Commit b99965e4 authored by Alberto Garcia's avatar Alberto Garcia Committed by Alberto
Browse files

Move analysis-tools to the how-to section

parent 2ea436de
:sequential_nav: next
.. _tutorial-basic-analysis-tools:
.. _how-to-analysis-tools:
Analysis tools
==============
.. note::
Rather than a tutorial per-se, this is a repository of
information with pointers on how to analyze and plot particular
items of data generated by Siesta. In that sense it is more of a
how-to, and it will be moved to that section
This is a repository (**under construction**) of information with pointers on how to analyze
and plot particular items of data generated by Siesta.
.. note::
Some of the tools mentioned in this how-to are covered in this
excellent `slide presentation <https://drive.google.com/file/d/1oQs0xGMoqJ02khKfC1x3jPiwkxwUIHNy/view?usp=sharing>`_
by Andrei Postnikov.
Electronic Structure
--------------------
......@@ -19,7 +20,7 @@ Electronic Structure
* Band structures
Use the ``gnubands`` program (with the modern options), plus
gnuplot. See examples :ref:`here<tutorial-kpoint-sampling>`.
gnuplot. See examples :ref:`here<tutorial-basic-kpoint-convergence>`.
* Fermi surfaces
......@@ -101,12 +102,6 @@ Forces on atoms, normal modes, etc
* Forces on atoms
.. note::
Some of the tools mentioned in this tutorial are covered in this
excellent `slide presentation <https://drive.google.com/file/d/1oQs0xGMoqJ02khKfC1x3jPiwkxwUIHNy/view?usp=sharing>`_
by Andrei Postnikov.
......
......@@ -30,6 +30,7 @@ Visualization
.. toctree::
:maxdepth: 1
analysis-tools.rst
orbitals.rst
stm_utils.rst
dos-pdos.rst
......
:sequential_nav: next
.. _tutorial-basic-ch4:
A first encounter with Siesta
========================================
.. sidebar:: **Have you set up the local environment?**
If not, :ref:`do that now <local_installation>` before proceeding.
In this exercise we will focus on the basic input parameters and
outputs of the SIESTA program. We will study two simple molecules
(CH4 and CH3)
..note:: (Enter the directory 'CH4')
You will find an input file for the SIESTA program named ch4.fdf along
with the files C.psf and H.psf containing the information about the
pseudopotentials. The ch4.fdf file sets the value of several
parameters which specify both the system we want to study and the
accuracy of the calculation. Of course the parameters specifying the
system are mandatory (number of atoms, atomic numbers, label
associated with each atomic specie, etc..). All other parameters have
some default values and, in principle, it is not necessary to
explicitly include them in the input file. However, it is important to
note that the default values do not always guarantee a converged
calculation.
In the file ch4.fdf you can find first the inputs that specify the
system. Pay special attention to the block ChemicalSpeciesLabel. In
this block you assign an index and a label to each atomic species. The
label will allow to recognize the files containing the information
about the pseudopotential and the basis set (when provided).
Check the input of the coordinates (they are just some guess
coordinates, not the optimized equilibrium ones).
The file ch4.fdf contains the most important parameters to take into
account to perform a molecular calculation. Namely:
......@@ -284,7 +284,7 @@ In response to these lines, SIESTA produced two extra files:
More details on how to visualize the charge density and other
quantities represented on the real-space grid are given in :ref:`this
tutorial <tutorial-basic-analysis-tools>`. For this tutorial we will
how-to <how-to-analysis-tools>`. For this tutorial we will
use Xcrysden. Execute::
rho2xsf < rho2xsf.inp
......
......@@ -11,24 +11,23 @@ Magnetism
:author: Daniel Sanchez-Portal and Andrei Postnikov (2010)
Initialization of different magnetic order in a magnetic insulator
(MnO), and analyzing the results.
Initialization of different magnetic orders in a magnetic insulator
(MnO), and analysis of the results.
.. warning::
As it is, this exercise is a bit "hard", because it demands some
.. As it is, this exercise is a bit "hard", because it demands some
skill in setting up the AF structures, and in analyzing the
output. We could tag it as such, or provide a bit more input
material. I still need to flex out the content of the
:ref:`analysis tools<tutorial-basic-analysis-tools>`
tutorial.
output. There are hints in Answers for now
The aim of the exercise: to learn setting up a calculation
in a bulk (crystal) system composed of "magnetic" (i.e., `3d`)
and "non-magnetic" (`s-p`) atoms, whereby spin moments of "magnetic"
atoms may be arranged in different types of magnetic orderings,
and hence allow different (metastable) magnetic solutions.
Analyze the results of converged calculations, demonstrating the type
of magnetic ordering in each of the cases considered.
The aims of the exercise:
* To learn to set up a calculation in a bulk (crystal) system composed
of "magnetic" (i.e., `3d`) and "non-magnetic" (`s-p`) atoms, whereby
spin moments of "magnetic" atoms may be arranged in different types
of magnetic orderings, and hence allow different (metastable)
magnetic solutions.
* To analyze the results of converged calculations, demonstrating the type
of magnetic ordering in each of the cases considered.
.. note::
3d oxydes are notorious examples of systems in which Coulomb correlation
......@@ -78,7 +77,7 @@ In order to run a spin-polarized calculation, we set::
and moreover initialize non-zero (in fact, maximal) spin on Mn site::
%block DM.InitSpin # Iitial magnetic order (on Mn only)
%block DM.InitSpin # Initial magnetic order (on Mn only)
1 +
%endblock DM.InitSpin
......@@ -99,7 +98,7 @@ magnetic orderings.
Tasks:
1. When the first calculation is done, check the local (on Mn and O sites)
and total (per unit cell) magntic moments. Plot the spin-resolved
and total (per unit cell) magnetic moments. Plot the spin-resolved
density of states (total and that for Mn and O sites).
2. Prepare the input file(s) for antiferromagnetc structures of MnO
......
......@@ -28,7 +28,6 @@ for more experienced users.
basic/first-crystals/index
basic/pseudopotentials/index
basic/basis-sets/index
basic/analysis-tools/index
basic/grid-convergence/index
basic/kpoint-convergence/index
basic/scf-convergence/index
......
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