diff --git a/README.md b/README.md index 2a8aeb2..3e4f8fb 100644 --- a/README.md +++ b/README.md @@ -26,11 +26,10 @@ MoreRed is built on top of [SchNetPack 2.0](https://github.com/atomistic-machine + [News](/README.md##News) + [Installation](/README.md##Installation) -+ [Training](/README.md##Training) -+ [Pre-trained models](/README.md##Pre-trained-models) -+ [Molecular relaxation](/README.md##Molecular-relaxation) -+ [Molecular structure generation](/README.md##Molecular-structure-generation) ++ [Using pre-trained models](/README.md##Using-pre-trained-models) ++ [Molecular relaxation and structure generation](/README.md##Molecular-relaxation-relaxation-and-structure-generation) + [Tutorials](/README.md##Tutorials) ++ [Training your own models](/README.md##Training-your-own-models) + [How to cite](/README.md##How-to-cite) ## News @@ -58,8 +57,19 @@ Now to install the package, inside the folder `MoreRed` run: ``` pip install . ``` +## Using pre-trained models +Under the folder `models`, you can find the final models trained on QM9 and Qm7-X datasets until complete convergence. You can load the models using `torch.load()` command. Besides, the tutorial notebooks provide details on how to use the models. + +## Molecular relaxation and structure generation +The notebook `notebooks/denoising_tutorial.ipynb` explains how the trained models can be used for denoising and generation from scratch using different samplers. +Under `src/morered/sampling`, you can find ready-to-use Python classes implementing the different samplers: `MoreRed-ITP`, `MoreRed-JT`, `MoreRed-AS`, `DDPM`. The same classes can be used for denoising/relaxation of noisy structures as well as for new structure generation. + +## Tutorials +Under `notebooks`, we provide different tutorials in the form of Jupyter notebooks, that will be continually updated: + - `diffusion_tutorial.ipynb`: explains how to use the diffusion processes implemented in `morered`. + - `denoising_tutorial.ipynb`: explains how to use the trained models with the different samplers implemented in `morered` for noisy structure relaxation or generation from scratch. Under the folder `models`, we provide final models trained on QM9 and QM7-X datasets until complete convergence. -## Training +## Training your own models The human-readable and customizable YAML configuration files under `src/morered/configs` are all you need to train and run customizable experiments with `morered`. They follow the configuration structure used in [SchNetPack 2.0](https://github.com/atomistic-machine-learning/schnetpack/tree/master). Here, we explain how to train and use the different models. Installing `morered` using pip adds the new CLI command `mrdtrain`, which can be used to train the different models by running the command: @@ -105,18 +115,6 @@ mrdtrain --config-dir= experiment= ``` More about overwriting configurations in the CLI can be found in the [SchNetPack 2.0](https://github.com/atomistic-machine-learning/schnetpack/tree/master) documentation. -## Pre-trained models -Under the folder `models`, you can find the final models trained on QM9 and Qm7-X datasets until complete convergence. You can load the models using `torch.load()` command. Besides, the tutorial notebooks provide details on how to use the models. - -## Molecular relaxation/generation -The notebook `notebooks/denoising_tutorial.ipynb` explains how the trained models can be used for denoising and generation from scratch using different samplers. -Under `src/morered/sampling`, you can find ready-to-use Python classes implementing the different samplers: `MoreRed-ITP`, `MoreRed-JT`, `MoreRed-AS`, `DDPM`. The same classes can be used for denoising/relaxation of noisy structures as well as for new structure generation. - -## Tutorials -Under `notebooks`, we provide different tutorials in the form of Jupyter notebooks, that will be continually updated: - - `diffusion_tutorial.ipynb`: explains how to use the diffusion processes implemented in `morered`. - - `denoising_tutorial.ipynb`: explains how to use the trained models with the different samplers implemented in `morered` for noisy structure relaxation or generation from scratch. Under the folder `models`, we provide final models trained on QM9 and QM7-X datasets until complete convergence. - ## How to cite if you use MoreRed in your research, please cite the corresponding publication: