# Open SourceMolecular Dynamics

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exercises:2018_uzh_cmest:faq

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 exercises:2018_uzh_cmest:faq [2018/09/17 12:52] exercises:2018_uzh_cmest:faq [2018/09/17 12:52] (current) Line 1: Line 1: + ===== Which basis sets and/or pseudopotentials should I use? ===== + When in doubt, always use the ''​DZVP-MOLOPT-GTH''​ basis set and the ''​GTH-PBE''​ pseudopotential. + + In some cases (for example for tin) there is only a short-range basis set available, called ''​DZVP-MOLOPT-SR-GTH''​. + + You can find all available MOLOPT basis sets in ''​BASIS_MOLOPT'',​ which is located in the folder ''​$CP2K_DATA_DIR''​ (after loading the CP2K module). + + ===== How do I run CP2K in parallel? ===== + + The command ''​cp2k.sopt''​ is the single-process variant of CP2K. + + To run CP2K in parallel, you have to use a different executable named ''​cp2k.popt''​ and prefix that with ''​mpirun -n 8''​ to run it on 8 CPUs in parallel. So, a complete command line to run CP2K on 8 CPUs would then be: + + <​code>​ +$ mpirun -n 8 cp2k.popt -i yourinput.inp -o youroutput.out + ​ + + + ===== How do I obtain a charge density difference? ===== + + In [[exercises:​2016_uzh_cmest:​basic_electronic_structure|Exercise 2]] a series of ''​*.cube''​ files was already produced for MOs. + To obtain the electronic charge density in a ''​*.cube'',​ file the following snippet of input file can be used (see also the [[https://​manual.cp2k.org/​trunk/​CP2K_INPUT/​FORCE_EVAL/​DFT/​PRINT/​E_DENSITY_CUBE.html|reference manual]]): + <​code>​ + &​FORCE_EVAL + &DFT + &PRINT + &​E_DENSITY_CUBE + &END E_DENSITY_CUBE + ... + &END PRINT + ... ... + &END DFT + &END FORCE_EVAL + ​ + + The [[tools:​cubecruncher|cubecruncher]] tool can be used to obtain charge density differences. A precompiled executable is available on the server ''​tcopt3'',​ its path being ''/​users/​scaravat/​bin/​cubecruncher.x''​. + + The basic usage to obtain a charge density difference is: + <​code>​ + $/​users/​scaravat/​bin/​cubecruncher.x -i input.cube -o output.cube -subtract subsystem.cube + ​ + + ===== How do I build a slab model for a surface? ===== + + E.g. by using [[http://​jp-minerals.org/​vesta/​en/​|VESTA]]. + A tutorial is available [[http://​hjklol.mit.edu/​content/​building-slab-geometries-catalysis-vesta|here]]. + + Vesta comes preinstalled on ''​tcopt3'',​ provided that you load the proper module. + <​code>​ +$ module load vesta + ​ + + ===== How do I obtain the stress tensor? ===== + + You have to add the following snippet to the input file: + <​code>​ + &​FORCE_EVAL + ... + STRESS_TENSOR ANALYTICAL + &PRINT + &​STRESS_TENSOR + &END STRESS_TENSOR + &END PRINT + ... + &END FORCE_EVAL + ​ + + Your calculation should be set up in such a way that forces are being calculated: + e.g. ''​RUN_TYPE''​ set to ''​GEO_OPT''​ or ''​ENERGY_FORCE'';​ instead ''​RUN_TYPE ENERGY''​ won't work!​ + + + ===== My calculation does not converge ===== + + ==== ... and I use MULTIPLE_UNIT_CELL ==== + + * first make sure that you actually need ''​MULTIPLE_UNIT_CELL''​. In case you want to do band structure calculation,​ you most definitely do **not** want it + * if you are sure that you need it, make sure that it is specified two times: once in the [[https://​manual.cp2k.org/​trunk/​CP2K_INPUT/​FORCE_EVAL/​SUBSYS/​CELL.html#​MULTIPLE_UNIT_CELL|''​CELL''​ section]] and a second time in the [[https://​manual.cp2k.org/​trunk/​CP2K_INPUT/​FORCE_EVAL/​SUBSYS/​TOPOLOGY.html#​desc_MULTIPLE_UNIT_CELL|''​TOPOLOGY''​ section]], otherwise your calculation may or may not converge + + + ===== Error after changing coordinates ===== + + If you get an error after copy and pasting coordinates from a website/​service/​other file into a CP2K input file and you get an error afterwards when trying to run it, please make sure that you are only using spaces as delimiters between the atomic kind and each of the coordinates.