/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/symmetry/ |
H A D | test_symmetry.py | 13 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)
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H A D | test_symmetry_ft.py | 13 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)
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/ |
H A D | symmetry.py | 110 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 …]
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H A D | pair_overlap.py | 29 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 …]
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H A D | pair_density.py | 11 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)
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H A D | density.py | 194 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 …]
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H A D | hamiltonian.py | 101 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 …]
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/wavefunctions/ |
H A D | fdpw.py | 19 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 …]
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/exx/ |
H A D | test_forces_ut.py | 57 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)
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H A D | test_derivs.py | 42 spos_ac = np.zeros((1, 3)) + 0.25 59 pt.set_positions(spos_ac) 65 xx = (kd, [Setup()], pt, coulomb, spos_ac)
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/dports/science/py-ase/ase-3.22.0/ase/test/neighbor/ |
H A D | test_neighbor.py | 138 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)
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/analyse/ |
H A D | hirshfeld.py | 30 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)
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/lcao/ |
H A D | newoverlap.py | 9 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)
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H A D | tci.py | 30 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 …]
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H A D | overlap.py | 404 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 …]
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/utilities/ |
H A D | ibz2bz.py | 32 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]
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H A D | dipole.py | 45 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)
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H A D | grid.py | 71 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)),
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/hybrids/ |
H A D | symmetry.py | 75 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),
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/lfc/ |
H A D | test_second_derivative.py | 11 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)
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H A D | test_derivatives.py | 11 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)
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/wannier/ |
H A D | overlaps.py | 144 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)
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/pw/ |
H A D | test_reallfc.py | 22 spos_ac = np.array([(0.15, 0.45, 0.95)]) 44 lfc.set_positions(spos_ac) 46 lfcr.set_positions(spos_ac)
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H A D | test_stresstest.py | 23 spos_ac = np.array([(0.15, 0.45, 0.95)]) 33 lfc.set_positions(spos_ac) 59 lfc.set_positions(spos_ac)
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/tddft/ |
H A D | tdopers.py | 20 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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