# Crystal structure prediction of materials with high symmetry using differential evolution

arXiv: https://arxiv.org/abs/2104.09764 · HTML: https://mlsanity.com/paper/2104.09764/

## Key facts

- Cited by 9 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 20 Apr 2021.

## Built on by (most cited first, 9 of 9)

- [Crystal Diffusion Variational Autoencoder for Periodic Material Generation](https://mlsanity.com/paper/2110.06197/) (2021)
- [Crystal Structure Prediction by Joint Equivariant Diffusion](https://mlsanity.com/paper/2309.04475/) (2023)
- [FlowMM: Generating Materials with Riemannian Flow Matching](https://mlsanity.com/paper/2406.04713/) (2024)
- [Space Group Constrained Crystal Generation](https://mlsanity.com/paper/2402.03992/) (2024)
- [MOFFlow: Flow Matching for Structure Prediction of Metal-Organic Frameworks](https://mlsanity.com/paper/2410.17270/) (2024)
- [A Periodic Bayesian Flow for Material Generation](https://mlsanity.com/paper/2502.02016/) (2025)
- [Equivariant Diffusion for Crystal Structure Prediction](https://mlsanity.com/paper/2512.07289/) (2025)
- [A Generic Performance Model for Deep Learning in a Distributed Environment](https://mlsanity.com/paper/2305.11665/) (2023)
- [Fundamental Limits of Crystalline Equivariant Graph Neural Networks: A Circuit Complexity Perspective](https://mlsanity.com/paper/2510.05494/) (2025)

## Abstract (arXiv)

Crystal structure determines properties of materials. With the crystal structure of a chemical substance, many physical and chemical properties can be predicted by first-principles calculations or machine learning models. Since it is relatively easy to generate a hypothetical chemically valid formula, crystal structure prediction becomes an important method for discovering new materials. In our previous work, we proposed a contact map-based crystal structure prediction method, which uses global optimization algorithms such as genetic algorithms to maximize the match between the contact map of the predicted structure and the contact map of the real crystal structure to search for the coordinates at the Wyckoff Positions(WP). However, when predicting the crystal structure with high symmetry, we found that the global optimization algorithm has difficulty to find an effective combination of WPs that satisfies the chemical formula, which is mainly caused by the inconsistency between the dimensionality of the contact map of the predicted crystal structure and the dimensionality of the contact map of the target crystal structure. This makes it challenging to predict the crystal structures of high-symmetry crystals. In order to solve this problem, here we propose to use PyXtal to generate and filter random crystal structures with given symmetry constraints based on the information such as chemical formulas and space groups. With contact map as the optimization goal, we use differential evolution algorithms to search for non-special coordinates at the Wyckoff positions to realize the structure prediction of high-symmetry crystal materials. Our experimental results show that our proposed algorithm CMCrystalHS can effectively solve the problem of inconsistent contact map dimensions and predict the crystal structures with high symmetry.