std::vector<uint32_t> CycleCreator::countPossibleCycles() {
uint32_t N = countN();
std::vector<uint32_t> cycleIds(0);
cycleIds.reserve(problem.approxCyclesCount());
uint16_t cycleSize = 0, cargo = 0;
for (uint32_t id = 1; id <= N; ++id) {
cycleSize = NumberOfSetBits(id);
if (cycleSize >= problem.getMinNodes() && cycleSize <= problem.getMaxNodes()) {
cargo = SumDemand(id, problem.getNodes());
if (cargo >= problem.getMinCapacity() && cargo <= problem.getMaxCapacity()) {
cycleIds.push_back(id);
}
}
}
return cycleIds;
}
/* returns the total potential energy for the system and updates our observables */
double energy(system_t *system) {
// molecule_t *molecule_ptr; (unused variable)
double potential_energy, rd_energy, coulombic_energy, polar_energy, vdw_energy, three_body_energy;
double kinetic_energy;
// struct timeval old_time, new_time; (unused variable)
// char linebuf[MAXLINE]; (unused variable)
#ifdef POLARTIMING
static double timing = 0;
static int count = 0;
#endif
/* zero the initial values */
kinetic_energy = 0;
potential_energy = 0;
rd_energy = 0;
coulombic_energy = 0;
polar_energy = 0;
vdw_energy = 0;
three_body_energy = 0;
system->natoms = countNatoms(system);
/* get the pairwise terms necessary for the energy calculation */
pairs(system);
/* only on the first simulation step, make sure that all recalculate flags are set */
/* if we made a volume change (or just reverted from one) set recalculate flags OR if replaying a trajectory */
// we set last_volume at the end of this function
if ( system->last_volume != system->pbc->volume
|| system->ensemble==ENSEMBLE_REPLAY
|| system->observables->energy == 0.0 )
flag_all_pairs(system);
/* get the electrostatic potential */
if(!(system->sg || system->rd_only)) {
if(system->spectre)
coulombic_energy = coulombic_nopbc(system->molecules);
else if(system->gwp) {
coulombic_energy = coulombic_nopbc_gwp(system);
kinetic_energy = coulombic_kinetic_gwp(system);
system->observables->kinetic_energy = kinetic_energy;
} else
coulombic_energy = coulombic(system);
system->observables->coulombic_energy = coulombic_energy;
/* get the polarization potential */
if(system->polarization) {
#ifdef POLARTIMING
/* get timing of polarization energy function for cuda comparison */
gettimeofday(&old_time, NULL);
#endif
#ifdef CUDA
if(system->cuda)
polar_energy = (double)polar_cuda(system);
else
polar_energy = polar(system);
#else
polar_energy = polar(system);
#endif /* CUDA */
#ifdef POLARTIMING
gettimeofday(&new_time, NULL);
timing = timing * (double)count/((double)count+1.0)
+ (double)((new_time.tv_sec-old_time.tv_sec)*1e6+(new_time.tv_usec-old_time.tv_usec)) * 1.0/((double)count +1.0);
count++;
if ( system->corrtime ) {
if ( count % system->corrtime == 0 ) sprintf(linebuf, "OUTPUT: Polarization energy function took %lf us\n", timing);
output(linebuf);
}
else {
sprintf(linebuf, "OUTPUT: Polarization energy function took %lf us\n", timing);
output(linebuf);
}
#endif
system->observables->polarization_energy = polar_energy;
}
if (system->polarvdw) {
#ifdef CUDA
if (system->cuda) {
error("error: cuda polarvdw not yet implemented!\n");
die(-1);
}
else
vdw_energy = vdw(system);
#else
vdw_energy = vdw(system);
#endif
system->observables->vdw_energy = vdw_energy;
}
}
/* get the repulsion/dispersion potential */
if(system->rd_anharmonic)
rd_energy = anharmonic(system);
else if(system->sg)
rd_energy = sg(system);
else if(system->dreiding)
rd_energy = dreiding(system);
else if(system->lj_buffered_14_7)
rd_energy = lj_buffered_14_7(system);
else if(system->disp_expansion)
rd_energy = disp_expansion(system);
else if(system->cdvdw_exp_repulsion)
rd_energy = exp_repulsion(system);
else if(!system->gwp)
rd_energy = lj(system);
system->observables->rd_energy = rd_energy;
if (system->axilrod_teller)
{
three_body_energy = axilrod_teller(system);
system->observables->three_body_energy = three_body_energy;
}
/* sum the total potential energy */
potential_energy = rd_energy + coulombic_energy + polar_energy + vdw_energy + three_body_energy;
/* not truly potential, but stick it there for convenience of MC */
/**
* POSSIBLE BUG: kinetic_energy was uninitialized, and previously only given a value inside the conditional:
*
* if(!(system->sg || system->rd_only)) {}
*
* If this conditional fails, but (system->gwp) is true (idk if this is possible), an un-initialized value would have been
* added to potential_energy. Now, 0 is being added, but am not sure if this is the desired behavior. -bt
**/
if(system->gwp) potential_energy += kinetic_energy;
system->observables->energy = potential_energy;
countN(system);
system->observables->spin_ratio /= system->observables->N;
/* for NVE */
if(system->ensemble == ENSEMBLE_NVE) {
system->observables->kinetic_energy = system->total_energy - potential_energy;
system->observables->temperature = (2.0/3.0)*system->observables->kinetic_energy/system->observables->N;
}
/* need this for the isosteric heat */
system->observables->NU = system->observables->N*system->observables->energy;
/* set last known volume*/
system->last_volume = system->pbc->volume;
if(system->cavity_autoreject_absolute)
potential_energy += cavity_absolute_check( system );
return(potential_energy);
}
/*==========================================
* main
*========================================== */
int main(int argc, char* argv[])
{
int T; // number of topics
int W; // number of unique words
int D; // number of docs
int N; // number of words in corpus
int i, iter, seed;
int *w, *d, *z, *order;
double **Nwt, **Ndt, *Nt;
double alpha, beta;
if (argc == 1) {
fprintf(stderr, "usage: %s T iter seed\n", argv[0]);
exit(-1);
}
T = atoi(argv[1]);
assert(T>0);
iter = atoi(argv[2]);
assert(iter>0);
seed = atoi(argv[3]);
assert(seed>0);
N = countN("docword.txt");
w = ivec(N);
d = ivec(N);
z = ivec(N);
read_dw("docword.txt", d, w, &D, &W);
Nwt = dmat(W,T);
Ndt = dmat(D,T);
Nt = dvec(T);
alpha = 0.05 * N / (D * T);
beta = 0.01;
printf("seed = %d\n", seed);
printf("N = %d\n", N);
printf("W = %d\n", W);
printf("D = %d\n", D);
printf("T = %d\n", T);
printf("iter = %d\n", iter);
printf("alpha = %f\n", alpha);
printf("beta = %f\n", beta);
srand48(seed);
randomassignment_d(N,T,w,d,z,Nwt,Ndt,Nt);
order = randperm(N);
add_smooth_d(D,T,Ndt,alpha);
add_smooth_d(W,T,Nwt,beta);
add_smooth1d( T,Nt, W*beta);
for (i = 0; i < iter; i++) {
sample_chain_d(N,W,T,w,d,z,Nwt,Ndt,Nt,order);
printf("iter %d \n", i);
}
printf("In-Sample Perplexity = %.2f\n",pplex_d(N,W,T,w,d,Nwt,Ndt));
add_smooth_d(D,T,Ndt,-alpha);
add_smooth_d(W,T,Nwt,-beta);
add_smooth1d( T,Nt, -W*beta);
write_sparse_d(W,T,Nwt,"Nwt.txt");
write_sparse_d(D,T,Ndt,"Ndt.txt");
write_ivec(N,z,"z.txt");
return 0;
}
