Added Axilrod-Teller manybody potential

doc/src/Eqs/pair_atm.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{equation}
+E=\nu\frac{1+3\cos\gamma_1\cos\gamma_2\cos\gamma_3}{r_{12}^3r_{23}^3r_{31}^3}
+\end{equation}                           
+
+\end{document}

doc/src/pair_atm.txt

@@ -0,0 +1,85 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style atm command :h3
+
+[Syntax:]
+
+pair_style atm args = cutoff :pre
+
+[Examples:]
+
+pair_style 2.5
+pair_coeff * * * 0.072 :pre
+
+pair_style	hybrid/overlay lj/cut 6.5 atm 2.5
+pair_coeff	* * lj/cut 1.0 1.0
+pair_coeff	* * atm * 0.072 :pre
+
+[Description:]
+
+The {atm} style computes a 3-body "Axilrod-Teller-Muto"_#Axilrod
+potential for the energy E of a system of atoms as
+
+:c,image(Eqs/pair_atm.jpg)
+
+where r12, r23 and r31 are the distances between the atoms,
+gamma1 is included by the sides r12 and r31
+with similar definitions for gamma2 and gamma3,
+nu is the three-body interaction strength (energy times distance^9 units).
+
+The {atm} is typically used in compination with some two-body potential
+using "hybrid/overlay"_pair_hybrid.html style as in an example above.
+
+The calculations are not undertaken if the distances between atoms satisfy
+r12 r23 r31 > curoff^3. Virtual cutoff distance based on a user defined
+tolerance tol is not used.
+
+The Axilrod-Teller-Muto potential file must contain entries for all the
+elements listed in the pair_coeff command.  It can also contain
+entries for additional elements not being used in a particular
+simulation; LAMMPS ignores those entries.
+
+For a single-element simulation, only a single entry is required
+(e.g. 1 1 1).  For a two-element simulation, the file must contain 4
+entries (eg. 1 1 1, 1 1 2, 1 2 2, 2 2 2), that
+specify ATM parameters for all combinations of the two elements
+interacting in three-body configurations.  Thus for 3 elements, 10
+entries would be required, etc.
+
+:line
+
+[Shift, table, tail correction, rRESPA info]:
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command.  It does not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+This pair style is part of the MANYBODY package.  It is only enabled
+if LAMMPS was built with that package.  See
+the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
+:link(Axilrod)
+[(Axilrod)]
+Axilrod and Teller, J Chem Phys, 11, 299 (1943);
+Muto, Nippon Sugaku Butsuri Gakkwaishi 17, 629 (1943).

examples/in.atm

@@ -0,0 +1,29 @@
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 10*$x
+variable	yy equal 10*$y
+variable	zz equal 10*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.65
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+
+pair_style	hybrid/overlay lj/cut 4.5 atm 2.5
+pair_coeff	* * lj/cut 1.0 1.0
+pair_coeff	* * atm * 0.072
+
+mass		* 1.0
+velocity	all create 1.033 12345678 loop geom
+
+fix		1 all nvt temp 1.033 1.033 0.05
+
+timestep        0.002
+thermo		1
+
+run 		50

src/MANYBODY/pair_atm.cpp

@@ -0,0 +1,317 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Sergey Lishchuk
+------------------------------------------------------------------------- */
+
+#include "pair_atm.h"
+
+#include <math.h>
+
+#include "atom.h"
+#include "citeme.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+
+using namespace LAMMPS_NS;
+
+static const char cite_atm_package[] =
+  "ATM package:\n\n"
+  "@Article{Lishchuk:2012:164501,\n"
+  " author = {S. V. Lishchuk},\n"
+  " title = {Role of three-body interactions in formation of bulk viscosity in liquid argon},\n"
+  " journal = {J.~Chem.~Phys.},\n"
+  " year =    2012,\n"
+  " volume =  136,\n"
+  " pages =   {164501}\n"
+  "}\n\n";
+
+/* ---------------------------------------------------------------------- */
+
+PairATM::PairATM(LAMMPS *lmp) : Pair(lmp)
+{
+  if (lmp->citeme) lmp->citeme->add(cite_atm_package);
+
+  single_enable = 0;
+  restartinfo = 0;
+  one_coeff = 1;
+  manybody_flag = 1;
+}
+
+/* ----------------------------------------------------------------------
+   check if allocated, since class can be destructed when incomplete
+------------------------------------------------------------------------- */
+
+PairATM::~PairATM()
+{
+  if (copymode) return;
+  if (allocated) {
+    memory->destroy(nu);
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   workhorse routine that computes pairwise interactions
+------------------------------------------------------------------------- */
+
+void PairATM::compute(int eflag, int vflag)
+{
+  int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
+  double xi,yi,zi,evdwl;
+  double rij2,rik2,rjk2,r6;
+  double rij[3],rik[3],rjk[3],fj[3],fk[3];
+  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;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    xi = x[i][0];
+    yi = x[i][1];
+    zi = x[i][2];
+
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+    jnumm1 = jnum - 1;
+
+    for (jj = 0; jj < jnumm1; jj++) {
+      j = jlist[jj];
+      j &= NEIGHMASK;
+      rij[0] = x[j][0] - xi;
+      rij[1] = x[j][1] - yi;
+      rij[2] = x[j][2] - zi;
+      rij2 = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2];
+
+      for (kk = jj+1; kk < jnum; kk++) {
+        k = jlist[kk];
+        k &= NEIGHMASK;
+
+        rik[0] = x[k][0] - xi;
+        rik[1] = x[k][1] - yi;
+        rik[2] = x[k][2] - zi;
+        rik2 = rik[0]*rik[0] + rik[1]*rik[1] + rik[2]*rik[2];
+
+        rjk[0] = x[k][0] - x[j][0];
+        rjk[1] = x[k][1] - x[j][1];
+        rjk[2] = x[k][2] - x[j][2];
+        rjk2 = rjk[0]*rjk[0] + rjk[1]*rjk[1] + rjk[2]*rjk[2];
+
+        r6 = rij2*rik2*rjk2;
+        if (r6 > cut_sixth) continue;
+
+        interaction_ddd(nu[type[i]][type[j]][type[k]],
+                  r6,rij2,rik2,rjk2,rij,rik,rjk,fj,fk,eflag,evdwl);
+
+        f[i][0] -= fj[0] + fk[0];
+        f[i][1] -= fj[1] + fk[1];
+        f[i][2] -= fj[2] + fk[2];
+        f[j][0] += fj[0];
+        f[j][1] += fj[1];
+        f[j][2] += fj[2];
+        f[k][0] += fk[0];
+        f[k][1] += fk[1];
+        f[k][2] += fk[2];
+
+        if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,rij,rik);
+      }
+    }
+  }
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+   reads the input script line with arguments you define
+------------------------------------------------------------------------- */
+
+void PairATM::settings(int narg, char **arg)
+{
+  if (narg != 1) error->all(FLERR,"Illegal pair_style command");
+  cut_global = force->numeric(FLERR,arg[0]);
+}
+
+/* ----------------------------------------------------------------------
+   set coefficients for one i,j,k type triplet
+------------------------------------------------------------------------- */
+
+void PairATM::coeff(int narg, char **arg)
+{
+  if (narg != 4)
+    error->all(FLERR,"Incorrect args for pair coefficients");
+  if (!allocated) allocate();
+
+  int ilo,ihi,jlo,jhi,klo,khi;
+  force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+  force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+  force->bounds(FLERR,arg[2],atom->ntypes,klo,khi);
+
+  double nu_one = force->numeric(FLERR,arg[3]);
+
+  cut_sixth = cut_global*cut_global;
+  cut_sixth = cut_sixth*cut_sixth*cut_sixth;
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo,i); j<=jhi; j++) {
+      for (int k = MAX(klo,j); k<=khi; k++) {
+        nu[i][j][k] = nu[i][k][j] = 
+        nu[j][i][k] = nu[j][k][i] = 
+        nu[k][i][j] = nu[k][j][i] = nu_one;
+        count++;
+      }
+      setflag[i][j] = 1;
+    }
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairATM::init_style()
+{
+  // need a full neighbor list
+  int irequest = neighbor->request(this,instance_me);
+  neighbor->requests[irequest]->half = 0;
+  neighbor->requests[irequest]->full = 1;
+}
+
+/* ----------------------------------------------------------------------
+   perform initialization for one i,j type pair
+------------------------------------------------------------------------- */
+
+double PairATM::init_one(int i, int j)
+{
+  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+  return cut_global;
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairATM::write_restart(FILE *fp)
+{
+  write_restart_settings(fp);
+
+  int i,j,k;
+  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]) for (k = i; k <= atom->ntypes; k++) fwrite(&nu[i][j][k],sizeof(double),1,fp);
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairATM::read_restart(FILE *fp)
+{
+  read_restart_settings(fp);
+  allocate();
+
+  int i,j,k;
+  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]) for (k = i; k <= atom->ntypes; k++) {
+        if (me == 0) fread(&nu[i][j][k],sizeof(double),1,fp);
+        MPI_Bcast(&nu[i][j][k],1,MPI_DOUBLE,0,world);
+      }
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairATM::write_restart_settings(FILE *fp)
+{
+  fwrite(&cut_global,sizeof(double),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairATM::read_restart_settings(FILE *fp)
+{
+  int me = comm->me;
+  if (me == 0) fread(&cut_global,sizeof(double),1,fp);
+  MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairATM::allocate()
+{
+  allocated = 1;
+  int n = atom->ntypes;
+  memory->create(nu,n+1,n+1,n+1,"pair:a");
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
+}
+
+/* ----------------------------------------------------------------------
+   Axilrod-Teller-Muto (dipole-dipole-dipole) potential
+------------------------------------------------------------------------- */
+
+void PairATM::interaction_ddd(double nu,
+                       double r6, double rij2, double rik2, double rjk2,
+                       double *rij, double *rik, double *rjk,
+                       double *fj, double *fk, int eflag, double &eng)
+{
+  double r5inv,rri,rrj,rrk,rrr;
+  r5inv = nu / (r6*r6*sqrt(r6));
+  rri = rik[0]*rij[0] + rik[1]*rij[1] + rik[2]*rij[2];
+  rrj = rij[0]*rjk[0] + rij[1]*rjk[1] + rij[2]*rjk[2];
+  rrk = rjk[0]*rik[0] + rjk[1]*rik[1] + rjk[2]*rik[2];
+  rrr = 5.0*rri*rrj*rrk;
+  for (int i=0; i<3; i++) {
+    fj[i] = rrj*(rrk - rri)*rik[i]
+      - (rrk*rri - rjk2*rik2 + rrr/rij2)*rij[i]
+      + (rrk*rri - rik2*rij2 + rrr/rjk2)*rjk[i];
+    fj[i] *= 3.0*r5inv;
+    fk[i] = rrk*(rri + rrj)*rij[i]
+      + (rri*rrj + rik2*rij2 - rrr/rjk2)*rjk[i]
+      + (rri*rrj + rij2*rjk2 - rrr/rik2)*rik[i];
+    fk[i] *= 3.0*r5inv;
+  }
+  if (eflag) eng = (r6 - 0.6*rrr)*r5inv;
+}

src/MANYBODY/pair_atm.h

@@ -0,0 +1,76 @@
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Sergey Lishchuk
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(atm,PairATM)
+
+#else
+
+#ifndef LMP_PAIR_ATM_H
+#define LMP_PAIR_ATM_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairATM : public Pair {
+ public:
+  PairATM(class LAMMPS *);
+  virtual ~PairATM();
+  virtual void compute(int, int);
+  void settings(int, char **);
+  virtual void coeff(int, char **);
+  virtual void init_style();
+  virtual double init_one(int, int);
+  void write_restart(FILE *);
+  void read_restart(FILE *);
+  void write_restart_settings(FILE *);
+  void read_restart_settings(FILE *);
+
+ protected:
+  double cut_global, cut_sixth;
+  double ***nu;
+
+ protected:
+  virtual void allocate();
+  void interaction_ddd(double, double, double, double, double, double *, double *, double *, double *, double *, int, double &);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal pair_style 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.
+
+*/