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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/
H A Dxcrysden.py46 cart_coords = self.structure.cart_coords
49 app(" %d 1" % len(cart_coords))
51 for site, coord in zip(self.structure, cart_coords):
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/lammps/
H A Dutils.py79 start_monomer.translate_sites(range(len(start_monomer)), -monomer.cart_coords[s_head])
80 monomer.translate_sites(range(len(monomer)), -monomer.cart_coords[head])
81 end_monomer.translate_sites(range(len(end_monomer)), -monomer.cart_coords[e_head])
82 self.mon_vector = monomer.cart_coords[tail] - monomer.cart_coords[head]
99 end_mon_vector = end_monomer.cart_coords[e_tail] - end_monomer.cart_coords[e_head]
157 translate_by = self.molecule.cart_coords[self.end] + self.link_distance * move_direction
260 …length = max([np.max(mol.cart_coords[:, i]) - np.min(mol.cart_coords[:, i]) for i in range(3)]) + …
/dports/science/py-abipy/abipy-0.9.0/abipy/iotools/
H A Dxsf.py47 cart_coords = struct.cart_coords
57 fwrite(' %d 1\n' % len(cart_coords))
59 for a in range(len(cart_coords)):
61 fwrite(' %20.14f %20.14f %20.14f' % tuple(cart_coords[a]))
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/electronic_structure/tests/
H A Dtest_bandstructure.py41 self.assertEqual(self.kpoint.cart_coords[0], 1.0)
42 self.assertEqual(self.kpoint.cart_coords[1], 4.0)
43 self.assertEqual(self.kpoint.cart_coords[2], -5.0)
67 self.assertEqual(kpoint.cart_coords[0], 1.0)
68 self.assertEqual(kpoint.cart_coords[1], 4.0)
69 self.assertEqual(kpoint.cart_coords[2], -5.0)
115 self.assertAlmostEqual(self.one_kpoint.cart_coords[0], 0.64918757)
116 self.assertAlmostEqual(self.one_kpoint.cart_coords[1], 1.29837513)
117 self.assertAlmostEqual(self.one_kpoint.cart_coords[2], 0.0)
302 self.assertAlmostEqual(bs_p.kpoints[8].cart_coords[2], 0.0)
[all …]
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/transformations/tests/
H A Dtest_advanced_transformations.py602 self.assertArrayAlmostEqual(slab_from_gen.cart_coords, slab_from_trans.cart_coords)
610 self.assertArrayAlmostEqual(slab_from_gen.cart_coords, slab_from_trans.cart_coords)
632 self.assertArrayAlmostEqual(gb_from_generator.cart_coords, gb_from_trans.cart_coords)
753 self.assertFalse(np.allclose(s.cart_coords, s_trans.cart_coords, atol=0.01))
754 self.assertTrue(np.allclose(s.cart_coords, s_trans.cart_coords, atol=1))
759 self.assertTrue(np.allclose(s_trans.cart_coords, s_trans2.cart_coords))
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/tests/
H A Dtest_xyz.py131 list(mxyz.all_molecules[0].cart_coords[0]),
135 list(mxyz.all_molecules[-1].cart_coords[-1]),
139 list(mxyz.molecule.cart_coords[-1]),
H A Dtest_gaussian.py173 self.assertEqual(gau.to_string(cart_coords=False), gau_str)
406 self.assertAlmostEqual(gau.opt_structures[-1].cart_coords.tolist(), coords)
427 self.assertAlmostEqual(gau.opt_structures[-1].cart_coords[:3].tolist(), coords)
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/core/tests/
H A Dtest_interface.py84 init_coords = self.interface.cart_coords
91 assert np.allclose(init_coords, interface.cart_coords)
/dports/science/py-abipy/abipy-0.9.0/abipy/core/
H A Dkpoints.py638 def cart_coords(self): member in Kpoint
676 return "(%+.3f, %+.3f, %+.3f)" % tuple(self.cart_coords)
754 return np.sqrt(np.dot(self.cart_coords, self.cart_coords))
1033 return np.reshape([k.cart_coords for k in self], (-1, 3))
1330 cart_bounds = [self[line[0]].cart_coords for line in self.lines]
1331 cart_bounds.append(self[self.lines[-1][-1]].cart_coords)
1334 def find_points_along_path(self, cart_coords, dist_tol=1e-12): argument
1339 return find_points_along_path(self.cart_bounds, cart_coords, dist_tol=dist_tol)
1854 def find_points_along_path(cart_bounds, cart_coords, dist_tol): argument
1883 for ik, k in enumerate(cart_coords):
[all …]
H A Dstructure.py348 def boxed_molecule(cls, pseudos, cart_coords, acell=3*(10,)): argument
358 cart_coords = np.atleast_2d(cart_coords)
359 molecule = Molecule([p.symbol for p in pseudos], cart_coords)
366 def boxed_atom(cls, pseudo, cart_coords=3*(0,), acell=3*(10,)): argument
375 return cls.boxed_molecule([pseudo], cart_coords, acell=acell)
1107 def get_kcoords_from_names(self, knames, cart_coords=False): argument
1128 if cart_coords:
2188 with_spglib=True, cart_coords=False): argument
2232 if cart_coords:
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/
H A Dmolecule_matcher.py794 p_coord, q_coord = p.cart_coords, self.target.cart_coords
909 p_coord, q_coord = p.cart_coords, q.cart_coords
1007 p_coord, q_coord = p.cart_coords, self.target.cart_coords
1296 p_coords, q_coords = p.cart_coords, self.target.cart_coords
H A Dstructure_analyzer.py285 cart_coords = np.array(self.s.cart_coords)
287 all_sites = cart_coords[:, None, :] + self.cart_offsets[None, :, :]
/dports/science/py-abipy/abipy-0.9.0/abipy/abio/tests/
H A Dtest_abivars.py144 self.assert_almost_equal(s0.cart_coords.ravel() / bohr_to_ang, [-0.7, 0, 0, 0.7, 0, 0])
145 self.assert_almost_equal(s1.cart_coords.ravel() / bohr_to_ang, [-0.8, 0, 0, 0.8, 0, 0])
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/core/
H A Dlattice.py160 def get_fractional_coords(self, cart_coords: ArrayLike) -> np.ndarray:
170 return dot(cart_coords, self.inv_matrix)
172 def get_vector_along_lattice_directions(self, cart_coords: ArrayLike) -> np.ndarray:
190 return self.lengths * self.get_fractional_coords(cart_coords)
1492 cart_coords = self.get_cartesian_coords(frac_points)
1494 all_coords=cart_coords,
1558 cart_coords = self.get_cartesian_coords(frac_points)
1560 all_coords=cart_coords,
1646 cart_coords = self.get_cartesian_coords(fcoords)
1648 coords = cart_coords[:, None, None, None, :] + cart_images[None, :, :, :, :]
/dports/net/mpich2/mpich2-1.5/src/mpi/topo/
H A D.state-cache5 <file name="cart_coords.c" info="1348192932"/>
45 <fileinfo name="cart_coords.c">
H A DMakefile.mk8 src/mpi/topo/cart_coords.c \
/dports/net/openmpi3/openmpi-3.1.6/ompi/mca/topo/base/
H A Dtopo_base_comm_select.c254 if (NULL == module->topo.cart.cart_coords) { in fill_null_pointers()
255 module->topo.cart.cart_coords = mca_topo_base_cart_coords; in fill_null_pointers()
/dports/net/openmpi/openmpi-4.1.1/ompi/mca/topo/base/
H A Dtopo_base_comm_select.c254 if (NULL == module->topo.cart.cart_coords) { in fill_null_pointers()
255 module->topo.cart.cart_coords = mca_topo_base_cart_coords; in fill_null_pointers()
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/electronic_structure/
H A Dbandstructure.py94 def cart_coords(self): member in Kpoint
125 return "{} {} {}".format(self.frac_coords, self.cart_coords, self.label)
134 "ccoords": self.cart_coords.tolist(),
501 cbm["kpoint"].cart_coords - vbm["kpoint"].cart_coords
805 …self.distance.append(np.linalg.norm(kpt.cart_coords - previous_kpoint.cart_coords) + previous_dist…
/dports/net/openmpi3/openmpi-3.1.6/ompi/mpi/c/
H A Dcart_coords.c78 err = comm->c_topo->topo.cart.cart_coords(comm, rank, maxdims, coords); in MPI_Cart_coords()
/dports/net/openmpi/openmpi-4.1.1/ompi/mpi/c/
H A Dcart_coords.c78 err = comm->c_topo->topo.cart.cart_coords(comm, rank, maxdims, coords); in MPI_Cart_coords()
/dports/net/mpich/mpich-3.4.3/src/mpi/topo/
H A DMakefile.mk7 src/mpi/topo/cart_coords.c \
/dports/science/py-abipy/abipy-0.9.0/abipy/core/tests/
H A Dtest_structure.py230 … bmol = Structure.boxed_molecule(pseudos, cart_coords=[[0, 0, 0], [5, 5, 5]], acell=[10, 10, 10])
312 …dfs = dataframes_from_structures([mgb2, sic, alas], index=None, with_spglib=True, cart_coords=True)
313 …fs = dataframes_from_structures([mgb2, sic, alas], index=None, with_spglib=True, cart_coords=False)
/dports/science/py-abipy/abipy-0.9.0/abipy/eph/
H A Dcommon.py87 qcs = qpoint.cart_coords
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/vis/
H A Dstructure_chemview.py65 mv = MolecularViewer(s.cart_coords, topology={"atom_types": atom_types, "bonds": bonds})

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