This Python package is intended to help running multiple CP2k calculations for the same system or multiple similar systems. In particular, it is used by KPFM_simulation_tools package to run geometry optimizations for multiple tip-sample distances and bias voltages. The parameters are separated in two Python modules called cp2k_common_params and cp2k_system_params, the first of which contains computational parameters common to a wide range of calculations and the second contains parameters for a specific system, like the used basis sets. The atomic geometry is expected to be defined as an Atoms object of Atomic Simulation Environment (ASE). pycp2k is used to write the CP2k input file and run the calculation.
- Python 3.X (originally 2.7)
- Atomic Simulation Environment (ASE), https://wiki.fysik.dtu.dk/ase/
- pycp2k, https://github.com/SINGROUP/pycp2k
Put this directory containing the Python modules to your PYTHONPATH environment variable. Create file cp2k_common_params.py based on the file templates in parameter_file_templates folder and place it to a directory that fits the scope in which you want to use those parameters (for example the root directory of a set of simulations). There are actually 2 sets of parameters the original one - used for NaCl systems - and more recent one called style_metallic - used for systems of organics on metallic substrates and CO-metallic tips - which has to be renamed to the original form, before usage. Make sure that directory is also in your PYTHONPATH.
cp2k_init is the main module containing CP2k_init class that defines CP2k initializer objects. Import that class to your Python script where you define and run your CP2k calculation. The initializer object is created using command
cp2k_initializer = CP2k_init(project_name, atoms)
where project_name is used in the output files created by the calculation and atoms is an ASE Atoms object defining the geometry of your model. The initializer object creates a CP2K object of pycp2k and sets the parameters from cp2k_common_params and cp2k_system_params to it, loads the atomic coordinates, cell vectors and boundary conditions based on the given Atoms object and tries to guess a Poisson solver that would work for the given boundary conditions. You should have the cp2k_common_params in your PYTHONPATH and cp2k_system_params files in the directory where you run the calculation (or both in the PYTHONPATH or in the working directory). See the parameter_file_templates folder for templates for these files. After that, you should call the correct initialize method based on the type of calculation you want to run. For example,
cp2k_calc = cp2k_initializer.init_geometry_optimization()
sets parameters needed for a geometry optimization and returns an object of type CP2K defined in pycp2k package. There are multiple initialize methods defined in cp2k_init but you can also define your own if you cannot find a suitable one. To run the actual calculation, use command
cp2k_calc.run()
See the documentation of pycp2k for more information. See also examples folder for a usage examples.
Contains get_grid_size function that returns the number of grid points along each cell vector in the finest grid used by CP2k. The number of points in the finest grid depends on the cell vectors and the plane wave cutoff, and it must be compatible for the FFT method that CP2k uses. You should use use_extended_fft_lengths=False unless you have allowed extended FFT lengths in the CP2k input file.
Contains some functions for obtaining data, such as total energy and forces on atoms, from the CP2k output file.
Juha Ritala (2016) [email protected]
Ondrej Krejci (2022) [email protected]