git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13378 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/KOKKOS/angle_charmm_kokkos.h

@@ -57,7 +57,7 @@ class AngleCharmmKokkos : public AngleCharmm {
                      const F_FLOAT &delx2, const F_FLOAT &dely2, const F_FLOAT &delz2) const;
 
  protected:
-  class AtomKokkos *atomKK;
+  
   class NeighborKokkos *neighborKK;
  
   typename ArrayTypes<DeviceType>::t_x_array_randomread x;

src/KOKKOS/angle_harmonic_kokkos.h

@@ -58,7 +58,7 @@ class AngleHarmonicKokkos : public AngleHarmonic {
                      const F_FLOAT &delx2, const F_FLOAT &dely2, const F_FLOAT &delz2) const;
 
  protected:
-  class AtomKokkos *atomKK;
+  
   class NeighborKokkos *neighborKK;
  
   typename ArrayTypes<DeviceType>::t_x_array_randomread x;

src/KOKKOS/atom_vec_kokkos.h

@@ -63,7 +63,7 @@ class AtomVecKokkos : public AtomVec {
   //{return 0;};
 
  protected:
-  class AtomKokkos *atomKK;
+  
   class CommKokkos *commKK;
 };
 

src/KOKKOS/bond_fene_kokkos.h

@@ -57,7 +57,7 @@ class BondFENEKokkos : public BondFENE {
                   const F_FLOAT &dely, const F_FLOAT &delz) const;
 
  protected:
-  class AtomKokkos *atomKK;
+  
   class NeighborKokkos *neighborKK;
  
   typename ArrayTypes<DeviceType>::t_x_array_randomread x;

src/KOKKOS/bond_harmonic_kokkos.h

@@ -57,7 +57,7 @@ class BondHarmonicKokkos : public BondHarmonic {
                   const F_FLOAT &dely, const F_FLOAT &delz) const;
 
  protected:
-  class AtomKokkos *atomKK;
+  
   class NeighborKokkos *neighborKK;
  
   typename ArrayTypes<DeviceType>::t_x_array_randomread x;

src/KOKKOS/comm_kokkos.h

@@ -21,7 +21,7 @@ namespace LAMMPS_NS {
 
 class CommKokkos : public CommBrick {
  public:
-  class AtomKokkos *atomKK;
+  
 
   bool exchange_comm_classic;
   bool forward_comm_classic;

src/KOKKOS/dihedral_charmm_kokkos.h

@@ -122,7 +122,7 @@ class DihedralCharmmKokkos : public DihedralCharmm {
                 const F_FLOAT &dely, const F_FLOAT &delz) const;
 
  protected:
-  class AtomKokkos *atomKK;
+  
   class NeighborKokkos *neighborKK;
  
   typename AT::t_x_array_randomread x;

src/KOKKOS/dihedral_opls_kokkos.h

@@ -59,7 +59,7 @@ class DihedralOPLSKokkos : public DihedralOPLS {
                           const F_FLOAT &vb3x, const F_FLOAT &vb3y, const F_FLOAT &vb3z) const;
 
  protected:
-  class AtomKokkos *atomKK;
+  
   class NeighborKokkos *neighborKK;
  
   typename AT::t_x_array_randomread x;

src/KOKKOS/domain_kokkos.h

@@ -21,7 +21,7 @@ namespace LAMMPS_NS {
 
 class DomainKokkos : public Domain {
  public:
-  class AtomKokkos *atomKK;
+  
 
   DomainKokkos(class LAMMPS *);
   ~DomainKokkos() {}

src/KOKKOS/fix_langevin_kokkos.h

@@ -92,7 +92,7 @@ namespace LAMMPS_NS {
 
   private:
     class CommKokkos *commKK;
-    class AtomKokkos *atomKK;
+    
     double *rmass;
     typename ArrayTypes<DeviceType>::tdual_double_2d k_franprev;
     typename ArrayTypes<DeviceType>::t_double_2d d_franprev;

src/KOKKOS/fix_nve_kokkos.h

@@ -55,7 +55,7 @@ class FixNVEKokkos : public FixNVE {
   void final_integrate_rmass_item(int) const;
 
  private:
-  class AtomKokkos *atomKK;
+  
 
   typename ArrayTypes<DeviceType>::t_x_array x;
   typename ArrayTypes<DeviceType>::t_v_array v;

src/KOKKOS/improper_harmonic_kokkos.h

@@ -59,7 +59,7 @@ class ImproperHarmonicKokkos : public ImproperHarmonic {
                           const F_FLOAT &vb3x, const F_FLOAT &vb3y, const F_FLOAT &vb3z) const;
 
  protected:
-  class AtomKokkos *atomKK;
+  
   class NeighborKokkos *neighborKK;
  
   typename AT::t_x_array_randomread x;

src/KOKKOS/modify_kokkos.h

@@ -61,7 +61,7 @@ class ModifyKokkos : public Modify {
   int min_reset_ref();
 
  protected:
-  class AtomKokkos *atomKK;
+  
 };
 
 }

src/KOKKOS/neigh_bond_kokkos.h

@@ -80,7 +80,7 @@ class NeighBondKokkos : protected Pointers  {
   int me;
 
  private:
-  class AtomKokkos *atomKK;
+  
 
   DAT::tdual_int_1d k_map_array;
   typename AT::t_int_1d_randomread map_array;

src/KOKKOS/neigh_list_kokkos.h

@@ -30,7 +30,7 @@ class AtomNeighbors
   KOKKOS_INLINE_FUNCTION
   AtomNeighbors(int* const & firstneigh, const int & _num_neighs, 
                 const int & stride):
-  num_neighs(_num_neighs), _firstneigh(firstneigh), _stride(stride) {};
+  _firstneigh(firstneigh), _stride(stride), num_neighs(_num_neighs) {};
   KOKKOS_INLINE_FUNCTION
   int& operator()(const int &i) const {
     return _firstneigh[i*_stride];
@@ -45,12 +45,12 @@ class AtomNeighborsConst
 {
  public:
   const int* const _firstneigh;
-  const int num_neighs;
+  const int numneigh;
 
   KOKKOS_INLINE_FUNCTION
-  AtomNeighborsConst(int* const & firstneigh, const int & _num_neighs, 
+  AtomNeighborsConst(int* const & firstneigh, const int & _numneigh, 
                      const int & stride):
-  _firstneigh(firstneigh), num_neighs(_num_neighs), _stride(stride) {};
+  _firstneigh(firstneigh), _stride(stride), numneigh(_numneigh) {};
   KOKKOS_INLINE_FUNCTION
   const int& operator()(const int &i) const {
     return _firstneigh[i*_stride];

src/KOKKOS/neighbor_kokkos.h

@@ -285,7 +285,7 @@ class NeighborKokkos : public Neighbor {
  public:
   typedef int value_type;
 
-  class AtomKokkos *atomKK;
+  
 
   int nlist_host;                       // pairwise neighbor lists on Host
   NeighListKokkos<LMPHostType> **lists_host;

src/KOKKOS/pair_buck_coul_cut_kokkos.h

@@ -101,7 +101,7 @@ class PairBuckCoulCutKokkos : public PairBuckCoulCut {
   typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
   typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
 
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_buck_coul_long_kokkos.h

@@ -105,7 +105,7 @@ class PairBuckCoulLongKokkos : public PairBuckCoulLong {
   typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
     d_rtable, d_drtable, d_ftable, d_dftable,
     d_ctable, d_dctable, d_etable, d_detable;
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_buck_kokkos.h

@@ -87,7 +87,7 @@ class PairBuckKokkos : public PairBuck {
   typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
   typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
 
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_coul_cut_kokkos.h

@@ -44,7 +44,9 @@ class PairCoulCutKokkos : public PairCoulCut {
   double init_one(int, int);
 
   struct params_coul{
+    KOKKOS_INLINE_FUNCTION
     params_coul(){cutsq=0,scale=0;};
+    KOKKOS_INLINE_FUNCTION
     params_coul(int i){cutsq=0,scale=0;};
     F_FLOAT cutsq, scale;
   };
@@ -102,7 +104,7 @@ class PairCoulCutKokkos : public PairCoulCut {
   typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
   typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
 
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_coul_debye_kokkos.h

@@ -102,7 +102,7 @@ class PairCoulDebyeKokkos : public PairCoulDebye {
   typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
   typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
 
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_coul_dsf_kokkos.h

@@ -73,7 +73,7 @@ class PairCoulDSFKokkos : public PairCoulDSF {
   DAT::t_efloat_1d d_eatom;
   DAT::t_virial_array d_vatom;
 
-  class AtomKokkos *atomKK;
+  
   int neighflag,newton_pair;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_coul_long_kokkos.h

@@ -109,7 +109,7 @@ class PairCoulLongKokkos : public PairCoulLong {
   typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
     d_rtable, d_drtable, d_ftable, d_dftable,
     d_ctable, d_dctable, d_etable, d_detable;
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_coul_wolf_kokkos.h

@@ -73,7 +73,7 @@ class PairCoulWolfKokkos : public PairCoulWolf {
   DAT::t_efloat_1d d_eatom;
   DAT::t_virial_array d_vatom;
 
-  class AtomKokkos *atomKK;
+  
   int neighflag,newton_pair;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_eam_kokkos.h

@@ -158,7 +158,7 @@ class PairEAMKokkos : public PairEAM {
   typename AT::t_int_2d d_sendlist;
   typename AT::t_xfloat_1d_um v_buf;
 
-  class AtomKokkos *atomKK;
+  
   int neighflag,newton_pair;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h

@@ -105,7 +105,7 @@ class PairLJCharmmCoulCharmmImplicitKokkos : public PairLJCharmmCoulCharmmImplic
   typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
     d_rtable, d_drtable, d_ftable, d_dftable,
     d_ctable, d_dctable, d_etable, d_detable;
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h

@@ -105,7 +105,7 @@ class PairLJCharmmCoulCharmmKokkos : public PairLJCharmmCoulCharmm {
   typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
     d_rtable, d_drtable, d_ftable, d_dftable,
     d_ctable, d_dctable, d_etable, d_detable;
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h

@@ -105,7 +105,7 @@ class PairLJCharmmCoulLongKokkos : public PairLJCharmmCoulLong {
   typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
     d_rtable, d_drtable, d_ftable, d_dftable,
     d_ctable, d_dctable, d_etable, d_detable;
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h

@@ -98,7 +98,6 @@ class PairLJClass2CoulCutKokkos : public PairLJClass2CoulCut {
   typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
   typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
 
-  class AtomKokkos *atomKK;
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_class2_coul_long_kokkos.h

@@ -102,7 +102,7 @@ class PairLJClass2CoulLongKokkos : public PairLJClass2CoulLong {
   typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
     d_rtable, d_drtable, d_ftable, d_dftable,
     d_ctable, d_dctable, d_etable, d_detable;
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_class2_kokkos.h

@@ -91,7 +91,6 @@ class PairLJClass2Kokkos : public PairLJClass2 {
   typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
   typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
 
-  class AtomKokkos *atomKK;
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h

@@ -44,7 +44,9 @@ class PairLJCutCoulCutKokkos : public PairLJCutCoulCut {
   double init_one(int, int);
 
   struct params_lj_coul{
+    KOKKOS_INLINE_FUNCTION
     params_lj_coul(){cut_ljsq=0;cut_coulsq=0;lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
+    KOKKOS_INLINE_FUNCTION
     params_lj_coul(int i){cut_ljsq=0;cut_coulsq=0;lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
     F_FLOAT cut_ljsq,cut_coulsq,lj1,lj2,lj3,lj4,offset;
   };
@@ -98,7 +100,7 @@ class PairLJCutCoulCutKokkos : public PairLJCutCoulCut {
   typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
   typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
 
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h

@@ -98,7 +98,7 @@ class PairLJCutCoulDebyeKokkos : public PairLJCutCoulDebye {
   typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
   typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
 
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h

@@ -97,7 +97,7 @@ class PairLJCutCoulDSFKokkos : public PairLJCutCoulDSF {
   typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
   typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
 
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_cut_coul_long_kokkos.h

@@ -102,7 +102,7 @@ class PairLJCutCoulLongKokkos : public PairLJCutCoulLong {
   typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
     d_rtable, d_drtable, d_ftable, d_dftable,
     d_ctable, d_dctable, d_etable, d_detable;
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_cut_kokkos.h

@@ -44,7 +44,9 @@ class PairLJCutKokkos : public PairLJCut {
   double init_one(int, int);
 
   struct params_lj{
+    KOKKOS_INLINE_FUNCTION
     params_lj(){cutsq=0,lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
+    KOKKOS_INLINE_FUNCTION
     params_lj(int i){cutsq=0,lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
     F_FLOAT cutsq,lj1,lj2,lj3,lj4,offset;
   };
@@ -85,7 +87,7 @@ class PairLJCutKokkos : public PairLJCut {
   typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
   typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
 
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_expand_kokkos.h

@@ -91,7 +91,7 @@ class PairLJExpandKokkos : public PairLJExpand {
   typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
   typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
 
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h

@@ -105,7 +105,7 @@ class PairLJGromacsCoulGromacsKokkos : public PairLJGromacsCoulGromacs {
   typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
     d_rtable, d_drtable, d_ftable, d_dftable,
     d_ctable, d_dctable, d_etable, d_detable;
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_lj_gromacs_kokkos.h

@@ -108,7 +108,7 @@ class PairLJGromacsKokkos : public PairLJGromacs {
   typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
     d_rtable, d_drtable, d_ftable, d_dftable,
     d_ctable, d_dctable, d_etable, d_detable;
-  class AtomKokkos *atomKK;
+  
   int neighflag;
   int nlocal,nall,eflag,vflag;
 

src/KOKKOS/pair_table_kokkos.h

@@ -147,7 +147,7 @@ class PairTableKokkos : public Pair {
 
  protected:
   int nlocal,nall,eflag,vflag,neighflag,newton_pair;
-  class AtomKokkos *atomKK;
+  
   int update_table;
   void create_kokkos_tables();
   void cleanup_copy();

src/KOKKOS/verlet_kokkos.h

@@ -33,7 +33,7 @@ class VerletKokkos : public Verlet {
   void run(int);
 
  protected:
-  class AtomKokkos *atomKK;
+  
 
   void force_clear();
 };

src/USER-CG-CMM/pair_lj_sdk.h

@@ -35,9 +35,9 @@ class PairLJSDK : public Pair {
   PairLJSDK(LAMMPS *);
   virtual ~PairLJSDK();
   virtual void compute(int, int);
-  void settings(int, char **);
+  virtual void settings(int, char **);
-  void coeff(int, char **);
+  virtual void coeff(int, char **);
-  double init_one(int, int);
+  virtual double init_one(int, int);
   void write_restart(FILE *);
   void read_restart(FILE *);
   void write_restart_settings(FILE *);
@@ -63,7 +63,7 @@ class PairLJSDK : public Pair {
 
   double cut_global;
 
-  void allocate();
+  virtual void allocate();
 
  private:
   template <int EVFLAG, int EFLAG, int NEWTON_PAIR> void eval();