Adding documentation, misc changes
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jtclemm
378
src/MISC/fix_pair_tracker.cpp
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378
src/MISC/fix_pair_tracker.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 "fix_pair_tracker.h"
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#include "pair_tracker.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "update.h"
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#include "memory.h"
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#include "modify.h"
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#include "error.h"
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#include "group.h"
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#include "tokenizer.h"
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#include <cstring>
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using namespace LAMMPS_NS;
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using namespace FixConst;
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#define DELTA 1000
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/* ---------------------------------------------------------------------- */
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FixPairTracker::FixPairTracker(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg),
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nvalues(0),
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array(NULL), vector(NULL), pack_choice(NULL)
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{
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if (narg < 3) error->all(FLERR,"Illegal fix pair/tracker command");
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local_flag = 1;
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nevery = utils::inumeric(FLERR,arg[3],false,lmp);
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if (nevery <= 0) error->all(FLERR,"Illegal fix pair/tracker command");
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local_freq = nevery;
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// If optional arguments included, this will be oversized
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nvalues = narg - 4;
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pack_choice = new FnPtrPack[nvalues];
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tmin = -1;
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type_filter = nullptr;
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int iarg = 4;
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nvalues = 0;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"id1") == 0) {
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pack_choice[nvalues++] = &FixPairTracker::pack_id1;
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} else if (strcmp(arg[iarg],"id2") == 0) {
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pack_choice[nvalues++] = &FixPairTracker::pack_id2;
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} else if (strcmp(arg[iarg],"time/created") == 0) {
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pack_choice[nvalues++] = &FixPairTracker::pack_time_created;
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} else if (strcmp(arg[iarg],"time/broken") == 0) {
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pack_choice[nvalues++] = &FixPairTracker::pack_time_broken;
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} else if (strcmp(arg[iarg],"time/total") == 0) {
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pack_choice[nvalues++] = &FixPairTracker::pack_time_total;
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} else if (strcmp(arg[iarg],"x") == 0) {
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pack_choice[nvalues++] = &FixPairTracker::pack_x;
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} else if (strcmp(arg[iarg],"y") == 0) {
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pack_choice[nvalues++] = &FixPairTracker::pack_y;
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} else if (strcmp(arg[iarg],"z") == 0) {
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pack_choice[nvalues++] = &FixPairTracker::pack_z;
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} else if (strcmp(arg[iarg],"r/min") == 0) {
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pack_choice[nvalues++] = &FixPairTracker::pack_rmin;
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} else if (strcmp(arg[iarg],"r/ave") == 0) {
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pack_choice[nvalues++] = &FixPairTracker::pack_rave;
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} else if (strcmp(arg[iarg],"time/min") == 0) {
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if (iarg + 1 >= narg) error->all(FLERR, "Invalid keyword in fix pair/tracker command");
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tmin = utils::numeric(FLERR,arg[iarg+1],false,lmp);
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iarg ++;
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} else if (strcmp(arg[iarg],"type/include") == 0) {
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if (iarg + 1 >= narg) error->all(FLERR, "Invalid keyword in fix pair/tracker command");
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int ntypes = atom->ntypes;
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int i, j, itype, jtype, in, jn, infield, jnfield;
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int inlo, inhi, jnlo, jnhi;
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char *istr, *jstr;
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if (! type_filter) {
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memory->create(type_filter,ntypes+1,ntypes+1,"fix/pair/tracker:type_filter");
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for (i = 0; i <= ntypes; i ++) {
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for (j = 0; j <= ntypes; j ++) {
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type_filter[i][j] = 0;
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}
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}
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}
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in = strlen(arg[iarg+1]) + 1;
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istr = new char[in];
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strcpy(istr,arg[iarg+1]);
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std::vector<std::string> iwords = Tokenizer(istr, ",").as_vector();
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infield = iwords.size();
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jn = strlen(arg[iarg+2]) + 1;
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jstr = new char[jn];
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strcpy(jstr,arg[iarg+2]);
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std::vector<std::string> jwords = Tokenizer(jstr, ",").as_vector();
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jnfield = jwords.size();
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for (i = 0; i < infield; i++) {
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const char * ifield = iwords[i].c_str();
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utils::bounds(FLERR,ifield,1,ntypes,inlo,inhi,error);
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for (j = 0; j < jnfield; j++) {
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const char * jfield = jwords[j].c_str();
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utils::bounds(FLERR,jfield,1,ntypes,jnlo,jnhi,error);
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for (itype = inlo; itype <= inhi; itype++) {
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for (jtype = jnlo; jtype <= jnhi; jtype++) {
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type_filter[itype][jtype] = 1;
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type_filter[jtype][itype] = 1;
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}
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}
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}
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}
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delete [] istr;
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delete [] jstr;
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iarg += 2;
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} else error->all(FLERR, "Invalid keyword in fix pair/tracker command");
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iarg ++;
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}
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if (nvalues == 1) size_local_cols = 0;
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else size_local_cols = nvalues;
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nmax = 0;
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ncount = 0;
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vector = NULL;
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array = NULL;
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}
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/* ---------------------------------------------------------------------- */
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FixPairTracker::~FixPairTracker()
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{
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delete [] pack_choice;
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memory->destroy(vector);
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memory->destroy(array);
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memory->destroy(type_filter);
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}
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/* ---------------------------------------------------------------------- */
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int FixPairTracker::setmask()
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{
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int mask = 0;
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mask |= POST_FORCE;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::init()
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{
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// Set size of array/vector
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ncount = 0;
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if (ncount > nmax)
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reallocate(ncount);
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size_local_rows = ncount;
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}
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::lost_contact(int i, int j, double nstep_tmp, double rsum_tmp, double time_tmp)
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{
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double time = update->atime + (update->ntimestep-update->atimestep)*update->dt;
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if ((time-time_tmp) < tmin) return;
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if (type_filter) {
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int *type = atom->type;
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if (type_filter[type[i]][type[j]] == 0) return;
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}
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int *mask = atom->mask;
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if (!(mask[i] & groupbit)) return;
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if (!(mask[j] & groupbit)) return;
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if (ncount == nmax) reallocate(ncount);
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index_i = i;
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index_j = j;
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rmin = rmin_tmp;
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rsum = rsum_tmp;
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time_initial = time_tmp;
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// fill vector or array with local values
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if (nvalues == 1) {
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(this->*pack_choice[0])(0);
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} else {
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for (int k = 0; k < nvalues; k++) {
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(this->*pack_choice[k])(k);
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}
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}
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ncount += 1;
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}
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::post_force(int /*vflag*/)
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{
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if (update->ntimestep % nevery == 0) {
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size_local_rows = ncount;
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ncount = 0;
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::reallocate(int n)
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{
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// grow vector or array
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while (nmax <= n) nmax += DELTA;
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if (nvalues == 1) {
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memory->grow(vector,nmax,"fix_pair_tracker:vector");
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vector_local = vector;
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} else {
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memory->grow(array,nmax,nvalues,"fix_pair_tracker:array");
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array_local = array;
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local data
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------------------------------------------------------------------------- */
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double FixPairTracker::memory_usage()
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{
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double bytes = nmax*nvalues * sizeof(double);
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bytes += nmax*2 * sizeof(int);
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return bytes;
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}
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/* ----------------------------------------------------------------------
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one method for every keyword fix property/local can output
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the atom property is packed into buf starting at n with stride nvalues
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customize a new keyword by adding a method
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------------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::pack_time_created(int n)
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{
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if (nvalues == 1)
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vector[ncount] = time_initial;
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else
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array[ncount][n] = time_initial;
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}
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::pack_time_broken(int n)
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{
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double time = update->atime + (update->ntimestep-update->atimestep)*update->dt;
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if (nvalues == 1)
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vector[ncount] = time;
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else
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array[ncount][n] = time;
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}
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::pack_time_total(int n)
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{
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double time = update->atime + (update->ntimestep-update->atimestep)*update->dt;
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if (nvalues == 1)
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vector[ncount] = time-time_initial;
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else
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array[ncount][n] = time-time_initial;
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}
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::pack_id1(int n)
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{
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tagint *tag = atom->tag;
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if (nvalues == 1)
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vector[ncount] = tag[index_i];
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else
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array[ncount][n] = tag[index_i];
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}
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::pack_id2(int n)
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{
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tagint *tag = atom->tag;
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if (nvalues == 1)
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vector[ncount] = tag[index_j];
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else
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array[ncount][n] = tag[index_j];
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}
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::pack_x(int n)
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{
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double **x = atom->x;
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if (nvalues == 1)
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vector[ncount] = (x[index_i][0] + x[index_j][0])/2;
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else
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array[ncount][n] = (x[index_i][0] + x[index_j][0])/2;
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}
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::pack_y(int n)
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{
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double **x = atom->x;
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if (nvalues == 1)
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vector[ncount] = (x[index_i][1] + x[index_j][1])/2;
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else
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array[ncount][n] = (x[index_i][1] + x[index_j][1])/2;
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}
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::pack_z(int n)
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{
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double **x = atom->x;
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if (nvalues == 1)
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vector[ncount] = (x[index_i][2] + x[index_j][2])/2;
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else
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array[ncount][n] = (x[index_i][2] + x[index_j][2])/2;
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}
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::pack_rmin(int n)
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{
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if (nvalues == 1)
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vector[ncount] = rmin;
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else
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array[ncount][n] = rmin;
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}
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/* ---------------------------------------------------------------------- */
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void FixPairTracker::pack_rave(int n)
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{
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if (nvalues == 1)
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vector[ncount] = rsum/(update->ntimestep-nstep_initial);
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else
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array[ncount][n] = rsum/(update->ntimestep-nstep_initial);
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}
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