git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2902 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -15,6 +15,7 @@
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#include "string.h"
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#include "compute_temp_sphere.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "update.h"
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#include "force.h"
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#include "domain.h"
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@ -35,9 +36,6 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
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if (narg != 3 && narg != 4)
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error->all("Illegal compute temp/sphere command");
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if (!atom->omega_flag)
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error->all("Compute temp/sphere requires atom attribute omega");
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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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@ -54,23 +52,51 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
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}
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vector = new double[6];
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inertia = new double[atom->ntypes+1];
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// error checks
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if (!atom->omega_flag)
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error->all("Compute temp/sphere requires atom attribute omega");
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if (!atom->radius_flag && !atom->avec->shape_type)
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error->all("Compute temp/sphere requires atom attribute "
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"radius or shape");
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}
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/* ---------------------------------------------------------------------- */
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ComputeTempSphere::~ComputeTempSphere()
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{
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delete [] id_bias;
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delete [] vector;
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delete [] inertia;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempSphere::init()
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{
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int i,itype;
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// if shape used, check that all particles are spherical
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// point particles are allowed
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if (atom->radius == NULL) {
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double **shape = atom->shape;
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int *type = atom->type;
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int *mask = atom->mask;
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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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itype = type[i];
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if (shape[itype][0] != shape[itype][1] ||
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shape[itype][0] != shape[itype][2])
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error->one("Compute temp/sphere requires "
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"spherical particle shapes");
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}
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}
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if (tempbias) {
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int i = modify->find_compute(id_bias);
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i = modify->find_compute(id_bias);
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if (i < 0) error->all("Could not find compute ID for temperature bias");
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tbias = modify->compute[i];
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if (tbias->tempflag == 0)
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@ -85,44 +111,119 @@ void ComputeTempSphere::init()
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}
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fix_dof = 0;
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for (int i = 0; i < modify->nfix; i++)
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for (i = 0; i < modify->nfix; i++)
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fix_dof += modify->fix[i]->dof(igroup);
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dof_compute();
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if (atom->mass) {
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double *mass = atom->mass;
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double **shape = atom->shape;
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for (int i = 1; i <= atom->ntypes; i++) {
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if (shape[i][0] != shape[i][1] || shape[i][0] != shape[i][2])
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error->all("Compute temp/sphere requires spherical particle shapes");
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inertia[i] = INERTIA * shape[i][0]*shape[i][0] * mass[i];
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempSphere::dof_compute()
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{
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double natoms = group->count(igroup);
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int nper = 6;
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if (domain->dimension == 2) nper = 3;
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dof = nper * natoms;
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int count,count_all;
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if (tempbias) {
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if (tempbias == 1) dof -= tbias->dof_remove(-1) * natoms;
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else {
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int count = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (tbias->dof_remove(i)) count++;
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int count_all;
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MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
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dof -= nper * count_all;
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// 6 or 3 dof for extended/point particles for 3d
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// 3 or 2 dof for extended/point particles for 2d
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// assume full rotation of extended particles
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// user can correct this via compute_modify if needed
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int dimension = domain->dimension;
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double *radius = atom->radius;
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double **shape = atom->shape;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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count = 0;
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if (dimension == 3) {
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if (radius) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (radius[i] == 0.0) count += 3;
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else count += 6;
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}
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}
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} else {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (shape[type[i]][0] == 0.0) count += 3;
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else count += 6;
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}
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}
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}
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} else {
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if (radius) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (radius[i] == 0.0) count += 2;
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else count += 3;
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}
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}
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} else {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (shape[type[i]][0] == 0.0) count += 2;
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else count += 3;
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}
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}
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}
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}
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MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
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dof = count_all;
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// additional adjustments to dof
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if (tempbias == 1) {
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double natoms = group->count(igroup);
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dof -= tbias->dof_remove(-1) * natoms;
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} else if (tempbias == 2) {
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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count = 0;
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if (dimension == 3) {
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if (radius) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (tbias->dof_remove(i)) {
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if (radius[i] == 0.0) count += 3;
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else count += 6;
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}
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}
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (tbias->dof_remove(i)) {
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if (shape[type[i]][0] == 0.0) count += 3;
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else count += 6;
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}
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}
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}
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} else {
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if (radius) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (tbias->dof_remove(i)) {
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if (radius[i] == 0.0) count += 2;
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else count += 3;
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}
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}
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (tbias->dof_remove(i)) {
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if (shape[type[i]][0] == 0.0) count += 2;
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else count += 3;
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}
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}
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}
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}
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MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
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dof -= count_all;
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}
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dof -= extra_dof + fix_dof;
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@ -134,6 +235,8 @@ void ComputeTempSphere::dof_compute()
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double ComputeTempSphere::compute_scalar()
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{
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int i,itype;
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invoked_scalar = update->ntimestep;
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if (tempbias) {
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@ -143,30 +246,65 @@ double ComputeTempSphere::compute_scalar()
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double **v = atom->v;
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double **omega = atom->omega;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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double *radius = atom->radius;
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double *rmass = atom->rmass;
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double *mass = atom->mass;
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double **shape = atom->shape;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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// 4 cases depending on radius vs shape and rmass vs mass
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// point particles will not contribute rotation due to radius or shape = 0
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double t = 0.0;
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if (rmass) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
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t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
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omega[i][2]*omega[i][2]) * INERTIA*radius[i]*radius[i]*rmass[i];
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}
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if (radius) {
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if (rmass) {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
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rmass[i];
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t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
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omega[i][2]*omega[i][2]) *
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INERTIA*radius[i]*radius[i]*rmass[i];
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}
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} else {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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itype = type[i];
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t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
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mass[itype];
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t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
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omega[i][2]*omega[i][2]) *
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INERTIA*radius[i]*radius[i]*mass[itype];
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}
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}
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
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mass[type[i]];
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t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
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omega[i][2]*omega[i][2]) * inertia[type[i]];
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}
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if (rmass) {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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itype = type[i];
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t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
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rmass[i];
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t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
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omega[i][2]*omega[i][2]) *
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INERTIA*shape[itype][0]*shape[itype][0]*rmass[i];
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}
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} else {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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itype = type[i];
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t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
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mass[itype];
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t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
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omega[i][2]*omega[i][2]) *
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INERTIA*shape[itype][0]*shape[itype][0]*mass[itype];
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}
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}
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}
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if (tempbias) tbias->restore_bias_all();
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@ -181,7 +319,7 @@ double ComputeTempSphere::compute_scalar()
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void ComputeTempSphere::compute_vector()
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{
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int i;
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int i,itype;
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invoked_vector = update->ntimestep;
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@ -195,51 +333,103 @@ void ComputeTempSphere::compute_vector()
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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double *radius = atom->radius;
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double **shape = atom->shape;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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// 4 cases depending on radius vs shape and rmass vs mass
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// point particles will not contribute rotation due to radius or shape = 0
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double massone,inertiaone,t[6];
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for (i = 0; i < 6; i++) t[i] = 0.0;
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if (rmass) {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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massone = rmass[i];
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t[0] += massone * v[i][0]*v[i][0];
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t[1] += massone * v[i][1]*v[i][1];
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t[2] += massone * v[i][2]*v[i][2];
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t[3] += massone * v[i][0]*v[i][1];
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t[4] += massone * v[i][0]*v[i][2];
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t[5] += massone * v[i][1]*v[i][2];
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if (radius) {
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if (rmass) {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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massone = rmass[i];
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t[0] += massone * v[i][0]*v[i][0];
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t[1] += massone * v[i][1]*v[i][1];
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t[2] += massone * v[i][2]*v[i][2];
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t[3] += massone * v[i][0]*v[i][1];
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t[4] += massone * v[i][0]*v[i][2];
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t[5] += massone * v[i][1]*v[i][2];
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inertiaone = INERTIA*radius[i]*radius[i]*rmass[i];
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t[0] += inertiaone * omega[i][0]*omega[i][0];
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t[1] += inertiaone * omega[i][1]*omega[i][1];
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t[2] += inertiaone * omega[i][2]*omega[i][2];
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t[3] += inertiaone * omega[i][0]*omega[i][1];
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t[4] += inertiaone * omega[i][0]*omega[i][2];
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t[5] += inertiaone * omega[i][1]*omega[i][2];
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}
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} else {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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itype = type[i];
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massone = mass[itype];
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t[0] += massone * v[i][0]*v[i][0];
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t[1] += massone * v[i][1]*v[i][1];
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t[2] += massone * v[i][2]*v[i][2];
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t[3] += massone * v[i][0]*v[i][1];
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t[4] += massone * v[i][0]*v[i][2];
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t[5] += massone * v[i][1]*v[i][2];
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inertiaone = INERTIA*radius[i]*radius[i]*mass[itype];
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t[0] += inertiaone * omega[i][0]*omega[i][0];
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t[1] += inertiaone * omega[i][1]*omega[i][1];
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t[2] += inertiaone * omega[i][2]*omega[i][2];
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t[3] += inertiaone * omega[i][0]*omega[i][1];
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t[4] += inertiaone * omega[i][0]*omega[i][2];
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t[5] += inertiaone * omega[i][1]*omega[i][2];
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}
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}
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inertiaone = INERTIA*radius[i]*radius[i]*rmass[i];
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t[0] += inertiaone * omega[i][0]*omega[i][0];
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t[1] += inertiaone * omega[i][1]*omega[i][1];
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t[2] += inertiaone * omega[i][2]*omega[i][2];
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t[3] += inertiaone * omega[i][0]*omega[i][1];
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t[4] += inertiaone * omega[i][0]*omega[i][2];
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t[5] += inertiaone * omega[i][1]*omega[i][2];
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}
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} else {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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massone = mass[type[i]];
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t[0] += massone * v[i][0]*v[i][0];
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t[1] += massone * v[i][1]*v[i][1];
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t[2] += massone * v[i][2]*v[i][2];
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t[3] += massone * v[i][0]*v[i][1];
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t[4] += massone * v[i][0]*v[i][2];
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t[5] += massone * v[i][1]*v[i][2];
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if (rmass) {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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itype = type[i];
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massone = rmass[i];
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t[0] += massone * v[i][0]*v[i][0];
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t[1] += massone * v[i][1]*v[i][1];
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t[2] += massone * v[i][2]*v[i][2];
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t[3] += massone * v[i][0]*v[i][1];
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t[4] += massone * v[i][0]*v[i][2];
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t[5] += massone * v[i][1]*v[i][2];
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inertiaone = INERTIA*shape[itype][0]*shape[itype][0]*rmass[i];
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t[0] += inertiaone * omega[i][0]*omega[i][0];
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t[1] += inertiaone * omega[i][1]*omega[i][1];
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t[2] += inertiaone * omega[i][2]*omega[i][2];
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t[3] += inertiaone * omega[i][0]*omega[i][1];
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t[4] += inertiaone * omega[i][0]*omega[i][2];
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t[5] += inertiaone * omega[i][1]*omega[i][2];
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}
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inertiaone = inertia[type[i]];
|
||||
t[0] += inertiaone * omega[i][0]*omega[i][0];
|
||||
t[1] += inertiaone * omega[i][1]*omega[i][1];
|
||||
t[2] += inertiaone * omega[i][2]*omega[i][2];
|
||||
t[3] += inertiaone * omega[i][0]*omega[i][1];
|
||||
t[4] += inertiaone * omega[i][0]*omega[i][2];
|
||||
t[5] += inertiaone * omega[i][1]*omega[i][2];
|
||||
}
|
||||
} else {
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
itype = type[i];
|
||||
massone = mass[itype];
|
||||
t[0] += massone * v[i][0]*v[i][0];
|
||||
t[1] += massone * v[i][1]*v[i][1];
|
||||
t[2] += massone * v[i][2]*v[i][2];
|
||||
t[3] += massone * v[i][0]*v[i][1];
|
||||
t[4] += massone * v[i][0]*v[i][2];
|
||||
t[5] += massone * v[i][1]*v[i][2];
|
||||
|
||||
inertiaone = INERTIA*shape[itype][0]*shape[itype][0]*mass[itype];
|
||||
t[0] += inertiaone * omega[i][0]*omega[i][0];
|
||||
t[1] += inertiaone * omega[i][1]*omega[i][1];
|
||||
t[2] += inertiaone * omega[i][2]*omega[i][2];
|
||||
t[3] += inertiaone * omega[i][0]*omega[i][1];
|
||||
t[4] += inertiaone * omega[i][0]*omega[i][2];
|
||||
t[5] += inertiaone * omega[i][1]*omega[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (tempbias) tbias->restore_bias_all();
|
||||
|
||||
Reference in New Issue
Block a user