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| # Using MDIMechanic | ||
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| :::{admonition} Prerequisites | ||
| :class: note | ||
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| Before completing this section, make sure you have completed the setup instructions in the [previous section](setup.md). | ||
| ::: | ||
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| In this tutorial, we will use the MDIMechanic package to run our code. | ||
| MDIMechanic is a Python package that provides an interface for running environments and MDI Engines. | ||
| It orchestrates Docker containers using a streamlined set up process. | ||
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| The file `mdimechanic.yml` contains the configuration for the MDIMechanic environment. | ||
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| To get started, execute the following command in your terminal: | ||
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| :::{tab-set} | ||
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| ````{tab-item} bash | ||
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| ```bash | ||
| mdimechanic build | ||
| ``` | ||
| ```` | ||
| ::: | ||
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| While your image is building, we can examine the `mdimechanic.yaml` file to see what is happening. | ||
| Looking at the file, you will see the following: | ||
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| ```yaml | ||
| code_name: 'mdi-ani-tutorial' | ||
| docker: | ||
| image_name: 'mdi-ani-tutorial' | ||
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| build_image: | ||
| - apt-get update && apt-get install -y curl | ||
| - curl "http://vergil.chemistry.gatech.edu/psicode-download/Psi4conda-1.9.1-py311-Linux-x86_64.sh" -o Psi4conda-1.9.1-py311-Linux-x86_64.sh --keepalive-time 2 | ||
| - bash Psi4conda-1.9.1-py311-Linux-x86_64.sh -b -p $HOME/psi4conda | ||
| - echo $'. $HOME/psi4conda/etc/profile.d/conda.sh\nconda activate' >> ~/.bashrc | ||
| - source ~/.bashrc | ||
| - /root/psi4conda/bin/pip install pymdi | ||
| - /root/psi4conda/bin/pip install numpy | ||
| - /root/psi4conda/bin/pip install torch --index-url https://download.pytorch.org/whl/cpu | ||
| - /root/psi4conda/bin/pip install torchani | ||
| - /root/psi4conda/bin/pip install matplotlib | ||
| - /root/psi4conda/bin/pip install tabulate | ||
| - /root/psi4conda/bin/pip cache purge | ||
| ``` | ||
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| This file specifies the name of the code, the Docker image to use, and the commands to run to build the image. | ||
| The Docker image is built from a base image for MDI that has compilers and other necessary software installed. | ||
| The `build_image` section specifies the commands to run to install the necessary software for the tutorial. | ||
| We are installing Psi4, pymdi, numpy, torch, torchani, and matplotlib. | ||
| Notice that this container is configured to install the CPU version of PyTorch (to save space and improve build time). | ||
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| ## Using the Image | ||
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| MDIMechanic has a command called `mdimechanic interactive` that will mount your local directory as a volume in the container and open a shell in the container. | ||
| Execute MDIMechanic interactive with the following command: | ||
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| :::{tab-set} | ||
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| ````{tab-item} bash | ||
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| ```bash | ||
| mdimechanic interactive | ||
| ``` | ||
| ```` | ||
| ::: | ||
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| You are now in the container and can use the software installed. | ||
| Check the directory contents using `ls` and confirm that it is the same as your local directory. | ||
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| Open a Python interpreter and confirm that you can import torch and Psi4: | ||
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| :::{tab-set} | ||
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| ````{tab-item} python | ||
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| ```python | ||
| import torch | ||
| import psi4 | ||
| ``` | ||
| ```` | ||
| ::: | ||
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| If you can import these packages, you have successfully set up your environment and are ready to run the tutorial. | ||
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| The other important section in `mdimechanic.yml` is the `run_scripts` section. | ||
| In that section, you will see commands for launching LAMMPS as well as the MDI Driver we will be writing. | ||
| If you are familiar with Docker, you may be interested to know that this section is used to specify a configuration for Docker Compose. | ||
| It will be discussed further in the [Driver Tutorial](driver_tutorial.md). | ||
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| In the next section, we will use MDI Mechanic and the `mdimechanic interactive` mode to run Psi4 and ANI for energy calculations. |
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