def setUp(self):
tmp_system = dpdata.System()
tmp_system.from_vasp_poscar(os.path.join('poscars', 'POSCAR.oh.d'))
# tmp_system.from_lammps_lmp(os.path.join('poscars', 'conf.lmp'), type_map = ['O', 'H'])
tmp_system.to_vasp_poscar('tmp.POSCAR')
self.system = dpdata.System()
self.system.from_vasp_poscar('tmp.POSCAR')
def test_failed_append(self):
sys1 = dpdata.System('poscars/POSCAR.h2o.md', fmt='vasp/poscar')
sys2 = dpdata.System('poscars/POSCAR.h4o3', fmt='vasp/poscar')
with self.assertRaises(Exception) as c:
sys1.append(sys2)
self.assertTrue("systems with inconsistent formula could not be append"
in str(c.exception))
def setUp(self):
self.system_1 = dpdata.System('amber/sqm.out', fmt='sqm/out')
self.system_1.to('deepmd/npy', 'tmp.deepmd.npy')
self.system_2 = dpdata.System('tmp.deepmd.npy', fmt='deepmd/npy')
self.places = 5
self.e_places = 4
self.f_places = 6
self.v_places = 6
def setUp(self, random_mock):
random_mock.rand = ConstGenerator().rand
random_mock.randn = ConstGenerator().randn
system_1_origin = dpdata.System('poscars/POSCAR.SiC',
fmt='vasp/poscar')
self.system_1 = system_1_origin.perturb(1, 0.05, 0.6, 'const')
self.system_2 = dpdata.System('poscars/POSCAR.SiC.const',
fmt='vasp/poscar')
self.places = 6
def setUp(self):
self.system_1 = dpdata.System('poscars/POSCAR.SiC', fmt='vasp/poscar')
self.system_1.replicate((
1,
2,
3,
))
self.system_2 = dpdata.System('poscars/POSCAR.SiC', fmt='vasp/poscar')
self.places = 6
def test_dump_vasp_type_map(self):
system0 = dpdata.System(os.path.join('poscars', 'POSCAR.oh.d'),
fmt='vasp/poscar',
type_map=['H', 'O'])
system0.to_vasp_poscar('POSCAR.tmp.1')
system1 = dpdata.System(os.path.join('poscars', 'POSCAR.oh.d'),
fmt='vasp/poscar',
type_map=['C', 'H', 'A', 'O', 'B'])
system1.to_vasp_poscar('POSCAR.tmp.2')
myfilecmp(self, 'POSCAR.tmp.1', 'POSCAR.tmp.2')
def setUp(self, random_mock):
random_mock.choice = ConstGenerator().choice
self.system_1 = dpdata.System('poscars/POSCAR.P42nmc',
fmt='vasp/poscar')
self.system_1.replace('Hf', 'Zr', 8)
# print(self.system_1.data)
self.system_2 = dpdata.System('poscars/POSCAR.P42nmc.replace',
fmt='vasp/poscar')
# print(self.system_2.data)
self.places = 6
def setUp(self):
self.system_1 = dpdata.System('poscars/POSCAR.h2o.md',
fmt='vasp/poscar')
self.system_1.to_deepmd_raw('tmp.deepmd')
self.system_2 = dpdata.System('tmp.deepmd',
fmt='deepmd/raw',
type_map=['O', 'H'])
self.places = 6
self.e_places = 6
self.f_places = 6
self.v_places = 6
def setUp(self):
system_1 = dpdata.System()
system_1.from_lammps_lmp(os.path.join('poscars', 'conf.lmp'),
type_map=['O', 'H'])
write('tmp.POSCAR', system_1.to_ase_structure()[0], vasp5=True)
self.system_1 = system_1
self.system_2 = dpdata.System('tmp.POSCAR')
self.places = 6
self.e_places = 6
self.f_places = 6
self.v_places = 6
def setUp(self):
system_1 = dpdata.System()
system_1.from_lammps_lmp(os.path.join('poscars', 'conf.lmp'),
type_map=['O', 'H'])
system_1.to_pymatgen_structure()[0].to('poscar', 'tmp.POSCAR')
self.system_1 = system_1
self.system_2 = dpdata.System('tmp.POSCAR')
self.places = 6
self.e_places = 6
self.f_places = 6
self.v_places = 6
def setUp(self):
sys0 = dpdata.System('poscars/POSCAR.oh.d', fmt = 'vasp/poscar')
sys0.data['atom_names'] = ['A', 'H', 'B', 'O', 'D']
sys0.data['atom_numbs'] = [ 0, 1, 0, 1, 0]
sys0.data['atom_types'] = np.array([ 3, 1], dtype = int)
sys1 = dpdata.System('poscars/POSCAR.oh.d', fmt = 'vasp/poscar', type_map = ['A', 'H', 'B', 'O', 'D'])
self.system_1 = sys0
self.system_2 = sys1
self.places = 6
self.e_places = 6
self.f_places = 6
self.v_places = 6
def setUp(self):
self.system_1 = dpdata.System('poscars/POSCAR.h2o.md',
fmt='vasp/poscar')
self.system_1.to_deepmd_npy('tmp.deepmd.npy',
prec=np.float64,
set_size=2)
self.system_2 = dpdata.System('tmp.deepmd.npy',
fmt='deepmd/npy',
type_map=['O', 'H'])
self.places = 6
self.e_places = 6
self.f_places = 6
self.v_places = 6
def setUp(self):
self.system_1 = dpdata.System(os.path.join('poscars', 'conf.5.dump'),
type_map=['O', 'H'],
begin=1,
step=2)
self.system_2 = dpdata.System(os.path.join('poscars', 'conf.5.dump'),
type_map = ['O', 'H'],
begin = 0,
step = 1) \
.sub_system(np.arange(1,5,2))
self.places = 6
self.e_places = 6
self.f_places = 6
self.v_places = 4
def setUp(self):
self.system_1 = dpdata.System(os.path.join('pwscf.traj', 'traj6'),
fmt = 'pwscf/traj',
begin = 1,
step = 2)
self.system_2 = dpdata.System(os.path.join('pwscf.traj', 'traj6'),
fmt = 'pwscf/traj',
begin = 0,
step = 1) \
.sub_system(np.arange(1,6,2))
self.places = 6
self.e_places = 6
self.f_places = 6
self.v_places = 4
def setUp(self):
self.system = dpdata.System()
self.system.from_lammps_lmp(os.path.join('poscars', 'conf.waterion.lmp'),
type_map = ['O', 'H'])
self.bonds = dpdata.md.water.compute_bonds(self.system.data['cells'][0],
self.system.data['coords'][0],
self.system.data['atom_types'])
def test_read_file(self):
system = dpdata.System('gromacs/multi_frames.gro', type_map=['H', 'O'])
self.assertTrue('H' in system['atom_names'])
self.assertTrue('O' in system['atom_names'])
self.assertEqual(system['atom_numbs'], [6, 3])
for cc, ii in enumerate([1, 0, 0, 1, 0, 0, 1, 0, 0]):
self.assertEqual(system['atom_types'][cc], ii)
self.assertEqual(len(system['cells']), 2)
self.assertEqual(len(system['coords']), 2)
for ii in range(3):
for jj in range(3):
if ii != jj:
self.assertAlmostEqual(system['cells'][0][ii][jj],
0) # frame no.1
self.assertAlmostEqual(system['cells'][1][ii][jj],
0) # frame no.2
# frame no.1
self.assertAlmostEqual(system['cells'][0][0][0], 7.822838765564372)
self.assertAlmostEqual(system['cells'][0][1][1], 7.353572647182051)
self.assertAlmostEqual(system['cells'][0][2][2], 9.036518515423753)
self.assertAlmostEqual(system['coords'][0][8][0], 7.43)
self.assertAlmostEqual(system['coords'][0][8][1], 5.12)
self.assertAlmostEqual(system['coords'][0][8][2], 3.36)
# frame no.2
self.assertAlmostEqual(system['cells'][1][0][0], 7.822838765564372)
self.assertAlmostEqual(system['cells'][1][1][1], 7.353572647182051)
self.assertAlmostEqual(system['cells'][1][2][2], 9.036518515423753)
self.assertAlmostEqual(system['coords'][1][8][0], 7.43)
self.assertAlmostEqual(system['coords'][1][8][1], 5.12)
self.assertAlmostEqual(system['coords'][1][8][2], 3.36)
def setUp(self):
self.dir_name = 'tmp.deepmd.npy.nol'
natoms = 3
atom_names = ['O', 'H']
atom_numbs = [1, 2]
atom_types = np.array([0, 1, 1], dtype=np.int32)
nframes = 11
half_n = 6
idx = [range(0, half_n), range(half_n, nframes)]
os.makedirs(self.dir_name, exist_ok=True)
os.makedirs(os.path.join(self.dir_name, 'set.000'), exist_ok=True)
os.makedirs(os.path.join(self.dir_name, 'set.001'), exist_ok=True)
np.savetxt(os.path.join(self.dir_name, 'type.raw'),
atom_types,
fmt='%d')
coords = np.random.random([nframes, natoms, 3])
cells = np.random.random([nframes, 3, 3])
np.save(os.path.join(self.dir_name, 'set.000', 'coord.npy'),
coords[idx[0]])
np.save(os.path.join(self.dir_name, 'set.000', 'box.npy'),
cells[idx[0]])
np.save(os.path.join(self.dir_name, 'set.001', 'coord.npy'),
coords[idx[1]])
np.save(os.path.join(self.dir_name, 'set.001', 'box.npy'),
cells[idx[1]])
data = {
'atom_names': atom_names,
'atom_types': atom_types,
'atom_numbs': atom_numbs,
'coords': coords,
'cells': cells,
'orig': np.zeros(3),
}
self.system_1 = dpdata.System(self.dir_name,
fmt='deepmd/npy',
type_map=['O', 'H'])
self.system_2 = dpdata.System()
self.system_2.data = data
self.places = 6
self.e_places = 6
self.f_places = 6
self.v_places = 6
def setUpClass(cls) -> None:
sp.check_output([
"dpdata", "poscars/conf.lmp", "--type-map", "O", "H",
"-olammps/lmp", "-O", "tmp.lmp", "--no-labeled"
])
cls.system = dpdata.System('tmp.lmp',
fmt='lammps/lmp',
type_map=['O', 'H'])
def setUp(self):
self.places = 6
xml_sys = dpdata.LabeledSystem()
xml_sys.from_vasp_xml('poscars/vasprun.h2o.md.xml')
# init_sys = dpdata.System()
# init_sys.from_vasp_poscar('poscars/POSCAR.h2o.md')
finl_sys = dpdata.System()
finl_sys.from_vasp_poscar('poscars/CONTCAR.h2o.md')
self.system_1 = finl_sys
self.system_2 = xml_sys.sub_system([-1])
def test_no_format_atom_name(self):
system = dpdata.System("gromacs/case_for_format_atom_name.gro",
fmt='gromacs/gro',
format_atom_name=False)
atoms = [
'CL1', 'H6', 'C4', 'C3', 'C6', 'C11', 'H10', 'C2', 'N3', 'C14',
'H7', 'H8', 'C13', 'H2', 'H1', 'H4', 'O2', 'H9', 'O1', 'N2', 'C9',
'H3', 'C5', 'H11', 'N1', 'C7', 'C10', 'CL2', 'H5', 'C1', 'C8',
'C12'
]
for at in atoms:
self.assertTrue(at in system['atom_names'])
def test_to_xyz(self):
with tempfile.NamedTemporaryFile('r') as f_xyz:
dpdata.System(data={
"atom_names": ["C", "O"],
"atom_numbs": [1, 1],
"atom_types": np.array([0, 1]),
"coords": np.arange(6).reshape((1,2,3)),
"cells": np.zeros((1,3,3)),
"orig": np.zeros(3),
}).to("xyz", f_xyz.name)
xyz0 = f_xyz.read().strip()
xyz1 = "2\n\nC 0.000000 1.000000 2.000000\nO 3.000000 4.000000 5.000000"
self.assertEqual(xyz0, xyz1)
def setUp(self):
self.system = dpdata.System()
self.system.data['atom_types'] = np.array([0, 1])
self.system.data['atom_names'] = ['O', 'H']
nframes = 10
cell_size = 5
self.system.data['cells'] = np.tile(cell_size * np.eye(3),
(nframes, 1, 1))
self.system.data['coords'] = np.zeros([nframes, 2, 3])
for ff in range(nframes):
self.system.data['coords'][ff][0] = 1.0 * ff * np.array([1, 0, 0])
self.system.data['coords'][ff][1] = 2.0 * ff * np.array([1, 0, 0])
self.system.data['coords'] = self.system.data['coords'] % cell_size
def setUp(self):
self.dir_name = 'tmp.deepmd.nol'
natoms = 3
atom_names = ['O', 'H']
atom_numbs = [1, 2]
atom_types = np.array([0, 1, 1], dtype=np.int32)
nframes = 11
os.makedirs(self.dir_name, exist_ok=True)
np.savetxt(os.path.join(self.dir_name, 'type.raw'),
atom_types,
fmt='%d')
coords = np.random.random([nframes, natoms, 3])
cells = np.random.random([nframes, 3, 3])
np.savetxt(os.path.join(self.dir_name, '', 'coord.raw'),
np.reshape(coords, [nframes, -1]))
np.savetxt(os.path.join(self.dir_name, '', 'box.raw'),
np.reshape(cells, [nframes, -1]))
data = {
'atom_names': atom_names,
'atom_types': atom_types,
'atom_numbs': atom_numbs,
'coords': coords,
'cells': cells,
'orig': np.zeros(3),
}
self.system_1 = dpdata.System(self.dir_name,
fmt='deepmd/raw',
type_map=['O', 'H'])
self.system_2 = dpdata.System()
self.system_2.data = data
self.places = 6
self.e_places = 6
self.f_places = 6
self.v_places = 6
def test_poscar_to_molecule(self):
tmp_system = dpdata.System()
tmp_system.from_vasp_poscar(os.path.join('pymatgen', 'mol2.vasp'))
natoms = len(tmp_system['coords'][0])
tmpcoord = tmp_system['coords'][0]
cog = np.average(tmpcoord, axis=0)
dist = tmpcoord - np.tile(cog, [natoms, 1])
max_dist_0 = np.max(np.linalg.norm(dist, axis=1))
mols = tmp_system.to("pymatgen/molecule")
cog = np.average(mols[-1].cart_coords, axis=0)
dist = mols[-1].cart_coords - np.tile(cog, [natoms, 1])
max_dist_1 = np.max(np.linalg.norm(dist, axis=1))
self.assertAlmostEqual(max_dist_0, max_dist_1)
def test_pbc(self):
nframes = 10
natoms = 20
data = {}
data['coords'] = np.random.random([nframes, natoms, 3]) + [5, 5, 5]
data['cells'] = np.tile(10 * np.eye(3), [nframes, 1, 1])
data['cells'] += np.random.random([nframes, 3, 3])
shift = 20 * (np.random.random([nframes, natoms, 3]) - 0.5)
shift = shift.astype(int)
bk_coord = np.copy(data['coords'])
data['coords'] += np.matmul(shift, data['cells'])
sys = dpdata.System()
sys.data = data
sys.apply_pbc()
for ii in range(nframes):
for jj in range(natoms):
for dd in range(3):
self.assertAlmostEqual(sys['coords'][ii][jj][dd],
bk_coord[ii][jj][dd],
msg='coord[%d][%d][%d] failed' %
(ii, jj, dd))
def test_read_file_tri(self):
system = dpdata.System('gromacs/1h.tri.gro')
self.assertEqual(system['atom_names'], ['H', 'O'])
self.assertEqual(system['atom_numbs'], [6, 3])
for cc,ii in enumerate([1, 0, 0, 1, 0, 0, 1, 0, 0]):
self.assertEqual(system['atom_types'][cc], ii)
self.assertEqual(len(system['cells']), 1)
self.assertEqual(len(system['coords']), 1)
count = 0
for ii in range(3):
for jj in range(3):
if ii != jj:
self.assertAlmostEqual(system['cells'][0][ii][jj], count)
count += 1
self.assertAlmostEqual(system['cells'][0][0][0], 7.822838765564372)
self.assertAlmostEqual(system['cells'][0][1][1], 7.353572647182051)
self.assertAlmostEqual(system['cells'][0][2][2], 9.036518515423753)
self.assertAlmostEqual(system['coords'][0][8][0], 7.43)
self.assertAlmostEqual(system['coords'][0][8][1], 5.12)
self.assertAlmostEqual(system['coords'][0][8][2], 3.36)
system.to('vasp/poscar', 'POSCAR')
def test_data_empty(self):
data = {
'atom_names': ['A', 'B'],
'atom_numbs': [0, 0],
'atom_types': np.array([], dtype=int),
'orig': np.array([0, 0, 0]),
'cells': np.array([]),
'coords': np.array([]),
}
sys1 = dpdata.System(data=data)
data = {
'atom_names': ['A', 'B'],
'atom_numbs': [0, 0],
'atom_types': np.array([], dtype=int),
'orig': np.array([0, 0, 0]),
'cells': np.array([]),
'coords': np.array([]),
'forces': np.array([]),
'energies': np.array([]),
'virials': np.array([]),
}
sys2 = dpdata.LabeledSystem(data=data)
def test_remove(self):
coords = np.array([[[-1, -1, 2], [-1, -1, -3], [-1, -1, 7]],
[[3, -1, 3], [-1, -1, 3], [7, -1, 3]]],
dtype=float)
cogs = np.average(coords, axis=1)
data = {
'atom_names': ['A', 'B'],
'atom_numbs': [1, 2],
'atom_types': np.array([1, 0, 1], dtype=int),
'orig': np.array([0, 0, 0]),
'coords': coords,
'cells': np.random.random([2, 3, 3]),
}
sys = dpdata.System(data=data)
proct = 9.0
mol_size = np.array([5, 4], dtype=float)
cell_size = (mol_size + proct) * 2.0
sys.remove_pbc(proct)
for ff in range(2):
ref = cell_size[ff] * np.eye(3)
for ii in range(3):
for jj in range(3):
self.assertAlmostEqual(sys['cells'][ff][ii][jj],
ref[ii][jj],
msg='%d %d %d' % (ff, ii, jj))
dists = []
for ii in range(sys.get_natoms()):
for jj in range(3):
dists.append(np.abs(sys['coords'][ff][ii][jj]))
dists.append(
np.abs(sys['cells'][ff][jj][jj] -
sys['coords'][ff][ii][jj]))
self.assertAlmostEqual(np.min(dists), proct)
def setUp(self):
tmp_system = dpdata.System(os.path.join('poscars', 'conf.lmp'),
type_map=['O', 'H'])
tmp_system.to_lammps_lmp('tmp.lmp')
self.system = dpdata.System()
self.system.from_lammps_lmp('tmp.lmp', type_map=['O', 'H'])
def setUp(self):
self.system = dpdata.System()
self.system.from_vasp_poscar(os.path.join('poscars', 'POSCAR.oh.c'))