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tutorials/advanced/embeddings.html | 6 +- tutorials/advanced/fine-tuning-in-python.html | 6 +- tutorials/advanced/fine-tuning-toc.html | 6 +- tutorials/advanced/mass-inference.html | 12 +- tutorials/fine-tuning/fine-tuning-oxides.html | 8 +- tutorials/gotchas.html | 6 +- tutorials/intro.html | 36 +- videos/intro_series.html | 6 +- videos/technical_talks.html | 6 +- 175 files changed, 1930 insertions(+), 730 deletions(-) delete mode 100644 _sources/autoapi/ocpmodels/common/model_registry/index.rst create mode 100644 _sources/autoapi/ocpmodels/models/model_registry/index.rst create mode 100644 _sources/core/QUICKSTART.md rename autoapi/ocpmodels/{common => models}/model_registry/index.html (78%) create mode 100644 core/QUICKSTART.html diff --git a/_sources/autoapi/ocpmodels/common/index.rst b/_sources/autoapi/ocpmodels/common/index.rst index 20d96be2c..df4749a65 100644 --- a/_sources/autoapi/ocpmodels/common/index.rst +++ b/_sources/autoapi/ocpmodels/common/index.rst @@ -33,7 +33,6 @@ Submodules gp_utils/index.rst hpo_utils/index.rst logger/index.rst - model_registry/index.rst registry/index.rst transforms/index.rst tutorial_utils/index.rst diff --git a/_sources/autoapi/ocpmodels/common/model_registry/index.rst b/_sources/autoapi/ocpmodels/common/model_registry/index.rst deleted file mode 100644 index f6efc71c4..000000000 --- a/_sources/autoapi/ocpmodels/common/model_registry/index.rst +++ /dev/null @@ -1,34 +0,0 @@ -:py:mod:`ocpmodels.common.model_registry` -========================================= - -.. py:module:: ocpmodels.common.model_registry - - -Module Contents ---------------- - - -Functions -~~~~~~~~~ - -.. autoapisummary:: - - ocpmodels.common.model_registry.model_name_to_local_file - - - -Attributes -~~~~~~~~~~ - -.. autoapisummary:: - - ocpmodels.common.model_registry.MODEL_REGISTRY - - -.. py:data:: MODEL_REGISTRY - - - -.. py:function:: model_name_to_local_file(model_name: str, local_cache: str) -> str | None - - diff --git a/_sources/autoapi/ocpmodels/models/index.rst b/_sources/autoapi/ocpmodels/models/index.rst index 51c7291ea..d2c6d2d40 100644 --- a/_sources/autoapi/ocpmodels/models/index.rst +++ b/_sources/autoapi/ocpmodels/models/index.rst @@ -28,6 +28,45 @@ Submodules base/index.rst dimenet_plus_plus/index.rst + model_registry/index.rst schnet/index.rst +Package Contents +---------------- + + +Functions +~~~~~~~~~ + +.. autoapisummary:: + + ocpmodels.models.model_name_to_local_file + + + +Attributes +~~~~~~~~~~ + +.. autoapisummary:: + + ocpmodels.models.available_pretrained_models + + +.. py:data:: available_pretrained_models + + + +.. py:function:: model_name_to_local_file(model_name: str, local_cache: str | pathlib.Path) -> str + + Download a pretrained checkpoint if it does not exist already + + :param model_name: the model name. See available_pretrained_checkpoints. + :type model_name: str + :param local_cache: + :type local_cache: str + + Returns: + + + diff --git a/_sources/autoapi/ocpmodels/models/model_registry/index.rst b/_sources/autoapi/ocpmodels/models/model_registry/index.rst new file mode 100644 index 000000000..3ddf1db32 --- /dev/null +++ b/_sources/autoapi/ocpmodels/models/model_registry/index.rst @@ -0,0 +1,49 @@ +:py:mod:`ocpmodels.models.model_registry` +========================================= + +.. py:module:: ocpmodels.models.model_registry + + +Module Contents +--------------- + + +Functions +~~~~~~~~~ + +.. autoapisummary:: + + ocpmodels.models.model_registry.model_name_to_local_file + + + +Attributes +~~~~~~~~~~ + +.. autoapisummary:: + + ocpmodels.models.model_registry.MODEL_REGISTRY + ocpmodels.models.model_registry.available_pretrained_models + + +.. py:data:: MODEL_REGISTRY + + + +.. py:data:: available_pretrained_models + + + +.. py:function:: model_name_to_local_file(model_name: str, local_cache: str | pathlib.Path) -> str + + Download a pretrained checkpoint if it does not exist already + + :param model_name: the model name. See available_pretrained_checkpoints. + :type model_name: str + :param local_cache: + :type local_cache: str + + Returns: + + + diff --git a/_sources/core/INSTALL.md b/_sources/core/INSTALL.md index 04df9863f..9602f5e95 100644 --- a/_sources/core/INSTALL.md +++ b/_sources/core/INSTALL.md @@ -1,4 +1,24 @@ -## Installation +# Installation + +## pip (fast, easy to get started) + +Installing the OCP package and necessary dependencies is now as easy as: + +(GPU) +``` +pip install torch==1.13.1+cu117 torchvision==0.14.1+cu117 torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu117 +pip install pyg_lib torch_scatter torch_sparse -f https://data.pyg.org/whl/torch-1.13.1+cu117.html +pip install -i https://test.pypi.org/simple/ ocp-models +``` + +or if you want the CPU-only install (no cuda/etc): +``` +pip install torch==1.13.1 torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu # install CPU torch +pip install pyg_lib torch_scatter torch_sparse -f https://data.pyg.org/whl/torch-1.13.1+cpu.html +pip install -i https://test.pypi.org/simple/ ocp-models +``` + +## Conda (preferred for model training & development) - We'll use `conda` to install dependencies and set up the environment. We recommend using the [Python 3.9 Miniconda installer](https://docs.conda.io/en/latest/miniconda.html#linux-installers). diff --git a/_sources/core/QUICKSTART.md b/_sources/core/QUICKSTART.md new file mode 100644 index 000000000..fee7abfac --- /dev/null +++ b/_sources/core/QUICKSTART.md @@ -0,0 +1,55 @@ +--- +jupytext: + text_representation: + extension: .md + format_name: myst + format_version: 0.13 + jupytext_version: 1.16.1 +kernelspec: + display_name: Python 3 (ipykernel) + language: python + name: python3 +--- + +Quickstart simulation using pre-trained models +---------- + +1. First, install OCP in a fresh python environment using one of the approaches in [installation documentation](INSTALL). +2. See what pre-trained potentials are available +```{code-cell} ipython3 +from ocpmodels.models.model_registry import available_pretrained_models +print(available_pretrained_models) +``` +3. Choose a checkpoint you want to use and download it automatically! We'll use the GemNet-OC potential, trained on both the OC20 and OC22 datasets. +```{code-cell} ipython3 +from ocpmodels.models.model_registry import model_name_to_local_file +checkpoint_path = model_name_to_local_file('GemNet-OC OC20+OC22', local_cache='/tmp/ocp_checkpoints/') +checkpoint_path +``` +4. Finally, use this checkpoint in an ASE calculator for a simple relaxation! +``` +from ocpmodels.common.relaxation.ase_utils import OCPCalculator +from ase.build import fcc111, add_adsorbate +from ase.optimize import BFGS +import matplotlib.pyplot as plt +from ase.visualize.plot import plot_atoms + +# Define the model atomic system, a Pt(111) slab with an *O adsorbate! +slab = fcc111('Pt', size=(2, 2, 5), vacuum=10.0) +add_adsorbate(slab, 'O', height=1.2, position='fcc') + +# Load the pre-trained checkpoint! +calc = OCPCalculator(checkpoint_path=checkpoint_path, cpu=False) +slab.set_calculator(calc) + +# Run the optimization! +opt = BFGS(slab) +opt.run(fmax=0.05, steps=100) + +# Visualize the result! +fig, axs = plt.subplots(1, 2) +plot_atoms(slab, axs[0]); +plot_atoms(slab, axs[1], rotation=('-90x')) +axs[0].set_axis_off() +axs[1].set_axis_off() +``` \ No newline at end of file diff --git a/_sources/core/datasets/oc20.md b/_sources/core/datasets/oc20.md index 72de8cbc3..eaea373fe 100644 --- a/_sources/core/datasets/oc20.md +++ b/_sources/core/datasets/oc20.md @@ -331,87 +331,83 @@ Please consider citing the following paper in any research manuscript using the ## Per-adsorbate trajectories - -Download links are in the table below: - -|Adsorbate symbol |Downloadable path |size |MD5 checksum | -|--- |--- |--- |--- | -|*O |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/0.tar |1006M |d4151542856b4b6405f276808f75358a | -|*H |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/1.tar |850M |3697f04faf04251a23da8b88a78209f7 | -|*OH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/2.tar |1.6G |a21081f3f55eb0c98a91021bbe3dac44 | -|*OH2 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/3.tar |1.8G |b12b706854f5d899e02a9ae6578b5d45 | -|*C |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/4.tar |1.1G |e4fe9890764fcf59e01e3ceab089b978 | -|*CH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/6.tar |1.4G |ec9aa2c4c4bd4419359438ba7fbb881d | -|*CHO |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/7.tar |1.4G |d32200f74ad5c3bfd42e8835f36d57ab | -|*COH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/8.tar |1.6G |5418a1b331f6c7689a5405cca4cc8d15 | -|*CH2 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/9.tar |1.6G |8ee1066149c305d7c17c219b369c5a73 | -|*CH2*O |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/10.tar |1.7G |960c2450814024b66f3c79121179ac60 | -|*CHOH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/11.tar |1.8G |60ac9f965f9589a3389483e3d1e58144 | -|*CH3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/12.tar |1.7G |7e123e6f4fb10d6897be3f47721dfd4a | -|*OCH3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/13.tar |1.8G |0823047bbbe05fa0e63f9d83ec601487 | -|*CH2OH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/14.tar |1.9G |9ac71e198d75b1427182cd34abb73e4d | -|*CH4 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/15.tar |1.9G |a405ce403018bf8afbd4425d5c0b34d5 | -|*OHCH3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/16.tar |2.1G |d3c829f1952db6e4f428273ee05f59b1 | -|*C*C |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/17.tar |1.5G |d687a151345305897b9245af4b0f9967 | -|*CCO |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/18.tar |1.7G |214ca96e620c5ec6e8a6ff8144a22a04 | -|*CCH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/19.tar |1.6G |da2268545e80ca1664026449dd2fdd24 | -|*CHCO |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/20.tar |1.7G |386c99407fe63080d26cda525dfdd8cd | -|*CCHO |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/21.tar |1.8G |918b20960438494ab160a9dbd9668157 | -|*COCHO |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/22.tar |1.8G |84424aa2ad30301e23ece1438ea39923 | -|*CCHOH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/23.tar |2.0G |3cc90425ec042a70085ba7eb2916a79a | -|*CCH2 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/24.tar |1.8G |9dbcf7566e40965dd7f8a186a75a718e | -|*CH*CH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/25.tar |1.7G |a193b4c72f915ba0b21a41790696b23c | -|CH2*CO |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/26.tar |1.8G |de83cf50247f5556fa4f9f64beff1eeb | -|*CHCHO |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/27.tar |1.9G |1d140aaa2e7b287124ab38911a711d70 | -|*CH*COH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/28.tar |1.3G |682d8a6b05ca5948b34dc5e5f6bbcd61 | -|*COCH2O |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/29.tar |1.9G |c8742faa8ca40e8edb4110069817fa70 | -|*CHO*CHO |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/30.tar |2.0G |8cfbb67beb312b98c40fcb891dfa480a | -|*COHCHO |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/31.tar |1.9G |6ffa903a62d8ec3319ecec6a03b06276 | -|*COHCOH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/32.tar |2.0G |caca0058b641bfdc9f8de4527e60feb7 | -|*CCH3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/33.tar |1.8G |906543aaefc171edab388ff4f0fe8a20 | -|*CHCH2 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/34.tar |1.8G |4dfab479495f76179749c1956046fbd8 | -|*COCH3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/35.tar |1.9G |29d1b992715054e920e8bb2afe97b393 | -|*CHCHOH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/38.tar |2.0G |9e5912df6f7b11706d1046cdb9e3087e | -|*CCH2OH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/39.tar |2.1G |7bcae43cee451306e34ec416588a7f09 | -|*CHOCHOH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/40.tar |2.0G |f98866d08fe3451ae7ebc47bb51599aa | -|*COCH2OH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/41.tar |1.4G |bfaf689e5827fcf26c51e567bb8dd1be | -|*COHCHOH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/42.tar |2.0G |236fe4e950aa2fbdde94ef2821fb48d2 | -|*OCHCH3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/44.tar |2.1G |66acc5460a999625c3364f0f3bcca871 | -|*COHCH3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/45.tar |2.1G |bb4a01956736399c8cee5e219f8c1229 | -|*CHOHCH2 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/46.tar |2.1G |e836de4ec146b1b611533f1ef682cace | -|*CHCH2OH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/47.tar |2.0G |66df44121806debef6dc038df7115d1d | -|*OCH2CHOH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/48.tar |2.2G |ff6981fdbcd2e65d351505c15d218d76 | -|*CHOCH2OH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/49.tar |2.1G |448f7d352ab6e32f754e24de64ca302a | -|*COHCH2OH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/50.tar |2.1G |8bff6bf3e10cc84acc4a283a375fcc23 | -|*CHOHCHOH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/51.tar |2.0G |9c9e4d617d306751760a80f1453e71f1 | -|*CH2CH3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/52.tar |2.0G |ec1e964d2ee6f468fa5773743e3994a4 | -|*OCH2CH3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/53.tar |2.1G |d297b27b02822f9b6af80bdb64aee819 | -|*CHOHCH3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/54.tar |2.1G |368de083dafdc3bbdb560d35e2a102c0 | -|*CH2CH2OH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/55.tar |2.1G |3c1aaf790659f7ff89bf1eed8b396b63 | -|*CHOHCH2OH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/56.tar |2.2G |2d71adb9e305e6f3bca49e5df9b5a86a | -|*OHCH2CH3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/57.tar |2.3G |cf51128f8522b7b66fc68d79980d6def | -|*NH2N(CH3)2 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/58.tar |1.6G |36ba974d80c20ff636431f7c0ad225da | -|*ONN(CH3)2 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/59.tar |2.3G |fdc4cd19977496909d61be4aee61c4f1 | -|*OHNNCH3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/60.tar |2.1G |50a6ff098f9ba7adbba9ac115726cc5a | -|*ONH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/62.tar |1.8G |47573199c545afe46c554ff756c3e38f | -|*NHNH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/63.tar |1.7G |dd456b7e19ef592d9f0308d911b91d7c | -|*N*NH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/65.tar |1.6G |c05289fd56d64c74306ebf57f1061318 | -|*NO2NO2 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/67.tar |2.1G |4822a06f6c5f41bdefd3cbbd8856c11f | -|*N*NO |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/68.tar |1.6G |2a27de122d32917cc5b6ac0a21c63c1c | -|*N2 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/69.tar |1.5G |cc668fecf679b6edaac8fd8fb9cdd404 | -|*ONNH2 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/70.tar |2.1G |dff880f1a5baa7f67b52fd3ed745443d | -|*NH2 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/71.tar |1.6G |c7f383b50faa6244e265c9611466cb8f | -|*NH3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/72.tar |1.9G |2b355741f9300445703270e0e4b8c01c | -|*NONH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/73.tar |1.8G |48877a0c6f2994baac82cb722711aaa2 | -|*NH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/74.tar |1.4G |7979b9e7ab557d6979b33e352486f0ef | -|*NO2 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/75.tar |1.7G |9f352fbc32bb2b8caf4788aba28b2eb7 | -|*NO |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/76.tar |1.4G |482ee306a5ae2eee78cac40d10059ebc | -|*N |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/77.tar |1.1G |bfb6e03d4a687987ff68976f0793cc46 | -|*NO3 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/78.tar |1.8G |700834326e789a6e38bf3922d9fcb792 | -|*OHNH2 |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/79.tar |2.1G |fa24472e0c02c34d91f3ffe6b77bfb11 | -|*ONOH |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/80.tar |1.4G |4ddcccd62a834a76fe6167461f512529 | -|*CN |https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/81.tar |1.5G |bc7c55330ece006d09496a5ff01d5d50 | - +|Adsorbate symbol |Size |MD5 checksum (download link) | +|--- |--- |--- | +|*O |1006M |[d4151542856b4b6405f276808f75358a](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/0.tar) | +|*H |850M |[3697f04faf04251a23da8b88a78209f7](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/1.tar) | +|*OH |1.6G |[a21081f3f55eb0c98a91021bbe3dac44](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/2.tar) | +|*OH2 |1.8G |[b12b706854f5d899e02a9ae6578b5d45](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/3.tar) | +|*C |1.1G |[e4fe9890764fcf59e01e3ceab089b978](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/4.tar) | +|*CH |1.4G |[ec9aa2c4c4bd4419359438ba7fbb881d](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/6.tar) | +|*CHO |1.4G |[d32200f74ad5c3bfd42e8835f36d57ab](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/7.tar) | +|*COH |1.6G |[5418a1b331f6c7689a5405cca4cc8d15](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/8.tar) | +|*CH2 |1.6G |[8ee1066149c305d7c17c219b369c5a73](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/9.tar) | +|*CH2*O |1.7G |[960c2450814024b66f3c79121179ac60](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/10.tar) | +|*CHOH |1.8G |[60ac9f965f9589a3389483e3d1e58144](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/11.tar) | +|*CH3 |1.7G |[7e123e6f4fb10d6897be3f47721dfd4a](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/12.tar) | +|*OCH3 |1.8G |[0823047bbbe05fa0e63f9d83ec601487](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/13.tar) | +|*CH2OH |1.9G |[9ac71e198d75b1427182cd34abb73e4d](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/14.tar) | +|*CH4 |1.9G |[a405ce403018bf8afbd4425d5c0b34d5](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/15.tar) | +|*OHCH3 |2.1G |[d3c829f1952db6e4f428273ee05f59b1](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/16.tar) | +|*C*C |1.5G |[d687a151345305897b9245af4b0f9967](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/17.tar) | +|*CCO |1.7G |[214ca96e620c5ec6e8a6ff8144a22a04](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/18.tar) | +|*CCH |1.6G |[da2268545e80ca1664026449dd2fdd24](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/19.tar) | +|*CHCO |1.7G |[386c99407fe63080d26cda525dfdd8cd](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/20.tar) | +|*CCHO |1.8G |[918b20960438494ab160a9dbd9668157](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/21.tar) | +|*COCHO |1.8G |[84424aa2ad30301e23ece1438ea39923](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/22.tar) | +|*CCHOH |2.0G |[3cc90425ec042a70085ba7eb2916a79a](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/23.tar) | +|*CCH2 |1.8G |[9dbcf7566e40965dd7f8a186a75a718e](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/24.tar) | +|*CH*CH |1.7G |[a193b4c72f915ba0b21a41790696b23c](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/25.tar) | +|CH2*CO |1.8G |[de83cf50247f5556fa4f9f64beff1eeb](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/26.tar) | +|*CHCHO |1.9G |[1d140aaa2e7b287124ab38911a711d70](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/27.tar) | +|*CH*COH |1.3G |[682d8a6b05ca5948b34dc5e5f6bbcd61](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/28.tar) | +|*COCH2O |1.9G |[c8742faa8ca40e8edb4110069817fa70](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/29.tar) | +|*CHO*CHO |2.0G |[8cfbb67beb312b98c40fcb891dfa480a](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/30.tar) | +|*COHCHO |1.9G |[6ffa903a62d8ec3319ecec6a03b06276](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/31.tar) | +|*COHCOH |2.0G |[caca0058b641bfdc9f8de4527e60feb7](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/32.tar) | +|*CCH3 |1.8G |[906543aaefc171edab388ff4f0fe8a20](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/33.tar) | +|*CHCH2 |1.8G |[4dfab479495f76179749c1956046fbd8](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/34.tar) | +|*COCH3 |1.9G |[29d1b992715054e920e8bb2afe97b393](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/35.tar) | +|*CHCHOH |2.0G |[9e5912df6f7b11706d1046cdb9e3087e](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/38.tar) | +|*CCH2OH |2.1G |[7bcae43cee451306e34ec416588a7f09](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/38.tar) | +|*CHOCHOH |2.0G |[f98866d08fe3451ae7ebc47bb51599aa](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/40.tar) | +|*COCH2OH |1.4G |[bfaf689e5827fcf26c51e567bb8dd1be](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/41.tar) | +|*COHCHOH |2.0G |[236fe4e950aa2fbdde94ef2821fb48d2](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/42.tar) | +|*OCHCH3 |2.1G |[66acc5460a999625c3364f0f3bcca871](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/44.tar) | +|*COHCH3 |2.1G |[bb4a01956736399c8cee5e219f8c1229](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/45.tar) | +|*CHOHCH2 |2.1G |[e836de4ec146b1b611533f1ef682cace](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/46.tar) | +|*CHCH2OH |2.0G |[66df44121806debef6dc038df7115d1d](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/47.tar) | +|*OCH2CHOH |2.2G |[ff6981fdbcd2e65d351505c15d218d76](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/48.tar) | +|*CHOCH2OH |2.1G |[448f7d352ab6e32f754e24de64ca302a](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/49.tar) | +|*COHCH2OH |2.1G |[8bff6bf3e10cc84acc4a283a375fcc23](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/50.tar) | +|*CHOHCHOH |2.0G |[9c9e4d617d306751760a80f1453e71f1](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/51.tar) | +|*CH2CH3 |2.0G |[ec1e964d2ee6f468fa5773743e3994a4](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/52.tar) | +|*OCH2CH3 |2.1G |[d297b27b02822f9b6af80bdb64aee819](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/53.tar) | +|*CHOHCH3 |2.1G |[368de083dafdc3bbdb560d35e2a102c0](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/54.tar) | +|*CH2CH2OH |2.1G |[3c1aaf790659f7ff89bf1eed8b396b63](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/55.tar) | +|*CHOHCH2OH |2.2G |[2d71adb9e305e6f3bca49e5df9b5a86a](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/56.tar) | +|*OHCH2CH3 |2.3G |[cf51128f8522b7b66fc68d79980d6def](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/57.tar) | +|*NH2N(CH3)2 |1.6G |[36ba974d80c20ff636431f7c0ad225da](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/58.tar) | +|*ONN(CH3)2 |2.3G |[fdc4cd19977496909d61be4aee61c4f1](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/59.tar) | +|*OHNNCH3 |2.1G |[50a6ff098f9ba7adbba9ac115726cc5a](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/60.tar) | +|*ONH |1.8G |[47573199c545afe46c554ff756c3e38f](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/62.tar) | +|*NHNH |1.7G |[dd456b7e19ef592d9f0308d911b91d7c](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/63.tar) | +|*N*NH |1.6G |[c05289fd56d64c74306ebf57f1061318](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/65.tar) | +|*NO2NO2 |2.1G |[4822a06f6c5f41bdefd3cbbd8856c11f](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/67.tar) | +|*N*NO |1.6G |[2a27de122d32917cc5b6ac0a21c63c1c](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/68.tar) | +|*N2 |1.5G |[cc668fecf679b6edaac8fd8fb9cdd404](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/69.tar) | +|*ONNH2 |2.1G |[dff880f1a5baa7f67b52fd3ed745443d](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/70.tar) | +|*NH2 |1.6G |[c7f383b50faa6244e265c9611466cb8f](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/71.tar) | +|*NH3 |1.9G |[2b355741f9300445703270e0e4b8c01c](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/72.tar) | +|*NONH |1.8G |[48877a0c6f2994baac82cb722711aaa2](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/73.tar) | +|*NH |1.4G |[7979b9e7ab557d6979b33e352486f0ef](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/74.tar) | +|*NO2 |1.7G |[9f352fbc32bb2b8caf4788aba28b2eb7](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/75.tar) | +|*NO |1.4G |[482ee306a5ae2eee78cac40d10059ebc](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/76.tar) | +|*N |1.1G |[bfb6e03d4a687987ff68976f0793cc46](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/77.tar) | +|*NO3 |1.8G |[700834326e789a6e38bf3922d9fcb792](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/78.tar) | +|*OHNH2 |2.1G |[fa24472e0c02c34d91f3ffe6b77bfb11](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/79.tar) | +|*ONOH |1.4G |[4ddcccd62a834a76fe6167461f512529](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/80.tar) | +|*CN |1.5G |[bc7c55330ece006d09496a5ff01d5d50](https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/81.tar) | Note - A few adsorbates are intentionally left out for the test splits. diff --git a/_sources/tutorials/NRR/NRR_example.md b/_sources/tutorials/NRR/NRR_example.md index d99f599f9..3a07ae2c8 100644 --- a/_sources/tutorials/NRR/NRR_example.md +++ b/_sources/tutorials/NRR/NRR_example.md @@ -121,7 +121,7 @@ You need to provide the calculator with a path to a model checkpoint file. That Running the model with BFGS prints at each relaxation step is a lot to print. So we will just run one to demonstrate what happens on each iteration. ```{code-cell} ipython3 -from ocpmodels.common.model_registry import model_name_to_local_file +from ocpmodels.models.model_registry import model_name_to_local_file checkpoint_path = model_name_to_local_file('eSCN-L6-M3-Lay20All+MD', local_cache='/tmp/ocp_checkpoints/') diff --git a/_sources/tutorials/OCP-introduction.md b/_sources/tutorials/OCP-introduction.md index 655ade029..4420ffefa 100644 --- a/_sources/tutorials/OCP-introduction.md +++ b/_sources/tutorials/OCP-introduction.md @@ -58,7 +58,7 @@ The first step is getting a checkpoint for the model we want to use. eSCN is cur The different models have different compute requirements. If you find your kernel is crashing, it probably means you have exceeded the allowed amount of memory. This checkpoint works fine in this example, but it may crash your kernel if you use it in the NRR example. ```{code-cell} -from ocpmodels.common.model_registry import model_name_to_local_file +from ocpmodels.models.model_registry import model_name_to_local_file checkpoint_path = model_name_to_local_file('eSCN-L6-M3-Lay20All+MD', local_cache='/tmp/ocp_checkpoints/') ``` diff --git a/_sources/tutorials/advanced/mass-inference.md b/_sources/tutorials/advanced/mass-inference.md index 61c157dc2..110b74ed1 100644 --- a/_sources/tutorials/advanced/mass-inference.md +++ b/_sources/tutorials/advanced/mass-inference.md @@ -33,13 +33,13 @@ You can retrieve the dataset below. In this notebook we learn how to do "mass in You have to choose a checkpoint to start with. The newer checkpoints may require too much memory for this environment. ```{code-cell} ipython3 -from ocpmodels.common.model_registry import MODEL_REGISTRY -print(MODEL_REGISTRY.keys()) +from ocpmodels.models.model_registry import available_pretrained_models +print(available_pretrained_models) ``` ```{code-cell} ipython3 -from ocpmodels.common.model_registry import model_name_to_local_file +from ocpmodels.models.model_registry import model_name_to_local_file checkpoint_path = model_name_to_local_file('GemNet-dT OC22', local_cache='/tmp/ocp_checkpoints/') checkpoint_path diff --git a/_sources/tutorials/fine-tuning/fine-tuning-oxides.md b/_sources/tutorials/fine-tuning/fine-tuning-oxides.md index 7710afbc3..73ccbc02e 100644 --- a/_sources/tutorials/fine-tuning/fine-tuning-oxides.md +++ b/_sources/tutorials/fine-tuning/fine-tuning-oxides.md @@ -27,7 +27,7 @@ First we get the checkpoint that we want. According to the [MODELS](../../core/M We get this checkpoint here. ```{code-cell} ipython3 -from ocpmodels.common.model_registry import model_name_to_local_file +from ocpmodels.models.model_registry import model_name_to_local_file checkpoint_path = model_name_to_local_file('GemNet-OC OC20+OC22', local_cache='/tmp/ocp_checkpoints/') ``` diff --git a/_sources/tutorials/intro.md b/_sources/tutorials/intro.md index 25906ed1c..31d301303 100644 --- a/_sources/tutorials/intro.md +++ b/_sources/tutorials/intro.md @@ -14,7 +14,7 @@ kernelspec: Intro and background on OCP and DFT ---------- -# Abstract +## Abstract The most recent, state of the art machine learned potentials in atomistic simulations are based on graph models that are trained on large (1M+) datasets. These models can be downloaded and used in a wide array of applications ranging from catalysis to materials properties. These pre-trained models can be used on their own, to accelerate DFT calculation, and they can also be used as a starting point to fine-tune new models for specific tasks. In this workshop we will focus on large, graph-based, pre-trained machine learned models from the Open Catalyst Project (OCP) to showcase how they can be used for these purposes. OCP provides several pre-trained models for a variety of tasks related to atomistic simulations. We will explain what these models are, how they differ, and details of the datasets they are trained from. We will introduce an Atomic Simulation Environment (ase) calculator that leverages an OCP pre-trained model for typical simulation tasks including adsorbate geometry relaxation, adsorption energy calculations, and reaction energies. We will show how pre-trained models can be fine-tuned on new data sets for new tasks. We will also discuss current limitations of the models and opportunities for future research. Participants will need a laptop with internet capability. @@ -24,7 +24,7 @@ The most recent, state of the art machine learned potentials in atomistic simula +++ -# Introduction +## Introduction Density functional theory (DFT) has been a mainstay in molecular simulation, but its high computational cost limits the number and size of simulations that are practical. Over the past two decades machine learning has increasingly been used to build surrogate models to supplement DFT. We call these models machine learned potentials (MLP) In the early days, neural networks were trained using the cartesian coordinates of atomistic systems as features with some success. These features lack important physical properties, notably they lack invariance to rotations, translations and permutations, and they are extensive features, which limit them to the specific system being investigated. About 15 years ago, a new set of features called symmetry functions were developed that were intensive, and which had these invariances. These functions enabled substantial progress in MLP, but they had a few important limitations. First, the size of the feature vector scaled quadratically with the number of elements, practically limiting the MLP to 4-5 elements. Second, composition was usually implicit in the functions, which limited the transferrability of the MLP to new systems. Finally, these functions were "hand-crafted", with limited or no adaptability to the systems being explored, thus one needed to use judgement and experience to select them. While progess has been made in mitigating these limitations, a new approach has overtaken these methods. @@ -40,45 +40,45 @@ The [Open Catalyst Project (OCP)](https://github.com/Open-Catalyst-Project) is a +++ -## Models +### Models OCP provides several [models](../core/MODELS). Each model represents a different approach to featurization, and a different machine learning architecture. The models can be used for different tasks, and you will find different checkpoints associated with different datasets and tasks. +++ -## Datasets / Tasks +### Datasets / Tasks OCP provides several different datasets like [OC20](../core/datasets/oc20) that correspond to different tasks that range from predicting energy and forces from structures to Bader charges, relaxation energies, and others. +++ -## Checkpoints +### Checkpoints To use a pre-trained model you need to have [ocp](https://github.com/Open-Catalyst-Project/ocp) installed. Then you need to choose a checkpoint and config file which will be loaded to configure OCP for the predictions you want to make. There are two approaches to running OCP, via scripts in a shell, or using an ASE compatible calculator. We will focus on the ASE compatible calculator here. To facilitate using the checkpoints, there is a set of [utilities](./ocp-tutorial) for this tutorial. You can list the checkpoints that are readily available here: ```{code-cell} ipython3 -from ocpmodels.common.model_registry import MODEL_REGISTRY -print(MODEL_REGISTRY.keys()) +from ocpmodels.models.model_registry import available_pretrained_models +print(available_pretrained_models) ``` You can get a checkpoint file with one of the keys listed above like this. The resulting string is the name of the file downloaded, and you use that when creating an OCP calculator later. ```{code-cell} ipython3 -from ocpmodels.common.model_registry import model_name_to_local_file +from ocpmodels.models.model_registry import model_name_to_local_file checkpoint_path = model_name_to_local_file('GemNet-OC OC20+OC22', local_cache='/tmp/ocp_checkpoints/') checkpoint_path ``` -# Goals for this tutorial +## Goals for this tutorial This tutorial will start by using OCP in a Jupyter notebook to setup some simple calculations that use OCP to compute energy and forces, for structure optimization, and then an example of fine-tuning a model with new data. +++ -# About the compute environment +## About the compute environment [ocp-tutorial.ipynb](./ocp_tutorial_helper.py) provides `describe_ocp` to output information that might be helpful in debugging. diff --git a/autoapi/index.html b/autoapi/index.html index 16391ad28..ed797e430 100644 --- a/autoapi/index.html +++ b/autoapi/index.html @@ -177,9 +177,10 @@ -

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    Installation & License

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    Contents

    @@ -674,10 +685,54 @@

    Submodulesocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • +
    +

    Package Contents#

    +
    +

    Functions#

    + + + + + + +

    model_name_to_local_file(→ str)

    Download a pretrained checkpoint if it does not exist already

    +
    +
    +

    Attributes#

    + + + + + + +

    available_pretrained_models

    +
    +
    +ocpmodels.models.available_pretrained_models#
    +
    + +
    +
    +ocpmodels.models.model_name_to_local_file(model_name: str, local_cache: str | pathlib.Path) str#
    +

    Download a pretrained checkpoint if it does not exist already

    +
    +
    Parameters:
    +
      +
    • model_name (str) – the model name. See available_pretrained_checkpoints.

    • +
    • local_cache (str) –

    • +
    +
    +
    +

    Returns:

    +
    + +
    +
    - + - - + + @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
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  • @@ -283,20 +285,19 @@ diff --git a/autoapi/ocpmodels/models/schnet/index.html b/autoapi/ocpmodels/models/schnet/index.html index 64c4c07cd..ca5bdbbbf 100644 --- a/autoapi/ocpmodels/models/schnet/index.html +++ b/autoapi/ocpmodels/models/schnet/index.html @@ -64,7 +64,7 @@ - + @@ -179,9 +179,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -212,6 +213,7 @@ +
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  • ocpmodels.common.gp_utils
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  • ocpmodels.models.utils
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  • @@ -695,12 +697,12 @@

    Classes#<

    previous

    -

    ocpmodels.models.dimenet_plus_plus

    +

    ocpmodels.models.model_registry

    -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

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  • @@ -291,7 +293,6 @@
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  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
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  • ocpmodels.common.tutorial_utils
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  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
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  • ocpmodels.models.schnet
  • diff --git a/autoapi/ocpmodels/trainers/base_trainer/index.html b/autoapi/ocpmodels/trainers/base_trainer/index.html index aa0786a7f..a48979e68 100644 --- a/autoapi/ocpmodels/trainers/base_trainer/index.html +++ b/autoapi/ocpmodels/trainers/base_trainer/index.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
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  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
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  • ocpmodels.models.schnet
  • diff --git a/autoapi/ocpmodels/trainers/index.html b/autoapi/ocpmodels/trainers/index.html index 8b2b94dfe..f190f9a7a 100644 --- a/autoapi/ocpmodels/trainers/index.html +++ b/autoapi/ocpmodels/trainers/index.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
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  • diff --git a/autoapi/ocpmodels/trainers/ocp_trainer/index.html b/autoapi/ocpmodels/trainers/ocp_trainer/index.html index 9f925165b..d81bc3584 100644 --- a/autoapi/ocpmodels/trainers/ocp_trainer/index.html +++ b/autoapi/ocpmodels/trainers/ocp_trainer/index.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
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  • @@ -320,6 +321,7 @@
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  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
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  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • diff --git a/core/FAQ.html b/core/FAQ.html index ffa1eea3c..a9f2d4430 100644 --- a/core/FAQ.html +++ b/core/FAQ.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

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  • Simple simulations using the OCP ASE calculator
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  • ocpmodels.models.schnet
  • diff --git a/core/INSTALL.html b/core/INSTALL.html index e142d3508..964a0b04b 100644 --- a/core/INSTALL.html +++ b/core/INSTALL.html @@ -61,7 +61,7 @@ - + @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
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  • ocpmodels.common.gp_utils
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  • ocpmodels.common.logger
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  • @@ -549,8 +551,12 @@

    Contents

    @@ -562,8 +568,26 @@

    Contents

    -
    +

    Installation#

    +
    +

    pip (fast, easy to get started)#

    +

    Installing the OCP package and necessary dependencies is now as easy as:

    +

    (GPU)

    +
    pip install torch==1.13.1+cu117 torchvision==0.14.1+cu117 torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu117
    +pip install pyg_lib torch_scatter torch_sparse -f https://data.pyg.org/whl/torch-1.13.1+cu117.html
    +pip install -i https://test.pypi.org/simple/ ocp-models
    +
    +
    +

    or if you want the CPU-only install (no cuda/etc):

    +
    pip install torch==1.13.1 torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu # install CPU torch
    +pip install pyg_lib torch_scatter torch_sparse -f https://data.pyg.org/whl/torch-1.13.1+cpu.html
    +pip install -i https://test.pypi.org/simple/ ocp-models
    +
    +
    +
    +
    +

    Conda (preferred for model training & development)#

    @@ -603,12 +605,12 @@

    License#<

    previous

    -

    Installation

    +

    Quickstart simulation using pre-trained models

    -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -212,6 +213,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -293,7 +295,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
  • ocpmodels.common.model_registry
  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -322,6 +323,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • diff --git a/core/QUICKSTART.html b/core/QUICKSTART.html new file mode 100644 index 000000000..9eaa9f94c --- /dev/null +++ b/core/QUICKSTART.html @@ -0,0 +1,719 @@ + + + + + + + + + + + Quickstart simulation using pre-trained models — Open Catalyst Project Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    +
    +
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    +
    + + + + +
    +
    + + + +
    + + + + + + + + + + + + + +
    + +
    + + + +
    + +
    +
    + +
    +
    + +
    + +
    + +
    + + +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + +
    + +
    +
    + + + +
    +

    Quickstart simulation using pre-trained models

    + +
    +
    + +
    +
    +
    + + + + +
    + +
    +

    Quickstart simulation using pre-trained models#

    +
      +
    1. First, install OCP in a fresh python environment using one of the approaches in installation documentation.

    2. +
    3. See what pre-trained potentials are available

    4. +
    +
    +
    +
    from ocpmodels.models.model_registry import available_pretrained_models
    +print(available_pretrained_models)
    +
    +
    +
    +
    +
      +
    1. Choose a checkpoint you want to use and download it automatically! We’ll use the GemNet-OC potential, trained on both the OC20 and OC22 datasets.

    2. +
    +
    +
    +
    from ocpmodels.models.model_registry import model_name_to_local_file
    +checkpoint_path = model_name_to_local_file('GemNet-OC OC20+OC22', local_cache='/tmp/ocp_checkpoints/')
    +checkpoint_path
    +
    +
    +
    +
    +
      +
    1. Finally, use this checkpoint in an ASE calculator for a simple relaxation!

    2. +
    +
    from ocpmodels.common.relaxation.ase_utils import OCPCalculator
    +from ase.build import fcc111, add_adsorbate
    +from ase.optimize import BFGS
    +import matplotlib.pyplot as plt
    +from ase.visualize.plot import plot_atoms
    +
    +# Define the model atomic system, a Pt(111) slab with an *O adsorbate!
    +slab = fcc111('Pt', size=(2, 2, 5), vacuum=10.0)
    +add_adsorbate(slab, 'O', height=1.2, position='fcc')
    +
    +# Load the pre-trained checkpoint!
    +calc = OCPCalculator(checkpoint_path=checkpoint_path, cpu=False)
    +slab.set_calculator(calc)
    +
    +# Run the optimization!
    +opt = BFGS(slab)
    +opt.run(fmax=0.05, steps=100)
    +
    +# Visualize the result!
    +fig, axs = plt.subplots(1, 2)
    +plot_atoms(slab, axs[0]);
    +plot_atoms(slab, axs[1], rotation=('-90x'))
    +axs[0].set_axis_off()
    +axs[1].set_axis_off()
    +
    +
    +
    + + + + +
    + + + + + + + + +
    + + + +
    + + +
    +
    + + +
    + + +
    +
    +
    + + + + + +
    +
    + + \ No newline at end of file diff --git a/core/TRAIN.html b/core/TRAIN.html index a2c0edf0d..fb86de7d3 100644 --- a/core/TRAIN.html +++ b/core/TRAIN.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
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  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • diff --git a/core/datasets/oc20.html b/core/datasets/oc20.html index 776342ed7..02de9e94c 100644 --- a/core/datasets/oc20.html +++ b/core/datasets/oc20.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
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  • ocpmodels.common.registry
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  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • @@ -1027,390 +1029,313 @@

    Citing OC20

    Per-adsorbate trajectories#

    -

    Download links are in the table below:

    - - - + + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - + - - +

    Adsorbate symbol

    Downloadable path

    size

    MD5 checksum

    Size

    MD5 checksum (download link)

    *O

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/0.tar

    1006M

    d4151542856b4b6405f276808f75358a

    d4151542856b4b6405f276808f75358a

    *H

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/1.tar

    850M

    3697f04faf04251a23da8b88a78209f7

    3697f04faf04251a23da8b88a78209f7

    *OH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/2.tar

    1.6G

    a21081f3f55eb0c98a91021bbe3dac44

    a21081f3f55eb0c98a91021bbe3dac44

    *OH2

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/3.tar

    1.8G

    b12b706854f5d899e02a9ae6578b5d45

    b12b706854f5d899e02a9ae6578b5d45

    *C

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/4.tar

    1.1G

    e4fe9890764fcf59e01e3ceab089b978

    e4fe9890764fcf59e01e3ceab089b978

    *CH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/6.tar

    1.4G

    ec9aa2c4c4bd4419359438ba7fbb881d

    ec9aa2c4c4bd4419359438ba7fbb881d

    *CHO

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/7.tar

    1.4G

    d32200f74ad5c3bfd42e8835f36d57ab

    d32200f74ad5c3bfd42e8835f36d57ab

    *COH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/8.tar

    1.6G

    5418a1b331f6c7689a5405cca4cc8d15

    5418a1b331f6c7689a5405cca4cc8d15

    *CH2

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/9.tar

    1.6G

    8ee1066149c305d7c17c219b369c5a73

    8ee1066149c305d7c17c219b369c5a73

    CH2O

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/10.tar

    1.7G

    960c2450814024b66f3c79121179ac60

    960c2450814024b66f3c79121179ac60

    *CHOH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/11.tar

    1.8G

    60ac9f965f9589a3389483e3d1e58144

    60ac9f965f9589a3389483e3d1e58144

    *CH3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/12.tar

    1.7G

    7e123e6f4fb10d6897be3f47721dfd4a

    7e123e6f4fb10d6897be3f47721dfd4a

    *OCH3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/13.tar

    1.8G

    0823047bbbe05fa0e63f9d83ec601487

    0823047bbbe05fa0e63f9d83ec601487

    *CH2OH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/14.tar

    1.9G

    9ac71e198d75b1427182cd34abb73e4d

    9ac71e198d75b1427182cd34abb73e4d

    *CH4

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/15.tar

    1.9G

    a405ce403018bf8afbd4425d5c0b34d5

    a405ce403018bf8afbd4425d5c0b34d5

    *OHCH3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/16.tar

    2.1G

    d3c829f1952db6e4f428273ee05f59b1

    d3c829f1952db6e4f428273ee05f59b1

    CC

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/17.tar

    1.5G

    d687a151345305897b9245af4b0f9967

    d687a151345305897b9245af4b0f9967

    *CCO

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/18.tar

    1.7G

    214ca96e620c5ec6e8a6ff8144a22a04

    214ca96e620c5ec6e8a6ff8144a22a04

    *CCH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/19.tar

    1.6G

    da2268545e80ca1664026449dd2fdd24

    da2268545e80ca1664026449dd2fdd24

    *CHCO

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/20.tar

    1.7G

    386c99407fe63080d26cda525dfdd8cd

    386c99407fe63080d26cda525dfdd8cd

    *CCHO

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/21.tar

    1.8G

    918b20960438494ab160a9dbd9668157

    918b20960438494ab160a9dbd9668157

    *COCHO

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/22.tar

    1.8G

    84424aa2ad30301e23ece1438ea39923

    84424aa2ad30301e23ece1438ea39923

    *CCHOH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/23.tar

    2.0G

    3cc90425ec042a70085ba7eb2916a79a

    3cc90425ec042a70085ba7eb2916a79a

    *CCH2

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/24.tar

    1.8G

    9dbcf7566e40965dd7f8a186a75a718e

    9dbcf7566e40965dd7f8a186a75a718e

    CHCH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/25.tar

    1.7G

    a193b4c72f915ba0b21a41790696b23c

    a193b4c72f915ba0b21a41790696b23c

    CH2*CO

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/26.tar

    1.8G

    de83cf50247f5556fa4f9f64beff1eeb

    de83cf50247f5556fa4f9f64beff1eeb

    *CHCHO

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/27.tar

    1.9G

    1d140aaa2e7b287124ab38911a711d70

    1d140aaa2e7b287124ab38911a711d70

    CHCOH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/28.tar

    1.3G

    682d8a6b05ca5948b34dc5e5f6bbcd61

    682d8a6b05ca5948b34dc5e5f6bbcd61

    *COCH2O

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/29.tar

    1.9G

    c8742faa8ca40e8edb4110069817fa70

    c8742faa8ca40e8edb4110069817fa70

    CHOCHO

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/30.tar

    2.0G

    8cfbb67beb312b98c40fcb891dfa480a

    8cfbb67beb312b98c40fcb891dfa480a

    *COHCHO

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/31.tar

    1.9G

    6ffa903a62d8ec3319ecec6a03b06276

    6ffa903a62d8ec3319ecec6a03b06276

    *COHCOH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/32.tar

    2.0G

    caca0058b641bfdc9f8de4527e60feb7

    caca0058b641bfdc9f8de4527e60feb7

    *CCH3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/33.tar

    1.8G

    906543aaefc171edab388ff4f0fe8a20

    906543aaefc171edab388ff4f0fe8a20

    *CHCH2

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/34.tar

    1.8G

    4dfab479495f76179749c1956046fbd8

    4dfab479495f76179749c1956046fbd8

    *COCH3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/35.tar

    1.9G

    29d1b992715054e920e8bb2afe97b393

    29d1b992715054e920e8bb2afe97b393

    *CHCHOH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/38.tar

    2.0G

    9e5912df6f7b11706d1046cdb9e3087e

    9e5912df6f7b11706d1046cdb9e3087e

    *CCH2OH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/39.tar

    2.1G

    7bcae43cee451306e34ec416588a7f09

    7bcae43cee451306e34ec416588a7f09

    *CHOCHOH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/40.tar

    2.0G

    f98866d08fe3451ae7ebc47bb51599aa

    f98866d08fe3451ae7ebc47bb51599aa

    *COCH2OH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/41.tar

    1.4G

    bfaf689e5827fcf26c51e567bb8dd1be

    bfaf689e5827fcf26c51e567bb8dd1be

    *COHCHOH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/42.tar

    2.0G

    236fe4e950aa2fbdde94ef2821fb48d2

    236fe4e950aa2fbdde94ef2821fb48d2

    *OCHCH3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/44.tar

    2.1G

    66acc5460a999625c3364f0f3bcca871

    66acc5460a999625c3364f0f3bcca871

    *COHCH3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/45.tar

    2.1G

    bb4a01956736399c8cee5e219f8c1229

    bb4a01956736399c8cee5e219f8c1229

    *CHOHCH2

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/46.tar

    2.1G

    e836de4ec146b1b611533f1ef682cace

    e836de4ec146b1b611533f1ef682cace

    *CHCH2OH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/47.tar

    2.0G

    66df44121806debef6dc038df7115d1d

    66df44121806debef6dc038df7115d1d

    *OCH2CHOH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/48.tar

    2.2G

    ff6981fdbcd2e65d351505c15d218d76

    ff6981fdbcd2e65d351505c15d218d76

    *CHOCH2OH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/49.tar

    2.1G

    448f7d352ab6e32f754e24de64ca302a

    448f7d352ab6e32f754e24de64ca302a

    *COHCH2OH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/50.tar

    2.1G

    8bff6bf3e10cc84acc4a283a375fcc23

    8bff6bf3e10cc84acc4a283a375fcc23

    *CHOHCHOH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/51.tar

    2.0G

    9c9e4d617d306751760a80f1453e71f1

    9c9e4d617d306751760a80f1453e71f1

    *CH2CH3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/52.tar

    2.0G

    ec1e964d2ee6f468fa5773743e3994a4

    ec1e964d2ee6f468fa5773743e3994a4

    *OCH2CH3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/53.tar

    2.1G

    d297b27b02822f9b6af80bdb64aee819

    d297b27b02822f9b6af80bdb64aee819

    *CHOHCH3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/54.tar

    2.1G

    368de083dafdc3bbdb560d35e2a102c0

    368de083dafdc3bbdb560d35e2a102c0

    *CH2CH2OH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/55.tar

    2.1G

    3c1aaf790659f7ff89bf1eed8b396b63

    3c1aaf790659f7ff89bf1eed8b396b63

    *CHOHCH2OH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/56.tar

    2.2G

    2d71adb9e305e6f3bca49e5df9b5a86a

    2d71adb9e305e6f3bca49e5df9b5a86a

    *OHCH2CH3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/57.tar

    2.3G

    cf51128f8522b7b66fc68d79980d6def

    cf51128f8522b7b66fc68d79980d6def

    *NH2N(CH3)2

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/58.tar

    1.6G

    36ba974d80c20ff636431f7c0ad225da

    36ba974d80c20ff636431f7c0ad225da

    *ONN(CH3)2

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/59.tar

    2.3G

    fdc4cd19977496909d61be4aee61c4f1

    fdc4cd19977496909d61be4aee61c4f1

    *OHNNCH3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/60.tar

    2.1G

    50a6ff098f9ba7adbba9ac115726cc5a

    50a6ff098f9ba7adbba9ac115726cc5a

    *ONH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/62.tar

    1.8G

    47573199c545afe46c554ff756c3e38f

    47573199c545afe46c554ff756c3e38f

    *NHNH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/63.tar

    1.7G

    dd456b7e19ef592d9f0308d911b91d7c

    dd456b7e19ef592d9f0308d911b91d7c

    NNH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/65.tar

    1.6G

    c05289fd56d64c74306ebf57f1061318

    c05289fd56d64c74306ebf57f1061318

    *NO2NO2

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/67.tar

    2.1G

    4822a06f6c5f41bdefd3cbbd8856c11f

    4822a06f6c5f41bdefd3cbbd8856c11f

    NNO

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/68.tar

    1.6G

    2a27de122d32917cc5b6ac0a21c63c1c

    2a27de122d32917cc5b6ac0a21c63c1c

    *N2

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/69.tar

    1.5G

    cc668fecf679b6edaac8fd8fb9cdd404

    cc668fecf679b6edaac8fd8fb9cdd404

    *ONNH2

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/70.tar

    2.1G

    dff880f1a5baa7f67b52fd3ed745443d

    dff880f1a5baa7f67b52fd3ed745443d

    *NH2

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/71.tar

    1.6G

    c7f383b50faa6244e265c9611466cb8f

    c7f383b50faa6244e265c9611466cb8f

    *NH3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/72.tar

    1.9G

    2b355741f9300445703270e0e4b8c01c

    2b355741f9300445703270e0e4b8c01c

    *NONH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/73.tar

    1.8G

    48877a0c6f2994baac82cb722711aaa2

    48877a0c6f2994baac82cb722711aaa2

    *NH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/74.tar

    1.4G

    7979b9e7ab557d6979b33e352486f0ef

    7979b9e7ab557d6979b33e352486f0ef

    *NO2

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/75.tar

    1.7G

    9f352fbc32bb2b8caf4788aba28b2eb7

    9f352fbc32bb2b8caf4788aba28b2eb7

    *NO

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/76.tar

    1.4G

    482ee306a5ae2eee78cac40d10059ebc

    482ee306a5ae2eee78cac40d10059ebc

    *N

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/77.tar

    1.1G

    bfb6e03d4a687987ff68976f0793cc46

    bfb6e03d4a687987ff68976f0793cc46

    *NO3

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/78.tar

    1.8G

    700834326e789a6e38bf3922d9fcb792

    700834326e789a6e38bf3922d9fcb792

    *OHNH2

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/79.tar

    2.1G

    fa24472e0c02c34d91f3ffe6b77bfb11

    fa24472e0c02c34d91f3ffe6b77bfb11

    *ONOH

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/80.tar

    1.4G

    4ddcccd62a834a76fe6167461f512529

    4ddcccd62a834a76fe6167461f512529

    *CN

    https://dl.fbaipublicfiles.com/opencatalystproject/data/per_adsorbate_is2res/81.tar

    1.5G

    bc7c55330ece006d09496a5ff01d5d50

    bc7c55330ece006d09496a5ff01d5d50

    diff --git a/core/datasets/oc22.html b/core/datasets/oc22.html index a5f0f3ef9..468dcc365 100644 --- a/core/datasets/oc22.html +++ b/core/datasets/oc22.html @@ -177,9 +177,10 @@ -

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  • @@ -913,10 +915,10 @@

    A

  • (class in ocpmodels.datasets.ase_datasets)
  • - - + @@ -2219,9 +2227,13 @@

    M

  • ml_relax() (in module ocpmodels.common.relaxation.ml_relaxation)
  • -
  • model_name_to_local_file() (in module ocpmodels.common.model_registry) +
  • model_name_to_local_file() (in module ocpmodels.models) + +
  • +
  • MODEL_REGISTRY (in module ocpmodels.models.model_registry)
  • module @@ -2242,8 +2254,6 @@

    M

  • ocpmodels.common.hpo_utils
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  • @@ -2418,6 +2428,8 @@

    M

  • ocpmodels.models.gemnet_oc.layers.spherical_basis
  • ocpmodels.models.gemnet_oc.utils +
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  • ocpmodels.models.painn
  • @@ -2630,13 +2642,6 @@

    O

    -
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    O

  • module
  • - -
    • ocpmodels.models.gemnet.layers.interaction_block @@ -3033,6 +3036,8 @@

      O

    • module
    + +
    • ocpmodels.models.gemnet.layers.radial_basis @@ -3248,6 +3253,13 @@

      O

    • +
    • + ocpmodels.models.model_registry + +
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  • diff --git a/legacy_tutorials/OCP_Tutorial.html b/legacy_tutorials/OCP_Tutorial.html index c0aeab55c..2cf4628eb 100644 --- a/legacy_tutorials/OCP_Tutorial.html +++ b/legacy_tutorials/OCP_Tutorial.html @@ -179,9 +179,10 @@ -

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  • ocpmodels.models.schnet
  • diff --git a/objects.inv b/objects.inv index cb55e26d29a91cf27572a8c0be6e54685469f360..21c859ce67c4cb6c6ebef97f043bdceef00d34a1 100644 GIT binary patch delta 11961 zcmV;qE=JL|U722xc|JI@=3T!+W;2I*hho)J-ukALlv&xWtt3^IwT+Fz5F`}A7PkUO zNm0Lku#iDAf(v%?9a0&=fcy8su{l5ok+&s(mq_)~|33fe?C^U4z&pYu&NBd*rU;hs z{J*F5^c948n&#OI3z2A+j7SzR5}<$>CJ9R9H1|ZbaDuNefmw*6udobv&oC_#gc*34 zKtcv>GKZ}RO3NfJ5f%lKqH>o@ zu#D@f?v&HR)#Fv3B(U^Q0XtZ<;6wV*N69~z6!5i5u47W-cvF=q^3~$Tp*^;{2@(s} zJ@6|ecc_GXAaGq4U9cdnKhU4c9fK}#ULaiVU7>I4rq7;~abw=sDhv5%d#JRKt1_M) zsvG4^a_M2L5eQi8-BRm`W+au9AutJl6pW%OL@rS_n2rM>B&AD`FhMY@3YQRD+MY4Y z-dtmR z+XuvvT*=r(e$BB<;O~66|AzC_pP45yott_Z-Lbi!xZmT~+>@Bj%{`6o*xb({EU6dZ zvk#eqbZ+cPaL2X=*OxDs;PLW*>GJmW<`#T^diecOX2j7z`u=qJ_^Tf%wds&H0QiW@ z9Uc9nD9*MH(bVQ$8UUn7;?lK#P@;_F4ojt;*MV)}5Q7f+pv(dP`LG&5OK7XGlAsP7 z#qV*1_~KBwL*X09a*CNkrof>^X@OPLf2Qc}FzTlCO2-=CR%O0>MC%KG&a1*Xipp|; zHi-IqfF9J=i`BM1thV)IHH|eCbr3ofIqzk~V6;ekCBji!p#SAdI8Fza633~lvfCB8 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What should I do?": [[128, "i-m-trying-to-run-gemnet-oc-gemnet-dt-but-it-throws-an-error-that-scaling-factors-are-not-fitted-what-should-i-do"]], "I\u2019m trying to run GemNet-OC on my data, but it errors out on sph_basis = self.spherical_basis(cos\u03c6_cab, \u03b8_cabd).": [[128, "i-m-trying-to-run-gemnet-oc-on-my-data-but-it-errors-out-on-sph-basis-self-spherical-basis-cos-cab-cabd"]], "Installation": [[129, "installation"], [137, "installation"]], "GPU machines": [[129, "gpu-machines"]], "CPU-only machines": [[129, "cpu-only-machines"]], "License": [[130, "license"], [137, "license"]], "Pretrained OCP model checkpoints": [[131, "pretrained-ocp-model-checkpoints"]], "Open Catalyst 2020 (OC20)": [[131, "open-catalyst-2020-oc20"], [133, "open-catalyst-2020-oc20"]], "S2EF models: optimized for EFwT": [[131, "s2ef-models-optimized-for-efwt"]], "S2EF models: optimized for force only": [[131, "s2ef-models-optimized-for-force-only"]], "IS2RE models": [[131, "is2re-models"]], "Open 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"Acknowledgements": [[137, "acknowledgements"]], "Citing ocp": [[137, "citing-ocp"]], "Open Catalyst Project Tutorial Notebook": [[138, "open-catalyst-project-tutorial-notebook"]], "Table of Contents": [[138, "table-of-contents"]], "Background ": [[138, "background"]], "Objective ": [[138, "objective"]], "Climate Impact": [[138, "climate-impact"]], "Target Audience": [[138, "target-audience"]], "Background & Prerequisites": [[138, "background-prerequisites"]], "Background References": [[138, "background-references"]], "Software Requirements": [[138, "software-requirements"]], "Dataset Overview": [[138, "dataset-overview"]], "Tutorial Use": [[138, "tutorial-use"]], "Data Download [~1min] ": [[138, "data-download-1min"]], "Data Visualization ": [[138, "data-visualization"]], "Understanding the data": [[138, "understanding-the-data"], [140, "understanding-the-data"]], "Generating sample data": [[138, "generating-sample-data"], [140, "generating-sample-data"]], "Structural relaxations": 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"Train the Model": [[138, "id5"]], "Validate the Model": [[138, "id6"]], "Test the model": [[138, "test-the-model"]], "Initial Structure to Relaxed Structure (IS2RS) ": [[138, "initial-structure-to-relaxed-structure-is2rs"]], "Steps for making IS2RS predictions": [[138, "steps-for-making-is2rs-predictions"]], "Download pretrained checkpoint": [[138, "download-pretrained-checkpoint"], [138, "id14"]], "Run relaxations": [[138, "run-relaxations"]], "Visualize ML-driven relaxations": [[138, "visualize-ml-driven-relaxations"]], "Model development ": [[138, "model-development"]], "Atom and Edge Embeddings": [[138, "atom-and-edge-embeddings"]], "Message passing": [[138, "message-passing"]], "Training the model": [[138, "training-the-model"]], "Incorporating triplets and training GemNet-T": [[138, "incorporating-triplets-and-training-gemnet-t"]], "(Optional) OCP Calculator ": [[138, "optional-ocp-calculator"]], "Using the OCP Calculator": [[138, "using-the-ocp-calculator"]], "(Optional) Creating your own LMDBs for use in the OCP repository": [[138, "optional-creating-your-own-lmdbs-for-use-in-the-ocp-repository"]], "Initial Structure to Relaxed Energy (IS2RE) LMDBs": [[138, "initial-structure-to-relaxed-energy-is2re-lmdbs"]], "Structure to Energy and Forces (S2EF) LMDBs": [[138, "structure-to-energy-and-forces-s2ef-lmdbs"], [142, "structure-to-energy-and-forces-s2ef-lmdbs"]], "Running on command line [Preferred way to train models] ": [[138, "running-on-command-line-preferred-way-to-train-models"]], "Limitations ": [[138, "limitations"]], "Next Steps ": [[138, "next-steps"]], "References": [[138, "references"]], "OCP Data Preprocessing Tutorial": [[139, "ocp-data-preprocessing-tutorial"]], "Generate toy dataset: Relaxation of CO on Cu": [[139, "generate-toy-dataset-relaxation-of-co-on-cu"], [142, "generate-toy-dataset-relaxation-of-co-on-cu"]], "Convert Atoms object to Data object": [[139, "convert-atoms-object-to-data-object"]], "Adding additional info to your Data objects": [[139, "adding-additional-info-to-your-data-objects"]], "OCP Data Visualization": [[140, "ocp-data-visualization"]], "Saving a trajectory video": [[140, "saving-a-trajectory-video"]], "Data contents": [[140, "data-contents"]], "Energy": [[140, "energy"]], "Forces": [[140, "forces"]], "Resources": [[140, "resources"]], "Legacy [deprecated] Tutorials": [[141, "legacy-deprecated-tutorials"]], "OCP LMDB Dataset Tutorial": [[142, "ocp-lmdb-dataset-tutorial"]], "Initial Structure to Relaxed Energy/Structure (IS2RE/IS2RS) LMDBs": [[142, "initial-structure-to-relaxed-energy-structure-is2re-is2rs-lmdbs"]], "Initialize AtomsToGraph feature extractor": [[142, "initialize-atomstograph-feature-extractor"]], "Initialize LMDB file": [[142, "initialize-lmdb-file"]], "Write data to LMDB": [[142, "write-data-to-lmdb"]], "Advanced usage": [[142, "advanced-usage"]], "Interacting with the LMDBs": [[142, "interacting-with-the-lmdbs"]], "Using OCP to enumerate adsorbates on catalyst surfaces": [[143, "using-ocp-to-enumerate-adsorbates-on-catalyst-surfaces"]], "Introduction": [[143, "introduction"], [144, "introduction"], [154, "introduction"]], "Enumerate the adsorbate-slab configurations to run relaxations on": [[143, "enumerate-the-adsorbate-slab-configurations-to-run-relaxations-on"], [144, "enumerate-the-adsorbate-slab-configurations-to-run-relaxations-on"]], "Work out a single example": [[143, "work-out-a-single-example"], [144, "work-out-a-single-example"]], "Run an ML relaxation": [[143, "run-an-ml-relaxation"], [144, "run-an-ml-relaxation"]], "Run all the systems": [[143, "run-all-the-systems"], [144, "run-all-the-systems"]], "Parse the trajectories and post-process": [[143, "parse-the-trajectories-and-post-process"], [144, "parse-the-trajectories-and-post-process"]], "Make parity plots for values obtained by ML v. reported in the paper": [[143, "make-parity-plots-for-values-obtained-by-ml-v-reported-in-the-paper"], [144, "make-parity-plots-for-values-obtained-by-ml-v-reported-in-the-paper"]], "Make figure 6b and compare to literature results": [[143, "make-figure-6b-and-compare-to-literature-results"], [144, "make-figure-6b-and-compare-to-literature-results"]], "Using OCP to enumerate adsorbates on alloy catalyst surfaces": [[144, "using-ocp-to-enumerate-adsorbates-on-alloy-catalyst-surfaces"]], "Next steps": [[144, "next-steps"], [146, "next-steps"], [152, "next-steps"]], "Screening catalysts with OCP": [[145, "screening-catalysts-with-ocp"]], "Simple simulations using the OCP ASE calculator": [[146, "simple-simulations-using-the-ocp-ase-calculator"]], "Calculating adsorption energies": [[146, "calculating-adsorption-energies"]], "Exercises": [[146, "exercises"], [146, "id1"]], "Trends in adsorption energies across metals.": [[146, "trends-in-adsorption-energies-across-metals"]], "Site correlations": [[146, "site-correlations"]], "Convergence study": [[146, "convergence-study"]], "Effects of number of layers": [[146, "effects-of-number-of-layers"]], "Effects of relaxation": [[146, "effects-of-relaxation"]], "Unit cell size": [[146, "unit-cell-size"]], "Summary": [[146, "summary"]], "Advanced OCP usage": [[147, "advanced-ocp-usage"]], "Working with embeddings": [[148, "working-with-embeddings"]], "A diagnostic example": [[148, "a-diagnostic-example"]], "Bulk Cu equation of state example": [[148, "bulk-cu-equation-of-state-example"]], "A clustering example": [[148, "a-clustering-example"]], "Clustering individual atoms": [[148, "clustering-individual-atoms"]], "A simple vector search example": [[148, "a-simple-vector-search-example"]], "Fine-tuning with Python": [[149, "fine-tuning-with-python"]], "Split the data into train, test, val sets": [[149, "split-the-data-into-train-test-val-sets"]], "Setup the training code": [[149, "setup-the-training-code"]], "Setup the training task": [[149, "setup-the-training-task"]], "Run the training task": [[149, "run-the-training-task"]], "Advanced example: Fine-tuning": [[150, "advanced-example-fine-tuning"]], "Mass inference": [[151, "mass-inference"]], "The ASE calculator way": [[151, "the-ase-calculator-way"]], "Comparing ASE calculator and main.py": [[151, "comparing-ase-calculator-and-main-py"]], "Fine tuning a model": [[152, "fine-tuning-a-model"]], "Fine tuning the checkpoint": [[152, "fine-tuning-the-checkpoint"]], "Make the train, test, val splits": [[152, "make-the-train-test-val-splits"]], "Setting up the configuration yaml file": [[152, "setting-up-the-configuration-yaml-file"]], "Running the training job": [[152, "running-the-training-job"]], "Common gotchas with OCP": [[153, "common-gotchas-with-ocp"]], "OutOfMemoryError": [[153, "outofmemoryerror"]], "I want the energy of a gas phase atom": [[153, "i-want-the-energy-of-a-gas-phase-atom"]], "I get wildly different energies from the different models": [[153, "i-get-wildly-different-energies-from-the-different-models"]], "Miscellaneous warnings": [[153, "miscellaneous-warnings"]], "Unrecognized arguments": [[153, "unrecognized-arguments"]], "Unable to identify OCP trainer": [[153, "unable-to-identify-ocp-trainer"]], "Request entity too large - can\u2019t save your Notebook": [[153, "request-entity-too-large-can-t-save-your-notebook"]], "You need at least four atoms for molecules with some models": [[153, "you-need-at-least-four-atoms-for-molecules-with-some-models"]], "To tag or not?": [[153, "to-tag-or-not"]], "Stochastic simulation results": [[153, "stochastic-simulation-results"]], "The forces don\u2019t sum to zero": [[153, "the-forces-don-t-sum-to-zero"]], "Intro and background on OCP and DFT": [[154, "intro-and-background-on-ocp-and-dft"]], "Abstract": [[154, "abstract"]], "Walkthrough video": [[154, "walkthrough-video"]], "Datasets / Tasks": [[154, "datasets-tasks"]], "Checkpoints": [[154, "checkpoints"]], "Goals for this tutorial": [[154, "goals-for-this-tutorial"]], "About the compute environment": [[154, 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"associated_legendre_polynomials() (in module ocpmodels.models.gemnet_gp.layers.basis_utils)": [[73, "ocpmodels.models.gemnet_gp.layers.basis_utils.associated_legendre_polynomials"]], "bessel_basis() (in module ocpmodels.models.gemnet_gp.layers.basis_utils)": [[73, "ocpmodels.models.gemnet_gp.layers.basis_utils.bessel_basis"]], "ocpmodels.models.gemnet_gp.layers.basis_utils": [[73, "module-ocpmodels.models.gemnet_gp.layers.basis_utils"]], "real_sph_harm() (in module ocpmodels.models.gemnet_gp.layers.basis_utils)": [[73, "ocpmodels.models.gemnet_gp.layers.basis_utils.real_sph_harm"]], "sph_harm_prefactor() (in module ocpmodels.models.gemnet_gp.layers.basis_utils)": [[73, "ocpmodels.models.gemnet_gp.layers.basis_utils.sph_harm_prefactor"]], "spherical_bessel_formulas() (in module ocpmodels.models.gemnet_gp.layers.basis_utils)": [[73, "ocpmodels.models.gemnet_gp.layers.basis_utils.spherical_bessel_formulas"]], "efficientinteractionbilinear (class in ocpmodels.models.gemnet_gp.layers.efficient)": [[74, "ocpmodels.models.gemnet_gp.layers.efficient.EfficientInteractionBilinear"]], "efficientinteractiondownprojection (class in ocpmodels.models.gemnet_gp.layers.efficient)": [[74, "ocpmodels.models.gemnet_gp.layers.efficient.EfficientInteractionDownProjection"]], "forward() (ocpmodels.models.gemnet_gp.layers.efficient.efficientinteractionbilinear method)": [[74, "ocpmodels.models.gemnet_gp.layers.efficient.EfficientInteractionBilinear.forward"]], "forward() (ocpmodels.models.gemnet_gp.layers.efficient.efficientinteractiondownprojection method)": [[74, "ocpmodels.models.gemnet_gp.layers.efficient.EfficientInteractionDownProjection.forward"]], "ocpmodels.models.gemnet_gp.layers.efficient": [[74, "module-ocpmodels.models.gemnet_gp.layers.efficient"]], "reset_parameters() (ocpmodels.models.gemnet_gp.layers.efficient.efficientinteractionbilinear method)": [[74, 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"ocpmodels.models.gemnet_gp.layers.embedding_block": [[75, "module-ocpmodels.models.gemnet_gp.layers.embedding_block"]], "ocpmodels.models.gemnet_gp.layers": [[76, "module-ocpmodels.models.gemnet_gp.layers"]], "interactionblocktripletsonly (class in ocpmodels.models.gemnet_gp.layers.interaction_block)": [[77, "ocpmodels.models.gemnet_gp.layers.interaction_block.InteractionBlockTripletsOnly"]], "tripletinteraction (class in ocpmodels.models.gemnet_gp.layers.interaction_block)": [[77, "ocpmodels.models.gemnet_gp.layers.interaction_block.TripletInteraction"]], "forward() (ocpmodels.models.gemnet_gp.layers.interaction_block.interactionblocktripletsonly method)": [[77, "ocpmodels.models.gemnet_gp.layers.interaction_block.InteractionBlockTripletsOnly.forward"]], "forward() (ocpmodels.models.gemnet_gp.layers.interaction_block.tripletinteraction method)": [[77, "ocpmodels.models.gemnet_gp.layers.interaction_block.TripletInteraction.forward"]], "ocpmodels.models.gemnet_gp.layers.interaction_block": [[77, "module-ocpmodels.models.gemnet_gp.layers.interaction_block"]], "bernsteinbasis (class in ocpmodels.models.gemnet_gp.layers.radial_basis)": [[78, "ocpmodels.models.gemnet_gp.layers.radial_basis.BernsteinBasis"]], "exponentialenvelope (class in ocpmodels.models.gemnet_gp.layers.radial_basis)": [[78, "ocpmodels.models.gemnet_gp.layers.radial_basis.ExponentialEnvelope"]], "polynomialenvelope (class in ocpmodels.models.gemnet_gp.layers.radial_basis)": [[78, "ocpmodels.models.gemnet_gp.layers.radial_basis.PolynomialEnvelope"]], "radialbasis (class in ocpmodels.models.gemnet_gp.layers.radial_basis)": [[78, "ocpmodels.models.gemnet_gp.layers.radial_basis.RadialBasis"]], "sphericalbesselbasis (class in ocpmodels.models.gemnet_gp.layers.radial_basis)": [[78, "ocpmodels.models.gemnet_gp.layers.radial_basis.SphericalBesselBasis"]], "forward() (ocpmodels.models.gemnet_gp.layers.radial_basis.bernsteinbasis method)": [[78, "ocpmodels.models.gemnet_gp.layers.radial_basis.BernsteinBasis.forward"]], "forward() (ocpmodels.models.gemnet_gp.layers.radial_basis.exponentialenvelope method)": [[78, "ocpmodels.models.gemnet_gp.layers.radial_basis.ExponentialEnvelope.forward"]], "forward() (ocpmodels.models.gemnet_gp.layers.radial_basis.polynomialenvelope method)": [[78, "ocpmodels.models.gemnet_gp.layers.radial_basis.PolynomialEnvelope.forward"]], "forward() (ocpmodels.models.gemnet_gp.layers.radial_basis.radialbasis method)": [[78, "ocpmodels.models.gemnet_gp.layers.radial_basis.RadialBasis.forward"]], "forward() (ocpmodels.models.gemnet_gp.layers.radial_basis.sphericalbesselbasis method)": [[78, "ocpmodels.models.gemnet_gp.layers.radial_basis.SphericalBesselBasis.forward"]], "ocpmodels.models.gemnet_gp.layers.radial_basis": [[78, "module-ocpmodels.models.gemnet_gp.layers.radial_basis"]], "circularbasislayer (class in ocpmodels.models.gemnet_gp.layers.spherical_basis)": [[79, "ocpmodels.models.gemnet_gp.layers.spherical_basis.CircularBasisLayer"]], "forward() (ocpmodels.models.gemnet_gp.layers.spherical_basis.circularbasislayer method)": [[79, "ocpmodels.models.gemnet_gp.layers.spherical_basis.CircularBasisLayer.forward"]], "ocpmodels.models.gemnet_gp.layers.spherical_basis": [[79, "module-ocpmodels.models.gemnet_gp.layers.spherical_basis"]], "calculate_interatomic_vectors() (in module ocpmodels.models.gemnet_gp.utils)": [[80, "ocpmodels.models.gemnet_gp.utils.calculate_interatomic_vectors"]], "inner_product_normalized() (in module ocpmodels.models.gemnet_gp.utils)": [[80, "ocpmodels.models.gemnet_gp.utils.inner_product_normalized"]], "mask_neighbors() (in module ocpmodels.models.gemnet_gp.utils)": [[80, "ocpmodels.models.gemnet_gp.utils.mask_neighbors"]], "ocpmodels.models.gemnet_gp.utils": [[80, "module-ocpmodels.models.gemnet_gp.utils"]], "ragged_range() (in module ocpmodels.models.gemnet_gp.utils)": [[80, "ocpmodels.models.gemnet_gp.utils.ragged_range"]], "read_json() (in module ocpmodels.models.gemnet_gp.utils)": [[80, "ocpmodels.models.gemnet_gp.utils.read_json"]], "read_value_json() (in module ocpmodels.models.gemnet_gp.utils)": [[80, "ocpmodels.models.gemnet_gp.utils.read_value_json"]], "repeat_blocks() (in module ocpmodels.models.gemnet_gp.utils)": [[80, "ocpmodels.models.gemnet_gp.utils.repeat_blocks"]], "update_json() (in module ocpmodels.models.gemnet_gp.utils)": [[80, "ocpmodels.models.gemnet_gp.utils.update_json"]], "write_json() (in module ocpmodels.models.gemnet_gp.utils)": [[80, "ocpmodels.models.gemnet_gp.utils.write_json"]], "gemnetoc (class in ocpmodels.models.gemnet_oc.gemnet_oc)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC"]], "calculate_quad_angles() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.calculate_quad_angles"]], "forward() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.forward"]], "generate_graph_dict() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.generate_graph_dict"]], "get_bases() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.get_bases"]], "get_graphs_and_indices() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.get_graphs_and_indices"]], "init_basis_functions() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.init_basis_functions"]], "init_shared_basis_layers() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.init_shared_basis_layers"]], "num_params (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc property)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.num_params"]], "ocpmodels.models.gemnet_oc.gemnet_oc": [[81, "module-ocpmodels.models.gemnet_oc.gemnet_oc"]], "select_symmetric_edges() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.select_symmetric_edges"]], "set_cutoffs() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.set_cutoffs"]], "set_max_neighbors() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.set_max_neighbors"]], "subselect_edges() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.subselect_edges"]], "subselect_graph() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.subselect_graph"]], "symmetrize_edges() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[81, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.symmetrize_edges"]], "ocpmodels.models.gemnet_oc": [[82, "module-ocpmodels.models.gemnet_oc"]], "_standardize() (in module ocpmodels.models.gemnet_oc.initializers)": [[83, "ocpmodels.models.gemnet_oc.initializers._standardize"]], "get_initializer() (in module ocpmodels.models.gemnet_oc.initializers)": [[83, "ocpmodels.models.gemnet_oc.initializers.get_initializer"]], "grid_init() (in module ocpmodels.models.gemnet_oc.initializers)": [[83, "ocpmodels.models.gemnet_oc.initializers.grid_init"]], "he_orthogonal_init() (in module ocpmodels.models.gemnet_oc.initializers)": [[83, "ocpmodels.models.gemnet_oc.initializers.he_orthogonal_init"]], "log_grid_init() (in module ocpmodels.models.gemnet_oc.initializers)": [[83, "ocpmodels.models.gemnet_oc.initializers.log_grid_init"]], "ocpmodels.models.gemnet_oc.initializers": [[83, "module-ocpmodels.models.gemnet_oc.initializers"]], "get_mixed_triplets() (in module ocpmodels.models.gemnet_oc.interaction_indices)": [[84, "ocpmodels.models.gemnet_oc.interaction_indices.get_mixed_triplets"]], "get_quadruplets() (in module ocpmodels.models.gemnet_oc.interaction_indices)": [[84, "ocpmodels.models.gemnet_oc.interaction_indices.get_quadruplets"]], "get_triplets() (in module ocpmodels.models.gemnet_oc.interaction_indices)": [[84, "ocpmodels.models.gemnet_oc.interaction_indices.get_triplets"]], "ocpmodels.models.gemnet_oc.interaction_indices": [[84, "module-ocpmodels.models.gemnet_oc.interaction_indices"]], "atomupdateblock (class in ocpmodels.models.gemnet_oc.layers.atom_update_block)": [[85, "ocpmodels.models.gemnet_oc.layers.atom_update_block.AtomUpdateBlock"]], "outputblock (class in ocpmodels.models.gemnet_oc.layers.atom_update_block)": [[85, "ocpmodels.models.gemnet_oc.layers.atom_update_block.OutputBlock"]], "forward() (ocpmodels.models.gemnet_oc.layers.atom_update_block.atomupdateblock method)": [[85, "ocpmodels.models.gemnet_oc.layers.atom_update_block.AtomUpdateBlock.forward"]], "forward() 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ocpmodels.models.gemnet_oc.layers.basis_utils)": [[87, "ocpmodels.models.gemnet_oc.layers.basis_utils.associated_legendre_polynomials"]], "bessel_basis() (in module ocpmodels.models.gemnet_oc.layers.basis_utils)": [[87, "ocpmodels.models.gemnet_oc.layers.basis_utils.bessel_basis"]], "get_sph_harm_basis() (in module ocpmodels.models.gemnet_oc.layers.basis_utils)": [[87, "ocpmodels.models.gemnet_oc.layers.basis_utils.get_sph_harm_basis"]], "ocpmodels.models.gemnet_oc.layers.basis_utils": [[87, "module-ocpmodels.models.gemnet_oc.layers.basis_utils"]], "real_sph_harm() (in module ocpmodels.models.gemnet_oc.layers.basis_utils)": [[87, "ocpmodels.models.gemnet_oc.layers.basis_utils.real_sph_harm"]], "sph_harm_prefactor() (in module ocpmodels.models.gemnet_oc.layers.basis_utils)": [[87, "ocpmodels.models.gemnet_oc.layers.basis_utils.sph_harm_prefactor"]], "spherical_bessel_formulas() (in module ocpmodels.models.gemnet_oc.layers.basis_utils)": [[87, "ocpmodels.models.gemnet_oc.layers.basis_utils.spherical_bessel_formulas"]], "basisembedding (class in ocpmodels.models.gemnet_oc.layers.efficient)": [[88, "ocpmodels.models.gemnet_oc.layers.efficient.BasisEmbedding"]], "efficientinteractionbilinear (class in ocpmodels.models.gemnet_oc.layers.efficient)": [[88, "ocpmodels.models.gemnet_oc.layers.efficient.EfficientInteractionBilinear"]], "forward() (ocpmodels.models.gemnet_oc.layers.efficient.basisembedding method)": [[88, "ocpmodels.models.gemnet_oc.layers.efficient.BasisEmbedding.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.efficient.efficientinteractionbilinear method)": [[88, "ocpmodels.models.gemnet_oc.layers.efficient.EfficientInteractionBilinear.forward"]], "ocpmodels.models.gemnet_oc.layers.efficient": [[88, "module-ocpmodels.models.gemnet_oc.layers.efficient"]], "reset_parameters() (ocpmodels.models.gemnet_oc.layers.efficient.basisembedding method)": [[88, 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"module-ocpmodels.models.gemnet_oc.layers.embedding_block"]], "forcescaler (class in ocpmodels.models.gemnet_oc.layers.force_scaler)": [[90, "ocpmodels.models.gemnet_oc.layers.force_scaler.ForceScaler"]], "calc_forces() (ocpmodels.models.gemnet_oc.layers.force_scaler.forcescaler method)": [[90, "ocpmodels.models.gemnet_oc.layers.force_scaler.ForceScaler.calc_forces"]], "calc_forces_and_update() (ocpmodels.models.gemnet_oc.layers.force_scaler.forcescaler method)": [[90, "ocpmodels.models.gemnet_oc.layers.force_scaler.ForceScaler.calc_forces_and_update"]], "ocpmodels.models.gemnet_oc.layers.force_scaler": [[90, "module-ocpmodels.models.gemnet_oc.layers.force_scaler"]], "scale() (ocpmodels.models.gemnet_oc.layers.force_scaler.forcescaler method)": [[90, "ocpmodels.models.gemnet_oc.layers.force_scaler.ForceScaler.scale"]], "unscale() (ocpmodels.models.gemnet_oc.layers.force_scaler.forcescaler method)": [[90, "ocpmodels.models.gemnet_oc.layers.force_scaler.ForceScaler.unscale"]], "update() 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"ocpmodels.models.gemnet_oc.layers.spherical_basis.CircularBasisLayer"]], "sphericalbasislayer (class in ocpmodels.models.gemnet_oc.layers.spherical_basis)": [[94, "ocpmodels.models.gemnet_oc.layers.spherical_basis.SphericalBasisLayer"]], "forward() (ocpmodels.models.gemnet_oc.layers.spherical_basis.circularbasislayer method)": [[94, "ocpmodels.models.gemnet_oc.layers.spherical_basis.CircularBasisLayer.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.spherical_basis.sphericalbasislayer method)": [[94, "ocpmodels.models.gemnet_oc.layers.spherical_basis.SphericalBasisLayer.forward"]], "ocpmodels.models.gemnet_oc.layers.spherical_basis": [[94, "module-ocpmodels.models.gemnet_oc.layers.spherical_basis"]], "calculate_interatomic_vectors() (in module ocpmodels.models.gemnet_oc.utils)": [[95, "ocpmodels.models.gemnet_oc.utils.calculate_interatomic_vectors"]], "get_angle() (in module ocpmodels.models.gemnet_oc.utils)": [[95, "ocpmodels.models.gemnet_oc.utils.get_angle"]], "get_edge_id() (in module ocpmodels.models.gemnet_oc.utils)": [[95, "ocpmodels.models.gemnet_oc.utils.get_edge_id"]], "get_inner_idx() (in module ocpmodels.models.gemnet_oc.utils)": [[95, "ocpmodels.models.gemnet_oc.utils.get_inner_idx"]], "get_neighbor_order() (in module ocpmodels.models.gemnet_oc.utils)": [[95, "ocpmodels.models.gemnet_oc.utils.get_neighbor_order"]], "get_projected_angle() (in module ocpmodels.models.gemnet_oc.utils)": [[95, "ocpmodels.models.gemnet_oc.utils.get_projected_angle"]], "inner_product_clamped() (in module ocpmodels.models.gemnet_oc.utils)": [[95, "ocpmodels.models.gemnet_oc.utils.inner_product_clamped"]], "mask_neighbors() (in module ocpmodels.models.gemnet_oc.utils)": [[95, "ocpmodels.models.gemnet_oc.utils.mask_neighbors"]], "masked_select_sparsetensor_flat() (in module ocpmodels.models.gemnet_oc.utils)": [[95, "ocpmodels.models.gemnet_oc.utils.masked_select_sparsetensor_flat"]], "ocpmodels.models.gemnet_oc.utils": [[95, 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ocpmodels.models.painn.painn)": [[98, "ocpmodels.models.painn.painn.PaiNNUpdate"]], "__repr__() (ocpmodels.models.painn.painn.painn method)": [[98, "ocpmodels.models.painn.painn.PaiNN.__repr__"]], "aggregate() (ocpmodels.models.painn.painn.painnmessage method)": [[98, "ocpmodels.models.painn.painn.PaiNNMessage.aggregate"]], "forward() (ocpmodels.models.painn.painn.gatedequivariantblock method)": [[98, "ocpmodels.models.painn.painn.GatedEquivariantBlock.forward"]], "forward() (ocpmodels.models.painn.painn.painn method)": [[98, "ocpmodels.models.painn.painn.PaiNN.forward"]], "forward() (ocpmodels.models.painn.painn.painnmessage method)": [[98, "ocpmodels.models.painn.painn.PaiNNMessage.forward"]], "forward() (ocpmodels.models.painn.painn.painnoutput method)": [[98, "ocpmodels.models.painn.painn.PaiNNOutput.forward"]], "forward() (ocpmodels.models.painn.painn.painnupdate method)": [[98, "ocpmodels.models.painn.painn.PaiNNUpdate.forward"]], "generate_graph_values() 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"ocpmodels.models.scn.scn.SphericalChannelNetwork.energy_fc2"]], "energy_fc3 (ocpmodels.models.scn.scn.sphericalchannelnetwork attribute)": [[103, "ocpmodels.models.scn.scn.SphericalChannelNetwork.energy_fc3"]], "force_fc1 (ocpmodels.models.scn.scn.sphericalchannelnetwork attribute)": [[103, "ocpmodels.models.scn.scn.SphericalChannelNetwork.force_fc1"]], "force_fc2 (ocpmodels.models.scn.scn.sphericalchannelnetwork attribute)": [[103, "ocpmodels.models.scn.scn.SphericalChannelNetwork.force_fc2"]], "force_fc3 (ocpmodels.models.scn.scn.sphericalchannelnetwork attribute)": [[103, "ocpmodels.models.scn.scn.SphericalChannelNetwork.force_fc3"]], "forward() (ocpmodels.models.scn.scn.distanceblock method)": [[103, "ocpmodels.models.scn.scn.DistanceBlock.forward"]], "forward() (ocpmodels.models.scn.scn.edgeblock method)": [[103, "ocpmodels.models.scn.scn.EdgeBlock.forward"]], "forward() (ocpmodels.models.scn.scn.messageblock method)": [[103, "ocpmodels.models.scn.scn.MessageBlock.forward"]], "forward() (ocpmodels.models.scn.scn.sphericalchannelnetwork method)": [[103, "ocpmodels.models.scn.scn.SphericalChannelNetwork.forward"]], "num_params (ocpmodels.models.scn.scn.sphericalchannelnetwork property)": [[103, "ocpmodels.models.scn.scn.SphericalChannelNetwork.num_params"]], "ocpmodels.models.scn.scn": [[103, "module-ocpmodels.models.scn.scn"]], "gaussiansmearing (class in ocpmodels.models.scn.smearing)": [[104, "ocpmodels.models.scn.smearing.GaussianSmearing"]], "linearsigmoidsmearing (class in ocpmodels.models.scn.smearing)": [[104, "ocpmodels.models.scn.smearing.LinearSigmoidSmearing"]], "silusmearing (class in ocpmodels.models.scn.smearing)": [[104, "ocpmodels.models.scn.smearing.SiLUSmearing"]], "sigmoidsmearing (class in ocpmodels.models.scn.smearing)": [[104, "ocpmodels.models.scn.smearing.SigmoidSmearing"]], "forward() (ocpmodels.models.scn.smearing.gaussiansmearing method)": [[104, "ocpmodels.models.scn.smearing.GaussianSmearing.forward"]], "forward() 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"ocpmodels.models.scn.spherical_harmonics.SphericalHarmonicsHelper.FromGrid"]], "initwignerdmatrix() (ocpmodels.models.scn.spherical_harmonics.sphericalharmonicshelper method)": [[105, "ocpmodels.models.scn.spherical_harmonics.SphericalHarmonicsHelper.InitWignerDMatrix"]], "inityrotmapping() (ocpmodels.models.scn.spherical_harmonics.sphericalharmonicshelper method)": [[105, "ocpmodels.models.scn.spherical_harmonics.SphericalHarmonicsHelper.InitYRotMapping"]], "rotate() (ocpmodels.models.scn.spherical_harmonics.sphericalharmonicshelper method)": [[105, "ocpmodels.models.scn.spherical_harmonics.SphericalHarmonicsHelper.Rotate"]], "rotateinv() (ocpmodels.models.scn.spherical_harmonics.sphericalharmonicshelper method)": [[105, "ocpmodels.models.scn.spherical_harmonics.SphericalHarmonicsHelper.RotateInv"]], "rotatewigner() (ocpmodels.models.scn.spherical_harmonics.sphericalharmonicshelper method)": [[105, "ocpmodels.models.scn.spherical_harmonics.SphericalHarmonicsHelper.RotateWigner"]], "rotationmatrix() (ocpmodels.models.scn.spherical_harmonics.sphericalharmonicshelper method)": [[105, "ocpmodels.models.scn.spherical_harmonics.SphericalHarmonicsHelper.RotationMatrix"]], "rotationtowignerdmatrix() (ocpmodels.models.scn.spherical_harmonics.sphericalharmonicshelper method)": [[105, "ocpmodels.models.scn.spherical_harmonics.SphericalHarmonicsHelper.RotationToWignerDMatrix"]], "sphericalharmonicshelper (class in ocpmodels.models.scn.spherical_harmonics)": [[105, "ocpmodels.models.scn.spherical_harmonics.SphericalHarmonicsHelper"]], "togrid() (ocpmodels.models.scn.spherical_harmonics.sphericalharmonicshelper method)": [[105, "ocpmodels.models.scn.spherical_harmonics.SphericalHarmonicsHelper.ToGrid"]], "_jd (in module ocpmodels.models.scn.spherical_harmonics)": [[105, "ocpmodels.models.scn.spherical_harmonics._Jd"]], "_z_rot_mat() (in module ocpmodels.models.scn.spherical_harmonics)": [[105, "ocpmodels.models.scn.spherical_harmonics._z_rot_mat"]], "ocpmodels.models.scn.spherical_harmonics": [[105, "module-ocpmodels.models.scn.spherical_harmonics"]], "wigner_d() (in module ocpmodels.models.scn.spherical_harmonics)": [[105, "ocpmodels.models.scn.spherical_harmonics.wigner_D"]], "act (class in ocpmodels.models.utils.activations)": [[106, "ocpmodels.models.utils.activations.Act"]], "forward() (ocpmodels.models.utils.activations.act method)": [[106, "ocpmodels.models.utils.activations.Act.forward"]], "ocpmodels.models.utils.activations": [[106, "module-ocpmodels.models.utils.activations"]], "basis (class in ocpmodels.models.utils.basis)": [[107, "ocpmodels.models.utils.basis.Basis"]], "fouriersmearing (class in ocpmodels.models.utils.basis)": [[107, "ocpmodels.models.utils.basis.FourierSmearing"]], "gaussiansmearing (class in ocpmodels.models.utils.basis)": [[107, "ocpmodels.models.utils.basis.GaussianSmearing"]], "sinesmearing (class in ocpmodels.models.utils.basis)": [[107, "ocpmodels.models.utils.basis.SINESmearing"]], "siren (class in ocpmodels.models.utils.basis)": [[107, "ocpmodels.models.utils.basis.SIREN"]], "sine (class in ocpmodels.models.utils.basis)": [[107, "ocpmodels.models.utils.basis.Sine"]], "sphericalsmearing (class in ocpmodels.models.utils.basis)": [[107, "ocpmodels.models.utils.basis.SphericalSmearing"]], "forward() (ocpmodels.models.utils.basis.basis method)": [[107, "ocpmodels.models.utils.basis.Basis.forward"]], "forward() (ocpmodels.models.utils.basis.fouriersmearing method)": [[107, "ocpmodels.models.utils.basis.FourierSmearing.forward"]], "forward() (ocpmodels.models.utils.basis.gaussiansmearing method)": [[107, "ocpmodels.models.utils.basis.GaussianSmearing.forward"]], "forward() (ocpmodels.models.utils.basis.sinesmearing method)": [[107, "ocpmodels.models.utils.basis.SINESmearing.forward"]], "forward() (ocpmodels.models.utils.basis.siren method)": [[107, "ocpmodels.models.utils.basis.SIREN.forward"]], "forward() (ocpmodels.models.utils.basis.sine method)": [[107, 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121, 122, 124, 125, 127, 150, 154], "directori": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 17, 18, 19, 23, 24, 25, 27, 28, 30, 31, 32, 44, 45, 46, 51, 53, 54, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 76, 77, 78, 79, 80, 82, 83, 84, 85, 86, 87, 88, 89, 91, 92, 93, 94, 98, 99, 100, 102, 103, 104, 105, 106, 107, 109, 111, 113, 121, 122, 124, 125, 126, 127, 131, 133, 134, 139, 143, 153], "tree": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 17, 18, 19, 23, 24, 27, 28, 30, 31, 32, 33, 34, 37, 40, 44, 45, 46, 51, 53, 54, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 76, 77, 78, 79, 80, 82, 83, 84, 85, 86, 87, 88, 89, 91, 92, 93, 94, 98, 99, 100, 102, 103, 104, 105, 106, 107, 109, 111, 112, 113, 116, 117, 121, 122, 124, 125, 127], "ocpcollat": 1, "otf_graph": [1, 25, 27, 31, 32, 36, 38, 51, 52, 54, 67, 80, 98, 100, 103, 139], "bool": [1, 2, 4, 7, 8, 9, 11, 13, 17, 19, 25, 26, 27, 29, 31, 32, 33, 34, 36, 37, 38, 39, 40, 43, 44, 45, 46, 49, 51, 52, 54, 57, 58, 59, 65, 66, 67, 70, 71, 72, 78, 79, 80, 83, 84, 85, 86, 89, 91, 92, 93, 94, 98, 99, 100, 103, 104, 106, 107, 110, 112, 116, 117, 118, 121, 122, 125, 126, 127, 139, 140], "fals": [1, 2, 4, 8, 11, 13, 17, 19, 25, 26, 27, 32, 33, 34, 36, 38, 43, 45, 46, 49, 51, 52, 54, 58, 59, 65, 66, 67, 71, 72, 78, 79, 80, 83, 85, 86, 91, 92, 93, 94, 98, 99, 100, 103, 107, 110, 118, 121, 122, 125, 126, 127, 131, 132, 133, 139, 140, 141, 143, 144, 145, 147, 149, 150, 152, 153, 154], "__call__": [1, 14, 17, 48, 120], "data_list": [1, 17, 25, 27, 121, 122], "list": [1, 2, 9, 14, 15, 17, 19, 25, 26, 27, 31, 36, 38, 39, 41, 42, 43, 44, 48, 49, 51, 52, 53, 59, 72, 80, 86, 98, 107, 117, 121, 122, 131, 134, 139, 149, 153, 155], "torch_geometr": [1, 13, 17, 18, 25, 27, 98, 100, 120, 121, 122, 139, 140], "data": [1, 2, 4, 13, 14, 15, 17, 18, 19, 25, 26, 27, 28, 31, 32, 34, 36, 38, 51, 52, 54, 66, 67, 79, 80, 98, 100, 103, 120, 121, 122, 125, 126, 129, 142, 144, 145, 147, 149, 151, 152, 153, 155], 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122, 128, 129, 133, 134, 135, 136, 141, 144, 145, 147, 149, 151, 152, 154, 155], "alwai": [1, 98], "insert": [1, 9], "largest": [1, 139, 143], "element": [1, 23, 24, 36, 38, 59, 66, 72, 79, 86, 87, 94, 99, 128, 141, 154, 155], "smallest": 1, "_hasmetadata": 1, "protocol": [1, 139, 143], "ar": [1, 4, 9, 17, 19, 25, 26, 27, 28, 33, 34, 36, 37, 38, 40, 41, 45, 46, 54, 56, 59, 67, 69, 72, 80, 82, 83, 86, 98, 110, 121, 122, 126, 127, 129, 131, 132, 133, 134, 135, 136, 138, 139, 141, 144, 145, 147, 149, 150, 152, 153, 154, 155], "defin": [1, 4, 80, 83, 94, 98, 132, 134, 140, 141, 143, 144, 145, 150, 153], "proto": 1, "def": [1, 4, 31, 32, 33, 34, 37, 40, 41, 44, 58, 71, 85, 92, 98, 103, 104, 106, 107, 112, 116, 117, 139, 143], "meth": 1, "self": [1, 9, 14, 19, 26, 31, 32, 33, 34, 37, 40, 41, 44, 58, 71, 85, 92, 98, 103, 104, 106, 107, 112, 116, 117, 134, 139], "Such": 1, "primarili": 1, "us": [1, 4, 8, 11, 15, 17, 19, 21, 25, 26, 27, 28, 32, 34, 36, 38, 39, 40, 41, 43, 44, 45, 46, 48, 49, 51, 52, 53, 54, 57, 58, 61, 63, 65, 67, 70, 71, 74, 76, 78, 80, 83, 84, 85, 87, 88, 89, 91, 94, 98, 100, 103, 105, 110, 114, 121, 122, 125, 126, 127, 128, 129, 130, 131, 134, 135, 136, 138, 140, 141, 142, 143, 146, 149, 150, 152, 153, 154, 155], "static": [1, 4, 19, 25, 125, 126], "checker": 1, "recogn": 1, "structur": [1, 11, 17, 19, 25, 27, 28, 31, 32, 33, 34, 37, 40, 44, 45, 46, 58, 71, 85, 92, 98, 103, 104, 106, 107, 112, 116, 117, 121, 122, 126, 127, 128, 131, 138, 141, 142, 144, 145, 147, 149, 152, 153, 155], "subtyp": 1, "duck": 1, "For": [1, 17, 19, 25, 27, 28, 39, 40, 43, 48, 49, 94, 117, 128, 131, 133, 134, 135, 136, 138, 139, 141, 144, 145, 147, 149, 153, 154], "exampl": [1, 4, 9, 17, 19, 25, 31, 32, 33, 34, 37, 39, 40, 41, 43, 44, 45, 46, 49, 58, 66, 71, 79, 85, 92, 94, 98, 99, 103, 104, 106, 107, 112, 116, 117, 126, 127, 128, 133, 134, 135, 139, 147, 153, 154, 155], "return": [1, 4, 8, 14, 15, 17, 19, 25, 27, 31, 32, 33, 34, 36, 37, 38, 40, 41, 43, 44, 54, 57, 58, 59, 60, 61, 63, 66, 67, 70, 71, 72, 73, 74, 76, 79, 80, 83, 84, 85, 86, 87, 88, 91, 92, 94, 95, 96, 98, 99, 103, 104, 106, 107, 110, 112, 116, 117, 121, 122, 139, 141, 143, 147, 149], "0": [1, 4, 9, 11, 13, 14, 15, 17, 25, 26, 27, 28, 29, 32, 33, 34, 36, 38, 40, 45, 46, 49, 51, 52, 54, 56, 59, 64, 66, 67, 69, 72, 76, 77, 79, 80, 82, 86, 89, 91, 92, 94, 98, 99, 100, 103, 104, 106, 107, 121, 122, 125, 126, 127, 128, 129, 131, 132, 133, 134, 135, 136, 139, 140, 141, 143, 144, 145, 147, 149, 152, 153, 154], "func": [1, 51], "x": [1, 2, 16, 31, 32, 33, 34, 37, 40, 41, 43, 44, 49, 51, 58, 59, 66, 71, 72, 79, 85, 86, 92, 94, 98, 100, 103, 104, 105, 106, 107, 112, 116, 117, 139, 141, 144, 145, 147], "pass": [1, 4, 8, 17, 19, 49, 51, 52, 54, 63, 67, 76, 80, 91, 98, 100, 103, 128, 141, 144, 145, 155], "check": [1, 128, 129, 138, 139, 140, 143, 144, 145, 153, 157], "see": [1, 4, 19, 25, 26, 34, 95, 96, 98, 128, 131, 132, 133, 134, 138, 139, 141, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154], 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79, 80, 82, 83, 86, 94, 98, 99, 100, 110, 114, 117, 119, 129, 130, 131, 132, 134, 135, 136, 138, 139, 140, 141, 143, 144, 145, 147, 149, 150, 152, 153, 155], "In": [1, 19, 25, 59, 61, 72, 74, 83, 86, 98, 128, 133, 134, 135, 139, 140, 141, 143, 144, 145, 147, 149, 152, 153, 154, 155], "case": [1, 17, 19, 25, 98, 133, 139, 143], "veri": [1, 133, 139, 143, 149, 152, 153, 154], "larg": [1, 19, 25, 128, 131, 136, 139, 141, 143, 145, 147, 150, 152, 153, 155], "we": [1, 17, 26, 33, 36, 38, 40, 44, 48, 54, 67, 80, 98, 128, 129, 132, 133, 134, 135, 136, 137, 138, 139, 141, 142, 143, 144, 145, 147, 149, 150, 152, 153, 155], "one": [1, 19, 33, 36, 38, 39, 49, 51, 52, 54, 63, 67, 76, 80, 82, 91, 98, 117, 132, 133, 134, 137, 139, 141, 144, 145, 147, 149, 153, 154, 155], "when": [1, 8, 11, 19, 25, 31, 32, 33, 34, 36, 37, 38, 39, 40, 44, 49, 56, 58, 69, 71, 80, 82, 85, 87, 92, 98, 103, 104, 106, 107, 110, 112, 116, 117, 121, 122, 134, 139, 144, 145, 153, 154, 155], "resum": 1, "want": [1, 9, 19, 25, 129, 132, 133, 139, 144, 145, 147, 150, 153, 155], "sampler": [1, 25, 27, 125, 126], "__iter__": 1, "set_epoch_and_start_iter": 1, "start_it": 1, "balancedbatchsampl": [1, 125, 126], "num_replica": 1, "rank": [1, 45, 46, 126, 127], "devic": [1, 2, 11, 13, 17, 44, 53, 102, 113, 125, 126], "mode": [1, 4, 31, 32, 33, 34, 37, 40, 44, 45, 46, 58, 71, 85, 92, 98, 103, 104, 106, 107, 112, 116, 117, 126, 127, 128, 133, 139, 144, 145, 150, 152, 153], "str": [1, 2, 5, 7, 8, 9, 11, 13, 14, 16, 17, 18, 19, 25, 26, 32, 34, 36, 38, 40, 41, 44, 45, 46, 49, 51, 52, 54, 57, 58, 61, 63, 64, 66, 67, 70, 71, 74, 76, 77, 79, 80, 84, 85, 88, 91, 92, 95, 96, 98, 100, 102, 103, 106, 107, 109, 112, 114, 115, 116, 117, 121, 122, 125, 126, 127], "atom": [1, 9, 13, 17, 19, 20, 21, 25, 26, 32, 36, 38, 39, 49, 51, 52, 54, 57, 61, 63, 66, 67, 70, 74, 76, 79, 80, 83, 84, 87, 88, 91, 94, 98, 100, 103, 121, 122, 128, 132, 133, 134, 135, 136, 142, 143, 144, 145, 147, 152, 153, 155], "true": [1, 4, 8, 9, 13, 17, 19, 25, 26, 32, 33, 36, 38, 39, 40, 43, 44, 49, 51, 52, 54, 57, 58, 59, 66, 67, 70, 71, 72, 79, 80, 83, 84, 85, 86, 89, 91, 94, 98, 99, 100, 103, 116, 117, 121, 122, 125, 126, 127, 128, 133, 134, 139, 140, 141, 143, 144, 145, 147, 149, 150, 152, 153, 154], "drop_last": 1, "force_balanc": 1, "throw_on_error": 1, "all": [1, 4, 9, 15, 17, 19, 25, 26, 27, 31, 32, 33, 34, 36, 37, 38, 40, 41, 43, 44, 49, 51, 54, 58, 67, 71, 80, 83, 85, 92, 98, 103, 104, 106, 107, 112, 116, 117, 121, 122, 128, 130, 131, 133, 134, 135, 136, 138, 139, 140, 141, 146, 149, 150, 153, 154, 155], "everi": [1, 17, 19, 25, 48, 54, 67, 80, 98, 110, 133, 139], "subclass": [1, 4, 9, 25, 27, 31, 32, 33, 34, 37, 40, 44, 58, 71, 85, 92, 98, 103, 104, 106, 107, 112, 116, 117], "ha": [1, 4, 9, 17, 19, 54, 59, 67, 72, 80, 86, 94, 98, 103, 134, 138, 139, 140, 144, 145, 147, 152, 153, 154, 155, 156], "provid": [1, 25, 27, 32, 98, 125, 126, 128, 130, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 149, 153, 155], "an": 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"module-ocpmodels.modules.scaling.compat"]], "ocpmodels.modules.scaling.fit": [[115, "module-ocpmodels.modules.scaling.fit"]], "ocpmodels.modules.scaling": [[116, "module-ocpmodels.modules.scaling"]], "ocpmodels.modules.scaling.scale_factor": [[117, "module-ocpmodels.modules.scaling.scale_factor"]], "ocpmodels.modules.scaling.util": [[118, "module-ocpmodels.modules.scaling.util"]], "ocpmodels.modules.scheduler": [[119, "module-ocpmodels.modules.scheduler"]], "ocpmodels.modules.transforms": [[120, "module-ocpmodels.modules.transforms"]], "ocpmodels.preprocessing.atoms_to_graphs": [[121, "module-ocpmodels.preprocessing.atoms_to_graphs"]], "ocpmodels.preprocessing": [[122, "module-ocpmodels.preprocessing"]], "ocpmodels.tasks": [[123, "module-ocpmodels.tasks"]], "ocpmodels.tasks.task": [[124, "module-ocpmodels.tasks.task"]], "ocpmodels.trainers.base_trainer": [[125, "module-ocpmodels.trainers.base_trainer"]], "ocpmodels.trainers": [[126, "module-ocpmodels.trainers"]], "ocpmodels.trainers.ocp_trainer": [[127, "module-ocpmodels.trainers.ocp_trainer"]], "Frequently Asked Questions": [[128, "frequently-asked-questions"]], "Models": [[128, "models"], [155, "models"]], "Are predictions from OCP models deterministic?": [[128, "are-predictions-from-ocp-models-deterministic"]], "How do I train a model on OC20 total energies?": [[128, "how-do-i-train-a-model-on-oc20-total-energies"]], "I\u2019m trying to run GemNet-OC / GemNet-dT, but it throws an error that scaling factors are not fitted. What should I do?": [[128, "i-m-trying-to-run-gemnet-oc-gemnet-dt-but-it-throws-an-error-that-scaling-factors-are-not-fitted-what-should-i-do"]], "I\u2019m trying to run GemNet-OC on my data, but it errors out on sph_basis = self.spherical_basis(cos\u03c6_cab, \u03b8_cabd).": [[128, "i-m-trying-to-run-gemnet-oc-on-my-data-but-it-errors-out-on-sph-basis-self-spherical-basis-cos-cab-cabd"]], "Installation": [[129, "installation"], [138, "installation"]], "pip (fast, easy to get started)": [[129, "pip-fast-easy-to-get-started"]], "Conda (preferred for model training & development)": [[129, "conda-preferred-for-model-training-development"]], "GPU machines": [[129, "gpu-machines"]], "CPU-only machines": [[129, "cpu-only-machines"]], "License": [[130, "license"], [138, "license"]], "Pretrained OCP model checkpoints": [[131, "pretrained-ocp-model-checkpoints"]], "Open Catalyst 2020 (OC20)": [[131, "open-catalyst-2020-oc20"], [134, "open-catalyst-2020-oc20"]], "S2EF models: optimized for EFwT": [[131, "s2ef-models-optimized-for-efwt"]], "S2EF models: optimized for force only": [[131, "s2ef-models-optimized-for-force-only"]], "IS2RE models": [[131, "is2re-models"]], "Open Catalyst 2022 (OC22)": [[131, "open-catalyst-2022-oc22"], [135, "open-catalyst-2022-oc22"]], "S2EF-Total models": [[131, "s2ef-total-models"]], "Open Direct Air Capture 2023 (ODAC23)": [[131, "open-direct-air-capture-2023-odac23"], [136, "open-direct-air-capture-2023-odac23"]], "S2EF models": [[131, "s2ef-models"]], "IS2RE Direct models": [[131, "is2re-direct-models"]], "IS2RS": [[131, "is2rs"]], "Quickstart simulation using pre-trained models": [[132, "quickstart-simulation-using-pre-trained-models"]], "Training and evaluating models on OCP datasets": [[133, "training-and-evaluating-models-on-ocp-datasets"]], "Getting Started": [[133, "getting-started"]], "OC20": [[133, "oc20"]], "Initial Structure to Relaxed Energy prediction (IS2RE)": [[133, "initial-structure-to-relaxed-energy-prediction-is2re"]], "IS2RE Relaxations": [[133, "is2re-relaxations"]], "Structure to Energy and Forces (S2EF)": [[133, "structure-to-energy-and-forces-s2ef"]], "Training OC20 models with total energies (IS2RE/S2EF)": [[133, "training-oc20-models-with-total-energies-is2re-s2ef"]], "Overriding YAML config parameters from the command line": [[133, "overriding-yaml-config-parameters-from-the-command-line"]], "Initial Structure to Relaxed Structure (IS2RS)": [[133, "initial-structure-to-relaxed-structure-is2rs"]], "Create EvalAI OC20 submission files": [[133, "create-evalai-oc20-submission-files"]], "S2EF/IS2RE:": [[133, "s2ef-is2re"]], "IS2RS:": [[133, "is2rs"]], "OC22": [[133, "oc22"]], "Initial Structure to Total Relaxed Energy (IS2RE-Total)": [[133, "initial-structure-to-total-relaxed-energy-is2re-total"]], "Structure to Total Energy and Forces (S2EF-Total)": [[133, "structure-to-total-energy-and-forces-s2ef-total"]], "Joint Training": [[133, "joint-training"]], "Create EvalAI OC22 submission files": [[133, "create-evalai-oc22-submission-files"]], "S2EF-Total/IS2RE-Total:": [[133, "s2ef-total-is2re-total"]], "Using Your Own Data": [[133, "using-your-own-data"]], "Writing an LMDB": [[133, "writing-an-lmdb"]], "Using an ASE Database": [[133, "using-an-ase-database"]], "Using ASE-Readable Files": [[133, "using-ase-readable-files"]], "Single-Structure Files": [[133, "single-structure-files"]], "Multi-structure Files": [[133, "multi-structure-files"]], "Download and preprocess the dataset": [[134, "download-and-preprocess-the-dataset"]], "Structure to Energy and Forces (S2EF) task": [[134, "structure-to-energy-and-forces-s2ef-task"], [136, "structure-to-energy-and-forces-s2ef-task"]], "Initial Structure to Relaxed Structure (IS2RS) and Initial Structure to Relaxed Energy (IS2RE) tasks": [[134, "initial-structure-to-relaxed-structure-is2rs-and-initial-structure-to-relaxed-energy-is2re-tasks"]], "Relaxation Trajectories": [[134, "relaxation-trajectories"], [135, "relaxation-trajectories"]], "Adsorbate+catalyst system trajectories (optional download)": [[134, "adsorbate-catalyst-system-trajectories-optional-download"]], "Per-adsorbate trajectories (optional download)": [[134, "per-adsorbate-trajectories-optional-download"]], "Catalyst system trajectories (optional download)": [[134, "catalyst-system-trajectories-optional-download"]], "Bader charge data": [[134, "bader-charge-data"]], "OC20 mappings": [[134, "oc20-mappings"]], "Data mapping information": [[134, "data-mapping-information"], [135, "data-mapping-information"]], "Adsorbate-catalyst system to catalyst system mapping information": [[134, "adsorbate-catalyst-system-to-catalyst-system-mapping-information"]], "Dataset changelog": [[134, "dataset-changelog"]], "September 2021": [[134, "september-2021"]], "March 2021": [[134, "march-2021"]], "Version 2, Feb 2021": [[134, "version-2-feb-2021"]], "Version 1, Oct 2020": [[134, "version-1-oct-2020"]], "Citing OC20": [[134, "citing-oc20"]], "Per-adsorbate trajectories": [[134, "per-adsorbate-trajectories"]], "Structure to Total Energy and Forces (S2EF-Total) task": [[135, "structure-to-total-energy-and-forces-s2ef-total-task"]], "Initial Structure to Relaxed Structure (IS2RS) and Initial Structure to Relaxed Total Energy (IS2RE-Total) tasks": [[135, "initial-structure-to-relaxed-structure-is2rs-and-initial-structure-to-relaxed-total-energy-is2re-total-tasks"]], "System trajectories (optional download)": [[135, "system-trajectories-optional-download"]], "OC22 Mappings": [[135, "oc22-mappings"]], "": [[135, "id1"], [135, "id2"]], "OC20 reference information": [[135, "oc20-reference-information"]], "Citing OC22": [[135, "citing-oc22"]], "Initial Structure to Relaxed Structure (IS2RS) / Relaxed Energy (IS2RE) tasks": [[136, "initial-structure-to-relaxed-structure-is2rs-relaxed-energy-is2re-tasks"]], "DDEC Charges": [[136, "ddec-charges"]], "Citing ODAC23": [[136, "citing-odac23"]], "Notebook execution times": [[137, "notebook-execution-times"]], "ocp by Open Catalyst Project": [[138, "ocp-by-open-catalyst-project"]], "Download data": [[138, "download-data"]], "Train and evaluate models": [[138, "train-and-evaluate-models"]], "Pretrained model weights": [[138, "pretrained-model-weights"]], "Discussion": [[138, "discussion"]], "Acknowledgements": [[138, "acknowledgements"]], "Citing ocp": [[138, "citing-ocp"]], "Open Catalyst Project Tutorial Notebook": [[139, "open-catalyst-project-tutorial-notebook"]], "Table of Contents": [[139, "table-of-contents"]], "Background ": [[139, "background"]], "Objective ": [[139, "objective"]], "Climate Impact": [[139, "climate-impact"]], "Target Audience": [[139, "target-audience"]], "Background & Prerequisites": [[139, "background-prerequisites"]], "Background References": [[139, "background-references"]], "Software Requirements": [[139, "software-requirements"]], "Dataset Overview": [[139, "dataset-overview"]], "Tutorial Use": [[139, "tutorial-use"]], "Data Download [~1min] ": [[139, "data-download-1min"]], "Data Visualization ": [[139, "data-visualization"]], "Understanding the data": [[139, "understanding-the-data"], [141, "understanding-the-data"]], "Generating sample data": [[139, "generating-sample-data"], [141, "generating-sample-data"]], "Structural relaxations": [[139, "structural-relaxations"]], "Reading a trajectory": [[139, "reading-a-trajectory"], [141, "reading-a-trajectory"]], "Viewing a trajectory": [[139, "viewing-a-trajectory"], [141, "viewing-a-trajectory"]], "Data contents ": [[139, "data-contents"]], "Atomic numbers": [[139, "atomic-numbers"], [141, "atomic-numbers"]], "Atomic symbols": [[139, "atomic-symbols"], [141, "atomic-symbols"]], "Unit cell": [[139, "unit-cell"], [141, "unit-cell"]], "Periodic boundary conditions (PBC)": [[139, "periodic-boundary-conditions-pbc"], [141, "periodic-boundary-conditions-pbc"]], "Tags": [[139, "tags"], [141, "tags"]], "Fixed atoms constraint": [[139, "fixed-atoms-constraint"], [141, "fixed-atoms-constraint"]], "Adsorption energy": [[139, "adsorption-energy"]], "Plot energy profile of toy trajectory": [[139, "plot-energy-profile-of-toy-trajectory"]], "Force": [[139, "force"]], "Interacting with the OC20 datasets": [[139, "interacting-with-the-oc20-datasets"]], "Additional Resources": [[139, "additional-resources"]], "Tasks": [[139, "tasks"]], "Structure to Energy and Forces (S2EF) ": [[139, "structure-to-energy-and-forces-s2ef"]], "Steps for training an S2EF model": [[139, "steps-for-training-an-s2ef-model"]], "Imports": [[139, "imports"], [139, "id1"], [139, "id8"], [139, "id13"]], "Dataset": [[139, "dataset"], [139, "id2"], [139, "id9"]], "Normalize data": [[139, "normalize-data"], [139, "id3"]], "Define the Config": [[139, "define-the-config"], [139, "id4"], [139, "id10"]], "Create the trainer": [[139, "create-the-trainer"], [139, "id11"]], "Train the model": [[139, "train-the-model"]], "Validate the model": [[139, "validate-the-model"]], "Load the best checkpoint": [[139, "load-the-best-checkpoint"], [139, "id7"], [139, "id12"]], "Run on the test set": [[139, "run-on-the-test-set"]], "Initial Structure to Relaxed Energy (IS2RE) ": [[139, "initial-structure-to-relaxed-energy-is2re"]], "Steps for training an IS2RE model": [[139, "steps-for-training-an-is2re-model"]], "Train the Model": [[139, "id5"]], "Validate the Model": [[139, "id6"]], "Test the model": [[139, "test-the-model"]], "Initial Structure to Relaxed Structure (IS2RS) ": [[139, "initial-structure-to-relaxed-structure-is2rs"]], "Steps for making IS2RS predictions": [[139, "steps-for-making-is2rs-predictions"]], "Download pretrained checkpoint": [[139, "download-pretrained-checkpoint"], [139, "id14"]], "Run relaxations": [[139, "run-relaxations"]], "Visualize ML-driven relaxations": [[139, "visualize-ml-driven-relaxations"]], "Model development ": [[139, "model-development"]], "Atom and Edge Embeddings": [[139, "atom-and-edge-embeddings"]], "Message passing": [[139, "message-passing"]], "Training the model": [[139, "training-the-model"]], "Incorporating triplets and training GemNet-T": [[139, "incorporating-triplets-and-training-gemnet-t"]], "(Optional) OCP Calculator ": [[139, "optional-ocp-calculator"]], "Using the OCP Calculator": [[139, "using-the-ocp-calculator"]], "(Optional) Creating your own LMDBs for use in the OCP repository": [[139, "optional-creating-your-own-lmdbs-for-use-in-the-ocp-repository"]], "Initial Structure to Relaxed Energy (IS2RE) LMDBs": [[139, "initial-structure-to-relaxed-energy-is2re-lmdbs"]], "Structure to Energy and Forces (S2EF) LMDBs": [[139, "structure-to-energy-and-forces-s2ef-lmdbs"], [143, "structure-to-energy-and-forces-s2ef-lmdbs"]], "Running on command line [Preferred way to train models] ": [[139, "running-on-command-line-preferred-way-to-train-models"]], "Limitations ": [[139, "limitations"]], "Next Steps ": [[139, "next-steps"]], "References": [[139, "references"]], "OCP Data Preprocessing Tutorial": [[140, "ocp-data-preprocessing-tutorial"]], "Generate toy dataset: Relaxation of CO on Cu": [[140, "generate-toy-dataset-relaxation-of-co-on-cu"], [143, "generate-toy-dataset-relaxation-of-co-on-cu"]], "Convert Atoms object to Data object": [[140, "convert-atoms-object-to-data-object"]], "Adding additional info to your Data objects": [[140, "adding-additional-info-to-your-data-objects"]], "OCP Data Visualization": [[141, "ocp-data-visualization"]], "Saving a trajectory video": [[141, "saving-a-trajectory-video"]], "Data contents": [[141, "data-contents"]], "Energy": [[141, "energy"]], "Forces": [[141, "forces"]], "Resources": [[141, "resources"]], "Legacy [deprecated] Tutorials": [[142, "legacy-deprecated-tutorials"]], "OCP LMDB Dataset Tutorial": [[143, "ocp-lmdb-dataset-tutorial"]], "Initial Structure to Relaxed Energy/Structure (IS2RE/IS2RS) LMDBs": [[143, "initial-structure-to-relaxed-energy-structure-is2re-is2rs-lmdbs"]], "Initialize AtomsToGraph feature extractor": [[143, "initialize-atomstograph-feature-extractor"]], "Initialize LMDB file": [[143, "initialize-lmdb-file"]], "Write data to LMDB": [[143, "write-data-to-lmdb"]], "Advanced usage": [[143, "advanced-usage"]], "Interacting with the LMDBs": [[143, "interacting-with-the-lmdbs"]], "Using OCP to enumerate adsorbates on catalyst surfaces": [[144, "using-ocp-to-enumerate-adsorbates-on-catalyst-surfaces"]], "Introduction": [[144, "introduction"], [145, "introduction"], [155, "introduction"]], "Enumerate the adsorbate-slab configurations to run relaxations on": [[144, "enumerate-the-adsorbate-slab-configurations-to-run-relaxations-on"], [145, "enumerate-the-adsorbate-slab-configurations-to-run-relaxations-on"]], "Work out a single example": [[144, "work-out-a-single-example"], [145, "work-out-a-single-example"]], "Run an ML relaxation": [[144, "run-an-ml-relaxation"], [145, "run-an-ml-relaxation"]], "Run all the systems": [[144, "run-all-the-systems"], [145, "run-all-the-systems"]], "Parse the trajectories and post-process": [[144, "parse-the-trajectories-and-post-process"], [145, "parse-the-trajectories-and-post-process"]], "Make parity plots for values obtained by ML v. reported in the paper": [[144, "make-parity-plots-for-values-obtained-by-ml-v-reported-in-the-paper"], [145, "make-parity-plots-for-values-obtained-by-ml-v-reported-in-the-paper"]], "Make figure 6b and compare to literature results": [[144, "make-figure-6b-and-compare-to-literature-results"], [145, "make-figure-6b-and-compare-to-literature-results"]], "Using OCP to enumerate adsorbates on alloy catalyst surfaces": [[145, "using-ocp-to-enumerate-adsorbates-on-alloy-catalyst-surfaces"]], "Next steps": [[145, "next-steps"], [147, "next-steps"], [153, "next-steps"]], "Screening catalysts with OCP": [[146, "screening-catalysts-with-ocp"]], "Simple simulations using the OCP ASE calculator": [[147, "simple-simulations-using-the-ocp-ase-calculator"]], "Calculating adsorption energies": [[147, "calculating-adsorption-energies"]], "Exercises": [[147, "exercises"], [147, "id1"]], "Trends in adsorption energies across metals.": [[147, "trends-in-adsorption-energies-across-metals"]], "Site correlations": [[147, "site-correlations"]], "Convergence study": [[147, "convergence-study"]], "Effects of number of layers": [[147, "effects-of-number-of-layers"]], "Effects of relaxation": [[147, "effects-of-relaxation"]], "Unit cell size": [[147, "unit-cell-size"]], "Summary": [[147, "summary"]], "Advanced OCP usage": [[148, "advanced-ocp-usage"]], "Working with embeddings": [[149, "working-with-embeddings"]], "A diagnostic example": [[149, "a-diagnostic-example"]], "Bulk Cu equation of state example": [[149, "bulk-cu-equation-of-state-example"]], "A clustering example": [[149, "a-clustering-example"]], "Clustering individual atoms": [[149, "clustering-individual-atoms"]], "A simple vector search example": [[149, "a-simple-vector-search-example"]], "Fine-tuning with Python": [[150, "fine-tuning-with-python"]], "Split the data into train, test, val sets": [[150, "split-the-data-into-train-test-val-sets"]], "Setup the training code": [[150, "setup-the-training-code"]], "Setup the training task": [[150, "setup-the-training-task"]], "Run the training task": [[150, "run-the-training-task"]], "Advanced example: Fine-tuning": [[151, "advanced-example-fine-tuning"]], "Mass inference": [[152, "mass-inference"]], "The ASE calculator way": [[152, "the-ase-calculator-way"]], "Comparing ASE calculator and main.py": [[152, "comparing-ase-calculator-and-main-py"]], "Fine tuning a model": [[153, "fine-tuning-a-model"]], "Fine tuning the checkpoint": [[153, "fine-tuning-the-checkpoint"]], "Make the train, test, val splits": [[153, "make-the-train-test-val-splits"]], "Setting up the configuration yaml file": [[153, "setting-up-the-configuration-yaml-file"]], "Running the training job": [[153, "running-the-training-job"]], "Common gotchas with OCP": [[154, "common-gotchas-with-ocp"]], "OutOfMemoryError": [[154, "outofmemoryerror"]], "I want the energy of a gas phase atom": [[154, "i-want-the-energy-of-a-gas-phase-atom"]], "I get wildly different energies from the different models": [[154, "i-get-wildly-different-energies-from-the-different-models"]], "Miscellaneous warnings": [[154, "miscellaneous-warnings"]], "Unrecognized arguments": [[154, "unrecognized-arguments"]], "Unable to identify OCP trainer": [[154, "unable-to-identify-ocp-trainer"]], "Request entity too large - can\u2019t save your Notebook": [[154, "request-entity-too-large-can-t-save-your-notebook"]], "You need at least four atoms for molecules with some models": [[154, "you-need-at-least-four-atoms-for-molecules-with-some-models"]], "To tag or not?": [[154, "to-tag-or-not"]], "Stochastic simulation results": [[154, "stochastic-simulation-results"]], "The forces don\u2019t sum to zero": [[154, "the-forces-don-t-sum-to-zero"]], "Intro and background on OCP and DFT": [[155, 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"ocpmodels.models.gemnet_gp.layers.interaction_block": [[76, "module-ocpmodels.models.gemnet_gp.layers.interaction_block"]], "bernsteinbasis (class in ocpmodels.models.gemnet_gp.layers.radial_basis)": [[77, "ocpmodels.models.gemnet_gp.layers.radial_basis.BernsteinBasis"]], "exponentialenvelope (class in ocpmodels.models.gemnet_gp.layers.radial_basis)": [[77, "ocpmodels.models.gemnet_gp.layers.radial_basis.ExponentialEnvelope"]], "polynomialenvelope (class in ocpmodels.models.gemnet_gp.layers.radial_basis)": [[77, "ocpmodels.models.gemnet_gp.layers.radial_basis.PolynomialEnvelope"]], "radialbasis (class in ocpmodels.models.gemnet_gp.layers.radial_basis)": [[77, "ocpmodels.models.gemnet_gp.layers.radial_basis.RadialBasis"]], "sphericalbesselbasis (class in ocpmodels.models.gemnet_gp.layers.radial_basis)": [[77, "ocpmodels.models.gemnet_gp.layers.radial_basis.SphericalBesselBasis"]], "forward() (ocpmodels.models.gemnet_gp.layers.radial_basis.bernsteinbasis method)": [[77, "ocpmodels.models.gemnet_gp.layers.radial_basis.BernsteinBasis.forward"]], "forward() (ocpmodels.models.gemnet_gp.layers.radial_basis.exponentialenvelope method)": [[77, "ocpmodels.models.gemnet_gp.layers.radial_basis.ExponentialEnvelope.forward"]], "forward() (ocpmodels.models.gemnet_gp.layers.radial_basis.polynomialenvelope method)": [[77, "ocpmodels.models.gemnet_gp.layers.radial_basis.PolynomialEnvelope.forward"]], "forward() (ocpmodels.models.gemnet_gp.layers.radial_basis.radialbasis method)": [[77, "ocpmodels.models.gemnet_gp.layers.radial_basis.RadialBasis.forward"]], "forward() (ocpmodels.models.gemnet_gp.layers.radial_basis.sphericalbesselbasis method)": [[77, "ocpmodels.models.gemnet_gp.layers.radial_basis.SphericalBesselBasis.forward"]], "ocpmodels.models.gemnet_gp.layers.radial_basis": [[77, "module-ocpmodels.models.gemnet_gp.layers.radial_basis"]], "circularbasislayer (class in ocpmodels.models.gemnet_gp.layers.spherical_basis)": [[78, "ocpmodels.models.gemnet_gp.layers.spherical_basis.CircularBasisLayer"]], "forward() (ocpmodels.models.gemnet_gp.layers.spherical_basis.circularbasislayer method)": [[78, "ocpmodels.models.gemnet_gp.layers.spherical_basis.CircularBasisLayer.forward"]], "ocpmodels.models.gemnet_gp.layers.spherical_basis": [[78, "module-ocpmodels.models.gemnet_gp.layers.spherical_basis"]], "calculate_interatomic_vectors() (in module ocpmodels.models.gemnet_gp.utils)": [[79, "ocpmodels.models.gemnet_gp.utils.calculate_interatomic_vectors"]], "inner_product_normalized() (in module ocpmodels.models.gemnet_gp.utils)": [[79, "ocpmodels.models.gemnet_gp.utils.inner_product_normalized"]], "mask_neighbors() (in module ocpmodels.models.gemnet_gp.utils)": [[79, "ocpmodels.models.gemnet_gp.utils.mask_neighbors"]], "ocpmodels.models.gemnet_gp.utils": [[79, "module-ocpmodels.models.gemnet_gp.utils"]], "ragged_range() (in module ocpmodels.models.gemnet_gp.utils)": [[79, "ocpmodels.models.gemnet_gp.utils.ragged_range"]], "read_json() (in module ocpmodels.models.gemnet_gp.utils)": [[79, "ocpmodels.models.gemnet_gp.utils.read_json"]], "read_value_json() (in module ocpmodels.models.gemnet_gp.utils)": [[79, "ocpmodels.models.gemnet_gp.utils.read_value_json"]], "repeat_blocks() (in module ocpmodels.models.gemnet_gp.utils)": [[79, "ocpmodels.models.gemnet_gp.utils.repeat_blocks"]], "update_json() (in module ocpmodels.models.gemnet_gp.utils)": [[79, "ocpmodels.models.gemnet_gp.utils.update_json"]], "write_json() (in module ocpmodels.models.gemnet_gp.utils)": [[79, "ocpmodels.models.gemnet_gp.utils.write_json"]], "gemnetoc (class in ocpmodels.models.gemnet_oc.gemnet_oc)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC"]], "calculate_quad_angles() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.calculate_quad_angles"]], "forward() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.forward"]], "generate_graph_dict() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.generate_graph_dict"]], "get_bases() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.get_bases"]], "get_graphs_and_indices() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.get_graphs_and_indices"]], "init_basis_functions() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.init_basis_functions"]], "init_shared_basis_layers() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.init_shared_basis_layers"]], "num_params (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc property)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.num_params"]], "ocpmodels.models.gemnet_oc.gemnet_oc": [[80, "module-ocpmodels.models.gemnet_oc.gemnet_oc"]], "select_symmetric_edges() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.select_symmetric_edges"]], "set_cutoffs() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.set_cutoffs"]], "set_max_neighbors() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.set_max_neighbors"]], "subselect_edges() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.subselect_edges"]], "subselect_graph() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.subselect_graph"]], "symmetrize_edges() (ocpmodels.models.gemnet_oc.gemnet_oc.gemnetoc method)": [[80, "ocpmodels.models.gemnet_oc.gemnet_oc.GemNetOC.symmetrize_edges"]], "ocpmodels.models.gemnet_oc": [[81, "module-ocpmodels.models.gemnet_oc"]], "_standardize() (in module ocpmodels.models.gemnet_oc.initializers)": [[82, "ocpmodels.models.gemnet_oc.initializers._standardize"]], "get_initializer() (in module ocpmodels.models.gemnet_oc.initializers)": [[82, "ocpmodels.models.gemnet_oc.initializers.get_initializer"]], "grid_init() (in module ocpmodels.models.gemnet_oc.initializers)": [[82, "ocpmodels.models.gemnet_oc.initializers.grid_init"]], "he_orthogonal_init() (in module ocpmodels.models.gemnet_oc.initializers)": [[82, "ocpmodels.models.gemnet_oc.initializers.he_orthogonal_init"]], "log_grid_init() (in module ocpmodels.models.gemnet_oc.initializers)": [[82, "ocpmodels.models.gemnet_oc.initializers.log_grid_init"]], "ocpmodels.models.gemnet_oc.initializers": [[82, "module-ocpmodels.models.gemnet_oc.initializers"]], "get_mixed_triplets() (in module ocpmodels.models.gemnet_oc.interaction_indices)": [[83, "ocpmodels.models.gemnet_oc.interaction_indices.get_mixed_triplets"]], "get_quadruplets() (in module ocpmodels.models.gemnet_oc.interaction_indices)": [[83, "ocpmodels.models.gemnet_oc.interaction_indices.get_quadruplets"]], "get_triplets() (in module ocpmodels.models.gemnet_oc.interaction_indices)": [[83, "ocpmodels.models.gemnet_oc.interaction_indices.get_triplets"]], "ocpmodels.models.gemnet_oc.interaction_indices": [[83, "module-ocpmodels.models.gemnet_oc.interaction_indices"]], "atomupdateblock (class in ocpmodels.models.gemnet_oc.layers.atom_update_block)": [[84, "ocpmodels.models.gemnet_oc.layers.atom_update_block.AtomUpdateBlock"]], "outputblock (class in ocpmodels.models.gemnet_oc.layers.atom_update_block)": [[84, "ocpmodels.models.gemnet_oc.layers.atom_update_block.OutputBlock"]], "forward() (ocpmodels.models.gemnet_oc.layers.atom_update_block.atomupdateblock method)": [[84, "ocpmodels.models.gemnet_oc.layers.atom_update_block.AtomUpdateBlock.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.atom_update_block.outputblock method)": [[84, "ocpmodels.models.gemnet_oc.layers.atom_update_block.OutputBlock.forward"]], "get_mlp() (ocpmodels.models.gemnet_oc.layers.atom_update_block.atomupdateblock method)": [[84, "ocpmodels.models.gemnet_oc.layers.atom_update_block.AtomUpdateBlock.get_mlp"]], "ocpmodels.models.gemnet_oc.layers.atom_update_block": [[84, "module-ocpmodels.models.gemnet_oc.layers.atom_update_block"]], "dense (class in ocpmodels.models.gemnet_oc.layers.base_layers)": [[85, "ocpmodels.models.gemnet_oc.layers.base_layers.Dense"]], "residuallayer (class in ocpmodels.models.gemnet_oc.layers.base_layers)": [[85, "ocpmodels.models.gemnet_oc.layers.base_layers.ResidualLayer"]], "scaledsilu (class in ocpmodels.models.gemnet_oc.layers.base_layers)": [[85, "ocpmodels.models.gemnet_oc.layers.base_layers.ScaledSiLU"]], "forward() (ocpmodels.models.gemnet_oc.layers.base_layers.dense method)": [[85, "ocpmodels.models.gemnet_oc.layers.base_layers.Dense.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.base_layers.residuallayer method)": [[85, "ocpmodels.models.gemnet_oc.layers.base_layers.ResidualLayer.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.base_layers.scaledsilu method)": [[85, "ocpmodels.models.gemnet_oc.layers.base_layers.ScaledSiLU.forward"]], "ocpmodels.models.gemnet_oc.layers.base_layers": [[85, "module-ocpmodels.models.gemnet_oc.layers.base_layers"]], "reset_parameters() (ocpmodels.models.gemnet_oc.layers.base_layers.dense method)": [[85, "ocpmodels.models.gemnet_oc.layers.base_layers.Dense.reset_parameters"]], "jn() (in module ocpmodels.models.gemnet_oc.layers.basis_utils)": [[86, "ocpmodels.models.gemnet_oc.layers.basis_utils.Jn"]], "jn_zeros() (in module ocpmodels.models.gemnet_oc.layers.basis_utils)": [[86, "ocpmodels.models.gemnet_oc.layers.basis_utils.Jn_zeros"]], "associated_legendre_polynomials() (in module ocpmodels.models.gemnet_oc.layers.basis_utils)": [[86, "ocpmodels.models.gemnet_oc.layers.basis_utils.associated_legendre_polynomials"]], "bessel_basis() (in module ocpmodels.models.gemnet_oc.layers.basis_utils)": [[86, "ocpmodels.models.gemnet_oc.layers.basis_utils.bessel_basis"]], "get_sph_harm_basis() (in module ocpmodels.models.gemnet_oc.layers.basis_utils)": [[86, "ocpmodels.models.gemnet_oc.layers.basis_utils.get_sph_harm_basis"]], "ocpmodels.models.gemnet_oc.layers.basis_utils": [[86, "module-ocpmodels.models.gemnet_oc.layers.basis_utils"]], "real_sph_harm() (in module ocpmodels.models.gemnet_oc.layers.basis_utils)": [[86, "ocpmodels.models.gemnet_oc.layers.basis_utils.real_sph_harm"]], "sph_harm_prefactor() (in module ocpmodels.models.gemnet_oc.layers.basis_utils)": [[86, "ocpmodels.models.gemnet_oc.layers.basis_utils.sph_harm_prefactor"]], "spherical_bessel_formulas() (in module ocpmodels.models.gemnet_oc.layers.basis_utils)": [[86, "ocpmodels.models.gemnet_oc.layers.basis_utils.spherical_bessel_formulas"]], "basisembedding (class in ocpmodels.models.gemnet_oc.layers.efficient)": [[87, "ocpmodels.models.gemnet_oc.layers.efficient.BasisEmbedding"]], "efficientinteractionbilinear (class in ocpmodels.models.gemnet_oc.layers.efficient)": [[87, "ocpmodels.models.gemnet_oc.layers.efficient.EfficientInteractionBilinear"]], "forward() (ocpmodels.models.gemnet_oc.layers.efficient.basisembedding method)": [[87, "ocpmodels.models.gemnet_oc.layers.efficient.BasisEmbedding.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.efficient.efficientinteractionbilinear method)": [[87, "ocpmodels.models.gemnet_oc.layers.efficient.EfficientInteractionBilinear.forward"]], "ocpmodels.models.gemnet_oc.layers.efficient": [[87, "module-ocpmodels.models.gemnet_oc.layers.efficient"]], "reset_parameters() (ocpmodels.models.gemnet_oc.layers.efficient.basisembedding method)": [[87, "ocpmodels.models.gemnet_oc.layers.efficient.BasisEmbedding.reset_parameters"]], "weight (ocpmodels.models.gemnet_oc.layers.efficient.basisembedding attribute)": [[87, "ocpmodels.models.gemnet_oc.layers.efficient.BasisEmbedding.weight"]], "atomembedding (class in ocpmodels.models.gemnet_oc.layers.embedding_block)": [[88, "ocpmodels.models.gemnet_oc.layers.embedding_block.AtomEmbedding"]], "edgeembedding (class in ocpmodels.models.gemnet_oc.layers.embedding_block)": [[88, "ocpmodels.models.gemnet_oc.layers.embedding_block.EdgeEmbedding"]], "forward() (ocpmodels.models.gemnet_oc.layers.embedding_block.atomembedding method)": [[88, "ocpmodels.models.gemnet_oc.layers.embedding_block.AtomEmbedding.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.embedding_block.edgeembedding method)": [[88, "ocpmodels.models.gemnet_oc.layers.embedding_block.EdgeEmbedding.forward"]], "ocpmodels.models.gemnet_oc.layers.embedding_block": [[88, "module-ocpmodels.models.gemnet_oc.layers.embedding_block"]], "forcescaler (class in ocpmodels.models.gemnet_oc.layers.force_scaler)": [[89, "ocpmodels.models.gemnet_oc.layers.force_scaler.ForceScaler"]], "calc_forces() (ocpmodels.models.gemnet_oc.layers.force_scaler.forcescaler method)": [[89, "ocpmodels.models.gemnet_oc.layers.force_scaler.ForceScaler.calc_forces"]], "calc_forces_and_update() (ocpmodels.models.gemnet_oc.layers.force_scaler.forcescaler method)": [[89, "ocpmodels.models.gemnet_oc.layers.force_scaler.ForceScaler.calc_forces_and_update"]], "ocpmodels.models.gemnet_oc.layers.force_scaler": [[89, "module-ocpmodels.models.gemnet_oc.layers.force_scaler"]], "scale() (ocpmodels.models.gemnet_oc.layers.force_scaler.forcescaler method)": [[89, "ocpmodels.models.gemnet_oc.layers.force_scaler.ForceScaler.scale"]], "unscale() (ocpmodels.models.gemnet_oc.layers.force_scaler.forcescaler method)": [[89, "ocpmodels.models.gemnet_oc.layers.force_scaler.ForceScaler.unscale"]], "update() (ocpmodels.models.gemnet_oc.layers.force_scaler.forcescaler method)": [[89, "ocpmodels.models.gemnet_oc.layers.force_scaler.ForceScaler.update"]], "ocpmodels.models.gemnet_oc.layers": [[90, "module-ocpmodels.models.gemnet_oc.layers"]], "interactionblock (class in ocpmodels.models.gemnet_oc.layers.interaction_block)": [[91, "ocpmodels.models.gemnet_oc.layers.interaction_block.InteractionBlock"]], "pairinteraction (class in ocpmodels.models.gemnet_oc.layers.interaction_block)": [[91, "ocpmodels.models.gemnet_oc.layers.interaction_block.PairInteraction"]], "quadrupletinteraction (class in ocpmodels.models.gemnet_oc.layers.interaction_block)": [[91, "ocpmodels.models.gemnet_oc.layers.interaction_block.QuadrupletInteraction"]], "tripletinteraction (class in ocpmodels.models.gemnet_oc.layers.interaction_block)": [[91, "ocpmodels.models.gemnet_oc.layers.interaction_block.TripletInteraction"]], "forward() (ocpmodels.models.gemnet_oc.layers.interaction_block.interactionblock method)": [[91, "ocpmodels.models.gemnet_oc.layers.interaction_block.InteractionBlock.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.interaction_block.pairinteraction method)": [[91, "ocpmodels.models.gemnet_oc.layers.interaction_block.PairInteraction.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.interaction_block.quadrupletinteraction method)": [[91, "ocpmodels.models.gemnet_oc.layers.interaction_block.QuadrupletInteraction.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.interaction_block.tripletinteraction method)": [[91, "ocpmodels.models.gemnet_oc.layers.interaction_block.TripletInteraction.forward"]], "ocpmodels.models.gemnet_oc.layers.interaction_block": [[91, "module-ocpmodels.models.gemnet_oc.layers.interaction_block"]], "bernsteinbasis (class in ocpmodels.models.gemnet_oc.layers.radial_basis)": [[92, "ocpmodels.models.gemnet_oc.layers.radial_basis.BernsteinBasis"]], "exponentialenvelope (class in ocpmodels.models.gemnet_oc.layers.radial_basis)": [[92, "ocpmodels.models.gemnet_oc.layers.radial_basis.ExponentialEnvelope"]], "gaussianbasis (class in ocpmodels.models.gemnet_oc.layers.radial_basis)": [[92, "ocpmodels.models.gemnet_oc.layers.radial_basis.GaussianBasis"]], "polynomialenvelope (class in ocpmodels.models.gemnet_oc.layers.radial_basis)": [[92, "ocpmodels.models.gemnet_oc.layers.radial_basis.PolynomialEnvelope"]], "radialbasis (class in ocpmodels.models.gemnet_oc.layers.radial_basis)": [[92, "ocpmodels.models.gemnet_oc.layers.radial_basis.RadialBasis"]], "sphericalbesselbasis (class in ocpmodels.models.gemnet_oc.layers.radial_basis)": [[92, "ocpmodels.models.gemnet_oc.layers.radial_basis.SphericalBesselBasis"]], "forward() (ocpmodels.models.gemnet_oc.layers.radial_basis.bernsteinbasis method)": [[92, "ocpmodels.models.gemnet_oc.layers.radial_basis.BernsteinBasis.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.radial_basis.exponentialenvelope method)": [[92, "ocpmodels.models.gemnet_oc.layers.radial_basis.ExponentialEnvelope.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.radial_basis.gaussianbasis method)": [[92, "ocpmodels.models.gemnet_oc.layers.radial_basis.GaussianBasis.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.radial_basis.polynomialenvelope method)": [[92, "ocpmodels.models.gemnet_oc.layers.radial_basis.PolynomialEnvelope.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.radial_basis.radialbasis method)": [[92, "ocpmodels.models.gemnet_oc.layers.radial_basis.RadialBasis.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.radial_basis.sphericalbesselbasis method)": [[92, "ocpmodels.models.gemnet_oc.layers.radial_basis.SphericalBesselBasis.forward"]], "ocpmodels.models.gemnet_oc.layers.radial_basis": [[92, "module-ocpmodels.models.gemnet_oc.layers.radial_basis"]], "circularbasislayer (class in ocpmodels.models.gemnet_oc.layers.spherical_basis)": [[93, "ocpmodels.models.gemnet_oc.layers.spherical_basis.CircularBasisLayer"]], "sphericalbasislayer (class in ocpmodels.models.gemnet_oc.layers.spherical_basis)": [[93, "ocpmodels.models.gemnet_oc.layers.spherical_basis.SphericalBasisLayer"]], "forward() (ocpmodels.models.gemnet_oc.layers.spherical_basis.circularbasislayer method)": [[93, "ocpmodels.models.gemnet_oc.layers.spherical_basis.CircularBasisLayer.forward"]], "forward() (ocpmodels.models.gemnet_oc.layers.spherical_basis.sphericalbasislayer method)": [[93, "ocpmodels.models.gemnet_oc.layers.spherical_basis.SphericalBasisLayer.forward"]], "ocpmodels.models.gemnet_oc.layers.spherical_basis": [[93, "module-ocpmodels.models.gemnet_oc.layers.spherical_basis"]], "calculate_interatomic_vectors() (in module ocpmodels.models.gemnet_oc.utils)": [[94, "ocpmodels.models.gemnet_oc.utils.calculate_interatomic_vectors"]], "get_angle() (in module ocpmodels.models.gemnet_oc.utils)": [[94, "ocpmodels.models.gemnet_oc.utils.get_angle"]], "get_edge_id() (in module ocpmodels.models.gemnet_oc.utils)": [[94, "ocpmodels.models.gemnet_oc.utils.get_edge_id"]], "get_inner_idx() (in module ocpmodels.models.gemnet_oc.utils)": [[94, "ocpmodels.models.gemnet_oc.utils.get_inner_idx"]], "get_neighbor_order() (in module ocpmodels.models.gemnet_oc.utils)": [[94, "ocpmodels.models.gemnet_oc.utils.get_neighbor_order"]], "get_projected_angle() (in module ocpmodels.models.gemnet_oc.utils)": [[94, "ocpmodels.models.gemnet_oc.utils.get_projected_angle"]], "inner_product_clamped() (in module ocpmodels.models.gemnet_oc.utils)": [[94, "ocpmodels.models.gemnet_oc.utils.inner_product_clamped"]], "mask_neighbors() (in module ocpmodels.models.gemnet_oc.utils)": [[94, "ocpmodels.models.gemnet_oc.utils.mask_neighbors"]], "masked_select_sparsetensor_flat() (in module ocpmodels.models.gemnet_oc.utils)": [[94, "ocpmodels.models.gemnet_oc.utils.masked_select_sparsetensor_flat"]], "ocpmodels.models.gemnet_oc.utils": [[94, 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"ocpmodels.trainers.ocp_trainer.OCPTrainer.train"]]}}) \ No newline at end of file diff --git a/tutorials/NRR/NRR_example-gemnet.html b/tutorials/NRR/NRR_example-gemnet.html index 1aebd25af..6fb5daeea 100644 --- a/tutorials/NRR/NRR_example-gemnet.html +++ b/tutorials/NRR/NRR_example-gemnet.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
  • ocpmodels.common.model_registry
  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • diff --git a/tutorials/NRR/NRR_example.html b/tutorials/NRR/NRR_example.html index 60137f88c..5308746ea 100644 --- a/tutorials/NRR/NRR_example.html +++ b/tutorials/NRR/NRR_example.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
  • ocpmodels.common.model_registry
  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • @@ -684,7 +686,7 @@

    Run an ML relaxationRunning the model with BFGS prints at each relaxation step is a lot to print. So we will just run one to demonstrate what happens on each iteration.

    -
    from ocpmodels.common.model_registry import model_name_to_local_file
    +
    from ocpmodels.models.model_registry import model_name_to_local_file
     
     checkpoint_path = model_name_to_local_file('eSCN-L6-M3-Lay20All+MD', local_cache='/tmp/ocp_checkpoints/')
     
    diff --git a/tutorials/NRR/NRR_toc.html b/tutorials/NRR/NRR_toc.html
    index e387bdcb8..577246d6d 100644
    --- a/tutorials/NRR/NRR_toc.html
    +++ b/tutorials/NRR/NRR_toc.html
    @@ -177,9 +177,10 @@
                     
                 
             
    -        

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
  • ocpmodels.common.model_registry
  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • diff --git a/tutorials/OCP-introduction.html b/tutorials/OCP-introduction.html index 6a607d35d..3168f8fa4 100644 --- a/tutorials/OCP-introduction.html +++ b/tutorials/OCP-introduction.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
  • ocpmodels.common.model_registry
  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • @@ -620,7 +622,7 @@

    Calculating adsorption energies
    -
    from ocpmodels.common.model_registry import model_name_to_local_file
    +
    from ocpmodels.models.model_registry import model_name_to_local_file
     
     checkpoint_path = model_name_to_local_file('eSCN-L6-M3-Lay20All+MD', local_cache='/tmp/ocp_checkpoints/')
     
    diff --git a/tutorials/advanced/advanced_toc.html b/tutorials/advanced/advanced_toc.html index d47c188b0..c19c52865 100644 --- a/tutorials/advanced/advanced_toc.html +++ b/tutorials/advanced/advanced_toc.html @@ -177,9 +177,10 @@
    -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
  • ocpmodels.common.model_registry
  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • diff --git a/tutorials/advanced/embeddings.html b/tutorials/advanced/embeddings.html index b7f726f14..fb1112144 100644 --- a/tutorials/advanced/embeddings.html +++ b/tutorials/advanced/embeddings.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
  • ocpmodels.common.model_registry
  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • diff --git a/tutorials/advanced/fine-tuning-in-python.html b/tutorials/advanced/fine-tuning-in-python.html index e19323957..643547752 100644 --- a/tutorials/advanced/fine-tuning-in-python.html +++ b/tutorials/advanced/fine-tuning-in-python.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
  • ocpmodels.common.model_registry
  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • diff --git a/tutorials/advanced/fine-tuning-toc.html b/tutorials/advanced/fine-tuning-toc.html index 7d81a8440..8db488772 100644 --- a/tutorials/advanced/fine-tuning-toc.html +++ b/tutorials/advanced/fine-tuning-toc.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
  • ocpmodels.common.model_registry
  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • diff --git a/tutorials/advanced/mass-inference.html b/tutorials/advanced/mass-inference.html index aabc28db4..b9441c710 100644 --- a/tutorials/advanced/mass-inference.html +++ b/tutorials/advanced/mass-inference.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
  • ocpmodels.common.model_registry
  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • @@ -587,15 +589,15 @@

    Mass inference
    -
    from ocpmodels.common.model_registry import MODEL_REGISTRY
    -print(MODEL_REGISTRY.keys())
    +
    from ocpmodels.models.model_registry import available_pretrained_models
    +print(available_pretrained_models)
     
    -
    from ocpmodels.common.model_registry import model_name_to_local_file
    +
    from ocpmodels.models.model_registry import model_name_to_local_file
     
     checkpoint_path = model_name_to_local_file('GemNet-dT OC22', local_cache='/tmp/ocp_checkpoints/')
     checkpoint_path
    diff --git a/tutorials/fine-tuning/fine-tuning-oxides.html b/tutorials/fine-tuning/fine-tuning-oxides.html
    index 5c10e53de..16eebeead 100644
    --- a/tutorials/fine-tuning/fine-tuning-oxides.html
    +++ b/tutorials/fine-tuning/fine-tuning-oxides.html
    @@ -177,9 +177,10 @@
                     
                 
             
    -        

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
  • ocpmodels.common.model_registry
  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • @@ -579,7 +581,7 @@

    Fine tuning a model
    -
    from ocpmodels.common.model_registry import model_name_to_local_file
    +
    from ocpmodels.models.model_registry import model_name_to_local_file
     
     checkpoint_path = model_name_to_local_file('GemNet-OC OC20+OC22', local_cache='/tmp/ocp_checkpoints/')
     
    diff --git a/tutorials/gotchas.html b/tutorials/gotchas.html index 9ae4c4a78..c405d5c15 100644 --- a/tutorials/gotchas.html +++ b/tutorials/gotchas.html @@ -177,9 +177,10 @@
    -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
  • ocpmodels.common.model_registry
  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • diff --git a/tutorials/intro.html b/tutorials/intro.html index 71debc3e9..e0d96765d 100644 --- a/tutorials/intro.html +++ b/tutorials/intro.html @@ -177,9 +177,10 @@ -

    Installation & License

    +

    Quickstart & Installation

    Released Datasets & Models

    @@ -210,6 +211,7 @@ +
  • Simple simulations using the OCP ASE calculator
  • @@ -291,7 +293,6 @@
  • ocpmodels.common.gp_utils
  • ocpmodels.common.hpo_utils
  • ocpmodels.common.logger
  • -
  • ocpmodels.common.model_registry
  • ocpmodels.common.registry
  • ocpmodels.common.transforms
  • ocpmodels.common.tutorial_utils
  • @@ -320,6 +321,7 @@
  • ocpmodels.models.utils
  • ocpmodels.models.base
  • ocpmodels.models.dimenet_plus_plus
  • +
  • ocpmodels.models.model_registry
  • ocpmodels.models.schnet
  • @@ -550,10 +552,8 @@

    Contents