Electrochemistry project, Chemistry Department, November Ab-initio Molecular Dynamics Simulation
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1 Electrochemistry project, Chemistry Department, November 2006 Ab-initio Molecular Dynamics Simulation
2 Outline Introduction Ab-initio concepts Total energy concepts Adsorption energy calculation Project objective Ab-initio total energy calculation Density Functional Theory Implementation to total energy calculation Ionic relaxation (Geometry optimization)
3 Ab-initio concepts Computational Ab-initio simulation Classical simulations Classical simulations and some theories use experimental values, while in ab-initio calculations no experimental value is needed. Experiment Theory Ab-initio -> No experimental data in needed as an input for the calculation
4 Total energy concepts Assumption: T=0K (no kinetics energy for nucleus) Total energy of an atom in gas phase Classical view r 2 E = E + E atom tot e ion e e E = ev ev atom tot 0 e ion 0 e e r 1 nucleus electrons E atom tot We use atomic unit: 3 z 1 = + r r r e 0 i= 1 i i> j= 1 i j 1 = 1, = 1 4πεε 0 E < atom tot 0 Total energy : The require energy to take apart all electrons from the nucleus
5 Total energy of a molecule in gas phase E = E + E + E mol tot e ion e e ion ion E = ev ev + zev mol tot 0 e ion 0 e e 0 ion ion r j R i E mol tot i= 2, j= 6 6 i= 2, j= 2 2 z 1 z = + + R r r r R R i= 1, j= 1 i j i, j= 1 i j i> j= 1 i j mol E < 0 Total energy : The require energy to take apart tot all electrons AND nucleus
6 mol E tot atom E tot What is mol tot E = E E atom tot It is the binding energy of a molecule: the require energy to take apart two atoms of a molecule
7 Adsorption energy Definition: The require energy to take apart the adsorbate from the surface Example: CO adsorption on Pt CO/Pt Clean Pt slab CO in gas phase slab CO E + slab tot E tot CO E tot
8 Project Objective Hydrogen and CO adsorption energies on Pt(111), Pt(110) and Pt(100)
9 Ab-initio total energy calculation of a system of nucleons and electrons The electrons and ions are very small therefore quantum consider is needed Approximation 1: ions are much bigger compare to electrons -> ions as classical particles. Electrons -> Quantum particles -> Wavefunction -> Charge density n(r) -> Schrödinger eq. Nucleons -> Classical particles -> Point charge -> Newton (coulomb) law ions (classic) electrons (quantum)
10 Schrödinger equation for system of electrons HΨ = where Ψ is the total wavefunction of the system. EΨ Kohn-Sham orbitals The charge density is given by Ψ = ϕ... 1ϕ2 ϕn N nr ( ) = ϕi i= 1 2 H is the Hamiltonian. H = T + Ve e+ V V ext is the interaction with an external potential. In our case the external potential is just electron-proton interaction: ext V ext [ n] = N i= 1 z r R i x z r R i y r-r i R i is the position of ions.
11 V e-e is electron-electron coulomb interaction: z r r r-r n(r ) Ve e[ n] = nr ( ') dr' r r' V ext V ext V ext x y Charge density of electrons n(r) V ext
12 H = T + V e-e + V ext x T is the kinetic energy of electrons of the interacting system. The bad news is that there no solution for T and Ψ therefore there is no solution for Schrödinger equation.
13 Density Functional Theory (DFT) Theory1: External potential is a unique functional of the density n(r). That means if we have a system of electrons, the ground state density n 0 (r) corresponding to an external potential (like the potential from the protons) V ext can not be reproduced using any other potential V ext. Theory 2: The correct ground state density n 0 (r) minimizes the total energy functional. Interacting particles (electrons) Non interacting particles H = T + V e-e + V ext DFT H s = T s + V eff V ext V eff electrons at ground state n 0 (r) non-interacting particles n(r) if E tot =E min n=n 0 (r)
14 Based on the DFT many body problem of fully interacting particles in an external potential V ext is simply replaced by a system of non-interacting particles in a effective potential V eff giving the same ground state charge density n 0 (r). T s is now the kinetic operator of a non-interacting system with N particles which can be easily given by: The effective potential V eff is: T s N 2 2 d = 2 i= 1 2mdr V eff = V e-e + V ext + V xc V xc : The extra term which contains all the energy contribution which were not taking into account in the transition from the interacting system to the non-interacting system. V xc is called exchange-correlation potential
15 The exchange-correlation potential can be expressed as: Vxc [n] = dexc[n] dn where E xc [n] is the exchange-corralation energy. The above DFT is formally exact, but it is impossible to find a exact from for Vxc The most common approach is the Local Density Approximation LDA E xc [n] = ε xc (n)n(r)dr where ε xc (n) is the energy of a homogeneous electron gas and it is known. Therefore the E xc [n] and hence V xc [n] are all known. Various approximations have been introduced in the course of the years to improve LDA. The Generalized Gradient Approximation (GGA) is one of those approximations which is more or less commonly accepted to be an improvement over LDA. In GGA approximation the Vxc depends not only on charge density n(r) but also on the magnitude of the gradient of the charge density n Vxc [n] in GGA approximation [ n, n ] V xc
16 Implementation to total energy calculation Etot = Eel + Eion ion In order to calculate to E el we need to solve the following Schrödinger equation. H s Ψ = E el Ψ ( T + V [ n] + V [ n] + V [ n]) ϕ = Eϕ i = 1, 2,.., N s e e ext XC i i N nr ( ) = ϕi i= 1 2 The effective potential depends on the density, the density depends on Kohn-Sham orbitals (φ i ) and Kohn-Sham orbitals depends on the effective potential!!
17 Ion-ion interaction term Etot = Eel + Eion ion where E ion-ion is just the coulomb interaction between ions z R j E ion 2 Z =,, R R iji j i j 2 R i x y
18 Trial charge density n(r) Set up Hamiltonian H=T s +V e-e +V ext +V xc new ϕ i calculate the orbitals and the total energy E tot from one-particle Shrodinger Equation new ϕ i, E new ϕ ϕ < 10 i i 5 Yes Output new ϕ i, Eel,n(r) No N new n ( r) = ϕ i= 1 i 2
19 Basis set-plane wave In this section we are going to briefly explain how we can solve the Kohn-Sham equation and obtain the wavefunctions and energies. If we multiply both sides of the Kohn-Sham Eq.? by φ* i (r) and take an integral from both sides we gets: 2 2m 2 * d ϕi (r). ϕi(r).dr + 2 dr * ϕ (r) i * ( Ve e[n] + Vext[n] + Vxc[n] ) ϕi(r)dr = εi ϕi (r) ϕi(r) dr One way to solve the Kohn-Sham equation is to expand the wavefunction φ i in a plane wave basis set. Using plane wave as a basis set has some advantages and some disadvantage. The advantage of using the plane wave is that it which help us to simplify the above Kohn-Sham equation. ϕ (r) = i k= 1 C i,k.exp(ik.r) where mathematically the sum is over a infinite number of plane wave but of course in practice we see that it already converges for a large number of plane wave. By substituting this equation into the above Shrodinger equation and using the following mathematical principal: exp( ik r).exp( ik' r ) dr = δkk' We end up with a matrix with N max x N max elements where N max is the number of the plane waves. N max depends very much to the size of your system. i.e. number of atoms in your system and also the elements you use. it can be as big as 1e+5 number of plane waves. In order to get φi and εi from the matrix we need to diagonal it which of course needs a powerful computer or even several computers working as parallel. Reminding: When φ i and ε i are calculated in the next iteration a new charge density should be constructed and again a new matrix should be diagonalized. Usually iterations in needed to get the total energy of the system self consistently.
20 The calculated total energy in this way depends very strongly on the position of the tions. The position of the atoms is given by you, and it is not precise enough. Therefore the total energy calculation will be absolutely wrong Solution Geometry optimization It is possible to calculate the force on each ion from the total energy calculation de F i = dr we can move the ions a little bit along the forces and redo the total energy calculation we repeat the above calculation until the total force on ions becomes almost zero tot i Initial configuration F ion Next ionic iteration F ion Next ionic iteration
21 Trial charge density n(r) Set up Hamiltonian H=T s +V e-e +V ext +V xc new ϕ i calculate the orbitals and the total energy E tot from one-particle Shrodinger Equation new ϕ i, E new ϕ ϕ < 10 i i 5 Yes Caculate the force on ions F ion N new n ( r) = ϕ i= 1 No i 2 Yes End F ion < 10-3 No Move the ions along the forces
22 References: W. E. Pickett, Pseudo potential methods in condensed matter application, Computer Phys. Report, 9:115, 1989 E. Kohn and L. J. Sham., Self-consistent equations including exchange and correlation effects, Phys. Rev., 140: A1133, 1965 R. O. Jones and O. Gunnarsson. The density functional formalism, its application and prospects:, Rev. Mod., Phys., 61:689, 1989 Ata Roudgar, Local reactivity of bimetallic overlayer and cluster systems, PhD thesis,
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