Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F91189293
compute_gyration_molecule.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Fri, Nov 8, 19:31
Size
5 KB
Mime Type
text/x-c
Expires
Sun, Nov 10, 19:31 (2 d)
Engine
blob
Format
Raw Data
Handle
22149269
Attached To
rLAMMPS lammps
compute_gyration_molecule.cpp
View Options
/* ----------------------------------------------------------------------
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 "math.h"
#include "compute_gyration_molecule.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeGyrationMolecule::ComputeGyrationMolecule(LAMMPS *lmp,
int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal compute gyration/molecule command");
if (atom->molecular == 0)
error->all("Compute gyration/molecule requires molecular atom style");
vector_flag = 1;
extvector = 0;
// setup molecule-based data
nmolecules = molecules_in_group(idlo,idhi);
size_vector = nmolecules;
massproc = (double *) memory->smalloc(nmolecules*sizeof(double),
"gyration/molecule:massproc");
masstotal = (double *) memory->smalloc(nmolecules*sizeof(double),
"gyration/molecule:masstotal");
com = memory->create_2d_double_array(nmolecules,3,"gyration/molecule:com");
comall = memory->create_2d_double_array(nmolecules,3,
"gyration/molecule:comall");
rg = (double *) memory->smalloc(nmolecules*sizeof(double),
"gyration/molecule:rg");
rgall = (double *) memory->smalloc(nmolecules*sizeof(double),
"gyration/molecule:rgall");
vector = rgall;
// 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);
}
/* ---------------------------------------------------------------------- */
ComputeGyrationMolecule::~ComputeGyrationMolecule()
{
memory->sfree(massproc);
memory->sfree(masstotal);
memory->destroy_2d_double_array(com);
memory->destroy_2d_double_array(comall);
memory->sfree(rg);
memory->sfree(rgall);
}
/* ---------------------------------------------------------------------- */
void ComputeGyrationMolecule::init()
{
int ntmp = molecules_in_group(idlo,idhi);
if (ntmp != nmolecules)
error->all("Molecule count changed in compute gyration/molecule");
}
/* ---------------------------------------------------------------------- */
void ComputeGyrationMolecule::compute_vector()
{
int i,imol;
double xbox,ybox,zbox,dx,dy,dz;
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] + xbox*xprd) * massone;
com[imol][1] += (x[i][1] + ybox*yprd) * massone;
com[imol][2] += (x[i][2] + zbox*zprd) * 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];
}
for (i = 0; i < nmolecules; i++) rg[i] = 0.0;
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;
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
else imol--;
dx = (x[i][0] + xbox*xprd) - comall[imol][0];
dy = (x[i][1] + ybox*yprd) - comall[imol][1];
dz = (x[i][2] + zbox*zprd) - comall[imol][2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
rg[imol] += (dx*dx + dy*dy + dz*dz) * massone;
}
MPI_Allreduce(rg,rgall,nmolecules,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < nmolecules; i++) rgall[i] = sqrt(rgall[i]/masstotal[i]);
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeGyrationMolecule::memory_usage()
{
double bytes = 4*nmolecules * sizeof(double);
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
bytes += 2*nmolecules*3 * sizeof(double);
return bytes;
}
Event Timeline
Log In to Comment