From: jzhou <jzhou>
Date: Tue, 11 Nov 2008 23:02:32 +0000 (+0000)
Subject: add the JGF MolDyn benchmark
X-Git-Tag: buildscript^7~39
X-Git-Url: http://demsky.eecs.uci.edu/git/?a=commitdiff_plain;h=4cb00fe5bf54ff63dcb82c1133f9776ef61bbc30;p=IRC.git

add the JGF MolDyn benchmark
---

diff --git a/Robust/src/Benchmarks/Scheduling/JGFMolDyn/JGFMolDynBench.java b/Robust/src/Benchmarks/Scheduling/JGFMolDyn/JGFMolDynBench.java
new file mode 100644
index 00000000..c8287f02
--- /dev/null
+++ b/Robust/src/Benchmarks/Scheduling/JGFMolDyn/JGFMolDynBench.java
@@ -0,0 +1,121 @@
+/** Banboo Version */
+
+/**************************************************************************
+*                                                                         *
+*         Java Grande Forum Benchmark Suite - Thread Version 1.0          *
+*                                                                         *
+*                            produced by                                  *
+*                                                                         *
+*                  Java Grande Benchmarking Project                       *
+*                                                                         *
+*                                at                                       *
+*                                                                         *
+*                Edinburgh Parallel Computing Centre                      *
+*                                                                         * 
+*                email: epcc-javagrande@epcc.ed.ac.uk                     *
+*                                                                         *
+*                                                                         *
+*      This version copyright (c) The University of Edinburgh, 2001.      *
+*                         All rights reserved.                            *
+*                                                                         *
+**************************************************************************/
+
+task t1(StartupObject s{initialstate}) {
+    //System.printString("task t1\n");
+    
+    int datasize = 2;
+    int group = 16;
+    
+    MD md = new MD(datasize, group){initialise};
+    
+    taskexit(s{!initialstate});
+}
+
+task t2(MD md{initialise}) {
+    //System.printString("task t2\n");
+    md.initialise();
+    taskexit(md{!initialise, move});
+}
+
+task t3(MD md{move}) {
+    //System.printString("task t3\n");
+    
+    md.domove();
+    md.init();
+    //System.printI(0xd0);
+    for(int i = 0; i < md.group; ++i) {
+	MDRunner runner = new MDRunner(i, md){run};
+	runner.init();
+	//System.printI(0xd1);
+    }
+    //System.printI(0xd2);
+    taskexit(md{!move,update});
+}
+
+/*task t4(MD md{fire}, MDRunner runner{wait}) {
+    System.printString("task t4\n");
+    
+    runner.init();
+    md.counter++;
+    //System.printString("counter: " + md.counter + "\n");
+    if(md.counter == md.group) {
+	//System.printString("Fire finished: " + md.move + "\n");
+	taskexit(md{!fire, update}, runner{!wait, run});
+    } else {
+	taskexit(md{fire}, runner{!wait, run});
+    }
+}*/
+
+task t5(MDRunner runner{run}) {
+    //System.printString("task t5\n");
+    
+    runner.run();
+    
+    taskexit(runner{update, !run});
+}
+
+task t6(MD md{update}, MDRunner runner{update}) {
+    //System.printString("task t6\n");
+    
+    md.update(runner);
+    md.counter++;
+    if(md.counter == md.group) {
+	md.sum();
+	md.scale();
+	if(md.finish()) {
+	    taskexit(md{!update, validate}, runner{!update/*, scale*/});
+	} else {
+	    taskexit(md{!update, move}, runner{!update/*, scale*/});
+	}
+    } else {
+	taskexit(md{update}, runner{!update/*, scale*/});
+    }
+}
+
+/*task t7(MD md{scale}, MDRunner runner{scale}) {
+    //System.printString("task t7\n");
+    
+    md.counter--;
+    
+    if(md.counter == 0) {
+	if(md.finish()) {
+	    // finished
+	    taskexit(md{!scale, validate}, runner{!scale, !wait});
+	}
+	taskexit(md{!scale, move}, runner{!scale, !wait});
+    } else {
+	if(md.finish()) {
+	    taskexit(md{scale}, runner{!scale, !wait});
+	}
+	taskexit(md{scale}, runner{!scale, !wait});
+    }
+}*/
+
+task t8(MD md{validate}) {
+    //System.printString("task t8\n");
+    
+    md.validate();
+    
+    taskexit(md{!validate, finish});
+}
+ 
diff --git a/Robust/src/Benchmarks/Scheduling/JGFMolDyn/MD.java b/Robust/src/Benchmarks/Scheduling/JGFMolDyn/MD.java
new file mode 100644
index 00000000..75fd7def
--- /dev/null
+++ b/Robust/src/Benchmarks/Scheduling/JGFMolDyn/MD.java
@@ -0,0 +1,356 @@
+/** Banboo Version */
+
+/**************************************************************************
+ *                                                                         *
+ *             Java Grande Forum Benchmark Suite - Version 2.0             *
+ *                                                                         *
+ *                            produced by                                  *
+ *                                                                         *
+ *                  Java Grande Benchmarking Project                       *
+ *                                                                         *
+ *                                at                                       *
+ *                                                                         *
+ *                Edinburgh Parallel Computing Centre                      *
+ *                                                                         * 
+ *                email: epcc-javagrande@epcc.ed.ac.uk                     *
+ *                                                                         *
+ *                  Original version of this code by                       *
+ *                         Dieter Heermann                                 * 
+ *                       converted to Java by                              *
+ *                Lorna Smith  (l.smith@epcc.ed.ac.uk)                     *
+ *                   (see copyright notice below)                          *
+ *                                                                         *
+ *      This version copyright (c) The University of Edinburgh, 2001.      *
+ *                         All rights reserved.                            *
+ *                                                                         *
+ **************************************************************************/
+
+public class MD {
+    flag initialise;
+    flag move;
+    flag fire;
+    flag update;
+    flag scale;
+    flag validate;
+    flag finish;
+    
+    public int mm;
+    public int group;
+    public int mdsize;
+    public int move;
+    public int movemx;
+ 
+    public float side;
+    float hsq, hsq2, den, h, vaver,vaverh;
+    float tref, tscale;
+    int irep;
+    int istop;
+    int iprint;
+    
+    public Particle[] one;
+    public float[][] sh_force;
+    //public float[] epot;
+    //public float[] vir;
+    //public float[] ek;
+    public float epot;
+    public float vir;
+    public float ek;
+    float ekin;
+    
+    public int counter;
+    
+    public void MD(int d, int g) {
+	this.mm = d;
+	this.group = g;
+	this.mdsize = this.mm * this.mm * this.mm * 4;
+	this.one = new Particle [this.mdsize];
+	this.sh_force = new float[3][this.mdsize];
+	this.move = 0;
+	this.movemx = 2;
+	this.den = (float)0.83134;
+	this.h = (float)0.064;
+	this.side = Math.powf((float)(this.mdsize/this.den),(float)0.3333333);
+	this.hsq = this.h * this.h;
+	this.hsq2 = this.hsq * (float)0.5;
+	this.vaver = (float)1.13 * Math.sqrtf((float)this.tref / (float)24.0);
+	this.vaverh = this.vaver * this.h;
+	this.irep = 10;
+	this.istop = 19;
+	//this.epot = (float)0.0;
+	//this.vir = (float)0.0;
+	this.tref = (float)0.722;
+	this.tscale = (float)16.0 / ((float)1.0 * (float)this.mdsize - (float)1.0);
+	this.iprint = 10;
+	this.counter = 0;
+	
+	this.epot = (float)0.0;//new float[this.group + 1];
+	this.vir = (float)0.0;//new float[this.group + 1];
+	this.ek = (float)0.0;//new float[this.group + 1];
+    }
+    
+    public void init() {
+	/*for(int i = 0; i < this.group + 1; i++) {
+	    this.epot[i] = (float)0.0;
+	    this.vir[i] = (float)0.0;
+	}*/
+	this.epot = (float)0.0;
+	this.vir = (float)0.0;
+	for(int j = 0; j < 3; j++) {
+	    for (int i = 0; i < this.mdsize; i++) {
+		this.sh_force[j][i] = (float)0.0;
+	    }
+	}
+	this.counter = 0;
+    }
+
+    public void initialise() {
+	
+	/* Particle Generation */
+	float xvelocity, yvelocity, zvelocity;
+	int ijk, lg, i, j, k;
+	float a = this.side/this.mm;
+	xvelocity = (float)0.0;
+	yvelocity = (float)0.0;
+	zvelocity = (float)0.0;
+	//System.printString("here 1\n");
+	//System.printI(0xa0);
+	ijk = 0;
+	for (lg=0; lg<=1; lg++) {
+	    for (i=0; i<mm; i++) {
+		for (j=0; j<mm; j++) {
+		    for (k=0; k<mm; k++) {
+			one[ijk] = new Particle((float)(i*a+lg*a*(float)0.5),(float)(j*a+lg*a*(float)0.5),(k*a),
+				xvelocity,yvelocity,zvelocity,this);
+			ijk = ijk + 1;
+		    }
+		}
+	    }
+	}
+	for (lg=1; lg<=2; lg++) {
+	    for (i=0; i<mm; i++) {
+		for (j=0; j<mm; j++) {
+		    for (k=0; k<mm; k++) {
+			one[ijk] = new Particle((float)(i*a+(2-lg)*a*(float)0.5),(float)(j*a+(lg-1)*a*(float)0.5),
+				(float)(k*a+a*(float)0.5),xvelocity,yvelocity,zvelocity,this);
+			ijk = ijk + 1;
+		    }
+		}
+	    }
+	}
+	//System.printString("here 2\n");
+	//System.printI(0xa1);
+	/* Initialise velocities */
+	int iseed;
+	float v1,v2, r;
+	iseed = 0;
+	v1 = (float)0.0;
+	v2 = (float)0.0;
+	
+	MyRandom random = new MyRandom(iseed,v1,v2);
+	//System.printString("here 3\n");
+	//System.printI(0xa2);
+	for (i=0; i<this.mdsize; i+=2) {
+	    r  = random.seed();
+	    one[i].xvelocity = r*random.v1;
+	    one[i+1].xvelocity  = r*random.v2;
+	}
+	//System.printString("here 4\n");
+	//System.printI(0xa3);
+	for (i=0; i<this.mdsize; i+=2) {
+	    r  = random.seed();
+	    one[i].yvelocity = r*random.v1;
+	    one[i+1].yvelocity  = r*random.v2;
+	}
+	//System.printString("here 5\n");
+	//System.printI(0xa4);
+	for (i=0; i<this.mdsize; i+=2) {
+	    r  = random.seed();
+	    one[i].zvelocity = r*random.v1;
+	    one[i+1].zvelocity  = r*random.v2;
+	}
+
+	/*for(i = 0; i < this.mdsize; i++) {
+		System.printString("xvel: " + (int)(one[i].xvelocity*100000) + "; yvel: " + (int)(one[i].yvelocity*100000) + "; zvel: " + (int)(one[i].zvelocity*100000) + "\n");
+	}*/
+	
+	//System.printString("here 6\n");
+	//System.printI(0xa5);
+	/* velocity scaling */
+	float sp, ts, sc;
+	ekin = (float)0.0;
+	sp = (float)0.0;
+	//System.printString("here 7\n");
+	//System.printI(0xa6);
+	for(i=0;i<this.mdsize;i++) {
+	    sp = sp + one[i].xvelocity;
+	}
+	sp = sp / this.mdsize;
+	//System.printString("here 8\n");
+	//System.printI(0xa7);
+	for(i=0;i<this.mdsize;i++) {
+	    one[i].xvelocity = one[i].xvelocity - sp;
+	    ekin = ekin + one[i].xvelocity*one[i].xvelocity;
+	}
+	//System.printString("here 9\n");
+	//System.printI(0xa8);
+	sp = (float)0.0;
+	for(i=0;i<this.mdsize;i++) {
+	    sp = sp + one[i].yvelocity;
+	}
+	sp = sp / this.mdsize;
+	//System.printString("here 10\n");
+	//System.printI(0xa9);
+	for(i=0;i<this.mdsize;i++) {
+	    one[i].yvelocity = one[i].yvelocity - sp;
+	    ekin = ekin + one[i].yvelocity*one[i].yvelocity;
+	}
+	//System.printString("here 11\n");
+	//System.printI(0xa10);
+	sp = (float)0.0;
+	for(i=0;i<this.mdsize;i++) {
+	    sp = sp + one[i].zvelocity;
+	}
+	sp = sp / this.mdsize;
+	//System.printString("here 12\n");
+	//System.printI(0xa11);
+	for(i=0;i<this.mdsize;i++) {
+	    one[i].zvelocity = one[i].zvelocity - sp;
+	    ekin = ekin + one[i].zvelocity*one[i].zvelocity;
+	}
+	//System.printString("here 13\n");
+	//System.printI(0xa12);
+	ts = this.tscale * ekin;
+	sc = h * Math.sqrtf(this.tref/ts);
+
+	for(i=0;i<this.mdsize;i++) {
+	    one[i].xvelocity = one[i].xvelocity * sc;     
+	    one[i].yvelocity = one[i].yvelocity * sc;     
+	    one[i].zvelocity = one[i].zvelocity * sc;     
+	}
+	//System.printString("here 14\n");
+	//System.printI(0xa13);
+    }
+
+
+    public void domove(){
+	for (int i=0;i<this.mdsize;i++) {
+	    one[i].domove(this.side,i);       
+	}
+	
+	/*for(int j=0;j<3;j++) {
+	    for (int i=0;i<mdsize;i++) {
+		sh_force[j][i] = (float)0.0;
+	    }
+	}*/
+	
+	this.move++;
+    }
+    
+    public boolean finish() {
+	if(this.move == this.movemx) {
+	    return true;
+	} 
+	return false;
+    }
+
+    public void update(MDRunner runner) {
+	float sum, vel,velt, count, sc;
+	float etot,temp,pres,rp;
+	
+	/* update force arrays */
+	for(int k=0;k<3;k++) {
+	    for(int i=0;i<this.mdsize;i++) {
+		sh_force[k][i] += runner.sh_force2[k][i];
+	    }
+	}
+	
+	//runner.init();
+
+	//this.epot[runner.id + 1] = runner.epot;
+	//this.vir[runner.id + 1] = runner.vir;
+	this.epot += runner.epot;
+	this.vir += runner.vir;
+    }
+    
+    public void sum() {
+	float sum = (float)0.0; 
+	
+	for (int j=0;j<3;j++) {
+	    for (int i=0;i<this.mdsize;i++) {
+		sh_force[j][i] = sh_force[j][i] * hsq2;
+	    }
+	}
+	
+	sum = (float)0.0;
+	for (int i=0;i<this.mdsize;i++) {
+	    sum = sum + this.one[i].mkekin(hsq2,i);  
+	}
+	ekin = (float)(sum/hsq);
+    }
+    
+    public void scale() {
+	float sum, vel,velt, count, sc;
+	float etot,temp,pres,rp;
+	
+	//runner.epot = this.epot[0];
+	//runner.vir = this.vir[0];
+
+	vel = (float)0.0;
+	count = (float)0.0;
+
+	/* average velocity */
+	for (int i=0;i<this.mdsize;i++) {
+	    velt = this.one[i].velavg(vaverh,h);
+	    if(velt > vaverh) { 
+		count = count + (float)1.0; 
+	    }
+	    vel = vel + velt;                    
+	}
+	vel = (float)(vel / h);
+
+	/* temperature scale if required */
+	if((this.move < this.istop) && (((this.move+1) % this.irep) == 0)) {
+	    sc = Math.sqrtf(this.tref / (this.tscale*ekin));
+	    for (int i=0;i<mdsize;i++) {
+		one[i].dscal(sc,1);
+	    }
+	    ekin = (float)(this.tref / this.tscale);
+	}
+
+	/* sum to get full potential energy and virial */
+	if(((this.move+1) % this.iprint) == 0) {
+	    /*this.ek[runner.id+1] = (float)24.0*ekin;
+	    this.epot[runner.id+1] = (float)4.0*this.epot[runner.id+1];
+	    etot = this.ek[runner.id+1] + this.epot[runner.id+1];
+	    temp = this.tscale * ekin;
+	    pres = den * (float)16.0 * (ekin - this.vir[runner.id+1]) / mdsize;
+	    vel = vel / this.mdsize; 
+	    rp = (count / this.mdsize) * (float)100.0;
+	    
+	    if(this.counter == this.group) {*/
+		this.ek = (float)24.0*ekin;
+		//this.epot[0] = (float)4.0*this.epot[0];
+		//etot = this.ek[0] + this.epot[0];
+		//temp = this.tscale * ekin;
+		//pres = den * (float)16.0 * (ekin - this.vir[0]) / mdsize;
+		//vel = vel / this.mdsize; 
+		//rp = (count / this.mdsize) * (float)100.0;
+		//System.printString("ek: " + (int)(this.ek*1000000) + " (" + this.move + ")\n");
+	    //}
+	}
+    }
+    
+    public void validate() {
+	float refval = (float)1731.4306625334357;
+	float dev = Math.abs(this.ek - refval);
+	if (dev > 1.0e-10 ){
+	    //System.printString("Validation failed\n");
+	    //System.printString("Kinetic Energy = " + (int)(this.ek*1000000) + ";  " + (int)(refval*1000000) + "\n");
+	    //System.printI(0xdddf);
+	    //System.printI((int)(this.ek[0]*1000000));
+	    //System.printI((int)(refval*1000000));
+	    //System.printI((int)(ek*10000));
+	    //System.printI((int)(refval*10000));
+	}
+    }
+}
diff --git a/Robust/src/Benchmarks/Scheduling/JGFMolDyn/MDRunner.java b/Robust/src/Benchmarks/Scheduling/JGFMolDyn/MDRunner.java
new file mode 100644
index 00000000..7b755511
--- /dev/null
+++ b/Robust/src/Benchmarks/Scheduling/JGFMolDyn/MDRunner.java
@@ -0,0 +1,72 @@
+public class MDRunner {
+    flag wait;
+    flag run;
+    flag update;
+    flag scale;
+    
+    public int id;  
+    int mm;
+    int mdsize;
+    public int group;
+    public int ilow, iupper;
+    //float l;
+    float rcoff;
+    //rcoffs,
+    float side/*sideh,*/;
+    //float rand;
+    public float [][] sh_force2;
+    public float epot;
+    public float vir;
+    public float ek;
+    //int npartm,tint;
+    //int iprint = 10;
+    MD md;
+    Particle[] one;
+
+    public MDRunner(int id, MD m) {
+	this.id=id;
+	this.md = m;
+	this.mm=this.md.mm;
+	//this.l = 50e-10;
+	this.mdsize = this.md.mdsize;
+	this.group = this.md.group;
+	this.side = this.md.side;
+	this.rcoff = this.mm/(float)4.0;
+//	this.rcoffs = this.rcoff * this.rcoff;
+	//this.sideh = this.side * 0.5;
+	//this.npartm = this.mdsize - 1;
+	//this.iprint = 10;
+	int slice = (this.mdsize - 1) / this.group + 1; 
+	this.ilow = this.id * slice; 
+	this.iupper = (this.id+1) * slice; 
+	if (this.iupper > this.mdsize )  {
+	    iupper = this.mdsize; 
+	}
+	sh_force2 = new float[3][this.mdsize];
+	
+	this.one = this.md.one;
+	this.epot = (float)0.0;//this.md.epot[id+1];
+	this.vir = (float)0.0;//this.md.vir[id+1];
+	this.ek = (float)0.0;//this.md.ek[id+1];
+    }
+    
+    public void init() {
+	this.epot = (float)0.0;
+	this.vir = (float)0.0;
+	for(int i = 0; i < this.mdsize; i++) {
+	    for(int j = 0; j < 3; j++) {
+		this.sh_force2[j][i] = (float)0.0;
+	    }
+	}
+    }
+
+    public void run() {
+	/* compute forces */
+	//System.printString("here 1: " + this.id + "\n");
+	for (int i = this.ilow; i < this.iupper; i++) {
+	    one[i].force(side,rcoff,mdsize,i,this); 
+	}
+	//System.printString("here 2: " + this.id + "\n");
+    }
+
+}
\ No newline at end of file
diff --git a/Robust/src/Benchmarks/Scheduling/JGFMolDyn/MyRandom.java b/Robust/src/Benchmarks/Scheduling/JGFMolDyn/MyRandom.java
new file mode 100644
index 00000000..3fdb7e47
--- /dev/null
+++ b/Robust/src/Benchmarks/Scheduling/JGFMolDyn/MyRandom.java
@@ -0,0 +1,61 @@
+public class MyRandom {
+
+    public int iseed;
+    public float v1,v2;
+
+    public MyRandom(int iseed, float v1, float v2) {
+	this.iseed = iseed;
+	this.v1 = v1;
+	this.v2 = v2;
+    }
+
+    public float update() {
+
+	float rand;
+	float scale= (float)4.656612875e-10;
+
+	int is1,is2,iss2;
+	int imult= 16807;
+	int imod = 2147483647;
+
+	if (iseed<=0) { 
+	    iseed = 1; 
+	    }
+
+	is2 = iseed % 32768;
+	is1 = (iseed-is2)/32768;
+	iss2 = is2 * imult;
+	is2 = iss2 % 32768;
+	is1 = (is1 * imult+(iss2-is2) / 32768) % (65536);
+
+	iseed = (is1 * 32768 + is2) % imod;
+
+	rand = scale * iseed;
+
+	return rand;
+
+    }
+
+    public float seed() {
+
+	float s,u1,u2,r;
+	s = (float)1.0;
+	//do {
+	    //System.printI(0xb1);
+	    u1 = update();
+	    u2 = update();
+
+	//System.printI(0xb2);
+	    v1 = (float)2.0 * u1 - (float)1.0;
+	    v2 = (float)2.0 * u2 - (float)1.0;
+	    s = v1*v1 + v2*v2;
+	//System.printI(0xb3);
+	//} while (s >= (float)1.0);
+	 s = s - (int)s;
+	//System.printI(0xb4);
+	r = Math.sqrtf((float)(-2.0*Math.logf(s))/(float)s);
+	//System.printI(0xb5);
+	return r;
+
+    }
+}
diff --git a/Robust/src/Benchmarks/Scheduling/JGFMolDyn/Particle.java b/Robust/src/Benchmarks/Scheduling/JGFMolDyn/Particle.java
new file mode 100644
index 00000000..5376afa7
--- /dev/null
+++ b/Robust/src/Benchmarks/Scheduling/JGFMolDyn/Particle.java
@@ -0,0 +1,139 @@
+public class Particle {
+
+    public float xcoord, ycoord, zcoord;
+    public float xvelocity,yvelocity,zvelocity;
+    int id;
+    //float [][] sh_force;
+    //float [][][] sh_force2;
+    MD md;
+
+    public Particle(float xcoord, float ycoord, float zcoord, float xvelocity,
+	    float yvelocity,float zvelocity,/*float [][] sh_force, 
+	    float [][][] sh_force2, int id, */MD m) {
+
+	this.xcoord = xcoord; 
+	this.ycoord = ycoord; 
+	this.zcoord = zcoord;
+	this.xvelocity = xvelocity;
+	this.yvelocity = yvelocity;
+	this.zvelocity = zvelocity;
+	//this.sh_force = sh_force;
+	//this.sh_force2 = sh_force2;
+	this.id=id;
+	this.md=m;
+    }
+
+    public void domove(float side,int part_id) {
+	xcoord = xcoord + xvelocity + this.md.sh_force[0][part_id];
+	ycoord = ycoord + yvelocity + this.md.sh_force[1][part_id];
+	zcoord = zcoord + zvelocity + this.md.sh_force[2][part_id];
+
+	if(xcoord < 0) { xcoord = xcoord + side; } 
+	if(xcoord > side) { xcoord = xcoord - side; }
+	if(ycoord < 0) { ycoord = ycoord + side; }
+	if(ycoord > side) { ycoord = ycoord - side; }
+	if(zcoord < 0) { zcoord = zcoord + side; }
+	if(zcoord > side) { zcoord = zcoord - side; }
+
+	xvelocity = xvelocity + this.md.sh_force[0][part_id];
+	yvelocity = yvelocity + this.md.sh_force[1][part_id];
+	zvelocity = zvelocity + this.md.sh_force[2][part_id];
+	//System.printI(0xc0);
+    }
+
+    public void force(float side, float rcoff,int mdsize,int x, MDRunner runner) {
+	float sideh;
+	float rcoffs;
+
+	float fxi,fyi,fzi;
+	float rd,rrd,rrd2,rrd3,rrd4,rrd6,rrd7,r148;
+	float forcex,forcey,forcez;
+	
+	float xx, yy, zz;
+
+	sideh = (float)0.5*side; 
+	rcoffs = rcoff*rcoff;
+
+	fxi = (float)0.0;
+	fyi = (float)0.0;
+	fzi = (float)0.0;
+	//System.printString("here 111: " + runner.id + "\n");
+	for (int i=x+1;i<mdsize;i++) {
+	    xx = this.xcoord - this.md.one[i].xcoord;
+	    yy = this.ycoord - this.md.one[i].ycoord;
+	    zz = this.zcoord - this.md.one[i].zcoord;
+
+	    if(xx < (-sideh)) { xx = xx + side; }
+	    if(xx > (sideh))  { xx = xx - side; }
+	    if(yy < (-sideh)) { yy = yy + side; }
+	    if(yy > (sideh))  { yy = yy - side; }
+	    if(zz < (-sideh)) { zz = zz + side; }
+	    if(zz > (sideh))  { zz = zz - side; }
+
+
+	    rd = xx*xx + yy*yy + zz*zz;
+
+	    if(rd <= rcoffs) {
+		rrd = (float)1.0/rd;
+		rrd2 = rrd*rrd;
+		rrd3 = rrd2*rrd;
+		rrd4 = rrd2*rrd2;
+		rrd6 = rrd2*rrd4;
+		rrd7 = rrd6*rrd;
+		runner.epot = runner.epot + (rrd6 - rrd3);
+		r148 = rrd7 - (float)0.5*rrd4;
+		runner.vir = runner.vir - rd*r148;
+		forcex = xx * r148;
+		fxi = fxi + forcex;
+
+		runner.sh_force2[0][i] = runner.sh_force2[0][i] - forcex;
+
+		forcey = yy * r148;
+		fyi = fyi + forcey;
+
+		runner.sh_force2[1][i] = runner.sh_force2[1][i] - forcey;
+
+		forcez = zz * r148;
+		fzi = fzi + forcez;
+
+		runner.sh_force2[2][i] = runner.sh_force2[2][i] - forcez;
+
+		//this.md.interacts[id]++;
+	    }
+
+	}
+	//System.printString("here 222: " + runner.id + "\n");
+	runner.sh_force2[0][x] = runner.sh_force2[0][x] + fxi;
+	runner.sh_force2[1][x] = runner.sh_force2[1][x] + fyi;
+	runner.sh_force2[2][x] = runner.sh_force2[2][x] + fzi;
+	//System.printString("here 333: " + runner.id + "\n");
+    }
+
+    public float mkekin(float hsq2,int part_id) {
+	float sumt = (float)0.0; 
+
+	xvelocity = xvelocity + this.md.sh_force[0][part_id]; 
+	yvelocity = yvelocity + this.md.sh_force[1][part_id]; 
+	zvelocity = zvelocity + this.md.sh_force[2][part_id]; 
+
+	sumt = (xvelocity*xvelocity)+(yvelocity*yvelocity)+(zvelocity*zvelocity);
+	return sumt;
+    }
+
+    public float velavg(float vaverh,float h) {
+	float velt;
+	float sq;
+
+	sq = Math.sqrtf(xvelocity*xvelocity + yvelocity*yvelocity + zvelocity*zvelocity);
+
+	velt = sq;
+	return velt;
+    }
+
+    public void dscal(float sc,int incx) {
+	xvelocity = xvelocity * sc;
+	yvelocity = yvelocity * sc;   
+	zvelocity = zvelocity * sc;   
+    }
+
+}
\ No newline at end of file