git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@255 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
466
src/atom_vec_hybrid.cpp
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466
src/atom_vec_hybrid.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 "string.h"
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#include "atom_vec_hybrid.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 MIN(A,B) ((A) < (B)) ? (A) : (B)
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#define MAX(A,B) ((A) > (B)) ? (A) : (B)
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#define DELTA 10000
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/* ---------------------------------------------------------------------- */
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AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
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AtomVec(lmp, narg, arg)
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{
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int i,m;
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if (narg < 1) error->all("Illegal atom_style command");
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// create sub-styles
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nstyles = narg;
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styles = new AtomVec*[nstyles];
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keywords = new char*[nstyles];
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for (i = 0; i < narg; i++) {
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for (m = 0; m < i; m++)
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if (strcmp(arg[i],keywords[m]) == 0)
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error->all("Atom style hybrid cannot use same atom style twice");
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if (strcmp(arg[i],"hybrid") == 0)
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error->all("Atom style hybrid cannot have hybrid as an argument");
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styles[i] = atom->new_avec(arg[i],0,NULL);
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keywords[i] = new char[strlen(arg[i])+1];
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strcpy(keywords[i],arg[i]);
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}
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// hybrid settings are MAX or MIN of sub-style settings
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// size_border has +1 for hybrid[] value that is also communicated
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for (m = 0; m < nstyles; m++) {
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molecular = MAX(molecular,styles[m]->molecular);
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bonds_allow = MAX(bonds_allow,styles[m]->bonds_allow);
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angles_allow = MAX(angles_allow,styles[m]->angles_allow);
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dihedrals_allow = MAX(dihedrals_allow,styles[m]->dihedrals_allow);
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impropers_allow = MAX(impropers_allow,styles[m]->impropers_allow);
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mass_type = MAX(mass_type,styles[m]->mass_type);
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dipole_type = MAX(dipole_type,styles[m]->dipole_type);
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comm_x_only = MIN(comm_x_only,styles[m]->comm_x_only);
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comm_f_only = MIN(comm_f_only,styles[m]->comm_f_only);
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size_comm = MAX(size_comm,styles[m]->size_comm);
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size_reverse = MAX(size_reverse,styles[m]->size_reverse);
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size_border = MAX(size_border,styles[m]->size_border) + 1;
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}
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}
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/* ---------------------------------------------------------------------- */
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AtomVecHybrid::~AtomVecHybrid()
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{
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for (int m = 0; m < nstyles; m++) delete styles[m];
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delete [] styles;
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for (int m = 0; m < nstyles; m++) delete [] keywords[m];
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delete [] keywords;
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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 AtomVecHybrid::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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int tmp = atom->nextra_grow;
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for (int m = 0; m < nstyles; m++) {
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atom->nextra_grow = 0;
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styles[m]->grow(nmax);
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atom->nextra_grow = tmp;
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}
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// pointers for arrays used directly by hybrid style
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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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hybrid = atom->hybrid = (int *)
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memory->srealloc(atom->hybrid,nmax*sizeof(int),"atom:hybrid");
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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 AtomVecHybrid::reset_ptrs()
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{
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for (int m = 0; m < nstyles; m++) styles[m]->reset_ptrs();
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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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hybrid = atom->hybrid;
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}
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/* ----------------------------------------------------------------------
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copy array values based on hybrid style of atom i
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zero auxiliary arrays for all other styles before copy
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------------------------------------------------------------------------- */
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void AtomVecHybrid::copy(int i, int j)
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{
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int ihybrid = hybrid[i];
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for (int m = 0; m < nstyles; m++)
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if (m != ihybrid) styles[m]->zero_owned(j);
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styles[ihybrid]->copy(i,j);
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hybrid[j] = ihybrid;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecHybrid::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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m += styles[hybrid[j]]->pack_comm_one(j,&buf[m]);
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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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m += styles[hybrid[j]]->pack_comm_one(j,&buf[m]);
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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 AtomVecHybrid::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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m += styles[hybrid[i]]->unpack_comm_one(i,&buf[m]);
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}
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecHybrid::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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m += styles[hybrid[i]]->pack_reverse_one(i,&buf[m]);
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecHybrid::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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m += styles[hybrid[j]]->unpack_reverse_one(j,&buf[m]);
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}
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecHybrid::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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buf[m++] = hybrid[j];
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m += styles[hybrid[j]]->pack_border_one(j,&buf[m]);
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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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buf[m++] = hybrid[j];
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m += styles[hybrid[j]]->pack_border_one(j,&buf[m]);
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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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unpack border ghost atom data
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zero auxiliary ghost arrays for all styles before unpack
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grow() is called in zero_ghost() and here (in case zero_ghost is no-op)
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------------------------------------------------------------------------- */
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void AtomVecHybrid::unpack_border(int n, int first, double *buf)
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{
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int i,m,last;
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for (m = 0; m < nstyles; m++) styles[m]->zero_ghost(n,first);
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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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hybrid[i] = static_cast<int> (buf[m++]);
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m += styles[hybrid[i]]->unpack_border_one(i,&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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sub-style does packing
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append hybrid[i] and increment count stored in buf[0]
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------------------------------------------------------------------------- */
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int AtomVecHybrid::pack_exchange(int i, double *buf)
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{
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int m = styles[hybrid[i]]->pack_exchange(i,buf);
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buf[m++] = hybrid[i];
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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 single atom received from another proc
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sub-style does unpacking
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grow() must occur here so arrays for all sub-styles are grown
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extract hybrid[nlocal] from end of buf
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------------------------------------------------------------------------- */
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int AtomVecHybrid::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 = static_cast<int> (buf[0]);
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hybrid[nlocal] = static_cast<int> (buf[m-1]);
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int tmp = styles[hybrid[nlocal]]->unpack_exchange(buf);
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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 AtomVecHybrid::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 = 0;
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for (i = 0; i < nlocal; i++)
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n += styles[hybrid[i]]->size_restart_one(i);
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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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pack atom I's data for restart file including extra quantities
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sub-style does packing
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append hybrid[i] and increment count stored in buf[0]
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------------------------------------------------------------------------- */
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int AtomVecHybrid::pack_restart(int i, double *buf)
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{
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int m = styles[hybrid[i]]->pack_restart(i,buf);
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buf[m++] = hybrid[i];
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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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sub-style does unpacking
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grow() must occur here so arrays for all sub-styles are grown
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zero auxiliary arrays for all other styles before unpack
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extract hybrid[nlocal] from end of buf
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------------------------------------------------------------------------- */
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int AtomVecHybrid::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 = static_cast<int> (buf[0]);
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int ihybrid = static_cast<int> (buf[m-1]);
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for (int m = 0; m < nstyles; m++)
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if (m != ihybrid) styles[m]->zero_owned(nlocal);
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hybrid[nlocal] = ihybrid;
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// size of extra unpack in sub-style includes end-of-buf entry of hybrid
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// avoid this by resetting buf[0] to one less
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buf[0] = m-1;
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int tmp = styles[ihybrid]->unpack_restart(buf);
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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 for ihybrid style
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sub-style does create
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grow() must occur here so arrays for all sub-styles are grown
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zero auxiliary arrays for all other styles before create
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------------------------------------------------------------------------- */
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void AtomVecHybrid::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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for (int m = 0; m < nstyles; m++)
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if (m != ihybrid) styles[m]->zero_owned(nlocal);
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hybrid[nlocal] = ihybrid;
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styles[ihybrid]->create_atom(itype,x0,y0,z0,0);
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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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zero auxiliary arrays for all other styles before unpack
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sub-style will increment nlocal
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------------------------------------------------------------------------- */
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void AtomVecHybrid::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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for (int m = 0; m < nstyles; m++)
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if (m != ihybrid) styles[m]->zero_owned(nlocal);
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hybrid[nlocal] = ihybrid;
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styles[ihybrid]->data_atom(xtmp,ytmp,ztmp,imagetmp,values,0);
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}
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/* ----------------------------------------------------------------------
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unpack one line from Velocities section of data file
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------------------------------------------------------------------------- */
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void AtomVecHybrid::data_vel(int m, char *line, int ihybrid)
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{
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styles[ihybrid]->data_vel(m,line,0);
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}
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/* ----------------------------------------------------------------------
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set data file parameters for ihybrid sub-style
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------------------------------------------------------------------------- */
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void AtomVecHybrid::data_params(int ihybrid)
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{
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size_data_atom = styles[ihybrid]->size_data_atom;
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size_data_vel = styles[ihybrid]->size_data_vel;
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xcol_data = styles[ihybrid]->xcol_data;
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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 AtomVecHybrid::memory_usage()
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{
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int bytes = 0;
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for (int m = 0; m < nstyles; m++)
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bytes += styles[m]->memory_usage();
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if (atom->memcheck("hybrid")) bytes += nmax * sizeof(int);
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return bytes;
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}
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