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openPMD: Handle Zero Particles Well #2980

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merged 5 commits into from
Mar 22, 2022
Merged

openPMD: Handle Zero Particles Well #2980

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75ce5fa
openPMD: Handle Zero Particles Well
ax3l Mar 17, 2022
b6e7271
openPMD: Emtpy Particle Writes
ax3l Mar 18, 2022
d655604
Re-order: ED-PIC & Constant Particle Records
ax3l Mar 21, 2022
8df7b1e
Enable BTD for ADIOS :)
ax3l Mar 21, 2022
d07cf66
Fix lingo in comments (Reva)
ax3l Mar 21, 2022
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1 change: 0 additions & 1 deletion Docs/source/usage/parameters.rst
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Expand Up @@ -1908,7 +1908,6 @@ In-situ capabilities can be used by turning on Sensei or Ascent (provided they a
``bp`` is the `ADIOS I/O library <https://csmd.ornl.gov/adios>`_, ``h5`` is the `HDF5 format <https://www.hdfgroup.org/solutions/hdf5/>`_, and ``json`` is a `simple text format <https://en.wikipedia.org/wiki/JSON>`_.
``json`` only works with serial/single-rank jobs.
When WarpX is compiled with openPMD support, the first available backend in the order given above is taken.
Note that when using ``BackTransformed`` diagnostic type, the openpmd format supports only ``h5`` backend for both species and fields, while ``bp`` backend can be used for visualizing fields, but not particles. The code will abort if ``bp`` is selected for particle output.

* ``<diag_name>.openpmd_encoding`` (optional, ``v`` (variable based), ``f`` (file based) or ``g`` (group based) ) only read if ``<diag_name>.format = openpmd``.
openPMD `file output encoding <https://openpmd-api.readthedocs.io/en/0.14.0/usage/concepts.html#iteration-and-series>`__.
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22 changes: 1 addition & 21 deletions Source/Diagnostics/FlushFormats/FlushFormatOpenPMD.cpp
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Expand Up @@ -100,26 +100,6 @@ FlushFormatOpenPMD::FlushFormatOpenPMD (const std::string& diag_name)
engine_type, engine_parameters,
warpx.getPMLdirections()
);

// Temporarily adding Abort for adios filetype if species is selected for BTD output
bool species_output = true;
int write_species = 1;
std::vector< std::string > output_species_names;
bool species_specified = pp_diag_name.queryarr("species", output_species_names);
if (species_specified == true and output_species_names.size() > 0) {
species_output = true;
} else {
// By default species output is computed for all diagnostics, if write_species is not set to 0
species_output = true;
}
// Check user-defined option to turn off species output
pp_diag_name.query("write_species", write_species);
if (write_species == 0) species_output = false;
if (diag_type_str == "BackTransformed" and species_output == true) {
if (m_OpenPMDPlotWriter->OpenPMDFileType() == "bp") {
amrex::Abort(" Currently BackTransformed diagnostics type does not support species output for ADIOS backend. Please select h5 as openpmd backend");
}
}
}

void
Expand Down Expand Up @@ -155,7 +135,7 @@ FlushFormatOpenPMD::WriteToFile (
varnames, mf, geom, output_levels, output_iteration, time, isBTD, full_BTD_snapshot);

// particles: all (reside only on locally finest level)
m_OpenPMDPlotWriter->WriteOpenPMDParticles(particle_diags, isBTD, totalParticlesFlushedAlready);
m_OpenPMDPlotWriter->WriteOpenPMDParticles(particle_diags, isBTD, isLastBTDFlush, totalParticlesFlushedAlready);

// signal that no further updates will be written to this iteration
m_OpenPMDPlotWriter->CloseStep(isBTD, isLastBTDFlush);
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33 changes: 24 additions & 9 deletions Source/Diagnostics/WarpXOpenPMD.H
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Expand Up @@ -135,6 +135,7 @@ public:
void WriteOpenPMDParticles (
const amrex::Vector<ParticleDiag>& particle_diags,
const bool isBTD = false,
const bool isLastBTDFlush = false,
const amrex::Vector<int>& totalParticlesFlushedAlready = amrex::Vector<int>());

/** Write out all openPMD fields for all active MR levels
Expand Down Expand Up @@ -209,18 +210,31 @@ private:
std::string& comp_name
) const;

/** This function sets up the entries for storing the particle positions, global IDs, and constant records (charge, mass)
/** This function sets up the entries for storing the particle positions and global IDs
*
* @param[in] currSpecies Corresponding openPMD species
* @param[in] np Number of particles
* @param[in] charge Charge of the particles (note: fix for ions)
* @param[in] mass Mass of the particles
* @param[in] isBTD Is this a back-transformed diagnostics output?
*/
void SetupPos (
openPMD::ParticleSpecies& currSpecies,
const unsigned long long& np,
bool const isBTD = false);

/** This function sets constant particle records and ED-PIC attributes.
*
* Sets the entries for storing particle position offset, constant records (charge, mass) and ED-PIC attributes.
*
* @param[in] currSpecies Corresponding openPMD species
* @param[in] np Number of particles
* @param[in] charge Charge of the particles (note: fix for ions)
* @param[in] mass Mass of the particles
*/
void SetConstParticleRecordsEDPIC (
openPMD::ParticleSpecies& currSpecies,
const unsigned long long& np,
amrex::ParticleReal const charge,
amrex::ParticleReal const mass, bool const isBTD = false);
amrex::ParticleReal const mass);

/** This function sets up the entries for particle properties
*
Expand Down Expand Up @@ -269,7 +283,9 @@ private:
* @param[in] int_comp_names The int attribute names, from WarpX
* @param[in] charge Charge of the particles (note: fix for ions)
* @param[in] mass Mass of the particles
* @param[in] isBTD is this a backtransformed diagnostics write?
* @param[in] isBTD is this a backtransformed diagnostics (BTD) write?
* @param[in] isLastBTDFlush is this the last time we will flush this BTD station?
* @param[in] ParticleFlushOffset previously flushed number of particles in BTD
*/
void DumpToFile (ParticleContainer* pc,
const std::string& name,
Expand All @@ -279,7 +295,9 @@ private:
const amrex::Vector<std::string>& real_comp_names,
const amrex::Vector<std::string>& int_comp_names,
amrex::ParticleReal const charge,
amrex::ParticleReal const mass, const bool isBTD = false,
amrex::ParticleReal const mass,
const bool isBTD = false,
const bool isLastBTDFlush = false,
int ParticleFlushOffset = 0);

/** Get the openPMD-api filename for openPMD::Series
Expand All @@ -294,9 +312,6 @@ private:

std::unique_ptr<openPMD::Series> m_Series;

/** To set particle meta-data for the openpmd dump. */
bool m_doParticleSetUp = true;

/** This is the output directory
*
* This usually does not yet end in a `/`.
Expand Down
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