forked from lijiext/lammps
296 lines
8.2 KiB
C++
296 lines
8.2 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: Naveen Michaud-Agrawal (Johns Hopkins University)
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------------------------------------------------------------------------- */
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#include "stdlib.h"
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#include "string.h"
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#include "fix_spring_self.h"
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#include "atom.h"
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#include "update.h"
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#include "domain.h"
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#include "respa.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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/* ---------------------------------------------------------------------- */
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FixSpringSelf::FixSpringSelf(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg != 4) error->all("Illegal fix spring/self command");
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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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extscalar = 1;
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k = atof(arg[3]);
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if (k <= 0.0) error->all("Illegal fix spring/self 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 = NULL;
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grow_arrays(atom->nmax);
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atom->add_callback(0);
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atom->add_callback(1);
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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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int *image = atom->image;
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int nlocal = atom->nlocal;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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int xbox,ybox,zbox;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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xbox = (image[i] & 1023) - 512;
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ybox = (image[i] >> 10 & 1023) - 512;
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zbox = (image[i] >> 20) - 512;
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xoriginal[i][0] = x[i][0] + xbox*xprd;
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xoriginal[i][1] = x[i][1] + ybox*yprd;
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xoriginal[i][2] = x[i][2] + zbox*zprd;
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} else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
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}
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espring = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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FixSpringSelf::~FixSpringSelf()
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{
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// unregister callbacks to this fix from Atom class
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atom->delete_callback(id,0);
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atom->delete_callback(id,1);
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// delete locally stored array
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memory->destroy_2d_double_array(xoriginal);
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}
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/* ---------------------------------------------------------------------- */
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int FixSpringSelf::setmask()
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{
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int mask = 0;
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mask |= POST_FORCE;
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mask |= THERMO_ENERGY;
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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 FixSpringSelf::init()
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{
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if (strcmp(update->integrate_style,"respa") == 0)
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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}
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/* ---------------------------------------------------------------------- */
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void FixSpringSelf::setup(int vflag)
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{
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if (strcmp(update->integrate_style,"verlet") == 0)
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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 FixSpringSelf::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 FixSpringSelf::post_force(int vflag)
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{
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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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int *image = atom->image;
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int nlocal = atom->nlocal;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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int xbox,ybox,zbox;
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double dx,dy,dz;
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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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xbox = (image[i] & 1023) - 512;
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ybox = (image[i] >> 10 & 1023) - 512;
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zbox = (image[i] >> 20) - 512;
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dx = x[i][0] + xbox*xprd - xoriginal[i][0];
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dy = x[i][1] + ybox*yprd - xoriginal[i][1];
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dz = x[i][2] + zbox*zprd - xoriginal[i][2];
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f[i][0] -= k*dx;
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f[i][1] -= k*dy;
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f[i][2] -= 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 FixSpringSelf::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 FixSpringSelf::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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energy of stretched springs
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------------------------------------------------------------------------- */
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double FixSpringSelf::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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memory usage of local atom-based array
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------------------------------------------------------------------------- */
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double FixSpringSelf::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 FixSpringSelf::grow_arrays(int nmax)
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{
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xoriginal =
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memory->grow_2d_double_array(xoriginal,nmax,3,"fix_spring/self: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 FixSpringSelf::copy_arrays(int i, int j)
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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 FixSpringSelf::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 FixSpringSelf::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 FixSpringSelf::pack_restart(int i, double *buf)
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{
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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 FixSpringSelf::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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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 FixSpringSelf::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 FixSpringSelf::size_restart(int nlocal)
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{
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return 4;
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}
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