From 5fd2d422eea15fdeb065f38c97b3a3483d5d1627 Mon Sep 17 00:00:00 2001
From: Rafael Ravedutti <rafaelravedutti@gmail.com>
Date: Wed, 2 Feb 2022 00:49:55 +0100
Subject: [PATCH] Adjust kernels to work with MxN loops

Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
---
 gromacs/force_lj.c |  4 ++--
 gromacs/pbc.c      | 12 +++++++++---
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/gromacs/force_lj.c b/gromacs/force_lj.c
index f55dbf0..1392731 100644
--- a/gromacs/force_lj.c
+++ b/gromacs/force_lj.c
@@ -61,7 +61,7 @@ double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *s
         for(int k = 0; k < numneighs; k++) {
             int cj = neighs[k];
             MD_FLOAT *cjptr = cluster_pos_ptr(cj);
-            for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) {
+            for(int cii = 0; cii < CLUSTER_DIM_M; cii++) {
                 MD_FLOAT xtmp = cluster_x(ciptr, cii);
                 MD_FLOAT ytmp = cluster_y(ciptr, cii);
                 MD_FLOAT ztmp = cluster_z(ciptr, cii);
@@ -69,7 +69,7 @@ double computeForceLJ(Parameter *param, Atom *atom, Neighbor *neighbor, Stats *s
                 MD_FLOAT fiy = 0;
                 MD_FLOAT fiz = 0;
 
-                for(int cjj = 0; cjj < atom->clusters[cj].natoms; cjj++) {
+                for(int cjj = 0; cjj < CLUSTER_DIM_N; cjj++) {
                     if(ci != cj || cii != cjj) {
                         MD_FLOAT delx = xtmp - cluster_x(cjptr, cjj);
                         MD_FLOAT dely = ytmp - cluster_y(cjptr, cjj);
diff --git a/gromacs/pbc.c b/gromacs/pbc.c
index 3d93c3b..5a303c3 100644
--- a/gromacs/pbc.c
+++ b/gromacs/pbc.c
@@ -44,7 +44,7 @@ void initPbc(Atom* atom) {
 
 /* update coordinates of ghost atoms */
 /* uses mapping created in setupPbc */
-void updatePbc(Atom *atom, Parameter *param, int updateBoundingBoxes) {
+void updatePbc(Atom *atom, Parameter *param, int firstUpdate) {
     int *border_map = atom->border_map;
     int nlocal = atom->Nclusters_local;
     MD_FLOAT xprd = param->xprd;
@@ -68,7 +68,7 @@ void updatePbc(Atom *atom, Parameter *param, int updateBoundingBoxes) {
             cluster_y(cptr, cii) = ytmp;
             cluster_z(cptr, cii) = ztmp;
 
-            if(updateBoundingBoxes) {
+            if(firstUpdate) {
                 // TODO: To create the bounding boxes faster, we can use SIMD operations
                 if(bbminx > xtmp) { bbminx = xtmp; }
                 if(bbmaxx < xtmp) { bbmaxx = xtmp; }
@@ -79,7 +79,13 @@ void updatePbc(Atom *atom, Parameter *param, int updateBoundingBoxes) {
             }
         }
 
-        if(updateBoundingBoxes) {
+        if(firstUpdate) {
+            for(int cii = atom->clusters[ci].natoms; cii < CLUSTER_DIM_M; cii++) {
+                cluster_x(cptr, cii) = INFINITY;
+                cluster_y(cptr, cii) = INFINITY;
+                cluster_z(cptr, cii) = INFINITY;
+            }
+
             atom->clusters[ci].bbminx = bbminx;
             atom->clusters[ci].bbmaxx = bbmaxx;
             atom->clusters[ci].bbminy = bbminy;