CES for DCE 6-body
- System requirements
- Operating system: Windows OS (tested on Windows 10, standard desktop configuration)
- Python version: 3.12.3 (installed via Anaconda distribution, standard options)
- Dependencies:
- fast-histogram
- Standard Python scientific libraries: numpy, pandas, matplotlib, etc.
- Hardware: Standard desktop; no special hardware required.
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Installation guide
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Install Anaconda (https://www.anaconda.com/download) and create/activate a Python 3.12.3 environment.
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Install the required packages: pip install fast-histogram
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Store the simulation script in your working directory.
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Demo
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Instructions:
- Open the provided script Static_Simulations_RandomGeoms_DCE_ML_Paper.py.
- Adjust simulation parameters in the script if desired (see Section 4).
- Run the script in your Python environment (Spyder, terminal, etc.).
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Expected output:
- A pandas DataFrame containing event-by-event simulation results.
- The DataFrame includes initial geometries, initial velocities, final momenta (Cartesian), and KE for each simulated event.
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Expected runtime: Typically a few minutes on a standard desktop.
- Instructions for use
- The cis-1,2-DCE Cartesian coordinates are embedded directly in the script as the starting geometry.
- Randomized geometries are generated based on parameters in the script.
- Key user-adjustable parameters inside the script:
- params: Controls random variations in geometry and the initial kinetic energy of the molecules.
- Number of geometries to simulate.
- Fragment charges.
- To use custom settings:
- Edit the relevant variables in the script.
- Run the script to generate the DataFrame.
- Save the DataFrame to file (DataFrame.to_csv() or to_hdf()).
- Reproduction instructions
- Run the script with default parameters to reproduce the results described in the manuscript.
- The generated DataFrame will contain:
- XYZ coordinates of all atoms for each event.
- Final velocities and momenta (Cartesian).
- Kinetic energies.
License: MIT