155 lines
4.5 KiB
C++
155 lines
4.5 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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This is a time integrator for position, velocity and concentration (x,
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v and cc) using the modified velocity-Verlet (MVV) algorithm.
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Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm.
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Contributing author: Zhen Li (Brown University)
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Email: zhen_li@brown.edu
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Please cite the related publication:
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Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. "Transport
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dissipative particle dynamics model for mesoscopic advection-diffusion
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-reaction problems". The Journal of Chemical Physics, 2015, 143: 014101.
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------------------------------------------------------------------------- */
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#include "fix_mvv_tdpd.h"
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#include <cstring>
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#include "atom.h"
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#include "force.h"
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#include "update.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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FixMvvTDPD::FixMvvTDPD(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (strcmp(style,"tdpd/verlet") != 0 && narg < 3)
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error->all(FLERR,"Illegal fix mvv/tdpd command");
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verlet = 0.5;
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if(narg > 3) verlet = utils::numeric(FLERR,arg[3],false,lmp);
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cc_species = atom->cc_species;
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dynamic_group_allow = 1;
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time_integrate = 1;
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}
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/* ---------------------------------------------------------------------- */
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int FixMvvTDPD::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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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixMvvTDPD::init()
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{
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dtv = update->dt;
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dtf = 0.5 * update->dt * force->ftm2v;
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}
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/* ----------------------------------------------------------------------
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allow for both per-type and per-atom mass
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------------------------------------------------------------------------- */
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void FixMvvTDPD::initial_integrate(int /*vflag*/)
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{
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double dtfm;
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// update v and x and cc of atoms in group
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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 **cc = atom->cc;
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double **cc_flux = atom->cc_flux;
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double **vest = atom->vest;
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double *rmass = atom->rmass;
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double *mass = atom->mass;
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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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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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if (rmass) dtfm = dtf / rmass[i];
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else dtfm = dtf / mass[type[i]];
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vest[i][0] = v[i][0] + dtfm * f[i][0];
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vest[i][1] = v[i][1] + dtfm * f[i][1];
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vest[i][2] = v[i][2] + dtfm * f[i][2];
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x[i][0] += dtv * vest[i][0];
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x[i][1] += dtv * vest[i][1];
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x[i][2] += dtv * vest[i][2];
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v[i][0] += 2.0 * verlet * dtfm * f[i][0];
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v[i][1] += 2.0 * verlet * dtfm * f[i][1];
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v[i][2] += 2.0 * verlet * dtfm * f[i][2];
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for(int k = 0; k < cc_species; k++)
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cc[i][k] += 0.5 * dtv * cc_flux[i][k];
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixMvvTDPD::final_integrate()
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{
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double dtfm;
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// update v of atoms in group
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double **v = atom->v;
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double **f = atom->f;
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double **cc = atom->cc;
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double **cc_flux = atom->cc_flux;
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double **vest = atom->vest;
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double *rmass = atom->rmass;
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double *mass = atom->mass;
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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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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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if (rmass) dtfm = dtf / rmass[i];
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else dtfm = dtf / mass[type[i]];
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v[i][0] = vest[i][0] + dtfm * f[i][0];
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v[i][1] = vest[i][1] + dtfm * f[i][1];
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v[i][2] = vest[i][2] + dtfm * f[i][2];
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for(int k = 0; k < cc_species; k++)
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cc[i][k] += 0.5 * dtv * cc_flux[i][k];
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixMvvTDPD::reset_dt()
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{
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dtv = update->dt;
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dtf = 0.5 * update->dt * force->ftm2v;
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}
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