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-rw-r--r--Makefile.am27
-rw-r--r--Makefile.in72
-rw-r--r--src/check_hkl.c1
-rw-r--r--src/compare_hkl.c1
-rw-r--r--src/diffraction-gpu.c1
-rw-r--r--src/diffraction.c1
-rw-r--r--src/dirax.c1
-rw-r--r--src/get_hkl.c105
-rw-r--r--src/index.c1
-rw-r--r--src/indexamajig.c1
-rw-r--r--src/mosflm.c1
-rw-r--r--src/pattern_sim.c1
-rw-r--r--src/process_hkl.c1
-rw-r--r--src/sfac.c542
-rw-r--r--src/sfac.h64
15 files changed, 70 insertions, 750 deletions
diff --git a/Makefile.am b/Makefile.am
index 738c8949..50631ced 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -25,7 +25,7 @@ LDADD = $(top_builddir)/lib/libgnu.a @IGNORE_UNUSED_LIBRARIES_CFLAGS@
src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c src/utils.c \
src/image.c src/cell.c src/hdf5-file.c \
- src/detector.c src/sfac.c src/peaks.c \
+ src/detector.c src/peaks.c \
src/reflections.c src/beam-parameters.c \
src/symmetry.c src/thread-pool.c src/reflist.c
if HAVE_OPENCL
@@ -41,7 +41,7 @@ tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c src/utils.c \
src/image.c
endif
-src_process_hkl_SOURCES = src/process_hkl.c src/sfac.c src/statistics.c \
+src_process_hkl_SOURCES = src/process_hkl.c src/statistics.c \
src/cell.c src/utils.c \
src/symmetry.c src/stream.c src/beam-parameters.c \
src/thread-pool.c src/image.c src/detector.c \
@@ -50,7 +50,7 @@ src_process_hkl_SOURCES = src/process_hkl.c src/sfac.c src/statistics.c \
src_indexamajig_SOURCES = src/indexamajig.c src/hdf5-file.c src/utils.c \
src/cell.c src/image.c src/peaks.c src/index.c \
src/filters.c src/diffraction.c src/detector.c \
- src/sfac.c src/dirax.c src/mosflm.c \
+ src/dirax.c src/mosflm.c \
src/reflections.c src/symmetry.c \
src/geometry.c src/thread-pool.c \
src/beam-parameters.c src/reflist.c src/stream.c \
@@ -66,15 +66,15 @@ src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c src/render.c \
src/thread-pool.c src/detector.c
endif
-src_get_hkl_SOURCES = src/get_hkl.c src/sfac.c src/cell.c src/utils.c \
+src_get_hkl_SOURCES = src/get_hkl.c src/cell.c src/utils.c \
src/reflections.c src/symmetry.c src/beam-parameters.c \
src/thread-pool.c
-src_compare_hkl_SOURCES = src/compare_hkl.c src/sfac.c src/cell.c src/utils.c \
+src_compare_hkl_SOURCES = src/compare_hkl.c src/cell.c src/utils.c \
src/reflections.c src/statistics.c src/symmetry.c \
src/thread-pool.c
-src_check_hkl_SOURCES = src/check_hkl.c src/sfac.c src/cell.c src/utils.c \
+src_check_hkl_SOURCES = src/check_hkl.c src/cell.c src/utils.c \
src/reflections.c src/statistics.c src/symmetry.c \
src/thread-pool.c
@@ -115,7 +115,7 @@ tests_list_check_SOURCES = tests/list_check.c src/reflist.c src/thread-pool.c \
INCLUDES = "-I$(top_srcdir)/data"
EXTRA_DIST += src/cell.h src/hdf5-file.h src/image.h src/utils.h \
- src/diffraction.h src/detector.h src/sfac.h src/reflections.h \
+ src/diffraction.h src/detector.h src/reflections.h \
src/list_tmp.h src/statistics.h src/dw-hdfsee.h \
src/render.h src/hdfsee.h src/dirax.h src/mosflm.h src/peaks.h \
src/index.h src/filters.h src/diffraction-gpu.h src/cl-utils.h \
@@ -125,16 +125,9 @@ EXTRA_DIST += src/cell.h src/hdf5-file.h src/image.h src/utils.h \
src/reflist.h
crystfeldir = $(datadir)/crystfel
-crystfel_DATA = data/diffraction.cl data/defs.h data/sfac/Ca.nff \
- data/sfac/C.nff data/sfac/Fe.nff data/sfac/H.nff \
- data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff \
- data/sfac/P.nff data/sfac/S.nff data/sfac/f0_WaasKirf.dat \
- data/hdfsee.ui
-
-EXTRA_DIST += data/sfac/Ca.nff data/sfac/C.nff data/sfac/Fe.nff \
- data/sfac/H.nff data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff \
- data/sfac/P.nff data/sfac/S.nff data/sfac/f0_WaasKirf.dat \
- data/defs.h data/diffraction.cl data/hdfsee.ui
+crystfel_DATA = data/diffraction.cl data/defs.h data/hdfsee.ui
+
+EXTRA_DIST += $(crystfel_DATA)
crystfeldocdir = $(docdir)
crystfeldoc_DATA = doc/geometry.txt doc/indexamajig.txt doc/pattern_sim.txt \
diff --git a/Makefile.in b/Makefile.in
index 499a2447..f8d4bf23 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -89,15 +89,15 @@ am_src_calibrate_detector_OBJECTS = src/calibrate_detector.$(OBJEXT) \
src_calibrate_detector_OBJECTS = $(am_src_calibrate_detector_OBJECTS)
src_calibrate_detector_LDADD = $(LDADD)
src_calibrate_detector_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
-am_src_check_hkl_OBJECTS = src/check_hkl.$(OBJEXT) src/sfac.$(OBJEXT) \
- src/cell.$(OBJEXT) src/utils.$(OBJEXT) \
- src/reflections.$(OBJEXT) src/statistics.$(OBJEXT) \
- src/symmetry.$(OBJEXT) src/thread-pool.$(OBJEXT)
+am_src_check_hkl_OBJECTS = src/check_hkl.$(OBJEXT) src/cell.$(OBJEXT) \
+ src/utils.$(OBJEXT) src/reflections.$(OBJEXT) \
+ src/statistics.$(OBJEXT) src/symmetry.$(OBJEXT) \
+ src/thread-pool.$(OBJEXT)
src_check_hkl_OBJECTS = $(am_src_check_hkl_OBJECTS)
src_check_hkl_LDADD = $(LDADD)
src_check_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
am_src_compare_hkl_OBJECTS = src/compare_hkl.$(OBJEXT) \
- src/sfac.$(OBJEXT) src/cell.$(OBJEXT) src/utils.$(OBJEXT) \
+ src/cell.$(OBJEXT) src/utils.$(OBJEXT) \
src/reflections.$(OBJEXT) src/statistics.$(OBJEXT) \
src/symmetry.$(OBJEXT) src/thread-pool.$(OBJEXT)
src_compare_hkl_OBJECTS = $(am_src_compare_hkl_OBJECTS)
@@ -119,10 +119,10 @@ am__src_cubeit_SOURCES_DIST = src/cubeit.c src/cell.c src/hdf5-file.c \
src_cubeit_OBJECTS = $(am_src_cubeit_OBJECTS)
src_cubeit_LDADD = $(LDADD)
src_cubeit_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
-am_src_get_hkl_OBJECTS = src/get_hkl.$(OBJEXT) src/sfac.$(OBJEXT) \
- src/cell.$(OBJEXT) src/utils.$(OBJEXT) \
- src/reflections.$(OBJEXT) src/symmetry.$(OBJEXT) \
- src/beam-parameters.$(OBJEXT) src/thread-pool.$(OBJEXT)
+am_src_get_hkl_OBJECTS = src/get_hkl.$(OBJEXT) src/cell.$(OBJEXT) \
+ src/utils.$(OBJEXT) src/reflections.$(OBJEXT) \
+ src/symmetry.$(OBJEXT) src/beam-parameters.$(OBJEXT) \
+ src/thread-pool.$(OBJEXT)
src_get_hkl_OBJECTS = $(am_src_get_hkl_OBJECTS)
src_get_hkl_LDADD = $(LDADD)
src_get_hkl_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
@@ -141,18 +141,18 @@ src_hdfsee_LDADD = $(LDADD)
src_hdfsee_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
am__src_indexamajig_SOURCES_DIST = src/indexamajig.c src/hdf5-file.c \
src/utils.c src/cell.c src/image.c src/peaks.c src/index.c \
- src/filters.c src/diffraction.c src/detector.c src/sfac.c \
- src/dirax.c src/mosflm.c src/reflections.c src/symmetry.c \
- src/geometry.c src/thread-pool.c src/beam-parameters.c \
- src/reflist.c src/stream.c src/reflist-utils.c \
- src/diffraction-gpu.c src/cl-utils.c
+ src/filters.c src/diffraction.c src/detector.c src/dirax.c \
+ src/mosflm.c src/reflections.c src/symmetry.c src/geometry.c \
+ src/thread-pool.c src/beam-parameters.c src/reflist.c \
+ src/stream.c src/reflist-utils.c src/diffraction-gpu.c \
+ src/cl-utils.c
@HAVE_OPENCL_TRUE@am__objects_1 = src/diffraction-gpu.$(OBJEXT) \
@HAVE_OPENCL_TRUE@ src/cl-utils.$(OBJEXT)
am_src_indexamajig_OBJECTS = src/indexamajig.$(OBJEXT) \
src/hdf5-file.$(OBJEXT) src/utils.$(OBJEXT) src/cell.$(OBJEXT) \
src/image.$(OBJEXT) src/peaks.$(OBJEXT) src/index.$(OBJEXT) \
src/filters.$(OBJEXT) src/diffraction.$(OBJEXT) \
- src/detector.$(OBJEXT) src/sfac.$(OBJEXT) src/dirax.$(OBJEXT) \
+ src/detector.$(OBJEXT) src/dirax.$(OBJEXT) \
src/mosflm.$(OBJEXT) src/reflections.$(OBJEXT) \
src/symmetry.$(OBJEXT) src/geometry.$(OBJEXT) \
src/thread-pool.$(OBJEXT) src/beam-parameters.$(OBJEXT) \
@@ -174,13 +174,13 @@ src_partialator_LDADD = $(LDADD)
src_partialator_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
am__src_pattern_sim_SOURCES_DIST = src/pattern_sim.c src/diffraction.c \
src/utils.c src/image.c src/cell.c src/hdf5-file.c \
- src/detector.c src/sfac.c src/peaks.c src/reflections.c \
+ src/detector.c src/peaks.c src/reflections.c \
src/beam-parameters.c src/symmetry.c src/thread-pool.c \
src/reflist.c src/diffraction-gpu.c src/cl-utils.c
am_src_pattern_sim_OBJECTS = src/pattern_sim.$(OBJEXT) \
src/diffraction.$(OBJEXT) src/utils.$(OBJEXT) \
src/image.$(OBJEXT) src/cell.$(OBJEXT) src/hdf5-file.$(OBJEXT) \
- src/detector.$(OBJEXT) src/sfac.$(OBJEXT) src/peaks.$(OBJEXT) \
+ src/detector.$(OBJEXT) src/peaks.$(OBJEXT) \
src/reflections.$(OBJEXT) src/beam-parameters.$(OBJEXT) \
src/symmetry.$(OBJEXT) src/thread-pool.$(OBJEXT) \
src/reflist.$(OBJEXT) $(am__objects_1)
@@ -195,7 +195,7 @@ src_powder_plot_OBJECTS = $(am_src_powder_plot_OBJECTS)
src_powder_plot_LDADD = $(LDADD)
src_powder_plot_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
am_src_process_hkl_OBJECTS = src/process_hkl.$(OBJEXT) \
- src/sfac.$(OBJEXT) src/statistics.$(OBJEXT) src/cell.$(OBJEXT) \
+ src/statistics.$(OBJEXT) src/cell.$(OBJEXT) \
src/utils.$(OBJEXT) src/symmetry.$(OBJEXT) \
src/stream.$(OBJEXT) src/beam-parameters.$(OBJEXT) \
src/thread-pool.$(OBJEXT) src/image.$(OBJEXT) \
@@ -558,18 +558,14 @@ top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
EXTRA_DIST = configure m4/gnulib-cache.m4 src/cell.h src/hdf5-file.h \
src/image.h src/utils.h src/diffraction.h src/detector.h \
- src/sfac.h src/reflections.h src/list_tmp.h src/statistics.h \
+ src/reflections.h src/list_tmp.h src/statistics.h \
src/dw-hdfsee.h src/render.h src/hdfsee.h src/dirax.h \
src/mosflm.h src/peaks.h src/index.h src/filters.h \
src/diffraction-gpu.h src/cl-utils.h src/symmetry.h \
src/povray.h src/index-priv.h src/geometry.h src/render_hkl.h \
src/stream.h src/thread-pool.h src/beam-parameters.h \
src/post-refinement.h src/hrs-scaling.h src/reflist.h \
- data/sfac/Ca.nff data/sfac/C.nff data/sfac/Fe.nff \
- data/sfac/H.nff data/sfac/Mg.nff data/sfac/N.nff \
- data/sfac/O.nff data/sfac/P.nff data/sfac/S.nff \
- data/sfac/f0_WaasKirf.dat data/defs.h data/diffraction.cl \
- data/hdfsee.ui doc/geometry.txt doc/indexamajig.txt \
+ $(crystfel_DATA) doc/geometry.txt doc/indexamajig.txt \
doc/pattern_sim.txt doc/process_hkl.txt doc/symmetry.txt \
doc/twin-calculator.pdf doc/0-INDEX doc/examples/lcls-dec.geom \
doc/examples/lcls-june-r0013-r0128.geom \
@@ -592,7 +588,7 @@ AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -I$(top_srcdir)/l
LDADD = $(top_builddir)/lib/libgnu.a @IGNORE_UNUSED_LIBRARIES_CFLAGS@
src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c \
src/utils.c src/image.c src/cell.c src/hdf5-file.c \
- src/detector.c src/sfac.c src/peaks.c src/reflections.c \
+ src/detector.c src/peaks.c src/reflections.c \
src/beam-parameters.c src/symmetry.c src/thread-pool.c \
src/reflist.c $(am__append_3)
@HAVE_OPENCL_TRUE@tests_gpu_sim_check_SOURCES = tests/gpu_sim_check.c src/utils.c \
@@ -601,7 +597,7 @@ src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c \
@HAVE_OPENCL_TRUE@ src/symmetry.c src/detector.c src/hdf5-file.c \
@HAVE_OPENCL_TRUE@ src/image.c
-src_process_hkl_SOURCES = src/process_hkl.c src/sfac.c src/statistics.c \
+src_process_hkl_SOURCES = src/process_hkl.c src/statistics.c \
src/cell.c src/utils.c \
src/symmetry.c src/stream.c src/beam-parameters.c \
src/thread-pool.c src/image.c src/detector.c \
@@ -609,23 +605,23 @@ src_process_hkl_SOURCES = src/process_hkl.c src/sfac.c src/statistics.c \
src_indexamajig_SOURCES = src/indexamajig.c src/hdf5-file.c \
src/utils.c src/cell.c src/image.c src/peaks.c src/index.c \
- src/filters.c src/diffraction.c src/detector.c src/sfac.c \
- src/dirax.c src/mosflm.c src/reflections.c src/symmetry.c \
- src/geometry.c src/thread-pool.c src/beam-parameters.c \
- src/reflist.c src/stream.c src/reflist-utils.c $(am__append_6)
+ src/filters.c src/diffraction.c src/detector.c src/dirax.c \
+ src/mosflm.c src/reflections.c src/symmetry.c src/geometry.c \
+ src/thread-pool.c src/beam-parameters.c src/reflist.c \
+ src/stream.c src/reflist-utils.c $(am__append_6)
@BUILD_HDFSEE_TRUE@src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c src/render.c \
@BUILD_HDFSEE_TRUE@ src/hdf5-file.c src/utils.c src/image.c src/filters.c \
@BUILD_HDFSEE_TRUE@ src/thread-pool.c src/detector.c
-src_get_hkl_SOURCES = src/get_hkl.c src/sfac.c src/cell.c src/utils.c \
+src_get_hkl_SOURCES = src/get_hkl.c src/cell.c src/utils.c \
src/reflections.c src/symmetry.c src/beam-parameters.c \
src/thread-pool.c
-src_compare_hkl_SOURCES = src/compare_hkl.c src/sfac.c src/cell.c src/utils.c \
+src_compare_hkl_SOURCES = src/compare_hkl.c src/cell.c src/utils.c \
src/reflections.c src/statistics.c src/symmetry.c \
src/thread-pool.c
-src_check_hkl_SOURCES = src/check_hkl.c src/sfac.c src/cell.c src/utils.c \
+src_check_hkl_SOURCES = src/check_hkl.c src/cell.c src/utils.c \
src/reflections.c src/statistics.c src/symmetry.c \
src/thread-pool.c
@@ -663,12 +659,7 @@ tests_list_check_SOURCES = tests/list_check.c src/reflist.c src/thread-pool.c \
INCLUDES = "-I$(top_srcdir)/data"
crystfeldir = $(datadir)/crystfel
-crystfel_DATA = data/diffraction.cl data/defs.h data/sfac/Ca.nff \
- data/sfac/C.nff data/sfac/Fe.nff data/sfac/H.nff \
- data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff \
- data/sfac/P.nff data/sfac/S.nff data/sfac/f0_WaasKirf.dat \
- data/hdfsee.ui
-
+crystfel_DATA = data/diffraction.cl data/defs.h data/hdfsee.ui
crystfeldocdir = $(docdir)
crystfeldoc_DATA = doc/geometry.txt doc/indexamajig.txt doc/pattern_sim.txt \
doc/process_hkl.txt doc/symmetry.txt \
@@ -811,7 +802,6 @@ src/calibrate_detector$(EXEEXT): $(src_calibrate_detector_OBJECTS) $(src_calibra
$(AM_V_CCLD)$(LINK) $(src_calibrate_detector_OBJECTS) $(src_calibrate_detector_LDADD) $(LIBS)
src/check_hkl.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-src/sfac.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
src/cell.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
src/reflections.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
@@ -963,7 +953,6 @@ mostlyclean-compile:
-rm -f src/reflist.$(OBJEXT)
-rm -f src/render.$(OBJEXT)
-rm -f src/render_hkl.$(OBJEXT)
- -rm -f src/sfac.$(OBJEXT)
-rm -f src/statistics.$(OBJEXT)
-rm -f src/stream.$(OBJEXT)
-rm -f src/sum_stack.$(OBJEXT)
@@ -1010,7 +999,6 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/reflist.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/render.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/render_hkl.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/sfac.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/statistics.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/stream.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/sum_stack.Po@am__quote@
diff --git a/src/check_hkl.c b/src/check_hkl.c
index b36150b2..fb6d02d5 100644
--- a/src/check_hkl.c
+++ b/src/check_hkl.c
@@ -22,7 +22,6 @@
#include <getopt.h>
#include "utils.h"
-#include "sfac.h"
#include "reflections.h"
#include "statistics.h"
#include "symmetry.h"
diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index dca4a298..abe8bc6a 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -22,7 +22,6 @@
#include <getopt.h>
#include "utils.h"
-#include "sfac.h"
#include "reflections.h"
#include "statistics.h"
#include "symmetry.h"
diff --git a/src/diffraction-gpu.c b/src/diffraction-gpu.c
index 74eca439..c0814e79 100644
--- a/src/diffraction-gpu.c
+++ b/src/diffraction-gpu.c
@@ -29,7 +29,6 @@
#include "utils.h"
#include "cell.h"
#include "diffraction.h"
-#include "sfac.h"
#include "cl-utils.h"
#include "beam-parameters.h"
diff --git a/src/diffraction.c b/src/diffraction.c
index e3d7435c..cd372a28 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -22,7 +22,6 @@
#include "utils.h"
#include "cell.h"
#include "diffraction.h"
-#include "sfac.h"
#include "beam-parameters.h"
#include "symmetry.h"
diff --git a/src/dirax.c b/src/dirax.c
index 35a2b1ce..291dc85b 100644
--- a/src/dirax.c
+++ b/src/dirax.c
@@ -36,7 +36,6 @@
#include "image.h"
#include "dirax.h"
#include "utils.h"
-#include "sfac.h"
#include "peaks.h"
diff --git a/src/get_hkl.c b/src/get_hkl.c
index cddb54b8..f8a43ddb 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -1,9 +1,9 @@
/*
* get_hkl.c
*
- * Small program to write out a list of h,k,l,I values given a structure
+ * Small program to manipulate reflection lists
*
- * (c) 2006-2010 Thomas White <taw@physics.org>
+ * (c) 2006-2011 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
@@ -22,7 +22,6 @@
#include <getopt.h>
#include "utils.h"
-#include "sfac.h"
#include "reflections.h"
#include "symmetry.h"
#include "beam-parameters.h"
@@ -32,27 +31,34 @@ static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
printf(
-"Create reflections lists.\n"
+"Manipulate reflection lists.\n"
"\n"
" -h, --help Display this help message.\n"
"\n"
-" -t, --template=<filename> Only include reflections mentioned in file.\n"
+" -i, --input=<file> Read reflections from <file>.\n"
+" -y, --symmetry=<sym> The symmetry of the input reflection list.\n"
+"\n"
+"You can add noise to the reflections with either of:\n"
" --poisson Simulate Poisson samples.\n"
" --noise Add 10%% random noise.\n"
-" -y, --symmetry=<sym> The symmetry of the input file (-i).\n"
+"\n"
+"To calculate Poisson samples accurately, you must also give:\n"
+" -b, --beam=<file> Get beam parameters from file.\n"
+"\n"
+"You can artificially 'twin' the reflections, or expand them out:\n"
" -w, --twin=<sym> Generate twinned data according to the given\n"
" point group.\n"
" -e, --expand=<sym> Expand reflections to this point group.\n"
-" -o, --output=<filename> Output filename (default: stdout).\n"
-" -i, --intensities=<file> Read intensities from file instead of\n"
-" calculating them from scratch. You might use\n"
-" this if you need to apply noise or twinning.\n"
-" -p, --pdb=<file> PDB file from which to get the structure.\n"
-" --no-phases Do not try to use phases in the input file.\n"
+"\n"
+"You can restrict which reflections are written out:\n"
+" -t, --template=<filename> Only include reflections mentioned in file.\n"
+"\n"
+"You might sometimes need to do this:\n"
" --multiplicity Multiply intensities by the number of\n"
" equivalent reflections.\n"
-" -b, --beam=<file> Get beam parameters from file (used for sigmas).\n"
-" --max-res=<d> Calculate structure factors out to d=<d> nm.\n"
+"\n"
+"Don't forget to specify the output filename:\n"
+" -o, --output=<filename> Output filename (default: stdout).\n"
);
}
@@ -253,7 +259,6 @@ int main(int argc, char *argv[])
double *ideal_ref;
double *phases;
double *esds;
- struct molecule *mol;
char *template = NULL;
int config_noise = 0;
int config_poisson = 0;
@@ -269,10 +274,7 @@ int main(int argc, char *argv[])
ReflItemList *write_items;
UnitCell *cell = NULL;
char *beamfile = NULL;
- char *rval;
- struct beam_params *beam; /* Beam parameters for SF calculation */
- int have_max_res = 0;
- double max_res = 0.0;
+ struct beam_params *beam; /* Beam parameters for Poisson calculation */
/* Long options */
const struct option longopts[] = {
@@ -285,16 +287,13 @@ int main(int argc, char *argv[])
{"twin", 1, NULL, 'w'},
{"expand", 1, NULL, 'e'},
{"intensities", 1, NULL, 'i'},
- {"pdb", 1, NULL, 'p'},
- {"no-phases", 0, &config_nophase, 1},
{"multiplicity", 0, &config_multi, 1},
{"beam", 1, NULL, 'b'},
- {"max-res", 1, NULL, 2},
{0, 0, NULL, 0}
};
/* Short options */
- while ((c = getopt_long(argc, argv, "ht:o:i:p:w:y:e:b:",
+ while ((c = getopt_long(argc, argv, "ht:o:i:w:y:e:b:",
longopts, NULL)) != -1) {
switch (c) {
@@ -314,10 +313,6 @@ int main(int argc, char *argv[])
input = strdup(optarg);
break;
- case 'p' :
- filename = strdup(optarg);
- break;
-
case 'y' :
mero = strdup(optarg);
break;
@@ -334,16 +329,6 @@ int main(int argc, char *argv[])
beamfile = strdup(optarg);
break;
- case 2 :
- max_res = strtod(optarg, &rval);
- if ( *rval != '\0' ) {
- ERROR("Invalid maximum resolution.\n");
- return 1;
- }
- max_res = 1.0 / (max_res * 1.0e-9);
- have_max_res = 1;
- break;
-
case 0 :
break;
@@ -363,7 +348,6 @@ int main(int argc, char *argv[])
exit(1);
}
- mol = load_molecule(filename);
cell = load_cell_from_pdb(filename);
if ( !config_nophase ) {
phases = new_list_phase();
@@ -371,44 +355,15 @@ int main(int argc, char *argv[])
phases = NULL;
}
esds = new_list_sigma();
- if ( input == NULL ) {
-
- if ( beamfile == NULL ) {
- ERROR("To calculate structure factors, you must"
- " provide a beam parameters file (use -b)\n");
- return 1;
- }
-
- beam = get_beam_parameters(beamfile);
- if ( beam == NULL ) {
- ERROR("Failed to read beam parameters from '%s'\n", beamfile);
- return 1;
- }
- free(beamfile);
-
- if ( !have_max_res ) {
- STATUS("You didn't specify the maximum resolution to"
- " calculate structure factors. I'll go to"
- " d = 0.5 nm.\n");
- max_res = 1.0/0.5e-9;
- }
-
- input_items = new_items();
- ideal_ref = get_reflections(mol, eV_to_J(beam->photon_energy),
- max_res, phases, input_items);
-
- } else {
-
- ideal_ref = new_list_intensity();
- input_items = read_reflections(input, ideal_ref, phases,
- NULL, esds);
- free(input);
- if ( check_symmetry(input_items, mero) ) {
- ERROR("The input reflection list does not appear to"
- " have symmetry %s\n", mero);
- return 1;
- }
+ ideal_ref = new_list_intensity();
+ input_items = read_reflections(input, ideal_ref, phases,
+ NULL, esds);
+ free(input);
+ if ( check_symmetry(input_items, mero) ) {
+ ERROR("The input reflection list does not appear to"
+ " have symmetry %s\n", mero);
+ return 1;
}
if ( config_poisson ) poisson_reflections(ideal_ref, input_items);
diff --git a/src/index.c b/src/index.c
index d24b5852..317c9200 100644
--- a/src/index.c
+++ b/src/index.c
@@ -26,7 +26,6 @@
#include "peaks.h"
#include "dirax.h"
#include "mosflm.h"
-#include "sfac.h"
#include "detector.h"
#include "index.h"
#include "index-priv.h"
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 80dd7e50..f53e4d85 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -30,7 +30,6 @@
#include "index.h"
#include "peaks.h"
#include "detector.h"
-#include "sfac.h"
#include "filters.h"
#include "reflections.h"
#include "thread-pool.h"
diff --git a/src/mosflm.c b/src/mosflm.c
index fe6cfca7..593b04eb 100644
--- a/src/mosflm.c
+++ b/src/mosflm.c
@@ -61,7 +61,6 @@
#include "image.h"
#include "mosflm.h"
#include "utils.h"
-#include "sfac.h"
#include "peaks.h"
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index 18b009eb..6d3c07ab 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -29,7 +29,6 @@
#include "hdf5-file.h"
#include "detector.h"
#include "peaks.h"
-#include "sfac.h"
#include "reflections.h"
#include "beam-parameters.h"
#include "symmetry.h"
diff --git a/src/process_hkl.c b/src/process_hkl.c
index 90428426..6ff40159 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -23,7 +23,6 @@
#include "utils.h"
#include "statistics.h"
-#include "sfac.h"
#include "reflist-utils.h"
#include "symmetry.h"
#include "stream.h"
diff --git a/src/sfac.c b/src/sfac.c
deleted file mode 100644
index 8b69f2e3..00000000
--- a/src/sfac.c
+++ /dev/null
@@ -1,542 +0,0 @@
-/*
- * sfac.c
- *
- * Scattering factors
- *
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-
-#include <stdlib.h>
-#include <math.h>
-#include <stdio.h>
-#include <complex.h>
-#include <string.h>
-#include <ctype.h>
-
-#include "utils.h"
-#include "sfac.h"
-
-
-#define N_MEMO 1024
-
-
-/* Look up f1 and f2 for this atom at this energy (in J/photon) */
-static double complex get_f1f2(const char *n, double en)
-{
- FILE *fh;
- char filename[64];
- char line[1024];
- char *rval;
- double last_E, last_f1, last_f2;
- static char *memo_n[N_MEMO];
- static int memo_eV[N_MEMO];
- static double complex memo_res[N_MEMO];
- static int n_memo = 0;
- int eV;
- int i;
-
- eV = (int)rint(J_to_eV(en));
-
- for ( i=0; i<n_memo; i++ ) {
- if ( (memo_eV[i] == eV) && (strcmp(memo_n[i], n) == 0) ) {
- return memo_res[i];
- }
- }
-
- snprintf(filename, 63, DATADIR"/crystfel/%s.nff", n);
- fh = fopen(filename, "r");
- if ( fh == NULL ) {
- ERROR("Couldn't open file '%s'\n", filename);
- return 0.0;
- }
-
- en = J_to_eV(en);
-
- /* Discard first line */
- fgets(line, 1023, fh);
-
- last_E = 0.0;
- last_f1 = 0.0;
- last_f2 = 0.0;
- do {
-
- int r;
- double E, f1, f2;
- float E_f, f1_f, f2_f;
-
- rval = fgets(line, 1023, fh);
-
- r = sscanf(line, "%f %f %f", &E_f, &f1_f, &f2_f);
- if ( r != 3 ) {
- STATUS("I couldn't understand a line in the f1f2 "
- "tables\n");
- continue;
- }
- /* Promote to double precision */
- E = E_f; f1 = f1_f; f2 = f2_f;
-
- /* Find the first energy greater than the required value */
- if ( E < en ) {
- /* Store old values ready for interpolation*/
- last_E = E;
- last_f1 = f1;
- last_f2 = f2;
- } else {
-
- /* Perform (linear) interpolation */
- double f;
- double actual_f1, actual_f2;
- double complex res;
-
- f = (en - last_E) / (E - last_E);
-
- actual_f1 = last_f1 + f * (f1 - last_f1);
- actual_f2 = last_f2 + f * (f2 - last_f2);
-
- fclose(fh);
-
- res = actual_f1 + I*actual_f2;
-
- memo_n[n_memo] = strdup(n);
- memo_eV[n_memo] = eV;
- memo_res[n_memo++] = res;
- n_memo = n_memo % N_MEMO;
-
- return res;
-
- }
-
- } while ( rval != NULL );
-
- fclose(fh);
-
- ERROR("Couldn't find scattering factors for '%s' at %f eV!\n", n, en);
-
- return 0.0;
-}
-
-
-struct waas_kirf_factors {
- char *n;
- float a1;
- float a2;
- float a3;
- float a4;
- float a5;
- float b1;
- float b2;
- float b3;
- float b4;
- float b5;
- float c;
-};
-
-/* s = sin(theta)/lambda in metres^-1*/
-static double get_waas_kirf(const char *n, double s)
-{
- FILE *fh;
- char *rval;
- double f;
- float a1, a2, a3, a4, a5, c, b1, b2, b3, b4, b5;
- double s2;
- int i;
- static struct waas_kirf_factors waaskirfcache[N_MEMO];
- int found;
- static int n_waaskirfcache = 0;
-
- found = 0;
- for ( i=0; i<n_waaskirfcache; i++ ) {
- if ( strcmp(waaskirfcache[i].n, n) == 0 ) {
-
- found = 1;
-
- a1 = waaskirfcache[n_waaskirfcache].a1;
- a2 = waaskirfcache[n_waaskirfcache].a2;
- a3 = waaskirfcache[n_waaskirfcache].a3;
- a4 = waaskirfcache[n_waaskirfcache].a4;
- a5 = waaskirfcache[n_waaskirfcache].a5;
- b1 = waaskirfcache[n_waaskirfcache].b1;
- b2 = waaskirfcache[n_waaskirfcache].b2;
- b3 = waaskirfcache[n_waaskirfcache].b3;
- b4 = waaskirfcache[n_waaskirfcache].b4;
- b5 = waaskirfcache[n_waaskirfcache].b5;
- c = waaskirfcache[n_waaskirfcache].c;
-
- break;
- }
- }
-
- if ( !found ) {
-
- fh = fopen(DATADIR"/crystfel/f0_WaasKirf.dat", "r");
- if ( fh == NULL ) {
- ERROR("Couldn't open f0_WaasKirf.dat\n");
- return 0.0;
- }
-
- do {
-
- int r;
- char line[1024];
- char sp[1024];
- int Z;
-
- rval = fgets(line, 1023, fh);
-
- if ( (line[0] != '#') || (line[1] != 'S') ) continue;
-
- r = sscanf(line, "#S %i %s", &Z, sp);
- if ( (r != 2) || (strcmp(sp, n) != 0) ) continue;
-
- /* Skip two lines */
- fgets(line, 1023, fh);
- fgets(line, 1023, fh);
-
- /* Read scattering coefficients */
- rval = fgets(line, 1023, fh);
- r = sscanf(line,
- " %f %f %f %f %f %f %f %f %f %f %f",
- &a1, &a2, &a3, &a4, &a5, &c,
- &b1, &b2, &b3, &b4, &b5);
- if ( r != 11 ) {
- ERROR("Couldn't read scattering "
- "factors (WaasKirf)\n");
- return 0.0;
- }
-
- break;
-
- } while ( rval != NULL );
-
- fclose(fh);
-
- waaskirfcache[n_waaskirfcache].a1 = a1;
- waaskirfcache[n_waaskirfcache].a2 = a2;
- waaskirfcache[n_waaskirfcache].a3 = a3;
- waaskirfcache[n_waaskirfcache].a4 = a4;
- waaskirfcache[n_waaskirfcache].a5 = a5;
- waaskirfcache[n_waaskirfcache].c = c;
- waaskirfcache[n_waaskirfcache].b1 = b1;
- waaskirfcache[n_waaskirfcache].b2 = b2;
- waaskirfcache[n_waaskirfcache].b3 = b3;
- waaskirfcache[n_waaskirfcache].b4 = b4;
- waaskirfcache[n_waaskirfcache].b5 = b5;
- waaskirfcache[n_waaskirfcache++].n = strdup(n);
- n_waaskirfcache = n_waaskirfcache % N_MEMO; /* Unlikely */
-
- }
-
- s2 = pow(s/1e10, 2.0); /* s2 is s squared in Angstroms^-2 */
- f = c + a1*exp(-b1*s2) + a2*exp(-b2*s2) + a3*exp(-b3*s2)
- + a4*exp(-b4*s2) + a5*exp(-b5*s2);
-
- return f;
-}
-
-
-/* Get complex scattering factors for element 'n' at energy 'en' (J/photon),
- * at resolution 's' = sin(theta)/lambda (in m^-1) */
-static double complex get_sfac(const char *n, double s, double en)
-{
- double complex f1f2;
- double fq;
-
- /* Anomalous part (point-like K-shell electrons only) */
- f1f2 = get_f1f2(n, en);
-
- /* Atomic form factor part (not complex-valued) */
- fq = get_waas_kirf(n, s) - get_waas_kirf(n, 0.0);
-
- return fq + f1f2;
-}
-
-
-static void centre_molecule(struct molecule *mol)
-{
- int i;
- double tx = 0.0;
- double ty = 0.0;
- double tz = 0.0;
- double total = 0.0;
-
- /* Atoms are grouped by species for faster calculation */
- for ( i=0; i<mol->n_species; i++ ) {
-
- struct mol_species *spec;
- int j;
-
- spec = mol->species[i];
-
- for ( j=0; j<spec->n_atoms; j++ ) {
-
- double sfac = get_waas_kirf(spec->species, 0.0);
-
- tx += spec->x[j] * sfac;
- ty += spec->y[j] * sfac;
- tz += spec->z[j] * sfac;
- total += sfac;
-
- }
-
- }
-
- mol->xc = tx / total;
- mol->yc = ty / total;
- mol->zc = tz / total;
-
- for ( i=0; i<mol->n_species; i++ ) {
-
- struct mol_species *spec;
- int j;
-
- spec = mol->species[i];
-
- for ( j=0; j<spec->n_atoms; j++ ) {
-
- spec->x[j] -= mol->xc;
- spec->y[j] -= mol->yc;
- spec->z[j] -= mol->zc;
-
- }
-
- }
-
- STATUS("The atoms were shifted by %5.3f, %5.3f, %5.3f nm\n",
- mol->xc*1e9, mol->yc*1e9, mol->zc*1e9);
-}
-
-
-/* Load PDB file into a memory format suitable for efficient(ish) structure
- * factor calculation */
-struct molecule *load_molecule(const char *filename)
-{
- struct molecule *mol;
- FILE *fh;
- char line[1024];
- char *rval;
- int i;
-
- mol = malloc(sizeof(struct molecule));
- if ( mol == NULL ) return NULL;
- mol->n_species = 0;
- mol->reflections = NULL;
- mol->cell = NULL;
-
- fh = fopen(filename, "r");
- if ( fh == NULL ) {
- ERROR("Couldn't open PDB file\n");
- return NULL;
- }
-
- do {
-
- int j, r;
- int done = 0;
- char xs[8];
- char ys[8];
- char zs[8];
- char occs[6];
- char Bs[6];
- char el[3];
- float xf, yf, zf, occf, Bf;
- double x, y, z, occ, B;
-
- rval = fgets(line, 1023, fh);
-
- /* Only interested in atoms */
- if ( (strncmp(line, "HETATM", 6) != 0)
- && (strncmp(line, "ATOM ", 6) != 0) ) continue;
-
- chomp(line);
- if ( strlen(line) != 80 ) {
- STATUS("Line does not have the correct length (%i):\n",
- (int)strlen(line));
- STATUS("'%s'\n", line);
- continue;
- }
-
- /* Separate out fixed-width fields */
- memcpy(xs, line+30, 5); xs[7] = '\0';
- memcpy(ys, line+38, 5); ys[7] = '\0';
- memcpy(zs, line+46, 5); zs[7] = '\0';
- memcpy(occs, line+54, 5); occs[5] = '\0';
- memcpy(Bs, line+60, 5); Bs[5] = '\0';
- memcpy(el, line+76, 2); el[2] = '\0';
-
- /* Convert fields */
- r = sscanf(xs, "%f", &xf);
- r += sscanf(ys, "%f", &yf);
- r += sscanf(zs, "%f", &zf);
- r += sscanf(occs, "%f", &occf);
- r += sscanf(Bs, "%f", &Bf);
- if ( el[0] == ' ' ) {
- el[0] = el[1];
- el[1] = '\0';
- } else {
- el[1] = tolower(el[1]);
- }
-
- /* Promote to double precision */
- x = xf; y = yf; z = zf; occ = occf; B = Bf;
-
- for ( j=0; j<mol->n_species; j++ ) {
-
- struct mol_species *spec;
- int n;
-
- spec = mol->species[j];
-
- if ( strcmp(spec->species, el) != 0 ) continue;
-
- n = mol->species[j]->n_atoms;
-
- spec->x[n] = x*1.0e-10; /* Convert to m */
- spec->y[n] = y*1.0e-10;
- spec->z[n] = z*1.0e-10;
- spec->occ[n] = occ;
- spec->B[n] = B*1.0e-20; /* Convert to m^2 */
- mol->species[j]->n_atoms++;
- if ( mol->species[j]->n_atoms == MAX_ATOMS ) {
- ERROR("Too many atoms of type '%s'!\n", el);
- exit(1);
- }
-
- done = 1;
-
- }
-
- if ( !done ) {
-
- /* Need to create record for this species */
- struct mol_species *spec;
-
- spec = malloc(sizeof(struct mol_species));
-
- memcpy(spec->species, el, 1+strlen(el));
- spec->x[0] = x*1.0e-10; /* Convert to m */
- spec->y[0] = y*1.0e-10;
- spec->z[0] = z*1.0e-10;
- spec->occ[0] = occ;
- spec->B[0] = B*1.0e-20; /* Convert to m^2 */
- spec->n_atoms = 1;
-
- mol->species[mol->n_species] = spec;
- mol->n_species++;
-
- }
-
- } while ( rval != NULL );
-
- fclose(fh);
-
- centre_molecule(mol);
-
- STATUS("There are %i species:\n", mol->n_species); fflush(stderr);
- for ( i=0; i<mol->n_species; i++ ) {
- STATUS("%3s : %6i\n", mol->species[i]->species,
- mol->species[i]->n_atoms);
- }
-
- mol->cell = load_cell_from_pdb(filename);
- if ( mol->cell == NULL ) {
- ERROR("No unit cell found in PDB file\n");
- return NULL;
- }
-
- return mol;
-}
-
-
-void free_molecule(struct molecule *mol)
-{
- int i;
-
- for ( i=0; i<mol->n_species; i++ ) {
- free(mol->species[i]);
- }
-
- free(mol->cell);
- free(mol);
-}
-
-
-double *get_reflections(struct molecule *mol, double en, double res,
- double *phases, ReflItemList *items)
-{
- double *reflections;
- double asx, asy, asz;
- double bsx, bsy, bsz;
- double csx, csy, csz;
- signed int h, k, l;
- const int do_thermal = 1;
-
- cell_get_reciprocal(mol->cell, &asx, &asy, &asz,
- &bsx, &bsy, &bsz,
- &csx, &csy, &csz);
-
- reflections = new_list_intensity();
-
- for ( h=-INDMAX; h<=INDMAX; h++ ) {
- for ( k=-INDMAX; k<=INDMAX; k++ ) {
- for ( l=-INDMAX; l<=INDMAX; l++ ) {
-
- double complex F = 0.0;
- int i;
- double s, oneoverd;
-
- /* We need sin(theta)/lambda = 1/2d */
- s = resolution(mol->cell, h, k, l);
- oneoverd = 2.0 * s;
- if ( oneoverd > res ) continue;
-
- /* Atoms are grouped by species for faster calculation */
- for ( i=0; i<mol->n_species; i++ ) {
-
- double complex sfac;
- double complex contrib = 0.0;
- struct mol_species *spec;
- int j;
-
- spec = mol->species[i];
-
- for ( j=0; j<spec->n_atoms; j++ ) {
-
- double ph, u, v, w;
- double complex cpart;
-
- u = h*asx + k*bsx + l*csx;
- v = h*asy + k*bsy + l*csy;
- w = h*asz + k*bsz + l*csz;
-
- ph = u*spec->x[j] + v*spec->y[j] + w*spec->z[j];
-
- /* Conversion from revolutions to radians */
- cpart = cexp(-2.0*M_PI*I*ph);
- if ( do_thermal ) {
- cpart *= exp(-2.0 * spec->B[j] * s * s);
- }
- contrib += cpart;
-
- }
-
- sfac = get_sfac(spec->species, s, en);
- F += sfac * contrib;
-
- }
-
- set_intensity(reflections, h, k, l, pow(cabs(F), 2.0));
- if ( phases != NULL ) set_phase(phases, h, k, l, carg(F));
- if ( items != NULL ) add_item(items, h, k, l);
-
- }
- progress_bar((k+INDMAX)+IDIM*(h+INDMAX), IDIM*IDIM-1,
- "Calculating reflection intensities");
- }
- }
-
- return reflections;
-}
diff --git a/src/sfac.h b/src/sfac.h
deleted file mode 100644
index e05b3ddf..00000000
--- a/src/sfac.h
+++ /dev/null
@@ -1,64 +0,0 @@
-/*
- * sfac.h
- *
- * Scattering factors
- *
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#ifndef SFAC_H
-#define SFAC_H
-
-#include <complex.h>
-
-#include "cell.h"
-#include "utils.h"
-
-
-#define MAX_ATOMS (128*1024)
-
-
-struct mol_species
-{
- char species[4]; /* Species name */
- int n_atoms; /* Number of atoms of this species */
-
- double x[MAX_ATOMS];
- double y[MAX_ATOMS];
- double z[MAX_ATOMS];
- double occ[MAX_ATOMS];
- double B[MAX_ATOMS];
-};
-
-
-struct molecule
-{
- int n_species;
- struct mol_species *species[32];
-
- /* Unit cell */
- UnitCell *cell;
-
- /* Reflection intensities at Bragg positions */
- double complex *reflections;
-
- /* Offset to molecule's centre of scattering power */
- double xc;
- double yc;
- double zc;
-};
-
-extern struct molecule *load_molecule(const char *filename);
-extern void free_molecule(struct molecule *mol);
-extern double *get_reflections(struct molecule *mol, double en, double res,
- double *phases, ReflItemList *items);
-
-
-#endif /* SFAC_H */
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