diff --git a/pynta/main.py b/pynta/main.py index 477e8584..0ec2b93b 100644 --- a/pynta/main.py +++ b/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 != []: