Metadata-Version: 1.0
Name: expectra
Version: 0.1.0
Summary: Code for simulating EXAFS calculations from molecular dynamics trajectories or normal modes using FEFF
Home-page: https://github.com/SamChill/expectra
Author: Samuel T. Chill
Author-email: samchill@gmail.com
License: LICENSE.txt
Description: 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 <http://www.feffproject.org/>`__, which was written at the
        University of Washington by J.J. Rehr and co-workers.1
        
        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
        
        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
        
Platform: UNKNOWN
