/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 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 …]
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H A D | tools.py | 255 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]) [all …]
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/dports/science/py-ase/ase-3.22.0/ase/test/atoms/ |
H A D | test_compare_atoms.py | 15 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"}
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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 27 assert atoms2 == atoms3
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxana/ |
H A D | gmx_confrms.cpp | 354 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() [all …]
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/dports/science/py-ase/ase-3.22.0/ase/calculators/ |
H A D | combine_mm.py | 50 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 …]
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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 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 [all …]
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H A D | diff.py | 163 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'
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/dports/science/py-ase/ase-3.22.0/ase/test/ |
H A D | test_mixingcalc.py | 26 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()
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/dports/science/py-ase/ase-3.22.0/ase/test/fio/ |
H A D | test_exciting.py | 14 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)
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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) 12 assert np.array_equal(atoms1.arrays[name], atoms2.arrays[name]), name
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H A D | test_v_sim.py | 209 atoms2 = read(copy) 212 assert sum(abs((atoms.positions - atoms2.positions).ravel())) < tol 213 assert sum(abs((atoms.cell - atoms2.cell).ravel())) < tol
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H A D | test_nwchem.py | 9 atoms2 = io.read('nwchem.nwi') 13 check = sum(abs((atoms.positions - atoms2.positions).ravel()) > tol)
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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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/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 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]
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/dports/science/py-ase/ase-3.22.0/ase/test/forcefields/ |
H A D | test_combine_mm2.py | 24 atoms2 = make_atoms() 25 atoms2.translate([0., 3, 0]) 26 atoms2.rotate(180, 'y') 27 atoms2.translate([3, 0, 0]) 28 atoms += atoms2
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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 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() [all …]
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/ |
H A D | test_davidson_scalapack.py | 34 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)
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/dports/science/py-ase/ase-3.22.0/ase/test/calculator/ |
H A D | test_gulp_opt.py | 15 atoms2 = atoms.copy() 17 with calc2.get_optimizer(atoms2) as opt2: 32 atoms2 = atoms.copy() 34 with calc2.get_optimizer(atoms2) as opt2:
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H A D | test_lj.py | 56 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
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/trajectoryanalysis/tests/ |
H A D | topologyinformation.cpp | 77 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()
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/more/ |
H A D | MdTopReader.java | 101 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()
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/dports/multimedia/opentoonz/opentoonz-1.5.0/toonz/sources/common/tiio/ |
H A D | movsettings.cpp | 162 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()
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/dports/science/py-gpaw/gpaw-21.6.0/gpaw/test/solvation/ |
H A D | test_spinpol.py | 34 atoms2 = atoms.copy() 35 atoms2.set_initial_magnetic_moments(None) 37 atomss = (atoms, atoms2)
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/dports/science/molscript/MolScript-280abee/code/ |
H A D | graphics.c | 314 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() [all …]
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