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While I don't know how particular protonation / tautomer tools work, most are trained with various ML models to predict pKa in water. Fortunately, we have a lot of experimental data for that task, although sometimes of varying quality.
For pKa prediction, there are a few public databases:
DataWarrior includes a set prepared by Thomas Sander
ChEMBL 25 ...
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Atomsk
Creating surface based on Miller indices is tough work if it is not cubic lattice. for example $\langle011\rangle$ direction and $(011)$ plane normal in case of $c>a$ is not same. So, in case you are trying to create orthogonal simulation box, you may end up in a situation where orthogonal box is quite large or periodicity is not found. Dependency ...
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Not a fully GUI solution but if we can assume you get a primitive cell to work with, Atomic Simulation Environment can generate your surface.
For some extra spice, its common to want to make root surfaces such as $\sqrt{2}$x$\sqrt{2}$, so I included a final step which will do this assuming there is a valid $\sqrt{2}$x$\sqrt{2}$ to make. There is also a ...
1
The Atomic Simulation Environment can generate surfaces and run LAMMPS.
1
You can take a look here about how to generate UPF pseudos using the software ld1.x that is part of QuantumEspresso.
In principle, you will need an input file with the information about the atom you want to generate the pseudopotential. Here is an example of an input file (infile) to generate the UPF pseudopotential for Si:
&input
title = 'all-electron ...
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