| ---
|
| configs:
|
| - config_name: default
|
| data_files:
|
| - split: train
|
| path: Dataset_A_MatterGen_Reproduction.parquet
|
| - config_name: no_lanthanoids
|
| data_files:
|
| - split: train
|
| path: Dataset_A_No_Lanthanoids.parquet
|
| - config_name: extension
|
| data_files:
|
| - split: train
|
| path: Dataset_B_Extension.parquet
|
| ---
|
|
|
| # Le-Mat-Bulk_matgen_constrained
|
|
|
| This repository contains preprocessed datasets from the LeMat-Bulk dataset prepared for MatterGen-style retraining.
|
|
|
| ---
|
|
|
| ## 🚀 Loading the Dataset
|
|
|
| Since this repository is public, you can load the dataset subsets directly without authentication using the Hugging Face `datasets` library:
|
|
|
| ```python
|
| from datasets import load_dataset
|
|
|
| # Load Default (Dataset A)
|
| dataset_a = load_dataset("youssefsassi/Le-Mat-Bulk_matgen_constrained", name="default")
|
|
|
| # Load No Lanthanoids
|
| dataset_no_lan = load_dataset("youssefsassi/Le-Mat-Bulk_matgen_constrained", name="no_lanthanoids")
|
|
|
| # Load Extension (Dataset B)
|
| dataset_b = load_dataset("youssefsassi/Le-Mat-Bulk_matgen_constrained", name="extension")
|
| ```
|
|
|
| ---
|
|
|
| ## 🛠️ Generation Procedure and Filter Counts
|
|
|
| To save computation time (since `pymatgen` and `spglib` primitive structure standardization are highly expensive CPU operations), the pipeline performs **primitivization only once on the broader Dataset B superset** (which uses looser constraints). The stricter Dataset A and its subsets are then derived directly from the pre-primitivized Dataset B.
|
|
|
| ### Step-by-Step Preprocessing Flow:
|
| 1. **Joined Inputs**: Loads and joins the structures from `LeMaterial/LeMat-Bulk` (config `compatible_pbe`) and DFT hulls from `LeMaterial/LeMat-Bulk-DFT-Hull-All` on `immutable_id`.
|
| 2. **Element Exclusions**: Excludes noble gases, Technetium (`Tc`), Promethium (`Pm`), and elements with atomic numbers greater than 84 (`> Po`).
|
| 3. **DFT Hull Pre-filtering**:
|
| * Dataset B filter: `dft_hull <= 0.15`
|
| * Dataset A filter: `dft_hull <= 0.10`
|
| 4. **Primitivization (Symmetry Standardization)**:
|
| * Performed on the Dataset B candidates. Spglib standardizes the structures and obtains primitive cells.
|
| 5. **Post-primitive Site Filtering**:
|
| * Applies the site count filter `nsites <= 40` on Dataset B's standardized primitive cells.
|
| 6. **Deduplication**:
|
| * Removes any duplicate entries to produce the final **Dataset B (Extension)**.
|
| 7. **Derivation of Dataset A (MatterGen Reproduction)**:
|
| * Applies stricter filters to the deduplicated Dataset B primitive superset: `dft_hull <= 0.10` and `nsites <= 20`.
|
| 8. **Derivation of Dataset A No Lanthanoids**:
|
| * Derived from the finalized Dataset A by removing all Lanthanoids (`La`, `Ce`, `Pr`, `Nd`, `Sm`, `Eu`, `Gd`, `Tb`, `Dy`, `Ho`, `Er`, `Tm`, `Yb`, `Lu`).
|
|
|
| ---
|
|
|
| ## 📐 Primitive Structure Standardization Statistics
|
|
|
| Symmetry standardization using `spglib` and `pymatgen`'s SpacegroupAnalyzer was run to reduce structures to their standard primitive form. By comparing the site counts (`nsites`) before and after the standardization pass, we find the following ratios of structures that were **already primitive** (i.e., their site counts remained unchanged):
|
|
|
| * **Dataset B (Extension)**:
|
| * Total matched structures: **1,664,351**
|
| * Already primitive before standardization: **1,639,324**
|
| * Ratio: **98.50%**
|
| * **Dataset A (MatterGen)**:
|
| * Total matched structures: **1,181,982**
|
| * Already primitive before standardization: **1,165,630**
|
| * Ratio: **98.62%**
|
|
|
| This indicates that **~98.5%** of the LeMat-Bulk structures matching our initial constraints were already in their primitive standardized representation, with only **~1.5%** being conventional cells that standard-reduced to a smaller site count.
|
|
|
| ---
|
|
|
| ## 📊 Detailed Filtering and Exclusion Statistics
|
|
|
| ### Step-Wise Preprocessing Pipeline Counts:
|
|
|
| | Dataset / Subset | Preprocessing Step | Row Count | Details |
|
| | :--- | :--- | :--- | :--- |
|
| | **All** | Joined Input (Initial) | **5,335,286** | Initial raw join on `immutable_id` |
|
| | **All** | After Element Exclusions | **4,426,249** | Excluded noble gases, Tc, Pm, and Z > 84 |
|
| | **Dataset B (Candidate)** | After DFT Hull Filtering | **1,699,744** | Cutoff: `dft_hull <= 0.15` |
|
| | **Dataset B (Candidate)** | Primitivization Success | **1,699,744** | Standardized primitive cells (0 failures) |
|
| | **Dataset B (Candidate)** | After Post-primitive `nsites` Filter | **1,664,358** | Cutoff: post-primitive `nsites <= 40` |
|
| | **Dataset B (Extension)** | **Final Deduplicated Output** | **1,664,351** | Final Dataset B count |
|
| | **Dataset A** | Primitive Superset Input | **1,664,351** | Input from finalized Dataset B |
|
| | **Dataset A (MatterGen)** | **Final Derived Output** | **1,181,982** | Stricter filters: `dft_hull <= 0.10` and `nsites <= 20` |
|
| | **Dataset A (No Lanthanoids)**| **Final Derived Output** | **611,142** | Excluded 14 Lanthanoids from Dataset A |
|
|
|
| ---
|
|
|
| ### Step-Wise Element Exclusions Simulation (Initial Join):
|
| When processing the initial raw joined dataset of **5,335,265** rows:
|
| 1. **Exclude Noble Gases** (Ar, He, Kr, Ne, Rn, Xe):
|
| * Dropped: **280** rows
|
| * Remaining: **5,334,985** rows
|
| 2. **Exclude MatterGen Excluded Elements** (Pm, Tc):
|
| * Dropped: **368,159** rows
|
| * Remaining: **4,966,826** rows
|
| 3. **Exclude Z > 84 elements**:
|
| * Dropped: **540,598** rows
|
| * Remaining: **4,426,228** rows (Total Baseline Excluded dropped: **909,037** rows)
|
|
|
| ---
|
|
|
| ### Specific Excluded Element Occurrences in Joined Structures:
|
| The number of structures in the initial joined dataset containing each of the excluded/ablation elements (sorted by occurrence count):
|
|
|
| | Element Group | Element | Row Count | % of Joined |
|
| | :--- | :--- | :--- | :--- |
|
| | **Lanthanoids** | La | 282,978 | 5.3039% |
|
| | **MatterGen Excluded** | Pm | 201,275 | 3.7725% |
|
| | **Lanthanoids** | Nd | 199,001 | 3.7299% |
|
| | **Lanthanoids** | Dy | 196,523 | 3.6835% |
|
| | **Lanthanoids** | Pr | 196,414 | 3.6814% |
|
| | **Lanthanoids** | Sm | 196,112 | 3.6758% |
|
| | **Lanthanoids** | Tb | 195,823 | 3.6704% |
|
| | **Lanthanoids** | Ho | 193,884 | 3.6340% |
|
| | **Lanthanoids** | Tm | 189,611 | 3.5539% |
|
| | **Lanthanoids** | Er | 188,347 | 3.5302% |
|
| | **MatterGen Excluded** | Tc | 168,798 | 3.1638% |
|
| | **Z > 84** | Ac | 159,246 | 2.9848% |
|
| | **Lanthanoids** | Ce | 130,640 | 2.4486% |
|
| | **Z > 84** | Th | 121,488 | 2.2771% |
|
| | **Z > 84** | Pu | 109,016 | 2.0433% |
|
| | **Z > 84** | Pa | 95,786 | 1.7953% |
|
| | **Z > 84** | U | 66,848 | 1.2529% |
|
| | **Lanthanoids** | Lu | 61,123 | 1.1456% |
|
| | **Lanthanoids** | Gd | 60,788 | 1.1394% |
|
| | **Z > 84** | Np | 59,124 | 1.1082% |
|
| | **Lanthanoids** | Eu | 33,606 | 0.6299% |
|
| | **Lanthanoids** | Yb | 10,032 | 0.1880% |
|
| | **Noble Gases** | Xe | 215 | 0.0040% |
|
| | **Noble Gases** | Kr | 29 | 0.0050% |
|
| | **Noble Gases** | He | 19 | 0.0004% |
|
| | **Noble Gases** | Ar | 10 | 0.0002% |
|
| | **Noble Gases** | Ne | 7 | 0.0001% |
|
|
|
| ---
|
|
|
| ## ⚛️ Atom Type (Element) Frequencies
|
| The overall atom occurrences (by total count across all sites in the joined dataset) for all **89** unique elements present in the structures:
|
|
|
| * **O**: 466,021
|
| * **Li**: 325,150
|
| * **Se**: 315,703
|
| * **Cu**: 311,939
|
| * **In**: 309,555
|
| * **Tl**: 306,728
|
| * **Zn**: 306,426
|
| * **Ag**: 303,354
|
| * **Te**: 302,900
|
| * **Mg**: 299,780
|
| * **Au**: 290,434
|
| * **Cd**: 286,238
|
| * **Ni**: 285,705
|
| * **Y**: 284,036
|
| * **La**: 282,978
|
| * **Hg**: 282,741
|
| * **Pd**: 273,467
|
| * **Pt**: 271,824
|
| * **Al**: 269,539
|
| * **S**: 264,889
|
| * **Sc**: 256,428
|
| * **Ga**: 255,553
|
| * **Co**: 252,470
|
| * **P**: 251,653
|
| * **As**: 247,732
|
| * **Pb**: 242,001
|
| * **Si**: 238,068
|
| * **N**: 237,804
|
| * **Sb**: 233,741
|
| * **Rh**: 232,227
|
| * **Ir**: 232,066
|
| * **Sn**: 229,583
|
| * **Cl**: 229,435
|
| * **K**: 229,055
|
| * **Ba**: 221,147
|
| * **Br**: 219,288
|
| * **Ca**: 218,521
|
| * **Sr**: 218,021
|
| * **Fe**: 217,204
|
| * **Ge**: 214,440
|
| * **Na**: 213,838
|
| * **Zr**: 202,165
|
| * **Pm**: 201,275
|
| * **Nd**: 199,001
|
| * **Dy**: 196,523
|
| * **Pr**: 196,414
|
| * **Sm**: 196,112
|
| * **Tb**: 195,823
|
| * **Ho**: 193,884
|
| * **Tm**: 189,611
|
| * **Er**: 188,347
|
| * **Mn**: 187,062
|
| * **Ru**: 182,009
|
| * **Rb**: 179,613
|
| * **H**: 176,728
|
| * **I**: 175,575
|
| * **Bi**: 173,363
|
| * **Os**: 172,771
|
| * **Tc**: 168,798
|
| * **F**: 167,288
|
| * **Ta**: 166,574
|
| * **Mo**: 160,262
|
| * **Be**: 160,154
|
| * **Ac**: 159,246
|
| * **W**: 149,643
|
| * **Re**: 148,063
|
| * **Cr**: 146,883
|
| * **Cs**: 143,895
|
| * **Hf**: 142,792
|
| * **C**: 141,806
|
| * **B**: 137,847
|
| * **Nb**: 131,949
|
| * **Ce**: 130,640
|
| * **Ti**: 126,835
|
| * **Th**: 121,488
|
| * **Pu**: 109,016
|
| * **V**: 108,048
|
| * **Pa**: 95,786
|
| * **U**: 66,848
|
| * **Lu**: 61,123
|
| * **Gd**: 60,788
|
| * **Np**: 59,124
|
| * **Eu**: 33,606
|
| * **Yb**: 10,032
|
| * **Xe**: 215
|
| * **Kr**: 29
|
| * **He**: 19
|
| * **Ar**: 10
|
| * **Ne**: 7
|
|
|
| ---
|
|
|
| ## Dataset Subsets Summary
|
|
|
| * **`default`** (Dataset A - MatterGen Reproduction): 1,181,982 rows.
|
| * **`no_lanthanoids`** (Dataset A Robustness Subset): 611,142 rows.
|
| * **`extension`** (Dataset B): 1,664,351 rows.
|
| |
