GRSQ: Structure-Factors and X-ray Scattering from Radial Distribution Functions
A package to calculate structure factors and x-ray (solution) scattering signals from Radial Distribution Functions (RDFs), sampled from Molecular Dynamics (MD) simulations.
Includes 3 different finite-size RDF-corrections, as well as a set of Fourier truncation window functions.
Please see https://doi.org/10.1063/5.0164365 for details (and cite it if you use this tool).
Example: X-ray Scattering from liquid water
from grsq.grsq import rdfset_from_dir
V = 122900.85207774633 # volume of MD box
stoich = {'H_v': 8190, 'O_v': 4095} # number of atoms in MD box
# Helper function to create RDFSet, a set of RDFs
# that comprises all possible combinations of atom-types
# in water: O-O, O-H, H-H.
rdfs = rdfset_from_dir('tests/data/xray_water/',
volume=V, stoich=stoich)
qvec = np.arange(0, 10, 0.05) # create q vector
ig_u = rdfs.get_iq(qvec) # Calculate scattering
rdfs.vdv_correct() # apply finite-size corrections
ig_c = rdfs.get_iq(qvec) # Calculate scattering again
fig, ax = plt.subplots(1, 1, figsize=(9, 5))
ax.plot(qvec, ig_u, label='Raw')
ax.plot(qvec, ig_c, label='Corrected')
ax.set_xlim([0, 10])
ax.set_xlabel('Q (Å$^{-1})$')
ax.set_ylabel('I(Q)')
ax.legend(loc='best');
fig.tight_layout()
