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Copy file name to clipboardExpand all lines: docs/introduction/quickstart.ipynb
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"- Use the installed ontologies to instantiate ontology individuals\n",
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"- Demonstrate the usage of wrappers to achieve interoperability\n",
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"\n",
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"In the tutorial, you will go through the following workflow:\n",
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"You will go through the workflow in the figure shown below.\n",
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"\n",
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"1. Make the SimLAMMPS ontology that will be used to describe the data available to SimPhoNy.\n",
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"2. Describe the positions and velocities of a set of atoms using said ontology.\n",
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"3. Save the ontology individuals that the description consists of in an SQLite database.\n",
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"4. Make them available to the [LAMMPS molecular dynamics simulation engine](https://www.lammps.org/).\n",
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"5. Add extra ontology individuals that describe LAMMPS input parameters, including the integration time.\n",
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"6. Let LAMMPS compute the new positions and velocities of the atoms and write the changes back to the ontology individuals.\n",
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"7. Overwrite the data in the SQLite database with the simulation results.\n",
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"\n",
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"\n",
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"Following the tutorial on your own machine requires the installation of [SimPhoNy](../installation.md#installation) and the [SimLAMMPS](https://github.com/simphony/simphony-osp-simlammps) wrapper. We recommend that you use the button above to follow the tutorial online using Binder."
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