calphy.def

BootStrap: library
From: ubuntu:22.04

%labels
    Author: Sebastian Havens
    Image for a calphy container
%environment
    export PATH=/scripts:$PATH
    export OMP_NUM_THREADS=1
    . /singularity-venv/bin/activate
    source /singularity-venv/bin/activate 

%post
    # Update package lists and install necessary packages
    export DEBIAN_FRONTEND=noninteractive
    echo . /singularity-venv/bin/activate

    apt-get update -y
    apt-get install -y build-essential libopenmpi-dev libmpich-dev vim emacs htop \
                       mpi-default-bin mpi-default-dev mpich libjpeg-dev libpng-dev git \
                       fftw3 fftw3-dev software-properties-common

    # Add repository and install Python 3.8
    add-apt-repository ppa:deadsnakes/ppa
    apt-get update -y
    apt-get install -y python3.8-dev python3.8-venv
   
   # Setup Python virtual environment
    python3.8 -m venv /singularity-venv
    . /singularity-venv/bin/activate

    # Install packages
    pip install numpy==1.24.4 ase==3.23.0 mpi4py==3.1.5
    pip install mendeleev==0.17.0 pylammpsmpi==0.2.16 pyscal==0.12 pyyaml==6.0.2 scipy==1.10.1 tqdm==4.66.2
    pip install calphy

        # Clone lammps source and make
    git clone https://github.com/lammps/lammps.git --branch patch_2Aug2023_update3
    cd /lammps/src/
    sed -i '35s/.*/LMP_INC = -DLAMMPS_GZIP -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG -DLAMMPS_EXCEPTIONS/' MAKE/MACHINES/Makefile.ubuntu
    make yes-manybody
    make yes-meam
    make yes-EXTRA-FIX
    make yes-EXTRA-PAIR
    make -j 8 ubuntu mode=shlib
    make install-python
    cp liblammps_ubuntu.so  /singularity-venv/lib/python3.8/site-packages/lammps
    cd ../../
%runscript

    echo "Input file: $1"
    echo "Calculation starting"
    calphy_kernel -i $1 -k 0
    exec echo "Calculation finished"



%help
    This is a container for carrying out calphy calculations which perform free energy calculations.
    The container is designed to run locally or on HPC machines.

    The calphy calcualtion can be initiated via the container with the following command:
    singularity exec --bind $PWD --pwd $PWD {location_of_.sif_image} calphy_kernel -i {input_file} -k 0
    This line can be contained within a slurm script

    The scheduler used in the calphy input file should be 'local'.
    On HPC machines the singularity executable can usually be loaded via 'module load singularity' or it will already be within your
    path.

    In the calphy input file, the scheduler should be set to local.
    The OpenMPI version on the host system must be at least 4.1.2, which will need to be loaded if you are using a HPC machine.