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_spring_rg.cpp
+++ b/src/fix_spring_rg.cpp
@ -0,0 +1,135 @@
+/* ----------------------------------------------------------------------
+   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)
+                        Paul Crozier (SNL)
+------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdlib.h"
+#include "string.h"
+#include "fix_spring_rg.h"
+#include "atom.h"
+#include "update.h"
+#include "group.h"
+#include "respa.h"
+#include "domain.h"
+#include "error.h"
+
+/* ---------------------------------------------------------------------- */
+
+FixSpringRG::FixSpringRG(int narg, char **arg) : Fix(narg, arg)
+{
+  if (narg != 5) error->all("Illegal fix spring/rg command");
+
+  k = atof(arg[3]);
+  rg0_flag = 0;
+  if (strcmp(arg[4],"NULL") == 0) rg0_flag = 1;
+  else rg0 = atof(arg[4]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixSpringRG::setmask()
+{
+  int mask = 0;
+  mask |= POST_FORCE;
+  mask |= POST_FORCE_RESPA;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixSpringRG::init()
+{
+  masstotal = group->mass(igroup);
+
+  // if rg0 was specified as NULL, compute current Rg
+  // only occurs on 1st run
+
+  if (rg0_flag) {
+    double xcm[3];
+    group->xcm(igroup,masstotal,xcm);
+    rg0 = group->gyration(igroup,masstotal,xcm);
+    rg0_flag = 0;
+  }
+
+  if (strcmp(update->integrate_style,"respa") == 0)
+    nlevels_respa = ((Respa *) update->integrate)->nlevels;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixSpringRG::setup()
+{
+  if (strcmp(update->integrate_style,"verlet") == 0)
+    post_force(1);
+  else {
+    ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
+    post_force_respa(1,nlevels_respa-1,0);
+    ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixSpringRG::post_force(int vflag)
+{
+  // compute current Rg and center-of-mass
+
+  double xcm[3];
+  group->xcm(igroup,masstotal,xcm);
+  double rg = group->gyration(igroup,masstotal,xcm);
+
+  // apply restoring force to atoms in group
+  // f = -k*(r-r0)*mass/masstotal
+
+  double dx,dy,dz,term1;
+
+  double **f = atom->f;
+  double **x = atom->x;
+  int *mask = atom->mask;
+  int *type = atom->type;
+  int *image = atom->image;
+  double *mass = atom->mass;
+  int nlocal = atom->nlocal;
+  
+  double massfrac;
+  double xprd = domain->xprd;
+  double yprd = domain->yprd;
+  double zprd = domain->zprd;
+   
+  int xbox,ybox,zbox;
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      term1 = 2.0 * k * (1.0 - rg0/rg);
+      xbox = (image[i] & 1023) - 512;
+      ybox = (image[i] >> 10 & 1023) - 512;
+      zbox = (image[i] >> 20) - 512;
+      dx = (x[i][0] + xbox*xprd) - xcm[0];
+      dy = (x[i][1] + ybox*yprd) - xcm[1];
+      dz = (x[i][2] + zbox*zprd) - xcm[2];
+      massfrac = mass[type[i]]/masstotal;
+      f[i][0] -= term1*dx*massfrac;
+      f[i][1] -= term1*dy*massfrac;
+      f[i][2] -= term1*dz*massfrac;
+    }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixSpringRG::post_force_respa(int vflag, int ilevel, int iloop)
+{
+  if (ilevel == nlevels_respa-1) post_force(vflag);
+}