Overview

ADAQ automates the following steps in the theoretical process of calculating point defects:

  • relaxes the host unit cell.

  • creates the defect supercells with arbitrarily sized defect clusters.

  • screens these defects for the most relevant properties.

  • fully characterizes the point defects including zero phonon lines (ZPL), zero field splitting (ZFS), and hyperfine coupling parameters.

This overview introduces the ADAQ commands and folder structure.. More details are found in Tutorial.

Ensure to source httk and ADAQ as well as activate the conda enviroment:

$ source /path/to/httk/init.shell
$ source /path/to/ADAQ/init.shell
$ conda activate adaq

ADAQ commands

The ADAQ commands are available after sourcing ADAQ/init.shell. They all start with adaq-. More details are found in Commands.

ADAQ project

Here is how a ADAQ project is created. Navigate to where you would like to store the ADAQ project. Run the following ADAQ command:

$ adaq-set-up-project <name>

Where <name> refers to the host material.

You will then be prompted to provide a POSCAR for the unit cell. It does not need to be relaxed, there are ADAQ workflows to do that.

One also needs to provide additional parameters that are not calculated. These are: * dielectric constant * refractive index

As well as meta data about the project. These are: * title * contributors

The command will also set up a httk project. You will be prompted to set up a public key that identifies you as the owner, which is recommended.

ADAQ folder

After the adaq-set-up-project command has finished. You will now have a folder titled <name> with subfolders for the different workflows. It will also contain:

  • <name>.vasp that is the POSCAR of the unit cell.

  • <name>.data that contains the dielectric constant and refractive index.

  • project.meta that contains meta data about the project.

  • parameters.py that have the settings for the defect generation.

  • ht.project that has the settings for the defect generation.

You will also need to set up a supercomputer with the httk command:

$ httk-computer-setup

Follow the prompt to set up a new computer. This will add a computer to the computers folder inside the ht.project. There is also a config file that you can edit in case you need to change something.

Depending on your supercomputer cluster, you may need to edit the ht.project/computers/<computer name>/start-taskmgr to load module or python environments during the runs.

To install httk at the remote computer, run the following command:

$ httk-computer-install <computer name>

Go to Tutorial to calculate the single defects in 4H-SiC using ADAQ.

Linköping University specifics

Here are the following settings to set up a computer for tetralith:

  • Add a project computer

  • Use the ssh-slurm templete

  • Name: tetralith

  • Remote Hostname: tetralith.nsc.liu.se

  • Username: x_abcde

  • Directory on remote host: /proj/theophys/users/x_abcde/httk (Important keep as short as possible)

  • Command to run vasp: mpprun /software/sse/manual/vasp/5.4.4.16052018/nsc2/vasp_gam

  • VASP pseudopotential path: /software/sse/manual/vasp/POTCARs/PBE/2015-09-21/

  • Slurm project to submit jobs to: naissYYYY-X-Z

  • Slurm job timeout: 168:00:00 (max walltime at tetralith)

  • Taskmanager timeout max time per task in seconds: 604800 (max walltime in seconds)

When using dedur and tetralith, also change these:

In ht.project/computers/name/pull, change: -az to -rltz

In ht.project/computers/name/start-taskmgr, add:

module load Anaconda/2023.09-0-hpc1
conda activate adaq2

after source "\$HTTK_DIR/setup.shell"

ADAQ database

Once a project is finished, the data can be added to the ADAQ database. Go to database for more information.