Adding pair_exp6_rx_kokkos files

src/KOKKOS/Install.sh

@@ -134,6 +134,8 @@ action pair_eam_alloy_kokkos.cpp pair_eam_alloy.cpp
 action pair_eam_alloy_kokkos.h pair_eam_alloy.h
 action pair_eam_fs_kokkos.cpp pair_eam_fs.cpp
 action pair_eam_fs_kokkos.h pair_eam_fs.h
+action pair_exp6_rx_kokkos.cpp pair_exp6_rx.cpp
+action pair_exp6_rx_kokkos.h pair_exp6_rx.h
 action pair_kokkos.h
 action pair_lj_charmm_coul_charmm_implicit_kokkos.cpp pair_lj_charmm_coul_charmm_implicit.cpp
 action pair_lj_charmm_coul_charmm_implicit_kokkos.h pair_lj_charmm_coul_charmm_implicit.h

src/KOKKOS/atom_kokkos.cpp

@@ -227,6 +227,63 @@ void AtomKokkos::grow(unsigned int mask){
   }
 }
 
+/* ----------------------------------------------------------------------
+   add a custom variable with name of type flag = 0/1 for int/double
+   assumes name does not already exist
+   return index in ivector or dvector of its location
+------------------------------------------------------------------------- */
+
+int AtomKokkos::add_custom(const char *name, int flag)
+{
+  int index;
+
+  if (flag == 0) {
+    index = nivector;
+    nivector++;
+    iname = (char **) memory->srealloc(iname,nivector*sizeof(char *),
+                                       "atom:iname");
+    int n = strlen(name) + 1;
+    iname[index] = new char[n];
+    strcpy(iname[index],name);
+    ivector = (int **) memory->srealloc(ivector,nivector*sizeof(int *),
+                                        "atom:ivector");
+    memory->create(ivector[index],nmax,"atom:ivector");
+  } else {
+    index = ndvector;
+    ndvector++;
+    dname = (char **) memory->srealloc(dname,ndvector*sizeof(char *),
+                                       "atom:dname");
+    int n = strlen(name) + 1;
+    dname[index] = new char[n];
+    strcpy(dname[index],name);
+    memory->grow_kokkos(k_dvector,dvector,ndvector,nmax,
+                        "atom:dvector");
+  }
+
+  return index;
+}
+
+/* ----------------------------------------------------------------------
+   remove a custom variable of type flag = 0/1 for int/double at index
+   free memory for vector and name and set ptrs to NULL
+   ivector/dvector and iname/dname lists never shrink
+------------------------------------------------------------------------- */
+
+void AtomKokkos::remove_custom(int flag, int index)
+{
+  if (flag == 0) {
+    memory->destroy(ivector[index]);
+    ivector[index] = NULL;
+    delete [] iname[index];
+    iname[index] = NULL;
+  } else {
+    //memory->destroy_kokkos(dvector);
+    dvector[index] = NULL;
+    delete [] dname[index];
+    dname[index] = NULL;
+  }
+}
+
 /* ---------------------------------------------------------------------- */
 
 void AtomKokkos::deallocate_topology()

src/KOKKOS/atom_kokkos.h

@@ -51,6 +51,8 @@ class AtomKokkos : public Atom {
   DAT::tdual_int_2d k_improper_type;
   DAT::tdual_tagint_2d k_improper_atom1, k_improper_atom2, k_improper_atom3, k_improper_atom4;
 
+  DAT::tdual_float_2d k_dvector;
+
 
 // USER-DPD package
   DAT::tdual_efloat_1d k_uCond, k_uMech, k_uChem, k_uCG, k_uCGnew,
@@ -66,6 +68,8 @@ class AtomKokkos : public Atom {
   void sync_overlapping_device(const ExecutionSpace space, unsigned int mask);
   virtual void sort();
   virtual void grow(unsigned int mask);
+  int add_custom(const char *, int);
+  void remove_custom(int, int);
   virtual void deallocate_topology();
   void sync_modify(ExecutionSpace, unsigned int, unsigned int);
  private:

src/KOKKOS/pair_exp6_rx_kokkos.h

@@ -0,0 +1,204 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(exp6/rx/kk,PairExp6rxKokkos<LMPDeviceType>)
+PairStyle(exp6/rx/kk/device,PairExp6rxKokkos<LMPDeviceType>)
+PairStyle(exp6/rx/kk/host,PairExp6rxKokkos<LMPHostType>)
+
+#else
+
+#ifndef LMP_PAIR_EXP6_RX_KOKKOS_H
+#define LMP_PAIR_EXP6_RX_KOKKOS_H
+
+#include "pair_exp6_rx.h"
+#include "kokkos_type.h"
+#include "pair_kokkos.h"
+
+namespace LAMMPS_NS {
+
+// Create a structure to hold the parameter data for all
+// local and neighbor particles. Pack inside this struct
+// to avoid any name clashes.
+
+template<class DeviceType>
+struct PairExp6ParamDataTypeKokkos
+{
+  typedef ArrayTypes<DeviceType> AT;
+
+   int n;
+   typename AT::t_float_1d epsilon1, alpha1, rm1, fraction1,
+          epsilon2, alpha2, rm2, fraction2,
+          epsilonOld1, alphaOld1, rmOld1, fractionOld1,
+          epsilonOld2, alphaOld2, rmOld2, fractionOld2;
+
+   // Default constructor -- nullify everything.
+   PairExp6ParamDataTypeKokkos<DeviceType>(void)
+      : n(0)
+   {}
+};
+
+struct TagPairExp6rxgetParamsEXP6{};
+
+template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+struct TagPairExp6rxCompute{};
+
+template<class DeviceType>
+class PairExp6rxKokkos : public PairExp6rx {
+ public:
+  typedef DeviceType device_type;
+  typedef ArrayTypes<DeviceType> AT;
+  typedef EV_FLOAT value_type;
+
+  PairExp6rxKokkos(class LAMMPS *);
+  virtual ~PairExp6rxKokkos();
+  virtual void compute(int, int);
+
+  template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairExp6rxCompute<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int&, EV_FLOAT&) const;
+
+  template<int NEIGHFLAG, int NEWTON_PAIR, int EVFLAG>
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairExp6rxCompute<NEIGHFLAG,NEWTON_PAIR,EVFLAG>, const int&) const;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairExp6rxgetParamsEXP6, const int&) const;
+
+  template<int NEIGHFLAG, int NEWTON_PAIR>
+  KOKKOS_INLINE_FUNCTION
+  void ev_tally(EV_FLOAT &ev, const int &i, const int &j,
+      const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx,
+                  const F_FLOAT &dely, const F_FLOAT &delz) const;
+
+  KOKKOS_INLINE_FUNCTION
+  int sbmask(const int& j) const;
+
+ protected:
+  int eflag,vflag;
+  int nlocal,newton_pair,neighflag;
+  double special_coul[4];
+  double special_lj[4];
+
+  typename AT::t_x_array_randomread x;
+  typename AT::t_f_array f;
+  typename AT::t_int_1d_randomread type;
+  typename AT::t_efloat_1d uCG, uCGnew;
+  typename AT::t_float_2d dvector;
+
+  DAT::tdual_efloat_1d k_eatom;
+  DAT::tdual_virial_array k_vatom;
+  DAT::t_efloat_1d d_eatom;
+  DAT::t_virial_array d_vatom;
+
+  typename AT::t_neighbors_2d d_neighbors;
+  typename AT::t_int_1d_randomread d_ilist;
+  typename AT::t_int_1d_randomread d_numneigh;
+
+  PairExp6ParamDataTypeKokkos<DeviceType> PairExp6ParamData;
+
+  void allocate();
+  DAT::tdual_int_1d k_mol2param;               // mapping from molecule to parameters
+  typename AT::t_int_1d_randomread d_mol2param;
+
+  typedef Kokkos::DualView<Param*,Kokkos::LayoutRight,DeviceType> tdual_param_1d;
+  typedef typename tdual_param_1d::t_dev_const_randomread t_param_1d_randomread;
+
+  tdual_param_1d k_params;                // parameter set for an I-J-K interaction
+  t_param_1d_randomread d_params;                // parameter set for an I-J-K interaction
+
+  typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
+  typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
+
+  void read_file(char *);
+  void setup();
+
+  KOKKOS_INLINE_FUNCTION
+  void getParamsEXP6(int, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &, double &) const;
+
+  KOKKOS_INLINE_FUNCTION
+  double func_rin(const double &) const;
+
+  KOKKOS_INLINE_FUNCTION
+  double expValue(const double) const;
+
+  friend void pair_virial_fdotr_compute<PairExp6rxKokkos>(PairExp6rxKokkos*);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E:  alpha_ij is 6.0 in pair exp6
+
+Self-explanatory
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory.  Check the input script or data file.
+
+E: PairExp6rxKokkos requires a fix rx command
+
+The fix rx command must come before the pair style command in the input file
+
+E:  There are no rx species specified
+
+There must be at least one species specified through the fix rx command
+
+E:  Site1 name not recognized in pair coefficients
+
+The site1 keyword does not match the species keywords specified throug the fix rx command
+
+E: All pair coeffs are not set
+
+All pair coefficients must be set in the data file or by the
+pair_coeff command before running a simulation.
+
+E:  Cannot open exp6/rx potential file %s
+
+Self-explanatory
+
+E:  Incorrect format in exp6/rx potential file
+
+Self-explanatory
+
+E:  Illegal exp6/rx parameters.  Rm and Epsilon must be greater than zero.  Alpha cannot be negative.
+
+Self-explanatory
+
+E:  Illegal exp6/rx parameters.  Interaction potential does not exist.
+
+Self-explanatory
+
+E:  Potential file has duplicate entry.
+
+Self-explanatory
+
+E:  The number of molecules in CG particle is less than 1e-8.
+
+Self-explanatory.  Check the species concentrations have been properly set
+and check the reaction kinetic solver parameters in fix rx to more for
+sufficient accuracy.
+
+
+*/

src/USER-DPD/pair_exp6_rx.cpp

@@ -77,6 +77,8 @@ PairExp6rx::PairExp6rx(LAMMPS *lmp) : Pair(lmp)
 
 PairExp6rx::~PairExp6rx()
 {
+  if (copymode) return;
+
   for (int i=0; i < nparams; ++i) {
     delete[] params[i].name;
     delete[] params[i].potential;

src/atom.h

@@ -255,8 +255,8 @@ class Atom : protected Pointers {
   void update_callback(int);
 
   int find_custom(const char *, int &);
-  int add_custom(const char *, int);
-  void remove_custom(int, int);
+  virtual int add_custom(const char *, int);
+  virtual void remove_custom(int, int);
 
   virtual void sync_modify(ExecutionSpace, unsigned int, unsigned int) {}