Photon Matter Interaction

Input/Output data description

The input/output data is expected in hdf5 format, and the glossary can be found below. Photon matter interaction module is responsible for reading in and writing out in the format specified below.

pmi_out_<7 digit ID>.h5 (Output HDF glossary)

Field name Description Data type Units
data/snp_<7 digit index>/ff Atomic form factor in 2D array (number of unique ions x length of atomFormFactorQ) Float  
data/snp_<7 digit index>/halfQ Reciprocal space spanned by the atomic form factor in 1D array (number of samples of reciprocal q) Float 1/Å
data/snp_<7 digit index>/Nph Numbers of photons in the beam Int ph
data/snp_<7 digit index>/r Atomic position in real space in 2D array (number of ions x 3D coordinates {x,y,z}) Float  
data/snp_<7 digit index>/T List of unique ID numbers given to each atomFormFactor in 1D array (number of unique ions) Int  
data/snp_<7 digit index>/Z List of atomType present at atomPosition in 1D array (number of ions x number of frames) Int  
data/snp_<7 digit index>/xyz List of indices of ff for each atom in Z Int  
data/snp_<7 digit index>/Sq_halfQ Reciprocal space spanned by the Compton scattering in 1D array (number of samples of reciprocal q) Float 1/Å
data/snp_<7 digit index>/Sq_bound Compton scattering by bound electrons in 1D array (length of Sq_Q) Float  
data/snp_<7 digit index>/Sq_free Compton scattering by free electrons in 1D array (length of Sq_Q) Float  
history Information about input data    
history/parent/detail Details of the parent inclusing /data, /info, /misc, /params    
history/parent/parent Iteratively list parent modules    
info/package_version Package version    
info/contact Contact details of author    
info/data_description Short description of what the data is    
info/method_description Short description of what method was used to generate the data    
misc/ Miscellaneous information    
params/ Parameters used to run the module    
version hdf5 format version Float 0.1

Python script for HDF

Script on bitbucket