/* ---------------------------------------------------------------------- This is the ██╗ ██╗ ██████╗ ██████╗ ██████╗ ██╗ ██╗████████╗███████╗ ██║ ██║██╔════╝ ██╔════╝ ██╔════╝ ██║ ██║╚══██╔══╝██╔════╝ ██║ ██║██║ ███╗██║ ███╗██║ ███╗███████║ ██║ ███████╗ ██║ ██║██║ ██║██║ ██║██║ ██║██╔══██║ ██║ ╚════██║ ███████╗██║╚██████╔╝╚██████╔╝╚██████╔╝██║ ██║ ██║ ███████║ ╚══════╝╚═╝ ╚═════╝ ╚═════╝ ╚═════╝ ╚═╝ ╚═╝ ╚═╝ ╚══════╝® DEM simulation engine, released by DCS Computing Gmbh, Linz, Austria http://www.dcs-computing.com, office@dcs-computing.com LIGGGHTS® is part of CFDEM®project: http://www.liggghts.com | http://www.cfdem.com Core developer and main author: Christoph Kloss, christoph.kloss@dcs-computing.com LIGGGHTS® is open-source, distributed under the terms of the GNU Public License, version 2 or later. It is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. You should have received a copy of the GNU General Public License along with LIGGGHTS®. If not, see http://www.gnu.org/licenses . See also top-level README and LICENSE files. LIGGGHTS® and CFDEM® are registered trade marks of DCS Computing GmbH, the producer of the LIGGGHTS® software and the CFDEM®coupling software See http://www.cfdem.com/terms-trademark-policy for details. ------------------------------------------------------------------------- Contributing author and copyright for this file: This file is from LAMMPS 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. ------------------------------------------------------------------------- */ #include #include "compute_msd.h" #include "atom.h" #include "update.h" #include "group.h" #include "domain.h" #include "modify.h" #include "fix_store.h" #include "error.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeMSD::ComputeMSD(LAMMPS *lmp, int &iarg, int narg, char **arg) : Compute(lmp, iarg, narg, arg) { if (narg < iarg) error->all(FLERR,"Illegal compute msd command"); vector_flag = 1; size_vector = 4; extvector = 0; // optional args comflag = 0; while (iarg < narg) { if (strcmp(arg[iarg],"com") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal compute msd command"); if (strcmp(arg[iarg+1],"no") == 0) comflag = 0; else if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1; else error->all(FLERR,"Illegal compute msd command"); iarg += 2; } else error->all(FLERR,"Illegal compute msd command"); } // create a new fix STORE style // id = compute-ID + COMPUTE_STORE, fix group = compute group int n = strlen(id) + strlen("_COMPUTE_STORE") + 1; id_fix = new char[n]; strcpy(id_fix,id); strcat(id_fix,"_COMPUTE_STORE"); char **newarg = new char*[5]; newarg[0] = id_fix; newarg[1] = group->names[igroup]; newarg[2] = (char *) "STORE"; newarg[3] = (char *) "1"; newarg[4] = (char *) "3"; modify->add_fix(5,newarg); fix = (FixStore *) modify->fix[modify->nfix-1]; delete [] newarg; // calculate xu,yu,zu for fix store array // skip if reset from restart file if (fix->restart_reset) fix->restart_reset = 0; else { double **xoriginal = fix->astore; double **x = atom->x; int *mask = atom->mask; tagint *image = atom->image; int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]); else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0; // adjust for COM if requested if (comflag) { double cm[3]; masstotal = group->mass(igroup); group->xcm(igroup,masstotal,cm); for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { xoriginal[i][0] -= cm[0]; xoriginal[i][1] -= cm[1]; xoriginal[i][2] -= cm[2]; } } } // displacement vector vector = new double[4]; } /* ---------------------------------------------------------------------- */ ComputeMSD::~ComputeMSD() { // check nfix in case all fixes have already been deleted if (modify->nfix) modify->delete_fix(id_fix); delete [] id_fix; delete [] vector; } /* ---------------------------------------------------------------------- */ void ComputeMSD::init() { // set fix which stores original atom coords int ifix = modify->find_fix(id_fix); if (ifix < 0) error->all(FLERR,"Could not find compute msd fix ID"); fix = (FixStore *) modify->fix[ifix]; // nmsd = # of atoms in group nmsd = group->count(igroup); masstotal = group->mass(igroup); } /* ---------------------------------------------------------------------- */ void ComputeMSD::compute_vector() { invoked_vector = update->ntimestep; // cm = current center of mass double cm[3]; if (comflag) group->xcm(igroup,masstotal,cm); else cm[0] = cm[1] = cm[2] = 0.0; // dx,dy,dz = displacement of atom from original position // original unwrapped position is stored by fix // relative to center of mass if comflag is set // for triclinic, need to unwrap current atom coord via h matrix double **xoriginal = fix->astore; double **x = atom->x; int *mask = atom->mask; tagint *image = atom->image; int nlocal = atom->nlocal; double *h = domain->h; double xprd = domain->xprd; double yprd = domain->yprd; double zprd = domain->zprd; double dx,dy,dz; int xbox,ybox,zbox; double msd[4]; msd[0] = msd[1] = msd[2] = msd[3] = 0.0; if (domain->triclinic == 0) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { xbox = (image[i] & IMGMASK) - IMGMAX; ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0]; dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1]; dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2]; msd[0] += dx*dx; msd[1] += dy*dy; msd[2] += dz*dz; msd[3] += dx*dx + dy*dy + dz*dz; } } else { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { xbox = (image[i] & IMGMASK) - IMGMAX; ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - cm[0] - xoriginal[i][0]; dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1]; dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2]; msd[0] += dx*dx; msd[1] += dy*dy; msd[2] += dz*dz; msd[3] += dx*dx + dy*dy + dz*dz; } } MPI_Allreduce(msd,vector,4,MPI_DOUBLE,MPI_SUM,world); if (nmsd) { vector[0] /= nmsd; vector[1] /= nmsd; vector[2] /= nmsd; vector[3] /= nmsd; } }