MagneticOrderingsWF get_wf() method leading to kwarg error
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Dan Davies
Aug 30, 2019, 7:46:51 AM8/30/19
to atomate
I am trying to produce a workflow to determine the ground state magnetic ordering of a structure. I am getting an error about unexpected keyword args. For other workflows I have mostly relied on presets from `vasp.workflows.presets` so maybe I'm not actually using the `MagneticOrderingsWF` class correctly at all. I would expect the following to return a Fireworks Workflow. Full traceback (making use of stackprinter):
[1]: struct
[1]: Structure Summary
Lattice
abc : 3.15302065 3.15302065 5.12425282
angles : 90.0 90.0 119.99999999999999
volume : 44.117897832868465
A : 3.15302065 0.0 1.9306683233340037e-16
B : -1.5765103249999994 2.730595981556924 1.9306683233340037e-16
C : 0.0 0.0 5.12425282
PeriodicSite: Li (0.0000, 1.8204, 3.2925) [0.3333, 0.6667, 0.6425]
PeriodicSite: Li (1.5765, 0.9102, 1.8318) [0.6667, 0.3333, 0.3575]
PeriodicSite: Co (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]
PeriodicSite: O (0.0000, 1.8204, 1.2151) [0.3333, 0.6667, 0.2371]
PeriodicSite: O (1.5765, 0.9102, 3.9092) [0.6667, 0.3333, 0.7629]
orig_wf = MOWF.get_wf()
File /Users/dan/anaconda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py, line 2963, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File <ipython-input-9-625e53ec6470>, line 2, in <module>
1 MOWF = MagneticOrderingsWF(struct)
--> 2 orig_wf = MOWF.get_wf()
..................................................
MOWF = <atomate.vasp.workflows.base.magnetism.MagneticOrderingsWF o
bject at 0x1c1e0d4940>
MagneticOrderingsWF = <class 'atomate.vasp.workflows.base.magnetism.MagneticOrderi
ngsWF'>
struct = Structure Summary
Lattice
abc : 3.15302065 3.15302065 5.12425282
angles : 90.0 90.0 119.99999999999999
volume : 44.117897832868465
A : 3.15302065 0.0 1.9306683233340037e-16
B : -1.5765103249999994 2.730595981556924 1.9306683233
340037e-16
C : 0.0 0.0 5.12425282
PeriodicSite: Li (0.0000, 1.8204, 3.2925) [0.3333, 0.6667, 0
.6425]
PeriodicSite: Li (1.5765, 0.9102, 1.8318) [0.6667, 0.3333, 0
.3575]
PeriodicSite: Co (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0
.0000]
PeriodicSite:...
MOWF.get_wf = <method 'MagneticOrderingsWF.get_wf' of <atomate.vasp.workfl
ows.base.magnetism.MagneticOrderingsWF object at 0x1c1e0d494
0> magnetism.py:201>
..................................................
File /Users/dan/anaconda3/lib/python3.6/site-packages/atomate/vasp/workflows/base/magnetism.py, line 346, in get_wf
201 def get_wf(
202 self, scan=False, perform_bader=True, num_orderings_hard_limit=16, c=None
203 ):
(...)
342 parent_structure=self.sanitized_structure,
343 origins=ordered_structure_origins,
344 input_index=self.input_index,
345 perform_bader=perform_bader,
--> 346 scan=scan,
347 ),
..................................................
self = <atomate.vasp.workflows.base.magnetism.MagneticOrderingsWF o
bject at 0x1c1e0d4940>
scan = False
perform_bader = True
num_orderings_hard_limit = 16
c = {'VASP_CMD': '>>vasp_cmd<<',
'DB_FILE': '>>db_file<<',
'user_incar_settings': {'ISYM': 0,
'LASPH': True,
'EDIFFG': -0.05}}
self.sanitized_structure = Structure Summary
Lattice
abc : 3.15302065 3.15302065 5.12425282
angles : 90.0 90.0 119.99999999999999
volume : 44.117897832868465
A : 3.15302065 0.0 1.9306683233340037e-16
B : -1.5765103249999994 2.730595981556924 1.9306683233
340037e-16
C : 0.0 0.0 5.12425282
PeriodicSite: Li (0.0000, 1.8204, 3.2925) [0.3333, 0.6667, 0
.6425]
PeriodicSite: Li (1.5765, 0.9102, 1.8318) [0.6667, 0.3333, 0
.3575]
PeriodicSite: Co (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0
.0000]
PeriodicSite:...
ordered_structure_origins = ['fm', 'afm', 'afm', 'afm', 'afm', 'afm', 'afm', 'afm', 'afm
', 'afm', 'afm', 'afm', ]
self.input_index = None
..................................................
File /Users/dan/anaconda3/lib/python3.6/site-packages/fireworks/core/firework.py, line 70, in __init__
57 def __init__(self, *args, **kwargs):
(...)
66 if self.optional_params is not None:
67 allowed_params = required_params + self.optional_params
68 for k in kwargs:
69 if k not in allowed_params:
--> 70 raise RuntimeError("Invalid keyword argument specified for: {}. You specified: {}. Allowed values are: {}.".format(self.__class__, k, allowed_params))
..................................................
self = MagneticOrderingsToDB
{'db_file': '>>db_file<<',
'wf_uuid': 'be373e28-0d83-495f-835b-46f27135bc3a',
'auto_generated': False,
'name': 'MagneticOrderingsToDB',
'parent_structure': Structure Summary
Lattice
abc : 3.15302065 3.15302065 5.12425
282
angles : 90.0 90.0 119.99999999999999
volume : 44.117897832868465
A : 3.15302065 0.0 1.930668323334
0037e-16
B...
args = ()
kwargs = {'db_file': '>>db_file<<',
'wf_uuid': 'be373e28-0d83-495f-835b-46f27135bc3a',
'auto_generated': False,
'name': 'MagneticOrderingsToDB',
'parent_structure': Structure Summary
Lattice
abc : 3.15302065 3.15302065 5.12425
282
angles : 90.0 90.0 119.99999999999999
volume : 44.117897832868465
A : 3.15302065 0.0 1.930668323334
0037e-16
B : -1.5765103249999994...
self.optional_params = ['origins', 'input_index', ]
allowed_params = ['db_file', 'wf_uuid', 'parent_structure', 'perform_bader',
'scan', 'origins', 'input_index', ]
required_params = ['db_file', 'wf_uuid', 'parent_structure', 'perform_bader',
'scan', ]
k = 'auto_generated'
self.__class__ = <class 'atomate.vasp.firetasks.parse_outputs.MagneticOrderin
gsToDB'>
..................................................
---- (full traceback above) ----
File /Users/dan/anaconda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py, line 2963, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File <ipython-input-9-625e53ec6470>, line 2, in <module>
orig_wf = MOWF.get_wf()
File /Users/dan/anaconda3/lib/python3.6/site-packages/atomate/vasp/workflows/base/magnetism.py, line 346, in get_wf
scan=scan,
File /Users/dan/anaconda3/lib/python3.6/site-packages/fireworks/core/firework.py, line 70, in __init__
raise RuntimeError("Invalid keyword argument specified for: {}. You specified: {}. Allowed values are: {}.".format(self.__class__, k, allowed_params))
RuntimeError: Invalid keyword argument specified for: <class 'atomate.vasp.firetasks.parse_outputs.MagneticOrderingsToDB'>. You specified: auto_generated. Allowed values are: ['db_file', 'wf_uuid', 'parent_structure', 'perform_bader', 'scan', 'origins', 'input_index'].
I assume that 'auto_generated' and 'name' should be allowed as they look to be set to sensible values?
Matthew Horton
Aug 30, 2019, 10:58:19 AM8/30/19
to atomate
Hi Dan,
This has been fixed in master but not in the released version yet.
This is as a result of more strict checking for keyword args, which is helping us find a few places where there are old args that don’t do anything any more.
My one note if using this workflow is to be mindful of the version of enumlib you have installed. The version available on the conda matsci channel should be fine, but the latest version compiled from source has a known bug.
Best,
Matt
This has been fixed in master but not in the released version yet.
This is as a result of more strict checking for keyword args, which is helping us find a few places where there are old args that don’t do anything any more.
My one note if using this workflow is to be mindful of the version of enumlib you have installed. The version available on the conda matsci channel should be fine, but the latest version compiled from source has a known bug.
Best,
Matt
Anubhav Jain
Aug 30, 2019, 12:43:03 PM8/30/19
to atomate
I just pushed v0.9.3 which should include the patch (I didn't realize that commit had a bugfix in it, otherwise I would have released earlier!)
Hopefully it works now.
Dan Davies
Sep 2, 2019, 2:40:29 AM9/2/19
to atomate
Thanks both, it's all working fine now!
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