Coherent Diffraction

Input/Output data description

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

diffr_params_SingFEL (Input Parameter glossary)

Field name Description DataType
–input_dir Input directory where pmi_out files are stored String
–output_dir Output directory where diffr_out files will be stored String
–config_file Full path and filename of this file String
-b Experimental beam file String
-g Experimental geometry file String
–uniformRotation Rotations are selected uniformly in given rotation space Int
–calculateCompton Calculate Compton scattering in diffraction pattern Int
–sliceInterval Interval to calculates diffraction Int
–numSlices Number of time slices to use for calculating diffraction Int
–pmiStartID Start ID of PMI trajectory Int
–pmiEndID End ID of PMI trajectory Int
–dpID Diffraction pattern index for current pmiID Int
–numDP Number of diffraction patterns to generate per pmiID Int
–USE_GPU Options to use GPU (1) or not (0) Int
version SingFEL version 0.1

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

Field name Description Data type Units
data/data Diffraction pattern in 2D matrix Float  
data/diffr Diffracted intensity before Poisson noise (Optional) Float  
data/angle Additional rotation applied to the rotated pmi_out position. Initial rotation angle can be found in pmi_out/data/angle. Active right handed rotations applied in quaternion. Float  
history/ Information about input data    
history/parent/detail Details of the parent including /data, /info, /misc, /params /data should be soft-linked with a relative path    
history/parent/parent Iteratively list parent modules    
info/ Information    
info/package_version Package name and version String  
info/contact Contact details of author String  
info/data_description Short description of what the data is String  
info/method_description Short description of what method was used to generate the data String  
misc/ Miscellaneous information    
params/ Parameters used for coherent diffraction    
params/geom/detectorDist Detector distance from point of interaction Float m
params/geom/pixelWidth Pixel width Float m
params/geom/pixelHeight Pixel height Float m
params/geom/mask Mask of a diffraction pattern to indicate Int  
  pixel ON (1) or OFF (0) in 2D array    
params/beam/photonEnergy Photon energy Float eV
params/beam/photons Number of photons in the beam Int ph
params/beam/focusArea Beam focus area Float
params/info Input for Coherent diffraction program String  
version hdf5 format version Float 0.1


Python script displays /data/data and /data/diffr at completion of the module execution.

Scaling behaviour of SingFEL

Calculation time using single processor vs number of atoms is non-linear, perhaps quadratic.

Detector number of pixels: 131x131

Benzoic acid: 15 atoms Chignolin: 2484 atoms 2YBE: 3240 atoms 2NIP: 4735 atoms 4AS4: 4963 atoms