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Diffstat (limited to 'doc/man/indexamajig.1')
| -rw-r--r-- | doc/man/indexamajig.1 | 6 |
1 files changed, 0 insertions, 6 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index a912e19a..66bb51ad 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -446,9 +446,7 @@ These set low-level parameters for the XGANDALF indexing algorithm. .IP \fB--pinkIndexer-tolerance=\fIn\fR .IP \fB--pinkIndexer-reflection-radius=\fIn\fR .IP \fB--pinkIndexer-max-resolution-for-indexing=\fIn\fR -.IP \fB--pinkIndexer-multi\fR .IP \fB--pinkIndexer-thread-count=\fIn\fR -.IP \fB--pinkIndexer-no-check-indexed\fR .IP \fB--pinkIndexer-max-refinement-disbalance=\fIn\fR .IP \fB--pinkIndexer-override-bandwidth=\fIn\fR .IP \fB--pinkIndexer-override-visible-energy-range=\fImin-max\fR @@ -468,12 +466,8 @@ These set low-level parameters for the PinkIndexer indexing algorithm. .IP \fB--pinkIndexer-max-resolution-for-indexing\fR sets the maximum resolition in 1/A used for indexing. Peaks at high resolution don't add much information, but they add a lot of computation time. Default is infinity. Does not influence the refinement. .IP -\fB--pinkIndexer-multi\fR Use pinkIndexers own multi indexing. Should be combined with the --no-multi flag. -.IP \fB--pinkIndexer-thread-count\fR sets the thread count for internal parallelization. Default is 1. Very useful for small datasets (e.g. for screening). Internal parallelization does not significantly increase the amount of RAM needed, whereas CrystFEL's parallelization does. For HPCs typically a mixture of both parallelizations leads to best results. .IP -\fB--pinkIndexer-no-check-indexed\fR Leave the check whether a pattern is indexed completely to CrystFEL. Useful for monochromatic (since CrystFEL's prediction model is smarter than the one of pinkIndexer) or in combnation with --no-check-peaks for geometry optimization. This flag is meant to eventually disappear, when the full pink pipeline is implemented. -.IP \fB--pinkIndexer-max-refinement-disbalance Indexing solutions are dismissed if the refinement refined very well to one side of the detector and very badly to the other side. Allowed values range from 0 (no disbalance) to 2 (extreme disbalance), default 0.4. Disbalance after refinement usually appears for bad geometries or bad prior unit cell parameters. .IP \fB--pinkIndexer-override-bandwidth=\fIn\fR Overrides the bandwidth in (delta energy)/(mean energy) to use for indexing (which usually is defined in the geometry file). Should be used together with \fB--pinkIndexer-override-photon-energy=\fIn\fR. Note: this option sets the borders for the spectrum, whereas the option in the geometry file sets the standard deviation for a Gaussian that fits the spectrum. Internally, the standard deviation is multiplied by 5 to compute the hard borders of the spectrum. I.e., photon_energy_bandwith = 0.005 in the geometry file equals --pinkIndexer-override-bandwidth=0.025. For monochromatic experiments usually --pinkIndexer-override-bandwidth=0.02 is sufficiently large. If in doubt, use --pinkIndexer-override-visible-energy-range. |