158 lines
4.3 KiB
C++
158 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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#include "math.h"
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#include "stdio.h"
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#include "string.h"
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#include "fix_nve_tri.h"
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#include "math_extra.h"
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#include "atom.h"
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#include "atom_vec_tri.h"
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#include "domain.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixNVETri::FixNVETri(LAMMPS *lmp, int narg, char **arg) :
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FixNVE(lmp, narg, arg)
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{
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if (narg != 3) error->all(FLERR,"Illegal fix nve/tri command");
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time_integrate = 1;
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}
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/* ---------------------------------------------------------------------- */
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int FixNVETri::setmask()
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{
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int mask = 0;
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mask |= INITIAL_INTEGRATE;
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mask |= FINAL_INTEGRATE;
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mask |= INITIAL_INTEGRATE_RESPA;
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mask |= FINAL_INTEGRATE_RESPA;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixNVETri::init()
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{
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int i,itype;
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// error checks
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avec = (AtomVecTri *) atom->style_match("tri");
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if (!avec) error->all(FLERR,"Fix nve/tri requires atom style tri");
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if (domain->dimension != 3)
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error->all(FLERR,"Fix nve/tri can only be used for 3d simulations");
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// check that all particles are triangles
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// no point particles allowed
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int *tri = atom->tri;
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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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if (tri[i] < 0) error->one(FLERR,"Fix nve/tri requires tri particles");
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}
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FixNVE::init();
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}
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/* ---------------------------------------------------------------------- */
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void FixNVETri::initial_integrate(int vflag)
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{
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double dtfm;
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double omega[3];
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AtomVecTri::Bonus *bonus = avec->bonus;
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int *tri = atom->tri;
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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double **angmom = atom->angmom;
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double **torque = atom->torque;
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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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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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dtfm = dtf / rmass[i];
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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x[i][0] += dtv * v[i][0];
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x[i][1] += dtv * v[i][1];
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x[i][2] += dtv * v[i][2];
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// update angular momentum by 1/2 step
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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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// 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],bonus[tri[i]].quat,
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bonus[tri[i]].inertia,omega);
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MathExtra::richardson(bonus[tri[i]].quat,angmom[i],omega,
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bonus[tri[i]].inertia,dtq);
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixNVETri::final_integrate()
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{
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double dtfm;
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double **v = atom->v;
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double **f = atom->f;
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double **angmom = atom->angmom;
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double **torque = atom->torque;
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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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// update v,omega for all particles
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// d_omega/dt = torque / inertia
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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dtfm = dtf / rmass[i];
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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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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