/dports/science/py-ase/ase-3.22.0/ase/test/ |
H A D | test_mixingcalc.py | 22 atoms1 = atoms.copy() 24 atoms1.calc = calc1 34 atoms1[0].x += 0.2 39 assert np.isclose(0, atoms1.get_forces()).all() 43 atoms1 = atoms.copy() 45 atoms1.calc = calc1 57 atoms1[0].x += 0.2 72 atoms1 = atoms.copy() 73 atoms1.calc = EMT() 74 E_tot = atoms1.get_potential_energy() [all …]
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H A D | test_external_viewer.py | 46 (atoms1, name1) = view(atoms, viewer='sage') 48 assert atoms1 == atoms 58 atoms1 = read(path) 62 assert all(atoms1.symbols == atoms.symbols)
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/dports/science/py-ase/ase-3.22.0/ase/test/atoms/ |
H A D | test_compare_atoms.py | 14 atoms1 = Atoms(cell=cell1) 16 assert set(compare_atoms(atoms1, atoms2)) == {"cell"} 21 atoms1 = Atoms() 23 assert set(compare_atoms(atoms1, atoms2)) == {"positions", "numbers"} 27 atoms1 = Atoms(numbers=[0], positions=[[0, 0, 0]]) 29 assert set(compare_atoms(atoms1, atoms2)) == {"positions"} 32 assert set(compare_atoms(atoms1, atoms2, excluded_properties={"positions"})) == set() 42 atoms1 = Atoms(numbers=[0], positions=[[0, 0, 0]]) 44 assert set(compare_atoms(atoms1, atoms2)) == {"initial_charges"}
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H A D | test_atoms_instantiation.py | 25 def test_atoms(atoms1=a1, atoms2=a2, atoms3=a3): argument 26 assert atoms1 == atoms2
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/dports/science/py-ase/ase-3.22.0/ase/test/fio/ |
H A D | test_cif.py | 390 labels = atoms1.info['_atom_site_label'] 405 print(atoms1.info) 503 atoms1 = roundtrip(atoms) 505 assert str(atoms1.symbols) == 'CO' 506 assert all(atoms1.pbc) 508 atoms1.cell.cellpar(), abs=1e-5) 510 atoms1.get_scaled_positions(), abs=1e-5) 515 atoms1 = roundtrip(atoms) 533 atoms1 = roundtrip(atoms) 536 assert all(atoms1.pbc) [all …]
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H A D | test_jsonio_atoms.py | 8 def assert_equal(atoms1, atoms2): argument 9 assert atoms1 == atoms2 10 assert set(atoms1.arrays) == set(atoms2.arrays) 11 for name in atoms1.arrays: 12 assert np.array_equal(atoms1.arrays[name], atoms2.arrays[name]), name 19 atoms1 = decode(txt) 20 print('decoded', atoms1) 21 txt1 = encode(atoms1) 23 assert_equal(atoms, atoms1)
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H A D | test_xyz.py | 9 def atoms_equal(atoms1, atoms2): argument 11 return compare_atoms(atoms1, atoms2, tol=1e-8) == [] 23 atoms1 = read('1.xyz', format='xyz') 24 assert atoms_equal(atoms, atoms1), 'Read failed' 49 atoms1 = read('1.xyz', format='xyz') 50 assert atoms_equal(atoms, atoms1), 'Read failed' 77 for atoms, atoms1 in zip(images, images1): 78 assert atoms_equal(atoms, atoms1), 'Read failed'
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H A D | test_pickle_bundle_trajectory.py | 31 atoms1 = atoms.copy() 32 atoms1.rattle() 33 images = [atoms, atoms1] 50 return [atoms, atoms1] 69 for atoms1, atoms2 in zip(images1, images2): 70 differences = compare_atoms(atoms1, atoms2)
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H A D | test_pdb_cell_io.py | 101 atoms1 = images[0] 102 write('grumbles.pdb', atoms1) 105 spos1 = (atoms1.get_scaled_positions() + 0.5) % 1.0
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H A D | test_traj_bytesio.py | 19 for atoms1, atoms2 in zip(images, images2): 20 assert atoms1 == atoms2
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H A D | test_atoms_bytes.py | 12 atoms1 = parse_atoms(buf) 14 err = compare_atoms(atoms, atoms1)
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/dports/science/py-ase/ase-3.22.0/ase/cli/ |
H A D | template.py | 98 def get_field_data(atoms1, atoms2, field): argument 107 data = atoms1.get_tags() 109 data = atoms1.numbers 113 data = np.arange(len(atoms1)) 119 y = atoms1.positions 138 y = atoms1.get_forces() 159 def rmsd(atoms1, atoms2): argument 165 def energy_delta(atoms1, atoms2): argument 166 E1 = atoms1.get_potential_energy() 311 def make(self, atoms1, atoms2, csv=False): argument [all …]
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H A D | diff.py | 158 atoms1 = read(actual_filename, index) 159 natoms1 = len(atoms1) 163 atoms2 = atoms1 190 atoms1 = natoms2 * atoms1 198 atoms2 = atoms1.copy() 199 atoms1 = atoms1[:-1] 220 output += table.make(atoms1[counter],
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/dports/science/py-ase/ase-3.22.0/ase/calculators/ |
H A D | combine_mm.py | 49 self.atoms1 = None 69 self.atoms1 = atoms[self.mask] 74 self.atoms1.calc = self.calc1 89 if self.atoms1 is None: 94 self.atoms1.set_positions(pos1) 99 spm1 = self.atoms1.calc.sites_per_mol 104 xc1 = self.atoms1.calc.get_virtual_charges(self.atoms1) 121 fi1 = self.atoms1.get_forces() 133 if self.atoms1 is None: 235 atoms1 = self.atoms1.copy() [all …]
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxana/ |
H A D | gmx_confrms.cpp | 352 resinfo1 = atoms1->resinfo; in find_matching_names() 353 atnms1 = atoms1->atomname; in find_matching_names() 358 snew(rindex1, atoms1->nres); in find_matching_names() 530 t_atoms * atoms1, *atoms2; in gmx_confrms() local 566 atoms1 = &(top1->atoms); in gmx_confrms() 567 …fprintf(stderr, "%s\nContaining %d atoms in %d residues\n", *top1->name, atoms1->nr, atoms1->nres); in gmx_confrms() 571 rm_gropbc(atoms1, x1, box1); in gmx_confrms() 707 for (i = 0; i < atoms1->nr; i++) in gmx_confrms() 731 srenew(atoms1->pdbinfo, atoms1->nr); in gmx_confrms() 732 srenew(atoms1->atom, atoms1->nr); /* Why renew atom? */ in gmx_confrms() [all …]
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/dports/science/py-ase/ase-3.22.0/ase/build/ |
H A D | attach.py | 20 def nearest(atoms1, atoms2, cell=None, pbc=None): argument 22 p1 = atoms1.get_positions() 29 def attach(atoms1, atoms2, distance, direction=(1, 0, 0), argument 47 atoms = atoms1.copy() 74 def attach_randomly(atoms1, atoms2, distance, argument 94 return attach(atoms1, atoms2, distance, 98 def attach_randomly_and_broadcast(atoms1, atoms2, distance, argument 120 joined = attach_randomly(atoms1, atoms2, distance, rng)
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H A D | tools.py | 254 atoms1 = atoms1.copy() 257 for atoms in [atoms1, atoms2]: 269 cell1 = atoms1.cell.copy() 291 atoms1_strained = atoms1.copy() 312 atoms1.center() 317 atoms1.translate(t1) 319 atoms1.cell[axis] *= 1.0 + h1 322 atoms2.translate(atoms1.cell[axis]) 324 atoms1.extend(atoms2) 327 atoms1 = sort(atoms1) [all …]
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/dports/science/py-ase/ase-3.22.0/ase/test/calculator/ |
H A D | test_gulp_opt.py | 10 atoms1 = atoms.copy() 11 atoms1.calc = GULP(library='reaxff.lib') 12 with BFGS(atoms1) as opt1: 25 atoms1 = atoms.copy() 26 atoms1.calc = GULP(keywords='conp gradient stress_out', 28 atoms1f = ExpCellFilter(atoms1)
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/ |
H A D | test_davidson_scalapack.py | 33 atoms1 = atoms.copy() 36 atoms1.calc = get_calculator(sl_auto=True, kpoint_gamma=kpoint_gamma) 39 e1 = atoms1.get_potential_energy() 42 for n, kpoint in enumerate(atoms1.calc.get_bz_k_points()): 43 eigvals1 = atoms1.calc.get_eigenvalues(kpt=n, spin=0)
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/dports/science/py-hiphive/hiphive-0.7.1/hiphive/core/ |
H A D | structure_alignment.py | 278 def are_nonpaired_configurations_equal(atoms1, atoms2): argument 299 n_atoms = len(atoms1) 300 if not (np.allclose(atoms1.cell, atoms2.cell, atol=1e-4) and 302 sorted(atoms1.numbers) == sorted(atoms2.numbers) and 303 all(atoms1.pbc == atoms2.pbc)): 305 new_cell = (atoms1.cell + atoms2.cell) / 2 306 pos = [a.position for a in atoms1] + [a.position for a in atoms2] 307 num = [a.number for a in atoms1] + [a.number for a in atoms2]
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/trajectoryanalysis/tests/ |
H A D | topologyinformation.cpp | 75 auto atoms1 = topInfo.copyAtoms(); in TEST() local 76 EXPECT_TRUE(atoms1); in TEST() 79 EXPECT_NE(atoms1.get(), atoms2.get()); in TEST() 80 EXPECT_EQ(0, atoms1->nr); in TEST() 106 auto atoms1 = topInfo.copyAtoms(); in runCommonTests() local 107 EXPECT_TRUE(atoms1); in runCommonTests() 111 EXPECT_NE(atoms1.get(), atoms2.get()); in runCommonTests() 114 EXPECT_NE(atoms1.get(), atoms); in runCommonTests()
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/dports/science/molscript/MolScript-280abee/code/ |
H A D | graphics.c | 338 atoms2 = atoms1; in ball_and_stick() 352 if (atoms1 == NULL) { in ball_and_stick() 356 free (atoms1); in ball_and_stick() 432 free (atoms1); in ball_and_stick() 435 free (atoms1); in ball_and_stick() 464 atoms2 = atoms1; in bonds() 486 free (atoms1); in bonds() 539 atoms1[slot1]->rval++; in bonds() 569 atoms1[slot1]->rval++; in bonds() 626 free (atoms1); in bonds() [all …]
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/dports/multimedia/opentoonz/opentoonz-1.5.0/toonz/sources/common/tiio/ |
H A D | movsettings.cpp | 161 void compareAtoms(const QTAtomContainer &atoms1, QTAtom parent1, in compareAtoms() argument 165 assert(QTCountChildrenOfType(atoms1, parent1, 0) == in compareAtoms() 169 if (QTNextChildAnyType(atoms1, parent1, curr1, &curr1) != noErr) in compareAtoms() 181 QTGetAtomTypeAndID(atoms1, curr1, &atomType1, &id1); in compareAtoms() 185 int sonCount1 = QTCountChildrenOfType(atoms1, curr1, 0); in compareAtoms() 189 compareAtoms(atoms1, curr1, atoms2, curr2); in compareAtoms() 195 if (QTGetAtomDataPtr(atoms1, curr1, &size1, (char **)&atomData1) != noErr) in compareAtoms()
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/response/ |
H A D | test_two-aluminum_chi_RPA.py | 22 atoms1 = bulk('Al', 'fcc', a=a) 23 atoms2 = atoms1.repeat((2, 1, 1)) 32 atoms1.calc = calc1 33 atoms1.get_potential_energy()
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/dports/science/py-ase/ase-3.22.0/ase/optimize/ |
H A D | minimahopping.py | 361 def __call__(self, atoms1, atoms2): argument 362 atoms1 = atoms1.copy() 367 dmax = self._translated_compare(atoms1, atoms2) 370 def _translated_compare(self, atoms1, atoms2): argument 378 atoms1.set_constraint() 381 assert atoms1.pbc[index] == atoms2.pbc[index] 382 least = self._get_least_common(atoms1) 404 standard = atoms1.copy() 405 standard.translate(-atoms1[indices1[0]].position) 424 def _indistinguishable_compare(self, atoms1, atoms2): argument [all …]
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