aimat-lab / ml4pxrds

Contains code to train neural networks based on simulated powder XRDs from synthetic crystals.

ML for pXRDs using synthetic crystals

This repository contains the code of the publication "Neural networks trained on synthetically generated crystals can extract structural information from ICSD powder X-ray diffractograms". It can be used to train machine learning models (e.g., for the classification of space groups) on powder XRD diffractograms simulated on-the-fly from synthetically generated random crystal structures.

You can find details about this project in our paper. If you want to cite our work, you can use the provided bibtex file CITATION.bib.

If you have any problems using the provided software, if documentation is missing, or if you find any bugs, feel free to add a new issue on GitHub.

The repository contains the following components:

1. Optimized simulation

   The code of the optimized simulation of powder XRDs (using numba LLVM just-in-time compilation) can be found in ./ml4pxrd_tools/simulation/. This code is based on the implementation found in the pymatgen library.

2. Generation of synthetic crystals

   The code of the generation of synthetic crystals can be found in ./ml4pxrd_tools/generation/.

3. Distributed training

   The code of the distributed training architecture uses tensorflow with the distributed computing framework ray. The relevant script files can be found in ./training/.

Documentation

Getting started

For convenience, the code for the optimized simulation of pXRDs and generation of synthetic crystals is provided as a package called ml4pxrd_tools. Before training, this should be installed, ideally in a separate virtual environment or anaconda environment. We tested the package with python 3.8.0 on Ubuntu, but it should also work for other python versions and operating systems.

To install the package, call pip in the root of the repository:

pip install -e .

This will further install all required dependencies.

To further run the training script and some of the analysis scripts in ./training/analysis, the following additional dependencies can be installed using pip:

• ray
• psutil
• ase
• tensorflow
• tensorflow-addons

We tested and recommend TensorFlow version 2.10.0. Also, make sure that the CUDA and cuDNN dependencies of tensorflow are installed and that the versions are compatible (we refer to the table available at https://www.tensorflow.org/install/source#tested_build_configurations). For TensorFlow 2.10.0, you can simply install the required CUDA and cuDNN dependencies using conda:

conda install -c conda-forge cudatoolkit==11.2.0
conda install -c conda-forge cudnn==8.1.0.77

Loading statistics of the ICSD

In order to be able to generate synthetic crystals, some general statistics (e.g., about the occupation of the Wyckoff positions for each space group) need to be extracted from the ICSD. If you only want to generate synthetic crystals (and simulate pXRDs based on them) without running your own training experiments, you can use the statistical data provided by us in ./public_statistics. We refer to section Training of this README if you want to create your own dataset and extract your own statistics from the ICSD.

The required data can be loaded using the function ml4pxrd_tools.manage_dataset.load_dataset_info with parameter load_public_statistics_only=True. The returned objects can then be passed to the respective functions to generate synthetic crystals and simulate pXRDs (see below).

from ml4pxrd_tools.manage_dataset import load_dataset_info

(
    probability_per_spg_per_element,
    probability_per_spg_per_element_per_wyckoff,
    NO_unique_elements_prob_per_spg,
    NO_repetitions_prob_per_spg_per_element,
    denseness_factors_density_per_spg,
    denseness_factors_conditional_sampler_seeds_per_spg,
    lattice_paras_density_per_lattice_type,
    per_element,
    represented_spgs,
    probability_per_spg,
) = load_dataset_info(load_public_statistics_only=True)

Generating synthetic crystals

After loading the statistics, you can use the statistics to generate synthetic structures of a given space group (here for space group 125):

from ml4pxrd_tools.generation.structure_generation import generate_structures

structures = generate_structures(
    125,
    N=1,
    probability_per_spg_per_element=probability_per_spg_per_element,
    probability_per_spg_per_element_per_wyckoff=probability_per_spg_per_element_per_wyckoff,
    NO_unique_elements_prob_per_spg=NO_unique_elements_prob_per_spg,
    NO_repetitions_prob_per_spg_per_element=NO_repetitions_prob_per_spg_per_element,
    denseness_factors_conditional_sampler_seeds_per_spg=denseness_factors_conditional_sampler_seeds_per_spg,
    lattice_paras_density_per_lattice_type=lattice_paras_density_per_lattice_type,
)

Simulating pXRDs

This repository provides various functions to simulate powder XRD diffractograms:

• Use function ml4pxrd_tools.simulation.simulation_core.get_pattern_optimized for fast simulation of the angles and intensities of all peaks in a given $2\theta$ range. This uses an optimized version of the pymatgen implementation.
• Use function ml4pxrd_tools.simulation.simulation_smeared.get_smeared_patterns to simulate one or more smeared patterns (peaks convoluted with a Gaussian preak profile) for a given structure object.
• Use function ml4pxrd_tools.simulation.simulation_smeared.get_synthetic_smeared_patterns to generate synthetic crystals and simulate pXRDs based on them.

Here is an example of how to call get_synthetic_smeared_patterns using the statistics loaded using load_dataset_info (see above):

from ml4pxrd_tools.simulation.simulation_smeared import get_synthetic_smeared_patterns

patterns, labels = get_synthetic_smeared_patterns(
    [125],
    N_structures_per_spg=5,
    wavelength=1.5406,
    two_theta_range=(5, 90),
    N=8501,
    NO_corn_sizes=1,
    probability_per_spg_per_element=probability_per_spg_per_element,
    probability_per_spg_per_element_per_wyckoff=probability_per_spg_per_element_per_wyckoff,
    NO_unique_elements_prob_per_spg=NO_unique_elements_prob_per_spg,
    NO_repetitions_prob_per_spg_per_element=NO_repetitions_prob_per_spg_per_element,
    denseness_factors_conditional_sampler_seeds_per_spg=denseness_factors_conditional_sampler_seeds_per_spg,
    lattice_paras_density_per_lattice_type=lattice_paras_density_per_lattice_type,
)

The functions get_smeared_patterns and get_synthetic_smeared_patterns calculate the FWHM of the gaussian peak profiles using the Scherrer equation with a random crystallite size uniformly sampled in the range pymatgen_crystallite_size_gauss_min=20 to pymatgen_crystallite_size_gauss_max=100 (in nm). You can change the default range at the top of script file ./ml4pxrd_tools/simulation/simulation_smeared.py.

Training

You can find the weights of our largest model (ResNet-101) trained using synthetic crystals and the weights of the ResNet-50 trained with experimental imperfections in our latest release.

Pre-simulate patterns for testing

If you want to run your own ML experiments, you need to generate your own dataset from the ICSD that contains the required simulated diffractograms and crystals. This is needed to test the accuracy of the ML models.

In order to generate a dataset, a license for the ICSD database is needed. If you have the license and downloaded the database, you need to first simulate powder diffractograms based on the ICSD crystals. This can be accomplished by running the script ./ml4pxrd_tools/simulation/icsd_simulator.py. Before running this script, make sure that you change the variables at the top of this script file, of the file simulation_worker.py, and of simulation_smeared.py.

Instead of running the script directly, you can also use the provided slurm script submit_icsd_simulation_slurm.slr to run it on a cluster. Make sure to adapt it to your cluster first and potentially change the path to your .bashrc file and the name of your anaconda environment.

As a point of reference, it takes ~14 hours to simulate the full ICSD on 8 cores.

Extract statistics and generate dataset split

To generate a new dataset with prototype-based split using the just simulated patterns, you can use the script ./ml4pxrd_tools/manage_dataset.py. Please first change the variables at the top of this script file. Then, you can generate the dataset and extract the statistics:

python manage_dataset.py

This will take a while (~5 hours). Finally, you can find the prepared dataset including the statistics in the directory ./prepared_dataset.

Run experiments

At the top of the training script (./trainig/train_random_classifier.py), you can find some variables / options of the training experiment including detailed explanations. While you should look through all options, the following options always need to be changed:

• path_to_patterns
• path_to_icsd_directory_local or path_to_icsd_directory_cluster

Furthermore, you might want to change the used model (see line model = build_model_XX(...)). You can find the models implemented by us in the file ./training/models.py.

You can call the training script like this:

python train_classifier.py <Unique name / ID of experiment> head-only <number of ray workers>

Instead of calling the script directly, you can also use the slurm script files contained in ./training/submit_scripts_slurm/ to perform the training runs. You can use submit_head_only.sh to run an experiment on a single node containing one or more GPUs.

However, to obtain reasonable training times, we recommend using additional compute nodes to generate synthetic crystals and simulate their powder diffractogram. Depending on the model size, the number of needed cores to not throttle the training process changes (bigger models train slower and need less compute cores). You can use the script submit.sh (execute with bash, not sbatch) to automatically spawn three slurm jobs on different compute nodes: one head job and two compute worker jobs. The three jobs will wait until all jobs are started and then initiate the training experiment. If your cluster supports heterogeneous jobs, feel free to adapt the scripts accordingly.

Make sure to adapt all submit scripts to the exact specifications of your cluster and change the name of the anaconda environment and potentially the path to your .bashrc file in all submit scripts.

Each training experiment will put its data (TensorBoard data, logs, checkpoint files) in a separate run directory. The current run directory will be printed in the beginning of the training script.

The easiest way to track the progress and results of your training runs is to use TensorBoard. Simply navigate to the run directory in your terminal and execute tensorboard --logdir ..

There are several metrics that are logged to TensorBoard during a run:

• accuracy/loss all: Performance on ICSD test dataset
• accuracy/loss match: Performance on ICSD test dataset, only using structures that match the simulation parameters (volume < 7000 angstroms, less than 100 atoms in asymmetric unit)
• accuracy/loss random: Performance on pXRDs from synthetically generated crystals (same distribution as training data)
• accuracy/loss match_correct_spgs: Performance on ICSD test dataset, only using structures that match the simulation parameters. Furthermore, the space group labels obtained using spglib are used instead of those provided by the ICSD.
• accuracy/loss match_correct_spgs_pure: Performance on ICSD test dataset, only using structures that match the simulation parameters. Furthermore, the space group labels obtained using spglib are used instead of those provided by the ICSD. Also, only structures without partial occupancies are used.
• accuracy gap: accuracy random - accuracy match

Additionally to those metrics, after each epoch, the current learning rate and the current size of the ray queue object (indicating if enough workers are used) are logged.

Inference

You can either use one of the models provided in our latest release or your own trained models to run inference on new diffractograms.

import tensorflow.keras as keras

model = keras.models.load_model("path/to/your/model")

predictions = model.predict(your_diffractograms, batch_size=145)