Add relative (no vacuum) alignment feature #1

kavanase · 2020-01-12T11:57:31Z

Use the optional arguments --eg and --vbo or --cbo to specify relative alignments of bands. I've added an example to README.md and help information. bapt knows which plot to produce
(vacuum alignment or not) based on whether --eg & --vbo/--cbo or --ip & --ea was specified.
"Vacuum level" changes to "conduction band", and the axis limits are set so that the highest CBM is 1 eV below the upper limit, and the lowest VBM is 1 eV above the lower limit.

Example:
bapt -n Cs\$_2\$AgBiBr\$_6\$,Cs\$_2\$AgSbBr\$_6\$,Cs\$_2\$AgSbCl\$_6\$ -eg 1.774,1.366,1.6 -cbo 0.247,-0.4 -o alignment.png --font-size 10 --show-axis gives:

Checking that the original plot function works as expected:
bapt --name "ZnO,MOF-5,HKUST-1,ZIF-8" --ip 7.7,7.3,6.0,6.4 --ea 4.4,2.7,5.1,1.9 -o normalalign.png gives:

Checking the errors work as expected:

Checking bapt -h works as expected:

Note:
If merging, you might need to change the image source line in README.md from <img src="https://raw.githubusercontent.com/kavanase/bapt/master/examples/cli_novac.png" height="300"> to <img src="https://raw.githubusercontent.com/utf/bapt/master/examples/cli_novac.png" height="300">

utf · 2020-01-14T17:06:25Z

bapt/__init__.py

+                ax.text(x + bar_width/2., ip + 1.65*pad,
+                        f"VBO: {compound['vbo'] - data[i-1]['vbo']:+.2f} eV", zorder=2,
+                        ha='center', va='top', size=label_size-3, color=name_colour,
+                        fontfamily='serif')


Can you keep this the default font to be consistent with the rest of the style of the plot.

Yep no problem. Thought it looked slightly nicer with a different font at the time, but I see that a consistent style is better 😃

utf

Hi @kavanase, thanks for this, I think this is a nice idea!

I've made some comments on the PR.

Basically, try and keep the plot style consistent:

The same font should be used throughout
Not more than 2 font sizes in the plot (ideally use 1 but I think a smaller font for the offset is ok).
Lines should all be the same thickness.

Finally, can you add a yaml file example also?

Thanks again for this. Nice to see bapt getting some love.

utf · 2020-01-14T17:06:33Z

bapt/__init__.py

+                ax.text(x + bar_width/2., ea - pad,
+                        f"CBO: {compound['cbo'] - data[i-1]['cbo']:+.2f} eV", zorder=2,
+                        ha='center', va='top', size=label_size-3, color=name_colour,
+                        fontfamily='serif')


utf · 2020-01-14T17:07:44Z

bapt/__init__.py

+        ax.yaxis.set_major_locator(MultipleLocator(1))
+        for spine in ax.spines.values():
+            spine.set_zorder(5)
+        ax.tick_params(which='major', width=1.75*_linewidth) # prettify


Is the width controlling the thickness of the line? In which case, can you keep the line thickness the same as all other axis lines for consistency.

Yeah this was just to change the major axis tick linewidth to make it obvious that the zero of energy was set to the VBM of the first compound:
To give this:

Instead of this:

Either way, I suppose it's clear enough without changing the width, and looks a bit cleaner and more consistent, without changing it, so I'll change it now.

utf · 2020-01-14T17:09:52Z

bapt/cli.py

    parser.add_argument('-i', '--ip',
                        help='List of ionisation potentials (comma separated).')
    parser.add_argument('-e', '--ea',
                        help='List of electron affinities (comma separated).')
+    parser.add_argument('-cbo', '--cbo', default=None,


Abbreviated arguments should only be one letter long. I.e., if the long argument is --cbo, the short one should be something like -c. If -c is already taken by another option, you can either come up with a different letter or leave it as a long argument only.

So this option, vbo and eg, should should be:

-c, --cbo -v, --vbo -e, --eg

utf · 2020-01-14T17:10:53Z

bapt/cli.py

+    parser.add_argument('-vbo', '--vbo', default=None,
+                        help='List of valence band offsets (comma separated). ' +
+                        '(Relative to first compound)(-> No vacuum alignment)')
+    parser.add_argument('-eg', '--eg',


I think --band-gap is actually a better long argument. It is more clear what it means immediately. You can use -b as an abbreviation.

Sounds good, will do.

utf · 2020-01-14T17:17:39Z

The yaml file should be along these lines:
https://github.com/utf/bapt/blob/master/examples/basic.yaml

utf · 2020-01-14T17:18:56Z

Also, can you go ahead and make the change in the readme to point to the new image url.

utf · 2020-01-14T17:24:15Z

One final thing: I added a contributors section to the readme! :)

kavanase · 2020-01-14T18:07:05Z

Ok, I've made all requested changes, and checked that it all still works as it should. I've added a yaml file to the examples folder, with the output shown in README. The two added example images don't currently display (as the html link is to utf/bapt/examples, but the filenames are correct, so once the pull request is merged they should display in README.
Appreciate the shoutout!

utf · 2020-01-14T23:08:17Z

Thanks again for this.

Just to let you know, I made a few more edits, such as removing the "VBO:" and "CBO:" strings from the plot.

I also, removed the reliance on f-strings. They are really nice but I don't think the adoption of python 3.6+ is high enough just yet.

kavanase · 2020-01-15T08:34:33Z

No worries, sounds good!

…

________________________________ From: Alex Ganose <[email protected]> Sent: Tuesday, January 14, 2020 11:08:17 PM To: utf/bapt <[email protected]> Cc: Kavanagh, Sean <[email protected]>; Mention <[email protected]> Subject: Re: [utf/bapt] Add relative (no vacuum) alignment feature (#1) This email from [email protected] originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. Thanks again for this. Just to let you know, I made a few more edits, such as removing the "VBO:" and "CBO:" strings from the plot. I also, removed the reliance on f-strings. They are really nice but I don't think the adoption of python 3.6+ is high enough just yet. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#1?email_source=notifications&email_token=AMIYBIPWU4XWPAF2VVNBKK3Q5ZAWDA5CNFSM4KFXIIYKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEI6ONUA#issuecomment-574416592>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMIYBILEDNKRPVFMNYG2PUDQ5ZAWDANCNFSM4KFXIIYA>.

kavanase added 14 commits January 12, 2020 10:42

Add get_plot_novac function to __init__.py

82d99a6

Update plotting.py

ec7b887

Add cbo/vbo optional parser arguments, error messages etc

88d00c9

Import from bapt

8963d4b

Import from bapt

e1d7ba7

PEP8 Formatting

9dce11c

Move linewidth and minor y-tick variation to get_plot_novac

ae5547b

Update plotting.py

ebf0665

Move linewidth and minor y-tick variation to get_plot_novac

3564937

Quick example of get_plot_novac

2fb724a

Add files via upload

357a657

Update README.md

5dfb727

Update README.md

519e5c2

Update README.md

3c09100

utf reviewed Jan 14, 2020

View reviewed changes

Remove font change for CBO & VBO

27dbd47

utf reviewed Jan 14, 2020

View reviewed changes

kavanase added 10 commits January 14, 2020 17:32

Remove y-axis major tick linewidth change

9e0336a

Change cli arguments

349259e

Update __init__.py to deal with new cli arguments

e6bc2c0

Add band_offset.yaml example

e265e72

Update README.md to point to yaml example

175579a

Update README.md

c94fa1d

Update band_offset.yaml

90afe73

Add files via upload

21da852

Update README.md

7088a9a

Merge branch 'master' into master

ccbf7f6

utf merged commit 9214b6d into utf:master Jan 14, 2020

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Add relative (no vacuum) alignment feature #1

Add relative (no vacuum) alignment feature #1

kavanase commented Jan 12, 2020

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Add relative (no vacuum) alignment feature #1

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kavanase commented Jan 12, 2020

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utf commented Jan 14, 2020

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