https://www.cp2k.org/ 2026-05-02T09:03:59+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:2014_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 angle… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_ethz_mmm:alanine_modify?rev=1598004913&do=diff Modification of the dihedral parameters commented [exercise_2.3.zip] * For the non-restrained optimizations to get A and B configurations, inp.a and inp.b * For the restrained optimization along a chain, line_ij and inp_ff.templ, respectively the script to generate the text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_ethz_mmm:basis_sets?rev=1598004913&do=diff Basis Sets In this exericse you will compare different basis sets and use them for computing the binding energy of an H2 molecule. The cp2k basis set format is described in detail here. Part I: Different basis sets for H and H2 1.Step Run a calculation with the following input file. Comment lines are marked with !\[ \sum E_\text{products} - \sum E_\text{rectants} = E(H_2) - 2 \cdot E(H) \] text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_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:2014_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, one needs to run a self-consistent field ( text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_ethz_mmm:c2h2_bond_energy?rev=1598004913&do=diff C2H2 and C2H4 bond energy REMEMBER TO LOAD THE MODULE FOR THE CP2K TRUNK VERSION: module load cp2k/trunk.2.5.13191 and to submit the job chain with bsub < c2h2.a.chain Create a new directory for this exercise: you@brutusX ~$ mkdir mmm_exercise_2.1 you@brutusX ~$ cd mmm_exercise_2.1 text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_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:2014_ethz_mmm:geometry_optimization?rev=1598004913&do=diff Geometry Optimization In this exercise you will run a geometry optimization calculation, for two Ar atoms placed at distance $r=2.00Å$. 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:2014_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:2014_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 2014. Lecture 1 * Single Point Energy Calculation * Geometry Optimization * Nudged Elastic Band Lecture 2 * Bond Strength in a molecule * Alanine dipeptide: Ramachandran plot * Alanine dipeptide: Modifying the parameters of the force field Lecture 3 * surface energy of Cu(111), Cu(110), Cu(100) and Wulff plot * surface energy of Au(… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_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:2014_ethz_mmm:ls_scf?rev=1598004913&do=diff Linear Scaling Self Consistent Field Methods In this exercise we will compare linear scaling 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:2014_ethz_mmm:md_ala?rev=1598004913&do=diff Molecular Dynamics simulation of a small molecule this paper In this exercise, we will extensively use vmd for visualizing the results of the cp2k simulations. As always, give the commands: module load cp2k/trunk.2.5.13191 module load vmd mkdir EX_4.1 cd EX_4.1 text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_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 text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_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. text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_ethz_mmm:monte_carlo_ice?rev=1598004913&do=diff Properties of Ice from Monte Carlo Simulations * Add the line PRINT_COORDS .FALSE. in the TMC section. It disables the output of the coordinate trajectory and thus avoids the files-size problem. * Add the line RND_DETERMINISTIC 42 to the TMC section to choose a random number seed. You have to replace \begin{equation} \epsilon = 1 + \left(\frac{4 \pi}{3 \epsilon_0 V k_B T } \right ) \operatorname{Var}(M) \ , \end{equation}$M$$\operatorname{Var}(M)$\begin{equation} \operatorname{Var}(M) = (\… text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_ethz_mmm:nacl_free_energy?rev=1598004913&do=diff Free Energy Profile of NaCl Dissociation * You'll have to run many similar simulations. Try to automatize as much as possible. * The first two task can be run directly on the login node, i.e. without using bsub. * The third task should be run on 4 cores with $F(x)$$x$\begin{equation} \Delta A = -\int_a^b F(x)\, dx \end{equation}$d_{min}$\begin{equation} A(d) = -\int_{d_{min}}^d F(x)\, dx \end{equation} text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_ethz_mmm:nacl_md?rev=1598004913&do=diff Observer NaCl dissociation Perform a MD simulation of NaCl in water by running the input-file NaCl_in_water.inp. Use VMD to calculate the Na-Cl distance for each frame of the trajectory. This can be done in the following way: * Load the trajectory with VMD$g(r)$$g(r)$ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_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, by using the NEB method. The NEB method requires at least the starting and the ending configuration between which the path is to be computed. In addition is good to add a guess of the intermediate configuration. This is useful in particular when two or more reaction paths are possible and you want to compute the activation energy of a determined path. By adding the … text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_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, O2, is a triplet diradical, a property which can explain why liquid oxygen is paramagnetic and attracted to the poles of a magnet. text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_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:2014_ethz_mmm:single_point_calculation?rev=1598004913&do=diff Computation of the Lennard Jones curve for two Ar atoms In this exercise you will compute the Lennard-Jones energy curve for a system of two Ar atoms. In Part I you find the instructions for computing the energy of two Ar atoms at a distance $r=3.00 Å$. In Part II you find the instructions for getting the energy profile as a function of $r$$ r=3.00 Å$$ k_\text{b} = 3.1668154 \cdot 10^{-6} \frac{E_\text{H}}{\text{K}} $ text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_ethz_mmm:surface_au?rev=1598004913&do=diff Calculation of surface energies of Au Take the above table as reference for the orders of magnitude of surface energies. You can download the commented inputs by downloading from the wiki: [exercise_3.2.zip]) the necessary files for computing the surface energies of all 3 high symmetry faces of gold. In principle all reconstructed phases should be with a lower surface energy, but this text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_ethz_mmm:surface_cu?rev=1598004913&do=diff Surface energies of Copper high-symmetry surfaces In this exercise we will compute the surface energies of Cu using the EAM potential. As a reference, we report the table from the Gross book: [http://example.com|External Link] * Copy the files from from the wiki: [exercise_3.1.zip] (all inputs are commented text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_ethz_mmm:t_melting?rev=1598004913&do=diff Determination of the melting temperature of copper 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 copper. As usual, connect to brutus and enter the following commands: text/html 2020-08-21T10:15:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://www.cp2k.org/exercises:2014_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:2014_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:2014_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.