https://www.cp2k.org/ 2026-04-29T09:42:59+00:00 https://www.cp2k.org/ https://www.cp2k.org/_media/wiki:logo.png text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:alanine_dipeptide?rev=1598004913&do=diff Ramachandran plot for Alanine Dipeptide Alanine dipeptide is often studied in theoretical work because it is among the simplest systems to exhibit some of the important features common to biomolecules. It has more than one long-lived conformational state. The relevant angles are the dihedral angles of the backbone, commonly called Φ and Ψ (see figure). In the following scheme, light blue atoms are carbons, white ones are hydrogens, red are oxygens, and blue are nitrogens. So the torsional ang… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:alanine_modify?rev=1598004913&do=diff Modification of the dihedral parameters Download the 2.3 exercise into your $HOME folder and unzip it. you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_2.3.zip you@eulerX ~$ unzip exercises:2015_ethz_mmm:exercise_2.3.zip text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:bands_1?rev=1598004913&do=diff Crystallographic point groups, free electron model Starting from 2006 Hafnium silicates replaced SiON as gate oxide in MOSFETS. The high dielectric constant of HfO2 and the ability of HfO2 to form silicates played a key role in the industrial transition. text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:bands_2?rev=1598004913&do=diff Calculation of the bandstructure of Si by means of DFT with different settings ssh -X EMPA-USER@jump1.empa.ch ssh -X hypatia module load python/2.7.12 go to your scratch directory: cd /mnt/scratch/your_username cp /home/cpi/exercise_11.tar ./ tar -xvf exercise_11.tar cd exercise_11 text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:basis_sets?rev=1598004913&do=diff Basis Sets In this exercise you will compare different basis sets and use them for computing the binding energy of an H$_2$ molecule. The cp2k basis set format is described in detail here. Part I: Different basis sets for H and H$_2$ 1.Step Run a calculation with the following input file. Comment lines are marked with !$E_h$$_2$$_2$\[ \sum E_\text{products} - \sum E_\text{reactants} = E(H_2) - 2 \cdot E(H) \]$E_h$$_2$$E_h$$_2$$Å$$_2$$E_h$$_2$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:benzene_dimer?rev=1598004913&do=diff Binding Energy of the Benzene Dimer The goal of this exercise is to compute the interaction energy for a π-stacked benzene dimer, with three different methods: * PBE with no dispersion interaction * PBE with parametrized dispersion interaction (\[E_\text{interaction}= E_\text{dimer}- 2 E_\text{benzene}\]$\pi$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:bs?rev=1598004913&do=diff 1. Running an SCF job and calculating the band structure and DOS of graphene Here we give some notes on how to use QUANTUM ESPRESSO to perform one of the standard tasks e.g. band structure calculation. In this exercise, we calculate the band structure of graphene along the high-symmetry lines (Γ-M-K-Γ) of the Brillouin zone (BZ). First, we do a self-consistent field (scf) calculation and then 'bands' calculation with a set of k-points (along high-symmetry lines). Please have a look at the end o… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:c2h2_bond_energy?rev=1598004913&do=diff C2H2 and C2H4 bond energy REMEMBER: this is the command to load the module for the cp2k program: you@eulerX ~$ module load cp2k and to submit the job: you@eulerX ~$ bsub < jobname Download the 2.1 exercise into your $HOME folder and unzip it. text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:c2h2_pdga?rev=1598004913&do=diff Adsorption of C2H2 on PdGa(111) In this exercise you will compute the adsorption energy of acetylene on a intermetallic catalyst. This process is important during the production of polyethylene, and the system is described in this paper: 10.1021%2Fja505936b. * In the first part of the exercise you will consider the optimized configuration (already in the directory) and study the pure electronic adsorption energy, namely the difference between the total energy of the surface-molecule system … text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:dye_tio?rev=1598004913&do=diff Dye anchoring to TiO$_2$ In this exercise you will compare two possible binding modes of acetic acid to anatase TiO$_2$. Acetic acid contains the carboxylic group. It is commonly used in Dye-Sensitized Solar Cells as an anchoring moiety to bind light harvesting dyes to semi-conducting substrates. We will therefore use acetic acid as a model of the more complex dye molecules, as done in this paper: $_2$$_2$\[ E_\text{binding}=\sum E_\text{products} - \sum E_\text{reactants} \]$_2$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:geometry_optimization?rev=1598004913&do=diff Geometry Optimization In this exercise you will run a geometry optimization calculation, for two Kr atoms placed at distance $r=3.00Å$. 1. Step Save the following commented CP2K input file to a file named geopt.inp &GLOBAL RUN_TYPE GEO_OPT PROJECT_NAME geopt ! the calculation will produce a few output files, that will be labeled with this name &END GLOBAL &FORCE_EVAL METHOD FIST &MM &FORCEFIELD &SPLINE EMAX_SPLINE 10000 ! numeric parameter to ensu… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:hfx_h2ion?rev=1598004913&do=diff Hartree-Fock exchange for the dihydrogen cation The goal of this exercise is to calculate the dissociate enery profile of the dihydrogen cation $H_2^+$. The curve should be record for three different fractions of Hartree-Fock exchange: * 0% HF exchange, 100% PBE exchange$H^+_2$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:index?rev=1598004913&do=diff Exercises The following exercises are part of the the course Molecular and Materials Modelling held at ETH Zürich during the spring semester 2017. Lecture 1 * 3D 38 Atom Lennard-Jones cluster - optimization * 3D 38 Atom Lennard-Jones cluster - transition paths Lecture 2 * 3D 38 Atom Lennard-Jones Molecular dynamics Lecture 3 * Monte Carlo simulations for the diffusion of "sumanene" molecules on the Ag(111) surface * Kinetic Monte Carlo simulations for the diffusion o… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:infra_red?rev=1598004913&do=diff Infrared spectroscopy with molecular dynamics In this exercise, we will compare the vibrational spectrum of two molecules (methanol and benzene) computed with a static method (diagonalization of the dynamical matrix) and with molecular dynamics. The spectra for methanol are available in this paper text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:lennard_jones_cluster_neb?rev=1598004913&do=diff 38 atom Lennard-Jones cluster: nudged elastic band In this second exercise we will find a transition path between a icosahedral-like minimum and a fcc-like minimum. Download the 1.1 exercise into your $HOME folder and unzip it. you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2017_ethz_mmm:exercise_1.2.zip you@eulerX ~$ unzip exercises:2017_ethz_mmm:exercise_1.2.zip text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:lennard_jones_cluster?rev=1598004913&do=diff 38 atom Lennard-Jones cluster (picture by Luke Abraham) REMEMBER: this is the command to load the module for the cp2k program: you@eulerX ~$ module load cp2k and to submit the job (note: since all the examples of this week are ultrafast, we will run them interactively, and NOT on a compute node. This is not the normal procedure for the next lectures). text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:ls_scf?rev=1598004913&do=diff Linear Scaling Self Consistent Field Methods In this exercise we will compare linear scaling SCF 10.1021/ct200897x with normal SCF methods. We will run simulations on a 2D polymer system containing up to 2400 atoms. The 2D polymer system is described in more detail in this recent publication text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:mc_and_kmc_2?rev=1598004913&do=diff Kinetic Monte Carlo simulations for the diffusion of molecules on a substrate The molecule shown in the image (hexaiodo-substituted macrocycle cyclohexa-m-phenylene (CHP) ), when deposited on a noble metal substrate such as Cu(111) , Ag(111) or Au(111), at room temperature looses the I atoms and starts diffusing. text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:mc_and_kmc?rev=1598004913&do=diff Monte Carlo simulations for the estimation of molecule pair interatcion In this exercise you will perform a MC simulation for different coverages of “sumanene” mlecules adsorbed on a Ag(111) substrate hypothesizing different posisble values for the nearest neighbor energy in the molecule-molecule interaction text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:md_ala?rev=1598004913&do=diff Molecular Dynamics simulation of a small molecule REMEMBER: this is the command to load the module for the cp2k program: you@eulerX ~$ module load new cp2k and to submit the job: you@eulerX ~$ bsub < jobname Download the 4.1 exercise into your $HOME folder and unzip it: text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:md_slab?rev=1598004913&do=diff Hot gold This exercise deals with heating a gold slab, namely the (100) reconstructed that you already simulated last time. The goal is to plot a density profile in the direction orthogonal to the slab, and to compute (using vmd) the radial distribution function g( r ) at various temperatures. text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:mo_ethene?rev=1598004913&do=diff Molecular orbitals of Ethene In this exercise, you will perform an electronic structure calculation to obtain the ethene molecular orbitals (MOs). If performed correctly, your calculations will produce a list of occupied and non occupied MOs and a series of *.cube files, that allow the visualization of the oribital with VMD. $\pi$$\pi^*$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:monte_carlo_ice?rev=1598004913&do=diff Properties of Ice from Monte Carlo Simulations In this exercise we will use Monte Carlo sampling to calculate the dielectric constant of the disordered hexagonal phase (Ih) of water ice. In order to speed up the calculation, we are going to use the SPC/E water model. The model is a non polarizable forcefield model, with parameters for:$ U_{bond}= k_{bond}⋅(r-r_{eq})^2$$ U_{angle}= k_{angle}⋅(θ-θ_{eq})^2$\begin{equation} \epsilon = 1 + \left(\frac{4 \pi}{3 \epsilon_0 V k_B T } \right ) \oper… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:nacl_free_energy?rev=1598004913&do=diff Free Energy Profile of NaCl Dissociation In this exercise, you will run different simulations to compute the NaCl dissociation curve in both gas and solution environments. * You'll have to run many similar simulations. Try to automatize as much as possible (we can help you).$F(x)$$x$\begin{equation} \Delta A = -\int_a^b F(x)\, dx \end{equation}$d_{min}$\begin{equation} A(d) = -\int_{d_{min}}^d F(x)\, dx \end{equation} text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:nacl_md?rev=1598004913&do=diff Observe NaCl dissociation This short task will help you to familiarize with Molecular Dynamics simulations. The simulation is based on forcefields, with parameters of the same type of those we used for ice (See: Properties of Ice from Monte Carlo Simulations). * You can perform the simulation of NaCl in water by running the input-file: $g(r)$$g(r)$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:nudged_elastic_band?rev=1598004913&do=diff Nudged Elastic Band In this exercise you will compute the energy profile for a simple reaction in a planar cluster of 7 Ar atoms with the NEB method. The NEB method requires at least the start- and end-configuration between which the reaction path should be computed. In addition it is advantageous to add a guess for an intermediate configuration. This is useful in particular when multiple reaction paths are possible and one is interested in a specific one. By adding a suitable intermediate con… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:pythonmd?rev=1598004913&do=diff 38 atom Lennard-Jones cluster: molecular dynamics with python In this exercise you will perform molecular dynamics with a python program that you may inspect and modify directly. Then, you will perform the same kind of dynamics using cp2k and compare the performance. text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:qmmm?rev=1598004913&do=diff Validation of a KCl QMMM model (exercise by Matthew Watkins, University college, London) In this exercise you will validate the mixed quamtum/classical model for a KCl slab. The present exercise is referring to the following paper: 10.1002/jcc.23904. * You will optimize the geometry of a KCL slab with the same arrangement as the one depicted below text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:reaction_energy_2017?rev=1598004913&do=diff Dehydration of ethanol We will investigate today a very important chemical reaction, the production of ethene (ethylene) from ethanol. Ethanol is heated with an excess of concentrated sulphuric acid at a temperature of 170°C. The gases produced are passed through sodium hydroxide solution to remove the carbon dioxide and sulphur dioxide produced from side reactions. Another way to favor this reaction is in presence of a catalyst surface, which makes the reaction exothermic even at room temperat… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:reaction_energy?rev=1598004913&do=diff Reaction Energy In this exercise, you will calculate the reaction energy for the methane combustion reaction: \[ CH_4 + 2O_2 \rightarrow CO_2 + 2H_2O \] Reaction energy: \[ \sum E_\text{products} - \sum E_\text{rectants} = \left (2\cdot E_{H_2O} + E_{CO_2} \right) - \left(E_{CH_4} + 2\cdot E_{O_2}\right) \] Ground state oxygen, O$_2$, is a triplet diradical, a property which can explain why liquid oxygen is paramagnetic and attracted to the poles of a magnet. $_2$$_4$$_4$$_2$$_2$$_2$$_4$$_2… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:replica_2017?rev=1598004913&do=diff Replica exchange of the disordering of a cluster HYPATIA HYPATIA User-specific information (note: TMP-PASSW1 ist the password for jump1, that is the FIRST one, but is listed as second): EMPA-USER:TMP-PASSW2:TMP-PASSW1 [you@hypatia ~]$ mmm-init [you@hypatia ~]$ cd /mnt/scratch/YOURUSER/ [you@hypatia ~]$ cp -r /home/psd/exercise_7 . [you@hypatia ~]$ cd exercise_7 text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:simple_stm?rev=1598004913&do=diff Simple STM images In this exercise we will consider different termination of two polyantryl molecules that are an intermediate step for the formation of a long armchair nanoribbon. 10.1021/ja311099k. We will show how a simple change in the termination (1 vs. 2 Hydrogens) changes the state structure completely. text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:single_point_calculation?rev=1598004913&do=diff Computation of the Lennard Jones curve In this exercise you will compute the Lennard-Jones energy curve for a system of two Krypton (Kr) atoms. In Part I you find the instructions for computing the energy of two Kr atoms at a distance $r=4.00 Å$. In Part II you find the instructions for getting the energy profile as a function of $r$$ r=4.00 Å$$ k_\text{b} = 3.1668154 \cdot 10^{-6} \frac{E_\text{H}}{\text{K}} $$$ \sigma_{ij}= \sqrt{\sigma_i\sigma_j}$$$$ \epsilon_{ij}= \sqrt{\epsilon_i\epsilon… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:stm?rev=1598004913&do=diff Simulation of STM and AFM images for a graphene nanoribbons adsorbed on a metallic substrate ssh -X EMPA-USER@jump1.empa.ch ssh -X hypatia module load python/2.7.12 go to your scratch directory: cd /mnt/scratch/your_username cp /home/cpi/exercise_12.tar ./ tar -xvf exercise_12.tar cd exercise_12 text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:surface_au?rev=1598004913&do=diff Calculation of surface energies of Au In this exercise, we will build three small slabs based on the following figures; the cell is an orthorombic cell with repetition along z. Figure out what is (in nearest neighbor units) the length of the three vectors Lx, Ly, Lz for the three high-symmetry surfaces. text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:surface_cu?rev=1598004913&do=diff Surface energies of Copper high-symmetry surfaces REMEMBER: this is the command to load the module for the cp2k program: you@eulerX ~$ module load new cp2k and to submit the job: you@eulerX ~$ bsub < jobname In this exercise we will compute the surface energies of Cu using the text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:t_melting_2017?rev=1598004913&do=diff Determination of the melting temperature of copper HYPATIA HYPATIA [you@hypatia ~]$ mmm-init [you@hypatia ~]$ cd exercise_5.1 REMEMBER: this is the command to run interactively cp2k: [you@hypatia ~]$ cp2k.popt -i file.inp -o file.out text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:t_melting?rev=1598004913&do=diff Determination of the melting temperature of a LJ system REMEMBER: this is the command to load the module for the cp2k program: you@eulerX ~$ module load new cp2k and to submit the job: you@eulerX ~$ bsub < jobname In this exercise, we will use a slab geometry (without vacuum region, so without a surface) with full periodic boundary conditions to study the melting behavior of nobel gases. text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:tio2_gap?rev=1598004913&do=diff TiO$_2$ Band Gap as a function of %hfx One problem with standard DFT is that correlation effects can lead to errors in evaluating certain system properties, such as the band gap of semiconductors. More information can be found here: 10.1126/science.1158722 A common approach to correct for electronic self-interaction is the $_2$$_2$$_{gap}$$_{gap}$$\mathcal{O}(N^4)$$E_\text{gap}$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:uv?rev=1598004913&do=diff Absorption spectroscopy with time-dependent density functional theory In this exercise we will compute the UV absorption spectrum of a water molecule, using the quantum chemistry software NWCHEM. The present exercise follows what is already available in the online manual of this open source software: text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2017_ethz_mmm:wannier?rev=1598004913&do=diff Maximally Localized Wannier Functions In this exercise we will explore alternative ways to divide the electronic densities into orbitals. By requiring that orbitals should be as localized as possible one obtains a representation, which closely resembles the typical text-book pictures of molecular orbitals.