openPMD RZ modes dumped in thetaMode (#2878)

* [Draft] openPMD: RZ Modes

* Change 'theta' to 't' and 'J' to 'j'

* Docs: openPMD rz notes

* editing docs openPMD RZ note

* erase cartesian E,B,j from openPMD rz diags list

* openpmd rz: theta->t, exclude xyz dumps

* openpmd rz: axes r,z, save as comp[mode][r][z]

* catch logic bugs tracking when in rz mode

* change return type to c++17 tuple in helper fn

* allow divB functor to store in theta mode

* tuple bindings / account for theta mode variables

* only r,t,z componets in RZ, separate rz field init

* separate rz field init, arbitrary diags in RZ

* docs: xyz comps in cartesian, rtz in rz geometry

* docs : remove mention of dump_rz_modes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* clarify documentation of InitializeFieldFunctorsRZ

* n_rz_modes = 1 if not in RZ

* style change for brackets

* style, documentation, clarify magic constants

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* add helper getVec

* transpose RZ openPMD data for proper viewing

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* safe for 2d and rz

* fix transpose order of limits, add tinyProfiler

* document transpose function, lack of optimization

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Fix divB num components

* keeping changes to openPMD+RZ, not general RZ

* divB made more similar to divE

* eliminate or document unused variables

* fix openPMD+RZ documentation

* change thetaMode parser to regex

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* replace n_rz_azimuthal_modes with warpx variable ncomps

* Ignore Unused Var in Cartesian

* add rz openpmd analysis

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Fix warnings: unused vars

* clarify documentation of dump_rz_modes

* cleaning up before sending to PR

* remove divB, divE, test in a different PR

* Update Source/Diagnostics/WarpXOpenPMD.cpp

fix Dxygen strings

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* clean up doxygen, note issue in divB

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* fixing rz_opmd test, still not passing

* Fix: Unused <diag>.dump_rz_modes

* updating openPMD+rz analysis

* Regression Setup: set `outputFile`

* Use HDF5 Backend

This is most likely installed by all developers, so we use it for
tests.

* Code Style Updates

* simplify test and reduce code redundancy

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* reduce redundancy 1 less line

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* Keep HDF5

HDF5 is easier to install for developers and provided in CI.

* Style fixes

* Style fix

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

1 files changed, 21 insertions, 0 deletions

diff --git a/Examples/Tests/openpmd_rz/analysis_openpmd_rz.py b/Examples/Tests/openpmd_rz/analysis_openpmd_rz.py
new file mode 100755
index 000000000..0a15173b6
--- /dev/null
+++ b/Examples/Tests/openpmd_rz/analysis_openpmd_rz.py
@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+
+import openpmd_api as io
+
+series = io.Series("LaserAccelerationRZ_opmd_plt/openpmd_%T.h5", io.Access.read_only)
+
+assert len(series.iterations) == 3, 'improper number of iterations stored'
+
+ii = series.iterations[20]
+
+assert len(ii.meshes) == 7, 'improper number of meshes'
+
+jt = ii.meshes['j']['t']
+(Nm, Nr, Nz) = jt.shape
+
+assert Nm == 3, 'Wrong number of angular modes stored or possible incorrect ordering when flushed'
+assert Nr == 64, 'Wrong number of radial points stored or possible incorrect ordering when flushed'
+assert Nz == 512, 'Wrong number of z points stored or possible incorrect ordering when flushed'
+
+assert ii.meshes['part_per_grid'][io.Mesh_Record_Component.SCALAR].shape == [64,512], 'problem with part_per_grid'
+assert ii.meshes['rho_electrons'][io.Mesh_Record_Component.SCALAR].shape == [3, 64, 512], 'problem with rho_electrons'