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Oleksii Turkot
CrystFEL
Commits
93cc3f13
Commit
93cc3f13
authored
Nov 27, 2009
by
Thomas White
Browse files
Improve help messages
parent
7c521735
Changes
1
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Inline
Side-by-side
src/pattern_sim.c
View file @
93cc3f13
...
...
@@ -30,24 +30,67 @@
static
void
show_help
(
const
char
*
s
)
{
printf
(
"Syntax: %s
\n\n
"
,
s
);
printf
(
"Simulate diffraction patterns from small crystals
\n
"
);
printf
(
" probed with femosecond pulses from a free electron laser.
\n\n
"
);
printf
(
" -h, --help Display this help message
\n
"
);
printf
(
" --simulation-details Show details of the simulation
\n
"
);
printf
(
" --near-bragg Output h,k,l,I near Bragg conditions
\n
"
);
printf
(
" -r, --random-orientation Use a randomly generated orientation
\n
"
);
printf
(
" (a new orientation will be used for each image)
\n
"
);
printf
(
" -n, --number=<N> Generate N images. Default 1
\n
"
);
printf
(
"Simulate diffraction patterns from small crystals probed with femosecond
\n
"
"pulses of X-rays from a free electron laser.
\n
"
"
\n
"
" -h, --help Display this help message
\n
"
" --simulation-details Show technical details of the simulation
\n
"
" --near-bragg Output h,k,l,I near Bragg conditions
\n
"
" -r, --random-orientation Use a randomly generated orientation
\n
"
" (a new orientation will be used for each image)
\n
"
" -n, --number=<N> Generate N images. Default 1
\n
"
);
}
static
void
show_details
()
{
printf
(
"This program simulates diffraction patterns from small crystals illuminated
\n
"
);
printf
(
"with femtosecond X-ray pulses from a free electron laser.
\n\n
"
);
printf
(
"Scattering Factors
\n
"
);
printf
(
"------------------
\n
"
);
printf
(
"Scattering factors
\n
"
);
printf
(
"This program simulates diffraction patterns from small crystals illuminated
\n
"
"with femtosecond X-ray pulses from a free electron laser.
\n
"
"
\n
"
"The lattice transform from the specified number of unit cells is calculated
\n
"
"using the closed-form solution for a truncated lattice:
\n
"
"
\n
"
"F(q) = sin(pi*na*q.a)/sin(pi*q.a)
\n
"
" * sin(pi*nb*q.b)/sin(pi*q.b)
\n
"
" * sin(pi*nc*q.c)/sin(pi*q.c)
\n
"
"
\n
"
"na = number of unit cells in 'a' direction (likewise nb, nc)
\n
"
" q = reciprocal vector (1/d convention, not 2pi/d)
\n
"
"
\n
"
"This value is multiplied by the complex structure factor at the nearest
\n
"
"Bragg position, i.e. the gradient of the shape transform across each
\n
"
"appearance of the shape transform is not included, for speed of calculation.
\n
"
"
\n
"
"Complex structure factors are calculated using a combination of the Henke
\n
"
"and Waasmeier-Kirfel scattering factors. The Henke factors are complex
\n
"
"and energy dependence, whereas the Waas-Kirf values are real-valued and
\n
"
"|q|-dependent. The difference between the Waas-Kirf value at the
\n
"
"appropriate |q| and the same value at |q|=0 is subtracted from the Henke
\n
"
"value. The Henke values are linearly interpolated from the provided tables
\n
"
"(note that the interpolation should really be exponential).
\n
"
"
\n
"
"The modulus of the structure factor is taken and squared. Intensity from
\n
"
"water is then added according to the first term of equation 5 from
\n
"
"Phys Chem Chem Phys 20033 (5) 1981--1991.
\n
"
"
\n
"
"Expected intensities at the CCD are then calculated using:
\n
"
"
\n
"
"I(q) = I0 * r^2 * |F(q)|^2 * S
\n
"
"
\n
"
"I0 = number of photons per unit area in the incident beam
\n
"
" r = Thomson radius
\n
"
" S = solid angle of corresponding pixel
\n
"
"
\n
"
"Poisson counts are generated from the expected intensities using Knuth's
\n
"
"algorithm.
\n
"
"
\n
"
"Bloom of the CCD is included. Any excess intensity in a particular pixel
\n
"
"is divided between the neighbouring pixels. Diagonal neighbours receive
\n
"
"half the contribution of adjacent pixels. This process is repeated for
\n
"
"every pixel until all pixels are below the saturation value. Note that this
\n
"
"process is slow for very saturated images.
\n
"
);
}
...
...
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