ONETEP Spring School 2010

Organized by

Chris-Kriton Skylaris (University of Southampton)
Mike Payne (University of Cambridge)
Nicholas Hine (University of Cambridge)
Peter Haynes (Imperial College London)
Arash A. Mostofi (Imperial College London)

The list of participants is available on the CECAM website
Schedule and Talk Slides

Tuesday, April 13

0900 : Welcome and introductions
0930 : Lecture 1 : Overview of first principles calculations (M. C. Payne) PDF Δ
1030 : Lecture 2 : Overview of linear-scaling methods (P. D. Haynes) PDF
1130 : Coffee break
1200 : Lecture 3 : Introduction to ONETEP (C.-K. Skylaris) PDF
1300 : Lunch
1400 : Practical session 1 : Setting up Simple ONETEP Calculations PDF
1800 : Close

Wednesday, April 14

0900 : Lecture 4 : Density matrices (P. D. Haynes) JPG
1000 : Short talks : Applications to biological systems
1000 : Daniel Cole : Protein-protein interactions from linear-scaling DFT calculations PDF
1020 : Stephen Fox : Protein-ligand interactions PDF
1040 : Jacek Dziedzic : Implicit Solvation Models in ONETEP PDF
1100 : Coffee break
1130 : Lecture 5 : Basis states: psincs and the FFT box (A. A. Mostofi) PDF
1230 : Participants’ talks
1230 : Oliviero Andreussi : Computational Design and Evaluation of Room Temperature Ionic Liquids for Rechargeable Lithium Batteries Applications PDF Δ
1300 : Lunch
1400 : Practical session 2 : Geometry optimisation PDF
1800 : Close

Thursday, April 15

0900 : Lecture 6 : Electronic energy minimisation (C.-K. Skylaris) PDF
1000 : Short talks : Applications to nanostructures
1000 : Fabiano Corsetti : Phonon calculations in ONETEP with the finite displacement method PDF
1020 : Phil Avraam : Charge distribution in GaAs nanorods
PDF
1040 : Nicholas Zonias : Large-scale DFT calculations on H-passivated Si nanorods using the ONETEP code PDF
1100 : Coffee break
1130 : Lecture 7 : Parallel implementation (N. D. M. Hine) PDF
1230 : Group discussion : The ONETEP Wiki
1300 : Lunch
1400 : Practical session 3 : Analysis and visualisation PDF
1800 : Close

Friday, April 16

0900 : Lecture 8 : Beyond DFT with ONETEP (N. D. M. Hine) PDF
0945: Short talks : Future developments
0945 : David O’Regan : Linear-scaling and projector self-consistent DFT+U for electronic correlations in large systems
1005 : Alvaro Ruiz Serrano : Pulay Forces and Multiple Accuracy Approach in ONETEP PDF
1025 : Laura Ratcliff : Towards the calculation of experimental spectra using linear-scaling density-functional theory PDF
1045 : Jacek Dziedzic : Hartree-Fock Exchange and Hybrid Exchange-Correlation Functionals PDF
1100 : Coffee break
1130 : Simon Dubois : Quantum transport in graphene based nanostructures PDF
1200 : Lecture 9 : Multiscale modelling with ONETEP (A. A. Mostofi)
1300 : Lunch

Location

Lectures and practical sessions will take place in the Theory of Condensed Matter (TCM) group’s seminar room in the Cavendish Laboratory. Extensive instructions on travel arrangements to the Cavendish are available on the TCM group website but do not hesitate to contact the organizers if you have further questions.
Accommodation in Cambridge for the ONETEP spring school participants has been arranged with Corpus Christi College in the centre of Cambridge.
Financial Support

Funding from the Psi-K Training programme for this ONETEP Spring School is gratefully acknowledged.
Eligible applicants received funding for full-board accommodation at Corpus Christi, and up to 200 euro towards travel expenses by rail or air.
Description

First-principles simulations based on density-functional theory (DFT), in particular the plane-wave pseudopotential (PWP) method, have become established as a powerful tool for gaining insight into complex atomistic processes and predicting the properties of new materials. Methods for performing such calculations are being developed and applied by a growing number of scientists including not just physicists, chemists and materials scientists but also biochemists and geologists.
However the system-sizes accessible to first-principles simulations is limited by the computational scaling of traditional implementations, which grows with the cube of the number of atoms and restricts them to the study of several hundreds of atoms even with modern supercomputers.
There has therefore been much interest in the development of so-called linear-scaling methods for insulators, which promise to revolutionise the scope and scale of simulations based upon DFT and facilitate calculations involving thousands of atoms. These new methods all abandon the conventional description of the fictitious Kohn-Sham system in terms of extended Bloch states in order to exploit the localisation of the density-matrix and/or Wannier functions. This also means that linear-scaling calculations are more amenable to embedding within other calculations and hence incorporation within multiscale simulations. This is reflected by the incorporation within Working Group 2 (Multiscale Methods) of the Psi-k Network.
However only a few general purpose linear-scaling codes have emerged over the last decade. The ONETEP code has been applied to systems consisting of up to thirty thousand atoms and ranging from proteins to nanostructures. In ONETEP, local orbitals associated with each atom are described in terms of a systematic basis set equivalent to a set of plane-waves and individually optimised in situ to obtain high accuracy and transferability.
While ONETEP inherits a number of desirable features from its relationship with the PWP method, it is nonetheless based on a reformulation of DFT in terms of the density-matrix whose truncation requires a considerably more complex (and sometimes conflicting) convergence procedure. Hence this tutorial is required to introduce the new principles and practices associated with ONETEP both to experienced practitioners and novices alike.
Although ONETEP is marketed commercially by Accelrys, it is available to academic users worldwide direct from the University of Cambridge via an inexpensive license to cover administrative costs. These users are encouraged to participate in the self-supporting ONETEP user community through the Wiki: www.onetep.org.
The first ONETEP summer school was held in Cambridge in July 2008 and was intended mainly for prospective developers. The attendees were almost exclusively from the UK. The aim of this tutorial is rather different: to provide training for new users from across Europe and beyond and to help them to exploit the new opportunities that ONETEP provides for their research. Participants will be expected to be familiar with electronic structure calculations within density-functional theory but no knowledge of ONETEP or linear-scaling methods in general is required.
Scientific Objectives

The tutorial will comprise lectures, practical sessions and short talks. Lectures by members of the ONETEP Developers’ Group will cover the theory underlying the method, its implementation in a general purpose computational scheme and future development work in progress and beyond. The practical sessions will provide a comprehensive overview to compiling and running the code and analysing the results obtained. Short talks from current ONETEP users will highlight the range of applications and development work currently under way and some participants will also be invited to speak about their plans for using ONETEP in their research. There will also be a group discussion about how to develop the ONETEP Wiki to promote effective communication across the ONETEP user community.
The objectives are to provide both new and experienced first-principles simulators with:

a basic grasp of the relevant theory underlying ONETEP
a clear understanding of the parameters that must be converged to obtain reliable results
the practical know-how to set up and run calculations that use the whole range of functionality currently in ONETEP
experience in trouble-shooting common problems that arise
tools for analysing the results of ONETEP simulations
an invitation to participate in the ONETEP user community and Wiki
enthusiasm to employ ONETEP in their future research

References

Review of linear-scaling methods

Linear scaling electronic structure methods, Stefan Goedecker, Rev. Mod. Phys. 71, 1085-1123 (1999)

Principal ONETEP reference

Introducing ONETEP: Linear-scaling density functional simulations on parallel computers, Chris-Kriton Skylaris, Peter D. Haynes, Arash A. Mostofi and Mike C. Payne, J. Chem. Phys. 122, 084119 (2005)

General overview

ONETEP: linear-scaling density-functional theory with local orbitals and plane waves, Peter D. Haynes, Chris-Kriton Skylaris, Arash A. Mostofi and Mike C. Payne, phys. stat. sol. (b) 243 2489-2499 (2006)

Implementation

Nonorthogonal generalized Wannier function pseudopotential plane-wave method, Chris-Kriton Skylaris, Arash A. Mostofi, Peter D. Haynes, Oswaldo Di�guez and Mike C. Payne, Phys. Rev. B 66, 035119 (2002)
Total-energy calculations on a real space grid with localized functions and a plane-wave basis, A. A. Mostofi, C.-K. Skylaris, P. D. Haynes and M. C. Payne, Comput. Phys. Commun. 147, 788-802 (2002)
Preconditioned iterative minimisation for linear-scaling electronic structure calculations, Arash A. Mostofi, Peter D. Haynes, Chris-Kriton Skylaris and Mike C. Payne, J. Chem. Phys. 119, 8842-8848 (2003)
Implementation of linear-scaling plane wave density functional theory on parallel computers, Chris-Kriton Skylaris, Peter D. Haynes, Arash A. Mostofi and Mike C. Payne, phys. stat. sol. (b) 243, 973-988 (2006)
Density kernel optimisation in the ONETEP code, P. D. Haynes, C.-K. Skylaris, A. A. Mostofi and M. C. Payne, J. Phys.: Condens. Matter 20, 294207 (2008)
Linear-scaling density-functional theory with tens of thousands of atoms: Expanding the scope and scale of calculations with ONETEP, N. D. M. Hine, P. D. Haynes, A. A. Mostofi, C.-K. Skylaris and M. C. Payne Comput. Phys. Commun. 180, 1041-1053 (2009)

Applications

Using ONETEP for accurate and efficient O(N) density functional calculations, Chris-Kriton Skylaris, Peter D. Haynes, Arash A. Mostofi and Mike C. Payne, J. Phys.: Condens. Matter 17, 5757-5769 (2005)
Novel structural features of CDK inhibition revealed by an ab initio computational method combined with dynamic simulations, L. Heady, M. Fernandez-Serra, R. L. Mancera, S. Joyce, A. R. Venkitaraman, E. Artacho, C.-K. Skylaris, L. Colombi Ciacchi and M. C. Payne, J. Med. Chem. 49, 5141-5153 (2006)
Achieving plane wave accuracy in linear-scaling density functional theory applied to periodic systems: A case study on crystalline silicon, Chris-Kriton Skylaris and Peter D. Haynes, J. Chem. Phys. 127, 164712 (2007)
Linear-scaling first-principles study of a quasicrystalline molecular material, M. Robinson and P. D. Haynes, Chem. Phys. Lett. 476, 73-77 (2009)

ONETEP Summer School 2008

The inaugural ONETEP Summer School was held in Cambridge
Tuesday 8th July

13.30 Lecture 1: Overview of first principles calculations (Mike Payne)
14.30 Lecture 2: Introduction to ONETEP (Peter Haynes) PDF
15.30 Coffee
16.00 Practical session 1 PDF

Wednesday 9th July

09.00 Lecture 3: Density matrices (Peter Haynes)
10.00 Lecture 4: Psinc functions and FFT boxes (Arash Mostofi) PDF
11.00 Coffee
11.30 Lecture 5: Electronic energy minimisation (Chris Skylaris) PDF
12.30 Lunch
13.30 Practical session 2 PDF
15.00 Practical session 3 PDF
16.00 Coffee
16.30 Lecture 6: ONETEP parallelisation (Nick Hine) PDF
19.00 Dinner

Thursday 10th July

09.00 Lecture 7: Forces and geometry optimisation (Arash Mostofi)
10.00 Lecture 8: Overview of ONETEP applications (Chris Skylaris, David O’Regan, Mark Robinson, Quintin Hill and Phil Avraam)
11.00 Coffee
11.30 General discussion of future plans for ONETEP and creating a user community (Chris Skylaris)
12.30 Close


Photos