Hi !
I encountered a new problem when I tried to calculate the surface energy of Ni(111) (or any miller index) with the procedure described in one of the matgenb notebook.
The problem occurs when I tried to include the bulk optimization with the corresponding option (include_bulk_opt). The first fireworks (for bulk) finished successfully but the second one fizzled. In fact, when looking in the file, it never started and the input files corresponds to the bulk one. In the log file, after creating the launcher directory and copying the files, nothing happens while checking FW every 60 s.
2020-09-10 11:03:43,343 INFO Hostname/IP lookup (this will take a few seconds)
2020-09-10 11:03:45,236 INFO Created new dir /home/f-gimbert/SLAB111/launcher_2020-09-10-02-03-45-236264
2020-09-10 11:03:45,236 INFO Launching Rocket
2020-09-10 11:03:45,406 INFO RUNNING fw_id: 5 in directory: /home/f-gimbert/SLAB111/launcher_2020-09-10-02-03-45-236264
2020-09-10 11:03:45,515 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}.
2020-09-10 11:03:45,598 INFO Task completed: {{atomate.vasp.firetasks.write_inputs.WriteVaspFromIOSet}}
2020-09-10 11:03:45,614 INFO Task started: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}.
2020-09-10 12:50:11,935 INFO Task completed: {{atomate.vasp.firetasks.run_calc.RunVaspCustodian}}
2020-09-10 12:50:11,956 INFO Task started: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}.
2020-09-10 12:50:11,957 INFO Task completed: {{atomate.common.firetasks.glue_tasks.PassCalcLocs}}
2020-09-10 12:50:11,978 INFO Task started: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}.
2020-09-10 12:50:11,979 INFO atomate.vasp.firetasks.parse_outputs PARSING DIRECTORY: /home/f-gimbert/SLAB111/launcher_20
20-09-10-02-03-45-236264
2020-09-10 12:50:11,979 INFO atomate.vasp.drones Getting task doc for base dir :/home/f-gimbert/SLAB111/launcher_2020-09
-10-02-03-45-236264
2020-09-10 12:50:18,632 INFO atomate.vasp.drones Post-processing dir:/home/f-gimbert/SLAB111/launcher_2020-09-10-02-03-4
5-236264
2020-09-10 12:50:18,632 WARNING atomate.vasp.drones Transformations file does not exist.
2020-09-10 12:50:18,739 INFO atomate.vasp.drones Post-processed /home/f-gimbert/SLAB111/launcher_2020-09-10-02-03-45-236
264
2020-09-10 12:50:19,096 INFO atomate.utils.database Inserting atlas06:/home/f-gimbert/SLAB111/launcher_2020-09-10-02-03-
45-236264 with taskid = 11
2020-09-10 12:50:19,197 INFO atomate.vasp.firetasks.parse_outputs Finished parsing with task_id: 11
2020-09-10 12:50:19,201 INFO Task completed: {{atomate.vasp.firetasks.parse_outputs.VaspToDb}}
2020-09-10 12:50:19,399 INFO Rocket finished
2020-09-10 12:50:19,444 INFO Created new dir /home/f-gimbert/SLAB111/launcher_2020-09-10-03-50-19-443795
2020-09-10 12:50:19,444 INFO Launching Rocket
2020-09-10 12:50:19,645 INFO RUNNING fw_id: 4 in directory: /home/f-gimbert/SLAB111/launcher_2020-09-10-03-50-19-443795
2020-09-10 12:50:19,677 INFO Task started: {{atomate.vasp.firetasks.glue_tasks.CopyVaspOutputs}}.
2020-09-10 12:50:19,892 INFO Task completed: {{atomate.vasp.firetasks.glue_tasks.CopyVaspOutputs}}
2020-09-10 12:50:19,910 INFO Task started: {{atomate.vasp.firetasks.write_inputs.WriteTransmutedStructureIOSet}}.
2020-09-10 12:50:20,100 INFO Rocket finished
2020-09-10 12:50:20,357 INFO Sleeping for 60 secs
2020-09-10 12:51:20,418 INFO Checking for FWs to run...
2020-09-10 12:51:20,483 INFO Sleeping for 60 secs
Another thing very weird is when I tried to do the same workflow without the bulk option (for (2,1,0) surface). The workflows finished successfully (Completed) but in the output log, the same lines appear (Checking for FWs to run / Sleeping for 60 seconds) and the job is still in the queue (while finished !).
That’s the first time something like this happens for slab (never tried before with bulk) aI recently modified my MongoDB database so it could be a configuration problem.
When I do lpad get_wflows, I have this:
{
"state": "COMPLETED",
"name": "Ni1_(2, 1, 0) slab workflow--1",
"created_on": "2020-09-10T00:41:05.420000",
"states_list": "C"
},
{
"state": "FIZZLED",
"name": "Ni1_(1, 1, 1) slab workflow--4",
"created_on": "2020-09-10T02:03:31.639000",
"states_list": "F-C"
},
]
The script I am using:
> struct = mpr.get_structure_by_material_id("mp-23") # fcc Ni
> struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
> slabs = generate_all_slabs(struct, 1, 10.0, 10.0, center_slab=True)
> slab_dict = {slab.miller_index:slab for slab in slabs}
>
> ni_slab_111 = slab_dict[(1, 1, 1)]
> wf = get_wf_slab(ni_slab_111,include_bulk_opt=True, db_file='/home/f-gimbert/atomate/config/db.json')
> new_wf = add_additional_fields_to_taskdocs(wf, {"system":"surface"})
> lpad.add_wf(new_wf)
and after qlaunch singleshot.
What did I miss this time ?