mathcryst

 

International Scientific School
«Combined topological and DFT methods
for prediction of new materials»

 


Registration

 

Information

Combined topological
and DFT methods
for prediction
of new materials


An international school
under
Russian-Chinese partnership
 
September 14 — 20, 2015. Samara.

TOPOS

Organization fee is USD 40

 

Accommodation of participants
will be paid by organizers

 

Contact the organizers


Introduction and motivation

In the previous (August 2014) school we dwelled on the topological approach to description and prediction of structure and properties of new crystalline substances and materials. This field of science has been rapidly developed in the past 15 years. The program package, where the corresponding methods, algorithms, and software are implemented most comprehensively is ToposPro; other programs like Gavrog Systre and 3dt Gavrog Systre and 3dt are intended for more special tasks. The topological databases (TOPOS TTD, TTO, TTR, TTM, TTL, and TTN collections, RCSR and EPINET databases) include more than 100000 topological types of nets that can occur in extended crystalline architectures as well as in molecular crystals. Many of these resources are available for free and become more and more popular; now the description of the overall topology of new structures is ordinal in such journals as CrystEngComm or Crystal Growth & Design. The search for relations between local topology of coordination groups, coordination abilities of metal atoms and ligands on the one hand and the overall topology of the whole network becomes one of the important tasks in the structure investigations.

These relations could be important to create first expert systems in crystal design; the knowledge database of such systems could rest upon the topological databases, while the inference machine could use the relations to provide an expert conclusion about the possibility of appearance of a particular topological motif. Thus the topological approaches are crucial for taxonomy of the experimental information and for developing predictive tools.

At the same time, the topological methods, being able to work with large samples of crystallographic data, provide only qualitative or semi-quantitative prediction. To make it precise we need to merge the topological methods with the quantitative methods of mathematical modelling. Recent progress in theoretical materials science is especially caused by development of Density Functional Theory (DFT), which is a basis of quantum mechanical calculations of various crystal properties. The present state of theoretical calculations in quantum chemistry and solid state physics can be considered as an ab initio approach. It means that we can describe already known crystalline structures, predict new crystalline materials and perform calculations of their physical properties without any empirical parameters. An important part of this ab initio approach is the high-performance numerical calculations on supercomputers or cluster systems.


Contents and objectives

The main goal of this tutorial is to give an introduction to this whole new area that we call Topological Crystal Chemistry and to show how the topological methods and tools can be used together with the DFT methods for creating expert systems in materials science. An important difference of this school compared to previous ones is that it consists of two interrelating parts. The first part will contain the full introduction to the topological methods while the second part will be devoted to how they can be combined with the DFT methods. There will be large time dedicated to hands-on session on the use of the novel and still not so widespread computer methods/software/databases so the student at the end of the course should be able to analyse any kind of extended structure through the eye of the topology and describe it in term of nets, entanglements, catenation etc. A special attention will be paid to the analysis of various classes of crystalline materials, in particular, MOFs, supramolecular crystals, zeolites, fast-ion conductors. All participants will have an ability to analyze their own crystal structures with the help of tutors that will be available also in the evening time. A special session will be devoted to summarize the results of such personal/free works.

The tutorial will start with a theoretical introduction where the background of the topological methods will be briefly, but rigorously, considered. No special mathematical skills are required, but the participants have to be aware of crystal chemistry and crystallography basics. The main abilities, problems, and perspectives of topological analysis of crystalline networks will be outlined.

The main part of the tutorial will be devoted to practical works with the computer programs ToposPro, Systre, and 3dt with a special attention to ToposPro. All participants will get the ToposPro Practical Manual that contains the detailed description of all practical works.

The second part includes a brief introduction into the Density Functional Theory and its application combined with the topological methods to design new materials. Two popular program DFT packages, VASP and CRYSTAL, will be used to solve some practical tasks, where the trial structures are generated with ToposPro and Systre, while the optimization and calculation of physical properties are performed with VASP and CRYSTAL.

 

As a result, the participants will gain the following knowledge:

1. A general view of modern topological and DFT methods in crystal chemistry and materials science, the corresponding algorithms, software, databases, and expert systems.

2. A skill of application of these tools to various classes of crystal structures and crystalline materials.

A vision of how to apply the software and databases to investigate the participant’s own specific field of science.

Important

Dear participants!

We recommend you to familiarize yourself with the materials prepared for you by the organizers of the School (download address will be sent to your e-mail).

New version TOPOS Practical Manual is available at: TOPOS_practical_manual_112.pdf

For fruitful work during the school you need have a laptop with Windows OS. You should download the distributive of TOPOS package and install it on your laptop.

Links for downloading:
ToposPro_Setup_x32.exe — for 32 bits versions Windows OS
ToposPro_Setup_x64.exe — for 64 bits versions Windows OS

 
We also recommend you to bring along the crystallographic data (in the form of *.cif or *.res files) on the structures that you’d like to explore on your own with the help of TOPOS — they will be used for individual tasks.

Please, let us know which classes of structures or crystal-chemical tasks you work on, we will find the individual tasks for you and assign a personal advisor on your topic.

If you have any questions, please, contact the organizers of school immediately.

Visas

The citizens of the following countries do not need visa to come to Russia:
 
Azerbaijan, Argentina, Armenia, Belarus, Bosnia and Herzegovina, Brazil, Chile, Colombia, Cuba, Ecuador, Fiji, Guatemala, Hong Kong (up to 14 days), Macao (up to 30 days), Israel, Kazakhstan, Kyrgyzstan, Macedonia, Moldova, Montenegro, Nicaragua, Peru, Republic of Korea, Serbia, Tajikistan, Thailand, Turkey, Uzbekistan, Ukraine, Uruguay, Venezuela.
 
Please, note that visa invitation processing time depends on the country of your citizenship. In order to plan visa process timely, please, contact Maria V. Mikheykina, Head, International Relations Sector, Samara State University, E-mail: miheykina@samsu.ru
To obtain visa invitation, please, fill in the Visa-invitation-form and send it to Maria V. Mikheykina (E-mail: miheykina@samsu.ru) together with a photocopy of your valid travel passport.

Fees

Dear participants!

After your registration and approving of your participation in the School you need to pay the registration fee.
 
Early bird registration fee (before July 1, 2015) is 40 USD.
Late registration fee (after July 1, 2015) is 60 USD.
 

Wire transfer in EUR to the benefit of Federal State-funded Educational Institution of Higher Professional Education «Samara State University». Please, use the following bank details to expedite credit of funds:
 

Receiver’s Correspondent DEUTDEFF
Корреспондент получателя Deutsche Bank AG, Frankfurt am Main
Account With Institution SABRRUMM
Банк бенефициара (получателя) SBERBANK, MOSCOW
Beneficiary Customer / 40503978954021000527

SAMARA STATE UNIVERSITY

INN 6316003560

AKADEMIKA PAVLOVA 1

SAMARA RU

Wire transfer in USD to the benefit of Federal State-funded Educational Institution of Higher Professional Education «Samara State University». Please, use the following bank details to expedite credit of funds:
 

Receiver’s Correspondent CHASUS33
Корреспондент получателя JPMorgan Chase Bank, New York
Account With Institution SABRRUMM
Банк бенефициара (получателя) SBERBANK, MOSCOW
Beneficiary Customer / 40503840354021000527

SAMARA STATE UNIVERSITY

INN 6316003560

AKADEMIKA PAVLOVA 1

SAMARA RU

Program

Lecturers:

Prof. Vladislav A. Blatov
Samara Center for Theoretical Materials Science (SCTMS), Samara State University
 
Prof. Davide M. Proserpio
Università degli Studi di Milano (Italy)

Samara Center for Theoretical Materials Science (SCTMS), Samara State University
 
Prof. Vladimir A. Saleev
Samara Center for Theoretical Materials Science (SCTMS), Samara State University

 

Tutors:

Dr. Eugeny V. Alexandrov
Dr. Artem A. Kabanov
Dr. Alexander P. Shevchenko
Dr. Alexandra V. Shipilova
Andrey A. Golov
Natalia A. Kabanova
Arina A. Pankova
Nikita S. Zakharov
Pavel N. Zolotarev

 

TOTAL VOLUME IS 52 HOURS (4 HOURS *13 HALF-DAYS). Working language ​​- English

 

THEORY (14 hours)
 
1. Computer crystallochemical analysis: an overview
2. Applied computer crystallochemical analysis: software, databases, expert systems
3. Periodic Structures and Crystal Chemistry… aka the Topological Approach to
Crystal Chemistry
4. Graph, Nets & Tilings (Quotient Graphs & Natural Tilings)
5. Topological Analysis of Entanglement : interpenetration, polycatenation, self-catenation
6. DFT as a basis of modern theoretical material science.
7. Introduction to VASP and CRYSTAL.

 
PRACTICE WITH PROGRAMS ToposPro, Systre, 3dt

 
Module 1. Standard topological analysis and classification of nets in MOFs
(Metal-Organic Frameworks), organic and inorganic crystals (6 hours)

1.1. Creating a database from CIF, SHELX or Systre formats
1.2. Computing adjacency matrix (complete set of interatomic bonds) for chemical compounds with different chemical bonding (valence, H bonding, specific interactions, intermetallic compounds)
1.3. Visualizing 0D, 1D, 2D and 3D structures
1.4. Standard simplified representations of MOFs or hydrogen-bonded organic crystals
1.5. Computing topological indices (coordination sequences, point and vertex symbols)
1.6. Topological identification of nets. Working with TTD collection and Systre
1.7. Taxonomy of nets. Working with TTO and TTR collections

 
Module 2. Special topological methods of searching for building units in crystal structures (4 hours)

2.1. Special methods of simplification. Edge nets and ring nets. Analysis of synthons
2.2. Standard cluster representation of MOFs
2.3. Nanocluster representation of intermetallic compounds

 
Module 3. Analysis of entanglements in MOFs and molecular crystals (4 hours)

3.1. Visualization, topological analysis and classification of interpenetrating MOFs
3.2. Detection and description of other types of entanglement in MOFs: polycatenation, self-catenation and polythreading. Classification of entanglements with Hopf ring nets

 
Module 4. Analysis of microporous materials and fast-ion conductors with natural tilings (4 hours)

4.1. Computing natural tilings and their parameters. Visualizing tiles and tilings (ToposPro & 3dt). Simple and isohedral tilings. Constructing dual nets
4.2. Analysis of zeolites and other microporous materials, constructing migration paths in fast-ion conductors

 
Module 5. Crystal design and topological relations between crystal structures (2 hours)

5.1. Group-subgroup relations in periodic nets. Subnets and supernets
5.2. Maximum-symmetry embedding of the periodic net, working with the Systre program
5.3. Searching for topological relations between nets and working with net relation graph
5.4. Applications of net relations to reconstructive phase transitions

 
Module 6. Toward expert systems in crystal design (2 hours)

6.1. Searching for topological relations with TTD, TTO, TTR, TTL, TTM, and TTN collections
6.2. Estimating probabilities of occurrence of topological motifs depending on the chemical composition of reactants

 
Module 7. Combined topological and DFT methods (12 hours)

7.1. VASP (geometrical optimization, mechanical properties, electronic properties)
7.2. CRYSTAL (geometrical optimization, mechanical properties, electronic properties)
7.3. TOPOS+VASP/CRYSTAL (applications for crystal design and prediction of physical properties)

 
Module 8. Work with the tasks based on the participants’ own structures (4 hours)

Participants are invited to bring their own data/structures to be analysed as well as personal computers to install the software.

 
Basic literature

 

  1. V.A. Blatov, D.M. Proserpio (2014) ToposPro Practical Manual 1.1.1.
  2. V.A. Blatov, A.P. Shevchenko, D.M. Proserpio (2014) Cryst. Growth Des., 14, 3576-3586.
  3. L. Ohrstrom, K. Larsson (2005) Molecule-Based Materials: The Structural Network Approach, Elsevier, Amsterdam.
  4. L. Carlucci, G. Ciani, D. M. Proserpio (2007) Chapter 1.3 in Making Crystals by Design: Methods, Techniques and Applications, ed. D. Braga and F. Grepioni, Wiley-VCH, Weinheim.
  5. S. R. Batten, S. M. Neville, D. R. Turner (2009) Coordination Polymers: Design, Analysis and Application, Royal Society of Chemistry, Cambridge.
  6. O. Delgado-Friedrichs, M. D. Foster, M. O’Keeffe, D. M. Proserpio, M. M. J. Treacy, O. M. Yaghi (2005) J. Solid State Chem., 178, 2533-2554.
  7. V.A. Blatov, D.M. Proserpio (2011) Chapter 1 in: «Modern Methods of Crystal Structure Prediction», Ed. A.R. Oganov, Weinheim: Wiley-VCH.
  8. V.A. Blatov (2011) Struct. Bond., 138, 31-66.
  9. M. O’Keeffe, O. M. Yaghi (2012) Chem. Rev., 112, 675-702.
  10. M. Li, D. Li, M. O’Keeffe, O. M. Yaghi (2014) Chem. Rev., 114, 1343-1370.
  11. V.A. Blatov, T.G. Mitina (2013) Cryst. Growth & Des., 13, 1655-1664.
  12. L. Carlucci, G. Ciani, D.M. Proserpio, T.G. Mitina, V.A. Blatov (2014) Chem. Rev., 114, 7557-7580.

Schedule

PROGRAMME

of the International Scientific School

Combined topological and DFT methods for prediction of new materials

Monday, September 14th, SCTMS conference hall

9.00-9.15 Welcome and Introduction
9.15-10.45 V.A. Blatov, Lecture “Computer crystallochemical analysis: an introduction”
10.45-11.00 Coffee break
11.00-12.30 V.A.Blatov, D.M. Proserpio, Exercises “Introduction to TOPOS”
12.30-14.00 Lunch
14.00-15.30 V.A.Blatov, D.M. Proserpio, Exercises “Visualization of 0D, 1D, 2D and 3D structures”
15.30-15.45 Coffee break
15.45-17.15 V.A. Blatov, Lecture “Methods, software, databases, and expert systems for crystallochemical analysis”
17.15-18.45 D.M. Proserpio, Lecture “Graphs, nets, and tilings- I”

 

Tuesday, September 15th, SCTMS conference hall
9.00-10.30 D.M. Proserpio, Lecture “Graphs, nets, and tilings- II”
10.30-10.45 Coffee break
10.45-12.30 V.A. Blatov, D.M. Proserpio, Exercises “Standard methods of simplification of crystal structures”
12.30-13.30 Lunch
13.30-16.30 – Excursion to Stalin’s bunker and short sightseeing of Samara
16.30-16.45 Coffee break
16.45-18.00 V.A. Blatov, D.M. Proserpio, Exercises “Topological identification of nets. Working with the TTD collection and Systre”
18.00-18.30 Q&A

 

Wednesday, September 16th, SCTMS conference hall
9.00-10.30 D.M. Proserpio, Lecture “Topological analysis of entanglements”
10.30-10.45 Coffee break
10.45-12.30 V.A. Blatov, D.M. Proserpio, Exercises “Special methods of simplification of crystal structures”
12.30-14.00 Lunch
14.00-15.30 V.A. Blatov, D.M. Proserpio, Exercises “Visualization, topological analysis and classification of MOFs and coordination polymers”
15.30-15.45 Coffee break
15.45-17.15 V.A. Blatov, D.M. Proserpio, Exercises “Visualization, topological analysis and classification of entangled networks”
17.15-18.00 Q&A

 

Thursday, September 17th, SCTMS conference hall
9.00-10.30 V.A. Blatov, D.M. Proserpio, Exercises “Computing natural tilings and their parameters with TOPOS. Analysis of zeolites and fast-ion conductors”
10.30-10.45 Coffee break
10.45-12.30 V.A. Blatov, D.M. Proserpio, Exercises “Work with Systre and 3dt programs”
12.30-14.00 Lunch
14.00-15.30 V.A. Blatov, D.M. Proserpio, Exercises “Nanocluster representation of intermetallic compounds”
15.30-15.45 Coffee break
15.45-17.15 V.A. Blatov, E.V.Alexandrov, Exercises “Creating knowledge databases for crystal chemistry and materials science”
17.15 -18.00 Q&A

 

Friday, September 18th, SCTMS conference hall
9.00-10.30 D.M. Proserpio, Lecture “The topological approach to crystal chemistry: An historical account”
10.30-10.45 Coffee break
10.45-12.30 V.A. Saleev, Lecture “DFT as a basis of modern theoretical materials science”
12.30-14.00 Lunch
14.00-15.30 A.V. Shipilova, “Introduction to VASP”
15.30-15.45 Coffee break
15.45-17.15 A.V.Shipilova, Exercises “Running VASP”
17.15 -18.00 Q&A

 

Saturday, September 19th, SCTMS conference hall
9.00-10.30 V.A. Saleev, “Introduction to CRYSTAL”
10.30-10.45 Coffee break
10.45-12.30 A.A. Kabanov, Exercises “DFT and topological investigations of ionic conductivity in solids”
12.30-14.00 Lunch
14.00-15.30 V.A. Saleev, Exercises “Running CRYSTAL — I”
15.30-15.45 Coffee break
15.45-17.15 V.A. Saleev, Exercises “Running CRYSTAL — II”
17.15 -18.00 Q&A

 

Sunday, September 20th, SCTMS conference hall
9.00-10.30 A.V. Shipilova, Exercises “Hybrid topological-DFT methods for the prediction of new materials”
10.30-10.45 Coffee break
10.45-12.15 V.A. Blatov, D.M. Proserpio, V.A. Saleev, Exercises “Solving individual tasks based on the participants’ own structures”
12.15-12.30 Summary and Conclusions

List of participants

 
 
   Germany
 
Michael Böhme — Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena
Oluseun Akintola — Institut für Anorganische und Analytische Chemie, Friedrich-Schiller-Universität, Jena
Falk Meutzner — TU Bergakademie Freiberg
Tilmann Leisegang — TU Bergakademie Freiberg

 
   India
 
Sumit Srivastava — University of Delhi
Ashok Yadav — Indian Institute of Science Education and Research

 

   Italy
 
Jacopo Tessarolo — University of Padova
 

   Russian Federation
 
Pavel Gavryushkin — V.S. Sobolev Institute of Geology and Mineralogy SB RAS
Sergey Sozykin — South Ural State University
Pavel Poltarak — Nikolaev Institute of Inorganic Chemistry
Stanislav Fedotov — Lomonosov Moscow State University
 
   South Korea
 
Eunji Lee — Gyeongsang National University
Huiyeong Ju — Gyeongsang National University
 

   United Kingdom
 
Sam Jobbins — Cardiff University
Timothy Flack — Cardiff University
Duncan Hardie — Cardiff University
 
   Viet Nam
 
Ha Nguyen — Vietnam National University