git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@255 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
455
src/atom_vec_atomic.cpp
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455
src/atom_vec_atomic.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "stdlib.h"
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#include "atom_vec_atomic.h"
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#include "atom.h"
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#include "domain.h"
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#include "modify.h"
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#include "fix.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define DELTA 10000
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/* ---------------------------------------------------------------------- */
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AtomVecAtomic::AtomVecAtomic(LAMMPS *lmp, int narg, char **arg) :
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AtomVec(lmp, narg, arg)
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{
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mass_type = 1;
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size_comm = 3;
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size_reverse = 3;
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size_border = 6;
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size_data_atom = 5;
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size_data_vel = 4;
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xcol_data = 3;
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}
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/* ----------------------------------------------------------------------
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grow atom arrays
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n = 0 grows arrays by DELTA
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n > 0 allocates arrays to size n
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------------------------------------------------------------------------- */
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void AtomVecAtomic::grow(int n)
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{
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if (n == 0) nmax += DELTA;
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else nmax = n;
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atom->nmax = nmax;
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tag = atom->tag = (int *)
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memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
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type = atom->type = (int *)
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memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
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mask = atom->mask = (int *)
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memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
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image = atom->image = (int *)
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memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
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x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
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v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
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f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecAtomic::reset_ptrs()
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{
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tag = atom->tag;
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type = atom->type;
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mask = atom->mask;
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image = atom->image;
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x = atom->x;
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v = atom->v;
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f = atom->f;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecAtomic::copy(int i, int j)
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{
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tag[j] = tag[i];
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type[j] = type[i];
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mask[j] = mask[i];
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image[j] = image[i];
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x[j][0] = x[i][0];
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x[j][1] = x[i][1];
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x[j][2] = x[i][2];
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v[j][0] = v[i][0];
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v[j][1] = v[i][1];
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v[j][2] = v[i][2];
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::pack_comm(int n, int *list, double *buf, int *pbc_flags)
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{
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int i,j,m;
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m = 0;
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if (pbc_flags[0] == 0) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0];
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buf[m++] = x[j][1];
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buf[m++] = x[j][2];
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}
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} else {
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0] + pbc_flags[1]*xprd;
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buf[m++] = x[j][1] + pbc_flags[2]*yprd;
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buf[m++] = x[j][2] + pbc_flags[3]*zprd;
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecAtomic::unpack_comm(int n, int first, double *buf)
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{
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int i,m,last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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x[i][0] = buf[m++];
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x[i][1] = buf[m++];
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x[i][2] = buf[m++];
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}
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::pack_reverse(int n, int first, double *buf)
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{
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int i,m,last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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buf[m++] = f[i][0];
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buf[m++] = f[i][1];
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buf[m++] = f[i][2];
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecAtomic::unpack_reverse(int n, int *list, double *buf)
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{
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int i,j,m;
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m = 0;
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for (i = 0; i < n; i++) {
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j = list[i];
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f[j][0] += buf[m++];
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f[j][1] += buf[m++];
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f[j][2] += buf[m++];
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}
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::pack_border(int n, int *list, double *buf, int *pbc_flags)
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{
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int i,j,m;
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m = 0;
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if (pbc_flags[0] == 0) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0];
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buf[m++] = x[j][1];
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buf[m++] = x[j][2];
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buf[m++] = tag[j];
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buf[m++] = type[j];
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buf[m++] = mask[j];
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}
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} else {
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0] + pbc_flags[1]*xprd;
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buf[m++] = x[j][1] + pbc_flags[2]*yprd;
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buf[m++] = x[j][2] + pbc_flags[3]*zprd;
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buf[m++] = tag[j];
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buf[m++] = type[j];
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buf[m++] = mask[j];
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecAtomic::unpack_border(int n, int first, double *buf)
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{
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int i,m,last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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if (i == nmax) grow(0);
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x[i][0] = buf[m++];
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x[i][1] = buf[m++];
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x[i][2] = buf[m++];
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tag[i] = static_cast<int> (buf[m++]);
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type[i] = static_cast<int> (buf[m++]);
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mask[i] = static_cast<int> (buf[m++]);
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}
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}
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/* ----------------------------------------------------------------------
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pack data for atom I for sending to another proc
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xyz must be 1st 3 values, so comm::exchange() can test on them
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------------------------------------------------------------------------- */
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int AtomVecAtomic::pack_exchange(int i, double *buf)
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{
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int m = 1;
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buf[m++] = x[i][0];
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buf[m++] = x[i][1];
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buf[m++] = x[i][2];
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buf[m++] = v[i][0];
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buf[m++] = v[i][1];
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buf[m++] = v[i][2];
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buf[m++] = tag[i];
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buf[m++] = type[i];
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buf[m++] = mask[i];
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buf[m++] = image[i];
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
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buf[0] = m;
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::unpack_exchange(double *buf)
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{
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int nlocal = atom->nlocal;
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if (nlocal == nmax) grow(0);
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int m = 1;
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x[nlocal][0] = buf[m++];
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x[nlocal][1] = buf[m++];
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x[nlocal][2] = buf[m++];
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v[nlocal][0] = buf[m++];
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v[nlocal][1] = buf[m++];
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v[nlocal][2] = buf[m++];
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tag[nlocal] = static_cast<int> (buf[m++]);
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type[nlocal] = static_cast<int> (buf[m++]);
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mask[nlocal] = static_cast<int> (buf[m++]);
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image[nlocal] = static_cast<int> (buf[m++]);
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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m += modify->fix[atom->extra_grow[iextra]]->
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unpack_exchange(nlocal,&buf[m]);
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atom->nlocal++;
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return m;
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}
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/* ----------------------------------------------------------------------
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size of restart data for all atoms owned by this proc
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include extra data stored by fixes
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------------------------------------------------------------------------- */
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int AtomVecAtomic::size_restart()
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{
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int i;
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int nlocal = atom->nlocal;
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int n = 11 * nlocal;
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if (atom->nextra_restart)
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for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
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for (i = 0; i < nlocal; i++)
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n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
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return n;
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}
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/* ----------------------------------------------------------------------
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size of restart data for atom I
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do not include extra data stored by fixes, included by caller
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------------------------------------------------------------------------- */
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int AtomVecAtomic::size_restart_one(int i)
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{
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return 11;
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}
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/* ----------------------------------------------------------------------
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pack atom I's data for restart file including extra quantities
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xyz must be 1st 3 values, so that read_restart can test on them
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molecular types may be negative, but write as positive
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------------------------------------------------------------------------- */
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int AtomVecAtomic::pack_restart(int i, double *buf)
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{
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int m = 1;
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buf[m++] = x[i][0];
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buf[m++] = x[i][1];
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buf[m++] = x[i][2];
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buf[m++] = tag[i];
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buf[m++] = type[i];
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buf[m++] = mask[i];
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buf[m++] = image[i];
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buf[m++] = v[i][0];
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buf[m++] = v[i][1];
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buf[m++] = v[i][2];
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if (atom->nextra_restart)
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for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
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m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
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buf[0] = m;
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return m;
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}
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/* ----------------------------------------------------------------------
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unpack data for one atom from restart file including extra quantities
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------------------------------------------------------------------------- */
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int AtomVecAtomic::unpack_restart(double *buf)
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{
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int nlocal = atom->nlocal;
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if (nlocal == nmax) {
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grow(0);
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if (atom->nextra_store)
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atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
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atom->nextra_store,
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"atom:extra");
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}
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int m = 1;
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x[nlocal][0] = buf[m++];
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x[nlocal][1] = buf[m++];
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x[nlocal][2] = buf[m++];
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tag[nlocal] = static_cast<int> (buf[m++]);
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type[nlocal] = static_cast<int> (buf[m++]);
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mask[nlocal] = static_cast<int> (buf[m++]);
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image[nlocal] = static_cast<int> (buf[m++]);
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v[nlocal][0] = buf[m++];
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v[nlocal][1] = buf[m++];
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v[nlocal][2] = buf[m++];
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double **extra = atom->extra;
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if (atom->nextra_store) {
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int size = static_cast<int> (buf[0]) - m;
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for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
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}
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atom->nlocal++;
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return m;
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}
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/* ----------------------------------------------------------------------
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create one atom of type itype at x0,y0,z0
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set other values to defaults
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------------------------------------------------------------------------- */
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void AtomVecAtomic::create_atom(int itype, double x0, double y0, double z0,
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int ihybrid)
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{
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int nlocal = atom->nlocal;
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if (nlocal == nmax) grow(0);
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tag[nlocal] = 0;
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type[nlocal] = itype;
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x[nlocal][0] = x0;
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x[nlocal][1] = y0;
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x[nlocal][2] = z0;
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mask[nlocal] = 1;
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image[nlocal] = (512 << 20) | (512 << 10) | 512;
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v[nlocal][0] = 0.0;
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v[nlocal][1] = 0.0;
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v[nlocal][2] = 0.0;
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atom->nlocal++;
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}
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/* ----------------------------------------------------------------------
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unpack one line from Atoms section of data file
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initialize other atom quantities
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------------------------------------------------------------------------- */
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void AtomVecAtomic::data_atom(double xtmp, double ytmp, double ztmp,
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int imagetmp, char **values, int ihybrid)
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{
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int nlocal = atom->nlocal;
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if (nlocal == nmax) grow(0);
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tag[nlocal] = atoi(values[0]);
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if (tag[nlocal] <= 0)
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error->one("Invalid atom ID in Atoms section of data file");
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type[nlocal] = atoi(values[1]);
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if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
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error->one("Invalid atom type in Atoms section of data file");
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x[nlocal][0] = xtmp;
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x[nlocal][1] = ytmp;
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x[nlocal][2] = ztmp;
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image[nlocal] = imagetmp;
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mask[nlocal] = 1;
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v[nlocal][0] = 0.0;
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v[nlocal][1] = 0.0;
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v[nlocal][2] = 0.0;
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atom->nlocal++;
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}
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/* ----------------------------------------------------------------------
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return # of bytes of allocated memory
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------------------------------------------------------------------------- */
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int AtomVecAtomic::memory_usage()
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{
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int bytes = 0;
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if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
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if (atom->memcheck("type")) bytes += nmax * sizeof(int);
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if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
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if (atom->memcheck("image")) bytes += nmax * sizeof(int);
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if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
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if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
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if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
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return bytes;
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}
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