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);
}
}
// ---------------------------------------------------------------------------------------------------------------------
// PicParams : open & parse the input data file, test that parameters are coherent
// ---------------------------------------------------------------------------------------------------------------------
PicParams::PicParams(InputData &ifile) {
// --------------
// Stop & Restart
// --------------
dump_step=1;
ifile.extract("dump_step", dump_step);
dump_minutes=0.0;
ifile.extract("dump_minutes", dump_minutes);
exit_after_dump=true;
ifile.extract("exit_after_dump", exit_after_dump);
restart=false;
ifile.extract("restart", restart);
if (restart) MESSAGE("Code running from restart"); //! \todo Give info on restart properties
//!\todo MG is this still used ?? I cannot find it anywhere
check_stop_file=false;
ifile.extract("check_stop_file", check_stop_file);
dump_file_sequence=2;
ifile.extract("dump_file_sequence", dump_file_sequence);
dump_file_sequence=std::max((unsigned int)1,dump_file_sequence);
// ---------------------
// Normalisation & units
// ---------------------
wavelength_SI = 0.;
ifile.extract("wavelength_SI",wavelength_SI);
// -------------------
// Simulation box info
// -------------------
// geometry of the simulation
ifile.extract("dim", geometry);
if (geometry!="1d3v" && geometry!="2d3v") {
ERROR("Geometry " << geometry << " does not exist");
}
setDimensions();
// interpolation order
ifile.extract("interpolation_order", interpolation_order);
/*
if (interpolation_order!=2 && interpolation_order!=4) {
ERROR("Interpolation/projection order " << interpolation_order << " not defined");
}
if (geometry=="2d3v" && interpolation_order==4) {
ERROR("Interpolation/projection order " << interpolation_order << " not yet defined in 2D");
}
*/
//!\todo (MG to JD) Please check if this parameter should still appear here
// Disabled, not compatible for now with particles sort
// if ( !ifile.extract("exchange_particles_each", exchange_particles_each) )
exchange_particles_each = 1;
// TIME & SPACE RESOLUTION/TIME-STEPS
// reads timestep & cell_length
ifile.extract("timestep", timestep);
res_time = 1.0/timestep;
ifile.extract("cell_length",cell_length);
if (cell_length.size()!=nDim_field) {
ERROR("Dimension of cell_length ("<< cell_length.size() << ") != " << nDim_field << " for geometry " << geometry);
}
res_space.resize(nDim_field);
for (unsigned int i=0;i<nDim_field;i++){
res_space[i] = 1.0/cell_length[i];
}
time_fields_frozen=0.0;
ifile.extract("time_fields_frozen", time_fields_frozen);
// testing the CFL condition
//!\todo (MG) CFL cond. depends on the Maxwell solv. ==> Move this computation to the ElectroMagn Solver
double res_space2=0;
for (unsigned int i=0; i<nDim_field; i++) {
res_space2 += res_space[i]*res_space[i];
}
dtCFL=1.0/sqrt(res_space2);
if ( timestep>dtCFL ) {
//ERROR("CFL problem: timestep=" << timestep << " should be smaller than " << dtCFL);
}
// simulation duration & length
ifile.extract("sim_time", sim_time);
ifile.extract("sim_length",sim_length);
if (sim_length.size()!=nDim_field) {
ERROR("Dimension of sim_length ("<< sim_length.size() << ") != " << nDim_field << " for geometry " << geometry);
}
//! Boundary conditions for ElectroMagnetic Fields
if ( !ifile.extract("bc_em_type_x", bc_em_type_x) ) {
ERROR("Electromagnetic boundary condition type (bc_em_type_x) not defined" );
}
if (bc_em_type_x.size()==1) { // if just one type is specified, then take the same bc type in a given dimension
bc_em_type_x.resize(2); bc_em_type_x[1]=bc_em_type_x[0];
}
if ( !ifile.extract("bc_em_value_x", bc_em_value_x) ) {
ERROR("Electromagnetic boundary condition type (bc_em_type_x) not defined" );
}
if (bc_em_value_x.size()==1) { // if just one type is specified, then take the same bc type in a given dimension
bc_em_value_x.resize(2); bc_em_value_x[1]=bc_em_value_x[0];
}
if ( geometry == "2d3v" || geometry == "3d3v" ) {
if ( !ifile.extract("bc_em_type_y", bc_em_type_y) )
ERROR("Electromagnetic boundary condition type (bc_em_type_y) not defined" );
if (bc_em_type_y.size()==1) { // if just one type is specified, then take the same bc type in a given dimension
bc_em_type_y.resize(2); bc_em_type_y[1]=bc_em_type_y[0];
}
}
if ( geometry == "3d3v" ) {
if ( !ifile.extract("bc_em_type_z", bc_em_type_z) )
ERROR("Electromagnetic boundary condition type (bc_em_type_z) not defined" );
if (bc_em_type_z.size()==1) { // if just one type is specified, then take the same bc type in a given dimension
bc_em_type_z.resize(2); bc_em_type_z[1]=bc_em_type_z[0];
}
}
// ------------------------
// Moving window parameters
// ------------------------
if (!ifile.extract("clrw",clrw)) {
clrw = 1;
}
// ------------------
// Species properties
// ------------------
readSpecies(ifile);
global_every=0;
ifile.extract("every",global_every);
// --------------------
// Number of processors
// --------------------
if ( !ifile.extract("number_of_procs", number_of_procs) )
number_of_procs.resize(nDim_field, 0);
// -------------------------------------------------------
// Compute usefull quantities and introduce normalizations
// also defines defaults values for the species lengths
// -------------------------------------------------------
compute();
computeSpecies();
}