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fix_smd_integrate_ulsph.cpp
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rLAMMPS lammps
fix_smd_integrate_ulsph.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.
------------------------------------------------------------------------- */
#include <stdio.h>
#include <string.h>
#include "fix_smd_integrate_ulsph.h"
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
#include "pair.h"
#include "domain.h"
#include <Eigen/Eigen>
using namespace Eigen;
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixSMDIntegrateUlsph::FixSMDIntegrateUlsph(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg) {
if ((atom->e_flag != 1) || (atom->vfrac_flag != 1))
error->all(FLERR, "fix smd/integrate_ulsph command requires atom_style with both energy and volume");
if (narg < 3)
error->all(FLERR, "Illegal number of arguments for fix smd/integrate_ulsph command");
adjust_radius_flag = false;
xsphFlag = false;
vlimit = -1.0;
int iarg = 3;
if (comm->me == 0) {
printf("\n>>========>>========>>========>>========>>========>>========>>========>>========\n");
printf("fix smd/integrate_ulsph is active for group: %s \n", arg[1]);
}
while (true) {
if (iarg >= narg) {
break;
}
if (strcmp(arg[iarg], "xsph") == 0) {
xsphFlag = true;
if (comm->me == 0) {
error->one(FLERR, "XSPH is currently not available");
printf("... will use XSPH time integration\n");
}
} else if (strcmp(arg[iarg], "adjust_radius") == 0) {
adjust_radius_flag = true;
iarg++;
if (iarg == narg) {
error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max");
}
adjust_radius_factor = force->numeric(FLERR, arg[iarg]);
iarg++;
if (iarg == narg) {
error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max");
}
min_nn = force->inumeric(FLERR, arg[iarg]);
iarg++;
if (iarg == narg) {
error->all(FLERR, "expected three numbers following adjust_radius: factor, min, max");
}
max_nn = force->inumeric(FLERR, arg[iarg]);
if (comm->me == 0) {
printf("... will adjust smoothing length dynamically with factor %g to achieve %d to %d neighbors per particle.\n ",
adjust_radius_factor, min_nn, max_nn);
}
} else if (strcmp(arg[iarg], "limit_velocity") == 0) {
iarg++;
if (iarg == narg) {
error->all(FLERR, "expected number following limit_velocity");
}
vlimit = force->numeric(FLERR, arg[iarg]);
if (comm->me == 0) {
printf("... will limit velocities to <= %g\n", vlimit);
}
} else {
char msg[128];
sprintf(msg, "Illegal keyword for smd/integrate_ulsph: %s\n", arg[iarg]);
error->all(FLERR, msg);
}
iarg++;
}
if (comm->me == 0) {
printf(">>========>>========>>========>>========>>========>>========>>========>>========\n\n");
}
// set comm sizes needed by this fix
atom->add_callback(0);
time_integrate = 1;
}
/* ---------------------------------------------------------------------- */
int FixSMDIntegrateUlsph::setmask() {
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixSMDIntegrateUlsph::init() {
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
vlimitsq = vlimit * vlimit;
}
/* ----------------------------------------------------------------------
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
void FixSMDIntegrateUlsph::initial_integrate(int vflag) {
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **vest = atom->vest;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int i, itmp;
double dtfm, vsq, scale;
double vxsph_x, vxsph_y, vxsph_z;
//printf("initial_integrate at timestep %d\n", update->ntimestep);
/*
* get smoothed velocities from ULSPH pair style
*/
Vector3d *smoothVel = (Vector3d *) force->pair->extract("smd/ulsph/smoothVel_ptr", itmp);
if (xsphFlag) {
if (smoothVel == NULL) {
error->one(FLERR, "fix smd/integrate_ulsph failed to access smoothVel array");
}
}
if (igroup == atom->firstgroup)
nlocal = atom->nfirst;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
if (vlimit > 0.0) {
vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
if (vsq > vlimitsq) {
scale = sqrt(vlimitsq / vsq);
v[i][0] *= scale;
v[i][1] *= scale;
v[i][2] *= scale;
vest[i][0] = v[i][0];
vest[i][1] = v[i][1];
vest[i][2] = v[i][2];
}
}
if (xsphFlag) {
// construct XSPH velocity
vxsph_x = v[i][0] - 0.5 * smoothVel[i](0);
vxsph_y = v[i][1] - 0.5 * smoothVel[i](1);
vxsph_z = v[i][2] - 0.5 * smoothVel[i](2);
vest[i][0] = vxsph_x + dtfm * f[i][0];
vest[i][1] = vxsph_y + dtfm * f[i][1];
vest[i][2] = vxsph_z + dtfm * f[i][2];
x[i][0] += dtv * vxsph_x;
x[i][1] += dtv * vxsph_y;
x[i][2] += dtv * vxsph_z;
} else {
// extrapolate velocity from half- to full-step
vest[i][0] = v[i][0] + dtfm * f[i][0];
vest[i][1] = v[i][1] + dtfm * f[i][1];
vest[i][2] = v[i][2] + dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixSMDIntegrateUlsph::final_integrate() {
double **v = atom->v;
double **f = atom->f;
double *e = atom->e;
double *de = atom->de;
double *vfrac = atom->vfrac;
double *radius = atom->radius;
double *contact_radius = atom->contact_radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup)
nlocal = atom->nfirst;
double dtfm, vsq, scale;
double *rmass = atom->rmass;
double vol_increment;
Matrix3d D;
/*
* get current number of SPH neighbors from ULSPH pair style
*/
int itmp;
int *nn = (int *) force->pair->extract("smd/ulsph/numNeighs_ptr", itmp);
if (nn == NULL) {
error->one(FLERR, "fix smd/integrate_ulsph failed to accesss num_neighs array");
}
Matrix3d *L = (Matrix3d *) force->pair->extract("smd/ulsph/velocityGradient_ptr", itmp);
if (L == NULL) {
error->one(FLERR, "fix smd/integrate_ulsph failed to accesss velocityGradient array");
}
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
if (vlimit > 0.0) {
vsq = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
if (vsq > vlimitsq) {
scale = sqrt(vlimitsq / vsq);
v[i][0] *= scale;
v[i][1] *= scale;
v[i][2] *= scale;
}
}
e[i] += dtf * de[i];
if (adjust_radius_flag) {
if (nn[i] < min_nn) {
radius[i] *= adjust_radius_factor;
} else if (nn[i] > max_nn) {
radius[i] /= adjust_radius_factor;
}
radius[i] = MAX(radius[i], 1.25 * contact_radius[i]);
radius[i] = MIN(radius[i], 4.0 * contact_radius[i]);
}
D = 0.5 * (L[i] + L[i].transpose());
vol_increment = vfrac[i] * update->dt * D.trace(); // Jacobian of deformation
vfrac[i] += vol_increment;
}
}
}
/* ---------------------------------------------------------------------- */
void FixSMDIntegrateUlsph::reset_dt() {
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
}
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