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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3610 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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commit
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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 "stdlib.h"
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#include "string.h"
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#include "fix_coord_original.h"
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#include "atom.h"
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#include "domain.h"
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#include "group.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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FixCoordOriginal::FixCoordOriginal(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 3) error->all("Illegal fix coord/original command");
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restart_peratom = 1;
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peratom_flag = 1;
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size_peratom_cols = 3;
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peratom_freq = 1;
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// optional args
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int comflag = 0;
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"com") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix coord/original command");
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if (strcmp(arg[iarg+1],"no") == 0) comflag = 0;
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else if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1;
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else error->all("Illegal fix coord/original command");
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iarg += 2;
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} else error->all("Illegal fix coord/original command");
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}
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// perform initial allocation of atom-based array
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// register with Atom class
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xoriginal = NULL;
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grow_arrays(atom->nmax);
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atom->add_callback(0);
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atom->add_callback(1);
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// cm = original center of mass
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double cm[3];
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if (comflag) {
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double masstotal = group->mass(igroup);
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group->xcm(igroup,masstotal,cm);
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}
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// xoriginal = initial unwrapped positions of atoms
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// relative to center of mass if comflag is set
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double **x = atom->x;
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int *mask = atom->mask;
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int *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) {
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domain->unmap(x[i],image[i],xoriginal[i]);
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if (comflag) {
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xoriginal[i][0] -= cm[0];
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xoriginal[i][1] -= cm[1];
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xoriginal[i][2] -= cm[2];
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}
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} else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
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}
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}
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/* ---------------------------------------------------------------------- */
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FixCoordOriginal::~FixCoordOriginal()
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{
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// unregister callbacks to this fix from Atom class
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atom->delete_callback(id,0);
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atom->delete_callback(id,1);
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// delete locally stored array
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memory->destroy_2d_double_array(xoriginal);
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}
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/* ---------------------------------------------------------------------- */
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int FixCoordOriginal::setmask()
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{
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int mask = 0;
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return mask;
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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 FixCoordOriginal::memory_usage()
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{
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double bytes = atom->nmax*3 * sizeof(double);
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return bytes;
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}
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/* ----------------------------------------------------------------------
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allocate atom-based array
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------------------------------------------------------------------------- */
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void FixCoordOriginal::grow_arrays(int nmax)
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{
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xoriginal =
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memory->grow_2d_double_array(xoriginal,nmax,3,"fix_msd:xoriginal");
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array_atom = xoriginal;
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}
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/* ----------------------------------------------------------------------
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copy values within local atom-based array
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------------------------------------------------------------------------- */
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void FixCoordOriginal::copy_arrays(int i, int j)
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{
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xoriginal[j][0] = xoriginal[i][0];
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xoriginal[j][1] = xoriginal[i][1];
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xoriginal[j][2] = xoriginal[i][2];
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}
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/* ----------------------------------------------------------------------
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pack values in local atom-based array for exchange with another proc
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------------------------------------------------------------------------- */
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int FixCoordOriginal::pack_exchange(int i, double *buf)
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{
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buf[0] = xoriginal[i][0];
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buf[1] = xoriginal[i][1];
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buf[2] = xoriginal[i][2];
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return 3;
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}
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/* ----------------------------------------------------------------------
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unpack values in local atom-based array from exchange with another proc
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------------------------------------------------------------------------- */
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int FixCoordOriginal::unpack_exchange(int nlocal, double *buf)
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{
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xoriginal[nlocal][0] = buf[0];
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xoriginal[nlocal][1] = buf[1];
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xoriginal[nlocal][2] = buf[2];
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return 3;
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}
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/* ----------------------------------------------------------------------
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pack values in local atom-based arrays for restart file
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------------------------------------------------------------------------- */
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int FixCoordOriginal::pack_restart(int i, double *buf)
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{
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buf[0] = 4;
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buf[1] = xoriginal[i][0];
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buf[2] = xoriginal[i][1];
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buf[3] = xoriginal[i][2];
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return 4;
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}
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/* ----------------------------------------------------------------------
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unpack values from atom->extra array to restart the fix
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------------------------------------------------------------------------- */
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void FixCoordOriginal::unpack_restart(int nlocal, int nth)
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{
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double **extra = atom->extra;
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// skip to Nth set of extra values
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int m = 0;
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for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
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m++;
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xoriginal[nlocal][0] = extra[nlocal][m++];
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xoriginal[nlocal][1] = extra[nlocal][m++];
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xoriginal[nlocal][2] = extra[nlocal][m++];
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}
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/* ----------------------------------------------------------------------
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maxsize of any atom's restart data
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------------------------------------------------------------------------- */
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int FixCoordOriginal::maxsize_restart()
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{
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return 4;
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}
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/* ----------------------------------------------------------------------
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size of atom nlocal's restart data
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------------------------------------------------------------------------- */
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int FixCoordOriginal::size_restart(int nlocal)
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{
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return 4;
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}
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@ -1,43 +0,0 @@
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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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#ifndef FIX_COORD_ORIGINAL_H
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#define FIX_COORD_ORIGINAL_H
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#include "fix.h"
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namespace LAMMPS_NS {
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class FixCoordOriginal : public Fix {
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public:
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FixCoordOriginal(class LAMMPS *, int, char **);
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~FixCoordOriginal();
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int setmask();
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double memory_usage();
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void grow_arrays(int);
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void copy_arrays(int, int);
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int pack_exchange(int, double *);
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int unpack_exchange(int, double *);
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int pack_restart(int, double *);
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void unpack_restart(int, int);
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int size_restart(int);
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int maxsize_restart();
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private:
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double **xoriginal; // original coords of atoms
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};
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}
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#endif
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@ -189,7 +189,6 @@ DumpStyle(xyz,DumpXYZ)
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#include "fix_ave_spatial.h"
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#include "fix_ave_time.h"
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#include "fix_box_relax.h"
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#include "fix_coord_original.h"
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#include "fix_deform.h"
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#include "fix_deposit.h"
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#include "fix_drag.h"
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#include "fix_spring.h"
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#include "fix_spring_rg.h"
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#include "fix_spring_self.h"
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#include "fix_store_coord.h"
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#include "fix_store_force.h"
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#include "fix_temp_berendsen.h"
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#include "fix_temp_rescale.h"
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#include "fix_thermal_conductivity.h"
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@ -248,7 +249,6 @@ FixStyle(ave/histo,FixAveHisto)
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FixStyle(ave/spatial,FixAveSpatial)
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FixStyle(ave/time,FixAveTime)
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FixStyle(box/relax,FixBoxRelax)
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FixStyle(coord/original,FixCoordOriginal)
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FixStyle(deform,FixDeform)
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FixStyle(deposit,FixDeposit)
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FixStyle(drag,FixDrag)
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@ -287,6 +287,8 @@ FixStyle(SHEAR_HISTORY,FixShearHistory)
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FixStyle(spring,FixSpring)
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FixStyle(spring/rg,FixSpringRG)
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FixStyle(spring/self,FixSpringSelf)
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FixStyle(store/coord,FixStoreCoord)
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FixStyle(store/force,FixStoreForce)
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FixStyle(temp/berendsen,FixTempBerendsen)
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FixStyle(temp/rescale,FixTempRescale)
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FixStyle(thermal/conductivity,FixThermalConductivity)
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