Catalysis research group publishes diffusion–reaction model code

Written by Jänis Järvilehto (https://linkedin.com/in/janisj)

The Catalysis research group has published its first-ever open code! Coined DReaM-ALD, the recently published Matlab script provides an implementation of a diffusion–reaction model developed by Ylilammi et al. (J. Appl. Phys. 123, 205301 (2018), DOI: 10.1063/1.5028178). The model simulates atomic layer deposition in high-aspect-ratio structures and generates saturation profiles, which show how the film thickness evolves with penetration into the structure. This Matlab implementation was originally written by Emma Verkama in 2019 by request of Prof. Riikka Puurunen, and the code was later published by Jänis Järvilehto. In addition to Github, the code was also made available on Zenodo

There was a significant delay (~3 years) between the creation and publication of the code. As there was no prior history of open code in the group, the barrier to publication was relatively high. Questions, such as…

Where should we publish the code? What kind of information would be useful for a potential user? How does the process work in general? Where do I click???

…may arise. While the best practices may seem obvious to a software engineer, generating research code can be a messy affair in other fields. Often, these researchers in other fields are less acquainted with the tools of the trade, such as a version control system like Github. Someone in the group would have to figure out how and where to publish the code so that it is easily accessible and citable. This causes useful and interesting projects to end up forgotten on university network drives, instead of being available for anyone to extend and experiment with. It is also difficult to replicate the results of a published work without access to the original code. 

As a starting point or inspiration for other groups that are unsure about open code, we’ve summarized the steps we went through to get our code out there. We’ve also linked some helpful resources we’ve run into during the process!

Step 1: Set up an Organization on Github

If your research group has not published on Github yet, it is a good idea to think about how the repositories should be organized. We opted to create an Organization for the research group — this way the repository’s association with the Catalysis research group is clear. Remember to assign a second Organization Owner for your Organization, just in case. The other research group members can be added as Organization Members

Step 2: Decide on a license

Choose a license for the software you intend to publish, if you haven’t already done so. Keep in mind that there may be restrictions on the type of license you can use, set by your organization or funding source. You can find an overview of common licenses at https://choosealicense.com/, for example. In our case, we opted for the MIT license. 

Step 3: Set up a repository

Next, it is time to set up a repository for the project. There are two paths to take here: either one directly creates the repository to be published later, or, a draft repository can be created first. On Github, all changes to a repository can be traced back, so a potential editing history of, for example, the README.md file will be publicly visible. We decided to forgo the draft repository, as we had already prepared the repository content elsewhere. However, we set the repository to Private at this stage. At this point, you can push your code and a LICENSE.txt file to the repository. 

Step 4: Create a README.md file

The README.md file is displayed whenever someone visits the repository. You can use the README.md as an opportunity to give a brief description of the project, reference relevant literature, explain how to use the code, and how you would like others to cite it in their work. We also decided to include a DOI badge, among others, at the top of the README.md. We used https://shields.io/ to generate the badges (shields) for our README.md file. 

Step 5: Make the repository (easily) citable

Anyone can cite the repository as-is, however, there are some things you can do to make it more straightforward. For starters, we included a Citing section in our README.md to give an example on how to cite the repository. Furthermore, we created a CITATION.cff file in the root of the repository using cffinit. The CITATION.cff file causes Github to display a Cite this repository button in the About section of the repository, which provides a preformatted citation and BibTeX entry. The file contains citation information in a machine-readable format; you can find further information at https://citation-file-format.github.io/

At this point, we also created a .zenodo.json file for the Zenodo synchronization (enabled in Step 7). This json file is placed at the root of the repository and Zenodo uses it to generate the deposit metadata. There are various fields you can fill out using the .zenodo.json file, a complete list of which can be found at here. We also validated our file before pushing it using a json validator, as it is easy to mess up the formatting. 

Step 6: Publish!

Here, the procedure varies slightly depending whether a draft repository was created or not. If you created a draft repository, simply copy its contents to a new, public repository. As we were satisfied with our repository, we simply changed its visibility to Public. Now the code is publicly available on Github!

Step 7: Synchronize the repository with Zenodo

To obtain a DOI for our repository, we archived it as a Zenodo deposit. The most efficient way to achieve this is to connect your Github account to Zenodo, enable synchronization for the repository on Zenodo, and finally create a Release on Github. You can find more information on how to connect the accounts on https://help.zenodo.org/. After this, Zenodo will automatically issue a new versioned DOI whenever a new Release is created on Github. Notably, this only works if no prior Releases have been created before enabling synchronization. After obtaining our first DOI, we decided to update it in the README.md and CITATION.cff files as well. 

Hopefully this blog post has been helpful in condensing the most relevant learnings of the process we went through to get our project published. While the steps may seem convoluted, the whole process should only take a few minutes, provided that the files have been prepared in advance. For further reading on research code, you can check out:

Update 28.9.2023 (Riikka Puurunen): A video is available in Youtube, where a code is published, using these instructions. Access it at: https://youtu.be/ksxAIaytv68?si=3eWQF9lG2zbQ7ftP.

Posted by Riikka Puurunen

Associate professor, Catalysis Science and Technology, at Aalto since February 2017
atomic layer deposition , openness - Comments Off on Catalysis research group publishes diffusion–reaction model code

Catalysis research group end-of-the-year summary 2022

The year 2022 is soon coming to end.

Oh, what a challenging year it was, in so many ways. February 24 started a new chapter in history, and recovery from Covid-19 has only been going on still. Related to Catalysis Professor’s Open, I did not even manage to create a single post, although there were also positive news among all the turmoil and challenges.

Here is a recap of some of the good news from 2022. For example, my group was heavily involved in organizing the 19th Nordic Symposium on Catalysis in Espoo, Finland. Several from the group had their first-ever in-person conference participation experience at ALD 2022, Ghent, June 2022. I got interviewed to the ALD Stories podcast about conformality in atomic layer deposition (ALD). Five Master’s thesis were completed under my supervision. The three projects we have with external funding (HDN cat, COOLCAT, ALDI), progressed well, and funding was acquired for one more (GreenAro) — I am looking forward to working with zeolites and collaboration with VTT and Åbo Akademi in GreenAro. Also, I gave my tenured professor’s installation talk: Catalysis meets atomic layer deposition, video available at https://youtu.be/Wd7lQOGpjfQ.

In 2022, the Catalysis research group published four scientific articles (one of them a proceedings paper). I am especially happy to see the first article out related to research initiated by me as professor at Aalto University, with grant from Academy of Finland (Applied Catalysis B). Good news is that there is more in the pipeline :).

Wishing everyone a Merry Christmas and Happy New Year,

Riikka

2022O.M.E. Ylivaara, A. Langner, S. Ek, J. Malm, J. Julin, M. Laitinen, S. Ali, S. Sintonen, T. Sajavaara, H. Lipsanen, R. L. Puurunen,Thermomechanical properties of aluminum oxide thin films made by atomic layer deposition,Journal of Vacuum Science & Technology A 40, 062414 (2022)https://doi.org/10.1116/6.0002095
2022Aitor Arandia, Jihong Yim, Hassaan Warraich, Emilia Leppäkangas, René Bes, Aku Lempelto, Lars Gell, Hua Jiang, Kristoffer Meinander, Tiia Viinikainen, Simo Huotari, Karoliina Honkala, Riikka L. PuurunenEffect of atomic layer deposited zinc promoter on the activity of copper-on-zirconia catalysts in the hydrogenation of carbon dioxide to methanolApplied Catalysis B: Environmental, 321 (2023) art. 122046.https://doi.org/10.1016/j.apcatb.2022.122046
2022Mikko Utriainen, Kimmo Saastamoinen, Heikki Rekola, Oili M. E. Ylivaara, Riikka L. Puurunen, and Pasi HyttinenOptical metrology of 3D thin film conformality by LHAR chip assisted methodProc. SPIE 12008, Photonic Instrumentation Engineering IX, 120080D (5 March 2022) [Note: non-peer-reviewed conference proceedings publication]https://doi.org/10.1117/12.2609643
2022Jihong Yim, Emma Verkama, Jorge Velasco, Karsten Arts, and Riikka L. Puurunen,Conformality of atomic layer deposition in microchannels: impact of process parameters on the simulated thickness profile,Phys. Chem. Chem. Phys. 24 (2022) 8645-8660.https://doi.org/10.1039/D1CP04758B

Posted by Riikka Puurunen

Associate professor, Catalysis Science and Technology, at Aalto since February 2017
Uncategorized - Comments Off on Catalysis research group end-of-the-year summary 2022

Season’s Greetings from the Aalto Catalysis group

[distributed also via email by RLP]

Dear past, present and potential future colleagues and collaborators; dear friends:

 

Another year is over, and it is good to take a moment to look back.

 

In 2021 – my fifth year as a professor at Aalto University – a lot of experimental progress took place in all three projects of the Catalysis group (HDN catalysis project funded by Neste & COOLCAT and ALDI projects funded by the Academy of Finland). While this progress is not yet seen in our publications (2021 list at the end of the email), some of our activities can be seen in an introductory video we made of the COOLCAT project – turned out quite nice!

 

There are some particular advances related to teaching, research, events and theses I would like to recap from 2021.

 

As for teaching in 2021:

  • Scientific Article Exercise (SAE) was carried out for the first time with all first-year M.Sc. students of School of Chemical Engineering. SAE is a new module which I have been developing, with the goal that students better understand the fundamental differences between scientific articles and e.g. webpages.
  • A new type of co-creation group work was experimented with in the CHEM-E1130 Catalysis course (theme: methanol economy). This received overall positive feedback from students and will be a clear “keeper” (next theme: hydrogen economy).
  • A new concept was tried related to individual research projects for students (10 ECTS). Attention was given e.g. to report writing and feedback in several steps. The overall concept seemed to work and this seems as a “keeper”, too.

 

As for research in 2021:

  • After years of aiming for it, the first open data set related to our research has been published: https://zenodo.org/record/3974438#.Yb7Xo71BxQI.
  • The Kirk-Othmer Encyclopedia of Chemical Technology (finally!) has a chapter on atomic layer deposition (ALD), https://doi.org/10.1002/0471238961.koe00059, which I had the honor to co-author with researchers from TU Delft. Notably, many new illustrations were created, separately published with a Creative Commons license for easy reuse. Images in Wikimedia Commons (category: atomic layer deposition), and one in Zenodo.org.
  • I gave an introductory “ALD 101” tutorial on the fundamentals of ALD at the international AVS ALD conference. Tutorial available e.g. in Youtube.

 

As for event organization:

 

As for theses in 2021, two doctoral theses were successfully defended (Irene Coronado and Eveliina Mäkelä) and four Master’s thesis were finalized (list here).

 

In 2021, was also granted tenure at Aalto University: I will be happy and honoured to continue contributing to Aalto’s success in the coming years.

 

With this letter, and the Aalto card, I wish everyone a happy Christmas time and all the best for the year 2022. 

 

Riikka Puurunen

Riikka Puurunen, Associate professor, Catalysis Science and Technology

Aalto University, School of Chemical Engineering, Department of Chemical and Metallurgical Engineering

Visiting address: Kemistintie 1, 02150 Espoo, Finland, room: E412

Mail address: P.O. Box 16100, FI-00076 AALTO, Finland
Tel: +358 50 337 8161 [] LinkedIn, @rlpuu, @AaltoCatalysis, ORCID:0000-0001-8722-4864

aalto.fi/cmet/catalysis, research.aalto.fi, blog catprofopen, vph-ald.com, aldhistory.blogspot.fi,

 

2021 Oili M. E. Ylivaara, A. Langner, X. Liu, D. Schneider, K. Arstila, J. Julin, S. Sintonen, S. Ali, T. Sajavaara, H. Lipsanen, R. L. Puurunen, Mechanical and system properties of titanium dioxide from titanium tetrachloride and water on silicon by atomic layer deposition. Thin Solid Films 732 (2021) 138758 https://doi.org/10.1016/j.tsf.2021.138758
2021 E. Haimi, O. M. E. Ylivaara, J. Yim, R. L. Puurunen, Thickness profile measurement of atomic layer deposited film by x-ray microanalysis on lateral high-aspect-ratio structure Applied Surface Science Advances (2021) 100102 https://doi.org/10.1016/j.apsadv.2021.100102
2021 K. Arts, H. Thepass, N. Verheijen, R. L. Puurunen, W.M.M. Kessels, H. Knoops, Impact of ions on film conformality and crystallinity during plasma-assisted atomic layer deposition of TiO2. Chemistry of Materials 33 (2021) 5002–5009 https://doi.org/10.1021/acs.chemmater.1c00781
2021 K. Arts, J.H. Deijkers, R.L. Puurunen, W.M.M. (Erwin) Kessels, H.C.M. Knoops, Oxygen recombination probability data for plasma-assisted atomic layer deposition of SiO2 and TiO2. The Journal of Physical Chemistry C 125 (2021) 8244–8252. https://doi.org/10.1021/acs.jpcc.1c01505
2021 J. R .van Ommen, A. Goulas, R. L. Puurunen, Atomic layer deposition Kirk-Othmer Encyclopedia of Chemical Technology, 2021 https://doi.org/10.1002/0471238961.koe00059

 

 

Posted by Riikka Puurunen

Associate professor, Catalysis Science and Technology, at Aalto since February 2017
Uncategorized - Comments Off on Season’s Greetings from the Aalto Catalysis group

Copy of email: 2021 November Networking – ALD at Aalto University

Yesterday, in-person registration to 2021 November Networking – ALD at Aalto University closed. We have now in total 90 registered participants. There are still two days when you can enroll to get the Zoom link, register via: https://www.aalto.fi/en/events/2021-november-networking-ald-at-aalto-university.

Below is copy of an email message that was just sent to all registered participants via our joint catalysis @ … account.

Riikka Puurunen, 23.11.2021

read more >>

Posted by Riikka Puurunen

Associate professor, Catalysis Science and Technology, at Aalto since February 2017
atomic layer deposition , events - Comments Off on Copy of email: 2021 November Networking – ALD at Aalto University

New Podcasts section in ALD OpenLearning site (Nov 20, 2021)

Yesterday (Nov 20, 2021), a new section was published in the OpenLearning site on atomic layer deposition  (ALD). The site is available at the OpenLearning platform of Aalto University https://openlearning.aalto.fi/, direct link https://openlearning.aalto.fi/course/view.php?id=100 (can be found by searching for “ALD” or “atomic layer deposition”).

The Podcasts section contains each podcast (that the author of this blog and the author/curator of the ALD OpenLearning site currently is aware of) as a separate “page” (as in defined the Moodle platform). Currently, the following podcasts have their own page: ALD Stories by Beneq, Nanovation, STG podcasts, Suomalaisten Kemistien Seura (a Finnish society), People Behind the Science and ALD Pulse.

In each page, named according to the specific podcast, direct links have been included to ALD-related episodes, which were available at the time of opening the Podcasts section (Nov 20, 2021). Most podcasts are in English. One podcasts in Finnish has also been linked to, and in the future more links to podcasts in other languages than English can also be included. The episodes in English contain interviews of many ALD scientists, including such internationally known names like Dr. Tuomo Suntola (the Finnish inventor of ALD), Prof. Seán Barry, Prof. Stacey Bent, Prof. Erwin Kessels, Prof. Mikko Ritala, Dr. Jonas Sundqvist, Prof. Ruud van Ommen and Prof. Charles Winter (list in alphabetical order, except for Suntola). The author of this blog (Prof. Riikka Puurunen) also had the honor of being interviewed for the ALD Stories podcast by Beneq (related to the history of ALD).

If some podcast or episode is missing from the list, I will be happy to add it. Please let me know of missing items — email to firstname.lastname@aalto.fi (replace with my info) should work well. Also, if someone would *not* like to have their podcast/episode included in this collection, it can be removed — please in such case contact me as well.

Espoo, Finland, November 21, 2021

Riikka Puurunen

Posted by Riikka Puurunen

Associate professor, Catalysis Science and Technology, at Aalto since February 2017
atomic layer deposition , teaching - Comments Off on New Podcasts section in ALD OpenLearning site (Nov 20, 2021)

Poster DL postponed: 2021 November Networking — ALD at Aalto University

Already about seventy persons registered to participate at 2021 November Networking — ALD at Aalto University!

The original deadline (DL) for registering with poster presentations was last Sunday. However, there is still space for more posters, and with the light organization that we have, we realized that we can take in registrations with the same schedule as other in-person registrations. So, we decided to postpone the DL.

Updated registration DLs according to type of participation:

  • Local in-person participation (with or without poster): registration DL Mon 22.11.2021. The number of posters may need to be limited; “first come, first serve”.
  • Zoom participation: registration DL Wed 24.11.2021. The number of participants might need to be limited (but likely not); if limiting is needed, “first come, first serve”.

Event website, with registration link: https://www.aalto.fi/en/events/2021-november-networking-ald-at-aalto-university.

Logo 2

Posted by Riikka Puurunen

Associate professor, Catalysis Science and Technology, at Aalto since February 2017
atomic layer deposition , events - Comments Off on Poster DL postponed: 2021 November Networking — ALD at Aalto University

Registration open: 2021 November Networking – ALD at Aalto University

Preparations for the 2021 November Networking — ALD at Aalto University (Nov 26, starting at 13) have progressed. Registration is now open in:  https://link.webropol.com/s/2021novembernetworkingald.

Registration deadlines (DL) according to type of participation:

  • Local participation with posters: registration DL Sun 14.11.2021. The number of posters may need to be limited; “first come, first serve”.
  • Local in-person participation: registration DL Mon 22.11.2021. The number of participants may need to be limited; “first come, first serve”.
  • Zoom participation: registration DL Wed 24.11.2021. The number of participants might need to be limited (but likely not); if limiting is needed, “first come, first serve”.

Info on the event is for the moment being collected and updated in: https://blogs.aalto.fi/catprofopen/ald-networking-nov-2021/. Maybe we will manage to get an “Event” page, too, in Aalto University systems – let’s see!

Posted by Riikka Puurunen

Associate professor, Catalysis Science and Technology, at Aalto since February 2017
atomic layer deposition , events - Comments Off on Registration open: 2021 November Networking – ALD at Aalto University

Save the date: November Networking – ALD at Aalto University, 26.11.2021

November Networking – ALD at Aalto University will be organized again! This time, on Friday 26.11.2021, at 13 on, at Aalto University School of Chemical Engineering (lecture hall Ke 2).

The decision to organize the event was made just a few days ago. At the moment, the organizing committee is formed by myself (Riikka Puurunen) and a postdoc in my group, Jorge Velasco. Programme is still under planning. Expect at least:

  • Posters by researchers. Not online as in the 2020 event, but in person! We have the downstairs lobby reserved for this — just like in the 2019 event.
  • Presentation on recent (1) book and (2) encyclopedia chapter on ALD. (1) Prof. Sean Barry (Carleton University, Canada) has published (/will publish: the book is not quite yet out! see: https://www.degruyter.com/document/isbn/9783110712513/html) a book on ALD chemistry; and (2) Prof. Ruud van Ommen (TU Delft, The Netherlands) has published (with A. Goulas and R.L. Puurunen) an introductory chapter on ALD for the Kirk-Othmer Encyclopedia of Chemical Techonology (https://doi.org/10.1002/0471238961.koe00059). Both Barry and van Ommen plan to be present at the event in person!
  • Discussion on the history of ALD and on the next steps in the VPHA project. The third coordinated reading effort in the Virtual Project on the History of ALD (VPHA, http://vph-ald.com) is about to start. Everyone interested in understanding the early history of ALD is welcome to join this open science type effort. A recent presentation on the VPHA in perspective here: https://youtu.be/7p8-pB7wsm8 (abstract and slides available via: https://vph-ald.com/ALD-history-publications.html).

read more >>

Posted by Riikka Puurunen

Associate professor, Catalysis Science and Technology, at Aalto since February 2017
atomic layer deposition , events - Comments Off on Save the date: November Networking – ALD at Aalto University, 26.11.2021

Mäkelä doctoral thesis defence 8.10., Riisager invited talk 7.10.

There is a doctoral thesis defence coming on 8.10.2021: M.Sc. Eveliina Mäkelä, “Hydrotreatment of lignocellulose-derived molecules to renewable fuels and chemicals”. Thesis is available at: https://aaltodoc.aalto.fi/handle/123456789/109881. The defence is organized in a hybrid manner, and it can be attended in Zoom: https://aalto.zoom.us/j/67830072574, starting at 12:00.

The opponent Prof. Anders Riisager will give an invited talk on the day before, 7.19.2021, starting at 15:00 (same Zoom link): “Valorization of biomass-derived resources with new heterogeneous catalysts“. Short biography of Prof. Riisager and abstract of the presentation below. read more >>

Posted by Riikka Puurunen

Associate professor, Catalysis Science and Technology, at Aalto since February 2017
Uncategorized - Comments Off on Mäkelä doctoral thesis defence 8.10., Riisager invited talk 7.10.

Invited tutorial on atomic layer deposition (ALD) at ALD 2021 conference

June 27-30, 2021, there was the 21st International Conference on Atomic Layer Deposition (ALD 2021), https://ald2021.avs.org/, organized as a virtual meeting.  I had the honour of giving an invited tutorial:  Fundamentals of atomic layer deposition: an introduction (“ALD101”). The pre-recorded tutorial is easy to access also after the conference – enjoy!

Posted by Riikka Puurunen

Associate professor, Catalysis Science and Technology, at Aalto since February 2017
atomic layer deposition - Comments Off on Invited tutorial on atomic layer deposition (ALD) at ALD 2021 conference