160 lines
4.6 KiB
C++
160 lines
4.6 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://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: Mike Brown (SNL)
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------------------------------------------------------------------------- */
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#include "fix_nh_asphere.h"
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#include "math_extra.h"
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#include "atom.h"
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#include "atom_vec_ellipsoid.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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FixNHAsphere::FixNHAsphere(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 FixNHAsphere::init()
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{
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avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
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if (!avec)
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error->all(FLERR,
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"Compute nvt/nph/npt asphere requires atom style ellipsoid");
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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 *ellipsoid = atom->ellipsoid;
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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 (ellipsoid[i] < 0)
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error->one(FLERR,"Fix nvt/nph/npt asphere requires extended particles");
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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 FixNHAsphere::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 FixNHAsphere::nve_x()
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{
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double omega[3];
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// standard nve_x position update
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FixNH::nve_x();
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AtomVecEllipsoid::Bonus *bonus = avec->bonus;
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int *ellipsoid = atom->ellipsoid;
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double **angmom = atom->angmom;
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double *rmass = atom->rmass;
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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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// returns new normalized quaternion
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// principal moments of inertia
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double *shape,*quat;
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double inertia[3];
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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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shape = bonus[ellipsoid[i]].shape;
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quat = bonus[ellipsoid[i]].quat;
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inertia[0] = rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]) / 5.0;
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inertia[1] = rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]) / 5.0;
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inertia[2] = rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]) / 5.0;
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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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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 FixNHAsphere::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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