forked from lijiext/lammps
154 lines
4.3 KiB
C++
154 lines
4.3 KiB
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
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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 FixNHAsphere
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------------------------------------------------------------------------- */
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#include <string.h>
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#include <stdlib.h>
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#include <math.h>
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#include "math_extra.h"
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#include "fix_nh_body.h"
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#include "atom.h"
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#include "atom_vec_body.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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using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixNHBody::FixNHBody(LAMMPS *lmp, int narg, char **arg) :
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FixNH(lmp, narg, arg)
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{
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}
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/* ---------------------------------------------------------------------- */
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void FixNHBody::init()
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{
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avec = (AtomVecBody *) atom->style_match("body");
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if (!avec)
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error->all(FLERR,
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"Compute nvt/nph/npt body requires atom style body");
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// check that all particles are finite-size
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// no point particles allowed, spherical is OK
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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,"Fix nvt/nph/npt body requires bodies");
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FixNH::init();
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}
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/* ----------------------------------------------------------------------
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perform half-step update of angular momentum
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-----------------------------------------------------------------------*/
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void FixNHBody::nve_v()
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{
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// standard nve_v velocity update
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FixNH::nve_v();
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double **angmom = atom->angmom;
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double **torque = atom->torque;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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// update angular momentum by 1/2 step for all particles
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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angmom[i][0] += dtf*torque[i][0];
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angmom[i][1] += dtf*torque[i][1];
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angmom[i][2] += dtf*torque[i][2];
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}
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}
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}
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/* ----------------------------------------------------------------------
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perform full-step update of orientation
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-----------------------------------------------------------------------*/
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void FixNHBody::nve_x()
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{
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double omega[3];
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double *quat,*inertia;
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// standard nve_x position update
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FixNH::nve_x();
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AtomVecBody::Bonus *bonus = avec->bonus;
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int *body = atom->body;
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double **angmom = atom->angmom;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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// set timestep here since dt may have changed or come via rRESPA
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dtq = 0.5 * dtv;
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// update quaternion a full step via Richardson iteration
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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// compute omega at 1/2 step from angmom at 1/2 step and current q
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// update quaternion a full step via Richardson iteration
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// returns new normalized quaternion
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inertia = bonus[body[i]].inertia;
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quat = bonus[body[i]].quat;
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MathExtra::mq_to_omega(angmom[i],quat,inertia,omega);
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MathExtra::richardson(quat,angmom[i],omega,inertia,dtq);
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}
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}
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/* ----------------------------------------------------------------------
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perform half-step temperature scaling of angular momentum
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-----------------------------------------------------------------------*/
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void FixNHBody::nh_v_temp()
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{
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// standard nh_v_temp scaling
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FixNH::nh_v_temp();
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double **angmom = atom->angmom;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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angmom[i][0] *= factor_eta;
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angmom[i][1] *= factor_eta;
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angmom[i][2] *= factor_eta;
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}
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}
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}
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