Update

.gitignore

@@ -1,3 +1,168 @@
+# Created by https://www.toptal.com/developers/gitignore/api/visualstudiocode,pycharm,macos,windows,linux,python
+# Edit at https://www.toptal.com/developers/gitignore?templates=visualstudiocode,pycharm,macos,windows,linux,python
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### macOS Patch ###
+# iCloud generated files
+*.icloud
+
+### PyCharm ###
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# AWS User-specific
+.idea/**/aws.xml
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# SonarLint plugin
+.idea/sonarlint/
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### PyCharm Patch ###
+# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721
+
+# *.iml
+# modules.xml
+# .idea/misc.xml
+# *.ipr
+
+# Sonarlint plugin
+# https://plugins.jetbrains.com/plugin/7973-sonarlint
+.idea/**/sonarlint/
+
+# SonarQube Plugin
+# https://plugins.jetbrains.com/plugin/7238-sonarqube-community-plugin
+.idea/**/sonarIssues.xml
+
+# Markdown Navigator plugin
+# https://plugins.jetbrains.com/plugin/7896-markdown-navigator-enhanced
+.idea/**/markdown-navigator.xml
+.idea/**/markdown-navigator-enh.xml
+.idea/**/markdown-navigator/
+
+# Cache file creation bug
+# See https://youtrack.jetbrains.com/issue/JBR-2257
+.idea/$CACHE_FILE$
+
+# CodeStream plugin
+# https://plugins.jetbrains.com/plugin/12206-codestream
+.idea/codestream.xml
+
+# Azure Toolkit for IntelliJ plugin
+# https://plugins.jetbrains.com/plugin/8053-azure-toolkit-for-intellij
+.idea/**/azureSettings.xml
+
+### Python ###
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -158,3 +323,55 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+### VisualStudioCode ###
+.vscode
+
+# Local History for Visual Studio Code
+.history/
+
+# Built Visual Studio Code Extensions
+*.vsix
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+.ionide
+
+### Windows ###
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode,pycharm,macos,windows,linux,python

README.md

@@ -1,8 +1,8 @@
 # pyiron File Reader
-*OVITO* Python file reader for the h5 data containers written by *pyiron*.
+OVITO Python file reader for the h5 data containers written by *pyiron*.
 
 ## Description
-Python file reader for *OVITO* that reads structural data from the hdf5 containers written by [*pyiron*](https://pyiron.org/). After installation, *OVITO* will auto-detect *pyiron* files and open them for analysis and visualization. 
+Python file reader for OVITO that reads structural data from the hdf5 containers written by [*pyiron*](https://pyiron.org/). After installation, OVITO will auto-detect *pyiron* files and open them for analysis and visualization. 
 Note that the *"status"* of the pyiron job needs to be *"finished"* before its file can be read.
 The following table gives an overview over all *particle properties* and *attributes* currently understood by this parser. Optional properties will be skipped if they are not included in the file **and** the parser is not in strict mode.
 
@@ -25,7 +25,7 @@ The following table gives an overview over all *particle properties* and *attrib
 | `generic/temperature` | `Temperature` | 1 | x |
 | `generic/energy_tot` | `Total energy` | 1 | x |
 
-The file reader can be installed either into *OVITO Pro* or the [*OVITO* Python module](https://pypi.org/project/ovito/) Python module using *pip*.
+The file reader can be installed either into OVITO Pro or the [OVITO Python module](https://pypi.org/project/ovito/) Python module using *pip*.
 
 ## Parameters
 - `roundCell` / "Round cell to orthogonal": Round the off-diagonal components of the simulation cell to `0` if they are below a threshold value currently hard-coded to `1e-8` A.
@@ -34,25 +34,26 @@ The file reader can be installed either into *OVITO Pro* or the [*OVITO* Python
 ## Example
 1. [Example 01](Examples/example_01.py) loads the [`lmp.h5` structure file](Examples/example_01/lmp.h5) and prints all *particle properties* and *attributes* found therein.
 
-The following image shows the same file in the *OVITO PRO* desktop application.
+The following image shows the same file in the OVITO Pro desktop application.
 ![Example 01](Examples/example_01.png)
 
 ### Example data generation
 The example data was generated using the [`generate_example_data_01.py`](Examples/generate_example_data_01.py) script using `pyiron`. For more information visit their [website](https://pyiron.org/).
 
 ## Installation
-- OVITO PRO built-in Python interpreter
-```
-ovitos -m pip install --user git+https://github.com/nnn911/pyironFileReader.git
-``` 
-- Standalone Python package or Conda environment
-```
-pip install --user git+https://github.com/nnn911/pyironFileReader.git
-```
-- Please note that the `--user` tag is recommended but optional and depends on your Python installation.
+- OVITO Pro [integrated Python interpreter](https://docs.ovito.org/python/introduction/installation.html#ovito-pro-integrated-interpreter):
+  ```
+  ovitos -m pip install --user git+https://github.com/nnn911/pyironFileReader.git
+  ``` 
+  The `--user` option is recommended and [installs the package in the user's site directory](https://pip.pypa.io/en/stable/user_guide/#user-installs).
+
+- Other Python interpreters or Conda environments:
+  ```
+  pip install git+https://github.com/nnn911/pyironFileReader.git
+  ```
 
 ## Technical information / dependencies
-- Tested with *OVITO* 3.9.0
+- Tested with OVITO 3.9.1
 - Depends on:
     - `numpy` 
     - `h5py`