git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@26 f3b2605a-c512-4ea7-a41b-209d697bcdaa

2006-09-27 19:51:33 +00:00
parent 3422cb245c
commit 222c95507e
536 changed files with 108384 additions and 0 deletions
--- a/src/fix_recenter.cpp
+++ b/src/fix_recenter.cpp
@ -0,0 +1,166 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   www.cs.sandia.gov/~sjplimp/lammps.html
+   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+
+   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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
+------------------------------------------------------------------------- */
+
+#include "stdlib.h"
+#include "string.h"
+#include "fix_recenter.h"
+#include "atom.h"
+#include "group.h"
+#include "domain.h"
+#include "modify.h"
+#include "comm.h"
+#include "error.h"
+
+/* ---------------------------------------------------------------------- */
+
+FixRecenter::FixRecenter(int narg, char **arg) : Fix(narg, arg)
+{
+  if (narg < 6) error->all("Illegal fix recenter command");
+
+  xcom = ycom = zcom = 0.0;
+  xflag = yflag = zflag = 1;
+  xinitflag = yinitflag = zinitflag = 0;
+
+  if (strcmp(arg[3],"NULL") == 0) xflag = 0;
+  else if (strcmp(arg[3],"INIT") == 0) xinitflag = 1;
+  else xcom = atof(arg[3]);
+  if (strcmp(arg[4],"NULL") == 0) yflag = 0;
+  else if (strcmp(arg[4],"INIT") == 0) yinitflag = 1;
+  else ycom = atof(arg[4]);
+  if (strcmp(arg[5],"NULL") == 0) zflag = 0;
+  else if (strcmp(arg[5],"INIT") == 0) zinitflag = 1;
+  else zcom = atof(arg[5]);
+
+  // optional args
+
+  group2bit = groupbit;
+  scaleflag = 1;
+
+  int iarg = 6;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg],"shift") == 0) {
+      int igroup2 = group->find(arg[iarg]);
+      if (igroup2 < 0) error->all("Could not find fix recenter group ID");
+      group2bit = group->bitmask[igroup2];
+      iarg += 2;
+    } else if (strcmp(arg[iarg],"units") == 0) {
+      if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
+      else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
+      else if (strcmp(arg[iarg+1],"fraction") == 0) scaleflag = 2;
+      else error->all("Illegal fix indent command");
+      iarg += 2;
+    } else error->all("Illegal fix recenter command");
+  }
+
+  // scale xcom,ycom,zcom
+
+  double xscale,yscale,zscale;
+  if (scaleflag == 1) {
+    xscale = domain->xlattice;
+    yscale = domain->ylattice;
+    zscale = domain->zlattice;
+  }
+  else xscale = yscale = zscale = 1.0;
+
+  xcom *= xscale;
+  ycom *= yscale;
+  zcom *= zscale;
+
+  // cannot have 0 atoms in group
+
+  if (group->count(igroup) == 0.0)
+    error->all("Fix recenter group has no atoms");
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixRecenter::setmask()
+{
+  int mask = 0;
+  mask |= INITIAL_INTEGRATE;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixRecenter::init()
+{
+  // warn if any integrate fix comes after this one
+
+  int after = 0;
+  int flag = 0;
+  for (int i = 0; i < modify->nfix; i++) {
+    if (strcmp(id,modify->fix[i]->id) == 0) after = 1;
+    else if ((modify->fmask[i] & INITIAL_INTEGRATE) && after) flag = 1;
+  }
+  if (flag && comm->me == 0)
+    error->warning("Fix recenter should come after all other integration fixes");
+
+  masstotal = group->mass(igroup);
+
+  // if any components of requested COM were INIT, store initial COM
+
+  if (xinitflag || yinitflag || zinitflag) {
+    double xcm[3];
+    group->xcm(igroup,masstotal,xcm);
+    xinit = xcm[0];
+    yinit = xcm[1];
+    zinit = xcm[2];
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixRecenter::initial_integrate()
+{
+  // target COM
+
+  double xtarget,ytarget,ztarget;
+
+  if (xinitflag) xtarget = xinit;
+  else if (scaleflag == 2)
+    xtarget = domain->boxxlo + xcom*(domain->boxxhi - domain->boxxlo);
+  else xtarget = xcom;
+
+  if (yinitflag) ytarget = yinit;
+  else if (scaleflag == 2)
+    ytarget = domain->boxylo + ycom*(domain->boxyhi - domain->boxylo);
+  else ytarget = ycom;
+
+  if (zinitflag) ztarget = zinit;
+  else if (scaleflag == 2)
+    ztarget = domain->boxzlo + zcom*(domain->boxzhi - domain->boxzlo);
+  else ztarget = zcom;
+
+  // current COM
+
+  double xcm[3];
+  group->xcm(igroup,masstotal,xcm);
+
+  // shift coords by difference between actual COM and requested COM
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & group2bit) {
+      if (xflag) x[i][0] += xtarget - xcm[0];
+      if (yflag) x[i][1] += ytarget - xcm[1];
+      if (zflag) x[i][2] += ztarget - xcm[2];
+    }
+}