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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/symmetry/
H A Dtest_symmetry.py13 spos_ac = np.array([(.00, .00, .00),
21 symm.analyze(spos_ac)
36 symm.analyze(spos_ac)
45 symm.analyze(spos_ac)
54 spos_ac = np.array([[0.125, 0.5, 0.5],
64 symm.analyze(spos_ac)
77 spos_ac = np.array([[0., 0., 0.],
87 symm.analyze(spos_ac)
H A Dtest_symmetry_ft.py13 spos_ac = np.array([(.00, .00, .00),
21 symm.analyze(spos_ac)
36 symm.analyze(spos_ac)
45 symm.analyze(spos_ac)
59 spos_ac = np.array([[0., 0., 0.],
69 symm.analyze(spos_ac)
84 spos_ac = np.array([(0.000000000, 0.000000000, 0.000000000),
97 symm.analyze(spos_ac)
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/
H A Dsymmetry.py110 def analyze(self, spos_ac): argument
157 if len(spos_ac) == 0:
176 ftrans_sc = spos_ac[a_j[1:]] - spos_ac[a_j[0]]
224 a_a = np.zeros(len(spos_ac), int)
226 spos_jc = spos_ac[a_j]
241 def check(self, spos_ac): argument
245 self.prune_symmetries_atoms(spos_ac)
327 def symmetrize_positions(self, spos_ac): argument
329 spos_tmp_ac = np.zeros_like(spos_ac)
330 spos_new_ac = np.zeros_like(spos_ac)
[all …]
H A Dpair_overlap.py29 def calculate_overlaps(self, spos_ac, lfc1, lfc2=None): argument
38 def calculate_overlaps(self, spos_ac, lfc1, lfc2=None): argument
45 return self.calculate_overlaps2(spos_ac, lfc1, lfc2)
71 (a1, spos_ac[a1], rcut1, self.setups[a1].ni))
84 spos_ac[a1], rcut1,
106 spos_ac[a2], rcut2,
158 def calculate_overlaps2(self, spos_ac, lfc1, lfc2=None): argument
193 (a1, spos_ac[a1], rcut1, self.setups[a1].ni),
211 spos_ac[a1], rcut1,
221 spos_ac[a2], rcut2,
[all …]
H A Dpair_density.py11 def __init__(self, density, spos_ac, finegrid): argument
23 density.Ghat.set_positions(spos_ac)
81 self.spos_ac = paw.spos_ac
170 self.density.Ghat.set_positions(self.spos_ac)
214 self.__class__.phi.set_positions(self.spos_ac)
215 self.__class__.phit.set_positions(self.spos_ac)
220 self.__class__.Phi.set_positions(self.spos_ac)
221 self.__class__.Phit.set_positions(self.spos_ac)
H A Ddensity.py194 def set_positions(self, spos_ac, atom_partition): argument
196 self.nct.set_positions(spos_ac, atom_partition)
428 if spos_ac is None:
483 phi.set_positions(spos_ac)
484 phit.set_positions(spos_ac)
485 nc.set_positions(spos_ac)
486 nct.set_positions(spos_ac)
488 I_sa = np.zeros((self.nspins, len(spos_ac)))
617 spos_ac = np.zeros((natoms, 3)) # XXXX
683 def set_positions(self, spos_ac, atom_partition): argument
[all …]
H A Dhamiltonian.py101 self.spos_ac = None
176 def set_positions_without_ruining_everything(self, spos_ac, argument
178 self.spos_ac = spos_ac
197 self.atomdist = self.redistributor.get_atom_distributions(spos_ac)
199 def set_positions(self, spos_ac, atom_partition): argument
200 self.vbar.set_positions(spos_ac, atom_partition)
201 self.xc.set_positions(spos_ac)
202 self.set_positions_without_ruining_everything(spos_ac, atom_partition)
350 self.xc.set_positions(self.spos_ac)
575 def set_positions(self, spos_ac, rank_a): argument
[all …]
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/wavefunctions/
H A Dfdpw.py19 def cut_wfs(self, wfs, spos_ac): argument
41 def cut_wfs(self, wfs, spos_ac): argument
52 phit.set_positions(wfs.spos_ac, wfs.atom_partition)
58 (spos_ac - wfs.spos_ac).T.round()))
72 phit.set_positions(spos_ac, wfs.atom_partition)
114 def cut_wfs(self, wfs, spos_ac): argument
179 spos_ac, wfs.spos_ac, wfs.setups, wfs.initksl.Mstart)
184 bfs.set_positions(spos_ac)
261 self.spos_ac is not None)
275 self.pt.set_positions(spos_ac, atom_partition)
[all …]
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/exx/
H A Dtest_forces_ut.py57 def __init__(self, spos_ac): argument
58 self.spos_ac = np.array(spos_ac)
59 self.wfs = WFS(self.spos_ac)
68 def __init__(self, spos_ac): argument
69 self.spos_ac = spos_ac
85 self.pt.set_positions(self.spos_ac)
138 e1, e2 = calculate_energy(kpts, paw_s[0], wfs, sym, coulomb, wfs.spos_ac)
H A Dtest_derivs.py42 spos_ac = np.zeros((1, 3)) + 0.25
59 pt.set_positions(spos_ac)
65 xx = (kd, [Setup()], pt, coulomb, spos_ac)
/dports/science/py-ase/ase-3.22.0/ase/test/neighbor/
H A Dtest_neighbor.py138 spos_ac = np.array([[0., 0., 0.],
145 nl.update(pbc_c, cell_cv, spos_ac)
146 nl2.update(pbc_c, cell_cv, spos_ac)
150 d0 = np.dot(spos_ac[a0] + offsets0 - spos_ac[0], cell_cv)
152 d1 = np.dot(spos_ac[a1] + offsets1 - spos_ac[1], cell_cv)
165 d0 = np.dot(spos_ac[a0] + offsets0 - spos_ac[0], cell_cv)
168 d1 = np.dot(spos_ac[a1] + offsets1 - spos_ac[1], cell_cv)
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/analyse/
H A Dhirshfeld.py30 def set_positions(self, spos_ac, atom_partition): argument
37 self.atomdist = self.redistributor.get_atom_distributions(spos_ac)
38 self.nct.set_positions(spos_ac)
39 self.ghat.set_positions(spos_ac)
71 spos_ac = atoms.get_scaled_positions()
84 rank_a = self.gd.get_ranks_from_positions(spos_ac)
85 self.set_positions(spos_ac, AtomPartition(self.gd.comm, rank_a))
90 basis_functions.set_positions(spos_ac)
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/lcao/
H A Dnewoverlap.py9 def __init__(self, nl, spos_ac, cell_cv): argument
16 for a1, spos1_c in enumerate(spos_ac):
19 spos2_c = spos_ac[a2] + offset
32 def newoverlap(wfs, spos_ac): argument
51 atoms.set_scaled_positions(spos_ac)
81 dists_and_offsets = DistsAndOffsets(neighbors, spos_ac, gd.cell_cv)
H A Dtci.py30 def __init__(self, cutoff_a, pbc_c, cell_cv, spos_ac): argument
35 nl.update(pbc=pbc_c, cell=cell_cv, coordinates=spos_ac)
41 for a1, spos1_c in enumerate(spos_ac):
44 spos2_c = spos_ac[a2] + offset
100 def get_tci_calculator(self, cell_cv, spos_ac, pbc_c, ibzk_qc, dtype): argument
101 return TCICalculator(self, cell_cv, spos_ac, pbc_c, ibzk_qc, dtype)
103 def get_manytci_calculator(self, setups, gd, spos_ac, ibzk_qc, dtype, argument
105 return ManyTCICalculator(self, setups, gd, spos_ac, ibzk_qc, dtype,
136 def __init__(self, tciexpansions, cell_cv, spos_ac, pbc_c, ibzk_qc, argument
151 self.a1a2 = AtomPairRegistry(cutoff_a, pbc_c, cell_cv, spos_ac)
[all …]
H A Doverlap.py404 def set_positions(self, spos_ac): argument
405 self.spos_ac = spos_ac
406 self.neighbors.update(self.pbc_c, self.cell_cv, spos_ac)
410 for a1, spos1_c in enumerate(self.spos_ac):
413 spos2_c = self.spos_ac[a2] + offset
422 def set_positions(self, spos_ac): argument
423 self.pairs.set_positions(spos_ac)
811 self.atoms_close.set_positions(spos_ac)
820 self.atompairs.set_positions(spos_ac)
842 def evaluate(self, spos_ac, Theta_qMM, T_qMM, P_aqMi): argument
[all …]
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/utilities/
H A Dibz2bz.py32 spos_ac = calc.atoms.get_scaled_positions()
43 calc.wfs.kd, calc.wfs.setups, spos_ac, K)
99 def construct_symmetry_operators(kd, setups, spos_ac, K): argument
123 S_c = np.dot(spos_ac[a], U_cc) - spos_ac[b]
H A Ddipole.py45 spos_ac = np.linalg.solve(gd.cell_cv.T, position_av.T).T % 1.0
46 spos_ac -= scenter_c - 0.5
47 spos_ac %= 1.0
48 spos_ac += scenter_c - 0.5
49 position_av = spos_ac.dot(gd.cell_cv)
H A Dgrid.py71 def get_atom_distributions(self, spos_ac): argument
73 self.gd, self.aux_gd, spos_ac)
77 def __init__(self, comm, broadcast_comm, gd, aux_gd, spos_ac): argument
83 rank_a = gd.get_ranks_from_positions(spos_ac)
84 aux_rank_a = aux_gd.get_ranks_from_positions(spos_ac)
93 self.work_partition = AtomPartition(comm, np.zeros(len(spos_ac)),
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/hybrids/
H A Dsymmetry.py75 S_c = np.dot(wfs.spos_ac[a], U_cc) - wfs.spos_ac[b]
81 def apply_symmetry(self, s: int, rsk, wfs, spos_ac): argument
111 S_c = np.dot(spos_ac[a], U_cc) - spos_ac[b]
122 def pairs(self, kpts, wfs, spos_ac): argument
203 self.apply_symmetry(s, rsk2, wfs, spos_ac),
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/lfc/
H A Dtest_second_derivative.py11 spos_ac = np.array([[0.252, 0.15, 0.35], [0.503, 0.5, 0.5]])
15 c.set_positions(spos_ac)
30 pos_av = np.dot(spos_ac, gd.cell_cv)
H A Dtest_derivatives.py11 spos_ac = np.array([[0.25, 0.15, 0.35], [0.5, 0.5, 0.5]])
16 c.set_positions(spos_ac)
36 pos_av = np.dot(spos_ac, gd.cell_cv)
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/wannier/
H A Doverlaps.py144 spos_ac = calc.spos_ac
170 Z_nn *= np.exp(2j * np.pi * phase_c.dot(spos_ac[a]))
240 spos_ac: Array2D,
244 kd, setups, spos_ac, bz_index)
306 spos_ac = calc.spos_ac
335 wf1 = wf.transform(kd, gd, setups, spos_ac, bz_index)
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/pw/
H A Dtest_reallfc.py22 spos_ac = np.array([(0.15, 0.45, 0.95)])
44 lfc.set_positions(spos_ac)
46 lfcr.set_positions(spos_ac)
H A Dtest_stresstest.py23 spos_ac = np.array([(0.15, 0.45, 0.95)])
33 lfc.set_positions(spos_ac)
59 lfc.set_positions(spos_ac)
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/tddft/
H A Dtdopers.py20 def __init__(self, wfs, spos_ac, hamiltonian, td_potential): argument
59 self.spos_ac = spos_ac
235 self.wfs, self.spos_ac, psit, hpsit,
319 def __init__(self, wfs, spos_ac, strength=[0.0, 0.0, 1e-3]): argument
334 self.spos_ac = spos_ac
398 add_linear_field(self.wfs, self.spos_ac, psit, hpsit,
798 def add_linear_field(wfs, spos_ac, a_nG, b_nG, strength, kpt): argument
846 c0 = np.dot(spos_ac[a] * gd.cell_cv.diagonal(), strength)

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