lammps-src/atom_vec_pi.cpp

/* ----------------------------------------------------------------------
 LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 https://lammps.sandia.gov/, 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.

 Modifed by NMC 19/01/2024 from sph style atom. Including settings for stmic, stfluid and gradv// Upgrqding to uptodate lammsp version

 ------------------------------------------------------------------------- */

#include "atom_vec_pi.h"

#include "atom.h"

#include <cstring>

using namespace LAMMPS_NS;

/* ---------------------------------------------------------------------- */

AtomVecPi::AtomVecPi(LAMMPS *lmp) : AtomVec(lmp)
{
  molecular = Atom::ATOMIC;
  mass_type = PER_TYPE;
  forceclearflag = 1;

  atom->esph_flag = 1;
  atom->rho_flag = 1;
  atom->cv_flag = 1;
  atom->vest_flag = 1;
  atom->stmic_flag =1; // Modifed by NMC
  atom->stfluid_flag =1; // Modifed by NMC
  atom->gradv_flag =1; // Modifed by NMC

  // strings with peratom variables to include in each AtomVec method
  // strings cannot contain fields in corresponding AtomVec default strings
  // order of fields in a string does not matter
  // except: fields_data_atom & fields_data_vel must match data fil


  fields_grow = {"rho", "drho", "esph", "desph", "cv", "vest", "stmic", "stfluid", "gradv"};
  fields_copy = {"rho", "drho", "esph", "desph", "cv", "vest", "stmic", "stfluid", "gradv"};
  fields_comm = {"rho", "esph", "vest", "stmic", "stfluid", "gradv"};
  fields_comm_vel = {"rho", "esph", "vest", "stmic", "stfluid", "gradv"};
  fields_reverse = {"drho", "desph", "gradv"}; //gradv is needed to communicate for sph pi for macroscale to compute gradv
  fields_border = {"rho", "esph", "cv", "vest", "stmic", "stfluid", "gradv"};
  fields_border_vel = {"rho", "esph", "cv", "vest", "stmic", "stfluid", "gradv"};
  fields_exchange = {"rho", "esph", "cv", "vest", "stmic", "stfluid", "gradv"};
  fields_restart = {"rho", "esph", "cv", "vest", "stmic", "stfluid", "gradv"};
  fields_create = {"rho", "esph", "cv", "vest", "desph", "drho", "stmic", "stfluid", "gradv"};
  fields_data_atom = {"id", "type", "rho", "esph", "cv", "x"};
  fields_data_vel = {"id", "v"};


  setup_fields();
}

/* ----------------------------------------------------------------------
   set local copies of all grow ptrs used by this class, except defaults
   needed in replicate when 2 atom classes exist and it calls pack_restart()
------------------------------------------------------------------------- */

void AtomVecPi::grow_pointers()
{
  rho = atom->rho;
  drho = atom->drho;
  esph = atom->esph;
  desph = atom->desph;
  cv = atom->cv;
  vest = atom->vest;
  //Modified by NMC
  stmic = atom->stmic;
  stfluid = atom->stfluid;
  gradv = atom->gradv;
}

/* ----------------------------------------------------------------------
   clear extra forces starting at atom N
   nbytes = # of bytes to clear for a per-atom vector
------------------------------------------------------------------------- */

void AtomVecPi::force_clear(int n, size_t nbytes)
{
  memset(&desph[n],0,nbytes);
  memset(&drho[n],0,nbytes);

  // LAMMPS stores 2D peratom arrays as one contiguous block (row-major,
  // gradv[i] points to gradv[0] + 9*i). Clearing nlocal rows of 9 doubles
  // each needs a single memset of 9*nbytes, NOT 9 memsets of nbytes.
  memset(&gradv[n][0], 0, 9 * nbytes);
}

/* ----------------------------------------------------------------------
   initialize non-zero atom quantities
------------------------------------------------------------------------- */

void AtomVecPi::create_atom_post(int ilocal)
{
  cv[ilocal] = 1.0;
}

/* ----------------------------------------------------------------------
   modify what AtomVec::data_atom() just unpacked
   or initialize other atom quantities
------------------------------------------------------------------------- */

void AtomVecPi::data_atom_post(int ilocal)
{
  vest[ilocal][0] = 0.0;
  vest[ilocal][1] = 0.0;
  vest[ilocal][2] = 0.0;
  desph[ilocal] = 0.0;
  drho[ilocal] = 0.0;

  // Modifed by NMC
  stmic[ilocal][0] = 0.0;
  stmic[ilocal][1] = 0.0;
  stmic[ilocal][2] = 0.0;
  stmic[ilocal][3] = 0.0;
  stmic[ilocal][4] = 0.0;
  stmic[ilocal][5] = 0.0;

  stfluid[ilocal][0] = 0.0;
  stfluid[ilocal][1] = 0.0;
  stfluid[ilocal][2] = 0.0;
  stfluid[ilocal][3] = 0.0;
  stfluid[ilocal][4] = 0.0;
  stfluid[ilocal][5] = 0.0;

// Modifed by NMC

  gradv[ilocal][0] = 0.0;
  gradv[ilocal][1] = 0.0;
  gradv[ilocal][2] = 0.0;
  gradv[ilocal][3] = 0.0;
  gradv[ilocal][4] = 0.0;
  gradv[ilocal][5] = 0.0;
  gradv[ilocal][6] = 0.0;
  gradv[ilocal][7] = 0.0;
  gradv[ilocal][8] = 0.0;

}

/* ----------------------------------------------------------------------
   assign an index to named atom property and return index
   return -1 if name is unknown to this atom style
------------------------------------------------------------------------- */

int AtomVecPi::property_atom(const std::string &name)
{

  if (name == "rho") return 0;
  if (name == "drho") return 1;
  if (name == "esph") return 2;
  if (name == "desph") return 3;
  if (name == "cv") return 4;



  //////////////Return each component of the tensors separately
  //Modified by NMC to include the prop atom for the new tensors
  if (name == "stfxx") return 5;
  if (name == "stfyy") return 6;
  if (name == "stfzz") return 7;
  if (name == "stfxy") return 8;
  if (name == "stfxz") return 9;
  if (name == "stfyz") return 10;

  if (name == "stmxx") return 11;
  if (name == "stmyy") return 12;
  if (name == "stmzz") return 13;
  if (name == "stmxy") return 14;
  if (name == "stmxz") return 15;
  if (name == "stmyz") return 16;

  if (name == "gdvxx") return 17;
  if (name == "gdvyy") return 18;
  if (name == "gdvzz") return 19;
  if (name == "gdvxy") return 20;
  if (name == "gdvxz") return 21;
  if (name == "gdvyz") return 22;
  if (name == "gdvyx") return 23;
  if (name == "gdvzx") return 24;
  if (name == "gdvzy") return 25;
  return -1;
}

/* ----------------------------------------------------------------------
   pack per-atom data into buf for ComputePropertyAtom
   index maps to data specific to this atom style
------------------------------------------------------------------------- */

void AtomVecPi::pack_property_atom(int index, double *buf,
                                     int nvalues, int groupbit)
{
  int *mask = atom->mask;
  int nlocal = atom->nlocal;
  int n = 0;

  if (index == 0) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = rho[i];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 1) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = drho[i];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 2) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = esph[i];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 3) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = desph[i];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 4) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = cv[i];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 5) {  //Modified from here to include the prop atome for the new tensors
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = stfluid[i][0];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 6) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = stfluid[i][1];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 7) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = stfluid[i][2];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 8) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = stfluid[i][3];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 9) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = stfluid[i][4];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 10) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = stfluid[i][5];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 11) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = stmic[i][0];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 12) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = stmic[i][1];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 13) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = stmic[i][2];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 14) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = stmic[i][3];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 15) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = stmic[i][4];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 16) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = stmic[i][5];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 17) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = gradv[i][0];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 18) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = gradv[i][1];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 19) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = gradv[i][2];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 20) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = gradv[i][3];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 21) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = gradv[i][4];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 22) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = gradv[i][5];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 23) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = gradv[i][6];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 24) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = gradv[i][7];
      else buf[n] = 0.0;
      n += nvalues;
    }
  } else if (index == 25) {
    for (int i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) buf[n] = gradv[i][8];
      else buf[n] = 0.0;
      n += nvalues;
    }
  }
}