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| -rw-r--r-- | Docs/source/visualization/ascent.rst | 188 | ||||
| -rw-r--r-- | Source/Diagnostics/WarpXIO.cpp | 56 |
2 files changed, 194 insertions, 50 deletions
diff --git a/Docs/source/visualization/ascent.rst b/Docs/source/visualization/ascent.rst index 4f8a2bbd9..12a11d38a 100644 --- a/Docs/source/visualization/ascent.rst +++ b/Docs/source/visualization/ascent.rst @@ -45,65 +45,153 @@ The supported parameters are described in the following table. +-------------------------+------------------------------------------------------+---------+ A typical use case is setting :code:`insitu.int` to a value of one or greater and -:code:`insitu.start` to the first time step where in situ analyswhere in situ analysis should be +:code:`insitu.start` to the first time step where in situ analysis should be performed. Visualization/Analysis Pipeline Configuration --------------------------------------------- -Ascent uses the file :code:`ascent_actions.json` to configure analysis and -visualization pipelines. For example, the following :code:`ascent_actions.json` +Ascent uses the file :code:`ascent_actions.yaml` to configure analysis and +visualization pipelines. Ascent looks for the :code:`ascent_actions.yaml` file +in the current working directory. + +For example, the following :code:`ascent_actions.yaml` file extracts an isosurface of the field Ex for 15 levels and saves the resulting images to :code:`levels_<nnnn>.png`. `Ascent Actions <https://ascent.readthedocs.io/en/latest/Actions/index.html>`_ provides an overview over all available analysis and visualization actions. .. code-block:: json +- + action: "add_pipelines" + pipelines: + p1: + f1: + type: "contour" + params: + field: "Ex" + levels: 15 +- + action: "add_scenes" + scenes: + scene1: + image_prefix: "levels_%04d" + plots: + plot1: + type: "pseudocolor" + pipeline: "p1" + field: "Ex" + +Here is another :code:`ascent_actions.yaml` example that renders isosurfaces +and particles: - [ - { - "action": "add_pipelines", - "pipelines": - { - "p1": - { - "f1": - { - "type" : "contour", - "params" : - { - "field" : "Ex", - "levels": 15 - } - } - } - } - }, - { - "action": "add_scenes", - "scenes": - { - "s1": - { - "image_prefix": "levels_%04d", - "plots": - { - "p1": - { - "type": "pseudocolor", - "pipeline": "p1", - "field": "Ex" - } - } - } - } - }, - - { - "action": "execute" - }, - - { - "action": "reset" - } - ] +.. code-block:: json +- + action: "add_pipelines" + pipelines: + p1: + f1: + type: "contour" + params: + field: "Bx" + levels: 3 +- + action: "add_scenes" + scenes: + scene1: + plots: + plot1: + type: "pseudocolor" + pipeline: "p1" + field: "Bx" + plot2: + type: "pseudocolor" + field: "particle_electrons_Bx" + points: + radius: 0.0000005 + renders: + r1: + camera: + azimuth: 100 + elevation: 10 + image_prefix: "out_render_3d_%06d" + + +Finally, here is a more complex :code:`ascent_actions.yaml` example that +creates the same images as the prior example, but adds a trigger that +creates a Cinema Database at cycle 300: +.. code-block:: json +- + action: "add_triggers" + triggers: + t1: + params: + condition: "cycle() == 300" + actions_file: "trigger.yaml" +- + action: "add_pipelines" + pipelines: + p1: + f1: + type: "contour" + params: + field: "jy" + iso_values: [ 1000000000000.0, -1000000000000.0] +- + action: "add_scenes" + scenes: + scene1: + plots: + plot1: + type: "pseudocolor" + pipeline: "p1" + field: "jy" + plot2: + type: "pseudocolor" + field: "particle_electrons_w" + points: + radius: 0.0000002 + renders: + r1: + camera: + azimuth: 100 + elevation: 10 + image_prefix: "out_render_jy_part_w_3d_%06d" + + +When the trigger condition is meet, `cycle() == 300`, the actions in +:code:`trigger.yaml` are also executed: + +.. code-block:: json +- + action: "add_pipelines" + pipelines: + p1: + f1: + type: "contour" + params: + field: "jy" + iso_values: [ 1000000000000.0, -1000000000000.0] +- + action: "add_scenes" + scenes: + scene1: + plots: + plot1: + type: "pseudocolor" + pipeline: "p1" + field: "jy" + plot2: + type: "pseudocolor" + field: "particle_electrons_w" + points: + radius: 0.0000001 + renders: + r1: + type: "cinema" + phi: 10 + theta: 10 + db_name: "cinema_out" + +You can view the Cinema Database result by opening +:code:`cinema_databases/cinema_out/index.html`. diff --git a/Source/Diagnostics/WarpXIO.cpp b/Source/Diagnostics/WarpXIO.cpp index c944c464d..4dfe9b3e3 100644 --- a/Source/Diagnostics/WarpXIO.cpp +++ b/Source/Diagnostics/WarpXIO.cpp @@ -459,6 +459,7 @@ WarpX::UpdateInSitu () const #endif #ifdef AMREX_USE_ASCENT + // wrap mesh data conduit::Node bp_mesh; MultiLevelToBlueprint(finest_level+1, amrex::GetVecOfConstPtrs(mf_avg), @@ -469,6 +470,61 @@ WarpX::UpdateInSitu () const refRatio(), bp_mesh); + // wrap particle data for each species + // we prefix the fields with "particle_{species_name}" b/c we + // want to to uniquely name all the fields that can be plotted + + std::vector<std::string> species_names = mypc->GetSpeciesNames(); + + for (unsigned i = 0, n = species_names.size(); i < n; ++i) + { + + Vector<std::string> particle_varnames; + Vector<std::string> particle_int_varnames; + std::string prefix = "particle_" + species_names[i]; + + // Get pc for species + auto& pc = mypc->GetParticleContainer(i); + + // get names of real comps + std::map<std::string, int> real_comps_map = pc.getParticleComps(); + std::map<std::string, int>::const_iterator r_itr = real_comps_map.begin(); + + // TODO: Looking at other code paths, I am not sure compile time + // QED field is included in getParticleComps()? + while (r_itr != real_comps_map.end()) + { + // get next real particle name + std::string varname = r_itr->first; + particle_varnames.push_back(prefix + "_" + varname); + r_itr++; + } + + // get names of int comps + std::map<std::string, int> int_comps_map = pc.getParticleiComps(); + std::map<std::string, int>::const_iterator i_itr = int_comps_map.begin(); + + while (i_itr != int_comps_map.end()) + { + // get next real particle name + std::string varname = i_itr->first; + particle_int_varnames.push_back(prefix + "_" + varname); + i_itr++; + } + + // wrap pc for current species into a blueprint topology + amrex::ParticleContainerToBlueprint(pc, + particle_varnames, + particle_int_varnames, + bp_mesh, + prefix); + } + + // // If you want to save blueprint HDF5 files w/o using an Ascent + // // extract, you can call the following AMReX helper: + // const auto step = istep[0]; + // WriteBlueprintFiles(bp_mesh,"bp_export",step,"hdf5"); + ascent::Ascent ascent; conduit::Node opts; opts["exceptions"] = "catch"; |