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/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/coordinates/
H A DXYZ.py146 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 DXDR.py139 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 DGRO.py177 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 DTRJ.py220 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 DTRZ.py169 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 DDCD.py140 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 DCRD.py86 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 DINPCRD.py56 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 DMOL2.py144 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 Dphonopy.py95 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 Dtest_netcdf.py68 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 Dtest_memory.py43 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 Ddata.py64 .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 Dforce_constants.py36 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 DGROParser.py88 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 Dtest_minimal.py59 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 Ddummy.py80 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 Dmkdcd_f77.f14 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 Dfind_dimension.py55 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 Dchemical_series.py25 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 Defield.c65 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 Dtopology.py204 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 Dcreate_data.py7 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 DXYZ.pm96 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 DXYZ.pm96 my $n_atoms;
98 $n_atoms = shift @lines;
104 $n_atoms = @lines unless $n_atoms;
111 last if $i > $n_atoms;

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