diff --git a/README.md b/README.md index 81cb2841b4cb0d87b38251a40d84163534cff038..a28fa4202f03fd435a01c24fa47d5c77545113df 100644 --- a/README.md +++ b/README.md @@ -1,33 +1,78 @@ -# LAMMPS Parser +This is a NOMAD parser for [LAMMPS](https://lammps.sandia.gov/). It will read LAMMPS input and +output files and provide all information in NOMAD's unified Metainfo based Archive format. -This is the parser for [LAMMPS](http://lammps.sandia.gov/). -It is part of the [NOMAD Laboratory](http://nomad-lab.eu). -The official version lives at +## Preparing code input and output file for uploading to NOMAD - git@gitlab.mpcdf.mpg.de:nomad-lab/parser-lammps.git +NOMAD accepts `.zip` and `.tar.gz` archives as uploads. Each upload can contain arbitrary +files and directories. NOMAD will automatically try to choose the right parser for you files. +For each parser (i.e. for each supported code) there is one type of file that the respective +parser can recognize. We call these files `mainfiles` as they typically are the main +output file a code. For each `mainfile` that NOMAD discovers it will create an entry +in the database that users can search, view, and download. NOMAD will associate all files +in the same directory as files that also belong to that entry. Parsers +might also read information from these auxillary files. This way you can add more files +to an entry, even if the respective parser/code might not directly support it. -you can browse it at +For lammps please provide at least the files from this table if applicable to your +calculations (remember that you can provide more files if you want): - https://gitlab.mpcdf.mpg.de/nomad-lab/parser-lammps -It relies on having the nomad-meta-info and the python common repositories one level higher. -The simplest way to have this is to check out nomad-lab-base recursively: - git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git +To create an upload with all calculations in a directory structure: -then this will be in parsers/lammps. +``` +zip -r <upload-file>.zip <directory>/* +``` -# Running and Testing the Parser +Go to the [NOMAD upload page](https://nomad-lab.eu/prod/rae/gui/uploads) to upload files +or find instructions about how to upload files from the command line. -## Usage -LAMMPS input/output files can be parsed with: +## Using the parser - python LAMMPSParserControl.py ../../test/examples/input.1_methyl_naphthalene +You can use NOMAD's parsers and normalizers locally on your computer. You need to install +NOMAD's pypi package: -## Test Files -Example input/output files of LAMMPS can be found in the directory test/examples. +``` +pip install nomad-lab +``` - - /methane/ : NVT simulation on pure CH4 with different logging styles (see input file name) - - /methane_MD_traj/ : NVT simulation on pure CH4 with different trajectory styles (see input file name) - - /hexane_cyclohexane/ : NVT simulation on a binary (equimolar mixture) - - /1_methyl_naphthalene/ : NVT simualtion on pure 1-methylnaphthalene (no trajectory) +To parse code input/output from the command line, you can use NOMAD's command line +interface (CLI) and print the processing results output to stdout: + +``` +nomad parse --show-archive <path-to-file> +``` + +To parse a file in Python, you can program something like this: +```python +import sys +from nomad.cli.parse import parse, normalize_all + +# match and run the parser +backend = parse(sys.argv[1]) +# run all normalizers +normalize_all(backend) + +# get the 'main section' section_run as a metainfo object +section_run = backend.resource.contents[0].section_run[0] + +# get the same data as JSON serializable Python dict +python_dict = section_run.m_to_dict() +``` + +## Developing the parser + +Also install NOMAD's pypi package: + +``` +pip install nomad-lab +``` + +Clone the parser project and install it in development mode: + +``` +git clone https://gitlab.mpcdf.mpg.de/nomad-lab/parser-lammps parser-lammps +pip install -e parser-lammps +``` + +Running the parser now, will use the parser's Python code from the clone project. diff --git a/metadata.yml b/metadata.yml new file mode 100644 index 0000000000000000000000000000000000000000..6fdeca9b7c33f1b5d72da95c71de522568a0bad4 --- /dev/null +++ b/metadata.yml @@ -0,0 +1,6 @@ +code-label: LAMMPS +code-label-style: All in capitals +code-url: https://lammps.sandia.gov/ +parser-dir-name: dependencies/parsers/lammps/ +parser-git-url: https://gitlab.mpcdf.mpg.de/nomad-lab/parser-lammps +table-of-files: ''