Tcod February 2014

tcod@lists.crystallography.net

5 participants
4 discussions

Fwd: some discussion topics related to TCOD
by Stefaan Cottenier 31 Jul '14

31 Jul '14

(as it seems there have been technical problems about TCOD, I'm not sure whether this 3-months-ago mail actually reached all or you or not. I just resend it.) -------- Original Message -------- Subject: some discussion topics related to TCOD Date: Fri, 24 May 2013 14:34:08 +0200 From: Stefaan Cottenier <Stefaan.Cottenier(a)UGent.be> To: tcod(a)lists.crystallography.net Dear colleagues, Today, we held a group discussion at CMM (http://molmod.ugent.be) about TCOD from the perspective of users and/or structure donators. That did not lead to clear conclusions, but rather to a series of thoughts that can be a starting point for further discussions or actions. I'll list those here (I guess that is what this mailing list is meant for): 1) You are probably aware of other database initiatives for computed crystal structures. Is there a vision on whether TCOD wants to 'compete' with those, or whether TCOD tries to fill a niche that is not served by other databases? For instance, consider https://www.materialsproject.org/. This is a database that aims doing a VASP geometry optimization for every structure in ICSD, starting from the ICSD cif (quite ironically, you can read their starting geometry (=ICSD info) for free, without having an ICSD yourself...). They use their own dedicated supercomputer infrastructure to run all this, and upload only results achieved by themselves. No input by others, this in order to keep control over quality and consistency. It has over 30.000 crystals by now, and apart from the structure info also computed properties are being added. I quote here a paragraph from a project proposal which we submitted earlier this year, and which contains info/references about other databases: "As is often the case for revolutions, this idea has been realized simultaneously and more or less independently at several places, emphasizing different aspects. The Materials Project [Jai11,MP] is an initiative at MIT, where basic properties of all crystalline solids documented in the (experimental) Inorganic Crystal Structure Database (ICSD) [ICSD] have been computed by DFT. The computed formation energies are used to construct secondary data bases of binary and ternary phase diagrams [Ong08, Jai11b]. Similar initiatives, each with their own focus and in different stages of growth are AFLOWLIB [Set10,Cur12] (Duke University), OQMD [Wol12] (Northwestern University) and CompES [CES] (NIMS, Japan). Other database initiatives that emphasize collaborative data sharing (see also Sec. 2.3, WP3) are ESTEST [Yua10,Yua12] at UC Davis (US), the Computational Materials Repository (CMR) [Lan12] at DTU (Denmark) and the AIDA environment [Koz13]." [Jai11] A. Jain et al. Computational Materials Science 50 (2011) 2295 [Jai11b] A. Jain et al., Physical Review B 84 (2011) 045115. [Ong08] S. P. Ong, L. Wang, B. Kang, G. Ceder, Chemistry of Materials 20 (2008) 1798 [Set10] W. Setyawan, S. Curtarolo, Computational Materials Science 49 (2010) 299 [Cur12] S. Curtarolo et al., Computational Materials Science 58 (2012) 227 [Wol12] Open Quantum Mechanical Database, http://wolverton.northwestern.edu/oqmd (no public access yet) [CES] http://caldb.nims.go.jp/index_en.html (Y. Chen, A. Nogami, H. Ohtani, N. Tatara) [Yua10] G. Yuan, F. Gygi, Computational Science & Discovery 3 (2010) 015004 [Yua12] G. Yuan, F. Gygi, Computer Physics Communications 183 (2012) 1744 [Lan12] D. Landis et al., Computing in Science and Engineering, nov/dec 2012, p. 51 (http://dx.doi.org/10.1109/MCSE.2012.16) [Koz13] B. Kozinsky, N. Marzari, N. Bonini, J. Garg, G. Pizzi, A. Cepellotti, M. Fornari, contributions at the MRS Fall meeting (Boston, Nov. 2012) and the DPG Spring meeting (Regensburg, March 2013). (2) From our perspective, we don't understand the need to separate experimental and computational databases. As long as every structure is properly tagged as 'experimental' or 'computed', we see no reason to separate them. It will only lead to the burden of having to run queries twice. In any case, a unified search web page that searches in both data bases simultaneously seems useful to us (that is, de facto, treating (T)COD as one database). (3) Quality control. If a deposited computed structure has been published, the reference to the publication serves as quality control. That's probably similar for deposited experimental structures, isn't it? If a computed structure has not (yet) been published, how to assess its quality? Well, let us turn the question around: if a not yet published experimental structure is deposited, how do you judge its quality...? It makes sense to do it in the same way: as long as basic information is provided on how the calculation has been done, later users should make their own judgement. (4) A quality control measure that could make sense for both experimental and computed structures, is to allow people to add remarks that appear on the web page of that structure ('considering the small basis set that has been used, I do not trust this result', or 'this result has been contradicted by <ref>'). Such information by the community can help people who are not experts in either computing or measuring crystal structures to decide to which extent they can trust a particular result. (Another variant is a feature on the web page of each structure to flag it if you have doubts, such that experts can look at it). (5) COD has cifs as entries only. If you want to go as far as including input info to reproduce each calculation, it might be hard to stick cifs-only for TCOD. It will then be necessary to link additional files to the cif of each entry. (6) We are split over whether it makes sense to require that each deposited calculation is exactly reproducible. Some basic information should be given, of course. This will be mainly information about the method that does not depend on the specific implementation (code). Furthermore, the main technical input parameters that are specific for the code used, should be given as well (if you want to do that in a structured way, you will immediately hit the problem that the required set of numbers will be a different kind of set for every other code...). Third in line should then be a free field for 'any other special settings' that could apply. With this kind of info, people can reproduce to a large extent (95%) the same calculation. If you want to have it reproduced exactly, then much more input (files) will be required. Which might not be worth the effort. (7) One of our enthusiastic PhD students with many years of experience in web design and databases immediately had a mental map about how to implement an automated version of (6) -- if the TCOD-team is willing to take him aboard to code that, he'll probably agree ;-). (8) In any case, it should be clear for the one who provides the structure, what exactly is requested. A web form where the information under (6) can be filled out (or the automated tool of (7) that extracts all this info from the output of each mainstream code) will be required in order to have consistent data. (9) Which kind of computed structures will TCOD accept? Ground state structures, obviously? Metastable structures probably as well? Also if they are not dynamically stable (soft phonon mode)? (that is not routinely examined) And what about transition state structures? (never observable in experiment, yet very useful to know -- and hard to find -- in order to understand reactions) If the latter are allowed, then they should be tagged as such. Best regards, Stefaan -- Stefaan Cottenier Center for Molecular Modeling (CMM) & Department of Materials Science and Engineering (DMSE) Ghent University Technologiepark 903 BE-9052 Zwijnaarde Belgium http://molmod.Ugent.be http://www.ugent.be/ea/dmse/en email: Stefaan . Cottenier /at/ UGent . be

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Presenting TCOD at the IUCr 23rd Congress?
by Saulius Gražulis 10 Feb '14

10 Feb '14

Dear colleagues, as I am going to the 23rd Congress of IUCr this year, I though that this would be a good opportunity to present TCOD to crystallographic and chemical community there. Unfortunately, the deadline of abstract submission is tomorrow, 2014-02-11, so I need a short feedback from you ASAP... I apologize for such a short notice. At this stage, TCOD poster/talk is not to present some spectacular results, but rather to inform community and to make sure that everyone is invited, so that nobody is excluded. Only in this case will the TCOD have its value. I attach a project of an abstract and an author list. If you do not mind, I present the abstract as a presenting author and thus put my name first; otherwise the list is alphabetical. If the NWchem people, or anyone else, would wish to participate and to provide their input about computational data representation and ontologies, I'd be glad to include them as co-authors. At the moment, I have included people on the tcod mailing list (except that I do not know the full name of , and Peter and Nicola with whom we discussed TCOD in detail; I hope you will participate :). Since we are a new team, I'll do as follows: a) those who e-mail me till tomorrow (2014-02-11) that they participate in the presentation I leave on the author list; b) those people who do not agree or *do not reply* by 2014-02-11 I will leave out as not consenting with their authorship; c) If no one from the theoretical community replies, I'll probably refrain from submitting the abstract. d) If you join the team, I'll submit the abstract and the author list tomorrow, on 2014-02-11. Me, Andrius and Antanas will do all the technical editing of the poster or slides; any comments on the text from you are welcome (but please keep in mind that the abstract is limited to 2000 chars). The most important contribution from you wold be the ideas: -- how to describe the computation data so that it is useful and reusable (what parameters need to be specified for different methods)? -- what quality criteria do we want to put on structures in TCOD (and in general on published DFT and other structures)? In other words, what computed structures will we be happy with? After the abstract submission we will have some time to polish TCOD policy details, data dictionaries (initial version can be found here: http://www.crystallography.net/tcod/cif/dictionaries/) and software pipeline (we will take care of this last bit in Vilnius, but participants are welcome :). Regards, Saulius -- Dr. Saulius Gražulis Vilnius University Institute of Biotechnology, Graiciuno 8 LT-02241 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556 mobile: (+370-684)-49802, (+370-614)-36366

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Re: [TCOD] Presenting TCOD at the IUCr 23rd Congress?
by Björkman Torbjörn 10 Feb '14

10 Feb '14

Dear Saulius and everyone else, I'll be happy to join. (I realize that people already have replied, sorry for not accounting for that, but I need to send this quickly now.) One question back regarding your second question: -- What are the existing quality criteria for COD? I know that I have to give Fabs, but that only applies if the data is not "old". However, data that is "old" (I forget the cutoff year) is still considered acceptable, so clearly it has been decided that the most important thing is not that a number is accurate but that an experienced person can see HOW accurate it is. I think that we should calibrate our mindsets to this "intermediately liberal" attitude and would prefer a rather liberal attitude when it comes to the pure convergence parameters as long as the most important ones are given. That would be (in addition to which code was used...) a description of the basis set (e.g. something like "400 eV" for a plane wave pseudopotential code or perhaps "tier 1" if you use FHI-AIMS), k-point set and the force/cell convergence criterion. Then we could have a rough classification resulting in a little green, yellow or red label for well, intermediately and poorly converged calculations. A major problem is that the choice of functional may not be as easily tagged as good or bad. There are a number of pointers that all of us in the business know, and of course we can collect these into a sort of heuristic. The modern thing would of course be to crosslink structures in TCOD with corresponding structures in COD and let some kind of neural network (or similar) generate a new heuristic free from our biases, although of course biased by only accounting for the crystal structure. Regards, Torbjörn P.S. OK, so maybe someone has to go first and get complained at by everoyne else for his sloppy standards... Here a suggestion for marking up the two most important convergence parameters: Max residual force on atoms < 0.01 eV/Å = good, 0.1-0.01 = intermediate, > 0.1 = low K-point resolution < 0.2 Å^{-1} = good, 0.75-0.2 = intermediate, > 0.75 = low There, I took the plunge, now to hide under my desk.... /T.B. --- Torbjörn Björkman, PhD COMP, Aalto University School of Science Espoo, Finland ________________________________________ Från: tcod-bounces(a)lists.crystallography.net [tcod-bounces(a)lists.crystallography.net] för Saulius Gražulis [grazulis(a)ibt.lt] Skickat: den 10 februari 2014 15:14 Till: tcod(a)lists.crystallography.net; blueobelisk-discuss(a)lists.sourceforge.net; Nicola Marzari; Peter Murray-Rust; Antanas Vaitkus; Andrius; Chateigner Daniel Ämne: [TCOD] Presenting TCOD at the IUCr 23rd Congress? Dear colleagues, as I am going to the 23rd Congress of IUCr this year, I though that this would be a good opportunity to present TCOD to crystallographic and chemical community there. Unfortunately, the deadline of abstract submission is tomorrow, 2014-02-11, so I need a short feedback from you ASAP... I apologize for such a short notice. At this stage, TCOD poster/talk is not to present some spectacular results, but rather to inform community and to make sure that everyone is invited, so that nobody is excluded. Only in this case will the TCOD have its value. I attach a project of an abstract and an author list. If you do not mind, I present the abstract as a presenting author and thus put my name first; otherwise the list is alphabetical. If the NWchem people, or anyone else, would wish to participate and to provide their input about computational data representation and ontologies, I'd be glad to include them as co-authors. At the moment, I have included people on the tcod mailing list (except that I do not know the full name of , and Peter and Nicola with whom we discussed TCOD in detail; I hope you will participate :). Since we are a new team, I'll do as follows: a) those who e-mail me till tomorrow (2014-02-11) that they participate in the presentation I leave on the author list; b) those people who do not agree or *do not reply* by 2014-02-11 I will leave out as not consenting with their authorship; c) If no one from the theoretical community replies, I'll probably refrain from submitting the abstract. d) If you join the team, I'll submit the abstract and the author list tomorrow, on 2014-02-11. Me, Andrius and Antanas will do all the technical editing of the poster or slides; any comments on the text from you are welcome (but please keep in mind that the abstract is limited to 2000 chars). The most important contribution from you wold be the ideas: -- how to describe the computation data so that it is useful and reusable (what parameters need to be specified for different methods)? -- what quality criteria do we want to put on structures in TCOD (and in general on published DFT and other structures)? In other words, what computed structures will we be happy with? After the abstract submission we will have some time to polish TCOD policy details, data dictionaries (initial version can be found here: http://www.crystallography.net/tcod/cif/dictionaries/) and software pipeline (we will take care of this last bit in Vilnius, but participants are welcome :). Regards, Saulius -- Dr. Saulius Gražulis Vilnius University Institute of Biotechnology, Graiciuno 8 LT-02241 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556 mobile: (+370-684)-49802, (+370-614)-36366

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First version of TCOD dictionaries
by Saulius Gražulis 10 Feb '14

10 Feb '14

Dear colleagues, after some unfortunate period of silence, I have finally put together two CIF dictionaries for the TCOD, using the input provided by Linas and Torbjorn. They can now be parsed by CIF parsers. You can find the current versions here: http://www.crystallography.net/tcod/cif/dictionaries/ files: http://www.crystallography.net/tcod/cif/dictionaries/cif_dft.dic http://www.crystallography.net/tcod/cif/dictionaries/cif_tcod.dic The cif_tcod.dic is intended as a general house-keeping dictionary and method identification meta-data, and cif_dft.dic is the first method-specific dictionary (and there might be more if needed, for different methods). All TCOD entries validate against these dictionaries, but for a trivial reason: the data items described there are not yet used in real data files. The dictionaries however open us possibility to start thinking about these data items, putting together their descriptions and setting up requirements that structures which we want to see in TCOD should fulfill :) Regards, Saulius PS. I am thinking that it would be good to announce TCOD in the upcoming IUCr meeting. I will send you an abstract project in a short while. S.G. -- Dr. Saulius Gražulis Vilnius University Institute of Biotechnology, Graiciuno 8 LT-02241 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556 mobile: (+370-684)-49802, (+370-614)-36366

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