Matlantis offers an integration package (matlantis-lammps) with the LAMMPS simulation software. matlantis-lammps can be installed to run LAMMPS calculations with PFP as the force field.The Matlantis-lammps environment is available for use in the Matlantis environment.This section describes how to install matlantis-lammps in a Matlantis environment (each figure can be enlarged by clicking on it).
Please refer to the official manual and the example scripts it contains for instructions on how to use LAMMPS.
- LAMMPS Manual: https://docs.lammps.org/Intro.html
- Example Scripts: https://docs.lammps.org/Examples.html
Ref : Guidelines for Creating LAMMPS Inputs Using matlantis-lammps
Step1. Download of matlantis-lammps from Package Launcher
- Click "Open Package Launcher" button in the directory where you want to do the installation.
- Package Launcher tab opens.
- In the Package Launcher tab -> Experimental Packages -> matlantis-lammps -> v0.0.16 (the latest version at the time of writing), click "Copy zip file to the current directory" button.
- Download will start and "matlantis-lammps-v0.0.16.zip" will be saved in the working directory.
Step2. Installing matlantis-lammps
- Right-click the downloaded "matlantis-lammps-v0.0.16.zip" and select "Extract Archive".
- "matlantis-lammps-v0.0.16" is generated.
- Go to "matlantis-lammps-v0.0.16" and open "how_to_use_lammps.ipynb".
- (If you want to use PLUMED as an extension, open the "how_to_use_plumed.ipynb" instead.)
- With the python environment you want to install selected, do the following.
- Execute the cell following Install LAMMPS with CMake, and proceed with the installation (the installation log is output, about ten or so minutes).
- (For "how_to_use_plumed.ipynb", proceed with Install PLUMED and Install LAMMPS with additional packages).
Step3. matlantis-lammps execution test
- Execute the cell following LAMMPS Run.
- （For "how_to_use_plumed.ipynb", execute the cells following Run LAMMPS + PLUMED example.）
- If the installation is successful, LAMMPS calculations are started with the sample input, and the log of the LAMMPS calculation will be shown in the output cell.
- In addition, a series of LAMMPS output files are generated in the working directory (log.lammps, output.data, etc.)
- For information on how to install LAMMPS from the terminal or the LAMMPS python module, please refer to the notes following "When using terminal" or "When using Python module".
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