# CP2K Open Source Molecular Dynamics

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exercises:2017_ethz_mmm:qmmm

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 exercises:2017_ethz_mmm:qmmm [2017/06/02 02:26]dpasserone exercises:2017_ethz_mmm:qmmm [2020/08/21 10:15] Line 1: Line 1: - ====== Validation of a KCl QMMM model ====== - ==(exercise by Matthew Watkins, University college, London) == - 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: [[doi>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 and the energy of the molecule alone and surface alone **in the same geometry as the surface-molecule system minimum structure**. This will allow to show the binding pattern of the electronic density. - * In the second part, you will optimize the surface and the molecule separately; this will allow to compute the total adsorption energy. - - - - {{ :exercises:2017_ethz_mmm:master.img-002.jpg?nolink&600 |}} - - - ===== 1. Task: Familiarize yourself  ===== - The coordinates of the optimized configuration are provided to you as ''S_M.opt.xyz'' (S stands for "Substrate", M for "Molecule", opt for "optimized"). Visualize the geometry with VMD and familiarize yourself with the system. - - ===== 2. Task: Bond induced density differences ===== - Compute the density difference induced by the adsorption bonding. - For this you will have to run three separate energy calculations, using the *.ene.inp files. - - combined system  (file ''S_M.opt.xyz'') - - lone acetylene (file ''M.S_M.xyz'') - - lone slab (file ''S.S_M.xyz'') - - In order to output the electronic densities as cube files, your input file has to contain the following snipped: - - &DFT - &PRINT - &E_DENSITY_CUBE - &END E_DENSITY_CUBE - &END - &END DFT - - - - The calculations involving the slab should be run on at least 16 cores with ''qsub run -v INP=prefix''. Check the  ''run'' file for the number of nodes. - - - To process the cube files we are going to use the [[tools:cubecruncher | cubecruncher]] tool. It is part of CP2K and is in your exercise directory. - - you@eulerX ~$./cubecruncher.x -i S_M-ELECTRON_DENSITY-1_0.cube -subtract S-ELECTRON_DENSITY-1_0.cube -o tmp.cube - you@eulerX ~$ ./cubecruncher.x -i tmp.cube -subtract M-ELECTRON_DENSITY-1_0.cube -o Delta_ads.cube - - - - The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool: - - you@eulerX ~\$ ./cubecruncher.x -center geo -i Delta_ads.cube -o Delta_ads-centered.cube - - - You can visualize the resulting file ''delta_ads-centered.cube'' with VMD. This has been covered in a [[reaction_energy_2017| previous exercise]]. - - What you get should look similar to this: - {{ dye_tio_bonding_density.png?300 |}} - - ===== 3. Task: Bonding energies  ===== - Compute the binding energy: - - $E_\text{binding}=\sum E_\text{products} - \sum E_\text{reactants}$ - - For this you will need the energy values of three systems: - - lone acetylene molecule (run geometry optimization, use energy of last step) - - lone  slab  (you can use the already geometry optimized coordinates from ''S.opt.xyz'' at the end of the exercise) - - combined system adsorbed (can be reused from previous task) - - - You can not reuse the energy values for the lone sub-systems from the previous task. Since the unbound subsystems might relax into a different geometry, they have to be geometry optimized first. - - - - ===== Questions ===== - * Sketch briefly the geometry of the molecule **when adsorbed** and **in the gas phase**. - * Report the system energy for the bonded system, lone slab, and lone molecule. - * Can you estimate the contribution due to the geometry relaxation? - * Briefly report the bond induced density difference on the system. - - ===== Required Files ===== - When you are dealing with big systems and multiple atomic species, the input can be simplified by splitting it into multiple files. We are going to use separate files for the coordinates, the basis-sets, and the pseudo-potentials. All these files should reside in the same directory as the main input file. - - - The provided files are all in the directory ''/home/psd/Exercise_9''. Change the name of the xyz file accordingly in the input files. - - - - - &FORCE_EVAL - METHOD Quickstep - &DFT - &PRINT - &E_DENSITY_CUBE - &END E_DENSITY_CUBE - &END - BASIS_SET_FILE_NAME ./BR - POTENTIAL_FILE_NAME ./GR - &QS - EPS_DEFAULT 1.0E-10 - METHOD GPW - EXTRAPOLATION ASPC - EXTRAPOLATION_ORDER 3 - &END QS - &MGRID - CUTOFF 400 - NGRIDS 5 - &END - &SCF - MAX_SCF 20 - SCF_GUESS RESTART - EPS_SCF 1.0E-5 - &OT - PRECONDITIONER  FULL_SINGLE_INVERSE - MINIMIZER  CG - &END - &OUTER_SCF - MAX_SCF 50 - EPS_SCF 1.0E-5 - &END - &PRINT - &RESTART - &EACH - GEO_OPT 2 - &END - ADD_LAST NUMERIC - FILENAME RESTART - &END - &RESTART_HISTORY OFF - &END - &END - &END SCF - &XC - &XC_FUNCTIONAL PBE - &END XC_FUNCTIONAL - &END XC - &END DFT - &SUBSYS - &CELL - A [angstrom] 14.08557 0 0 - B [angstrom] 0 12.1985 0 - C [angstrom] 0.000000      0.000000    15.0 - &END CELL - &TOPOLOGY - COORD_FILE_NAME ./S_M.opt.xyz - COORDINATE xyz - &END - &KIND Pd - BASIS_SET DZVP-MOLOPT-SR-GTH-q18 - POTENTIAL GTH-PBE-q18 - &END KIND - &KIND Ga - BASIS_SET DZVP-MOLOPT-SR-GTH-q13 - POTENTIAL GTH-PBE-q13 - &END KIND - &KIND C - BASIS_SET TZV2P-MOLOPT-GTH - POTENTIAL GTH-PBE-q4 - &END KIND - &KIND H - BASIS_SET TZV2P-MOLOPT-GTH - POTENTIAL GTH-PBE-q1 - &END KIND - &END SUBSYS - &END FORCE_EVAL - &GLOBAL - PRINT_LEVEL LOW - PROJECT S_M - RUN_TYPE ENERGY - &END GLOBAL - -