Error of ferroelectric workflow generation

Atomate
1

Hello,

I am a new user of atomate, I am trying to generate polarization workflows with the following codes:

import numpy as np
from atomate.vasp.workflows.base.ferroelectric import get_wf_ferroelectric

from pymatgen import MPRester, Structure
with MPRester() as mp:
s = mp.get_structure_by_material_id(‘mp-19845’) # TiPbO3

pert_coords = []
for site in s.sites:
if site.specie.symbol == ‘Ti’:
pert_coords.append( site.coords + np.array( [0., 0., 0.25])) # add displacement on Ti
else:
pert_coords.append( site.coords)
pert_struct = Structure( s.lattice, s.species, pert_coords, coords_are_cartesian=True)

wf = get_wf_ferroelectric(s, pert_struct, vasp_cmd=">>vasp_cmd<<", db_file=’>>db_file<<’,
vasp_input_set_polar=“MPStaticSet”,
vasp_input_set_nonpolar=“MPStaticSet”,
vasp_relax_input_set_polar=“MPRelaxSet”,
vasp_relax_input_set_nonpolar=“MPRelaxSet”,
add_analysis_task=True)

from fireworks.core.launchpad import LaunchPad
lpad_file_path = ‘path_to_my_launchpad.yaml’

lp = LaunchPad().from_file(lpad_file_path)
lp.add_wf(wf)

However, I got the following error:
RuntimeError: Invalid keyword argument specified for: <class 'atomate.vasp.firetasks.parse_outputs.PolarizationToDb'>. You specified: name. Allowed values are: ['db_file'].

After I set add_analysis_task=True in function get_wf_ferroelectric, the error is gone, but interpolation workflows are FIZZLED and first two workflows COMPLETED (TiPbO3-_polar_polarization, TiPbO3-_nonpolar_polarization).

My question is why add_analysis_task=True get me that error? Am I doing something wrong?

Many thanks!
Yichen

2

I got an update from my post last time. So far, by reinstall and configure atomate from the scratch in another anaconda environment, the get_wf_ferroelectric function is worked with setting
add_analysis_task=True, but interpolation workflows are still FIZZLED with the first two workflows (polar and nonpolar ones) completed.

3

Hi Yichen,

Are you able to provide more information on the FIZZLED Fireworks? Do you know which FireTask is failing and what the error message is?

Best,
Alex

4

Hi Alex,

I am really sorry for the delayed reply.

The error message in FW_job.error file is:

Traceback (most recent call last):
File “/home/yig319/.conda/envs/atomate1/lib/python3.7/site-packages/fireworks/core/rocket.py”, line 262, in run
m_action = t.run_task(my_spec)
File “/home/yig319/.conda/envs/atomate1/lib/python3.7/site-packages/atomate/vasp/firetasks/write_inputs.py”, line 132, in run_task
structure = GetInterpolatedPOSCAR.interpolate_poscar(self, fw_spec)
File “/home/yig319/.conda/envs/atomate1/lib/python3.7/site-packages/atomate/vasp/firetasks/glue_tasks.py”, line 270, in interpolate_poscar
s1 = Structure.from_file(os.path.join(interpolate_folder, “CONTCAR_0”))
File “/home/yig319/.conda/envs/atomate1/lib/python3.7/site-packages/pymatgen/core/structure.py”, line 2326, in from_file
with zopen(filename, “rt”) as f:
File “/home/yig319/.conda/envs/atomate1/lib/python3.7/site-packages/monty/io.py”, line 43, in zopen
return io.open(filename, *args, **kwargs)
FileNotFoundError: [Errno 2] No such file or directory: ‘interpolate/CONTCAR_0’

I am not sure when CONTCAR_0 should be created, and it seems like FireTask should create or pass CONTCAR_O file to the “interpolate” folder for interpolation workflow, but it didn’t.

From the source codes of atomate, I found that the function get_wf_ferroelectric is using a Class LcalcpolFW, which will use parameter start and end to locate output structures (CONTCAR) of previous calculations. And my friend told me the LcalcpolFW uses PassCalcLoc in atomate.common.glue_tasks to keeps track of the location of the current calculation to pass on to the next firework, which needs to use that information.

Regards,
Yichen

5

I ran into the same error and found the solution on this forum page: Ferroelectric job error - #4 by Bikash. Bikash explained that the error went away when he set {‘gzip_output’: False} in run_calc.py inside /atomate/vasp/firetasks at line no. 127. It has something to do with the Firetask not being able to find/pass the file when it is zipped.