make irc_obj_dict optional in MolecularTSEstimate

fix typo

add irc_mode to ts_task

typo fixed (stupid uppercase)...

typo fix

delete empty IRC_obj_dict

collect_firework() added again

define IRC_obj_dict key value in run_task

fix typo (case sensitive)

add IRC_opj_dict in optional_params

indentation fix

define IRC_obj_dict key value in run_task

fix typo (case sensitive)

add IRC_opj_dict in optional_params

indentation fix

make irc_obj_dict optional in MolecularTSEstimate

fix typo

add irc_mode to ts_task

typo fixed (stupid uppercase)...

typo fix

delete empty IRC_obj_dict

collect_firework() added again

pynta/tasks.py

@@ -617,7 +617,15 @@ def run_task(self, fw_spec):
 
         if spawn_jobs:
             print(irc_mode)
-            if irc_mode == "relaxed" or irc_mode == "fixed":
+            if irc_mode == "skip":
+                ctask = MolecularCollect({"xyzs":xyzsout,"check_symm":True,"fw_generators": ["optimize_firework",["vibrations_firework"]],
+                        "fw_generator_dicts": [self["opt_obj_dict"],[self["vib_obj_dict"]]],
+                        "out_names": ["opt.xyz",["vib.json"]],"future_check_symms": [True,False], "label": "TS"+str(index)+"_"+rxn_name})
+                cfw = Firework([ctask],name="TS"+str(index)+"_"+rxn_name+"_collect",spec={"_allow_fizzled_parents": True, "_priority": 5})
+                newwf = Workflow([cfw],name='rxn_'+str(index)+str(rxn_name))
+                return FWAction(detours=newwf) #using detour allows us to inherit children from the original collect to the subsequent collects
+
+            else:
                 irc_obj_dict_forward = deepcopy(self["IRC_obj_dict"])
                 irc_obj_dict_forward["forward"] = True
                 irc_obj_dict_reverse = deepcopy(self["IRC_obj_dict"])
@@ -629,17 +637,18 @@ def run_task(self, fw_spec):
                 cfw = Firework([ctask],name="TS"+str(index)+"_"+rxn_name+"_collect",spec={"_allow_fizzled_parents": True, "_priority": 5})
                 newwf = Workflow([cfw],name='rxn_'+str(index)+str(rxn_name))
                 return FWAction(detours=newwf) #using detour allows us to inherit children from the original collect to the subsequent collects
-
-            #if irc_mode == "skip":
-            else:
-                ctask = MolecularCollect({"xyzs":xyzsout,"check_symm":True,"fw_generators": ["optimize_firework",["vibrations_firework"]],
-                        "fw_generator_dicts": [self["opt_obj_dict"],[self["vib_obj_dict"]]],
-                        "out_names": ["opt.xyz",["vib.json"]],"future_check_symms": [True,False], "label": "TS"+str(index)+"_"+rxn_name})
-                cfw = Firework([ctask],name="TS"+str(index)+"_"+rxn_name+"_collect",spec={"_allow_fizzled_parents": True, "_priority": 5})
-                newwf = Workflow([cfw],name='rxn_'+str(index)+str(rxn_name))
-                return FWAction(detours=newwf) #using detour allows us to inherit children from the original collect to the subsequent collects
         else:
             return FWAction()
+
+def collect_firework(xyzs,check_symm,fw_generators,fw_generator_dicts,out_names,future_check_symms,parents=[],label="",allow_fizzled_parents=False):
+    task = MolecularCollect({"xyzs": xyzs, "check_symm": check_symm, "fw_generators": fw_generators,
+        "fw_generator_dicts": fw_generator_dicts, "out_names": out_names, "future_check_symms": future_check_symms, "label": label})
+    return Firework([task],parents=parents,name=label+"collect",spec={"_allow_fizzled_parents": allow_fizzled_parents,"_priority": 5})
+
+def collect_firework(xyzs,check_symm,fw_generators,fw_generator_dicts,out_names,future_check_symms,parents=[],label="",allow_fizzled_parents=False):
+    task = MolecularCollect({"xyzs": xyzs, "check_symm": check_symm, "fw_generators": fw_generators,
+        "fw_generator_dicts": fw_generator_dicts, "out_names": out_names, "future_check_symms": future_check_symms, "label": label})
+    return Firework([task],parents=parents,name=label+"collect",spec={"_allow_fizzled_parents": allow_fizzled_parents,"_priority": 5})
 
 def collect_firework(xyzs,check_symm,fw_generators,fw_generator_dicts,out_names,future_check_symms,parents=[],label="",allow_fizzled_parents=False):
     task = MolecularCollect({"xyzs": xyzs, "check_symm": check_symm, "fw_generators": fw_generators,