README.md

Phasecalculator

Phasecalculator is a python package designed to automate calculation of FGIPs, solvent similarity and VLE informatio n using SSIMPLE, pulling together analysis and calculation modules in a higher l evel repository for easier use by experimental chemists.

How do I get set up?

Required modules

The other modules produced by Mark Driver required for this work to function are:

* xmlvalidator [bitbucket](https://bitbucket.org/mdd31/xmlvalidator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/utils/xmlvalidator)
* puresolventinformation [bitbucket](https://bitbucket.org/mdd31/puresolventinformation) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/puresolventinformation)
* resultsanalysis [bitbucket](https://bitbucket.org/mdd31/resultsanalysis) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/utils/resultsanalysis)
* phasexmlparser [bitbucket](https://bitbucket.org/mdd31/phasexmlparser) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/phasexmlparser)
* phasexmlcreator [bitbucket](https://bitbucket.org/mdd31/phasexmlcreator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/phasexmlcreator)
* solventmapcreator [bitbucket](https://bitbucket.org/mdd31/solventmapcreator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/solventmapcreator)
* ssip (specifically phasetransfer module) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssip)

Clone this repository

From bitbucket:

    git clone https://bitbucket.org/mdd31/phasecalculator.git

From University of Cambridge gitlab:

Setting up the python environment

Change to the repository:

    cd phasecalculator

Details of an anaconda environment is provided in the repository with the required dependencies for this package.

    conda env create -f environment.yml

This creates and environment callled 'resultsanalysis' which can be loaded using:

    conda activate resultsanalysis

Install dependencies

Before installing this module please make sure that the required modules listed previously are installed in the current python environment. Before cloning the dependent repositories please change up a directory and follow install instructions to install in this environment.

For the SSIP phasetransfer module please compile a jar with dependencies as detailed in the repository documentation (This requires version 6.0.0 or greater). A pre-compiled jar with dependencies may be available on the repository ___ page.

Using pip to install module

To install in your environment using pip run:

    pip install .

This installs it in your current python environment.

Expected usage

This module contains methods for the running of FGIP, similarity and VLE calculations for solvent mixtures at specified temperatures. The calculation process can be run through the use of an XML data format. For the specification of this format please see the Phase Calculator schema on the Hunter Group website. The CLI has been implemented to enable operation in two modes:

1. Run calculations from input XML.

This uses the calculate option of the CLI.

2. Generate input XML for default solvents.

This uses the inpgen option of the CLI.

See the help arguments for more information about the options.

Example calculations

Please see the examples included in the bottom of the help statements for the inpgen and calculate modules.

Notes about file formats

CSV file format for phase information

The CSV file of phase information used by inpgen to create the phase calculator XML has the following specification.

• The file is tab '\t' delimited, and fields are not quoted.

• One solvent/phase entry per row.

• First column contains the temperature.

• Subsequent columns contain molecule name and molefraction for each molecule present in the solvent/phase.

• Illustrative line is below:

  TEMP MOL_NAME1 MOL_FRAC1 MOL_NAME2 MOL_FRAC2 ...

Default solvent names for inclusion in the CSV file can be found by running:

python -m phasecalculator solventnames

This lists the accepted names of components for use with the CLI. For more advanced usage please see the source code documentation.

Documentation

Documentation can be rendered using sphinx.

    cd docs
    make html

The rendered HTML can then be found in the build sub folder.

In progress: display of this documentation in a project wiki.

Contribution guidelines

This code has been released under the AGPLv3 license. If you find any bugs please file an issue ticket. Submission of pull requests for open issues or improvements are welcomed.

Who do I talk to?

Any queries please contact Mark Driver.

Licensing

This is released under the AGPLv3 license.