diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp new file mode 100644 index 0000000000..8a4de20b3d --- /dev/null +++ b/src/compute_coord_atom.cpp @@ -0,0 +1,128 @@ +/* ---------------------------------------------------------------------- + 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 "stdlib.h" +#include "compute_coord_atom.h" +#include "atom.h" +#include "modify.h" +#include "neighbor.h" +#include "force.h" +#include "pair.h" +#include "comm.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 4) error->all("Illegal compute centro/atom command"); + + cutoff = atof(arg[3]); + + peratom_flag = 1; + size_peratom = 0; + neigh_full_once = 1; + + nmax = 0; + coordination = NULL; +} + +/* ---------------------------------------------------------------------- */ + +ComputeCoordAtom::~ComputeCoordAtom() +{ + memory->sfree(coordination); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeCoordAtom::init() +{ + if (force->pair == NULL || cutoff > force->pair->cutforce) + error->all("Compute coord/atom cutoff is longer than pairwise cutoff"); + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style,"coord/atom") == 0) count++; + if (count > 1 && comm->me == 0) + error->warning("More than one compute coord/atom defined"); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeCoordAtom::compute_peratom() +{ + int j,k,jj,kk,n,numneigh; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighs; + + // grow coordination array if necessary + + if (atom->nlocal > nmax) { + memory->sfree(coordination); + nmax = atom->nmax; + coordination = (double *) + memory->smalloc(nmax*sizeof(double),"compute/coord/atom:coordination"); + scalar_atom = coordination; + } + + // if needed, build a full neighbor list + + if (!neighbor->full_every) neighbor->build_full(); + + // compute coordination number for each atom in group + // use full neighbor list to count atoms less than cutoff + + double **x = atom->x; + int *mask = atom->mask; + int nlocal = atom->nlocal; + int nall = atom->nlocal + atom->nghost; + double cutsq = cutoff*cutoff; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + neighs = neighbor->firstneigh_full[i]; + numneigh = neighbor->numneigh_full[i]; + + n = 0; + for (k = 0; k < numneigh; k++) { + j = neighs[k]; + if (j >= nall) j %= nall; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + if (rsq < cutsq) n++; + } + + coordination[i] = n; + } +} +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +int ComputeCoordAtom::memory_usage() +{ + int bytes = nmax * sizeof(double); + return bytes; +} diff --git a/src/compute_coord_atom.h b/src/compute_coord_atom.h new file mode 100644 index 0000000000..74ff941087 --- /dev/null +++ b/src/compute_coord_atom.h @@ -0,0 +1,37 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifndef COMPUTE_COORD_ATOM_H +#define COMPUTE_COORD_ATOM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeCoordAtom : public Compute { + public: + ComputeCoordAtom(class LAMMPS *, int, char **); + ~ComputeCoordAtom(); + void init(); + void compute_peratom(); + int memory_usage(); + + private: + int nmax; + double cutoff; + double *coordination; +}; + +} + +#endif diff --git a/src/style.h b/src/style.h index 1ff730a2a8..2302a116d8 100644 --- a/src/style.h +++ b/src/style.h @@ -73,6 +73,7 @@ CommandStyle(write_restart,WriteRestart) #ifdef ComputeInclude #include "compute_centro_atom.h" +#include "compute_coord_atom.h" #include "compute_epair_atom.h" #include "compute_etotal_atom.h" #include "compute_ke_atom.h" @@ -90,6 +91,7 @@ CommandStyle(write_restart,WriteRestart) #ifdef ComputeClass ComputeStyle(centro/atom,ComputeCentroAtom) +ComputeStyle(coord/atom,ComputeCoordAtom) ComputeStyle(epair/atom,ComputeEpairAtom) ComputeStyle(etotal/atom,ComputeEtotalAtom) ComputeStyle(ke/atom,ComputeKEAtom)