Application for processing files for EXtreme-scale Electronic Structure System (EXESS) with a focus on lattice-energy type calculations using python.
- QCP (https://github.com/zoeseeger/qcp-python-app) and change sys.path.append(path_to_qcp)
- tqdm
- numpy
- pandas
- h5py (for reading from a restart file)
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Make separate dimer/trimer/tetramer calculations
Separates a json mbe calculation into single dimer, trimer and tetramer calculations. -
Make job from json files
Makes Gadi scripts for the json files in the current directory in batches determined by the user. -
CSV from log files
Makes a csv from the ouput of an exess fragmentation calculation. If folder 'dimers' exists, it will attempt to get the energies from separate log files existing in folders 'dimers', 'trimers' and 'tetramers' as per the 'Make separate dimer/trimer/tetramer calculations' function of this script. If the file 'frag_ids.txt' exists - it is expected to contain all of the 'grep "<-" *log' lines of a run - the script will get the energies from the restart file ending in '*h5'. Else, the script will read from the end of a log file in the current directory. -
json to xyz
An xyz file is created from an exess input file (json). The json can be given as a command line argument, otherwise the first json found in the working directory will be used. -
Make smaller shell from json
Given a EXESS MBE input file (json) fragments whose center of mass lie within a given distance to the central fragment will be written to a new input file. The fragment IDs used to make the new input file are written to "indexes.txt". The json can be given as a command line argument, otherwise the first json found in the working directory will be used. -
xyz to json
Make an EXESS MBE or non-MBE exess input file from an xyz. Choose whether to pair molecules to closest oppositely charged guy - only available for ions - or keep as single molecules per monomer. -
Get geometry from frag list
Will make a full ab initio file for a list of monomers supplied.