The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
We can create structural files for DFT or Molecular Dynamics software with ASE. We could also create inputs with Materials Studio, but that is paid software.
See example in [[Week 2024-11-04 MDanse#Xray and Neutron Responses]]
For example, we can perform DFT calculations with CASTEP, obtaining CIF structural files. Then, to perform molecular dynamics calculations to these structures, we can use ASE to transform the CIF files into the PDB format (Protein DataBase) that CP2K can read. We can do that with ase.io as follows:
>>> from ase.io import read
>>> test = read("test.cif")
>>> test.write("test.pdb")
We can export outputs from programs such as QuantumESPRESSO to a .CIF format.
Sometimes we need the cell parameters: for example, on [[CP2K#CP2K Input|CP2K]] inputs we must specify cell parameters in the &CELL section. In order to do that, we can check the cell parameters with the atoms.cell object:
>>> from ase.io import read
>>> test = read("dumped.pdb")
>>> test.cell[:]
array([[35.767, 0. , 0. ],
[ 0. , 37.99 , 0. ],
[ 0. , 0. , 33.906]])
Optionally, we could just translate the structural file into a *.cell file, and copy the %BLOCK LATTICE_CART section:
>>> test.write("test.cell")
~$ cat test.cell
%BLOCK LATTICE_CART
35.767000 0.000000 0.000000
0.000000 37.990000 0.000000
0.000000 0.000000 33.906000
%ENDBLOCK LATTICE_CART
We can check structural files with VESTA, but we can also visualize them with ase.visualize.view as follows:
>>> from ase.io import read
>>> from ase.visualize import view
>>> test = read("test.pdb")
>>> view(test)
We can calculate the dipole moment with the get_dipole_moment() method, by using another program as a calculator. We can use programs such as CP2K as calculators, but seems like CP2K in particular does not support the dipole moment. I checked other programs, but in the end it was a mess and I gave up.