Commit f5eb7d15 authored by Thomas White's avatar Thomas White
Browse files

pattern_sim: Update --simulation-details

parent fe514e51
......@@ -95,33 +95,34 @@ static void show_details()
"with femtosecond X-ray pulses from a free electron laser.\n"
"The lattice transform from the specified number of unit cells is calculated\n"
"using the closed-form solution for a truncated lattice:\n"
"using the closed-form solution for a truncated lattice faceted on the\n"
"(001), (010) and (100) planes:\n"
"F(q) = sin(pi*na*q.a)/sin(pi*q.a)\n"
" * sin(pi*nb*q.b)/sin(pi*q.b)\n"
" * sin(pi*nc*q.c)/sin(pi*q.c)\n"
"I_latt(q) = sin^2(pi*na*q.a)/sin^2(pi*q.a)\n"
" * sin^2(pi*nb*q.b)/sin^2(pi*q.b)\n"
" * sin^2(pi*nc*q.c)/sin^2(pi*q.c)\n"
"na = number of unit cells in 'a' direction (likewise nb, nc)\n"
" q = reciprocal vector (1/d convention, not 2pi/d)\n"
"This square modulus of this value is taken, and multiplied by the Bragg\n"
"intensitiy at the neares Bragg position. That means that the gradient of\n"
"the underlying molecule transform is not included, for speed of calculation.\n"
"The Bragg intensities are taken from the file specified on the command line\n"
"with the --intensities option.\n"
"This is multiplied by a model of the underlying molecular transform, I_mol(q).\n"
"This can be approximated to varying levels of accuracy by the methods given by\n"
"the '--gradients' option.\n"
"Intensity from water is then added according to the first term of equation\n"
"5 from Phys Chem Chem Phys 2003 (5) 1981--1991. This simulates the\n"
"Intensity from water is added according to the first term of equation 5\n"
"from Phys Chem Chem Phys 2003 (5) 1981--1991. This simulates the\n"
"coherent, elastic part of the diffuse scattering from the water jet only.\n"
"Expected intensities at the CCD are then calculated using:\n"
"I(q) = I0 * r^2 * |F(q)|^2 * S\n"
"I(q) = I0 * r^2 * I_latt(q) * I_mol(q) * S\n"
"I0 = number of photons per unit area in the incident beam\n"
" r = Thomson radius\n"
" S = solid angle of corresponding pixel\n"
"where |F(q)|^2 is the value calculated as described above.\n"
"Polarisation is not currently included in pattern_sim, although it is included\n"
"in the analysis of Bragg peaks by 'indexamajig'.\n"
"Poisson counts are generated from the expected intensities using Knuth's\n"
"algorithm. When the intensity is sufficiently high that Knuth's algorithm\n"
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