Final MPI version

lammps/includes/atom.h

@@ -4,8 +4,9 @@
  * Use of this source code is governed by a LGPL-3.0
  * license that can be found in the LICENSE file.
  */
-#include <parameter.h>
 
+#include <box.h>
+#include <parameter.h>
 #ifndef __ATOM_H_
 #define __ATOM_H_
 
@@ -56,6 +57,8 @@ typedef struct {
     MD_FLOAT *sigma6;
     MD_FLOAT *cutforcesq;
     MD_FLOAT *cutneighsq;
+    //TODO: insert the id number
+    //MD_FLOAT *Atom_id;
 
     // DEM
     MD_FLOAT *radius;
@@ -64,6 +67,9 @@ typedef struct {
 
     // Device data
     DeviceAtom d_atom;
+     
+    //Info Subdomain
+    Box mybox;            
 } Atom;
 
 extern void initAtom(Atom*);
@@ -73,9 +79,19 @@ extern int readAtom_pdb(Atom*, Parameter*);
 extern int readAtom_gro(Atom*, Parameter*);
 extern int readAtom_dmp(Atom*, Parameter*);
 extern int readAtom_in(Atom*, Parameter*);
-extern void writeAtom(Atom*, Parameter*);
 extern void growAtom(Atom*);
 
+int  packGhost(Atom*, int, MD_FLOAT*, int*);
+int  unpackGhost(Atom*, int, MD_FLOAT*);
+int  packExchange(Atom*, int, MD_FLOAT*);
+int  unpackExchange(Atom*, int, MD_FLOAT*);
+void packForward(Atom*, int, int*, MD_FLOAT*, int*); 
+void unpackForward(Atom*, int, int, MD_FLOAT*);
+void packReverse(Atom* , int , int , MD_FLOAT*);
+void unpackReverse(Atom*, int, int*, MD_FLOAT*);
+void pbc(Atom*);
+void copy(Atom*, int, int);
+
 #ifdef AOS
 #   define POS_DATA_LAYOUT     "AoS"
 #   define atom_x(i)           atom->x[(i) * 3 + 0]
@@ -100,4 +116,8 @@ extern void growAtom(Atom*);
 #   define atom_fz(i)          atom->fz[i]
 #endif
 
+#   define buf_x(i)            buf[3*(i)] 
+#   define buf_y(i)            buf[3*(i)+1]
+#   define buf_z(i)            buf[3*(i)+2]
+
 #endif

lammps/includes/neighbor.h

@@ -20,9 +20,14 @@ typedef struct {
     int ncalls;
     int maxneighs;
     int half_neigh;
+    int half_stencil;
     int *neighbors;
     int *numneigh;
-
+    //MPI
+    int Nshell;         //# of atoms in listShell
+    int *numNeighShell; //# of neighs for each atom in listShell
+    int *neighshell;    //list of neighs for each atom in listShell
+    int *listshell;     //Atoms to compute the force
     // Device data
     DeviceNeighbor d_neighbor;
 } Neighbor;

lammps/includes/vtk.h

@@ -5,8 +5,11 @@
  * license that can be found in the LICENSE file.
  */
 #include <atom.h>
+#include <comm.h>
+#include <parameter.h>
 
 #ifndef __VTK_H_
 #define __VTK_H_
 extern int write_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep);
+extern void printvtk(const char* filename, Comm* comm, Atom* atom ,Parameter* param, int timestep);
 #endif