Setting up the local working environment for the tutorial exercises¶
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.
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:
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.