public void compute_line_normal(int nstart, int n)
{
int p1, p2;
double[] z = new double[3], delta = new double[3], norm = new double[3];
z[0] = 0.0; z[1] = 0.0; z[2] = 1.0;
int m = nstart;
for (int i = 0; i < n; i++)
{
p1 = lines[m].p1;
p2 = lines[m].p2;
MathExtra.sub3(pts[p2].x, pts[p1].x, delta);
MathExtra.cross3(z, delta, norm);
MathExtra.norm3(norm);
norm[2] = 0.0;
Line line = lines[m];
line.norm = new double[3];
line.norm[0] = norm[0];
line.norm[1] = norm[1];
line.norm[2] = norm[2];
lines[m] = line;
m++;
}
}
//public double axi_line_size(int);
public double tri_size(int m, out double len)
{
double[] delta12 = new double[3], delta13 = new double[3],
delta23 = new double[3], cross = new double[3];
MathExtra.sub3(pts[tris[m].p2].x, pts[tris[m].p1].x, delta12);
MathExtra.sub3(pts[tris[m].p3].x, pts[tris[m].p1].x, delta13);
MathExtra.sub3(pts[tris[m].p3].x, pts[tris[m].p2].x, delta23);
len = Math.Min(MathExtra.len3(delta12), MathExtra.len3(delta13));
len = Math.Min(len, MathExtra.len3(delta23));
MathExtra.cross3(delta12, delta13, cross);
double area = 0.5 * MathExtra.len3(cross);
return(area);
}
public void compute_tri_normal(int nstart, int n)
{
int p1, p2, p3;
double[] delta12 = new double[3], delta13 = new double[3];
int m = nstart;
for (int i = 0; i < n; i++)
{
p1 = tris[m].p1;
p2 = tris[m].p2;
p3 = tris[m].p3;
MathExtra.sub3(pts[p2].x, pts[p1].x, delta12);
MathExtra.sub3(pts[p3].x, pts[p1].x, delta13);
MathExtra.cross3(delta12, delta13, tris[m].norm);
MathExtra.norm3(tris[m].norm);
m++;
}
}
public void end(int flag, double time_multiple_runs)
{
int i;
int[] histo = new int[10];
int loopflag, statsflag, timeflag, histoflag;
double time, tmp = 0, ave = 0, max = 0, min = 0;
double time_loop = 0, time_other = 0;
int me = 0, nprocs = 0;
sparta.mpi.MPI_Comm_rank(sparta.world, ref me);
sparta.mpi.MPI_Comm_size(sparta.world, ref nprocs);
// choose flavors of statistical output
// flag = 0 = just loop summary
// flag = 1 = dynamics or minimization
loopflag = 1;
statsflag = timeflag = histoflag = 0;
if (flag == 1)
{
statsflag = timeflag = histoflag = 1;
}
// loop stats
// time_multiple_runs used for moves/CPU/proc statistic below
if (loopflag != 0)
{
time_other = sparta.timer.array[(int)EnumTime.Time_LOOP] -
(sparta.timer.array[(int)EnumTime.Time_MOVE] + sparta.timer.array[(int)EnumTime.Time_COLLIDE] +
sparta.timer.array[(int)EnumTime.Time_SORT] + sparta.timer.array[(int)EnumTime.Time_COMM] +
sparta.timer.array[(int)EnumTime.Time_MODIFY] + sparta.timer.array[(int)EnumTime.Time_OUTPUT]);
time_loop = sparta.timer.array[(int)EnumTime.Time_LOOP];
sparta.mpi.MPI_Allreduce(ref time_loop, ref tmp, 1, MPI.MPI_DOUBLE, MPI.MPI_SUM, sparta.world);
time_loop = tmp / nprocs;
if (time_multiple_runs == 0.0)
{
time_multiple_runs = time_loop;
}
else
{
tmp = time_multiple_runs;
sparta.mpi.MPI_Allreduce(ref tmp, ref time_multiple_runs, 1, MPI.MPI_DOUBLE, MPI.MPI_SUM, sparta.world);
time_multiple_runs /= nprocs;
}
}
// recalculate nglobal
Int64 n = sparta.particle.nlocal;
sparta.mpi.MPI_Allreduce(ref n, ref sparta.particle.nglobal, 1, MPI.MPI_LONG_LONG, MPI.MPI_SUM, sparta.world);
// overall loop time
if (me == 0)
{
string str = string.Format("Loop time of {0} on {1} procs for {2} steps with {3} particles\n", time_loop, nprocs, sparta.update.nsteps, sparta.particle.nglobal);
Console.WriteLine(str);
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine(str);
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine(str);
}
}
// cummulative stats over entire run
if (statsflag != 0)
{
Int64 nmove_total = 0, ntouch_total = 0, ncomm_total = 0;
Int64 nboundary_total = 0, nexit_total = 0;
Int64 nscheck_total = 0, nscollide_total = 0, nsreact_total = 0;
Int64 nattempt_total = 0;
Int64 ncollide_total = 0;
Int64 nreact_total = 0;
int stuck_total = 0;
sparta.mpi.MPI_Allreduce(ref sparta.update.nmove_running, ref nmove_total, 1,
MPI.MPI_LONG_LONG, MPI.MPI_SUM, sparta.world);
sparta.mpi.MPI_Allreduce(ref sparta.update.ntouch_running, ref ntouch_total, 1,
MPI.MPI_LONG_LONG, MPI.MPI_SUM, sparta.world);
sparta.mpi.MPI_Allreduce(ref sparta.update.ncomm_running, ref ncomm_total, 1,
MPI.MPI_LONG_LONG, MPI.MPI_SUM, sparta.world);
sparta.mpi.MPI_Allreduce(ref sparta.update.nboundary_running, ref nboundary_total, 1,
MPI.MPI_LONG_LONG, MPI.MPI_SUM, sparta.world);
sparta.mpi.MPI_Allreduce(ref sparta.update.nexit_running, ref nexit_total, 1,
MPI.MPI_LONG_LONG, MPI.MPI_SUM, sparta.world);
sparta.mpi.MPI_Allreduce(ref sparta.update.nscheck_running, ref nscheck_total, 1,
MPI.MPI_LONG_LONG, MPI.MPI_SUM, sparta.world);
sparta.mpi.MPI_Allreduce(ref sparta.update.nscollide_running, ref nscollide_total, 1,
MPI.MPI_LONG_LONG, MPI.MPI_SUM, sparta.world);
sparta.mpi.MPI_Allreduce(ref sparta.surf.nreact_running, ref nsreact_total, 1,
MPI.MPI_LONG_LONG, MPI.MPI_SUM, sparta.world);
if (sparta.collide != null)
{
sparta.mpi.MPI_Allreduce(ref sparta.collide.nattempt_running, ref nattempt_total, 1,
MPI.MPI_LONG_LONG, MPI.MPI_SUM, sparta.world);
sparta.mpi.MPI_Allreduce(ref sparta.collide.ncollide_running, ref ncollide_total, 1,
MPI.MPI_LONG_LONG, MPI.MPI_SUM, sparta.world);
sparta.mpi.MPI_Allreduce(ref sparta.collide.nreact_running, ref nreact_total, 1,
MPI.MPI_LONG_LONG, MPI.MPI_SUM, sparta.world);
}
sparta.mpi.MPI_Allreduce(ref sparta.update.nstuck, ref stuck_total, 1, MPI.MPI_INT, MPI.MPI_SUM, sparta.world);
double pms, pmsp, ctps, cis, pfc, pfcwb, pfeb, schps, sclps, srps, caps, cps, rps;
pms = pmsp = ctps = cis = pfc = pfcwb = pfeb =
schps = sclps = srps = caps = cps = rps = 0.0;
Int64 elapsed = sparta.update.ntimestep - sparta.update.first_running_step;
if (elapsed != 0)
{
pms = 1.0 * nmove_total / elapsed;
}
if (nmove_total != 0)
{
pmsp = 1.0 * nmove_total / time_multiple_runs / nprocs;
ctps = 1.0 * ntouch_total / nmove_total;
cis = 1.0 * sparta.update.niterate_running / elapsed;
pfc = 1.0 * ncomm_total / nmove_total;
pfcwb = 1.0 * nboundary_total / nmove_total;
pfeb = 1.0 * nexit_total / nmove_total;
schps = 1.0 * nscheck_total / nmove_total;
sclps = 1.0 * nscollide_total / nmove_total;
srps = 1.0 * nsreact_total / nmove_total;
caps = 1.0 * nattempt_total / nmove_total;
cps = 1.0 * ncollide_total / nmove_total;
rps = 1.0 * nreact_total / nmove_total;
}
string str;
if (me == 0)
{
str = "\n";
str += string.Format("Particle moves = {0} {1}\n",
nmove_total, MathExtra.num2str(nmove_total));
str += string.Format("Cells touched = {0} {1}\n",
ntouch_total, MathExtra.num2str(ntouch_total));
str += string.Format("Particle comms = {0} {1}\n",
ncomm_total, MathExtra.num2str(ncomm_total));
str += string.Format("Boundary collides = {0} {1}\n",
nboundary_total, MathExtra.num2str(nboundary_total));
str += string.Format("Boundary exits = {0} {1}\n",
nboundary_total, MathExtra.num2str(nexit_total));
str += string.Format("SurfColl checks = {0} {1}\n",
nscheck_total, MathExtra.num2str(nscheck_total));
str += string.Format("SurfColl occurs = {0} {1}\n",
nscollide_total, MathExtra.num2str(nscollide_total));
str += string.Format("Surf reactions = {0} {1}\n",
nsreact_total, MathExtra.num2str(nsreact_total));
str += string.Format("Collide attempts = {0} {1}\n",
nattempt_total, MathExtra.num2str(nattempt_total));
str += string.Format("Collide occurs = {0} {1}\n",
ncollide_total, MathExtra.num2str(ncollide_total));
str += string.Format("Gas reactions = {0} {1}\n",
nreact_total, MathExtra.num2str(nreact_total));
str += string.Format("Particles stuck = {0}\n", stuck_total);
str += string.Format("\n");
str += string.Format("Particle-moves/CPUsec/proc: {0}\n", pmsp);
str += string.Format("Particle-moves/step: {0}\n", pms);
str += string.Format("Cell-touches/particle/step: {0}\n", ctps);
str += string.Format("Particle comm iterations/step: {0}\n", cis);
str += string.Format("Particle fraction communicated: {0}\n", pfc);
str += string.Format("Particle fraction colliding with boundary: {0}\n", pfcwb);
str += string.Format("Particle fraction exiting boundary: {0}\n", pfeb);
str += string.Format("Surface-checks/particle/step: {0}\n", schps);
str += string.Format("Surface-collisions/particle/step: {0}\n", sclps);
str += string.Format("Surface-reactions/particle/step: {0}\n", srps);
str += string.Format("Collision-attempts/particle/step: {0}\n", caps);
str += string.Format("Collisions/particle/step: {0}\n", cps);
str += string.Format("Gas-reactions/particle/step: {0}\n", rps);
Console.WriteLine(str);
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine(str);
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine(str);
}
}
}
// timing breakdowns
if (timeflag != 0)
{
if (me == 0)
{
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine("\n");
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine("\n");
}
}
time = sparta.timer.array[(int)EnumTime.Time_MOVE];
sparta.mpi.MPI_Allreduce(ref time, ref tmp, 1, MPI.MPI_DOUBLE, MPI.MPI_SUM, sparta.world);
time = tmp / nprocs;
if (me == 0)
{
Console.WriteLine("Move time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine("Move time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine("Move time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
}
time = sparta.timer.array[(int)EnumTime.Time_COLLIDE];
sparta.mpi.MPI_Allreduce(ref time, ref tmp, 1, MPI.MPI_DOUBLE, MPI.MPI_SUM, sparta.world);
time = tmp / nprocs;
if (me == 0)
{
Console.WriteLine("Coll time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine("Coll time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine("Coll time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
}
time = sparta.timer.array[(int)EnumTime.Time_SORT];
sparta.mpi.MPI_Allreduce(ref time, ref tmp, 1, MPI.MPI_DOUBLE, MPI.MPI_SUM, sparta.world);
time = tmp / nprocs;
if (me == 0)
{
Console.WriteLine("Sort time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine("Sort time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine("Sort time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
}
time = sparta.timer.array[(int)EnumTime.Time_COMM];
sparta.mpi.MPI_Allreduce(ref time, ref tmp, 1, MPI.MPI_DOUBLE, MPI.MPI_SUM, sparta.world);
time = tmp / nprocs;
if (me == 0)
{
Console.WriteLine("Comm time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine("Comm time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine("Comm time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
}
time = sparta.timer.array[(int)EnumTime.Time_MODIFY];
sparta.mpi.MPI_Allreduce(ref time, ref tmp, 1, MPI.MPI_DOUBLE, MPI.MPI_SUM, sparta.world);
time = tmp / nprocs;
if (me == 0)
{
Console.WriteLine("Modfy time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine("Modfy time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine("Modfy time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
}
time = sparta.timer.array[(int)EnumTime.Time_OUTPUT];
sparta.mpi.MPI_Allreduce(ref time, ref tmp, 1, MPI.MPI_DOUBLE, MPI.MPI_SUM, sparta.world);
time = tmp / nprocs;
if (me == 0)
{
Console.WriteLine("Outpt time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine("Outpt time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine("Outpt time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
}
time = time_other;
sparta.mpi.MPI_Allreduce(ref time, ref tmp, 1, MPI.MPI_DOUBLE, MPI.MPI_SUM, sparta.world);
time = tmp / nprocs;
if (me == 0)
{
Console.WriteLine("Other time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine("Other time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine("Other time (%%) = {0} ({1})\n",
time, time / time_loop * 100.0);
}
}
}
// histograms
if (histoflag != 0)
{
if (me == 0)
{
Console.WriteLine("\n");
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine("\n");
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine("\n");
}
}
tmp = sparta.particle.nlocal;
stats(1, ref tmp, ref ave, ref max, ref min, 10, ref histo);
if (me == 0)
{
string str = string.Format("Particles: {0} ave {1} max {2} min\n", ave, max, min);
str += "Histogram:";
for (int a = 0; a < 10; a++)
{
str += string.Format(" {0}", histo[a]);
}
str += "\n";
Console.WriteLine(str);
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine(str);
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine(str);
}
}
tmp = sparta.grid.nlocal;
stats(1, ref tmp, ref ave, ref max, ref min, 10, ref histo);
if (me == 0)
{
string str = string.Format("Cells: {0} ave {1} max {2} min\n", ave, max, min);
str += "Histogram:";
for (int a = 0; a < 10; a++)
{
str += string.Format(" {0}", histo[a]);
}
str += "\n";
Console.WriteLine(str);
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine(str);
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine(str);
}
}
tmp = sparta.grid.nghost;
stats(1, ref tmp, ref ave, ref max, ref min, 10, ref histo);
if (me == 0)
{
string str = string.Format("GhostCell: {0} ave {1} max {2} min\n", ave, max, min);
str += "Histogram:";
for (int a = 0; a < 10; a++)
{
str += string.Format(" {0}", histo[a]);
}
str += "\n";
Console.WriteLine(str);
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine(str);
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine(str);
}
}
tmp = sparta.grid.nempty;
stats(1, ref tmp, ref ave, ref max, ref min, 10, ref histo);
if (me == 0)
{
string str = string.Format("EmptyCell: {0} ave {1} max {2} min\n", ave, max, min);
str += "Histogram:";
for (int a = 0; a < 10; a++)
{
str += string.Format(" {0}", histo[a]);
}
str += "\n";
Console.WriteLine(str);
if (sparta.screen != null)
{
new StreamWriter(sparta.screen).WriteLine(str);
}
if (sparta.logfile != null)
{
new StreamWriter(sparta.logfile).WriteLine(str);
}
}
}
if (sparta.logfile != null)
{
sparta.logfile.Flush();
}
}
//public void quad_corner_point(int, double*, double*, double*);
//public void hex_corner_point(int, double*, double*, double*);
public double line_size(int m)
{
double[] delta = new double[3];
MathExtra.sub3(pts[lines[m].p2].x, pts[lines[m].p1].x, delta);
return(MathExtra.len3(delta));
}
protected RanPark random; // RNG for particle reflection
void diffuse(Particle.OnePart p, double[] norm)
{
// specular reflection
// reflect incident v around norm
if (random.uniform() > acc)
{
MathExtra.reflect3(p.v, norm);
// diffuse reflection
// vrm = most probable speed of species, eqns (4.1) and (4.7)
// vperp = velocity component perpendicular to surface along norm, eqn (12.3)
// vtan12 = 2 velocity components tangential to surface
// tangent1 = component of particle v tangential to surface,
// check if tangent1 = 0 (normal collision), set randomly
// tangent2 = norm x tangent1 = orthogonal tangential direction
// tangent12 are both unit vectors
}
else
{
double[] tangent1 = new double[3], tangent2 = new double[3];
List <Particle.Species> species = sparta.particle.species;
int ispecies = p.ispecies;
double vrm = Math.Sqrt(2.0 * sparta.update.boltz * twall / species[ispecies].mass);
double vperp = vrm * Math.Sqrt(-Math.Log(random.uniform()));
double theta = MyConst.MY_2PI * random.uniform();
double vtangent = vrm * Math.Sqrt(-Math.Log(random.uniform()));
double vtan1 = vtangent * Math.Sin(theta);
double vtan2 = vtangent * Math.Cos(theta);
double[] v = p.v;
double dot = MathExtra.dot3(v, norm);
double beta_un, normalized_distbn_fn;
tangent1[0] = v[0] - dot * norm[0];
tangent1[1] = v[1] - dot * norm[1];
tangent1[2] = v[2] - dot * norm[2];
if (MathExtra.lensq3(tangent1) == 0.0)
{
tangent2[0] = random.uniform();
tangent2[1] = random.uniform();
tangent2[2] = random.uniform();
MathExtra.cross3(norm, tangent2, tangent1);
}
MathExtra.norm3(tangent1);
MathExtra.cross3(norm, tangent1, tangent2);
// add in translation or rotation vector if specified
// only keep portion of vector tangential to surface element
if (trflag != 0)
{
double vxdelta, vydelta, vzdelta;
if (tflag != 0)
{
vxdelta = vx; vydelta = vy; vzdelta = vz;
double adot = vxdelta * norm[0] + vydelta * norm[1] + vzdelta * norm[2];
if (Math.Abs(adot) > 0.001)
{
adot /= vrm;
do
{
do
{
beta_un = (6.0 * random.uniform() - 3.0);
} while (beta_un + adot < 0.0);
normalized_distbn_fn = 2.0 * (beta_un + adot) /
(adot + Math.Sqrt(adot * adot + 2.0)) *
Math.Exp(0.5 + (0.5 * adot) * (adot - Math.Sqrt(adot * adot + 2.0)) -
beta_un * beta_un);
} while (normalized_distbn_fn < random.uniform());
vperp = beta_un * vrm;
}
}
else
{
double[] x = p.x;
vxdelta = wy * (x[2] - pz) - wz * (x[1] - py);
vydelta = wz * (x[0] - px) - wx * (x[2] - pz);
vzdelta = wx * (x[1] - py) - wy * (x[0] - px);
double adot = vxdelta * norm[0] + vydelta * norm[1] + vzdelta * norm[2];
vxdelta -= adot * norm[0];
vydelta -= adot * norm[1];
vzdelta -= adot * norm[2];
}
v[0] = vperp * norm[0] + vtan1 * tangent1[0] + vtan2 * tangent2[0] + vxdelta;
v[1] = vperp * norm[1] + vtan1 * tangent1[1] + vtan2 * tangent2[1] + vydelta;
v[2] = vperp * norm[2] + vtan1 * tangent1[2] + vtan2 * tangent2[2] + vzdelta;
// no translation or rotation
}
else
{
v[0] = vperp * norm[0] + vtan1 * tangent1[0] + vtan2 * tangent2[0];
v[1] = vperp * norm[1] + vtan1 * tangent1[1] + vtan2 * tangent2[1];
v[2] = vperp * norm[2] + vtan1 * tangent1[2] + vtan2 * tangent2[2];
}
p.erot = sparta.particle.erot(ispecies, twall, random);
p.evib = sparta.particle.evib(ispecies, twall, random);
}
}