/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/coordinates/ |
H A D | XYZ.py | 146 self.n_atoms = n_atoms 211 if ts_full.n_atoms == atoms.n_atoms: 233 if self.n_atoms is not None: 234 if self.n_atoms != ts.n_atoms: 239 ''.format(ts.n_atoms, self.n_atoms)) 319 def n_atoms(self): member in XYZReader 337 linesPerFrame = self.n_atoms + 2 372 for i in range(self.n_atoms): 419 if n_atoms is None: 420 n_atoms = self.n_atoms [all …]
|
H A D | XDR.py | 139 self.n_atoms = len(self._sub) 141 self.n_atoms = self._xdr.n_atoms 167 n_atoms = f.n_atoms 168 return n_atoms 189 n_atoms_ok = self._xdr.n_atoms == data['n_atoms'] 210 n_atoms=self._xdr.n_atoms) 256 def Writer(self, filename, n_atoms=None, **kwargs): argument 258 if n_atoms is None: 259 n_atoms = self.n_atoms 260 return self._writer(filename, n_atoms=n_atoms, **kwargs) [all …]
|
H A D | GRO.py | 177 self.n_atoms = n_atoms = int(grofile.readline()) 184 velocities = np.zeros((n_atoms, 3), dtype=np.float32) 186 self.ts = ts = self._Timestep(n_atoms, 194 if pos == n_atoms: 231 def Writer(self, filename, n_atoms=None, **kwargs): argument 244 if n_atoms is None: 245 n_atoms = self.n_atoms 246 return GROWriter(filename, n_atoms=n_atoms, **kwargs) 329 self.n_atoms = n_atoms 398 atom_indices = range(1, ag_or_ts.n_atoms+1) [all …]
|
H A D | TRJ.py | 220 if n_atoms is None: 315 if self.n_atoms == 1: 369 def n_atoms(self): member in TRJReader 519 if n_atoms is not None and n_atoms != self.n_atoms: 522 "is used!".format(n_atoms, self.n_atoms)) 543 return n_atoms 631 n_atoms = kwargs.pop('n_atoms', self.n_atoms) 742 n_atoms, argument 750 if n_atoms == 0: 752 self.n_atoms = n_atoms [all …]
|
H A D | TRZ.py | 169 if n_atoms is None: 174 self._n_atoms = n_atoms 177 self.ts = Timestep(self.n_atoms, 184 readarg = str(n_atoms) + '<f4' 283 def n_atoms(self): member in TRZReader 423 if n_atoms is None: 425 n_atoms = self.ts.n_atoms 467 if n_atoms is None: 469 if n_atoms == 0: 471 self.n_atoms = n_atoms [all …]
|
H A D | DCD.py | 140 self.n_atoms = self._file.header['natoms'] 166 n_atoms = f.header['natoms'] 167 return n_atoms 207 if n_atoms is None: 208 n_atoms = self.n_atoms 211 n_atoms=n_atoms, 327 atom_numbers = list(range(self.n_atoms)) 355 n_atoms, argument 396 if n_atoms is None: 398 self.n_atoms = n_atoms [all …]
|
H A D | CRD.py | 86 self.n_atoms = len(coords_list) 95 if self.n_atoms != natoms: 97 "should be %d coordinates." % (self.n_atoms, self.filename, natoms)) 185 n_atoms = len(atoms) 189 if n_atoms > 99999: 206 ('resids', np.ones(n_atoms, dtype=np.int)), 238 if n_atoms > 99999: 239 crd.write(self.fmt['NUMATOMS_EXT'].format(n_atoms)) 241 crd.write(self.fmt['NUMATOMS'].format(n_atoms)) 248 range(n_atoms), coor, attrs['resnames'], attrs['names'],
|
H A D | INPCRD.py | 56 self.n_atoms = int(line[0]) 58 self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs) 67 for p in range(self.n_atoms // 2): 74 if self.n_atoms % 2: 83 n_atoms = int(f.readline().split()[0]) 84 return n_atoms
|
H A D | MOL2.py | 144 self.n_atoms = None 158 self.n_atoms = len(coords) 160 self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs) 180 elif self.n_atoms is None: 182 self.n_atoms = len(atom_lines) 183 elif len(atom_lines) != self.n_atoms: 188 "".format(self.n_atoms, len(atom_lines))) 194 coords = np.zeros((self.n_atoms, 3), dtype=np.float32) 276 def __init__(self, filename, n_atoms=None, convert_units=None): argument
|
/dports/science/py-hiphive/hiphive-0.7.1/hiphive/input_output/ |
H A D | phonopy.py | 95 n_atoms = fc2_array.shape[0] 96 if fc2_array.shape != (n_atoms, n_atoms, 3, 3): 147 n_atoms = fc3_array.shape[0] 148 if fc3_array.shape != (n_atoms, n_atoms, n_atoms, 3, 3, 3): 164 n_atoms = line_ints[0] 167 n_atoms = line_ints[0] 170 fc2 = np.full((n_atoms, n_atoms, 3, 3), np.nan) 200 n_atoms = fc2.shape[0] 202 f.write('{:5d} {:5d}\n'.format(n_atoms, n_atoms)) 203 for i, j in product(range(n_atoms), repeat=2):
|
/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/coordinates/ |
H A D | test_netcdf.py | 68 assert w.n_atoms == len(universe.atoms) 74 assert w.n_atoms == 42 355 with mda.Writer(outfile, n_atoms=p.n_atoms, format="ncdf") as W: 391 n_atoms = 3 variable in TestNCDFWriterVelsForces 397 ts._pos[:] = np.arange(self.n_atoms * 3).reshape(self.n_atoms, 3) 398 ts._velocities[:] = np.arange(self.n_atoms * 3).reshape(self.n_atoms, 400 ts._forces[:] = np.arange(self.n_atoms * 3).reshape(self.n_atoms, 408 ts._pos[:] = np.arange(self.n_atoms * 3).reshape(self.n_atoms, 3) + 300 409 ts._velocities[:] = np.arange(self.n_atoms * 3).reshape(self.n_atoms, 411 ts._forces[:] = np.arange(self.n_atoms * 3).reshape(self.n_atoms, [all …]
|
H A D | test_memory.py | 43 self.n_atoms = self.universe.trajectory.n_atoms 51 self.first_frame = Timestep(self.n_atoms) 56 self.second_frame = Timestep(self.n_atoms) 61 self.last_frame = Timestep(self.n_atoms) 310 n_atoms = 10 variable in TestMemoryReaderModifications 316 self.n_frames, self.n_atoms, 3) 318 self.n_frames, self.n_atoms, 3) + 200 320 self.n_frames, self.n_atoms, 3) + 400 330 u = mda.Universe.empty(self.n_atoms) 343 assert ts.positions.shape == (self.n_atoms, 3) [all …]
|
/dports/science/py-ase/ase-3.22.0/ase/vibrations/ |
H A D | data.py | 64 .reshape(3 * n_atoms, 3 * n_atoms).copy()) 90 n_atoms = cls._check_dimensions(atoms, hessian_2d_array, 93 return cls(atoms, hessian_2d_array.reshape(n_atoms, 3, n_atoms, 3), 142 n_atoms = len(atoms[indices]) 145 ref_shape = [n_atoms * 3, n_atoms * 3] 149 ref_shape = [n_atoms, 3, n_atoms, 3] 154 return n_atoms 200 n_atoms = int(self._hessian2d.shape[0] / 3) 201 return self._hessian2d.reshape(n_atoms, 3, n_atoms, 3).copy() 260 n_atoms = len(active_atoms) [all …]
|
/dports/science/py-hiphive/hiphive-0.7.1/hiphive/ |
H A D | force_constants.py | 36 def n_atoms(self) -> int: member in ForceConstants 129 self.n_atoms * 3, self.n_atoms * 3) 164 atomic_indices = range(self.n_atoms) 279 n_atoms = len(supercell) 283 if fc2_array.shape != (n_atoms, n_atoms, 3, 3): 290 if fc3_array.shape != (n_atoms, n_atoms, n_atoms, 3, 3, 3): 563 n_atoms = fc_array.shape[0] 664 n_atoms = fc2.shape[0] 665 if len(masses) != n_atoms: 670 fc2_tmp = np.zeros((n_atoms, n_atoms, 3, 3)) [all …]
|
/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/topology/ |
H A D | GROParser.py | 88 n_atoms = int(next(inf)) 91 resids = np.zeros(n_atoms, dtype=np.int32) 92 resnames = np.zeros(n_atoms, dtype=object) 93 names = np.zeros(n_atoms, dtype=object) 94 indices = np.zeros(n_atoms, dtype=np.int32) 97 if i == n_atoms: 153 top = Topology(n_atoms=n_atoms, n_res=len(new_resids), n_seg=1,
|
/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/topology/ |
H A D | test_minimal.py | 59 assert top.n_atoms == expected_n_atoms 76 def test_minimal_parser_fail(filename,n_atoms): argument 83 def test_minimal_n_atoms_kwarg(filename, n_atoms): argument 85 u = mda.Universe(filename, n_atoms=n_atoms) 87 assert len(u.atoms) == n_atoms 107 assert top.n_atoms == 10
|
/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/ |
H A D | dummy.py | 80 n_atoms, n_residues, n_segments = size 83 n_atoms=n_atoms, 87 np.arange(n_residues), n_atoms // n_residues), 102 ts.positions = np.arange(3 * n_atoms).reshape(n_atoms, 3) 105 ts.velocities = np.arange(3 * n_atoms).reshape(n_atoms, 3) + 100 107 ts.forces = np.arange(3 * n_atoms).reshape(n_atoms, 3) + 10000
|
/dports/science/lammps/lammps-stable_29Sep2021/tools/ch2lmp/other/ |
H A D | mkdcd_f77.f | 14 4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter, local 43 4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter, local 80 read(21,*) n_atoms 91 if (n_atoms > max_atoms) write(6,*) "n_atoms > max_atoms" 94 do i = 1, n_atoms 103 if (n_atoms_recenter < n_atoms) i_recenter_flag = 1 118 4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter, local 162 4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter, local 216 4 n_atoms, n_frozen_atoms, n_atoms_dump, n_atoms_recenter, local 233 read(21,*) n_atoms [all …]
|
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/ |
H A D | find_dimension.py | 55 n_atoms = len(struct.species) 65 for i in range(n_atoms): 66 for j in range(i + 1, n_atoms): 102 n_atoms = len(struct.species) 103 if len(np.unique(connected_list)) != n_atoms: 105 if n_atoms == 0: 109 for atom in range(n_atoms): 132 if n_atoms in cluster_sizes:
|
/dports/science/py-OpenFermion/OpenFermion-1.3.0/src/openfermion/chem/ |
H A D | chemical_series.py | 25 def make_atomic_ring(n_atoms, argument 50 theta = 2. * numpy.pi / float(n_atoms) 52 for atom in range(n_atoms): 58 n_electrons = n_atoms * periodic_hash_table[atom_type] 110 n_atoms = nx_atoms * ny_atoms * nz_atoms 111 n_electrons = n_atoms * periodic_hash_table[atom_type]
|
/dports/science/libefp/libefp-1.5.0/efpmd/src/ |
H A D | efield.c | 65 size_t n_atoms; in sim_efield() local 67 check_fail(efp_get_frag_atom_count(state->efp, i, &n_atoms)); in sim_efield() 68 atoms = xmalloc(n_atoms * sizeof(struct efp_atom)); in sim_efield() 69 check_fail(efp_get_frag_atoms(state->efp, i, n_atoms, atoms)); in sim_efield() 71 for (size_t j = 0; j < n_atoms; j++) { in sim_efield()
|
/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/core/ |
H A D | topology.py | 204 n_atoms, n_residues, n_segments, # Size of tables argument 207 self.n_atoms = n_atoms 213 self._AR = np.zeros(n_atoms, dtype=np.intp) 216 if not len(self._AR) == n_atoms: 231 return self.__class__(self.n_atoms, self.n_residues, self.n_segments, 237 return (self.n_atoms, self.n_residues, self.n_segments) 446 def __init__(self, n_atoms=1, n_res=1, n_seg=1, argument 467 self.tt = TransTable(n_atoms, n_res, n_seg, 494 def n_atoms(self): member in Topology 495 return self.tt.n_atoms
|
/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/data/coordinates/ |
H A D | create_data.py | 7 n_atoms = uni.atoms.n_atoms 8 pos = np.arange(3 * n_atoms).reshape(n_atoms, 3) 14 with mda.Writer(fname, n_atoms) as w:
|
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-File-XYZ-0.11/ |
H A D | XYZ.pm | 96 my $n_atoms; 98 $n_atoms = shift @lines; 104 $n_atoms = @lines unless $n_atoms; 111 last if $i > $n_atoms;
|
/dports/science/p5-Chemistry-File-XYZ/Chemistry-File-XYZ-0.11/ |
H A D | XYZ.pm | 96 my $n_atoms; 98 $n_atoms = shift @lines; 104 $n_atoms = @lines unless $n_atoms; 111 last if $i > $n_atoms;
|