Add flexible_molecules_JCP2021 files

README.md

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+---
+configs:
+- config_name: default
+  data_files: "co/*.parquet"
+- config_name: info
+  data_files: "ds.parquet"
+- config_name: configuration_sets
+  data_files: "cs/*.parquet"
+- config_name: config_set_mapping
+  data_files: "cs_co_map/*.parquet"
+license: cc0-1.0
+tags:
+- molecular dynamics
+- mlip
+- interatomic potential
+pretty_name: flexible molecules JCP2021
+---
+### <details><summary>Cite this dataset </summary>Vassilev-Galindo, V., Fonseca, G., Poltavsky, I., and Tkatchenko, A. _flexible molecules JCP2021_. ColabFit, 2023. https://doi.org/10.60732/71f8031b</details>  
+#### This dataset has been curated and formatted for the ColabFit Exchange  
+#### This dataset is also available on the ColabFit Exchange:  
+https://materials.colabfit.org/id/DS_i23sbm1o45sj_0  
+#### Visit the ColabFit Exchange to search additional datasets by author, description, element content and more.  
+https://materials.colabfit.org
+<br><hr>  
+# Dataset  Name  
+flexible molecules JCP2021  
+### Description  
+Configurations of azobenzene featuring a cis to trans thermal inversion through three channels: inversion, rotation, and rotation assisted by inversion; and configurations of glycine as a simpler comparison molecule. All calculations were performed in FHI-aims software using the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional with the Tkatchenko-Scheffler (TS) method to account for van der Waals (vdW) interactions. The azobenzene sets contain calculations from several different MD simulations, including two long simulations initialized at 300 K; short simulations (300 steps) initialized at 300 K and shorter (.5fs) timestep; four simulations, two starting from each of cis and trans isomer, at 750 K (initialized at 3000 K); and simulations at 50 K (initialized at 300 K). The glycine isomerization set was built using one MD simulation starting from each of two different minima. Initializatin and simulation temperature were 500 K.  
+### Dataset authors  
+Valentin Vassilev-Galindo, Gregory Fonseca, Igor Poltavsky, Alexandre Tkatchenko  
+### Publication  
+https://doi.org/10.1063/5.0038516  
+### Original data link  
+https://doi.org/10.1063/5.0038516  
+### License  
+CC0-1.0  
+### Number of unique molecular configurations  
+69174  
+### Number of atoms  
+1520162  
+### Elements included  
+C, H, N, O  
+### Properties included  
+energy, atomic forces, cauchy stress  
+<br>
+<hr>  
+
+# Usage  
+- `ds.parquet` : Aggregated dataset information.  
+- `co/` directory: Configuration rows each include a structure, calculated properties, and metadata.  
+- `cs/` directory : Configuration sets are subsets of configurations grouped by some common characteristic. If `cs/` does not exist, no configurations sets have been defined for this dataset.  
+- `cs_co_map/` directory : The mapping of configurations to configuration sets (if defined).  
+<br>
+#### ColabFit Exchange documentation includes descriptions of content and example code for parsing parquet files:  
+- [Parquet parsing: example code](https://materials.colabfit.org/docs/how_to_use_parquet)  
+- [Dataset info schema](https://materials.colabfit.org/docs/dataset_schema)  
+- [Configuration schema](https://materials.colabfit.org/docs/configuration_schema)  
+- [Configuration set schema](https://materials.colabfit.org/docs/configuration_set_schema)  
+- [Configuration set to configuration mapping schema](https://materials.colabfit.org/docs/cs_co_mapping_schema)  

co/co_0.parquet

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+version https://git-lfs.github.com/spec/v1
+oid sha256:3d8cf0699ff78a58f5c6d2c93d1fc425eadfc20a61ccbbb4dc03422c10093786
+size 70044987

cs/cs_0.parquet

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+version https://git-lfs.github.com/spec/v1
+oid sha256:325927077791c0d545b8f4f14b77ef396c7d43dd0ba7e1e463c69a7f2876388a
+size 7964

cs_co_map/cs_co_map_0.parquet

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+version https://git-lfs.github.com/spec/v1
+oid sha256:3d50f9b3ed5b8baf2b2f9203f98621f0a99598a40f8d07458be2f1b0b3ba4048
+size 807283

ds.parquet

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+version https://git-lfs.github.com/spec/v1
+oid sha256:09bad87cfabf499b0a738ef42be98c4433b9c4f32e3c9195309565f325da2ce6
+size 20171