In case GPAW is ahead of ASE

When next time (like in 2024), GPAW refers to a beta-version of ASE to that

conda install -c conda-forge gpaw
conda remove --force ase
pip install --upgrade git+https://gitlab.com/ase/ase.git@master

Present of year 2023

I wish everyone a Merry Christmas and a Happy New Year!

As I present, let me share the discovery of this year.

Ferdium is a program that combines all messengers in a single window! I tried to distinguish between work and life using different messengers for years. For work, I used fleep.io. Unfortunately, they decided to close all freemium accounts and raise the prices this year. So, I switched to other messengers and eventually mixed them up. Luckily, I found Ferdium! Just see my print screen – all messengers in one app:

Go to ferdium.org to get it.

By the way, Opera provides a similar functionality, but it does not have so many app in it. For example, it does not have Element.

Simulating colour blindness in GIMP

A simple check whether your colours are suitable for illustrations is implemented in GIMP.

view > display filters > color deficient vision

Also

image > mode > grayscale

For details see: https://docs.gimp.org/2.10/en/gimp-display-filter-dialog.html#gimp-deficient-vision

Type hinting in python

[a note for myself]

var: str='text'
from typing import Optional
def function(variable: str|float, number: int|float, variable: bool=False, a_kwarg: Optional[int]=None):
    pass
from typing import Tuple
def function() -> Tuble[str,str]:
    return 'Hello', 'World!'

Zotero + chatGPT via pdfGEAR

Some time ago (in 2023), I linked Zotero with chatGPT by creating an environment with paper-qa and pyzotero like this:
conda create -n Zotero
conda activate Zotero
conda install pip
pip install paper-qa
pip install pyzotero
pip install bs4

That worked but felt way too complicated … like I am not going to use it on a daily basis. It also reminded me the very first experience with the Meta AI in late 2022 (which everyone already forgot).

Here is a much simpler recipe:

  1. Install Zotero add-on from github.com/retorquere/zotero-open-pdf to enable opening with external pdf viewers.
  2. Install pdfGEAR as your default pdf viewer (external to Zotero).

See how it works on my YouTube channel: youtu.be/4JSy2RsBLDE?si=Hbj7oq7gaOiq6END

Fonts for grant proposals

The reference font for the body text of European proposals is Times New Roman (Windows platforms), Times/Times New Roman (Apple platforms) or Nimbus Roman No. 9 L (Linux distributions). The Roman family is from a pre-digital age and has well-recognizable features.

Is it the best font in terms of readability? On the one hand, there is a tendency to move from Times-type fonts to plainer fonts, like Calibri. On the other hand, many studies (with controversial results) account for aspects like Dyslexia, typeface anatomy, and Display vs. Print. The effect of font choice on readability and compression on big numbers seems small or insignificant. However, my point is that a proposal must be clear to a few reviewers, who might have difficulties understanding the proposal due to age, Dyslexia, and colour vision deficiency. These few people will have some feelings about how the text is formatted. For that reason and also because of my artistic education in caligraphy, I have been looking for and playing with font combinations for a long time. Here is what I have tried and liked.

1. STIX two and Source Sans form a pair of Serif and Sans fonts. STIX two resulted from a collaborative effort from the most prominent academic publishing companies. Its predecessor (STIX one) has exactly the same metrics as Times New Roman. STIX two is somewhat bigger, which is not prohibited by the EU funding agencies. The main benefit of using STIX fonts is that these are mathematical fonts and, thus, can be natively used in MS Equation Editor (instead of Cambria) and LaTeX (as XITS or STIX2).

2. An excellent substitution for Times New Roman is Zilla Slab – a unique font by the Mozilla foundation – which has the same metrics as Times New Roman, is a Sans font, yet looks like a monospace one, does have features of a Dyslexia-friendly typeface, and looks great in print and on screen. It is freely available from Google fonts. It can be used with Times New Roman (or similar) as a pair of Serif and Sans fonts.

3. Libertinus Serif + Gill Sans is my favourite Serif and Sans pair. You can see Linux Libertine in the Wikipedia logo. Gill Sans Nova is commonly fond in the University of Tartu (Estonia) press. Although Libertinus Serif has an original Sans counterpart, its combination with Gill Sans looks most natural. I love Libertinus because of its amazingly looking ligatures, and it is also compatible with MS Equation Editor and LaTeX.

PS One can play with fonts in the EU projects to make their proposal more appealing. Like Estonian grants, I prefer calls, where applicants fill out online forms without changing the text appearance. Of course, the text looks ugly due to nasty line breaks, horrible chemical formulas and mathematical equations, and poor typography. Still, the competition is more fair because everyone is in the same conditions. 

Reference style for an MSCA proposal

Dani Bodor created a nice reference style that is suitable for writing an MSCA proposal:

marie-sklodowska-curie-actions.csl

See forums.zotero.org/discussion/73275/foot-notes-for-a-marie-curie-application.

This style is similar to what I used in my LaTeX template:

www.overleaf.com/latex/templates/msca-template/dskmdjpzbhkg

Here is the code for that style:

<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="note" version="1.0" demote-non-dropping-particle="never" page-range-format="chicago" default-locale="en-GB">
  <!-- This style was edited with the Visual CSL Editor (http://editor.citationstyles.org/visualEditor/) -->
  <info>
    <title>Marie Skłodowska-Curie actions</title>
    <id>http://www.zotero.org/styles/marie-sklodowska-curie-actions</id>
    <link href="http://www.zotero.org/styles/marie-sklodowska-curie-actions" rel="self"/>
    <link href="https://forums.zotero.org/discussion/comment/262041/#Comment_262041" rel="documentation"/>
    <author>
      <name>Dani Bodor</name>
      <email>d.bodor@ucl.ac.uk</email>
    </author>
    <category citation-format="note"/>
    <category field="generic-base"/>
    <summary>For use in application to H2020 Marie Skłodowska-Curie Actions fellowship</summary>
    <updated>2017-07-31T17:37:20+00:00</updated>
    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
  </info>
  <locale xml:lang="en">
    <terms>
      <term name="editor" form="verb-short">ed.</term>
      <term name="translator" form="verb-short">trans.</term>
      <term name="editortranslator" form="verb-short">
        <single>ed. and trans.</single>
        <multiple>ed. and trans.</multiple>
      </term>
      <term name="editortranslator" form="verb">
        <single>Edited and translated by</single>
        <multiple>Edited and translated by</multiple>
      </term>
      <term name="translator" form="short">trans.</term>
    </terms>
  </locale>
  <macro name="secondary-contributors">
    <choose>
      <if type="chapter paper-conference" match="none">
        <names variable="editor translator" delimiter=". ">
          <label form="verb" text-case="capitalize-first" suffix=" "/>
          <name and="text" delimiter=", "/>
        </names>
      </if>
    </choose>
  </macro>
  <macro name="container-contributors">
    <choose>
      <if type="chapter paper-conference" match="any">
        <group delimiter=", ">
          <choose>
            <if variable="author">
              <choose>
                <if variable="container-author" match="any">
                  <names variable="container-author">
                    <label form="verb-short" text-case="lowercase" suffix=" "/>
                    <name and="text" delimiter=", "/>
                  </names>
                </if>
              </choose>
              <choose>
                <if variable="container-author author" match="all">
                  <group delimiter=". ">
                    <text variable="page"/>
                    <names variable="editor translator" delimiter=", ">
                      <label form="verb" suffix=" "/>
                      <name and="text" delimiter=", "/>
                    </names>
                  </group>
                </if>
                <else>
                  <names variable="editor translator" delimiter=", ">
                    <label form="verb" text-case="lowercase" suffix=" "/>
                    <name and="text" delimiter=", "/>
                  </names>
                </else>
              </choose>
            </if>
          </choose>
        </group>
      </if>
    </choose>
  </macro>
  <macro name="recipient-note">
    <names variable="recipient" delimiter=", ">
      <label form="verb" text-case="lowercase" suffix=" "/>
      <name and="text" delimiter=", "/>
    </names>
  </macro>
  <macro name="editor">
    <names variable="editor">
      <name name-as-sort-order="first" and="text" sort-separator=", " delimiter=", " delimiter-precedes-last="always"/>
      <label form="short" prefix=", "/>
    </names>
  </macro>
  <macro name="translator">
    <names variable="translator">
      <name name-as-sort-order="first" and="text" sort-separator=", " delimiter=", " delimiter-precedes-last="always"/>
      <label form="verb-short" prefix=", "/>
    </names>
  </macro>
  <macro name="recipient">
    <group delimiter=" ">
      <choose>
        <if type="personal_communication">
          <choose>
            <if variable="genre">
              <text variable="genre" text-case="capitalize-first"/>
            </if>
            <else>
              <text term="letter" text-case="capitalize-first"/>
            </else>
          </choose>
        </if>
      </choose>
      <text macro="recipient-note"/>
    </group>
  </macro>
  <macro name="contributors">
    <group delimiter=". ">
      <names variable="author">
        <name name-as-sort-order="first" and="text" sort-separator=", " delimiter=", " delimiter-precedes-last="always"/>
        <substitute>
          <text macro="editor"/>
          <text macro="translator"/>
        </substitute>
      </names>
      <text macro="recipient"/>
    </group>
  </macro>
  <macro name="recipient-short">
    <names variable="recipient">
      <label form="verb" text-case="lowercase" suffix=" "/>
      <name form="short" and="text" delimiter=", "/>
    </names>
  </macro>
  <macro name="contributors-short">
    <group delimiter=" ">
      <names variable="author">
        <name form="short" and="symbol"/>
        <substitute>
          <names variable="editor"/>
          <names variable="translator"/>
        </substitute>
      </names>
      <text macro="recipient-short"/>
    </group>
  </macro>
  <macro name="interviewer">
    <names variable="interviewer" delimiter=", ">
      <label form="verb" text-case="capitalize-first" suffix=" "/>
      <name and="text" delimiter=", "/>
    </names>
  </macro>
  <macro name="title">
    <choose>
      <if variable="title" match="none">
        <choose>
          <if type="personal_communication" match="none">
            <text variable="genre" text-case="capitalize-first"/>
          </if>
        </choose>
      </if>
      <else-if type="bill book graphic legislation motion_picture song" match="any">
        <text variable="title" text-case="title" font-style="italic"/>
        <group prefix=" (" suffix=")" delimiter=" ">
          <text term="version"/>
          <text variable="version"/>
        </group>
      </else-if>
      <else-if variable="reviewed-author">
        <group delimiter=", ">
          <text variable="title" font-style="italic" prefix="Review of "/>
          <names variable="reviewed-author">
            <label form="verb-short" text-case="lowercase" suffix=" "/>
            <name and="text" delimiter=", "/>
          </names>
        </group>
      </else-if>
      <else-if type="legal_case interview patent" match="any">
        <text variable="title"/>
      </else-if>
      <else>
        <text variable="title" text-case="title" quotes="true"/>
      </else>
    </choose>
  </macro>
  <macro name="description">
    <group delimiter=", ">
      <group delimiter=". ">
        <text macro="interviewer"/>
        <text variable="medium" text-case="capitalize-first"/>
      </group>
      <choose>
        <if variable="title" match="none"/>
        <else-if type="thesis speech" match="any"/>
        <else-if type="patent">
          <group delimiter=" ">
            <text variable="authority"/>
            <text variable="number"/>
          </group>
        </else-if>
        <else>
          <text variable="genre" text-case="capitalize-first"/>
        </else>
      </choose>
    </group>
  </macro>
  <macro name="container-title">
    <group delimiter=" ">
      <choose>
        <if type="chapter paper-conference" match="any">
          <text term="in" text-case="capitalize-first"/>
        </if>
      </choose>
      <choose>
        <if type="legal_case" match="none">
          <text variable="container-title" text-case="title" font-style="italic"/>
        </if>
      </choose>
    </group>
  </macro>
  <macro name="collection-title">
    <choose>
      <if match="none" type="article-journal">
        <choose>
          <if match="none" is-numeric="collection-number">
            <group delimiter=", ">
              <text variable="collection-title" text-case="title"/>
              <text variable="collection-number"/>
            </group>
          </if>
          <else>
            <group delimiter=" ">
              <text variable="collection-title" text-case="title"/>
              <text variable="collection-number"/>
            </group>
          </else>
        </choose>
      </if>
    </choose>
  </macro>
  <macro name="collection-title-journal">
    <choose>
      <if type="article-journal">
        <group delimiter=" ">
          <text variable="collection-title"/>
          <text variable="collection-number"/>
        </group>
      </if>
    </choose>
  </macro>
  <macro name="edition-note">
    <choose>
      <if type="bill book chapter graphic legal_case legislation motion_picture paper-conference report song" match="any">
        <choose>
          <if is-numeric="edition">
            <group delimiter=" ">
              <number variable="edition" form="ordinal"/>
              <text term="edition" form="short"/>
            </group>
          </if>
          <else>
            <text variable="edition"/>
          </else>
        </choose>
      </if>
    </choose>
  </macro>
  <macro name="edition">
    <choose>
      <if type="bill book chapter graphic legal_case legislation motion_picture paper-conference report song" match="any">
        <choose>
          <if is-numeric="edition">
            <group delimiter=" ">
              <number variable="edition" form="ordinal"/>
              <text term="edition" form="short"/>
            </group>
          </if>
          <else>
            <text variable="edition" text-case="capitalize-first" suffix="."/>
          </else>
        </choose>
      </if>
    </choose>
  </macro>
  <macro name="locators-note">
    <choose>
      <if type="article-journal">
        <group delimiter=", ">
          <text macro="collection-title-journal"/>
          <number variable="volume"/>
          <group delimiter=" ">
            <text term="issue" form="short"/>
            <number variable="issue"/>
          </group>
        </group>
      </if>
      <else-if type="legal_case">
        <group delimiter=", ">
          <group delimiter=" ">
            <number variable="volume"/>
            <text variable="container-title"/>
            <text variable="page"/>
          </group>
          <text variable="locator"/>
        </group>
      </else-if>
      <else-if type="bill book chapter graphic legal_case legislation motion_picture paper-conference report song" match="any">
        <group delimiter=", ">
          <text macro="edition-note"/>
          <group delimiter=" ">
            <text term="volume" form="short"/>
            <number variable="volume" form="numeric"/>
          </group>
          <choose>
            <if variable="locator" match="none">
              <group delimiter=" ">
                <number variable="number-of-volumes" form="numeric"/>
                <text term="volume" form="short" plural="true"/>
              </group>
            </if>
          </choose>
        </group>
      </else-if>
    </choose>
  </macro>
  <macro name="locators-join-with-space">
    <choose>
      <if type="article-journal" variable="volume" match="all">
        <choose>
          <if match="none" variable="collection-title">
            <text macro="locators"/>
          </if>
        </choose>
      </if>
    </choose>
  </macro>
  <macro name="locators-join-with-comma">
    <choose>
      <if type="legal_case chapter paper-conference" match="any">
        <text macro="locators"/>
      </if>
      <else-if type="article-journal">
        <choose>
          <if variable="volume" match="none">
            <text macro="locators"/>
          </if>
          <else-if match="any" variable="collection-title">
            <text macro="locators"/>
          </else-if>
        </choose>
      </else-if>
    </choose>
  </macro>
  <macro name="locators-join-with-period">
    <choose>
      <if type="legal_case article-journal chapter paper-conference" match="none">
        <text macro="locators"/>
      </if>
    </choose>
  </macro>
  <macro name="locators">
    <choose>
      <if type="article-journal">
        <group delimiter=", ">
          <text macro="collection-title-journal"/>
          <number variable="volume"/>
          <group delimiter=" ">
            <text term="issue" form="short"/>
            <number variable="issue"/>
          </group>
        </group>
      </if>
      <else-if type="legal_case">
        <group delimiter=" ">
          <number variable="volume"/>
          <text variable="container-title"/>
          <text variable="page"/>
        </group>
      </else-if>
      <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
        <group delimiter=". ">
          <text macro="edition"/>
          <group delimiter=" ">
            <text term="volume" form="short" text-case="capitalize-first"/>
            <number variable="volume" form="numeric"/>
          </group>
          <group delimiter=" ">
            <number variable="number-of-volumes" form="numeric"/>
            <text term="volume" form="short" plural="true"/>
          </group>
        </group>
      </else-if>
      <else-if type="chapter paper-conference" match="any">
        <group delimiter=". ">
          <text macro="edition"/>
          <choose>
            <if variable="page" match="none">
              <group delimiter=" ">
                <text term="volume" form="short" text-case="capitalize-first"/>
                <number variable="volume" form="numeric"/>
              </group>
            </if>
          </choose>
        </group>
      </else-if>
    </choose>
  </macro>
  <macro name="locators-newspaper">
    <choose>
      <if type="article-newspaper">
        <group delimiter=", ">
          <group delimiter=" ">
            <number variable="edition"/>
            <text term="edition"/>
          </group>
          <group delimiter=" ">
            <text term="section" form="short"/>
            <text variable="section"/>
          </group>
        </group>
      </if>
    </choose>
  </macro>
  <macro name="event">
    <choose>
      <if variable="title">
        <group delimiter=" ">
          <text term="presented at"/>
          <text variable="event"/>
        </group>
      </if>
      <else>
        <group delimiter=" ">
          <text term="presented at" text-case="capitalize-first"/>
          <text variable="event"/>
        </group>
      </else>
    </choose>
  </macro>
  <macro name="originally-published">
    <group delimiter=", ">
      <group delimiter=": ">
        <text variable="original-publisher-place"/>
        <text variable="original-publisher"/>
      </group>
      <date variable="original-date" form="text" date-parts="year"/>
    </group>
  </macro>
  <macro name="reprint">
    <choose>
      <if variable="original-date issued" match="all">
        <text value="reprint" text-case="capitalize-first"/>
      </if>
    </choose>
  </macro>
  <macro name="publisher">
    <choose>
      <if type="thesis">
        <text variable="publisher"/>
      </if>
      <else-if type="speech">
        <text variable="event-place"/>
      </else-if>
      <else>
        <group delimiter=": ">
          <text variable="publisher-place"/>
          <text variable="publisher"/>
        </group>
      </else>
    </choose>
  </macro>
  <macro name="issued">
    <choose>
      <if variable="issued">
        <choose>
          <if type="graphic report" match="any">
            <date variable="issued" form="text"/>
          </if>
          <else-if type="legal_case">
            <group delimiter=" ">
              <text variable="authority"/>
              <date variable="issued">
                <date-part name="year"/>
              </date>
            </group>
          </else-if>
          <else-if type="bill book chapter graphic legal_case legislation motion_picture paper-conference report song thesis" match="any">
            <date variable="issued">
              <date-part name="year"/>
            </date>
          </else-if>
          <else-if type="patent">
            <group delimiter=", ">
              <group delimiter=" ">
                <text value="filed"/>
                <date variable="submitted" form="text"/>
              </group>
              <group delimiter=" ">
                <choose>
                  <if variable="issued submitted" match="all">
                    <text term="and"/>
                  </if>
                </choose>
                <text value="issued"/>
                <date variable="issued" form="text"/>
              </group>
            </group>
          </else-if>
          <else>
            <date variable="issued" form="text"/>
          </else>
        </choose>
      </if>
      <else-if variable="status">
        <text variable="status"/>
      </else-if>
      <else-if variable="accessed URL" match="all"/>
      <else>
        <text term="no date" form="short"/>
      </else>
    </choose>
  </macro>
  <macro name="point-locators-subsequent">
    <choose>
      <if type="legal_case"/>
      <else-if variable="locator">
        <choose>
          <if locator="page" match="none">
            <group delimiter=" ">
              <choose>
                <if type="bill book graphic legislation motion_picture report song" match="any">
                  <choose>
                    <if variable="volume">
                      <group delimiter=", ">
                        <group delimiter=" ">
                          <text term="volume" form="short"/>
                          <number variable="volume" form="numeric"/>
                        </group>
                        <label variable="locator" form="short"/>
                      </group>
                    </if>
                    <else>
                      <label variable="locator" form="short"/>
                    </else>
                  </choose>
                </if>
                <else>
                  <label variable="locator" form="short"/>
                </else>
              </choose>
              <text variable="locator"/>
            </group>
          </if>
          <else-if type="bill book graphic legislation motion_picture report song" match="any">
            <group delimiter=":">
              <number variable="volume" form="numeric"/>
              <text variable="locator"/>
            </group>
          </else-if>
          <else>
            <text variable="locator"/>
          </else>
        </choose>
      </else-if>
    </choose>
  </macro>
  <macro name="locators-chapter">
    <choose>
      <if type="chapter paper-conference" match="any">
        <choose>
          <if variable="author container-author" match="all"/>
          <else>
            <choose>
              <if variable="page">
                <number variable="volume" suffix=":"/>
                <text variable="page"/>
              </if>
            </choose>
          </else>
        </choose>
      </if>
    </choose>
  </macro>
  <macro name="locators-journal-join-with-colon">
    <choose>
      <if type="article-journal">
        <choose>
          <if variable="volume issue" match="any">
            <text variable="page"/>
          </if>
        </choose>
      </if>
    </choose>
  </macro>
  <macro name="locators-journal-join-with-comma">
    <choose>
      <if type="article-journal">
        <choose>
          <if variable="volume issue" match="none">
            <text variable="page"/>
          </if>
        </choose>
      </if>
    </choose>
  </macro>
  <macro name="archive">
    <choose>
      <if type="thesis">
        <group delimiter=" ">
          <text variable="archive"/>
          <text variable="archive_location" prefix="(" suffix=")"/>
        </group>
      </if>
      <else>
        <group delimiter=". ">
          <text variable="archive_location" text-case="capitalize-first"/>
          <text variable="archive"/>
          <text variable="archive-place"/>
        </group>
      </else>
    </choose>
  </macro>
  <macro name="issue-join-with-space">
    <choose>
      <if type="article-journal legal_case" match="any">
        <choose>
          <if variable="issue volume" match="any">
            <text macro="issue"/>
          </if>
        </choose>
      </if>
    </choose>
  </macro>
  <macro name="issue-join-with-period">
    <choose>
      <if type="article-journal legal_case" match="none">
        <choose>
          <if type="speech" variable="publisher publisher-place" match="any">
            <text macro="issue"/>
          </if>
        </choose>
      </if>
    </choose>
  </macro>
  <macro name="issue-join-with-comma">
    <choose>
      <if type="article-journal legal_case" match="none">
        <choose>
          <if type="speech" variable="publisher publisher-place" match="none">
            <text macro="issue"/>
          </if>
        </choose>
      </if>
      <else-if variable="volume issue" match="none">
        <text macro="issue"/>
      </else-if>
    </choose>
  </macro>
  <macro name="issue">
    <choose>
      <if type="legal_case" match="any">
        <text macro="issued" prefix="(" suffix=")"/>
      </if>
      <else-if type="article-journal">
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PAW Setups & PseudoPotentials

GPAW has a large set of PAW setups (updated in 2016) for elements from H to Rn, excluding lanthanides, actinides, and radioactive elements. One can generate new setups with a PAW generating build-in tool and their own risk. One can use optimized norm-conserving Vanderbilt SG15 pseudopotentials (updated in 2017) or norm-conserving Hartwigsen-Goedecker-Hutter HGH pseudopotentials (see also GPAW intro) or even JTH pseudopotentials from ABINIT. There are even more setups, including f-elements, listed on the QE webpage. The great thing about these setups is that they use a similar format – either xml or upfApparently, GPAW can read both formats, although there is no relevant documentation. So, there are many ways to run calculations with elements that are missing in the GPAW default setups set. QuantumATK webpage provides an overview of pseudopotentials and even suggests mixing them. I hope that in the future, these and new PAWs will be gathered together like basis sets at the basis sets exchange portal.

P.S. Interesting https://esl.cecam.org/data/ and https://molmod.ugent.be/deltacodesdft

DFT geometry optimizers

These are undeservedly less attention to optimizers than density functionals (concerning Jacob’s ladder). It is not even covered in the recent review: Best-Practice DFT Protocols for Basic Molecular Computational Chemistry. At the same time, in my current projects, the most resource-demanding was geometry optimization – the time spent on optimizing structures was much longer than a single-point calculation. Papers that introduce new (AI-based) optimizers promise significant speed-up. However, there are always some problems:

  1. The tested systems are different from my electrochemical interfaces.
  2. The code is not available or difficult to install.
  3. The code is outdated and contains bugs.
  4. Optimizers perform worse than the common ones, like QuasiNewton in ASE.

ASE wiki lists all internal and some external optimizers and provides their comparison. I have checked the most promising on a high-entropy alloy slab.

Observation 1. QuasiNewton outperforms all other optimizers. Point. I have run a standard GPAW/DFT/PBE/PW optimization with various optimizers:

Observation 2. Pre-optimizing the slab with a cheaper method does not reduce the number of optimization steps. I have preoptimized the geometry with TBLITE/DFTB/GFN1-xTB to continue with GPAW/DFT/PBE/PW. Preoptimization takes just some minutes and the obtained geometry looks similar to the DFT one but that does not reduce the number of DFT optimization steps.

OptimizerN steps*Time$N steps*#Total time#
BFGS1602:44:271703:01:26
LBFGS1502:30:351602:55:04
BondMin1202:46:271302:45:07
GPMin1205:26:233108:14:22
MLMin38verylong2812:31:29
FIRE3805:06:564405:56:54
QuasiNewton801:36:23902:00:10

Note * – the printed number of steps might different from the actuall number of calculations because each calculator has a different way of reporting that number.

Note $ – the time between the end of the first and last steps.

Note # – started from the TBLITE/DFTB/GFN1-xTB preoptimized geometry.

N.B! I have done my test only once in two runs: starting with slab.xyz and preoptized geometry. Runs were on similar nodes and all optimizations were done on the same node.

Conclusion. Do not believe in claims in articles advertizing new optimizers – Run your tests before using them.

A practical finding. The usual problem with calculations that require many optimization steps is that they need to fit into HPC time limits. On the restart, ASE usually rewrites the trajectory. Some optimizers (GPMin and AI-based) could benefit from reading the full trajectory. So, I started writing two trajectories and a restart file like this.

# Restarting
if os.path.exists(f'{name}_last.gpw') == True and os.stat(f'{name}_last.gpw').st_size > 0:
    atoms,calc = restart(f'{name}_last.gpw', txt=None)
    parprint(f'Restart from the gpw geometry.')
elif os.path.exists(f'{name}_full.traj') == True and os.stat(f'{name}_full.traj').st_size > 0:
    atoms = read(f'{name}_full.traj',-1)
    parprint(f'Restart with the traj geometry.')
else:
    atoms = read(f'{name}_init.xyz')
    parprint(f'Start with the initial xyz geometry.')

# Optimizing
opt = QuasiNewton(atoms, trajectory=f'{name}.traj', logfile=f'{name}.log')
traj= Trajectory(f'{name}_full.traj', 'a', atoms)
opt.attach(traj.write, interval=1)
def writegpw():
    calc.write(f'{name}_last.gpw')
opt.attach(writegpw, interval=1)
opt.run(fmax=0.05, steps=42)

Here are some details on the tests.

My gpaw_opt.py for DFT calculations on 24 cores:

# Load modules
from ase import Atom, Atoms
from ase.build import add_adsorbate, fcc100, fcc110, fcc111, fcc211, molecule
from ase.calculators.mixing import SumCalculator
from ase.constraints import FixAtoms, FixedPlane, FixInternals
from ase.data.vdw_alvarez import vdw_radii
from ase.db import connect
from ase.io import write, read
from ase.optimize import BFGS, GPMin, LBFGS, FIRE, QuasiNewton
from ase.parallel import parprint
from ase.units import Bohr
from bondmin import BondMin
from catlearn.optimize.mlmin import MLMin
from dftd4.ase import DFTD4
from gpaw import GPAW, PW, FermiDirac, PoissonSolver, Mixer, restart
from gpaw.dipole_correction import DipoleCorrection
from gpaw.external import ConstantElectricField
from gpaw.utilities import h2gpts
import numpy as np
import os

atoms = read('slab.xyz')
atoms.set_constraint([FixAtoms(indices=[atom.index for atom in atoms if atom.tag in [1,2]])])

# Set calculator
kwargs = dict(poissonsolver={'dipolelayer':'xy'},
              xc='RPBE',
              kpts=(4,4,1),
              gpts=h2gpts(0.18, atoms.get_cell(), idiv=4),
              mode=PW(400),
              basis='dzp',
              parallel={'augment_grids':True,'sl_auto':True,'use_elpa':True},
             )
calc = GPAW(**kwargs)

#atoms.calc = SumCalculator([DFTD4(method='RPBE'), calc])
#atoms.calc = calc

# Optimization paramters
maxf = 0.05

# Run optimization
###############################################################################

# 2.A. Optimize structure using MLMin (CatLearn).
initial_mlmin = atoms.copy()
initial_mlmin.set_calculator(calc)
mlmin_opt = MLMin(initial_mlmin, trajectory='results_mlmin.traj')
mlmin_opt.run(fmax=maxf, kernel='SQE', full_output=True)

# 2.B Optimize using GPMin.
initial_gpmin = atoms.copy()
initial_gpmin.set_calculator(calc)
gpmin_opt = GPMin(initial_gpmin, trajectory='results_gpmin.traj', logfile='results_gpmin.log', update_hyperparams=True)
gpmin_opt.run(fmax=maxf)

# 2.C Optimize using LBFGS.
initial_lbfgs = atoms.copy()
initial_lbfgs.set_calculator(calc)
lbfgs_opt = LBFGS(initial_lbfgs, trajectory='results_lbfgs.traj', logfile='results_lbfgs.log')
lbfgs_opt.run(fmax=maxf)

# 2.D Optimize using FIRE.
initial_fire = atoms.copy()
initial_fire.set_calculator(calc)
fire_opt = FIRE(initial_fire, trajectory='results_fire.traj', logfile='results_fire.log')
fire_opt.run(fmax=maxf)

# 2.E Optimize using QuasiNewton.
initial_qn = atoms.copy()
initial_qn.set_calculator(calc)
qn_opt = QuasiNewton(initial_qn, trajectory='results_qn.traj', logfile='results_qn.log')
qn_opt.run(fmax=maxf)

# 2.F Optimize using BFGS.
initial_bfgs = atoms.copy()
initial_bfgs.set_calculator(calc)
bfgs_opt = LBFGS(initial_bfgs, trajectory='results_bfgs.traj', logfile='results_bfgs.log')
bfgs_opt.run(fmax=maxf)

# 2.G. Optimize structure using BondMin.
initial_bondmin = atoms.copy()
initial_bondmin.set_calculator(calc)
bondmin_opt = BondMin(initial_bondmin, trajectory='results_bondmin.traj',logfile='results_bondmin.log')
bondmin_opt.run(fmax=maxf)

# Summary of the results
###############################################################################

fire_results = read('results_fire.traj', ':')
parprint('Number of function evaluations using FIRE:',
         len(fire_results))

lbfgs_results = read('results_lbfgs.traj', ':')
parprint('Number of function evaluations using LBFGS:',
         len(lbfgs_results))

gpmin_results = read('results_gpmin.traj', ':')
parprint('Number of function evaluations using GPMin:',
         gpmin_opt.function_calls)

bfgs_results = read('results_bfgs.traj', ':')
parprint('Number of function evaluations using BFGS:',
         len(bfgs_results))

qn_results = read('results_qn.traj', ':')
parprint('Number of function evaluations using QN:',
         len(qn_results))

catlearn_results = read('results_mlmin.traj', ':')
parprint('Number of function evaluations using MLMin:',
         len(catlearn_results))

bondmin_results = read('results_bondmin.traj', ':')
parprint('Number of function evaluations using BondMin:',
         len(bondmin_results))

Initial slab.xyz file:

45
Lattice="8.529357696932532 0.0 0.0 4.264678848466266 7.386640443507905 0.0 0.0 0.0 29.190908217261956" Properties=species:S:1:pos:R:3:tags:I:1 pbc="T T F"
Ir       0.00000000       1.62473838      10.00000000        5
Ru       2.81412943       1.62473838      10.00000000        5
Pt       5.62825885       1.62473838      10.00000000        5
Pd       1.40706471       4.06184595      10.00000000        5
Ag       4.22119414       4.06184595      10.00000000        5
Ag       7.03532356       4.06184595      10.00000000        5
Ag       2.81412943       6.49895353      10.00000000        5
Ru       5.62825885       6.49895353      10.00000000        5
Pt       8.44238828       6.49895353      10.00000000        5
Pt       0.00000000       0.00000000      12.29772705        4
Ag       2.81412943       0.00000000      12.29772705        4
Ru       5.62825885       0.00000000      12.29772705        4
Ru       1.40706471       2.43710757      12.29772705        4
Ir       4.22119414       2.43710757      12.29772705        4
Ag       7.03532356       2.43710757      12.29772705        4
Ag       2.81412943       4.87421514      12.29772705        4
Ir       5.62825885       4.87421514      12.29772705        4
Pd       8.44238828       4.87421514      12.29772705        4
Pd       1.40706471       0.81236919      14.59545411        3
Ir       4.22119414       0.81236919      14.59545411        3
Pt       7.03532356       0.81236919      14.59545411        3
Ag       2.81412943       3.24947676      14.59545411        3
Ir       5.62825885       3.24947676      14.59545411        3
Ir       8.44238828       3.24947676      14.59545411        3
Pd       4.22119414       5.68658433      14.59545411        3
Pt       7.03532356       5.68658433      14.59545411        3
Ag       9.84945299       5.68658433      14.59545411        3
Pd       0.00000000       1.62473838      16.89318116        2
Pd       2.81412943       1.62473838      16.89318116        2
Ag       5.62825885       1.62473838      16.89318116        2
Pt       1.40706471       4.06184595      16.89318116        2
Ag       4.22119414       4.06184595      16.89318116        2
Ag       7.03532356       4.06184595      16.89318116        2
Ru       2.81412943       6.49895353      16.89318116        2
Ru       5.62825885       6.49895353      16.89318116        2
Ru       8.44238828       6.49895353      16.89318116        2
Ir       0.00000000       0.00000000      19.19090822        1
Ag       2.81412943       0.00000000      19.19090822        1
Pt       5.62825885       0.00000000      19.19090822        1
Pd       1.40706471       2.43710757      19.19090822        1
Ag       4.22119414       2.43710757      19.19090822        1
Pd       7.03532356       2.43710757      19.19090822        1
Ag       2.81412943       4.87421514      19.19090822        1
Ru       5.62825885       4.87421514      19.19090822        1
Ir       8.44238828       4.87421514      19.19090822        1

My tblite_opt.py for DFTB calcualation with just one core. It takes some minutes but eventually crashes 🙁

# Load modules
from ase import Atom, Atoms
from ase.build import add_adsorbate, fcc100, fcc110, fcc111, fcc211, molecule
from ase.calculators.mixing import SumCalculator
from ase.constraints import FixAtoms, FixedPlane, FixInternals
from ase.data.vdw_alvarez import vdw_radii
from ase.db import connect
from ase.io import write, read
from ase.optimize import BFGS, GPMin, LBFGS, FIRE, QuasiNewton
from ase.parallel import parprint
from ase.units import Bohr
from tblite.ase import TBLite
import numpy as np
import os

# https://tblite.readthedocs.io/en/latest/users/ase.html

atoms = read('slab.xyz')
atoms.set_constraint([FixAtoms(indices=[atom.index for atom in atoms if atom.tag in [1,2]])])

# Set calculator
calc = TBLite(method="GFN1-xTB",accuracy=1000,electronic_temperature=300,max_iterations=300)
atoms.set_calculator(calc)
qn_opt = QuasiNewton(atoms, trajectory='results_qn.traj', logfile='results_qn.log', maxstep=0.1)
qn_opt.run(fmax=0.1)

To compare structures I have used MDanalysis, which unfortunately does not work with ASE traj, so I prepared xyz-files with “ase convert -n -1 file.traj file.xyz”

import MDAnalysis as mda
from MDAnalysis.analysis.rms import rmsd
import sys

def coord(file_name):
    file  = mda.Universe(f"{file_name}.xyz")
    atoms = file.select_atoms("index 1:9")
    return  atoms.positions.copy()

print(rmsd(coord(sys.argv[1]),coord(sys.argv[2])))

An instruction on installation of GPAW. TBLITE can be installed as “conda install -c conda-forge tblite”.