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CPP KD Tree Review Fixes #100

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Merged
seanebum merged 16 commits into from
Mar 29, 2021
Merged

CPP KD Tree Review Fixes #100

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7f91251
Merge branch 'cpp-fluid-dynamics-fix' of https://github.com/StochSS/S…
seanebum Mar 8, 2021
e4cebc7
updated some pointer / loop architecture
seanebum Mar 10, 2021
649a028
Fixed several small errors
makdl Mar 19, 2021
4e8d165
still trying to compile, moved some things around including template …
seanebum Mar 22, 2021
b9130e2
Use reference instead of pointer
makdl Mar 22, 2021
624de39
undo bogus attempt to move template function definition to cpp
seanebum Mar 22, 2021
64a4c56
undoing unhelpful changes
seanebum Mar 22, 2021
ad152a9
resolved merge conflicts
seanebum Mar 23, 2021
e60b466
Resolve merge conflicts
makdl Mar 23, 2021
717255f
Merge conflict
makdl Mar 23, 2021
d19eaf0
Merge remote-tracking branch 'origin/cpp-rdme-nrm-stuff' into cpp-kd-…
makdl Mar 23, 2021
9860246
welp... it compiles now!
seanebum Mar 23, 2021
1c21abd
resolve conflicts
seanebum Mar 23, 2021
9a4df3a
Fixed bug diffusing species below 0; Changed diffusion event zero che…
makdl Mar 23, 2021
cc0f467
CylinderDemo3D works in C++
makdl Mar 23, 2021
cb1cbd8
More accurate filenames, cleanup formatting, whitespace, imports
makdl Mar 28, 2021
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2 changes: 1 addition & 1 deletion spatialpy/ssa_sdpd-c-simulation-engine/build/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ SIMFLAGS = -l. -std=c++14 -Wall -O3
LFLAGS = -pthread -lm
INCDIR = $(ROOTINC)/include/ $(ROOTINC)/external/ $(ROOTINC)/external/ANN/include/
INCDIRPARAMS = $(INCDIR:%=-I%)
OBJ = particle.o simulate.o count_cores.o output.o simulate_rdme.o simulate_threads.o model.o pthread_barrier.o
OBJ = particle.o NRMConstant_v5.o simulate.o count_cores.o output.o simulate_rdme.o simulate_threads.o model.o pthread_barrier.o
ANNOBJECTS = ANN.o brute.o kd_tree.o kd_util.o kd_split.o \
kd_dump.o kd_search.o kd_pr_search.o kd_fix_rad_search.o \
bd_tree.o bd_search.o bd_pr_search.o bd_fix_rad_search.o \
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4 changes: 2 additions & 2 deletions spatialpy/ssa_sdpd-c-simulation-engine/src/particle.cpp
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Expand Up @@ -53,7 +53,7 @@ namespace Spatialpy{
}

NeighborNode::NeighborNode(Particle *data, double dist, double dWdr, double D_i_j):data(data), dist(dist), dWdr(dWdr), D_i_j(D_i_j){}
EventNode::EventNode(Particle *data, double tt):data(data), tt(tt){}
// EventNode::EventNode(Particle *data, double tt):data(data), tt(tt){}

void Particle::check_particle_nan(){
if(
Expand Down Expand Up @@ -123,7 +123,7 @@ namespace Spatialpy{
// double c = x[2] - neighbor.x[2];
// double r2 = ( a*a + b*b + c*c);
// Make sure the distance was actually set by the annkFRSearch
double r2_old = r2;
//double r2_old = r2;
if(r2 == ANN_DIST_INF) {
r2 = particle_dist_sqrd(neighbor) ;
}
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21 changes: 11 additions & 10 deletions spatialpy/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp
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Expand Up @@ -70,8 +70,8 @@ namespace Spatialpy{
}
/**************************************************************************/
void destroy_rdme(ParticleSystem*system){
if(debug_flag) printf("NSM: total # reacton events %lu\n",system->rdme->total_reactions);
if(debug_flag) printf("NSM: total # diffusion events %lu\n",system->rdme->total_diffusion);
if(debug_flag) printf("NSM: total # reacton events %lu\n",system->total_reactions);
if(debug_flag) printf("NSM: total # diffusion events %lu\n",system->total_diffusion);
}


Expand All @@ -92,7 +92,7 @@ namespace Spatialpy{
p2 = nn.data;
printf("%i: nn->D_i_j=%e \n",p2->id,nn.D_i_j);
}

}

/*void nsm_core(const size_t *irD,const size_t *jcD,const double *prD,
Expand Down Expand Up @@ -324,7 +324,7 @@ namespace Spatialpy{
Particle *p ;
p = &system->particles[i] ;
//p = e->data;

//long unsigned int srng = rng() ;
//long unsigned int rng_max = rng.max() ;
//double tt = -log(1.0-(rng() * 1.0 / rng.max())) / (p->srrate+p->sdrate);
Expand All @@ -333,10 +333,10 @@ namespace Spatialpy{
if(propensities[i] > 0){
activeChannels++
}
if(p.particle_index != i){
if(p->particle_index != i){
// particles can move around in the sys->particles vector,
// this ensures that we know where in the vector each particle is
p.particle_index = i;
p->particle_index = i;
}

//system->event_v.emplace_back(p, tt) ;
Expand All @@ -345,7 +345,7 @@ namespace Spatialpy{
// ordered_list_sort(system->heap);

double timeOffset = system->current_step * system->dt;

// TODO: does this deallocate memory on the 2nd call? No
// TODO: make a deallocation function
system->rdme_event_q.build(propensities, rng, propensitySum, activeChannels,
Expand Down Expand Up @@ -533,7 +533,8 @@ namespace Spatialpy{
double totrate,cum,rdelta,rrdelta;
int event,errcode = 0;
long unsigned int re, spec = 0 ;
Particle*subvol;
Particle *subvol;
int subvol_index;
size_t i,j = 0;
//double old_rrate = 0.0,old_drate = 0.0;
double rand1,rand2,cum2,old;
Expand Down Expand Up @@ -579,7 +580,7 @@ namespace Spatialpy{
timeRxnPair = system->rdme_event_q.selectReaction();
tt = timeRxnPair.first;
subvol_index = timeRxnPair.second;
subvol = system->particles[subvol_index];
subvol = &system->particles[subvol_index];
vol = (subvol->mass / subvol->rho);

if(debug_flag){printf("nsm: tt=%e subvol=%i\n",tt,subvol->id);}
Expand Down Expand Up @@ -855,7 +856,7 @@ namespace Spatialpy{
// }
//ordered_list_bubble_up_down(system->heap, dest_subvol->heap_index);

system->rdme_event_q.update(dest_subvol.particle_index, totrate, tt, rng);
system->rdme_event_q.update(dest_subvol->particle_index, totrate, tt, rng);
}

// re-sort the heap
Expand Down