Polarizable Embedding


Table of Contents


PyFraME

Examples of use can be found at Runs cripts.

Local installation

Use pip installer python -m pip install PyFraME

Installation of computer clusters

On some clusters the python environment is the generic one from the employed operating linux system (i.e. often quite old). To get an updated python environment, install miniconda:

  1. wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
  2. run bash Miniconda3-latest-Linux-x86_64.sh (the file can be deleted after)
  3. Answer yes to Do you wish the installer to initialize Miniconda3 by running conda init? - this will add the updated python to your bashrc (e.g.~/home/erikh/.bashrc in my case)
  4. run Source ~/home/erikh/.bashrc - replace erikh with your username
  5. run python -m pip install PyFraME
  6. Test that works by import pyframe in a python environment.

Note: use conda config --set auto_activate_base false if you want to revert to your orginal python. Altenatively remove the extra lines added to .bashrc.

Examples of use can be found at Runs cripts.

  • GenomeDK
    source /faststorage/project/DeiC-SDU-L-10/Modules/setup_modules.sh # to get module loading system
    ./setup --fc=mpifort --cc=mpicc --cxx=mpicxx build_master_ompi && cd build_master_ompi && make -j4

  • Parallel installation GenomeDK (Intel/MKL)
    source /faststorage/project/DeiC-SDU-L-10/Modules/setup_modules.sh # to get module loading system
    module load cmake/3.21.1 intel-mpi/2021.3 intel-mkl/2021.3
    ./setup --mpi build_master_impi && cd build_master_impi && make -j4

Examples of inputs

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