void PicParams::readSpecies(InputData &ifile) {
bool ok;
for (int ispec = 0; ispec < ifile.nComponents("Species"); ispec++) {
SpeciesStructure tmpSpec;
ifile.extract("species_type",tmpSpec.species_type,"Species",ispec);
if(tmpSpec.species_type.empty()) {
ERROR("For species #" << ispec << " empty species_type");
}
ifile.extract("initPosition_type",tmpSpec.initPosition_type ,"Species",ispec);
if (tmpSpec.initPosition_type.empty()) {
ERROR("For species #" << ispec << " empty initPosition_type");
} else if ( (tmpSpec.initPosition_type!="regular")&&(tmpSpec.initPosition_type!="random") ) {
ERROR("For species #" << ispec << " bad definition of initPosition_type " << tmpSpec.initPosition_type);
}
ifile.extract("initMomentum_type",tmpSpec.initMomentum_type ,"Species",ispec);
if ( (tmpSpec.initMomentum_type=="mj") || (tmpSpec.initMomentum_type=="maxj") ) {
tmpSpec.initMomentum_type="maxwell-juettner";
}
if ( (tmpSpec.initMomentum_type!="cold")
&& (tmpSpec.initMomentum_type!="maxwell-juettner")
&& (tmpSpec.initMomentum_type!="rectangular") ) {
ERROR("For species #" << ispec << " bad definition of initMomentum_type");
}
tmpSpec.c_part_max = 1.0;// default value
ifile.extract("c_part_max",tmpSpec.c_part_max,"Species",ispec);
if( !ifile.extract("mass",tmpSpec.mass ,"Species",ispec) ) {
ERROR("For species #" << ispec << ", mass not defined.");
}
tmpSpec.dynamics_type = "norm"; // default value
if (!ifile.extract("dynamics_type",tmpSpec.dynamics_type ,"Species",ispec) )
WARNING("For species #" << ispec << ", dynamics_type not defined: assumed = 'norm'.");
if (tmpSpec.dynamics_type!="norm"){
ERROR("dynamics_type different than norm not yet implemented");
}
tmpSpec.time_frozen = 0.0; // default value
ifile.extract("time_frozen",tmpSpec.time_frozen ,"Species",ispec);
if (tmpSpec.time_frozen > 0 && \
tmpSpec.initMomentum_type!="cold") {
WARNING("For species #" << ispec << " possible conflict between time-frozen & not cold initialization");
}
tmpSpec.radiating = false; // default value
ifile.extract("radiating",tmpSpec.radiating ,"Species",ispec);
if (tmpSpec.dynamics_type=="rrll" && (!tmpSpec.radiating)) {
WARNING("For species #" << ispec << ", dynamics_type='rrll' forcing radiating=True");
tmpSpec.radiating=true;
}
if (!ifile.extract("bc_part_type_west",tmpSpec.bc_part_type_west,"Species",ispec) )
ERROR("For species #" << ispec << ", bc_part_type_west not defined");
if (!ifile.extract("bc_part_type_east",tmpSpec.bc_part_type_east,"Species",ispec) )
ERROR("For species #" << ispec << ", bc_part_type_east not defined");
if (nDim_particle>1) {
if (!ifile.extract("bc_part_type_south",tmpSpec.bc_part_type_south,"Species",ispec) )
ERROR("For species #" << ispec << ", bc_part_type_south not defined");
if (!ifile.extract("bc_part_type_north",tmpSpec.bc_part_type_north,"Species",ispec) )
ERROR("For species #" << ispec << ", bc_part_type_north not defined");
}
// for thermalizing BCs on particles check if thermT is correctly defined
bool thermTisDefined=false;
if ( (tmpSpec.bc_part_type_west=="thermalize") || (tmpSpec.bc_part_type_east=="thermalize") ){
thermTisDefined=ifile.extract("thermT",tmpSpec.thermT,"Species",ispec);
if (!thermTisDefined) ERROR("thermT needs to be defined for species " <<ispec<< " due to x-BC thermalize");
}
if ( (nDim_particle==2) && (!thermTisDefined) &&
(tmpSpec.bc_part_type_south=="thermalize" || tmpSpec.bc_part_type_north=="thermalize") ) {
thermTisDefined=ifile.extract("thermT",tmpSpec.thermT,"Species",ispec);
if (!thermTisDefined) ERROR("thermT needs to be defined for species " <<ispec<< " due to y-BC thermalize");
}
if (thermTisDefined) {
if (tmpSpec.thermT.size()==1) {
tmpSpec.thermT.resize(3);
for (unsigned int i=1; i<3;i++)
tmpSpec.thermT[i]=tmpSpec.thermT[0];
}
} else {
tmpSpec.thermT.resize(3);
for (unsigned int i=0; i<3;i++)
tmpSpec.thermT[i]=0.0;
}
tmpSpec.ionization_model = "none"; // default value
ifile.extract("ionization_model", tmpSpec.ionization_model, "Species",ispec);
ok = ifile.extract("atomic_number", tmpSpec.atomic_number, "Species",ispec);
if( !ok && tmpSpec.ionization_model!="none" ) {
ERROR("For species #" << ispec << ", `atomic_number` not found => required for the ionization model .");
}
tmpSpec.isTest = false; // default value
ifile.extract("isTest",tmpSpec.isTest ,"Species",ispec);
if (tmpSpec.ionization_model!="none" && (!tmpSpec.isTest)) {
ERROR("Disabled for now : test & ionized");
}
// Species geometry
// ----------------
// Density
bool ok1, ok2;
ok1 = extractOneProfile(ifile, "nb_density" , tmpSpec.dens_profile, ispec);
ok2 = extractOneProfile(ifile, "charge_density", tmpSpec.dens_profile, ispec);
if( ok1 && ok2 ) ERROR("For species #" << ispec << ", cannot define both `nb_density` and `charge_density`.");
if( !ok1 && !ok2 ) ERROR("For species #" << ispec << ", must define `nb_density` or `charge_density`.");
if( ok1 ) tmpSpec.density_type = "nb";
if( ok2 ) tmpSpec.density_type = "charge";
// Number of particles per cell
if( !extractOneProfile(ifile, "n_part_per_cell", tmpSpec.ppc_profile, ispec) )
ERROR("For species #" << ispec << ", n_part_per_cell not found or not understood");
// Charge
if( !extractOneProfile(ifile, "charge", tmpSpec.charge_profile, ispec) )
ERROR("For species #" << ispec << ", charge not found or not understood");
// Mean velocity
vector<ProfileStructure*> vecMvel;
extractVectorOfProfiles(ifile, "mean_velocity", vecMvel, ispec);
tmpSpec.mvel_x_profile = *(vecMvel[0]);
tmpSpec.mvel_y_profile = *(vecMvel[1]);
tmpSpec.mvel_z_profile = *(vecMvel[2]);
// Temperature
vector<ProfileStructure*> vecTemp;
extractVectorOfProfiles(ifile, "temperature", vecTemp, ispec);
tmpSpec.temp_x_profile = *(vecTemp[0]);
tmpSpec.temp_y_profile = *(vecTemp[1]);
tmpSpec.temp_z_profile = *(vecTemp[2]);
// Save the Species params
// -----------------------
species_param.push_back(tmpSpec);
}
}
