public int PARTSIZE;
- public double[] epot;
- public double[] vir;
- public double[] ek;
+ public DoubleWrapper[] epot;
+ public DoubleWrapper[] vir;
+ public DoubleWrapper[] ek;
int size,mm;
int[] datasizes;
public int interactions;
- public int[] interacts;
+ public IntWrapper[] interacts;
public int nthreads;
public JGFInstrumentor instr;
mid[2] = (128<<24)|(195<<16)|(175<<8)|78;
mid[3] = (128<<24)|(195<<16)|(175<<8)|73;
- atomic {
- mold.epot = global new double [mold.nthreads];
- mold.vir = global new double [mold.nthreads];
- mold.ek = global new double [mold.nthreads];
- mold.interacts = global new int [mold.nthreads];
- }
-
+ double sh_force [][];
+ double sh_force2 [][][];
int partsize, numthreads;
atomic {
partsize = mold.PARTSIZE;
mybarr = global new BarrierServer(numthreads);
}
mybarr.start(mid[0]);
-
- double sh_force [][];
- double sh_force2 [][][];
+
atomic {
sh_force = global new double[3][partsize];
sh_force2 = global new double[3][numthreads][partsize];
+ mold.epot = global new DoubleWrapper[numthreads];
+ mold.vir = global new DoubleWrapper[numthreads];
+ mold.ek = global new DoubleWrapper[numthreads];
+ mold.interacts = global new IntWrapper[numthreads];
+ for(int i=0;i<numthreads;i++) {
+ mold.epot[i]=global new DoubleWrapper();
+ mold.vir[i]=global new DoubleWrapper();
+ mold.ek[i]=global new DoubleWrapper();
+ mold.interacts[i]=global new IntWrapper();
+ }
}
-
+
// spawn threads
- mdRunner[] thobjects;
+ MDWrap[] thobjects = new MDWrap[numthreads];
+
atomic {
- thobjects = global new mdRunner[numthreads];
+ for(int i=0;i<numthreads;i++) {
+ thobjects[i] = new MDWrap(global new mdRunner(i,mold.mm,sh_force,sh_force2,mold.nthreads,mold));
+ }
}
- mdRunner tmp;
-
+
boolean waitfordone=true;
while(waitfordone) {
atomic{
- if(mybarr.done)
+ if (mybarr.done)
waitfordone=false;
}
}
-
- for(int i=1;i<numthreads;i++) {
- atomic {
- thobjects[i] = global new mdRunner(i,mold.mm,sh_force,sh_force2,mold.nthreads,mold);
- tmp = thobjects[i];
- }
- tmp.start(mid[i]);
+
+ for(int i=0;i<numthreads;i++) {
+ thobjects[i].md.start(mid[i]);
}
-
- atomic {
- thobjects[0] = global new mdRunner(0,mold.mm,sh_force,sh_force2,mold.nthreads,mold);
- tmp = thobjects[0];
+
+ for(int i=0;i<numthreads;i++) {
+ thobjects[i].md.join();
}
- tmp.start(mid[0]);
- tmp.join();
-
- for(int i=1;i<numthreads;i++) {
- atomic {
- tmp = thobjects[i];
- }
- tmp.join();
- }
- }
+ }
public void JGFvalidate(){
double[] refval = new double[2];
refval[0] = 1731.4306625334357;
refval[1] = 7397.392307839352;
- double dev = Math.fabs(ek[0] - refval[size]);
+ double dev = Math.fabs(ek[0].d - refval[size]);
if (dev > 1.0e-10 ){
//System.printString("Validation failed\n");
//System.printString("Kinetic Energy = " + (long)ek[0] + " " + (long)dev + " " + size + "\n");
class mdRunner extends Thread {
double count;
- int id,i,j,k,lg,mdsize,mm;
+ int id,i,j,k,lg,mm;
double l,rcoff,rcoffs,side,sideh,hsq,hsq2,vel,velt;
double a,r,sum,tscale,sc,ekin,ts,sp;
double den;
double h;
double vaver,vaverh,rand;
double etot,temp,pres,rp;
- double u1,u2,v1,v2,s, xx, yy, zz;
+ double u1, u2, s, xx, yy, zz;
double xvelocity, yvelocity, zvelocity;
double [][] sh_force;
int istop;
int iprint;
- random randnum;
JGFMolDynBench mymd;
int nthreads;
- particle[] one;
-
public mdRunner(int id, int mm, double [][] sh_force, double [][][] sh_force2,
int nthreads, JGFMolDynBench mymd) {
this.id=id;
}
public void run() {
-
/* Parameter determination */
-
- int tmpmdsize;
+
+ int mdsize;
double tmpden;
int movemx=50;
- Barrier barr;
- barr = new Barrier("128.195.175.79");
+ Barrier barr=new Barrier("128.195.175.79");
+ particle[] one;
atomic {
mdsize = mymd.PARTSIZE;
- one = global new particle[mdsize];
+ one=new particle[mdsize];
l = mymd.LENGTH;
- tmpmdsize = mdsize;
tmpden = den;
- side = Math.pow((tmpmdsize/tmpden),0.3333333);
+ side = Math.pow((mdsize/tmpden),0.3333333);
rcoff = mm/4.0;
a = side/mm;
sideh = side*0.5;
hsq = h*h;
hsq2 = hsq*0.5;
- npartm = tmpmdsize - 1;
+ npartm = mdsize - 1;
rcoffs = rcoff * rcoff;
- tscale = 16.0 / (1.0 * tmpmdsize - 1.0);
+ tscale = 16.0 / (1.0 * mdsize - 1.0);
vaver = 1.13 * Math.sqrt(tref / 24.0);
vaverh = vaver * h;
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);
+ one[ijk] = new particle((i*a+lg*a*0.5),(j*a+lg*a*0.5),(k*a),
+ xvelocity,yvelocity,zvelocity,sh_force,sh_force2,id,one);
ijk = ijk + 1;
}
}
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);
+ one[ijk] = 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,one);
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) {
+ double v1 = 0.0;
+ double v2 = 0.0;
+ random randnum = new random(iseed,v1,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) {
+ 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<tmpmdsize; i+=2) {
+ for (i=0; i<mdsize; i+=2) {
r = randnum.seed();
one[i].zvelocity = r*randnum.v1;
one[i+1].zvelocity = r*randnum.v2;
ekin = 0.0;
sp = 0.0;
- for(i=0;i<tmpmdsize;i++) {
+ for(i=0;i<mdsize;i++) {
sp = sp + one[i].xvelocity;
}
- sp = sp / tmpmdsize;
+ sp = sp / mdsize;
- for(i=0;i<tmpmdsize;i++) {
+ for(i=0;i<mdsize;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++) {
+ for(i=0;i<mdsize;i++) {
sp = sp + one[i].yvelocity;
}
- sp = sp / tmpmdsize;
+ sp = sp / mdsize;
- for(i=0;i<tmpmdsize;i++) {
+ 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++) {
+ for(i=0;i<mdsize;i++) {
sp = sp + one[i].zvelocity;
}
- sp = sp / tmpmdsize;
+ sp = sp / mdsize;
- for(i=0;i<tmpmdsize;i++) {
+ for(i=0;i<mdsize;i++) {
one[i].zvelocity = one[i].zvelocity - sp;
ekin = ekin + one[i].zvelocity*one[i].zvelocity;
}
sc = h * Math.sqrt(tref/ts);
- for(i=0;i<tmpmdsize;i++) {
+ for(i=0;i<mdsize;i++) {
one[i].xvelocity = one[i].xvelocity * sc;
one[i].yvelocity = one[i].yvelocity * sc;
for (int move=0;move<movemx;move++) {
atomic {
/* move the particles and update velocities */
-
- for (i=0;i<tmpmdsize;i++) {
+ for (i=0;i<mdsize;i++) {
one[i].domove(side,i);
}
}
Barrier.enterBarrier(barr);
atomic {
-
if(id==0) {
for(j=0;j<3;j++) {
- for (i=0;i<tmpmdsize;i++) {
+ for (i=0;i<mdsize;i++) {
sh_force[j][i] = 0.0;
}
}
}
-
- mymd.epot[id] = 0.0;
- mymd.vir[id] = 0.0;
- mymd.interacts[id] = 0;
+
+ mymd.epot[id].d = 0.0;
+ mymd.vir[id].d = 0.0;
+ mymd.interacts[id].i = 0;
}
/* Barrier */
Barrier.enterBarrier(barr);
-
+
atomic {
/* compute forces */
-
- for (i=0+id;i<tmpmdsize;i+=nthreads) {
- one[i].force(side,rcoff,tmpmdsize,i,xx,yy,zz,mymd);
+
+ for (i=0+id;i<mdsize;i+=nthreads) {
+ one[i].force(side,rcoff,mdsize,i,xx,yy,zz,mymd);
}
-
}
+
/* Barrier */
Barrier.enterBarrier(barr);
/* update force arrays */
atomic {
-
if(id == 0) {
for(int k=0;k<3;k++) {
- for(i=0;i<tmpmdsize;i++) {
+ 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(i=0;i<mdsize;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];
+ mymd.epot[0].d += mymd.epot[j].d;
+ mymd.vir[0].d += mymd.vir[j].d;
}
for(j=1;j<nthreads;j++) {
- mymd.epot[j] = mymd.epot[0];
- mymd.vir[j] = mymd.vir[0];
+ mymd.epot[j].d = mymd.epot[0].d;
+ mymd.vir[j].d = mymd.vir[0].d;
}
for(j=0;j<nthreads;j++) {
- mymd.interactions += mymd.interacts[j];
- }
- }
- }
-
- /* Barrier */
- Barrier.enterBarrier(barr);
-
- 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;
- }
+ mymd.interactions += mymd.interacts[j].i;
}
- }
- sum = 0.0;
+ for (j=0;j<3;j++) {
+ for (i=0;i<mdsize;i++) {
+ sh_force[j][i] = sh_force[j][i] * hsq2;
+ }
+ }
+ }
}
-
/* Barrier */
Barrier.enterBarrier(barr);
atomic {
/*scale forces, update velocities */
-
- for (i=0;i<tmpmdsize;i++) {
+ sum = 0.0;
+ for (i=0;i<mdsize;i++) {
sum = sum + one[i].mkekin(hsq2,i);
}
/* average velocity */
- for (i=0;i<tmpmdsize;i++) {
+ for (i=0;i<mdsize;i++) {
velt = one[i].velavg(vaverh,h);
if(velt > vaverh) { count = count + 1.0; }
vel = vel + velt;
if((move < istop) && (((move+1) % irep) == 0)) {
sc = Math.sqrt(tref / (tscale*ekin));
- for (i=0;i<tmpmdsize;i++) {
+ for (i=0;i<mdsize;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];
+ mymd.ek[id].d = 24.0*ekin;
+ mymd.epot[id].d = 4.0*mymd.epot[id].d;
+ etot = mymd.ek[id].d + mymd.epot[id].d;
temp = tscale * ekin;
- pres = tmpden * 16.0 * (ekin - mymd.vir[id]) / tmpmdsize;
- vel = vel / tmpmdsize;
- rp = (count / tmpmdsize) * 100.0;
+ pres = tmpden * 16.0 * (ekin - mymd.vir[id].d) / mdsize;
+ vel = vel / mdsize;
+ rp = (count / mdsize) * 100.0;
}
}
Barrier.enterBarrier(barr);
public double xvelocity,yvelocity,zvelocity;
int part_id;
int id;
- double [][] sh_force;
- double [][][] sh_force2;
- mdRunner runner;
-
+ global double [][] sh_force;
+ global double [][][] sh_force2;
+ particle[] one;
+
public particle(double xcoord, double ycoord, double zcoord, double xvelocity,
- double yvelocity,double zvelocity,double [][] sh_force,
- double [][][] sh_force2,int id,mdRunner runner) {
+ double yvelocity,double zvelocity, double [][] sh_force,
+ double [][][] sh_force2,int id, particle[] one) {
this.xcoord = xcoord;
this.ycoord = ycoord;
this.sh_force = sh_force;
this.sh_force2 = sh_force2;
this.id=id;
- this.runner=runner;
+ this.one=one;
}
public void domove(double side,int part_id) {
fzi = 0.0;
for (int i=x+1;i<mdsize;i++) {
- xx = this.xcoord - runner.one[i].xcoord;
- yy = this.ycoord - runner.one[i].ycoord;
- zz = this.zcoord - runner.one[i].zcoord;
+ xx = this.xcoord - one[i].xcoord;
+ yy = this.ycoord - one[i].ycoord;
+ zz = this.zcoord - one[i].zcoord;
if(xx < (-sideh)) { xx = xx + side; }
if(xx > (sideh)) { xx = xx - side; }
rrd4 = rrd2*rrd2;
rrd6 = rrd2*rrd4;
rrd7 = rrd6*rrd;
- mymd.epot[id] = mymd.epot[id] + (rrd6 - rrd3);
+ mymd.epot[id].d += (rrd6 - rrd3);
r148 = rrd7 - 0.5*rrd4;
- mymd.vir[id] = mymd.vir[id] - rd*r148;
+ mymd.vir[id].d += - rd*r148;
forcex = xx * r148;
fxi = fxi + forcex;
sh_force2[2][id][i] = sh_force2[2][id][i] - forcez;
- mymd.interacts[id]++;
+ mymd.interacts[id].i++;
}
}
}
public void dscal(double sc,int incx) {
-
xvelocity = xvelocity * sc;
yvelocity = yvelocity * sc;
zvelocity = zvelocity * sc;
-
-
-
}
-
}
class random {
projects / IRC.git / commitdiff