@@ -54,7 +46,7 @@ This creates and environment callled 'resultsanalysis' which can be loaded using
Before installing this module please make sure that the required modules listed previously are installed in the current python environment. Before cloning the dependent repositories please change up a directory and follow install instructions to install in this environment.
For the SSIP phasetransfer module please compile a jar with dependencies as detailed in the repository documentation.
For the SSIP phasetransfer module please compile a jar with dependencies as detailed in the repository documentation (This requires version 6.0.0 or greater). A pre-compiled jar with dependencies may be available on the repository \_\_\_ page.
### Using pip to install module ###
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@@ -75,25 +67,38 @@ The CLI has been implemented to enable operation in two modes:
1) Run calculations from input XML.
This uses the
This uses the calculate option of the CLI.
2) Generate input XML for default solvents.
This uses the
This uses the inpgen option of the CLI.
See the help arguments for more information about the options.
#### Example calculations ####
The
Please see the examples included in the bottom of the help statements for the inpgen and calculate modules.
### Notes about file formats ###
#### CSV file format for phase information ####
The CSV file of phase information used by inpgen to create the phase calculator XML has the following specification.
- The file is tab '\t' delimited, and fields are not quoted.
- One solvent/phase entry per row.
- First column contains the temperature.
- Subsequent columns contain molecule name and molefraction for each molecule present in the solvent/phase.
- Illustrative line is below:
TEMP MOL_NAME1 MOL_FRAC1 MOL_NAME2 MOL_FRAC2 ...
The csv file of solvent information is in
Default solvent names for inclusion in the CSV file can be found by running:
python -m phasecalculator #ADD method- new subprocessor.
python -m phasecalculator solventnames
This lists the accepted names of components for use with the CLI. For more advanced usage please see the source code documentation.
