Examples

A number of examples with a small amount of comments can be found in the projects examples folder, which you can find at the GitHub Repository These should cover the basic use of XHARPy.

Here is the list of available examples, with connected keywords. All examples are written as jupyter notebooks. So to run them, go to the respective folder and type jupyter lab. If you are unfamiliar with jupyter, please consult one of the myriad tutorials on Youtube or the internet in general.

Calculation with GPAW

L-Alanin with GPAW

  • Folder: L-Alanin_gpaw

  • Original data doi: 10.1021/j100315a022

  • Program: GPAW

  • SCAN calculation

  • Using MPI

  • Constant Core calculation

Urea with GPAW

  • Folder: Urea_gpaw

  • Original data doi: 10.1107/S0108767304015120

  • Program: GPAW

  • SCAN calculation

  • Using MPI

  • Constant Core calculation

  • Multi-Step refinement

  • Save core density

  • Gram-Charlier Refinement

  • Atom table from refined parameters

Xylitol with GPAW

  • Folder: Xylitol_gpaw_extinction

  • Original data doi: 10.1107/S0108767304018306

  • Program: GPAW

  • SCAN calculation

  • Using MPI

  • Constant Core calculation

  • SHELXL-style extinction correction

CpNa with GPAW

  • Folder: CpNa_gpaw_special_position

  • Original data doi: 10.1002/anie.201304498

  • Program: GPAW

  • RPBE calculation

  • Constant core calculation

  • Read xd.hkl

  • Disorder on special position / skip atoms

Hexaqua magnesium hydrogen maleate with GPAW

  • Folder: HMa_Mg_gpaw

  • Original data doi: 10.1039/D0CE00378F

  • Program: GPAW

  • SCAN calculation

  • Using MPI

  • Constant Core calculation

8-Hydroxy quinoline hydrogen maleate with GPAW

  • Folder: HMa_8HQ_gpaw

  • Original data doi: 10.1039/D0CE00378F

  • Program: GPAW

  • SCAN calculation

  • Using MPI

  • Constant Core calculation

Calculation with Quantum Espresso

L-Alanin with Quantum Espresso

  • Folder: L-Alanin_qe

  • Original data doi: 10.1021/j100315a022

  • Program: Quantum Espresso

  • PBE calculation

  • Constant core calculation

Urea with Quantum Espresso

  • Folder: Urea_qe

  • Original data doi: 10.1107/S0108767304015120

  • Program: Quantum Espresso

  • B3LYP calculation from PBE files

  • Core scaling

Calculation with NoSpherA2/ORCA

L-Alanin with NoSpherA2/Orca

  • Folder: L-Alanin_nosphera2_orca

  • Original data doi: 10.1107/S0108767304015120

  • Program: NoSpherA2/Orca

  • B3LYP calculation

  • 8 Angstroem cluster charges

Calculation with the Independent Atom model

L-Alanin with the Independent Atom Model

  • Folder: L-Alanin_iam

  • Original data doi: 10.1021/j100315a022

  • Independent Atom Model

  • Isotropic Hydrogen Refinement

L-Alanin with the Independent Atom Model and Hydrogen Constraints

  • Folder: L-Alanin_iam_HConstraints

  • Original data doi: 10.1021/j100315a022

  • Independent Atom Model

  • Isotropic Hydrogen Refinement

  • Position constraints for sp3 hydrogen atoms

  • U(equiv) constraints

Export to .tsc file

L-Alanin with GPAW

  • Folder: L-Alanin_tscexport_gpaw

  • Original data doi: 10.1021/j100315a022

  • Example for the export of atomic form factors to a .tsc file

  • Running (only) under Linux

  • Program: GPAW

  • SCAN calculation

  • Using MPI

  • Constant Core calculation

Urea with Quantum Espresso under Windows

  • Folder: Urea_tscexport_qe_windows

  • Original data doi: 10.1107/S0108767304015120

  • Example for the export of atomic form factors to a .tsc file

  • Running (only) under Windows

  • Program: Quantum Espresso

  • PBE calculation

  • Using MPI

  • Constant Core calculation