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authorThomas White <taw@physics.org>2014-01-22 13:49:36 +0100
committerThomas White <taw@physics.org>2014-01-22 13:49:36 +0100
commit364ef8cbcec43e22cac41439284eb13eb7796e84 (patch)
treecc4b7752e2e2b4fd58916fc990f00334805de7c1
parent98879100c72e0db3e1861f0bb3b6557f834be133 (diff)
pattern_sim: Update man page, simplify --help
-rw-r--r--doc/man/pattern_sim.112
-rw-r--r--src/pattern_sim.c44
2 files changed, 18 insertions, 38 deletions
diff --git a/doc/man/pattern_sim.1 b/doc/man/pattern_sim.1
index a9528654..e34bf11d 100644
--- a/doc/man/pattern_sim.1
+++ b/doc/man/pattern_sim.1
@@ -120,6 +120,18 @@ Generate random crystal sizes between \fImin\fR and \fImax\fR nanometres. These
.PD
Do not calculate Poisson noise.
+.PD 0
+.IP "\fB-s\fR \fIn\fR"
+.IP \fB--sample-spectrum=\fR\fIn\fR
+.PD
+Include \fIn\fR samples from the spectrum in the calculation.
+
+.PD 0
+.IP "\fB-x\fR \fItype\fR"
+.IP \fB--spectrum=\fR\fItype\fR
+.PD
+Use \fItype\fR of spectrum. \fItype\fR can be one of \fBtophat\fR or \fBsase\fR.
+
.SH REFLECTION LISTS
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 5ea328bf..7be2acfb 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -73,54 +73,22 @@ static void show_help(const char *s)
" available devices.\n"
" -g, --geometry=<file> Get detector geometry from file.\n"
" -b, --beam=<file> Get beam parameters from file.\n"
-"\n"
" -n, --number=<N> Generate N images. Default 1.\n"
" --no-images Do not output any HDF5 files.\n"
" -o, --output=<filename> Output HDF5 filename. Default: sim.h5.\n"
-" If you choose to simulate more than one pattern,\n"
-" the filename given will be postfixed with a\n"
-" hyphen, the image number and '.h5'. In this\n"
-" case, the default value is 'sim', such that the\n"
-" files produced are sim-1.h5, sim-2.h5 and so on.\n"
-" -r, --random-orientation Use a randomly generated orientation\n"
-" (a new orientation will be used for each image).\n"
+" -r, --random-orientation Use randomly generated orientations.\n"
" --powder=<file> Write a summed pattern of all images simulated by\n"
" this invocation as the given filename.\n"
" -i, --intensities=<file> Specify file containing reflection intensities\n"
" (and phases) to use.\n"
" -y, --symmetry=<sym> The symmetry of the intensities file.\n"
-" -t, --gradients=<method> Use <method> for the calculation of shape\n"
-" transform intensities. Choose from:\n"
-" mosaic : Take the intensity of the nearest\n"
-" Bragg position. This is the\n"
-" fastest method and the only one\n"
-" supported on the GPU.\n"
-" interpolate : Interpolate trilinearly between\n"
-" six adjacent Bragg intensities.\n"
-" This method has intermediate\n"
-" accuracy.\n"
-" phased : As 'interpolate', but take phase\n"
-" values into account. This is the\n"
-" most accurate method, but the\n"
-" slowest.\n"
-" --really-random Use really random numbers for the orientation and\n"
-" crystal size. By default, the same sequence\n"
-" will be used for each new run.\n"
-" --min-size=<s> Generate random crystal sizes using <s> as the\n"
-" minimum crystal size in nm. --max-size is also\n"
-" required.\n"
-" --max-size=<s> Use <s> as the maximum crystal size in nm.\n"
-" --min-size is also required.\n"
+" -t, --gradients=<method> Select method for calculation of shape transforms\n"
+" --really-random Seed the random number generator with /dev/urandom.\n"
+" --min-size=<s> Minimum crystal size in nm.\n"
+" --max-size=<s> Naximum crystal size in nm.\n"
" --no-noise Do not calculate Poisson noise.\n"
" -s, --sample-spectrum=<N> Use N samples from spectrum. Default 3.\n"
-" -x, --spectrum=<type> Use <type> for the calculation of spectrum.\n"
-" Choose from:\n"
-" tophat : Tophat spectrum. Bandwidth is\n"
-" taken from beam parameters.\n"
-" SASE : SASE spectrum. Random SASE pulse \n"
-" is generated from a model.\n"
-" Bandwidth is taken from beam \n"
-" parameters.\n"
+" -x, --spectrum=<type> Type of spectrum to simulate.\n"
);
}