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Searched refs:peratom (Results 1 – 25 of 141) sorted by relevance

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/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/src/
H A Dfix_minimize.cpp62 peratom = NULL; in FixMinimize()
81 memory->destroy(peratom); in ~FixMinimize()
99 memory->grow(peratom,nvector+1,"minimize:peratom"); in add_vector()
100 peratom[nvector] = n; in add_vector()
204 bytes += atom->nmax*peratom[m]*sizeof(double); in memory_usage()
215 memory->grow(vectors[m],peratom[m]*nmax,"minimize:vector"); in grow_arrays()
227 nper = peratom[m]; in copy_arrays()
244 nper = peratom[m]; in pack_exchange()
261 nper = peratom[m]; in unpack_exchange()
H A Dcompute_atom_molecule.cpp260 vone[imol] += peratom[j]; in compute_vector()
292 aone[imol][m] += peratom[j]; in compute_array()
325 peratom = compute->vector_atom; in compute_one()
328 if (compute->array_atom) peratom = &compute->array_atom[0][aidx-1]; in compute_one()
329 else peratom = NULL; in compute_one()
342 peratom = fix->vector_atom; in compute_one()
345 peratom = &fix->array_atom[0][aidx-1]; in compute_one()
356 peratom = scratch; in compute_one()
359 input->variable->compute_atom(vidx,igroup,peratom,1,0); in compute_one()
H A Dfix_minimize.h81 int *peratom;
H A Dcompute_atom_molecule.h79 double *peratom;
/dports/science/lammps/lammps-stable_29Sep2021/src/
H A Dfix_minimize.cpp27 nvector(0), peratom(nullptr), vectors(nullptr) in FixMinimize()
45 memory->destroy(peratom); in ~FixMinimize()
65 memory->grow(peratom,nvector+1,"minimize:peratom"); in add_vector()
66 peratom[nvector] = n; in add_vector()
170 bytes += (double)atom->nmax*peratom[m]*sizeof(double); in memory_usage()
181 memory->grow(vectors[m],peratom[m]*nmax,"minimize:vector"); in grow_arrays()
193 nper = peratom[m]; in copy_arrays()
210 nper = peratom[m]; in pack_exchange()
227 nper = peratom[m]; in unpack_exchange()
H A Datom.cpp105 peratom = nullptr; in Atom()
301 delete [] peratom[i].name; in ~Atom()
302 memory->sfree(peratom); in ~Atom()
381 delete [] peratom[i].name; in peratom_create()
382 memory->sfree(peratom); in peratom_create()
384 peratom = nullptr; in peratom_create()
567 peratom = (PerAtom *) in add_peratom()
574 peratom[nperatom].cols = cols; in add_peratom()
591 peratom[i].cols = cols; in add_peratom_change_columns()
615 peratom = (PerAtom *) in add_peratom_vary()
[all …]
H A Dfix_minimize.h49 int *peratom; variable
/dports/science/py-ase/ase-3.22.0/ase/md/
H A Dlogger.py28 peratom=False, mode="a"): argument
37 self.peratom = peratom
44 if self.peratom:
77 if self.peratom:
/dports/science/lammps/lammps-stable_29Sep2021/doc/src/
H A DDeveloper_notes.rst14 virial of the system, both in a global and peratom sense. Fixes that
67 * For peratom energy, invoke the ev_init(eflag,vflag) function each
75 * For global and/or peratom virial, invoke the v_init(vflag) function
86 peratom virial contributions. Thus you do not need to invoke the
87 v_init() and v_tally() methods, if the fix also calculates peratom
91 these contributions to the global/peratom energy/virial of the system.
95 * *thermo_energy* = 1, for global and peratom energy
96 * *thermo_virial* = 1, for global and peratom virial
108 If the fix contributes to any of the global/peratom energy/virial
117 * peratom energy in :doc:`compute pe/atom <compute_pe_atom>`
[all …]
H A Dcompute_voronoi_atom.rst17 or *face_threshold* or *neighbors* or *peratom*
35 *peratom* value = *yes* or *no* = per-atom quantities accessible or no
62 plus any exterior faces (see note below). If the *peratom* keyword
200 options. If the *peratom* keyword is set to "no", the per-atom array
216 quantity. This effect can be eliminated by using the *peratom*
242 *neighbors* no, *peratom* yes
H A DPython_scatter.rst18 The gather methods collect peratom info of the requested type (atom
21 functions do the inverse. They distribute a vector of peratom values,
/dports/science/lammps/lammps-stable_29Sep2021/src/KOKKOS/
H A Dfix_minimize_kokkos.cpp49 memory->grow(peratom,nvector+1,"minimize:peratom"); in add_vector_kokkos()
50 peratom[nvector] = n; in add_vector_kokkos()
232 nper = peratom[m]; in pack_exchange()
251 nper = peratom[m]; in unpack_exchange()
/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/atc/two_temperature/
H A Drestart.screen12 ATC: peratom PE compute created with ID: 3
103 ATC: peratom PE compute created with ID: 3
/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/atc/elastic/
H A Dbar1d_thermo_elastic.screen56 ATC: peratom PE compute created with ID: 3
109 ATC: peratom PE compute created with ID: 3
/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/awpmd/
H A Din.h_molecule32 compute peratom all stress/atom NULL
H A Din.h_atom32 compute peratom all stress/atom NULL
/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/eff/H/
H A Din.h_atom.spe.ang23 compute peratom all stress/atom NULL
H A Din.h_atom.spe.bohr22 compute peratom all stress/atom NULL
/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/interlayer/drip/
H A Din.C_drip17 compute peratom all pe/atom
H A Din.CH_drip18 compute peratom all pe/atom
/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/eff/fixed-core/CH4/
H A Din.CH4fc.spe.bohr26 compute peratom all stress/atom NULL
H A Din.CH4fc.spe.ang27 compute peratom all stress/atom NULL
/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/rann/
H A Din.rann18 compute peratom all pe/atom
/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/eff/Li-solid/
H A Din.Li.bohr19 compute peratom all stress/atom NULL
/dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxpreprocess/
H A Deditconf.cpp215 …fac(int natoms, int nres, t_atoms* atoms, int n_bfac, double* bfac, int* bfac_nr, gmx_bool peratom) in set_pdb_conf_bfac() argument
223 peratom = TRUE; in set_pdb_conf_bfac()
274 if (!peratom) in set_pdb_conf_bfac()
595 static gmx_bool peratom = FALSE, bLegend = FALSE, bOrient = FALSE, bMead = FALSE, in gmx_editconf() local
663 { "-atom", FALSE, etBOOL, { &peratom }, "Force B-factor attachment per atom" }, in gmx_editconf()
1277 set_pdb_conf_bfac(atoms.nr, atoms.nres, &atoms, n_bfac, bfac, bfac_nr, peratom); in gmx_editconf()

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