communication-free EAM implementation

LAMMPS_plugin/install.sh

@@ -22,3 +22,8 @@ ln -sf $(pwd)/src/pair_hybrid_overlay_mlml.h ${lammps}/src/pair_hybrid_overlay_m
 ln -sf $(pwd)/src/pair_hybrid_overlay_mlml.cpp ${lammps}/src/pair_hybrid_overlay_mlml.cpp
 ln -sf $(pwd)/src/KOKKOS/pair_hybrid_overlay_mlml_kokkos.h ${lammps}/src/KOKKOS/pair_hybrid_overlay_mlml_kokkos.h
 ln -sf $(pwd)/src/KOKKOS/pair_hybrid_overlay_mlml_kokkos.cpp ${lammps}/src/KOKKOS/pair_hybrid_overlay_mlml_kokkos.cpp
+
+ln -sf $(pwd)/src/pair_eam_mlml.h ${lammps}/src/pair_eam_mlml.h
+ln -sf $(pwd)/src/pair_eam_mlml.cpp ${lammps}/src/pair_eam_mlml.cpp
+ln -sf $(pwd)/src/pair_eam_fs_mlml.h ${lammps}/src/pair_eam_fs_mlml.h
+ln -sf $(pwd)/src/pair_eam_fs_mlml.cpp ${lammps}/src/pair_eam_fs_mlml.cpp

LAMMPS_plugin/src/pair_eam_fs_mlml.cpp

@@ -0,0 +1,372 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, [email protected]
+
+   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 authors:
+   originally
+   Tim Lau (MIT)
+   removing communication within compute
+   David Immel ([email protected], FZJ, Germany)
+------------------------------------------------------------------------- */
+
+#include "pair_eam_fs_mlml.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "memory.h"
+#include "potential_file_reader.h"
+
+#include <cstring>
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairEAMFSMLML::PairEAMFSMLML(LAMMPS *lmp) : PairEAMMLML(lmp)
+{
+  one_coeff = 1;
+  manybody_flag = 1;
+  he_flag = 0;
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more type pairs
+   read EAM Finnis-Sinclair file
+------------------------------------------------------------------------- */
+
+void PairEAMFSMLML::coeff(int narg, char **arg)
+{
+  int i,j;
+
+  if (!allocated) allocate();
+
+  if (narg != 3 + atom->ntypes)
+    error->all(FLERR,"Incorrect args for pair coefficients");
+
+  // insure I,J args are * *
+
+  if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
+    error->all(FLERR,"Incorrect args for pair coefficients");
+
+  // read EAM Finnis-Sinclair file
+
+  if (fs) {
+    for (i = 0; i < fs->nelements; i++) delete [] fs->elements[i];
+    delete [] fs->elements;
+    memory->destroy(fs->mass);
+    memory->destroy(fs->frho);
+    memory->destroy(fs->rhor);
+    memory->destroy(fs->z2r);
+    delete fs;
+  }
+  fs = new Fs();
+  read_file(arg[2]);
+
+  // read args that map atom types to elements in potential file
+  // map[i] = which element the Ith atom type is, -1 if "NULL"
+
+  for (i = 3; i < narg; i++) {
+    if (strcmp(arg[i],"NULL") == 0) {
+      map[i-2] = -1;
+      continue;
+    }
+    for (j = 0; j < fs->nelements; j++)
+      if (strcmp(arg[i],fs->elements[j]) == 0) break;
+    if (j < fs->nelements) map[i-2] = j;
+    else error->all(FLERR,"No matching element in EAM potential file");
+  }
+
+  // clear setflag since coeff() called once with I,J = * *
+
+  int n = atom->ntypes;
+  for (i = 1; i <= n; i++)
+    for (j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  // set setflag i,j for type pairs where both are mapped to elements
+  // set mass of atom type if i = j
+
+  int count = 0;
+  for (i = 1; i <= n; i++) {
+    for (j = i; j <= n; j++) {
+      if (map[i] >= 0 && map[j] >= 0) {
+        setflag[i][j] = 1;
+        if (i == j) atom->set_mass(FLERR,i,fs->mass[map[i]]);
+        count++;
+      }
+      scale[i][j] = 1.0;
+    }
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   read a multi-element DYNAMO setfl file
+------------------------------------------------------------------------- */
+
+void PairEAMFSMLML::read_file(char *filename)
+{
+  Fs *file = fs;
+
+  // read potential file
+  if (comm->me == 0) {
+    PotentialFileReader reader(lmp, filename, he_flag ? "eam/he" : "eam/fs",
+                               unit_convert_flag);
+
+    // transparently convert units for supported conversions
+
+    int unit_convert = reader.get_unit_convert();
+    double conversion_factor = utils::get_conversion_factor(utils::ENERGY,
+                                                            unit_convert);
+    try {
+      reader.skip_line();
+      reader.skip_line();
+      reader.skip_line();
+
+      // extract element names from nelements line
+      ValueTokenizer values = reader.next_values(1);
+      file->nelements = values.next_int();
+
+      if ((int)values.count() != file->nelements + 1)
+        error->one(FLERR,"Incorrect element names in EAM potential file");
+
+      file->elements = new char*[file->nelements];
+      for (int i = 0; i < file->nelements; i++) {
+        const std::string word = values.next_string();
+        const int n = word.length() + 1;
+        file->elements[i] = new char[n];
+        strcpy(file->elements[i], word.c_str());
+      }
+
+      //
+
+      if (he_flag) values = reader.next_values(6);
+      else values = reader.next_values(5);
+      file->nrho = values.next_int();
+      file->drho = values.next_double();
+      file->nr   = values.next_int();
+      file->dr   = values.next_double();
+      file->cut  = values.next_double();
+      if (he_flag) rhomax = values.next_double();
+
+      if ((file->nrho <= 0) || (file->nr <= 0) || (file->dr <= 0.0))
+        error->one(FLERR,"Invalid EAM potential file");
+
+      memory->create(file->mass, file->nelements, "pair:mass");
+      memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
+      memory->create(file->rhor, file->nelements, file->nelements, file->nr + 1, "pair:rhor");
+      memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
+
+      for (int i = 0; i < file->nelements; i++) {
+        values = reader.next_values(2);
+        values.next_int(); // ignore
+        file->mass[i] = values.next_double();
+
+        reader.next_dvector(&file->frho[i][1], file->nrho);
+        if (unit_convert) {
+          for (int j = 1; j <= file->nrho; ++j)
+            file->frho[i][j] *= conversion_factor;
+        }
+
+        for (int j = 0; j < file->nelements; j++) {
+          reader.next_dvector(&file->rhor[i][j][1], file->nr);
+        }
+      }
+
+      for (int i = 0; i < file->nelements; i++) {
+        for (int j = 0; j <= i; j++) {
+          reader.next_dvector(&file->z2r[i][j][1], file->nr);
+          if (unit_convert) {
+            for (int k = 1; k <= file->nr; ++k)
+              file->z2r[i][j][k] *= conversion_factor;
+          }
+        }
+      }
+    } catch (TokenizerException &e) {
+      error->one(FLERR, e.what());
+    }
+  }
+
+  // broadcast potential information
+  MPI_Bcast(&file->nelements, 1, MPI_INT, 0, world);
+
+  MPI_Bcast(&file->nrho, 1, MPI_INT, 0, world);
+  MPI_Bcast(&file->drho, 1, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&file->nr, 1, MPI_INT, 0, world);
+  MPI_Bcast(&file->dr, 1, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&file->cut, 1, MPI_DOUBLE, 0, world);
+  MPI_Bcast(&rhomax, 1, MPI_DOUBLE, 0, world);
+
+  // allocate memory on other procs
+  if (comm->me != 0) {
+    file->elements = new char*[file->nelements];
+    for (int i = 0; i < file->nelements; i++) file->elements[i] = nullptr;
+    memory->create(file->mass, file->nelements, "pair:mass");
+    memory->create(file->frho, file->nelements, file->nrho + 1, "pair:frho");
+    memory->create(file->rhor, file->nelements, file->nelements, file->nr + 1, "pair:rhor");
+    memory->create(file->z2r, file->nelements, file->nelements, file->nr + 1, "pair:z2r");
+  }
+
+  // broadcast file->elements string array
+  for (int i = 0; i < file->nelements; i++) {
+    int n;
+    if (comm->me == 0) n = strlen(file->elements[i]) + 1;
+    MPI_Bcast(&n, 1, MPI_INT, 0, world);
+    if (comm->me != 0) file->elements[i] = new char[n];
+    MPI_Bcast(file->elements[i], n, MPI_CHAR, 0, world);
+  }
+
+  // broadcast file->mass, frho, rhor
+  for (int i = 0; i < file->nelements; i++) {
+    MPI_Bcast(&file->mass[i], 1, MPI_DOUBLE, 0, world);
+    MPI_Bcast(&file->frho[i][1], file->nrho, MPI_DOUBLE, 0, world);
+
+    for (int j = 0; j < file->nelements; j++) {
+      MPI_Bcast(&file->rhor[i][j][1], file->nr, MPI_DOUBLE, 0, world);
+    }
+  }
+
+  // broadcast file->z2r
+  for (int i = 0; i < file->nelements; i++) {
+    for (int j = 0; j <= i; j++) {
+      MPI_Bcast(&file->z2r[i][j][1], file->nr, MPI_DOUBLE, 0, world);
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   copy read-in setfl potential to standard array format
+------------------------------------------------------------------------- */
+
+void PairEAMFSMLML::file2array()
+{
+  int i,j,m,n;
+  int ntypes = atom->ntypes;
+
+  // set function params directly from fs file
+
+  nrho = fs->nrho;
+  nr = fs->nr;
+  drho = fs->drho;
+  dr = fs->dr;
+  if (he_flag) rhomin = rhomax - (nrho-1) * drho;
+  else rhomax = (nrho-1) * drho;
+
+  // ------------------------------------------------------------------
+  // setup frho arrays
+  // ------------------------------------------------------------------
+
+  // allocate frho arrays
+  // nfrho = # of fs elements + 1 for zero array
+
+  nfrho = fs->nelements + 1;
+  memory->destroy(frho);
+  memory->create(frho,nfrho,nrho+1,"pair:frho");
+
+  // copy each element's frho to global frho
+
+  for (i = 0; i < fs->nelements; i++)
+    for (m = 1; m <= nrho; m++) frho[i][m] = fs->frho[i][m];
+
+  // add extra frho of zeroes for non-EAM types to point to (pair hybrid)
+  // this is necessary b/c fp is still computed for non-EAM atoms
+
+  for (m = 1; m <= nrho; m++) frho[nfrho-1][m] = 0.0;
+
+  // type2frho[i] = which frho array (0 to nfrho-1) each atom type maps to
+  // if atom type doesn't point to element (non-EAM atom in pair hybrid)
+  // then map it to last frho array of zeroes
+
+  for (i = 1; i <= ntypes; i++)
+    if (map[i] >= 0) type2frho[i] = map[i];
+    else type2frho[i] = nfrho-1;
+
+  // ------------------------------------------------------------------
+  // setup rhor arrays
+  // ------------------------------------------------------------------
+
+  // allocate rhor arrays
+  // nrhor = square of # of fs elements
+
+  nrhor = fs->nelements * fs->nelements;
+  memory->destroy(rhor);
+  memory->create(rhor,nrhor,nr+1,"pair:rhor");
+
+  // copy each element pair rhor to global rhor
+
+  n = 0;
+  for (i = 0; i < fs->nelements; i++)
+    for (j = 0; j < fs->nelements; j++) {
+      for (m = 1; m <= nr; m++) rhor[n][m] = fs->rhor[i][j][m];
+      n++;
+    }
+
+  // type2rhor[i][j] = which rhor array (0 to nrhor-1) each type pair maps to
+  // for fs files, there is a full NxN set of rhor arrays
+  // OK if map = -1 (non-EAM atom in pair hybrid) b/c type2rhor not used
+
+  for (i = 1; i <= ntypes; i++)
+    for (j = 1; j <= ntypes; j++)
+      type2rhor[i][j] = map[i] * fs->nelements + map[j];
+
+  // ------------------------------------------------------------------
+  // setup z2r arrays
+  // ------------------------------------------------------------------
+
+  // allocate z2r arrays
+  // nz2r = N*(N+1)/2 where N = # of fs elements
+
+  nz2r = fs->nelements * (fs->nelements+1) / 2;
+  memory->destroy(z2r);
+  memory->create(z2r,nz2r,nr+1,"pair:z2r");
+
+  // copy each element pair z2r to global z2r, only for I >= J
+
+  n = 0;
+  for (i = 0; i < fs->nelements; i++)
+    for (j = 0; j <= i; j++) {
+      for (m = 1; m <= nr; m++) z2r[n][m] = fs->z2r[i][j][m];
+      n++;
+    }
+
+  // type2z2r[i][j] = which z2r array (0 to nz2r-1) each type pair maps to
+  // set of z2r arrays only fill lower triangular Nelement matrix
+  // value = n = sum over rows of lower-triangular matrix until reach irow,icol
+  // swap indices when irow < icol to stay lower triangular
+  // if map = -1 (non-EAM atom in pair hybrid):
+  //   type2z2r is not used by non-opt
+  //   but set type2z2r to 0 since accessed by opt
+
+  int irow,icol;
+  for (i = 1; i <= ntypes; i++) {
+    for (j = 1; j <= ntypes; j++) {
+      irow = map[i];
+      icol = map[j];
+      if (irow == -1 || icol == -1) {
+        type2z2r[i][j] = 0;
+        continue;
+      }
+      if (irow < icol) {
+        irow = map[j];
+        icol = map[i];
+      }
+      n = 0;
+      for (m = 0; m < irow; m++) n += m + 1;
+      n += icol;
+      type2z2r[i][j] = n;
+    }
+  }
+}