mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3427 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
a66aa5e0f6
commit
5062206d36
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@ -16,14 +16,11 @@
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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_colloid.h"
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#include "atom.h"
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#include "atom_vec.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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@ -32,74 +29,7 @@ using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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FixWallColloid::FixWallColloid(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg != 8) error->all("Illegal fix wall/colloid command");
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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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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/colloid command");
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coord = atof(arg[4]);
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hamaker = atof(arg[5]);
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sigma = atof(arg[6]);
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cutoff = atof(arg[7]);
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coeff1 = -4.0/315.0 * hamaker * pow(sigma,6.0);
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coeff2 = -2.0/3.0 * hamaker;
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coeff3 = hamaker * pow(sigma,6.0)/7560.0;
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coeff4 = hamaker/6.0;
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double rinv = 1.0/cutoff;
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double r2inv = rinv*rinv;
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double r4inv = r2inv*r2inv;
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offset = coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv;
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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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}
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/* ---------------------------------------------------------------------- */
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int FixWallColloid::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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FixWall(lmp, narg, arg) {}
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/* ---------------------------------------------------------------------- */
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@ -135,34 +65,33 @@ void FixWallColloid::init()
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MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
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if (flagall) error->all("Fix wall/colloid requires extended particles");
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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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FixWall::init();
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}
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/* ---------------------------------------------------------------------- */
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void FixWallColloid::setup(int vflag)
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void FixWallColloid::precompute(int m)
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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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coeff1[m] = -4.0/315.0 * epsilon[m] * pow(sigma[m],6.0);
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coeff2[m] = -2.0/3.0 * epsilon[m];
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coeff3[m] = epsilon[m] * pow(sigma[m],6.0)/7560.0;
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coeff4[m] = epsilon[m]/6.0;
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double rinv = 1.0/cutoff[m];
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double r2inv = rinv*rinv;
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double r4inv = r2inv*r2inv;
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offset[m] = coeff3[m]*r4inv*r4inv*rinv - coeff4[m]*r2inv*rinv;
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}
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/* ---------------------------------------------------------------------- */
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void FixWallColloid::min_setup(int vflag)
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void FixWallColloid::wall_particle(int m, double coord)
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{
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post_force(vflag);
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}
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double delta,delta2,rinv,r2inv,r4inv,r8inv,fwall;
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double r2,rinv2,r2inv2,r4inv2,r6inv2;
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double r3,rinv3,r2inv3,r4inv3,r6inv3;
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double rad,rad2,rad4,rad8,diam,new_coeff2;
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/* ---------------------------------------------------------------------- */
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void FixWallColloid::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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double **shape = atom->shape;
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@ -170,21 +99,17 @@ void FixWallColloid::post_force(int vflag)
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double delta,delta2,rinv,r2inv,r4inv,r8inv,fwall;
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double r2,rinv2,r2inv2,r4inv2,r6inv2;
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double r3,rinv3,r2inv3,r4inv3,r6inv3;
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double rad,rad2,rad4,rad8,diam,new_coeff2;
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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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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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rad = shape[type[i]][0];
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new_coeff2 = coeff2*rad*rad*rad;
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new_coeff2 = coeff2[m]*rad*rad*rad;
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diam = 2.0*rad;
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rad2 = rad*rad;
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rad4 = rad2*rad2;
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@ -194,7 +119,7 @@ void FixWallColloid::post_force(int vflag)
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r2inv = rinv*rinv;
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r4inv = r2inv*r2inv;
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r8inv = r4inv*r4inv;
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fwall = (coeff1*(rad8*rad + 27.0*rad4*rad2*rad*pow(delta,2.0)
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fwall = (coeff1[m]*(rad8*rad + 27.0*rad4*rad2*rad*pow(delta,2.0)
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+ 63.0*rad4*rad*pow(delta,4.0)
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+ 21.0*rad2*rad*pow(delta,6.0))*r8inv -
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new_coeff2*r2inv) * side;
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@ -209,54 +134,10 @@ void FixWallColloid::post_force(int vflag)
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r2inv3 = rinv3*rinv3;
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r4inv3 = r2inv3*r2inv3;
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r6inv3 = r4inv3*r2inv3;
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wall[0] += coeff3*((-3.5*diam+delta)*r4inv2*r2inv2*rinv2
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ewall[0] += coeff3[m]*((-3.5*diam+delta)*r4inv2*r2inv2*rinv2
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+ (3.5*diam+delta)*r4inv3*r2inv3*rinv3) -
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coeff4*((-diam*delta+r2*r3*(log(-r2)-log(r3)))*
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(-rinv2)*rinv3) - offset;
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wall[dim+1] += fwall;
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coeff4[m]*((-diam*delta+r2*r3*(log(-r2)-log(r3)))*
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(-rinv2)*rinv3) - 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 FixWallColloid::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 FixWallColloid::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 FixWallColloid::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 FixWallColloid::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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@ -14,31 +14,19 @@
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#ifndef FIX_WALL_COLLOID_H
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#define FIX_WALL_COLLOID_H
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#include "fix.h"
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#include "fix_wall.h"
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namespace LAMMPS_NS {
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class FixWallColloid : public Fix {
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class FixWallColloid : public FixWall {
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public:
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FixWallColloid(class LAMMPS *, int, char **);
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~FixWallColloid() {}
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int setmask();
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void init();
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void setup(int);
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void min_setup(int);
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void post_force(int);
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void post_force_respa(int, int, int);
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void min_post_force(int);
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double compute_scalar();
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double compute_vector(int);
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void precompute(int);
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void wall_particle(int, double);
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private:
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int dim,side,thermo_flag,eflag_enable;
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double coord,hamaker,sigma,cutoff;
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double coeff1,coeff2,coeff3,coeff4,offset;
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double wall[4],wall_all[4];
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int wall_flag;
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int nlevels_respa;
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double coeff1[6],coeff2[6],coeff3[6],coeff4[6],offset[6];
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};
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}
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@ -0,0 +1,222 @@
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/* ----------------------------------------------------------------------
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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 "stdlib.h"
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#include "string.h"
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#include "fix_wall.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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enum{XLO,XHI,YLO,YHI,ZLO,ZHI};
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/* ---------------------------------------------------------------------- */
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FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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scalar_flag = 1;
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vector_flag = 1;
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size_vector = 6;
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scalar_vector_freq = 1;
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extscalar = 1;
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extvector = 1;
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// parse args
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for (int m = 0; m < 6; m++) wflag[m] = 0;
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vflag = 0;
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aflag = 0;
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int iarg = 3;
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if ((strcmp(arg[iarg],"xlo") == 0) || (strcmp(arg[iarg],"xhi") == 0) ||
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(strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) ||
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(strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) {
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if (iarg+5 > narg) error->all("Illegal fix wall command");
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int m;
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if (strcmp(arg[iarg],"xlo") == 0) m = XLO;
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else if (strcmp(arg[iarg],"xhi") == 0) m = XHI;
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else if (strcmp(arg[iarg],"ylo") == 0) m = YLO;
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else if (strcmp(arg[iarg],"yhi") == 0) m = YHI;
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else if (strcmp(arg[iarg],"zlo") == 0) m = ZLO;
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else if (strcmp(arg[iarg],"zhi") == 0) m = ZHI;
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wflag[m] = 1;
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coord0[m] = atof(arg[iarg+1]);
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epsilon[m] = atof(arg[iarg+2]);
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sigma[m] = atof(arg[iarg+3]);
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cutoff[m] = atof(arg[iarg+4]);
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iarg += 5;
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} else if (strcmp(arg[iarg],"vel") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix wall command");
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vflag = 1;
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vel = atof(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"wiggle") == 0) {
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if (iarg+3 > narg) error->all("Illegal fix wall command");
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aflag = 1;
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amplitude = atof(arg[iarg+1]);
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period = atof(arg[iarg+2]);
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iarg += 3;
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} else error->all("Illegal fix wall command");
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// error check
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int flag = 0;
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for (int m = 0; m < 6; m++) if (wflag[m]) flag;
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if (!flag) error->all("Illegal fix wall command");
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if (vflag && aflag)
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error->all("Cannot set both vel and wiggle in fix wall command");
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if ((wflag[XLO] || wflag[XHI]) && domain->xperiodic)
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error->all("Cannot use fix wall in periodic dimension");
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if ((wflag[YLO] || wflag[YHI]) && domain->yperiodic)
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error->all("Cannot use fix wall in periodic dimension");
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if ((wflag[ZLO] || wflag[ZHI]) && domain->xperiodic)
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error->all("Cannot use fix wall in periodic zimension");
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// setup oscillations
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if (aflag) {
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double PI = 4.0 * atan(1.0);
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omega = 2.0*PI / period;
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}
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eflag = 0;
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for (int m = 0; m < 7; m++) ewall[m] = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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int FixWall::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 FixWall::init()
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{
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dt = update->dt;
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// setup coefficients
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for (int m = 0; m < 6; m++)
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if (wflag[m]) precompute(m);
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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 FixWall::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 FixWall::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 FixWall::post_force(int vflag)
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{
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eflag = 0;
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for (int m = 0; m < 7; m++) ewall[m] = 0.0;
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// coord0 = initial position of wall
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// coord = current position of wall
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double delta = (update->ntimestep - update->beginstep) * dt;
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double coord;
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for (int m = 0; m < 6; m++) {
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if (wflag[m] == 0) continue;
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if (vflag) {
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if (m/2 == 0) coord = coord0[m] + delta*vel;
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else coord = coord0[m] - delta*vel;
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} else if (aflag) {
|
||||
if (m/2 == 0) coord = coord0[m] + amplitude*sin(omega*delta);
|
||||
else coord = coord0[m] - amplitude*sin(omega*delta);
|
||||
} else coord = coord0[m];
|
||||
|
||||
wall_particle(m,coord);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWall::post_force_respa(int vflag, int ilevel, int iloop)
|
||||
{
|
||||
if (ilevel == nlevels_respa-1) post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWall::min_post_force(int vflag)
|
||||
{
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
energy of wall interaction
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixWall::compute_scalar()
|
||||
{
|
||||
// only sum across procs one time
|
||||
|
||||
if (eflag == 0) {
|
||||
MPI_Allreduce(ewall,ewall_all,7,MPI_DOUBLE,MPI_SUM,world);
|
||||
eflag = 1;
|
||||
}
|
||||
return ewall_all[0];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
components of force on wall
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixWall::compute_vector(int n)
|
||||
{
|
||||
// only sum across procs one time
|
||||
|
||||
if (eflag == 0) {
|
||||
MPI_Allreduce(ewall,ewall_all,7,MPI_DOUBLE,MPI_SUM,world);
|
||||
eflag = 1;
|
||||
}
|
||||
return ewall_all[n+1];
|
||||
}
|
||||
|
|
@ -0,0 +1,51 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef FIX_WALL_H
|
||||
#define FIX_WALL_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixWall : public Fix {
|
||||
public:
|
||||
FixWall(class LAMMPS *, int, char **);
|
||||
virtual ~FixWall() {}
|
||||
int setmask();
|
||||
virtual void init();
|
||||
void setup(int);
|
||||
void min_setup(int);
|
||||
void post_force(int);
|
||||
void post_force_respa(int, int, int);
|
||||
void min_post_force(int);
|
||||
double compute_scalar();
|
||||
double compute_vector(int);
|
||||
|
||||
virtual void precompute(int) = 0;
|
||||
virtual void wall_particle(int, double) = 0;
|
||||
|
||||
protected:
|
||||
int wflag[6];
|
||||
double coord0[6],epsilon[6],sigma[6],cutoff[6];
|
||||
int vflag,aflag;
|
||||
double vel,amplitude,period,omega;
|
||||
int eflag;
|
||||
double ewall[7],ewall_all[7];
|
||||
int nlevels_respa;
|
||||
double dt;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
|
@ -11,212 +11,57 @@
|
|||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Mark Stevens (SNL)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "fix_wall_lj126.h"
|
||||
#include "atom.h"
|
||||
#include "domain.h"
|
||||
#include "update.h"
|
||||
#include "output.h"
|
||||
#include "respa.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixWallLJ126::FixWallLJ126(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg)
|
||||
FixWall(lmp, narg, arg) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ126::precompute(int m)
|
||||
{
|
||||
if (narg < 8) error->all("Illegal fix wall/lj126 command");
|
||||
coeff1[m] = 48.0 * epsilon[m] * pow(sigma[m],12.0);
|
||||
coeff2[m] = 24.0 * epsilon[m] * pow(sigma[m],6.0);
|
||||
coeff3[m] = 4.0 * epsilon[m] * pow(sigma[m],12.0);
|
||||
coeff4[m] = 4.0 * epsilon[m] * pow(sigma[m],6.0);
|
||||
|
||||
scalar_flag = 1;
|
||||
vector_flag = 1;
|
||||
size_vector = 3;
|
||||
scalar_vector_freq = 1;
|
||||
extscalar = 1;
|
||||
extvector = 1;
|
||||
|
||||
// set defaults
|
||||
|
||||
if (strcmp(arg[3],"xlo") == 0) {
|
||||
dim = 0;
|
||||
side = -1;
|
||||
} else if (strcmp(arg[3],"xhi") == 0) {
|
||||
dim = 0;
|
||||
side = 1;
|
||||
} else if (strcmp(arg[3],"ylo") == 0) {
|
||||
dim = 1;
|
||||
side = -1;
|
||||
} else if (strcmp(arg[3],"yhi") == 0) {
|
||||
dim = 1;
|
||||
side = 1;
|
||||
} else if (strcmp(arg[3],"zlo") == 0) {
|
||||
dim = 2;
|
||||
side = -1;
|
||||
} else if (strcmp(arg[3],"zhi") == 0) {
|
||||
dim = 2;
|
||||
side = 1;
|
||||
} else error->all("Illegal fix wall/lj126 command");
|
||||
|
||||
coord0 = atof(arg[4]);
|
||||
epsilon = atof(arg[5]);
|
||||
sigma = atof(arg[6]);
|
||||
cutoff = atof(arg[7]);
|
||||
|
||||
// read options
|
||||
|
||||
vel = 0.0;
|
||||
|
||||
int iarg = 8;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"vel") == 0) {
|
||||
if (iarg+2 > narg) error->all("Illegal fix wall/lj126 command");
|
||||
vel = atof(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else error->all("Illegal fix wall/lj126 command");
|
||||
}
|
||||
|
||||
coeff1 = 48.0 * epsilon * pow(sigma,12.0);
|
||||
coeff2 = 24.0 * epsilon * pow(sigma,6.0);
|
||||
coeff3 = 4.0 * epsilon * pow(sigma,12.0);
|
||||
coeff4 = 4.0 * epsilon * pow(sigma,6.0);
|
||||
|
||||
double r2inv = 1.0/(cutoff*cutoff);
|
||||
double r2inv = 1.0/(cutoff[m]*cutoff[m]);
|
||||
double r6inv = r2inv*r2inv*r2inv;
|
||||
offset = r6inv*(coeff3*r6inv - coeff4);
|
||||
|
||||
if (dim == 0 && domain->xperiodic)
|
||||
error->all("Cannot use wall in periodic dimension");
|
||||
if (dim == 1 && domain->yperiodic)
|
||||
error->all("Cannot use wall in periodic dimension");
|
||||
if (dim == 2 && domain->zperiodic)
|
||||
error->all("Cannot use wall in periodic dimension");
|
||||
|
||||
wall_flag = 0;
|
||||
wall[0] = wall[1] = wall[2] = wall[3] = 0.0;
|
||||
offset[m] = r6inv*(coeff3[m]*r6inv - coeff4[m]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixWallLJ126::setmask()
|
||||
void FixWallLJ126::wall_particle(int m, double coord)
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= POST_FORCE;
|
||||
mask |= THERMO_ENERGY;
|
||||
mask |= POST_FORCE_RESPA;
|
||||
mask |= MIN_POST_FORCE;
|
||||
return mask;
|
||||
}
|
||||
double delta,rinv,r2inv,r6inv,fwall;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ126::init()
|
||||
{
|
||||
if (strcmp(update->integrate_style,"respa") == 0)
|
||||
nlevels_respa = ((Respa *) update->integrate)->nlevels;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ126::setup(int vflag)
|
||||
{
|
||||
if (strcmp(update->integrate_style,"verlet") == 0)
|
||||
post_force(vflag);
|
||||
else {
|
||||
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
|
||||
post_force_respa(vflag,nlevels_respa-1,0);
|
||||
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ126::min_setup(int vflag)
|
||||
{
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ126::post_force(int vflag)
|
||||
{
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double delta,rinv,r2inv,r6inv,fwall;
|
||||
wall[0] = wall[1] = wall[2] = wall[3] = 0.0;
|
||||
wall_flag = 0;
|
||||
|
||||
// coord = current position of wall
|
||||
// coord0 = initial position of wall
|
||||
|
||||
double delt = (update->ntimestep - update->beginstep) * update->dt;
|
||||
double coord = coord0 + delt*vel;
|
||||
int dim = m/2;
|
||||
int side = m % 2;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
if (side == -1) delta = x[i][dim] - coord;
|
||||
if (side == 0) delta = x[i][dim] - coord;
|
||||
else delta = coord - x[i][dim];
|
||||
if (delta <= 0.0) continue;
|
||||
if (delta > cutoff) continue;
|
||||
if (delta > cutoff[m]) continue;
|
||||
rinv = 1.0/delta;
|
||||
r2inv = rinv*rinv;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
fwall = side * r6inv*(coeff1*r6inv - coeff2) * rinv;
|
||||
fwall = side * r6inv*(coeff1[m]*r6inv - coeff2[m]) * rinv;
|
||||
f[i][dim] -= fwall;
|
||||
wall[0] += r6inv*(coeff3*r6inv - coeff4) - offset;
|
||||
wall[dim+1] += fwall;
|
||||
ewall[0] += r6inv*(coeff3[m]*r6inv - coeff4[m]) - offset[m];
|
||||
ewall[m+1] += fwall;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ126::post_force_respa(int vflag, int ilevel, int iloop)
|
||||
{
|
||||
if (ilevel == nlevels_respa-1) post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ126::min_post_force(int vflag)
|
||||
{
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
energy of wall interaction
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixWallLJ126::compute_scalar()
|
||||
{
|
||||
// only sum across procs one time
|
||||
|
||||
if (wall_flag == 0) {
|
||||
MPI_Allreduce(wall,wall_all,4,MPI_DOUBLE,MPI_SUM,world);
|
||||
wall_flag = 1;
|
||||
}
|
||||
return wall_all[0];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
components of force on wall
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixWallLJ126::compute_vector(int n)
|
||||
{
|
||||
// only sum across procs one time
|
||||
|
||||
if (wall_flag == 0) {
|
||||
MPI_Allreduce(wall,wall_all,4,MPI_DOUBLE,MPI_SUM,world);
|
||||
wall_flag = 1;
|
||||
}
|
||||
return wall_all[n+1];
|
||||
}
|
||||
|
|
|
|||
|
|
@ -14,34 +14,19 @@
|
|||
#ifndef FIX_WALL_LJ126_H
|
||||
#define FIX_WALL_LJ126_H
|
||||
|
||||
#include "fix.h"
|
||||
#include "fix_wall.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixWallLJ126 : public Fix {
|
||||
class FixWallLJ126 : public FixWall {
|
||||
public:
|
||||
FixWallLJ126(class LAMMPS *, int, char **);
|
||||
int setmask();
|
||||
void init();
|
||||
void setup(int);
|
||||
void min_setup(int);
|
||||
void post_force(int);
|
||||
void post_force_respa(int, int, int);
|
||||
void min_post_force(int);
|
||||
double compute_scalar();
|
||||
double compute_vector(int);
|
||||
void precompute(int);
|
||||
void wall_particle(int, double);
|
||||
|
||||
private:
|
||||
int dim,side,thermo_flag,eflag_enable;
|
||||
double coord,epsilon,sigma,cutoff;
|
||||
double coeff1,coeff2,coeff3,coeff4,offset;
|
||||
double wall[4],wall_all[4];
|
||||
double vel,coord0;
|
||||
int wall_flag;
|
||||
int nlevels_respa;
|
||||
double coeff1[6],coeff2[6],coeff3[6],coeff4[6],offset[6];
|
||||
};
|
||||
|
||||
#endif
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -12,209 +12,59 @@
|
|||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "fix_wall_lj93.h"
|
||||
#include "atom.h"
|
||||
#include "domain.h"
|
||||
#include "update.h"
|
||||
#include "output.h"
|
||||
#include "respa.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixWallLJ93::FixWallLJ93(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg)
|
||||
FixWall(lmp, narg, arg) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ93::precompute(int m)
|
||||
{
|
||||
if (narg < 8) error->all("Illegal fix wall/lj93 command");
|
||||
coeff1[m] = 6.0/5.0 * epsilon[m] * pow(sigma[m],9.0);
|
||||
coeff2[m] = 3.0 * epsilon[m] * pow(sigma[m],3.0);
|
||||
coeff3[m] = 2.0/15.0 * epsilon[m] * pow(sigma[m],9.0);
|
||||
coeff4[m] = epsilon[m] * pow(sigma[m],3.0);
|
||||
|
||||
scalar_flag = 1;
|
||||
vector_flag = 1;
|
||||
size_vector = 3;
|
||||
scalar_vector_freq = 1;
|
||||
extscalar = 1;
|
||||
extvector = 1;
|
||||
|
||||
// set defaults
|
||||
|
||||
if (strcmp(arg[3],"xlo") == 0) {
|
||||
dim = 0;
|
||||
side = -1;
|
||||
} else if (strcmp(arg[3],"xhi") == 0) {
|
||||
dim = 0;
|
||||
side = 1;
|
||||
} else if (strcmp(arg[3],"ylo") == 0) {
|
||||
dim = 1;
|
||||
side = -1;
|
||||
} else if (strcmp(arg[3],"yhi") == 0) {
|
||||
dim = 1;
|
||||
side = 1;
|
||||
} else if (strcmp(arg[3],"zlo") == 0) {
|
||||
dim = 2;
|
||||
side = -1;
|
||||
} else if (strcmp(arg[3],"zhi") == 0) {
|
||||
dim = 2;
|
||||
side = 1;
|
||||
} else error->all("Illegal fix wall/lj93 command");
|
||||
|
||||
coord0 = atof(arg[4]);
|
||||
epsilon = atof(arg[5]);
|
||||
sigma = atof(arg[6]);
|
||||
cutoff = atof(arg[7]);
|
||||
|
||||
// read options
|
||||
|
||||
vel = 0.0;
|
||||
|
||||
int iarg = 8;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"vel") == 0) {
|
||||
if (iarg+2 > narg) error->all("Illegal fix wall/lj93 command");
|
||||
vel = atof(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else error->all("Illegal fix wall/lj93 command");
|
||||
}
|
||||
|
||||
coeff1 = 6.0/5.0 * epsilon * pow(sigma,9.0);
|
||||
coeff2 = 3.0 * epsilon * pow(sigma,3.0);
|
||||
coeff3 = 2.0/15.0 * epsilon * pow(sigma,9.0);
|
||||
coeff4 = epsilon * pow(sigma,3.0);
|
||||
|
||||
double rinv = 1.0/cutoff;
|
||||
double rinv = 1.0/cutoff[m];
|
||||
double r2inv = rinv*rinv;
|
||||
double r4inv = r2inv*r2inv;
|
||||
offset = coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv;
|
||||
|
||||
if (dim == 0 && domain->xperiodic)
|
||||
error->all("Cannot use wall in periodic dimension");
|
||||
if (dim == 1 && domain->yperiodic)
|
||||
error->all("Cannot use wall in periodic dimension");
|
||||
if (dim == 2 && domain->zperiodic)
|
||||
error->all("Cannot use wall in periodic dimension");
|
||||
|
||||
wall_flag = 0;
|
||||
wall[0] = wall[1] = wall[2] = wall[3] = 0.0;
|
||||
offset[m] = coeff3[6]*r4inv*r4inv*rinv - coeff4[6]*r2inv*rinv;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixWallLJ93::setmask()
|
||||
void FixWallLJ93::wall_particle(int m, double coord)
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= POST_FORCE;
|
||||
mask |= THERMO_ENERGY;
|
||||
mask |= POST_FORCE_RESPA;
|
||||
mask |= MIN_POST_FORCE;
|
||||
return mask;
|
||||
}
|
||||
double delta,rinv,r2inv,r4inv,r10inv,fwall;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ93::init()
|
||||
{
|
||||
if (strcmp(update->integrate_style,"respa") == 0)
|
||||
nlevels_respa = ((Respa *) update->integrate)->nlevels;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ93::setup(int vflag)
|
||||
{
|
||||
if (strcmp(update->integrate_style,"verlet") == 0)
|
||||
post_force(vflag);
|
||||
else {
|
||||
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
|
||||
post_force_respa(vflag,nlevels_respa-1,0);
|
||||
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ93::min_setup(int vflag)
|
||||
{
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ93::post_force(int vflag)
|
||||
{
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double delta,rinv,r2inv,r4inv,r10inv,fwall;
|
||||
wall[0] = wall[1] = wall[2] = wall[3] = 0.0;
|
||||
wall_flag = 0;
|
||||
|
||||
// coord = current position of wall
|
||||
// coord0 = initial position of wall
|
||||
|
||||
double delt = (update->ntimestep - update->beginstep) * update->dt;
|
||||
double coord = coord0 + delt*vel;
|
||||
int dim = m/2;
|
||||
int side = m % 2;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
if (side == -1) delta = x[i][dim] - coord;
|
||||
if (side == 0) delta = x[i][dim] - coord;
|
||||
else delta = coord - x[i][dim];
|
||||
if (delta <= 0.0) continue;
|
||||
if (delta > cutoff) continue;
|
||||
if (delta > cutoff[m]) continue;
|
||||
rinv = 1.0/delta;
|
||||
r2inv = rinv*rinv;
|
||||
r4inv = r2inv*r2inv;
|
||||
r10inv = r4inv*r4inv*r2inv;
|
||||
fwall = (coeff1*r10inv - coeff2*r4inv) * side;
|
||||
fwall = (coeff1[m]*r10inv - coeff2[m]*r4inv) * side;
|
||||
f[i][dim] -= fwall;
|
||||
wall[0] += coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv - offset;
|
||||
wall[dim+1] += fwall;
|
||||
ewall[0] += coeff3[m]*r4inv*r4inv*rinv -
|
||||
coeff4[m]*r2inv*rinv - offset[m];
|
||||
ewall[m+1] += fwall;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ93::post_force_respa(int vflag, int ilevel, int iloop)
|
||||
{
|
||||
if (ilevel == nlevels_respa-1) post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallLJ93::min_post_force(int vflag)
|
||||
{
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
energy of wall interaction
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixWallLJ93::compute_scalar()
|
||||
{
|
||||
// only sum across procs one time
|
||||
|
||||
if (wall_flag == 0) {
|
||||
MPI_Allreduce(wall,wall_all,4,MPI_DOUBLE,MPI_SUM,world);
|
||||
wall_flag = 1;
|
||||
}
|
||||
return wall_all[0];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
components of force on wall
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixWallLJ93::compute_vector(int n)
|
||||
{
|
||||
// only sum across procs one time
|
||||
|
||||
if (wall_flag == 0) {
|
||||
MPI_Allreduce(wall,wall_all,4,MPI_DOUBLE,MPI_SUM,world);
|
||||
wall_flag = 1;
|
||||
}
|
||||
return wall_all[n+1];
|
||||
}
|
||||
|
|
|
|||
|
|
@ -14,32 +14,18 @@
|
|||
#ifndef FIX_WALL_LJ93_H
|
||||
#define FIX_WALL_LJ93_H
|
||||
|
||||
#include "fix.h"
|
||||
#include "fix_wall.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixWallLJ93 : public Fix {
|
||||
class FixWallLJ93 : public FixWall {
|
||||
public:
|
||||
FixWallLJ93(class LAMMPS *, int, char **);
|
||||
~FixWallLJ93() {}
|
||||
int setmask();
|
||||
void init();
|
||||
void setup(int);
|
||||
void min_setup(int);
|
||||
void post_force(int);
|
||||
void post_force_respa(int, int, int);
|
||||
void min_post_force(int);
|
||||
double compute_scalar();
|
||||
double compute_vector(int);
|
||||
void precompute(int);
|
||||
void wall_particle(int, double);
|
||||
|
||||
private:
|
||||
int dim,side,thermo_flag,eflag_enable;
|
||||
double coord,epsilon,sigma,cutoff;
|
||||
double coeff1,coeff2,coeff3,coeff4,offset;
|
||||
double wall[4],wall_all[4];
|
||||
double vel,coord0;
|
||||
int wall_flag;
|
||||
int nlevels_respa;
|
||||
double coeff1[6],coeff2[6],coeff3[6],coeff4[6],offset[6];
|
||||
};
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue