Expectra
Introduction
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).
Requirements
- gfortran
- MPI (e.g. OpenMPI or MPICH)
- Python
- numpy
- mpi4py
- ASE
Installation
This program is distributed as a Python package. It requires a Fortran compiler (e.g. gfortran) to build the FEFF6-lite program that is redistributed with the code. A MPI library (e.g. OpenMPI) is also required.
The first step is to install Python, GFortran, and MPICH. On Ubuntu this can be accomplished like so:
$ sudo apt-get install build-essential gfortran mpich python python-pip
Once the dependencies are installed expectra (and the Python packages it depends on) can be installed using pip:
$ pip install --user expectra
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] [--skip SKIP]
[--every EVERY]
TRAJ [TRAJ ...]
positional arguments:
TRAJ trajectory file (POSCAR, con, xyz)
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
--skip SKIP number of frames to skip at the beginning
--every EVERY number of frames to between each step
Installing from source
If installing Expectra from source instead of pip, clone the source code
from GitHub:
git clone https://github.com/SamChill/expectra.git
After all the dependency requirements have been satisfied, build the feff binary,
and move it to expectra/expectra/:
cd expectra/feff
# To use ifort instead of gfortran, set FC=ifort in ./Makefile
make clean
make # should create the feff binary
mv ./feff ../expectra
Finally, set relevant environmental variables (assuming Expectra was installed at $HOME):
# consider including these in ~/.bash_profile, ~/.profile, or ~/.bashrc
export PATH=$HOME/expectra/bin:$PATH
export PYTHONPATH=$HOME/expectra:$PYTHONPATH
Note from developers
Expectra was recently migrated from Python2 to Python3. Please report any bugs to sunghjung3@utexas.edu.
