Adding files for BPM

src/fix_store_local.cpp

@@ -0,0 +1,200 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/ Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "fix_store_local.h"
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "memory.h"
+#include "update.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+#define DELTA 1000
+
+/* ---------------------------------------------------------------------- */
+
+FixStoreLocal::FixStoreLocal(LAMMPS *lmp, int narg, char **arg) :
+    Fix(lmp, narg, arg), nvalues(0), vector(nullptr), array(nullptr)
+{
+  if (narg != 5) error->all(FLERR, "Illegal fix store/local command");
+  local_flag = 1;
+
+  nevery = utils::inumeric(FLERR, arg[3], false, lmp);
+  if (nevery <= 0) error->all(FLERR, "Illegal fix store/local command");
+  local_freq = nevery;
+
+  nvalues = utils::inumeric(FLERR, arg[4], false, lmp);
+  
+  if (nvalues <= 0) error->all(FLERR, "Illegal fix store/local command");
+  if (nvalues == 1)
+    size_local_cols = 0;
+  else
+    size_local_cols = nvalues;
+  size_local_rows = 0;
+  
+  vector = nullptr;
+  array = nullptr;  
+  nmax = 0;
+  ncount = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixStoreLocal::~FixStoreLocal()
+{
+  memory->destroy(vector);
+  memory->destroy(array);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixStoreLocal::setmask()
+{
+  int mask = 0;
+  mask |= POST_FORCE;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixStoreLocal::add_data(double *input_data, int i, int j)
+{
+  int *mask = atom->mask;
+  if (!(mask[i] & groupbit)) return;
+  if (!(mask[j] & groupbit)) return;
+  
+  if (ncount >= nmax) reallocate(ncount);
+  
+  // fill vector or array with local values
+  if (nvalues == 1) {
+    vector[ncount] = input_data[0];
+  } else {
+    for (int i = 0; i < nvalues; i++) array[ncount][i] = input_data[i];
+  }
+
+  ncount += 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixStoreLocal::post_force(int /*vflag*/)
+{
+  if (update->ntimestep % nevery == 0) {
+    size_local_rows = ncount;
+    ncount = 0;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixStoreLocal::reallocate(int n)
+{
+  // grow vector or array
+  while (nmax <= n) nmax += DELTA;
+
+  if (nvalues == 1) {
+    memory->grow(vector, nmax, "fix_store_local:vector");
+    vector_local = vector;
+  } else {
+    memory->grow(array, nmax, nvalues, "fix_store_local:array");
+    array_local = array;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   write global array to restart file 
+------------------------------------------------------------------------- */
+
+void FixStoreLocal::write_restart(FILE *fp)
+{
+  // fill rbuf with size and vec/array values
+
+  rbuf[0] = nmax;
+  rbuf[1] = nvalues;
+  if (nvalues == 1) memcpy(&rbuf[2],vector,sizeof(double)*nmax);
+  else memcpy(&rbuf[2],&array[0][0],sizeof(double)*nmax*nvalues);
+
+  int n = nmax*nvalues + 2;
+  if (comm->me == 0) {
+    int size = n * sizeof(double);
+    fwrite(&size,sizeof(int),1,fp);
+    fwrite(rbuf,sizeof(double),n,fp);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   use global array from restart file to restart the Fix
+------------------------------------------------------------------------- */
+
+void FixStoreLocal::restart(char *buf)
+{
+  // first 2 values in buf are vec/array sizes
+
+  double *dbuf = (double *) buf;
+  int nrow_restart = dbuf[0];
+  int ncol_restart = dbuf[1];
+
+  // if size of vec/array has changed,
+  //   means the restart file is setting size of vec or array and doing init
+  //   because caller did not know size at time this fix was instantiated
+  // reallocate vector or array accordingly
+
+  if (nmax != nrow_restart || nvalues != ncol_restart) {
+    memory->destroy(vector);
+    memory->destroy(array);
+    memory->destroy(rbuf);
+    vector = nullptr;
+    array = nullptr;
+
+    nmax = nrow_restart;
+    nvalues = ncol_restart;
+    if (nvalues == 1) memory->create(vector,nmax,"fix/store/local:vector");
+    else memory->create(array,nmax,nvalues,"fix/store/local:array");
+    memory->create(rbuf,nmax*nvalues+2,"fix/store:rbuf");
+  }
+
+  int n = nmax*nvalues;
+  if (nvalues == 1) memcpy(vector,&dbuf[2],n*sizeof(double));
+  else memcpy(&array[0][0],&dbuf[2],n*sizeof(double));
+}
+
+/* ----------------------------------------------------------------------
+   maxsize of any atom's restart data
+------------------------------------------------------------------------- */
+
+int FixStoreLocal::maxsize_restart()
+{
+  return nvalues+1;
+}
+
+/* ----------------------------------------------------------------------
+   size of atom nlocal's restart data
+------------------------------------------------------------------------- */
+
+int FixStoreLocal::size_restart(int /*nlocal*/)
+{
+  return nvalues+1;
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local data
+------------------------------------------------------------------------- */
+
+double FixStoreLocal::memory_usage()
+{
+  double bytes = (double) nmax * (double) nvalues * sizeof(double);
+  return bytes;
+}
+