Tcod March 2014

tcod@lists.crystallography.net

2 participants
2 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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Merged cif_dft.dic and cif_tcod.dic
by Linas Vilciauskas 31 Mar '14

31 Mar '14

Dear TCOD'ers, I tried merging the two dictionaries for the tcod. I removed what looked like duplicate entries form the cif_dft.dic and cleaned up the cif_tcod.dic a little bit. Nevertheless, the cif_tcod is by any means final and we should continue cleaning it up and adding the necessary entries. Best, LV -- Linas Vilciauskas Postdoctoral Research Fellow Dept. of Chemistry New York University 100 Washington Square East / 830BB New York, NY 10003 linas.vilciauskas(a)nyu.edu Office: +1-212-998-3589 Cellular: +1-347- 614-6831

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Tcod March 2014