despasito 0.4.1

Determining Equilibrium State and Parametrization Application for SAFT, Intended for Thermodynamic Output

DESPASITO

DESPASITO: Determining Equilibrium State and Parametrization Application for SAFT, Intended for Thermodynamic Output

First open-source application for thermodynamic calculations and parameter fitting for the Statistical Associating Fluid Theory (SAFT) EOS and SAFT-𝛾-Mie coarse-grained simulations. This software has two primary facets.

The first facet is a means to evaluate implicit equations of state (EOS), such as the focus of this package, SAFT-𝛾-Mie. This framework allows easy implementation of more advanced thermodynamic calculations as well as additional forms of SAFT or other equations of state. Feel free to inform us of issues or contribute!

The second facet is parameterization of equations of state (EOS), some of which are useful for coarse-grained (CG) simulations. The SAFT-𝛾-Mie formalism is an attractive source of simulation parameters as it offers a means to directly link the intermolecular potential with thermodynamic properties. This application has the ability to fit EOS parameters to experimental thermodynamic data in a top down approach for self and cross interaction parameters.

In another published work, we present a method of predicting cross-interaction parameters for SAFT-𝛾-Mie from multipole moments derived from DFT calculations. This method is easily implemented in using the package, MAPSCI as a plug-in. It should be noted that additional, iterative fine tuning in simulation parameters may be desired, but previous works have found close agreement between simulation parameters and those fit to the EOS.

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Check out our Documentation first.

Documentation

Check out our Documentation:

Installation

NOTE: DESPASITO is not yet available in conda-forge, but it is available with pip.

Prerequisites:

• Python: Available for python 3.6 to 3.8 (limited by current compatibility issues with Numba)
• NumPy: If using cython, numpy is needed for running setup (distutils). Follow instructions outlined here for installation.

Options

Option 1: Install from pip: pip install despasito

Option 2: Install locally with pip.

• Step 1: Install the prerequisites listed above.
• Step 2: Download the master branch from our github page as a zip file, or clone it with git via git clone https://github.com/Santiso-Group/despasito to your working directory.
• Step 3: Install with pip install despasito/., or change directories and run pip install -e ..

NOTE If pip is unavailable, follow the instructions outlined here for installation.

Command Line Use

This package has been primarily designed as a command line tool but can be used as an imported package.

In any directory with the appropriate input files in .json format, run DESPASITO with python -m despasito -i input.json

See examples directory for input file structures.

Copyright

Copyright (c) 2019, Jennifer A Clark

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.0.