pattern_sim: Update --simulation-details

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"