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Oleksii Turkot
CrystFEL
Commits
3132451e
Commit
3132451e
authored
Feb 22, 2010
by
Thomas White
Browse files
Tidy some things up:
s convention detector geometry comments, help messages
parent
cc0db005
Changes
9
Hide whitespace changes
Inline
Side-by-side
src/cell.c
View file @
3132451e
...
...
@@ -554,6 +554,7 @@ done:
}
/* Return sin(theta)/lambda = 1/2d. Multiply by two if you want 1/d */
double
resolution
(
UnitCell
*
cell
,
signed
int
h
,
signed
int
k
,
signed
int
l
)
{
const
double
a
=
cell
->
a
;
...
...
src/compare_hkl.c
View file @
3132451e
...
...
@@ -28,7 +28,7 @@
static
void
show_help
(
const
char
*
s
)
{
printf
(
"Syntax: %s [options] <file1.hkl> <file2.hkl>
\n\n
"
,
s
);
printf
(
"Syntax: %s [options]
-a
<file1.hkl>
-b
<file2.hkl>
\n\n
"
,
s
);
printf
(
"Compare intensity lists.
\n
"
"
\n
"
...
...
src/detector.c
View file @
3132451e
...
...
@@ -191,6 +191,7 @@ void record_image(struct image *image, int do_water, int do_poisson,
return
;
}
/* FIXME: Move to diffraction.c somehow */
if
(
do_water
)
{
struct
rvec
q
;
...
...
src/geometry-lcls.tmp
0 → 100644
View file @
3132451e
/* Set up detector configuration */
image.det.n_panels = 2;
image.det.panels = malloc(2*sizeof(struct panel));
/* Upper panel */
image.det.panels[0].min_x = 0;
image.det.panels[0].max_x = 1023;
image.det.panels[0].min_y = 512;
image.det.panels[0].max_y = 1023;
image.det.panels[0].cx = 491.9;
image.det.panels[0].cy = 440.7;
image.det.panels[0].clen = 67.0e-3;
image.det.panels[0].res = 13333.3; /* 75 micron pixel size */
/* Lower panel */
image.det.panels[1].min_x = 0;
image.det.panels[1].max_x = 1023;
image.det.panels[1].min_y = 0;
image.det.panels[1].max_y = 511;
image.det.panels[1].cx = 492.0;
image.det.panels[1].cy = 779.7;
image.det.panels[1].clen = 75.0e-3;
image.det.panels[1].res = 13333.3; /* 75 micron pixel size */
src/indexamajig.c
View file @
3132451e
...
...
@@ -170,28 +170,7 @@ int main(int argc, char *argv[])
image
.
data
=
NULL
;
image
.
indexed_cell
=
NULL
;
/* Set up detector configuration */
image
.
det
.
n_panels
=
2
;
image
.
det
.
panels
=
malloc
(
2
*
sizeof
(
struct
panel
));
/* Upper panel */
image
.
det
.
panels
[
0
].
min_x
=
0
;
image
.
det
.
panels
[
0
].
max_x
=
1023
;
image
.
det
.
panels
[
0
].
min_y
=
512
;
image
.
det
.
panels
[
0
].
max_y
=
1023
;
image
.
det
.
panels
[
0
].
cx
=
491
.
9
;
image
.
det
.
panels
[
0
].
cy
=
440
.
7
;
image
.
det
.
panels
[
0
].
clen
=
67.0e-3
;
image
.
det
.
panels
[
0
].
res
=
13333
.
3
;
/* 75 micron pixel size */
/* Lower panel */
image
.
det
.
panels
[
1
].
min_x
=
0
;
image
.
det
.
panels
[
1
].
max_x
=
1023
;
image
.
det
.
panels
[
1
].
min_y
=
0
;
image
.
det
.
panels
[
1
].
max_y
=
511
;
image
.
det
.
panels
[
1
].
cx
=
492
.
0
;
image
.
det
.
panels
[
1
].
cy
=
779
.
7
;
image
.
det
.
panels
[
1
].
clen
=
75.0e-3
;
image
.
det
.
panels
[
1
].
res
=
13333
.
3
;
/* 75 micron pixel size */
#include
"geometry-lcls.tmp"
STATUS
(
"Processing '%s'
\n
"
,
line
);
...
...
src/pattern_sim.c
View file @
3132451e
/*
* main.c
* pattern_sim.c
*
* Simulate diffraction patterns from small crystals
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
...
...
@@ -227,27 +229,7 @@ int main(int argc, char *argv[])
image
.
lambda
=
ph_en_to_lambda
(
eV_to_J
(
2.0e3
));
/* Wavelength */
image
.
molecule
=
load_molecule
();
/* Set up detector configuration */
image
.
det
.
n_panels
=
2
;
image
.
det
.
panels
=
malloc
(
2
*
sizeof
(
struct
panel
));
/* Upper panel */
image
.
det
.
panels
[
0
].
min_x
=
0
;
image
.
det
.
panels
[
0
].
max_x
=
1023
;
image
.
det
.
panels
[
0
].
min_y
=
512
;
image
.
det
.
panels
[
0
].
max_y
=
1023
;
image
.
det
.
panels
[
0
].
cx
=
491
.
9
;
image
.
det
.
panels
[
0
].
cy
=
440
.
7
;
image
.
det
.
panels
[
0
].
clen
=
67.0e-3
;
image
.
det
.
panels
[
0
].
res
=
13333
.
3
;
/* 75 micron pixel size */
/* Lower panel */
image
.
det
.
panels
[
1
].
min_x
=
0
;
image
.
det
.
panels
[
1
].
max_x
=
1023
;
image
.
det
.
panels
[
1
].
min_y
=
0
;
image
.
det
.
panels
[
1
].
max_y
=
511
;
image
.
det
.
panels
[
1
].
cx
=
492
.
0
;
image
.
det
.
panels
[
1
].
cy
=
779
.
7
;
image
.
det
.
panels
[
1
].
clen
=
75.0e-3
;
image
.
det
.
panels
[
1
].
res
=
13333
.
3
;
/* 75 micron pixel size */
#include
"geometry-lcls.tmp"
powder
=
calloc
(
image
.
width
*
image
.
height
,
sizeof
(
*
powder
));
...
...
src/process_hkl.c
View file @
3132451e
...
...
@@ -78,7 +78,7 @@ static void write_RvsQ(const char *name, double *ref, double *trueref,
for
(
h
=-
INDMAX
;
h
<
INDMAX
;
h
++
)
{
for
(
k
=-
INDMAX
;
k
<
INDMAX
;
k
++
)
{
for
(
l
=-
INDMAX
;
l
<
INDMAX
;
l
++
)
{
double
s
=
resolution
(
cell
,
h
,
k
,
l
);
double
s
=
2
.
0
*
resolution
(
cell
,
h
,
k
,
l
);
if
(
(
lookup_count
(
counts
,
h
,
k
,
l
)
>
0
)
&&
(
s
>
smax
)
)
{
smax
=
s
;
}
...
...
@@ -105,7 +105,7 @@ static void write_RvsQ(const char *name, double *ref, double *trueref,
if
(
(
h
==
0
)
&&
(
k
==
0
)
&&
(
l
==
0
)
)
continue
;
c
=
lookup_count
(
counts
,
h
,
k
,
l
);
s
=
resolution
(
cell
,
h
,
k
,
l
);
s
=
2
.
0
*
resolution
(
cell
,
h
,
k
,
l
);
if
((
s
>=
sbracket
)
&&
(
s
<
sbracket
+
smax
/
RVQDV
)
&&
(
c
>
0
))
{
double
obs
,
calc
,
obsi
;
...
...
src/reflections.c
View file @
3132451e
...
...
@@ -45,7 +45,6 @@ void write_reflections(const char *filename, unsigned int *counts,
fprintf
(
fh
,
"a %5.3f nm
\n
"
,
a
*
1e9
);
fprintf
(
fh
,
"b %5.3f nm
\n
"
,
b
*
1e9
);
fprintf
(
fh
,
"angle %5.3f deg
\n
"
,
rad2deg
(
gamma
));
fprintf
(
fh
,
"scale 10
\n
"
);
}
for
(
h
=-
INDMAX
;
h
<
INDMAX
;
h
++
)
{
...
...
@@ -65,7 +64,7 @@ void write_reflections(const char *filename, unsigned int *counts,
F
=
lookup_intensity
(
ref
,
h
,
k
,
l
)
/
N
;
if
(
zone_axis
&&
(
l
!=
0
)
)
continue
;
s
=
resolution
(
cell
,
h
,
k
,
l
);
s
=
2
.
0
*
resolution
(
cell
,
h
,
k
,
l
);
/* h, k, l, I, sigma(I), s */
fprintf
(
fh
,
"%3i %3i %3i %f %f %f
\n
"
,
h
,
k
,
l
,
F
,
0
.
0
,
s
/
1.0e9
);
...
...
src/sfac.c
View file @
3132451e
...
...
@@ -456,6 +456,7 @@ double complex *get_reflections(struct molecule *mol, double en)
int
i
;
double
s
;
/* We need sin(theta)/lambda = 1/2d */
s
=
resolution
(
mol
->
cell
,
h
,
k
,
l
);
/* Atoms are grouped by species for faster calculation */
...
...
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