def create_random_xyz_traj_to_write(request):
natoms, frames, comment, expected_cell, precision = request.param
a, b, c, alpha, beta, gamma = mt.h2abc_deg(expected_cell)
fmt_header = "# CELL(abcABC): %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f %s"
comment = fmt_header % (a, b, c, alpha, beta, gamma, comment)
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(natoms, frames, comment)
filedesc.seek(0)
masses = [Elements.mass(_am) for _am in atom_names]
cell_list = []
atoms_list = []
for _fr in xrange(frames):
cell = Cell(expected_cell)
atoms = Atoms(natoms)
atoms.q[:] = xyz[_fr * natoms * 3:(_fr + 1) * natoms * 3]
atoms.names = atom_names[_fr * natoms:(_fr + 1) * natoms]
atoms.m[:] = masses[_fr * natoms:(_fr + 1) * natoms]
atoms_list.append(atoms)
cell_list.append(cell)
return (filedesc, atoms_list, cell_list, comment, precision)
def test_process_units_object(units_preparation):
natoms, frames, comment, conver_xyz, conver_cell = units_preparation
output = 'objects'
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(
natoms, frames, comment)
cell = mt.abc2h(1.0, 1.0, 1.0, np.pi / 2.0, np.pi / 2.0, np.pi / 2.0)
masses = []
_count = 0
for _at in atom_names:
print(Elements.mass(_at), _count, _at)
masses.append(Elements.mass(_at))
_count += 1
masses = np.array(masses)
res = testing.process_units(comment,
cell.copy(),
xyz.copy(),
np.array(atom_names).copy(),
np.array(masses).copy(),
output=output)
npt.assert_array_almost_equal(res['atoms'].q, xyz * conver_xyz, 5)
npt.assert_array_almost_equal(res['atoms'].m, masses, 5)
npt.assert_array_almost_equal(res['cell'].h, cell * conver_cell, 5)
npt.assert_array_equal(res['atoms'].names, atom_names, 5)
def test_process_units_noobj(units_preparation):
natoms, frames, comment, conver_xyz, conver_cell = units_preparation
output = 'noobj'
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(
natoms, frames, comment)
cell = mt.abc2h(1.0, 1.0, 1.0, np.pi / 2.0, np.pi / 2.0, np.pi / 2.0)
masses = []
_count = 0
print('atom_names', atom_names)
for _at in atom_names:
print(Elements.mass(_at), _count, _at)
masses.append(Elements.mass(_at))
_count += 1
masses = np.array(masses)
type(masses)
res = testing.process_units(comment,
cell.copy(),
xyz.copy(),
np.array(atom_names).copy(),
np.array(masses).copy(),
output=output)
print(xyz, res['data'])
npt.assert_array_almost_equal(res['data'], xyz * conver_xyz, 5)
npt.assert_array_almost_equal(res['masses'], masses, 5)
npt.assert_array_almost_equal(res['cell'], cell * conver_cell, 5)
npt.assert_array_equal(res['names'], atom_names, 5)
assert res['natoms'] == natoms
def test_process_units_object(units_preparation):
natoms, frames, comment, conver_xyz, conver_cell = units_preparation
output = 'objects'
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(natoms,
frames, comment)
cell = mt.abc2h(1.0, 1.0, 1.0, np.pi / 2.0, np.pi / 2.0, np.pi / 2.0)
masses = []
_count = 0
for _at in atom_names:
print Elements.mass(_at), _count, _at
masses.append(Elements.mass(_at))
_count += 1
masses = np.array(masses)
res = testing.process_units(comment, cell.copy(), xyz.copy(), np.array(atom_names).copy(), np.array(masses).copy(), output=output)
npt.assert_array_almost_equal(res['atoms'].q, xyz * conver_xyz, 5)
npt.assert_array_almost_equal(res['atoms'].m, masses, 5)
npt.assert_array_almost_equal(res['cell'].h, cell * conver_cell, 5)
npt.assert_array_equal(res['atoms'].names, atom_names, 5)
def test_process_units_noobj(units_preparation):
natoms, frames, comment, conver_xyz, conver_cell = units_preparation
output = 'noobj'
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(natoms,
frames, comment)
cell = mt.abc2h(1.0, 1.0, 1.0, np.pi / 2.0, np.pi / 2.0, np.pi / 2.0)
masses = []
_count = 0
print 'atom_names', atom_names
for _at in atom_names:
print Elements.mass(_at), _count, _at
masses.append(Elements.mass(_at))
_count += 1
masses = np.array(masses)
type(masses)
res = testing.process_units(comment, cell.copy(), xyz.copy(), np.array(atom_names).copy(), np.array(masses).copy(), output=output)
print xyz, res['data']
npt.assert_array_almost_equal(res['data'], xyz * conver_xyz, 5)
npt.assert_array_almost_equal(res['masses'], masses, 5)
npt.assert_array_almost_equal(res['cell'], cell * conver_cell, 5)
npt.assert_array_equal(res['names'], atom_names, 5)
assert res['natoms'] == natoms
def create_xyz_sample_file(request):
""" Create a fake xyz file and build the atoms and cell object from it.
"""
natoms, frames, comment, expected_cell, units_conv_at, units_conv_cell = request.param
filedesc, xyz, atoms_names = xyz_gen.xyz_traj_filedesc(natoms, frames, comment)
# init_file needs to read from a real file...
tmp_file = tmp.NamedTemporaryFile(mode='wr', prefix='ipi_testing-tmp', delete=False)
tmp_file.seek(0)
tmp_file.write(filedesc.read())
tmp_file.close()
filedesc.close()
masses = np.zeros(natoms * frames)
for _ii, _at in enumerate(atoms_names):
masses[_ii] = Elements.mass(_at)
ratoms = []
for _fr in range(frames):
ratoms.append(Atoms(natoms))
ratoms[-1].q = xyz[_fr * natoms * 3:3 * (_fr + 1) * natoms] * units_conv_at
ratoms[-1].m = masses[_fr * natoms:(_fr + 1) * natoms]
ratoms[-1].names = atoms_names[_fr * natoms:(_fr + 1) * natoms]
cell = Cell(expected_cell * units_conv_cell)
# remove temp file created during this test
def delete_files_after_testing():
if os.path.isfile(tmp_file.name):
os.remove(tmp_file.name)
request.addfinalizer(delete_files_after_testing)
return tmp_file, cell, ratoms
def prepare_read_file(request):
natoms, nframes, comment, output_type, file_type, expected_cell, unit_conv_cell, unit_conv_q = request.param
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(natoms, nframes, comment)
expected_q = xyz.copy()
expected_names = atom_names[:]
# if comment.find('CELL') < 0:
# unit_conv_cell = 1.0
return file_type, filedesc, output_type, expected_q, expected_cell, expected_names, unit_conv_cell, unit_conv_q
def prepare_read_file(request):
natoms, nframes, comment, output_type, file_type, expected_cell, unit_conv_cell, unit_conv_q = request.param
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(natoms, nframes, comment)
expected_q = xyz.copy()
expected_names = atom_names[:]
if comment.find('CELL') < 0:
unit_conv_cell = 1.0
return file_type, filedesc, output_type, expected_q, expected_cell, expected_names, unit_conv_cell, unit_conv_q
def create_random_xyz_traj_to_read(request):
natoms, frames, comment, expected_cell, precision = request.param
filedesc, xyz, atom_names = xyz_gen.xyz_traj_filedesc(natoms,
frames, comment)
filedesc.seek(0)
check_comment = re.match('# CELL[\(\[\{]H[\)\]\}]: ([-0-9\.?Ee ]*)\s*', comment) # pylint: disable=W1401
if check_comment:
genh = np.array(check_comment.group(1).split()[:9], float).reshape((3, 3))
invgenh = np.linalg.inv(genh)
for _ui in xrange(natoms * frames):
_uu = np.array([xyz[3 * _ui], xyz[3 * _ui + 1], xyz[3 * _ui + 2]])
_us = np.dot(_uu, invgenh)
_uu = np.dot(expected_cell, _us)
xyz[3 * _ui], xyz[3 * _ui + 1], xyz[3 * _ui + 2] = _uu
return (filedesc, xyz, atom_names, natoms, frames,
comment, expected_cell, precision)
