Add restart function and machine keyword option for restart

pynta/main.py

@@ -21,8 +21,7 @@
 from fireworks.core.fworker import FWorker
 import fireworks.fw_config
 import logging
-#restart RHE
-import pickle
+#restart RHE+KSA
 import time
 from pynta.polaris import createFWorkers
 from pynta.utils import copyDataAndSave
@@ -43,10 +42,10 @@ def __init__(self,path,rxns_file,surface_type,metal,label,launchpad_path=None,fw
         TS_opt_software_kwargs=None,
         lattice_opt_software_kwargs={'kpts': (25,25,25), 'ecutwfc': 70, 'degauss':0.02, 'mixing_mode': 'plain'},
         reset_launchpad=False,queue_adapter_path=None,num_jobs=25,max_num_hfsp_opts=None,#max_num_hfsp_opts is mostly for fast testing
-        Eharmtol=3.0,Eharmfiltertol=30.0,Ntsmin=5,frozen_layers=2,fmaxopt=0.05,fmaxirc=0.1,fmaxopthard=0.05,pickled=0):
+        Eharmtol=3.0,Eharmfiltertol=30.0,Ntsmin=5,frozen_layers=2,fmaxopt=0.05,fmaxirc=0.1,fmaxopthard=0.05):
 
         self.surface_type = surface_type
-        self.pickled = pickled
+
 
         if launchpad_path:
             launchpad = LaunchPad.from_file(launchpad_path)
@@ -180,28 +179,6 @@ def analyze_slab(self):
             self.double_site_bond_params_lists = double_site_bond_params_lists
             self.double_sites_lists = unique_site_pairs_lists
 
-            my_dictionary_to_pickled  = {'cas' : cas,
-                                        'single_site_bond_params_list': single_site_bond_params_lists,
-                                        'single_sites_lists': unique_site_lists,
-                                        'double_site_bond_params_lists': double_site_bond_params_lists,
-                                        'double_sites_lists_full': unique_site_pairs_lists}
-
-            print("Save as a pickle")
-            with open('analize_slab.pickle', 'wb') as myfile:
-                pickle.dump(my_dictionary_to_pickled, myfile)
-
-        else :
-            with open('analize_slab.pickle', 'rb') as myfile:
-                my_dict = pickle.load(myfile)
-
-            print("Load from a pickle")
-
-            self.cas = my_dict['cas']
-            self.single_site_bond_params_lists = my_dict['single_site_bond_params_list']
-            self.single_sites_lists = my_dict['unique_site_lists']
-            self.double_site_bond_params_lists = my_dict['double_site_bond_params_lists']
-            self.double_sites_lists = my_dict['unique_site_pairs_lists']
-
     def generate_mol_dict(self):
         """
         generates all unique Molecule objects based on the reactions and generates a dictionary
@@ -589,7 +566,7 @@ def execute_from_initial_ad_guesses(self):
         self.launch()
 
 #restart option: RHE + KSA
-    def reset(self,wfid):
+    def restart(self,wfid):
 
         id_number = int(wfid)
         # Get the information of the workflow
@@ -617,19 +594,6 @@ def reset(self,wfid):
                             '{{pynta.tasks.MolecularVibrationsTask}}',
                             '{{pynta.tasks.MolecularIRC}}']
 
-                #if nameTask in nameTasks:
-                #    opt_method = newd['_tasks'][0]['opt_method'] if 'opt_method' in newd['_tasks'][0] else None
-
-                #    if self.software == "Espresso" or self.software == "PWDFT":
-                #        print(" Change: ", newd['_tasks'][0]['software_kwargs']['command'], end='')
-                #        node = MapTaskToNodes()
-                #        newcommand = node.getCommand()
-                #        newd['_tasks'][0]['software_kwargs']['command'] = newcommand
-                #        print(" by: ", newcommand)
-                # Here we work with reset the optimization task
-                # We load the trajectory file and save this structure in the
-                # tree of each uncompleted task
-
                 if 'opt' in task_name:
                     dirs = wf_launchers[task_name]
                     if dirs != []: