157 lines
5.0 KiB
C++
157 lines
5.0 KiB
C++
/* -*- c++ -*- ----------------------------------------------------------
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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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Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
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------------------------------------------------------------------------- */
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#include "compute_mesont.h"
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#include <cstring>
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#include "atom.h"
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#include "update.h"
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#include "comm.h"
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#include "force.h"
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#include "modify.h"
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#include "memory.h"
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#include "error.h"
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#include "pair.h"
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#include <string>
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeMesoNT::ComputeMesoNT(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg), energy(NULL) {
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if (narg != 4) error->all(FLERR,"Illegal compute mesont command");
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std::string ctype = arg[3];
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if (ctype == "estretch") compute_type = ES;
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else if (ctype == "ebend") compute_type = EB;
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else if (ctype == "etube") compute_type = ET;
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else error->all(FLERR,"Illegal compute mesont command");
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peratom_flag = 1;
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size_peratom_cols = 0;
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peatomflag = 1;
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timeflag = 1;
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comm_reverse = 1;
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extscalar = 1;
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scalar_flag = 1;
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nmax = 0;
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}
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/* ---------------------------------------------------------------------- */
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ComputeMesoNT::~ComputeMesoNT() {
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memory->destroy(energy);
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}
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/* ---------------------------------------------------------------------- */
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double ComputeMesoNT::compute_scalar() {
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invoked_scalar = update->ntimestep;
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if (update->eflag_global != invoked_scalar)
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error->all(FLERR,"Energy was not tallied on needed timestep");
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int i;
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double* ptr = NULL;
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if (compute_type == ES)
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ptr = static_cast<double*>(force->pair->extract("mesonttpm_Es_tot",i));
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else if (compute_type == EB)
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ptr = static_cast<double*>(force->pair->extract("mesonttpm_Eb_tot",i));
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else if (compute_type == ET)
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ptr = static_cast<double*>(force->pair->extract("mesonttpm_Et_tot",i));
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else error->all(FLERR,"Illegal compute mesont command");
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if (!ptr) error->all(FLERR,
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"compute mesont is allowed only with mesont/tpm pair style");
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MPI_Allreduce(ptr,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
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return scalar;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeMesoNT::compute_peratom() {
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invoked_peratom = update->ntimestep;
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if (update->eflag_atom != invoked_peratom)
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error->all(FLERR,"Per-atom energy was not tallied on needed timestep");
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// grow local energy array if necessary
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// needs to be atom->nmax in length
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if (atom->nmax > nmax) {
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memory->destroy(energy);
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nmax = atom->nmax;
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memory->create(energy,nmax,"mesont_Eb:energy");
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vector_atom = energy;
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}
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// npair includes ghosts if newton_bond is set
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// ntotal includes ghosts if either newton flag is set
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int nlocal = atom->nlocal;
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int npair = nlocal;
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if (force->newton) npair += atom->nghost;
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int ntotal = nlocal;
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if (force->newton) ntotal += atom->nghost;
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int i;
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// clear local energy array
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for (int i = 0; i < ntotal; i++) energy[i] = 0.0;
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double* ptr = NULL;
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if (compute_type == ES)
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ptr = static_cast<double*>(force->pair->extract("mesonttpm_Es",i));
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else if (compute_type == EB)
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ptr = static_cast<double*>(force->pair->extract("mesonttpm_Eb",i));
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else if (compute_type == ET)
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ptr = static_cast<double*>(force->pair->extract("mesonttpm_Et",i));
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else error->all(FLERR,"Illegal compute mesont command");
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if (ptr) for (i = 0; i < npair; i++) energy[i] += ptr[i];
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else error->all(FLERR,
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"compute mesont is allowed only with mesont/tpm pair style");
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// communicate ghost energy between neighbor procs
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if (force->newton) comm->reverse_comm_compute(this);
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// zero energy of atoms not in group
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// only do this after comm since ghost contributions must be included
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int *mask = atom->mask;
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for (int i = 0; i < nlocal; i++)
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if (!(mask[i] & groupbit)) energy[i] = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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int ComputeMesoNT::pack_reverse_comm(int n, int first, double *buf) {
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int m = 0;
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int last = first + n;
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for (int i = first; i < last; i++) buf[m++] = energy[i];
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeMesoNT::unpack_reverse_comm(int n, int *list, double *buf) {
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int m = 0;
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for (int i = 0; i < n; i++) {
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int j = list[i];
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energy[j] += buf[m++];
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based array
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------------------------------------------------------------------------- */
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double ComputeMesoNT::memory_usage() {
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double bytes = nmax * sizeof(double);
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return bytes;
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}
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