90 lines
2.1 KiB
Markdown
90 lines
2.1 KiB
Markdown
# PyLammps and Jupyter Notebooks
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This folder contains examples showcasing the usage of the PyLammps Python
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interface and Jupyter notebooks. To use this you will need LAMMPS compiled as
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a shared library and the LAMMPS Python package installed.
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An extensive guide on how to achieve this is documented in the [LAMMPS manual](https://lammps.sandia.gov/doc/Python_install.html). There is also a [PyLammps tutorial](https://lammps.sandia.gov/doc/Howto_pylammps.html).
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The following will show one way of creating a Python virtual environment
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which has both LAMMPS and its Python package installed:
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1. Clone the LAMMPS source code
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```shell
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$ git clone https://github.com/lammps/lammps.git
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$ cd lammps
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```
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2. Create a build folder
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```shell
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$ mkdir build
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$ cd build
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```
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3. Create a virtual environment for Python
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```shell
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$ python3 -m venv myenv
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```
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4. Extend `LD_LIBRARY_PATH` (Unix/Linux) or `DYLD_LIBRARY_PATH` (MacOS)
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On Unix/Linux:
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```shell
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$ echo 'export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH' >> myenv/bin/activate
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```
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On MacOS:
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```shell
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echo 'export DYLD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$DYLD_LIBRARY_PATH' >> myenv/bin/activate
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```
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5. Activate the virtual environment
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```shell
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$ source myenv/bin/activate
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(myenv)$
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```
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6. Configure LAMMPS compilation (CMake)
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```shell
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(myenv)$ cmake -C ../cmake/presets/minimal.cmake \
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-D BUILD_SHARED_LIBS=on \
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-D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on \
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-D CMAKE_INSTALL_PREFIX=$VIRTUAL_ENV \
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../cmake
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```
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7. Compile LAMMPS
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```shell
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(myenv)$ cmake --build .
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```
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8. Install LAMMPS and Python package into virtual environment
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```shell
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(myenv)$ cmake --install .
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```
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9. Install other Python packages into virtual environment
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```shell
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(myenv)$ pip install jupyter matplotlib mpi4py
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```
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10. Navigate to pylammps examples folder
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```shell
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(myenv)$ cd ../python/examples/pylammmps
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```
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11. Launch Jupyter and work inside browser
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```shell
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(myenv)$ jupyter notebook
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```
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