forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1292 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
b4fabf0d0c
commit
0808bd4c86
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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 "math.h"
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#include "string.h"
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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 "modify.h"
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#include "fix.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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#define INVOKED_PERATOM 4
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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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{
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if (narg != 4) error->all("Illegal compute displace/atom command");
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peratom_flag = 1;
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size_peratom = 4;
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// store fix ID which stores original atom coords
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int n = strlen(arg[3]) + 1;
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id_fix = new char[n];
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strcpy(id_fix,arg[3]);
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int ifix = modify->find_fix(id_fix);
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if (ifix < 0) error->all("Could not find compute displace/atom fix ID");
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nmax = 0;
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displace = NULL;
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}
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/* ---------------------------------------------------------------------- */
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ComputeDisplaceAtom::~ComputeDisplaceAtom()
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{
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delete [] id_fix;
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memory->destroy_2d_double_array(displace);
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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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// check if is correct style
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int ifix = modify->find_fix(id_fix);
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if (ifix < 0) error->all("Could not find compute displace/atom fix ID");
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fix = modify->fix[ifix];
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if (strcmp(fix->style,"coord/original") != 0)
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error->all("Invalid fix style used in compute displace/atom command");
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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 |= INVOKED_PERATOM;
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// grow local displacement array if necessary
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if (atom->nmax > nmax) {
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memory->destroy_2d_double_array(displace);
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nmax = atom->nmax;
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displace =
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memory->create_2d_double_array(nmax,4,"compute/displace/atom:displace");
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vector_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->vector_atom;
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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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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] & 1023) - 512;
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ybox = (image[i] >> 10 & 1023) - 512;
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zbox = (image[i] >> 20) - 512;
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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] & 1023) - 512;
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ybox = (image[i] >> 10 & 1023) - 512;
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zbox = (image[i] >> 20) - 512;
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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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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 = nmax*4 * sizeof(double);
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return bytes;
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}
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@ -0,0 +1,38 @@
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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 COMPUTE_DISPLACE_ATOM_H
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#define COMPUTE_DISPLACE_ATOM_H
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#include "compute.h"
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namespace LAMMPS_NS {
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class ComputeDisplaceAtom : public Compute {
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public:
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ComputeDisplaceAtom(class LAMMPS *, int, char **);
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~ComputeDisplaceAtom();
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void init();
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void compute_peratom();
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double memory_usage();
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private:
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int nmax;
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double **displace;
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char *id_fix;
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class Fix *fix;
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};
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}
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#endif
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@ -0,0 +1,184 @@
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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 = 3;
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peratom_freq = 1;
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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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// xoriginal = initial unwrapped positions of atoms
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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) 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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}
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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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vector_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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@ -0,0 +1,43 @@
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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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@ -78,6 +78,7 @@ CommandStyle(write_restart,WriteRestart)
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#ifdef ComputeInclude
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#include "compute_centro_atom.h"
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#include "compute_coord_atom.h"
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#include "compute_displace_atom.h"
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#include "compute_ke_atom.h"
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#include "compute_pe.h"
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#include "compute_pe_atom.h"
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@ -96,6 +97,7 @@ CommandStyle(write_restart,WriteRestart)
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#ifdef ComputeClass
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ComputeStyle(centro/atom,ComputeCentroAtom)
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ComputeStyle(coord/atom,ComputeCoordAtom)
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ComputeStyle(displace/atom,ComputeDisplaceAtom)
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ComputeStyle(ke/atom,ComputeKEAtom)
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ComputeStyle(pe,ComputePE)
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ComputeStyle(pe/atom,ComputePEAtom)
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@ -138,6 +140,7 @@ 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_com.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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@ -190,6 +193,7 @@ FixStyle(aveforce,FixAveForce)
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FixStyle(ave/spatial,FixAveSpatial)
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FixStyle(ave/time,FixAveTime)
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FixStyle(com,FixCOM)
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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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