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authorThomas White <taw@physics.org>2015-10-27 14:43:01 +0100
committerThomas White <taw@physics.org>2015-10-27 14:43:01 +0100
commit8e29e4a7f588db22aa716a7172dbb56e471f8260 (patch)
tree3c1dc0a5f0b9f6fce773e6631afe4fa202595db7 /doc/man
parentdc7ef64b2699221d80cfbf447ab46b91fa9d0b79 (diff)
Update docs for pattern_sim
Diffstat (limited to 'doc/man')
-rw-r--r--doc/man/pattern_sim.122
1 files changed, 21 insertions, 1 deletions
diff --git a/doc/man/pattern_sim.1 b/doc/man/pattern_sim.1
index 85c199f1..7c761c71 100644
--- a/doc/man/pattern_sim.1
+++ b/doc/man/pattern_sim.1
@@ -126,7 +126,7 @@ Include \fIn\fR samples from the spectrum in the calculation.
.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.
+Use \fItype\fR of spectrum. \fItype\fR can be one of \fBtophat\fR, \fBsase\fR or \fBtwocolour\fR. See the section \fBSPECTRUM TYPES\fR below.
.PD 0
.IP \fB--background=\fR\fIn\fR
@@ -158,6 +158,10 @@ Set the central photon energy, in eV, for the incident beam. The default is \fB
.PD
Set the number of photons per X-ray pulse. The default is \fB--nphotons=1e12\fR. A physically reasonable value is such that the pulse energy (number of photons multiplied by photon energy) is about 1 mJ.
+.IP "\fB--beam-radius=\fIval\fR"
+.PD
+Set the radius of the X-ray beam, in metres. The default is \fB--beam-radius=1e-6\fR, i.e. a beam of 2 microns' diameter.
+
.SH REFLECTION LISTS
You'll need to create a file containing the intensities of the reflections. The normal way to do this is to use CCP4 via the "gen-sfs" script in CrystFEL's script folder. Run it like this:
@@ -219,6 +223,22 @@ Interpolate trilinearly between six adjacent Bragg intensities. This method has
.PD
As 'interpolate', but take phase values into account. This is the most accurate method, but the slowest.
+.SH SPECTRUM TYPES
+
+The available options for \fB--spectrum\fR are:
+
+.IP \fBtophat\fR
+.PD
+The spectrum samples will be distributed equidistantly either side of the specified photon energy to give a uniform distribution.
+
+.IP \fBsase\fR
+.PD
+A self-amplified spontaneous emission (SASE) spectrum will be simulated, as follows. First, a central photon energy will be chosen using a Gaussian distribution centered on the specified photon energy with a standard deviation of 8 eV. A Gaussian spectrum will then be calculated using the specified bandwidth, and noise added to simulatie the SASE 'spikes'.
+
+.IP \fBtwocolour\fR
+.PD
+The spectrum will consist of two Gaussian peaks separated by the specified bandwidth, each with a standard deviation of one fifth the specified bandwidth.
+
.SH AUTHOR
This page was written by Thomas White.