implement fix wall/morse based on fix wall/region and fix wall/harmonic

doc/src/fix_wall.txt

@@ -12,22 +12,25 @@ fix wall/lj126 command :h3
 fix wall/lj1043 command :h3
 fix wall/colloid command :h3
 fix wall/harmonic command :h3
+fix wall/morse command :h3
 
 [Syntax:]
 
 fix ID group-ID style face args ... keyword value ... :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
-style = {wall/lj93} or {wall/lj126} or {wall/lj1043} or {wall/colloid} or {wall/harmonic} :l
+style = {wall/lj93} or {wall/lj126} or {wall/lj1043} or {wall/colloid} or {wall/harmonic} or {wall/morse} :l
 one or more face/arg pairs may be appended :l
 face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
-  args = coord epsilon sigma cutoff
+  args = coord epsilon \[alpha\] sigma cutoff
     coord = position of wall = EDGE or constant or variable
       EDGE = current lo or hi edge of simulation box
       constant = number like 0.0 or -30.0 (distance units)
       variable = "equal-style variable"_variable.html like v_x or v_wiggle
     epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
       epsilon can be a variable (see below)
+    alpha = width factor for wall-particle interaction (1/distance units)
+      [only] for {wall/morse}. alpha can be a variable (see below)
     sigma = size factor for wall-particle interaction (distance units)
       sigma can be a variable (see below)
     cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
@@ -48,6 +51,7 @@ keyword = {units} or {fld} :l
 
 fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
 fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
+fix wallhi all wall/morse xhi EDGE 1.0 1.0 1.0 2.5 units box
 fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
 fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 :pre
 
@@ -80,6 +84,10 @@ potential:
 
 :c,image(Eqs/fix_wall_harmonic.jpg)
 
+For style {wall/morse}, the energy E is given by a Morse potential:
+
+:c,image(Eqs/pair_morse.jpg)
+
 In all cases, {r} is the distance from the particle to the wall at
 position {coord}, and Rc is the {cutoff} distance at which the
 particle and wall no longer interact.  The energy of the wall
@@ -147,7 +155,15 @@ constant K, and has units (energy/distance^2).  The input parameter
 spring is at the {cutoff}.  This is a repulsive-only spring since the
 interaction is truncated at the {cutoff}
 
-For any wall, the {epsilon} and/or {sigma} parameter can be specified
+For the {wall/morse} style, one additional parameter {alpha} is required.
+Thus the parameters are in this order: {epsilon} as the depth of the
+Morse potential (D_0), {alpha} as the width parameter of the Morse
+potential, and {sigma} the location of the minimum (r_0)
+the wall.  {D_0} has energy units, {alpha} inverse distance units, and
+{r_0} distance units.
+
+For any wall, the {epsilon} and/or {sigma} and/or {alpha} parameter can
+be specified
 as an "equal-style variable"_variable.html, in which case it should be
 specified as v_name, where name is the variable name.  As with a
 variable wall position, the variable is evaluated each timestep and

src/fix_wall.cpp

@@ -23,6 +23,7 @@
 #include "respa.h"
 #include "error.h"
 #include "force.h"
+#include "utils.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -99,6 +100,19 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
         estyle[nwall] = CONSTANT;
       }
 
+      if (utils::strmatch(style,"^wall/morse")) {
+        if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
+          int n = strlen(&arg[iarg+3][2]) + 1;
+          astr[nwall] = new char[n];
+          strcpy(astr[nwall],&arg[iarg+3][2]);
+          astyle[nwall] = VARIABLE;
+        } else {
+          alpha[nwall] = force->numeric(FLERR,arg[iarg+3]);
+          astyle[nwall] = CONSTANT;
+        }
+        ++iarg;
+      }
+
       if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
         int n = strlen(&arg[iarg+3][2]) + 1;
         sstr[nwall] = new char[n];

src/fix_wall.h

@@ -45,12 +45,12 @@ class FixWall : public Fix {
   virtual void wall_particle(int, int, double) = 0;
 
  protected:
-  double epsilon[6],sigma[6],cutoff[6];
+  double epsilon[6],sigma[6],alpha[6],cutoff[6];
   double ewall[7],ewall_all[7];
   double xscale,yscale,zscale;
-  int estyle[6],sstyle[6],wstyle[6];
+  int estyle[6],sstyle[6],astyle[6],wstyle[6];
   int eindex[6],sindex[6];
-  char *estr[6],*sstr[6];
+  char *estr[6],*sstr[6],*astr[6];
   int varflag;                // 1 if any wall position,epsilon,sigma is a var
   int eflag;                  // per-wall flag for energy summation
   int ilevel_respa;

src/fix_wall_morse.cpp

@@ -0,0 +1,87 @@
+/* ----------------------------------------------------------------------
+   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 "fix_wall_morse.h"
+#include <cmath>
+#include "atom.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ---------------------------------------------------------------------- */
+
+FixWallMorse::FixWallMorse(LAMMPS *lmp, int narg, char **arg) :
+  FixWall(lmp, narg, arg)
+{
+  dynamic_group_allow = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixWallMorse::precompute(int m)
+{
+  coeff1[m] = 2.0 * epsilon[m] * alpha[m];
+  const double alpha_dr = -alpha[m] * (cutoff[m] - sigma[m]);
+  offset[m] = epsilon[m] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
+}
+
+/* ----------------------------------------------------------------------
+   interaction of all particles in group with a wall
+   m = index of wall coeffs
+   which = xlo,xhi,ylo,yhi,zlo,zhi
+   error if any particle is on or behind wall
+------------------------------------------------------------------------- */
+
+void FixWallMorse::wall_particle(int m, int which, double coord)
+{
+  double delta,fwall;
+  double vn;
+
+  double **x = atom->x;
+  double **f = atom->f;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  int dim = which / 2;
+  int side = which % 2;
+  if (side == 0) side = -1;
+
+  int onflag = 0;
+
+  for (int i = 0; i < nlocal; i++) {
+    if (mask[i] & groupbit) {
+      if (side < 0) delta = x[i][dim] - coord;
+      else delta = coord - x[i][dim];
+      if (delta >= cutoff[m]) continue;
+      if (delta <= 0.0) {
+        onflag = 1;
+        continue;
+      }
+      double dr = delta - sigma[m];
+      double dexp = exp(-alpha[m] * dr);
+      fwall = side * coeff1[m] * (dexp*dexp - dexp) / delta;
+      ewall[0] += epsilon[m] * (dexp*dexp - 2.0*dexp) - offset[m];
+      f[i][dim] -= fwall;
+      ewall[m+1] += fwall;
+
+      if (evflag) {
+        if (side < 0) vn = -fwall*delta;
+        else vn = fwall*delta;
+        v_tally(dim, i, vn);
+      }
+    }
+  }
+
+  if (onflag) error->one(FLERR,"Particle on or inside fix wall surface");
+}

src/fix_wall_morse.h

@@ -0,0 +1,49 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(wall/morse,FixWallMorse)
+
+#else
+
+#ifndef LMP_FIX_WALL_MORSE_H
+#define LMP_FIX_WALL_MORSE_H
+
+#include "fix_wall.h"
+
+namespace LAMMPS_NS {
+
+class FixWallMorse : public FixWall {
+ public:
+  FixWallMorse(class LAMMPS *, int, char **);
+  void precompute(int);
+  void wall_particle(int, int, double);
+
+ private:
+  double coeff1[6],offset[6];
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Particle on or inside fix wall surface
+
+Particles must be "exterior" to the wall in order for energy/force to
+be calculated.
+
+*/