Merge branch 'master' into tom/speed

3 files changed, 116 insertions, 8 deletions

diff --git a/doc/man/check_hkl.1 b/doc/man/check_hkl.1
index df1f857e..39dd97ac 100644
--- a/doc/man/check_hkl.1
+++ b/doc/man/check_hkl.1
@@ -37,12 +37,6 @@ Specify the symmetry of the reflections.
 Discard reflections with I/sigma(I) < \fIn\fR.  Default: -infinity (no cutoff).
 
 .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--rmin=\fR\fI1/d\fR
 .PD
 Fix the lower resolution limit for the resolutions shells, as 1/d in m^-1.
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index ac443906..5bc3f7c0 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -216,7 +216,6 @@ these.  The defaults are probably not appropriate for your situation.
 .PD
 The default is \fB--int-radius=4,5,7\fR.
 
-
 .PD 0
 .IP \fB--basename\fR
 .PD
@@ -296,9 +295,18 @@ Run \fIn\fR analyses in parallel.  Default: 1.
 Don't attempt to correct the prefix (see \fB--prefix\fR) if it doesn't look correct.
 
 .PD 0
+.IP \fB--closer-peak\fR
+.PD
+If you use this option, indexamajig will integrate around the location of a detected peak instead of the predicted peak location if one is found close to the predicted position, within ten pixels.  \fBDon't use this option\fR, because
+there is currently no way to set the definition of 'nearby' to be appropriate
+for your data.
+
+.PD 0
 .IP \fB--no-closer-peak\fR
 .PD
-Normally, indexamajig will integrate around the location of a detected peak instead of the predicted peak location if one is found close to the predicted position.  This option disables this behaviour.  Normally it doesn't make much difference either way.
+This is the opposite of \fB--closer-peak\fR, and is provided for compatibility
+with old scripts because this option selects the behaviour which is now the
+default.
 
 .PD 0
 .IP \fB--insane\fR
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.