From 4982d28ecb1677fcb59a72b4da5dfaa82312f00a Mon Sep 17 00:00:00 2001
From: yeom <yeom>
Date: Fri, 12 Nov 2010 02:38:19 +0000
Subject: [PATCH] changes on MolDyn: increases workload and re-arranges
 unnecessary stall sites.

---
 .../Benchmarks/oooJava/moldyn/JGFMolDynBench.java | 15 +++++++++------
 .../oooJava/moldyn/JGFMolDynBenchSizeB.java       |  2 +-
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/Robust/src/Benchmarks/oooJava/moldyn/JGFMolDynBench.java b/Robust/src/Benchmarks/oooJava/moldyn/JGFMolDynBench.java
index 75cd1d11..5f3b0946 100644
--- a/Robust/src/Benchmarks/oooJava/moldyn/JGFMolDynBench.java
+++ b/Robust/src/Benchmarks/oooJava/moldyn/JGFMolDynBench.java
@@ -259,7 +259,7 @@ class mdRunner {
   public void doinit(int mdsize) {
     for (int j = 0; j < 3; j++) {
       double[] sh = sh_force[j];
-      for (int i = 0; i < mdsize; i++) {
+      for (int i = 0; i < sh.length; i++) {
         sh[i] = 0.0;
       }
     }
@@ -357,7 +357,7 @@ class mdRunner {
 
     for (int move = 0; move < movemx; move++) {
       /* move the particles and update velocities */
-      for (int i = 0; i < mdsize; i++) {
+      for (int i = 0; i < one.length; i++) {
         one[i].domove(side, i);
       }
 
@@ -423,11 +423,12 @@ class mdRunner {
       }
       
       mymd.epot[0] =l_epot;
+//      System.out.println("SEQ_START");
       mymd.vir[0] = l_vir;
       mymd.interactions = l_interacts;
       
       for (int k = 0; k < 3; k++) {
-        for (int j = 0; j < mdsize; j++) {
+        for (int j = 0; j <  sh_force[k].length; j++) {
           sh_force[k][j] = sh_force[k][j] * hsq2;
         }
       }
@@ -438,10 +439,12 @@ class mdRunner {
       // }
 
       /* scale forces, update velocities */
-      sum = 0.0;
-      for (int i = 0; i < mdsize; i++) {
-        sum = sum + one[i].mkekin(hsq2, i);
+      double l_sum=0.0;
+      int maxIdx=one.length;
+      for (int i = 0; i < maxIdx; i++) {
+        l_sum = l_sum + one[i].mkekin(hsq2, i);
       }
+      sum=l_sum;
 
       ekin = sum / hsq;
 
diff --git a/Robust/src/Benchmarks/oooJava/moldyn/JGFMolDynBenchSizeB.java b/Robust/src/Benchmarks/oooJava/moldyn/JGFMolDynBenchSizeB.java
index 3331e9df..f7007ad5 100644
--- a/Robust/src/Benchmarks/oooJava/moldyn/JGFMolDynBenchSizeB.java
+++ b/Robust/src/Benchmarks/oooJava/moldyn/JGFMolDynBenchSizeB.java
@@ -29,7 +29,7 @@ public class JGFMolDynBenchSizeB {
       System.printString("The no of threads has not been specified, defaulting to 1\n");
       System.printString("  " + "\n");
       nthreads = 1;
-      workload=100;
+      workload=300;
     }
 
 //    JGFInstrumentor instr = new JGFInstrumentor();
-- 
2.34.1