coherent_diffraction.rst

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/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	m^2
params/info	Input for Coherent diffraction program	String
version	hdf5 format version	Float	0.1

Diagnostic

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