delete a couple more files, that don't belong into src/

/* ----------------------------------------------------------------------

   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

   http://lammps.sandia.gov, Sandia National Laboratories

   Steve Plimpton, sjplimp@sandia.gov

   Copyright (2003) Sandia Corporation.  Under the terms of Contract

   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

   certain rights in this software.  This software is distributed under

   the GNU General Public License.

   See the README file in the top-level LAMMPS directory.

------------------------------------------------------------------------- */

/* ----------------------------------------------------------------------

   Contributing authors: 

   James Larentzos and Timothy I. Mattox (Engility Corporation)

------------------------------------------------------------------------- */

#include "npair_halffull_newton_ssa.h"

#include "neighbor.h"

#include "neigh_list.h"

#include "atom.h"

#include "atom_vec.h"

#include "molecule.h"

#include "domain.h"

#include "my_page.h"

#include "error.h"

using namespace LAMMPS_NS;

// allocate space for static class variable

// prototype for non-class function

static int *ssaAIRptr;

static int cmp_ssaAIR(const void *, const void *);

/* ---------------------------------------------------------------------- */

NPairHalffullNewtonSSA::NPairHalffullNewtonSSA(LAMMPS *lmp) : NPair(lmp) {}

/* ----------------------------------------------------------------------

   build half list from full list for use by Shardlow Spliting Algorithm

   pair stored once if i,j are both owned and i < j

   if j is ghost, only store if j coords are "above and to the right" of i

   works if full list is a skip list

------------------------------------------------------------------------- */

void NPairHalffullNewtonSSA::build(NeighList *list)

{

  int i,j,ii,jj,n,jnum,joriginal;

  int *neighptr,*jlist;

  int nlocal = atom->nlocal;

  int *ssaAIR = atom->ssaAIR;

  int *ilist = list->ilist;

  int *numneigh = list->numneigh;

  int **firstneigh = list->firstneigh;

  MyPage<int> *ipage = list->ipage;

  int *ilist_full = list->listfull->ilist;

  int *numneigh_full = list->listfull->numneigh;

  int **firstneigh_full = list->listfull->firstneigh;

  int inum_full = list->listfull->inum;

  int inum = 0;

  ipage->reset();

  // loop over parent full list

  for (ii = 0; ii < inum_full; ii++) {

    int AIRct[8] = { 0 };

    n = 0;

    neighptr = ipage->vget();

    i = ilist_full[ii];

    // loop over full neighbor list

    jlist = firstneigh_full[i];

    jnum = numneigh_full[i];

    for (jj = 0; jj < jnum; jj++) {

      joriginal = jlist[jj];

      j = joriginal & NEIGHMASK;

      if (j < nlocal) {

        if (i > j) continue;

        ++(AIRct[0]);

      } else {

        if (ssaAIR[j] < 2) continue; // skip ghost atoms not in AIR

        ++(AIRct[ssaAIR[j] - 1]);

      }

      neighptr[n++] = joriginal;

    }

    ilist[inum++] = i;

    firstneigh[i] = neighptr;

    numneigh[i] = n;

    ipage->vgot(n);

    if (ipage->status())

      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");

    // sort the locals+ghosts in the neighbor list by their ssaAIR number

    ssaAIRptr = atom->ssaAIR;

    qsort(&(neighptr[0]), n, sizeof(int), cmp_ssaAIR);

    // do a prefix sum on the counts to turn them into indexes

    list->ndxAIR_ssa[i][0] = AIRct[0];

    for (int ndx = 1; ndx < 8; ++ndx) {

      list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];

    }

  }

  list->inum = inum;

}

/* ----------------------------------------------------------------------

   comparison function invoked by qsort()

   accesses static class member ssaAIRptr, set before call to qsort()

------------------------------------------------------------------------- */

static int cmp_ssaAIR(const void *iptr, const void *jptr)

{

  int i = *((int *) iptr);

  int j = *((int *) jptr);

  if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;

  if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;

  return 0;

}

/* -*- c++ -*- ----------------------------------------------------------

   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

   http://lammps.sandia.gov, Sandia National Laboratories

   Steve Plimpton, sjplimp@sandia.gov

   Copyright (2003) Sandia Corporation.  Under the terms of Contract

   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

   certain rights in this software.  This software is distributed under

   the GNU General Public License.

   See the README file in the top-level LAMMPS directory.

------------------------------------------------------------------------- */

#ifdef NPAIR_CLASS

NPairStyle(halffull/newton/ssa,

           NPairHalffullNewtonSSA,

           NP_HALFFULL | NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON | 

           NP_ORTHO | NP_TRI | NP_SSA)

#else

#ifndef LMP_NPAIR_HALFFULL_NEWTON_SSA_H

#define LMP_NPAIR_HALFFULL_NEWTON_SSA_H

#include "npair.h"

namespace LAMMPS_NS {

class NPairHalffullNewtonSSA : public NPair {

 public:

  NPairHalffullNewtonSSA(class LAMMPS *);

  ~NPairHalffullNewtonSSA() {}

  void build(class NeighList *);

};

}

#endif

#endif

/* ERROR/WARNING messages:

*/