int main(int argc, char** argv){
const char *image_path = IMAGE;
//TODO : declare ALL variables here
LoadBMPFile(&h_Src, &imageW, &imageH, image_path);
D = (float *)malloc(imageW*imageH*sizeof(float));
//printf("Input Image\n");
for(r=0;r<imageH;r++){
for(c=0;c<imageW;c++){
D[r*imageW+c] = h_Src[r*imageW+c].x;
/*printf("%3.0f ", D[r*imageW+c]);*/
}
//printf("\n");
}
N = imageW*imageH;
for(i=0;i<N;i++){
D[i] = EPSILON - abs(D[i] - THRESHOLD);
}
//printf("Speed Function\n");
//for(int r=0;r<imageH;r++){
// for(int c=0;c<imageW;c++){
// printf("%3.0f ", D[r*imageW+c]);
// }
// printf("\n");
//}
// Set up CUDA Timer
cutCreateTimer(&Timer);
cutCreateTimer(&ReInitTimer);
cutStartTimer(Timer);
init_phi();
if((contour=(float *)malloc(imageW*imageH*sizeof(float)))==NULL)printf("Contour\n");
if((phi1=(float *)malloc(imageW*imageH*sizeof(float)))==NULL)printf("GRADPHI\n");
//update_phi();
// GL initialisation
glutInit(&argc, argv);
glutInitDisplayMode(GLUT_ALPHA | GLUT_DOUBLE);
glutInitWindowSize(imageW,imageH);
glutInitWindowPosition(100,100);
glutCreateWindow("GL Level Set Evolution");
glClearColor(0.0,0.0,0.0,0.0);
glutDisplayFunc(disp);
glutMainLoop();
//printf("phi+1\n");
//for(int r=0;r<imageH;r++){
// for(int c=0;c<imageW;c++){
// printf("%6.3f ", phi[r*imageW+c]);
// }
// printf("\n");
//}
}
/*
* learn dictionary and find optimum code.
*/
int MedSTC::train(char* start, char* directory, Corpus* pC, Params *param)
{
m_dDeltaEll = param->DELTA_ELL;
m_dLambda = param->LAMBDA;
m_dRho = param->RHO;
m_dGamma = m_dLambda;
long runtime_start = get_runtime();
// allocate variational parameters
double ***phi = (double***)malloc(sizeof(double**) * pC->num_docs);
for ( int d=0; d<pC->num_docs; d++ ) {
phi[d] = (double**)malloc(sizeof(double*)*pC->docs[d].length);
for (int n=0; n<pC->docs[d].length; n++) {
phi[d][n] = (double*)malloc(sizeof(double) * param->NTOPICS);
}
}
double **theta = (double**)malloc(sizeof(double*)*(pC->num_docs));
for (int d=0; d<pC->num_docs; d++) {
theta[d] = (double*)malloc(sizeof(double) * param->NTOPICS);
}
for ( int d=0; d<pC->num_docs; d++ ) {
init_phi(&(pC->docs[d]), phi[d], theta[d], param);
}
// initialize model
if (strcmp(start, "random")==0) {
new_model(pC->num_docs, pC->num_terms, param->NTOPICS,
param->NLABELS, param->INITIAL_C);
init_param( pC );
} else {
load_model(start);
m_dC = param->INITIAL_C;
}
strcpy(m_directory, directory);
char filename[100];
// run expectation maximization
sprintf(filename, "%s/lhood.dat", directory);
FILE* lhood_file = fopen(filename, "w");
Document *pDoc = NULL;
double dobj, obj_old = 1, converged = 1;
int nIt = 0;
while (((converged < 0) || (converged > param->EM_CONVERGED)
|| (nIt <= 2)) && (nIt <= param->EM_MAX_ITER))
{
dobj = 0;
double dLogLoss = 0;
for ( int d=0; d<pC->num_docs; d++ ) {
pDoc = &(pC->docs[d]);
dobj += sparse_coding( pDoc, d, param, theta[d], phi[d] );
dLogLoss += m_dLogLoss;
}
// m-step
dict_learn(pC, theta, phi, param, false);
if ( param->SUPERVISED == 1 ) { // for supervised MedLDA.
char buff[512];
get_train_filename( buff, m_directory, param );
outputLowDimData( buff, pC, theta );
svmStructSolver(buff, param, m_dMu);
if ( param->PRIMALSVM == 1 ) { // solve svm in the primal form
for ( int d=0; d<pC->num_docs; d++ ) {
loss_aug_predict( &(pC->docs[d]), theta[d] );
}
}
dobj += m_dsvm_primalobj;
} else ;
// check for convergence
converged = fabs(1 - dobj / obj_old);
obj_old = dobj;
// output model and lhood
if ( param->SUPERVISED == 1 ) {
fprintf(lhood_file, "%10.10f\t%10.10f\t%5.5e\t%.5f\n", dobj-m_dsvm_primalobj, dobj, converged, dLogLoss);
} else {
fprintf(lhood_file, "%10.10f\t%5.5e\t%.5f\n", dobj, converged, dLogLoss);
}
fflush(lhood_file);
if ( nIt > 0 && (nIt % LAG) == 0) {
sprintf( filename, "%s/%d", directory, nIt + 1);
save_model( filename, -1 );
sprintf( filename, "%s/%d.theta", directory, nIt + 1 );
save_theta( filename, theta, pC->num_docs, m_nK );
}
nIt ++;
}
// learn the final SVM.
if ( param->SUPERVISED == 0 ) {
char buff[512];
get_train_filename(buff, m_directory, param);
outputLowDimData(buff, pC, theta);
svmStructSolver(buff, param, m_dMu);
}
long runtime_end = get_runtime();
double dTrainTime = ((double)runtime_end-(double)runtime_start) / 100.0;
// output the final model
sprintf( filename, "%s/final", directory);
save_model( filename, dTrainTime );
// output the word assignments (for visualization)
int nNum = 0, nAcc = 0;
sprintf(filename, "%s/word-assignments.dat", directory);
FILE* w_asgn_file = fopen(filename, "w");
for (int d=0; d<pC->num_docs; d++) {
sparse_coding( &(pC->docs[d]), d, param, theta[d], phi[d] );
write_word_assignment(w_asgn_file, &(pC->docs[d]), phi[d]);
nNum ++;
pC->docs[d].predlabel = predict(theta[d]);
if ( pC->docs[d].gndlabel == pC->docs[d].predlabel ) nAcc ++;
}
fclose(w_asgn_file);
fclose(lhood_file);
sprintf(filename,"%s/train.theta",directory);
save_theta(filename, theta, pC->num_docs, m_nK);
for (int d=0; d<pC->num_docs; d++) {
free( theta[d] );
for (int n=0; n<pC->docs[d].length; n++)
free( phi[d][n] );
free( phi[d] );
}
free( theta );
free( phi );
return nIt;
}
int
main (int argc, char* argv[])
{
BoxLib::Initialize(argc,argv);
// What time is it now? We'll use this to compute total run time.
Real strt_time = ParallelDescriptor::second();
std::cout << std::setprecision(15);
// ParmParse is way of reading inputs from the inputs file
ParmParse pp;
int verbose = 0;
pp.query("verbose", verbose);
// We need to get n_cell from the inputs file - this is the number of cells on each side of
// a square (or cubic) domain.
int n_cell;
pp.get("n_cell",n_cell);
int max_grid_size;
pp.get("max_grid_size",max_grid_size);
// Default plot_int to 1, allow us to set it to something else in the inputs file
// If plot_int < 0 then no plot files will be written
int plot_int = 1;
pp.query("plot_int",plot_int);
// Default nsteps to 0, allow us to set it to something else in the inputs file
int nsteps = 0;
pp.query("nsteps",nsteps);
pp.query("do_tiling", do_tiling);
// Define a single box covering the domain
IntVect dom_lo(0,0,0);
IntVect dom_hi(n_cell-1,n_cell-1,n_cell-1);
Box domain(dom_lo,dom_hi);
// Initialize the boxarray "bs" from the single box "bx"
BoxArray bs(domain);
// Break up boxarray "bs" into chunks no larger than "max_grid_size" along a direction
bs.maxSize(max_grid_size);
// This defines the physical size of the box. Right now the box is [-1,1] in each direction.
RealBox real_box;
for (int n = 0; n < BL_SPACEDIM; n++) {
real_box.setLo(n,-1.0);
real_box.setHi(n, 1.0);
}
// This says we are using Cartesian coordinates
int coord = 0;
// This sets the boundary conditions to be doubly or triply periodic
int is_per[BL_SPACEDIM];
for (int i = 0; i < BL_SPACEDIM; i++) is_per[i] = 1;
// This defines a Geometry object which is useful for writing the plotfiles
Geometry geom(domain,&real_box,coord,is_per);
// This defines the mesh spacing
Real dx[BL_SPACEDIM];
for ( int n=0; n<BL_SPACEDIM; n++ )
dx[n] = ( geom.ProbHi(n) - geom.ProbLo(n) )/domain.length(n);
// Nghost = number of ghost cells for each array
int Nghost = 1;
// Ncomp = number of components for each array
int Ncomp = 1;
pp.query("ncomp", Ncomp);
// Allocate space for the old_phi and new_phi -- we define old_phi and new_phi as
PArray < MultiFab > phis(2, PArrayManage);
phis.set(0, new MultiFab(bs, Ncomp, Nghost));
phis.set(1, new MultiFab(bs, Ncomp, Nghost));
MultiFab* old_phi = &phis[0];
MultiFab* new_phi = &phis[1];
// Initialize both to zero (just because)
old_phi->setVal(0.0);
new_phi->setVal(0.0);
// Initialize phi by calling a Fortran routine.
// MFIter = MultiFab Iterator
#ifdef _OPENMP
#pragma omp parallel
#endif
for ( MFIter mfi(*new_phi,true); mfi.isValid(); ++mfi )
{
const Box& bx = mfi.tilebox();
init_phi(bx.loVect(),bx.hiVect(),
BL_TO_FORTRAN((*new_phi)[mfi]),Ncomp,
dx,geom.ProbLo(),geom.ProbHi());
}
// Call the compute_dt routine to return a time step which we will pass to advance
Real dt = compute_dt(dx[0]);
// Write a plotfile of the initial data if plot_int > 0 (plot_int was defined in the inputs file)
if (plot_int > 0) {
int n = 0;
const std::string& pltfile = BoxLib::Concatenate("plt",n,5);
writePlotFile(pltfile, *new_phi, geom);
}
Real adv_start_time = ParallelDescriptor::second();
for (int n = 1; n <= nsteps; n++)
{
// Swap the pointers so we don't have to allocate and de-allocate data
std::swap(old_phi, new_phi);
// new_phi = old_phi + dt * (something)
advance(old_phi, new_phi, dx, dt, geom);
// Tell the I/O Processor to write out which step we're doing
if (verbose && ParallelDescriptor::IOProcessor())
std::cout << "Advanced step " << n << std::endl;
// Write a plotfile of the current data (plot_int was defined in the inputs file)
if (plot_int > 0 && n%plot_int == 0) {
const std::string& pltfile = BoxLib::Concatenate("plt",n,5);
writePlotFile(pltfile, *new_phi, geom);
}
}
// Call the timer again and compute the maximum difference between the start time and stop time
// over all processors
Real advance_time = ParallelDescriptor::second() - adv_start_time;
Real stop_time = ParallelDescriptor::second() - strt_time;
const int IOProc = ParallelDescriptor::IOProcessorNumber();
ParallelDescriptor::ReduceRealMax(stop_time,IOProc);
ParallelDescriptor::ReduceRealMax(advance_time,IOProc);
ParallelDescriptor::ReduceRealMax(kernel_time,IOProc);
ParallelDescriptor::ReduceRealMax(FB_time,IOProc);
// Tell the I/O Processor to write out the "run time"
if (ParallelDescriptor::IOProcessor()) {
std::cout << "Kernel time = " << kernel_time << std::endl;
std::cout << "FB time = " << FB_time << std::endl;
std::cout << "Advance time = " << advance_time << std::endl;
std::cout << "Total run time = " << stop_time << std::endl;
}
// Say goodbye to MPI, etc...
BoxLib::Finalize();
}
/*============================================================================*/
int *ghmm_dpmodel_viterbi_variable_tb(ghmm_dpmodel *mo, ghmm_dpseq * X, ghmm_dpseq * Y,
double *log_p, int *path_length,
int start_traceback_with) {
#define CUR_PROC "ghmm_dpmodel_viterbi"
int u, v, j, i, off_x, off_y, current_state_index;
double value, max_value, previous_prob;
plocal_store_t *pv;
int *state_seq = NULL;
int emission;
double log_b_i, log_in_a_ij;
double (*log_in_a)(plocal_store_t*, int, int, ghmm_dpseq*, ghmm_dpseq*, int, int);
/* printf("---- viterbi -----\n"); */
i_list * state_list;
state_list = ighmm_list_init_list();
log_in_a = &sget_log_in_a;
/* int len_path = mo->N*len; the length of the path is not known apriori */
/* if (mo->model_type & kSilentStates && */
/* mo->silent != NULL && */
/* mo->topo_order == NULL) { */
/* ghmm_dmodel_topo_order( mo ); */
/* } */
/* Allocate the matrices log_in_a, log_b,Vektor phi, phi_new, Matrix psi */
pv = pviterbi_alloc(mo, X->length, Y->length);
if (!pv) { GHMM_LOG_QUEUED(LCONVERTED); goto STOP; }
/* Precomputing the log(a_ij) and log(bj(ot)) */
pviterbi_precompute(mo, pv);
/* Initialize the lookback matrix (for positions [-offsetX,0], [-1, len_y]*/
init_phi(pv, X, Y);
/* u > max_offset_x , v starts -1 to allow states with offset_x == 0
which corresponds to a series of gap states before reading the first
character of x at position x=0, y=v */
/** THIS IS THE MAIN RECURRENCE **/
for (u = mo->max_offset_x + 1; u < X->length; u++) {
for (v = -mo->max_offset_y; v < Y->length; v++) {
for (j = 0; j < mo->N; j++)
{
/** initialization of phi (lookback matrix), psi (traceback) **/
set_phi(pv, u, v, j, +1);
set_psi(pv, u, v, j, -1);
}
for (i = 0; i < mo->N; i++) {
/* Determine the maximum */
/* max_phi = phi[i] + log_in_a[j][i] ... */
if (!(mo->model_type & GHMM_kSilentStates) || !mo->silent[i] ) {
max_value = -DBL_MAX;
set_psi(pv, u, v, i, -1);
for (j = 0; j < mo->s[i].in_states; j++) {
/* look back in the phi matrix at the offsets */
previous_prob = get_phi(pv, u, v, mo->s[i].offset_x, mo->s[i].offset_y, mo->s[i].in_id[j]);
log_in_a_ij = (*log_in_a)(pv, i, j, X, Y, u, v);
if ( previous_prob != +1 && log_in_a_ij != +1) {
value = previous_prob + log_in_a_ij;
if (value > max_value) {
max_value = value;
set_psi(pv, u, v, i, mo->s[i].in_id[j]);
}
}
else
{;} /* fprintf(stderr, " %d --> %d = %f, \n", i,i,v->log_in_a[i][i]); */
}
emission = ghmm_dpmodel_pair(ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(Y, mo->s[i].alphabet, v),
mo->size_of_alphabet[mo->s[i].alphabet],
mo->s[i].offset_x, mo->s[i].offset_y);
#ifdef DEBUG
if (emission > ghmm_dpmodel_emission_table_size(mo, i)){
printf("State %i\n", i);
ghmm_dpmodel_state_print(&(mo->s[i]));
printf("charX: %i charY: %i alphabet size: %i emission table: %i emission index: %i\n",
ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(Y, mo->s[i].alphabet, v),
mo->size_of_alphabet[mo->s[i].alphabet],
ghmm_dpmodel_emission_table_size(mo, i), emission);
}
#endif
log_b_i = log_b(pv, i, ghmm_dpmodel_pair(ghmm_dpseq_get_char(X, mo->s[i].alphabet, u),
ghmm_dpseq_get_char(Y, mo->s[i].alphabet, v),
mo->size_of_alphabet[mo->s[i].alphabet],
mo->s[i].offset_x, mo->s[i].offset_y));
/* No maximum found (that is, state never reached)
or the output O[t] = 0.0: */
if (max_value == -DBL_MAX ||/* and then also: (v->psi[t][j] == -1) */
log_b_i == +1 ) {
set_phi(pv, u, v, i, +1);
}
else
set_phi(pv, u, v, i, max_value + log_b_i);
}
} /* complete time step for emitting states */
/* last_osc = osc; */
/* save last transition class */
/*if (mo->model_type & kSilentStates) {
p__viterbi_silent( mo, t, v );
}*/ /* complete time step for silent states */
/**************
for (j = 0; j < mo->N; j++)
{
printf("\npsi[%d],in:%d, phi=%f\n", t, v->psi[t][j], v->phi[j]);
}
for (i = 0; i < mo->N; i++){
printf("%d\t", former_matchcount[i]);
}
for (i = 0; i < mo->N; i++){
printf("%d\t", recent_matchcount[i]);
}
****************/
} /* End for v in Y */
/* Next character in X */
push_back_phi(pv, Y->length);
} /* End for u in X */
/* Termination */
max_value = -DBL_MAX;
ighmm_list_append(state_list, -1);
/* if start_traceback_with is -1 (it is by default) search for the most
likely state at the end of both sequences */
if (start_traceback_with == -1) {
for (j = 0; j < mo->N; j++){
#ifdef DEBUG
printf("phi(len_x)(len_y)(%i)=%f\n", j, get_phi(pv, u, Y->length-1, 0, 0, j));
#endif
if ( get_phi(pv, u, Y->length-1, 0, 0, j) != +1 &&
get_phi(pv, u, Y->length-1, 0, 0, j) > max_value) {
max_value = get_phi(pv, X->length-1, Y->length-1, 0, 0, j);
state_list->last->val = j;
}
}
}
/* this is the special traceback mode for the d & c algorithm that also
connects the traceback to the first state of the rest of the path */
else {
#ifdef DEBUG
printf("D & C traceback from state %i!\n", start_traceback_with);
printf("Last characters emitted X: %i, Y: %i\n",
ghmm_dpseq_get_char(X, mo->s[start_traceback_with].alphabet,
X->length-1),
ghmm_dpseq_get_char(Y, mo->s[start_traceback_with].alphabet,
Y->length-1));
for (j = 0; j < mo->N; j++){
printf("phi(len_x)(len_y)(%i)=%f\n", j, get_phi(pv, X->length-1, Y->length-1, 0, 0, j));
}
#endif
max_value = get_phi(pv, X->length-1, Y->length-1, 0, 0, start_traceback_with);
if (max_value != 1 && max_value > -DBL_MAX)
state_list->last->val = start_traceback_with;
}
if (max_value == -DBL_MAX) {
/* Sequence can't be generated from the model! */
*log_p = +1;
/* Backtracing doesn't work, because state_seq[*] allocated with -1 */
/* for (t = len - 2; t >= 0; t--)
state_list->last->val = -1; */
}
else {
/* Backtracing, should put DEL path nicely */
*log_p = max_value;
/* removed the handling of silent states here */
/* start trace back at the end of both sequences */
u = X->length - 1;
v = Y->length - 1;
current_state_index = state_list->first->val;
off_x = mo->s[current_state_index].offset_x;
off_y = mo->s[current_state_index].offset_y;
while (u - off_x >= -1 && v - off_y >= -1 && current_state_index != -1) {
/* while (u > 0 && v > 0) { */
/* look up the preceding state and save it in the first position of the
state list */
/* printf("Current state %i at (%i,%i) -> preceding state %i\n",
current_state_index, u, v, get_psi(pv, u, v, current_state_index)); */
/* update the current state */
current_state_index = get_psi(pv, u, v, current_state_index);
if (current_state_index != -1)
ighmm_list_insert(state_list, current_state_index);
/* move in the alignment matrix */
u -= off_x;
v -= off_y;
/* get the next offsets */
off_x = mo->s[current_state_index].offset_x;
off_y = mo->s[current_state_index].offset_y;
}
}
/* Free the memory space */
pviterbi_free(&pv, mo->N, X->length, Y->length, mo->max_offset_x ,
mo->max_offset_y);
/* printf("After traceback: last state = %i\n", state_list->last->val); */
state_seq = ighmm_list_to_array(state_list);
*path_length = state_list->length;
/* PRINT PATH */
/* fprintf(stderr, "Viterbi path: " ); */
/* int t; */
/* for(t=0; t < *path_length; t++) */
/* if (state_seq[t] >= 0) fprintf(stderr, " %d ", state_seq[t]); */
/* fprintf(stderr, "\n Freeing ... \n"); */
return (state_seq);
STOP: /* Label STOP from ARRAY_[CM]ALLOC */
/* Free the memory space */
pviterbi_free(&pv, mo->N, X->length, Y->length, mo->max_offset_x,
mo->max_offset_y);
m_free(state_seq);
ighmm_list_free(state_list);
return NULL;
#undef CUR_PROC
} /* viterbi */
void main_main ()
{
// What time is it now? We'll use this to compute total run time.
Real strt_time = ParallelDescriptor::second();
std::cout << std::setprecision(15);
int n_cell, max_grid_size, nsteps, plot_int, is_periodic[BL_SPACEDIM];
// Boundary conditions
Array<int> lo_bc(BL_SPACEDIM), hi_bc(BL_SPACEDIM);
// inputs parameters
{
// ParmParse is way of reading inputs from the inputs file
ParmParse pp;
// We need to get n_cell from the inputs file - this is the number of cells on each side of
// a square (or cubic) domain.
pp.get("n_cell",n_cell);
// Default nsteps to 0, allow us to set it to something else in the inputs file
pp.get("max_grid_size",max_grid_size);
// Default plot_int to 1, allow us to set it to something else in the inputs file
// If plot_int < 0 then no plot files will be written
plot_int = 1;
pp.query("plot_int",plot_int);
// Default nsteps to 0, allow us to set it to something else in the inputs file
nsteps = 0;
pp.query("nsteps",nsteps);
// Boundary conditions - default is periodic (INT_DIR)
for (int i = 0; i < BL_SPACEDIM; ++i)
{
lo_bc[i] = hi_bc[i] = INT_DIR; // periodic boundaries are interior boundaries
}
pp.queryarr("lo_bc",lo_bc,0,BL_SPACEDIM);
pp.queryarr("hi_bc",hi_bc,0,BL_SPACEDIM);
}
// make BoxArray and Geometry
BoxArray ba;
Geometry geom;
{
IntVect dom_lo(IntVect(D_DECL(0,0,0)));
IntVect dom_hi(IntVect(D_DECL(n_cell-1, n_cell-1, n_cell-1)));
Box domain(dom_lo, dom_hi);
// Initialize the boxarray "ba" from the single box "bx"
ba.define(domain);
// Break up boxarray "ba" into chunks no larger than "max_grid_size" along a direction
ba.maxSize(max_grid_size);
// This defines the physical size of the box. Right now the box is [-1,1] in each direction.
RealBox real_box;
for (int n = 0; n < BL_SPACEDIM; n++) {
real_box.setLo(n,-1.0);
real_box.setHi(n, 1.0);
}
// This says we are using Cartesian coordinates
int coord = 0;
// This sets the boundary conditions to be doubly or triply periodic
int is_periodic[BL_SPACEDIM];
for (int i = 0; i < BL_SPACEDIM; i++)
{
is_periodic[i] = 0;
if (lo_bc[i] == 0 && hi_bc[i] == 0) {
is_periodic[i] = 1;
}
}
// This defines a Geometry object
geom.define(domain,&real_box,coord,is_periodic);
}
// Boundary conditions
PhysBCFunct physbcf;
BCRec bcr(&lo_bc[0], &hi_bc[0]);
physbcf.define(geom, bcr, BndryFunctBase(phifill)); // phifill is a fortran function
// define dx[]
const Real* dx = geom.CellSize();
// Nghost = number of ghost cells for each array
int Nghost = 1;
// Ncomp = number of components for each array
int Ncomp = 1;
// time = starting time in the simulation
Real time = 0.0;
// we allocate two phi multifabs; one will store the old state, the other the new
// we swap the indices each time step to avoid copies of new into old
PArray<MultiFab> phi(2, PArrayManage);
phi.set(0, new MultiFab(ba, Ncomp, Nghost));
phi.set(1, new MultiFab(ba, Ncomp, Nghost));
// Initialize both to zero (just because)
phi[0].setVal(0.0);
phi[1].setVal(0.0);
// Initialize phi[init_index] by calling a Fortran routine.
// MFIter = MultiFab Iterator
int init_index = 0;
for ( MFIter mfi(phi[init_index]); mfi.isValid(); ++mfi )
{
const Box& bx = mfi.validbox();
init_phi(phi[init_index][mfi].dataPtr(),
bx.loVect(), bx.hiVect(), &Nghost,
geom.CellSize(), geom.ProbLo(), geom.ProbHi());
}
// compute the time step
Real dt = 0.9*dx[0]*dx[0] / (2.0*BL_SPACEDIM);
// Write a plotfile of the initial data if plot_int > 0 (plot_int was defined in the inputs file)
if (plot_int > 0)
{
int n = 0;
const std::string& pltfile = BoxLib::Concatenate("plt",n,5);
writePlotFile(pltfile, phi[init_index], geom, time);
}
// build the flux multifabs
PArray<MultiFab> flux(BL_SPACEDIM, PArrayManage);
for (int dir = 0; dir < BL_SPACEDIM; dir++)
{
// flux(dir) has one component, zero ghost cells, and is nodal in direction dir
BoxArray edge_ba = ba;
edge_ba.surroundingNodes(dir);
flux.set(dir, new MultiFab(edge_ba, 1, 0));
}
int old_index = init_index;
for (int n = 1; n <= nsteps; n++, old_index = 1 - old_index)
{
int new_index = 1 - old_index;
// new_phi = old_phi + dt * (something)
advance(phi[old_index], phi[new_index], flux, time, dt, geom, physbcf, bcr);
time = time + dt;
// Tell the I/O Processor to write out which step we're doing
if (ParallelDescriptor::IOProcessor())
std::cout << "Advanced step " << n << std::endl;
// Write a plotfile of the current data (plot_int was defined in the inputs file)
if (plot_int > 0 && n%plot_int == 0)
{
const std::string& pltfile = BoxLib::Concatenate("plt",n,5);
writePlotFile(pltfile, phi[new_index], geom, time);
}
}
// Call the timer again and compute the maximum difference between the start time and stop time
// over all processors
Real stop_time = ParallelDescriptor::second() - strt_time;
const int IOProc = ParallelDescriptor::IOProcessorNumber();
ParallelDescriptor::ReduceRealMax(stop_time,IOProc);
// Tell the I/O Processor to write out the "run time"
if (ParallelDescriptor::IOProcessor()) {
std::cout << "Run time = " << stop_time << std::endl;
}
}
