CP2K Open Source Molecular Dynamics

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exercises:2019_conexs_newcastle:ex3 [2019/09/10 14:50] – [MgO] abussyexercises:2019_conexs_newcastle:ex3 [2019/09/10 16:49] – abussy
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 Do not forget to put in your work directory the files ''GTH_POTENTIALS'' and ''GTH_BASIS_SETS'', which contain the parameters for the pseudopotentials and basis sets used in the calculations. Do not forget to put in your work directory the files ''GTH_POTENTIALS'' and ''GTH_BASIS_SETS'', which contain the parameters for the pseudopotentials and basis sets used in the calculations.
  
-To run the calculation, type in your terminal:+To run the calculation follow the instructions on the page [[exercises:2019_conexs_newcastle:ex0|Connecting to the HPC cluster]].
  
-<code> 
-./cp2k.sopt -i MgO_opt.inp -o MgO_opt.out &  
-</code>  
  
 After the calculation is finished, you can check the files created in your directory. First open the output file ''MgO_opt.out'' and search for the following banner:  After the calculation is finished, you can check the files created in your directory. First open the output file ''MgO_opt.out'' and search for the following banner: 
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 <note important>Even though we are not changing the name of the basis set or pseupotential used, cp2k will use the parameters for the sulfur atom now, since the ''ELEMENT'' type is different. However, it is important to check in the ''GTH_BASIS_SET'' and ''GTH_POTENTIALS'' files whether the names are the same for different atoms.</note> <note important>Even though we are not changing the name of the basis set or pseupotential used, cp2k will use the parameters for the sulfur atom now, since the ''ELEMENT'' type is different. However, it is important to check in the ''GTH_BASIS_SET'' and ''GTH_POTENTIALS'' files whether the names are the same for different atoms.</note>
  
-Now the input is ready, and can be run in the same way as before, just changing the input and output files names. +Now the input is ready and it can be run in the same way as before, just remember to change the file ''cp2k.sh''.
- +
-<code> +
-./cp2k.sopt -i MgS_opt.inp -o MgS_opt.out &  +
-</code> +
  
 After the calculation is finished, open the output file ''MgS_opt.out'' and look for the same banner as before. The optimized atomic positions are written in the file ''MgS-pos-1.xyz''. After the calculation is finished, open the output file ''MgS_opt.out'' and look for the same banner as before. The optimized atomic positions are written in the file ''MgS-pos-1.xyz''.
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 <note important>At this time we are using cartesian coordinates to indicate the position of the atoms, so the keyword ''SCALED'' should be removed.</note> <note important>At this time we are using cartesian coordinates to indicate the position of the atoms, so the keyword ''SCALED'' should be removed.</note>
  
-To run this calculation type in terminal: +To run this calculation proceed as you did before.
- +
-<code> +
-./cp2k.sopt -i MgS_xas.inp -o MgS_xas.out & +
-</code>+
  
 This calculation should take longer than the geometry optimization to run. Once it is finished, check the number of warnings and if the calculation converged. Sometimes it does not converge within the maximum number of iterations we set in the input file. If this is the case, you can increase the number using the keyword ''MAX_SCF''. This calculation should take longer than the geometry optimization to run. Once it is finished, check the number of warnings and if the calculation converged. Sometimes it does not converge within the maximum number of iterations we set in the input file. If this is the case, you can increase the number using the keyword ''MAX_SCF''.
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 </code> </code>
  
-For the MgS system, for example, run the calculation typing  +instead of ''TP_HH'', and you can run the calculation in the same way as you did before.
- +
-<code> +
-./cp2k.sopt -i MgS_dscf.inp -o MgS_dscf.out & +
-</code>+
  
-After the calculation ran, look for the message+After the calculation is done, look for the message
  
 <code> <code>
exercises/2019_conexs_newcastle/ex3.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1