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Author: tom-bickley

.gitignore

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+.DS_Store

LICENSE

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+# extending_digitaldiscovery_data
+
+This repository contains supplimentary data for the publication "Extending Quantum Computing through Subspace, Embedding and Classical Molecular Dynamics Techniques".
+
+The data is structured as follows:
+- `input/` - contains the input data and scripts required to run the QM/MM simulation presented in Section 5.
+- `quantum/` - contains the Hamiltonian data from the QM/MM simulation and the the scripts for pre- and post-processing circuit executions.
+- `plot/` - contains the data and scripts needed to plot Figure 9.
+- `LICENSE` - this repository is distributed under the GNU General Public License v2 (GPLv2), because it incorporates code adapted from [LAMMPS](https://github.com/lammps/lammps). In particular, the file `input/run.py` is adapted from the LAMMPS source code. The full GPLv2 license for LAMMPS is included here.

README.md

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+# input/
+
+This folder contains the data and scripts required to run the QM/MM simulation presented in Section 5.
+
+A prerequisite is the installation of LAMMPS with the `mdi`, `molecule`, and `kspace` flags switched on. Instructions for this can be found in the [LAMMPS documentation](https://github.com/lammps/lammps/blob/0d479cae298abb73ffd8b1460197a8a74c63bc5e/examples/QUANTUM/PySCF/README).
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+Then, the script `run.sh` should be executable and can be edited to run simulations for each of the starting geometries. The LAMMPS input geometries are found in the `data.*` files. For example, `data.19_200` corresponds to the geometry for $d_{\mathrm{OO}} = 1.9$ Å and $d_{\mathrm{OH}} = 0.200$, and similarly for the other files. The output from running the script will be the Hamiltonian data in a pickle file.