Calculation Interface

Calculation of Thermodynamics

The JThermodynamic calculation interface has four parts:

Setup: This is the information needed to perform the calculation.
Result: This is the summary of the individual contributions leading to the total value. The total information available, which includes the source, both bibilographic and components, of the contributions is also available.
Json: This is the JSON representation, the internal representation of all data in the database, of the contribution.
Logs: With the calculations, some logging is done showing the contributions. This could be useful if the calculation did no perform properly.

Calculation Setup

This is the basic interface to the caluculation:

Title: This is a title to the calculation. This can be used for future reference of the user, especially when used with comparisons
Thermodynamic Calculation: This is actually a pull-down list of the types of calculations that can be made. Full calculations can be made using the TherGas method or the THERM methods. Also available, for reference and checking, are individual component calculations, such as the different symmetries, the disassociation energy contribution, the steric contributions and ring strain.
Dataset Collection Label: This specifies which combination of fundamental data components, meaning Benson rules, symmetry objects, meta atoms, etc. The dataset behind this particular collection is setup elsewhere.
Object Maintainer: This is used in combination with Dataset Collection Label to determine which dataset collection to use. The dataset collections are user oriented.
Structure Name: This is label given to the structure. This is also for reference by the user.
Representation: This is the type of linear form that is used to create the 2D-graphical species. The linear form defined by the CNRS Nancy is the standard. SMILES InChI are also used. If appropriate meta atoms are defined, the Nancy Linear form can include structural groups, such as 'co', co2, etc. Note the the interpretation of SMILE and InChI are dependent on the CDK (Chemistry Development Kit) interpretation.
Structure Definition: This is the linear form specification of the type given by 'Representation'

Units of Calculation Results

The result contributions of the JThermodynamic calculation are given as Standard Entropy, Standard Entropy and a set of Heat Capacity value given at a specified number of temperatures. Within the setup of the thermodynamic calculation, the units of the final answer(s) can be given. So for each of parameter values, the units are specified through 'Units of Value'. This is a pull down list of possibilities as specified by the 'Unit Class'. Only the 'Unit Class' and the 'Parameter Label' should/can be modified (the interface may be simplified in later versions -- The current presentation represents the total parameter specification).

Thermodynamic Contributions

In the 'Result' tab is the individual contributions that have be found are visualized. This includes:

Name: This is the contribution name. From the name, the type and specific element of that type can be determined.
Enthalpy: The standard enthalpy associated with the contribution
Entropy: The standard entropy associated with the contribution
Temperatures: This is the set of temperatures. In each column are the heat capacities associated with that temperature.

Further information, the information behind the summarized contributions, can be found. The 'Show Units' button reveals the exact parameter specification of the parameters (this is basically the same as the 'Setup' menu. On the right side of each contribution row, there is a button which can be used to provide additional information about the contribution. this includes the original database object associated with the contribution which holds, among other things, bibiliographic references and links to the source of the database object (traceability of the contribution).

JSON Representation

Under the Json tab is the JSON representation of the thermodynamic contribution. Basically, the raw data and the source of the contribution from the database. JSON is the representation used by the database.

This is meant mainly for debugging purposes.

Logs

During the calculation, a log of how the contributions were calculated is given. This output could be useful if, for example, a specific contribution is wrong or is missing. This log gives an accounting of what happened during the calculation.