Comments (12)
Considering the plotting/
, I understand this is not linked to the autoparallelize
, but I wonder if you don't want to provide some standard plots (one may add more) which could help users to monitor progress of potential training?
If this is not wanted in the wfl/
code maybe it makes sense to move it out of it, but keep it separately in the repo?
from workflow.
I don't even know what's in plotting/
, but maybe we need a different repo for analysis?
from workflow.
I mean that's up to you and maybe a separate repo is easier to maintain. I personally think that providing some analysis tools for workflow in the same repo would be more convenient, though. So far some of us have been using functions like plot_ef_correlation.py
producing detailed energy and force correlation plots. Of course we could generalize and refactor the contained functions and add some more of our own which could fit in there -- we also happily do this if you chose to make a separate analysis repo.
from workflow.
@gabor1 where should we put these things?
from workflow.
Just to collect some other things to revise:
devtools
(in particulardevtools/scripts/pretty_pca.py
)- (to be continued)
from workflow.
@bernstei what's wrong with vib.py
?
from workflow.
It's sort of OK, since it does use ConfigSet
, but wouldn't it be more modular to have functions that just generate the necessary configurations, then use the existing autoparallelized generic eval loop, and then routines that analyze them? Given that the calculations will almost certainly dominate the cost that seems like a more useful packaging of the work.
from workflow.
Very small nitpick, but might I suggest that all style elements be removed from the plotting section? Seems like that is something that the users can easily set via their plt.rcParams. So instead of defining a sequence of colors, we just define:
colors = plt.rcParams['axes.prop_cycle'].by_key()['color']
and iterate through those parameters. The figsizes, labelsizes, etc. would then all be taken directly from the user's individual setups.
The added benefit would be that the code becomes a lot shorter.
An alternative approach would be to provide a default rcParams file somewhere, which would then be the fallback.
from workflow.
providing a default rcParams would be good. not everyone controls their styles by rcParams files
from workflow.
Comments on what's there now:
reactions_processing/
: routines specific to @stenczelt workflow, not really workflow ops [note - by this reasoning, should gap-rss-iter-fit be moved out of workflow as well, or at least refactored in things that belong a things that don't?]plotting/
: nice for analysis, but not really using any workflow stuff- some things in
generate/
,neb
: not using any workflow featurests
: not using any workflow featuresvib
: using autoparallelize over configs xor Hessian displacements in each config.radicals
: not using any workflow features
I think that vib
has a good reason to stay, but all the others should probably be moved outside of wfl
, whether that's some user or system specific directory distributed with the workflow, or entirely separate. I've tentatively moved them to workflow/deprecated
.
As for vib
, we should think about the best interface, and perhaps also making it uniform with the equivalent functionality for periodic systems (using phonopy
). I have routines for that, but would need to think about how to unify the two interfaces.
from workflow.
Current plan:
reactions_processing
,neb
,ts
,radicals
touser/reactions
(name to be finalized)plotting
todeprecate/plotting
, to be moved into a separate directory or repo for analysisvib
unchanged for now, pending thought about merging withphononpy
based code for periodic systems.
@gabor1 sounds OK to you? Do we have a better name for the user directory for Tamas's code?
from workflow.
from workflow.
Related Issues (20)
- duplicate configs in output
- Successful MD job not transferred to local machine HOT 21
- unexpectedly changed rng state confuses detection of identical jobs HOT 1
- failed calculation doesn't respect user's choice of keep_files
- _ConfigSet_loc geting increasingly nested for no reason HOT 3
- Error in MD run (related to rng?) HOT 3
- Errorr encountered when trying to submit remote jobs. HOT 4
- conflict in compatible ASE version? HOT 31
- Coupling NEB with wfl. HOT 1
- error in configset HOT 2
- Renaming the package HOT 2
- `config_type` get concatenated over different operations HOT 8
- Error related to profile HOT 2
- Update Calculators to work with ASE v3.23 Profiles HOT 15
- RDKit is dependency HOT 4
- reconsider complex env-var dict mechanism for associating autopara info with specific function calls
- "Iterative GAP fitting" example using ase Vasp calculator? HOT 1
- Attaching user defined logfile to MD wrapper. HOT 10
- MACE descriptor HOT 9
- copying back generated logfile HOT 1
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from workflow.