openPMD plugin for VisIt

:warning: This reader plugin has been integrated into mainline VisIt :tada: All further development happens in the VisIt repository.

Table of Contents

1. Presentation
2. Repository and code structure
3. Installation

Presentation

This repository contains the sources of an openPMD plugin for the visualization software VisIt. This plugin now handles openPMD files in HDF5. It works both in sequential and parallel. The plugin can read Cartesian and axisymmetrical geometry (referred to as thetaMode in the standard).

Repository and code structure

Files

This repository contains:

• The C++ source files
• An xml file OpenPMD.xml essential for building the plugin with VisIt tools
• The directory docs that contains the documentation
• The resources to generate a doxygen doc (in the directory /Doxygen) that describes the different classes
• This README.md file

Sources are composed of files generated by VisIt:

• avtOpenPMDFileFormat.C: class for reading and converting file format in vtk
• OpenPMDEnginePluginInfo.C
• OpenPMDMDServerPluginInfo.C
• OpenPMDCommonPluginInfo.C
• OpenPMDPluginInfo.C

And external C++ classes developed for reading openPMD files:

• PMDFile.C: Open, scan and print openPMD file structures
• PMDiteration.C: class for the iteration groups
• PMDField.C: class for the field groups
• PMDParticle.C: class for the particle groups

The docs directory contains:

• CONTRIBUTING.md with instructions on how to contribute to this plugin
• ISSUE_TEMPLATE.md

How works this plugin

VisIt plugins basically read outputs with some specific code or data formats to convert them internally into vtk readable data.

How to generate the Doxygen documentation

First, download and install Doxygen.

You can create the documentation by command line (see this page for more information)

doxygen Doxygen/Doxyfile

You can also use the GUI frontend. Open Doxygen/Doxyfile, go to Run, click on Run Doxygen and finally Show HTML output.

Installation

For more information about how to generate install a plugin, please, consider the following links:

• Getting Data Into Visit (official pdf)
• NERSC Visit presentation and instructions

Visit contains a series of tools that makes it easy to create and generate plugins. Without going to the details, we will use one of them (xml2cmake) to install this plugin. These tools are located in the directory <Visit application directory>/Contents/Resources/bin/.

You also need to install a recent version of cmake.

You can find instructions to install and use the plugin depending on your system in docs/installation:

• Ubuntu
• MacOs
• NERSC