JThermodynamics 1.0 is an line command based version using mySQL as an interface. The corresponding code is on github, with a compiled version in the releases. The command line code can be downloaded, compiled and run or with use of the releases. The database is based on mySQL which needs to be installed. Follow the instructions in the Quick Start page.
The following is a summary of the basic commands of JThermodynamics 1.0.
The line commands enable the user to calculate the thermodynamics of species using several methods and formats and also to modify and query the database.
There are three sets of methods to calculate the thermodynamics:
Thermo: This is the calculation of thermodynamics of a single species
ThermoSet: This calculates a set of species (through an input file of species specifications)
ThermoCompare: This allows the comparisons of calculations with each other and with external sources.
The database on which the calculations are based can be modified with the following commands:
Benson: This parses a file of benson rules and corrections (ex Table A.1 and Table 2.14)
Molecules: This parses a file of thermodynamics, in Benson format of standard enthalpy, standard entropy and heat capacities, for molecules (ex. Tables A.7 to A.11 in Benson)
Structures: This reads in species structures and substructures.
SubstructureThermo: This reads in the thermodynamics, , in Benson format of standard enthalpy, standard entropy and heat capacities, for substructures. This is used for reading in corrections based on substructures. (such as ring compound estimates in Table A.1 in Benson).
Meta-Atoms: This defines a set of meta-atoms, including structure, name and type. The type governs how JTHERMODYNAMICS interprets it.
SymmetryDefinition: This reads a file of internal, external and optical symmetries definitions.
Vibrational: This reads in the vibrational structure and its corresponding frequency (ex. Table A.13 in Benson).
BondLengths: This reads in the database of bond lengths (ex Table A.14 in Benson)
DisassociationEnergies: The hydrogen disassociation energies of different species.
Testing structure correction recognition. A species can be tested against the entire set of elements or a single element:
OpticalSymmetryTest: Recognize optical symmetry in the species.
BensonAtomTest: Tests the substition of benson meta atoms (for use in Benson atom rule definition)
LinearAtomTest: Tests the substitution of linear structures (for use with symmetry recognition)
BensonRuleTest: Tests the recognition of benson rules
Examine the database elements:
OpticalSymmetry: Examine the optical symmetry elements.
BensonAtom: Examine the benson atoms that are substituted in a species, for example c/d , c/t, c/a for double, triple and aromatic carbons.
BensonRule: Examine the benson rules.
LinearAtom: Examine the linear atom definitions. The definition of linear atoms is important for symmetry recognition.