int main(int argc, char ** argv)
{
invalid_argument er(
"Bond angle correlation function\n"
#ifdef use_periodic
"Syntax : periodic_g6 [path]filename NbOfBins Nb dx dy dz [mode=0 [l=6]]\n"
#else
"Syntax : g6 [path]filename radius NbOfBins range [mode=0 [l=6 [zmin zmax]]]\n"
" range is in diameter unit\n"
#endif
" mode\t0 raw boo\n"
" \t1 coarse grained boo\n"
);
try
{
if(argc<3) throw er;
const string filename(argv[1]);
const string inputPath = filename.substr(0,filename.find_last_of("."));
vector<size_t> inside;
//construct the particle container out of the datafile
#ifdef use_periodic
if(argc<7) throw er;
const size_t Nbins = atoi(argv[2]);
const size_t Nb = atoi(argv[3]);
double nbDiameterCutOff =atof(argv[4]);
BoundingBox b;
for(size_t d=0;d<3;++d)
{
b.edges[d].first=0.0;
b.edges[d].second = atof(argv[4+d]);
if(nbDiameterCutOff>b.edges[d].second)
nbDiameterCutOff=b.edges[d].second;
}
nbDiameterCutOff /=4.0;
const bool mode = (argc<8)?0:atoi(argv[7]);
const size_t l = (argc<9)?6:atoi(argv[8]);
PeriodicParticles Centers(Nb,b,filename,1.0);
cout << "With periodic boundary conditions"<<endl;
#else
const double radius = atof(argv[2]),
nbDiameterCutOff = atof(argv[4]);
const size_t Nbins = atoi(argv[3]);
const bool mode = (argc<6)?0:atoi(argv[5]);
const size_t l = (argc<7)?6:atoi(argv[6]);
Particles Centers(filename,radius);
#endif
cout << Centers.size() << " particles ... ";
//read q6m
vector<BooData> rawBoo, allBoo;
Centers.load_qlm(inputPath+".qlm", rawBoo);
if(mode)
{
Centers.makeNgbList(loadBonds(inputPath+".bonds"));
//select all particles who's all neighbours' qlms are not null
vector<size_t> second_inside;
second_inside.reserve(Centers.size());
for(size_t p=0; p<Centers.getNgbList().size(); ++p)
{
bool hasNullNgb = false;
for(size_t n=0; n<Centers.getNgbList()[p].size(); ++n)
hasNullNgb = (hasNullNgb || rawBoo[Centers.getNgbList()[p][n]].isnull());
if(!hasNullNgb)
second_inside.push_back(p);
}
cout<< second_inside.size()<< " have coarse grained qlms ... ";
Centers.getCgBOOs(second_inside, rawBoo, allBoo);
}
else
allBoo=rawBoo;
#ifndef use_periodic
vector<size_t> slab;
slab.reserve(Centers.size());
//Case where we ask to discard all points out of the interval [zmin, zmax]
if(argc>8)
{
const double zmin = atof(argv[7]),
zmax = atof(argv[8]);
//look for the particles that are in the slab and have non null qlm
for(size_t p=0; p<Centers.size(); ++p)
if(Centers[p][2]>zmin && Centers[p][2]<zmax && !allBoo[p].isnull())
slab.push_back(p);
}
else
for(size_t p=0; p<Centers.size(); ++p)
if(!allBoo[p].isnull())
slab.push_back(p);
//reduce the centers list
Particles cen;
cen.radius = Centers.radius;
cen.reserve(slab.size());
for(size_t p=0; p<slab.size(); ++p)
cen.push_back(Centers[slab[p]]);
Centers.swap(cen);
Centers.delNgbList();
//reduce the qlm
vector<BooData> boo(slab.size());
for(size_t p=0; p<slab.size(); ++p)
boo[p] = allBoo[slab[p]];
allBoo.swap(boo);
#endif
vector<size_t> nb(Nbins, 0);
vector<double> gl(Nbins, 0.0);
const double maxdistsq = pow(2.0*nbDiameterCutOff, 2);
for(size_t p=0; p<Centers.size(); ++p)
for(size_t q=p+1; q<Centers.size(); ++q)
{
Coord diff = Centers.getDiff(p, q);
const double distsq = (diff*diff).sum();
if(distsq<maxdistsq)
{
const size_t r = sqrt(distsq) / (2.0*nbDiameterCutOff) * Nbins;
nb[r]++;
gl[r] += allBoo[p].innerProduct(allBoo[q], l);
}
}
cout << " done !" << endl;
ostringstream rdffilename;
rdffilename << inputPath << (mode?".cg":".g") << l;
ofstream rdfFile(rdffilename.str().c_str(), ios::out | ios::trunc);
rdfFile << "#r\tg"<<l<<"(r)\tg(r)"<<endl;
for(size_t r=0; r<Nbins; ++r)
rdfFile<< r/(double)Nbins*nbDiameterCutOff <<"\t"<< gl[r] <<"\t"<< nb[r] <<"\n";
//all particles are "inside"
/*inside.reserve(Centers.size());
for(size_t p=0; p<Centers.size(); ++p)
inside[p] = p;
cout << Centers.size() << " inside ... ";
Centers.makeRTreeIndex();*/
//create binner
//Particles::GlBinner binner(Centers, Nbins, nbDiameterCutOff, allBoo, l);
//select particles and bin them
//vector<size_t> inside = Centers.selectInside(2.0*radius*(nbDiameterCutOff+(1+mode)*1.3/2));
//Case where we ask to discard all points out of the interval [zmin, zmax]
/*if(argc>8)
{
const double zmin = atof(argv[7]),
zmax = atof(argv[8]);
//cout<<"\tl="<<l<<"\tzmin="<<zmin<<"\tzmax="<<zmax;
vector<size_t> in;
in.reserve(inside.size());
for(vector<size_t>::const_iterator p=inside.begin(); p!=inside.end(); ++p)
if(Centers[*p][2]>=zmin && Centers[*p][2]<=zmax)
in.push_back(*p);
in.swap(inside);
}*/
/*binner << inside;
//binner.normalize(inside.size());
cout << " done !" << endl;
ostringstream rdffilename;
rdffilename << inputPath << (mode?".cg":".g") << l;
ofstream rdfFile(rdffilename.str().c_str(), ios::out | ios::trunc);
rdfFile << "#r\tg"<<l<<"(r)\tg(r)"<<endl;
for(size_t r=0; r<Nbins; ++r)
rdfFile<< r/(double)Nbins*nbDiameterCutOff <<"\t"<< binner.gl[r] <<"\t"<< binner.g[r] <<"\n";*/
}
catch(const std::exception &e)
{
cerr<<e.what() << endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
void WaterSimApp::resetParticles()
{
particles->clear_particles();
}
void add(Particle *p)
{
particles.push_back(p);
}
algebra::Vector3Ds CoarseCC::calc_derivatives(const DensityMap *em_map,
const DensityMap *model_map,
const Particles &model_ps,
const FloatKey &w_key,
KernelParameters *kernel_params,
const float &scalefac,
const algebra::Vector3Ds &dv) {
algebra::Vector3Ds dv_out;
dv_out.insert(dv_out.end(), dv.size(), algebra::Vector3D(0., 0., 0.));
double tdvx = 0., tdvy = 0., tdvz = 0., tmp, rsq;
int iminx, iminy, iminz, imaxx, imaxy, imaxz;
const DensityHeader *model_header = model_map->get_header();
const DensityHeader *em_header = em_map->get_header();
const float *x_loc = em_map->get_x_loc();
const float *y_loc = em_map->get_y_loc();
const float *z_loc = em_map->get_z_loc();
IMP_INTERNAL_CHECK(model_ps.size() == dv.size(),
"input derivatives array size does not match "
<< "the number of particles in the model map\n");
core::XYZRs model_xyzr = core::XYZRs(model_ps);
// this would go away once we have XYZRW decorator
const emreal *em_data = em_map->get_data();
float lim = kernel_params->get_lim();
long ivox;
// validate that the model and em maps are not empty
IMP_USAGE_CHECK(em_header->rms >= EPS,
"EM map is empty ! em_header->rms = " << em_header->rms);
// it may be that CG takes a too large step, which causes the particles
// to go outside of the density
// if (model_header->rms <= EPS){
// IMP_WARN("Model map is empty ! model_header->rms = " << model_header->rms
// <<" derivatives are not calculated. the model centroid is : " <<
// core::get_centroid(core::XYZs(model_ps))<<
// " the map centroid is " << em_map->get_centroid()<<
// "number of particles in model:"<<model_ps.size()
//<<std::endl);
// return;
// }
// Compute the derivatives
int nx = em_header->get_nx();
int ny = em_header->get_ny();
// int nz=em_header->get_nz();
IMP_INTERNAL_CHECK(em_map->get_rms_calculated(),
"RMS should be calculated for calculating derivatives \n");
long nvox = em_header->get_number_of_voxels();
double lower_comp = 1. * nvox * em_header->rms * model_header->rms;
for (unsigned int ii = 0; ii < model_ps.size(); ii++) {
float x, y, z;
x = model_xyzr[ii].get_x();
y = model_xyzr[ii].get_y();
z = model_xyzr[ii].get_z();
IMP_IF_LOG(VERBOSE) {
algebra::Vector3D vv(x, y, z);
IMP_LOG_VERBOSE(
"start value:: (" << x << "," << y << "," << z << " ) "
<< em_map->get_value(x, y, z) << " : "
<< em_map->get_dim_index_by_location(vv, 0) << ","
<< em_map->get_dim_index_by_location(vv, 1) << ","
<< em_map->get_dim_index_by_location(vv, 2)
<< std::endl);
}
const RadiusDependentKernelParameters ¶ms =
kernel_params->get_params(model_xyzr[ii].get_radius());
calc_local_bounding_box( // em_map,
model_map, x, y, z, params.get_kdist(), iminx, iminy, iminz, imaxx,
imaxy, imaxz);
IMP_LOG_WRITE(VERBOSE, params.show());
IMP_LOG_VERBOSE("local bb: [" << iminx << "," << iminy << "," << iminz
<< "] [" << imaxx << "," << imaxy << ","
<< imaxz << "] \n");
tdvx = .0;
tdvy = .0;
tdvz = .0;
for (int ivoxz = iminz; ivoxz <= imaxz; ivoxz++) {
for (int ivoxy = iminy; ivoxy <= imaxy; ivoxy++) {
ivox = ivoxz * nx * ny + ivoxy * nx + iminx;
for (int ivoxx = iminx; ivoxx <= imaxx; ivoxx++) {
/* if (em_data[ivox]<EPS) {
ivox++;
continue;
}*/
float dx = x_loc[ivox] - x;
float dy = y_loc[ivox] - y;
float dz = z_loc[ivox] - z;
rsq = dx * dx + dy * dy + dz * dz;
rsq = EXP(-rsq * params.get_inv_sigsq());
tmp = (x - x_loc[ivox]) * rsq;
if (std::abs(tmp) > lim) {
tdvx += tmp * em_data[ivox];
}
tmp = (y - y_loc[ivox]) * rsq;
if (std::abs(tmp) > lim) {
tdvy += tmp * em_data[ivox];
}
tmp = (z - z_loc[ivox]) * rsq;
if (std::abs(tmp) > lim) {
tdvz += tmp * em_data[ivox];
}
ivox++;
}
}
}
tmp = model_ps[ii]->get_value(w_key) * 2. * params.get_inv_sigsq() *
scalefac * params.get_normfac() / lower_comp;
IMP_LOG_VERBOSE("for particle:" << ii << " (" << tdvx << "," << tdvy << ","
<< tdvz << ")" << std::endl);
dv_out[ii][0] = tdvx * tmp;
dv_out[ii][1] = tdvy * tmp;
dv_out[ii][2] = tdvz * tmp;
} // particles
return dv_out;
}
void PusherPonderomotivePositionBorisV::operator()( Particles &particles, SmileiMPI *smpi, int istart, int iend, int ithread, int ipart_ref )
{
/////////// not vectorized
std::vector<double> *Phi_mpart = &( smpi->dynamics_PHI_mpart[ithread] );
std::vector<double> *GradPhi_mpart = &( smpi->dynamics_GradPHI_mpart[ithread] );
double charge_sq_over_mass_dts4, charge_over_mass_sq;
double gamma0, gamma0_sq, gamma_ponderomotive;
double pxsm, pysm, pzsm;
//int* cell_keys;
double *momentum[3];
for( int i = 0 ; i<3 ; i++ ) {
momentum[i] = &( particles.momentum( i, 0 ) );
}
double *position[3];
for( int i = 0 ; i<nDim_ ; i++ ) {
position[i] = &( particles.position( i, 0 ) );
}
#ifdef __DEBUG
double *position_old[3];
for( int i = 0 ; i<nDim_ ; i++ ) {
position_old[i] = &( particles.position_old( i, 0 ) );
}
#endif
short *charge = &( particles.charge( 0 ) );
int nparts = GradPhi_mpart->size()/3;
double *Phi_m = &( ( *Phi_mpart )[0*nparts] );
double *GradPhi_mx = &( ( *GradPhi_mpart )[0*nparts] );
double *GradPhi_my = &( ( *GradPhi_mpart )[1*nparts] );
double *GradPhi_mz = &( ( *GradPhi_mpart )[2*nparts] );
//particles.cell_keys.resize(nparts);
//cell_keys = &( particles.cell_keys[0]);
#pragma omp simd
for( int ipart=istart ; ipart<iend; ipart++ ) { // begin loop on particles
// ! ponderomotive force is proportional to charge squared and the field is divided by 4 instead of 2
charge_sq_over_mass_dts4 = ( double )( charge[ipart] )*( double )( charge[ipart] )*one_over_mass_*dts4;
// (charge over mass)^2
charge_over_mass_sq = ( double )( charge[ipart] )*one_over_mass_*( charge[ipart] )*one_over_mass_;
// compute initial ponderomotive gamma
gamma0_sq = 1. + momentum[0][ipart]*momentum[0][ipart] + momentum[1][ipart]*momentum[1][ipart] + momentum[2][ipart]*momentum[2][ipart] + ( *( Phi_m+ipart-ipart_ref ) )*charge_over_mass_sq;
gamma0 = sqrt( gamma0_sq ) ;
// ponderomotive force for ponderomotive gamma advance (Grad Phi is interpolated in time, hence the division by 2)
pxsm = charge_sq_over_mass_dts4 * ( *( GradPhi_mx+ipart-ipart_ref ) ) / gamma0_sq ;
pysm = charge_sq_over_mass_dts4 * ( *( GradPhi_my+ipart-ipart_ref ) ) / gamma0_sq ;
pzsm = charge_sq_over_mass_dts4 * ( *( GradPhi_mz+ipart-ipart_ref ) ) / gamma0_sq ;
// update of gamma ponderomotive
gamma_ponderomotive = gamma0 + ( pxsm*momentum[0][ipart]+pysm*momentum[1][ipart]+pzsm*momentum[2][ipart] ) ;
// Move the particle
#ifdef __DEBUG
for( int i = 0 ; i<nDim_ ; i++ ) {
position_old[i][ipart] = position[i][ipart];
}
#endif
for( int i = 0 ; i<nDim_ ; i++ ) {
position[i][ipart] += dt*momentum[i][ipart]/gamma_ponderomotive;
}
} // end loop on particles
//#pragma omp simd
//for (int ipart=0 ; ipart<nparts; ipart++ ) {
//
// for ( int i = 0 ; i<nDim_ ; i++ ){
// cell_keys[ipart] *= nspace[i];
// cell_keys[ipart] += round( (position[i][ipart]-min_loc_vec[i]) * dx_inv_[i] );
// }
//
//} // end loop on particles
}
// ---------------------------------------------------------------------------------------------------------------------
//! Project charge : frozen & diagFields timstep
// ---------------------------------------------------------------------------------------------------------------------
void Projector2D4Order::basic( double *rhoj, Particles &particles, unsigned int ipart, unsigned int type )
{
//Warning : this function is used for frozen species or initialization only and doesn't use the standard scheme.
//rho type = 0
//Jx type = 1
//Jy type = 2
//Jz type = 3
int iloc;
int ny( nprimy );
// (x,y,z) components of the current density for the macro-particle
double charge_weight = inv_cell_volume * ( double )( particles.charge( ipart ) )*particles.weight( ipart );
if( type > 0 ) {
charge_weight *= 1./sqrt( 1.0 + particles.momentum( 0, ipart )*particles.momentum( 0, ipart )
+ particles.momentum( 1, ipart )*particles.momentum( 1, ipart )
+ particles.momentum( 2, ipart )*particles.momentum( 2, ipart ) );
if( type == 1 ) {
charge_weight *= particles.momentum( 0, ipart );
} else if( type == 2 ) {
charge_weight *= particles.momentum( 1, ipart );
ny ++;
} else {
charge_weight *= particles.momentum( 2, ipart );
}
}
// variable declaration
double xpn, ypn;
double delta, delta2, delta3, delta4;
// arrays used for the Esirkepov projection method
double Sx1[7], Sy1[7];
for( unsigned int i=0; i<7; i++ ) {
Sx1[i] = 0.;
Sy1[i] = 0.;
}
// --------------------------------------------------------
// Locate particles & Calculate Esirkepov coef. S, DS and W
// --------------------------------------------------------
// locate the particle on the primal grid at current time-step & calculate coeff. S1
xpn = particles.position( 0, ipart ) * dx_inv_;
int ip = round( xpn + 0.5 * ( type==1 ) ); // index of the central node
delta = xpn - ( double )ip;
delta2 = delta*delta;
delta3 = delta2*delta;
delta4 = delta3*delta;
Sx1[1] = dble_1_ov_384 - dble_1_ov_48 * delta + dble_1_ov_16 * delta2 - dble_1_ov_12 * delta3 + dble_1_ov_24 * delta4;
Sx1[2] = dble_19_ov_96 - dble_11_ov_24 * delta + dble_1_ov_4 * delta2 + dble_1_ov_6 * delta3 - dble_1_ov_6 * delta4;
Sx1[3] = dble_115_ov_192 - dble_5_ov_8 * delta2 + dble_1_ov_4 * delta4;
Sx1[4] = dble_19_ov_96 + dble_11_ov_24 * delta + dble_1_ov_4 * delta2 - dble_1_ov_6 * delta3 - dble_1_ov_6 * delta4;
Sx1[5] = dble_1_ov_384 + dble_1_ov_48 * delta + dble_1_ov_16 * delta2 + dble_1_ov_12 * delta3 + dble_1_ov_24 * delta4;
ypn = particles.position( 1, ipart ) * dy_inv_;
int jp = round( ypn + 0.5*( type==2 ) );
delta = ypn - ( double )jp;
delta2 = delta*delta;
delta3 = delta2*delta;
delta4 = delta3*delta;
Sy1[1] = dble_1_ov_384 - dble_1_ov_48 * delta + dble_1_ov_16 * delta2 - dble_1_ov_12 * delta3 + dble_1_ov_24 * delta4;
Sy1[2] = dble_19_ov_96 - dble_11_ov_24 * delta + dble_1_ov_4 * delta2 + dble_1_ov_6 * delta3 - dble_1_ov_6 * delta4;
Sy1[3] = dble_115_ov_192 - dble_5_ov_8 * delta2 + dble_1_ov_4 * delta4;
Sy1[4] = dble_19_ov_96 + dble_11_ov_24 * delta + dble_1_ov_4 * delta2 - dble_1_ov_6 * delta3 - dble_1_ov_6 * delta4;
Sy1[5] = dble_1_ov_384 + dble_1_ov_48 * delta + dble_1_ov_16 * delta2 + dble_1_ov_12 * delta3 + dble_1_ov_24 * delta4;
// ---------------------------
// Calculate the total current
// ---------------------------
ip -= i_domain_begin + 3;
jp -= j_domain_begin + 3;
for( unsigned int i=0 ; i<7 ; i++ ) {
iloc = ( i+ip )*ny+jp;
for( unsigned int j=0 ; j<7 ; j++ ) {
rhoj[iloc+j] += charge_weight * Sx1[i]*Sy1[j];
}
}//i
}
unsigned int _take_particles(const Particles &ps) {
for (unsigned int i = 0; i < ps.size(); ++i) {
IMP_CHECK_OBJECT(ps[i]);
}
return ps.size();
}
ParticleIndexesAdaptor::ParticleIndexesAdaptor(const Particles &ps)
: tmp_(new ParticleIndexes(ps.size())), val_(tmp_.get()) {
*tmp_ = get_indexes(ParticlesTemp(ps.begin(), ps.end()));
}
// ---------------------------------------------------------------------------------------------------------------------
// 2nd Order Interpolation of the fields at a the particle position (3 nodes are used)
// ---------------------------------------------------------------------------------------------------------------------
void Interpolator2D1Order::operator() (ElectroMagn* EMfields, Particles &particles, int ipart, LocalFields* ELoc, LocalFields* BLoc)
{
// Static cast of the electromagnetic fields
Field2D* Ex2D = static_cast<Field2D*>(EMfields->Ex_);
Field2D* Ey2D = static_cast<Field2D*>(EMfields->Ey_);
Field2D* Ez2D = static_cast<Field2D*>(EMfields->Ez_);
Field2D* Bx2D = static_cast<Field2D*>(EMfields->Bx_m);
Field2D* By2D = static_cast<Field2D*>(EMfields->By_m);
Field2D* Bz2D = static_cast<Field2D*>(EMfields->Bz_m);
// Normalized particle position
double xpn = particles.position(0, ipart)*dx_inv_;
double ypn = particles.position(1, ipart)*dy_inv_;
// Indexes of the central nodes
ip_ = floor(xpn);
jp_ = floor(ypn);
// Declaration and calculation of the coefficient for interpolation
double delta;
delta = xpn - (double)ip_;
coeffxp_[0] = 1.0 - delta;
coeffxp_[1] = delta;
delta = ypn - (double)jp_;
coeffyp_[0] = 1.0 - delta;
coeffyp_[1] = delta;
//!\todo CHECK if this is correct for both primal & dual grids !!!
// First index for summation
ip_ = ip_ - i_domain_begin;
jp_ = jp_ - j_domain_begin;
// -------------------------
// Interpolation of Ex^(d,p)
// -------------------------
(*ELoc).x = compute( coeffxp_, coeffyp_, Ex2D, ip_, jp_);
// -------------------------
// Interpolation of Ey^(p,d)
// -------------------------
(*ELoc).y = compute( coeffxp_, coeffyp_, Ey2D, ip_, jp_);
// -------------------------
// Interpolation of Ez^(p,p)
// -------------------------
(*ELoc).z = compute( coeffxp_, coeffyp_, Ez2D, ip_, jp_);
// -------------------------
// Interpolation of Bx^(p,d)
// -------------------------
(*BLoc).x = compute( coeffxp_, coeffyp_, Bx2D, ip_, jp_);
// -------------------------
// Interpolation of By^(d,p)
// -------------------------
(*BLoc).y = compute( coeffxp_, coeffyp_, By2D, ip_, jp_);
// -------------------------
// Interpolation of Bz^(d,d)
// -------------------------
(*BLoc).z = compute( coeffxp_, coeffyp_, Bz2D, ip_, jp_);
} // END Interpolator2D1Order
//----------------------------------------------------------------------------
void ParticleSystems::CreateScene ()
{
mScene = new0 Node();
mWireState = new0 WireState();
mRenderer->SetOverrideWireState(mWireState);
VertexFormat* vformat = VertexFormat::Create(2,
VertexFormat::AU_POSITION, VertexFormat::AT_FLOAT3, 0,
VertexFormat::AU_TEXCOORD, VertexFormat::AT_FLOAT2, 0);
int vstride = vformat->GetStride();
const int numParticles = 32;
VertexBuffer* vbuffer = new0 VertexBuffer(4*numParticles, vstride);
Float4* positionSizes = new1<Float4>(numParticles);
for (int i = 0; i < numParticles; ++i)
{
positionSizes[i][0] = Mathf::SymmetricRandom();
positionSizes[i][1] = Mathf::SymmetricRandom();
positionSizes[i][2] = Mathf::SymmetricRandom();
positionSizes[i][3] = 0.25f*Mathf::UnitRandom();
}
Particles* particles = new0 Particles(vformat, vbuffer, sizeof(int),
positionSizes, 1.0f);
particles->AttachController(new0 BloodCellController());
mScene->AttachChild(particles);
// Create an image with transparency.
const int xsize = 32, ysize = 32;
Texture2D* texture = new0 Texture2D(Texture::TF_A8R8G8B8, xsize,
ysize, 1);
unsigned char* data = (unsigned char*)texture->GetData(0);
float factor = 1.0f/(xsize*xsize + ysize*ysize);
for (int y = 0, i = 0; y < ysize; ++y)
{
for (int x = 0; x < xsize; ++x)
{
// The image is red.
data[i++] = 0;
data[i++] = 0;
data[i++] = 255;
// Semitransparent within a disk, dropping off to zero outside the
// disk.
int dx = 2*x - xsize;
int dy = 2*y - ysize;
float value = factor*(dx*dx + dy*dy);
if (value < 0.125f)
{
value = Mathf::Cos(4.0f*Mathf::PI*value);
}
else
{
value = 0.0f;
}
data[i++] = (unsigned char)(255.0f*value);
}
}
Texture2DEffect* effect = new0 Texture2DEffect(Shader::SF_LINEAR);
effect->GetAlphaState(0, 0)->BlendEnabled = true;
effect->GetDepthState(0, 0)->Enabled = false;
particles->SetEffectInstance(effect->CreateInstance(texture));
}
void MapModel::verifyPoses(Particles& particles){
double minX, minY, minZ, maxX, maxY, maxZ;
m_map->getMetricMin(minX, minY, minZ);
m_map->getMetricMax(maxX, maxY, maxZ);
// find min. particle weight:
double minWeight = std::numeric_limits<double>::max();
for (Particles::iterator it = particles.begin(); it != particles.end(); ++it) {
if (it->weight < minWeight)
minWeight = it->weight;
}
minWeight -= 200;
unsigned numWall = 0;
unsigned numOut = 0;
unsigned numMotion = 0;
// TODO possible speedup: cluster particles by grid voxels first?
// iterate over samples, multi-threaded:
#pragma omp parallel for
for (unsigned i = 0; i < particles.size(); ++i){
octomap::point3d position(particles[i].pose.getOrigin().getX(),
particles[i].pose.getOrigin().getY(), particles[i].pose.getOrigin().getZ());
// see if outside of map bounds:
if (position(0) < minX || position(0) > maxX
|| position(1) < minY || position(1) > maxY
|| position(2) < minZ || position(2) > maxZ)
{
particles[i].weight = minWeight;
#pragma omp atomic
numOut++;
} else {
// see if occupied cell:
if (this->isOccupied(position)){
particles[i].weight = minWeight;
#pragma omp atomic
numWall++;
} else {
// see if current pose is a valid walking pose:
// TODO: need to check height over floor!
if (m_motionRangeZ >= 0.0 &&
std::abs(particles[i].pose.getOrigin().getZ() - m_motionMeanZ) > m_motionRangeZ)
{
particles[i].weight = minWeight;
#pragma omp atomic
numMotion++;
} else if (m_motionRangePitch >= 0.0 || m_motionRangeRoll >= 0.0){
double yaw, pitch, roll;
particles[i].pose.getBasis().getRPY(roll, pitch, yaw);
if ((m_motionRangePitch >= 0.0 && std::abs(pitch) > m_motionRangePitch)
|| (m_motionRangeRoll >= 0.0 && std::abs(roll) > m_motionRangeRoll))
{
particles[i].weight = minWeight;
#pragma omp atomic
numMotion++;
}
}
}
}
} // end loop over particles
if (numWall > 0 || numOut > 0 || numMotion > 0){
ROS_INFO("Particle weights minimized: %d out of map, %d in obstacles, %d out of motion range", numOut, numWall, numMotion);
}
if (numOut + numWall >= particles.size()){
ROS_WARN("All particles are out of the valid map area or in obstacles!");
}
}
Field TriCubicHermite::scalarCurl2D( const Particles& aParticles ) const
{
assert(data->nDim() == 2);
Field result("n/a","n/a", 1, aParticles.N());
return result;
};
Field TriCubicHermite::vectorDivergence( const Particles& aParticles ) const
{
assert(data->nDim() == 2);
Field result("n/a","n/a", 1, aParticles.N());
return result;
};
void FMM_load_balance(string file, int nbParticles, double dist, double tolerance, double maxEdge, int LBStrategy)
{
int size;
MPI_Comm_size(MPI_COMM_WORLD,&size);
decompo nb1ers(size);
int first = 0;
int last = nbParticles-1;
vec3D center(0,0,0);
Node<Particles> * treeHead = nullptr;
Gaspi_communicator * gComm = nullptr;
// tree creation
Particles p;
if ( LBStrategy == HIST_EXACT ||
LBStrategy == HIST_APPROX ||
LBStrategy == MORTON_MPI_SYNC)
{
p.loadCoordinatesASCII(nbParticles, file);
}
else
{
gComm = new Gaspi_communicator(512, nbParticles);
p.loadCoordinatesASCII(nbParticles, file, gComm);
}
p.scale();
treeHead = new Node<Particles>(p);
// Node Owners array
i64 * nodeOwners = nullptr;
// Load Balancing
LB_Base * LBB = nullptr;
switch (LBStrategy)
{
case HIST_EXACT :
cout <<"--> Exact Histograms" << endl;
LBB = new LoadBalancer<Particles, HistExact> (treeHead, nb1ers, dist, tolerance, first, last, maxEdge, center, gComm, nullptr, nodeOwners, 0);
LBB->run();
break;
case HIST_APPROX :
cout <<"--> Approx Histograms" << endl;
LBB = new LoadBalancer<Particles, HistApprox> (treeHead, nb1ers, dist, tolerance, first, last, maxEdge, center, gComm, nullptr, nodeOwners, 0);
LBB->run();
break;
case MORTON_MPI_SYNC :
cout <<"--> Morton DFS, with tolerance : " << tolerance << endl;
LBB = new LoadBalancer<Particles, MortonSyncMPI>(treeHead, nb1ers, dist, tolerance, first, last, maxEdge, center, gComm, nullptr, nodeOwners, 0);
LBB->run();
break;
case MORTON_GASPI_ASYNC :
cout <<"--> Morton DFS Async, with tolerance : " << tolerance << endl;
LBB = new LoadBalancer<Particles, MortonAsyncGASPI>(treeHead, nb1ers, dist, tolerance, first, last, maxEdge, center, gComm, nullptr, nodeOwners, 0);
LBB->run();
break;
default :
cerr << "No load balancing strategy detected !";
exit(5);
}
}
// ---------------------------------------------------------------------------------------------------------------------
//! Project current densities : main projector
// ---------------------------------------------------------------------------------------------------------------------
void Projector1D4Order::currents( double *Jx, double *Jy, double *Jz, Particles &particles, unsigned int ipart, double invgf, int *iold, double *delta )
{
// Declare local variables
int ipo, ip;
int ip_m_ipo;
double charge_weight = inv_cell_volume * ( double )( particles.charge( ipart ) )*particles.weight( ipart );
double xjn, xj_m_xipo, xj_m_xipo2, xj_m_xipo3, xj_m_xipo4, xj_m_xip, xj_m_xip2, xj_m_xip3, xj_m_xip4;
double crx_p = charge_weight*dx_ov_dt; // current density for particle moving in the x-direction
double cry_p = charge_weight*particles.momentum( 1, ipart )*invgf; // current density in the y-direction of the macroparticle
double crz_p = charge_weight*particles.momentum( 2, ipart )*invgf; // current density allow the y-direction of the macroparticle
double S0[7], S1[7], Wl[7], Wt[7], Jx_p[7]; // arrays used for the Esirkepov projection method
// Initialize variables
for( unsigned int i=0; i<7; i++ ) {
S0[i]=0.;
S1[i]=0.;
Wl[i]=0.;
Wt[i]=0.;
Jx_p[i]=0.;
}//i
// Locate particle old position on the primal grid
xj_m_xipo = *delta; // normalized distance to the nearest grid point
xj_m_xipo2 = xj_m_xipo * xj_m_xipo; // square of the normalized distance to the nearest grid point
xj_m_xipo3 = xj_m_xipo2 * xj_m_xipo; // cube of the normalized distance to the nearest grid point
xj_m_xipo4 = xj_m_xipo3 * xj_m_xipo; // 4th power of the normalized distance to the nearest grid point
// Locate particle new position on the primal grid
xjn = particles.position( 0, ipart ) * dx_inv_;
ip = round( xjn ); // index of the central node
xj_m_xip = xjn - ( double )ip; // normalized distance to the nearest grid point
xj_m_xip2 = xj_m_xip * xj_m_xip; // square of the normalized distance to the nearest grid point
xj_m_xip3 = xj_m_xip2 * xj_m_xip; // cube of the normalized distance to the nearest grid point
xj_m_xip4 = xj_m_xip3 * xj_m_xip; // 4th power of the normalized distance to the nearest grid point
// coefficients 4th order interpolation on 5 nodes
S0[1] = dble_1_ov_384 - dble_1_ov_48 * xj_m_xipo + dble_1_ov_16 * xj_m_xipo2 - dble_1_ov_12 * xj_m_xipo3 + dble_1_ov_24 * xj_m_xipo4;
S0[2] = dble_19_ov_96 - dble_11_ov_24 * xj_m_xipo + dble_1_ov_4 * xj_m_xipo2 + dble_1_ov_6 * xj_m_xipo3 - dble_1_ov_6 * xj_m_xipo4;
S0[3] = dble_115_ov_192 - dble_5_ov_8 * xj_m_xipo2 + dble_1_ov_4 * xj_m_xipo4;
S0[4] = dble_19_ov_96 + dble_11_ov_24 * xj_m_xipo + dble_1_ov_4 * xj_m_xipo2 - dble_1_ov_6 * xj_m_xipo3 - dble_1_ov_6 * xj_m_xipo4;
S0[5] = dble_1_ov_384 + dble_1_ov_48 * xj_m_xipo + dble_1_ov_16 * xj_m_xipo2 + dble_1_ov_12 * xj_m_xipo3 + dble_1_ov_24 * xj_m_xipo4;
// coefficients 2nd order interpolation on 5 nodes
ipo = *iold; // index of the central node
ip_m_ipo = ip-ipo-index_domain_begin;
S1[ip_m_ipo+1] = dble_1_ov_384 - dble_1_ov_48 * xj_m_xip + dble_1_ov_16 * xj_m_xip2 - dble_1_ov_12 * xj_m_xip3 + dble_1_ov_24 * xj_m_xip4;
S1[ip_m_ipo+2] = dble_19_ov_96 - dble_11_ov_24 * xj_m_xip + dble_1_ov_4 * xj_m_xip2 + dble_1_ov_6 * xj_m_xip3 - dble_1_ov_6 * xj_m_xip4;
S1[ip_m_ipo+3] = dble_115_ov_192 - dble_5_ov_8 * xj_m_xip2 + dble_1_ov_4 * xj_m_xip4;
S1[ip_m_ipo+4] = dble_19_ov_96 + dble_11_ov_24 * xj_m_xip + dble_1_ov_4 * xj_m_xip2 - dble_1_ov_6 * xj_m_xip3 - dble_1_ov_6 * xj_m_xip4;
S1[ip_m_ipo+5] = dble_1_ov_384 + dble_1_ov_48 * xj_m_xip + dble_1_ov_16 * xj_m_xip2 + dble_1_ov_12 * xj_m_xip3 + dble_1_ov_24 * xj_m_xip4;
// coefficients used in the Esirkepov method
for( unsigned int i=0; i<7; i++ ) {
Wl[i] = S0[i] - S1[i]; // for longitudinal current (x)
Wt[i] = 0.5 * ( S0[i] + S1[i] ); // for transverse currents (y,z)
}//i
// local current created by the particle
// calculate using the charge conservation equation
for( unsigned int i=1; i<7; i++ ) {
Jx_p[i] = Jx_p[i-1] + crx_p * Wl[i-1];
}
ipo -= 3 ;
// 4th order projection for the total currents & charge density
// At the 4th order, oversize = 3.
for( unsigned int i=0; i<7; i++ ) {
Jx[i + ipo] += Jx_p[i];
Jy[i + ipo] += cry_p * Wt[i];
Jz[i + ipo] += crz_p * Wt[i];
}//i
}
Particle& GetOrigin(){
return *(*m_particles.begin() );
}
Particles ResamplingResidual::resample(Particles* particles){
Particles resampledSet;
Particles stage1;
int count = 0;
resampledSet.samples = fmat(particles->samples.n_rows,particles->samples.n_cols);
resampledSet.weights = frowvec(particles->weights.n_cols);
fvec cumsum;
fvec random;
unsigned int number = particles->samples.n_cols;
unsigned int numberOfStage1 = 0;
// Generating copie information of every particle
ivec copies = zeros<ivec>(particles->samples.n_cols);
for (unsigned int i=0;i<particles->samples.n_cols;++i){
copies = (int) floor(number*particles->weights(i));
}
numberOfStage1 = sum(copies);
stage1.samples = fmat(particles->samples.n_rows,numberOfStage1);
stage1.weights = frowvec(numberOfStage1);
//Picking N_i = N*w_i copies of i-th particle
for (unsigned int i=1; i < copies.n_rows;++i){
for (int j=0;j<copies(i);++j){
for (unsigned int k=0;k<particles->samples.n_rows;++k){
stage1.samples(k,count) = particles->samples(k,i);
}
stage1.weights(count) = particles->weights(i) - (float)copies(i)/number;
count++;
}
}
// multinomial resampling with residuum weights w_i = w_i - N_i/N
cumsum = zeros<fvec>(numberOfStage1);
for (unsigned int i=1; i < stage1.weights.n_cols;++i){
cumsum(i) = cumsum(i-1) + stage1.weights(i);
}
// generate sorted random set
random = randu<fvec>(numberOfStage1);
random=random*cumsum(cumsum.n_rows-1);
random = sort(random);
for (unsigned int j=0; j < random.n_rows; ++j){
for (unsigned int i=0 ; i < cumsum.n_rows; ++i){
if (random(j) <= cumsum(i)){
if(i > 0){
if(random(j) >= cumsum(i-1)) {
for (unsigned int k=0;k<stage1.samples.n_rows;++k){
resampledSet.samples(k,j) = stage1.samples(k,i);
assignmentVec.push_back(i);
}
break;
}
}
else {
for (unsigned int k=0; k<stage1.samples.n_rows; ++k){
resampledSet.samples(k,j) = stage1.samples(k,i);
assignmentVec.push_back(i);
}
break;
}
}
// Normalize weights
resampledSet.weights(j) = 1.0f/particles->weights.n_cols;
}
}
return resampledSet;
}
Particle& GetEnd(){
return *(*m_particles.end() );
}
// ---------------------------------------------------------------------------------------------------------------------
//! Project current densities : main projector
// ---------------------------------------------------------------------------------------------------------------------
void Projector2D4Order::currents( double *Jx, double *Jy, double *Jz, Particles &particles, unsigned int ipart, double invgf, int *iold, double *deltaold )
{
int nparts = particles.size();
// -------------------------------------
// Variable declaration & initialization
// -------------------------------------
int iloc;
// (x,y,z) components of the current density for the macro-particle
double charge_weight = inv_cell_volume * ( double )( particles.charge( ipart ) )*particles.weight( ipart );
double crx_p = charge_weight*dx_ov_dt;
double cry_p = charge_weight*dy_ov_dt;
double crz_p = charge_weight*one_third*particles.momentum( 2, ipart )*invgf;
// variable declaration
double xpn, ypn;
double delta, delta2, delta3, delta4;
// arrays used for the Esirkepov projection method
double Sx0[7], Sx1[7], Sy0[7], Sy1[7], DSx[7], DSy[7], tmpJx[7];
for( unsigned int i=0; i<7; i++ ) {
Sx1[i] = 0.;
Sy1[i] = 0.;
tmpJx[i] = 0.;
}
Sx0[0] = 0.;
Sx0[6] = 0.;
Sy0[0] = 0.;
Sy0[6] = 0.;
// --------------------------------------------------------
// Locate particles & Calculate Esirkepov coef. S, DS and W
// --------------------------------------------------------
// locate the particle on the primal grid at former time-step & calculate coeff. S0
delta = deltaold[0*nparts];
delta2 = delta*delta;
delta3 = delta2*delta;
delta4 = delta3*delta;
Sx0[1] = dble_1_ov_384 - dble_1_ov_48 * delta + dble_1_ov_16 * delta2 - dble_1_ov_12 * delta3 + dble_1_ov_24 * delta4;
Sx0[2] = dble_19_ov_96 - dble_11_ov_24 * delta + dble_1_ov_4 * delta2 + dble_1_ov_6 * delta3 - dble_1_ov_6 * delta4;
Sx0[3] = dble_115_ov_192 - dble_5_ov_8 * delta2 + dble_1_ov_4 * delta4;
Sx0[4] = dble_19_ov_96 + dble_11_ov_24 * delta + dble_1_ov_4 * delta2 - dble_1_ov_6 * delta3 - dble_1_ov_6 * delta4;
Sx0[5] = dble_1_ov_384 + dble_1_ov_48 * delta + dble_1_ov_16 * delta2 + dble_1_ov_12 * delta3 + dble_1_ov_24 * delta4;
delta = deltaold[1*nparts];
delta2 = delta*delta;
delta3 = delta2*delta;
delta4 = delta3*delta;
Sy0[1] = dble_1_ov_384 - dble_1_ov_48 * delta + dble_1_ov_16 * delta2 - dble_1_ov_12 * delta3 + dble_1_ov_24 * delta4;
Sy0[2] = dble_19_ov_96 - dble_11_ov_24 * delta + dble_1_ov_4 * delta2 + dble_1_ov_6 * delta3 - dble_1_ov_6 * delta4;
Sy0[3] = dble_115_ov_192 - dble_5_ov_8 * delta2 + dble_1_ov_4 * delta4;
Sy0[4] = dble_19_ov_96 + dble_11_ov_24 * delta + dble_1_ov_4 * delta2 - dble_1_ov_6 * delta3 - dble_1_ov_6 * delta4;
Sy0[5] = dble_1_ov_384 + dble_1_ov_48 * delta + dble_1_ov_16 * delta2 + dble_1_ov_12 * delta3 + dble_1_ov_24 * delta4;
// locate the particle on the primal grid at current time-step & calculate coeff. S1
xpn = particles.position( 0, ipart ) * dx_inv_;
int ip = round( xpn );
int ipo = iold[0*nparts];
int ip_m_ipo = ip-ipo-i_domain_begin;
delta = xpn - ( double )ip;
delta2 = delta*delta;
delta3 = delta2*delta;
delta4 = delta3*delta;
Sx1[ip_m_ipo+1] = dble_1_ov_384 - dble_1_ov_48 * delta + dble_1_ov_16 * delta2 - dble_1_ov_12 * delta3 + dble_1_ov_24 * delta4;
Sx1[ip_m_ipo+2] = dble_19_ov_96 - dble_11_ov_24 * delta + dble_1_ov_4 * delta2 + dble_1_ov_6 * delta3 - dble_1_ov_6 * delta4;
Sx1[ip_m_ipo+3] = dble_115_ov_192 - dble_5_ov_8 * delta2 + dble_1_ov_4 * delta4;
Sx1[ip_m_ipo+4] = dble_19_ov_96 + dble_11_ov_24 * delta + dble_1_ov_4 * delta2 - dble_1_ov_6 * delta3 - dble_1_ov_6 * delta4;
Sx1[ip_m_ipo+5] = dble_1_ov_384 + dble_1_ov_48 * delta + dble_1_ov_16 * delta2 + dble_1_ov_12 * delta3 + dble_1_ov_24 * delta4;
ypn = particles.position( 1, ipart ) * dy_inv_;
int jp = round( ypn );
int jpo = iold[1*nparts];
int jp_m_jpo = jp-jpo-j_domain_begin;
delta = ypn - ( double )jp;
delta2 = delta*delta;
delta3 = delta2*delta;
delta4 = delta3*delta;
Sy1[jp_m_jpo+1] = dble_1_ov_384 - dble_1_ov_48 * delta + dble_1_ov_16 * delta2 - dble_1_ov_12 * delta3 + dble_1_ov_24 * delta4;
Sy1[jp_m_jpo+2] = dble_19_ov_96 - dble_11_ov_24 * delta + dble_1_ov_4 * delta2 + dble_1_ov_6 * delta3 - dble_1_ov_6 * delta4;
Sy1[jp_m_jpo+3] = dble_115_ov_192 - dble_5_ov_8 * delta2 + dble_1_ov_4 * delta4;
Sy1[jp_m_jpo+4] = dble_19_ov_96 + dble_11_ov_24 * delta + dble_1_ov_4 * delta2 - dble_1_ov_6 * delta3 - dble_1_ov_6 * delta4;
Sy1[jp_m_jpo+5] = dble_1_ov_384 + dble_1_ov_48 * delta + dble_1_ov_16 * delta2 + dble_1_ov_12 * delta3 + dble_1_ov_24 * delta4;
for( unsigned int i=0; i < 7; i++ ) {
DSx[i] = Sx1[i] - Sx0[i];
DSy[i] = Sy1[i] - Sy0[i];
}
// calculate Esirkepov coeff. Wx, Wy, Wz when used
double tmp, tmp2, tmp3, tmpY;
//Do not compute useless weights.
// ------------------------------------------------
// Local current created by the particle
// calculate using the charge conservation equation
// ------------------------------------------------
// ---------------------------
// Calculate the total current
// ---------------------------
ipo -= 3; //This minus 3 come from the order 4 scheme, based on a 7 points stencil from -3 to +3.
jpo -= 3;
// i =0
{
iloc = ipo*nprimy+jpo;
tmp2 = 0.5*Sx1[0];
tmp3 = Sx1[0];
Jz[iloc] += crz_p * ( Sy1[0]*tmp3 );
tmp = 0;
tmpY = Sx0[0] + 0.5*DSx[0];
for( unsigned int j=1 ; j<7 ; j++ ) {
tmp -= cry_p * DSy[j-1] * tmpY;
Jy[iloc+j+ipo] += tmp; //Because size of Jy in Y is nprimy+1.
Jz[iloc+j] += crz_p * ( Sy0[j]*tmp2 + Sy1[j]*tmp3 );
}
}//i
for( unsigned int i=1 ; i<7 ; i++ ) {
iloc = ( i+ipo )*nprimy+jpo;
tmpJx[0] -= crx_p * DSx[i-1] * ( 0.5*DSy[0] );
Jx[iloc] += tmpJx[0];
tmp2 = 0.5*Sx1[i] + Sx0[i];
tmp3 = 0.5*Sx0[i] + Sx1[i];
Jz[iloc] += crz_p * ( Sy1[0]*tmp3 );
tmp = 0;
tmpY = Sx0[i] + 0.5*DSx[i];
for( unsigned int j=1 ; j<7 ; j++ ) {
tmpJx[j] -= crx_p * DSx[i-1] * ( Sy0[j] + 0.5*DSy[j] );
Jx[iloc+j] += tmpJx[j];
tmp -= cry_p * DSy[j-1] * tmpY;
Jy[iloc+j+i+ipo] += tmp; //Because size of Jy in Y is nprimy+1.
Jz[iloc+j] += crz_p * ( Sy0[j]*tmp2 + Sy1[j]*tmp3 );
}
}//i
}
void calculateBoo(Particles &parts, const string& filename, const bool noZ=false, bool quiet=false)
{
const string inputPath = filename.substr(0,filename.find_last_of("."));
const string ext = filename.substr(filename.find_last_of(".")+1);
const string head = filename.substr(0,filename.rfind("_t"));
const string neck = filename.substr(head.size(), inputPath.size()-head.size());
//select interesting particles and load (or make) bonds
vector<size_t> inside, secondInside;
try
{
BondSet bonds = loadBonds(inputPath+".bonds");
parts.makeNgbList(bonds);
inside = parts.selectInside_noindex(1.3*parts.radius, noZ);
secondInside = parts.selectInside_noindex(2.0*1.3*parts.radius, noZ);
}
catch(invalid_argument &e)
{
if(!quiet) cout<<"bond network ";
boost::progress_timer *ti;
if(!quiet) ti = new boost::progress_timer();
parts.makeRTreeIndex();
parts.makeNgbList(1.3);
BondSet bonds = parts.getBonds();
ofstream bondFile((inputPath+".bonds").c_str(), ios::out | ios::trunc);
for(BondSet::const_iterator b=bonds.begin(); b!= bonds.end();++b)
bondFile<<b->low()<<" "<<b->high()<<"\n";
inside = parts.selectInside(1.3*parts.radius, noZ);
secondInside = parts.selectInside(2.0*1.3*parts.radius, noZ);
if(!quiet) delete ti;
}
const bool empty = inside.empty(), empty2 = secondInside.empty();
if(empty)
for(size_t p=0; p<parts.size(); ++p)
inside.insert(inside.end(), p);
if(empty2)
for(size_t p=0; p<parts.size(); ++p)
secondInside.insert(secondInside.end(), p);
//calculate and export qlm
vector<BooData> qlm, qlm_cg, qlm_sf;
{
boost::progress_timer *ti;
if(!quiet)
{
cout<<"boo with and without surface bonds for "<<inside.size()<<" particles ";
ti = new boost::progress_timer();
}
parts.getBOOs_SurfBOOs(qlm, qlm_sf);
if(!empty)
{
parts.removeOutside(inside, qlm);
parts.removeOutside(inside, qlm_sf);
}
if(!quiet) delete ti;
}
{
if(!quiet) cout<<"coarse grained for "<<secondInside.size()<<" particles ";
boost::progress_timer* ti;
if(!quiet) ti = new boost::progress_timer();
parts.getCgBOOs(secondInside, qlm, qlm_cg);
if(!quiet) delete ti;
}
ofstream qlmFile((inputPath+".qlm").c_str(), ios::out | ios::trunc);
copy(
qlm.begin(), qlm.end(),
ostream_iterator<BooData>(qlmFile,"\n")
);
qlmFile.close();
ofstream qlmcgFile((head+"_space"+neck+".qlm").c_str(), ios::out | ios::trunc);
copy(
qlm_cg.begin(), qlm_cg.end(),
ostream_iterator<BooData>(qlmcgFile,"\n")
);
qlmcgFile.close();
//calculate and export invarients
ofstream cloudFile((inputPath+".cloud").c_str(), ios::out | ios::trunc);
cloudFile<<"#q4\tq6\tq8\tq10\tw4\tw6\tw8\tw10"<<endl;
transform(
qlm.begin(), qlm.end(),
ostream_iterator<string>(cloudFile,"\n"),
cloud_exporter()
);
cloudFile.close();
ofstream cloud_cgFile((head+"_space"+neck+".cloud").c_str(), ios::out | ios::trunc);
cloud_cgFile<<"#Q4\tQ6\tQ8\tQ10\tW4\tW6\tW8\tW10"<<endl;
transform(
qlm_cg.begin(), qlm_cg.end(),
ostream_iterator<string>(cloud_cgFile,"\n"),
cloud_exporter()
);
cloud_cgFile.close();
ofstream cloud_sfFile((head+"_surf"+neck+".cloud").c_str(), ios::out | ios::trunc);
cloud_cgFile<<"#Q4\tQ6\tW4\tW6"<<endl;
transform(
qlm_sf.begin(), qlm_sf.end(),
ostream_iterator<string>(cloud_sfFile,"\n"),
cloud_exporter()
);
cloud_sfFile.close();
}
unsigned int _take_particles(Model *, const Particles &ps, base::TextOutput) {
for (unsigned int i = 0; i < ps.size(); ++i) {
IMP_CHECK_OBJECT(ps[i]);
}
return ps.size();
}
/**
* This function
* @param * nbElemPerNode : Array of number of elements, per octree node
* @param * firstElemAdress : Array of Indexes.
* Gives the index(address) first element's data in the Id's array fmmData%elem, per octree node.
* @param * nbSonsPerNode : Array of number of sons, per octree node
* @param * firstSonId : Array of number of first son Id, per octree node
* @param * nodeOwners : Array of responsible mpi ranks, per octree node. (From 1 to nbRanks, Fortran's style)
* The Result of the load balancing is read here.
* @param * nodeCenters : Array of octree node centers
* @param * endlev : Array of last octree node id, per octree level
* @param * nbLevels : Number of Octree levels
* @param * maxEdge : Edge of the first octree node. (the biggest)
* @param *LBstrategy : integer used to choose the load balancing strategy
*/
void fmm_load_balance_( i64 * nbElemPerNode, i64 * firstElemAdress, i64 * nbSonsPerNode, i64 * firstSonId, i64 * nodeOwners, double * nodeCenters, i64 * endlev,
i64 * nbLevels, double * maxEdge, int * LBstrategy)
{
// MPI parameters
int size; MPI_Comm_size(MPI_COMM_WORLD, &size);
int rank; MPI_Comm_rank(MPI_COMM_WORLD, &rank);
// create Particles
vec3D center(nodeCenters[0], nodeCenters[1], nodeCenters[2]);
scale(center);
Particles p;
p.setAttributes(0,nbElemPerNode[0],*maxEdge, center);
int nbElements = nbElemPerNode[0];
p.setNewCoordinates(elements, nbElements);
p.scale();
// creatre Octree
Node<Particles> * octree = nullptr;
octree = new Node<Particles>(p);
octree -> read_octree(nbElemPerNode, firstElemAdress, nbSonsPerNode, firstSonId, nodeCenters);
// Octree useful characteristics
int height = (*nbLevels) - 1;
int nbLeaves = endlev[height] - endlev[height-1];
int firstLeave = endlev[height-1]; // endlev[height-1] +1(next node) -1(F to C)
int firstElem = 0;
int lastElem = nbElemPerNode[0]-1;
int nbNodes = endlev[height]*3;
double * centers = new double[nbNodes];
// Load Balancing useful parameters
decompo nb1ers(size);
// Load Balance
LB_Base * LBB = nullptr;
switch (*LBstrategy)
{
case MORTON_MPI_SYNC :
cout << "*** ----- MORTON -----" << endl;
LBB = new LoadBalancer<Particles, MortonSyncMPI>(octree, nb1ers, 0, 0, firstElem, lastElem, *maxEdge, center, nullptr, nullptr/*centers*/, nodeOwners, 0);
break;
case HIST_APPROX :
cout << "*** ----- KD TREE -----" << endl;
// Get a copy of the octree centers, scale them and apply load balancing strategy
copyAndScaleArray(nodeCenters, centers, nbNodes);
LBB = new LoadBalancer<Particles, HistApprox>(octree, nb1ers, 0, 0, firstElem, lastElem, *maxEdge, center, nullptr, ¢ers[firstLeave*3], &nodeOwners[firstLeave], nbLeaves);
break;
case HIST_APPROX_X :
cout << "*** ----- SAUCISONNAGE EN X -----" << endl;
// Get a copy of the octree centers, scale them and apply load balancing strategy
copyAndScaleArray(nodeCenters, centers, nbNodes);
// test rapide - saucissonnage en X
cout << "Decomposition has been modified to : " << endl;
nb1ers._list.resize(1);
nb1ers._list[0] = size;
nb1ers.display();
LBB = new LoadBalancer<Particles, HistApprox>(octree, nb1ers, 0, 0, firstElem, lastElem, *maxEdge, center, nullptr, ¢ers[firstLeave*3], &nodeOwners[firstLeave], nbLeaves);
break;
default :
cerr << "No identified Load Balancing strategy" << endl;
exit(0);
}
LBB->run();
delete Particles::_coordinates;
cout << "---- Load Balancing ----> TERMINATED !" <<endl;
int * counters = new int[size + 1]();
}
bool Particle::update()
{
if (!mMap)
return false;
if (mLifetimeLeft == 0 && mAlive == ALIVE)
mAlive = DEAD_TIMEOUT;
Vector oldPos = mPos;
if (mAlive == ALIVE)
{
//calculate particle movement
if (mMomentum != 1.0f)
{
mVelocity *= mMomentum;
}
if (mTarget && mAcceleration != 0.0f)
{
Vector dist = mPos - mTarget->getPosition();
dist.x *= SIN45;
float invHypotenuse;
switch (Particle::fastPhysics)
{
case 1:
invHypotenuse = fastInvSqrt(
dist.x * dist.x + dist.y * dist.y + dist.z * dist.z);
break;
case 2:
invHypotenuse = 2.0f /
fabs(dist.x) + fabs(dist.y) + fabs(dist.z);
break;
default:
invHypotenuse = 1.0f / sqrt(
dist.x * dist.x + dist.y * dist.y + dist.z * dist.z);
break;
}
if (invHypotenuse)
{
if (mInvDieDistance > 0.0f && invHypotenuse > mInvDieDistance)
{
mAlive = DEAD_IMPACT;
}
float accFactor = invHypotenuse * mAcceleration;
mVelocity -= dist * accFactor;
}
}
if (mRandomness > 0)
{
mVelocity.x += (rand()%mRandomness - rand()%mRandomness) / 1000.0f;
mVelocity.y += (rand()%mRandomness - rand()%mRandomness) / 1000.0f;
mVelocity.z += (rand()%mRandomness - rand()%mRandomness) / 1000.0f;
}
mVelocity.z -= mGravity;
// Update position
mPos.x += mVelocity.x;
mPos.y += mVelocity.y * SIN45;
mPos.z += mVelocity.z * SIN45;
// Update other stuff
if (mLifetimeLeft > 0)
{
mLifetimeLeft--;
}
mLifetimePast++;
if (mPos.z < 0.0f)
{
if (mBounce > 0.0f)
{
mPos.z *= -mBounce;
mVelocity *= mBounce;
mVelocity.z = -mVelocity.z;
}
else
{
mAlive = DEAD_FLOOR;
}
}
else if (mPos.z > PARTICLE_SKY)
{
mAlive = DEAD_SKY;
}
// Update child emitters
if ((mLifetimePast-1)%Particle::emitterSkip == 0)
{
for (EmitterIterator e = mChildEmitters.begin();
e != mChildEmitters.end(); e++)
{
Particles newParticles = (*e)->createParticles(mLifetimePast);
for (ParticleIterator p = newParticles.begin();
p != newParticles.end(); p++)
{
(*p)->moveBy(mPos);
mChildParticles.push_back (*p);
}
}
}
}
// create death effect when the particle died
if (mAlive != ALIVE && mAlive != DEAD_LONG_AGO)
{
if ((mAlive & mDeathEffectConditions) > 0x00 && !mDeathEffect.empty())
{
Particle* deathEffect = particleEngine->addEffect(mDeathEffect, 0, 0);
deathEffect->moveBy(mPos);
}
mAlive = DEAD_LONG_AGO;
}
Vector change = mPos - oldPos;
// Update child particles
for (ParticleIterator p = mChildParticles.begin();
p != mChildParticles.end();)
{
//move particle with its parent if desired
if ((*p)->doesFollow())
{
(*p)->moveBy(change);
}
//update particle
if ((*p)->update())
{
p++;
}
else
{
delete (*p);
p = mChildParticles.erase(p);
}
}
if (mAlive != ALIVE && mChildParticles.empty() && mAutoDelete)
{
return false;
}
return true;
}
void PusherBorisV::operator()( Particles &particles, SmileiMPI *smpi, int istart, int iend, int ithread, int ipart_ref )
{
std::vector<double> *Epart = &( smpi->dynamics_Epart[ithread] );
std::vector<double> *Bpart = &( smpi->dynamics_Bpart[ithread] );
double *invgf = &( smpi->dynamics_invgf[ithread][0] );
double charge_over_mass_dts2;
double inv_det_T, Tx, Ty, Tz;
double local_invgf;
//int IX;
//int* cell_keys;
double *momentum[3];
for( int i = 0 ; i<3 ; i++ ) {
momentum[i] = &( particles.momentum( i, 0 ) );
}
double *position[3];
for( int i = 0 ; i<nDim_ ; i++ ) {
position[i] = &( particles.position( i, 0 ) );
}
#ifdef __DEBUG
double *position_old[3];
for( int i = 0 ; i<nDim_ ; i++ ) {
position_old[i] = &( particles.position_old( i, 0 ) );
}
#endif
short *charge = &( particles.charge( 0 ) );
int nparts = Epart->size()/3;
double *Ex = &( ( *Epart )[0*nparts] );
double *Ey = &( ( *Epart )[1*nparts] );
double *Ez = &( ( *Epart )[2*nparts] );
double *Bx = &( ( *Bpart )[0*nparts] );
double *By = &( ( *Bpart )[1*nparts] );
double *Bz = &( ( *Bpart )[2*nparts] );
//particles.cell_keys.resize(nparts);
//cell_keys = &( particles.cell_keys[0]);
double dcharge[nparts];
#pragma omp simd
for( int ipart=istart ; ipart<iend; ipart++ ) {
dcharge[ipart] = ( double )( charge[ipart] );
}
#pragma omp simd
for( int ipart=istart ; ipart<iend; ipart++ ) {
double psm[3], um[3];
charge_over_mass_dts2 = dcharge[ipart]*one_over_mass_*dts2;
// init Half-acceleration in the electric field
psm[0] = charge_over_mass_dts2*( *( Ex+ipart-ipart_ref ) );
psm[1] = charge_over_mass_dts2*( *( Ey+ipart-ipart_ref ) );
psm[2] = charge_over_mass_dts2*( *( Ez+ipart-ipart_ref ) );
//(*this)(particles, ipart, (*Epart)[ipart], (*Bpart)[ipart] , (*invgf)[ipart]);
um[0] = momentum[0][ipart] + psm[0];
um[1] = momentum[1][ipart] + psm[1];
um[2] = momentum[2][ipart] + psm[2];
// Rotation in the magnetic field
local_invgf = charge_over_mass_dts2 / sqrt( 1.0 + um[0]*um[0] + um[1]*um[1] + um[2]*um[2] );
Tx = local_invgf * ( *( Bx+ipart-ipart_ref ) );
Ty = local_invgf * ( *( By+ipart-ipart_ref ) );
Tz = local_invgf * ( *( Bz+ipart-ipart_ref ) );
inv_det_T = 1.0/( 1.0+Tx*Tx+Ty*Ty+Tz*Tz );
psm[0] += ( ( 1.0+Tx*Tx-Ty*Ty-Tz*Tz )* um[0] + 2.0*( Tx*Ty+Tz )* um[1] + 2.0*( Tz*Tx-Ty )* um[2] )*inv_det_T;
psm[1] += ( 2.0*( Tx*Ty-Tz )* um[0] + ( 1.0-Tx*Tx+Ty*Ty-Tz*Tz )* um[1] + 2.0*( Ty*Tz+Tx )* um[2] )*inv_det_T;
psm[2] += ( 2.0*( Tz*Tx+Ty )* um[0] + 2.0*( Ty*Tz-Tx )* um[1] + ( 1.0-Tx*Tx-Ty*Ty+Tz*Tz )* um[2] )*inv_det_T;
// finalize Half-acceleration in the electric field
local_invgf = 1. / sqrt( 1.0 + psm[0]*psm[0] + psm[1]*psm[1] + psm[2]*psm[2] );
invgf[ipart-ipart_ref] = local_invgf;
momentum[0][ipart] = psm[0];
momentum[1][ipart] = psm[1];
momentum[2][ipart] = psm[2];
// Move the particle
#ifdef __DEBUG
for( int i = 0 ; i<nDim_ ; i++ ) {
position_old[i][ipart] = position[i][ipart];
}
#endif
local_invgf *= dt;
for( int i = 0 ; i<nDim_ ; i++ ) {
position[i][ipart] += psm[i]*local_invgf;
}
}
// This is temporarily moved to SpeciesV.cpp
//#pragma omp simd
//for (int ipart=istart ; ipart<iend; ipart++ ) {
//
// for ( int i = 0 ; i<nDim_ ; i++ ){
// cell_keys[ipart] *= nspace[i];
// cell_keys[ipart] += round( (position[i][ipart]-min_loc_vec[i]) * dx_inv_[i] );
// }
//
//}
}
IMPCNMULTIFIT_BEGIN_NAMESPACE
Floats get_rmsd_for_models(const std::string param_filename,
const std::string trans_filename,
const std::string ref_filename, int start_model,
int end_model) {
std::string protein_filename, surface_filename;
int cn_symm_deg;
std::cout << "============= parameters ============" << std::endl;
std::cout << "params filename : " << param_filename << std::endl;
std::cout << "trans filename : " << trans_filename << std::endl;
std::cout << "ref filename : " << ref_filename << std::endl;
std::cout << "start index to rmsd : " << start_model << std::endl;
std::cout << "end index to rmsd : " << end_model << std::endl;
std::cout << "=====================================" << std::endl;
internal::Parameters params(param_filename.c_str());
protein_filename = params.get_unit_pdb_fn();
cn_symm_deg = params.get_cn_symm();
IMP_NEW(Model, mdl, ());
atom::Hierarchy asmb_ref;
atom::Hierarchies mhs;
// read the monomer
core::XYZs model_xyzs;
for (int i = 0; i < cn_symm_deg; i++) {
atom::Hierarchy h =
atom::read_pdb(protein_filename, mdl, new atom::CAlphaPDBSelector());
atom::Chain c = atom::get_chain(
atom::Residue(atom::get_residue(atom::Atom(core::get_leaves(h)[0]))));
c.set_id(std::string(1, char(65 + i)));
atom::add_radii(h);
atom::create_rigid_body(h);
mhs.push_back(h);
Particles leaves = core::get_leaves(h);
for (Particles::iterator it = leaves.begin(); it != leaves.end();
it++) {
model_xyzs.push_back(core::XYZ(*it));
}
}
// read the transformations
multifit::FittingSolutionRecords recs =
multifit::read_fitting_solutions(trans_filename.c_str());
// read the reference structure
asmb_ref = atom::read_pdb(ref_filename, mdl, new atom::CAlphaPDBSelector());
atom::Hierarchies ref_chains =
atom::Hierarchies(atom::get_by_type(asmb_ref, atom::CHAIN_TYPE));
std::cout << "number of records:" << recs.size() << std::endl;
Floats rmsd;
std::ofstream out;
out.open("rmsd.output");
if (end_model < 0 || end_model >= static_cast<int>(recs.size())) {
end_model = recs.size() - 1;
}
for (int i = start_model; i >= 0 && i <= end_model; ++i) {
algebra::Transformation3D t1 = recs[i].get_dock_transformation();
algebra::Transformation3D t2 = recs[i].get_fit_transformation();
algebra::Transformation3D t2_inv = t1.get_inverse();
transform_cn_assembly(mhs, t1);
for (unsigned int j = 0; j < model_xyzs.size(); j++) {
model_xyzs[j]
.set_coordinates(t2.get_transformed(model_xyzs[j].get_coordinates()));
}
std::cout << mhs.size() << "," << ref_chains.size() << std::endl;
Float cn_rmsd = get_cn_rmsd(mhs, ref_chains);
out << " trans:" << i << " rmsd: " << cn_rmsd
<< " cc: " << 1. - recs[i].get_fitting_score() << std::endl;
rmsd.push_back(cn_rmsd);
for (unsigned int j = 0; j < model_xyzs.size(); j++) {
model_xyzs[j].set_coordinates(
t2_inv.get_transformed(model_xyzs[j].get_coordinates()));
}
/* std::stringstream ss;
ss<<"asmb_"<<i<<".pdb";
atom::write_pdb(mhs,ss.str());*/
transform_cn_assembly(mhs, t1.get_inverse());
}
out.close();
return rmsd;
}
void PusherPonderomotiveBorisV::operator()( Particles &particles, SmileiMPI *smpi, int istart, int iend, int ithread, int ipart_ref )
{
std::vector<double> *Epart = &( smpi->dynamics_Epart[ithread] );
std::vector<double> *Bpart = &( smpi->dynamics_Bpart[ithread] );
std::vector<double> *GradPhipart = &( smpi->dynamics_GradPHIpart[ithread] );
std::vector<double> *dynamics_inv_gamma_ponderomotive = &( smpi->dynamics_inv_gamma_ponderomotive[ithread] );
double charge_over_mass_dts2, charge_sq_over_mass_sq_dts4;
double alpha, inv_det_T, Tx, Ty, Tz, Tx2, Ty2, Tz2;
double TxTy, TyTz, TzTx;
double one_ov_gamma_ponderomotive;
double *momentum[3];
for( int i = 0 ; i<3 ; i++ ) {
momentum[i] = &( particles.momentum( i, 0 ) );
}
short *charge = &( particles.charge( 0 ) );
int nparts = Epart->size()/3;
double *Ex = &( ( *Epart )[0*nparts] );
double *Ey = &( ( *Epart )[1*nparts] );
double *Ez = &( ( *Epart )[2*nparts] );
double *Bx = &( ( *Bpart )[0*nparts] );
double *By = &( ( *Bpart )[1*nparts] );
double *Bz = &( ( *Bpart )[2*nparts] );
double *GradPhix = &( ( *GradPhipart )[0*nparts] );
double *GradPhiy = &( ( *GradPhipart )[1*nparts] );
double *GradPhiz = &( ( *GradPhipart )[2*nparts] );
double *inv_gamma_ponderomotive = &( ( *dynamics_inv_gamma_ponderomotive )[0*nparts] );
double dcharge[nparts];
#pragma omp simd
for( int ipart=istart ; ipart<iend; ipart++ ) {
dcharge[ipart] = ( double )( charge[ipart] );
}
#pragma omp simd
for( int ipart=istart ; ipart<iend; ipart++ ) {
double psm[3], um[3];
charge_over_mass_dts2 = dcharge[ipart]*one_over_mass_*dts2;
// ! ponderomotive force is proportional to charge squared and the field is divided by 4 instead of 2
charge_sq_over_mass_sq_dts4 = ( double )( charge[ipart] )*( double )( charge[ipart] )*one_over_mass_*one_over_mass_*dts4;
// ponderomotive gamma buffered from susceptibility
one_ov_gamma_ponderomotive = ( *( inv_gamma_ponderomotive+ipart ) );
// init Half-acceleration in the electric field and ponderomotive force
psm[0] = charge_over_mass_dts2 * ( *( Ex+ipart-ipart_ref ) ) - charge_sq_over_mass_sq_dts4 * ( *( GradPhix+ipart-ipart_ref ) ) * one_ov_gamma_ponderomotive;
psm[1] = charge_over_mass_dts2 * ( *( Ey+ipart-ipart_ref ) ) - charge_sq_over_mass_sq_dts4 * ( *( GradPhiy+ipart-ipart_ref ) ) * one_ov_gamma_ponderomotive;
psm[2] = charge_over_mass_dts2 * ( *( Ez+ipart-ipart_ref ) ) - charge_sq_over_mass_sq_dts4 * ( *( GradPhiz+ipart-ipart_ref ) ) * one_ov_gamma_ponderomotive;
um[0] = momentum[0][ipart] + psm[0];
um[1] = momentum[1][ipart] + psm[1];
um[2] = momentum[2][ipart] + psm[2];
// Rotation in the magnetic field, using updated gamma ponderomotive
alpha = charge_over_mass_dts2 * one_ov_gamma_ponderomotive;
Tx = alpha * ( *( Bx+ipart-ipart_ref ) );
Ty = alpha * ( *( By+ipart-ipart_ref ) );
Tz = alpha * ( *( Bz+ipart-ipart_ref ) );
Tx2 = Tx*Tx;
Ty2 = Ty*Ty;
Tz2 = Tz*Tz;
TxTy = Tx*Ty;
TyTz = Ty*Tz;
TzTx = Tz*Tx;
inv_det_T = 1.0/( 1.0+Tx2+Ty2+Tz2 );
psm[0] += ( ( 1.0+Tx2-Ty2-Tz2 )* um[0] + 2.0*( TxTy+Tz )* um[1] + 2.0*( TzTx-Ty )* um[2] )*inv_det_T;
psm[1] += ( 2.0*( TxTy-Tz )* um[0] + ( 1.0-Tx2+Ty2-Tz2 )* um[1] + 2.0*( TyTz+Tx )* um[2] )*inv_det_T;
psm[2] += ( 2.0*( TzTx+Ty )* um[0] + 2.0*( TyTz-Tx )* um[1] + ( 1.0-Tx2-Ty2+Tz2 )* um[2] )*inv_det_T;
momentum[0][ipart] = psm[0];
momentum[1][ipart] = psm[1];
momentum[2][ipart] = psm[2];
}
}
void add_BallMover(Particles ps, double dx, core::MonteCarloMovers &mvs) {
for (unsigned int k = 0; k < ps.size(); ++k) {
IMP_NEW(core::BallMover, bmv, (ps[k]->get_model(), ps[k]->get_index(), dx));
mvs.push_back(bmv);
}
}
// ---------------------------------------------------------------------------------------------------------------------
//! Project charge : frozen & diagFields timstep
// ---------------------------------------------------------------------------------------------------------------------
void Projector1D4Order::basic( double *rhoj, Particles &particles, unsigned int ipart, unsigned int type )
{
//Warning : this function is used for frozen species or initialization only and doesn't use the standard scheme.
//rho type = 0
//Jx type = 1
//Jy type = 2
//Jz type = 3
// Declare local variables
//int ipo, ip, iloc;
int ip;
//int ip_m_ipo;
double charge_weight = inv_cell_volume * ( double )( particles.charge( ipart ) )*particles.weight( ipart );
double xjn, xj_m_xip, xj_m_xip2, xj_m_xip3, xj_m_xip4;
double S1[7]; // arrays used for the Esirkepov projection method
// Initialize variables
for( unsigned int i=0; i<7; i++ ) {
S1[i]=0.;
}//i
if( type > 0 ) {
charge_weight *= 1./sqrt( 1.0 + particles.momentum( 0, ipart )*particles.momentum( 0, ipart )
+ particles.momentum( 1, ipart )*particles.momentum( 1, ipart )
+ particles.momentum( 2, ipart )*particles.momentum( 2, ipart ) );
if( type == 1 ) {
charge_weight *= particles.momentum( 0, ipart );
} else if( type == 2 ) {
charge_weight *= particles.momentum( 1, ipart );
} else {
charge_weight *= particles.momentum( 2, ipart );
}
}
// Locate particle new position on the primal grid
xjn = particles.position( 0, ipart ) * dx_inv_;
ip = round( xjn + 0.5 * ( type==1 ) ); // index of the central node
xj_m_xip = xjn - ( double )ip; // normalized distance to the nearest grid point
xj_m_xip2 = xj_m_xip * xj_m_xip; // square of the normalized distance to the nearest grid point
xj_m_xip3 = xj_m_xip2 * xj_m_xip; // cube of the normalized distance to the nearest grid point
xj_m_xip4 = xj_m_xip3 * xj_m_xip; // 4th power of the normalized distance to the nearest grid point
// coefficients 2nd order interpolation on 5 nodes
//ip_m_ipo = ip-ipo;
S1[1] = dble_1_ov_384 - dble_1_ov_48 * xj_m_xip + dble_1_ov_16 * xj_m_xip2 - dble_1_ov_12 * xj_m_xip3 + dble_1_ov_24 * xj_m_xip4;
S1[2] = dble_19_ov_96 - dble_11_ov_24 * xj_m_xip + dble_1_ov_4 * xj_m_xip2 + dble_1_ov_6 * xj_m_xip3 - dble_1_ov_6 * xj_m_xip4;
S1[3] = dble_115_ov_192 - dble_5_ov_8 * xj_m_xip2 + dble_1_ov_4 * xj_m_xip4;
S1[4] = dble_19_ov_96 + dble_11_ov_24 * xj_m_xip + dble_1_ov_4 * xj_m_xip2 - dble_1_ov_6 * xj_m_xip3 - dble_1_ov_6 * xj_m_xip4;
S1[5] = dble_1_ov_384 + dble_1_ov_48 * xj_m_xip + dble_1_ov_16 * xj_m_xip2 + dble_1_ov_12 * xj_m_xip3 + dble_1_ov_24 * xj_m_xip4;
ip -= index_domain_begin + 3 ;
// 4th order projection for the charge density
// At the 4th order, oversize = 3.
for( unsigned int i=0; i<7; i++ ) {
//iloc = i + ipo - 3;
rhoj[i + ip ] += charge_weight * S1[i];
}//i
}
void remove(Particle *p)
{
removeList.push_back(p);
}
/** @brief get the centers as intensity centroids of local maxima neighbourhood
*
* Local maxima are taken as the bright pixels of centersMap
*/
Particles Tracker::getSubPixel(bool autoThreshold)
{
//boost::progress_timer ptimer;
//get the positions of the bright centers from flatten centersMap
if(!quiet) cout<<"get positions ... ";
list<size_t> flat_positions;
bool* b = centersMap.origin();
for(size_t i=0; i<centersMap.num_elements(); ++i)
if(*b++)
flat_positions.push_back(i);
//sort by increasing pixel intensity
if(!quiet) cout<<flat_positions.size()<<" potential centers ... ";
flat_positions.sort(compIntensities(data));
//Find the best intensity threshold
if(autoThreshold)
{
//construct the centers intensity histogram
const long double minhist = *(data+flat_positions.front()),
maxhist = *(data+flat_positions.back());
const long double scale = 100.0/(maxhist-minhist);
vector<size_t> hist(100, 0);
for(list<size_t>::const_iterator c = flat_positions.begin(); c!= flat_positions.end(); ++c)
{
size_t l = (*(data + (*c)) - minhist) * scale;
if(l<hist.size())
hist[l]++;
}
//find the population global maximum
vector<size_t>::iterator peak = max_element(hist.begin(), hist.end());
if(!quiet) cout<<"peak ="<<distance(hist.begin(), peak)<<" ... ";
//find the last non-null bin before the peak, and at the same time the bin with the minimum population between it and the peak
vector<size_t>::iterator non_z = lower_bound(hist.begin(), peak, 1);
vector<size_t>::iterator lowest = min_element(non_z, peak);
//cout<<"non_z="<<distance(hist.begin(),non_z)<<"\tlowest="<<distance(hist.begin(),lowest)<<endl;
while((*lowest)==0)
{
non_z = lowest;
lowest = min_element(lowest, peak);
//cout<<"non_z="<<distance(hist.begin(),non_z)<<"\tlowest="<<distance(hist.begin(),lowest)<<endl;
}
//lowest gives the position of the valley of the histogram, ie the best threshold
if(!quiet) cout<<"best threshold = "<<distance(hist.begin(), lowest)/scale + minhist<<" ("<<distance(hist.begin(), lowest)<<"%) ... ";
//We remove all centers that have lower intensity than the best threshold
list<size_t>::iterator i = flat_positions.begin();
advance(i, accumulate(hist.begin(), lowest, (size_t)0));
flat_positions.erase(flat_positions.begin(), i);
if(!quiet) cout<<flat_positions.size()<<" centers after auto thresholding ... ";
}
//centroid binning
if(!quiet) cout<<"centroid ... ";
list< valarray<double> > positions;
boost::array<size_t,3> shape;
copy(centersMap.shape(), centersMap.shape()+3, shape.begin());
transform(
flat_positions.rbegin(), flat_positions.rend(),
back_inserter(positions),
centroid(boost::multi_array_ref<float,3>(data,shape))
);
//removing marked centers
positions.remove_if(markedPositionRemover<valarray<double> >());
if(!quiet) cout<<positions.size()<<" are real local maxima ... ";
Particles centers;
for(size_t d=0;d<3;++d)
{
centers.bb.edges[d].first = 0;
centers.bb.edges[d].second = centersMap.shape()[d];
}
//centers.reserve(positions.size());
copy(positions.begin(), positions.end(), back_inserter(centers));
if(fortran_order)
{
//If the image was filled in row major ordering of the dimensions, the coordinates are given as z,y,x by the tracker.
//Here we convert to the human-readable x,y,z coordinates
for_each(centers.begin(), centers.end(), revert<valarray<double> >());
//don't forget the bounding box
swap(centers.bb.edges[0].second, centers.bb.edges[2].second);
}
if(!quiet) cout << "done!" << endl;
if(view)
{
markCenters();
display("Centers");
}
return centers;
}
