Rename default directory to lammps and reorganize gromacs variant steps

Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>

config.mk

@@ -1,7 +1,7 @@
 # Compiler tag (GCC/CLANG/ICC)
 TAG ?= ICC
-# Optimization scheme (default/gromacs/clusters_per_bin)
-OPT_SCHEME = default
+# Optimization scheme (lammps/gromacs/clusters_per_bin)
+OPT_SCHEME = lammps
 # Enable likwid (true or false)
 ENABLE_LIKWID ?= false
 # SP or DP

gromacs/includes/neighbor.h

@@ -39,4 +39,5 @@ extern void binatoms(Atom*);
 extern void buildNeighbor(Parameter*, Atom*, Neighbor*);
 extern void sortAtom(Atom*);
 extern void buildClusters(Parameter*, Atom*);
+extern void binGhostClusters(Parameter*, Atom*);
 #endif

gromacs/main.c

@@ -100,7 +100,7 @@ double setup(
     setupThermo(param, atom->Natoms);
     if(param->input_file == NULL) { adjustThermo(param, atom); }
     setupPbc(atom, param);
-    updatePbc(atom, param);
+    buildClusters(param, atom);
     buildNeighbor(param, atom, neighbor);
     E = getTimeStamp();
 
@@ -118,8 +118,6 @@ double reneighbour(
     LIKWID_MARKER_START("reneighbour");
     updateAtomsPbc(atom, param);
     setupPbc(atom, param);
-    updatePbc(atom, param);
-    //sortAtom(atom);
     buildNeighbor(param, atom, neighbor);
     LIKWID_MARKER_STOP("reneighbour");
     E = getTimeStamp();

gromacs/neighbor.c

@@ -219,10 +219,6 @@ void buildNeighbor(Parameter *param, Atom *atom, Neighbor *neighbor) {
         neighbor->neighbors = (int*) malloc(nmax * neighbor->maxneighs * sizeof(int*));
     }
 
-    /* bin local & ghost atoms */
-    binatoms(atom);
-    buildClusters(param, atom);
-
     const MD_FLOAT rBB = cutneighsq / 2.0; // TODO: change this
     int resize = 1;
 
@@ -413,6 +409,9 @@ void sortBinAtomsByZCoord(Parameter *param, Atom *atom, int bin) {
 }
 
 void buildClusters(Parameter *param, Atom *atom) {
+    /* bin local atoms */
+    binatoms(atom);
+
     for(int bin = 0; bin < mbins; bin++) {
         sortBinAtomsByZCoord(param, atom, bin);
     }

gromacs/pbc.c

@@ -26,6 +26,7 @@
 #include <pbc.h>
 #include <atom.h>
 #include <allocate.h>
+#include <neighbor.h>
 
 #define DELTA 20000
 
@@ -177,4 +178,8 @@ void setupPbc(Atom *atom, Parameter *param) {
     // increase by one to make it the ghost atom count
     atom->Nclusters_ghost = Nghost + 1;
     atom->Nclusters = atom->Nclusters_local + Nghost + 1;
+
+    // Update and bin created ghost clusters
+    updatePbc(atom, param);
+    binGhostClusters(param, atom);
 }