pysingfel

Python version of singfel, which is a C++ package calculating the propagation of the scattered light signal (including incoherent effects) to the detector plane.

Benchmark

+-------------+-------------+-------------+-------------+-------------+-------------+-------------+ | | C++ | pysingfel | +=============+=============+=============+=============+=============+=============+=============+ | No. of dp   | 100       | 200 | 400 | 100       | 200 | 400 | +-------------+-------------+-------------+-------------+-------------+-------------+-------------+ | Time (s)   | 72.514     | 143.179     | 283.113     | 75.768     | 150.969     | 302.367 | +-------------+-------------+-------------+-------------+-------------+-------------+-------------+ | Ave time (s)| 3.626       | 3.579       | 3.539       | 3.788       | 3.774       | 3.780 | +-------------+-------------+-------------+-------------+-------------+-------------+-------------+ Here 'dp' means diffraction pattern. On average pysingfel is only about 5.3% slower than the C++ version, thanks for the just-in-time optimization provided by Numba library.

Usage

1. Integrated inside the simex_platform. A python script named radiationDamageMPI has the same interface as the excutive radiationDamageMPI in the C++ version and could be used in the same way. Therefore simex_platform doesn't need to change.
2. Calculate diffraction patterns directly from Protein Data Bank (.pdb) file. See test_particle.test_calFromPDB() for more infomation.