diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/pattern_sim.c | 53 |
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"); |