forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14598 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
parent
e98647efb2
commit
3db8850f09
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/* ----------------------------------------------------------------------
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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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/* ----------------------------------------------------------------------
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Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
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based on ComputeTempAsphere
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------------------------------------------------------------------------- */
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#include <mpi.h>
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#include <string.h>
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#include "compute_temp_body.h"
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#include "math_extra.h"
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#include "atom.h"
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#include "atom_vec_body.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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#include "modify.h"
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#include "group.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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enum{ROTATE,ALL};
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/* ---------------------------------------------------------------------- */
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ComputeTempBody::ComputeTempBody(LAMMPS *lmp, 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 temp/body command");
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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 = 1;
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tempflag = 1;
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tempbias = 0;
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id_bias = NULL;
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mode = ALL;
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"bias") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute temp/body command");
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tempbias = 1;
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int n = strlen(arg[iarg+1]) + 1;
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id_bias = new char[n];
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strcpy(id_bias,arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"dof") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute temp/body command");
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if (strcmp(arg[iarg+1],"rotate") == 0) mode = ROTATE;
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else if (strcmp(arg[iarg+1],"all") == 0) mode = ALL;
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else error->all(FLERR,"Illegal compute temp/body command");
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iarg += 2;
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} else error->all(FLERR,"Illegal compute temp/body command");
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}
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vector = new double[6];
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}
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/* ---------------------------------------------------------------------- */
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ComputeTempBody::~ComputeTempBody()
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{
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delete [] id_bias;
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delete [] vector;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempBody::init()
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{
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// error check
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avec = (AtomVecBody *) atom->style_match("body");
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if (!avec)
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error->all(FLERR,"Compute temp/body requires atom style body");
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// check that all particles are finite-size, no point particles allowed
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int *body = atom->body;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (body[i] < 0)
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error->one(FLERR,"Compute temp/body requires bodies");
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if (tempbias) {
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int i = modify->find_compute(id_bias);
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if (i < 0)
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error->all(FLERR,"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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error->all(FLERR,"Bias compute does not calculate temperature");
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if (tbias->tempbias == 0)
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error->all(FLERR,"Bias compute does not calculate a velocity bias");
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if (tbias->igroup != igroup)
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error->all(FLERR,"Bias compute group does not match compute group");
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if (strcmp(tbias->style,"temp/region") == 0) tempbias = 2;
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else tempbias = 1;
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// init and setup bias compute because
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// this compute's setup()->dof_compute() may be called first
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tbias->init();
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tbias->setup();
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempBody::setup()
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{
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dynamic = 0;
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if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
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dof_compute();
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempBody::dof_compute()
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{
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adjust_dof_fix();
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// 6 dof for 3d, 3 dof for 2d
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// which dof are included also depends on mode
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// assume full rotation of extended particles
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// user should correct this via compute_modify if needed
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natoms_temp = group->count(igroup);
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int nper;
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if (domain->dimension == 3) {
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if (mode == ALL) nper = 6;
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else nper = 3;
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} else {
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if (mode == ALL) nper = 3;
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else nper = 1;
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}
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dof = nper*natoms_temp;
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// additional adjustments to dof
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if (tempbias == 1) {
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if (mode == ALL) dof -= tbias->dof_remove(-1) * natoms_temp;
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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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tbias->dof_remove_pre();
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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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}
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dof -= extra_dof + fix_dof;
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if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
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else tfactor = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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double ComputeTempBody::compute_scalar()
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{
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invoked_scalar = update->ntimestep;
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if (tempbias) {
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if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar();
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tbias->remove_bias_all();
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}
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AtomVecBody::Bonus *bonus = avec->bonus;
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double **v = atom->v;
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double **angmom = atom->angmom;
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double *rmass = atom->rmass;
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int *body = atom->body;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double *inertia,*quat;
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double wbody[3];
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double rot[3][3];
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// sum translational and rotational energy for each particle
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double t = 0.0;
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if (mode == ALL) {
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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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// principal moments of inertia
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inertia = bonus[body[i]].inertia;
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quat = bonus[body[i]].quat;
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// wbody = angular velocity in body frame
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MathExtra::quat_to_mat(quat,rot);
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MathExtra::transpose_matvec(rot,angmom[i],wbody);
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if (inertia[0] == 0.0) wbody[0] = 0.0;
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else wbody[0] /= inertia[0];
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if (inertia[1] == 0.0) wbody[1] = 0.0;
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else wbody[1] /= inertia[1];
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if (inertia[2] == 0.0) wbody[2] = 0.0;
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else wbody[2] /= inertia[2];
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t += inertia[0]*wbody[0]*wbody[0] +
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inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
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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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// principal moments of inertia
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inertia = bonus[body[i]].inertia;
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quat = bonus[body[i]].quat;
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// wbody = angular velocity in body frame
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MathExtra::quat_to_mat(quat,rot);
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MathExtra::transpose_matvec(rot,angmom[i],wbody);
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if (inertia[0] == 0.0) wbody[0] = 0.0;
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else wbody[0] /= inertia[0];
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if (inertia[1] == 0.0) wbody[1] = 0.0;
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else wbody[1] /= inertia[1];
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if (inertia[2] == 0.0) wbody[2] = 0.0;
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else wbody[2] /= inertia[2];
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t += inertia[0]*wbody[0]*wbody[0] +
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inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
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}
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}
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if (tempbias) tbias->restore_bias_all();
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MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
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if (dynamic || tempbias == 2) dof_compute();
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if (dof < 0.0 && natoms_temp > 0.0)
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error->all(FLERR,"Temperature compute degrees of freedom < 0");
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scalar *= tfactor;
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return scalar;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempBody::compute_vector()
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{
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int i;
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invoked_vector = update->ntimestep;
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if (tempbias) {
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if (tbias->invoked_vector != update->ntimestep) tbias->compute_vector();
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tbias->remove_bias_all();
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}
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AtomVecBody::Bonus *bonus = avec->bonus;
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double **v = atom->v;
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double **angmom = atom->angmom;
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double *rmass = atom->rmass;
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int *body = atom->body;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double *inertia,*quat;
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double wbody[3],t[6];
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double rot[3][3];
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double massone;
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// sum translational and rotational energy for each particle
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for (i = 0; i < 6; i++) t[i] = 0.0;
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if (mode == ALL) {
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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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// principal moments of inertia
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inertia = bonus[body[i]].inertia;
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quat = bonus[body[i]].quat;
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// wbody = angular velocity in body frame
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MathExtra::quat_to_mat(quat,rot);
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MathExtra::transpose_matvec(rot,angmom[i],wbody);
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if (inertia[0] == 0.0) wbody[0] = 0.0;
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else wbody[0] /= inertia[0];
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if (inertia[1] == 0.0) wbody[1] = 0.0;
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else wbody[1] /= inertia[1];
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if (inertia[2] == 0.0) wbody[2] = 0.0;
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else wbody[2] /= inertia[2];
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// rotational kinetic energy
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t[0] += inertia[0]*wbody[0]*wbody[0];
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t[1] += inertia[1]*wbody[1]*wbody[1];
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t[2] += inertia[2]*wbody[2]*wbody[2];
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t[3] += inertia[0]*wbody[0]*wbody[1];
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t[4] += inertia[1]*wbody[0]*wbody[2];
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t[5] += inertia[2]*wbody[1]*wbody[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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// principal moments of inertia
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inertia = bonus[body[i]].inertia;
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quat = bonus[body[i]].quat;
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massone = rmass[i];
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// wbody = angular velocity in body frame
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MathExtra::quat_to_mat(quat,rot);
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MathExtra::transpose_matvec(rot,angmom[i],wbody);
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if (inertia[0] == 0.0) wbody[0] = 0.0;
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else wbody[0] /= inertia[0];
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if (inertia[1] == 0.0) wbody[1] = 0.0;
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else wbody[1] /= inertia[1];
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if (inertia[2] == 0.0) wbody[2] = 0.0;
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else wbody[2] /= inertia[2];
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// rotational kinetic energy
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t[0] += inertia[0]*wbody[0]*wbody[0];
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t[1] += inertia[1]*wbody[1]*wbody[1];
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t[2] += inertia[2]*wbody[2]*wbody[2];
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t[3] += inertia[0]*wbody[0]*wbody[1];
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t[4] += inertia[1]*wbody[0]*wbody[2];
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t[5] += inertia[2]*wbody[1]*wbody[2];
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}
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}
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if (tempbias) tbias->restore_bias_all();
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MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
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for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
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}
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/* ----------------------------------------------------------------------
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remove velocity bias from atom I to leave thermal velocity
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------------------------------------------------------------------------- */
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void ComputeTempBody::remove_bias(int i, double *v)
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{
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if (tbias) tbias->remove_bias(i,v);
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}
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/* ----------------------------------------------------------------------
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add back in velocity bias to atom I removed by remove_bias()
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assume remove_bias() was previously called
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------------------------------------------------------------------------- */
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void ComputeTempBody::restore_bias(int i, double *v)
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{
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if (tbias) tbias->restore_bias(i,v);
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}
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@ -0,0 +1,96 @@
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/* -*- 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
|
||||
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.
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------------------------------------------------------------------------- */
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#ifdef COMPUTE_CLASS
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ComputeStyle(temp/body,ComputeTempBody)
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#else
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#ifndef LMP_COMPUTE_TEMP_BODY_H
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#define LMP_COMPUTE_TEMP_BODY_H
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#include "compute.h"
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namespace LAMMPS_NS {
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class ComputeTempBody : public Compute {
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public:
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ComputeTempBody(class LAMMPS *, int, char **);
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~ComputeTempBody();
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void init();
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void setup();
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double compute_scalar();
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void compute_vector();
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void remove_bias(int, double *);
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void restore_bias(int, double *);
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private:
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int mode;
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double tfactor;
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char *id_bias;
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class Compute *tbias; // ptr to additional bias compute
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class AtomVecBody *avec;
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void dof_compute();
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Compute temp/body requires atom style body
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Self-explanatory.
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E: Compute temp/body requires bodies
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This compute can only be applied to body particles.
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E: Could not find compute ID for temperature bias
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||||
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Self-explanatory.
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E: Bias compute does not calculate temperature
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The specified compute must compute temperature.
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E: Bias compute does not calculate a velocity bias
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The specified compute must compute a bias for temperature.
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E: Bias compute group does not match compute group
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The specified compute must operate on the same group as the parent
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compute.
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E: Temperature compute degrees of freedom < 0
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This should not happen if you are calculating the temperature
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on a valid set of atoms.
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U: Compute temp/asphere requires atom style ellipsoid
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Self-explanatory.
|
||||
|
||||
*/
|
|
@ -0,0 +1,154 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
|
||||
based on FixNHAsphere
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <string.h>
|
||||
#include <stdlib.h>
|
||||
#include <math.h>
|
||||
#include "math_extra.h"
|
||||
#include "fix_nh_body.h"
|
||||
#include "atom.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "group.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixNHBody::FixNHBody(LAMMPS *lmp, int narg, char **arg) :
|
||||
FixNH(lmp, narg, arg)
|
||||
{
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNHBody::init()
|
||||
{
|
||||
avec = (AtomVecBody *) atom->style_match("body");
|
||||
if (!avec)
|
||||
error->all(FLERR,
|
||||
"Compute nvt/nph/npt body requires atom style body");
|
||||
|
||||
// check that all particles are finite-size
|
||||
// no point particles allowed, spherical is OK
|
||||
|
||||
int *body = atom->body;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
if (body[i] < 0)
|
||||
error->one(FLERR,"Fix nvt/nph/npt body requires bodies");
|
||||
|
||||
FixNH::init();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
perform half-step update of angular momentum
|
||||
-----------------------------------------------------------------------*/
|
||||
|
||||
void FixNHBody::nve_v()
|
||||
{
|
||||
// standard nve_v velocity update
|
||||
|
||||
FixNH::nve_v();
|
||||
|
||||
double **angmom = atom->angmom;
|
||||
double **torque = atom->torque;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
// update angular momentum by 1/2 step for all particles
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
angmom[i][0] += dtf*torque[i][0];
|
||||
angmom[i][1] += dtf*torque[i][1];
|
||||
angmom[i][2] += dtf*torque[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
perform full-step update of orientation
|
||||
-----------------------------------------------------------------------*/
|
||||
|
||||
void FixNHBody::nve_x()
|
||||
{
|
||||
double omega[3];
|
||||
double *quat,*inertia;
|
||||
|
||||
// standard nve_x position update
|
||||
|
||||
FixNH::nve_x();
|
||||
|
||||
AtomVecBody::Bonus *bonus = avec->bonus;
|
||||
int *body = atom->body;
|
||||
double **angmom = atom->angmom;
|
||||
double *rmass = atom->rmass;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
// set timestep here since dt may have changed or come via rRESPA
|
||||
|
||||
dtq = 0.5 * dtv;
|
||||
|
||||
// update quaternion a full step via Richardson iteration
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
|
||||
// compute omega at 1/2 step from angmom at 1/2 step and current q
|
||||
// update quaternion a full step via Richardson iteration
|
||||
// returns new normalized quaternion
|
||||
|
||||
inertia = bonus[body[i]].inertia;
|
||||
quat = bonus[body[i]].quat;
|
||||
MathExtra::mq_to_omega(angmom[i],quat,inertia,omega);
|
||||
MathExtra::richardson(quat,angmom[i],omega,inertia,dtq);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
perform half-step temperature scaling of angular momentum
|
||||
-----------------------------------------------------------------------*/
|
||||
|
||||
void FixNHBody::nh_v_temp()
|
||||
{
|
||||
// standard nh_v_temp scaling
|
||||
|
||||
FixNH::nh_v_temp();
|
||||
|
||||
double **angmom = atom->angmom;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
angmom[i][0] *= factor_eta;
|
||||
angmom[i][1] *= factor_eta;
|
||||
angmom[i][2] *= factor_eta;
|
||||
}
|
||||
}
|
||||
}
|
|
@ -0,0 +1,50 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_FIX_NH_BODY_H
|
||||
#define LMP_FIX_NH_BODY_H
|
||||
|
||||
#include "fix_nh.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixNHBody : public FixNH {
|
||||
public:
|
||||
FixNHBody(class LAMMPS *, int, char **);
|
||||
virtual ~FixNHBody() {}
|
||||
void init();
|
||||
|
||||
protected:
|
||||
double dtq;
|
||||
class AtomVecBody *avec;
|
||||
|
||||
void nve_v();
|
||||
void nve_x();
|
||||
void nh_v_temp();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Compute nvt/nph/npt body requires atom style body
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix nvt/nph/npt body requires bodies
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
|
@ -0,0 +1,72 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <string.h>
|
||||
#include "fix_nph_body.h"
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixNPHBody::FixNPHBody(LAMMPS *lmp, int narg, char **arg) :
|
||||
FixNHBody(lmp, narg, arg)
|
||||
{
|
||||
if (tstat_flag)
|
||||
error->all(FLERR,"Temperature control can not be used with fix nph/body");
|
||||
if (!pstat_flag)
|
||||
error->all(FLERR,"Pressure control must be used with fix nph/body");
|
||||
|
||||
// create a new compute temp style
|
||||
// id = fix-ID + temp
|
||||
// compute group = all since pressure is always global (group all)
|
||||
// and thus its KE/temperature contribution should use group all
|
||||
|
||||
int n = strlen(id) + 6;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,id);
|
||||
strcat(id_temp,"_temp");
|
||||
|
||||
char **newarg = new char*[3];
|
||||
newarg[0] = id_temp;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "temp/body";
|
||||
|
||||
modify->add_compute(3,newarg);
|
||||
delete [] newarg;
|
||||
tflag = 1;
|
||||
|
||||
// create a new compute pressure style
|
||||
// id = fix-ID + press, compute group = all
|
||||
// pass id_temp as 4th arg to pressure constructor
|
||||
|
||||
n = strlen(id) + 7;
|
||||
id_press = new char[n];
|
||||
strcpy(id_press,id);
|
||||
strcat(id_press,"_press");
|
||||
|
||||
newarg = new char*[4];
|
||||
newarg[0] = id_press;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "pressure";
|
||||
newarg[3] = id_temp;
|
||||
modify->add_compute(4,newarg);
|
||||
delete [] newarg;
|
||||
pflag = 1;
|
||||
}
|
|
@ -0,0 +1,48 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nph/body,FixNPHBody)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NPH_BODY_H
|
||||
#define LMP_FIX_NPH_BODY_H
|
||||
|
||||
#include "fix_nh_body.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixNPHBody : public FixNHBody {
|
||||
public:
|
||||
FixNPHBody(class LAMMPS *, int, char **);
|
||||
~FixNPHBody() {}
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Temperature control can not be used with fix nph/body
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Pressure control must be used with fix nph/body
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
|
@ -0,0 +1,72 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <string.h>
|
||||
#include "fix_npt_body.h"
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixNPTBody::FixNPTBody(LAMMPS *lmp, int narg, char **arg) :
|
||||
FixNHBody(lmp, narg, arg)
|
||||
{
|
||||
if (!tstat_flag)
|
||||
error->all(FLERR,"Temperature control must be used with fix npt/body");
|
||||
if (!pstat_flag)
|
||||
error->all(FLERR,"Pressure control must be used with fix npt/body");
|
||||
|
||||
// create a new compute temp style
|
||||
// id = fix-ID + temp
|
||||
// compute group = all since pressure is always global (group all)
|
||||
// and thus its KE/temperature contribution should use group all
|
||||
|
||||
int n = strlen(id) + 6;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,id);
|
||||
strcat(id_temp,"_temp");
|
||||
|
||||
char **newarg = new char*[3];
|
||||
newarg[0] = id_temp;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "temp/body";
|
||||
|
||||
modify->add_compute(3,newarg);
|
||||
delete [] newarg;
|
||||
tflag = 1;
|
||||
|
||||
// create a new compute pressure style
|
||||
// id = fix-ID + press, compute group = all
|
||||
// pass id_temp as 4th arg to pressure constructor
|
||||
|
||||
n = strlen(id) + 7;
|
||||
id_press = new char[n];
|
||||
strcpy(id_press,id);
|
||||
strcat(id_press,"_press");
|
||||
|
||||
newarg = new char*[4];
|
||||
newarg[0] = id_press;
|
||||
newarg[1] = (char *) "all";
|
||||
newarg[2] = (char *) "pressure";
|
||||
newarg[3] = id_temp;
|
||||
modify->add_compute(4,newarg);
|
||||
delete [] newarg;
|
||||
pflag = 1;
|
||||
}
|
|
@ -0,0 +1,48 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(npt/body,FixNPTBody)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NPT_BODY_H
|
||||
#define LMP_FIX_NPT_BODY_H
|
||||
|
||||
#include "fix_nh_body.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixNPTBody : public FixNHBody {
|
||||
public:
|
||||
FixNPTBody(class LAMMPS *, int, char **);
|
||||
~FixNPTBody() {}
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Temperature control must be used with fix npt/body
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Pressure control must be used with fix npt/body
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
|
@ -0,0 +1,53 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <string.h>
|
||||
#include "fix_nvt_body.h"
|
||||
#include "group.h"
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixNVTBody::FixNVTBody(LAMMPS *lmp, int narg, char **arg) :
|
||||
FixNHBody(lmp, narg, arg)
|
||||
{
|
||||
if (!tstat_flag)
|
||||
error->all(FLERR,"Temperature control must be used with fix nvt/body");
|
||||
if (pstat_flag)
|
||||
error->all(FLERR,"Pressure control can not be used with fix nvt/body");
|
||||
|
||||
// create a new compute temp style
|
||||
// id = fix-ID + temp
|
||||
|
||||
int n = strlen(id) + 6;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,id);
|
||||
strcat(id_temp,"_temp");
|
||||
|
||||
char **newarg = new char*[3];
|
||||
newarg[0] = id_temp;
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char *) "temp/body";
|
||||
|
||||
modify->add_compute(3,newarg);
|
||||
delete [] newarg;
|
||||
tflag = 1;
|
||||
}
|
|
@ -0,0 +1,48 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nvt/body,FixNVTBody)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVT_BODY_H
|
||||
#define LMP_FIX_NVT_BODY_H
|
||||
|
||||
#include "fix_nh_body.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixNVTBody : public FixNHBody {
|
||||
public:
|
||||
FixNVTBody(class LAMMPS *, int, char **);
|
||||
~FixNVTBody() {}
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Temperature control must be used with fix nvt/body
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Pressure control can not be used with fix nvt/body
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
Loading…
Reference in New Issue