update to reademe.

README.md

@@ -10,13 +10,13 @@ evel repository for easier use by experimental chemists.
 
 The other modules produced by Mark Driver required for this work to function are:
 
-    * xmlvalidator [bitbucket](https://bitbucket.org/mdd31/xmlvalidator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/utils/xmlvalidator)
-    * puresolventinformation [bitbucket](https://bitbucket.org/mdd31/puresolventinformation) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/puresolventinformation)
-    * resultsanalysis [bitbucket](https://bitbucket.org/mdd31/resultsanalysis) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/utils/resultsanalysis)
-    * phasexmlparser [bitbucket](https://bitbucket.org/mdd31/phasexmlparser) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/phasexmlparser)
-    * phasexmlcreator [bitbucket](https://bitbucket.org/mdd31/phasexmlcreator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/phasexmlcreator)
-    * solventmapcreator [bitbucket](https://bitbucket.org/mdd31/solventmapcreator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/solventmapcreator)
-    * ssip (specifically phasetransfer module) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssip)
+* xmlvalidator [bitbucket](https://bitbucket.org/mdd31/xmlvalidator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/utils/xmlvalidator)
+* puresolventinformation [bitbucket](https://bitbucket.org/mdd31/puresolventinformation) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/puresolventinformation)
+* resultsanalysis [bitbucket](https://bitbucket.org/mdd31/resultsanalysis) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/utils/resultsanalysis)
+* phasexmlparser [bitbucket](https://bitbucket.org/mdd31/phasexmlparser) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/phasexmlparser)
+* phasexmlcreator [bitbucket](https://bitbucket.org/mdd31/phasexmlcreator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/phasexmlcreator)
+* solventmapcreator [bitbucket](https://bitbucket.org/mdd31/solventmapcreator) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/solventmapcreator)
+* ssip (specifically phasetransfer module) [CamGitlab](https://gitlab.developers.cam.ac.uk/ch/hunter/ssip)
     
 ### Clone this repository ###
 
@@ -25,8 +25,9 @@ The other modules produced by Mark Driver required for this work to function are
         git clone https://bitbucket.org/mdd31/phasecalculator.git
 
 
-*From University of Cambridge gitlab:*
+*From University of Cambridge gitlab (ussing ssh):*
 
+    git clone 
 
 ### Setting up the python environment ###
 
@@ -69,10 +70,57 @@ The CLI has been implemented to enable operation in two modes:
 
 This uses the calculate option of the CLI.
 
+    python -m phasecalculator calculate -h
+    usage: __main__.py calculate [-h] -i FILE [--memreq MEMREQ]
+
+    Calculation runner based on input System XML.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      -i FILE, -f FILE, --file FILE
+                            filename for SystemCollectionXML (default: None)
+      --memreq MEMREQ       memory specifier for jar call. Defaults to system
+                            default. (default: None)
+
+    Example Usage: 
+        python -m phasecalculator calculate -f systemcollection.xml
+
+    Where systemcollection.xml was generated with inpgen. For large phase sets you need to set memreq to match your current hardware limit.
+
+
 2) Generate input XML for default solvents.
 
 This uses the inpgen option of the CLI.
 
+    python -m phasecalculator inpgen -h
+    usage: __main__.py inpgen [-h] [-p PHASES] -j JAR [-x SCRATCH] [-o OUT_DIR]
+                              [-f] [-s] [--sim_type SIM_TYPE] [-v]
+                              [--filename FILENAME]
+
+    Input SystemCollection XML generation.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      -p PHASES, --phases PHASES
+      -j JAR, --jar JAR     Phasetransfer jar path. (default: None)
+      -x SCRATCH, --scratch SCRATCH
+                            scratch directory path. (default: scratch)
+      -o OUT_DIR, --out_dir OUT_DIR
+                            output directory for calculation results (default:
+                            output)
+      -f, --fgip            Calculate FGIPs for input solvents (default: False)
+      -s, --sim             Calculate similarity for input solvents (default:
+                            False)
+      --sim_type SIM_TYPE   similarity output type. (default: all)
+      -v, --vle             Calculate VLE for input solvents (default: False)
+      --filename FILENAME   filename for XML file. (default: systemcollection.xml)
+
+    Example usage: 
+        python -m phasecalculator inpgen -p $CONDA_PREFIX/lib/python3.7/site-packages/phasecalculator/test/resources/examplephasecomp.csv -f -j PATH_TO_JAR
+
+    Where PATH_TO_JAR is replaced with the SSIP phasetransfer jar file location.
+
+
 See the help arguments for more information about the options.
 
 #### Example calculations ####