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How to install PLUMED

  • Updated

In this article, we explain how to install PLUMED on Matlantis.

As of July 2024, Matlantis supports integration of PLUMED with LAMMPS and ASE (version 3.23 and above).

Installation of PLUMED for LAMMPS

Please follow the setup instructions in the `how_to_use_plumed.ipynb` file within the `matlantis-lammps` directory of the Matlantis Package Launcher for installing PLUMED for LAMMPS.

Installation of PLUMED for ASE

  1. Firstly, make sure to install the latest `pfp-api-client`, `matlantis features`, and `pfcc-extras`.
  2. Confirm that the version of ASE is 3.23 or higher.
    1. If it is below 3.23, run `pip install -U ase` to upgrade ASE and ensure it is at least version 3.23.
  3. Please install PLUMED by following these steps:
    1. Download an appropriate version from GitHub and upload it to Matlantis, then unzip it. Visit https://github.com/plumed/plumed2/releases
      We have confirmed operation with version 2.9.0.

    2. Compile PLUMED by executing the following commands:
       

      !cd ../plumed-2.9.0/ && ./configure --disable-mpi --prefix=/home/jovyan/plumed_local && make && make install

    3. Set the environment variables:

      !export LD_LIBRARY_PATH=/home/jovyan/plumed_local/lib:$LD_LIBRARY_PATH
!export PATH=/home/jovyan/plumed_local/bin:/usr/local/bin:$PATH
!export PKG_CONFIG_PATH=/home/jovyan/plumed_local/lib/pkgconfig:$PKG_CONFIG_PATH
!export PLUMED_KERNEL=/home/jovyan/plumed_local/lib/libplumedKernel.so

    4. Install plumed with pip:

      !pip install plumed==2.9.0

The setup is complete at this point.

To execute calculations with PLUMED with ASE, you will need to set up the environment variables in the notebook as follows:

import os
import sys
os.environ["PLUMED_KERNEL"]="/home/jovyan/plumed_local/lib/libplumedKernel.so"
os.environ["L"]="/home/jovyan/plumed_local/lib/libplumedKernel.so" # This may be a typo, double-check the variable name.
os.environ["PLUMED_TYPESAFE_IGNORE"]="yes"
sys.path.append('/home/jovyan/plumed_local/')

Furthermore, you should import the plumed calculator from ASE:

from ase.calculators.plumed import Plumed

 

 

 

 

 

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