389 lines
11 KiB
C++
389 lines
11 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 authors:
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Rodrigo Freitas (UC Berkeley) - rodrigof@berkeley.edu
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Mark Asta (UC Berkeley) - mdasta@berkeley.edu
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Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
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------------------------------------------------------------------------- */
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#include "fix_ti_spring.h"
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#include "atom.h"
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#include "citeme.h"
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#include "domain.h"
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#include "error.h"
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#include "memory.h"
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#include "respa.h"
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#include "update.h"
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#include <cstring>
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using namespace LAMMPS_NS;
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using namespace FixConst;
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static const char cite_fix_ti_spring[] =
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"ti/spring command:\n\n"
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"@article{freitas2016,\n"
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" author={Freitas, Rodrigo and Asta, Mark and de Koning, Maurice},\n"
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" title={Nonequilibrium free-energy calculation of solids using LAMMPS},\n"
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" journal={Computational Materials Science},\n"
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" volume={112},\n"
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" pages={333--341},\n"
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" year={2016},\n"
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" publisher={Elsevier}\n"
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"}\n\n";
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/* ---------------------------------------------------------------------- */
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FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (lmp->citeme) lmp->citeme->add(cite_fix_ti_spring);
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if (narg < 6 || narg > 8)
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error->all(FLERR,"Illegal fix ti/spring command");
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// Flags.
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restart_peratom = 1;
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scalar_flag = 1;
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global_freq = 1;
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vector_flag = 1;
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size_vector = 2;
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global_freq = 1;
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extscalar = 1;
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extvector = 1;
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energy_global_flag = 1;
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// disallow resetting the time step, while this fix is defined
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time_depend = 1;
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// Spring constant.
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k = utils::numeric(FLERR,arg[3],false,lmp);
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if (k <= 0.0) error->all(FLERR,"Illegal fix ti/spring command");
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// Perform initial allocation of atom-based array
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// Register with Atom class
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xoriginal = nullptr;
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grow_arrays(atom->nmax);
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atom->add_callback(Atom::GROW);
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atom->add_callback(Atom::RESTART);
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// xoriginal = initial unwrapped positions of atoms
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double **x = atom->x;
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int *mask = atom->mask;
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imageint *image = atom->image;
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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) domain->unmap(x[i],image[i],xoriginal[i]);
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else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
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}
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// Time variables.
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t0 = update->ntimestep; // timestep of original/starting coordinates
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t_switch = utils::bnumeric(FLERR,arg[4],false,lmp); // Number of steps for switching
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t_equil = utils::bnumeric(FLERR,arg[5],false,lmp); // Number of steps for equilibration
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if ((t_switch <= 0) || (t_equil < 0))
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error->all(FLERR,"Illegal fix ti/spring command");
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// Coupling parameter initialization
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sf = 1;
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if (narg > 6) {
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if (strcmp(arg[6], "function") == 0) sf = utils::inumeric(FLERR,arg[7],false,lmp);
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else error->all(FLERR,"Illegal fix ti/spring switching function");
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if ((sf!=1) && (sf!=2))
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error->all(FLERR,"Illegal fix ti/spring switching function");
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}
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lambda = switch_func(0);
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dlambda = dswitch_func(0);
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espring = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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FixTISpring::~FixTISpring()
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{
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// unregister callbacks to this fix from Atom class
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atom->delete_callback(id,Atom::GROW);
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atom->delete_callback(id,Atom::RESTART);
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// delete locally stored array
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memory->destroy(xoriginal);
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}
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/* ---------------------------------------------------------------------- */
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int FixTISpring::setmask()
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{
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int mask = 0;
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mask |= INITIAL_INTEGRATE;
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mask |= POST_FORCE;
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mask |= POST_FORCE_RESPA;
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mask |= MIN_POST_FORCE;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixTISpring::init()
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{
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if (strstr(update->integrate_style,"respa"))
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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}
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/* ---------------------------------------------------------------------- */
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void FixTISpring::setup(int vflag)
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{
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if (strstr(update->integrate_style,"verlet"))
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post_force(vflag);
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else {
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((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
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post_force_respa(vflag,nlevels_respa-1,0);
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((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixTISpring::min_setup(int vflag)
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{
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post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixTISpring::post_force(int /*vflag*/)
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{
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// do not calculate forces during equilibration
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if ((update->ntimestep - t0) < t_equil) return;
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double **x = atom->x;
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double **f = atom->f;
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int *mask = atom->mask;
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imageint *image = atom->image;
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int nlocal = atom->nlocal;
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double dx, dy, dz;
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double unwrap[3];
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espring = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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domain->unmap(x[i],image[i],unwrap);
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dx = unwrap[0] - xoriginal[i][0];
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dy = unwrap[1] - xoriginal[i][1];
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dz = unwrap[2] - xoriginal[i][2];
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f[i][0] = (1-lambda) * f[i][0] + lambda * (-k*dx);
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f[i][1] = (1-lambda) * f[i][1] + lambda * (-k*dy);
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f[i][2] = (1-lambda) * f[i][2] + lambda * (-k*dz);
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espring += k * (dx*dx + dy*dy + dz*dz);
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}
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espring *= 0.5;
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}
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/* ---------------------------------------------------------------------- */
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void FixTISpring::post_force_respa(int vflag, int ilevel, int /*iloop*/)
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{
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if (ilevel == nlevels_respa-1) post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixTISpring::min_post_force(int vflag)
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{
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post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixTISpring::initial_integrate(int /*vflag*/)
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{
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// Update the coupling parameter value if needed
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if ((update->ntimestep - t0) < t_equil) return;
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const bigint t = update->ntimestep - (t0+t_equil);
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const double r_switch = 1.0/t_switch;
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if ((t >= 0) && (t <= t_switch)) {
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lambda = switch_func(t*r_switch);
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dlambda = dswitch_func(t*r_switch);
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}
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if ((t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch))) {
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lambda = switch_func(1.0 - (t - t_switch - t_equil)*r_switch);
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dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)*r_switch);
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}
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}
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/* ----------------------------------------------------------------------
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energy of stretched springs
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------------------------------------------------------------------------- */
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double FixTISpring::compute_scalar()
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{
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double all;
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MPI_Allreduce(&espring,&all,1,MPI_DOUBLE,MPI_SUM,world);
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return all;
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}
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/* ----------------------------------------------------------------------
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information about coupling parameter
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------------------------------------------------------------------------- */
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double FixTISpring::compute_vector(int n)
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{
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linfo[0] = lambda;
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linfo[1] = dlambda;
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return linfo[n];
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based array
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------------------------------------------------------------------------- */
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double FixTISpring::memory_usage()
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{
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double bytes = atom->nmax*3 * sizeof(double);
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return bytes;
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}
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/* ----------------------------------------------------------------------
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allocate atom-based array
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------------------------------------------------------------------------- */
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void FixTISpring::grow_arrays(int nmax)
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{
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memory->grow(xoriginal,nmax,3,"fix_ti/spring:xoriginal");
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}
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/* ----------------------------------------------------------------------
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copy values within local atom-based array
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------------------------------------------------------------------------- */
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void FixTISpring::copy_arrays(int i, int j, int /*delflag*/)
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{
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xoriginal[j][0] = xoriginal[i][0];
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xoriginal[j][1] = xoriginal[i][1];
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xoriginal[j][2] = xoriginal[i][2];
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}
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/* ----------------------------------------------------------------------
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pack values in local atom-based array for exchange with another proc
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------------------------------------------------------------------------- */
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int FixTISpring::pack_exchange(int i, double *buf)
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{
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buf[0] = xoriginal[i][0];
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buf[1] = xoriginal[i][1];
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buf[2] = xoriginal[i][2];
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return 3;
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}
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/* ----------------------------------------------------------------------
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unpack values in local atom-based array from exchange with another proc
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------------------------------------------------------------------------- */
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int FixTISpring::unpack_exchange(int nlocal, double *buf)
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{
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xoriginal[nlocal][0] = buf[0];
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xoriginal[nlocal][1] = buf[1];
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xoriginal[nlocal][2] = buf[2];
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return 3;
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}
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/* ----------------------------------------------------------------------
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pack values in local atom-based arrays for restart file
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------------------------------------------------------------------------- */
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int FixTISpring::pack_restart(int i, double *buf)
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{
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// pack buf[0] this way because other fixes unpack it
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buf[0] = 4;
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buf[1] = xoriginal[i][0];
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buf[2] = xoriginal[i][1];
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buf[3] = xoriginal[i][2];
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return 4;
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}
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/* ----------------------------------------------------------------------
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unpack values from atom->extra array to restart the fix
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------------------------------------------------------------------------- */
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void FixTISpring::unpack_restart(int nlocal, int nth)
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{
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double **extra = atom->extra;
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// skip to Nth set of extra values
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// unpack the Nth first values this way because other fixes pack them
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int m = 0;
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for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
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m++;
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xoriginal[nlocal][0] = extra[nlocal][m++];
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xoriginal[nlocal][1] = extra[nlocal][m++];
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xoriginal[nlocal][2] = extra[nlocal][m++];
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}
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/* ----------------------------------------------------------------------
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maxsize of any atom's restart data
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------------------------------------------------------------------------- */
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int FixTISpring::maxsize_restart()
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{
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return 4;
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}
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/* ----------------------------------------------------------------------
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size of atom nlocal's restart data
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------------------------------------------------------------------------- */
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int FixTISpring::size_restart(int /*nlocal*/)
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{
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return 4;
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}
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/* ----------------------------------------------------------------------
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Switching function
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------------------------------------------------------------------------- */
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double FixTISpring::switch_func(double t)
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{
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if (sf == 1) return t;
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double t2 = t*t;
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double t5 = t2*t2*t;
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return ((70.0*t2*t2 - 315.0*t2*t + 540.0*t2 - 420.0*t + 126.0)*t5);
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}
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/* ----------------------------------------------------------------------
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Switching function derivative
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------------------------------------------------------------------------- */
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double FixTISpring::dswitch_func(double t)
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{
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if (sf == 1) return 1.0/t_switch;
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double t2 = t*t;
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double t4 = t2*t2;
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return ((630*t2*t2 - 2520*t2*t + 3780*t2 - 2520*t + 630)*t4) / t_switch;
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}
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