git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@254 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/CLASS2/Install.csh

@@ -1,7 +1,5 @@
 # Install/unInstall package classes in LAMMPS
 
-# pair_lj_class2_coul_long.h must always be in src
-
 if ($1 == 1) then
 
   cp style_class2.h ..
@@ -22,7 +20,7 @@ if ($1 == 1) then
 
   cp pair_lj_class2.h ..
   cp pair_lj_class2_coul_cut.h ..
-#  cp pair_lj_class2_coul_long.h ..
+  cp pair_lj_class2_coul_long.h ..
 
 else if ($1 == 0) then
 
@@ -45,6 +43,6 @@ else if ($1 == 0) then
 
   rm ../pair_lj_class2.h
   rm ../pair_lj_class2_coul_cut.h
-#  rm ../pair_lj_class2_coul_long.h
+  rm ../pair_lj_class2_coul_long.h
 
 endif

src/CLASS2/angle_class2.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -26,11 +26,15 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define SMALL 0.001
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays 
+
-------------------------------------------------------------------------- */
+AngleClass2::AngleClass2(LAMMPS *lmp) : Angle(lmp) {}
+
+/* ---------------------------------------------------------------------- */
 
 AngleClass2::~AngleClass2()
 {

src/CLASS2/angle_class2.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "angle.h"
 
+namespace LAMMPS_NS {
+
 class AngleClass2 : public Angle {
  public:
-  AngleClass2() {}
+  AngleClass2(class LAMMPS *);
   ~AngleClass2();
   void compute(int, int);
   void coeff(int, int, char **);
@@ -36,4 +38,6 @@ class AngleClass2 : public Angle {
   void allocate();
 };
 
+}
+
 #endif

src/CLASS2/bond_class2.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -26,9 +26,13 @@
 #include "memory.h"
 #include "error.h"
 
-/* ----------------------------------------------------------------------
+using namespace LAMMPS_NS;
-   free all arrays 
+
-------------------------------------------------------------------------- */
+/* ---------------------------------------------------------------------- */
+
+BondClass2::BondClass2(LAMMPS *lmp) : Bond(lmp) {}
+
+/* ---------------------------------------------------------------------- */
 
 BondClass2::~BondClass2()
 {

src/CLASS2/bond_class2.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "bond.h"
 
+namespace LAMMPS_NS {
+
 class BondClass2 : public Bond {
  public:
-  BondClass2() {}
+  BondClass2(class LAMMPS *);
   ~BondClass2();
   void compute(int, int);
   void coeff(int, char **);
@@ -34,4 +36,6 @@ class BondClass2 : public Bond {
   void allocate();
 };
 
+}
+
 #endif

src/CLASS2/dihedral_class2.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -27,24 +27,22 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(A,B) ((A) < (B)) ? (A) : (B)
 #define MAX(A,B) ((A) > (B)) ? (A) : (B)
 
 #define TOLERANCE 0.05
 #define SMALL     0.0000001
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   set all global defaults 
-------------------------------------------------------------------------- */
 
-DihedralClass2::DihedralClass2()
+DihedralClass2::DihedralClass2(LAMMPS *lmp) : Dihedral(lmp)
 {
   PI = 4.0*atan(1.0);
 }
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays 
-------------------------------------------------------------------------- */
 
 DihedralClass2::~DihedralClass2()
 {

src/CLASS2/dihedral_class2.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "dihedral.h"
 
+namespace LAMMPS_NS {
+
 class DihedralClass2 : public Dihedral {
  public:
-  DihedralClass2();
+  DihedralClass2(class LAMMPS *);
   ~DihedralClass2();
   void compute(int, int);
   void coeff(int, int, char **);
@@ -43,4 +45,6 @@ class DihedralClass2 : public Dihedral {
   void allocate();
 };
 
+}
+
 #endif

src/CLASS2/improper_class2.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -27,20 +27,18 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define SMALL 0.001
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   set all global defaults 
-------------------------------------------------------------------------- */
 
-ImproperClass2::ImproperClass2()
+ImproperClass2::ImproperClass2(LAMMPS *lmp) : Improper(lmp)
 {
   PI = 4.0*atan(1.0);
 }
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays 
-------------------------------------------------------------------------- */
 
 ImproperClass2::~ImproperClass2()
 {

src/CLASS2/improper_class2.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "improper.h"
 
+namespace LAMMPS_NS {
+
 class ImproperClass2 : public Improper {
  public:
-  ImproperClass2();
+  ImproperClass2(class LAMMPS *);
   ~ImproperClass2();
   void compute(int, int);
   void coeff(int, int, char **);
@@ -38,4 +40,6 @@ class ImproperClass2 : public Improper {
   double dot(double *, double *);
 };
 
+}
+
 #endif

src/CLASS2/pair_lj_class2.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -23,12 +23,16 @@
 #include "neighbor.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays 
+
-------------------------------------------------------------------------- */
+PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp) {}
+
+/* ---------------------------------------------------------------------- */
 
 PairLJClass2::~PairLJClass2()
 {

src/CLASS2/pair_lj_class2.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,9 +16,11 @@
 
 #include "pair.h"
 
+namespace LAMMPS_NS {
+
 class PairLJClass2 : public Pair {
  public:
-  PairLJClass2() {}
+  PairLJClass2(class LAMMPS *);
   ~PairLJClass2();
   void compute(int, int);
   void settings(int, char **);
@@ -39,4 +41,6 @@ class PairLJClass2 : public Pair {
   void allocate();
 };
 
+}
+
 #endif

src/CLASS2/pair_lj_class2_coul_cut.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -23,12 +23,16 @@
 #include "neighbor.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays 
+
-------------------------------------------------------------------------- */
+PairLJClass2CoulCut::PairLJClass2CoulCut(LAMMPS *lmp) : Pair(lmp) {}
+
+/* ---------------------------------------------------------------------- */
 
 PairLJClass2CoulCut::~PairLJClass2CoulCut()
 {
@@ -333,7 +337,7 @@ void PairLJClass2CoulCut::init_style()
 {
   // require an atom style with charge defined
 
-  if (atom->charge_allow == 0)
+  if (atom->q == NULL)
     error->all("Must use charged atom style with this pair style");
 }
 

src/CLASS2/pair_lj_class2_coul_cut.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,9 +16,11 @@
 
 #include "pair.h"
 
+namespace LAMMPS_NS {
+
 class PairLJClass2CoulCut : public Pair {
  public:
-  PairLJClass2CoulCut() {}
+  PairLJClass2CoulCut(class LAMMPS *);
   ~PairLJClass2CoulCut();
   void compute(int, int);
   void settings(int, char **);
@@ -41,4 +43,6 @@ class PairLJClass2CoulCut : public Pair {
   void allocate();
 };
 
+}
+
 #endif

src/CLASS2/pair_lj_class2_coul_long.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -25,6 +25,8 @@
 #include "neighbor.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
@@ -36,9 +38,11 @@
 #define A4       -1.453152027
 #define A5        1.061405429
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays 
+
-------------------------------------------------------------------------- */
+PairLJClass2CoulLong::PairLJClass2CoulLong(LAMMPS *lmp) : Pair(lmp) {}
+
+/* ---------------------------------------------------------------------- */
 
 PairLJClass2CoulLong::~PairLJClass2CoulLong()
 {
@@ -339,7 +343,7 @@ void PairLJClass2CoulLong::init_style()
 {
   // require an atom style with charge defined
 
-  if (atom->charge_allow == 0)
+  if (atom->q == NULL)
     error->all("Must use charged atom style with this pair style");
 
   cut_coulsq = cut_coul * cut_coul;
@@ -474,3 +478,10 @@ void PairLJClass2CoulLong::single(int i, int j, int itype, int jtype,
     } else one.eng_vdwl = 0.0;
   }
 }
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJClass2CoulLong::extract_long(double *p_cut_coul)
+{
+  *p_cut_coul = cut_coul;
+}

src/CLASS2/style_class2.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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

src/DPD/Install.csh

@@ -4,10 +4,10 @@ if ($1 == 1) then
 
   cp style_dpd.h ..
 
-  cp atom_dpd.cpp ..
+  cp atom_vec_dpd.cpp ..
   cp pair_dpd.cpp ..
 
-  cp atom_dpd.h ..
+  cp atom_vec_dpd.h ..
   cp pair_dpd.h ..
 
 else if ($1 == 0) then
@@ -15,10 +15,10 @@ else if ($1 == 0) then
   rm ../style_dpd.h
   touch ../style_dpd.h
 
-  rm ../atom_dpd.cpp
+  rm ../atom_vec_dpd.cpp
   rm ../pair_dpd.cpp
 
-  rm ../atom_dpd.h
+  rm ../atom_vec_dpd.h
   rm ../pair_dpd.h
 
 endif

src/DPD/atom_dpd.cpp

@@ -1,236 +0,0 @@
-/* ----------------------------------------------------------------------
-   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.
-------------------------------------------------------------------------- */
-
-#include "atom_dpd.h"
-#include "domain.h"
-#include "modify.h"
-#include "fix.h"
-
-/* ---------------------------------------------------------------------- */
-
-AtomDPD::AtomDPD(int narg, char **arg) : Atom(narg, arg) {}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomDPD::copy(int i, int j)
-{
-  tag[j] = tag[i];
-  type[j] = type[i];
-  mask[j] = mask[i];
-  image[j] = image[i];
-  x[j][0] = x[i][0];
-  x[j][1] = x[i][1];
-  x[j][2] = x[i][2];
-  v[j][0] = v[i][0];
-  v[j][1] = v[i][1];
-  v[j][2] = v[i][2];
-
-  if (nextra_grow)
-    for (int iextra = 0; iextra < nextra_grow; iextra++) 
-      modify->fix[extra_grow[iextra]]->copy_arrays(i,j);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomDPD::pack_comm(int n, int *list, double *buf, int *pbc_flags)
-{
-  int i,j,m;
-
-  m = 0;
-  if (pbc_flags[0] == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = x[j][0];
-      buf[m++] = x[j][1];
-      buf[m++] = x[j][2];
-      buf[m++] = v[j][0];
-      buf[m++] = v[j][1];
-      buf[m++] = v[j][2];
-    }
-  } else {
-    double xprd = domain->xprd;
-    double yprd = domain->yprd;
-    double zprd = domain->zprd;
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = x[j][0] + pbc_flags[1]*xprd;
-      buf[m++] = x[j][1] + pbc_flags[2]*yprd;
-      buf[m++] = x[j][2] + pbc_flags[3]*zprd;
-      buf[m++] = v[j][0];
-      buf[m++] = v[j][1];
-      buf[m++] = v[j][2];
-    }
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomDPD::unpack_comm(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++) {
-    x[i][0] = buf[m++];
-    x[i][1] = buf[m++];
-    x[i][2] = buf[m++];
-    v[i][0] = buf[m++];
-    v[i][1] = buf[m++];
-    v[i][2] = buf[m++];
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomDPD::pack_reverse(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++) {
-    buf[m++] = f[i][0];
-    buf[m++] = f[i][1];
-    buf[m++] = f[i][2];
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomDPD::unpack_reverse(int n, int *list, double *buf)
-{
-  int i,j,m;
-
-  m = 0;
-  for (i = 0; i < n; i++) {
-    j = list[i];
-    f[j][0] += buf[m++];
-    f[j][1] += buf[m++];
-    f[j][2] += buf[m++];
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomDPD::pack_border(int n, int *list, double *buf, int *pbc_flags)
-{
-  int i,j,m;
-
-  m = 0;
-  if (pbc_flags[0] == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = x[j][0];
-      buf[m++] = x[j][1];
-      buf[m++] = x[j][2];
-      buf[m++] = tag[j];
-      buf[m++] = type[j];
-      buf[m++] = mask[j];
-      buf[m++] = v[j][0];
-      buf[m++] = v[j][1];
-      buf[m++] = v[j][2];
-    }
-  } else {
-    double xprd = domain->xprd;
-    double yprd = domain->yprd;
-    double zprd = domain->zprd;
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = x[j][0] + pbc_flags[1]*xprd;
-      buf[m++] = x[j][1] + pbc_flags[2]*yprd;
-      buf[m++] = x[j][2] + pbc_flags[3]*zprd;
-      buf[m++] = tag[j];
-      buf[m++] = type[j];
-      buf[m++] = mask[j];
-      buf[m++] = v[j][0];
-      buf[m++] = v[j][1];
-      buf[m++] = v[j][2];
-    }
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomDPD::unpack_border(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++) {
-    if (i == nmax) grow(0);
-    x[i][0] = buf[m++];
-    x[i][1] = buf[m++];
-    x[i][2] = buf[m++];
-    tag[i] = static_cast<int> (buf[m++]);
-    type[i] = static_cast<int> (buf[m++]);
-    mask[i] = static_cast<int> (buf[m++]);
-    v[i][0] = buf[m++];
-    v[i][1] = buf[m++];
-    v[i][2] = buf[m++];
-  }
-}
-
-/* ----------------------------------------------------------------------
-   pack all atom quantities for shipping to another proc
-   xyz must be 1st 3 values, so that comm::exchange can test on them 
-------------------------------------------------------------------------- */
-
-int AtomDPD::pack_exchange(int i, double *buf)
-{
-  int m = 1;
-  buf[m++] = x[i][0];
-  buf[m++] = x[i][1];
-  buf[m++] = x[i][2];
-  buf[m++] = v[i][0];
-  buf[m++] = v[i][1];
-  buf[m++] = v[i][2];
-  buf[m++] = tag[i];
-  buf[m++] = type[i];
-  buf[m++] = mask[i];
-  buf[m++] = image[i];
-
-  if (nextra_grow)
-    for (int iextra = 0; iextra < nextra_grow; iextra++) 
-      m += modify->fix[extra_grow[iextra]]->pack_exchange(i,&buf[m]);
-
-  buf[0] = m;
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomDPD::unpack_exchange(double *buf)
-{
-  if (nlocal == nmax) grow(0);
-
-  int m = 1;
-  x[nlocal][0] = buf[m++];
-  x[nlocal][1] = buf[m++];
-  x[nlocal][2] = buf[m++];
-  v[nlocal][0] = buf[m++];
-  v[nlocal][1] = buf[m++];
-  v[nlocal][2] = buf[m++];
-  tag[nlocal] = static_cast<int> (buf[m++]);
-  type[nlocal] = static_cast<int> (buf[m++]);
-  mask[nlocal] = static_cast<int> (buf[m++]);
-  image[nlocal] = static_cast<int> (buf[m++]);
-
-  if (nextra_grow)
-    for (int iextra = 0; iextra < nextra_grow; iextra++) 
-      m += modify->fix[extra_grow[iextra]]->unpack_exchange(nlocal,&buf[m]);
-
-  nlocal++;
-  return m;
-}

src/DPD/atom_dpd.h

@@ -1,34 +0,0 @@
-/* ----------------------------------------------------------------------
-   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 ATOM_DPD_H
-#define ATOM_DPD_H
-
-#include "atom.h"
-
-class AtomDPD : public Atom {
- public:
-  AtomDPD(int, char **);
-  ~AtomDPD() {}
-  void copy(int, int);
-  void pack_comm(int, int *, double *, int *);
-  void unpack_comm(int, int, double *);
-  void pack_reverse(int, int, double *);
-  void unpack_reverse(int, int *, double *);
-  void pack_border(int, int *, double *, int *);
-  void unpack_border(int, int, double *);
-  int pack_exchange(int, double *);
-  int unpack_exchange(double *);
-};
-
-#endif

src/DPD/pair_dpd.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -28,6 +28,8 @@
 #include "neighbor.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
@@ -35,14 +37,12 @@
 
 /* ---------------------------------------------------------------------- */
 
-PairDPD::PairDPD()
+PairDPD::PairDPD(LAMMPS *lmp) : Pair(lmp)
 {
   random = NULL;
 }
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays 
-------------------------------------------------------------------------- */
 
 PairDPD::~PairDPD()
 {
@@ -208,7 +208,7 @@ void PairDPD::settings(int narg, char **arg)
   if (seed <= 0 || seed > 900000000)
     error->all("Illegal fix pair_style command");
   if (random) delete random;
-  random = new RanMars(seed + comm->me);
+  random = new RanMars(lmp,seed + comm->me);
 
   // reset cutoffs that have been explicitly set
 
@@ -372,7 +372,7 @@ void PairDPD::read_restart_settings(FILE *fp)
   // same seed that pair_style command initially specified
 
   if (random) delete random;
-  random = new RanMars(seed + comm->me);
+  random = new RanMars(lmp,seed + comm->me);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -381,15 +381,7 @@ void PairDPD::single(int i, int j, int itype, int jtype, double rsq,
 		     double factor_coul, double factor_dpd, int eflag,
 		     One &one)
 {
-  double r,rinv,dot,wd,randnum,phi;
+  double r,rinv,wd,phi;
-
-  double delx = atom->x[i][0] - atom->x[j][0];
-  double dely = atom->x[i][1] - atom->x[j][1];
-  double delz = atom->x[i][2] - atom->x[j][2];
-  double delvx = atom->v[i][0] - atom->v[j][0];
-  double delvy = atom->v[i][1] - atom->v[j][1];
-  double delvz = atom->v[i][2] - atom->v[j][2];
-  double dtinvsqrt = 1.0/sqrt(update->dt);
 
   r = sqrt(rsq);
   if (r < EPSILON) {
@@ -399,9 +391,7 @@ void PairDPD::single(int i, int j, int itype, int jtype, double rsq,
   }
 
   rinv = 1.0/r;
-  dot = delx*delvx + dely*delvy + delz*delvz;
   wd = 1.0 - r/cut[itype][jtype];
-  randnum = random->gaussian();
 
   one.fforce = a0[itype][jtype]*wd * factor_dpd*rinv;
   

src/DPD/pair_dpd.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,11 +16,11 @@
 
 #include "pair.h"
 
-class RanMars;
+namespace LAMMPS_NS {
 
 class PairDPD : public Pair {
  public:
-  PairDPD();
+  PairDPD(class LAMMPS *);
   ~PairDPD();
   void compute(int, int);
   void settings(int, char **);
@@ -39,9 +39,11 @@ class PairDPD : public Pair {
   double **cut;
   double **a0,**gamma;
   double **sigma;
-  RanMars *random;
+  class RanMars *random;
 
   void allocate();
 };
 
+}
+
 #endif

src/DPD/style_dpd.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #ifdef AtomInclude
-#include "atom_dpd.h"
+#include "atom_vec_dpd.h"
 #endif
 
 #ifdef AtomClass
-AtomStyle(dpd,AtomDPD)
+AtomStyle(dpd,AtomVecDPD)
 #endif
 
 #ifdef PairInclude

src/GRANULAR/Install.csh

@@ -1,28 +1,24 @@
 # Install/unInstall package classes in LAMMPS
 
-# fix_shear_history.h must always be in src
-
 if ($1 == 1) then
 
   cp style_granular.h ..
 
-  cp atom_granular.cpp ..
+  cp atom_vec_granular.cpp ..
   cp fix_freeze.cpp ..
   cp fix_gran_diag.cpp ..
   cp fix_nve_gran.cpp ..
   cp fix_pour.cpp ..
-  cp fix_shear_history.cpp ..
   cp fix_wall_gran.cpp ..
   cp pair_gran_hertzian.cpp ..
   cp pair_gran_history.cpp ..
   cp pair_gran_no_history.cpp ..
 
-  cp atom_granular.h ..
+  cp atom_vec_granular.h ..
   cp fix_freeze.h ..
   cp fix_gran_diag.h ..
   cp fix_nve_gran.h ..
   cp fix_pour.h ..
-#  cp fix_shear_history.h ..
   cp fix_wall_gran.h ..
   cp pair_gran_hertzian.h ..
   cp pair_gran_history.h ..
@@ -33,23 +29,21 @@ else if ($1 == 0) then
   rm ../style_granular.h
   touch ../style_granular.h
 
-  rm ../atom_granular.cpp
+  rm ../atom_vec_granular.cpp
   rm ../fix_freeze.cpp
   rm ../fix_gran_diag.cpp
   rm ../fix_nve_gran.cpp
   rm ../fix_pour.cpp
-  rm ../fix_shear_history.cpp
   rm ../fix_wall_gran.cpp
   rm ../pair_gran_hertzian.cpp
   rm ../pair_gran_history.cpp
   rm ../pair_gran_no_history.cpp
 
-  rm ../atom_granular.h
+  rm ../atom_vec_granular.h
   rm ../fix_freeze.h
   rm ../fix_gran_diag.h
   rm ../fix_nve_gran.h
   rm ../fix_pour.h
-#  rm ../fix_shear_history.h
   rm ../fix_wall_gran.h
   rm ../pair_gran_hertzian.h
   rm ../pair_gran_history.h

src/GRANULAR/atom_granular.cpp

@@ -1,322 +0,0 @@
-/* ----------------------------------------------------------------------
-   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.
-------------------------------------------------------------------------- */
-
-#include "string.h"
-#include "atom_granular.h"
-#include "domain.h"
-#include "modify.h"
-#include "fix.h"
-
-/* ---------------------------------------------------------------------- */
-
-AtomGranular::AtomGranular(int narg, char **arg) : Atom(narg, arg) {}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomGranular::copy(int i, int j)
-{
-  tag[j] = tag[i];
-  type[j] = type[i];
-  mask[j] = mask[i];
-  image[j] = image[i];
-  x[j][0] = x[i][0];
-  x[j][1] = x[i][1];
-  x[j][2] = x[i][2];
-  v[j][0] = v[i][0];
-  v[j][1] = v[i][1];
-  v[j][2] = v[i][2];
-  phix[j][0] = phix[i][0];
-  phix[j][1] = phix[i][1];
-  phix[j][2] = phix[i][2];
-  phiv[j][0] = phiv[i][0];
-  phiv[j][1] = phiv[i][1];
-  phiv[j][2] = phiv[i][2];
-  radius[j] = radius[i];
-  density[j] = density[i];
-  rmass[j] = rmass[i];
-
-  if (nextra_grow)
-    for (int iextra = 0; iextra < nextra_grow; iextra++) 
-      modify->fix[extra_grow[iextra]]->copy_arrays(i,j);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomGranular::pack_comm(int n, int *list, double *buf, int *pbc_flags)
-{
-  int i,j,m;
-
-  m = 0;
-  if (pbc_flags[0] == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = x[j][0];
-      buf[m++] = x[j][1];
-      buf[m++] = x[j][2];
-      buf[m++] = v[j][0];
-      buf[m++] = v[j][1];
-      buf[m++] = v[j][2];
-      buf[m++] = phiv[j][0];
-      buf[m++] = phiv[j][1];
-      buf[m++] = phiv[j][2];
-    }
-  } else {
-    double xprd = domain->xprd;
-    double yprd = domain->yprd;
-    double zprd = domain->zprd;
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = x[j][0] + pbc_flags[1]*xprd;
-      buf[m++] = x[j][1] + pbc_flags[2]*yprd;
-      buf[m++] = x[j][2] + pbc_flags[3]*zprd;
-      buf[m++] = v[j][0];
-      buf[m++] = v[j][1];
-      buf[m++] = v[j][2];
-      buf[m++] = phiv[j][0];
-      buf[m++] = phiv[j][1];
-      buf[m++] = phiv[j][2];
-    }
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomGranular::unpack_comm(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++) {
-    x[i][0] = buf[m++];
-    x[i][1] = buf[m++];
-    x[i][2] = buf[m++];
-    v[i][0] = buf[m++];
-    v[i][1] = buf[m++];
-    v[i][2] = buf[m++];
-    phiv[i][0] = buf[m++];
-    phiv[i][1] = buf[m++];
-    phiv[i][2] = buf[m++];
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomGranular::pack_reverse(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++) {
-    buf[m++] = f[i][0];
-    buf[m++] = f[i][1];
-    buf[m++] = f[i][2];
-    buf[m++] = phia[i][0];
-    buf[m++] = phia[i][1];
-    buf[m++] = phia[i][2];
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomGranular::unpack_reverse(int n, int *list, double *buf)
-{
-  int i,j,m;
-
-  m = 0;
-  for (i = 0; i < n; i++) {
-    j = list[i];
-    f[j][0] += buf[m++];
-    f[j][1] += buf[m++];
-    f[j][2] += buf[m++];
-    phia[j][0] += buf[m++];
-    phia[j][1] += buf[m++];
-    phia[j][2] += buf[m++];
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomGranular::pack_border(int n, int *list, double *buf, int *pbc_flags)
-{
-  int i,j,m;
-
-  m = 0;
-  if (pbc_flags[0] == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = x[j][0];
-      buf[m++] = x[j][1];
-      buf[m++] = x[j][2];
-      buf[m++] = tag[j];
-      buf[m++] = type[j];
-      buf[m++] = mask[j];
-      buf[m++] = v[j][0];
-      buf[m++] = v[j][1];
-      buf[m++] = v[j][2];
-      buf[m++] = phiv[j][0];
-      buf[m++] = phiv[j][1];
-      buf[m++] = phiv[j][2];
-      buf[m++] = radius[j];
-      buf[m++] = rmass[j];
-    }
-  } else {
-    double xprd = domain->xprd;
-    double yprd = domain->yprd;
-    double zprd = domain->zprd;
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = x[j][0] + pbc_flags[1]*xprd;
-      buf[m++] = x[j][1] + pbc_flags[2]*yprd;
-      buf[m++] = x[j][2] + pbc_flags[3]*zprd;
-      buf[m++] = tag[j];
-      buf[m++] = type[j];
-      buf[m++] = mask[j];
-      buf[m++] = v[j][0];
-      buf[m++] = v[j][1];
-      buf[m++] = v[j][2];
-      buf[m++] = phiv[j][0];
-      buf[m++] = phiv[j][1];
-      buf[m++] = phiv[j][2];
-      buf[m++] = radius[j];
-      buf[m++] = rmass[j];
-    }
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomGranular::unpack_border(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++) {
-    if (i == nmax) grow(0);
-    x[i][0] = buf[m++];
-    x[i][1] = buf[m++];
-    x[i][2] = buf[m++];
-    tag[i] = static_cast<int> (buf[m++]);
-    type[i] = static_cast<int> (buf[m++]);
-    mask[i] = static_cast<int> (buf[m++]);
-    v[i][0] = buf[m++];
-    v[i][1] = buf[m++];
-    v[i][2] = buf[m++];
-    phiv[i][0] = buf[m++];
-    phiv[i][1] = buf[m++];
-    phiv[i][2] = buf[m++];
-    radius[i] = buf[m++];
-    rmass[i] = buf[m++];
-  }
-}
-
-/* ----------------------------------------------------------------------
-   pack all atom quantities for shipping to another proc
-   xyz must be 1st 3 values, so that comm::exchange can test on them
-------------------------------------------------------------------------- */
-
-int AtomGranular::pack_exchange(int i, double *buf)
-{
-  int m = 1;
-  buf[m++] = x[i][0];
-  buf[m++] = x[i][1];
-  buf[m++] = x[i][2];
-  buf[m++] = v[i][0];
-  buf[m++] = v[i][1];
-  buf[m++] = v[i][2];
-  buf[m++] = phix[i][0];
-  buf[m++] = phix[i][1];
-  buf[m++] = phix[i][2];
-  buf[m++] = phiv[i][0];
-  buf[m++] = phiv[i][1];
-  buf[m++] = phiv[i][2];
-  buf[m++] = radius[i];
-  buf[m++] = density[i];
-  buf[m++] = rmass[i];
-  buf[m++] = tag[i];
-  buf[m++] = type[i];
-  buf[m++] = mask[i];
-  buf[m++] = image[i];
-
-  if (nextra_grow)
-    for (int iextra = 0; iextra < nextra_grow; iextra++) 
-      m += modify->fix[extra_grow[iextra]]->pack_exchange(i,&buf[m]);
-
-  buf[0] = m;
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomGranular::unpack_exchange(double *buf)
-{
-  if (nlocal == nmax) grow(0);
-
-  int m = 1;
-  x[nlocal][0] = buf[m++];
-  x[nlocal][1] = buf[m++];
-  x[nlocal][2] = buf[m++];
-  v[nlocal][0] = buf[m++];
-  v[nlocal][1] = buf[m++];
-  v[nlocal][2] = buf[m++];
-  phix[nlocal][0] = buf[m++];
-  phix[nlocal][1] = buf[m++];
-  phix[nlocal][2] = buf[m++];
-  phiv[nlocal][0] = buf[m++];
-  phiv[nlocal][1] = buf[m++];
-  phiv[nlocal][2] = buf[m++];
-  radius[nlocal] = buf[m++];
-  density[nlocal] = buf[m++];
-  rmass[nlocal] = buf[m++];
-  tag[nlocal] = static_cast<int> (buf[m++]);
-  type[nlocal] = static_cast<int> (buf[m++]);
-  mask[nlocal] = static_cast<int> (buf[m++]);
-  image[nlocal] = static_cast<int> (buf[m++]);
-
-  if (nextra_grow)
-    for (int iextra = 0; iextra < nextra_grow; iextra++) 
-      m += modify->fix[extra_grow[iextra]]->unpack_exchange(nlocal,&buf[m]);
-
-  nlocal++;
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   unpack vels & phis specific to granular data file
-------------------------------------------------------------------------- */
-
-void AtomGranular::unpack_vels(int n, char *buf)
-{
-  int m,tagtmp;
-  double vxtmp,vytmp,vztmp,phivxtmp,phivytmp,phivztmp;
-  char *next;
-
-  for (int i = 0; i < n; i++) {
-    next = strchr(buf,'\n');
-    *next = '\0';
-    sscanf(buf,"%d %lg %lg %lg %lg %lg %lg",
-	   &tagtmp,&vxtmp,&vytmp,&vztmp,
-	   &phivxtmp,&phivytmp,&phivztmp);
-    if ((m = map(tagtmp)) >= 0) {
-      v[m][0] = vxtmp;
-      v[m][1] = vytmp;
-      v[m][2] = vztmp;
-      phiv[m][0] = phivxtmp;
-      phiv[m][1] = phivytmp;
-      phiv[m][2] = phivztmp;
-    }
-    buf = next + 1;
-  }
-}

src/GRANULAR/atom_granular.h

@@ -1,36 +0,0 @@
-/* ----------------------------------------------------------------------
-   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 ATOM_GRANULAR_H
-#define ATOM_GRANULAR_H
-
-#include "atom.h"
-
-class AtomGranular : public Atom {
- public:
-  AtomGranular(int, char **);
-  ~AtomGranular() {}
-  void copy(int, int);
-  void pack_comm(int, int *, double *, int *);
-  void unpack_comm(int, int, double *);
-  void pack_reverse(int, int, double *);
-  void unpack_reverse(int, int *, double *);
-  void pack_border(int, int *, double *, int *);
-  void unpack_border(int, int, double *);
-  int pack_exchange(int, double *);
-  int unpack_exchange(double *);
-
-  void unpack_vels(int, char *);
-};
-
-#endif

src/GRANULAR/fix_freeze.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -18,9 +18,12 @@
 #include "comm.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 /* ---------------------------------------------------------------------- */
 
-FixFreeze::FixFreeze(int narg, char **arg) : Fix(narg, arg)
+FixFreeze::FixFreeze(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
 {
   if (narg != 3) error->all("Illegal fix freeze command");
 

src/GRANULAR/fix_freeze.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,14 +16,17 @@
 
 #include "fix.h"
 
+namespace LAMMPS_NS {
+
 class FixFreeze : public Fix {
  public:
-  FixFreeze(int, char **);
+  FixFreeze(class LAMMPS *, int, char **);
-  ~FixFreeze() {}
   int setmask();
   void init();
   void setup();
   void post_force(int);
 };
 
+}
+
 #endif

src/GRANULAR/fix_gran_diag.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,28 +17,29 @@
 
 #include "math.h"
 #include "stdlib.h"
+#include "string.h"
 #include "fix_gran_diag.h"
 #include "update.h"
 #include "force.h"
-#include "pair_gran_no_history.h"
+#include "pair.h"
-#include "pair_gran_history.h"
-#include "pair_gran_hertzian.h"
 #include "atom.h"
 #include "neighbor.h"
+#include "modify.h"
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
-#define NO_HISTORY 1
+enum{NO_HISTORY,HISTORY,HERTZIAN};
-#define HISTORY    2
-#define HERTZIAN   3
 
 /* ---------------------------------------------------------------------- */
 
-FixGranDiag::FixGranDiag(int narg, char **arg) : Fix(narg, arg)
+FixGranDiag::FixGranDiag(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
 {
   if (narg != 6) error->all("Illegal fix gran/diag command");
   nevery = atoi(arg[3]);
@@ -112,37 +113,38 @@ int FixGranDiag::setmask()
 
 void FixGranDiag::init()
 {
+  // insure use of granular pair_style
+  // set local values from Pair values
+
+  Pair *pair = force->pair_match("gran");
+  if (pair == NULL)
+    error->all("Fix gran/diag is incompatible with Pair style");
+  int dampflag;
+  double gamman;
+  pair->extract_gran(&xkk,&gamman,&xmu,&dampflag);
+
+  // same initialization as in pair_gran_history::init_style()
+
+  xkkt = xkk * 2.0/7.0;
   dt = update->dt;
+  double gammas = 0.5*gamman;
+  if (dampflag == 0) gammas = 0.0;
+  gamman_dl = gamman/dt;
+  gammas_dl = gammas/dt;
 
-  // set constants from pair style
+  // set pairstyle from granular pair style
 
-  Pair *anypair;
+  if (force->pair_match("gran/no_history")) pairstyle = NO_HISTORY;
-  if (anypair = force->pair_match("gran/no_history")) {
+  else if (force->pair_match("gran/history")) pairstyle = HISTORY;
-    pairstyle = NO_HISTORY;
+  else if (force->pair_match("gran/hertzian")) pairstyle = HERTZIAN;
-    xkk = ((PairGranNoHistory *) anypair)->xkk;
+
-    xkkt = ((PairGranNoHistory *) anypair)->xkkt;
+  // check for freeze Fix and set freeze_group_bit
-    xmu = ((PairGranNoHistory *) anypair)->xmu;
+
-    gamman_dl = ((PairGranNoHistory *) anypair)->gamman_dl;
+  int i;
-    gammas_dl = ((PairGranNoHistory *) anypair)->gammas_dl;
+  for (i = 0; i < modify->nfix; i++)
-    freeze_group_bit = ((PairGranNoHistory *) anypair)->freeze_group_bit;
+    if (strcmp(modify->fix[i]->style,"freeze") == 0) break;
-  } else if (anypair = force->pair_match("gran/history")) {
+  if (i < modify->nfix) freeze_group_bit = modify->fix[i]->groupbit;
-    pairstyle = HISTORY;
+  else freeze_group_bit = 0;
-    xkk = ((PairGranHistory *) anypair)->xkk;
-    xkkt = ((PairGranHistory *) anypair)->xkkt;
-    xmu = ((PairGranHistory *) anypair)->xmu;
-    gamman_dl = ((PairGranHistory *) anypair)->gamman_dl;
-    gammas_dl = ((PairGranHistory *) anypair)->gammas_dl;
-    freeze_group_bit = ((PairGranNoHistory *) anypair)->freeze_group_bit;
-  } else if (anypair = force->pair_match("gran/hertzian")) {
-    pairstyle = HERTZIAN;
-    xkk = ((PairGranHertzian *) anypair)->xkk;
-    xkkt = ((PairGranHertzian *) anypair)->xkkt;
-    xmu = ((PairGranHertzian *) anypair)->xmu;
-    gamman_dl = ((PairGranHertzian *) anypair)->gamman_dl;
-    gammas_dl = ((PairGranHertzian *) anypair)->gammas_dl;
-    freeze_group_bit = ((PairGranNoHistory *) anypair)->freeze_group_bit;
-  } else
-    error->all("Must use fix gran/diag with granular pair style");
 }
 
 /* ---------------------------------------------------------------------- */

src/GRANULAR/fix_gran_diag.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "fix.h"
 
+namespace LAMMPS_NS {
+
 class FixGranDiag : public Fix {
  public:
-  FixGranDiag(int, char **);
+  FixGranDiag(class LAMMPS *, int, char **);
   ~FixGranDiag();
   int setmask();
   void init();
@@ -50,4 +52,6 @@ class FixGranDiag : public Fix {
   void stress_hertzian();
 };
 
+}
+
 #endif

src/GRANULAR/fix_nve_gran.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -19,6 +19,8 @@
 #include "force.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 // moments of inertia for sphere and disk
 
 #define INERTIA3D 0.4
@@ -26,7 +28,8 @@
 
 /* ---------------------------------------------------------------------- */
 
-FixNVEGran::FixNVEGran(int narg, char **arg) : Fix(narg, arg)
+FixNVEGran::FixNVEGran(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
 {
   if (narg != 3) error->all("Illegal fix nve/gran command");
 

src/GRANULAR/fix_nve_gran.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,10 +16,11 @@
 
 #include "fix.h"
 
+namespace LAMMPS_NS {
+
 class FixNVEGran : public Fix {
  public:
-  FixNVEGran(int, char **);
+  FixNVEGran(class LAMMPS *, int, char **);
-  ~FixNVEGran() {}
   int setmask();
   void init();
   void initial_integrate();
@@ -29,4 +30,6 @@ class FixNVEGran : public Fix {
   double dtv,dtf,dtfphi;
 };
 
+}
+
 #endif

src/GRANULAR/fix_pour.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,6 +16,7 @@
 #include "string.h"
 #include "fix_pour.h"
 #include "atom.h"
+#include "atom_vec.h"
 #include "force.h"
 #include "update.h"
 #include "comm.h"
@@ -30,11 +31,14 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define EPSILON 0.001
 
 /* ---------------------------------------------------------------------- */
 
-FixPour::FixPour(int narg, char **arg) : Fix(narg, arg)
+FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
 {
   if (narg < 6) error->all("Illegal fix pour command");
 
@@ -151,7 +155,7 @@ FixPour::FixPour(int narg, char **arg) : Fix(narg, arg)
 
   // random number generator, same for all procs
 
-  random = new RanPark(seed);
+  random = new RanPark(lmp,seed);
 
   // allgather arrays
 
@@ -269,10 +273,11 @@ void FixPour::init()
 
   // check if a shear history fix exists
 
-  ifix_history = -1;
+  fix_history = NULL;
   if (force->pair_match("gran/history") || force->pair_match("gran/hertzian"))
     for (int i = 0; i < modify->nfix; i++)
-      if (strcmp(modify->fix[i]->style,"SHEAR_HISTORY") == 0) ifix_history = i;
+      if (strcmp(modify->fix[i]->style,"SHEAR_HISTORY") == 0)
+	fix_history = (FixShearHistory *) modify->fix[i];
 }
 
 /* ----------------------------------------------------------------------
@@ -403,7 +408,7 @@ void FixPour::pre_exchange()
     error->warning("Less insertions than requested");
 
   // check if new atom is in my sub-box or above it if I'm highest proc
-  // if so, add to my list via create_one()
+  // if so, add to my list via create_atom()
   // initialize info about the atom
   // type, diameter, density set from fix parameters
   // group mask set to "all" plus fix group
@@ -412,6 +417,7 @@ void FixPour::pre_exchange()
   // this gives continuous stream of atoms
   // set npartner for new atom to 0 (assume not touching any others)
 
+  AtomVec *avec = atom->avec;
   int m,flag;
   double denstmp,vxtmp,vytmp,vztmp;
   double g = 1.0;
@@ -445,7 +451,7 @@ void FixPour::pre_exchange()
 	     xtmp >= domain->subxlo && xtmp < domain->subxhi) flag = 1;
 
     if (flag) {
-      atom->create_one(ntype,xtmp,ytmp,ztmp);
+      avec->create_atom(ntype,xtmp,ytmp,ztmp,0);
       m = atom->nlocal - 1;
       atom->type[m] = ntype;
       atom->radius[m] = radtmp;
@@ -458,8 +464,7 @@ void FixPour::pre_exchange()
       atom->v[m][0] = vxtmp;
       atom->v[m][1] = vytmp;
       atom->v[m][2] = vztmp;
-      if (ifix_history >= 0)
+      if (fix_history) fix_history->npartner[m] = 0;
-	((FixShearHistory *) modify->fix[ifix_history])->npartner[m] = 0;
     }
   }
 

src/GRANULAR/fix_pour.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,7 +16,7 @@
 
 #include "fix.h"
 
-class RanPark;
+namespace LAMMPS_NS {
 
 class FixPour : public Fix {
   friend class PairGranHistory;
@@ -24,7 +24,7 @@ class FixPour : public Fix {
   friend class PairGranNoHistory;
 
  public:
-  FixPour(int, char **);
+  FixPour(class LAMMPS *, int, char **);
   ~FixPour();
   int setmask();
   void init();
@@ -47,12 +47,13 @@ class FixPour : public Fix {
   double PI;
   int nfreq,nfirst,ninserted,nper;
   double lo_current,hi_current;
-  int ifix_history;
+  class FixShearHistory *fix_history;
-
+  class RanPark *random;
-  RanPark *random;
 
   int overlap(int);
   void xyz_random(double, double &, double &, double &);
 };
 
+}
+
 #endif

src/GRANULAR/fix_shear_history.cpp

@@ -1,282 +0,0 @@
-/* ----------------------------------------------------------------------
-   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.
-------------------------------------------------------------------------- */
-
-#include "string.h"
-#include "stdio.h"
-#include "fix_shear_history.h"
-#include "atom.h"
-#include "neighbor.h"
-#include "force.h"
-#include "update.h"
-#include "modify.h"
-#include "memory.h"
-#include "error.h"
-
-#define MAXTOUCH 15
-
-/* ---------------------------------------------------------------------- */
-
-FixShearHistory::FixShearHistory(int narg, char **arg) : Fix(narg, arg)
-{
-  restart_peratom = 1;
-
-  // perform initial allocation of atom-based arrays
-  // register with atom class
-
-  npartner = NULL;
-  partner = NULL;
-  shearpartner = NULL;
-  grow_arrays(atom->nmax);
-  atom->add_callback(0);
-  atom->add_callback(1);
-
-  // initialize npartner to 0 so neighbor list creation is OK the 1st time
-
-  int nlocal = atom->nlocal;
-  for (int i = 0; i < nlocal; i++) npartner[i] = 0;
-}
-
-/* ---------------------------------------------------------------------- */
-
-FixShearHistory::~FixShearHistory()
-{
-  // if atom class still exists:
-  //   unregister this fix so atom class doesn't invoke it any more
-
-  if (atom) atom->delete_callback(id,0);
-  if (atom) atom->delete_callback(id,1);
-
-  // delete locally stored arrays
-
-  memory->sfree(npartner);
-  memory->destroy_2d_int_array(partner);
-  memory->destroy_3d_double_array(shearpartner);
-}
-
-/* ---------------------------------------------------------------------- */
-
-int FixShearHistory::setmask()
-{
-  int mask = 0;
-  mask |= PRE_EXCHANGE;
-  return mask;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void FixShearHistory::init()
-{
-  if (atom->tag_enable == 0) 
-    error->all("Pair style granular with history requires atoms have IDs");
-}
-
-/* ----------------------------------------------------------------------
-   copy shear partner info from neighbor lists to atom arrays
-   so can be exchanged with atoms
-------------------------------------------------------------------------- */
-
-void FixShearHistory::pre_exchange()
-{
-  int i,j,k,m;
-
-  // zero npartners for all current atoms
-
-  int nlocal = atom->nlocal;
-  for (i = 0; i < nlocal; i++) npartner[i] = 0;
-
-  // copy shear info from neighbor list atoms to atom arrays
-  // nlocal = nlocal_neighbor = nlocal when neighbor list last built,
-  //   which might be pre-insert on this step
-
-  int numneigh;
-  int *neighs,*touch;
-  double *firstshear,*shear;
-  int *tag = atom->tag;
-  nlocal = neighbor->nlocal_neighbor;
-
-  for (i = 0; i < nlocal; i++) {
-    neighs = neighbor->firstneigh[i];
-    touch = neighbor->firsttouch[i];
-    firstshear = neighbor->firstshear[i];
-    numneigh = neighbor->numneigh[i];
-    for (k = 0; k < numneigh; k++) {
-      if (touch[k]) {
-	shear = &firstshear[3*k];
-	j = neighs[k];
-	if (npartner[i] < MAXTOUCH) {
-	  m = npartner[i];
-	  partner[i][m] = tag[j];
-	  shearpartner[i][m][0] = shear[0];
-	  shearpartner[i][m][1] = shear[1];
-	  shearpartner[i][m][2] = shear[2];
-	}
-	npartner[i]++;
-	if (j < nlocal) {
-	  if (npartner[j] < MAXTOUCH) {
-	    m = npartner[j];
-	    partner[j][m] = tag[i];
-	    shearpartner[j][m][0] = -shear[0];
-	    shearpartner[j][m][1] = -shear[1];
-	    shearpartner[j][m][2] = -shear[2];
-	  }
-	  npartner[j]++;
-	}
-      }
-    }
-  }
-
-  // test for too many touching neighbors
-
-  int flag = 0;
-  for (i = 0; i < nlocal; i++)
-    if (npartner[i] >= MAXTOUCH) flag = 1;
-  int flag_all;
-  MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
-  if (flag_all) error->all("Too many touching neighbors - boost MAXTOUCH");
-}
-
-/* ----------------------------------------------------------------------
-   memory usage of local atom-based arrays
-------------------------------------------------------------------------- */
-
-int FixShearHistory::memory_usage()
-{
-  int nmax = atom->nmax;
-  int bytes = nmax * sizeof(int);
-  bytes += nmax*MAXTOUCH * sizeof(int);
-  bytes += nmax*MAXTOUCH*3 * sizeof(double);
-  return bytes;
-}
-
-/* ----------------------------------------------------------------------
-   allocate local atom-based arrays
-------------------------------------------------------------------------- */
-
-void FixShearHistory::grow_arrays(int nmax)
-{
-  npartner = (int *) memory->srealloc(npartner,nmax*sizeof(int),
-				      "shear_history:npartner");
-  partner = memory->grow_2d_int_array(partner,nmax,MAXTOUCH,
-				      "shear_history:partner");
-  shearpartner = 
-    memory->grow_3d_double_array(shearpartner,nmax,MAXTOUCH,3,
-				 "shear_history:shearpartner");
-}
-
-/* ----------------------------------------------------------------------
-   copy values within local atom-based arrays
-------------------------------------------------------------------------- */
-
-void FixShearHistory::copy_arrays(int i, int j)
-{
-  npartner[j] = npartner[i];
-  for (int m = 0; m < npartner[j]; m++) {
-    partner[j][m] = partner[i][m];
-    shearpartner[j][m][0] = shearpartner[i][m][0];
-    shearpartner[j][m][1] = shearpartner[i][m][1];
-    shearpartner[j][m][2] = shearpartner[i][m][2];
-  }
-}
-
-/* ----------------------------------------------------------------------
-   pack values in local atom-based arrays for exchange with another proc
-------------------------------------------------------------------------- */
-
-int FixShearHistory::pack_exchange(int i, double *buf)
-{
-  int m = 0;
-  buf[m++] = npartner[i];
-  for (int n = 0; n < npartner[i]; n++) {
-    buf[m++] = partner[i][n];
-    buf[m++] = shearpartner[i][n][0];
-    buf[m++] = shearpartner[i][n][1];
-    buf[m++] = shearpartner[i][n][2];
-  }
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   unpack values in local atom-based arrays from exchange with another proc
-------------------------------------------------------------------------- */
-
-int FixShearHistory::unpack_exchange(int nlocal, double *buf)
-{
-  int m = 0;
-  npartner[nlocal] = static_cast<int> (buf[m++]);
-  for (int n = 0; n < npartner[nlocal]; n++) {
-    partner[nlocal][n] = static_cast<int> (buf[m++]);
-    shearpartner[nlocal][n][0] = buf[m++];
-    shearpartner[nlocal][n][1] = buf[m++];
-    shearpartner[nlocal][n][2] = buf[m++];
-  }
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   pack values in local atom-based arrays for restart file
-------------------------------------------------------------------------- */
-
-int FixShearHistory::pack_restart(int i, double *buf)
-{
-  int m = 0;
-  buf[m++] = 4*npartner[i] + 2;
-  buf[m++] = npartner[i];
-  for (int n = 0; n < npartner[i]; n++) {
-    buf[m++] = partner[i][n];
-    buf[m++] = shearpartner[i][n][0];
-    buf[m++] = shearpartner[i][n][1];
-    buf[m++] = shearpartner[i][n][2];
-  }
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   unpack values from atom->extra array to restart the fix
-------------------------------------------------------------------------- */
-
-void FixShearHistory::unpack_restart(int nlocal, int nth)
-{
-  double **extra = atom->extra;
-
-  // skip to Nth set of extra values
-
-  int m = 0;
-  for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
-  m++;
-
-  npartner[nlocal] = static_cast<int> (extra[nlocal][m++]);
-  for (int n = 0; n < npartner[nlocal]; n++) {
-    partner[nlocal][n] = static_cast<int> (extra[nlocal][m++]);
-    shearpartner[nlocal][n][0] = extra[nlocal][m++];
-    shearpartner[nlocal][n][1] = extra[nlocal][m++];
-    shearpartner[nlocal][n][2] = extra[nlocal][m++];
-  }
-}
-
-/* ----------------------------------------------------------------------
-   maxsize of any atom's restart data
-------------------------------------------------------------------------- */
-
-int FixShearHistory::maxsize_restart()
-{
-  return 4*MAXTOUCH + 2;
-}
-
-/* ----------------------------------------------------------------------
-   size of atom nlocal's restart data
-------------------------------------------------------------------------- */
-
-int FixShearHistory::size_restart(int nlocal)
-{
-  return 4*npartner[nlocal] + 2;
-}

src/GRANULAR/fix_wall_gran.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -22,21 +22,15 @@
 #include "atom.h"
 #include "update.h"
 #include "force.h"
+#include "pair.h"
 #include "modify.h"
-#include "pair_gran_no_history.h"
-#include "pair_gran_history.h"
-#include "pair_gran_hertzian.h"
 #include "memory.h"
 #include "error.h"
 
-#define XPLANE    1
+using namespace LAMMPS_NS;
-#define YPLANE    2
-#define ZPLANE    3
-#define ZCYLINDER 4
 
-#define NO_HISTORY 1
+enum{XPLANE,YPLANE,ZPLANE,ZCYLINDER};
-#define HISTORY    2
+enum{NO_HISTORY,HISTORY,HERTZIAN};
-#define HERTZIAN   3
 
 #define BIG 1.0e20
 
@@ -45,7 +39,8 @@
 
 /* ---------------------------------------------------------------------- */
 
-FixWallGran::FixWallGran(int narg, char **arg) : Fix(narg, arg)
+FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
 {
   if (narg < 4) error->all("Illegal fix wall/gran command");
   
@@ -125,7 +120,7 @@ FixWallGran::FixWallGran(int narg, char **arg) : Fix(narg, arg)
   }
 
   // perform initial allocation of atom-based arrays
-  // register with atom class
+  // register with Atom class
 
   shear = NULL;
   grow_arrays(atom->nmax);
@@ -143,11 +138,10 @@ FixWallGran::FixWallGran(int narg, char **arg) : Fix(narg, arg)
 
 FixWallGran::~FixWallGran()
 {
-  // if atom class still exists:
+  // unregister callbacks to this fix from Atom class
-  //   unregister this fix so atom class doesn't invoke it any more
 
-  if (atom) atom->delete_callback(id,0);
+  atom->delete_callback(id,0);
-  if (atom) atom->delete_callback(id,1);
+  atom->delete_callback(id,1);
 
   // delete locally stored arrays
 
@@ -167,32 +161,29 @@ int FixWallGran::setmask()
 
 void FixWallGran::init()
 {
-  // set constants that depend on pair style
+  // insure use of granular pair_style
+  // set local values from Pair values
 
-  Pair *anypair;
+  Pair *pair = force->pair_match("gran");
-  if (anypair = force->pair_match("gran/no_history")) {
+  if (pair == NULL)
-    historystyle = 0;
+    error->all("Fix wall/gran is incompatible with Pair style");
-    pairstyle = NO_HISTORY;
+  int itmp;
-    xkk = ((PairGranNoHistory *) anypair)->xkk;
+  double tmp1,tmp2;
-    xkkt = ((PairGranNoHistory *) anypair)->xkkt;
+  pair->extract_gran(&xkk,&tmp1,&tmp2,&itmp);
-  } else if (anypair = force->pair_match("gran/history")) {
-    historystyle = 1;
-    pairstyle = HISTORY;
-    xkk = ((PairGranHistory *) anypair)->xkk;
-    xkkt = ((PairGranHistory *) anypair)->xkkt;
-  } else if (anypair = force->pair_match("gran/hertzian")) {
-    historystyle = 1;
-    pairstyle = HERTZIAN;
-    xkk = ((PairGranHertzian *) anypair)->xkk;
-    xkkt = ((PairGranHertzian *) anypair)->xkkt;
-  } else
-    error->all("Fix wall/gran can only be used with granular pair style");
 
-  // friction coeffs
+  // same initialization as in pair_gran_history::init_style()
 
+  xkkt = xkk * 2.0/7.0;
   dt = update->dt;
+  double gammas = 0.5*gamman;
   gamman_dl = gamman/dt;
-  gammas_dl = 0.5*gamman_dl;
+  gammas_dl = gammas/dt;
+
+  // set pairstyle from granular pair style
+
+  if (force->pair_match("gran/no_history")) pairstyle = NO_HISTORY;
+  else if (force->pair_match("gran/history")) pairstyle = HISTORY;
+  else if (force->pair_match("gran/hertzian")) pairstyle = HERTZIAN;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -274,7 +265,7 @@ void FixWallGran::post_force(int vflag)
       rsq = dx*dx + dy*dy + dz*dz;
 
       if (rsq > radius[i]*radius[i]) {
-	if (historystyle) {
+	if (pairstyle != NO_HISTORY) {
 	  shear[i][0] = 0.0;
 	  shear[i][1] = 0.0;
 	  shear[i][2] = 0.0;

src/GRANULAR/fix_wall_gran.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,9 +16,11 @@
 
 #include "fix.h"
 
+namespace LAMMPS_NS {
+
 class FixWallGran : public Fix {
  public:
-  FixWallGran(int, char **);
+  FixWallGran(class LAMMPS *, int, char **);
   ~FixWallGran();
   int setmask();
   void init();
@@ -36,7 +38,7 @@ class FixWallGran : public Fix {
   int maxsize_restart();
 
  private:
-  int wallstyle,pairstyle,historystyle,wiggle,axis;
+  int wallstyle,pairstyle,wiggle,axis;
   double xkk,xkkt,gamman,xmu;
   double lo,hi,cylradius;
   double dt,gamman_dl,gammas_dl;
@@ -55,4 +57,6 @@ class FixWallGran : public Fix {
 		double *);
 };
 
+}
+
 #endif

src/GRANULAR/pair_gran_hertzian.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -23,11 +23,20 @@
 #include "force.h"
 #include "neighbor.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
 /* ---------------------------------------------------------------------- */
 
+PairGranHertzian::PairGranHertzian(LAMMPS *lmp) : PairGranHistory(lmp)
+{
+  history = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
 void PairGranHertzian::compute(int eflag, int vflag)
 {
   int i,j,k,numneigh;

src/GRANULAR/pair_gran_hertzian.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,9 +16,14 @@
 
 #include "pair_gran_history.h"
 
+namespace LAMMPS_NS {
+
 class PairGranHertzian : public PairGranHistory {
  public:
+  PairGranHertzian(class LAMMPS *);
   void compute(int, int);
 };
 
+}
+
 #endif

src/GRANULAR/pair_gran_history.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -32,24 +32,27 @@
 #include "neighbor.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
 /* ---------------------------------------------------------------------- */
 
-PairGranHistory::PairGranHistory()
+PairGranHistory::PairGranHistory(LAMMPS *lmp) : Pair(lmp)
 {
   single_enable = 0;
 
   for (int i = 0; i < 6; i++) virial[i] = 0.0;
-  ifix_history = -1;
+  history = 1;
+  fix_history = NULL;
 }
 
 /* ---------------------------------------------------------------------- */
 
 PairGranHistory::~PairGranHistory()
 {
-  if (ifix_history >= 0) modify->delete_fix("SHEAR_HISTORY");
+  if (fix_history) modify->delete_fix("SHEAR_HISTORY");
 
   if (allocated) {
     memory->destroy_2d_int_array(setflag);
@@ -335,32 +338,21 @@ void PairGranHistory::init_style()
   if (atom->check_style("granular") == 0)
     error->all("Must use atom style granular with pair style granular");
 
-  // for pair choices with shear history:
+  // if shear history is stored:
   // check if newton flag is valid
   // if first init, create Fix needed for storing shear history
 
-  int history = 0;
-  if (force->pair_match("gran/history") || force->pair_match("gran/hertzian"))
-    history = 1;
-  
   if (history && force->newton_pair == 1)
     error->all("Potential with shear history requires newton pair off");
 
-  if (history && ifix_history == -1) {
+  if (history && fix_history == NULL) {
     char **fixarg = new char*[3];
     fixarg[0] = "SHEAR_HISTORY";
     fixarg[1] = "all";
     fixarg[2] = "SHEAR_HISTORY";
     modify->add_fix(3,fixarg);
     delete [] fixarg;
-  }
+    fix_history = (FixShearHistory *) modify->fix[modify->nfix-1];
-
-  // find associated SHEAR_HISTORY fix that must exist
-  // could have changed locations in fix list since created
-
-  if (history) {
-    for (i = 0; i < modify->nfix; i++)
-      if (strcmp(modify->fix[i]->style,"SHEAR_HISTORY") == 0) ifix_history = i;
   }
 
   // check for freeze Fix and set freeze_group_bit
@@ -452,3 +444,14 @@ void PairGranHistory::read_restart_settings(FILE *fp)
   MPI_Bcast(&xmu,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&dampflag,1,MPI_INT,0,world);
 }
+
+/* ---------------------------------------------------------------------- */
+
+void PairGranHistory::extract_gran(double *p_xkk, double *p_gamman,
+				   double *p_xmu, int *p_dampflag)
+{
+  *p_xkk = xkk;
+  *p_gamman = gamman;
+  *p_xmu = xmu;
+  *p_dampflag = dampflag;
+}

src/GRANULAR/pair_gran_history.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,13 +16,11 @@
 
 #include "pair.h"
 
-class PairGranHistory : public Pair {
+namespace LAMMPS_NS {
-  friend class Neighbor;
-  friend class FixWallGran;
-  friend class FixGranDiag;
 
+class PairGranHistory : public Pair {
  public:
-  PairGranHistory();
+  PairGranHistory(class LAMMPS *);
   ~PairGranHistory();
   virtual void compute(int, int);
   void settings(int, char **);
@@ -34,14 +32,20 @@ class PairGranHistory : public Pair {
   void write_restart_settings(FILE *);
   void read_restart_settings(FILE *);
 
+  void extract_gran(double *, double *, double *, int *);
+
  protected:
   double xkk,xkkt,xmu;
   int dampflag;
   double gamman;
   double dt,gamman_dl,gammas_dl;
-  int ifix_history,freeze_group_bit;
+  int freeze_group_bit;
+  int history;
+  class FixShearHistory *fix_history;
 
   void allocate();
 };
 
+}
+
 #endif

src/GRANULAR/pair_gran_no_history.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -23,11 +23,20 @@
 #include "force.h"
 #include "neighbor.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
 /* ---------------------------------------------------------------------- */
 
+PairGranNoHistory::PairGranNoHistory(LAMMPS *lmp) : PairGranHistory(lmp)
+{
+  history = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
 void PairGranNoHistory::compute(int eflag, int vflag)
 {
   int i,j,k,numneigh;

src/GRANULAR/pair_gran_no_history.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,9 +16,14 @@
 
 #include "pair_gran_history.h"
 
+namespace LAMMPS_NS {
+
 class PairGranNoHistory : public PairGranHistory {
  public:
+  PairGranNoHistory(class LAMMPS *);
   void compute(int, int);
 };
 
+}
+
 #endif

src/GRANULAR/style_granular.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #ifdef AtomInclude
-#include "atom_granular.h"
+#include "atom_vec_granular.h"
 #endif
 
 #ifdef AtomClass
-AtomStyle(granular,AtomGranular)
+AtomStyle(granular,AtomVecGranular)
 # endif
 
 #ifdef FixInclude

src/KSPACE/Install.csh

@@ -1,7 +1,5 @@
 # Install/unInstall package classes in LAMMPS
 
-# pair_lj_charmm_coul_long.h must always be in src
-
 if ($1 == 1) then
 
   cp style_kspace.h ..
@@ -24,7 +22,7 @@ if ($1 == 1) then
   cp pair_buck_coul_long.h ..
   cp pair_lj_cut_coul_long.h ..
   cp pair_lj_cut_coul_long_tip4p.h ..
-#  cp pair_lj_charmm_coul_long.h ..
+  cp pair_lj_charmm_coul_long.h ..
   cp fft3d.h ..
   cp fft3d_wrap.h ..
   cp remap.h ..
@@ -53,7 +51,7 @@ else if ($1 == 0) then
   rm ../pair_buck_coul_long.h
   rm ../pair_lj_cut_coul_long.h
   rm ../pair_lj_cut_coul_long_tip4p.h
-#  rm ../pair_lj_charmm_coul_long.h
+  rm ../pair_lj_charmm_coul_long.h
   rm ../fft3d.h
   rm ../fft3d_wrap.h
   rm ../remap.h

src/KSPACE/ewald.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -23,21 +23,19 @@
 #include "atom.h"
 #include "comm.h"
 #include "force.h"
-#include "pair_buck_coul_long.h"
+#include "pair.h"
-#include "pair_lj_cut_coul_long.h"
-#include "pair_lj_charmm_coul_long.h"
-#include "pair_lj_class2_coul_long.h"
-#include "pair_table.h"
 #include "domain.h"
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
 /* ---------------------------------------------------------------------- */
 
-Ewald::Ewald(int narg, char **arg) : KSpace(narg, arg)
+Ewald::Ewald(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
 {
   if (narg != 1) error->all("Illegal kspace_style ewald command");
 
@@ -90,27 +88,16 @@ void Ewald::init()
       error->all("Incorrect boundaries with slab Ewald");
   }
 
-  // insure use of pair_style with long-range Coulombics
+  // insure use of long (or table) pair_style with long-range Coulombics
-  // set cutoff to short-range Coulombic cutoff
+  // set cutoff to Pair's short-range Coulombic cutoff
 
   qqrd2e = force->qqrd2e;
 
+  Pair *pair = force->pair_match("long");
+  if (pair == NULL) pair = force->pair_match("table");
+  if (pair == NULL) error->all("KSpace style is incompatible with Pair style");
   double cutoff;
-
+  pair->extract_long(&cutoff);
-  Pair *anypair;
-  if (force->pair == NULL) 
-    error->all("KSpace style is incompatible with Pair style");
-  else if (anypair = force->pair_match("buck/coul/long"))
-    cutoff = ((PairBuckCoulLong *) anypair)->cut_coul;
-  else if (anypair = force->pair_match("lj/cut/coul/long"))
-    cutoff = ((PairLJCutCoulLong *) anypair)->cut_coul;
-  else if (anypair = force->pair_match("lj/charmm/coul/long"))
-    cutoff = ((PairLJCharmmCoulLong *) anypair)->cut_coul;
-  else if (anypair = force->pair_match("lj/class2/coul/long"))
-    cutoff = ((PairLJClass2CoulLong *) anypair)->cut_coul;
-  else if (anypair = force->pair_match("table"))
-    cutoff = ((PairTable *) anypair)->cut_coul();
-  else error->all("KSpace style is incompatible with Pair style");
 
   // compute qsum & qsqsum
 

src/KSPACE/ewald.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,9 +16,11 @@
 
 #include "kspace.h"
 
+namespace LAMMPS_NS {
+
 class Ewald : public KSpace {
  public:
-  Ewald(int, char **);
+  Ewald(class LAMMPS *, int, char **);
   ~Ewald();
   void init();
   void setup();
@@ -49,4 +51,6 @@ class Ewald : public KSpace {
 };
 
 #endif
+}
+
 

src/KSPACE/fft3d.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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

src/KSPACE/fft3d.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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

src/KSPACE/fft3d_wrap.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -15,14 +15,16 @@
 #include "fft3d_wrap.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 /* ---------------------------------------------------------------------- */
 
-FFT3d::FFT3d(MPI_Comm comm, int nfast, int nmid, int nslow,
+FFT3d::FFT3d(LAMMPS *lmp, MPI_Comm comm, int nfast, int nmid, int nslow,
 	     int in_ilo, int in_ihi, int in_jlo, int in_jhi,
 	     int in_klo, int in_khi,
 	     int out_ilo, int out_ihi, int out_jlo, int out_jhi,
 	     int out_klo, int out_khi,
-	     int scaled, int permute, int *nbuf)
+	     int scaled, int permute, int *nbuf) : Pointers(lmp)
 {
   plan = fft_3d_create_plan(comm,nfast,nmid,nslow,
 			    in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,

src/KSPACE/fft3d_wrap.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -14,12 +14,14 @@
 #ifndef FFT3D_WRAP_H
 #define FFT3D_WRAP_H
 
-#include "lammps.h"
+#include "pointers.h"
 #include "fft3d.h"
 
-class FFT3d : public LAMMPS {
+namespace LAMMPS_NS {
+
+class FFT3d : protected Pointers {
  public:
-  FFT3d(MPI_Comm,int,int,int,int,int,int,int,int,int,
+  FFT3d(class LAMMPS *, MPI_Comm,int,int,int,int,int,int,int,int,int,
 	int,int,int,int,int,int,int,int,int *);
   ~FFT3d();
   void compute(double *, double *, int);
@@ -29,4 +31,6 @@ class FFT3d : public LAMMPS {
   struct fft_plan_3d *plan;
 };
 
+}
+
 #endif

src/KSPACE/pair_buck_coul_long.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -25,6 +25,8 @@
 #include "neighbor.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
@@ -36,9 +38,11 @@
 #define A4       -1.453152027
 #define A5        1.061405429
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays
+
-------------------------------------------------------------------------- */
+PairBuckCoulLong::PairBuckCoulLong(LAMMPS *lmp) : Pair(lmp) {}
+
+/* ---------------------------------------------------------------------- */
 
 PairBuckCoulLong::~PairBuckCoulLong()
 {
@@ -305,7 +309,7 @@ void PairBuckCoulLong::init_style()
 {
   // require an atom style with charge defined
 
-  if (atom->charge_allow == 0)
+  if (atom->q == NULL)
     error->all("Must use charged atom style with this pair style");
 
   cut_coulsq = cut_coul * cut_coul;
@@ -444,3 +448,11 @@ void PairBuckCoulLong::single(int i, int j, int itype, int jtype,
     } else one.eng_vdwl = 0.0;
   }
 }
+
+/* ---------------------------------------------------------------------- */
+
+void PairBuckCoulLong::extract_long(double *p_cut_coul)
+{
+  *p_cut_coul = cut_coul;
+}
+

src/KSPACE/pair_buck_coul_long.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,11 +16,11 @@
 
 #include "pair.h"
 
+namespace LAMMPS_NS {
+
 class PairBuckCoulLong : public Pair {
  public:
-  double cut_coul;
+  PairBuckCoulLong(class LAMMPS *);
-
-  PairBuckCoulLong() {}
   ~PairBuckCoulLong();
   void compute(int, int);
   void settings(int, char **);
@@ -33,10 +33,12 @@ class PairBuckCoulLong : public Pair {
   void read_restart_settings(FILE *);
   void single(int, int, int, int, double, double, double, int, One &);
 
+  void extract_long(double *);
+
  private:
   double cut_lj_global;
   double **cut_lj,**cut_ljsq;
-  double cut_coulsq;
+  double cut_coul,cut_coulsq;
   double **a,**rho,**c;
   double **rhoinv,**buck1,**buck2,**offset;
   double g_ewald;
@@ -44,4 +46,6 @@ class PairBuckCoulLong : public Pair {
   void allocate();
 };
 
+}
+
 #endif

src/KSPACE/pair_lj_charmm_coul_long.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -31,6 +31,8 @@
 #include "neighbor.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
@@ -44,7 +46,7 @@
 
 /* ---------------------------------------------------------------------- */
 
-PairLJCharmmCoulLong::PairLJCharmmCoulLong()
+PairLJCharmmCoulLong::PairLJCharmmCoulLong(LAMMPS *lmp) : Pair(lmp)
 {
   respa_enable = 1;
   ftable = NULL;
@@ -763,7 +765,7 @@ void PairLJCharmmCoulLong::init_style()
 {
   // require an atom style with charge defined
 
-  if (atom->charge_allow == 0)
+  if (atom->q == NULL)
     error->all("Must use charged atom style with this pair style");
 
   // require cut_lj_inner < cut_lj
@@ -1158,3 +1160,25 @@ void PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype,
     } else one.eng_vdwl = 0.0;
   }
 }
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJCharmmCoulLong::extract_charmm(double ***p_lj14_1, 
+					  double ***p_lj14_2,
+					  double ***p_lj14_3,
+					  double ***p_lj14_4,
+					  int *p_implicit_flag)
+{
+  *p_lj14_1 = lj14_1;
+  *p_lj14_2 = lj14_2;
+  *p_lj14_3 = lj14_3;
+  *p_lj14_4 = lj14_4;
+  *p_implicit_flag = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJCharmmCoulLong::extract_long(double *p_cut_coul)
+{
+  *p_cut_coul = cut_coul;
+}

src/KSPACE/pair_lj_cut_coul_long.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -31,6 +31,8 @@
 #include "neighbor.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
@@ -44,15 +46,13 @@
 
 /* ---------------------------------------------------------------------- */
 
-PairLJCutCoulLong::PairLJCutCoulLong()
+PairLJCutCoulLong::PairLJCutCoulLong(LAMMPS *lmp) : Pair(lmp)
 {
   respa_enable = 1;
   ftable = NULL;
 }
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays
-------------------------------------------------------------------------- */
 
 PairLJCutCoulLong::~PairLJCutCoulLong()
 {
@@ -739,7 +739,7 @@ void PairLJCutCoulLong::init_style()
 
   // require an atom style with charge defined
 
-  if (atom->charge_allow == 0)
+  if (atom->q == NULL)
     error->all("Must use charged atom style with this pair style");
 
   cut_coulsq = cut_coul * cut_coul;
@@ -1102,3 +1102,10 @@ void PairLJCutCoulLong::single(int i, int j, int itype, int jtype,
     } else one.eng_vdwl = 0.0;
   }
 }
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJCutCoulLong::extract_long(double *p_cut_coul)
+{
+  *p_cut_coul = cut_coul;
+}

src/KSPACE/pair_lj_cut_coul_long.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,11 +16,11 @@
 
 #include "pair.h"
 
+namespace LAMMPS_NS {
+
 class PairLJCutCoulLong : public Pair {
  public:
-  double cut_coul;
+  PairLJCutCoulLong(class LAMMPS *);
-
-  PairLJCutCoulLong();
   ~PairLJCutCoulLong();
   virtual void compute(int, int);
   virtual void settings(int, char **);
@@ -36,11 +36,12 @@ class PairLJCutCoulLong : public Pair {
   void compute_inner();
   void compute_middle();
   void compute_outer(int, int);
+  void extract_long(double *);
 
  protected:
   double cut_lj_global;
   double **cut_lj,**cut_ljsq;
-  double cut_coulsq;
+  double cut_coul,cut_coulsq;
   double **epsilon,**sigma;
   double **lj1,**lj2,**lj3,**lj4,**offset;
   double *cut_respa;
@@ -56,4 +57,6 @@ class PairLJCutCoulLong : public Pair {
   void free_tables();
 };
 
+}
+
 #endif

src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -33,6 +33,8 @@
 #include "neighbor.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
@@ -46,7 +48,8 @@
 
 /* ---------------------------------------------------------------------- */
 
-PairLJCutCoulLongTIP4P::PairLJCutCoulLongTIP4P()
+PairLJCutCoulLongTIP4P::PairLJCutCoulLongTIP4P(LAMMPS *lmp) : 
+  PairLJCutCoulLong(lmp)
 {
   single_enable = 0;
 }
@@ -407,7 +410,7 @@ void PairLJCutCoulLongTIP4P::init_style()
     error->all("Pair style lj/cut/coul/long/tip4p requires atom IDs");
   if (!force->newton_pair) 
     error->all("Pair style lj/cut/coul/long/tip4p requires newton pair on");
-  if (atom->charge_allow == 0)
+  if (atom->q == NULL)
     error->all("Must use charged atom style with this pair style");
 
   cut_coulsq = cut_coul * cut_coul;
@@ -526,3 +529,16 @@ void PairLJCutCoulLongTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
   xM[1] = x[i][1] + alpha * (dely1 + dely2);
   xM[2] = x[i][2] + alpha * (delz1 + delz2);
 }
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJCutCoulLongTIP4P::extract_tip4p(double *p_qdist, 
+					   int *p_typeO, int *p_typeH,
+					   int *p_typeA, int *p_typeB)
+{
+  *p_qdist = qdist;
+  *p_typeO = typeO;
+  *p_typeH = typeH;
+  *p_typeA = typeA;
+  *p_typeB = typeB;
+}

src/KSPACE/pair_lj_cut_coul_long_tip4p.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,17 +16,19 @@
 
 #include "pair_lj_cut_coul_long.h"
 
-class PairLJCutCoulLongTIP4P : public PairLJCutCoulLong {
+namespace LAMMPS_NS {
-  friend class PPPM; 
 
+class PairLJCutCoulLongTIP4P : public PairLJCutCoulLong {
  public:
-  PairLJCutCoulLongTIP4P();
+  PairLJCutCoulLongTIP4P(class LAMMPS *);
   void compute(int, int);
   void settings(int, char **);
   void init_style();
   void write_restart_settings(FILE *fp);
   void read_restart_settings(FILE *fp);
 
+  void extract_tip4p(double *, int *, int *, int *, int *);
+
  private:
   int typeH,typeO;             // atom types of TIP4P water H and O atoms
   int typeA,typeB;             // angle and bond types of TIP4P water
@@ -38,4 +40,6 @@ class PairLJCutCoulLongTIP4P : public PairLJCutCoulLong {
   void find_M(int, int &, int &, double *);
 };
 
+}
+
 #endif

src/KSPACE/pppm.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -25,12 +25,7 @@
 #include "comm.h"
 #include "neighbor.h"
 #include "force.h"
-#include "pair_buck_coul_long.h"
+#include "pair.h"
-#include "pair_lj_cut_coul_long.h"
-#include "pair_lj_charmm_coul_long.h"
-#include "pair_lj_class2_coul_long.h"
-#include "pair_lj_cut_coul_long_tip4p.h"
-#include "pair_table.h"
 #include "bond.h"
 #include "angle.h"
 #include "domain.h"
@@ -39,6 +34,8 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
@@ -50,7 +47,7 @@
 
 /* ---------------------------------------------------------------------- */
 
-PPPM::PPPM(int narg, char **arg) : KSpace(narg, arg)
+PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
 {
   if (narg != 1) error->all("Illegal kspace_style pppm command");
 
@@ -128,41 +125,35 @@ void PPPM::init()
 
   deallocate();
 
-  // insure use of valid pair_style with long-range Coulombics
+  // insure use of long (or table) pair_style with long-range Coulombics
-  // set cutoff to short-range Coulombic cutoff
+  // set cutoff to Pair's short-range Coulombic cutoff
 
   qqrd2e = force->qqrd2e;
+
+  Pair *pair = force->pair_match("long");
+  if (pair == NULL) pair = force->pair_match("table");
+  if (pair == NULL) error->all("KSpace style is incompatible with Pair style");
+  pair->extract_long(&cutoff);
+
+  // insure use of TIP4P pair_style with TIP4P long-range Coulombics
+  // set TIP4P params from Pair's params
+
   qdist = 0.0;
 
-  Pair *anypair;
+  pair = force->pair_match("tip4p");
-  if (force->pair == NULL) 
+  if (strcmp(force->kspace_style,"pppm/tip4p") != 0 && pair != NULL)
-    error->all("Pair style is incompatible with KSpace style");
+    error->all("KSpace style is incompatible with Pair style");
-  else if (anypair = force->pair_match("buck/coul/long"))
+  if (strcmp(force->kspace_style,"pppm/tip4p") == 0 && pair == NULL)
-    cutoff = ((PairBuckCoulLong *) anypair)->cut_coul;
+    error->all("KSpace style is incompatible with Pair style");
-  else if (anypair = force->pair_match("lj/cut/coul/long"))
+  if (pair) {
-    cutoff = ((PairLJCutCoulLong *) anypair)->cut_coul;
+    int typeA,typeB;
-  else if (anypair = force->pair_match("lj/charmm/coul/long"))
+    pair->extract_tip4p(&qdist,&typeO,&typeH,&typeA,&typeB);
-    cutoff = ((PairLJCharmmCoulLong *) anypair)->cut_coul;
-  else if (anypair = force->pair_match("lj/class2/coul/long"))
-    cutoff = ((PairLJClass2CoulLong *) anypair)->cut_coul;
-  else if (anypair = force->pair_match("lj/cut/coul/long/tip4p")) {
-    if (strcmp(force->kspace_style,"pppm/tip4p") != 0)
-      error->all("Pair style is incompatible with KSpace style");
-    cutoff = ((PairLJCutCoulLongTIP4P *) anypair)->cut_coul;
-    qdist = ((PairLJCutCoulLongTIP4P *) anypair)->qdist;
-    typeO = ((PairLJCutCoulLongTIP4P *) anypair)->typeO;
-    typeH = ((PairLJCutCoulLongTIP4P *) anypair)->typeH;
-    int typeA = ((PairLJCutCoulLongTIP4P *) anypair)->typeA;
-    int typeB = ((PairLJCutCoulLongTIP4P *) anypair)->typeB;
     if (force->angle == NULL || force->bond == NULL)
       error->all("Bond and angle potentials must be defined for TIP4P");
     double theta = force->angle->equilibrium_angle(typeA);
     double blen = force->bond->equilibrium_distance(typeB);
     alpha = qdist / (2.0 * cos(0.5*theta) * blen);
   }
-  else if (anypair = force->pair_match("table"))
-    cutoff = ((PairTable *) anypair)->cut_coul();
-  else error->all("Pair style is incompatible with KSpace style");
 
   // compute qsum & qsqsum and warn if not charge-neutral
 
@@ -698,17 +689,17 @@ void PPPM::allocate()
 
   int tmp;
 
-  fft1 = new FFT3d(world,nx_pppm,ny_pppm,nz_pppm,
+  fft1 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
 		   nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
 		   nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
 		   0,0,&tmp);
 
-  fft2 = new FFT3d(world,nx_pppm,ny_pppm,nz_pppm,
+  fft2 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
 		   nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
 		   nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
 		   0,0,&tmp);
 
-  remap = new Remap(world,
+  remap = new Remap(lmp,world,
 		    nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
 		    nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
 		    1,0,0,2);

src/KSPACE/pppm.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,12 +16,11 @@
 
 #include "kspace.h"
 
-class FFT3d;
+namespace LAMMPS_NS {
-class Remap;
 
 class PPPM : public KSpace {
  public:
-  PPPM(int, char **);
+  PPPM(class LAMMPS *, int, char **);
   ~PPPM();
   void init();
   void setup();
@@ -61,8 +60,8 @@ class PPPM : public KSpace {
   double *gf_b;
   double **rho1d,**rho_coeff;
 
-  FFT3d *fft1,*fft2;
+  class FFT3d *fft1,*fft2;
-  Remap *remap;
+  class Remap *remap;
 
   int **part2grid;             // storage for particle -> grid mapping
   int nmax;
@@ -91,4 +90,6 @@ class PPPM : public KSpace {
   void slabcorr(int);
 };
 
+}
+
 #endif

src/KSPACE/pppm_tip4p.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -22,11 +22,14 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define OFFSET 4096
 
 /* ---------------------------------------------------------------------- */
 
-PPPMTIP4P::PPPMTIP4P(int narg, char **arg) : PPPM(narg, arg) {}
+PPPMTIP4P::PPPMTIP4P(LAMMPS *lmp, int narg, char **arg) :
+  PPPM(lmp, narg, arg) {}
 
 /* ----------------------------------------------------------------------
    find center grid pt for each of my particles

src/KSPACE/pppm_tip4p.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,9 +16,11 @@
 
 #include "pppm.h"
 
+namespace LAMMPS_NS {
+
 class PPPMTIP4P : public PPPM {
  public:
-  PPPMTIP4P(int, char **);
+  PPPMTIP4P(class LAMMPS *, int, char **);
 
  private:
   void particle_map();
@@ -28,4 +30,6 @@ class PPPMTIP4P : public PPPM {
   void find_M(int, int &, int &, double *); 
 };
 
+}
+
 #endif

src/KSPACE/remap.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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

src/KSPACE/remap.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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

src/KSPACE/remap_wrap.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -15,14 +15,16 @@
 #include "remap_wrap.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 /* ---------------------------------------------------------------------- */
 
-Remap::Remap(MPI_Comm comm,
+Remap::Remap(LAMMPS *lmp, MPI_Comm comm,
 	     int in_ilo, int in_ihi, int in_jlo, int in_jhi,
 	     int in_klo, int in_khi,
 	     int out_ilo, int out_ihi, int out_jlo, int out_jhi,
 	     int out_klo, int out_khi,
-	     int nqty, int permute, int memory, int precision)
+	     int nqty, int permute, int memory, int precision) : Pointers(lmp)
 {
   plan = remap_3d_create_plan(comm,
 			      in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,

src/KSPACE/remap_wrap.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -14,12 +14,14 @@
 #ifndef REMAP_WRAP_H
 #define REMAP_WRAP_H
 
-#include "lammps.h"
+#include "pointers.h"
 #include "remap.h"
 
-class Remap : public LAMMPS {
+namespace LAMMPS_NS {
+
+class Remap : protected Pointers {
  public:
-  Remap(MPI_Comm,int,int,int,int,int,int,
+  Remap(class LAMMPS *, MPI_Comm,int,int,int,int,int,int,
 	int,int,int,int,int,int,int,int,int,int);
   ~Remap();
   void perform(double *, double *, double *);
@@ -28,4 +30,6 @@ class Remap : public LAMMPS {
   struct remap_plan_3d *plan;
 };
 
+}
+
 #endif

src/KSPACE/style_kspace.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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

src/MAKE/Makefile.linux

@@ -8,6 +8,8 @@ SHELL = /bin/sh
 CC =		icc
 CCFLAGS =	-O -I/home/sjplimp/tools/mpich/include \
 		-I/home/sjplimp/tools/fftw/include -DFFT_FFTW -DGZIP
+#CCFLAGS =	-O -restrict -I/home/sjplimp/tools/mpich/include \
+#		-I/home/sjplimp/tools/fftw/include -DFFT_FFTW -DGZIP
 DEPFLAGS =	-M
 LINK =		icc
 LINKFLAGS =	-O -L/home/sjplimp/tools/mpich/lib \

src/MANYBODY/Install.csh

@@ -1,7 +1,5 @@
 # Install/unInstall package classes in LAMMPS
 
-# pair_eam.h must always be in src
-
 if ($1 == 1) then
 
   cp style_manybody.h ..
@@ -12,7 +10,7 @@ if ($1 == 1) then
   cp pair_sw.cpp ..
   cp pair_tersoff.cpp ..
 
-#  cp pair_eam.h ..
+  cp pair_eam.h ..
   cp pair_eam_alloy.h ..
   cp pair_eam_fs.h ..
   cp pair_sw.h ..
@@ -29,7 +27,7 @@ else if ($1 == 0) then
   rm ../pair_sw.cpp
   rm ../pair_tersoff.cpp
 
-#  rm ../pair_eam.h
+  rm ../pair_eam.h
   rm ../pair_eam_alloy.h
   rm ../pair_eam_fs.h
   rm ../pair_sw.h

src/MANYBODY/pair_eam.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -28,6 +28,8 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))
 
@@ -35,7 +37,7 @@
 
 /* ---------------------------------------------------------------------- */
 
-PairEAM::PairEAM()
+PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp)
 {
   nmax = 0;
   rho = NULL;
@@ -54,10 +56,14 @@ PairEAM::PairEAM()
   frho_spline = NULL;
   rhor_spline = NULL;
   z2r_spline = NULL;
+
+  // set comm size needed by this Pair
+
+  comm_forward = 1;
+  comm_reverse = 1;
 }
 
 /* ----------------------------------------------------------------------
-   free all arrays
    check if allocated, since class can be destructed when incomplete
 ------------------------------------------------------------------------- */
 
@@ -410,11 +416,6 @@ double PairEAM::init_one(int i, int j)
 
 void PairEAM::init_style()
 {
-  // set communication sizes in comm class
-
-  comm->maxforward_pair = MAX(comm->maxforward_pair,1);
-  comm->maxreverse_pair = MAX(comm->maxreverse_pair,1);
-
   // convert read-in file(s) to arrays and spline them
 
   file2array();
@@ -804,17 +805,16 @@ void PairEAM::single(int i, int j, int itype, int jtype,
 
 /* ---------------------------------------------------------------------- */
 
-void PairEAM::single_embed(int i, int itype, double &fpi,
+void PairEAM::single_embed(int i, int itype, double &phi)
-			   int eflag, double &phi)
 {
+  printf("AAA %d\n",i);
   double p = rho[i]*rdrho + 1.0;
   int m = static_cast<int> (p);
   m = MAX(1,MIN(m,nrho-1));
   p -= m;
   
   double *coeff = frho_spline[type2frho[itype]][m];
-  fpi = (coeff[0]*p + coeff[1])*p + coeff[2];
+  phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
-  if (eflag) phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
 }
 
 /* ---------------------------------------------------------------------- */
@@ -876,3 +876,14 @@ int PairEAM::memory_usage()
   int bytes = 2 * nmax * sizeof(double);
   return bytes;
 }
+
+/* ----------------------------------------------------------------------
+   swap fp array with one passed in by caller
+------------------------------------------------------------------------- */
+
+void PairEAM::extract_eam(double *fp_caller, double **fp_caller_hold)
+{
+  double *tmp = fp;
+  fp = fp_caller;
+  *fp_caller_hold = tmp;
+}

src/MANYBODY/pair_eam_alloy.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -24,8 +24,17 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MAXLINE 1024
 
+/* ---------------------------------------------------------------------- */
+
+PairEAMAlloy::PairEAMAlloy(LAMMPS *lmp) : PairEAM(lmp)
+{
+  one_coeff = 1;
+}
+
 /* ----------------------------------------------------------------------
    set coeffs for one or more type pairs
    read DYNAMO setfl file

src/MANYBODY/pair_eam_alloy.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,13 +16,21 @@
 
 #include "pair_eam.h"
 
-class PairEAMAlloy : public PairEAM {
+namespace LAMMPS_NS {
+
+// use virtual public since this class is parent in multiple inheritance
+
+class PairEAMAlloy : virtual public PairEAM {
  public:
+  PairEAMAlloy(class LAMMPS *);
+  virtual ~PairEAMAlloy() {}
   void coeff(int, char **);
 
- private:
+ protected:
   void read_file(char *);
   void file2array();
 };
 
+}
+
 #endif

src/MANYBODY/pair_eam_fs.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -24,8 +24,17 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MAXLINE 1024
 
+/* ---------------------------------------------------------------------- */
+
+PairEAMFS::PairEAMFS(LAMMPS *lmp) : PairEAM(lmp)
+{
+  one_coeff = 1;
+}
+
 /* ----------------------------------------------------------------------
    set coeffs for one or more type pairs
    read EAM Finnis-Sinclair file

src/MANYBODY/pair_eam_fs.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,13 +16,21 @@
 
 #include "pair_eam.h"
 
-class PairEAMFS : public PairEAM {
+namespace LAMMPS_NS {
+
+// use virtual public since this class is parent in multiple inheritance
+
+class PairEAMFS : virtual public PairEAM {
  public:
+  PairEAMFS(class LAMMPS *);
+  virtual ~PairEAMFS() {}
   void coeff(int, char **);
 
- private:
+ protected:
   void read_file(char *);
   void file2array();
 };
 
+}
+
 #endif

src/MANYBODY/pair_sw.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -29,12 +29,14 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MAXLINE 1024
 #define DELTA 4
 
 /* ---------------------------------------------------------------------- */
 
-PairSW::PairSW()
+PairSW::PairSW(LAMMPS *lmp) : Pair(lmp)
 {
   neigh_half_every = 0;
   neigh_full_every = 1;
@@ -50,7 +52,6 @@ PairSW::PairSW()
 }
 
 /* ----------------------------------------------------------------------
-   free all arrays
    check if allocated, since class can be destructed when incomplete
 ------------------------------------------------------------------------- */
 
@@ -211,7 +212,7 @@ void PairSW::settings(int narg, char **arg)
 
 void PairSW::coeff(int narg, char **arg)
 {
-  int i,j,m,n;
+  int i,j,n;
 
   if (!allocated) allocate();
 
@@ -325,7 +326,7 @@ void PairSW::read_file(char *file)
   // one set of params can span multiple lines
   // store params if all 3 element tags are in element list
 
-  int i,n,nwords,ielement,jelement,kelement;
+  int n,nwords,ielement,jelement,kelement;
   char line[MAXLINE],*ptr;
   int eof = 0;
 
@@ -491,7 +492,6 @@ void PairSW::twobody(Param *param, double rsq, double &fforce,
 		     int eflag, double &eng)
 {
   double r,rinvsq,rp,rq,rainv,rainvsq,expsrainv;
-  double delr[3];
 
   r = sqrt(rsq);
   rinvsq = 1.0/rsq;

src/MANYBODY/pair_sw.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,9 +16,11 @@
 
 #include "pair.h"
 
+namespace LAMMPS_NS {
+
 class PairSW : public Pair {
  public:
-  PairSW();
+  PairSW(class LAMMPS *);
   ~PairSW();
   void compute(int, int);
   void settings(int, char **);
@@ -55,4 +57,6 @@ class PairSW : public Pair {
 		 double *, double *, int, double &);
 };
 
+}
+
 #endif

src/MANYBODY/pair_tersoff.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -29,12 +29,14 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define MAXLINE 1024
 #define DELTA 4
 
 /* ---------------------------------------------------------------------- */
 
-PairTersoff::PairTersoff()
+PairTersoff::PairTersoff(LAMMPS *lmp) : Pair(lmp)
 {
   neigh_half_every = 0;
   neigh_full_every = 1;
@@ -53,7 +55,6 @@ PairTersoff::PairTersoff()
 }
 
 /* ----------------------------------------------------------------------
-   free all arrays
    check if allocated, since class can be destructed when incomplete
 ------------------------------------------------------------------------- */
 
@@ -248,7 +249,7 @@ void PairTersoff::settings(int narg, char **arg)
 
 void PairTersoff::coeff(int narg, char **arg)
 {
-  int i,j,m,n;
+  int i,j,n;
 
   if (!allocated) allocate();
 
@@ -361,7 +362,7 @@ void PairTersoff::read_file(char *file)
   // read each line out of file, skipping blank lines or leading '#'
   // store line of params if all 3 element tags are in element list
 
-  int i,n,nwords,ielement,jelement,kelement;
+  int n,nwords,ielement,jelement,kelement;
   char line[MAXLINE],*ptr;
   int eof = 0;
 

src/MANYBODY/pair_tersoff.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,9 +16,11 @@
 
 #include "pair.h"
 
+namespace LAMMPS_NS {
+
 class PairTersoff : public Pair {
  public:
-  PairTersoff();
+  PairTersoff(class LAMMPS *);
   ~PairTersoff();
   void compute(int, int);
   void settings(int, char **);
@@ -85,4 +87,6 @@ class PairTersoff : public Pair {
   }
 };
 
+}
+
 #endif

src/MANYBODY/style_manybody.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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

src/MOLECULE/Install.csh

@@ -13,10 +13,9 @@ if ($1 == 1) then
   cp angle_cosine_squared.cpp ..
   cp angle_harmonic.cpp ..
   cp angle_hybrid.cpp ..
-  cp atom_angle.cpp ..
+  cp atom_vec_angle.cpp ..
-  cp atom_bond.cpp ..
+  cp atom_vec_bond.cpp ..
-  cp atom_full.cpp ..
+  cp atom_vec_molecular.cpp ..
-  cp atom_molecular.cpp ..
   cp bond.cpp ..
   cp bond_fene.cpp ..
   cp bond_fene_expand.cpp ..
@@ -46,10 +45,9 @@ if ($1 == 1) then
   cp angle_cosine_squared.h ..
   cp angle_harmonic.h ..
   cp angle_hybrid.h ..
-  cp atom_angle.h ..
+  cp atom_vec_angle.h ..
-  cp atom_bond.h ..
+  cp atom_vec_bond.h ..
-  cp atom_full.h ..
+  cp atom_vec_molecular.h ..
-  cp atom_molecular.h ..
 #  cp bond.h ..
   cp bond_fene.h ..
   cp bond_fene_expand.h ..
@@ -84,10 +82,9 @@ else if ($1 == 0) then
   rm ../angle_cosine_squared.cpp
   rm ../angle_harmonic.cpp
   rm ../angle_hybrid.cpp
-  rm ../atom_angle.cpp
+  rm ../atom_vec_angle.cpp
-  rm ../atom_bond.cpp
+  rm ../atom_vec_bond.cpp
-  rm ../atom_full.cpp
+  rm ../atom_vec_molecular.cpp
-  rm ../atom_molecular.cpp
   rm ../bond.cpp
   rm ../bond_fene.cpp
   rm ../bond_fene_expand.cpp
@@ -117,10 +114,9 @@ else if ($1 == 0) then
   rm ../angle_cosine_squared.h
   rm ../angle_harmonic.h
   rm ../angle_hybrid.h
-  rm ../atom_angle.h
+  rm ../atom_vec_angle.h
-  rm ../atom_bond.h
+  rm ../atom_vec_bond.h
-  rm ../atom_full.h
+  rm ../atom_vec_molecular.h
-  rm ../atom_molecular.h
 #  rm ../bond.h
   rm ../bond_fene.h
   rm ../bond_fene_expand.h

src/MOLECULE/angle.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,9 +16,11 @@
 #include "atom.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 /* ---------------------------------------------------------------------- */
 
-Angle::Angle()
+Angle::Angle(LAMMPS *lmp) : Pointers(lmp)
 {
   allocated = 0;
   PI = 4.0*atan(1.0);

src/MOLECULE/angle_charmm.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -26,11 +26,15 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define SMALL 0.001
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays 
+
-------------------------------------------------------------------------- */
+AngleCharmm::AngleCharmm(LAMMPS *lmp) : Angle(lmp) {}
+
+/* ---------------------------------------------------------------------- */
 
 AngleCharmm::~AngleCharmm()
 {

src/MOLECULE/angle_charmm.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "angle.h"
 
+namespace LAMMPS_NS {
+
 class AngleCharmm : public Angle {
  public:
-  AngleCharmm() {}
+  AngleCharmm(class LAMMPS *);
   ~AngleCharmm();
   void compute(int, int);
   void coeff(int, int, char **);
@@ -34,4 +36,6 @@ class AngleCharmm : public Angle {
   void allocate();
 };
 
+}
+
 #endif

src/MOLECULE/angle_cosine.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -22,11 +22,15 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define SMALL 0.001
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays 
+
-------------------------------------------------------------------------- */
+AngleCosine::AngleCosine(LAMMPS *lmp) : Angle(lmp) {}
+
+/* ---------------------------------------------------------------------- */
 
 AngleCosine::~AngleCosine()
 {

src/MOLECULE/angle_cosine.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "angle.h"
 
+namespace LAMMPS_NS {
+
 class AngleCosine : public Angle {
  public:
-  AngleCosine() {}
+  AngleCosine(class LAMMPS *);
   ~AngleCosine();
   void compute(int, int);
   void coeff(int, int, char **);
@@ -34,4 +36,6 @@ class AngleCosine : public Angle {
   void allocate();
 };
 
+}
+
 #endif

src/MOLECULE/angle_cosine_squared.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -26,11 +26,15 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define SMALL 0.001
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays 
+
-------------------------------------------------------------------------- */
+AngleCosineSquared::AngleCosineSquared(LAMMPS *lmp) : Angle(lmp) {}
+
+/* ---------------------------------------------------------------------- */
 
 AngleCosineSquared::~AngleCosineSquared()
 {

src/MOLECULE/angle_cosine_squared.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "angle.h"
 
+namespace LAMMPS_NS {
+
 class AngleCosineSquared : public Angle {
  public:
-  AngleCosineSquared() {}
+  AngleCosineSquared(class LAMMPS *);
   ~AngleCosineSquared();
   void compute(int, int);
   void coeff(int, int, char **);
@@ -34,4 +36,6 @@ class AngleCosineSquared : public Angle {
   void allocate();
 };
 
+}
+
 #endif

src/MOLECULE/angle_harmonic.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -22,11 +22,15 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define SMALL 0.001
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays 
+
-------------------------------------------------------------------------- */
+AngleHarmonic::AngleHarmonic(LAMMPS *lmp) : Angle(lmp) {}
+
+/* ---------------------------------------------------------------------- */
 
 AngleHarmonic::~AngleHarmonic()
 {

src/MOLECULE/angle_harmonic.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "angle.h"
 
+namespace LAMMPS_NS {
+
 class AngleHarmonic : public Angle {
  public:
-  AngleHarmonic() {}
+  AngleHarmonic(class LAMMPS *);
   ~AngleHarmonic();
   void compute(int, int);
   void coeff(int, int, char **);
@@ -34,4 +36,6 @@ class AngleHarmonic : public Angle {
   void allocate();
 };
 
+}
+
 #endif

src/MOLECULE/angle_hybrid.cpp

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -22,20 +22,18 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define EXTRA 1000
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   set all global defaults 
-------------------------------------------------------------------------- */
 
-AngleHybrid::AngleHybrid()
+AngleHybrid::AngleHybrid(LAMMPS *lmp) : Angle(lmp)
 {
   nstyles = 0;
 }
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays
-------------------------------------------------------------------------- */
 
 AngleHybrid::~AngleHybrid()
 {

src/MOLECULE/angle_hybrid.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "angle.h"
 
+namespace LAMMPS_NS {
+
 class AngleHybrid : public Angle {
  public:
-  AngleHybrid();
+  AngleHybrid(class LAMMPS *);
   ~AngleHybrid();
   void compute(int, int);
   void settings(int, char **);
@@ -43,4 +45,6 @@ class AngleHybrid : public Angle {
   void allocate();
 };
 
+}
+
 #endif

src/MOLECULE/bond.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -16,12 +16,14 @@
 #include "atom.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 /* -----------------------------------------------------------------------
    set bond contribution to Vdwl energy to 0.0
    a particular bond style can override this
 ------------------------------------------------------------------------- */
 
-Bond::Bond()
+Bond::Bond(LAMMPS *lmp) : Pointers(lmp)
 {
   allocated = 0;
   eng_vdwl = 0.0;

src/MOLECULE/bond_fene.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -23,16 +23,16 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 /* ---------------------------------------------------------------------- */
 
-BondFENE::BondFENE()
+BondFENE::BondFENE(LAMMPS *lmp) : Bond(lmp)
 {
   TWO_1_3 = pow(2.0,(1.0/3.0));
 }
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays 
-------------------------------------------------------------------------- */
 
 BondFENE::~BondFENE()
 {

src/MOLECULE/bond_fene.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "bond.h"
 
+namespace LAMMPS_NS {
+
 class BondFENE : public Bond {
  public:
-  BondFENE();
+  BondFENE(class LAMMPS *);
   ~BondFENE();
   void compute(int, int);
   void coeff(int, char **);
@@ -35,4 +37,6 @@ class BondFENE : public Bond {
   void allocate();
 };
 
+}
+
 #endif

src/MOLECULE/bond_fene_expand.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -11,8 +11,6 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-// FENE bond potential, with repulsive LJ, with shift
-
 #include "math.h"
 #include "stdlib.h"
 #include "bond_fene_expand.h"
@@ -25,18 +23,16 @@
 #include "memory.h"
 #include "error.h"
 
-/* ----------------------------------------------------------------------
+using namespace LAMMPS_NS;
-   set all global defaults 
-------------------------------------------------------------------------- */
 
-BondFENEExpand::BondFENEExpand()
+/* ---------------------------------------------------------------------- */
+
+BondFENEExpand::BondFENEExpand(LAMMPS *lmp) : Bond(lmp)
 {
   TWO_1_3 = pow(2.0,(1.0/3.0));
 }
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays 
-------------------------------------------------------------------------- */
 
 BondFENEExpand::~BondFENEExpand()
 {

src/MOLECULE/bond_fene_expand.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "bond.h"
 
+namespace LAMMPS_NS {
+
 class BondFENEExpand : public Bond {
  public:
-  BondFENEExpand();
+  BondFENEExpand(class LAMMPS *);
   ~BondFENEExpand();
   void compute(int, int);
   void coeff(int, char **);
@@ -35,4 +37,6 @@ class BondFENEExpand : public Bond {
   void allocate();
 };
 
+}
+
 #endif

src/MOLECULE/bond_harmonic.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -22,9 +22,13 @@
 #include "memory.h"
 #include "error.h"
 
-/* ----------------------------------------------------------------------
+using namespace LAMMPS_NS;
-   free all arrays 
+
-------------------------------------------------------------------------- */
+/* ---------------------------------------------------------------------- */
+
+BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp) {}
+
+/* ---------------------------------------------------------------------- */
 
 BondHarmonic::~BondHarmonic()
 {

src/MOLECULE/bond_harmonic.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "bond.h"
 
+namespace LAMMPS_NS {
+
 class BondHarmonic : public Bond {
  public:
-  BondHarmonic() {}
+  BondHarmonic(class LAMMPS *);
   ~BondHarmonic();
   void compute(int, int);
   void coeff(int, char **);
@@ -34,4 +36,6 @@ class BondHarmonic : public Bond {
   void allocate();
 };
 
+}
+
 #endif

src/MOLECULE/bond_hybrid.cpp

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -22,20 +22,18 @@
 #include "memory.h"
 #include "error.h"
 
+using namespace LAMMPS_NS;
+
 #define EXTRA 1000
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   set all global defaults 
-------------------------------------------------------------------------- */
 
-BondHybrid::BondHybrid()
+BondHybrid::BondHybrid(LAMMPS *lmp) : Bond(lmp)
 {
   nstyles = 0;
 }
 
-/* ----------------------------------------------------------------------
+/* ---------------------------------------------------------------------- */
-   free all arrays
-------------------------------------------------------------------------- */
 
 BondHybrid::~BondHybrid()
 {

src/MOLECULE/bond_morse.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -26,9 +26,13 @@
 #include "memory.h"
 #include "error.h"
 
-/* ----------------------------------------------------------------------
+using namespace LAMMPS_NS;
-   free all arrays 
+
-------------------------------------------------------------------------- */
+/* ---------------------------------------------------------------------- */
+
+BondMorse::BondMorse(LAMMPS *lmp) : Bond(lmp) {}
+
+/* ---------------------------------------------------------------------- */
 
 BondMorse::~BondMorse()
 {

src/MOLECULE/bond_morse.h

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -17,9 +17,11 @@
 #include "stdio.h"
 #include "bond.h"
 
+namespace LAMMPS_NS {
+
 class BondMorse : public Bond {
  public:
-  BondMorse() {}
+  BondMorse(class LAMMPS *);
   ~BondMorse();
   void compute(int, int);
   void coeff(int, char **);
@@ -34,4 +36,6 @@ class BondMorse : public Bond {
   void allocate();
 };
 
+}
+
 #endif

src/MOLECULE/bond_nonlinear.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@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
@@ -22,9 +22,13 @@
 #include "memory.h"
 #include "error.h"
 
-/* ----------------------------------------------------------------------
+using namespace LAMMPS_NS;
-   free all arrays 
+
-------------------------------------------------------------------------- */
+/* ---------------------------------------------------------------------- */
+
+BondNonlinear::BondNonlinear(LAMMPS *lmp) : Bond(lmp) {}
+
+/* ---------------------------------------------------------------------- */
 
 BondNonlinear::~BondNonlinear()
 {