# Open SourceMolecular Dynamics

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exercises:2016_summer_school:geometry_and_cell_optimization

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 exercises:2016_summer_school:geometry_and_cell_optimization [2016/08/22 21:20]ibethune exercises:2016_summer_school:geometry_and_cell_optimization [2016/08/23 06:57]ibethune Both sides previous revision Previous revision 2016/08/23 19:18 ibethune 2016/08/23 06:57 ibethune 2016/08/22 21:29 ibethune 2016/08/22 21:20 ibethune 2016/08/22 21:18 ibethune 2016/08/22 21:16 ibethune 2016/08/22 21:12 ibethune created Next revision Previous revision 2016/08/23 19:18 ibethune 2016/08/23 06:57 ibethune 2016/08/22 21:29 ibethune 2016/08/22 21:20 ibethune 2016/08/22 21:18 ibethune 2016/08/22 21:16 ibethune 2016/08/22 21:12 ibethune created Last revision Both sides next revision Line 20: Line 20: ​ - where the template input ''​template.inp''​ is this geometry optimization using the classical forcefield FIST module of CP2K. + where the template input ''​template.inp''​ is this geometry optimization using the classical forcefield FIST module of CP2K.  You will also need to initial geometry file ''​NaCl.pdb''​. - + - You will also need to initial geometry file ''​NaCl.pdb'' ​which can be found in ''​cp2k/​tests/​Fist/​sample_pdb/​NaCl.pdb''​ + <​code>​ <​code>​ Line 218: Line 216: Copy the input template to a new file and change the ''​RUN_TYPE''​ to ''​CELL_OPT''​. You'll also need to ask the code to calculate the stress tensor (in ''​FORCE_EVAL''​ section) ''​ANALYTICAL''​ly! Also define the ''​CUTOFF''​ and ''​SCALING_FACTOR''​. Start the cell optimization from small cells (''​SCALING_FACTOR 0.85''​) or large cells (''​SCALING_FACTOR 1.10''​) - do you get the same results? ​ Copy the input template to a new file and change the ''​RUN_TYPE''​ to ''​CELL_OPT''​. You'll also need to ask the code to calculate the stress tensor (in ''​FORCE_EVAL''​ section) ''​ANALYTICAL''​ly! Also define the ''​CUTOFF''​ and ''​SCALING_FACTOR''​. Start the cell optimization from small cells (''​SCALING_FACTOR 0.85''​) or large cells (''​SCALING_FACTOR 1.10''​) - do you get the same results? ​ - If you have access a machine with several cores (16 or so ideally) ​check whether increasing the supercell size (''​NREP''​ variable) affects the results. + If you are running on ARCHER, use some larger parallel jobs to check whether increasing the supercell size (''​NREP''​ variable) affects the results.