tcnicholas / amorphous-calcium-carbonate

Repository supporting the manuscript: Geometrically-frustrated interactions drive structural complexity in amorphous calcium carbonate.

Research data for "Geometrically-frustrated interactions drive structural complexity in amorphous calcium carbonate"

Geometrically-frustrated interactions drive structural complexity in amorphous calcium carbonate
Thomas C. Nicholas, Adam E. Stones, Adam Patel, F. Marc Michel, Richard J. Reeder, Dirk G. A. L. Aarts, Volker L. Deringer, and Andrew L. Goodwin

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Repository overview

• Simulation scripts

  • HRMC simulation scripts. The custom scripts used to run the hybrid reverse Monte Carlo (HRMC) refinements. The program is under continual development, but the program version used for the work is archived here.

  • LJG simulator scripts. The custom scripts used to run the LJG simulations are included here.

• Simulation data

  • Hybrid reverse Monte Carlo model. The final model is included in both LAMMPS and CIF data formats here.

  • LJG coarse-grained models. We ran both Monte Carlo (MC) and molecular dynamics (MD) simulations using our LJG-parameterised effective Ca–Ca interaction potential. We ran 12 independent simulations for each method. Final configurations are provided in LAMMPS and CIF data formats. The radial distribution functions computed in LAMMPS are also provided as "rdf.rdf" for each configuration.

• Analysis scripts

• Plotting scripts

  • main.ipynb is a Jupyter Notebook containing the plotting scripts for generating the raw graphic data for the main text. Specifically, this includes:

    1. Comparing computed X-ray total scattering functions with experimental value for the RMC, HRMC, and MD methods (Fig. 1a).

    2. Comparing the relative energies and quality of fit-to-data metrics for the RMC, HRMC, and MD methods (Fig. 1b).

    3. Coordination number histograms for calcium and carbonate environments in the HRMC configuration (Fig. 2a and b).

    4. Comparison of the Ca–Ca partial radial distribution functions for the HRMC, RMC, and LJG with the Fourier transform of the X-ray total scattering function (Fig. 2e).

    5. The extracted effective Ca–Ca interaction potential from the test-particle insertion algorithm for the ACC configuration, together with the LJG parameterisation (Fig. 3a).

    6. Orientational correlation function for CO₃ and H₂O species (Fig. 3a).

  • si.ipynb is a Jupyter Notebook containing the plotting scripts for generating the raw graphic data for the supporting information. Specifically, this includes:

    1. Evolution of system properties during HRMC refinement and MD simulation (Fig. S1).

    2. Evolution of coarse-grained simulation ensemble energies (Fig. S2).

    3. HRMC partial radial distribution functions, averaged over the final 12 frames of the refinement trajectory (Fig. S3).

    4. Key bond-length and bond-angle distributions from the final HRMC structure (Fig. S4).

    5. Computed neutron total scattering measurements, as compared with three independent neutron total scattering measurements of ACC (Fig. S5).

    6. RDFs and particle cluster sizes pertinent to investigating the role of water in ACC (Fig. S6).

    7. Comparing properties of the Ca-only (coarse-grained) configurations from HRMC with those produced by LJG Monte Carlo and molecular dyanmics simulations. We compare distributions of Voronoi cell volumes, Voronoi cell face counts (neighbours), (strong) ring sizes, and a Ca-triplet three-body correlation function (Fig. S7–9).

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Citing this work

You can cite this work using the following BibTeX reference.

@misc{Nicholas_2023,
      title={Geometrically-frustrated interactions drive structural complexity in amorphous calcium carbonate}, 
      author={Thomas C. Nicholas and Adam E. Stones and Adam Patel and F. Marc Michel and Richard J. Reeder and Dirk G. A. L. Aarts and Volker L. Deringer and Andrew L. Goodwin},
      year={2023},
      eprint={2303.06178},
      archivePrefix={arXiv},
      primaryClass={cond-mat.mtrl-sci}
}

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License

This work is licensed under a Creative Commons Attribution 4.0 International License.