Installation

ADAQ requires a local installation, ideally in a location where the data does not have to be moved later. For example, an interfaceable storage archive.

The High-Throughput Toolkit (httk)

More info about httk, see https://docs.httk.org/en/latest/.

Install httk

Install the devel branch by following the instructions here:

$ git clone -b devel https://github.com/httk/httk.git

Ensure to use the devel branch.

Configure httk

httk uses other software to find symmetry and show crystal structures:

isotropy (required for ADAQ)
jmol (optional but recommended)

Place the isotropy files where you want and edit isotropy/findsym to find the absolute path:

export ISODATA=/path/to/isotropy/iso-9.3.1/
exec /path/to/isotropy/iso-9.3.1/findsym "$@"

Place jmol files where you want.

In the httk folder, run:

cp httk.cfg.example src/httk/httk.cfg

Edit the paths in src/httk/httk.cfg to link to isotropy and jmol (absoulute path):

isotropy=/path/to/isotropy
jmol=/path/to/jmol-14.4.0_2015.10.22b/jmol.sh

ADAQ

Install ADAQ

Clone the directory from github:

$ git clone <link to ADAQ when public>

The current version of ADAQ runs with python 2.7 and requires the python package tess. A suggestion is to make a virtualenv or conda with python 2.7 and tess:

$ conda create -n adaq python=2.7

activate this environment with:

$ conda activate adaq

and install tess with:

(adaq) $ pip install tess

Test installation

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

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

In the ADAQ folder, run:

(adaq) $ python test_installation.py

If you want to test with jmol, run:

(adaq) $ python test_installation.py jmol

Supercomputer

ADAQ and httk interfaces with a supercomputer to do the calculations. At the supercomputer, you require VASP and a python installation with numpy and scipy.

Linköping University specifics

Recommended to install httk and ADAQ at dedur01. At dedur01, the required files are located here:

istropy (/dedur01/data/shared/httk_libs/isotropy)
jmol (/dedur01/data/shared/httk_libs/jmol/jmol-14.4.0_2015.10.22b/jmol.sh)

Note

At dedur, you may need to install gcc compiler. use the following command: conda install compilers

It is also recommended to add configure ssh connection sharing at dedur. Add the following code to .ssh/config:

Host tetralith.nsc.liu.se
User x_abcde
ControlMaster auto
ControlPath ~/.ssh/cm-%r@%h:%p
ControlPersist 8h

When using tetralith or sigma, install a conda environment:

$ conda create -n adaq2 python=2.7 numpy scipy