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Diffstat (limited to 'doc/man/pattern_sim.1')
| -rw-r--r-- | doc/man/pattern_sim.1 | 106 |
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. |