forked from lijiext/lammps
274 lines
7.6 KiB
C++
274 lines
7.6 KiB
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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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "compute_gyration_molecule.h"
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#include "atom.h"
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#include "update.h"
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#include "domain.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeGyrationMolecule::ComputeGyrationMolecule(LAMMPS *lmp,
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int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg < 3) error->all(FLERR,"Illegal compute gyration/molecule command");
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if (atom->molecular == 0)
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error->all(FLERR,"Compute gyration/molecule requires molecular atom style");
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tensor = 0;
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"tensor") == 0) {
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tensor = 1;
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iarg++;
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} else error->all(FLERR,"Illegal compute gyration/molecule command");
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}
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// setup molecule-based data
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nmolecules = molecules_in_group(idlo,idhi);
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memory->create(massproc,nmolecules,"gyration/molecule:massproc");
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memory->create(masstotal,nmolecules,"gyration/molecule:masstotal");
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memory->create(com,nmolecules,3,"gyration/molecule:com");
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memory->create(comall,nmolecules,3,"gyration/molecule:comall");
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rg = vector = NULL;
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rgt = array = NULL;
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if (tensor) {
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memory->create(rgt,nmolecules,6,"gyration/molecule:rgt");
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memory->create(array,nmolecules,6,"gyration/molecule:array");
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array_flag = 1;
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size_array_rows = nmolecules;
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size_array_cols = 6;
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extarray = 0;
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} else {
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memory->create(rg,nmolecules,"gyration/molecule:rg");
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memory->create(vector,nmolecules,"gyration/molecule:vector");
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vector_flag = 1;
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size_vector = nmolecules;
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extvector = 0;
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}
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// compute masstotal for each molecule
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int *mask = atom->mask;
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int *molecule = atom->molecule;
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int *type = atom->type;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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int i,imol;
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double massone;
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for (i = 0; i < nmolecules; i++) massproc[i] = 0.0;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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massproc[imol] += massone;
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}
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MPI_Allreduce(massproc,masstotal,nmolecules,MPI_DOUBLE,MPI_SUM,world);
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}
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/* ---------------------------------------------------------------------- */
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ComputeGyrationMolecule::~ComputeGyrationMolecule()
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{
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memory->destroy(massproc);
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memory->destroy(masstotal);
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memory->destroy(com);
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memory->destroy(comall);
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memory->destroy(rg);
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memory->destroy(rgt);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeGyrationMolecule::init()
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{
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int ntmp = molecules_in_group(idlo,idhi);
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if (ntmp != nmolecules)
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error->all(FLERR,"Molecule count changed in compute gyration/molecule");
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}
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/* ---------------------------------------------------------------------- */
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void ComputeGyrationMolecule::compute_vector()
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{
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int i,imol;
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double dx,dy,dz,massone;
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double unwrap[3];
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invoked_array = update->ntimestep;
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molcom();
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for (i = 0; i < nmolecules; i++) rg[i] = 0.0;
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double **x = atom->x;
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int *mask = atom->mask;
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int *molecule = atom->molecule;
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int *type = atom->type;
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tagint *image = atom->image;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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domain->unmap(x[i],image[i],unwrap);
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dx = unwrap[0] - comall[imol][0];
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dy = unwrap[1] - comall[imol][1];
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dz = unwrap[2] - comall[imol][2];
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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rg[imol] += (dx*dx + dy*dy + dz*dz) * massone;
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}
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MPI_Allreduce(rg,vector,nmolecules,MPI_DOUBLE,MPI_SUM,world);
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for (i = 0; i < nmolecules; i++) vector[i] = sqrt(vector[i]/masstotal[i]);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeGyrationMolecule::compute_array()
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{
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int i,j,imol;
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double dx,dy,dz,massone;
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double unwrap[3];
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invoked_array = update->ntimestep;
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molcom();
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for (i = 0; i < nmolecules; i++)
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for (j = 0; j < 6; j++)
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rgt[i][j] = 0.0;
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double **x = atom->x;
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int *mask = atom->mask;
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int *molecule = atom->molecule;
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int *type = atom->type;
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tagint *image = atom->image;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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domain->unmap(x[i],image[i],unwrap);
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dx = unwrap[0] - comall[imol][0];
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dy = unwrap[1] - comall[imol][1];
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dz = unwrap[2] - comall[imol][2];
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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rgt[imol][0] += dx*dx * massone;
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rgt[imol][1] += dy*dy * massone;
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rgt[imol][2] += dz*dz * massone;
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rgt[imol][3] += dx*dy * massone;
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rgt[imol][4] += dx*dz * massone;
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rgt[imol][5] += dy*dz * massone;
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}
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if (nmolecules)
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MPI_Allreduce(&rgt[0][0],&array[0][0],nmolecules*6,
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MPI_DOUBLE,MPI_SUM,world);
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for (i = 0; i < nmolecules; i++)
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for (j = 0; j < 6; j++)
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array[i][j] /= masstotal[i];
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}
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/* ----------------------------------------------------------------------
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calculate per-molecule COM
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------------------------------------------------------------------------- */
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void ComputeGyrationMolecule::molcom()
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{
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int i,imol;
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double dx,dy,dz,massone;
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double unwrap[3];
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for (i = 0; i < nmolecules; i++)
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com[i][0] = com[i][1] = com[i][2] = 0.0;
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double **x = atom->x;
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int *mask = atom->mask;
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int *molecule = atom->molecule;
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int *type = atom->type;
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tagint *image = atom->image;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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imol = molecule[i];
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if (molmap) imol = molmap[imol-idlo];
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else imol--;
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domain->unmap(x[i],image[i],unwrap);
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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com[imol][0] += unwrap[0] * massone;
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com[imol][1] += unwrap[1] * massone;
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com[imol][2] += unwrap[2] * massone;
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}
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MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
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MPI_DOUBLE,MPI_SUM,world);
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for (i = 0; i < nmolecules; i++) {
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comall[i][0] /= masstotal[i];
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comall[i][1] /= masstotal[i];
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comall[i][2] /= masstotal[i];
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local data
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------------------------------------------------------------------------- */
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double ComputeGyrationMolecule::memory_usage()
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{
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double bytes = 2*nmolecules * sizeof(double);
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if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
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bytes += 2*nmolecules*3 * sizeof(double);
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if (tensor) bytes += 2*6*nmolecules * sizeof(double);
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else bytes += 2*nmolecules * sizeof(double);
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return bytes;
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}
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