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Open catalyst #211

Merged
merged 27 commits into from
Mar 18, 2024
Merged

Open catalyst #211

merged 27 commits into from
Mar 18, 2024

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allaffa
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@allaffa allaffa commented Mar 14, 2024

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allaffa and others added 23 commits March 9, 2024 22:18
@allaffa
open catalysts pre-load scripts added
dfed076
@allaffa
train.py added
6e61df1
@allaffa
data loading, data processing, and training added
d20e266
test set changed to validation because we need labels
a399d97
exception handler in data loader removed
d1f8c0d
skip command added if len(traj_logs) != len(traj_frames)
2634858
fix adios
b2f552b
@allaffa
Merge pull request #10 from jychoi-hpc/dev-open-catalyst
9e82185 
Data preocessing
removing second np.split
bf21bea
uncompress file added
3fe60ea
@allaffa
energy float converted into tensor
4141d06
@jychoi-hpc
add update_predicted_values in adios reader
df3880b
@jychoi-hpc
add var_config for adios
f34171c
@allaffa
Merge pull request #11 from jychoi-hpc/dev-open-catalyst
f055291 
Add update_data_object for adios
file reader uses glob.iglob
3a31ae0
Merge branch 'open_catalyst' of https://github.com/allaffa/HydraGNN i…
7bba7b6 
…nto open_catalyst
minor update
00c469a
@allaffa
Merge pull request #12 from jychoi-hpc/dev-open-catalyst
2b2a3e1 
Possible fix for handling large number of files
conflict merged
8bfa8d9
choice of adios or pickle in pre-loading
00caab7
@jychoi-hpc
minor fixes
4f715fc
@jychoi-hpc
Merge branch 'open_catalyst' into dev-open-catalyst
1eddd13
@allaffa
Merge pull request #13 from jychoi-hpc/dev-open-catalyst
48cc105 
Minor fixes
@allaffa allaffa added the enhancement New feature or request label Mar 14, 2024
@allaffa allaffa requested a review from jychoi-hpc March 14, 2024 13:09
@allaffa allaffa self-assigned this Mar 14, 2024
@allaffa allaffa requested a review from pzhanggit March 14, 2024 19:47
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I am getting the following error. Do I need to set any option?

Traceback (most recent call last):
  File "train.py", line 196, in <module>
    trainset = OpenCatalystDataset(
  File "train.py", line 90, in __init__
    write_images_to_adios(a2g, chunked_txt_files, self.data_path)
  File "/lustre/orion/cph161/world-shared/jyc/frontier/HydraGNN-oc/examples/open_catalyst_2020/utils/preprocess.py", line 48, in write_images_to_adios
    data_object = a2g.convert(frame)
  File "/lustre/orion/cph161/world-shared/jyc/frontier/HydraGNN-oc/examples/open_catalyst_2020/utils/atoms_to_graphs.py", line 111, in convert
    data = self.radius_graph_pbc(data)
  File "/lustre/orion/world-shared/cph161/jyc/frontier/HydraGNN-oc/hydragnn/preprocess/utils.py", line 144, in __call__
    assert hasattr(
AssertionError: The data must contain the size of the supercell to apply periodic boundary conditions.

@allaffa allaffa force-pushed the open_catalyst branch 2 times, most recently from e629c14 to fa100bd Compare March 15, 2024 21:54
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allaffa commented Mar 16, 2024

@jychoi-hpc @pzhanggit
After discussion with Jong, we decided not to apply periodic boundary conditions. Due to the variable size of the graphs, the feasibility of applying PBC is too case-dependent.

@jychoi-hpc jychoi-hpc requested review from jychoi-hpc and removed request for jychoi-hpc March 16, 2024 14:23
jychoi-hpc
jychoi-hpc approved these changes Mar 16, 2024
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This PR works for me on Frontier.

pzhanggit
pzhanggit reviewed Mar 18, 2024
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Looks good to me with minor comments

@allaffa allaffa requested a review from pzhanggit March 18, 2024 18:34
@allaffa allaffa merged commit a6ff278 into ORNL:main Mar 18, 2024
2 checks passed
@allaffa allaffa deleted the open_catalyst branch March 18, 2024 21:10
RylieWeaver pushed a commit to RylieWeaver/HydraGNN that referenced this pull request Oct 17, 2024
@allaffa @jychoi-hpc
Open catalyst (ORNL#211)
8b7f542 
* open catalysts pre-load scripts added

* train.py added

* data loading, data processing, and training added

* test set changed to validation because we need labels

* exception handler in data loader removed

* skip command added if len(traj_logs) != len(traj_frames)

* fix adios

* removing second np.split

* uncompress file added

* energy float converted into tensor

* add update_predicted_values in adios reader

* add var_config for adios

* file reader uses glob.iglob

* minor update

* choice of adios or pickle in pre-loading

* minor fixes

* formatting fixed

* black reformatting of utils/adiosdataset.py

* black reformarring of scripts in examples/open_catalyst_2020

* Dataset section in the JSON file is removed

---------

Co-authored-by: Massimiliano Lupo Pasini <[email protected]>
Co-authored-by: Massimiliano Lupo Pasini <[email protected]>
Co-authored-by: Jong Choi <[email protected]>
Co-authored-by: Massimiliano Lupo Pasini <[email protected]>
Co-authored-by: Massimiliano Lupo Pasini <[email protected]>
Co-authored-by: Jong Choi <[email protected]>
Co-authored-by: Massimiliano Lupo Pasini <[email protected]>
Co-authored-by: Jong Choi <[email protected]>
Co-authored-by: Massimiliano Lupo Pasini <[email protected]>
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@jychoi-hpc jychoi-hpc jychoi-hpc approved these changes

@pzhanggit pzhanggit pzhanggit approved these changes

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