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Parse and Visualize HYDRAD Results#

This example demonstrates how to configure a simple hydrad simulation and read in and visualize the outputs as a function of time and field-aligned spatial coordinate.

import pathlib
import tempfile

import astropy.units as u
from astropy.visualization import ImageNormalize, LogStretch

from pydrad.configure import Configure
from pydrad.configure.data import get_defaults
from pydrad.configure.util import get_clean_hydrad, run_shell_command
from pydrad.parse import Strand

tmpdir = pathlib.Path(tempfile.mkdtemp())  # Change to wherever you want to save your clean HYDRAD copy

HYDRAD prints all results to the Results directory in the main code directory. These filenames are in the format profile{index}.{ext} where index is the timestep number and ext can be one of the following filetypes,

  • phy – main physics results file containing temperature, density, etc.

  • amr – data related to the adaptive mesh

  • trm – equation terms at each grid cell

Parsing all of these files can be difficult. pydrad provides a convenient object, ~pydrad.parse.Strand, for easily accessing the data associated with a particular HYDRAD run.

First, we’ll setup a simple HYDRAD run and run the simulation. Grab a new copy of HYDRAD

hydrad_clean = tmpdir / 'hydrad-clean'
get_clean_hydrad(hydrad_clean, from_github=True)

We’ll start with the default configuration and setup a simple simulation for a 50 Mm loop lasting 500 s in which there are no heating events such that the loop is maintained in static equilibrium.

config = get_defaults()
config['general']['total_time'] = 500 * u.s
config['general']['output_interval'] = 10 * u.s
config['general']['loop_length'] = 50 * u.Mm
config['heating']['background']['use_initial_conditions'] = True
config['heating']['events'] = []

/home/docs/checkouts/readthedocs.org/user_builds/pydrad/envs/latest/lib/python3.11/site-packages/astropy/units/format/utils.py:219: UnitsWarning: The unit 'erg' has been deprecated in the VOUnit standard. Suggested: cm**2.g.s**-2.
  warnings.warn(message, UnitsWarning)

To reduce the commputation time and memory footprint of our example simulation, we reduce the degree to which our spatial grid is refined. In general, this is something that should be done cautiously. See Bradshaw and Cargill (2013) for more details on appropriately resolving gradients in the transition region. This is an especially important consideration in impulsive heating scenarios.

config['grid']['initial_refinement_level'] = 6
config['grid']['maximum_refinement_level'] = 6

Next, we’ll setup and run the simulation. We’ll run HYDRAD directly from Python, but this is easily done via the command line as well. This can take a few minutes.

c = Configure(config)
hydrad_results = tmpdir / 'steady-run'
c.setup_simulation(hydrad_results, hydrad_clean)
run_shell_command(hydrad_results / 'HYDRAD.exe')

WARNING: ../source/misc.cpp: In function ‘void GetConfigurationParameters(PARAMETERS*)’:
../source/misc.cpp:31:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   31 | fscanf( pFile, "%s", pParams->szOutputFilename );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp: In member function ‘void CElement::OpenRangesFile(char*)’:
../../Radiation_Model/source/element.cpp:63:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   63 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:66:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   66 | fscanf( pFile, "%i", &NumTemp );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:67:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   67 | fscanf( pFile, "%i", &NumDen );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:76:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   76 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:85:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   85 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp: In member function ‘void CElement::OpenAbundanceFile(char*)’:
../../Radiation_Model/source/element.cpp:105:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  105 | fscanf( pFile, "%i", &buffer );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:121:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  121 |     fscanf( pFile, "%i", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp: In member function ‘void CElement::OpenEmissivityFile(char*)’:
../../Radiation_Model/source/element.cpp:152:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  152 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:154:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  154 | fscanf( pFile, "%i", &NumIons );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:162:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  162 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:166:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  166 |     fscanf( pFile, "%i", &pSpecNum[i] );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:184:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  184 |         fscanf( pFile, "%c", &buffer );
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp: In member function ‘void CElement::OpenRatesFile(char*)’:
../../Radiation_Model/source/element.cpp:237:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  237 |     fscanf( pFile, "%s", buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:251:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  251 |     fscanf( pFile, "%s", buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp: In member function ‘void CRadiation::Initialise(char*)’:
../../Radiation_Model/source/radiation.cpp:92:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   92 | fscanf( pFile, "%s", buffer1 );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:96:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   96 | fscanf( pFile, "%s", buffer2 );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:99:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   99 | fscanf( pFile, "%s", buffer3 );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:103:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  103 | fscanf( pFile, "%s", buffer4 );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:106:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  106 | fscanf( pFile, "%i", &NumElements );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:117:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  117 |     fscanf( pFile, "%s", buffer1 );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:120:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  120 |     fscanf( pFile, "%i", &(pZ[i]) );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp: In member function ‘void CRadiation::OpenRangesFile(char*)’:
../../Radiation_Model/source/radiation.cpp:156:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  156 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:159:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  159 | fscanf( pFile, "%i", &NumTemp );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:160:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  160 | fscanf( pFile, "%i", &NumDen );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:169:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  169 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:178:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  178 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp: In member function ‘void CPieceWiseFit::OpenPieceWiseFit(char*)’:
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp:49:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   49 |                 fscanf( pInputFile, "%i", &iPolyOrder );
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp:51:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   51 |                 fscanf( pInputFile, "%i", &inumSD );
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp: In member function ‘void CPieceWiseFit::GeneratePieceWiseFit(char*, char*)’:
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp:92:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   92 |                 fscanf( pInputFile, "%i", &iPolyOrder );
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp:99:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   99 |                 fscanf( pInputFile, "%i", &inumSD );
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp:106:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  106 |                 fscanf( pInputFile, "%i", &inumPoints );
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Resources/source/file.cpp: In function ‘void ReadDouble(void*, double*)’:
../../Resources/source/file.cpp:24:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   24 | fscanf( pFile, "%s", buffer );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
 [pydrad.configure.util]
INFO:

Calculating initial hydrostatic conditions...

Peak heating range = 7.6913e-04 -> 7.7090e-04 erg cm^-3 s^-1

Optimum peak heating rate = 7.6952e-04 erg cm^-3 s^-1

Writing initial conditions file...

Done!

 [pydrad.configure.util]
WARNING: ../source/mesh.cpp: In member function ‘void CAdaptiveMesh::CreateInitialMesh()’:
../source/mesh.cpp:84:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   84 | fscanf( pFile, "%i", &iFileNumber );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../source/mesh.cpp:88:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   88 | fscanf( pFile, "%i", &Params.iNumberOfCells );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../source/mesh.cpp:112:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  112 |     fscanf( pFile, "%i", &(CellProperties.iRefinementLevel) );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../source/mesh.cpp:114:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  114 |         fscanf( pFile, "%i", &(CellProperties.iUniqueID[j]) );
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../source/eqns.cpp: In member function ‘void CEquations::Initialise()’:
../source/eqns.cpp:131:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  131 |                 fscanf( pFile, "%s", Params.Profiles );
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../source/eqns.cpp:133:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  133 |                 fscanf( pFile, "%s", Params.GravityFilename );
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../source/eqns.cpp:147:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  147 |                 fscanf( pFile, "%i", &iTemp );
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../../Heating_Model/source/heat.cpp: In member function ‘void CHeat::GetHeatingData()’:
../../Heating_Model/source/heat.cpp:104:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  104 | fscanf( pConfigFile, "%i", &NumActivatedEvents );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/ionfrac.cpp: In member function ‘void CIonFrac::Initialise(CIonFrac*, char*, PRADIATION)’:
../../Radiation_Model/source/ionfrac.cpp:49:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   49 |     fscanf( pFile, "%s", buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/ionfrac.cpp:52:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   52 |     fscanf( pFile, "%s", buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/ionfrac.cpp:55:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   55 |     fscanf( pFile, "%s", buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/ionfrac.cpp:58:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   58 |     fscanf( pFile, "%s", buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/ionfrac.cpp:61:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   61 |     fscanf( pFile, "%i", &NumElements );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/ionfrac.cpp:74:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   74 |         fscanf( pFile, "%s", buffer );
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/ionfrac.cpp:77:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   77 |         fscanf( pFile, "%i", &(pZ[i]) );
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/ionfrac.cpp: In member function ‘void CIonFrac::ReadAllIonFracFromFile(void*)’:
../../Radiation_Model/source/ionfrac.cpp:199:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  199 |     fscanf( (FILE*)pFile, "%i", &(pZ[i]) );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/ionfrac.cpp: In member function ‘void CIonFrac::ReadIonFracFromFile(void*, int)’:
../../Radiation_Model/source/ionfrac.cpp:216:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  216 | fscanf( (FILE*)pFile, "%i", &(pZ[i]) );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp: In member function ‘void CElement::OpenRangesFile(char*)’:
../../Radiation_Model/source/element.cpp:63:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   63 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:66:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   66 | fscanf( pFile, "%i", &NumTemp );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:67:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   67 | fscanf( pFile, "%i", &NumDen );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:76:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   76 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:85:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   85 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp: In member function ‘void CElement::OpenAbundanceFile(char*)’:
../../Radiation_Model/source/element.cpp:105:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  105 | fscanf( pFile, "%i", &buffer );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:121:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  121 |     fscanf( pFile, "%i", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp: In member function ‘void CElement::OpenEmissivityFile(char*)’:
../../Radiation_Model/source/element.cpp:152:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  152 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:154:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  154 | fscanf( pFile, "%i", &NumIons );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:162:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  162 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:166:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  166 |     fscanf( pFile, "%i", &pSpecNum[i] );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:184:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  184 |         fscanf( pFile, "%c", &buffer );
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp: In member function ‘void CElement::OpenRatesFile(char*)’:
../../Radiation_Model/source/element.cpp:237:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  237 |     fscanf( pFile, "%s", buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/element.cpp:251:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  251 |     fscanf( pFile, "%s", buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp: In member function ‘void CRadiation::Initialise(char*)’:
../../Radiation_Model/source/radiation.cpp:92:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   92 | fscanf( pFile, "%s", buffer1 );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:96:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   96 | fscanf( pFile, "%s", buffer2 );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:99:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   99 | fscanf( pFile, "%s", buffer3 );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:103:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  103 | fscanf( pFile, "%s", buffer4 );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:106:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  106 | fscanf( pFile, "%i", &NumElements );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:117:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  117 |     fscanf( pFile, "%s", buffer1 );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:120:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  120 |     fscanf( pFile, "%i", &(pZ[i]) );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp: In member function ‘void CRadiation::OpenRangesFile(char*)’:
../../Radiation_Model/source/radiation.cpp:156:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  156 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:159:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  159 | fscanf( pFile, "%i", &NumTemp );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:160:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  160 | fscanf( pFile, "%i", &NumDen );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:169:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  169 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Radiation_Model/source/radiation.cpp:178:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  178 |     fscanf( pFile, "%c", &buffer );
      |     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp: In member function ‘void CPieceWiseFit::OpenPieceWiseFit(char*)’:
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp:49:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   49 |                 fscanf( pInputFile, "%i", &iPolyOrder );
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp:51:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   51 |                 fscanf( pInputFile, "%i", &inumSD );
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp: In member function ‘void CPieceWiseFit::GeneratePieceWiseFit(char*, char*)’:
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp:92:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   92 |                 fscanf( pInputFile, "%i", &iPolyOrder );
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp:99:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   99 |                 fscanf( pInputFile, "%i", &inumSD );
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Resources/Utils/generatePieceWiseFit/source/piecewisefit.cpp:106:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  106 |                 fscanf( pInputFile, "%i", &inumPoints );
      |                 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../Resources/source/file.cpp: In function ‘void ReadDouble(void*, double*)’:
../../Resources/source/file.cpp:24:7: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   24 | fscanf( pFile, "%s", buffer );
      | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
 [pydrad.configure.util]
/home/docs/checkouts/readthedocs.org/user_builds/pydrad/envs/latest/lib/python3.11/site-packages/astropy/units/format/utils.py:219: UnitsWarning: The unit 'erg' has been deprecated in the VOUnit standard. Suggested: cm**2.g.s**-2.
  warnings.warn(message, UnitsWarning)
/home/docs/checkouts/readthedocs.org/user_builds/pydrad/envs/latest/lib/python3.11/site-packages/astropy/units/format/utils.py:219: UnitsWarning: The unit 'erg' has been deprecated in the VOUnit standard. Suggested: cm**2.g.s**-2.
  warnings.warn(message, UnitsWarning)
/home/docs/checkouts/readthedocs.org/user_builds/pydrad/envs/latest/lib/python3.11/site-packages/astropy/units/format/utils.py:219: UnitsWarning: The unit 'erg' has been deprecated in the VOUnit standard. Suggested: cm**2.g.s**-2.
  warnings.warn(message, UnitsWarning)
/home/docs/checkouts/readthedocs.org/user_builds/pydrad/envs/latest/lib/python3.11/site-packages/astropy/units/format/utils.py:219: UnitsWarning: The unit 'erg' has been deprecated in the VOUnit standard. Suggested: cm**2.g.s**-2.
  warnings.warn(message, UnitsWarning)
INFO:
Processing the initial conditions...

Solving...

model-time elapsed = 9.7295e+00 s; dt = 9.6230e-03 s
wall-time elapsed = 3.0760e-01 s; ~ wall-time remaining = 1.5500e+01 s
        wall-time/1000 steps = 3.0760e-01 s; wall-time/second = 3.1615e-02 s
        refinement level = 6/6; total grid cells = 202

model-time elapsed = 1.5989e+01 s; dt = 6.0930e-03 s
wall-time elapsed = 6.3283e-01 s; ~ wall-time remaining = 1.9157e+01 s
        wall-time/1000 steps = 3.2523e-01 s; wall-time/second = 3.9579e-02 s
        refinement level = 6/6; total grid cells = 209

model-time elapsed = 2.5415e+01 s; dt = 9.2978e-03 s
wall-time elapsed = 1.0597e+00 s; ~ wall-time remaining = 1.9789e+01 s
        wall-time/1000 steps = 4.2687e-01 s; wall-time/second = 4.1696e-02 s
        refinement level = 6/6; total grid cells = 199

model-time elapsed = 3.4885e+01 s; dt = 9.3214e-03 s
wall-time elapsed = 1.3859e+00 s; ~ wall-time remaining = 1.8478e+01 s
        wall-time/1000 steps = 3.2615e-01 s; wall-time/second = 3.9727e-02 s
        refinement level = 6/6; total grid cells = 209

model-time elapsed = 4.4357e+01 s; dt = 9.3359e-03 s
wall-time elapsed = 1.7049e+00 s; ~ wall-time remaining = 1.7513e+01 s
        wall-time/1000 steps = 3.1897e-01 s; wall-time/second = 3.8435e-02 s
        refinement level = 6/6; total grid cells = 204

model-time elapsed = 5.3855e+01 s; dt = 9.3367e-03 s
wall-time elapsed = 2.0243e+00 s; ~ wall-time remaining = 1.6770e+01 s
        wall-time/1000 steps = 3.1940e-01 s; wall-time/second = 3.7588e-02 s
        refinement level = 6/6; total grid cells = 204

model-time elapsed = 6.3105e+01 s; dt = 9.2969e-03 s
wall-time elapsed = 2.4356e+00 s; ~ wall-time remaining = 1.6862e+01 s
        wall-time/1000 steps = 4.1131e-01 s; wall-time/second = 3.8596e-02 s
        refinement level = 6/6; total grid cells = 213

model-time elapsed = 6.6273e+01 s; dt = 2.9953e-03 s
wall-time elapsed = 2.8438e+00 s; ~ wall-time remaining = 1.8611e+01 s
        wall-time/1000 steps = 4.0817e-01 s; wall-time/second = 4.2910e-02 s
        refinement level = 6/6; total grid cells = 212

model-time elapsed = 7.5565e+01 s; dt = 9.2687e-03 s
wall-time elapsed = 3.3283e+00 s; ~ wall-time remaining = 1.8694e+01 s
        wall-time/1000 steps = 4.8450e-01 s; wall-time/second = 4.4045e-02 s
        refinement level = 6/6; total grid cells = 201

model-time elapsed = 8.4994e+01 s; dt = 9.2844e-03 s
wall-time elapsed = 3.8330e+00 s; ~ wall-time remaining = 1.8715e+01 s
        wall-time/1000 steps = 5.0465e-01 s; wall-time/second = 4.5097e-02 s
        refinement level = 6/6; total grid cells = 209

model-time elapsed = 9.2869e+01 s; dt = 8.1498e-03 s
wall-time elapsed = 4.3149e+00 s; ~ wall-time remaining = 1.8916e+01 s
        wall-time/1000 steps = 4.8194e-01 s; wall-time/second = 4.6462e-02 s
        refinement level = 6/6; total grid cells = 200

model-time elapsed = 1.0052e+02 s; dt = 7.4367e-03 s
wall-time elapsed = 4.8143e+00 s; ~ wall-time remaining = 1.9133e+01 s
        wall-time/1000 steps = 4.9937e-01 s; wall-time/second = 4.7895e-02 s
        refinement level = 6/6; total grid cells = 207

model-time elapsed = 1.0992e+02 s; dt = 9.2432e-03 s
wall-time elapsed = 5.2865e+00 s; ~ wall-time remaining = 1.8761e+01 s
        wall-time/1000 steps = 4.7214e-01 s; wall-time/second = 4.8094e-02 s
        refinement level = 6/6; total grid cells = 199

model-time elapsed = 1.1930e+02 s; dt = 9.2350e-03 s
wall-time elapsed = 5.7596e+00 s; ~ wall-time remaining = 1.8379e+01 s
        wall-time/1000 steps = 4.7315e-01 s; wall-time/second = 4.8277e-02 s
        refinement level = 6/6; total grid cells = 196

model-time elapsed = 1.2611e+02 s; dt = 7.2317e-03 s
wall-time elapsed = 6.2934e+00 s; ~ wall-time remaining = 1.8659e+01 s
        wall-time/1000 steps = 5.3373e-01 s; wall-time/second = 4.9905e-02 s
        refinement level = 6/6; total grid cells = 221

model-time elapsed = 1.3551e+02 s; dt = 9.5554e-03 s
wall-time elapsed = 6.7794e+00 s; ~ wall-time remaining = 1.8235e+01 s
        wall-time/1000 steps = 4.8603e-01 s; wall-time/second = 5.0029e-02 s
        refinement level = 6/6; total grid cells = 201

model-time elapsed = 1.4461e+02 s; dt = 8.8333e-03 s
wall-time elapsed = 7.2450e+00 s; ~ wall-time remaining = 1.7806e+01 s
        wall-time/1000 steps = 4.6553e-01 s; wall-time/second = 5.0101e-02 s
        refinement level = 6/6; total grid cells = 222

model-time elapsed = 1.5392e+02 s; dt = 9.1968e-03 s
wall-time elapsed = 7.5603e+00 s; ~ wall-time remaining = 1.6998e+01 s
        wall-time/1000 steps = 3.1530e-01 s; wall-time/second = 4.9117e-02 s
        refinement level = 6/6; total grid cells = 202

model-time elapsed = 1.6330e+02 s; dt = 9.2610e-03 s
wall-time elapsed = 7.8901e+00 s; ~ wall-time remaining = 1.6269e+01 s
        wall-time/1000 steps = 3.2979e-01 s; wall-time/second = 4.8317e-02 s
        refinement level = 6/6; total grid cells = 211

model-time elapsed = 1.7144e+02 s; dt = 7.2235e-03 s
wall-time elapsed = 8.2209e+00 s; ~ wall-time remaining = 1.5755e+01 s
        wall-time/1000 steps = 3.3075e-01 s; wall-time/second = 4.7952e-02 s
        refinement level = 6/6; total grid cells = 212

model-time elapsed = 1.8092e+02 s; dt = 9.3172e-03 s
wall-time elapsed = 8.5266e+00 s; ~ wall-time remaining = 1.5038e+01 s
        wall-time/1000 steps = 3.0571e-01 s; wall-time/second = 4.7129e-02 s
        refinement level = 6/6; total grid cells = 196

model-time elapsed = 1.9037e+02 s; dt = 9.2807e-03 s
wall-time elapsed = 8.8588e+00 s; ~ wall-time remaining = 1.4408e+01 s
        wall-time/1000 steps = 3.3217e-01 s; wall-time/second = 4.6534e-02 s
        refinement level = 6/6; total grid cells = 213

model-time elapsed = 1.9421e+02 s; dt = 4.0456e-03 s
wall-time elapsed = 9.1826e+00 s; ~ wall-time remaining = 1.4458e+01 s
        wall-time/1000 steps = 3.2376e-01 s; wall-time/second = 4.7282e-02 s
        refinement level = 6/6; total grid cells = 211

model-time elapsed = 2.0200e+02 s; dt = 8.0129e-03 s
wall-time elapsed = 9.4943e+00 s; ~ wall-time remaining = 1.4006e+01 s
        wall-time/1000 steps = 3.1170e-01 s; wall-time/second = 4.7001e-02 s
        refinement level = 6/6; total grid cells = 201

model-time elapsed = 2.1142e+02 s; dt = 9.2711e-03 s
wall-time elapsed = 9.8108e+00 s; ~ wall-time remaining = 1.3391e+01 s
        wall-time/1000 steps = 3.1651e-01 s; wall-time/second = 4.6403e-02 s
        refinement level = 6/6; total grid cells = 202

model-time elapsed = 2.2083e+02 s; dt = 9.2336e-03 s
wall-time elapsed = 1.0144e+01 s; ~ wall-time remaining = 1.2823e+01 s
        wall-time/1000 steps = 3.3301e-01 s; wall-time/second = 4.5934e-02 s
        refinement level = 6/6; total grid cells = 213

model-time elapsed = 2.3019e+02 s; dt = 9.1875e-03 s
wall-time elapsed = 1.0471e+01 s; ~ wall-time remaining = 1.2273e+01 s
        wall-time/1000 steps = 3.2729e-01 s; wall-time/second = 4.5489e-02 s
        refinement level = 6/6; total grid cells = 209

model-time elapsed = 2.3952e+02 s; dt = 9.1823e-03 s
wall-time elapsed = 1.0790e+01 s; ~ wall-time remaining = 1.1735e+01 s
        wall-time/1000 steps = 3.1932e-01 s; wall-time/second = 4.5051e-02 s
        refinement level = 6/6; total grid cells = 207

model-time elapsed = 2.4203e+02 s; dt = 2.4089e-03 s
wall-time elapsed = 1.1146e+01 s; ~ wall-time remaining = 1.1881e+01 s
        wall-time/1000 steps = 3.5586e-01 s; wall-time/second = 4.6054e-02 s
        refinement level = 6/6; total grid cells = 228

model-time elapsed = 2.5152e+02 s; dt = 9.1384e-03 s
wall-time elapsed = 1.1466e+01 s; ~ wall-time remaining = 1.1328e+01 s
        wall-time/1000 steps = 3.1990e-01 s; wall-time/second = 4.5588e-02 s
        refinement level = 6/6; total grid cells = 206

model-time elapsed = 2.6089e+02 s; dt = 9.5380e-03 s
wall-time elapsed = 1.1795e+01 s; ~ wall-time remaining = 1.0811e+01 s
        wall-time/1000 steps = 3.2897e-01 s; wall-time/second = 4.5212e-02 s
        refinement level = 6/6; total grid cells = 206

model-time elapsed = 2.7030e+02 s; dt = 9.5660e-03 s
wall-time elapsed = 1.2105e+01 s; ~ wall-time remaining = 1.0287e+01 s
        wall-time/1000 steps = 3.1017e-01 s; wall-time/second = 4.4786e-02 s
        refinement level = 6/6; total grid cells = 198

model-time elapsed = 2.7970e+02 s; dt = 9.5389e-03 s
wall-time elapsed = 1.2416e+01 s; ~ wall-time remaining = 9.7797e+00 s
        wall-time/1000 steps = 3.1100e-01 s; wall-time/second = 4.4392e-02 s
        refinement level = 6/6; total grid cells = 202

model-time elapsed = 2.8908e+02 s; dt = 9.5329e-03 s
wall-time elapsed = 1.2736e+01 s; ~ wall-time remaining = 9.2924e+00 s
        wall-time/1000 steps = 3.1919e-01 s; wall-time/second = 4.4056e-02 s
        refinement level = 6/6; total grid cells = 204

model-time elapsed = 2.9847e+02 s; dt = 9.5375e-03 s
wall-time elapsed = 1.3061e+01 s; ~ wall-time remaining = 8.8188e+00 s
        wall-time/1000 steps = 3.2562e-01 s; wall-time/second = 4.3760e-02 s
        refinement level = 6/6; total grid cells = 208

model-time elapsed = 3.0781e+02 s; dt = 9.4345e-03 s
wall-time elapsed = 1.3371e+01 s; ~ wall-time remaining = 8.3486e+00 s
        wall-time/1000 steps = 3.0934e-01 s; wall-time/second = 4.3438e-02 s
        refinement level = 6/6; total grid cells = 198

model-time elapsed = 3.0979e+02 s; dt = 1.8934e-03 s
wall-time elapsed = 1.3710e+01 s; ~ wall-time remaining = 8.4182e+00 s
        wall-time/1000 steps = 3.3966e-01 s; wall-time/second = 4.4257e-02 s
        refinement level = 6/6; total grid cells = 219

model-time elapsed = 3.1457e+02 s; dt = 4.3378e-03 s
wall-time elapsed = 1.4027e+01 s; ~ wall-time remaining = 8.2684e+00 s
        wall-time/1000 steps = 3.1639e-01 s; wall-time/second = 4.4590e-02 s
        refinement level = 6/6; total grid cells = 203

model-time elapsed = 3.2309e+02 s; dt = 8.5466e-03 s
wall-time elapsed = 1.4338e+01 s; ~ wall-time remaining = 7.8510e+00 s
        wall-time/1000 steps = 3.1177e-01 s; wall-time/second = 4.4379e-02 s
        refinement level = 6/6; total grid cells = 200

model-time elapsed = 3.3099e+02 s; dt = 7.9878e-03 s
wall-time elapsed = 1.4676e+01 s; ~ wall-time remaining = 7.4942e+00 s
        wall-time/1000 steps = 3.3763e-01 s; wall-time/second = 4.4341e-02 s
        refinement level = 6/6; total grid cells = 216

model-time elapsed = 3.4025e+02 s; dt = 9.4452e-03 s
wall-time elapsed = 1.4988e+01 s; ~ wall-time remaining = 7.0374e+00 s
        wall-time/1000 steps = 3.1237e-01 s; wall-time/second = 4.4052e-02 s
        refinement level = 6/6; total grid cells = 200

model-time elapsed = 3.4875e+02 s; dt = 9.3853e-03 s
wall-time elapsed = 1.5306e+01 s; ~ wall-time remaining = 6.6384e+00 s
        wall-time/1000 steps = 3.1774e-01 s; wall-time/second = 4.3889e-02 s
        refinement level = 6/6; total grid cells = 207

model-time elapsed = 3.5815e+02 s; dt = 9.5709e-03 s
wall-time elapsed = 1.5620e+01 s; ~ wall-time remaining = 6.1863e+00 s
        wall-time/1000 steps = 3.1405e-01 s; wall-time/second = 4.3613e-02 s
        refinement level = 6/6; total grid cells = 201

model-time elapsed = 3.6306e+02 s; dt = 4.9369e-03 s
wall-time elapsed = 1.5965e+01 s; ~ wall-time remaining = 6.0220e+00 s
        wall-time/1000 steps = 3.4499e-01 s; wall-time/second = 4.3974e-02 s
        refinement level = 6/6; total grid cells = 217

model-time elapsed = 3.7242e+02 s; dt = 9.5545e-03 s
wall-time elapsed = 1.6272e+01 s; ~ wall-time remaining = 5.5744e+00 s
        wall-time/1000 steps = 3.0633e-01 s; wall-time/second = 4.3692e-02 s
        refinement level = 6/6; total grid cells = 196

model-time elapsed = 3.7692e+02 s; dt = 4.3461e-03 s
wall-time elapsed = 1.6601e+01 s; ~ wall-time remaining = 5.4211e+00 s
        wall-time/1000 steps = 3.2978e-01 s; wall-time/second = 4.4045e-02 s
        refinement level = 6/6; total grid cells = 215

model-time elapsed = 3.8632e+02 s; dt = 9.3150e-03 s
wall-time elapsed = 1.6915e+01 s; ~ wall-time remaining = 4.9774e+00 s
        wall-time/1000 steps = 3.1369e-01 s; wall-time/second = 4.3785e-02 s
        refinement level = 6/6; total grid cells = 201

model-time elapsed = 3.9174e+02 s; dt = 5.1060e-03 s
wall-time elapsed = 1.7270e+01 s; ~ wall-time remaining = 4.7724e+00 s
        wall-time/1000 steps = 3.5455e-01 s; wall-time/second = 4.4084e-02 s
        refinement level = 6/6; total grid cells = 227

model-time elapsed = 4.0118e+02 s; dt = 9.6066e-03 s
wall-time elapsed = 1.7580e+01 s; ~ wall-time remaining = 4.3303e+00 s
        wall-time/1000 steps = 3.0984e-01 s; wall-time/second = 4.3820e-02 s
        refinement level = 6/6; total grid cells = 198

model-time elapsed = 4.1018e+02 s; dt = 8.4934e-03 s
wall-time elapsed = 1.7915e+01 s; ~ wall-time remaining = 3.9229e+00 s
        wall-time/1000 steps = 3.3571e-01 s; wall-time/second = 4.3676e-02 s
        refinement level = 6/6; total grid cells = 213

model-time elapsed = 4.1948e+02 s; dt = 9.4870e-03 s
wall-time elapsed = 1.8229e+01 s; ~ wall-time remaining = 3.4991e+00 s
        wall-time/1000 steps = 3.1362e-01 s; wall-time/second = 4.3456e-02 s
        refinement level = 6/6; total grid cells = 204

model-time elapsed = 4.2386e+02 s; dt = 4.1776e-03 s
wall-time elapsed = 1.8547e+01 s; ~ wall-time remaining = 3.3315e+00 s
        wall-time/1000 steps = 3.1787e-01 s; wall-time/second = 4.3757e-02 s
        refinement level = 6/6; total grid cells = 204

model-time elapsed = 4.3164e+02 s; dt = 6.8167e-03 s
wall-time elapsed = 1.8863e+01 s; ~ wall-time remaining = 2.9875e+00 s
        wall-time/1000 steps = 3.1576e-01 s; wall-time/second = 4.3700e-02 s
        refinement level = 6/6; total grid cells = 203

model-time elapsed = 4.3462e+02 s; dt = 2.8103e-03 s
wall-time elapsed = 1.9190e+01 s; ~ wall-time remaining = 2.8869e+00 s
        wall-time/1000 steps = 3.2782e-01 s; wall-time/second = 4.4154e-02 s
        refinement level = 6/6; total grid cells = 214

model-time elapsed = 4.3673e+02 s; dt = 2.2891e-03 s
wall-time elapsed = 1.9501e+01 s; ~ wall-time remaining = 2.8251e+00 s
        wall-time/1000 steps = 3.1056e-01 s; wall-time/second = 4.4652e-02 s
        refinement level = 6/6; total grid cells = 203

model-time elapsed = 4.4605e+02 s; dt = 9.2978e-03 s
wall-time elapsed = 1.9804e+01 s; ~ wall-time remaining = 2.3953e+00 s
        wall-time/1000 steps = 3.0301e-01 s; wall-time/second = 4.4398e-02 s
        refinement level = 6/6; total grid cells = 194

model-time elapsed = 4.5312e+02 s; dt = 6.8158e-03 s
wall-time elapsed = 2.0143e+01 s; ~ wall-time remaining = 2.0840e+00 s
        wall-time/1000 steps = 3.3934e-01 s; wall-time/second = 4.4455e-02 s
        refinement level = 6/6; total grid cells = 216

model-time elapsed = 4.6246e+02 s; dt = 9.5104e-03 s
wall-time elapsed = 2.0458e+01 s; ~ wall-time remaining = 1.6605e+00 s
        wall-time/1000 steps = 3.1430e-01 s; wall-time/second = 4.4236e-02 s
        refinement level = 6/6; total grid cells = 201

model-time elapsed = 4.7187e+02 s; dt = 9.6121e-03 s
wall-time elapsed = 2.0764e+01 s; ~ wall-time remaining = 1.2378e+00 s
        wall-time/1000 steps = 3.0605e-01 s; wall-time/second = 4.4003e-02 s
        refinement level = 6/6; total grid cells = 196

model-time elapsed = 4.7804e+02 s; dt = 6.6761e-03 s
wall-time elapsed = 2.1104e+01 s; ~ wall-time remaining = 9.6961e-01 s
        wall-time/1000 steps = 3.4001e-01 s; wall-time/second = 4.4147e-02 s
        refinement level = 6/6; total grid cells = 221

model-time elapsed = 4.8754e+02 s; dt = 9.7215e-03 s
wall-time elapsed = 2.1430e+01 s; ~ wall-time remaining = 5.4788e-01 s
        wall-time/1000 steps = 3.2589e-01 s; wall-time/second = 4.3955e-02 s
        refinement level = 6/6; total grid cells = 208

model-time elapsed = 4.9197e+02 s; dt = 4.5820e-03 s
wall-time elapsed = 2.1759e+01 s; ~ wall-time remaining = 3.5529e-01 s
        wall-time/1000 steps = 3.2947e-01 s; wall-time/second = 4.4229e-02 s
        refinement level = 6/6; total grid cells = 211


Done!

 [pydrad.configure.util]

To parse the results of a simulation, we create a ~pydard.parse.Strand object which holds information about the entire simulation.

s = Strand(hydrad_results)
print(s)

HYDrodynamics and RADiation (HYDRAD) Code
-----------------------------------------
Results path: /tmp/tmpudrlx3gl/steady-run
Time interval: [0.0 s, 500.008 s]
Number of profiles: 51
Loop length: 50.000 Mm

We can get basic information about the simulation such as the time and loop length

print(s.time)
print(s.loop_length)

[  0.      10.0039  20.0028  30.0049  40.0001  50.0075  60.0027  70.0048
  80.0039  90.0039 100.005  110.003  120.005  130.005  140.005  150.009
 160.008  170.005  180.001  190.004  200.002  210.001  220.006  230.003
 240.002  250.006  260.007  270.004  280.007  290.007  300.002  310.005
 320.006  330.003  340.005  350.004  360.003  370.002  380.003  390.003
 400.006  410.003  420.004  430.004  440.002  450.001  460.003  470.008
 480.006  490.001  500.008 ] s
5000000000.0 cm

Indexing the ~pydrad.parse.Strand object, we get back a ~pydrad.parse.Profile object which holds information about a single snapshot of the simulation.

p = s[0]
print(p)

HYDRAD Timestep Profile
-----------------------
Filename: /tmp/tmpudrlx3gl/steady-run/Results/profile0.phy
Timestep #: 0

The ~pydrad.parse.Profile object also holds the thermodynamic quantities as a function of spatial coordinate at this particular timestep. Note that the quantity at each time step is stored as a separate 1D array as the spatial grid from one time step to the next need not be the same due to the use of the adaptively refined grid. Note that each profile is a ~astropy.units.Quantity and can be easily converted to any compatible unit.

print(p.electron_temperature)
print(p.ion_density)
print(p.velocity)

[  20000.       20000.       20000.       20000.       20000.
   20000.       20000.       20000.       20000.       20000.
   20000.       20000.       20000.       20000.       20000.
   20000.       20000.       20000.       20000.       20000.
   20000.       20000.       20000.       20000.       20000.
   20000.       20000.       20000.       20000.       20000.
   20000.       20000.       20000.       20000.       20000.
   20000.       20000.       20000.       20798.6104   19213.3114
   16440.7517   16556.2916   17438.2987   19170.8913   21267.7631
   23263.7091   25855.9661   29890.9259   36463.4647   48845.2523
   79874.1744  143781.469   180118.62    206425.8     236101.268
  267714.727   303543.35    341825.871   385390.725   432009.889
  485124.497   542009.211   607042.572   676869.65    756598.148
  841786.338   910176.801   967717.34   1017516.85   1061437.44
 1100695.86   1136137.09   1168374.93   1197871.1    1224982.73
 1249992.32   1273127.49   1294574.58   1314488.09   1332997.66
 1350212.95   1366227.74   1381122.67   1394967.52   1407822.95
 1419742.02   1430770.94   1440950.5    1450316.9    1458901.95
 1466733.46   1473835.92   1480230.83   1485936.97   1490970.67
 1495346.01   1499074.98   1502167.6    1504632.09   1506474.91
 1507700.83   1508310.45   1508306.1    1507700.98   1506475.15
 1504632.44   1502168.05   1499075.52   1495346.66   1490971.42
 1485937.83   1480231.79   1473836.99   1466734.64   1458903.24
 1450318.31   1440952.03   1430772.46   1419743.51   1407824.45
 1394969.04   1381124.24   1366229.32   1350214.55   1332999.28
 1314489.91   1294576.5    1273129.5    1249994.4    1224984.9
 1197873.35   1168377.29   1136139.63   1100698.66   1061440.54
 1017520.29    967721.312   910181.426   841791.994   756605.419
  676879.019   607054.645   542024.609   485144.328   432035.478
  385423.697   341868.265   303597.995   267785.062   236192.295
  206543.39    180271.102   144010.059    80338.6471   48992.318
   36529.7638   29915.7872   25881.2589   22147.3636   19226.0896
   16976.5598   16433.9347   19211.6163   20800.475    20000.
   20000.       20000.       20000.       20000.       20000.
   20000.       20000.       20000.       20000.       20000.
   20000.       20000.       20000.       20000.       20000.
   20000.       20000.       20000.       20000.       20000.
   20000.       20000.       20000.       20000.       20000.
   20000.       20000.       20000.       20000.       20000.
   20000.       20000.       20000.       20000.       20000.
   20000.       20000.    ] K
[1.79790804e+13 1.57162717e+13 1.37389400e+13 1.20111886e+13
 1.05015025e+13 9.18233680e+12 8.02961910e+12 7.02231377e+12
 6.14204058e+12 5.37274084e+12 4.70038519e+12 4.11271798e+12
 3.59903359e+12 3.14998090e+12 2.75739216e+12 2.41413354e+12
 2.11397432e+12 1.85147267e+12 1.62187581e+12 1.42103272e+12
 1.24531791e+12 1.09156485e+12 9.57007779e+11 8.39230902e+11
 7.36124010e+11 6.45843730e+11 5.66779694e+11 4.97524985e+11
 4.36850348e+11 3.83681658e+11 3.37080266e+11 2.96225823e+11
 2.60401301e+11 2.28979905e+11 2.01413650e+11 1.77223395e+11
 1.55990132e+11 1.37347388e+11 1.20064836e+11 1.21884349e+11
 1.35945915e+11 1.31751589e+11 1.23095759e+11 1.10199129e+11
 9.81626547e+10 8.90392578e+10 7.94861081e+10 6.82314258e+10
 5.55161363e+10 4.11478222e+10 2.49951898e+10 1.38660042e+10
 1.10579366e+10 9.64084088e+09 8.42016448e+09 7.41658492e+09
 6.53044933e+09 5.78778615e+09 5.12033370e+09 4.55378229e+09
 4.03873566e+09 3.59731940e+09 3.19127336e+09 2.84007253e+09
 2.51501772e+09 2.23324745e+09 2.04304830e+09 1.90244084e+09
 1.79258904e+09 1.70351338e+09 1.62933085e+09 1.56630315e+09
 1.51191838e+09 1.46441400e+09 1.42250960e+09 1.38524855e+09
 1.35189901e+09 1.32189006e+09 1.29476861e+09 1.27016986e+09
 1.24779651e+09 1.22740336e+09 1.20878632e+09 1.19177417e+09
 1.17622219e+09 1.16200722e+09 1.14902425e+09 1.13718295e+09
 1.12640518e+09 1.11662351e+09 1.10777982e+09 1.09982380e+09
 1.09271198e+09 1.08640686e+09 1.08087625e+09 1.07609272e+09
 1.07203312e+09 1.06867823e+09 1.06601245e+09 1.06402357e+09
 1.06270258e+09 1.06204632e+09 1.06205103e+09 1.06270247e+09
 1.06402340e+09 1.06601221e+09 1.06867792e+09 1.07203273e+09
 1.07609226e+09 1.08087571e+09 1.08640624e+09 1.09271128e+09
 1.09982301e+09 1.10777894e+09 1.11662255e+09 1.12640413e+09
 1.13718180e+09 1.14902312e+09 1.16200612e+09 1.17622109e+09
 1.19177307e+09 1.20878516e+09 1.22740218e+09 1.24779531e+09
 1.27016862e+09 1.29476711e+09 1.32188841e+09 1.35189723e+09
 1.38524660e+09 1.42250749e+09 1.46441166e+09 1.51191579e+09
 1.56630013e+09 1.62932720e+09 1.70350891e+09 1.79258351e+09
 1.90243356e+09 2.04303844e+09 2.23323291e+09 2.51499392e+09
 2.84003337e+09 3.19120971e+09 3.59721653e+09 4.03856919e+09
 4.55351017e+09 5.11989191e+09 5.78706260e+09 6.52926540e+09
 7.41462490e+09 8.41690227e+09 9.63532791e+09 1.10485494e+10
 1.38439363e+10 2.48504665e+10 4.10241755e+10 5.54154394e+10
 6.81746940e+10 7.94093741e+10 9.38936435e+10 1.09887654e+11
 1.27468944e+11 1.36004604e+11 1.21896682e+11 1.20055404e+11
 1.37349035e+11 1.55992002e+11 1.77225520e+11 2.01416065e+11
 2.28982651e+11 2.60404424e+11 2.96229376e+11 3.37084309e+11
 3.83686260e+11 4.36855588e+11 4.97530954e+11 5.66786493e+11
 6.45851479e+11 7.36132842e+11 8.39240972e+11 9.57019262e+11
 1.09157795e+12 1.24533285e+12 1.42104977e+12 1.62189528e+12
 1.85149490e+12 2.11399969e+12 2.41416252e+12 2.75742527e+12
 3.15001872e+12 3.59907681e+12 4.11276736e+12 4.70044163e+12
 5.37280536e+12 6.14211434e+12 7.02239811e+12 8.02971554e+12
 9.18244709e+12 1.05016286e+13 1.20113329e+13 1.37391051e+13
 1.57164605e+13 1.79792642e+13] 1 / cm3
[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.] cm / s

The ~pydrad.parse.Strand object also holds an additional ~pydrad.parse.Profile object for the initial conditions,

print(s.initial_conditions)

HYDRAD Timestep Profile
-----------------------
Filename: /tmp/tmpudrlx3gl/steady-run/Initial_Conditions/profiles/initial.amr.phy
Timestep #: 0

The ~pydrad.parse.Strand object can also be indexed in more complex ways in the same manner as a list or array to get the simulation only over a particular time range or at a particular time cadence. As an example, we can grab only the first 5 time steps or every other time step.

print(s[:5])
print(s[::2])

HYDrodynamics and RADiation (HYDRAD) Code
-----------------------------------------
Results path: /tmp/tmpudrlx3gl/steady-run
Time interval: [0.0 s, 40.0001 s]
Number of profiles: 5
Loop length: 50.000 Mm
HYDrodynamics and RADiation (HYDRAD) Code
-----------------------------------------
Results path: /tmp/tmpudrlx3gl/steady-run
Time interval: [0.0 s, 500.008 s]
Number of profiles: 26
Loop length: 50.000 Mm

The simplest way to visualize HYDRAD output is to look at a single time step as a function of field-aligned coordinate. The ~pydrad.parse.Profile object provides a simple quicklook method for this,

s[0].peek()
parse simulation

Similarly, we can call this method on a ~pydrad.parse.Strand to overplot every profile at each time step, where the time step is mapped to the colormap. For additional information about what arguments can be passed in here, see the ~pydrad.visualize.plot_profile documentation.

s.peek()
parse simulation

Often we want to visualize the whole loop as a function of time as a “time-distance” plot. The ~pydrad.parse.Strand object provides a convenience method for this visualization as well. Because of the differences in spatial grids between time steps, the quantities are reinterpolated onto a uniform grid of specified resolution, in this case 0.5 Mm, before plotting.

s.peek_time_distance('electron_temperature', 0.5*u.Mm)
parse simulation

This quicklook function is flexible enough to visualize multiple quantities on different colormaps

s.peek_time_distance(
    ['electron_temperature', 'electron_density', 'velocity'],
    0.5*u.Mm,
    cmap={'velocity': 'RdBu_r'},
    labels={'electron_temperature': r'$T_e$',
            'electron_density': r'$n_e$'},
    norm={'electron_density': ImageNormalize(vmin=1e8, vmax=1e12, stretch=LogStretch())},
    time_unit='h',
    space_unit='Mm',
)
parse simulation

Total running time of the script: (0 minutes 42.958 seconds)

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