git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14704 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/USER-MISC/README

@@ -61,5 +61,6 @@ pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
 pair_style lj/sf, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
 pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12
 pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12
+pair_style morse/smooth/linear, Stefan Paquay (TU Eindhoven), stefanpaquay at gmail.com, 29 Feb 16
 pair_style srp, Tim Sirk, tim.sirk at us.army.mil, 21 Nov 14
 pair_style tersoff/table, Luca Ferraro, luca.ferraro@caspur.it, 1 Dec 11

src/USER-MISC/pair_morse_smooth_linear.cpp

@@ -0,0 +1,370 @@
+/* ----------------------------------------------------------------------
+   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 <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "pair_morse_smooth_linear.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neigh_list.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+PairMorseSmoothLinear::PairMorseSmoothLinear(LAMMPS *lmp) : Pair(lmp)
+{
+  writedata = 1;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairMorseSmoothLinear::~PairMorseSmoothLinear()
+{
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(cut);
+    memory->destroy(d0);
+    memory->destroy(alpha);
+    memory->destroy(r0);
+    memory->destroy(morse1);
+    memory->destroy(der_at_cutoff);
+    memory->destroy(offset);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairMorseSmoothLinear::compute(int eflag, int vflag)
+{
+  int i,j,ii,jj,inum,jnum,itype,jtype;
+  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair, fpartial;
+  double rsq,r,dr,dexp,factor_lj;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+
+  evdwl = 0.0;
+  if (eflag || vflag) ev_setup(eflag,vflag);
+  else evflag = vflag_fdotr = 0;
+
+  double **x = atom->x;
+  double **f = atom->f;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+  double *special_lj = force->special_lj;
+  int newton_pair = force->newton_pair;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // loop over neighbors of my atoms
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    itype = type[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      factor_lj = special_lj[sbmask(j)];
+      j &= NEIGHMASK;
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+      jtype = type[j];
+
+      if (rsq < cutsq[itype][jtype]) {
+        r = sqrt(rsq);
+        dr = r - r0[itype][jtype];
+        dexp = exp(-alpha[itype][jtype] * dr);
+
+        fpartial = morse1[itype][jtype] * (dexp*dexp - dexp) / r;
+        fpair = factor_lj * ( fpartial - der_at_cutoff[itype][jtype] / r);
+
+        f[i][0] += delx*fpair;
+        f[i][1] += dely*fpair;
+        f[i][2] += delz*fpair;
+        if (newton_pair || j < nlocal) {
+          f[j][0] -= delx*fpair;
+          f[j][1] -= dely*fpair;
+          f[j][2] -= delz*fpair;
+        }
+
+        if (eflag) {
+          evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
+            offset[itype][jtype];
+          evdwl += ( r - cut[itype][jtype] ) * der_at_cutoff[itype][jtype];
+          evdwl *= factor_lj;
+        }
+
+        if (evflag) ev_tally(i,j,nlocal,newton_pair,
+                             evdwl,0.0,fpair,delx,dely,delz);
+      }
+    }
+  }
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairMorseSmoothLinear::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes;
+
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  for (int i = 1; i <= n; i++)
+    for (int j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+  memory->create(cut,n+1,n+1,"pair:cut");
+  memory->create(d0,n+1,n+1,"pair:d0");
+  memory->create(alpha,n+1,n+1,"pair:alpha");
+  memory->create(r0,n+1,n+1,"pair:r0");
+  memory->create(morse1,n+1,n+1,"pair:morse1");
+  memory->create(der_at_cutoff,n+1,n+1,"pair:der_at_cutoff");
+  memory->create(offset,n+1,n+1,"pair:offset");
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairMorseSmoothLinear::settings(int narg, char **arg)
+{
+  if (narg != 1) error->all(FLERR,"Illegal pair_style command");
+
+  cut_global = force->numeric(FLERR,arg[0]);
+
+  // reset cutoffs that have been explicitly set
+
+  if (allocated) {
+    int i,j;
+    for (i = 1; i <= atom->ntypes; i++)
+      for (j = i+1; j <= atom->ntypes; j++)
+        if (setflag[i][j]) cut[i][j] = cut_global;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairMorseSmoothLinear::coeff(int narg, char **arg)
+{
+  if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients");
+  if (!allocated) allocate();
+
+  int ilo,ihi,jlo,jhi;
+  force->bounds(arg[0],atom->ntypes,ilo,ihi);
+  force->bounds(arg[1],atom->ntypes,jlo,jhi);
+
+  double d0_one = force->numeric(FLERR,arg[2]);
+  double alpha_one = force->numeric(FLERR,arg[3]);
+  double r0_one = force->numeric(FLERR,arg[4]);
+
+  double cut_one = cut_global;
+  if (narg == 6) cut_one = force->numeric(FLERR,arg[5]);
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo,i); j <= jhi; j++) {
+      d0[i][j] = d0_one;
+      alpha[i][j] = alpha_one;
+      r0[i][j] = r0_one;
+      cut[i][j] = cut_one;
+      setflag[i][j] = 1;
+      count++;
+    }
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairMorseSmoothLinear::init_one(int i, int j)
+{
+  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+
+  morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
+
+  double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
+    
+  offset[i][j]        = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
+  der_at_cutoff[i][j] = -2.0*alpha[i][j]*d0[i][j] * (exp(2.0*alpha_dr) - exp(alpha_dr));
+
+  d0[j][i] = d0[i][j];
+  alpha[j][i] = alpha[i][j];
+  r0[j][i] = r0[i][j];
+  morse1[j][i] = morse1[i][j];
+  der_at_cutoff[j][i] = der_at_cutoff[i][j];
+  offset[j][i] = offset[i][j];
+
+  return cut[i][j];
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairMorseSmoothLinear::write_restart(FILE *fp)
+{
+  write_restart_settings(fp);
+
+  int i,j;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      fwrite(&setflag[i][j],sizeof(int),1,fp);
+      if (setflag[i][j]) {
+        fwrite(&d0[i][j],sizeof(double),1,fp);
+        fwrite(&alpha[i][j],sizeof(double),1,fp);
+        fwrite(&r0[i][j],sizeof(double),1,fp);
+        fwrite(&cut[i][j],sizeof(double),1,fp);
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairMorseSmoothLinear::read_restart(FILE *fp)
+{
+  read_restart_settings(fp);
+
+  allocate();
+
+  int i,j;
+  int me = comm->me;
+  for (i = 1; i <= atom->ntypes; i++)
+    for (j = i; j <= atom->ntypes; j++) {
+      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+      if (setflag[i][j]) {
+        if (me == 0) {
+          fread(&d0[i][j],sizeof(double),1,fp);
+          fread(&alpha[i][j],sizeof(double),1,fp);
+          fread(&r0[i][j],sizeof(double),1,fp);
+          fread(&cut[i][j],sizeof(double),1,fp);
+        }
+        MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+      }
+    }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairMorseSmoothLinear::write_restart_settings(FILE *fp)
+{
+  fwrite(&cut_global,sizeof(double),1,fp);
+  // fwrite(&offset_flag,sizeof(int),1,fp);
+  fwrite(&mix_flag,sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairMorseSmoothLinear::read_restart_settings(FILE *fp)
+{
+  if (comm->me == 0) {
+    fread(&cut_global,sizeof(double),1,fp);
+    // fread(&offset_flag,sizeof(int),1,fp);
+    fread(&mix_flag,sizeof(int),1,fp);
+  }
+  MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
+  // MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
+  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairMorseSmoothLinear::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp,"%d %g %g %g\n",i,d0[i][i],alpha[i][i],r0[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairMorseSmoothLinear::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp,"%d %d %g %g %g %g\n",
+              i,j,d0[i][j],alpha[i][j],r0[i][j],cut[i][j]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairMorseSmoothLinear::single(int i, int j, int itype, int jtype, double rsq,
+                                     double factor_coul, double factor_lj,
+                                     double &fforce)
+{
+  double r,dr,dexp,phi;
+
+  r = sqrt(rsq);
+  dr = r - r0[itype][jtype];
+  dexp = exp(-alpha[itype][jtype] * dr);
+  fforce = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
+
+  phi = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - offset[itype][jtype];
+  dr = cut[itype][jtype] - r0[itype][jtype];
+  phi += dr * der_at_cutoff[itype][jtype];
+
+  return factor_lj*phi;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *PairMorseSmoothLinear::extract(const char *str, int &dim)
+{
+  dim = 2;
+  if (strcmp(str,"d0") == 0) return (void *) d0;
+  if (strcmp(str,"r0") == 0) return (void *) r0;
+  if (strcmp(str,"alpha") == 0) return (void *) alpha;
+  return NULL;
+}

src/USER-MISC/pair_morse_smooth_linear.h

@@ -0,0 +1,80 @@
+/* -*- 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.
+  -------------------------------------------------------------------------
+  Contributed by Stefan Paquay @ Eindhoven University of Technology
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(morse/smooth/linear,PairMorseSmoothLinear)
+
+#else
+
+#ifndef LMP_PAIR_MORSE_SMOOTH_LINEAR_H
+#define LMP_PAIR_MORSE_SMOOTH_LINEAR_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairMorseSmoothLinear : public Pair {
+ public:
+  PairMorseSmoothLinear(class LAMMPS *);
+  virtual ~PairMorseSmoothLinear();
+
+  virtual void compute(int, int);
+  void settings(int, char **);
+  void coeff(int, char **);
+  double init_one(int, int);
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_restart_settings(FILE *);
+  void read_restart_settings(FILE *);
+  void write_data(FILE *);
+  void write_data_all(FILE *);
+  double single(int, int, int, int, double, double, double, double &);
+  void *extract(const char *, int &);
+
+ protected:
+  double cut_global;
+  double **cut;
+  double **d0,**alpha,**r0;
+  double **morse1;
+  double **der_at_cutoff;
+  double **offset;
+
+  void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+E: All pair coeffs are not set
+
+All pair coefficients must be set in the data file or by the
+pair_coeff command before running a simulation.
+
+*/