update CLI to allow option of polarised or unpolarised solvent descriptions.

phasecalculator/phasecalculatorcli.py

@@ -135,7 +135,7 @@ def create_system_collection(args):
         SystemCollection.
 
     """
-    phases = read_phasecsv(args.phases)
+    phases = read_phasecsv(args.phases, args.unpolarised_ssips)
     jar_path = args.jar
     scratch_dir = args.scratch
     output_dir = args.out_dir
@@ -216,13 +216,15 @@ def read_calculator_xml(xml_filename):
     return sysproc.read_system_collection_file(xml_filename)
 
 
-def read_phasecsv(csv_filename):
+def read_phasecsv(csv_filename, unpolarised_ssips):
     """Read CSV file containing phase infomration and create Phases object.
 
     Parameters
     ----------
     csv_filename : str
         phase information CSV file.
+    unpolarised_ssips : boolean
+        True if unpolarised SSIP descriptions are to be used.
 
     Returns
     -------
@@ -230,7 +232,7 @@ def read_phasecsv(csv_filename):
         Phases representation of information.
 
     """
-    return csvconv.convert_csv_file_to_phases(csv_filename)
+    return csvconv.convert_csv_file_to_phases(csv_filename, unpolarised_ssips)
 
 
 def run_system_collection(system_collection, **kwargs):
@@ -372,7 +374,12 @@ Where systemcollection.xml was generated with inpgen. For large phase sets you n
         "--filename", type=str, default="systemcollection.xml",
         help="filename for XML file.",
     )
-    inpgen_argparser.set_defaults(func=process_inputgen)
+    ssip_desc = inpgen_argparser.add_mutually_exclusive_group(required=False)
+    ssip_desc.add_argument("--polarised", action="store_false", dest="unpolarised_ssips",
+                           help="Use unpolarised SSIP descriptions in calculations")
+    ssip_desc.add_argument("--unpolarised", action="store_true", dest="unpolarised_ssips",
+                           help="Use polarised SSIP descriptions in calculations")
+    inpgen_argparser.set_defaults(func=process_inputgen, unpolarised_ssips=False)
     solvname_description = """Display acceptable solvent molecule names for inclusion in a phases csv file."""
     solvnames_epilog = "Solvent molecule names:\n" + get_acceptable_solvent_names() + "\n"
     solvent_nameparser = subparsers.add_parser(