convert to KSspace style rather than fix
This commit is contained in:
Steven J. Plimpton
308
src/USER-SCAFACOS/scafacos.cpp
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308
src/USER-SCAFACOS/scafacos.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Rene Halver (JSC)
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------------------------------------------------------------------------- */
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#include <cstdio>
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#include <cstring>
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#include <cstdlib>
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#include "scafacos.h"
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#include "atom.h"
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#include "comm.h"
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#include "domain.h"
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#include "force.h"
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#include "memory.h"
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#include "error.h"
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// ScaFaCoS library
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#include <string>
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#include <sstream>
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#include "fcs.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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Scafacos::Scafacos(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
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{
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if (narg < 2) error->all(FLERR,"Illegal scafacos command");
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int n = strlen(arg[0]) + 1;
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method = new char[n];
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strcpy(method,arg[0]);
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// additional args
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int tflag = 0;
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int iarg = 1;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"tolerance") == 0) {
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if (iarg+3 > narg) error->all(FLERR,"Illegal scafacos command");
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tflag = 1;
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if (strcmp(arg[iarg+1],"energy") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
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else if (strcmp(arg[iarg+1],"energy_rel") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
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else if (strcmp(arg[iarg+1],"field") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
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else if (strcmp(arg[iarg+1],"field_rel") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
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else if (strcmp(arg[iarg+1],"potential") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
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else if (strcmp(arg[iarg+1],"potential_rel") == 0)
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tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
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else error->all(FLERR,"Illegal scafacos command");
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tolerance = force->numeric(FLERR,arg[iarg+2]);
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iarg += 3;
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} else error->all(FLERR,"Illegal scafacos command");
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}
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if (!tflag) error->all(FLERR,"Must set tolerance in scafacos command");
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// initializations
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me = comm->me;
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initialized = 0;
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maxatom = 0;
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epot = NULL;
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efield = NULL;
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}
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/* ---------------------------------------------------------------------- */
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Scafacos::~Scafacos()
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{
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delete [] method;
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memory->destroy(epot);
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memory->destroy(efield);
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// NOTE: any clean-up call to ScaFaCoS needed?
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}
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/* ---------------------------------------------------------------------- */
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void Scafacos::init()
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{
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// error checks
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// NOTE: allow triclinic at some point
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if (domain->dimension == 2)
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error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation");
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if (domain->triclinic)
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error->all(FLERR,"Cannot use ScaFaCoS with triclinic domain yet");
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// one-time initialization of ScaFaCoS
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if (!initialized) {
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result = fcs_init(&fcs,method,world);
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check_result(result);
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setup_handle();
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result = fcs_set_tolerance(fcs,tolerance_type,tolerance);
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check_result(result);
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if (me == 0) fcs_print_parameters(fcs);
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double **x = atom->x;
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double *q = atom->q;
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int nlocal = atom->nlocal;
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result = fcs_tune(fcs,nlocal,&x[0][0],q);
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}
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initialized = 1;
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}
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/* ---------------------------------------------------------------------- */
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void Scafacos::setup() {}
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/* ---------------------------------------------------------------------- */
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void Scafacos::compute(int eflag, int vflag)
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{
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double **x = atom->x;
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double *q = atom->q;
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int nlocal = atom->nlocal;
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// if simluation box has changed, call fcs_tune()
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if (box_has_changed()) {
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printf("AAA\n");
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setup_handle();
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result = fcs_tune(fcs,nlocal,&x[0][0],q);
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check_result(result);
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}
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// grow epot & efield if necessary
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if (nlocal > maxatom) {
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memory->destroy(epot);
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memory->destroy(efield);
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maxatom = atom->nmax;
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memory->create(epot,maxatom,"scafacos:epot");
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memory->create(efield,maxatom,3,"scafacos:efield");
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}
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// initialize epot & efield
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// NOTE: is this necessary?
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for (int i = 0; i < nlocal; i++) {
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epot[i] = 0.0;
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efield[i][0] = efield[i][1] = efield[i][2] = 0.0;
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}
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// ScaFaCoS calculation of full Coulombics
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result = fcs_run(fcs,nlocal,&x[0][0],q,&efield[0][0],epot);
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check_result(result);
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// apply Efield to each particle
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// accumulate total energy
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double **f = atom->f;
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double qone;
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double myeng = 0.0;
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for (int i = 0; i < nlocal; i++) {
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qone = q[i];
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f[i][0] += qone * efield[i][0];
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f[i][1] += qone * efield[i][1];
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f[i][2] += qone * efield[i][2];
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myeng += 0.5 * qone * epot[i];
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}
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MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world);
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}
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/* ----------------------------------------------------------------------
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memory usage of local arrays
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------------------------------------------------------------------------- */
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double Scafacos::memory_usage()
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{
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double bytes = 0.0;
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bytes += maxatom * sizeof(double);
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bytes += 3*maxatom * sizeof(double);
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return bytes;
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}
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/* ----------------------------------------------------------------------
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setup of ScaFaCoS handle with common parameters
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------------------------------------------------------------------------- */
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void Scafacos::setup_handle()
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{
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// store simulation box params
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// NOTE: this assumes orthogonal box
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// NOTE: total particles may not be a 4-byte int
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// NOTE: what does SCFCS mean by offset?
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// it's an integer flag in LAMMPS
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old_periodicity[0] = domain->xperiodic;
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old_periodicity[1] = domain->yperiodic;
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old_periodicity[2] = domain->zperiodic;
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old_offset[0] = domain->boundary[0][0];
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old_offset[1] = domain->boundary[1][0];
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old_offset[2] = domain->boundary[2][0];
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old_box_x[0] = domain->prd[0];
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old_box_x[1] = old_box_x[2] = 0.0;
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old_box_y[1] = domain->prd[1];
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old_box_y[0] = old_box_y[2] = 0.0;
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old_box_z[2] = domain->prd[2];
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old_box_z[1] = old_box_z[0] = 0.0;
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old_natoms = atom->natoms;
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// set all required ScaFaCoS params
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result = fcs_set_box_a(fcs,old_box_x);
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check_result(result);
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result = fcs_set_box_b(fcs,old_box_y);
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check_result(result);
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result = fcs_set_box_c(fcs,old_box_z);
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check_result(result);
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result = fcs_set_box_origin(fcs,old_offset);
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check_result(result);
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result = fcs_set_periodicity(fcs,old_periodicity);
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check_result(result);
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result = fcs_set_total_particles(fcs,old_natoms);
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check_result(result);
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// NOTE: for now disable short-range calculations within LAMMPS
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int near_field_flag = 0;
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result = fcs_set_near_field_flag(fcs,near_field_flag);
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check_result(result);
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}
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/* ----------------------------------------------------------------------
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check if box parameters changed, requiring a new call to fcs_tune
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------------------------------------------------------------------------- */
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bool Scafacos::box_has_changed()
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{
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int *periodicity = domain->periodicity;
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double *prd = domain->prd;
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bool changed =
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(periodicity[0] != old_periodicity[0]) ||
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(periodicity[1] != old_periodicity[1]) ||
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(periodicity[2] != old_periodicity[2]) ||
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(domain->boundary[0][0] != old_offset[0]) ||
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(domain->boundary[1][0] != old_offset[1]) ||
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(domain->boundary[2][0] != old_offset[2]) ||
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(prd[0] != old_box_x[0]) ||
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(prd[1] != old_box_y[1]) ||
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(prd[2] != old_box_z[2]) ||
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(atom->natoms != old_natoms);
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return changed;
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}
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/* ----------------------------------------------------------------------
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check ScaFaCoS result for error condition
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NOTE: will all procs have same error?
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------------------------------------------------------------------------- */
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void Scafacos::check_result(FCSResult result)
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{
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if (!result) return;
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std::stringstream ss;
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ss << "ScaFaCoS: " << fcs_result_get_function(result) << "\n"
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<< fcs_result_get_message(result) << "\n";
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fcs_result_destroy(result);
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std::string err_msg = ss.str();
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const char *str = err_msg.c_str();
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error->one(FLERR,str);
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}
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