Wannier90 tutorial and example 32 (extracting SCDM parameters from projectability with projwfc.x) #300

VVitale · 2019-11-27T12:29:31Z

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…jwfc.x

…er90 into develop

codecov · 2019-11-27T16:33:39Z

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giovannipizzi

Three minor changes requested

giovannipizzi · 2019-11-29T13:52:41Z

doc/tutorial/tutorial.tex

+	{\tt xmgrace }
+
+	To Import the {\tt p\_vs\_e.dat} file, click on {\tt Data} from the top bar and then {\tt Import -> ASCII...}.
+	At this point a new window {\tt Grace: Read sets} should pop up . Select {\tt p\_vs\_e.dat} in the {\tt Files} section, click {\tt Ok} at the bottom and close the window. You should now be able to see a quite noisy function that is bounded between 1 and 0. You can modify the appearence of the plot by clicking on {\tt Plot} in the top bar and then {\tt Set appearance...}. In the {\tt Main} section of the pop-up window change the symbol type from {\tt None} to {\tt Circle} and symbol size from 100 to 25. Also change symbol color from black to blue. Change the line type from straight to none. Move to the {\tt Symbols} section and change the filling pattern from none to full (indentified by a full black square) and then close the window. For the fitting, go to {\tt Data -> Transformations -> Non-linear curve fitting}. In this window, select the source from the {\tt Set} box and in the {\tt Formula} box insert the following \\


Remove space after pop up before the dot.
Also, it is really needed to ask to use 'fill' as a pattern and to make dots blue? I would remove this as it just makes the description longer and it's not critical. I don't think it's a problem if the plot is slightly different from the figure.

Yes I think you are right. I'll remove the section where I describe how to modify the graph appearance.

giovannipizzi · 2019-11-29T13:53:56Z

doc/tutorial/tutorial.tex

+
+	{\tt y = 0.5 * erfc( ( x - A0 ) / A1 )}  \\
+
+Select 2 as number of parameters, give 40 as initial condition for {\tt A0} and 7 for {\tt A1}. Click {\tt Apply}. A new window should pop up with the stats of the fitting. In particular you should find a {\tt Correlation coefficient} of 0.96 and a value of $39.9756$ for {\tt A0} and $6.6529$ for {\tt A1}. These are the value of $\mu_{fit}$ and $\sigma_{fit}$ we are going to use for the SCDM method. In particular, $\mu_{SCDM} = \mu_{fit} - 3\sigma_{fit} = 20.0169$ eV and $\sigma_{SCDM} = \sigma_{fit} = 6.6529$ eV. You should now see the fitting function, as well as the projectabilities, in the graph (see Fig. \ref{fig:W_fit}-(a)).\\


Explain that the specific choice \mu_{SCDM} = \mu_{fit} - 3\sigma_{fit} and \sigma_{SCDM} = \sigma_{fit} has been introduced in Ref. [3] and that there is the motivation and validation in there. Maybe somewhere at the end of the exercise say to cite [3] if you use this approach to get mu and sigma?

giovannipizzi · 2019-11-29T18:59:59Z

examples/example32/generate_weights.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+for i in {1..21}; do


Add a rm e.dat p.dat tmp.dat here - to avoid that these files already exist for some reason.

Can you also add a comment saying that this script is specific for this system (e.g. the number 21)?

giovannipizzi · 2019-11-29T19:00:27Z

doc/tutorial/tutorial.tex

+
+	{\tt y = 0.5 * erfc( ( x - A0 ) / A1 )}  \\
+
+Select 2 as number of parameters, give 40 as initial condition for {\tt A0} and 7 for {\tt A1}. Click {\tt Apply}. A new window should pop up with the stats of the fitting. In particular you should find a {\tt Correlation coefficient} of 0.96 and a value of $39.9756$ for {\tt A0} and $6.6529$ for {\tt A1}. These are the value of $\mu_{fit}$ and $\sigma_{fit}$ we are going to use for the SCDM method. In particular, $\mu_{SCDM} = \mu_{fit} - 3\sigma_{fit} = 20.0169$ eV and $\sigma_{SCDM} = \sigma_{fit} = 6.6529$ eV.The motivation for this specific choice of $\mu_{fit}$ and $\sigma_{fit}$ may be found in Ref.~\cite{Vitale2019automated}, where the authors also show validation of this approach on a dataset of 200 materials.  You should now see the fitting function, as well as the projectabilities, in the graph (see Fig. \ref{fig:W_fit}-(a)).\\


Missing space after the dot: 6.6529$ eV.The motivation

giovannipizzi · 2019-11-29T19:01:31Z

doc/tutorial/tutorial.tex

+	{\tt xmgrace }
+
+	To Import the {\tt p\_vs\_e.dat} file, click on {\tt Data} from the top bar and then {\tt Import -> ASCII...}.
+	At this point a new window {\tt Grace: Read sets} should pop up. Select {\tt p\_vs\_e.dat} in the {\tt Files} section, click {\tt Ok} at the bottom and close the window. You should now be able to see a quite noisy function that is bounded between 1 and 0. You can modify the appearence of the plot by clicking on {\tt Plot} in the top bar and then {\tt Set appearance...}. For the fitting, go to {\tt Data -> Transformations -> Non-linear curve fitting}. In this window, select the source from the {\tt Set} box and in the {\tt Formula} box insert the following \\


Maybe now you removed more than I intended - I would leave the part where you make them remove the lines and put dots - or at least mention that lines are just added by xmgrace connecting dots, but they are not meaningful (but maybe, it's easier just to put back the part where you explain how to make dots).

giovannipizzi · 2019-11-29T20:41:20Z

examples/example32/generate_weights.sh

+        rm p.dat;
+fi
+
+if [ -f "p_vs_e.dat" ]; then


I am going to approve this, but I mention that this is not really correct - this file is anyway regenerated, while the file appended with >> is instead tmp.dat, this is the one that should be removed...

Also, you can just rm -f FILENAME to remove it and not complain if it does not exist, no need to check.

Finally, below if there is a problem, better to use exit 1 instead of exit, to mark an unsuccessful exit.

Wannier90 tutorial and example 32 (extracting SCDM parameters from projectability with projwfc.x)

VVitale added 2 commits November 27, 2019 12:23

Tutorial for extracting SCDM parameters from projectability using pro…

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…jwfc.x

Merge branch 'develop' of https://github.com/wannier-developers/wanni…

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…er90 into develop

VVitale requested a review from giovannipizzi November 27, 2019 12:43

Tutorial and example for extracting SCDM parameters from projectability

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VVitale changed the title ~~Wannier90 tutorial and example 31 (extracting SCDM parameters from projectability with projwfc.x)~~ Wannier90 tutorial and example 32 (extracting SCDM parameters from projectability with projwfc.x) Nov 27, 2019

giovannipizzi reviewed Nov 29, 2019

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VVitale added 2 commits November 29, 2019 15:22

Changed text in example32 as suggested by Pizzi

193a647

typo-fix in citation in example32

e145ae8

giovannipizzi requested changes Nov 29, 2019

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Further changes to tutorial.tex requested by G. Pizzi

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giovannipizzi reviewed Nov 29, 2019

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giovannipizzi approved these changes Nov 29, 2019

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Update generate_weights.sh

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giovannipizzi merged commit 8ab4d9d into wannier-developers:develop Dec 2, 2019

manxkim pushed a commit to manxkim/wannier90 that referenced this pull request Jan 10, 2021

Merge pull request wannier-developers#300 from VVitale/develop

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Wannier90 tutorial and example 32 (extracting SCDM parameters from projectability with projwfc.x)

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Wannier90 tutorial and example 32 (extracting SCDM parameters from projectability with projwfc.x) #300

Wannier90 tutorial and example 32 (extracting SCDM parameters from projectability with projwfc.x) #300

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		{\tt y = 0.5 * erfc( ( x - A0 ) / A1 )} \\

		Select 2 as number of parameters, give 40 as initial condition for {\tt A0} and 7 for {\tt A1}. Click {\tt Apply}. A new window should pop up with the stats of the fitting. In particular you should find a {\tt Correlation coefficient} of 0.96 and a value of $39.9756$ for {\tt A0} and $6.6529$ for {\tt A1}. These are the value of $\mu_{fit}$ and $\sigma_{fit}$ we are going to use for the SCDM method. In particular, $\mu_{SCDM} = \mu_{fit} - 3\sigma_{fit} = 20.0169$ eV and $\sigma_{SCDM} = \sigma_{fit} = 6.6529$ eV. You should now see the fitting function, as well as the projectabilities, in the graph (see Fig. \ref{fig:W_fit}-(a)).\\

Wannier90 tutorial and example 32 (extracting SCDM parameters from projectability with projwfc.x) #300

Wannier90 tutorial and example 32 (extracting SCDM parameters from projectability with projwfc.x) #300

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