====== Exercises ======

The following exercises are part of the the course [[http://www.vvz.ethz.ch/Vorlesungsverzeichnis/lerneinheitPre.do?lerneinheitId=113150&semkez=2017S | Molecular and Materials Modelling]] held at ETH Zürich during the spring semester 2017. 

===== Lecture 1 =====
  - [[lennard_jones_cluster| 3D 38 Atom Lennard-Jones cluster - optimization ]]
  - [[lennard_jones_cluster_neb| 3D 38 Atom Lennard-Jones cluster - transition paths ]]


===== Lecture 2 =====
  - [[pythonmd| 3D 38 Atom Lennard-Jones Molecular dynamics ]]


===== Lecture 3 =====
  - [[MC and KMC| Monte Carlo  simulations for the diffusion of "sumanene" molecules on the Ag(111) surface ]]
  - [[MC and KMC 2| Kinetic Monte Carlo simulations for the diffusion of Hexaiodobenzene molecules on noble metal substrates ]]

===== Lecture 4 =====
  - [[surface_Cu|surface energy of Cu(111), Cu(110), Cu(100) and Wulff plot]]
  - [[surface_Au|surface energy of Au(110): perfect and reconstructed and other faces]]

===== Lecture 5 =====
  - [[T_melting_2017|Determination of melting temperature of a copper system from molecular dynamics]]

===== Lecture 7 =====
  - [[replica_2017|Sampling the disordering of a cluster using replica exchange]]

===== Lecture 8 =====
  - [[Reaction_energy_2017|Dehydration of ethanol]]

===== Lecture 9 =====
  - [[c2h2_PdGa|Adsorption energy of acetylene on PdGa]]

===== Lecture 10 =====
  - [[bands_1|Crystallographic point groups, free electron model]]

===== Lecture 11 =====
  - [[bands_2|Bandstructure calculations]]

===== Lecture 12 =====
  - [[STM|Scanning Tunnelling Microscopy]]

===== Lecture 13 =====
  - [[QMMM|Validation of a QM/MM model for KCl]]

<!--  ===== Lecture 1 (tentative) =====
  - [[single_point_calculation|Single Point Energy Calculation]]
  - [[geometry_optimization|Geometry Optimization]]
  - [[nudged_elastic_band|Nudged Elastic Band]]

===== Lecture 2 (tentative) =====
  - [[c2h2_bond_energy|Bond Strength in a molecule]]
  - [[alanine_dipeptide|Alanine dipeptide: Ramachandran plot]]
  - [[alanine_modify|Alanine dipeptide: Modifying the parameters of the force field]]



===== Lecture 4 (tentative) =====
  - [[MD_ala|Molecular dynamics of alanine dipeptide]]
  - [[MD_slab|Molecular dynamics of Au 100 slab]]

===== Lecture 5 (tentative) =====
  - [[T_melting|Determination of melting temperature of a Lennard-Jones system from molecular dynamics]]

===== Lecture 5 (tentative) =====
  - [[T_melting|Determination of melting temperature of a Lennard-Jones system from molecular dynamics]]

===== Lecture 6 (tentative) ===
  - [[exercises:2015_ethz_mmm:monte_carlo_ice|Properties of Ice from Monte Carlo Simulations]]
  - [[nacl_md | Observer NaCl dissociation in water ]]
  - [[nacl_free_energy | Free Energy Profile of NaCl Dissociation ]]

===== Lecture 7 (tentative) =====
  - [[basis_sets|Basis Sets]]
  - [[reaction_energy|Reaction Energy]]
  - [[mo_ethene|Molecular orbitals of Ethene]]

===== Lecture 8 (tentative) =====
  - [[dye_tio|Dye anchoring to TiO$_2$]]

===== Lecture 9 (tentative)  =====
  - [[hfx_h2ion|Hartree-Fock exchange for the dihydrogen cation]]
  - [[tio2_gap|TiO$_2$ Band Gap as a function of %hfx]]
  - [[benzene_dimer|Binding Energy of the Benzene Dimer]]

===== Lecture 10 (tentative)  =====
  - [[ls_scf| Linear scaling SCF]]
  - [[wannier | Maximally Localized Wannier Functions]]

===== Lecture 11 (tentative) =====
  - [[infra_red | Infrared spectroscopy with MD ]]
  - [[simple_stm | Simple STM images ]]

===== Lecture 12 (tentative) =====
  - [[bs | band structure and DOS of graphene ]] ...-->

====== Euler Cheat Sheet ======
For more information have a look at the [[http://www.clusterwiki.ethz.ch/brutus/Getting_started_with_Euler | cluster-wiki]].

<code>
you@eulerX ~$ module load new cp2k vmd
you@eulerX ~$ bsub -n 1 mpirun cp2k.popt -i energy.inp -o energy.out
you@eulerX ~$ bjobs
JOBID      USER    STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
2955028    you     PEND  beta.4h    euler02                 *nergy.out Feb 12 14:21
you@eulerX ~$ bkill 2955028
Job <2955028> is being terminated
</code>

<note tip>Connecting to Euler from a Windows machine: install
  * putty [[http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe]]
  * xming [[http://sourceforge.net/projects/xming/files/latest/download]]
  * winscp [[http://winscp.net/download/winscp551setup.exe]]
</note>