Topic outline

  • Welcome to the Density-functional theory for experts course!

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    • Course Description:

      Density-functional theory (DFT) derives from the fundamental laws of quantum mechanics and describes the behavior of electrons - the glue that holds all matter together. Understanding the behavior of electrons therefore means understanding matter. DFT is a theoretical concept that has been turned into a computational tool with enormous success in physics, chemistry and materials science. DFT provides a parameter-free description of materials on the atomic scale and can be used to predict materials properties. DFT is also often used for training Machine Learning Force-Fields which are used for predicting material properties on atomistic levels on much larger scales than any Quantum Mechanics/Chemistry codes can handle. This course assumes that you are familiar with the basics of DFT. It will go into more detail on the theoretical foundations of DFT, in particular the exchange-correlation functional, cover pros and cons of DFT, delve into the numerical realization of DFT and teach the practical aspects of performing DFT calculations in hands-on tutorial sessions.

      Course level:

      The course is for students who have completed their Bachelor's degree and have a basic understanding of DFT. Completion of last years course Density-Functional Theory for Practitionersis beneficial, but not a prerequisite.

      Credits:

      5 ECR are awarded for the course.

      Content:

        • Theoretical foundations of density-functional theory (DFT)
        • Hierarchy of exchange-correlation functionals
        • Strengths and limitations of DFT
        • Beyond DFT schemes for e.g. describing excitations
        • DFT in computational materials modelling and chemistry
        • Expert usage of the DFT software package FHI-aims
        • High-performance computing environments
        • Numerical aspects (e.g. density mixing, optimization schemes)
        • Advanced modelling concepts (e.g. supercell concept, repeated slab approach)
        • Equilibrium structures of materials (e.g., molecules, solids, surfaces)
        • Elastic properties of materials
        • Magnetic properties of materials
        • Thermodynamics (e.g., free energy, phase diagrams)
        • Vibrations, phonons and vibrational spectroscopy
        • Band structures, excitation energies and photo-electron spectroscopy
        • Dielectric function and optical spectra
        • Point defects in materials
        • Properties of surfaces and interfaces

    • Course completion:

      Criteria:

      Attending the 5/6 hands-on labs (substitutional assignment in case of additional absence ). Attending 2/3 contact project checkpoints. Attending 2/3 seminars and presenting 1 seminar topics to the class. Project proposal send before the deadline (deadline stated on 1st lecture). Project report send before the deadline (deadline stated on 1st lecture).

      In the case of an extra reason for non-passing some of the criteria an extra assessment could be provided upon an agreement.

      Grading scale:

      Pass/Fail.

      Course outcomes:

      After completion of the course you:
      - have a good understanding of DFT-based materials modelling.
      - are familiar with the strengths and limitations of DFT.
      - are an advanced user of the FHI-aims DFT software package.
      - can use DFT software in a high-performance computing environment.
      - can solve physics, chemistry and material science problems with DFT.
      - can follow a presentation (e.g. conference or seminar) on DFT results.
      - can plan, execute, document and present a computational research project.
      - can give peer feedback.
    • forum icon
      Announcements Forum
    • forum icon
      General Discussion Forum
      Any question to the teachers, or even to your pears on the course.

  • Schedule and Teaching premises

    • Schedule Overview:

      The course is scheduled for both Autumn terms (I: 4.9 -15.10; II: 23.10-4.12), except for the exam period (16.10-22.10).

      The course consist of:

      • Monday lectures 10:15 -12:00 (voluntary).
      • Thursdays contact sessions 8:15 -12:00 (obligatory): Hands-on tutorials, Seminars and Project presentation sessions.
      • Two written assessments (obligatory): Project plan (1.10), Project Final report (4.12).

      Detailed Schedule:

      Sessions: Lectures (10:15 -12:00) Exercise (8:15-12:00) Maari B Written assesments
      Week: Monday: Where: Thursday: What: Deadline: What:
      36 4.9 U119  7.9 Tutorial    
      37 11.9 U119  14.9 Seminar    
      38 18.9 U119  21.9 Tutorial    
      39 25.9 U119  28.9 Project Intro 1.10 Project plan
      40 2.10 U119  5.10 Tutorial    
      41 9.10 U119  12.10 Seminar    
      42 Exam week
      43 23.10 M240 26.10 Tutorial    
      44 30.10 U119  2.11 Project checkpont    
      45 6.11 U119  9.11 Tutorial    
      46 13.11 U119  16.11 Seminar    
      47 20.11 U119  23.11 Tutorial    
      48 27.11 U119  30.11 Project final presentation 4.12 Project final report

      Premises:

      Map of Otakaari , with its classrooms for the course lectures.
      All the Monday lectures will take space in the Undergraduate center (Otakaari 1) mostly in U119 (left part of the image above). while on 23.10 it will take place in M240 (Right part of the image above).
      The Thursday contact sessions will take place in Maarintalo (Sähkömiehentie 3) - Maari B Linux computer room (see image bellow, for a map). You need a working Aalto key-card to get into Maarintalo main door.
      Map of maarintalo with the maari B computerroom

  • Registration

  • Lectures

  • Hands-on tutorials

    • On this page we will upload the study material and files important to the Thursday tutorials session (8-12). See for Schedule and Premises for additional information about the venue and exact dates.

    • resource icon
      grep cheatcheat File
      Text file
    • folder icon
      Tutorial 1 Folder
    • resource icon
      Tutorial 1 - pre-lecture video File
      Video file (MP4)
      Not available unless: You belong to A01 (SISU)
    • folder icon
      Tutorial 2 Folder
    • resource icon
      Tutorial 2 - pre-lecture video File
      Video file (MP4)
      Not available unless: You belong to A01 (SISU)

  • Seminars

    • On this page you can find the topics for the seminars. We also provide reference material, which you can access by visiting the page for the corresponding topic below. Each seminar should be about 20 minutes long and should include time for questions from the audience.

    • assign icon
      Slides for seminar Assignment

    • Here are the topics for 1st seminar: Thursday 14th September:

    • resource icon
      The Born-Oppenheimer approximation - taken! File
      PDF document

      Review the Born-Oppenheimer approximation. You can derive it and then discuss its implications and also when it might fail. You can use the material below, but please also conduct a search for additional information and reference material.

      References

      Chapter 6 of Principles of the theory of solids, J. M. Ziman, Cambridge University Press 1972

    • resource icon
      The exchange-correlation hole File
      PDF document

      Review the concept of the exchange-correlation hole in DFT. Then discuss how the exchange-correlation hole can be used to understand the good performance of the local-density approximation (LDA). You can use the material below, but please also conduct a search for additional information and reference material.

      References

      Density functional theory: Its origins, rise to prominence, and future, by R. O. Jones, Rev. Mod. Phys. 87, 897 (2015) (this article is also listed on the main Reference page)


    • resource icon
      Self-Interaction Corrections File
      PDF document

      Review the concept of the one-electron self-interaction error that was introduced by Perdew and Zunger. You can derive it and then discuss its performance and also its disadvantages (if any). You can use the material below, but please also conduct a search for additional information and reference material.

      References:

      Mark R. Pederson  and John P. Perdew, Psi-K Highlights 109 (2011)

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      The B3LYP hybrid functional File
      PDF document

      Review and present the B3LYP hybrid functional. The two original papers are listed below. We have also included a recent benchmarking paper that tests the performance of B3LYP for 622 molecules. You can of course also look for other benchmarking papers.

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      Transition states and the nudged elastic band method File
      PDF document

      Describe briefly what a transition state is and why it is a useful concept. Then introduce the Nudged Elastic Band (NEB) method as a means to find transition states. The more images and illustrations you can use, the better. Below you can find two book chapters on transition state search methods. We also found Graeme Henkelman's website quite illustrative. You can of course search for other material and publications.

    • resource icon
      Which functional should I choose? File
      PDF document

      Taken - Review Kieron Burke's article "Which functional should I choose?". A pdf of the article can be found below. You can of course include your own perspective on the question "which functional to choose" and also search for other studies and works that address this question.

    • folder icon
      Seminar presentations Folder

  • Project Work

  • Contact Information

    • Main Lecturer:

      Picture of Ondrej Krejci

      Ondřej Krejčí
      ondrej(dot)krejci(at)aalto(dot)fi
      Y 412, Otakaari 1 B
      Consultation hours: Tue 10-12

      Assistants:

      Dr. Orlando J. Silveira

      Orlando Silveira Júnior
      orlando(dot)silveirajunior(at)aalto(dot)fi
      Y 430c, Otakaari 1 B
      Consultation hours: Tue 10-12

      Dr. Pascal Henhell

      Pascal Henkel
      pascal(dot)henkel(at)aalto(dot)fi
      Y 426c, Otakaari 1 B
      Consultation hours: Tue 10-12

      Guarantor:

      prof. Patrick Rinke
      patrick(dot)rinke(at)aalto(dot)fi

  • Praise for DFT!

    • Density-functional theory has finally brought quantum mechanics into materials science. Its proven ability to produce correct predictions of properties of real materials means that it has taken over as the premier method in solid state materials, ultimately because of its suitability as a numerical method. Graeme Ackland, University of Edinburgh on the back cover of Materials Modelling using Density Functional Theory

      Density functional theory (DFT) is an incredible success story. The low computational cost, com- bined with useful (but not yet chemical) accuracy, has made DFT a standard technique in most branches of chemistry and materials science. Electronic structure problems in a dazzling variety of fields are currently being tackled. Kieron Burke in Perspective on density functional theory, J. Chem. Phys. 136, 150901 (2012).

  • Additional Literature

    • resource icon
      FHI-aims manual File
      PDF document

    • Working on Tutorials/Projects remotely or outside of the scheduled contact session:

      You can of course work on the Aalto Linux stations in your free time:

      Here you can find computer rooms and their utilization: https://computers.aalto.fi/

      You can also try to work on those things through remote access. Either through Linux vdi ( https://www.aalto.fi/en/services/vdiaaltofi-how-to-use-aalto-virtual-desktop-infrastructure ) or through connecting ( ssh -X ... )to kosh or taltta ( https://scicomp.aalto.fi/aalto/remoteaccess/ ) and then connecting to one of the computers in classrooms - ssh -X nameofcomputer.org.aalto.fi ; the names of computers are here. PLEASE, allway check if somebody is not using the computer heavilly. Try top command to see the workload on the particular computer.


    • Triton Cluster:


      For your project work, you can use:

      the Aalto Workstations with Ubuntu 20.04 abd Intel I5 11th generations with 12-cores - see here for remote access and where you can find those on the campus. 

      the Triton computational cluster ( overview here ) with different architectures, but which allows you to run your calculations up-to 192 cores. For getting the access (if you do not have already), please contact us. We can provide you a temporary acccess to the cluster - for the time of the course.
      You can login to the cluster through ssh -X YOUR_USERNAME@triton.aalto.fi, (don't forget to add your username) from any computer at Aalto. Otherwise use double ssh through kosh or taltta (see the remote access).
      You can start to create your input files in your scratch directory:
      /scratch/work/YOUR_USERNAME
      Navigate there, create new folder and you can start to create your files. Beware that not all the visualization software is on triton, and not all the pop-up windows can tunnel through ssh -X.

      DO NOT RUN YOUR CALCULATIONS ON THE LOGIN NODE!!! - You should put your calculations into a queue via slurm command.  The example of slurm script for running the FHI-aims code on Triton is provided here. You will submit it into the queue via:

      sbatch YOUR_SCRIPT

      You can check the status of your calculations through:

      squeue -u YOUR_USERNAME

      If there are no running jobs, check the output of your calculations - either they are already done, or there was a mistake somewhere in the inputs.
      The species for your calculations can be found in:
      /scratch/scip/PHYS-E0546/CODE/species_defaults/

      Good luck with your calculations!

  • The XC-challenge


    • The rules:

      • The question for the competition is: How many exchange-correlation functionals are there (in this world, today)?
      • Submit your answer in the class on Monday, September 18th. If you could not come to class, you can email me your answer.
      • During the course search for exchange-correlation functionals and enter them for the 2nd time in provided google doc.
      • The winner is, whose number (in avarage)  is closest to the number of unique exchange-correlation functionals will be announced on Monday 27.11.