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OpenPMDparams.cpp
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#include "OpenPMDparams.h"
using namespace std;
OpenPMDparams::OpenPMDparams( Params &p ):
axisLabels( 1 ),
fieldBoundary( 10 ),
fieldBoundaryParameters( 13 ),
particleBoundary( 0 ),
particleBoundaryParameters( 0 ),
params( &p )
{
version = "1.0.0";
extension = 0;
//extension = 1; // ED-PIC extension. Not supported yet
// Grid parameters
string xyz = "xyz";
gridGlobalOffset.resize( params->nDim_field, 0. );
gridOffset .resize( params->nDim_field, 0. );
gridSpacing .resize( params->nDim_field );
for( unsigned int idim=0; idim<params->nDim_field; idim++ ) {
axisLabels.addString( xyz.substr( idim, 1 ) );
gridSpacing[idim] = params->cell_length[idim];
}
fieldSolverParameters = "";
if( params->maxwell_sol == "Yee" ) {
fieldSolver = "Yee";
} else if( params->maxwell_sol == "Lehe" ) {
fieldSolver = "Lehe";
} else {
fieldSolver = "other";
fieldSolverParameters = params->maxwell_sol;
}
patchSize = params->patch_size_;
// Units
unitDimension.resize( SMILEI_NUNITS );
unitSI.resize( SMILEI_NUNITS );
double Wr = params->reference_angular_frequency_SI;
if( Wr==0. ) {
Wr=1.;
}
for( unsigned int unit_type=0; unit_type<SMILEI_NUNITS; unit_type++ ) {
if( unit_type == SMILEI_UNIT_NONE ) { // dimensionless
unitDimension[unit_type] = { 0., 0., 0., 0., 0., 0., 0. };
unitSI[unit_type] = 1.;
} else if( unit_type == SMILEI_UNIT_EFIELD ) {
unitDimension[unit_type] = { 1., 1., -3., -1., 0., 0., 0. };
unitSI[unit_type] = 1.704508807123e-3 * Wr; // me * c * Wr / e
} else if( unit_type == SMILEI_UNIT_BFIELD ) {
unitDimension[unit_type] = { 0., 1., -2., -1., 0., 0., 0. };
unitSI[unit_type] = 5.685629380e-12 * Wr; // me * Wr / e
} else if( unit_type == SMILEI_UNIT_CURRENT ) {
unitDimension[unit_type] = { -2., 0., 0., 1., 0., 0., 0. };
unitSI[unit_type] = 1.5092041114e-14 * Wr*Wr; // e0 * me * c * Wr^2 / e
} else if( unit_type == SMILEI_UNIT_DENSITY ) {
unitDimension[unit_type] = { -3., 0., 1., 1., 0., 0., 0. };
unitSI[unit_type] = 5.034163 * Wr*Wr; // e0 * me * Wr^2 / e
} else if( unit_type == SMILEI_UNIT_POSITION ) {
unitDimension[unit_type] = { 1., 0., 0., 0., 0., 0., 0. };
unitSI[unit_type] = 299792458. / Wr; // c / Wr
} else if( unit_type == SMILEI_UNIT_MOMENTUM ) {
unitDimension[unit_type] = { 1., 1., -1., 0., 0., 0., 0. };
unitSI[unit_type] = 2.7309240656e-22; // me * c
} else if( unit_type == SMILEI_UNIT_CHARGE ) {
unitDimension[unit_type] = { 0., 0., 1., 1., 0., 0., 0. };
unitSI[unit_type] = 1.602176565e-19; // e
} else if( unit_type == SMILEI_UNIT_TIME ) {
unitDimension[unit_type] = { 0., 0., 1., 0., 0., 0., 0. };
unitSI[unit_type] = 1. / Wr; // 1 / Wr
} else if( unit_type == SMILEI_UNIT_ENERGY ) {
unitDimension[unit_type] = { 2., 1., -2., 0., 0., 0., 0. };
unitSI[unit_type] = 8.187104382e-14; // me * c^2
} else if( unit_type == SMILEI_UNIT_WEIGHT ) {
const auto &n = params->nDim_particle;
unitDimension[unit_type] = { -3. + n, 0., 1., 1., 0., 0., 0. };
unitSI[unit_type] = 5.034163 * Wr*Wr * pow( 299792458. / Wr, n ); // Nr * Lr^n
}
}
// Boundary conditions
for( unsigned int i=0; i<params->EM_BCs.size(); i++ ) {
for( unsigned int j=0; j<2; j++ ) {
if( params->EM_BCs[i][j] == "periodic" ) {
fieldBoundary .addString( "periodic" );
fieldBoundaryParameters.addString( "periodic" );
} else if( params->EM_BCs[i][j] == "reflective" ) {
fieldBoundary .addString( "reflecting" );
fieldBoundaryParameters.addString( "reflecting" );
} else if( params->EM_BCs[i][j] == "silver-muller" ) {
fieldBoundary .addString( "open" );
fieldBoundaryParameters.addString( "silver-muller" );
} else if( params->EM_BCs[i][j] == "buneman" ) {
fieldBoundary .addString( "open" );
fieldBoundaryParameters.addString( "buneman" );
} else if( params->EM_BCs[i][j].substr(0,4) == "ramp" ) {
fieldBoundary .addString( "open" );
fieldBoundaryParameters.addString( params->EM_BCs[i][j] );
} else if( params->EM_BCs[i][j] == "PML" ) {
fieldBoundary .addString( "open" );
fieldBoundaryParameters.addString( "PML" );
} else {
ERROR( " impossible boundary condition: "<<params->EM_BCs[i][j] );
}
particleBoundary .addString( "" );
particleBoundaryParameters.addString( "" );
}
}
// Other parameters
currentSmoothing = "none";
currentSmoothingParameters = "";
if (params->currentFilter_passes.size() > 0){
if( *std::max_element(std::begin(params->currentFilter_passes), std::end(params->currentFilter_passes)) > 0 ) {
currentSmoothing = "Binomial";
ostringstream t( "" );
t << "numPasses="<<*std::max_element(std::begin(params->currentFilter_passes), std::end(params->currentFilter_passes));
currentSmoothingParameters = t.str();
}
}
}
void OpenPMDparams::writeRootAttributes( H5Write &location, string meshesPath, string particlesPath )
{
location.attr( "openPMDextension", extension, H5T_NATIVE_UINT32 );
location.attr( "openPMD", version );
location.attr( "basePath", "/data/%T/" );
location.attr( "software", "Smilei" );
location.attr( "softwareVersion", __VERSION );
location.attr( "date", getLocalTime() );
location.attr( "iterationEncoding", "groupBased" );
location.attr( "iterationFormat", "/data/%T/" );
location.attr( "meshesPath", meshesPath );
location.attr( "particlesPath", particlesPath );
}
void OpenPMDparams::writeBasePathAttributes( H5Write &location, unsigned int itime )
{
location.attr( "time", ( double )( itime * params->timestep ) );
location.attr( "dt", ( double )params->timestep );
location.attr( "timeUnitSI", unitSI[SMILEI_UNIT_TIME] );
}
void OpenPMDparams::writeParticlesAttributes( H5Write & )
{
}
void OpenPMDparams::writeMeshesAttributes( H5Write &location )
{
location.attr( "patchSize", patchSize ); // this one is not openPMD
location.attr( "fieldSolver", fieldSolver );
location.attr( "fieldSolverParameters", fieldSolverParameters );
location.attr( "fieldBoundary", fieldBoundary );
location.attr( "fieldBoundaryParameters", fieldBoundaryParameters );
location.attr( "particleBoundary", particleBoundary );
location.attr( "particleBoundaryParameters", particleBoundaryParameters );
location.attr( "currentSmoothing", currentSmoothing );
location.attr( "currentSmoothingParameters", currentSmoothingParameters );
location.attr( "chargeCorrection", "none" );
location.attr( "chargeCorrectionParameters", "" );
location.attr( "fieldSmoothing", "none" );
location.attr( "fieldSmoothingParameters", "" );
}
void OpenPMDparams::writeFieldAttributes( H5Write &location, vector<unsigned int> subgrid_start, vector<unsigned int> subgrid_step )
{
location.attr( "geometry", "cartesian" );
location.attr( "dataOrder", "C" );
location.attr( "axisLabels", axisLabels );
if( subgrid_start.size() == 0 ) {
location.attr( "gridSpacing", gridSpacing );
location.attr( "gridGlobalOffset", gridGlobalOffset );
} else {
unsigned int ndim = subgrid_start.size();
vector<double> subgridSpacing( ndim );
vector<double> subgridOffset( ndim );
for( unsigned int i=0; i<ndim; i++ ) {
subgridSpacing[i] = gridSpacing [i] * subgrid_step [i];
subgridOffset [i] = gridSpacing [i] * subgrid_start[i];
}
location.attr( "gridSpacing", subgridSpacing );
location.attr( "gridGlobalOffset", subgridOffset );
}
//location.attr( "gridOffset", gridOffset);
location.attr( "gridUnitSI", unitSI[SMILEI_UNIT_POSITION] );
}
void OpenPMDparams::writeSpeciesAttributes( H5Write & )
{
}
void OpenPMDparams::writeRecordAttributes( H5Write &location, unsigned int unit_type, double timeOffset )
{
location.attr( "unitDimension", unitDimension[unit_type] );
location.attr( "timeOffset", timeOffset );
}
void OpenPMDparams::writeFieldRecordAttributes( H5Write &location, vector<double> &stagger )
{
location.attr( "position", stagger );
}
void OpenPMDparams::writeComponentAttributes( H5Write &location, unsigned int unit_type )
{
location.attr( "unitSI", unitSI[unit_type] );
}
// WARNING: do not change the format. It is required for OpenPMD compatibility.
string OpenPMDparams::getLocalTime()
{
time_t t = time( 0 );
struct tm *now = localtime( & t );
char buffer[25];
strftime( buffer, 25, "%Y-%m-%d %H:%M:%S %z", now );
string s( buffer, 25 );
return s;
}