Python based Matter Modeling software

https://phonopy.github.io/phonopy/, https://pypi.org/project/pysmiles/, https://github.com/pyscf/pyscf, etc.
9d ago – sloshy
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Apr 4, 2023 13:41
But I don’t see why you need to reinvent the wheel when there are already existing libraries.
Feb 11, 2023 19:46
I will for sure be asking some things in the near future :)
Sep 1, 2022 04:00
@lela2011 The convergence is a red hearing. You can see that you aren't computing the correct Fock matrix from this simple example:
Jul 29, 2021 22:16
«Rome wasn't built in a day», but for now there is need for a rest. roger and out.
Feb 28, 2021 22:30
@NikeDattani sure
Aug 27, 2020 21:06
In ionic crystals (eg. Na Cl) you might need more. A robust way to check is to calculate the forces for the undistorted supercell (should be near 0, but numerically not exactly as we already learned) and then do a calculation for a displaced atom. You can read the forces on the atoms from the OUTCAR and determine how much the force changes on atoms far away from the displaced atom. If the cell is big enough, the force induced on the most distant atoms in the distorted cell should be negligible
Aug 27, 2020 20:57
PHONOPY will read the hessian elements (second derivatives of total energy with respect to atomic displacements) from VASP output and then determine the dynamical matrix. Phonopy does the same thing with finite displacements, the difference is really numerical vs. analytical differentiation. After this point, it is the same to use PHONOPY to compute dispersions, calculate thermodynamics properties, etc.