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Introduction to Quantum Espresso

Introduction to Quantum Espresso. ESPRESSO. ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation and Optimization

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Introduction to Quantum Espresso

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  1. Introduction to Quantum Espresso PPT by Heliokinesis Research Student Group

  2. ESPRESSO • ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation and Optimization • QE is an integrated suite of computer codes for electronic-structure calculations and material modeling, based on DFT, Plane waves, & Pseudopotential(numerical trick, replace nuclear potential by pseudopotential) PPT by Heliokinesis Research Student Group

  3. The QE Project • The two main goals of this project are: • to foster methodological innovation in the field of electronic-structure simulations • To provide a wide and diverse community of end users with hightly efficient, robust, and userfriendly software implementing the most recent innovations in this field. PPT by Heliokinesis Research Student Group

  4. The QE Project • Applications are run through text input files based on fortrannamelists • The QE distribution is written, mostly in Fortran-95, with some part in C or in Fortran-77 • Parallelization via standard MPI libraries. PPT by Heliokinesis Research Student Group

  5. Code • The codes are constructed around the use of periodic boundary conditions PPT by Heliokinesis Research Student Group

  6. Simulations • Calculation of the Kohn-Sham (KS) orbitals and energies for isolated or extended periodic system, and their ground-state energy • Complete structural optimizations of the microscopic (atomic coordinates) and macroscopic (unit cell) degrees of freedom, using Hellmann-Feynman forces and stresses PPT by Heliokinesis Research Student Group

  7. Simulations • Ground state of magnetic or spin-polarized system, including spin-orbit coupling and non collinear magnetism • ab initio molecular dynamics (MD), using either the Car-ParrinelloLagrangian or the Hellmann-Feynman forces calculated on the Born-Oppenheimer surface, in variety of thermodynamical ensembles, including NPT variable-cell MD PPT by Heliokinesis Research Student Group

  8. Simulations • Density-functional peturbation theory (DFPT), to calculate second and third derivatives of the total energy at any arbitrary wavelength, providing phonon dispersions, electron-phonon and phonon-phonon interactions, and static response functions (dielectric tensors, Born effective charges, IR spectra, and Raman tensors) PPT by Heliokinesis Research Student Group

  9. Simulations • Location of saddle points and transition states via transition-path optimization using the nudged elastic band (NEB) method • Ballistic conductance within the Landauer-Buttiker theory using the scattering approach PPT by Heliokinesis Research Student Group

  10. Simulations • Generation of maximally localized Wannier functions and related quantities • Calculation of nuclear magnetic resonance (NMR) and electronic paramagnetic resonance (EPR) parameters • Calculation of K-edge x-ray absorption spectra. PPT by Heliokinesis Research Student Group

  11. Data file format • Data files should ideally be: • Extensible • Self-documenting • Efficient • Structured file formats, notably Hierarchical Data Format (HDF) and network Common Data Form (netCDF), that have been widely used for years in other communities • File formats based on the Extensible Markup Language (XML) PPT by Heliokinesis Research Student Group

  12. QE Packages • The current version (4.1) includes: • 310000 lines of fortran-90/95 code, • 1000 lines of fortran-77 code, • 1000 lines of C code, • 30000 lines of Tcl code + external standard math libraries such as FFTW (Fast Fourier-Transform Package), BLAS (BASIC Linear Algebra Subroutine), LAPACK (Linear Algebra Package), & external toolkit iotk • There are 10000 lines of specific documentation, 100 different examples & +100 tests of the different functionalities. PPT by Heliokinesis Research Student Group

  13. QE Packages • PWscf • CP • PHonon • Atomic • PWcond • GIPAW • XPECTRA • Wannier90 • PostProc • Pwgui • We’ll mostly deal with PWSCF. Other components havesimilar input structure PPT by Heliokinesis Research Student Group

  14. QE Packages • PWscf (Plane-Wave Self-Consistent Field) • We will use this to perform total energy calculations • Density-functional & Hartree-Fock calculations of the energy electronic structure • Phonon dispersion curves, dielectric constants, & Born effective charges • PWSCF uses both norm-conserving pseudopotentials(PP), ultrasoftpseudopotential (US-PP) & projector augmented wave (PAW) potentials within DFT PPT by Heliokinesis Research Student Group

  15. QE Packages • CP (Car-Parrinello molecular dynamics) • The CP code is the specialized module performing Car–Parrinelloab initio MD. • the electron density is augmented through a Fourier interpolation scheme in real space (‘box grid’) that is particularly efficient for large-scale calculations. • CP implements the same functionals as PWscf,with the exception of hybrid functionals; a simplified one-electron self-interaction correction (SIC) is also available. PPT by Heliokinesis Research Student Group

  16. QE Packages • CP (Car-Parrinello molecular dynamics) • CP can also be used to directly minimize the electronic energy functional to self-consistency while keeping thenuclei fixed, or to perform structural minimizations of nuclear positions, using the ‘global minimization’ approaches of and damped dynamics or conjugate-gradients on the electronic or ionic degrees of freedom. • CP can perform NEB and metadynamics calculations PPT by Heliokinesis Research Student Group

  17. QE Packages • PHonon • The PHonon package implements density-functional perturbation theory (DFPT) for the calculation of second- and third-order derivatives of the energy with respect to atomic displacements and to electric fields • Advanced features of the PHonon package include the calculation of third-order energy derivatives and of electron–phonon or phonon–phonon interaction coefficients PPT by Heliokinesis Research Student Group

  18. QE Packages • Atomic • The atomic code performs three different tasks (These three tasks can be either separately executed or performed in a single run): • Solution of the self-consistent all-electron radial KS equations (with a Coulomb nuclear potential and spherically symmetric charge density) • generation of NC PPs, US PPs, or PAW datasets • test of the above PPs and data-sets. • Three different all-electron equations are available: • The nonrelativistic radial KS equations • the scalar relativistic approximation to the radial Dirac equations • The radial Dirac-like equations derived within relativistic densityfunctional theory PPT by Heliokinesis Research Student Group

  19. QE Packages • PWcond • The PWcond code implements the scattering approach proposed by Choi and Ihm for the study of coherent electron transport in atomic-sized nanocontacts within the Landauer–B¨uttiker theory PPT by Heliokinesis Research Student Group

  20. QE Packages • GIPAW • The GIPAW code allows for the calculation of physical parameters measured in: • NMR spectroscopy in insulators (the electric-field-gradient (EFG) tensors and the chemical shift tensors) • EPR spectroscopy for paramagnetic defects in solids or in radicals (the hyperfine tensors and the gtensor). • The code also computes the magnetic susceptibility of nonmagnetic insulators PPT by Heliokinesis Research Student Group

  21. QE Packages • XSPECTRA • The XSPECTRA code allows for the calculation of K-edge x-ray absorption spectra (XAS). PPT by Heliokinesis Research Student Group

  22. QE Packages • Wannier90 • Wannier90 is a code that calculates maximally localizedWannier functions in insulators or metals, a number of properties that can be conveniently expressed in a Wannier basis. PPT by Heliokinesis Research Student Group

  23. QE Packages • PostProc • The PostProc module contains a number of codes for postprocessing and analysis of data files produced by PWscf and CP • The following operations can be performed: • Interfacing to graphical and molecular graphics applications • Interfaces to other codes that use DFT results from QE for further calculations • Calculation of various quantities that are useful for the analysis of the results. PPT by Heliokinesis Research Student Group

  24. QE Packages • PWgui • PWgui is the graphical user interface (GUI) for the PWscf, PHonon, and atomic packages as well as for some of the main codes in PostProc • PWgui is an input file builder whose main goal is to lower the learning barrier for the newcomer, who would otherwise have to struggle with the input syntax PPT by Heliokinesis Research Student Group

  25. Parallelization • High performance on massively parallel architectures is achieved by distributing both data and computations in a hierarchical way across available processors PPT by Heliokinesis Research Student Group

  26. Parallelization PPT by Heliokinesis Research Student Group

  27. Parallelization • Image parallelization • by dividing processors into nimage groups, each taking care of one or more images • pool parallelization • by dividing each group of processors into npool pools of processors, each taking care of one or more k-points • plane-wave parallelization • by distributing real- and reciprocal-space grids across the nPWprocessors of each pool. • Task group parallelization • in which processors are divided into ntask task groups of nFFT= nPW/ntaskprocessors, each one taking care of different groups of electron states to be Fourier transformed, while each FFT is parallelized inside a task group PPT by Heliokinesis Research Student Group

  28. General Structure • Namelist-calculation specifications • &CONTROL: general variables controlling the run • &SYSTEM: structural information on the system under investigation • &ELECTRONS: electronic variables • &IONS (optional): ionic variables • &CELL (optional): variable-cell dynamics • &PHONON (optional): information required to produce data for • phonon calculations PPT by Heliokinesis Research Student Group

  29. General Structure • Nonoptional & optional cards • ATOMIC SPECIES • ATOMIC POSITIONS • K POINTS • CELL PARAMETERS(optional) • OCCUPATIONS(optional) • FIRST IMAGE(optional) • LAST IMAGE(optional) • CLIMBING IMAGES(optional) PPT by Heliokinesis Research Student Group

  30. Typical input file – diamond Si

  31. The namelist &control • calculation • scf: single point calculation without geometric optimization • nscf : non-self-consistent calculation • relax : geometric optimization • md : molecular dynamics • vc-relax : geometric optimization with variable unit cellcoordinates • restart_mode • from scratch : Start from an initial guess • restart : Start from earlier data • outdir: Directory where intermediates are dumped. • pseudo_dir: Directory where the pseudopotentials live. PPT by Heliokinesis Research Student Group

  32. The namelist &system • nat : number of atoms • ntyp : number of types of atoms • nbnd : number of states to be calculated (unoccupied statesas well) • ecutwfc : kinetic energy cutoff (for planewaves) • ecutrho : density cutoff (for the augmentation charge inUSPP ≈ 10× ecutwfc) PPT by Heliokinesis Research Student Group

  33. The namelist &system PPT by Heliokinesis Research Student Group

  34. The namelist &system PPT by Heliokinesis Research Student Group

  35. The namelist &system PPT by Heliokinesis Research Student Group

  36. The namelist &electrons PPT by Heliokinesis Research Student Group

  37. The namelist &ions PPT by Heliokinesis Research Student Group

  38. Cards PPT by Heliokinesis Research Student Group

  39. Cards PPT by Heliokinesis Research Student Group

  40. THANK YOU PPT by Heliokinesis Research Student Group

  41. References • Paolo Giannozzi et al 2009 J. Phys.: Condens. Matter21 395502 doi:10.1088/0953-8984/21/39/395502 • Ustunel, Hande 2007 Quantum-Espresso • www.quantum-espresso.org PPT by Heliokinesis Research Student Group

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