Write species concentration range in the RMG input file

Author: alongd

t3/utils/writer.py

@@ -94,7 +94,7 @@ def write_rmg_input_file(rmg: dict,
 
     # reactors
     reactors = rmg['reactors']
-    gas_batch_constant_t_p_template_template = """
+    gas_batch_constant_t_p_template = """
 simpleReactor(
     temperature=${temperature},
     pressure=${pressure},
@@ -104,7 +104,12 @@ def write_rmg_input_file(rmg: dict,
 )
 <%def name="concentrations()">
 % for spc in species_list:
+    % if isinstance(spc["concentration"], (int, float)):
         '${spc["label"]}': ${spc["concentration"]},
+    % endif
+    % if isinstance(spc["concentration"], (tuple, list)):
+        '${spc["label"]}': [${spc["concentration"][0]}, ${spc["concentration"][1]}],
+    % endif
 % endfor
 </%def>
 """
@@ -117,7 +122,12 @@ def write_rmg_input_file(rmg: dict,
 )
 <%def name="concentrations()">
 % for spc in species_list:
+    % if isinstance(spc["concentration"], (int, float)):
         '${spc["label"]}': (${spc["concentration"]}, 'mol/cm^3'),
+    % endif
+    % if isinstance(spc["concentration"], (tuple, list)):
+        '${spc["label"]}': [(${spc["concentration"][0]}, 'mol/cm^3'), (${spc["concentration"][1]}, 'mol/cm^3')],
+    % endif
 % endfor
 </%def>
 """
@@ -129,8 +139,13 @@ def write_rmg_input_file(rmg: dict,
         else:
             raise ValueError(f"The reactor temperature must be a float or a list,\n"
                              f"got {reactor['T']} which is a {type(reactor['T'])}.")
-        species_list = [{'label': spc['label'], 'concentration': spc['concentration']} for spc in species]
-        species_list.sort(key=lambda spc: spc['concentration'], reverse=True)
+        species_list = [{'label': spc['label'], 'concentration': spc['concentration']} for spc in species
+                        if isinstance(spc['concentration'], (list, tuple))
+                        or spc['concentration'] > 0
+                        or spc['balance'] or not spc['reactive']]
+        species_list.sort(key=lambda spc: spc['concentration'][0] if isinstance(spc['concentration'], (tuple, list))
+                          else spc['concentration'], reverse=True)
+        print(species_list)
         termination = ''
         if reactor['termination_conversion'] is not None:
             termination += f"terminationConversion={reactor['termination_conversion']},"
@@ -161,7 +176,7 @@ def write_rmg_input_file(rmg: dict,
                 if spc['balance']:
                     balance = f"\n    balanceSpecies='{spc['label']}',"
                     break
-            rmg_input += Template(gas_batch_constant_t_p_template_template).render(
+            rmg_input += Template(gas_batch_constant_t_p_template).render(
                 temperature=temperature,
                 pressure=pressure,
                 species_list=species_list,