ExVol

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Input

Input for ExVol consists of three text files:

• .json -- providing simulation parameters,
• .txt -- providing configuration of the crpwded box,
• .txt -- providing configuration of the inserted model,

Below we ellaborate on their structure and meaning.

.txt files

Configuration (.txt) files contain the information about the positions and sizes of beads. Each line follows a scheme:

label x y z a

The entries should be replaced with values specific to a given type of bead. Below their meanings are explained:

• label -- label (name) of the bead (string)
• x y z -- x, y and z cartesian coordinates of the bead center (float)
• a -- the radius of the bead (float)

.json file

Simulation parameters are provided in a standard JSON data format. It consists of multiple lines in a form of keyword: value pairs enclosed by a curly bracket. Some keywords are obligatory, but a majority is not -- for them default values will be loaded, if needed. pyBrown will inform you if it does not recognize some keywords in input .json file.

The complete list of keywords is provided below.

• "tracer_filename": string -- the name of the input inserted model configuration .txt file (see above), required
• "crowders_filename": string -- the name of the input crowded box configuration .txt file (see above), required
• "number_of_trials": int -- the total number of insertions, required
• "box_size": float -- length of the cubic simulation box, required
• "debug": boolean -- switching on/off the debug printout, default: false
• "verbose": boolean -- switching on/off the verbose printout, default: false
• "disable_progress_bar": boolean -- disabling the progress bar, default: false
• "seed": int -- seed for pseudorandom number generation algorithm, default np.random.randint(2**32 - 1)
• "omp_cores": int -- number of cores for parallel computation, default: all available

Author

The following people contributed to the development of ExVol.

• Tomasz Skóra -- creator, lead developer (contact: [email protected])