git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1292 f3b2605a-c512-4ea7-a41b-209d697bcdaa

2008-01-04 00:12:32 +00:00
parent b4fabf0d0c
commit 0808bd4c86
5 changed files with 419 additions and 0 deletions
--- a/src/compute_displace_atom.cpp
+++ b/src/compute_displace_atom.cpp
@ -0,0 +1,150 @@
+/* ----------------------------------------------------------------------
+   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 "math.h"
+#include "string.h"
+#include "compute_displace_atom.h"
+#include "atom.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define INVOKED_PERATOM 4
+
+/* ---------------------------------------------------------------------- */
+
+ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg)
+{
+  if (narg != 4) error->all("Illegal compute displace/atom command");
+
+  peratom_flag = 1;
+  size_peratom = 4;
+
+  // store fix ID which stores original atom coords
+
+  int n = strlen(arg[3]) + 1;
+  id_fix = new char[n];
+  strcpy(id_fix,arg[3]);
+
+  int ifix = modify->find_fix(id_fix);
+  if (ifix < 0) error->all("Could not find compute displace/atom fix ID");
+
+  nmax = 0;
+  displace = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeDisplaceAtom::~ComputeDisplaceAtom()
+{
+  delete [] id_fix;
+  memory->destroy_2d_double_array(displace);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeDisplaceAtom::init()
+{
+  // set fix which stores original atom coords
+  // check if is correct style
+
+  int ifix = modify->find_fix(id_fix);
+  if (ifix < 0) error->all("Could not find compute displace/atom fix ID");
+  fix = modify->fix[ifix];
+
+  if (strcmp(fix->style,"coord/original") != 0)
+    error->all("Invalid fix style used in compute displace/atom command");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeDisplaceAtom::compute_peratom()
+{
+  invoked |= INVOKED_PERATOM;
+
+  // grow local displacement array if necessary
+
+  if (atom->nmax > nmax) {
+    memory->destroy_2d_double_array(displace);
+    nmax = atom->nmax;
+    displace =
+      memory->create_2d_double_array(nmax,4,"compute/displace/atom:displace");
+    vector_atom = displace;
+  }
+
+  // dx,dy,dz = displacement of atom from original position
+  // original unwrapped position is stored by fix
+  // for triclinic, need to unwrap current atom coord via h matrix
+
+  double **xoriginal = fix->vector_atom;
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  int *image = atom->image;
+  int nlocal = atom->nlocal;
+
+  double *h = domain->h;
+  double xprd = domain->xprd;
+  double yprd = domain->yprd;
+  double zprd = domain->zprd;
+  int xbox,ybox,zbox;
+  double dx,dy,dz;
+
+  if (domain->triclinic == 0) {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+	xbox = (image[i] & 1023) - 512;
+	ybox = (image[i] >> 10 & 1023) - 512;
+	zbox = (image[i] >> 20) - 512;
+	dx = x[i][0] + xbox*xprd - xoriginal[i][0];
+	dy = x[i][1] + ybox*yprd - xoriginal[i][1];
+	dz = x[i][2] + zbox*zprd - xoriginal[i][2];
+	displace[i][0] = dx;
+	displace[i][1] = dy;
+	displace[i][2] = dz;
+	displace[i][3] = sqrt(dx*dx + dy*dy + dz*dz);
+      } else displace[i][0] = displace[i][1] =
+	       displace[i][2] = displace[i][3] = 0.0;
+
+  } else {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+	xbox = (image[i] & 1023) - 512;
+	ybox = (image[i] >> 10 & 1023) - 512;
+	zbox = (image[i] >> 20) - 512;
+	dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0];
+	dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1];
+	dz = x[i][2] + h[2]*zbox - xoriginal[i][2];
+	displace[i][0] = dx;
+	displace[i][1] = dy;
+	displace[i][2] = dz;
+	displace[i][3] = sqrt(dx*dx + dy*dy + dz*dz);
+      } else displace[i][0] = displace[i][1] =
+	       displace[i][2] = displace[i][3] = 0.0;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double ComputeDisplaceAtom::memory_usage()
+{
+  double bytes = nmax*4 * sizeof(double);
+  return bytes;
+}