Setting up the local working environment for the tutorial exercises

Execution environment

For the 2021 Siesta School we will be using the Siesta Mobile, a virtual machine based on the Quantum Mobile sponsored by the Marvel and MaX projects.

The virtual machine contains an Ubuntu operating system, plus school-related executables, python packages, and data files. Users just need to download the VM image and run it using the VirtualBox framework, which is available for most operating systems.

For more details about the setup and a link to download the VM image, please see this link.

Note

Using the Siesta Mobile is strongly recommended, since:

• It provides a cutting-edge version of Siesta with a number of features that are not yet in the latest officially released version (4.1.5):

  TD-DFT
  Spin-orbit coupling without the 'on-site approximation'
  Support for PSML pseudopotentials
  

• Contains the most relevant visualizers and analysis tools that are needed for the tutorials

• There is no need to deal with possibly complex installation issues, allowing full focus on learning how to use Siesta.

However, if using the Siesta Mobile is not possible for technical reasons, there are (less optimal) alternatives.

Working files for the tutorials

They are currently embedded in the source for the document repository you are reading, for consistency. One can obtain the whole distribution and generate an independent tree of working files:

git clone   https://gitlab.com/garalb/siesta-docs.git
cd siesta-docs
cd work-files
sh link.sh

During the school, new working files might be added, or typos or inconsistencies fixed. To get updated versions, one should do:

cd siesta-docs     # To be inside the git-controlled domain
git fetch
git pull

Now you are ready to update the working-files hierarchy in directory work-files for the actual work, but notice that the next step will potentially over-write files that you might have changed. For example, if you were working in the tutorials/basic/first-encounter/CH4 directory and had edited ch4.fdf to try some new feature, your changes will be lost. This only happens for files with the same name as the official files, so it is good practice to rename files in which you want to try new things that you might want to keep. In any case, you have also the option of copying your working directory to some other place for safekeeping.

After this step, you can do:

cd work-files
sh link.sh

You should read the docs online here, but could also regenerate them locally if desired using the above repo. (Check for availability of sphinx et al)

Things to add or download/compile later

Some items are not included in the Siesta Mobile for technical reasons:

• Extra programs

  The programs to process the PDOS/PDOS.xml files can be obtained and compiled very easily. See this how-to.

• The FLOS library

  This is needed for the simulation code implemented in Lua (e.g. NEB, new relaxation algorithms, etc). It is easily installed following the instructions in this how-to.

• Other tutorial-specific material (such as extra packages and potentially large data files).

When needed, each tutorial will provide information about any additional material needed.