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compute_com_molecule.cpp
62b27e591539efficient_neuronet

compute_com_molecule.cpp
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			/* ----------------------------------------------------------------------
			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.
			------------------------------------------------------------------------- */

			#include "compute_com_molecule.h"
			#include "atom.h"
			#include "update.h"
			#include "domain.h"
			#include "memory.h"
			#include "error.h"

			using namespace LAMMPS_NS;

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

			ComputeCOMMolecule::ComputeCOMMolecule(LAMMPS lmp, int narg, char *arg) :
			Compute(lmp, narg, arg)
			{
			if (narg != 3) error->all(FLERR,"Illegal compute com/molecule command");

			if (atom->molecular == 0)
			error->all(FLERR,"Compute com/molecule requires molecular atom style");

			array_flag = 1;
			size_array_cols = 3;
			extarray = 0;

			// setup molecule-based data

			nmolecules = molecules_in_group(idlo,idhi);
			size_array_rows = nmolecules;

			memory->create(massproc,nmolecules,"com/molecule:massproc");
			memory->create(masstotal,nmolecules,"com/molecule:masstotal");
			memory->create(com,nmolecules,3,"com/molecule:com");
			memory->create(comall,nmolecules,3,"com/molecule:comall");
			array = comall;

			// compute masstotal for each molecule

			int *mask = atom->mask;
			int *molecule = atom->molecule;
			int *type = atom->type;
			double *mass = atom->mass;
			double *rmass = atom->rmass;
			int nlocal = atom->nlocal;

			int i,imol;
			double massone;

			for (i = 0; i < nmolecules; i++) massproc[i] = 0.0;

			for (i = 0; i < nlocal; i++)
			if (mask[i] & groupbit) {
			if (rmass) massone = rmass[i];
			else massone = mass[type[i]];
			imol = molecule[i];
			if (molmap) imol = molmap[imol-idlo];
			else imol--;
			massproc[imol] += massone;
			}

			MPI_Allreduce(massproc,masstotal,nmolecules,MPI_DOUBLE,MPI_SUM,world);
			}

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

			ComputeCOMMolecule::~ComputeCOMMolecule()
			{
			memory->destroy(massproc);
			memory->destroy(masstotal);
			memory->destroy(com);
			memory->destroy(comall);
			}

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

			void ComputeCOMMolecule::init()
			{
			int ntmp = molecules_in_group(idlo,idhi);
			if (ntmp != nmolecules)
			error->all(FLERR,"Molecule count changed in compute com/molecule");
			}

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

			void ComputeCOMMolecule::compute_array()
			{
			int i,imol;
			double xbox,ybox,zbox;
			double massone;

			invoked_array = update->ntimestep;

			for (i = 0; i < nmolecules; i++)
			com[i][0] = com[i][1] = com[i][2] = 0.0;

			double **x = atom->x;
			int *mask = atom->mask;
			int *molecule = atom->molecule;
			int *type = atom->type;
			int *image = atom->image;
			double *mass = atom->mass;
			double *rmass = atom->rmass;
			int nlocal = atom->nlocal;

			double xprd = domain->xprd;
			double yprd = domain->yprd;
			double zprd = domain->zprd;

			for (int i = 0; i < nlocal; i++)
			if (mask[i] & groupbit) {
			xbox = (image[i] & 1023) - 512;
			ybox = (image[i] >> 10 & 1023) - 512;
			zbox = (image[i] >> 20) - 512;
			if (rmass) massone = rmass[i];
			else massone = mass[type[i]];
			imol = molecule[i];
			if (molmap) imol = molmap[imol-idlo];
			else imol--;
			com[imol][0] += (x[i][0] + xboxxprd) massone;
			com[imol][1] += (x[i][1] + yboxyprd) massone;
			com[imol][2] += (x[i][2] + zboxzprd) massone;
			}

			MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
			MPI_DOUBLE,MPI_SUM,world);
			for (i = 0; i < nmolecules; i++) {
			comall[i][0] /= masstotal[i];
			comall[i][1] /= masstotal[i];
			comall[i][2] /= masstotal[i];
			}
			}

			/* ----------------------------------------------------------------------
			memory usage of local data
			------------------------------------------------------------------------- */

			double ComputeCOMMolecule::memory_usage()
			{
			double bytes = 2nmolecules sizeof(double);
			if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
			bytes += 2nmolecules3 * sizeof(double);
			return bytes;
			}

lammps/src/compute_com_molecule.cpp62b27e591539efficient_neuronet

compute_com_molecule.cppView Options

lammps/src/compute_com_molecule.cpp
62b27e591539efficient_neuronet

compute_com_molecule.cpp
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