Atomic Simulation Environment Souheil Saadi Thomas Olsen Jens Jørgen Mortensen Ask Hjorth Larsen.

Presentation on theme: "Atomic Simulation Environment Souheil Saadi Thomas Olsen Jens Jørgen Mortensen Ask Hjorth Larsen."— Presentation transcript:

1 Atomic Simulation Environment Souheil Saadi saadi@fysik.dtu.dk Thomas Olsen tolsen@fysik.dtu.dk Jens Jørgen Mortensen jensj@fysik.dtu.dk Ask Hjorth Larsen askhl@fysik.dtu.dk

2 February 20, 200910302 Atomic Simulation Environment Toolbox for : ● Building atomic structures ● Molecular Dynamics ● Structure optimization ● Analysis ● Interface to several calculator codes: GPAW, ASAP, Dacapo...

3 February 20, 200910302 The Python programming language http://www.python.org/

4 February 20, 200910302 Energy Calculations

5 February 20, 200910302 ASE Objects

6 February 20, 200910302 Demonstration Atomization energy of a H 2 molecule [askhl@neumann ~]$ python atomize.py atomic energy: -0.74 eV molecular energy: -6.35 eV atomization energy: -4.86 eV

7 February 20, 200910302 Script

8 Simple example: CO on Cu(100) Part II

9 February 20, 200910302 Example: CO/Cu(100) ● Calculate adsorption energies for the p(2x2) structure using the PBE functional. ● This will be done by means of a structure relaxation. – Calculate forces, move atoms in general direction of forces, repeat until geometry converges. ● Experimental value: 0.53 eV - 0.57 eV

10 February 20, 200910302 How much vacuum?

11 February 20, 200910302 How thick should the slab be?

12 February 20, 200910302 Surface relaxations

13 February 20, 200910302 Number of k-points ● The 2D surface Brillouin zone is sampled uniformly with NxN points. ● GPAW language: kpts=(N, N, 1)

14 Useful Software and Websites Part III

15 February 20, 200910302 https://wiki.fysik.dtu.dk ● Exercises can be found on GPAW-> Exercises

16 February 20, 200910302 Software ● Python – The language that ASE uses http://www.python.orghttp://www.python.org and ● Scientific Python – Addon with nice tools http://www.scipy.org ● Jmol – Java based molecular viewer http://jmol.sourceforge.net/download/ ● VMD – Multiplatform Visualization tool http://www.ks.uiuc.edu/Research/vmd/

17 February 20, 200910302 Software for remote access ● You need a SHELL and X11 ● Putty: http://www.chiark.greenend.org.uk/~sgtatham/putty/http://www.chiark.greenend.org.uk/~sgtatham/putty/ ● Xming: http://sourceforge.net/projects/xming ● OSX and GNU/Linux run X11 and terminals natively ● Use your Campusnet login to connect to bohr.gbar.dtu.dk Example: ssh -X s021864@bohr.gbar.dtu.dk