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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
23 p2 = atoms2.get_positions()
29 def attach(atoms1, atoms2, distance, direction=(1, 0, 0), argument
48 atoms2 = atoms2.copy()
64 atoms += atoms2
68 atoms2.translate(direction * move)
74 def attach_randomly(atoms1, atoms2, distance, argument
91 atoms2 = atoms2.copy()
92 atoms2.rotate('x', random_unit_vector(rng),
93 center=atoms2.get_center_of_mass())
[all …]
H A Dtools.py255 atoms2 = atoms2.copy()
257 for atoms in [atoms1, atoms2]:
267 c2 = np.linalg.norm(atoms2.cell[axis])
270 cell2 = atoms2.cell.copy()
292 atoms2_strained = atoms2.copy()
307 pos2 = atoms2.positions + t2
313 atoms2.center()
318 atoms2.translate(t2)
320 atoms2.cell[axis] *= 1.0 + h2
322 atoms2.translate(atoms1.cell[axis])
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/dports/science/py-ase/ase-3.22.0/ase/test/atoms/
H A Dtest_compare_atoms.py15 atoms2 = Atoms(cell=cell2)
16 assert set(compare_atoms(atoms1, atoms2)) == {"cell"}
22 atoms2 = Atoms(numbers=[0], positions=[[0, 0, 0]])
23 assert set(compare_atoms(atoms1, atoms2)) == {"positions", "numbers"}
28 atoms2 = Atoms(numbers=[0], positions=[[1, 0, 0]])
29 assert set(compare_atoms(atoms1, atoms2)) == {"positions"}
32 assert set(compare_atoms(atoms1, atoms2, excluded_properties={"positions"})) == set()
43 atoms2 = Atoms(numbers=[0], positions=[[0, 0, 0]], charges=[1.13])
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
27 assert atoms2 == atoms3
/dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxana/
H A Dgmx_confrms.cpp354 resinfo2 = atoms2->resinfo; in find_matching_names()
355 atnms2 = atoms2->atomname; in find_matching_names()
360 snew(rindex2, atoms2->nres); in find_matching_names()
530 t_atoms * atoms1, *atoms2; in gmx_confrms() local
587 atoms2 = &(top2->atoms); in gmx_confrms()
588 …fprintf(stderr, "%s\nContaining %d atoms in %d residues\n", *top2->name, atoms2->nr, atoms2->nres); in gmx_confrms()
592 rm_gropbc(atoms2, x2, box2); in gmx_confrms()
655 snew(w_rls, atoms2->nr); in gmx_confrms()
656 snew(fit_x, atoms2->nr); in gmx_confrms()
763 srenew(atoms2->pdbinfo, atoms2->nr); in gmx_confrms()
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/dports/science/py-ase/ase-3.22.0/ase/calculators/
H A Dcombine_mm.py50 self.atoms2 = None
70 self.atoms2 = atoms[~self.mask]
75 self.atoms2.calc = self.calc2
95 self.atoms2.set_positions(pos2)
100 spm2 = self.atoms2.calc.sites_per_mol
105 xc2 = self.atoms2.calc.get_virtual_charges(self.atoms2)
124 fi2 = self.atoms2.get_forces()
239 atoms2 = self.atoms2.copy()
240 atoms2.calc = copy.copy(self.calc2)
241 atoms2.calc.atoms = atoms2
[all …]
/dports/science/py-ase/ase-3.22.0/ase/cli/
H A Dtemplate.py98 def get_field_data(atoms1, atoms2, field): argument
121 y = atoms2.positions
140 y = atoms2.get_forces()
159 def rmsd(atoms1, atoms2): argument
160 dpositions = atoms2.positions - atoms1.positions
165 def energy_delta(atoms1, atoms2): argument
167 E2 = atoms2.get_potential_energy()
311 def make(self, atoms1, atoms2, csv=False): argument
316 summary = self.make_summary(atoms1, atoms2)
335 def make_summary(self, atoms1, atoms2): argument
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H A Ddiff.py163 atoms2 = atoms1
170 atoms2 = read(actual_filename, index)
171 natoms2 = len(atoms2)
188 atoms2 = natoms1 * atoms2
198 atoms2 = atoms1.copy()
200 atoms2 = atoms2[1:]
221 atoms2[counter], csv=args.as_csv) + '\n'
/dports/science/py-ase/ase-3.22.0/ase/test/
H A Dtest_mixingcalc.py26 atoms2 = atoms.copy()
27 SumCalculator(calcs=[EMT(), EMT()], atoms=atoms2)
31 assert np.isclose(2 * forces, atoms2.get_forces()).all()
49 atoms2 = atoms.copy()
50 LinearCombinationCalculator([EMT(), EMT()], weights=[.5, .5], atoms=atoms2)
54 assert np.isclose(forces, atoms2.get_forces()).all()
/dports/science/py-ase/ase-3.22.0/ase/test/fio/
H A Dtest_exciting.py14 atoms2 = read('input.xml')
16 assert all(atoms.symbols == atoms2.symbols)
17 assert atoms.cell[:] == pytest.approx(atoms2.cell[:])
18 assert atoms.positions == pytest.approx(atoms2.positions)
H A Dtest_jsonio_atoms.py8 def assert_equal(atoms1, atoms2): argument
9 assert atoms1 == atoms2
10 assert set(atoms1.arrays) == set(atoms2.arrays)
12 assert np.array_equal(atoms1.arrays[name], atoms2.arrays[name]), name
H A Dtest_v_sim.py209 atoms2 = read(copy)
212 assert sum(abs((atoms.positions - atoms2.positions).ravel())) < tol
213 assert sum(abs((atoms.cell - atoms2.cell).ravel())) < tol
H A Dtest_nwchem.py9 atoms2 = io.read('nwchem.nwi')
13 check = sum(abs((atoms.positions - atoms2.positions).ravel()) > tol)
H A Dtest_traj_bytesio.py19 for atoms1, atoms2 in zip(images, images2):
20 assert atoms1 == atoms2
/dports/science/py-hiphive/hiphive-0.7.1/hiphive/core/
H A Dstructure_alignment.py278 def are_nonpaired_configurations_equal(atoms1, atoms2): argument
300 if not (np.allclose(atoms1.cell, atoms2.cell, atol=1e-4) and
301 n_atoms == len(atoms2) 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/py-ase/ase-3.22.0/ase/test/forcefields/
H A Dtest_combine_mm2.py24 atoms2 = make_atoms()
25 atoms2.translate([0., 3, 0])
26 atoms2.rotate(180, 'y')
27 atoms2.translate([3, 0, 0])
28 atoms += atoms2
/dports/science/py-ase/ase-3.22.0/ase/optimize/
H A Dminimahopping.py361 def __call__(self, atoms1, atoms2): argument
363 atoms2 = atoms2.copy()
370 def _translated_compare(self, atoms1, atoms2): argument
379 atoms2.set_constraint()
389 for bc in atoms2.pbc:
394 repeated = atoms2.repeat(repeat)
395 moved_cell = atoms2.cell * atoms2.pbc
398 repeated.set_cell(atoms2.cell)
428 atoms2 = atoms2.copy() # allow deletion
429 atoms2.set_constraint()
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/
H A Dtest_davidson_scalapack.py34 atoms2 = atoms.copy()
37 atoms2.calc = get_calculator(sl_auto=False, kpoint_gamma=kpoint_gamma)
40 e2 = atoms2.get_potential_energy()
44 eigvals2 = atoms2.calc.get_eigenvalues(kpt=n, spin=0)
/dports/science/py-ase/ase-3.22.0/ase/test/calculator/
H A Dtest_gulp_opt.py15 atoms2 = atoms.copy()
17 with calc2.get_optimizer(atoms2) as opt2:
32 atoms2 = atoms.copy()
34 with calc2.get_optimizer(atoms2) as opt2:
H A Dtest_lj.py56 atoms2 = Atoms('H2', positions=[[0, 0, 0], [r + h, 0, 0]])
58 atoms2.calc = calc
60 fd_force = (atoms2.get_potential_energy() - atoms.get_potential_energy()) / h
/dports/science/gromacs/gromacs-2021.4/src/gromacs/trajectoryanalysis/tests/
H A Dtopologyinformation.cpp77 auto atoms2 = topInfo.copyAtoms(); in TEST() local
78 ASSERT_TRUE(atoms2); in TEST()
79 EXPECT_NE(atoms1.get(), atoms2.get()); in TEST()
108 auto atoms2 = topInfo.copyAtoms(); in runCommonTests() local
109 EXPECT_TRUE(atoms2); in runCommonTests()
111 EXPECT_NE(atoms1.get(), atoms2.get()); in runCommonTests()
115 EXPECT_NE(atoms2.get(), atoms); in runCommonTests()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/more/
H A DMdTopReader.java101 Atom[] atoms2 = null; in finalizeSubclassReader() local
105 atoms2 = new Atom[atoms.length]; in finalizeSubclassReader()
109 atoms2[nAtoms++] = atoms[i]; in finalizeSubclassReader()
118 if (atoms2 != null) { in finalizeSubclassReader()
121 asc.addAtom(atoms2[i]); in finalizeSubclassReader()
/dports/multimedia/opentoonz/opentoonz-1.5.0/toonz/sources/common/tiio/
H A Dmovsettings.cpp162 const QTAtomContainer &atoms2, QTAtom parent2) { in compareAtoms() argument
166 QTCountChildrenOfType(atoms2, parent2, 0)); in compareAtoms()
172 if (QTNextChildAnyType(atoms2, parent2, curr2, &curr2) != noErr) in compareAtoms()
182 QTGetAtomTypeAndID(atoms2, curr2, &atomType2, &id2); in compareAtoms()
186 int sonCount2 = QTCountChildrenOfType(atoms2, curr2, 0); in compareAtoms()
189 compareAtoms(atoms1, curr1, atoms2, curr2); in compareAtoms()
197 if (QTGetAtomDataPtr(atoms2, curr2, &size2, (char **)&atomData2) != noErr) in compareAtoms()
/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/solvation/
H A Dtest_spinpol.py34 atoms2 = atoms.copy()
35 atoms2.set_initial_magnetic_moments(None)
37 atomss = (atoms, atoms2)
/dports/science/molscript/MolScript-280abee/code/
H A Dgraphics.c314 at3d **atoms1, **atoms2; in ball_and_stick() local
338 atoms2 = atoms1; in ball_and_stick()
353 if (atoms2 != NULL) free (atoms2); in ball_and_stick()
379 v2 = &(atoms2[slot2]->xyz); in ball_and_stick()
434 free (atoms2); in ball_and_stick()
446 at3d **atoms1, **atoms2; in bonds() local
464 atoms2 = atoms1; in bonds()
483 if (atoms2 != NULL) free (atoms2); in bonds()
540 atoms2[slot2]->rval++; in bonds()
570 atoms2[slot2]->rval++; in bonds()
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