Fixes in formula parser and CpfT with phase transition

Fixes for formula parser and CpfT for phase transition (#24)

* fix for Cp=f(T) phase transition, problems with the derivatives

* added default valences and fixed formula parser bug

* tests for formula parser and CpfT with phase transition

Tests for Ryzhenko Bryzgalin model, possibility to append elements

Append a new element with data for substances and reactions related to the element.

database.appendData('Fe-speciation-thermofun.json')

Const correctness fixes in ThermoEngine and Database class

Merge pull request #21 from allanleal/improve-const-correctness

Improve const-correctness for classes Database and ThermoEngine

Using units from database

If units are provided together with the properties and parameters in the database file, e.g.:

    "m_landau_phase_trans_props": {
        "values": [
            1926.8499755859,
            4,
            0.035000000149012
        ],
        "names": [
            "Tcr",
            "Smax",
            "Vmax"
        ],
        "units": [
            "degC",
            "J/(mol*K)",
            "J/bar"
        ]
    }

The user can provide parameters in any valid and convertible units, these will be converted to the default ones when reading the database file and used accordingly in the respective correction TPMethod.

BugFix

• fix check for H+ using symbol H+

• fix for HKF properties calculation close to the critical point. (TdegC>=355 && Pbar<500), use equations (32)-(44) of Shock and others (1992) to compute the function g and its partial derivatives on region 2.

• fix for calculation of reaction properties using logk_fpt_function

• check if reaction / dependent substance methods are correctly defined to avoid the case when a substance is defined by a reaction with no TPMethods.

v0.3.1: Origin bucket (#18)

• Database object can now be constructed using a file or a string containing a ThermoDataSet in valid JSON
• Bug-fixes

Append data, reaction equation parsing, imporved json database structure

Append data, reaction equation parsing, imporved json database structure

This release brings new functionality:

• Append additional data to the database from provided files in json database format.

import thermofun as thermofun
database = thermofun.Database('slop98-thermofun.json')
database.appendData('additional-data-thermofun.json')

• Calculate properties for a given reaction equation (reactants with with the symbols used in the equation should be present in the database)

import thermofun as thermofun
engine = thermofun.ThermoEngine('slop98-thermofun.json')
logK = engine.thermoPropertiesReaction(298.15, 1e5, "Cal = Ca+2 + CO3-2").log_equilibrium_constant.val

• Database files have an improved JSON format. A thermofun database file contains 'substances', 'reactions', and 'elements' lists, plus additional keys with information about the ThermoDataSet.

{
  "thermodataset": "slop98-inorganic",
  "datasources": [
    "db.thermohub.org",
    "[1998SHO/EA]"
  ],
  "date": "10.12.2019 13:43:37",
  "substances": ["..."],
  "reactions": ["..."],
  "elements": ["..."]
}

• using pytests in CI
• removed version pinning from pybind11 and nlohmann json libs
• bugfixes

v0.2.2: Merge pull request #12 from gdmiron/master

Sync with bitbucket

Improved database parsing (simpler thermodynamic database format)

bug fixes in parser, enabling the use of simplified database files containing only fields that are necessary for calculation.

v0.2.0: Merge pull request #9 from gdmiron/master

sync with bitbucket