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sjplimp
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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 "math.h"
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#include "string.h"
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#include "bond_hybrid.h"
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#include "atom.h"
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#include "neighbor.h"
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#include "domain.h"
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#include "comm.h"
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#include "force.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 EXTRA 1000
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/* ---------------------------------------------------------------------- */
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BondHybrid::BondHybrid(LAMMPS *lmp) : Bond(lmp)
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{
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nstyles = 0;
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}
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/* ---------------------------------------------------------------------- */
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BondHybrid::~BondHybrid()
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{
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if (nstyles) {
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for (int i = 0; i < nstyles; i++) delete styles[i];
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delete [] styles;
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for (int i = 0; i < nstyles; i++) delete [] keywords[i];
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delete [] keywords;
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}
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if (allocated) {
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memory->sfree(setflag);
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memory->sfree(map);
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delete [] nbondlist;
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delete [] maxbond;
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for (int i = 0; i < nstyles; i++)
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memory->destroy_2d_int_array(bondlist[i]);
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delete [] bondlist;
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}
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}
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/* ---------------------------------------------------------------------- */
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void BondHybrid::compute(int eflag, int vflag)
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{
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int i,j,m,n;
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// save ptrs to original bondlist
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int nbondlist_orig = neighbor->nbondlist;
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int **bondlist_orig = neighbor->bondlist;
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// if this is re-neighbor step, create sub-style bondlists
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// nbondlist[] = length of each sub-style list
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// realloc sub-style bondlist if necessary
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// load sub-style bondlist with 3 values from original bondlist
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if (neighbor->ago == 0) {
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for (m = 0; m < nstyles; m++) nbondlist[m] = 0;
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for (i = 0; i < nbondlist_orig; i++) {
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m = map[bondlist_orig[i][2]];
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if (m >= 0) nbondlist[m]++;
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}
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for (m = 0; m < nstyles; m++) {
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if (nbondlist[m] > maxbond[m]) {
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memory->destroy_2d_int_array(bondlist[m]);
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maxbond[m] = nbondlist[m] + EXTRA;
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bondlist[m] = (int **)
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memory->create_2d_int_array(maxbond[m],3,"bond_hybrid:bondlist");
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}
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nbondlist[m] = 0;
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}
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for (i = 0; i < nbondlist_orig; i++) {
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m = map[bondlist_orig[i][2]];
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if (m < 0) continue;
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n = nbondlist[m];
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bondlist[m][n][0] = bondlist_orig[i][0];
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bondlist[m][n][1] = bondlist_orig[i][1];
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bondlist[m][n][2] = bondlist_orig[i][2];
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nbondlist[m]++;
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}
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}
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// call each sub-style's compute function
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// set neighbor->bondlist to sub-style bondlist before call
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// accumulate sub-style global/peratom energy/virial in hybrid
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = 0;
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for (m = 0; m < nstyles; m++) {
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neighbor->nbondlist = nbondlist[m];
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neighbor->bondlist = bondlist[m];
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styles[m]->compute(eflag,vflag);
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if (eflag_global) energy += styles[m]->energy;
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if (vflag_global)
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for (n = 0; n < 6; n++) virial[n] += styles[m]->virial[n];
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if (eflag_atom) {
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n = atom->nlocal;
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if (force->newton_bond) n += atom->nghost;
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double *eatom_substyle = styles[m]->eatom;
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for (i = 0; i < n; i++) eatom[i] += eatom_substyle[i];
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}
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if (vflag_atom) {
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n = atom->nlocal;
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if (force->newton_bond) n += atom->nghost;
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double **vatom_substyle = styles[m]->vatom;
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for (i = 0; i < n; i++)
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for (j = 0; j < 6; j++)
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vatom[i][j] += vatom_substyle[i][j];
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}
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}
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// restore ptrs to original bondlist
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neighbor->nbondlist = nbondlist_orig;
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neighbor->bondlist = bondlist_orig;
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}
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/* ---------------------------------------------------------------------- */
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void BondHybrid::allocate()
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{
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allocated = 1;
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int n = atom->nbondtypes;
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map = (int *) memory->smalloc((n+1)*sizeof(int),"bond:map");
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setflag = (int *) memory->smalloc((n+1)*sizeof(int),"bond:setflag");
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for (int i = 1; i <= n; i++) setflag[i] = 0;
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nbondlist = new int[nstyles];
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maxbond = new int[nstyles];
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bondlist = new int**[nstyles];
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for (int m = 0; m < nstyles; m++) maxbond[m] = 0;
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for (int m = 0; m < nstyles; m++) bondlist[m] = NULL;
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}
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/* ----------------------------------------------------------------------
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create one bond style for each arg in list
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------------------------------------------------------------------------- */
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void BondHybrid::settings(int narg, char **arg)
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{
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nstyles = narg;
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styles = new Bond*[nstyles];
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keywords = new char*[nstyles];
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for (int m = 0; m < nstyles; m++) {
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for (int i = 0; i < m; i++)
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if (strcmp(arg[m],arg[i]) == 0)
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error->all("Bond style hybrid cannot use same bond style twice");
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if (strcmp(arg[m],"hybrid") == 0)
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error->all("Bond style hybrid cannot have hybrid as an argument");
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if (strcmp(arg[m],"none") == 0)
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error->all("Bond style hybrid cannot have none as an argument");
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styles[m] = force->new_bond(arg[m]);
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keywords[m] = new char[strlen(arg[m])+1];
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strcpy(keywords[m],arg[m]);
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}
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}
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/* ----------------------------------------------------------------------
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set coeffs for one type
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---------------------------------------------------------------------- */
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void BondHybrid::coeff(int narg, char **arg)
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{
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if (!allocated) allocate();
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int ilo,ihi;
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force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
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// 2nd arg = bond sub-style name
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// allow for "none" as valid sub-style name
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int m;
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for (m = 0; m < nstyles; m++)
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if (strcmp(arg[1],keywords[m]) == 0) break;
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int none = 0;
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if (m == nstyles) {
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if (strcmp(arg[1],"none") == 0) none = 1;
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else error->all("Bond coeff for hybrid has invalid style");
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}
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// move 1st arg to 2nd arg
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// just copy ptrs, since arg[] points into original input line
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arg[1] = arg[0];
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// invoke sub-style coeff() starting with 1st arg
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if (!none) styles[m]->coeff(narg-1,&arg[1]);
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// set setflag and which type maps to which sub-style
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// if sub-style is none: set hybrid setflag, wipe out map
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for (int i = ilo; i <= ihi; i++) {
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setflag[i] = 1;
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if (none) map[i] = -1;
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else map[i] = m;
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}
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}
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/* ---------------------------------------------------------------------- */
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void BondHybrid::init_style()
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{
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for (int m = 0; m < nstyles; m++)
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if (styles[m]) styles[m]->init_style();
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}
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/* ----------------------------------------------------------------------
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return an equilbrium bond length
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------------------------------------------------------------------------- */
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double BondHybrid::equilibrium_distance(int i)
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{
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if (map[i] < 0) error->one("Invoked bond equil distance on bond style none");
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return styles[map[i]]->equilibrium_distance(i);
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void BondHybrid::write_restart(FILE *fp)
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{
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fwrite(&nstyles,sizeof(int),1,fp);
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int n;
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for (int m = 0; m < nstyles; m++) {
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n = strlen(keywords[m]) + 1;
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fwrite(&n,sizeof(int),1,fp);
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fwrite(keywords[m],sizeof(char),n,fp);
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void BondHybrid::read_restart(FILE *fp)
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{
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int me = comm->me;
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if (me == 0) fread(&nstyles,sizeof(int),1,fp);
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MPI_Bcast(&nstyles,1,MPI_INT,0,world);
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styles = new Bond*[nstyles];
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keywords = new char*[nstyles];
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allocate();
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int n;
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for (int m = 0; m < nstyles; m++) {
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if (me == 0) fread(&n,sizeof(int),1,fp);
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MPI_Bcast(&n,1,MPI_INT,0,world);
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keywords[m] = new char[n];
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if (me == 0) fread(keywords[m],sizeof(char),n,fp);
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MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
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styles[m] = force->new_bond(keywords[m]);
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}
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}
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/* ---------------------------------------------------------------------- */
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double BondHybrid::single(int type, double rsq, int i, int j)
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{
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if (map[type] < 0) error->one("Invoked bond single on bond style none");
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return styles[map[type]]->single(type,rsq,i,j);
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}
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/* ----------------------------------------------------------------------
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memory usage
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------------------------------------------------------------------------- */
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double BondHybrid::memory_usage()
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{
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double bytes = maxeatom * sizeof(double);
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bytes += maxvatom*6 * sizeof(double);
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for (int m = 0; m < nstyles; m++) bytes += maxbond[m]*3 * sizeof(int);
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for (int m = 0; m < nstyles; m++)
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if (styles[m]) bytes += styles[m]->memory_usage();
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return bytes;
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}
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