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/dports/science/py-ase/ase-3.22.0/ase/test/
H A Dtest_mixingcalc.py22 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()
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H A Dtest_external_viewer.py46 (atoms1, name1) = view(atoms, viewer='sage')
48 assert atoms1 == atoms
58 atoms1 = read(path)
62 assert all(atoms1.symbols == atoms.symbols)
/dports/science/py-ase/ase-3.22.0/ase/test/atoms/
H A Dtest_compare_atoms.py14 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"}
H A Dtest_atoms_instantiation.py25 def test_atoms(atoms1=a1, atoms2=a2, atoms3=a3): argument
26 assert atoms1 == atoms2
/dports/science/py-ase/ase-3.22.0/ase/test/fio/
H A Dtest_cif.py390 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)
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H A Dtest_jsonio_atoms.py8 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)
H A Dtest_xyz.py9 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'
H A Dtest_pickle_bundle_trajectory.py31 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)
H A Dtest_pdb_cell_io.py101 atoms1 = images[0]
102 write('grumbles.pdb', atoms1)
105 spos1 = (atoms1.get_scaled_positions() + 0.5) % 1.0
H A Dtest_traj_bytesio.py19 for atoms1, atoms2 in zip(images, images2):
20 assert atoms1 == atoms2
H A Dtest_atoms_bytes.py12 atoms1 = parse_atoms(buf)
14 err = compare_atoms(atoms, atoms1)
/dports/science/py-ase/ase-3.22.0/ase/cli/
H A Dtemplate.py98 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
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H A Ddiff.py158 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],
/dports/science/py-ase/ase-3.22.0/ase/calculators/
H A Dcombine_mm.py49 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()
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxana/
H A Dgmx_confrms.cpp352 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()
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/dports/science/py-ase/ase-3.22.0/ase/build/
H A Dattach.py20 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)
H A Dtools.py254 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)
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/dports/science/py-ase/ase-3.22.0/ase/test/calculator/
H A Dtest_gulp_opt.py10 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)
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/
H A Dtest_davidson_scalapack.py33 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)
/dports/science/py-hiphive/hiphive-0.7.1/hiphive/core/
H A Dstructure_alignment.py278 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]
/dports/science/gromacs/gromacs-2021.4/src/gromacs/trajectoryanalysis/tests/
H A Dtopologyinformation.cpp75 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()
/dports/science/molscript/MolScript-280abee/code/
H A Dgraphics.c338 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()
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/dports/multimedia/opentoonz/opentoonz-1.5.0/toonz/sources/common/tiio/
H A Dmovsettings.cpp161 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()
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/response/
H A Dtest_two-aluminum_chi_RPA.py22 atoms1 = bulk('Al', 'fcc', a=a)
23 atoms2 = atoms1.repeat((2, 1, 1))
32 atoms1.calc = calc1
33 atoms1.get_potential_energy()
/dports/science/py-ase/ase-3.22.0/ase/optimize/
H A Dminimahopping.py361 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
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