134 lines
4.7 KiB
C++
134 lines
4.7 KiB
C++
/* ----------------------------------------------------------------------
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*
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* *** Smooth Mach Dynamics ***
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*
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* This file is part of the USER-SMD package for LAMMPS.
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* Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de
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* Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI,
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* Eckerstrasse 4, D-79104 Freiburg i.Br, Germany.
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*
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* ----------------------------------------------------------------------- */
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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 "compute_smd_tlsph_shape.h"
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#include <cstring>
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#include <Eigen/Eigen>
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "comm.h"
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#include "force.h"
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#include "memory.h"
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#include "error.h"
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#include "pair.h"
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using namespace Eigen;
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using namespace std;
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeSmdTlsphShape::ComputeSmdTlsphShape(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg) {
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if (narg != 3)
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error->all(FLERR, "Illegal compute smd/tlsph_strain command");
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peratom_flag = 1;
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size_peratom_cols = 7;
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nmax = 0;
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strainVector = NULL;
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}
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/* ---------------------------------------------------------------------- */
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ComputeSmdTlsphShape::~ComputeSmdTlsphShape() {
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memory->sfree(strainVector);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSmdTlsphShape::init() {
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int count = 0;
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for (int i = 0; i < modify->ncompute; i++)
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if (strcmp(modify->compute[i]->style, "smd/tlsph_strain") == 0)
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count++;
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if (count > 1 && comm->me == 0)
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error->warning(FLERR, "More than one compute smd/tlsph_strain");
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSmdTlsphShape::compute_peratom() {
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double *contact_radius = atom->contact_radius;
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invoked_peratom = update->ntimestep;
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// grow vector array if necessary
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if (atom->nmax > nmax) {
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memory->destroy(strainVector);
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nmax = atom->nmax;
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memory->create(strainVector, nmax, size_peratom_cols, "strainVector");
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array_atom = strainVector;
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}
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int itmp = 0;
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Matrix3d *R = (Matrix3d *) force->pair->extract("smd/tlsph/rotation_ptr", itmp);
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if (R == NULL) {
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error->all(FLERR, "compute smd/tlsph_shape failed to access rotation array");
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}
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Matrix3d *F = (Matrix3d *) force->pair->extract("smd/tlsph/Fincr_ptr", itmp);
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if (F == NULL) {
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error->all(FLERR, "compute smd/tlsph_shape failed to access deformation gradient array");
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}
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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Matrix3d E, eye;
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eye.setIdentity();
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Quaterniond q;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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E = 0.5 * (F[i].transpose() * F[i] - eye); // Green-Lagrange strain
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strainVector[i][0] = contact_radius[i] * (1.0 + E(0, 0));
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strainVector[i][1] = contact_radius[i] * (1.0 + E(1, 1));
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strainVector[i][2] = contact_radius[i] * (1.0 + E(2, 2));
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q = R[i]; // convert pure rotation matrix to quaternion
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strainVector[i][3] = q.w();
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strainVector[i][4] = q.x();
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strainVector[i][5] = q.y();
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strainVector[i][6] = q.z();
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} else {
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for (int j = 0; j < size_peratom_cols; j++) {
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strainVector[i][j] = 0.0;
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}
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}
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based array
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------------------------------------------------------------------------- */
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double ComputeSmdTlsphShape::memory_usage() {
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double bytes = size_peratom_cols * nmax * sizeof(double);
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return bytes;
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}
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