Metal oxides in the presence of water are covered in a hydration shell. To accurately perform simulations on such systems this fact needs to be taken into account. The motivation for this program lies therein and automatically adds hydration shells to arbitrary metal oxide surfaces.

Hydrates metal oxides in the pdb format with OH2 and OH. In config.wet the user specifies which metals to hydrate and in what ratio. Custom config files are included using the -c flag, if no config file is supplied the default config file is used. Defult name for the output pdb file is inputfilename_wet.pdbHydrating a crystal containing different metals is supported.

The program consists of four main modules: *Wetter *AtomCreator *pdbExplorer *potential

Calculates directional vectors which are the oxygen -> metal center vectors. From the sum of directional vectors of each center the coordinates where oxygen should be positioned is calculated.

The AtomCreator module holds methods for creating molecules according to specified coordinates and directional vectors from the Wetter module. Rotational matrices are set up and aligns the molecules accordning to the directional vectors.

This module handles writing and reading from the supplied .pdb file. It also handles the removal of low coordinated atoms (Nmax - 3, where Nmax is the maximum coordination of the metal) using the remove_lower_coordinated method at the start of the program.

Contains the objective function to be optimized and the Jacobian.

Clone repository and install with pip

pip install .

pip install -e .

python setup.py build_ext --inplace

To run the program with default settings, only a pdb-file is required as input

./mizzler input.pdb

optional flags:

-s (silent) -o (ouput filename) -c (config file) --check [none, metal, all] --log(output log file) -solver [L-BFGS-B, SLSQP] -maxiter (max iterations) -print_dist (output min and max distances in resulting pdb file.)

config.wet (This is also the default config file)

atom Ti: surface
	water: 1.0
	hydroxyl: 0.0

atom Ti: defect
	water: 0.5
	hydroxyl: 0.5
end
resname SOL

./mizzler input.pdb -c config.wet

will put water on all Nmax-1 (surface) coordinated Ti atoms, each Nmax-2 (defect) coordinated atom will have a 50/50 chance of being hydrated with water and/or hydroxyl.

*numpy
*scipy
*pandas
*radish