Beam file removal, part I

3 files changed, 53 insertions, 60 deletions

diff --git a/doc/man/crystfel_geometry.5 b/doc/man/crystfel_geometry.5
index 462b0e98..7886fd25 100644
--- a/doc/man/crystfel_geometry.5
+++ b/doc/man/crystfel_geometry.5
@@ -8,9 +8,7 @@
 
 .TH CRYSTFEL\_GEOMETRY 5
 .SH NAME
-CRYSTFEL DETECTOR GEOMETRY AND BEAM DESCRIPTION FILES
-
-See below for information about CrystFEL's beam description files.
+CRYSTFEL DETECTOR GEOMETRY DESCRIPTION FILES
 
 .SH CRYSTFEL DETECTOR GEOMETRY FILES
 The detector geometry is taken from a text file rather than hardcoded into the
@@ -178,53 +176,6 @@ badregionB/max_ss = 512
 .PP
 See the "examples" folder for some examples (look at the ones ending in .geom).
 
-.SH CRYSTFEL BEAM DESCRIPTION FILES
-CrystFEL beam description files, usually given with \fB--beam=\fR\fIfilename\fR,
-describe the beam parameters.  The syntax of each line in the beam file is simply this:
-
-.IP
-\fIparameter\fB = \fIvalue\fR
-
-.PP
-The possible parameters are:
-
-.PD 0
-.IP \fBbeam/fluence\fR
-.PD
-The number of photons per pulse.
-
-.PD 0
-.IP \fBbeam/radius\fR
-.PD
-The radius of X-ray beam, in metres.
-
-.PD 0
-.IP \fBbeam/photon_energy\fR
-.PD
-The photon energy in electron-Volts, or an HDF5 path to a stored wavelength value, also in eV.
-
-.PD 0
-.IP \fBbeam/photon_energy_scale\fR
-.PD
-Scaling factor for the photon energy, used if the photon energy itself is taken from the HDF5 file.  This can be useful to correct old data sets which have systematically wrong energies.
-
-.PD 0
-.IP \fBbeam/bandwidth\fR
-.PD
-Bandwidth: FWHM(wavelength) over wavelength.  Note: current simulation code just uses a rectangular distribution with this as its (full) width.
-
-.PD 0
-.IP \fBbeam/divergence\fR
-Beam divergence (full convergence angle, \fBnot\fR the half-angle) in radians.
-
-.PD 0
-.IP \fBprofile_radius\fR
-.PD
-Reciprocal space 3D profile radius in m^-1.  A sphere of this radius surrounds each reciprocal space, and if any part of the sphere is inside the excited volume of reciprocal space, the reflection will be predicted.  You can change the prediction of spots by altering this value - larger numbers give more spots;
-
-.PP
-The parameters \fBbeam/fluence\fR and \fBbeam/radius\fR are only relevant when simulations, e.g. with pattern_sim.  \fBbeam/bandwidth\fR, \fBbeam/divergence\fR and \fBprofile_radius\fR affect which spots are predicted for the final stages of integration.
-
 .SH AUTHOR
 This page was written by Thomas White and Valerio Mariani.
 
diff --git a/doc/man/partial_sim.1 b/doc/man/partial_sim.1
index 0c30ba73..1521b410 100644
--- a/doc/man/partial_sim.1
+++ b/doc/man/partial_sim.1
@@ -25,7 +25,7 @@ partial_sim \- calculate partial reflections
 partial_sim calculates the intensities of idealised partial reflections from crystals in random orientations, which is useful for testing the convergence of Monte Carlo integration or scaling/post-refinement techniques.
 
 .P
-You need to provide a CrystFEL geometry file (with \fB--geometry=\fR\fImy.geom\fR or \fB-g\fR \fImy.geom\fR), a beam description file (with \fB--beam=\fR\fImy.beam\fR or \fB-b\fR \fImy.beam\fR), a file containing the unit cell to use for the simulation (with \fB--pdb=\fR\fImy.pdb\fR or \fB-p\fR \fImy.pdb\fR), and an output filename with \fB--output=\fR\fImy.stream\fR or \fB-o\fR \fImy.stream\fR.
+You need to provide a CrystFEL geometry file (with \fB--geometry=\fR\fImy.geom\fR or \fB-g\fR \fImy.geom\fR), a file containing the unit cell to use for the simulation (with \fB--pdb=\fR\fImy.pdb\fR or \fB-p\fR \fImy.pdb\fR), and an output filename with \fB--output=\fR\fImy.stream\fR or \fB-o\fR \fImy.stream\fR.
 
 For each randomly generated orientation, partial_sim calculates which reflections would appear on the detector with the specified beam parameters.  It calculates the partiality for each reflection and multiplies it by the fully integrated intensity to produce a partial intensity.  The fully integrated intensities can be taken from a file you provide (see below), otherwise they will be randomly generated (by taking the absolute value of a Gaussian random number, mean zero and standard deviation 1000).  All the partial intensities for the orientation are multiplied by an overall scaling factor, which is randomly generated with a Gaussian distribution with mean 1 and standard deviation 0.3.  The partial intensities are written to the output stream, and the process repeated for as many different orientations as you ask for (see below, default: 2).
 
@@ -120,6 +120,29 @@ For each chunk in the output stream, write a 'sketch' image in HDF5 format to \f
 .PD
 Add a Poisson-distributed background with \fIval\fR photons to the sketches (see \fB--images\fR).  The default is \fB--background=3000\fR.\fR.
 
+.PD 0
+.B
+.IP "\fB--beam-divergence=\fIval\fR"
+.PD
+Set the convergence angle (the full angle, not "half-angle"/"semi-angle") for the incident beam.  The default is \fB--beam-divergence=0.001\fR, i.e. 1 mrad.\fR.
+
+.PD 0
+.B
+.IP "\fB--beam-bandwidth=\fIval\fR"
+.PD
+Set the bandwidth, expressed as a decimal fraction applying to to wavelengths (not the photon energies), for the incident beam.  The default is \fB--beam-bandwidth=0.01\fR, i.e. 1%.\fR.
+
+.PD 0
+.B
+.IP "\fB--profile-radius=\fIval\fR"
+.PD
+Set the radius of the scattering density surrounding each reciprocal lattice point, in m^-1.  The default is \fB--profile-radius=0.001e9\fR m^-1.
+
+.PD 0
+.B
+.IP "\fB--photon-energy=\fIval\fR"
+.PD
+Set the central photon energy, in eV, for the incident beam.  The default is \fB--photon-energy=9000\fR, i.e. 9 keV X-rays.\fR.
 
 .SH AUTHOR
 This page was written by Thomas White.
diff --git a/doc/man/pattern_sim.1 b/doc/man/pattern_sim.1
index 1c3a3b41..b709ed3e 100644
--- a/doc/man/pattern_sim.1
+++ b/doc/man/pattern_sim.1
@@ -13,7 +13,7 @@ pattern_sim \- Simulation of nanocrystal diffraction patterns
 .SH SYNOPSIS
 .PP
 .B pattern_sim
-\fB-g\fR \fIdetector.geom\fR \fB-b\fR \fImy.beam\fR \fB-p\fR \fImy.pdb\fR
+\fB-g\fR \fIdetector.geom\fR \fB-p\fR \fImy.pdb\fR
 [\fBoptions\fR] \fB...\fR
 .PP
 .B pattern_sim
@@ -23,9 +23,9 @@ pattern_sim \- Simulation of nanocrystal diffraction patterns
 
 pattern_sim simulates diffraction patterns from small crystals probed with femtosecond pulses of X-rays from a free electron laser.  Typical use might be of the form:
 
-pattern_sim -g mydetector.geom -b my.beam -p my.pdb -r -i myintensities.hkl
+pattern_sim -g mydetector.geom -p my.pdb -r -i myintensities.hkl
 
-The unit cell geometry will be taken from the unit cell file you provide, and the intensities of the reflections will be interpolated from the reflection list file you provide.  The reflection list format is the same as that output by process_hkl and handled by get_hkl.  You also need beam and geometry description files (-b and -g respectively).  See `man crystfel_geometry' for details of how to create a geometry file.  Examples of both files can be found in the installation directory, which is normally /usr/local/share/doc/crystfel.
+The unit cell geometry will be taken from the unit cell file you provide, and the intensities of the reflections will be interpolated from the reflection list file you provide.  The reflection list format is the same as that output by process_hkl and handled by get_hkl.  You also need a geometry description file (-g).  See `man crystfel_geometry' for details of how to create a geometry file.  Examples of both files can be found in the installation directory, which is normally /usr/local/share/doc/crystfel.
 
 The result will be written to an HDF5 file in the current directory with the name `sim.h5'.
 
@@ -55,12 +55,6 @@ Use GPU device number \fIn\fR.  If you omit this option, the list of GPU devices
 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
@@ -144,6 +138,31 @@ Add \fIn\fR photons of Poisson-distributed background uniformly over the detecto
 .PD
 Suppress the subsidiary maxima of the shape transforms by setting I_latt(q) to zero beyond the first minimum of the function.
 
+.PD 0
+.B
+.IP "\fB--beam-divergence=\fIval\fR"
+.PD
+Set the convergence angle (the full angle, not "half-angle"/"semi-angle") for the incident beam.  The default is \fB--beam-divergence=0.001\fR, i.e. 1 mrad.\fR.
+
+.PD 0
+.B
+.IP "\fB--beam-bandwidth=\fIval\fR"
+.PD
+Set the bandwidth, expressed as a decimal fraction applying to to wavelengths (not the photon energies), for the incident beam.  The default is \fB--beam-bandwidth=0.01\fR, i.e. 1%.\fR.
+.PD
+Note: When using the two-colour or SASE spectrum, the spectrum calculation actually takes this value to be the bandwidth applying to the photon energies instead of the wavelengths.  For small bandwidths, the difference should be very small.  Sorry for the horrifying inconsistency.
+
+.PD 0
+.B
+.IP "\fB--profile-radius=\fIval\fR"
+.PD
+Set the radius of the scattering density surrounding each reciprocal lattice point, in m^-1.  The default is \fB--profile-radius=0.001e9\fR m^-1.
+
+.PD 0
+.B
+.IP "\fB--photon-energy=\fIval\fR"
+.PD
+Set the central photon energy, in eV, for the incident beam.  The default is \fB--photon-energy=9000\fR, i.e. 9 keV X-rays.\fR.
 
 .SH REFLECTION LISTS