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lammps/src/USER-SMD/compute_smd_tlsph_shape.cpp
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compute_smd_tlsph_shape.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 <string.h>
#include "compute_smd_tlsph_shape.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
#include "pair.h"
#include <iostream>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <Eigen/Eigen>
#include <Eigen/Geometry>
using namespace Eigen;
using namespace std;
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeSmdTlsphShape::ComputeSmdTlsphShape(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg) {
if (narg != 3)
error->all(FLERR, "Illegal compute smd/tlsph_strain command");
peratom_flag = 1;
size_peratom_cols = 7;
nmax = 0;
strainVector = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeSmdTlsphShape::~ComputeSmdTlsphShape() {
memory->sfree(strainVector);
}
/* ---------------------------------------------------------------------- */
void ComputeSmdTlsphShape::init() {
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style, "smd/tlsph_strain") == 0)
count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR, "More than one compute smd/tlsph_strain");
}
/* ---------------------------------------------------------------------- */
void ComputeSmdTlsphShape::compute_peratom() {
double *contact_radius = atom->contact_radius;
invoked_peratom = update->ntimestep;
// grow vector array if necessary
if (atom->nmax > nmax) {
memory->destroy(strainVector);
nmax = atom->nmax;
memory->create(strainVector, nmax, size_peratom_cols, "strainVector");
array_atom = strainVector;
}
int itmp = 0;
Matrix3d *R = (Matrix3d *) force->pair->extract("smd/tlsph/rotation_ptr", itmp);
if (R == NULL) {
error->all(FLERR, "compute smd/tlsph_shape failed to access rotation array");
}
Matrix3d *F = (Matrix3d *) force->pair->extract("smd/tlsph/Fincr_ptr", itmp);
if (F == NULL) {
error->all(FLERR, "compute smd/tlsph_shape failed to access deformation gradient array");
}
int *mask = atom->mask;
int nlocal = atom->nlocal;
Matrix3d E, eye;
eye.setIdentity();
Quaterniond q;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
E = 0.5 * (F[i].transpose() * F[i] - eye); // Green-Lagrange strain
strainVector[i][0] = contact_radius[i] * (1.0 + E(0, 0));
strainVector[i][1] = contact_radius[i] * (1.0 + E(1, 1));
strainVector[i][2] = contact_radius[i] * (1.0 + E(2, 2));
q = R[i]; // convert pure rotation matrix to quaternion
strainVector[i][3] = q.w();
strainVector[i][4] = q.x();
strainVector[i][5] = q.y();
strainVector[i][6] = q.z();
} else {
for (int j = 0; j < size_peratom_cols; j++) {
strainVector[i][j] = 0.0;
}
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeSmdTlsphShape::memory_usage() {
double bytes = size_peratom_cols * nmax * sizeof(double);
return bytes;
}
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