diff options
Diffstat (limited to 'src/pattern_sim.c')
| -rw-r--r-- | src/pattern_sim.c | 27 |
1 files changed, 14 insertions, 13 deletions
diff --git a/src/pattern_sim.c b/src/pattern_sim.c index 7e2b46fa..227bbc85 100644 --- a/src/pattern_sim.c +++ b/src/pattern_sim.c @@ -95,33 +95,34 @@ static void show_details() "with femtosecond X-ray pulses from a free electron laser.\n" "\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" "\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" "\n" "na = number of unit cells in 'a' direction (likewise nb, nc)\n" " q = reciprocal vector (1/d convention, not 2pi/d)\n" "\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" "\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" "\n" "Expected intensities at the CCD are then calculated using:\n" "\n" -"I(q) = I0 * r^2 * |F(q)|^2 * S\n" +"I(q) = I0 * r^2 * I_latt(q) * I_mol(q) * S\n" "\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" +"\n" +"Polarisation is not currently included in pattern_sim, although it is included\n" +"in the analysis of Bragg peaks by 'indexamajig'.\n" "\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" |