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pair_smd_hertz.cpp
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Mon, Nov 11, 10:52

pair_smd_hertz.cpp
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/* ----------------------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
* This file is part of the USER-SMD package for LAMMPS.
* Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de
* Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI,
* Eckerstrasse 4, D-79104 Freiburg i.Br, Germany.
*
* ----------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <float.h>
#include <stdlib.h>
#include <string.h>
#include "pair_smd_hertz.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define SQRT2 1.414213562e0
/* ---------------------------------------------------------------------- */
PairHertz::PairHertz(LAMMPS *lmp) :
Pair(lmp) {
onerad_dynamic = onerad_frozen = maxrad_dynamic = maxrad_frozen = NULL;
bulkmodulus = NULL;
kn = NULL;
scale = 1.0;
}
/* ---------------------------------------------------------------------- */
PairHertz::~PairHertz() {
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(bulkmodulus);
memory->destroy(kn);
delete[] onerad_dynamic;
delete[] onerad_frozen;
delete[] maxrad_dynamic;
delete[] maxrad_frozen;
}
}
/* ---------------------------------------------------------------------- */
void PairHertz::compute(int eflag, int vflag) {
int i, j, ii, jj, inum, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz;
double rsq, r, evdwl, fpair;
int *ilist, *jlist, *numneigh, **firstneigh;
double rcut, r_geom, delta, ri, rj, dt_crit;
double *rmass = atom->rmass;
evdwl = 0.0;
if (eflag || vflag)
ev_setup(eflag, vflag);
else
evflag = vflag_fdotr = 0;
double **f = atom->f;
double **x = atom->x;
double **x0 = atom->x0;
int *type = atom->type;
int nlocal = atom->nlocal;
double *radius = atom->contact_radius;
double *sph_radius = atom->radius;
double rcutSq;
double delx0, dely0, delz0, rSq0, sphCut;
int newton_pair = force->newton_pair;
int periodic = (domain->xperiodic || domain->yperiodic || domain->zperiodic);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
stable_time_increment = 1.0e22;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
ri = scale * radius[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
rj = scale * radius[j];
rcut = ri + rj;
rcutSq = rcut * rcut;
if (rsq < rcutSq) {
/*
* self contact option:
* if pair of particles was initially close enough to interact via a bulk continuum mechanism (e.g. SPH), exclude pair from contact forces.
* this approach should work well if no updates of the reference configuration are performed.
*/
if (itype == jtype) {
delx0 = x0[j][0] - x0[i][0];
dely0 = x0[j][1] - x0[i][1];
delz0 = x0[j][2] - x0[i][2];
if (periodic) {
domain->minimum_image(delx0, dely0, delz0);
}
rSq0 = delx0 * delx0 + dely0 * dely0 + delz0 * delz0; // initial distance
sphCut = sph_radius[i] + sph_radius[j];
if (rSq0 < sphCut * sphCut) {
rcut = 0.5 * rcut;
rcutSq = rcut * rcut;
if (rsq > rcutSq) {
continue;
}
}
}
r = sqrt(rsq);
//printf("hertz interaction, r=%f, cut=%f, h=%f\n", r, rcut, sqrt(rSq0));
// Hertzian short-range forces
delta = rcut - r; // overlap distance
r_geom = ri * rj / rcut;
//assuming poisson ratio = 1/4 for 3d
fpair = 1.066666667e0 * bulkmodulus[itype][jtype] * delta * sqrt(delta * r_geom); // units: N
evdwl = fpair * 0.4e0 * delta; // GCG 25 April: this expression conserves total energy
dt_crit = 3.14 * sqrt(0.5 * (rmass[i] + rmass[j]) / (fpair / delta));
stable_time_increment = MIN(stable_time_increment, dt_crit);
if (r > 2.0e-16) {
fpair /= r; // divide by r and multiply with non-normalized distance vector
} else {
fpair = 0.0;
}
/*
* contact viscosity -- needs to be done, see GRANULAR package for normal & shear damping
* for now: no damping and thus no viscous energy deltaE
*/
if (evflag) {
ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
}
f[i][0] += delx * fpair;
f[i][1] += dely * fpair;
f[i][2] += delz * fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx * fpair;
f[j][1] -= dely * fpair;
f[j][2] -= delz * fpair;
}
}
}
}
// double stable_time_increment_all = 0.0;
// MPI_Allreduce(&stable_time_increment, &stable_time_increment_all, 1, MPI_DOUBLE, MPI_MIN, world);
// if (comm->me == 0) {
// printf("stable time step for pair smd/hertz is %f\n", stable_time_increment_all);
// }
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairHertz::allocate() {
allocated = 1;
int n = atom->ntypes;
memory->create(setflag, n + 1, n + 1, "pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(bulkmodulus, n + 1, n + 1, "pair:kspring");
memory->create(kn, n + 1, n + 1, "pair:kn");
memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); // always needs to be allocated, even with granular neighborlist
onerad_dynamic = new double[n + 1];
onerad_frozen = new double[n + 1];
maxrad_dynamic = new double[n + 1];
maxrad_frozen = new double[n + 1];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairHertz::settings(int narg, char **arg) {
if (narg != 1)
error->all(FLERR, "Illegal number of args for pair_style hertz");
scale = force->numeric(FLERR, arg[0]);
if (comm->me == 0) {
printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
printf("SMD/HERTZ CONTACT SETTINGS:\n");
printf("... effective contact radius is scaled by %f\n", scale);
printf(">>========>>========>>========>>========>>========>>========>>========>>========\n");
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairHertz::coeff(int narg, char **arg) {
if (narg != 3)
error->all(FLERR, "Incorrect args for pair coefficients");
if (!allocated)
allocate();
int ilo, ihi, jlo, jhi;
force->bounds(arg[0], atom->ntypes, ilo, ihi);
force->bounds(arg[1], atom->ntypes, jlo, jhi);
double bulkmodulus_one = atof(arg[2]);
// set short-range force constant
double kn_one = 0.0;
if (domain->dimension == 3) {
kn_one = (16. / 15.) * bulkmodulus_one; //assuming poisson ratio = 1/4 for 3d
} else {
kn_one = 0.251856195 * (2. / 3.) * bulkmodulus_one; //assuming poisson ratio = 1/3 for 2d
}
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo, i); j <= jhi; j++) {
bulkmodulus[i][j] = bulkmodulus_one;
kn[i][j] = kn_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0)
error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairHertz::init_one(int i, int j) {
if (!allocated)
allocate();
if (setflag[i][j] == 0)
error->all(FLERR, "All pair coeffs are not set");
bulkmodulus[j][i] = bulkmodulus[i][j];
kn[j][i] = kn[i][j];
// cutoff = sum of max I,J radii for
// dynamic/dynamic & dynamic/frozen interactions, but not frozen/frozen
double cutoff = maxrad_dynamic[i] + maxrad_dynamic[j];
cutoff = MAX(cutoff, maxrad_frozen[i] + maxrad_dynamic[j]);
cutoff = MAX(cutoff, maxrad_dynamic[i] + maxrad_frozen[j]);
if (comm->me == 0) {
printf("cutoff for pair smd/hertz = %f\n", cutoff);
}
return cutoff;
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairHertz::init_style() {
int i;
// error checks
if (!atom->contact_radius_flag)
error->all(FLERR, "Pair style smd/hertz requires atom style with contact_radius");
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->gran = 1;
// set maxrad_dynamic and maxrad_frozen for each type
// include future Fix pour particles as dynamic
for (i = 1; i <= atom->ntypes; i++)
onerad_dynamic[i] = onerad_frozen[i] = 0.0;
double *radius = atom->radius;
int *type = atom->type;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
onerad_dynamic[type[i]] = MAX(onerad_dynamic[type[i]], radius[i]);
}
MPI_Allreduce(&onerad_dynamic[1], &maxrad_dynamic[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
MPI_Allreduce(&onerad_frozen[1], &maxrad_frozen[1], atom->ntypes, MPI_DOUBLE, MPI_MAX, world);
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
optional granular history list
------------------------------------------------------------------------- */
void PairHertz::init_list(int id, NeighList *ptr) {
if (id == 0)
list = ptr;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairHertz::memory_usage() {
return 0.0;
}
void *PairHertz::extract(const char *str, int &i) {
//printf("in PairTriSurf::extract\n");
if (strcmp(str, "smd/hertz/stable_time_increment_ptr") == 0) {
return (void *) &stable_time_increment;
}
return NULL;
}

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