This is the main repository of the NOMAD parser for CP2K.

Example

    from cp2kparser import CP2KParser
    import matplotlib.pyplot as mpl

    # 1. Initialize a parser with a set of default units.
    default_units = ["eV"]
    parser = CP2KParser(default_units=default_units)

    # 2. Parse a file
    path = "path/to/main.file"
    results = parser.parse(path)

    # 3. Query the results with using the id's created specifically for NOMAD.
    scf_energies = results["energy_total_scf_iteration"]
    mpl.plot(scf_energies)
    mpl.show()

Installation

The code is python 2 and python 3 compatible. First download and install the nomadcore package:

git clone https://gitlab.mpcdf.mpg.de/nomad-lab/python-common.git
cd python-common
pip install -r requirements.txt
pip install -e .

Then download the metainfo definitions to the same folder where the 'python-common' repository was cloned:

git clone https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info.git

Finally download and install the parser:

git clone https://gitlab.mpcdf.mpg.de/nomad-lab/parser-cp2k.git
cd parser-cp2k
pip install -e .

Notes

The parser is based on CP2K 2.6.2.

The CP2K input setting PRINT_LEVEL controls the amount of details that are outputted during the calculation. The higher this setting is, the more can be parsed from the upload.

The parser will try to find the paths to all the input and output files, but if they are located very deep inside some folder structure or outside the folder where the output file is, the parser will not be able to locate them. For this reason it is recommended to keep the upload structure as flat as possible.

Here is a list of features/fixes that would make the parsing of CP2K results easier:

• The pdb trajectory output doesn't seem to conform to the actual standard as the different configurations are separated by the END keyword which is supposed to be written only once in the file. The format specification states that different configurations should start with MODEL and end with ENDMDL tags.
• The output file should contain the paths/filenames of different input and output files that are accessed during the program run. This data is already available for some files (input file, most files produced by MD), but many are not mentioned.