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README.md

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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.

Usage

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