Merge branch 'master' into tom/speed

1 files changed, 106 insertions, 0 deletions

diff --git a/doc/man/pattern_sim.1 b/doc/man/pattern_sim.1
index b0d2fa06..bd2b35e4 100644
--- a/doc/man/pattern_sim.1
+++ b/doc/man/pattern_sim.1
@@ -30,6 +30,96 @@ The result will be written to an HDF5 file in the current directory with the nam
 
 .SH OPTIONS
 
+.PD 0
+.IP "\fB-p\fR \fIunitcell.pdb\fR"
+.IP \fB--pdb=\fR\fIunitcell.pdb\fR
+.PD
+Specify the name of the PDB file containing at least a CRYST1 line describing the unit cell.
+
+.PD 0
+.IP \fB--gpu\fR
+.PD
+Use the GPU to speed up the calculation.  Requires that OpenCL libraries and drivers are available, and that CrystFEL was compiled with OpenCL enabled.
+
+.PD 0
+.IP \fB--gpu-dev=\fRIn\fR
+.PD
+Use GPU device number \fIn\fR.  If you omit this option, the list of GPU devices will be shown when you run pattern_sim.
+
+.PD 0
+.IP "\fB-g\fR \fIfilename\fR"
+.IP \fB--geometry=\fR\fIfilename\fR
+.PD
+Read the detector geometry description from \fIfilename\fR.  See \fBman crystfel_geometry\fR for more information.
+
+.PD 0
+.IP "\fB-b\fR \fIfilename\fR"
+.IP \fB--beam=\fR\fIfilename\fR
+.PD
+Read the beam description from \fIfilename\fR.  See \fBman crystfel_geometry\fR for more information.
+
+.PD 0
+.IP "\fB-n\fR \fn\fR"
+.IP \fB--number=\fR\fIn\fR
+.PD
+Simulate \fIn\fR patterns.  Default: \fB-n 1\fR.
+
+.PD 0
+.IP \fB--no-images\fR
+.PD
+Do not save any HDF5 files apart from the powder pattern (if requested).
+
+.PD 0
+.IP "\fB-o\fR \fIfilename\fR"
+.IP \fB--output=\fR\fIfilename\fR
+.PD
+Write the pattern to \fIfilename\fR.  The default is \fB--output=sim.5\fR.  If more than one pattern is to be simulated (see \fB--number\fR), the filename will be postfixed with a hyphen, the image number and then '.h5'.
+
+.PD 0
+.IP \fB-r\fR
+.IP \fB--random-orientation\fR
+.PD
+Make up a random orientation for each pattern simulated.
+
+.PD 0
+.IP \fB--powder=\fR\fIfilename\fR
+.PD
+Write the sum of all patterns to \fIfilename\fR.
+
+.PD 0
+.IP "\fB-i\fR \ffilename\fR"
+.IP \fB--intensities=\fR\fIfilename\fR
+.PD
+Get the intensities and phases at the reciprocal lattice points from \fIfilename\fR.
+
+.PD 0
+.IP "\fB-y\fR \fIpointgroup\fR"
+.IP \fB--symmetry=\fR\fIpointgroup\fR
+.PD
+Use \fIpointgroup\fR as the symmetry of the intensity list (see \fB--intensities\fR).
+
+.PD 0
+.IP "\fB-t\fR \fImethod\fR"
+.IP \fB--gradients=\fR\fImethod\fR
+.PD
+Use \fImethod\fR as way of calculating the molecular transform between reciprocal lattice points.  See the section \fBGRADIENT METHODS\fR below.
+
+.PD 0
+.IP \fB--really-random\fR
+.PD
+Seed the random number generator using the kernel random number generator (/dev/urandom).  This means that truly random numbers for the orientation and crystal size, instead of the same sequence being used for each new run.
+
+.PD 0
+.IP \fB--min-size=\fR\fImin\fR
+.IP \fB--min-size=\fR\fImax\fR
+.PD
+Generate random crystal sizes between \fImin\fR and \fImax\fR nanometres.  These options must be used together.
+
+.PD 0
+.IP \fB--no-noise\fR
+.PD
+Do not calculate Poisson noise.
+
 
 .SH REFLECTION LISTS
 
@@ -76,6 +166,22 @@ algorithm.  When the intensity is sufficiently high that Knuth's algorithm
 would result in machine precision problems, a normal distribution with
 standard deviation sqrt(I) is used instead.
 
+.SH GRADIENT METHODS
+
+The available options for \fB--gradients\fR as as follows:
+
+.IP \fBmosaic\fR
+.PD
+Take the intensity of the nearest Bragg position.  This is the fastest method and the only one supported on the GPU, but the least accurate.
+
+.IP \fBinterpolate\fR
+.PD
+Interpolate trilinearly between six adjacent Bragg intensities. This method has intermediate accuracy.
+
+.IP \fBphased\fR
+.PD
+As 'interpolate', but take phase values into account.  This is the most accurate method, but the slowest.
+
 .SH AUTHOR
 This page was written by Thomas White.