lammps-sys 0.6.0

/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   http://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.
------------------------------------------------------------------------- */

/* ----------------------------------------------------------------------
   Contributing author: Rene Halver (JSC)
------------------------------------------------------------------------- */

#include <cstdio>
#include <cstring>
#include <cstdlib>
#include "scafacos.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "memory.h"
#include "error.h"

// ScaFaCoS library

#include <string>
#include <sstream>
#include "fcs.h"

using namespace LAMMPS_NS;

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

Scafacos::Scafacos(LAMMPS *lmp) : KSpace(lmp)
{
  me = comm->me;
  initialized = 0;

  maxatom = 0;
  xpbc = NULL;
  epot = NULL;
  efield = NULL;
  fcs = NULL;
}

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

void Scafacos::settings(int narg, char **arg)
{
  if (narg != 2) error->all(FLERR,"Illegal scafacos command");

  int n = strlen(arg[0]) + 1;
  method = new char[n];
  strcpy(method,arg[0]);
  tolerance = force->numeric(FLERR,arg[1]);

  // optional ScaFaCoS library setting defaults
  // choose the correct default tolerance type for chosen method
  // throw an error if a not yet supported solver is chosen
  if (strcmp(method,"fmm") == 0) {
    tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
    fmm_tuning_flag = 0;
  } else if (strcmp(method,"p3m") == 0 ||
             strcmp(method,"p2nfft") == 0 ||
             strcmp(method,"ewald") == 0) {
    tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
  } else if (strcmp(method,"direct") == 0) {
    ; // direct summation has no tolerance type
  } else {
    error->all(FLERR,"Unsupported ScaFaCoS method");
  }
}

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

Scafacos::~Scafacos()
{
  delete [] method;

  memory->destroy(xpbc);
  memory->destroy(epot);
  memory->destroy(efield);

  // clean up of the ScaFaCoS handle and internal arrays
  fcs_destroy((FCS)fcs);
}

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

void Scafacos::init()
{
  // error checks
  if (screen && me == 0) fprintf(screen,
                         "Setting up ScaFaCoS with solver %s ...\n",method);
  if (logfile && me == 0) fprintf(logfile,
                          "Setting up ScaFaCoS with solver %s ...\n",method);

  if ((strcmp(method,"p3m") == 0) && (me == 0))
    error->warning(FLERR,"Virial computation for P3M not available");

  if ((strcmp(method,"ewald") == 0) && (me == 0))
    error->warning(FLERR,"Virial computation for Ewald not available");

  if (!atom->q_flag)
    error->all(FLERR,"Kspace style requires atom attribute q");

  if (domain->dimension == 2)
    error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation");

  if (domain->triclinic)
    error->all(FLERR,"Cannot use ScaFaCoS with triclinic domain yet");

  if (atom->natoms > INT_MAX && sizeof(int) != 8)
    error->all(FLERR,"Scafacos atom count exceeds 2B");

  if (atom->molecular > 0)
    error->all(FLERR,
               "Cannot use Scafacos with molecular charged systems yet");

  FCSResult result;

  // one-time initialization of ScaFaCoS

  qqrd2e = force->qqrd2e;

  if (!initialized) {
    result = fcs_init((FCS*)&fcs,method,world);
    check_result((void*)&result);

    setup_handle();

    // using other methods lead to termination of the program,
    // since they have no tolerance tuning methods
    if ( strcmp(method,"fmm") == 0 ||
         strcmp(method,"p3m") == 0 ||
         strcmp(method,"p2nfft") == 0 ||
         strcmp(method,"ewald") == 0)
    {
      result = fcs_set_tolerance((FCS)fcs,tolerance_type,tolerance);
      check_result((void*)&result);
    }

    double **x = atom->x;
    double *q = atom->q;
    int nlocal = atom->nlocal;

    if (strcmp(method,"fmm") == 0) {
      if (fmm_tuning_flag == 1)
        fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_INHOMOGENOUS_SYSTEM);
      else
        fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_HOMOGENOUS_SYSTEM);
    }

    // for the FMM at least one particle is required per process
    if (strcmp(method,"fmm") == 0) {
      int empty = (nlocal==0)?1:0;
      MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world);
      if (empty > 0)
        fcs_set_redistribute((FCS)fcs,1);
      else
        fcs_set_redistribute((FCS)fcs,0);
    }

    result = fcs_tune((FCS)fcs,nlocal,&x[0][0],q);
    check_result((void*)&result);
    // more useful here, since the parameters should be tuned now
    if (me == 0) fcs_print_parameters((FCS)fcs);
  }

  initialized = 1;
}

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

void Scafacos::compute(int eflag, int vflag)
{
  double **x = atom->x;
  double *q = atom->q;
  int nlocal = atom->nlocal;

  const double qscale = qqrd2e;
  FCSResult result;

  // for the FMM at least one particle is required per process
  if (strcmp(method,"fmm"))
  {
    int empty = (nlocal==0)?1:0;
    MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world);
    if (empty > 0)
      fcs_set_redistribute((FCS)fcs,1);
    else
      fcs_set_redistribute((FCS)fcs,0);
  }

  ev_init(eflag,vflag);

  // grow xpbc, epot, efield if necessary

  if (nlocal > maxatom || maxatom == 0) {
    memory->destroy(xpbc);
    memory->destroy(epot);
    memory->destroy(efield);
    maxatom = atom->nmax;
    memory->create(xpbc,3*maxatom,"scafacos:xpbc");
    memory->create(epot,maxatom,"scafacos:epot");
    memory->create(efield,maxatom,3,"scafacos:efield");
  }

  if (vflag_global) {

    // for P3M or Ewald we cannot compute the virial. skip it.

    if ((strcmp(method,"p3m") != 0)
        && (strcmp(method,"ewald") != 0)) {
      result = fcs_set_compute_virial((FCS)fcs,1);
      check_result((void*)&result);
    }
  }

  // pack coords into xpbc and apply PBC
  memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double));


  if (domain->xperiodic || domain -> yperiodic || domain -> zperiodic){
  int j = 0;
    for (int i = 0; i < nlocal; i++) {
      domain->remap(&xpbc[j]);
      j += 3;
    }
  }

  // if simulation box has changed, call fcs_tune()

  if (box_has_changed()) {
    setup_handle();
    result = fcs_tune((FCS)fcs,nlocal,xpbc,q);
    check_result((void*)&result);
  }

  // invoke ScaFaCoS solver

  result = fcs_run((FCS)fcs,nlocal,xpbc,q,&efield[0][0],epot);
  check_result((void*)&result);

  // extract virial

  if (vflag_global) {

    // for P3M or Ewald we cannot compute the virial. skip it.

    if ((strcmp(method,"p3m") != 0)
        && (strcmp(method,"ewald") != 0)) {
      result = fcs_get_virial((FCS)fcs,virial_int);
      check_result((void*)&result);

      virial[0] = virial_int[0];
      virial[1] = virial_int[1];
      virial[2] = virial_int[2];
      virial[3] = virial_int[4];
      virial[4] = virial_int[5];
      virial[5] = virial_int[8];
    }
  }

  // apply Efield to each particle
  // accumulate total energy

  double **f = atom->f;

  double qone;
  double myeng = 0.0;

  for (int i = 0; i < nlocal; i++) {
    qone = q[i] * qscale;
    f[i][0] += qone * efield[i][0];
    f[i][1] += qone * efield[i][1];
    f[i][2] += qone * efield[i][2];
    myeng += 0.5 * qone * epot[i];
  }

  if (eflag_atom) {
    for (int i = 0; i < nlocal; i++)
      eatom[i] = 0.5 * qscale * q[i] * epot[i];
  }

  MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world);
}

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

int Scafacos::modify_param(int narg, char **arg)
{
  // add any Scafacos options here you want to expose to LAMMPS
  // syntax: kspace_modify scafacos keyword value1 value2 ...
  //   keyword = tolerance
  //     value1 = energy, energy_rel, etc
  // everyone of these should have a default, so user doesn't need to set

  if (strcmp(arg[0],"scafacos") != 0) return 0;

  if (strcmp(arg[1],"tolerance") == 0) {
    if (narg < 3) error->all(FLERR,
                         "Illegal kspace_modify command (tolerance)");
    if (strcmp(arg[2],"energy") == 0)
      tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
    else if (strcmp(arg[2],"energy_rel") == 0)
      tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
    else if (strcmp(arg[2],"field") == 0)
      tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
    else if (strcmp(arg[2],"field_rel") == 0)
      tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
    else if (strcmp(arg[2],"potential") == 0)
      tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
    else if (strcmp(arg[2],"potential_rel") == 0)
      tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
    else error->all(FLERR,
                "Illegal kspace_modify command (tolerance argument)");
    // check if method is compatatible to chosen tolerance type
    if(
        (
          strcmp(method,"fmm") == 0 &&
          (
            tolerance_type != FCS_TOLERANCE_TYPE_ENERGY &&
            tolerance_type != FCS_TOLERANCE_TYPE_ENERGY_REL
          )
        ) ||
        (
          strcmp(method,"p2nfft") == 0 &&
          (
            tolerance_type != FCS_TOLERANCE_TYPE_FIELD &&
            tolerance_type != FCS_TOLERANCE_TYPE_POTENTIAL
          )
        ) ||
        (
          strcmp(method,"p3m") == 0 &&
          (
            tolerance_type != FCS_TOLERANCE_TYPE_FIELD
          )
        ) ||
        (
          strcmp(method,"ewald") == 0 &&
          (
            tolerance_type != FCS_TOLERANCE_TYPE_FIELD
          )
        )
      )
        error->all(FLERR,"Illegal kspace_modify command \
                          (invalid tolerance / method combination)");
    return 3;
  }

  //   keyword = fmm_inhomogen_tuning
  //     value1 = 0, 1
  //       0 -> homogenous system (default)
  //       1 -> inhomogenous system (more internal tuning is provided (sequential!))
  if (strcmp(arg[1],"fmm_tuning") == 0)
  {
    if (screen && me == 0) fprintf(screen,
                           "ScaFaCoS setting fmm inhomogen tuning ...\n");
    if (logfile && me == 0) fprintf(logfile,
                            "ScaFaCoS setting fmm inhomogen tuning ...\n");
    if (narg < 3) error->all(FLERR,
                         "Illegal kspace_modify command (fmm_tuning)");
    fmm_tuning_flag = atoi(arg[2]);
    return 3;
  }

  return 0;
}

/* ----------------------------------------------------------------------
   memory usage of local arrays
------------------------------------------------------------------------- */

double Scafacos::memory_usage()
{
  double bytes = 0.0;
  bytes += maxatom * sizeof(double);
  bytes += 3*maxatom * sizeof(double);
  return bytes;
}

/* ----------------------------------------------------------------------
    setup of ScaFaCoS handle with common parameters
------------------------------------------------------------------------- */

void Scafacos::setup_handle()
{
  FCSResult result;

  // store simulation box params

  // setup periodicity
  old_periodicity[0] = domain->xperiodic;
  old_periodicity[1] = domain->yperiodic;
  old_periodicity[2] = domain->zperiodic;

  // setup box origin (lower left front corner of the system)
  old_origin[0] = domain->boxlo[0];
  old_origin[1] = domain->boxlo[1];
  old_origin[2] = domain->boxlo[2];

  // setup box vectors (base vectors of the system box)
  old_box_x[0] = domain->prd[0];
  old_box_x[1] = old_box_x[2] = 0.0;
  old_box_y[1] = domain->prd[1];
  old_box_y[0] = old_box_y[2] = 0.0;
  old_box_z[2] = domain->prd[2];
  old_box_z[1] = old_box_z[0] = 0.0;

  // setup number of atoms in the system
  old_natoms = atom->natoms;

  // store parameters to ScaFaCoS handle
  result = fcs_set_box_a((FCS)fcs,old_box_x);
  check_result((void*)&result);

  result = fcs_set_box_b((FCS)fcs,old_box_y);
  check_result((void*)&result);

  result = fcs_set_box_c((FCS)fcs,old_box_z);
  check_result((void*)&result);

  result = fcs_set_box_origin((FCS)fcs,old_origin);
  check_result((void*)&result);

  result = fcs_set_periodicity((FCS)fcs,old_periodicity);
  check_result((void*)&result);

  result = fcs_set_total_particles((FCS)fcs,old_natoms);
  check_result((void*)&result);

  // allow ScaFaCoS to calculate the near field computations for now
  // TODO: allow the delegation of the near field computations
  //       within LAMMPS
  //       (near_field_flag = 1 -> enables the internal near field calcs
  //                          0 -> disables the internal near field calcs
  int near_field_flag = 1;
  result = fcs_set_near_field_flag((FCS)fcs,near_field_flag);
  check_result((void*)&result);
}

/* ----------------------------------------------------------------------
    check if box parameters changed, requiring a new call to fcs_tune
------------------------------------------------------------------------- */

bool Scafacos::box_has_changed()
{
  int *periodicity = domain->periodicity;
  double *prd = domain->prd;

  bool changed =
    (periodicity[0] != old_periodicity[0]) ||
    (periodicity[1] != old_periodicity[1]) ||
    (periodicity[2] != old_periodicity[2]) ||
    (domain->boundary[0][0] != old_origin[0]) ||
    (domain->boundary[1][0] != old_origin[1]) ||
    (domain->boundary[2][0] != old_origin[2]) ||
    (prd[0] != old_box_x[0]) ||
    (prd[1] != old_box_y[1]) ||
    (prd[2] != old_box_z[2]) ||
    (atom->natoms != old_natoms);

  return changed;
}

/* ----------------------------------------------------------------------
   check ScaFaCoS result for error condition
------------------------------------------------------------------------- */

void Scafacos::check_result(void* result_p)
{
  FCSResult result = *(FCSResult*)result_p;

  if (!result) return;

  std::stringstream ss;
  ss << "ScaFaCoS: " << fcs_result_get_function(result) << "\n"
     << fcs_result_get_message(result) << "\n";
  fcs_result_destroy(result);
  std::string err_msg = ss.str();
  const char *str = err_msg.c_str();

  error->one(FLERR,str);
}