git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13708 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/CORESHELL/Install.sh

@@ -30,3 +30,5 @@ action pair_born_coul_long_cs.cpp pair_born_coul_long.cpp
 action pair_buck_coul_long_cs.cpp pair_buck_coul_long.cpp
 action pair_born_coul_long_cs.h pair_born_coul_long.h
 action pair_buck_coul_long_cs.h pair_buck_coul_long.h
+action pair_coul_long_cs.cpp pair_coul_long.cpp
+action pair_coul_long_cs.h pair_coul_long.h

src/CORESHELL/pair_coul_long_cs.cpp

@@ -0,0 +1,159 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Added epsilon for use with CORESHELL and USER-DRUDE
+------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdio.h"
+#include "stdlib.h"
+#include "string.h"
+#include "pair_coul_long_cs.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "kspace.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "update.h"
+#include "integrate.h"
+#include "respa.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define EWALD_F   1.12837917
+#define EWALD_P   9.95473818e-1
+#define B0       -0.1335096380159268
+#define B1       -2.57839507e-1
+#define B2       -1.37203639e-1
+#define B3       -8.88822059e-3
+#define B4       -5.80844129e-3
+#define B5        1.14652755e-1
+
+/* ---------------------------------------------------------------------- */
+
+PairCoulLongCS::PairCoulLongCS(LAMMPS *lmp) : PairCoulLong(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+void PairCoulLongCS::compute(int eflag, int vflag)
+{
+  int i,j,ii,jj,inum,jnum,itable,itype,jtype;
+  double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
+  double fraction,table;
+  double r,r2inv,forcecoul,factor_coul;
+  double grij,expm2,prefactor,t,erfc,u;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+  double rsq;
+
+  ecoul = 0.0;
+  if (eflag || vflag) ev_setup(eflag,vflag);
+  else evflag = vflag_fdotr = 0;
+
+  double **x = atom->x;
+  double **f = atom->f;
+  double *q = atom->q;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+  double *special_coul = force->special_coul;
+  int newton_pair = force->newton_pair;
+  double qqrd2e = force->qqrd2e;
+
+  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];
+    qtmp = q[i];
+    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_coul = special_coul[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 < cut_coulsq) {
+        r2inv = 1.0/rsq;
+        r = sqrt(rsq);
+        if (!ncoultablebits || rsq <= tabinnersq) {
+          prefactor = qqrd2e * scale[itype][jtype] * qtmp*q[j];
+          grij = g_ewald * r;
+          expm2 = exp(-grij*grij);
+          t = 1.0 / (1.0 + EWALD_P*grij);
+	  u = 1. - t;
+          erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
+          prefactor /= r;
+          forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+          if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+        } else {
+          union_int_float_t rsq_lookup;
+          rsq_lookup.f = rsq;
+          itable = rsq_lookup.i & ncoulmask;
+          itable >>= ncoulshiftbits;
+          fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+          table = ftable[itable] + fraction*dftable[itable];
+          forcecoul = scale[itype][jtype] * qtmp*q[j] * table;
+          if (factor_coul < 1.0) {
+            table = ctable[itable] + fraction*dctable[itable];
+            prefactor = scale[itype][jtype] * qtmp*q[j] * table;
+            forcecoul -= (1.0-factor_coul)*prefactor;
+          }
+        }
+
+        fpair = forcecoul * r2inv;
+
+        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) {
+          if (!ncoultablebits || rsq <= tabinnersq)
+            ecoul = prefactor*erfc;
+          else {
+            table = etable[itable] + fraction*detable[itable];
+            ecoul = scale[itype][jtype] * qtmp*q[j] * table;
+          }
+          if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+        }
+
+        if (evflag) ev_tally(i,j,nlocal,newton_pair,
+                             0.0,ecoul,fpair,delx,dely,delz);
+      }
+    }
+  }
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}

src/CORESHELL/pair_coul_long_cs.h

@@ -0,0 +1,58 @@
+/* -*- 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 PAIR_CLASS
+
+PairStyle(coul/long/cs,PairCoulLongCS)
+
+#else
+
+#ifndef LMP_PAIR_COUL_LONG_CS_H
+#define LMP_PAIR_COUL_LONG_CS_H
+
+#include "pair_coul_long.h"
+
+namespace LAMMPS_NS {
+
+class PairCoulLongCS : public PairCoulLong {
+ public:
+  PairCoulLongCS(class LAMMPS *);
+  virtual void compute(int, int);
+};
+
+}
+
+#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: Pair style lj/cut/coul/long/drude requires atom attribute q
+
+The atom style defined does not have this attribute.
+
+E: Pair style requires a KSpace style
+
+No kspace style is defined.
+
+*/

src/Makefile

@@ -46,9 +46,9 @@ PACKAGE = asphere body class2 colloid coreshell dipole fld gpu granular kim \
 	  python qeq reax replica rigid shock snap srd voronoi xtc
 
 PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars user-cuda \
-	   user-diffraction user-eff user-fep user-intel user-lb user-misc \
+	   user-diffraction user-drude user-eff user-fep user-intel user-lb \
-	   user-molfile user-omp user-phonon user-qmmm user-qtb user-quip \
+	   user-misc user-molfile user-omp user-phonon user-qmmm user-qtb \
-	   user-reaxc user-sph
+	   user-quip user-reaxc user-sph
 
 PACKLIB = gpu kim kokkos meam poems python reax voronoi \
 	  user-atc user-awpmd user-colvars user-cuda user-molfile \

src/compute_chunk_atom.cpp

@@ -722,12 +722,17 @@ int ComputeChunkAtom::setup_chunks()
   // assign chunk IDs to atoms
   // will exclude atoms not in group or in optional region
   // for binning styles, need to setup bins and their volume first
+  //   else chunk_volume_scalar = box volume
   // IDs are needed to scan for max ID and for compress()
 
   if (binflag) {
     nchunk = setup_bins();
     bin_volumes();
+  } else {
+    chunk_volume_scalar = domain->xprd * domain->yprd;
+    if (domain->dimension == 3) chunk_volume_scalar *= domain->zprd;
   }
+
   assign_chunk_ids();
 
   // set nchunk for chunk styles other than binning

src/fix.cpp

@@ -66,6 +66,7 @@ Fix::Fix(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   wd_header = wd_section = 0;
   dynamic_group_allow = 0;
   dof_flag = 0;
+  special_alter_flag = 0;
   cudable_comm = 0;
 
   scalar_flag = vector_flag = array_flag = 0;

src/fix.h

@@ -50,6 +50,7 @@ class Fix : protected Pointers {
   int wd_section;                // # of sections fix writes to data file
   int dynamic_group_allow;       // 1 if can be used with dynamic group, else 0
   int dof_flag;                  // 1 if has dof() method (not min_dof())
+  int special_alter_flag;        // 1 if has special_alter() meth for spec lists
   int cudable_comm;              // 1 if fix has CUDA-enabled communication
 
   int scalar_flag;               // 0/1 if compute_scalar() function exists
@@ -194,6 +195,8 @@ class Fix : protected Pointers {
   virtual void zero_momentum() {}
   virtual void zero_rotation() {}
 
+  virtual void rebuild_special() {}
+
   virtual int modify_param(int, char **) {return 0;}
   virtual void *extract(const char *, int &) {return NULL;}
 

src/neighbor.cpp

@@ -310,6 +310,7 @@ void Neighbor::init()
   // flag = 1 if both LJ/Coulomb special values are 1.0
   // flag = 2 otherwise or if KSpace solver is enabled
   // pairwise portion of KSpace solver uses all 1-2,1-3,1-4 neighbors
+  // or selected Coulomb-approixmation pair styles require it
 
   if (force->special_lj[1] == 0.0 && force->special_coul[1] == 0.0)
     special_flag[1] = 0;
@@ -329,8 +330,8 @@ void Neighbor::init()
     special_flag[3] = 1;
   else special_flag[3] = 2;
 
-  if (force->kspace || force->pair_match("coul/wolf",0)
+  if (force->kspace || force->pair_match("coul/wolf",0) ||
-      || force->pair_match("coul/dsf",0))
+      force->pair_match("coul/dsf",0) || force->pair_match("thole",0))
      special_flag[1] = special_flag[2] = special_flag[3] = 2;
 
   // maxwt = max multiplicative factor on atom indices stored in neigh list

src/special.cpp

@@ -18,6 +18,8 @@
 #include "atom_vec.h"
 #include "force.h"
 #include "comm.h"
+#include "modify.h"
+#include "fix.h"
 #include "accelerator_kokkos.h"
 #include "memory.h"
 #include "error.h"
@@ -191,6 +193,7 @@ void Special::build()
       force->special_lj[3] == 1.0 && force->special_coul[3] == 1.0) {
     dedup();
     combine();
+    fix_alteration();
     return;
   }
 
@@ -307,6 +310,7 @@ void Special::build()
     dedup();
     if (force->special_angle) angle_trim();
     combine();
+    fix_alteration();
     return;
   }
 
@@ -419,6 +423,7 @@ void Special::build()
   if (force->special_angle) angle_trim();
   if (force->special_dihedral) dihedral_trim();
   combine();
+  fix_alteration();
 }
 
 /* ----------------------------------------------------------------------
@@ -1127,3 +1132,17 @@ void Special::ring_eight(int ndatum, char *cbuf)
     i += 2;
   }
 }
+
+/* ----------------------------------------------------------------------
+   allow fixes to alter special list
+   currently, only fix drude does this
+     so that both the Drude core and electron are same level of neighbor
+------------------------------------------------------------------------- */
+
+void Special::fix_alteration()
+{
+  for (int ifix = 0; ifix < modify->nfix; ifix++)
+    if (modify->fix[ifix]->special_alter_flag)
+      modify->fix[ifix]->rebuild_special();
+}
+

src/special.h

@@ -37,6 +37,7 @@ class Special : protected Pointers {
   void angle_trim();
   void dihedral_trim();
   void combine();
+  void fix_alteration();
 
   // static variable for ring communication callback to access class data
   // callback functions for ring communication