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creating_inputs [2018/10/24 13:18]
krejcio
creating_inputs [2021/09/30 13:06] (current)
krejcio Updated FHI-aims output; no need for parallel recompilation any more
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 +//Note:// If you work with the **flexible-tip**=**PP-AFM** adjust the geometry into the necessary box for the force-field calculations. Don't forget to put the top-most atoms above ''​0.0'',​ but lower part of the box in the //z// direction.
 +
 At the moment the PP-STM code can read inputs from following DFT codes: At the moment the PP-STM code can read inputs from following DFT codes:
  
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-== FHI-AIMS ==+== FHI-aims ==
 [[http://​aimsclub.fhi-berlin.mpg.de/​]] [[http://​aimsclub.fhi-berlin.mpg.de/​]]
  
-Works for PBC calculations, just add:+Works for PBC calculations ​serial or parallel (mpi.scalapack) version. Ideally with the final geometry run a single point calculation with the following outputs added to your __control.in__:
   output eigenvectors   output eigenvectors
   output band 0 0 0 0.5 0.5 0.0 2 G K   output band 0 0 0 0.5 0.5 0.0 2 G K
-into __control.in__.+      KS_method lapack_fast ​ # for mpi-version (mpi.scalapack): The error message with HDF5 is not true in the aims output; use this keywords instead of recompilation # 
 +See the [[https://​github.com/​ondrejkrejci/​PPSTM/​blob/​master/​tests/​CuPc/​control.in|CuPc example]] 
 In the case of hybrid functionals (B3LYP, PBE0, HSE) add also: In the case of hybrid functionals (B3LYP, PBE0, HSE) add also:
   exx_band_structure_version 1 ## for hybrid functionals only; both options 1 and 2 are working (1 takes more memory) ##   exx_band_structure_version 1 ## for hybrid functionals only; both options 1 and 2 are working (1 takes more memory) ##
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 The calculations produces: __KS_eigenvectors.band_1.kpt_1.out__ for spin-restricted calculations or __KS_eigenvectors_dn.band_1.kpt_1.out__ & __KS_eigenvectors_up.band_1.kpt_1.out__ in the case of spin-polarized calculations. The calculations produces: __KS_eigenvectors.band_1.kpt_1.out__ for spin-restricted calculations or __KS_eigenvectors_dn.band_1.kpt_1.out__ & __KS_eigenvectors_up.band_1.kpt_1.out__ in the case of spin-polarized calculations.
 +You will also need __geometry.in__ in the same directory. All of these files are supposed to be easily read by the __PPSTM_simple.py__ script or within __GUI.py__.
  
-Note: For cluster calculations Mathematica scripts have to be used for creating PP-STM inputs.+Note: Under normal conditions, please use PBC calculations,​ Just adjust the __geometry.in__ with a suitable ''​lattice_vector''​s (for small molecules ''​30.0 30.0 30.0''​ box is enough). There is a possibility to run strict ​cluster calculations, but additional parsing through ​Mathematica scripts ​(and some additional outputs) ​have to be used for creating PP-STM inputs.
  
-== CP2k ==+== CP2K ==
 [[http://​www.cp2k.org/​]] [[http://​www.cp2k.org/​]]
  
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 Examples of input (and output) files can be found in the code in __examples/​__ __4N-coronene/​__ __CuPc/__ and __TOAT/__ . Examples of input (and output) files can be found in the code in __examples/​__ __4N-coronene/​__ __CuPc/__ and __TOAT/__ .
 +
 +Note: CP2K reading procedure was mainly written by Ole Schütt, those days working at EMPA, Switzerland.
creating_inputs.1540379905.txt.gz · Last modified: 2018/10/24 13:18 by krejcio