Expectra is program to simulate EXAFS from the outputs of molecular dynamics simulations. It also has the ability to to sample structures based on a harmonic potential generated from a normal modes calculation.
The EXAFS multiple scattering calculations are performed using FEFF6-lite, which was written at the University of Washington by J.J. Rehr and co-workers.1
- J.J. Rehr, S.I. Zabinsky and R.C. Albers, "High-order multiple scattering calculations of x-ray-absorption fine structure", Phys. Rev. Lett. 69, 3397 (1992).
usage: expectra [-h] [--first-shell] [--neighbor-cutoff DISTANCE]
[--multiple-scattering] [--rmax DISTANCE] [--S02 FACTOR]
[--energy-shift ENERGY] [--absorber ELEMENT]
[--ignore-elements ELEMENTS] [--edge EDGE]
{snapshots,modes} ...
positional arguments:
{snapshots,modes} sub-command help
snapshots average EXAFS signal from snapshots of a trajectory
modes average EXAFS signal from harmonic approximation using
normal modes
optional arguments:
-h, --help show this help message and exit
--first-shell a single scattering calculation that uses an
automatically calculated reference path (default:
True)
--neighbor-cutoff DISTANCE
1st neighbor cutoff distance (default: 3.4)
--multiple-scattering
--rmax DISTANCE maximum scattering half-path length
--S02 FACTOR amplitude reduction factor
--energy-shift ENERGY
energy shift to apply in eV
--absorber ELEMENT atomic symbol of the xray absorber
--ignore-elements ELEMENTS
comma delimited list of elements to ignore in the
scattering calculation
--edge EDGE one of K, L1, L2, L3