partial_sim: Update documentation

2 files changed, 27 insertions, 12 deletions

diff --git a/doc/man/partial_sim.1 b/doc/man/partial_sim.1
index 7321b9ff..9e74b97b 100644
--- a/doc/man/partial_sim.1
+++ b/doc/man/partial_sim.1
@@ -1,7 +1,7 @@
 .\"
 .\" partial_sim man page
 .\"
-.\" Copyright © 2012-2013 Thomas White <taw@physics.org>
+.\" Copyright © 2012-2014 Thomas White <taw@physics.org>
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
 .\"
@@ -44,7 +44,7 @@ for information about CrystFEL geometry description files.
 Take the fully integrated reflection intensities from \fIfile.hkl\fR, instead of generating them randomly.
 
 .B
-.IP -n \fIn\fR
+.IP \fB-n\fR \fIn\fR
 Specify the number of different orientations to simulate.  Default: 2.
 
 .PD 0
@@ -87,7 +87,7 @@ Set the standard deviation of the distribution of overall scaling factors to \fI
 .B
 .IP "\fB--full-stddev=\fR\fIval\fR
 .PD
-Set the standard deviation of the distribution of randomly generated full intensities to \fIval\fR.  The distribution will be Gaussian, centered on zero, and the absolute value will be taken (i.e. there will be no negative values).  The default is \fB--full-stddev=1000.0\fR.  This option has no effect if you also use \fB-i\fR or \fR--input\fB.
+Set the standard deviation of the distribution of randomly generated full intensities to \fIval\fR.  The distribution will be Gaussian, centered on zero, and the absolute value will be taken (i.e. there will be no negative values).  The default is \fB--full-stddev=1000.0\fR.  This option has no effect if you also use \fB-i\fR or \fB--input\fR.
 
 .PD 0
 .B
@@ -95,6 +95,18 @@ Set the standard deviation of the distribution of randomly generated full intens
 .PD
 Set the standard deviation of the noise added to the partial intensities to \fIval\fR.  The noise will be Gaussian, and the same for all reflections.  The default is \fB--noise-stddev=20.0\fR.
 
+.PD 0
+.B
+.IP "\fB-j\fR \fIn\fR"
+.PD
+Use \fIn\fR threads for simulation.  Default: 1.
+
+.PD 0
+.B
+.IP "\fB--images=\fR\fIprefix\fR
+.PD
+For each chunk in the output stream, write an image in HDF5 format to \fIprefix\fR\fB/sim-\fR\fINNN\fR\fB.h5\fR, where \fINNN\fR is the sequence number of the chunk in the output stream.  This option is incompatible with \fB-j\fR.
+
 .SH AUTHOR
 This page was written by Thomas White.
 
diff --git a/src/partial_sim.c b/src/partial_sim.c
index e35c7ef2..bbcc5a63 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -230,11 +230,9 @@ static void show_help(const char *s)
 " -n <n>                   Simulate <n> patterns.  Default: 2.\n"
 " -r, --save-random=<file> Save randomly generated intensities to file.\n"
 "     --pgraph=<file>      Save a histogram of partiality values to file.\n"
-" -c, --cnoise=<val>       Add random noise, with a flat distribution, to the\n"
-"                          reciprocal lattice vector components given in the\n"
-"                          stream, with maximum error +/- <val> percent.\n"
-"     --osf-stddev=<val>   Set the standard deviation of the scaling factors.\n"
-"     --full-stddev=<val>  Set the standard deviation of the randomly\n"
+" -c, --cnoise=<val>       Amount of reciprocal space cell noise, in percent.\n"
+"     --osf-stddev=<val>   Standard deviation of the scaling factors.\n"
+"     --full-stddev=<val>  Standard deviation of the randomly\n"
 "                           generated full intensities, if not using -i.\n"
 "     --noise-stddev=<val>  Set the standard deviation of the noise.\n"
 "\n"
@@ -470,14 +468,14 @@ int main(int argc, char *argv[])
 			show_help(argv[0]);
 			return 0;
 
-			case 'o' :
-			output_file = strdup(optarg);
-			break;
-
 			case 'i' :
 			input_file = strdup(optarg);
 			break;
 
+			case 'o' :
+			output_file = strdup(optarg);
+			break;
+
 			case 'b' :
 			beamfile = strdup(optarg);
 			break;
@@ -579,6 +577,11 @@ int main(int argc, char *argv[])
 		return 1;
 	}
 
+	if ( (n_threads > 1) && (image_prefix != NULL) ) {
+		ERROR("Option \"--images\" is incompatible with \"-j\".\n");
+		return 1;
+	}
+
 	/* Load beam */
 	if ( beamfile == NULL ) {
 		ERROR("You need to provide a beam parameters file.\n");