public int PARTSIZE;
- public global double[] epot;
- public global double[] vir;
- public global double[] ek;
+ public double[] epot;
+ public double[] vir;
+ public double[] ek;
int size,mm;
int[] datasizes;
public int interactions;
public int[] interacts;
- public global int nthreads;
- public global JGFInstrumentor instr;
+ public int nthreads;
+ public JGFInstrumentor instr;
- public JGFMolDynBench(int nthreads, JGFInstrumentor instr) {
+ public JGFMolDynBench(int nthreads) {
this.nthreads=nthreads;
- this.instr = instr;
}
public void JGFsetsize(int size){
public void JGFinitialise(){
interactions = 0;
- datasizes = new int[2];
+ datasizes = global new int[2];
datasizes[0] = 8;
datasizes[1] = 13;
kb = 1.38066e-23;
TSIM = 50;
deltat = 5e-16;
-
- //initialise();
}
public static void JGFapplication(JGFMolDynBench mold) {
numthreads = mold.nthreads;
}
- double sh_force [][] = new double[3][partsize];
- double sh_force2 [][][] = new double[3][numthreads][partsize];
+ double sh_force [][];
+ double sh_force2 [][][];
+ atomic {
+ sh_force = global new double[3][partsize];
+ sh_force2 = global new double[3][numthreads][partsize];
+ }
// spawn threads
- //Thread thobjects[] = new Thread [nthreads];
mdRunner[] thobjects;
TournamentBarrier br;
atomic {
for(int i=1;i<numthreads;i++) {
atomic {
- thobjects[i] = global new mdRunner(i,mold.mm,sh_force,sh_force2,br,mold.instr,mold.nthreads,mold);
+ thobjects[i] = global new mdRunner(i,mold.mm,sh_force,sh_force2,br,mold.nthreads,mold);
tmp = thobjects[i];
}
tmp.start(mid);
}
atomic {
- thobjects[0] = global new mdRunner(0,mold.mm,sh_force,sh_force2,br,mold.instr,mold.nthreads,mold);
- thobjects[0].run();
+ thobjects[0] = global new mdRunner(0,mold.mm,sh_force,sh_force2,br,mold.nthreads,mold);
+ tmp = thobjects[0];
}
+ tmp.start(mid);
+ tmp.join();
for(int i=1;i<numthreads;i++) {
atomic {
refval[1] = 7397.392307839352;
double dev = Math.fabs(ek[0] - refval[size]);
if (dev > 1.0e-10 ){
- //System.printString("Validation failed");
- //System.printString("Kinetic Energy = " + (long)ek[0] + " " + (long)dev + " " + size);
+ //System.printString("Validation failed\n");
+ //System.printString("Kinetic Energy = " + (long)ek[0] + " " + (long)dev + " " + size + "\n");
}
}
}
TournamentBarrier br;
random randnum;
- JGFInstrumentor instr;
JGFMolDynBench mymd;
int nthreads;
particle[] one;
public mdRunner(int id, int mm, double [][] sh_force, double [][][] sh_force2,TournamentBarrier br,
- JGFInstrumentor instr, int nthreads, JGFMolDynBench mymd) {
+ int nthreads, JGFMolDynBench mymd) {
this.id=id;
this.mm=mm;
this.sh_force=sh_force;
this.sh_force2=sh_force2;
this.br=br;
- this.instr = instr;
this.nthreads = nthreads;
this.mymd = mymd;
count = 0.0;
atomic {
mdsize = mymd.PARTSIZE;
- }
- one = global new particle [mdsize];
- atomic {
+ one = global new particle[mdsize];
l = mymd.LENGTH;
}
- side = Math.pow((mdsize/den),0.3333333);
- rcoff = mm/4.0;
-
- a = side/mm;
- sideh = side*0.5;
- hsq = h*h;
- hsq2 = hsq*0.5;
- npartm = mdsize - 1;
- rcoffs = rcoff * rcoff;
- tscale = 16.0 / (1.0 * mdsize - 1.0);
- vaver = 1.13 * Math.sqrt(tref / 24.0);
- vaverh = vaver * h;
-
- /* Particle Generation */
-
- xvelocity = 0.0;
- yvelocity = 0.0;
- zvelocity = 0.0;
-
- ijk = 0;
+ int tmpmdsize;
+ double tmpden;
+ atomic {
+ tmpmdsize = mdsize;
+ tmpden = den;
+ }
+
+ atomic {
+ side = Math.pow((tmpmdsize/tmpden),0.3333333);
+ rcoff = mm/4.0;
+
+ a = side/mm;
+ sideh = side*0.5;
+ hsq = h*h;
+ hsq2 = hsq*0.5;
+ npartm = tmpmdsize - 1;
+ rcoffs = rcoff * rcoff;
+ tscale = 16.0 / (1.0 * tmpmdsize - 1.0);
+ vaver = 1.13 * Math.sqrt(tref / 24.0);
+ vaverh = vaver * h;
+
+ /* Particle Generation */
+
+ xvelocity = 0.0;
+ yvelocity = 0.0;
+ zvelocity = 0.0;
+ ijk = 0;
+ }
atomic {
for (lg=0; lg<=1; lg++) {
for (i=0; i<mm; i++) {
}
}
}
+
atomic {
for (lg=1; lg<=2; lg++) {
for (i=0; i<mm; i++) {
/* Initialise velocities */
- iseed = 0;
- v1 = 0.0;
- v2 = 0.0;
+ atomic {
+ iseed = 0;
+ v1 = 0.0;
+ v2 = 0.0;
+ randnum = global new random(iseed,v1,v2);
+
+ for (i=0; i<tmpmdsize; i+=2) {
+ r = randnum.seed();
+ one[i].xvelocity = r*randnum.v1;
+ one[i+1].xvelocity = r*randnum.v2;
+ }
- randnum = global new random(iseed,v1,v2);
+ for (i=0; i<tmpmdsize; i+=2) {
+ r = randnum.seed();
+ one[i].yvelocity = r*randnum.v1;
+ one[i+1].yvelocity = r*randnum.v2;
+ }
- for (i=0; i<mdsize; i+=2) {
- r = randnum.seed();
- one[i].xvelocity = r*randnum.v1;
- one[i+1].xvelocity = r*randnum.v2;
- }
+ for (i=0; i<tmpmdsize; i+=2) {
+ r = randnum.seed();
+ one[i].zvelocity = r*randnum.v1;
+ one[i+1].zvelocity = r*randnum.v2;
+ }
- for (i=0; i<mdsize; i+=2) {
- r = randnum.seed();
- one[i].yvelocity = r*randnum.v1;
- one[i+1].yvelocity = r*randnum.v2;
- }
- for (i=0; i<mdsize; i+=2) {
- r = randnum.seed();
- one[i].zvelocity = r*randnum.v1;
- one[i+1].zvelocity = r*randnum.v2;
- }
+ /* velocity scaling */
+ ekin = 0.0;
+ sp = 0.0;
- /* velocity scaling */
+ for(i=0;i<tmpmdsize;i++) {
+ sp = sp + one[i].xvelocity;
+ }
+ sp = sp / tmpmdsize;
- ekin = 0.0;
- sp = 0.0;
+ for(i=0;i<tmpmdsize;i++) {
+ one[i].xvelocity = one[i].xvelocity - sp;
+ ekin = ekin + one[i].xvelocity*one[i].xvelocity;
+ }
- for(i=0;i<mdsize;i++) {
- sp = sp + one[i].xvelocity;
- }
- sp = sp / mdsize;
+ sp = 0.0;
+ for(i=0;i<tmpmdsize;i++) {
+ sp = sp + one[i].yvelocity;
+ }
+ sp = sp / tmpmdsize;
- for(i=0;i<mdsize;i++) {
- one[i].xvelocity = one[i].xvelocity - sp;
- ekin = ekin + one[i].xvelocity*one[i].xvelocity;
- }
+ for(i=0;i<tmpmdsize;i++) {
+ one[i].yvelocity = one[i].yvelocity - sp;
+ ekin = ekin + one[i].yvelocity*one[i].yvelocity;
+ }
- sp = 0.0;
- for(i=0;i<mdsize;i++) {
- sp = sp + one[i].yvelocity;
- }
- sp = sp / mdsize;
- for(i=0;i<mdsize;i++) {
- one[i].yvelocity = one[i].yvelocity - sp;
- ekin = ekin + one[i].yvelocity*one[i].yvelocity;
- }
+ sp = 0.0;
+ for(i=0;i<tmpmdsize;i++) {
+ sp = sp + one[i].zvelocity;
+ }
+ sp = sp / tmpmdsize;
+ for(i=0;i<tmpmdsize;i++) {
+ one[i].zvelocity = one[i].zvelocity - sp;
+ ekin = ekin + one[i].zvelocity*one[i].zvelocity;
+ }
- sp = 0.0;
- for(i=0;i<mdsize;i++) {
- sp = sp + one[i].zvelocity;
- }
- sp = sp / mdsize;
+ ts = tscale * ekin;
+ sc = h * Math.sqrt(tref/ts);
- for(i=0;i<mdsize;i++) {
- one[i].zvelocity = one[i].zvelocity - sp;
- ekin = ekin + one[i].zvelocity*one[i].zvelocity;
- }
- ts = tscale * ekin;
- sc = h * Math.sqrt(tref/ts);
+ for(i=0;i<tmpmdsize;i++) {
+ one[i].xvelocity = one[i].xvelocity * sc;
+ one[i].yvelocity = one[i].yvelocity * sc;
+ one[i].zvelocity = one[i].zvelocity * sc;
- for(i=0;i<mdsize;i++) {
+ }
- one[i].xvelocity = one[i].xvelocity * sc;
- one[i].yvelocity = one[i].yvelocity * sc;
- one[i].zvelocity = one[i].zvelocity * sc;
- }
+ /* Synchronise threads and start timer before MD simulation */
+ br.DoBarrier(id);
+ //if (id == 0) JGFInstrumentor.startTimer("Section3:MolDyn:Run", instr.timers);
+ br.DoBarrier(id);
- /* Synchronise threads and start timer before MD simulation */
+ /* MD simulation */
- atomic {
- br.DoBarrier(id);
- }
- if (id == 0) JGFInstrumentor.startTimer("Section3:MolDyn:Run", instr.timers);
- atomic {
- br.DoBarrier(id);
- }
-
-
- /* MD simulation */
+ move = 0;
+ for (move=0;move<movemx;move++) {
- move = 0;
- for (move=0;move<movemx;move++) {
+ /* move the particles and update velocities */
- /* move the particles and update velocities */
-
- for (i=0;i<mdsize;i++) {
- one[i].domove(side,i);
- }
+ for (i=0;i<tmpmdsize;i++) {
+ one[i].domove(side,i);
+ }
- /* Barrier */
- br.DoBarrier(id);
+ /* Barrier */
+ br.DoBarrier(id);
- if(id==0) {
- for(j=0;j<3;j++) {
- for (i=0;i<mdsize;i++) {
- sh_force[j][i] = 0.0;
+ if(id==0) {
+ for(j=0;j<3;j++) {
+ for (i=0;i<tmpmdsize;i++) {
+ sh_force[j][i] = 0.0;
+ }
}
}
- }
-
- mymd.epot[id] = 0.0;
- mymd.vir[id] = 0.0;
- mymd.interacts[id] = 0;
-
- /* Barrier */
- br.DoBarrier(id);
+ mymd.epot[id] = 0.0;
+ mymd.vir[id] = 0.0;
+ mymd.interacts[id] = 0;
+ /* Barrier */
+ br.DoBarrier(id);
- /* compute forces */
+ /* compute forces */
- for (i=0+id;i<mdsize;i+=nthreads) {
- one[i].force(side,rcoff,mdsize,i,xx,yy,zz,mymd);
- }
+ for (i=0+id;i<tmpmdsize;i+=nthreads) {
+ one[i].force(side,rcoff,tmpmdsize,i,xx,yy,zz,mymd);
+ }
- /* Barrier */
- br.DoBarrier(id);
+ /* Barrier */
+ br.DoBarrier(id);
- /* update force arrays */
+ /* update force arrays */
- if(id == 0) {
- for(int k=0;k<3;k++) {
- for(i=0;i<mdsize;i++) {
- for(j=0;j<nthreads;j++) {
- sh_force[k][i] += sh_force2[k][j][i];
+ if(id == 0) {
+ for(int k=0;k<3;k++) {
+ for(i=0;i<tmpmdsize;i++) {
+ for(j=0;j<nthreads;j++) {
+ sh_force[k][i] += sh_force2[k][j][i];
+ }
}
}
}
- }
- if(id == 0) {
- for(int k=0;k<3;k++) {
- for(i=0;i<mdsize;i++) {
- for(j=0;j<nthreads;j++) {
- sh_force2[k][j][i] = 0.0;
+ if(id == 0) {
+ for(int k=0;k<3;k++) {
+ for(i=0;i<tmpmdsize;i++) {
+ for(j=0;j<nthreads;j++) {
+ sh_force2[k][j][i] = 0.0;
+ }
}
}
}
- }
- if(id==0) {
- for(j=1;j<nthreads;j++) {
- mymd.epot[0] += mymd.epot[j];
- mymd.vir[0] += mymd.vir[j];
- }
- for(j=1;j<nthreads;j++) {
- mymd.epot[j] = mymd.epot[0];
- mymd.vir[j] = mymd.vir[0];
- }
- for(j=0;j<nthreads;j++) {
- mymd.interactions += mymd.interacts[j];
+ if(id==0) {
+ for(j=1;j<nthreads;j++) {
+ mymd.epot[0] += mymd.epot[j];
+ mymd.vir[0] += mymd.vir[j];
+ }
+ for(j=1;j<nthreads;j++) {
+ mymd.epot[j] = mymd.epot[0];
+ mymd.vir[j] = mymd.vir[0];
+ }
+ for(j=0;j<nthreads;j++) {
+ mymd.interactions += mymd.interacts[j];
+ }
}
- }
- /* Barrier */
- br.DoBarrier(id);
+ /* Barrier */
+ br.DoBarrier(id);
- if(id == 0) {
- for (j=0;j<3;j++) {
- for (i=0;i<mdsize;i++) {
- sh_force[j][i] = sh_force[j][i] * hsq2;
+ if(id == 0) {
+ for (j=0;j<3;j++) {
+ for (i=0;i<tmpmdsize;i++) {
+ sh_force[j][i] = sh_force[j][i] * hsq2;
+ }
}
}
- }
- sum = 0.0;
+ sum = 0.0;
- /* Barrier */
- br.DoBarrier(id);
+ /* Barrier */
+ br.DoBarrier(id);
- /*scale forces, update velocities */
+ /*scale forces, update velocities */
- for (i=0;i<mdsize;i++) {
- sum = sum + one[i].mkekin(hsq2,i);
- }
+ for (i=0;i<tmpmdsize;i++) {
+ sum = sum + one[i].mkekin(hsq2,i);
+ }
- ekin = sum/hsq;
+ ekin = sum/hsq;
- vel = 0.0;
- count = 0.0;
+ vel = 0.0;
+ count = 0.0;
- /* average velocity */
+ /* average velocity */
- for (i=0;i<mdsize;i++) {
- velt = one[i].velavg(vaverh,h);
- if(velt > vaverh) { count = count + 1.0; }
- vel = vel + velt;
- }
+ for (i=0;i<tmpmdsize;i++) {
+ velt = one[i].velavg(vaverh,h);
+ if(velt > vaverh) { count = count + 1.0; }
+ vel = vel + velt;
+ }
- vel = vel / h;
+ vel = vel / h;
- /* temperature scale if required */
+ /* temperature scale if required */
- if((move < istop) && (((move+1) % irep) == 0)) {
- sc = Math.sqrt(tref / (tscale*ekin));
- for (i=0;i<mdsize;i++) {
- one[i].dscal(sc,1);
+ if((move < istop) && (((move+1) % irep) == 0)) {
+ sc = Math.sqrt(tref / (tscale*ekin));
+ for (i=0;i<tmpmdsize;i++) {
+ one[i].dscal(sc,1);
+ }
+ ekin = tref / tscale;
}
- ekin = tref / tscale;
- }
- /* sum to get full potential energy and virial */
+ /* sum to get full potential energy and virial */
+
+ if(((move+1) % iprint) == 0) {
+ mymd.ek[id] = 24.0*ekin;
+ mymd.epot[id] = 4.0*mymd.epot[id];
+ etot = mymd.ek[id] + mymd.epot[id];
+ temp = tscale * ekin;
+ pres = tmpden * 16.0 * (ekin - mymd.vir[id]) / tmpmdsize;
+ vel = vel / tmpmdsize;
+ rp = (count / tmpmdsize) * 100.0;
+ }
- if(((move+1) % iprint) == 0) {
- mymd.ek[id] = 24.0*ekin;
- mymd.epot[id] = 4.0*mymd.epot[id];
- etot = mymd.ek[id] + mymd.epot[id];
- temp = tscale * ekin;
- pres = den * 16.0 * (ekin - mymd.vir[id]) / mdsize;
- vel = vel / mdsize;
- rp = (count / mdsize) * 100.0;
+ br.DoBarrier(id);
}
- br.DoBarrier(id);
- }
+ br.DoBarrier(id);
+ //if (id == 0) JGFInstrumentor.stopTimer("Section3:MolDyn:Run", instr.timers);
- br.DoBarrier(id);
- if (id == 0) JGFInstrumentor.stopTimer("Section3:MolDyn:Run", instr.timers);
+ }
}