forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8271 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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commit
ee74e0f713
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@ -11,9 +11,12 @@
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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 "compute_gyration.h"
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#include "update.h"
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#include "atom.h"
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#include "group.h"
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#include "domain.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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@ -25,8 +28,19 @@ ComputeGyration::ComputeGyration(LAMMPS *lmp, int narg, char **arg) :
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{
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if (narg != 3) error->all(FLERR,"Illegal compute gyration command");
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scalar_flag = 1;
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scalar_flag = vector_flag = 1;
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size_vector = 6;
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extscalar = 0;
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extvector = 0;
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vector = new double[6];
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}
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/* ---------------------------------------------------------------------- */
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ComputeGyration::~ComputeGyration()
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{
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delete [] vector;
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}
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/* ---------------------------------------------------------------------- */
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@ -47,3 +61,57 @@ double ComputeGyration::compute_scalar()
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scalar = group->gyration(igroup,masstotal,xcm);
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return scalar;
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}
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/* ----------------------------------------------------------------------
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compute the radius-of-gyration tensor of group of atoms
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around center-of-mass cm
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must unwrap atoms to compute Rg tensor correctly
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------------------------------------------------------------------------- */
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void ComputeGyration::compute_vector()
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{
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invoked_vector = update->ntimestep;
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double masstotal;
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double xcm[3];
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group->xcm(igroup,masstotal,xcm);
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double **x = atom->x;
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int *mask = atom->mask;
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int *type = atom->type;
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int *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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int xbox,ybox,zbox;
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double dx,dy,dz,massone;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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double rg[6];
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rg[0] = rg[1] = rg[2] = rg[3] = rg[4] = rg[5] = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & 1023) - 512;
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ybox = (image[i] >> 10 & 1023) - 512;
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zbox = (image[i] >> 20) - 512;
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dx = (x[i][0] + xbox*xprd) - xcm[0];
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dy = (x[i][1] + ybox*yprd) - xcm[1];
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dz = (x[i][2] + zbox*zprd) - xcm[2];
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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rg[0] += dx*dx * massone;
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rg[1] += dy*dy * massone;
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rg[2] += dz*dz * massone;
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rg[3] += dx*dy * massone;
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rg[4] += dx*dz * massone;
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rg[5] += dy*dz * massone;
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}
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MPI_Allreduce(rg,vector,6,MPI_DOUBLE,MPI_SUM,world);
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if (masstotal == 0.0) return;
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for (int i = 0; i < 6; i++) vector[i] = sqrt(vector[i]/masstotal);
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}
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@ -27,9 +27,10 @@ namespace LAMMPS_NS {
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class ComputeGyration : public Compute {
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public:
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ComputeGyration(class LAMMPS *, int, char **);
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~ComputeGyration() {}
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~ComputeGyration();
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void init();
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double compute_scalar();
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void compute_vector();
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private:
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double masstotal;
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@ -12,6 +12,7 @@
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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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@ -27,26 +28,47 @@ 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 (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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vector_flag = 1;
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extvector = 0;
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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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size_vector = nmolecules;
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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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memory->create(rg,nmolecules,"gyration/molecule:rg");
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memory->create(rgall,nmolecules,"gyration/molecule:rgall");
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vector = rgall;
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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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@ -84,7 +106,7 @@ ComputeGyrationMolecule::~ComputeGyrationMolecule()
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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(rgall);
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memory->destroy(rgt);
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}
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/* ---------------------------------------------------------------------- */
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@ -106,6 +128,114 @@ void ComputeGyrationMolecule::compute_vector()
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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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int *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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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & 1023) - 512;
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ybox = (image[i] >> 10 & 1023) - 512;
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zbox = (image[i] >> 20) - 512;
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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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dx = (x[i][0] + xbox*xprd) - comall[imol][0];
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dy = (x[i][1] + ybox*yprd) - comall[imol][1];
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dz = (x[i][2] + zbox*zprd) - 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 xbox,ybox,zbox,dx,dy,dz;
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double massone;
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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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int *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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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & 1023) - 512;
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ybox = (image[i] >> 10 & 1023) - 512;
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zbox = (image[i] >> 20) - 512;
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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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dx = (x[i][0] + xbox*xprd) - comall[imol][0];
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dy = (x[i][1] + ybox*yprd) - comall[imol][1];
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dz = (x[i][2] + zbox*zprd) - 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] = sqrt(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 xbox,ybox,zbox,dx,dy,dz;
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double massone;
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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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@ -122,7 +252,7 @@ void ComputeGyrationMolecule::compute_vector()
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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for (int i = 0; i < nlocal; i++)
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & 1023) - 512;
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ybox = (image[i] >> 10 & 1023) - 512;
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@ -144,28 +274,6 @@ void ComputeGyrationMolecule::compute_vector()
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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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for (i = 0; i < nmolecules; i++) rg[i] = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & 1023) - 512;
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ybox = (image[i] >> 10 & 1023) - 512;
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zbox = (image[i] >> 20) - 512;
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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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dx = (x[i][0] + xbox*xprd) - comall[imol][0];
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dy = (x[i][1] + ybox*yprd) - comall[imol][1];
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dz = (x[i][2] + zbox*zprd) - 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,rgall,nmolecules,MPI_DOUBLE,MPI_SUM,world);
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for (i = 0; i < nmolecules; i++) rgall[i] = sqrt(rgall[i]/masstotal[i]);
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}
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/* ----------------------------------------------------------------------
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@ -174,8 +282,10 @@ void ComputeGyrationMolecule::compute_vector()
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double ComputeGyrationMolecule::memory_usage()
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{
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double bytes = 4*nmolecules * sizeof(double);
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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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@ -30,15 +30,20 @@ class ComputeGyrationMolecule : public Compute {
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~ComputeGyrationMolecule();
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void init();
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void compute_vector();
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void compute_array();
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double memory_usage();
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private:
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int tensor;
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int nmolecules;
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int idlo,idhi;
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double *massproc,*masstotal;
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double **com,**comall;
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double *rg,*rgall;
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double *rg;
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double **rgt;
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void molcom();
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};
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}
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