lammps/src/compute.cpp

// clang-format off
/* ----------------------------------------------------------------------
   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.
------------------------------------------------------------------------- */

#include "compute.h"

#include "atom_masks.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "group.h"
#include "memory.h"
#include "modify.h"

#include <cstring>

using namespace LAMMPS_NS;

static constexpr int DELTA = 4;

// allocate space for static class instance variable and initialize it

int Compute::instance_total = 0;

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

Compute::Compute(LAMMPS *lmp, int narg, char **arg) :
  Pointers(lmp), id(nullptr), style(nullptr), vector(nullptr), array(nullptr),
  vector_atom(nullptr), array_atom(nullptr), vector_local(nullptr), array_local(nullptr),
  extlist(nullptr), tlist(nullptr), vbiasall(nullptr)
{
  instance_me = instance_total++;

  if (narg < 3) utils::missing_cmd_args(FLERR,"compute", error);

  // compute ID, group, and style
  // ID must be all alphanumeric chars or underscores

  id = utils::strdup(arg[0]);
  if (!utils::is_id(id))
    error->all(FLERR,"Compute ID {} must only have alphanumeric or underscore characters", id);

  groupbit = group->get_bitmask_by_id(FLERR, arg[1], fmt::format("compute {}", arg[2]));
  igroup = group->find(arg[1]);
  if (igroup == -1) error->all(FLERR,"Could not find compute group ID {}", arg[1]);

  style = utils::strdup(arg[2]);

  // set child class defaults

  scalar_flag = vector_flag = array_flag = 0;
  extscalar = extvector = extarray = -1;
  peratom_flag = local_flag = pergrid_flag = 0;
  size_vector_variable = size_array_rows_variable = 0;

  tempflag = pressflag = peflag = 0;
  pressatomflag = peatomflag = 0;
  create_attribute = 0;
  tempbias = 0;
  scalar = 0.0;

  timeflag = 0;
  comm_forward = comm_reverse = 0;
  dynamic = 0;
  dynamic_group_allow = 1;

  initialized_flag = 0;
  invoked_scalar = invoked_vector = invoked_array = -1;
  invoked_peratom = invoked_local = -1;
  invoked_flag = INVOKED_NONE;

  // set modify defaults

  extra_dof = domain->dimension;
  dynamic_user = 0;
  fix_dof = 0.0;

  // setup list of timesteps

  ntime = maxtime = 0;

  // data masks

  execution_space = Host;
  datamask_read = ALL_MASK;
  datamask_modify = ALL_MASK;

  copymode = 0;
  kokkosable = 0;
}

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

Compute::~Compute()
{
  if (copymode) return;

  delete[] id;
  delete[] style;
  memory->destroy(tlist);
}

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

void Compute::init_flags()
{
  initialized_flag = 1;
  invoked_scalar = invoked_vector = invoked_array = -1;
  invoked_peratom = invoked_local = -1;

  if (scalar_flag && (extscalar < 0))
    error->all(FLERR, "Must set 'extscalar' when setting 'scalar_flag' for compute {}.  "
               "Contact the developer.", style);
  if (vector_flag && (extvector < 0) && !extlist)
    error->all(FLERR, "Must set 'extvector' or 'extlist' when setting 'vector_flag' for compute {}.  "
               "Contact the developer.", style);
  if (array_flag && (extarray < 0))
    error->all(FLERR, "Must set 'extarray' when setting 'array_flag' for compute {}.  "
               "Contact the developer.", style);
}

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

void Compute::modify_params(int narg, char **arg)
{
  if (narg == 0) error->all(FLERR,"Illegal compute_modify command");

  int iarg = 0;
  while (iarg < narg) {
    if (strcmp(arg[iarg],"extra/dof") == 0) {
      if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"compute_modify extra/dof", error);
      extra_dof = utils::numeric(FLERR,arg[iarg+1],false,lmp);
      iarg += 2;
    } else if (strcmp(arg[iarg],"dynamic/dof") == 0) {
      if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"compute_modify dynamic/dof", error);
      dynamic_user = utils::logical(FLERR,arg[iarg+1],false,lmp);
      iarg += 2;
    } else {
      int n = modify_param(narg-iarg, &arg[iarg]);
        if (n== 0)
          error->all(FLERR, iarg + 1, "Compute {} {} does not support compute_modify {} command",
                     id, style, arg[iarg]);
    }
  }
}

/* ----------------------------------------------------------------------
   calculate adjustment in DOF due to fixes
------------------------------------------------------------------------- */

void Compute::adjust_dof_fix()
{
  fix_dof = 0;
  for (auto &ifix : modify->get_fix_list())
    if (ifix->dof_flag)
      fix_dof += ifix->dof(igroup);
}

/* ----------------------------------------------------------------------
   reset extra_dof to its default value
------------------------------------------------------------------------- */

void Compute::reset_extra_dof()
{
  extra_dof = domain->dimension;
}

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

void Compute::reset_extra_compute_fix(const char *)
{
  error->all(FLERR,
             "Compute does not allow an extra compute or fix to be reset");
}

/* ----------------------------------------------------------------------
   add ntimestep to list of timesteps the compute will be called on
   do not add if already in list
   search from top downward, since list of times is in decreasing order
------------------------------------------------------------------------- */

void Compute::addstep(bigint ntimestep)
{
  // i = location in list to insert ntimestep

  int i;
  for (i = ntime-1; i >= 0; i--) {
    if (ntimestep == tlist[i]) return;
    if (ntimestep < tlist[i]) break;
  }
  i++;

  // extend list as needed

  if (ntime == maxtime) {
    maxtime += DELTA;
    memory->grow(tlist,maxtime,"compute:tlist");
  }

  // move remainder of list upward and insert ntimestep

  for (int j = ntime-1; j >= i; j--) tlist[j+1] = tlist[j];
  tlist[i] = ntimestep;
  ntime++;
}

/* ----------------------------------------------------------------------
   return 1/0 if ntimestep is or is not in list of calling timesteps
   if value(s) on top of list are less than ntimestep, delete them
   search from top downward, since list of times is in decreasing order
------------------------------------------------------------------------- */

int Compute::matchstep(bigint ntimestep)
{
  for (int i = ntime-1; i >= 0; i--) {
    if (ntimestep < tlist[i]) return 0;
    if (ntimestep == tlist[i]) return 1;
    if (ntimestep > tlist[i]) ntime--;
  }
  return 0;
}

/* ----------------------------------------------------------------------
   clean out list of timesteps to call the compute on
------------------------------------------------------------------------- */

void Compute::clearstep()
{
  ntime = 0;
}