aboutsummaryrefslogtreecommitdiff
path: root/src
diff options
context:
space:
mode:
Diffstat (limited to 'src')
-rw-r--r--src/pattern_sim.c53
1 files changed, 0 insertions, 53 deletions
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 634399c2..19f58589 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -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"
@@ -105,56 +104,11 @@ static void show_help(const char *s)
" required.\n"
" --max-size=<s> Use <s> as the maximum crystal size in nm.\n"
" --min-size is also required.\n"
-"\n"
-"By default, the simulation aims to be as accurate as possible. For greater\n"
-"speed, or for testing, you can choose to disable certain things using the\n"
-"following options.\n"
-"\n"
" --no-noise Do not calculate Poisson noise.\n"
);
}
-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 +236,6 @@ 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 +265,6 @@ 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 +399,6 @@ 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");