CHANGELOG

Changelog
=========


Release 1.0.0
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First python implementation of POMSimulator for isopolyoxometalates

./pomsimulator/modules:
- text_module.py : functions for parsing the ADF outputs, and reading/writing chemical files such as .mol and .xyz
- graph_module.py : function for creating molecular graphs, isomorphic matrix, and chemical reaction network
- msce_module.py : function for setting the speciation models, activity functions, and chemical equilibrium related features
- Database.py : file that contains the useful dictionaries and experimental data 

./Simulation:
- simulation_test.py : simulation file to check that POMSimulator was well installed
- simulation_tungstates.py : main simulation file that contains all the workflow of POMSimulator for isopolyoxotungstates

./Utilities:
- compute_isomorphism.py : calculates the isomorphic matrix from the molecular graphs derived from Bader QTAIM calculations
- generate_mol_file.py : converts the Bader QTAIM bond connectivity to .mol files
- monometal_phase.py : calculates the speciation phase data array for isopolyoxometalates
- monometal_speciation.py : calculations the speciation data array for isopolyoxometalates
- plot_phase_diagram.py :  plots the speciation phase data array
- plot_reac_map.py : plots the chemical reaction network
- plot_speciation_diagram.py : plots the speciation data array
- scale_constants.py : scales the theoretical formation constants respect to the experimental constants (in Database.py)

./Input: folder that contains the ADF output file subfolders

./Output: folder that contains the chemical reaction network, formation constants and simulation related files