248 lines
7.3 KiB
C++
248 lines
7.3 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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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_displace_atom.h"
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#include "atom.h"
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#include "domain.h"
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#include "error.h"
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#include "fix_store_peratom.h"
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#include "group.h"
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#include "input.h"
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#include "memory.h"
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#include "modify.h"
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#include "update.h"
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#include "variable.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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displace(nullptr), id_fix(nullptr)
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{
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if (narg < 3) error->all(FLERR,"Illegal compute displace/atom command");
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peratom_flag = 1;
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size_peratom_cols = 4;
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create_attribute = 1;
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// optional args
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refreshflag = 0;
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rvar = nullptr;
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"refresh") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute displace/atom command");
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refreshflag = 1;
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delete [] rvar;
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rvar = utils::strdup(arg[iarg+1]);
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iarg += 2;
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} else error->all(FLERR,"Illegal compute displace/atom command");
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}
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// error check
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if (refreshflag) {
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ivar = input->variable->find(rvar);
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if (ivar < 0)
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error->all(FLERR,"Variable name for compute displace/atom does not exist");
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if (input->variable->atomstyle(ivar) == 0)
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error->all(FLERR,"Compute displace/atom variable "
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"is not atom-style variable");
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}
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// create a new fix STORE style
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// id = compute-ID + COMPUTE_STORE, fix group = compute group
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id_fix = utils::strdup(std::string(id) + "_COMPUTE_STORE");
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fix = dynamic_cast<FixStorePeratom *>(
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modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 3", id_fix, group->names[igroup])));
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// calculate xu,yu,zu for fix store array
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// skip if reset from restart file
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if (fix->restart_reset) fix->restart_reset = 0;
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else {
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double **xoriginal = fix->astore;
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double **x = atom->x;
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int *mask = atom->mask;
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imageint *image = atom->image;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]);
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else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
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}
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// per-atom displacement array
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nmax = nvmax = 0;
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varatom = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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ComputeDisplaceAtom::~ComputeDisplaceAtom()
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{
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// check nfix in case all fixes have already been deleted
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if (modify->nfix) modify->delete_fix(id_fix);
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delete [] id_fix;
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memory->destroy(displace);
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delete [] rvar;
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memory->destroy(varatom);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeDisplaceAtom::init()
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{
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// set fix which stores original atom coords
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fix = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_fix));
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if (!fix) error->all(FLERR,"Could not find compute displace/atom fix with ID {}", id_fix);
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if (refreshflag) {
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ivar = input->variable->find(rvar);
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if (ivar < 0)
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error->all(FLERR,"Variable name for compute displace/atom does not exist");
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeDisplaceAtom::compute_peratom()
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{
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invoked_peratom = update->ntimestep;
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// grow local displacement array if necessary
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if (atom->nmax > nmax) {
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memory->destroy(displace);
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nmax = atom->nmax;
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memory->create(displace,nmax,4,"displace/atom:displace");
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array_atom = displace;
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}
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// dx,dy,dz = displacement of atom from original position
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// original unwrapped position is stored by fix
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// for triclinic, need to unwrap current atom coord via h matrix
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double **xoriginal = fix->astore;
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double **x = atom->x;
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int *mask = atom->mask;
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imageint *image = atom->image;
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int nlocal = atom->nlocal;
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double *h = domain->h;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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int xbox,ybox,zbox;
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double dx,dy,dz;
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if (domain->triclinic == 0) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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dx = x[i][0] + xbox*xprd - xoriginal[i][0];
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dy = x[i][1] + ybox*yprd - xoriginal[i][1];
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dz = x[i][2] + zbox*zprd - xoriginal[i][2];
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displace[i][0] = dx;
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displace[i][1] = dy;
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displace[i][2] = dz;
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displace[i][3] = sqrt(dx*dx + dy*dy + dz*dz);
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} else displace[i][0] = displace[i][1] =
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displace[i][2] = displace[i][3] = 0.0;
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0];
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dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1];
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dz = x[i][2] + h[2]*zbox - xoriginal[i][2];
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displace[i][0] = dx;
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displace[i][1] = dy;
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displace[i][2] = dz;
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displace[i][3] = sqrt(dx*dx + dy*dy + dz*dz);
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} else displace[i][0] = displace[i][1] =
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displace[i][2] = displace[i][3] = 0.0;
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}
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}
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/* ----------------------------------------------------------------------
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initialize one atom's storage values, called when atom is created
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------------------------------------------------------------------------- */
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void ComputeDisplaceAtom::set_arrays(int i)
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{
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double **xoriginal = fix->astore;
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double **x = atom->x;
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xoriginal[i][0] = x[i][0];
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xoriginal[i][1] = x[i][1];
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xoriginal[i][2] = x[i][2];
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}
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/* ----------------------------------------------------------------------
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reset per-atom storage values, based on atom-style variable evaluation
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called by dump when dump_modify refresh is set
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------------------------------------------------------------------------- */
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void ComputeDisplaceAtom::refresh()
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{
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if (atom->nmax > nvmax) {
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nvmax = atom->nmax;
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memory->destroy(varatom);
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memory->create(varatom,nvmax,"displace/atom:varatom");
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}
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input->variable->compute_atom(ivar,igroup,varatom,1,0);
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double **xoriginal = fix->astore;
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double **x = atom->x;
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imageint *image = atom->image;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (varatom[i]) domain->unmap(x[i],image[i],xoriginal[i]);
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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 ComputeDisplaceAtom::memory_usage()
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{
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double bytes = (double)nmax*4 * sizeof(double);
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bytes += (double)nvmax * sizeof(double);
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return bytes;
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}
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