Commit 136e3370 authored by Thomas White's avatar Thomas White
Browse files

pattern_sim: Remove --simulation-details, obsoleted by manpage

parent 4976035d
......@@ -61,7 +61,6 @@ static void show_help(const char *s)
" -p, --pdb=<file> PDB file from which to get the unit cell.\n"
" (The actual Bragg intensities come from the\n"
" intensities file)\n"
" --simulation-details Show technical details of the simulation.\n"
" --gpu Use the GPU to speed up the calculation.\n"
" --gpu-dev=<n> Use GPU device <n>. Omit this option to see the\n"
" available devices.\n"
......@@ -115,46 +114,6 @@ static void show_help(const char *s)
}
static void show_details()
{
printf(
"This program simulates diffraction patterns from small crystals illuminated\n"
"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 faceted on the\n"
"(001), (010) and (100) planes:\n"
"\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 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"
"Expected intensities at the CCD are then calculated using:\n"
"\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"
"\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"
"would result in machine precision problems, a normal distribution with\n"
"standard deviation sqrt(I) is used instead.\n"
);
}
static double *intensities_from_list(RefList *list)
{
Reflection *refl;
......@@ -282,7 +241,6 @@ int main(int argc, char *argv[])
char *rval;
double *phases;
unsigned char *flags;
int config_simdetails = 0;
int config_randomquat = 0;
int config_noimages = 0;
int config_nonoise = 0;
......@@ -312,7 +270,6 @@ int main(int argc, char *argv[])
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"simulation-details", 0, &config_simdetails, 1},
{"gpu", 0, &config_gpu, 1},
{"random-orientation", 0, NULL, 'r'},
{"number", 1, NULL, 'n'},
......@@ -447,11 +404,6 @@ int main(int argc, char *argv[])
sym = get_pointgroup(sym_str);
/* sym_str is used below */
if ( config_simdetails ) {
show_details();
return 0;
}
if ( grad_str == NULL ) {
STATUS("You didn't specify a gradient calculation method, so"
" I'm using the 'mosaic' method, which is fastest.\n");
......
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