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parameters.cpp
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parameters.cpp
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/*
* This file is part of Vlasiator.
* Copyright 2010-2016 Finnish Meteorological Institute
*
* For details of usage, see the COPYING file and read the "Rules of the Road"
* at http://www.physics.helsinki.fi/vlasiator/
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/
#include "parameters.h"
#include "object_wrapper.h"
#include "particle_species.h"
#include "readparameters.h"
#include <algorithm>
#include <cstdlib>
#include <iostream>
#include <limits>
#include <set>
#include <unistd.h>
#include "fieldtracing/fieldtracing.h"
#ifndef NAN
#define NAN 0
#endif
using namespace std;
typedef Parameters P;
// Using numeric_limits<Real>::max() leads to FP exceptions inside boost programoptions, use a slightly smaller value to
// avoid...
const Real LARGE_REAL = 1e20;
// Define static members:
int P::geometry = geometry::XYZ6D;
Real P::xmin = NAN;
Real P::xmax = NAN;
Real P::ymin = NAN;
Real P::ymax = NAN;
Real P::zmin = NAN;
Real P::zmax = NAN;
Real P::dx_ini = NAN;
Real P::dy_ini = NAN;
Real P::dz_ini = NAN;
uint P::xcells_ini = numeric_limits<uint>::max();
uint P::ycells_ini = numeric_limits<uint>::max();
uint P::zcells_ini = numeric_limits<uint>::max();
Real P::t = 0;
Real P::t_min = 0;
Real P::t_max = LARGE_REAL;
Real P::dt = NAN;
Real P::vlasovSolverMaxCFL = NAN;
Real P::vlasovSolverMinCFL = NAN;
Real P::fieldSolverMaxCFL = NAN;
Real P::fieldSolverMinCFL = NAN;
uint P::fieldSolverSubcycles = 1;
uint P::tstep = 0;
uint P::tstep_min = 0;
uint P::tstep_max = 0;
uint P::diagnosticInterval = numeric_limits<uint>::max();
bool P::writeInitialState = true;
bool P::writeFullBGB = false;
bool P::meshRepartitioned = true;
bool P::prepareForRebalance = false;
vector<CellID> P::localCells;
vector<string> P::systemWriteName;
vector<string> P::systemWritePath;
vector<Real> P::systemWriteTimeInterval;
vector<int> P::systemWriteDistributionWriteStride;
vector<int> P::systemWriteDistributionWriteXlineStride;
vector<int> P::systemWriteDistributionWriteYlineStride;
vector<int> P::systemWriteDistributionWriteZlineStride;
vector<Real> P::systemWriteDistributionWriteShellRadius;
vector<int> P::systemWriteDistributionWriteShellStride;
vector<bool> P::systemWriteFsGrid;
bool P::systemWriteAllDROs;
bool P::diagnosticWriteAllDROs;
vector<int> P::systemWrites;
vector<pair<string, string>> P::systemWriteHints;
vector<pair<string, string>> P::restartWriteHints;
vector<pair<string, string>> P::restartReadHints;
Real P::saveRestartWalltimeInterval = -1.0;
uint P::exitAfterRestarts = numeric_limits<uint>::max();
uint64_t P::vlsvBufferSize = 0;
int P::restartStripeFactor = 0;
int P::systemStripeFactor = 0;
string P::restartWritePath = string("");
uint P::transmit = 0;
bool P::recalculateStencils = true;
bool P::propagateVlasovAcceleration = true;
bool P::propagateVlasovTranslation = true;
bool P::propagateField = true;
bool P::dynamicTimestep = true;
Real P::maxWaveVelocity = 0.0;
uint P::maxFieldSolverSubcycles = 0.0;
int P::maxSlAccelerationSubcycles = 0.0;
Real P::resistivity = NAN;
bool P::fieldSolverDiffusiveEterms = true;
uint P::ohmHallTerm = 0;
uint P::ohmGradPeTerm = 0;
Real P::electronTemperature = 0.0;
Real P::electronDensity = 0.0;
Real P::electronPTindex = 1.0;
string P::restartFileName = string("");
bool P::isRestart = false;
int P::writeAsFloat = false;
int P::writeRestartAsFloat = false;
string P::loadBalanceAlgorithm = string("");
std::map<std::string, std::string> P::loadBalanceOptions;
uint P::rebalanceInterval = numeric_limits<uint>::max();
vector<string> P::outputVariableList;
vector<string> P::diagnosticVariableList;
string P::projectName = string("");
bool P::vlasovAccelerateMaxwellianBoundaries = false;
Real P::maxSlAccelerationRotation = 10.0;
Real P::hallMinimumRhom = physicalconstants::MASS_PROTON;
Real P::hallMinimumRhoq = physicalconstants::CHARGE;
bool P::bailout_write_restart = false;
Real P::bailout_min_dt = NAN;
Real P::bailout_max_memory = 1073741824.;
uint P::bailout_velocity_space_wall_margin = 0;
uint P::vamrMaxVelocityRefLevel = 0;
Realf P::vamrRefineLimit = 1.0;
Realf P::vamrCoarsenLimit = 0.5;
string P::vamrVelRefCriterion = string("");
bool P::amrTransShortPencils = false;
int P::amrMaxSpatialRefLevel = 0;
int P::amrMaxAllowedSpatialRefLevel = -1;
bool P::adaptRefinement = false;
bool P::refineOnRestart = false;
bool P::forceRefinement = false;
bool P::shouldFilter = false;
bool P::useAlpha1 = true;
Real P::alpha1RefineThreshold = 0.5;
Real P::alpha1CoarsenThreshold = -1.0;
bool P::useAlpha2 = true;
Real P::alpha2RefineThreshold = 0.5;
Real P::alpha2CoarsenThreshold = -1.0;
Real P::alphaDRhoWeight = 1.0;
Real P::alphaDUWeight = 1.0;
Real P::alphaDPSqWeight = 1.0;
Real P::alphaDBSqWeight = 1.0;
Real P::alphaDBWeight = 1.0;
uint P::refineCadence = 5;
Real P::refineAfter = 0.0;
Real P::refineRadius = LARGE_REAL;
Real P::refinementMinX = -LARGE_REAL;
Real P::refinementMinY = -LARGE_REAL;
Real P::refinementMinZ = -LARGE_REAL;
Real P::refinementMaxX = LARGE_REAL;
Real P::refinementMaxY = LARGE_REAL;
Real P::refinementMaxZ = LARGE_REAL;
int P::maxFilteringPasses = 0;
int P::amrBoxNumber = 0;
std::vector<uint> P::amrBoxHalfWidthX;
std::vector<uint> P::amrBoxHalfWidthY;
std::vector<uint> P::amrBoxHalfWidthZ;
std::vector<Realf> P::amrBoxCenterX;
std::vector<Realf> P::amrBoxCenterY;
std::vector<Realf> P::amrBoxCenterZ;
std::vector<int> P::amrBoxMaxLevel;
vector<string> P::blurPassString;
std::vector<int> P::numPasses; //numpasses
std::array<FsGridTools::Task_t,3> P::manualFsGridDecomposition = {0,0,0};
std::array<FsGridTools::Task_t,3> P::overrideReadFsGridDecomposition = {0,0,0};
std::string tracerString; /*!< Fieldline tracer to use for coupling ionosphere and magnetosphere */
bool P::computeCurvature;
bool P::addParameters() {
typedef Readparameters RP;
// the other default parameters we read through the add/get interface
RP::add("io.diagnostic_write_interval", "Write diagnostic output every arg time steps", numeric_limits<uint>::max());
RP::addComposing(
"io.system_write_t_interval",
"Save the simulation every arg simulated seconds. Negative values disable writes. [Define for all groups.]");
RP::addComposing("io.system_write_file_name",
"Save the simulation to this file name series. [Define for all groups.]");
RP::addComposing("io.system_write_path",
"Save this series in this location. Default is ./ [Define for all groups or none.]");
RP::addComposing("io.system_write_distribution_stride",
"Every this many cells write out their velocity space. 0 is none. [Define for all groups.]");
RP::addComposing("io.system_write_distribution_xline_stride",
"Every this many lines of cells along the x direction write out their velocity space. 0 is none. "
"[Define for all groups.]");
RP::addComposing("io.system_write_distribution_yline_stride",
"Every this many lines of cells along the y direction write out their velocity space. 0 is none. "
"[Define for all groups.]");
RP::addComposing("io.system_write_distribution_zline_stride",
"Every this many lines of cells along the z direction write out their velocity space. 0 is none. "
"[Define for all groups.]");
RP::addComposing("io.system_write_distribution_shell_radius",
"At cells intersecting spheres with those radii centred at the origin write out their velocity "
"space. 0 is none.");
RP::addComposing("io.system_write_distribution_shell_stride",
"Every this many cells for those on selected shells write out their velocity space. 0 is none.");
RP::addComposing("io.system_write_fsgrid_variables", "If 0 don't write fsgrid DROs, if 1 do write them.");
RP::addComposing(
"io.system_write_mpiio_hint_key",
"MPI-IO hint key passed to the non-restart IO. Has to be matched by io.system_write_mpiio_hint_value.");
RP::addComposing(
"io.system_write_mpiio_hint_value",
"MPI-IO hint value passed to the non-restart IO. Has to be matched by io.system_write_mpiio_hint_key.");
RP::addComposing(
"io.restart_write_mpiio_hint_key",
"MPI-IO hint key passed to the restart IO. Has to be matched by io.restart_write_mpiio_hint_value.");
RP::addComposing(
"io.restart_write_mpiio_hint_value",
"MPI-IO hint value passed to the restart IO. Has to be matched by io.restart_write_mpiio_hint_key.");
RP::addComposing(
"io.restart_read_mpiio_hint_key",
"MPI-IO hint key passed to the restart IO. Has to be matched by io.restart_read_mpiio_hint_value.");
RP::addComposing(
"io.restart_read_mpiio_hint_value",
"MPI-IO hint value passed to the restart IO. Has to be matched by io.restart_read_mpiio_hint_key.");
RP::add("io.write_initial_state",
"Write initial state, not even the 0.5 dt propagation is done. Do not use for restarting. ", false);
RP::add("io.write_full_bgb_data", "Write a dedicated file containing all BGB components and first derivatives, then exit.", false);
RP::add("io.restart_walltime_interval",
"Save the complete simulation in given walltime intervals. Negative values disable writes.", -1.0);
RP::add("io.number_of_restarts", "Exit the simulation after certain number of walltime-based restarts.",
numeric_limits<uint>::max());
RP::add("io.vlsv_buffer_size",
"Buffer size passed to VLSV writer (bytes, up to uint64_t), default 0 as this is sensible on sisu", 0);
RP::add("io.write_restart_stripe_factor", "Stripe factor for restart and initial grid writing. Default 0 to inherit.", 0);
RP::add("io.write_system_stripe_factor", "Stripe factor for bulk file writing. Default 0 to inherit.", 0);
RP::add("io.write_as_float", "If true, write in floats instead of doubles", false);
RP::add("io.restart_write_path",
"Path to the location where restart files should be written. Defaults to the local directory, also if the "
"specified destination is not writeable.",
string("./"));
RP::add("propagate_field", "Propagate magnetic field during the simulation", true);
RP::add("propagate_vlasov_acceleration",
"Propagate distribution functions during the simulation in velocity space. If false, it is propagated with "
"zero length timesteps.",
true);
RP::add("propagate_vlasov_translation",
"Propagate distribution functions during the simulation in ordinary space. If false, it is propagated with "
"zero length timesteps.",
true);
RP::add("dynamic_timestep", "If true, timestep is set based on CFL limits (default on)", true);
RP::add("hallMinimumRho",
"Minimum rho value used for the Hall and electron pressure gradient terms in the Lorentz force and in the "
"field solver. Default is very low and has no effect in practice.",
1.0);
RP::add("project",
"Specify the name of the project to use. Supported to date (20150610): Alfven Diffusion Dispersion "
"Distributions Firehose Flowthrough Fluctuations Harris KHB Larmor Magnetosphere Multipeak Riemann1 Shock "
"Shocktest Template test_fp testHall test_trans verificationLarmor",
string(""));
RP::add("restart.write_as_float", "If true, write restart fields in floats instead of doubles", false);
RP::add("restart.filename", "Restart from this vlsv file. No restart if empty file.", string(""));
RP::add(
"restart.overrideReadFsGridDecompositionX",
"Manual FsGridDecomposition for field solver grid stored in a restart file.", 0);
RP::add(
"restart.overrideReadFsGridDecompositionY",
"Manual FsGridDecomposition for field solver grid stored in a restart file.", 0);
RP::add(
"restart.overrideReadFsGridDecompositionZ",
"Manual FsGridDecomposition for field solver grid stored in a restart file.", 0);
RP::add("gridbuilder.geometry", "Simulation geometry XY4D,XZ4D,XY5D,XZ5D,XYZ6D", string("XYZ6D"));
RP::add("gridbuilder.x_min", "Minimum value of the x-coordinate.", NAN);
RP::add("gridbuilder.x_max", "Minimum value of the x-coordinate.", NAN);
RP::add("gridbuilder.y_min", "Minimum value of the y-coordinate.", NAN);
RP::add("gridbuilder.y_max", "Minimum value of the y-coordinate.", NAN);
RP::add("gridbuilder.z_min", "Minimum value of the z-coordinate.", NAN);
RP::add("gridbuilder.z_max", "Minimum value of the z-coordinate.", NAN);
RP::add("gridbuilder.x_length", "Number of cells in x-direction in initial grid.", 0);
RP::add("gridbuilder.y_length", "Number of cells in y-direction in initial grid.", 0);
RP::add("gridbuilder.z_length", "Number of cells in z-direction in initial grid.", 0);
RP::add("gridbuilder.dt", "Initial timestep in seconds.", 0.0);
RP::add("gridbuilder.t_max",
"Maximum simulation time, in seconds. If timestep_max limit is hit first this time will never be reached",
LARGE_REAL);
RP::add("gridbuilder.timestep_max",
"Max. value for timesteps. If t_max limit is hit first, this step will never be reached",
numeric_limits<uint>::max());
// Field solver parameters
RP::add("fieldsolver.maxWaveVelocity",
"Maximum wave velocity allowed in the fastest velocity determination in m/s, default unlimited", LARGE_REAL);
RP::add("fieldsolver.maxSubcycles", "Maximum allowed field solver subcycles", 1);
RP::add("fieldsolver.resistivity", "Resistivity for the eta*J term in Ohm's law.", 0.0);
RP::add("fieldsolver.diffusiveEterms", "Enable diffusive terms in the computation of E", true);
RP::add(
"fieldsolver.ohmHallTerm",
"Enable/choose spatial order of the Hall term in Ohm's law. 0: off, 1: 1st spatial order, 2: 2nd spatial order",
0);
RP::add(
"fieldsolver.ohmGradPeTerm",
"Enable/choose spatial order of the electron pressure gradient term in Ohm's law. 0: off, 1: 1st spatial order.",
0);
RP::add("fieldsolver.electronTemperature",
"Upstream electron temperature to be used for the electron pressure gradient term (K).", 0.0);
RP::add("fieldsolver.electronDensity",
"Upstream electron density to be used for the electron pressure gradient term (m^-3).", 0.0);
RP::add("fieldsolver.electronPTindex",
"Polytropic index for electron pressure gradient term. 0 is isobaric, 1 is isothermal, 1.667 is adiabatic "
"electrons, ",
0.0);
RP::add("fieldsolver.maxCFL",
"The maximum CFL limit for field propagation. Used to set timestep if dynamic_timestep is true.", 0.5);
RP::add("fieldsolver.minCFL",
"The minimum CFL limit for field propagation. Used to set timestep if dynamic_timestep is true.", 0.4);
RP::add(
"fieldsolver.manualFsGridDecompositionX",
"Manual FsGridDecomposition for field solver grid.", 0);
RP::add(
"fieldsolver.manualFsGridDecompositionY",
"Manual FsGridDecomposition for field solver grid.", 0);
RP::add(
"fieldsolver.manualFsGridDecompositionZ",
"Manual FsGridDecomposition for field solver grid.", 0);
// Vlasov solver parameters
RP::add("vlasovsolver.maxSlAccelerationRotation",
"Maximum rotation angle (degrees) allowed by the Semi-Lagrangian solver (Use >25 values with care)", 25.0);
RP::add("vlasovsolver.maxSlAccelerationSubcycles", "Maximum number of subcycles for acceleration", 1);
RP::add("vlasovsolver.maxCFL",
"The maximum CFL limit for vlasov propagation in ordinary space. Used to set timestep if dynamic_timestep "
"is true.",
0.99);
RP::add("vlasovsolver.minCFL",
"The minimum CFL limit for vlasov propagation in ordinary space. Used to set timestep if dynamic_timestep "
"is true.",
0.8);
RP::add("vlasovsolver.accelerateMaxwellianBoundaries",
"Propagate maxwellian boundary cell contents in velocity space. Default false.",
false);
// Load balancing parameters
RP::add("loadBalance.algorithm", "Load balancing algorithm to be used", string("RCB"));
RP::add("loadBalance.tolerance", "Load imbalance tolerance", string("1.05"));
RP::add("loadBalance.rebalanceInterval", "Load rebalance interval (steps)", 10);
RP::addComposing("loadBalance.optionKey", "Zoltan option key. Has to be matched by loadBalance.optionValue.");
RP::addComposing("loadBalance.optionValue", "Zoltan option value. Has to be matched by loadBalance.optionKey.");
// Output variable parameters
RP::add("io.system_write_all_data_reducers", "If 0 don't write all DROs, if 1 do write them.", false);
// NOTE Do not remove the : before the list of variable names as this is parsed by tools/check_vlasiator_cfg.sh
RP::addComposing("variables.output",
string() +
"List of data reduction operators (DROs) to add to the grid file output. Each variable to be "
"added has to be on a new line output = XXX. Names are case insensitive. " +
"Available (20230628): " + "fg_b fg_b_background fg_b_perturbed fg_b_background_vol fg_derivs_b_background fg_e " +
"vg_rhom vg_rhoq populations_vg_rho " + "fg_rhom fg_rhoq " + "vg_v fg_v populations_vg_v " +
"populations_vg_moments_thermal populations_vg_moments_nonthermal " +
"populations_vg_effectivesparsitythreshold populations_vg_rho_loss_adjust " +
"populations_vg_energydensity populations_vg_precipitationdifferentialflux " +
"populations_vg_heatflux " +
"populations_vg_nonmaxwellianity " +
"vg_maxdt_acceleration vg_maxdt_translation populations_vg_maxdt_acceleration " +
"populations_vg_maxdt_translation " +
"fg_maxdt_fieldsolver " + "vg_rank fg_rank fg_amr_level vg_loadbalance_weight " +
"vg_boundarytype fg_boundarytype vg_boundarylayer fg_boundarylayer " +
"populations_vg_blocks vg_f_saved " + "populations_vg_acceleration_subcycles " +
"vg_e_vol fg_e_vol " +
"fg_e_hall vg_e_gradpe fg_b_vol vg_b_vol vg_b_background_vol vg_b_perturbed_vol " +
"vg_pressure fg_pressure populations_vg_ptensor " + "vg_b_vol_derivatives fg_derivs " +
"ig_fac ig_latitude ig_chi0 ig_cellarea ig_upmappedarea ig_sigmap ig_sigmah ig_sigmaparallel ig_rhon " +
"ig_electrontemp ig_solverinternals ig_upmappednodecoords ig_upmappedb ig_openclosed ig_potential "+
"ig_precipitation ig_deltaphi "+
"ig_inplanecurrent ig_b ig_e vg_drift vg_ionospherecoupling vg_connection vg_fluxrope fg_curvature "+
"vg_amr_drho vg_amr_du vg_amr_dpsq vg_amr_dbsq vg_amr_db vg_amr_alpha1 vg_amr_reflevel vg_amr_alpha2 "+
"vg_amr_translate_comm vg_gridcoordinates fg_gridcoordinates ");
RP::addComposing(
"variables_deprecated.output",
string() + "List of deprecated names for data reduction operators (DROs). Names are case insensitive. " +
"Available (20190521): " + "B BackgroundB fg_BackgroundB PerturbedB fg_PerturbedB " + "E " +
"Rhom Rhoq populations_Rho " + "V populations_V " +
"populations_moments_Backstream populations_moments_NonBackstream " +
"populations_moments_thermal populations_moments_nonthermal " +
"populations_minvalue populations_EffectiveSparsityThreshold populations_RhoLossAdjust "
"populations_rho_loss_adjust" +
"populations_EnergyDensity populations_PrecipitationFlux populations_precipitationdifferentialflux" +
"LBweight vg_lbweight vg_loadbalanceweight MaxVdt MaxRdt populations_MaxVdt populations_MaxRdt " +
"populations_maxdt_acceleration populations_maxdt_translation MaxFieldsdt fg_maxfieldsdt" +
"MPIrank FsGridRank " + "FsGridBoundaryType BoundaryType FsGridBoundaryLayer BoundaryLayer " +
"populations_Blocks fSaved vg_fsaved" + "populations_accSubcycles populations_acceleration_subcycles" +
"VolE vg_VolE Evol E_vol fg_VolE fg_Evol " +
"HallE fg_HallE GradPeE e_gradpe VolB vg_VolB fg_VolB B_vol Bvol vg_Bvol fg_volB fg_Bvol " +
"BackgroundVolB PerturbedVolB " + "Pressure vg_Pressure fg_Pressure populations_PTensor " +
"BVOLderivs b_vol_derivs");
RP::add("io.diagnostic_write_all_data_reducers", "Write all available diagnostic reducers", false);
// NOTE Do not remove the : before the list of variable names as this is parsed by tools/check_vlasiator_cfg.sh
RP::addComposing("variables.diagnostic",
string() +
"List of data reduction operators (DROs) to add to the diagnostic runtime output. Each "
"variable to be added has to be on a new line diagnostic = XXX. Names are case insensitive. " +
"Available (20221221): " + "populations_vg_blocks " +
"vg_rhom populations_vg_rho_loss_adjust " + "vg_loadbalance_weight " +
"vg_maxdt_acceleration vg_maxdt_translation " + "fg_maxdt_fieldsolver " +
"populations_vg_maxdt_acceleration populations_vg_maxdt_translation " +
"populations_vg_maxdistributionfunction populations_vg_mindistributionfunction");
RP::addComposing("variables_deprecated.diagnostic",
string() +
"List of deprecated data reduction operators (DROs) to add to the diagnostic runtime output. "
"Names are case insensitive. " +
"Available (20201111): " + "rhom populations_rholossadjust populations_rho_loss_adjust " +
"populations_blocks lbweight loadbalance_weight " + "vg_lbweight vg_loadbalanceweight " +
"maxvdt maxdt_acceleration " + "maxrdt maxdt_translation " +
"populations_maxvdt populations_maxrdt " +
"populations_maxdt_acceleration populations_maxdt_translation " +
"populations_maxdistributionfunction populations_mindistributionfunction " +
"maxfieldsdt maxdt_fieldsolver fg_maxfieldsdt");
// bailout parameters
RP::add("bailout.write_restart",
"If 1, write a restart file on bailout. Gets reset when sending a STOP (1) or a KILL (0).", true);
RP::add("bailout.min_dt", "Minimum time step below which bailout occurs (s).", 1e-6);
RP::add("bailout.max_memory", "Maximum amount of memory used per node (in GiB) over which bailout occurs.",
1073741824.);
RP::add("bailout.velocity_space_wall_block_margin", "Distance from the velocity space limits in blocks, if the distribution function reaches that distance from the wall we bail out to avoid hitting the wall.", 1);
// Velocity Refinement parameters
RP::add("VAMR.vel_refinement_criterion", "Name of the velocity refinement criterion", string(""));
RP::add("VAMR.max_velocity_level", "Maximum velocity mesh refinement level", (uint)0);
RP::add("VAMR.refine_limit",
"If the refinement criterion function returns a larger value than this, block is refined", (Realf)1.0);
RP::add("VAMR.coarsen_limit",
"If the refinement criterion function returns a smaller value than this, block can be coarsened",
(Realf)0.5);
// Spatial Refinement parameters
RP::add("AMR.max_spatial_level", "Maximum absolute spatial mesh refinement level", (uint)0);
RP::add("AMR.max_allowed_spatial_level", "Maximum currently allowed spatial mesh refinement level", -1);
RP::add("AMR.should_refine","If false, do not refine Vlasov grid regardless of max spatial level",true);
RP::add("AMR.adapt_refinement","If true, re-refine vlasov grid every refine_cadence balance", false);
RP::add("AMR.refine_on_restart","If true, re-refine vlasov grid on restart. DEPRECATED, consider using the DOMR command", false);
RP::add("AMR.force_refinement","If true, refine/unrefine the vlasov grid to match the config on restart", false);
RP::add("AMR.should_filter","If true, filter vlasov grid with boxcar filter on restart",false);
RP::add("AMR.use_alpha1","Use the maximum of dimensionless gradients alpha_1 as a refinement index", true);
RP::add("AMR.alpha1_refine_threshold","Determines the minimum value of alpha_1 to refine cells", 0.5);
RP::add("AMR.alpha1_coarsen_threshold","Determines the maximum value of alpha_1 to unrefine cells, default half of the refine threshold", -1.0);
RP::add("AMR.use_alpha2","Use J/B_perp as a refinement index", true);
RP::add("AMR.alpha2_refine_threshold","Determines the minimum value of alpha_2 to refine cells", 0.5);
RP::add("AMR.alpha2_coarsen_threshold","Determines the maximum value of alpha_2 to unrefine cells, default half of the refine threshold", -1.0);
RP::add("AMR.refine_cadence","Refine every nth load balance", 5);
RP::add("AMR.refine_after","Start refinement after this many simulation seconds", 0.0);
RP::add("AMR.refine_radius","Maximum distance from origin to allow refinement within. Only induced refinement allowed outside this radius.", LARGE_REAL);
RP::add("AMR.refinement_min_x", "Refinement minimum X coordinate, no refinement at x < this value (m) except induced refinement.", -LARGE_REAL);
RP::add("AMR.refinement_min_y", "Refinement minimum Y coordinate, no refinement at y < this value (m) except induced refinement.", -LARGE_REAL);
RP::add("AMR.refinement_min_z", "Refinement minimum Z coordinate, no refinement at z < this value (m) except induced refinement.", -LARGE_REAL);
RP::add("AMR.refinement_max_x", "Refinement maximum X coordinate, no refinement at x > this value (m) except induced refinement.", LARGE_REAL);
RP::add("AMR.refinement_max_y", "Refinement maximum Y coordinate, no refinement at y > this value (m) except induced refinement.", LARGE_REAL);
RP::add("AMR.refinement_max_z", "Refinement maximum Z coordinate, no refinement at z > this value (m) except induced refinement.", LARGE_REAL);
RP::add("AMR.alpha1_drho_weight","Multiplier for delta rho in alpha calculation", 1.0);
RP::add("AMR.alpha1_du_weight","Multiplier for delta U in alpha calculation", 1.0);
RP::add("AMR.alpha1_dpsq_weight","Multiplier for delta p squared in alpha calculation", 1.0);
RP::add("AMR.alpha1_dbsq_weight","Multiplier for delta B squared in alpha calculation", 1.0);
RP::add("AMR.alpha1_db_weight","Multiplier for delta B in alpha calculation", 1.0);
RP::add("AMR.number_of_boxes", "How many boxes to be refined, that number of centers and sizes have to then be defined as well.", 0);
RP::addComposing("AMR.box_half_width_x", "Half width in x of the box that is refined");
RP::addComposing("AMR.box_half_width_y", "Half width in y of the box that is refined");
RP::addComposing("AMR.box_half_width_z", "Half width in z of the box that is refined");
RP::addComposing("AMR.box_center_x", "x coordinate of the center of the box that is refined");
RP::addComposing("AMR.box_center_y", "y coordinate of the center of the box that is refined");
RP::addComposing("AMR.box_center_z", "z coordinate of the center of the box that is refined");
RP::addComposing("AMR.box_max_level", "max refinement level of the box that is refined");
RP::add("AMR.transShortPencils", "if true, use one-cell pencils", false);
RP::addComposing("AMR.filterpasses", string("AMR filter passes for each individual refinement level"));
RP::add("fieldtracing.fieldLineTracer", "Field line tracing method to use for coupling ionosphere and magnetosphere (options are: Euler, BS)", std::string("Euler"));
RP::add("fieldtracing.tracer_max_allowed_error", "Maximum allowed error for the adaptive field line tracers ", 1000);
RP::add("fieldtracing.tracer_max_attempts", "Maximum allowed attempts for the adaptive field line tracers", 100);
RP::add("fieldtracing.tracer_min_dx", "Minimum allowed field line tracer step length for the adaptive field line tracers (m)", 100e3);
RP::add("fieldtracing.fullbox_and_fluxrope_max_absolute_distance_to_trace", "Maximum absolute distance in m to trace along the field line before ending. Defaults to the sum of the simulation box edge lengths LX+LY+LZ if set <= 0.", -1);
RP::add("fieldtracing.fullbox_max_incomplete_cells", "Maximum fraction of cells left incomplete when stopping tracing loop for full box tracing. Defaults to zero to process all, will be slow at scale! Both fluxrope_max_incomplete_cells and fullbox_max_incomplete_cells will be achieved.", 0);
RP::add("fieldtracing.fluxrope_max_incomplete_cells", "Maximum fraction of cells left incomplete when stopping loop for flux rope tracing. Defaults to zero to process all, will be slow at scale! Both fluxrope_max_incomplete_cells and fullbox_max_incomplete_cells will be achieved.", 0);
RP::add("fieldtracing.use_reconstruction_cache", "Use the cache to store reconstruction coefficients. (0: don't, 1: use)", 0);
RP::add("fieldtracing.fluxrope_max_curvature_radii_to_trace", "Maximum number of seedpoint curvature radii to trace forward and backward from each DCCRG cell to find flux ropes", 10);
RP::add("fieldtracing.fluxrope_max_curvature_radii_extent", "Maximum extent in seedpoint curvature radii from the seed a field line is allowed to extend to be counted as a flux rope", 2);
return true;
}
void Parameters::getParameters() {
typedef Readparameters RP;
// get numerical values of the parameters
RP::get("io.diagnostic_write_interval", P::diagnosticInterval);
RP::get("io.diagnostic_write_all_data_reducers", P::diagnosticWriteAllDROs);
RP::get("io.system_write_t_interval", P::systemWriteTimeInterval);
RP::get("io.system_write_file_name", P::systemWriteName);
RP::get("io.system_write_path", P::systemWritePath);
RP::get("io.system_write_distribution_stride", P::systemWriteDistributionWriteStride);
RP::get("io.system_write_distribution_xline_stride", P::systemWriteDistributionWriteXlineStride);
RP::get("io.system_write_distribution_yline_stride", P::systemWriteDistributionWriteYlineStride);
RP::get("io.system_write_distribution_zline_stride", P::systemWriteDistributionWriteZlineStride);
RP::get("io.system_write_distribution_shell_radius", P::systemWriteDistributionWriteShellRadius);
RP::get("io.system_write_distribution_shell_stride", P::systemWriteDistributionWriteShellStride);
RP::get("io.system_write_fsgrid_variables", P::systemWriteFsGrid);
RP::get("io.system_write_all_data_reducers", P::systemWriteAllDROs);
RP::get("io.write_initial_state", P::writeInitialState);
RP::get("io.write_full_bgb_data", P::writeFullBGB);
RP::get("io.restart_walltime_interval", P::saveRestartWalltimeInterval);
RP::get("io.number_of_restarts", P::exitAfterRestarts);
RP::get("io.vlsv_buffer_size", P::vlsvBufferSize);
RP::get("io.write_restart_stripe_factor", P::restartStripeFactor);
RP::get("io.write_system_stripe_factor", P::systemStripeFactor);
RP::get("io.restart_write_path", P::restartWritePath);
RP::get("io.write_as_float", P::writeAsFloat);
// Checks for validity of io and restart parameters
int myRank;
MPI_Comm_rank(MPI_COMM_WORLD, &myRank);
const string prefix = string("./");
if (access(&(P::restartWritePath[0]), W_OK) != 0) {
if (myRank == MASTER_RANK) {
cerr << "ERROR restart write path " << P::restartWritePath << " not writeable, defaulting to local directory."
<< endl;
}
P::restartWritePath = prefix;
}
size_t maxSize = 0;
maxSize = max(maxSize, P::systemWriteTimeInterval.size());
maxSize = max(maxSize, P::systemWriteName.size());
maxSize = max(maxSize, P::systemWritePath.size());
maxSize = max(maxSize, P::systemWriteDistributionWriteStride.size());
maxSize = max(maxSize, P::systemWriteDistributionWriteXlineStride.size());
maxSize = max(maxSize, P::systemWriteDistributionWriteYlineStride.size());
maxSize = max(maxSize, P::systemWriteDistributionWriteZlineStride.size());
if (P::systemWriteTimeInterval.size() != maxSize) {
if (myRank == MASTER_RANK) {
cerr << "ERROR io.system_write_t_interval should be defined for all file types." << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
}
if (P::systemWriteName.size() != maxSize) {
if (myRank == MASTER_RANK) {
cerr << "ERROR io.system_write_file_name should be defined for all file types." << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
}
if (P::systemWritePath.size() != maxSize && P::systemWritePath.size() != 0) {
if (myRank == MASTER_RANK) {
cerr << "ERROR io.system_write_path should be defined for all file types or none at all." << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
}
if (P::systemWriteDistributionWriteStride.size() != maxSize) {
if (myRank == MASTER_RANK) {
cerr << "ERROR io.system_write_distribution_stride should be defined for all file types." << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
}
if (P::systemWriteDistributionWriteXlineStride.size() != maxSize) {
if (myRank == MASTER_RANK) {
cerr << "ERROR io.system_write_distribution_xline_stride should be defined for all file types." << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
}
if (P::systemWriteDistributionWriteYlineStride.size() != maxSize) {
if (myRank == MASTER_RANK) {
cerr << "ERROR io.system_write_distribution_yline_stride should be defined for all file types." << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
}
if (P::systemWriteDistributionWriteZlineStride.size() != maxSize) {
if (myRank == MASTER_RANK) {
cerr << "ERROR io.system_write_distribution_zline_stride should be defined for all file types." << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
}
if (P::systemWriteDistributionWriteShellStride.size() != P::systemWriteDistributionWriteShellRadius.size()) {
if (myRank == MASTER_RANK) {
cerr << "ERROR You should set the same number of io.system_write_distribution_shell_stride "
<< "and io.system_write_distribution_shell_radius." << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
}
if (P::systemWriteFsGrid.size() != maxSize) {
if (P::systemWriteFsGrid.size() == 0) {
for (uint i = 0; i < maxSize; i++) {
P::systemWriteFsGrid.push_back(true);
}
} else {
if (myRank == MASTER_RANK) {
cerr << "ERROR io.system_write_fsgrid_variables should be defined for all file types (or none at all)." << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
}
}
if (P::systemWritePath.size() == 0) {
for (uint i = 0; i < P::systemWriteName.size(); i++) {
P::systemWritePath.push_back(string("./"));
}
} else {
for (uint i = 0; i < P::systemWritePath.size(); i++) {
if (access(&(P::systemWritePath.at(i)[0]), W_OK) != 0) {
if (myRank == MASTER_RANK) {
cerr << "ERROR " << P::systemWriteName.at(i) << " write path " << P::systemWritePath.at(i)
<< " not writeable, defaulting to local directory." << endl;
}
P::systemWritePath.at(i) = prefix;
}
}
}
bool includefSaved = false;
for(uint i=0; i<maxSize; i++) {
if(P::systemWriteDistributionWriteStride[i] != 0 ||
P::systemWriteDistributionWriteXlineStride[i] > 0 ||
P::systemWriteDistributionWriteYlineStride[i] > 0 ||
P::systemWriteDistributionWriteZlineStride[i] > 0) {
includefSaved = true;
}
}
for(uint i=0; i<P::systemWriteDistributionWriteShellRadius.size(); i++) {
if(P::systemWriteDistributionWriteShellRadius[i] > 0) {
includefSaved = true;
}
}
vector<string> mpiioKeys, mpiioValues;
RP::get("io.system_write_mpiio_hint_key", mpiioKeys);
RP::get("io.system_write_mpiio_hint_value", mpiioValues);
if (mpiioKeys.size() != mpiioValues.size()) {
if (myRank == MASTER_RANK) {
cerr << "WARNING the number of io.system_write_mpiio_hint_key and io.system_write_mpiio_hint_value do not "
"match. Disregarding these options."
<< endl;
}
} else {
for (uint i = 0; i < mpiioKeys.size(); i++) {
P::systemWriteHints.push_back({mpiioKeys[i], mpiioValues[i]});
}
}
mpiioKeys.clear();
mpiioValues.clear();
RP::get("io.restart_write_mpiio_hint_key", mpiioKeys);
RP::get("io.restart_write_mpiio_hint_value", mpiioValues);
if (mpiioKeys.size() != mpiioValues.size()) {
if (myRank == MASTER_RANK) {
cerr << "WARNING the number of io.restart_write_mpiio_hint_key and io.restart_write_mpiio_hint_value do not "
"match. Disregarding these options."
<< endl;
}
} else {
for (uint i = 0; i < mpiioKeys.size(); i++) {
P::restartWriteHints.push_back({mpiioKeys[i], mpiioValues[i]});
}
}
mpiioKeys.clear();
mpiioValues.clear();
RP::get("io.restart_read_mpiio_hint_key", mpiioKeys);
RP::get("io.restart_read_mpiio_hint_value", mpiioValues);
if (mpiioKeys.size() != mpiioValues.size()) {
if (myRank == MASTER_RANK) {
cerr << "WARNING the number of io.restart_read_mpiio_hint_key and io.restart_read_mpiio_hint_value do not "
"match. Disregarding these options."
<< endl;
}
} else {
for (uint i = 0; i < mpiioKeys.size(); i++) {
P::restartReadHints.push_back({mpiioKeys[i], mpiioValues[i]});
}
}
RP::get("propagate_field", P::propagateField);
RP::get("propagate_vlasov_acceleration", P::propagateVlasovAcceleration);
RP::get("propagate_vlasov_translation", P::propagateVlasovTranslation);
RP::get("dynamic_timestep", P::dynamicTimestep);
Real hallRho;
RP::get("hallMinimumRho", hallRho);
P::hallMinimumRhom = hallRho * physicalconstants::MASS_PROTON;
P::hallMinimumRhoq = hallRho * physicalconstants::CHARGE;
RP::get("restart.write_as_float", P::writeRestartAsFloat);
RP::get("restart.filename", P::restartFileName);
P::isRestart = (P::restartFileName != string(""));
// manual FsGrid decomposition should be complete with three values. If at least one is set but all are not set, abort
if ((RP::isSet("restart.overrideReadFsGridDecompositionX")||RP::isSet("restart.overrideReadFsGridDecompositionY")||RP::isSet("restart.overrideReadFsGridDecompositionZ")) &&
!(RP::isSet("restart.overrideReadFsGridDecompositionX")&&RP::isSet("restart.overrideReadFsGridDecompositionY")&&RP::isSet("restart.overrideReadFsGridDecompositionZ")) ) {
cerr << "ERROR all of restart.overrideReadFsGridDecompositionX,Y,Z should be defined." << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
FsGridTools::Task_t temp_task_t;
RP::get("restart.overrideReadFsGridDecompositionX", temp_task_t);
P::overrideReadFsGridDecomposition[0] = temp_task_t;
RP::get("restart.overrideReadFsGridDecompositionY", temp_task_t);
P::overrideReadFsGridDecomposition[1] = temp_task_t;
RP::get("restart.overrideReadFsGridDecompositionZ", temp_task_t);
P::overrideReadFsGridDecomposition[2] = temp_task_t;
RP::get("project", P::projectName);
if (RP::helpRequested) {
P::projectName = string("Magnetosphere");
}
/*get numerical values, let Readparameters handle the conversions*/
string geometryString;
RP::get("gridbuilder.geometry", geometryString);
RP::get("gridbuilder.x_min", P::xmin);
RP::get("gridbuilder.x_max", P::xmax);
RP::get("gridbuilder.y_min", P::ymin);
RP::get("gridbuilder.y_max", P::ymax);
RP::get("gridbuilder.z_min", P::zmin);
RP::get("gridbuilder.z_max", P::zmax);
RP::get("gridbuilder.x_length", P::xcells_ini);
RP::get("gridbuilder.y_length", P::ycells_ini);
RP::get("gridbuilder.z_length", P::zcells_ini);
RP::get("VAMR.max_velocity_level", P::vamrMaxVelocityRefLevel);
RP::get("VAMR.vel_refinement_criterion", P::vamrVelRefCriterion);
RP::get("VAMR.refine_limit", P::vamrRefineLimit);
RP::get("VAMR.coarsen_limit", P::vamrCoarsenLimit);
RP::get("AMR.max_spatial_level", P::amrMaxSpatialRefLevel);
RP::get("AMR.max_allowed_spatial_level", P::amrMaxAllowedSpatialRefLevel);
if(P::amrMaxAllowedSpatialRefLevel < 0) { // negative (default is -1) just goes to max
P::amrMaxAllowedSpatialRefLevel = P::amrMaxSpatialRefLevel; // set max allowed to the same as the absolute max
}
if(P::amrMaxSpatialRefLevel < P::amrMaxAllowedSpatialRefLevel) {
if(myRank == MASTER_RANK) {
cerr << "AMR.max_allowed_spatial_level cannot be greater than AMR.max_spatial_level!\n";
}
MPI_Abort(MPI_COMM_WORLD, 1);
}
RP::get("AMR.adapt_refinement",P::adaptRefinement);
RP::get("AMR.refine_on_restart",P::refineOnRestart);
RP::get("AMR.force_refinement",P::forceRefinement);
RP::get("AMR.should_filter",P::shouldFilter);
RP::get("AMR.use_alpha1",P::useAlpha1);
RP::get("AMR.alpha1_refine_threshold",P::alpha1RefineThreshold);
RP::get("AMR.alpha1_coarsen_threshold",P::alpha1CoarsenThreshold);
if (P::useAlpha1 && P::alpha1CoarsenThreshold < 0) {
P::alpha1CoarsenThreshold = P::alpha1RefineThreshold / 2.0;
}
if (P::useAlpha1 && P::alpha1RefineThreshold < 0) {
if (myRank == MASTER_RANK) {
cerr << "ERROR invalid alpha_1 refine threshold" << endl;
}
MPI_Abort(MPI_COMM_WORLD, 1);
}
RP::get("AMR.use_alpha2",P::useAlpha2);
RP::get("AMR.alpha2_refine_threshold",P::alpha2RefineThreshold);
RP::get("AMR.alpha2_coarsen_threshold",P::alpha2CoarsenThreshold);
if (P::useAlpha2 && P::alpha2CoarsenThreshold < 0) {
P::alpha2CoarsenThreshold = P::alpha2RefineThreshold / 2.0;
}
if (P::useAlpha2 && P::alpha2RefineThreshold < 0) {
if (myRank == MASTER_RANK) {
cerr << "ERROR invalid alpha_2 refine threshold" << endl;
}
MPI_Abort(MPI_COMM_WORLD, 1);
}
RP::get("AMR.refine_cadence",P::refineCadence);
RP::get("AMR.refine_after",P::refineAfter);
RP::get("AMR.refine_radius",P::refineRadius);
RP::get("AMR.refinement_min_x", P::refinementMinX);
RP::get("AMR.refinement_min_y", P::refinementMinY);
RP::get("AMR.refinement_min_z", P::refinementMinZ);
RP::get("AMR.refinement_max_x", P::refinementMaxX);
RP::get("AMR.refinement_max_y", P::refinementMaxY);
RP::get("AMR.refinement_max_z", P::refinementMaxZ);
RP::get("AMR.alpha1_drho_weight", P::alphaDRhoWeight);
RP::get("AMR.alpha1_du_weight", P::alphaDUWeight);
RP::get("AMR.alpha1_dpsq_weight", P::alphaDPSqWeight);
RP::get("AMR.alpha1_dbsq_weight", P::alphaDBSqWeight);
RP::get("AMR.alpha1_db_weight", P::alphaDBWeight);
RP::get("AMR.number_of_boxes", P::amrBoxNumber);
RP::get("AMR.box_max_level", P::amrBoxMaxLevel);
RP::get("AMR.box_half_width_x", P::amrBoxHalfWidthX);
RP::get("AMR.box_half_width_y", P::amrBoxHalfWidthY);
RP::get("AMR.box_half_width_z", P::amrBoxHalfWidthZ);
RP::get("AMR.box_center_x", P::amrBoxCenterX);
RP::get("AMR.box_center_y", P::amrBoxCenterY);
RP::get("AMR.box_center_z", P::amrBoxCenterZ);
RP::get("AMR.transShortPencils", P::amrTransShortPencils);
RP::get("AMR.filterpasses", P::blurPassString);
// We need the correct number of parameters for the AMR boxes
if( P::amrBoxNumber != (int)P::amrBoxHalfWidthX.size()
|| P::amrBoxNumber != (int)P::amrBoxHalfWidthY.size()
|| P::amrBoxNumber != (int)P::amrBoxHalfWidthZ.size()
|| P::amrBoxNumber != (int)P::amrBoxCenterX.size()
|| P::amrBoxNumber != (int)P::amrBoxCenterY.size()
|| P::amrBoxNumber != (int)P::amrBoxCenterZ.size()
|| P::amrBoxNumber != (int)P::amrBoxMaxLevel.size()
) {
cerr << "AMR.number_of_boxes is set to " << P::amrBoxNumber << " so the same number of values is required for AMR.box_half_width_[xyz] and AMR.box_center_[xyz]." << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
// If we are in an AMR run we need to set up the filtering scheme.
if (P::amrMaxSpatialRefLevel>0){
bool isEmpty = blurPassString.size() == 0;
if (!isEmpty){
//sanity check=> user should define a pass for every level
if ((int)blurPassString.size() != P::amrMaxSpatialRefLevel + 1) {
cerr << "Filter Passes=" << blurPassString.size() << "\t" << "AMR Levels=" << P::amrMaxSpatialRefLevel + 1 << endl;
cerr << "FilterPasses do not match AMR levels. \t" << " in " << __FILE__ << ":" << __LINE__ << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
//sort the filtering passes per refLevel
numPasses.clear();
//Parse to a vector of ints
for (auto pass : blurPassString){
P::numPasses.push_back(stoi(pass));
}
sort(numPasses.begin(),numPasses.end(),greater<int>());
}else{
//here we will default to manually constructing the number of passes
numPasses.clear();
auto g_sequence=[](int size){
int retval=1;
while(size!=0){
retval*=2;
size-=1;
}
return retval;
};
int maxPasses=g_sequence(P::amrMaxSpatialRefLevel-1);
for (int refLevel=0; refLevel<=P::amrMaxSpatialRefLevel; refLevel++){
numPasses.push_back(maxPasses);
maxPasses/=2;
}
//Overwrite passes for the highest refLevel. We do not want to filter there.
numPasses.at(P::amrMaxSpatialRefLevel) = 0;
}
P::maxFilteringPasses = numPasses[0];
}
if (geometryString == "XY4D") {
P::geometry = geometry::XY4D;
} else if (geometryString == "XZ4D") {
P::geometry = geometry::XZ4D;
} else if (geometryString == "XY5D") {
P::geometry = geometry::XY5D;
} else if (geometryString == "XZ5D") {
P::geometry = geometry::XZ5D;
} else if (geometryString == "XYZ6D") {
P::geometry = geometry::XYZ6D;
} else {
cerr << "Unknown simulation geometry " << geometryString << " in " << __FILE__ << ":" << __LINE__ << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
if (P::vamrCoarsenLimit >= P::vamrRefineLimit) {
cerr << "vamrRefineLimit must be smaller than vamrCoarsenLimit!" << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
if (P::xmax < P::xmin || (P::ymax < P::ymin || P::zmax < P::zmin)) {
cerr << "Box domain error!" << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
// Set some parameter values.
P::dx_ini = (P::xmax - P::xmin) / P::xcells_ini;
P::dy_ini = (P::ymax - P::ymin) / P::ycells_ini;
P::dz_ini = (P::zmax - P::zmin) / P::zcells_ini;
RP::get("gridbuilder.dt", P::dt);
RP::get("gridbuilder.t_max", P::t_max);
RP::get("gridbuilder.timestep_max", P::tstep_max);
if (P::dynamicTimestep)
P::dt = 0.0; // if dynamic timestep then first dt is always 0
// if we are restarting, t,t_min, tstep, tstep_min will be overwritten in readGrid
P::t_min = 0;
P::t = P::t_min;
P::tstep_min = 0;
P::tstep = P::tstep_min;
// Get field solver parameters
RP::get("fieldsolver.maxWaveVelocity", P::maxWaveVelocity);
RP::get("fieldsolver.maxSubcycles", P::maxFieldSolverSubcycles);
RP::get("fieldsolver.resistivity", P::resistivity);
RP::get("fieldsolver.diffusiveEterms", P::fieldSolverDiffusiveEterms);
RP::get("fieldsolver.ohmHallTerm", P::ohmHallTerm);
RP::get("fieldsolver.ohmGradPeTerm", P::ohmGradPeTerm);
RP::get("fieldsolver.electronTemperature", P::electronTemperature);
RP::get("fieldsolver.electronDensity", P::electronDensity);
RP::get("fieldsolver.electronPTindex", P::electronPTindex);
RP::get("fieldsolver.maxCFL", P::fieldSolverMaxCFL);
RP::get("fieldsolver.minCFL", P::fieldSolverMinCFL);
// manual FsGrid decomposition should be complete with three values. If at least one is set but all are not set, abort
if ((RP::isSet("fieldsolver.manualFsGridDecompositionX")||RP::isSet("fieldsolver.manualFsGridDecompositionY")||RP::isSet("fieldsolver.manualFsGridDecompositionZ")) &&
!(RP::isSet("fieldsolver.manualFsGridDecompositionX")&&RP::isSet("fieldsolver.manualFsGridDecompositionY")&&RP::isSet("fieldsolver.manualFsGridDecompositionZ")) ) {
cerr << "ERROR all of fieldsolver.manualFsGridDecompositionX,Y,Z should be defined." << endl;
MPI_Abort(MPI_COMM_WORLD, 1);
}
RP::get("fieldsolver.manualFsGridDecompositionX", temp_task_t);
P::manualFsGridDecomposition[0] = temp_task_t;
RP::get("fieldsolver.manualFsGridDecompositionY", temp_task_t);
P::manualFsGridDecomposition[1] = temp_task_t;
RP::get("fieldsolver.manualFsGridDecompositionZ", temp_task_t);
P::manualFsGridDecomposition[2] = temp_task_t;
// Get Vlasov solver parameters
RP::get("vlasovsolver.maxSlAccelerationRotation", P::maxSlAccelerationRotation);
RP::get("vlasovsolver.maxSlAccelerationSubcycles", P::maxSlAccelerationSubcycles);
RP::get("vlasovsolver.maxCFL", P::vlasovSolverMaxCFL);
RP::get("vlasovsolver.minCFL", P::vlasovSolverMinCFL);
RP::get("vlasovsolver.accelerateMaxwellianBoundaries", P::vlasovAccelerateMaxwellianBoundaries);
// Get load balance parameters
RP::get("loadBalance.algorithm", P::loadBalanceAlgorithm);
loadBalanceOptions["IMBALANCE_TOL"] = "";
RP::get("loadBalance.tolerance", loadBalanceOptions["IMBALANCE_TOL"]);
RP::get("loadBalance.rebalanceInterval", P::rebalanceInterval);
std::vector<std::string> loadBalanceKeys;
std::vector<std::string> loadBalanceValues;
RP::get("loadBalance.optionKey", loadBalanceKeys);
RP::get("loadBalance.optionValue", loadBalanceValues);
if (loadBalanceKeys.size() != loadBalanceValues.size()) {
if (myRank == MASTER_RANK) {
cerr << "WARNING the number of load balance keys and values do not match. Disregarding these options." << endl;
}
} else {
for (size_t i = 0; i < loadBalanceKeys.size(); ++i) {
loadBalanceOptions[loadBalanceKeys[i]] = loadBalanceValues[i];
}
}
// Get output variable parameters
RP::get("variables.output", P::outputVariableList);
RP::get("variables.diagnostic", P::diagnosticVariableList);
// Insert vg_f_saved to the list if necessary
if(includefSaved) {
P::outputVariableList.push_back("vg_f_saved");
}
// Filter duplicate variable names
set<string> dummy(P::outputVariableList.begin(), P::outputVariableList.end());
P::outputVariableList.clear();
P::outputVariableList.insert(P::outputVariableList.end(), dummy.begin(), dummy.end());
dummy.clear();
dummy.insert(P::diagnosticVariableList.begin(), P::diagnosticVariableList.end());
P::diagnosticVariableList.clear();
P::diagnosticVariableList.insert(P::diagnosticVariableList.end(), dummy.begin(), dummy.end());
// Get parameters related to bailout
RP::get("bailout.write_restart", P::bailout_write_restart);
RP::get("bailout.min_dt", P::bailout_min_dt);