diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp new file mode 100755 index 0000000000000000000000000000000000000000..8dca23bd8b54f66ce90e966b93d73a4a6a86e68c --- /dev/null +++ b/src/compute_vacf.cpp @@ -0,0 +1,139 @@ +/* ---------------------------------------------------------------------- + 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 ret + 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_vacf.h" +#include "atom.h" +#include "update.h" +#include "group.h" +#include "modify.h" +#include "fix_store.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeVACF::ComputeVACF(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg < 3) error->all(FLERR,"Illegal compute vacf command"); + + vector_flag = 1; + size_vector = 4; + extvector = 0; + + // 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; + + // store current velocities in fix store array + // skip if reset from restart file + + if (fix->restart_reset) fix->restart_reset = 0; + else { + double **voriginal = fix->astore; + + double **v = atom->v; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + voriginal[i][0] = v[i][0]; + voriginal[i][1] = v[i][1]; + voriginal[i][2] = v[i][2]; + } else voriginal[i][0] = voriginal[i][1] = voriginal[i][2] = 0.0; + } + + // displacement vector + + vector = new double[4]; +} + +/* ---------------------------------------------------------------------- */ + +ComputeVACF::~ComputeVACF() +{ + // check nfix in case all fixes have already been deleted + + if (modify->nfix) modify->delete_fix(id_fix); + + delete [] id_fix; + delete [] vector; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeVACF::init() +{ + // set fix which stores original atom velocities + + int ifix = modify->find_fix(id_fix); + if (ifix < 0) error->all(FLERR,"Could not find compute vacf fix ID"); + fix = (FixStore *) modify->fix[ifix]; + + // nvacf = # of atoms in group + + nvacf = group->count(igroup); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeVACF::compute_vector() +{ + invoked_vector = update->ntimestep; + + double **voriginal = fix->astore; + + double **v = atom->v; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + double vxsq,vysq,vzsq; + double vacf[4]; + vacf[0] = vacf[1] = vacf[2] = vacf[3] = 0.0; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + vxsq = v[i][0] * voriginal[i][0]; + vysq = v[i][1] * voriginal[i][1]; + vzsq = v[i][2] * voriginal[i][2]; + vacf[0] += vxsq; + vacf[1] += vysq; + vacf[2] += vzsq; + vacf[3] += vxsq + vysq + vzsq; + } + + MPI_Allreduce(vacf,vector,4,MPI_DOUBLE,MPI_SUM,world); + if (nvacf) { + vector[0] /= nvacf; + vector[1] /= nvacf; + vector[2] /= nvacf; + vector[3] /= nvacf; + } +} diff --git a/src/compute_vacf.h b/src/compute_vacf.h new file mode 100755 index 0000000000000000000000000000000000000000..6d4399ad638620bbfa75ecc7f44b749de21e1fd3 --- /dev/null +++ b/src/compute_vacf.h @@ -0,0 +1,57 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(vacf,ComputeVACF) + +#else + +#ifndef LMP_COMPUTE_VACF_H +#define LMP_COMPUTE_VACF_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeVACF : public Compute { + public: + ComputeVACF(class LAMMPS *, int, char **); + ~ComputeVACF(); + void init(); + virtual void compute_vector(); + + protected: + bigint nvacf; + char *id_fix; + class FixStore *fix; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Could not find compute msd fix ID + +Self-explanatory. + +*/