git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@144 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/fix_wall_lj126.cpp

@@ -0,0 +1,179 @@
+/* ----------------------------------------------------------------------
+   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: Mark Stevens (SNL)
+------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdlib.h"
+#include "string.h"
+#include "fix_wall_lj126.h"
+#include "atom.h"
+#include "update.h"
+#include "output.h"
+#include "respa.h"
+#include "error.h"
+
+/* ---------------------------------------------------------------------- */
+
+FixWallLJ126::FixWallLJ126(int narg, char **arg) : Fix(narg, arg)
+{
+  if (narg != 8) error->all("Illegal fix wall/lj126 command");
+
+  if (strcmp(arg[3],"xlo") == 0) {
+    dim = 0;
+    side = -1;
+  } else if (strcmp(arg[3],"xhi") == 0) {
+    dim = 0;
+    side = 1;
+  } else if (strcmp(arg[3],"ylo") == 0) {
+    dim = 1;
+    side = -1;
+  } else if (strcmp(arg[3],"yhi") == 0) {
+    dim = 1;
+    side = 1;
+  } else if (strcmp(arg[3],"zlo") == 0) {
+    dim = 2;
+    side = -1;
+  } else if (strcmp(arg[3],"zhi") == 0) {
+    dim = 2;
+    side = 1;
+  } else error->all("Illegal fix wall/lj126 command");
+
+  coord = atof(arg[4]);
+  epsilon = atof(arg[5]);
+  sigma = atof(arg[6]);
+  cutoff = atof(arg[7]);
+
+  coeff1 = 48.0 * epsilon * pow(sigma,12.0);
+  coeff2 = 24.0 * epsilon * pow(sigma,6.0);
+  coeff3 = 4.0 * epsilon * pow(sigma,12.0);
+  coeff4 = 4.0 * epsilon * pow(sigma,6.0);
+
+  double r2inv = 1.0/(cutoff*cutoff);
+  double r6inv = r2inv*r2inv*r2inv;
+  offset = r6inv*(coeff3*r6inv - coeff4);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixWallLJ126::setmask()
+{
+  int mask = 0;
+  mask |= POST_FORCE;
+  mask |= THERMO;
+  mask |= POST_FORCE_RESPA;
+  mask |= MIN_POST_FORCE;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixWallLJ126::init()
+{
+  if (strcmp(update->integrate_style,"respa") == 0)
+    nlevels_respa = ((Respa *) update->integrate)->nlevels;
+
+  if (thermo_print || thermo_energy) thermo_flag = 1;
+  else thermo_flag = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixWallLJ126::setup()
+{
+  eflag_on = 1;
+  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);
+  }
+  eflag_on = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixWallLJ126::min_setup()
+{
+  eflag_on = 1;
+  post_force(1);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixWallLJ126::post_force(int vflag)
+{
+  bool eflag = false;
+  if (thermo_flag) {
+    if (eflag_on) eflag = true;
+    else if (output->next_thermo == update->ntimestep) eflag = true;
+  }
+
+  double **x = atom->x;
+  double **f = atom->f;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  double delta,rinv,r2inv,r6inv;
+  if (eflag) eng = 0.0;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      if (side == -1) delta = x[i][dim] - coord;
+      else delta = coord - x[i][dim];
+      if (delta <= 0.0) continue;
+      if (delta > cutoff) continue;
+      rinv = 1.0/delta;
+      r2inv = rinv*rinv;
+      r6inv = r2inv*r2inv*r2inv;
+      f[i][dim] -= r6inv*(coeff1*r6inv - coeff2) * side;
+      if (eflag) eng += r6inv*(coeff3*r6inv - coeff4) - offset;
+    }
+
+  if (eflag) MPI_Allreduce(&eng,&etotal,1,MPI_DOUBLE,MPI_SUM,world);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixWallLJ126::post_force_respa(int vflag, int ilevel, int iloop)
+{
+  if (ilevel == nlevels_respa-1) post_force(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixWallLJ126::min_post_force(int vflag)
+{
+  post_force(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixWallLJ126::thermo_fields(int n, int *flags, char **keywords)
+{
+  if (n == 0) return 1;
+  flags[0] = 3;
+  strcpy(keywords[0],"Wall");
+  return 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixWallLJ126::thermo_compute(double *values)
+{
+  values[0] = etotal;
+  return 1;
+}

src/fix_wall_lj126.h

@@ -0,0 +1,43 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifndef FIX_WALL_LJ126_H
+#define FIX_WALL_LJ126_H
+
+#include "fix.h"
+
+class FixWallLJ126 : public Fix {
+ public:
+  FixWallLJ126(int, char **);
+  ~FixWallLJ126() {}
+  int setmask();
+  void init();
+  void setup();
+  void min_setup();
+  void post_force(int);
+  void post_force_respa(int, int, int);
+  void min_post_force(int);
+
+  int thermo_fields(int, int *, char **);
+  int thermo_compute(double *);
+
+ private:
+  int dim,side,thermo_flag,eflag_on;
+  double coord,epsilon,sigma,cutoff;
+  double coeff1,coeff2,coeff3,coeff4,offset;
+  double eng,etotal;
+  int nlevels_respa;
+};
+
+#endif
+

src/fix_wall_lj93.cpp

@@ -56,6 +56,12 @@ FixWallLJ93::FixWallLJ93(int narg, char **arg) : Fix(narg, arg)
   coeff2 = 3.0 * epsilon * pow(sigma,3.0);
   coeff3 = 2.0/15.0 * epsilon * pow(sigma,9.0);
   coeff4 = epsilon * pow(sigma,3.0);
+
+  double rinv = 1.0/cutoff;
+  double r2inv = rinv*rinv;
+  double r4inv = r2inv*r2inv;
+  double r10inv = r4inv*r4inv*r2inv;
+  offset = coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -133,7 +139,7 @@ void FixWallLJ93::post_force(int vflag)
       r4inv = r2inv*r2inv;
       r10inv = r4inv*r4inv*r2inv;
       f[i][dim] -= (coeff1*r10inv - coeff2*r4inv) * side;
-      if (eflag) eng += coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv;
+      if (eflag) eng += coeff3*r4inv*r4inv*rinv - coeff4*r2inv*rinv - offset;
     }
 
   if (eflag) MPI_Allreduce(&eng,&etotal,1,MPI_DOUBLE,MPI_SUM,world);

src/fix_wall_lj93.h

@@ -33,7 +33,7 @@ class FixWallLJ93 : public Fix {
  private:
   int dim,side,thermo_flag,eflag_on;
   double coord,epsilon,sigma,cutoff;
-  double coeff1,coeff2,coeff3,coeff4;
+  double coeff1,coeff2,coeff3,coeff4,offset;
   double eng,etotal;
   int nlevels_respa;
 };

src/style.h

@@ -130,6 +130,7 @@ DumpStyle(xyz,DumpXYZ)
 #include "fix_uniaxial.h"
 #include "fix_viscous.h"
 #include "fix_volume_rescale.h"
+#include "fix_wall_lj126.h"
 #include "fix_wall_lj93.h"
 #include "fix_wall_reflect.h"
 #include "fix_wiggle.h"
@@ -174,6 +175,7 @@ FixStyle(tmd,FixTMD)
 FixStyle(uniaxial,FixUniaxial)
 FixStyle(viscous,FixViscous)
 FixStyle(volume/rescale,FixVolRescale)
+FixStyle(wall/lj126,FixWallLJ126)
 FixStyle(wall/lj93,FixWallLJ93)
 FixStyle(wall/reflect,FixWallReflect)
 FixStyle(wiggle,FixWiggle)