopologicalTool.from_molecule(mol, points=cub.points)
# check NA
assert len(top.nna) == 3
assert sum([np.allclose(top.nna[0].coordinate, c, rtol=0.0)
for c in nna]) == 1
assert sum([np.allclose(top.nna[1].coordinate, c, rtol=0.0)
for c in nna]) == 1
assert sum([np.allclose(top.nna[2].coordinate, c, rtol=0.0)
for c in nna]) == 1
# check BCP
assert len(top.bcp) == 2
assert sum([np.allclose(top.bcp[0].coordinate, c, rtol=0.0)
for c in bcp]) == 1
assert sum([np.allclose(top.bcp[1].coordinate, c, rtol=0.0)
for c in bcp]) == 1
# check total number of CP
assert len(top.rcp) == 0
assert len(top.ccp) == 0
assert len(top.cps) == 5
assert top.poincare_hopf_equation
def from_molecule(cls, molecule, spin="ab", index=None, points=None):
"""Initialize class from ``Molecule`` object.
Parameters
----------
molecule : instance of `Molecule` class.
Instance of `Molecular` class.
spin : str, optional
The type of occupied spin orbitals; options are "a", "b" & "ab".
index : int or Sequence of int, optional
Sequence of integers representing the index of spin orbitals.
If None, all occupied spin orbitals are included.
points : np.ndarray, optional
Cartesian coordinates of points used for critical point search.
If None, cubic grid points with spacing=0.1 & extension=0.1 are used.
"""
if points is None:
points = UniformGrid.from_molecule(molecule,
spacing=0.1,
extension=0.1).points
func_dens = cls._wrapper_compute_density(molecule,
spin=spin,
index=index)
func_grad = cls._wrapper_compute_gradient(molecule,
spin=spin,
index=index)
func_hess = cls._wrapper_compute_hessian(molecule,
spin=spin,
index=index)
return cls(func_dens, func_grad, func_hess, points,
molecule.coordinates)
def _check_grid(molecule, grid):
if grid is None:
grid = UniformGrid.from_molecule(molecule, spacing=0.1, extension=2.0)
elif not hasattr(grid, 'points'):
raise ValueError('Argument grid should have "points" attribute!')
return grid
def load_molecule_and_grid(fname, cube):
"""Return instances of molecule and uniform cubic grid.
Parameters
----------
fname : str
Path to wave-function file.
cube : str
Uniform cubic grid specifications.
"""
# load molecule
mol = Molecule.from_file(fname)
if cube.endswith(".cube"):
# load & check cube file
cube = UniformGrid.from_cube(cube)
if np.allclose(mol.numbers, cube.numbers):
raise ValueError(
"Atomic number in {0} & {1} should be the same!".format(
fname, cube))
if np.allclose(mol.coordinates, cube.coordinates):
raise ValueError(
"Atomic coordinates in {0} & {1} should be the same!".format(
cube.fname, cube.cube))
elif len(cube.split(",")) == 2:
# make a cubic grid
spacing, extension = [float(item) for item in cube.split(",")]
cube = UniformGrid.from_molecule(mol,
spacing=spacing,
extension=extension,
rotate=True)
else:
raise ValueError("Argument cube={0} is not recognized!".format(cube))
return mol, cube
def generate_scripts(self, fname, spin='a', index=None, isosurf=0.05, grid=None):
"""Generate VMD script(s) and cube file(s) to visualize MO iso-surface of given orbitals.
Parameters
----------
fname : str
A string representing the path to a fname of generated files.
The VMD script and cube file will be named fname_mo{index}.vmd and
fname_mo{index}.cube, respectively.
spin : str, optional
The type of occupied spin orbitals. Choose either 'a' or 'b'.
index : int, optional
Integer representing the index of spin orbital to visualize. Spin orbitals are each
indexed from 1 to :attr:`nbasis`. If None, files for visualizing all orbitals are
generated.
isosurf : float, optional
Value of MO iso-surface used in VMD script.
grid : UniformGrid, optional
Instance of UniformGrid used for computation and generating cube file(s).
If None, a cubic grid is constructed from molecule with spacing=0.2 & extension=5.0.
"""
if spin not in ['a', 'b']:
raise ValueError('Argument spin can only be "a" or "b".')
if index is not None and not isinstance(index, int):
raise ValueError('Argument index is either None or an integer for visualization. '
'Given index={0}'.format(index))
if grid is None:
grid = UniformGrid.from_molecule(self._molecule, spacing=0.2, extension=5.0, rotate=True)
elif not isinstance(grid, UniformGrid):
raise ValueError('Argument grid should be a UniformGrid to generate cube files.')
if index is None:
spin_index = {'a': 0, 'b': 1}
index = range(1, self._molecule.mo.homo_index[spin_index[spin]] + 1)
else:
index = [index]
for mo_index in index:
vmdname = fname + '_mo{0}.vmd'.format(mo_index)
cubname = fname + '_mo{0}.cube'.format(mo_index)
mo_value = self.compute_orbital_expression(grid.points, spin=spin, index=mo_index)
grid.generate_cube(cubname, mo_value)
print_vmd_script_isosurface(vmdname, cubname, isosurf=isosurf, negative=True,
material='BlownGlass')
def test_uniformgrid_o2_raises():
with path('chemtools.data', 'o2_uhf.fchk') as fpath:
mol = Molecule.from_file(str(fpath))
cube = UniformGrid.from_molecule(mol)
tool = LocalConceptualDFT.from_file(str(fpath), model='linear', points=cube.points)
o = np.array([-3.0, -3.0, -3.0])
a = np.array([[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]])
s = np.array([3, 3, 3])
# check ValueError
assert_raises(ValueError, UniformGrid, mol.numbers, mol.pseudo_numbers, mol.coordinates,
np.array([0.]), a, s)
assert_raises(ValueError, UniformGrid, mol.numbers, mol.pseudo_numbers, mol.coordinates,
o, np.array([0.]), s)
assert_raises(ValueError, UniformGrid, mol.numbers, mol.pseudo_numbers, mol.coordinates,
o, a, np.array([0.]))
assert_raises(ValueError, UniformGrid.from_cube, 'test.wrong_end')
assert_raises(ValueError, cube.generate_cube, 'test.wrong_end', tool.ff_minus)
assert_raises(ValueError, cube.generate_cube, 'test.cube', np.array([0.]))
assert_raises(ValueError, cube.weights, method='erroneous')
assert_raises(ValueError, cube.integrate, np.array([0.]))
def test_uniformgrid_points_h2o():
# replace this test with a better one later
with path('chemtools.data', 'h2o_dimer_pbe_sto3g.fchk') as fpath:
cube = UniformGrid.from_file(fpath, spacing=2.0, extension=0.0, rotate=True)
expected = np.array([[-2.31329824e+00, -2.00000000e+00, 3.82735565e+00],
[-2.31329824e+00, -4.99999997e-09, 3.82735565e+00],
[-3.19696330e-01, -2.00000000e+00, 3.98720381e+00],
[-3.19696330e-01, -4.99999997e-09, 3.98720381e+00],
[-2.15345008e+00, -2.00000000e+00, 1.83375375e+00],
[-2.15345008e+00, -4.99999997e-09, 1.83375375e+00],
[-1.59848169e-01, -2.00000000e+00, 1.99360191e+00],
[-1.59848169e-01, -4.99999997e-09, 1.99360191e+00],
[-1.99360191e+00, -2.00000000e+00, -1.59848162e-01],
[-1.99360191e+00, -4.99999997e-09, -1.59848162e-01],
[-6.77400003e-09, -2.00000000e+00, 0.00000000e+00],
[-6.77400003e-09, -4.99999997e-09, 0.00000000e+00],
[-1.83375375e+00, -2.00000000e+00, -2.15345007e+00],
[-1.83375375e+00, -4.99999997e-09, -2.15345007e+00],
[ 1.59848155e-01, -2.00000000e+00, -1.99360191e+00],
[ 1.59848155e-01, -4.99999997e-09, -1.99360191e+00]])
assert_allclose(cube.points, expected, rtol=1.e-7, atol=1.e-7)
def test_cube_h2o_dimer():
# test against previous generated .cube files
with path('chemtools.data', 'h2o_dimer_pbe_sto3g-dens.cube') as file_path:
cube = UniformGrid.from_cube(file_path)
mol1 = Molecule.from_file(str(file_path))
with tmpdir('chemtools.test.test_base.test_cube_h2o_dimer') as dn:
cube2 = '%s/%s' % (dn, 'h2o_dimer_pbe_sto3g-dens.cube')
cube.generate_cube(cube2, mol1.cube_data)
cube2 = '%s/%s' % (dn, 'h2o_dimer_pbe_sto3g-dens.cube')
mol2 = Molecule.from_file(cube2)
# Check coordinates
np.testing.assert_array_almost_equal(mol1.coordinates, mol2.coordinates, decimal=6)
np.testing.assert_equal(mol1.numbers, mol2.numbers)
# Check grid data
ugrid1 = mol1.grid
ugrid2 = mol2.grid
np.testing.assert_array_almost_equal(ugrid1.grid_rvecs, ugrid2.grid_rvecs, decimal=6)
np.testing.assert_equal(ugrid1.shape, ugrid2.shape)
data1 = mol1.cube_data / mol1.cube_data
data2 = mol2.cube_data / mol1.cube_data
np.testing.assert_array_almost_equal(data1, data2, decimal=4)
np.testing.assert_equal(mol1.pseudo_numbers, mol2.pseudo_numbers)
def test_uniformgrid_from_file_o2_uhf():
with path('chemtools.data', 'o2_uhf.fchk') as fpath:
mol = Molecule.from_file(str(fpath))
# create cube file from file:
cube = UniformGrid.from_file(fpath, spacing=0.5, extension=6.0, rotate=False)
# test the cube gives the right result:
origin_result = [-6.0, -6.0, -7.25]
axes_result = [[0.5, 0.0, 0.0],
[0.0, 0.5, 0.0],
[0.0, 0.0, 0.5]]
shape_result = [24, 24, 29]
weight_result = np.full(cube.npoints, 0.125)
np.testing.assert_array_almost_equal(cube.origin, origin_result, decimal=7)
np.testing.assert_array_almost_equal(cube.axes, axes_result, decimal=7)
np.testing.assert_array_equal(cube.shape, shape_result)
np.testing.assert_array_equal(cube.numbers, mol.numbers)
np.testing.assert_array_almost_equal(cube.coordinates, mol.coordinates, decimal=10)
np.testing.assert_array_almost_equal(cube.pseudo_numbers, mol.pseudo_numbers, decimal=10)
np.testing.assert_array_almost_equal(cube.weights(), weight_result, decimal=7)
np.testing.assert_array_almost_equal(cube.weights(method='R0'), weight_result, decimal=7)
np.testing.assert_array_almost_equal(cube.weights(method='R'), weight_result, decimal=7)
def test_critical_point_c4h4():
# test against multiwfn 3.6 dev src
with path("chemtools.data",
"data_multiwfn36_fchk_c4h4_ub3lyp_ccpvdz.npz") as fname:
data = np.load(str(fname))
nna, bcp = data["nna_coords"], data["bcp_coords"]
rcp, ccp = data["rcp_coords"], data["ccp_coords"]
# find critical points
with path("chemtools.data", "c4h4_ub3lyp_ccpvdz.fchk") as fpath:
mol = Molecule.from_file(fpath)
cub = UniformGrid.from_molecule(mol,
spacing=0.25,
extension=0.1,
rotate=False)
top = TopologicalTool.from_molecule(mol, points=cub.points)
# check NA
assert len(top.nna) == 8
assert sum([
np.allclose(top.nna[0].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in nna
]) == 1
assert sum([
np.allclose(top.nna[1].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in nna
]) == 1
assert sum([
np.allclose(top.nna[2].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in nna
]) == 1
assert sum([
np.allclose(top.nna[3].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in nna
]) == 1
assert sum([
np.allclose(top.nna[4].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in nna
]) == 1
assert sum([
np.allclose(top.nna[5].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in nna
]) == 1
assert sum([
np.allclose(top.nna[6].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in nna
]) == 1
assert sum([
np.allclose(top.nna[7].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in nna
]) == 1
# check BCP
assert len(top.bcp) == 10
assert sum([
np.allclose(top.bcp[0].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in bcp
]) == 1
assert sum([
np.allclose(top.bcp[2].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in bcp
]) == 1
assert sum([
np.allclose(top.bcp[3].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in bcp
]) == 1
assert sum([
np.allclose(top.bcp[4].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in bcp
]) == 1
assert sum([
np.allclose(top.bcp[5].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in bcp
]) == 1
assert sum([
np.allclose(top.bcp[6].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in bcp
]) == 1
assert sum([
np.allclose(top.bcp[7].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in bcp
]) == 1
assert sum([
np.allclose(top.bcp[8].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in bcp
]) == 1
assert sum([
np.allclose(top.bcp[9].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in bcp
]) == 1
# check RCP
assert len(top.rcp) == 4
assert sum([
np.allclose(top.rcp[0].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in rcp
]) == 1
assert sum([
np.allclose(top.rcp[1].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in rcp
]) == 1
assert sum([
np.allclose(top.rcp[2].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in rcp
]) == 1
assert sum([
np.allclose(top.rcp[3].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in rcp
]) == 1
# check CCP
assert len(top.ccp) == 1
assert sum([
np.allclose(top.ccp[0].coordinate, c, rtol=0.0, atol=1.0e-5)
for c in ccp
]) == 1
# check total number of CP
assert len(top.cps) == 23
assert top.poincare_hopf_equation