QuAcK Apptainer Container

Overview

This repository provides an Apptainer (formerly Singularity) container for QuAcK. The container allows users to easily install and execute QuAcK on HPC clusters within a consistent and reproducible environment.

Building the Image

Before starting, make sure you have Apptainer installed on your system. If not, you can install it by following the instructions from the official Apptainer documentation. To build the Apptainer image (SIF file) for QuAcK, follow these steps:

1. Clone the Repository: Clone this repository to your machine.

   git clone https://github.com/AbdAmmar/QuAcK-apptainer.git
   cd QuAcK-apptainer

2. Build the Image: Use the Apptainer build command to create the SIF file.

   apptainer build quack.sif quack.def

   This command will create an image file named quack.sif based on the definitions provided in the quack.def file.

Running a Calculation

Once you have built the Apptainer image, you can run QuAcK to perform calculations by following these steps:

1. Prepare Input for QuAcK: QuAcK requires users to provide a molecular geometry, along with a file containing the methods and a file with the options for the calculation. These files should be placed in a working directory, for example named work_quack.

2. Run the Calculation: Launch QuAcK using the following command:

   apptainer run --cleanenv --no-mount home,cwd --bind path_to_work_quack quack.sif python3 PyDuck.py --working_dir path_to_work_quack arguments
   

In this command:

• --cleanenv ensures a clean environment for the execution.
• --no-mount home,cwd prevents mounting your home directory and current working directory for security and reproducibility.
• --bind path_to_work_quack binds your working directory to the container, allowing access to input files.
• arguments should be replaced with the specific options for your calculation.

To see all available options for the arguments, you can execute:

apptainer run --cleanenv --no-mount home,cwd --bind path_to_work_quack quack.sif python3 PyDuck.py --help

Example

In this section, we provide an example of running a Self-Consistent Field (SCF) calculation using the "cc-pvqz" basis set for a water molecule.

Step 1: Create a Working Directory

First, create a working directory named, for instance, work_quack:

mkdir work_quack

Next, navigate into this directory and prepare the input files.

Step 2: Prepare the Molecular Geometry

Inside the work_quack directory, create a subdirectory for the molecular geometry:

cd work_quack
mkdir mol && cd mol

Then, create a file named H2O.xyz to store the geometry in Angstroms:

touch H2O.xyz

Step 3: Prepare Input Files

Navigate back to the work_quack directory and create a subdirectory for input files:

cd ..
mkdir input && cd input

Download the template files for methods and options from the QuAcK repository:

curl -o options https://raw.githubusercontent.com/pfloos/QuAcK/master/input/options.default
curl -o methods https://raw.githubusercontent.com/pfloos/QuAcK/master/input/methods.default

Open the methods file and set RHF to T (True).

Step 4: Launch the Calculation

Now you are ready to launch the calculation. Navigate back to the main directory:

cd ../..

Run the following command to execute the SCF calculation:

apptainer run --cleanenv --no-mount home,cwd --bind $PWD/work_quack quack.sif python3 PyDuck.py --working_dir $PWD/work_quack -b "cc-pvqz" -x "H2O"

Here, the command $PWD ensures that you are providing the absolute path to the working directory.

QuAcK is supported by the PTEROSOR project that has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 863481).