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Predictive GFM 2025#318

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allaffa wants to merge 33 commits intoORNL:Predictive_GFM_2025ORNL/HydraGNN:Predictive_GFM_2025from allaffa:Predictive_GFM_2025allaffa/HydraGNN:Predictive_GFM_2025Copy head branch name to clipboard

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Commits on Jan 11, 2025

• data attributes updated for consistency across datasets

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  ba4cedc

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• non-normalized chemical composition added as data attribute

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• download_dataset.sh added for transition1x example

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• download dataset flag updated

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• scripts updated

  

  Massimiliano Lupo Pasini

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• development of tranistion1x scripts continues

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• transiton1x scripts completed

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• black formatting fixed

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• Merge pull request #21 from allaffa/transition1x

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• printouts removed

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• parallelizatin of data reading introduced

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• blsck formatting fixed

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• Merge pull request #22 from allaffa/transition1x

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• detach().clone() used to defined normalized energy per atom and black formatting

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• add compute_grad_energy=False as explicit argument

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Commits on Jan 12, 2025

• add data name as attributed to each data object

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• compute_grad_energy is parsed as input argument with default value set to False

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• edge_index, edge_attr, and edge_shifts explicitly itnroduced in the definition of the Data object

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Commits on Jan 13, 2025

• changed data.force into data.forces for ani1x and qm7x examples

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Commits on Jan 16, 2025

• smiles_string added as data attribute

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• remove redundant logic on energy normalization from omat24 example

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Commits on Jan 22, 2025

• force threshold value increased to 1000 for ani-1x

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Commits on Jan 23, 2025

• Reverted smiles_utils.py to version from commit 3c3c434

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• xyz2mol functionalities put in a separate file

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• download dataset script added for qm7x

  

  Massimiliano Lupo Pasini

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Commits on Jan 25, 2025

• renamed data.force as data.forces in ani1x

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• natoms converted into a tensor

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• verbosity level ntroduced for ani1x

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• Z corrected into atomic_numbers for qm7x example

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Commits on Jan 27, 2025

• bug fixed for data attributes in transition1x

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• try-except in transition1x rescoped

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• transform coordinates fixed in transition1x

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• iterate_tqdm used in utils.create_graph_data for transition1x example

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