The H 2 molecule without convergence studies Objectives: - the (pseudo)total energy - the bond length r HH Acknowledgment: exercise inspired on the first.

Slides:



Advertisements
Similar presentations
How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander.
Advertisements

Javier Junquera Exercises on basis set generation Convergence of the basis set with size.
Javier Junquera Exercises on basis set generation Control of the range of the second-ς orbital: the split norm.
Javier Junquera Exercises on basis set generation 1. The default basis set.
Javier Junquera Exercises on basis set generation Control of the range: the energy shift.
Introducing the coordinates in Z-matrix form Objectives study how to introduce the coordinates of a molecule in Z-matrix form.
Take-home postcard. Basis set: Atomic orbitals s p d f SIESTA: Strictly localized (zero beyond cut-off radius)
Molecular Bonds Molecular Spectra Molecules and Solids CHAPTER 10 Molecules and Solids Johannes Diderik van der Waals (1837 – 1923) “You little molecule!”
Pseudopotentials and Basis Sets
Molecular Bonding Molecular Schrödinger equation
Happyphysics.com Physics Lecture Resources Prof. Mineesh Gulati Head-Physics Wing Happy Model Hr. Sec. School, Udhampur, J&K Website: happyphysics.com.
DFT – Practice Simple Molecules & Solids [based on Chapters 5 & 2, Sholl & Steckel] Input files Supercells Molecules Solids.
Introduction to Molecular Orbitals
DFT Calculations Shaun Swanson.
Convergence with respect the number of k-points: bulk BaTiO 3 Objectives - study the convergence of the different phases of bulk BaTiO 3 with respect the.
Computational Solid State Physics 計算物性学特論 第2回 2.Interaction between atoms and the lattice properties of crystals.
Meeting 31, April 7 th Theory: ZnTe, ZnSe dispersion curves.
Performance Analysis and Monitoring Facilities in CPN Tools Tutorial CPN’05 October 25, 2005 Lisa Wells.
Computing lattice constant, bulk modulus and equilibrium energies of solids Bulk Si Diamond structure.
How to optimize automatically the parameters that determine the quality of the basis Javier Junquera Alberto García.
Introduction to run Siesta
Javier Junquera Exercises on basis set generation Increasing the angular flexibility: polarization orbitals.
Philippe Ghosez Lattice dynamics Andrei Postnikov Javier Junquera.
Interatomic Binding Quark binding in nuclear particles Radioactive β-decay Celestial mechanics, Structure of the universe Atomic forces, binding, Optics,
Molecular Modeling Part I Molecular Mechanics and Conformational Analysis ORG I Lab William Kelly.
Network for Computational Nanotechnology (NCN) Purdue, Norfolk State, Northwestern, MIT, Molecular Foundry, UC Berkeley, Univ. of Illinois, UTEP DFT Calculations.
BINF6201/8201 Principle components analysis (PCA) -- Visualization of amino acids using their physico-chemical properties
Lectures Introduction to computational modelling and statistics1 Potential models2 Density Functional.
Practical quantum Monte Carlo calculations: QWalk
NA-MIC National Alliance for Medical Image Computing shapeAnalysisMANCOVA_Wizar d Lucile Bompard, Clement Vacher, Beatriz Paniagua, Martin.
The Nuts and Bolts of First-Principles Simulation Durham, 6th-13th December : DFT Plane Wave Pseudopotential versus Other Approaches CASTEP Developers’
Incorporating the spherically symmetric potential energy we need to deal with the radial equation that came from separation of space variables, which contains.
The H 2 O molecule: converging the size of the simulation box Objectives - study the convergence of the properties with the size of the unit cell.
Quark binding in nuclear particles Radioactive β-decay Celestial mechanics, Structure of the universe Atomic forces, binding, Optics, electricity,... Binding.
How to run SIESTA Víctor García Suárez (thanks to J. Junquera and J. Ferrer)
How to generate a pseudopotential with non-linear core corrections Objectives Check whether the non-linear core-corrections are necessary and how to include.
- Compute and analyze the band structure of an ionic solid
The eggbox effect: converging the mesh cutoff Objectives - study the convergence of the energy and the forces with respect to the real space grid.
TBPW: A Modular Framework for Pedagogical Electronic Structure Codes Todd D. Beaudet, Dyutiman Das, Nichols A. Romero, William D. Mattson, Jeongnim Kim.
© Alejandro Strachan – Binding Curves for H2 and He2 Online simulations via nanoHUB: Binding curves for H 2 molecule In this tutorial: Density functional.
© Alejandro Strachan – Online simulations: electronic structure of oxygen Online simulations via nanoHUB: Exchange interaction in Oxygen In this tutorial:
How to generate a mixed pseudopotential Objectives Generate a mixed pseudopotential to be used in the Virtual Crystal Approximation or in simulations at.
How to generate a pseudopotential
Plotting the charge density of bulk Si
How to generate a pseudopotential with the semicore in the valence Objectives Check whether semicore states should be explicitly included in the valence.
The Nuts and Bolts of First-Principles Simulation Durham, 6th-13th December : Testing Testing. Basic procedure to “validate” calculations CASTEP.
2/25/2015PHY 752 Spring Lecture 181 PHY 752 Solid State Physics 11-11:50 AM MWF Olin 107 Plan for Lecture 18: Reading: Chapter 10 in MPM Ingredients.
Dissociation of H 2 Do HF calculations for different values of the H-H internuclear distance (this distance is fixed since we are in the Born- Oppenheimer.
How to prepare the interface between siesta and wannier90
Practice #2: Solid Yong-Hyun Kim NST551.
Computing lattice constant, bulk modulus and equilibrium energies of bulk cubic SrTiO 3 Bulk SrTiO 3 Cubic structure.
Practice #2: Solid Yong-Hyun Kim NST551.
Molecular Bonding Molecular Schrödinger equation
Chapter 8.
Van der Waals dispersion in density functional theory
How to plot fat bands with siesta
Band structure of a cubic perovskite oxide:
Online simulations via nanoHUB: The O2 molecule and spin
Other Kinds of Arrays Chapter 11
How to plot the Fermi surface using siesta and wannier90
shapeAnalysisMANCOVA_Wizard
Types of Chemical Bonds Chapter 8
Energies, forces, bonds - only shapes of atomic electron orbitals give us a hint of three-dimensional shapes of molecules more quantitative treatment requires.
Prof. Sanjay. V. Khare Department of Physics and Astronomy,
Intermolecular Forces
Covalent Bonds Main Concept:
• Explain how a permanent dipole can result in a polar bond.
Practice Problems Draw Lewis structures for the following molecules
Orbitals, Basis Sets and Other Topics
Intermolecular Forces
Presentation transcript:

The H 2 molecule without convergence studies Objectives: - the (pseudo)total energy - the bond length r HH Acknowledgment: exercise inspired on the first exercise of the Abinit tutorial (

H 2 molecule: example of a very simple input file Go to the directory where the exercise of the H 2 molecule is included Number of different species and atoms present in the unit cell List of different species Position of the atoms Example of a first-principles simulation: no input from experiment Inspect the input file, h2.fdf Examine in detail the different input variables, more information at and follow the link Documentations, Manual

Many variables will take the default value PAO.BasisSize(Basis set quality) DZP MeshCutoff(Fineness of real space integrations)100 Ry XC.Functional(Exchange and correlation functional)LDA XC.Authors(Flavour of the exchange and correlation)CA SpinPolarized(Are we performing an spin polarized calc.).false. … and many others. For a detailed list, see fdf.log after running the code.

H 2 molecule: the first run of Siesta (0.002 thousand of atoms) Check that you have all the required files A pseudopotential file (.vps or.psf) for every atomic specie included in the input file For H within LDA, you can download it from the Siesta web page. Run the code, siesta h out The name of the output file is free, but since we are running the H 2 molecule with an interatomic distance of 1 Å, this seems very sensible… Wait for a few seconds… and then you should have an output

H 2 molecule: taking a glance to the output files Let’s make a tour on the different output files: Inspect the output file where the forces are written, SystemLabel.FA What is the value of the force on each atom, in eV/Å? Is the system in the equilibrium configuration? Inspect the output file, h out How many SCF cycles were required to arrive to the convergence criterion? How much is the total energy of the system after SCF? How large is the unit cell automatically generated by Siesta? How much is the electric dipole of the molecule (in electrons  bohr)? For molecules,

H 2 molecule: the interatomic distance Goal: find the equilibrium structure of the molecule Method 1: - compute the total energy for different values of the interatomic distance, - make a fit through the different points, - determine the minimum of the fitting function. Method 2: - compute the forces for different values of the interatomic distance, - make a fit through the different points, - determine the zero of the fitting function. Method 3: - use an automatic algorithm to minimize the energy

H 2 molecule: the interatomic distance using Method 1 Run again the code, changing the interatomic distance from 0.40 Å to 3.00 Å by steps of 0.10 Å Modify the input file, changing the position of this atom Run the code, saving each output in a separate file siesta h2.your_interatomic_distance.out

H 2 molecule: the interatomic distance using Method 1 Tabulate the total energy as a function of the interatomic distance grep “Total =” h2.*.out > h2.distance.dat Edit the h2.distance.dat file, and leave only two columns Interatomic distance (Å)Total energy (eV) These numbers have been obtained with siesta-3.0-b, compiled with the g95 compiler and double precision in the grid. Numbers might change slightly depending on the platform, compiler and compilation flags

H 2 molecule: the interatomic distance using Method 1 Plot the total energy versus interatomic distance gnuplot plot “h2.distance.dat” using 1:2 with lines

H 2 molecule: the most important point: analyze the results When atoms or molecules get too close, they repel each other with a very large repulsion For non-polar molecules, the interaction at very large distances is an attraction, and varies inversely as the sixth power of the distance E  r -6 (Thought LDA does not capture Van- der-Waals interation) Minimum at the equilibrium distance, around 0.8 Å (For comparison, Abinit Å) At this point, the forces on the atoms vanish ( ) Close to the minimum, we can approximate the curve as a parabola (harmonic approximation)