Add APIP package.

src/APIP/pair_lambda_input.cpp

@@ -0,0 +1,218 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   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.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author: David Immel (d.immel@fz-juelich.de, FZJ, Germany)
+------------------------------------------------------------------------- */
+
+#include "pair_lambda_input.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "modify.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+#include "update.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairLambdaInput::PairLambdaInput(LAMMPS *lmp) : Pair(lmp), fix_lambda(nullptr), cut(nullptr)
+{
+
+  cut_global = -1;
+  ignore_group_bit = 0;
+  timer = 0;
+  n_calculations = 0;
+  time_per_atom = -1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairLambdaInput::~PairLambdaInput()
+{
+  if (copymode) return;
+
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(cut);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+void PairLambdaInput::coeff(int narg, char **arg)
+{
+  if (narg != 2) error->all(FLERR, "Incorrect args for pair coefficients");
+  if (!allocated) allocate();
+
+  int ilo, ihi, jlo, jhi;
+  utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
+  utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo, i); j <= jhi; j++) {
+      setflag[i][j] = 1;
+      cut[i][j] = cut_global;
+      count++;
+    }
+  }
+
+  if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairLambdaInput::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes + 1;
+
+  memory->create(setflag, n, n, "pair:setflag");
+  for (int i = 1; i < n; i++)
+    for (int j = i; j < n; j++) setflag[i][j] = 0;
+
+  memory->create(cutsq, n, n, "pair:cutsq");
+  memory->create(cut, n, n, "pair:cut");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLambdaInput::compute(int eflag, int vflag)
+{
+  // basic stuff (see pair_zero)
+  ev_init(eflag, vflag);
+  if (vflag_fdotr) virial_fdotr_compute();
+
+  double timer_start = platform::walltime();
+
+  n_calculations += calculate_lambda_input();
+
+  timer += platform::walltime() - timer_start;
+
+  fix_lambda->update_lambda_input_history();
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairLambdaInput::settings(int narg, char **arg)
+{
+  if (narg < 1) utils::missing_cmd_args(FLERR, "pair_style lambda_input", error);
+
+  cut_global = utils::numeric(FLERR, arg[0], false, lmp);
+
+  // reset cutoffs that have been explicitly set
+  if (allocated) {
+    int i, j;
+    for (i = 1; i <= atom->ntypes; i++)
+      for (j = i; j <= atom->ntypes; j++)
+        if (setflag[i][j]) cut[i][j] = cut_global;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairLambdaInput::init_style()
+{
+  if (!atom->lambda_input_flag)
+    error->all(FLERR, "pair_lambda input requires an atom style with lambda_input");
+
+  // find fix lambda
+  int count = 0;
+  for (int i = 0; i < modify->nfix; i++) {
+    if (strcmp(modify->fix[i]->style, "lambda") == 0) {
+      fix_lambda = (FixLambda *) modify->fix[i];
+      count++;
+    }
+  }
+  if (count != 1) error->all(FLERR, "Exact one fix lambda required");
+
+  // get group whose input is ignored from fix lambda
+  ignore_group_bit = fix_lambda->group_bit_ignore_lambda_input;
+
+  neighbor->add_request(this, NeighConst::REQ_FULL);
+}
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairLambdaInput::init_one(int i, int j)
+{
+  if (setflag[i][j] == 0) { cut[i][j] = mix_distance(cut[i][i], cut[j][j]); }
+  return cut[i][j];
+}
+
+/**
+  * Compute lambda_input and write it to atom->lambda_input.
+  * Count the number of computations and measure the compute time for
+  * fix apip_atom_weight.
+  */
+
+int PairLambdaInput::calculate_lambda_input()
+{
+  int i, ii, inum;
+  int *ilist;
+
+  inum = list->inum;
+  ilist = list->ilist;
+
+  double *lambda_input = atom->lambda_input;
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    // "compute" and set lambda input
+    lambda_input[i] = 0;
+  }
+  // return number of calculations
+  return inum;
+}
+
+/* ----------------------------------------------------------------------
+   set return values for timers and counted particles
+------------------------------------------------------------------------- */
+
+void PairLambdaInput::calculate_time_per_atom()
+{
+  if (n_calculations > 0)
+    time_per_atom = timer / n_calculations;
+  else
+    time_per_atom = -1;
+
+  // reset
+  timer = 0;
+  n_calculations = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *PairLambdaInput::extract(const char *str, int &dim)
+{
+  dim = 0;
+  if (strcmp(str, "lambda_input:time_per_atom") == 0) {
+    calculate_time_per_atom();
+    return (void *) &time_per_atom;
+  }
+  return nullptr;
+}