// spawn threads
mdRunner[] thobjects;
- TournamentBarrier br;
+ Barrier br;
atomic {
thobjects = global new mdRunner[numthreads];
- br= global new TournamentBarrier(numthreads);
+ br= global new Barrier(numthreads);
}
int mid = (128<<24)|(195<<16)|(175<<8)|73;
class mdRunner extends Thread {
double count;
- int id,i,j,k,lg,mdsize,move,mm;
+ int id,i,j,k,lg,mdsize,mm;
double l,rcoff,rcoffs,side,sideh,hsq,hsq2,vel,velt;
double a,r,sum,tscale,sc,ekin,ts,sp;
double den;
int irep;
int istop;
int iprint;
- int movemx;
- TournamentBarrier br;
+ Barrier br;
random randnum;
JGFMolDynBench mymd;
int nthreads;
particle[] one;
- public mdRunner(int id, int mm, double [][] sh_force, double [][][] sh_force2,TournamentBarrier br,
- int nthreads, JGFMolDynBench mymd) {
+ public mdRunner(int id, int mm, double [][] sh_force, double [][][] sh_force2,Barrier br,
+ int nthreads, JGFMolDynBench mymd) {
this.id=id;
this.mm=mm;
this.sh_force=sh_force;
irep = 10;
istop = 19;
iprint = 10;
- movemx = 50;
}
public void run() {
- /* Parameter determination */
-
- atomic {
- mdsize = mymd.PARTSIZE;
- one = global new particle[mdsize];
- l = mymd.LENGTH;
- }
-
- 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++) {
- for (j=0; j<mm; j++) {
- for (k=0; k<mm; k++) {
- one[ijk] = global new particle((i*a+lg*a*0.5),(j*a+lg*a*0.5),(k*a),
- xvelocity,yvelocity,zvelocity,sh_force,sh_force2,id,this);
- ijk = ijk + 1;
- }
- }
- }
- }
- }
-
- atomic {
- 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] = global new particle((i*a+(2-lg)*a*0.5),(j*a+(lg-1)*a*0.5),
- (k*a+a*0.5),xvelocity,yvelocity,zvelocity,sh_force,sh_force2,id,this);
- ijk = ijk + 1;
- }
- }
- }
- }
- }
-
-
- /* Initialise velocities */
-
- 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;
- }
-
- 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<tmpmdsize; 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;
-
- for(i=0;i<tmpmdsize;i++) {
- sp = sp + one[i].xvelocity;
- }
- sp = sp / tmpmdsize;
-
- for(i=0;i<tmpmdsize;i++) {
- one[i].xvelocity = one[i].xvelocity - sp;
- ekin = ekin + one[i].xvelocity*one[i].xvelocity;
- }
-
- sp = 0.0;
- for(i=0;i<tmpmdsize;i++) {
- sp = sp + one[i].yvelocity;
- }
- sp = sp / tmpmdsize;
-
- 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<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;
- }
-
- 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;
-
+ /* Parameter determination */
+
+ int tmpmdsize;
+ double tmpden;
+ int movemx=50;
+ Barrier tmpbr;
+
+ atomic {
+ tmpbr=br;
+ mdsize = mymd.PARTSIZE;
+ one = global new particle[mdsize];
+ l = mymd.LENGTH;
+ tmpmdsize = mdsize;
+ tmpden = den;
+ 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;
+
+ 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] = global new particle((i*a+lg*a*0.5),(j*a+lg*a*0.5),(k*a),
+ xvelocity,yvelocity,zvelocity,sh_force,sh_force2,id,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] = global new particle((i*a+(2-lg)*a*0.5),(j*a+(lg-1)*a*0.5),
+ (k*a+a*0.5),xvelocity,yvelocity,zvelocity,sh_force,sh_force2,id,this);
+ ijk = ijk + 1;
+ }
+ }
+ }
+ }
+
+ /* Initialise velocities */
+
+ 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;
+ }
+
+ 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<tmpmdsize; 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;
+
+ for(i=0;i<tmpmdsize;i++) {
+ sp = sp + one[i].xvelocity;
+ }
+ sp = sp / tmpmdsize;
+
+ for(i=0;i<tmpmdsize;i++) {
+ one[i].xvelocity = one[i].xvelocity - sp;
+ ekin = ekin + one[i].xvelocity*one[i].xvelocity;
+ }
+
+ sp = 0.0;
+ for(i=0;i<tmpmdsize;i++) {
+ sp = sp + one[i].yvelocity;
+ }
+ sp = sp / tmpmdsize;
+
+ 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<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;
+ }
+
+ 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;
+
+ }
}
-
/* Synchronise threads and start timer before MD simulation */
-
- br.DoBarrier(id);
+
+ Barrier.enterBarrier(tmpbr);
//if (id == 0) JGFInstrumentor.startTimer("Section3:MolDyn:Run", instr.timers);
- br.DoBarrier(id);
-
+ //Barrier.enterBarrier(tmpbr);
+
/* MD simulation */
-
- move = 0;
- for (move=0;move<movemx;move++) {
-
- /* move the particles and update velocities */
-
- for (i=0;i<tmpmdsize;i++) {
- one[i].domove(side,i);
- }
-
- /* Barrier */
- br.DoBarrier(id);
-
- 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);
-
- /* compute forces */
-
- for (i=0+id;i<tmpmdsize;i+=nthreads) {
- one[i].force(side,rcoff,tmpmdsize,i,xx,yy,zz,mymd);
- }
-
- /* Barrier */
- br.DoBarrier(id);
-
- /* update force arrays */
-
- 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<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];
- }
- }
-
- /* Barrier */
- br.DoBarrier(id);
-
- 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;
-
- /* Barrier */
- br.DoBarrier(id);
-
- /*scale forces, update velocities */
-
- for (i=0;i<tmpmdsize;i++) {
- sum = sum + one[i].mkekin(hsq2,i);
- }
-
- ekin = sum/hsq;
-
- vel = 0.0;
- count = 0.0;
-
- /* average velocity */
-
- 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;
-
- /* temperature scale if required */
-
- 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;
- }
-
- /* 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;
- }
-
- br.DoBarrier(id);
+
+ for (int move=0;move<movemx;move++) {
+ atomic {
+
+
+ /* move the particles and update velocities */
+
+ for (i=0;i<tmpmdsize;i++) {
+ one[i].domove(side,i);
+ }
+ }
+
+ /* Barrier */
+ Barrier.enterBarrier(tmpbr);
+ atomic {
+
+ 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 */
+ Barrier.enterBarrier(tmpbr);
+
+ atomic {
+ /* compute forces */
+
+ for (i=0+id;i<tmpmdsize;i+=nthreads) {
+ one[i].force(side,rcoff,tmpmdsize,i,xx,yy,zz,mymd);
+ }
+
+ }
+ /* Barrier */
+ Barrier.enterBarrier(tmpbr);
+
+ /* update force arrays */
+ atomic {
+
+ 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<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];
+ }
+ }
+ }
+
+ /* Barrier */
+ Barrier.enterBarrier(tmpbr);
+
+ atomic {
+ 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;
+ }
+
+
+ /* Barrier */
+ Barrier.enterBarrier(tmpbr);
+
+ atomic {
+ /*scale forces, update velocities */
+
+ for (i=0;i<tmpmdsize;i++) {
+ sum = sum + one[i].mkekin(hsq2,i);
+ }
+
+ ekin = sum/hsq;
+
+ vel = 0.0;
+ count = 0.0;
+
+ /* average velocity */
+
+ 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;
+
+ /* temperature scale if required */
+
+ 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;
+ }
+
+ /* 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;
+ }
+ }
+ Barrier.enterBarrier(tmpbr);
}
-
- br.DoBarrier(id);
+ Barrier.enterBarrier(tmpbr);
//if (id == 0) JGFInstrumentor.stopTimer("Section3:MolDyn:Run", instr.timers);
-
- }
-
}
}
projects / IRC.git / commitdiff