Vladislav Ivanistsev, Ritums Cepitis, Jan Rossmeisl, Nadezda Kongi
to be published in Chemical Society Reviews
https://chemrxiv.org/engage/chemrxiv/article-details/67ed469081d2151a02b33a98
All figures:
https://gitlab.com/doublelayer/chemsocrev_2025_scaling-relations
Some cool notebooks:
https://gitlab.com/doublelayer/electrocatalysis-on-a-laptop
AI-created podcast:
Youtube video:
The following video-presentation – for the CHEAC Summer school 2025 – retells our review on the scaling relations electrocatalysis https://chemrxiv.org/engage/chemrxiv/article-details/67ed469081d2151a02b33a98
From the beginning I decided to try AI to prepare the presentation. Eventually the only to record the video turned out to be by the traditional way. Together with co-authors Ritums and Nadezda, we used PowerPoint with its slide-by-slide recording feature. As we were in 3 different locations, we exchanged the presentation several time while recording. I used chatgpt 4o and 5 to write lecturer’s notes for every slide. In particular, I gave the chat our article’s pdf-file and then discussed every slide-text using canvas-feature to polish it iteratively. Nadezda also used chatgpt to refined her slides before reading them aloud. Overall, I have spend over two weeks planning the presentation. Then a week polishing the slides. Then several days to record and re-record slides. And finally I have got this the final video-presentation.
app.pictory.ai does a relatively good job on reading the lecturer’s notes in a ready presentation. Thought, it reads “Jan” and “OOH” in a funny way. And it adds a lot of 10–20 second pauses. Also the slide numbering is off as well as all animation. The picture is also cut from below. But overall, it takes around 2 hours to generate this voiced video and process it.
Does not work for me. Gemini wants to draw images. I just want to enter my own figures.
https://www.magicslides.app promises to do exactly that but I failed with a notice that below 5 Mb files are allowed.
SlideAI extension also does not do what I want.
Ufff … manual upload is still the fastest and most robust. Well, it is not so simple, as most of my figures are in pdf, so I wrote this script to convert everything to png. When it took me 2 mins to drag-and-drop all png figure to my presentation. Hurray!
#!/bin/bash
# Create output folder
mkdir -p png
# List of input files
files=(
"Figure 1 mechanisms.png"
"Figure 18 Timeline.png"
"FIgure 14 distances.pdf"
"Figure 11 relative.pdf"
"Figure 6 3dvolcano_withscaling.pdf"
"Figure 2 publications.pdf"
"Figure 5 3dvolcano.pdf"
"Figure 17 perspectives.pdf"
"Figure 16 O_bypassing.pdf"
"Figure 15 O_pushing.pdf"
"Figure 12 O_breaking.pdf"
"Figure 13 O_switching.png"
"Figure 10 O_tuning.pdf"
"Figure 7 projection_potential.pdf"
"Figure 9 projection_ads.pdf"
"Figure 8 timeline.pdf"
"Figure 3 ass_diss.png"
"Figure 4 scalings.png"
)
# Loop through files
for f in "${files[@]}"; do
base=$(basename "$f")
name="${base%.*}"
ext="${base##*.}"
if [[ "$ext" == "pdf" ]]; then
convert -density 300 "$f" -quality 100 "png/${name}.png"
elif [[ "$ext" == "png" ]]; then
cp "$f" "png/${name}.png"
else
echo "Unsupported file type: $f"
fi
donePretty cool – NotebookLM make a FAQ.
Scaling relations are correlations between the adsorption energies of reaction intermediates on a catalyst’s surface. They are crucial in multi-step electrocatalytic reactions, such as the oxygen reduction reaction (ORR), carbon dioxide reduction (CO2R), and nitrogen reduction (N2RR). The concept emerged in 2005 with the discovery of linear relations between adsorption energies of intermediates like OH, OOH, and O on metal surfaces. Understanding these relations is vital because they define fundamental chemical limitations in electrocatalytic reactions, impacting the design of more efficient catalysts for energy conversion technologies like electrolysers, fuel cells, and metal-air batteries.
In oxygen electrocatalysis, particularly the oxygen reduction reaction (ORR), the adsorption energies of key intermediates (OOH, OH, O) are correlated by scaling relations. These correlations constrain the achievable catalytic activity, often visualised on “volcano plots.” The OOH-OH and O-OH scaling relations, for instance, mean that if a catalyst binds one intermediate optimally, it might bind another too strongly or too weakly, preventing it from reaching the ideal catalytic activity (the “volcano top”). This limitation is significant, as experimental results have shown catalytic overpotentials converging to a limit set by these relations for over two decades, hindering progress in sustainable energy solutions.
Oxygen electrocatalysis primarily proceeds via two mechanisms: associative and dissociative. The associative mechanism, which dominates most known catalysts, involves intermediates like OOH, OH, and O adsorbing at a single active site. Geometrically, this requires only one atom in the active site. The dissociative mechanism, conversely, requires at least two neighbouring atoms to accommodate dissociation products (O and OH). On metal surfaces, a spatial mismatch often prevents the dissociative mechanism, as O preferentially adsorbs on hollow sites and OH on top sites. However, dual-atom site catalysts (DACs) can facilitate dissociative pathways by providing two adjacent sites, allowing for the adsorption of dissociation products. The inter-atomic distance within these active sites is a critical geometric parameter that influences the energy barrier for dissociation, balancing thermodynamics and kinetics.
The “volcano plot” is a theoretical framework used to understand electrocatalysis, typically representing overpotential or activity as an “altitude” against adsorption energy descriptors. For ORR, it correlates adsorption energies with deviations from the thermodynamic equilibrium potential. Scaling relations define the “paths” or “fixed climbing routes” on this volcano plot that are accessible to catalysts. For example, the OOH-OH scaling relation appears as a plane on the three-dimensional volcano, and catalysts following this relation are confined to a specific line on the volcano’s surface. This means that while an “ideal catalyst” (the volcano’s apex) might exist theoretically, scaling relations prevent most catalysts from reaching it, limiting the search for optimal catalysts to a two-dimensional projection.
The review outlines five general strategies for manipulating scaling relations to enhance electrocatalytic performance:
The “breaking” strategy focuses on reducing the intercept of the OOH-OH scaling relation (from approximately 3.2 eV to an ideal value of 2.46 eV) by selectively stabilising the OOH intermediate relative to OH. This typically involves introducing spectator groups or a second adsorption site near the active site. These spectators can form hydrogen bonds or other stabilising interactions with OOH, effectively shifting its adsorption energy without proportionally affecting OH. While challenging to achieve experimentally, this strategy has been demonstrated in oxygen evolution reactions (OER) and more recently in ORR using dual-atom catalysts (DACs) with specific active sites like PN3FeN3, where the phosphorus acts as a spectator to stabilise OOH through hydrogen bonding.
Single-Atom Site Catalysts (SACs) and Dual-Atom Site Catalysts (DACs) are crucial in manipulating scaling relations due to their distinct geometric and electronic properties. SACs typically allow for “on-top” adsorption, primarily favouring the associative mechanism in ORR. DACs, with their two neighbouring active sites, offer the possibility of accommodating two dissociation products simultaneously, thereby enabling the dissociative mechanism. This ability to switch mechanisms is key to the “switching” strategy, where DACs can replace the OOH intermediate with two distinct O and OH intermediates adsorbed at separate sites. Furthermore, the precise control over inter-atomic distances and curvature in DACs allows for fine-tuning of electronic structures and promoting specific interactions (like hydrogen bonding), contributing to “breaking” and “pushing” strategies.
The ultimate goal of manipulating scaling relations is to achieve ideal catalyst performance, ideally with zero overpotential, by overcoming the fundamental limitations imposed by these correlations. The “bypassing” strategy represents the most ambitious approach towards this goal. It seeks to completely decouple the adsorption energies of reaction intermediates by allowing the catalyst to switch between two or more distinct states (e.g., geometric, electronic, or photonic) during the reaction cycle. Each state would be optimally configured to bind specific intermediates at the ideal energy values required for efficient catalysis. While seemingly challenging in practice, this concept, inspired by natural enzymes like cytochrome c oxidase, offers a theoretical pathway to eliminate all scaling constraints and achieve the theoretical apex of the volcano plot, pushing the boundaries of what is currently achievable in electrocatalysis.
Join the DoubleLayer hub as a postdoctoral fellow at the University of Latvia!
If you are a post-doc seeking independence through training skills and gaining knowledge in a supportive environment, then this post is for you. That is an opportunity to advance your career through Marie Skłodowska-Curie Actions (MSCA) by focusing on competencies – academic writing, research methods, and supervision – essential for succeeding in academia and industry.
You need to submit just one proposal on 10 September 2025 to participate in at least three funding calls. The proposal is only 10 pages long. The first application is for the MSCA or MSCA4Ukraine postdoctoral fellowship, which provides funding for up to 24 months of research and training. To get this prestigious grant, one must gain more than 95% in the evaluation. However, passing the 85% threshold already opens the opportunity to be funded through the ERA Fellowship or MSCA Seal of Excellence in Estonia. Moreover, passing the 70% threshold makes you eligible to be funded by Latvia. Even more, there is a Latvian post-doc fellowship with the next call in early 2026. And the is also new EU initiative ‘Choose Europe for Science’ to attract 10,000 researchers from abroad. That MSCA COFUND call will open on 1 October 2025 and close on 3 December 2025. Submitting to all these 6! opportunities per 1 proposal increases your chances of fulfilling your research idea and advancing your career. These fellowships include funds for salary, mobility, research, and allowances described in the following table.
Disclaimer: The data in the table might be incorrect. CCC value is taken form 2025 program. Salary is estimated using this calculator.
| Latvian 1 | MSCA | ERA talents | Latvian 2 | |
| Submission | 16th May 2025 | 10th Sept 2025 | 10th Sept 2025 | March 2026 |
| Decision | Summer 2025 | Feb 2026 | Feb 2026 | May 2026 |
| Start | 6 M after approval | May–Dec 2026 | May–Dec 2026 | Sept–Dec 2026 |
| Threshold / % | tbu | 95 | 85 | 85 |
| Success / % | ≤50 (70 PF) | 15 (1700 PF) | (20 PF) | tbu |
| Link | lzp.gov.lv | ec.europa.eu | ec.europa.eu | lzp.gov.lv |
| Duration / M | 36 | 12–24 | 12–24 | 12–24 |
| Total salary / €/M | 3860 | 5990*0.838 | 5990*0.838 | 3860 |
| Net salary / €/M | 2080 | 2700 | 2700 | 2080 |
| Research / €/M | 1000 | 1000 | 1000 | 1000 |
| Overhead | 6% | 650 € | 650 € | 6% |
| Mobility / €/M | 700 | 710 | 710 | ? |
| Family / €/M | 660 | 660 | 660 | ? |
| Move / € | 710 (+660) | 6700 | 6700 | ? |
| Secondment / M | >2 (mandatory) >6 (optional) | (optional) | (optional) | (optional) |
Why University of Latvia?
Why the DoubleLayer hub?
Why Vladislav Ivanistsev as a mentor?
Further details
To be considered for the opportunity, you will undergo a pre-selection process based on your CV, project idea, and motivation letter. There are three main eligibility requirements:
For any other further questions, please contact vladislav.ivanistsev@doublelayer.eu. Prefix your email subject title with “DoubleLayer hub:”
Career planning is easy with the right tool. In the EU, such tool is supposed to be the ResearchCOMP … well, I have just made it interactive and useful at https://vladislavivanistsev.github.io/researchcomp.
You can make a self-evaluation of your skills and competences. Then you can copy, email, download the summary to use it in planning your career.
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.
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"/>
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</group>
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<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">
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<text macro="edition"/>
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<text term="volume" form="short" text-case="capitalize-first"/>
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<text macro="edition"/>
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<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"/>
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</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">
<choose>
<if variable="issue volume" match="any">
<text macro="issued" prefix="(" suffix=")"/>
</if>
<else>
<text macro="issued"/>
</else>
</choose>
</else-if>
<else-if type="speech">
<group delimiter=", ">
<group delimiter=" ">
<choose>
<if variable="title" match="none"/>
<else>
<text variable="genre" text-case="capitalize-first"/>
</else>
</choose>
<text macro="event"/>
</group>
<text variable="event-place"/>
<text macro="issued"/>
</group>
</else-if>
<else-if type="article-newspaper">
<text macro="issued"/>
</else-if>
<else-if variable="publisher-place publisher" match="any">
<group delimiter=", ">
<choose>
<if type="thesis">
<text variable="genre" text-case="capitalize-first"/>
</if>
</choose>
<group delimiter=". ">
<text macro="originally-published"/>
<group delimiter=", ">
<text macro="reprint"/>
<text macro="publisher"/>
</group>
</group>
<text macro="issued"/>
</group>
</else-if>
<else>
<text macro="issued"/>
</else>
</choose>
</macro>
<macro name="access">
<group delimiter=". ">
<choose>
<if type="graphic report" match="any">
<text macro="archive"/>
</if>
<else-if type="article-journal bill book chapter legal_case legislation motion_picture paper-conference" match="none">
<text macro="archive"/>
</else-if>
</choose>
<choose>
<if variable="issued" match="none">
<group delimiter=" ">
<text term="accessed" text-case="capitalize-first"/>
<date variable="accessed" form="text"/>
</group>
</if>
</choose>
<choose>
<if type="legal_case" match="none">
<choose>
<if variable="DOI">
<text variable="DOI" prefix="doi:"/>
</if>
<else>
<text variable="URL"/>
</else>
</choose>
</if>
</choose>
</group>
</macro>
<macro name="case-locator-subsequent">
<choose>
<if type="legal_case">
<text macro="locators-note"/>
</if>
</choose>
</macro>
<macro name="case-issue-subsequent">
<choose>
<if type="legal_case">
<text macro="issue"/>
</if>
</choose>
</macro>
<citation et-al-min="4" et-al-use-first="1" disambiguate-add-names="true">
<layout suffix="." delimiter="; ">
<choose>
<if match="all" position="subsequent">
<text variable="first-reference-note-number" prefix="see ref: "/>
</if>
<else-if type="webpage post-weblog" match="any">
<group delimiter=" ">
<text variable="title" suffix=": "/>
<text variable="URL"/>
</group>
</else-if>
<else>
<group delimiter=", ">
<text macro="contributors-short" strip-periods="true"/>
<text variable="title" font-style="italic" />
<group delimiter=" ">
<group delimiter=", ">
<date date-parts="year" form="numeric" variable="issued"/>
<text macro="case-locator-subsequent"/>
<choose>
<if type="chapter" match="any">
<group>
<text variable="title" form="short"/>
<text value="in: " prefix=", "/>
<text variable="container-title" form="short" font-style="italic" suffix=", "/>
<text variable="publisher" prefix="(" suffix=")"/>
<text variable="page" form="short" prefix=": "/>
</group>
</if>
<else>
<group delimiter=" ">
<text variable="container-title" form="short" strip-periods="true" font-style="italic"/>
<text variable="volume" strip-periods="true" font-weight="bold" suffix=":"/>
<text variable="page" form="short" strip-periods="false"/>
</group>
</else>
</choose>
</group>
<text macro="case-issue-subsequent"/>
</group>
<text macro="point-locators-subsequent"/>
</group>
</else>
</choose>
</layout>
</citation>
<bibliography hanging-indent="true" et-al-min="11" et-al-use-first="7" subsequent-author-substitute="———" entry-spacing="0">
<sort>
<key variable="call-number"/>
</sort>
<layout suffix=".">
<group delimiter=". ">
<group delimiter=": ">
<group delimiter=", ">
<group delimiter=" ">
<group delimiter=". ">
<group delimiter=" ">
<group delimiter=", ">
<group delimiter=". ">
<group delimiter=". ">
<text macro="contributors"/>
<text macro="title"/>
</group>
<text macro="description"/>
<text macro="secondary-contributors"/>
<group delimiter=", ">
<text macro="container-title"/>
<text macro="container-contributors"/>
</group>
<text macro="locators-join-with-period"/>
</group>
<text macro="locators-join-with-comma"/>
<text macro="locators-chapter"/>
</group>
<text macro="locators-join-with-space"/>
</group>
<text macro="collection-title"/>
<text macro="issue-join-with-period"/>
</group>
<text macro="issue-join-with-space"/>
</group>
<text macro="issue-join-with-comma"/>
<text macro="locators-journal-join-with-comma"/>
<text macro="locators-newspaper"/>
</group>
<text macro="locators-journal-join-with-colon"/>
</group>
<text macro="access"/>
</group>
</layout>
</bibliography>
</style>While preparing the final report on the past MSCA project, I found some memorable pictures. Here me, my wife and nephew are building a LEGO illustration for the project proposal. Yes, we had some fun while I was thinking about the concept.
The results looks pretty.
Still, as the concept illustration, I draw this figure. Today, I have reused it for the report illustration.
Try to use default parameters for the calculator. Simple and often useful.
Below you find a list of suggestions that should be considered when encountering a memory problem – when a calculation does not fit an allocated memory limit.
Note1: You can use –dry-run to make memory estimation and check for parallelization over kpts, domain, and bands as well as use of symmetry.
gpaw python --dry-run=N script.py
Mind that the memory estimation with –dry-run is underestimated. https://gitlab.com/gpaw/gpaw/-/issues/614
Note2: You can use def monkey_patch_timer() to write information about memory usage into mem.* files. Call the function before the actual work is started.
from gpaw.utilities.memory import monkey_patch_timer
monkey_patch_timer()
SUBMISSION OPTIONS
GEOMETRY
orthorhombic=False option.PARALLELIZATION
In general, parallelization over domains requires less memory than parallelization over bands and k-points, but the default order of parallelization is k-points, then domains, then bands. Remember the formula kpts×domain×bands = N, where N is the number of tasks (CPUs).
parallel = {'domain':1}. In the LCAO mode, you should check whether parallelizing over bands, like parallel = {'bands':2}, helps with the memory issue.CALCULATOR PARAMETERS
setups={'Pt': '10'}), basis (like basis={'H': 'sz', 'C': 'dz'}), etc. Check for convergence of properties, like in this tutorial: wiki.fysik.dtu.dk/gpaw/summerschools/summerschool22/catalysis/catalysis.html#extra-material-convergence-testBader analysis is a fast and simple way of getting atomic charges. It is especially useful for periodic calculations. The analysis can be done on the fly using pybader tool from pypi.org/project/pybader. I recommend using it within conda environments.
The installation is straightforward:
pip install pybader
The usage is less obvious. Here is a function for obtaining xmol-type xyz that can obtained with GPAW and visualized with ASE:
def xyzb(atoms, filename, nCPU):
from pybader.io import gpaw
from pybader.interface import Bader
import os
bader = Bader(*gpaw.read_obj(atoms.calc)) # read ASE object 'atoms'
bader(threads=nCPU) # specify the number of CPUs
f = open('{0}.xyz'.format(filename), 'w') # set xmol format
b = bader.atoms_charge # get number of electrons per atom
n = atoms.get_atomic_numbers() # get atomic numbers
a = atoms.get_chemical_symbols() # get chemical symbols
p = atoms.get_positions() # get positions of the atoms
f.write('{0}\n'.format(len(a)))
f.write('Properties=species:S:1:pos:R:3:charge:R:1\n') # ensure compatibility with ASE
for i in range(len(a)): # print symbol, positions, and charge
s = '{0}'.format(a[i])
x = '{0:.6f}'.format(round(p[i][0],6))
y = '{0:.6f}'.format(round(p[i][1],6))
z = '{0:.6f}'.format(round(p[i][2],6))
c = '{0:.3f}'.format(round(float(n[i]) - float(b[i]),3))
f.write('{0:<4}{1:>16}{2:>16}{3:>16}{4:>10}\n'.format(s,x,y,z,c))
f.close()
del bader
os.remove('bader.p')
Similarly one can obtain xmol-type xyz file with Hirshfeld charges:
def xyzh(atoms, filename):
from gpaw.analyse.hirshfeld import HirshfeldPartitioning
f = open('{0}.xyz'.format(filename), 'w') # set xmol format
a = atoms.get_chemical_symbols() # get chemical symbols
p = atoms.get_positions() # get positions of the atoms
h = HirshfeldPartitioning(atoms.calc).get_charges()
f.write('{0}\n'.format(len(a)))
f.write('Properties=species:S:1:pos:R:3:charge:R:1\n') # ensure compatibility with ASE
for i in range(len(a)): # print symbol, positions, and charge
s = '{0}'.format(a[i])
x = '{0:.6f}'.format(round(p[i][0],6))
y = '{0:.6f}'.format(round(p[i][1],6))
z = '{0:.6f}'.format(round(p[i][2],6))
c = '{0:.3f}'.format(round(h[i],3))
f.write('{0:<4}{1:>16}{2:>16}{3:>16}{4:>10}\n'.format(s,x,y,z,c))
f.close()
In the LCAO mode of GPAW one can also get the Mulliken charges. Test before using:
def xyzm(atoms, filename):
from gpaw.lcao.tools import get_mulliken
f = open('{0}.xyz'.format(filename), 'w') # set xmol format
a = atoms.get_chemical_symbols() # get chemical symbols
p = atoms.get_positions() # get positions of the atoms
m = get_mulliken(atoms.calc, range(len(a)))
f.write('{0}\n'.format(len(a)))
f.write('Properties=species:S:1:pos:R:3:charge:R:1\n') # ensure compatibility with ASE
for i in range(len(a)): # print symbol, positions, and charge
s = '{0}'.format(a[i])
x = '{0:.6f}'.format(round(p[i][0],6))
y = '{0:.6f}'.format(round(p[i][1],6))
z = '{0:.6f}'.format(round(p[i][2],6))
c = '{0:.3f}'.format(round(m[i],3))
f.write('{0:<4}{1:>16}{2:>16}{3:>16}{4:>10}\n'.format(s,x,y,z,c))
f.close()
