git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3427 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
@ -11,212 +11,57 @@
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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: Mark Stevens (SNL)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdlib.h"
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#include "string.h"
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#include "fix_wall_lj126.h"
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#include "atom.h"
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#include "domain.h"
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#include "update.h"
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#include "output.h"
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#include "respa.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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FixWallLJ126::FixWallLJ126(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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FixWallLJ126::FixWallLJ126(LAMMPS *lmp, int narg, char **arg) :
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FixWall(lmp, narg, arg) {}
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/* ---------------------------------------------------------------------- */
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void FixWallLJ126::precompute(int m)
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{
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if (narg < 8) error->all("Illegal fix wall/lj126 command");
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coeff1[m] = 48.0 * epsilon[m] * pow(sigma[m],12.0);
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coeff2[m] = 24.0 * epsilon[m] * pow(sigma[m],6.0);
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coeff3[m] = 4.0 * epsilon[m] * pow(sigma[m],12.0);
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coeff4[m] = 4.0 * epsilon[m] * pow(sigma[m],6.0);
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scalar_flag = 1;
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vector_flag = 1;
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size_vector = 3;
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scalar_vector_freq = 1;
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extscalar = 1;
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extvector = 1;
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// set defaults
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if (strcmp(arg[3],"xlo") == 0) {
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dim = 0;
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side = -1;
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} else if (strcmp(arg[3],"xhi") == 0) {
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dim = 0;
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side = 1;
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} else if (strcmp(arg[3],"ylo") == 0) {
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dim = 1;
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side = -1;
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} else if (strcmp(arg[3],"yhi") == 0) {
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dim = 1;
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side = 1;
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} else if (strcmp(arg[3],"zlo") == 0) {
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dim = 2;
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side = -1;
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} else if (strcmp(arg[3],"zhi") == 0) {
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dim = 2;
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side = 1;
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} else error->all("Illegal fix wall/lj126 command");
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coord0 = atof(arg[4]);
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epsilon = atof(arg[5]);
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sigma = atof(arg[6]);
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cutoff = atof(arg[7]);
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// read options
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vel = 0.0;
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int iarg = 8;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"vel") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix wall/lj126 command");
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vel = atof(arg[iarg+1]);
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iarg += 2;
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} else error->all("Illegal fix wall/lj126 command");
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}
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coeff1 = 48.0 * epsilon * pow(sigma,12.0);
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coeff2 = 24.0 * epsilon * pow(sigma,6.0);
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coeff3 = 4.0 * epsilon * pow(sigma,12.0);
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coeff4 = 4.0 * epsilon * pow(sigma,6.0);
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double r2inv = 1.0/(cutoff*cutoff);
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double r2inv = 1.0/(cutoff[m]*cutoff[m]);
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double r6inv = r2inv*r2inv*r2inv;
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offset = r6inv*(coeff3*r6inv - coeff4);
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if (dim == 0 && domain->xperiodic)
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error->all("Cannot use wall in periodic dimension");
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if (dim == 1 && domain->yperiodic)
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error->all("Cannot use wall in periodic dimension");
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if (dim == 2 && domain->zperiodic)
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error->all("Cannot use wall in periodic dimension");
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wall_flag = 0;
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wall[0] = wall[1] = wall[2] = wall[3] = 0.0;
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offset[m] = r6inv*(coeff3[m]*r6inv - coeff4[m]);
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}
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/* ---------------------------------------------------------------------- */
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int FixWallLJ126::setmask()
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void FixWallLJ126::wall_particle(int m, double coord)
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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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double delta,rinv,r2inv,r6inv,fwall;
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/* ---------------------------------------------------------------------- */
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void FixWallLJ126::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 FixWallLJ126::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 FixWallLJ126::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 FixWallLJ126::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 nlocal = atom->nlocal;
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double delta,rinv,r2inv,r6inv,fwall;
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wall[0] = wall[1] = wall[2] = wall[3] = 0.0;
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wall_flag = 0;
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// coord = current position of wall
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// coord0 = initial position of wall
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double delt = (update->ntimestep - update->beginstep) * update->dt;
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double coord = coord0 + delt*vel;
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int dim = m/2;
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int side = m % 2;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (side == -1) delta = x[i][dim] - coord;
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if (side == 0) delta = x[i][dim] - coord;
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else delta = coord - x[i][dim];
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if (delta <= 0.0) continue;
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if (delta > cutoff) continue;
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if (delta > cutoff[m]) continue;
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rinv = 1.0/delta;
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r2inv = rinv*rinv;
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r6inv = r2inv*r2inv*r2inv;
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fwall = side * r6inv*(coeff1*r6inv - coeff2) * rinv;
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fwall = side * r6inv*(coeff1[m]*r6inv - coeff2[m]) * rinv;
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f[i][dim] -= fwall;
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wall[0] += r6inv*(coeff3*r6inv - coeff4) - offset;
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wall[dim+1] += fwall;
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ewall[0] += r6inv*(coeff3[m]*r6inv - coeff4[m]) - offset[m];
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ewall[m+1] += fwall;
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixWallLJ126::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 FixWallLJ126::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 wall interaction
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------------------------------------------------------------------------- */
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double FixWallLJ126::compute_scalar()
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{
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// only sum across procs one time
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if (wall_flag == 0) {
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MPI_Allreduce(wall,wall_all,4,MPI_DOUBLE,MPI_SUM,world);
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wall_flag = 1;
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}
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return wall_all[0];
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}
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/* ----------------------------------------------------------------------
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components of force on wall
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------------------------------------------------------------------------- */
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double FixWallLJ126::compute_vector(int n)
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{
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// only sum across procs one time
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if (wall_flag == 0) {
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MPI_Allreduce(wall,wall_all,4,MPI_DOUBLE,MPI_SUM,world);
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wall_flag = 1;
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}
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return wall_all[n+1];
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}
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