---
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  
<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)