Ethylene carbonate data for graph2mat

Creators
------------
Pol Febrer ([e-mail], ORCID 0000-0003-0904-2234)
Peter Bjorn Jorgensen ([e-mail], ORCID 0000-0003-4404-7276)
Arghya Bhowmik ([e-mail], ORCID 0000-0003-3198-5116)

Related publication
-------------------
The dataset is published as part of the paper:
"GRAPH2MAT: UNIVERSAL GRAPH TO MATRIX CONVERSION FOR ELECTRON DENSITY PREDICTION"
(https://doi.org/10.26434/chemrxiv-2024-j4g21)
https://github.com/BIG-MAP/graph2mat

Short description
------------------
This dataset contains the Hamiltonian, Overlap, Density and Energy Density matrices
from SIESTA calculations of a subset of the MD17 aspirin dataset. The subset is taken
from the third split in (https://doi.org/10.6084/m9.figshare.12672038.v3).

SIESTA 5.0.0 was used to compute the dataset.

Contents
-----------------

The dataset has two directories:

- pseudos: Contains the pseudopotentials used for the calculation (obtained from
http://www.pseudo-dojo.org/, type NC SR (ONCVPSP v0.5), PBE, standard accuracy)
- splits: The data splits used in the published paper. Each file "splits_X.json"
contains the splits for training size X.

And then, three directories containing the calculations with different basis sets:
- matrix_dataset_defsplit: Uses the default split-valence DZP basis in SIESTA.
- matrix_dataset_optimsplit: Uses a split-valence DZP basis optimized for aspirin.
- matrix_dataset_defnodes: Uses the default nodes DZP basis in SIESTA.

Each of the basis directories has two subdirectories:
- basis: Contains the files specifying the basis used for each atom.
- runs: The results of running the SIESTA simulations. Contents are discussed next.

The "runs" directory contains one directory for each run, named with the index
of the run. Each directory contains:
- RUN.fdf, geom.fdf: The input files used for the SIESTA calculation.
- RUN.out: The log of the SIESTA run, which apar
- siesta.TSDE: Contains the Density and Energy Density matrices.
- siesta.TSHS: Contains the Hamiltonian and Overlap matrices.

Each matrix can be read using the sisl python package (https://github.com/zerothi/sisl)
like:

```python
import sisl

matrix = sisl.get_sile("RUN.fdf").read_X()
```

where X is hamiltonian, overlap, density_matrix or energy_density_matrix.

To reproduce the results presented in the paper, follow the documentation of the graph2mat
package (https://github.com/BIG-MAP/graph2mat).

Cite this data
------------------

https://doi.org/10.11583/DTU.c.7310005
© 2024 Technical University of Denmark

License
-----------------
This dataset is published under the CC BY 4.0 license.
This license allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator.

创作者
------------

Pol Febrer ([e-mail], ORCID 0000-0003-0904-2234)
Peter Bjorn Jorgensen ([e-mail], ORCID 0000-0003-4404-7276)
Arghya Bhowmik ([e-mail], ORCID 0000-0003-3198-5116)

相关出版物
-------------------
本数据集作为论文的一部分发布，论文标题为‘GRAPH2MAT：通用电子密度预测的图到矩阵转换’（https://doi.org/10.26434/chemrxiv-2024-j4g21），代码库地址为https://github.com/BIG-MAP/graph2mat。

简短描述
------------------
本数据集包含了MD17阿司匹林数据集子集的SIESTA计算中的哈密顿矩阵、重叠矩阵、密度矩阵和能量密度矩阵。该子集取自（https://doi.org/10.6084/m9.figshare.12672038.v3）中的第三次分割。
SIESTA 5.0.0版本被用于计算该数据集。

内容
-----------------
该数据集包含两个目录：

- pseudos：包含用于计算的伪势（从http://www.pseudo-dojo.org/获取，类型为NC SR (ONCVPSP v0.5)，PBE，标准精度）。
- splits：发布论文中使用的数据分割。每个文件“splits_X.”包含大小为X的训练分割。

此外，还包含三个包含不同基组的计算目录：

- matrix_dataset_defsplit：使用SIESTA中的默认分割价DZP基。
- matrix_dataset_optimsplit：使用针对阿司匹林优化的分割价DZP基。
- matrix_dataset_defnodes：使用SIESTA中的默认节点DZP基。

每个基组目录包含两个子目录：

- basis：包含指定每个原子的基组文件的文件。
- runs：SIESTA模拟的结果。具体内容将在下文讨论。

“runs”目录包含每个运行的一个目录，以运行的索引命名。每个目录包含以下内容：

- RUN.fdf, geom.fdf：用于SIESTA计算的输入文件。
- RUN.out：SIESTA运行的日志，其中包含...
- siesta.TSDE：包含密度矩阵和能量密度矩阵。
- siesta.TSHS：包含哈密顿矩阵和重叠矩阵。

每个矩阵可以使用sisl Python包（https://github.com/zerothi/sisl）读取，如下所示：

python
import sisl

matrix = sisl.get_sile('RUN.fdf').read_X()

其中X为哈密顿矩阵、重叠矩阵、密度矩阵或能量密度矩阵。

要重现论文中呈现的结果，请遵循graph2mat包的文档（https://github.com/BIG-MAP/graph2mat）。

引用此数据
------------------
https://doi.org/10.11583/DTU.c.7310005
© 2024 丹麦技术大学

许可
-----------------
本数据集在CC BY 4.0许可下发布。此许可允许使用者以任何媒体或格式分发、混合、改编和在此基础上构建材料，前提是必须给予创作者适当的归属。