Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Oleksii Turkot
CrystFEL
Commits
f5eb7d15
Commit
f5eb7d15
authored
Jun 05, 2010
by
Thomas White
Browse files
pattern_sim: Update --simulation-details
parent
fe514e51
Changes
1
Hide whitespace changes
Inline
Side-by-side
src/pattern_sim.c
View file @
f5eb7d15
...
...
@@ -95,33 +95,34 @@ static void show_details()
"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
"
"using the closed-form solution for a truncated lattice faceted on the
\n
"
"(001), (010) and (100) planes:
\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
"
"
I_latt
(q) = sin
^2
(pi*na*q.a)/sin
^2
(pi*q.a)
\n
"
"
* sin
^2
(pi*nb*q.b)/sin
^2
(pi*q.b)
\n
"
"
* sin
^2
(pi*nc*q.c)/sin
^2
(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 square modulus of this value is taken, and multiplied by the Bragg
\n
"
"intensitiy at the neares Bragg position. That means that the gradient of
\n
"
"the underlying molecule transform is not included, for speed of calculation.
\n
"
"The Bragg intensities are taken from the file specified on the command line
\n
"
"with the --intensities option.
\n
"
"This is multiplied by a model of the underlying molecular transform, I_mol(q).
\n
"
"This can be approximated to varying levels of accuracy by the methods given by
\n
"
"the '--gradients' option.
\n
"
"
\n
"
"Intensity from water is
then
added according to the first term of equation
\n
"
"
5
from Phys Chem Chem Phys 2003 (5) 1981--1991. This simulates the
\n
"
"Intensity from water is added according to the first term of equation
5
\n
"
"from Phys Chem Chem Phys 2003 (5) 1981--1991. This simulates the
\n
"
"coherent, elastic part of the diffuse scattering from the water jet only.
\n
"
"
\n
"
"Expected intensities at the CCD are then calculated using:
\n
"
"
\n
"
"I(q) = I0 * r^2 *
|F(q)|^2
* S
\n
"
"I(q) = I0 * r^2 *
I_latt(q) * I_mol(q)
* 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
"
"where |F(q)|^2 is the value calculated as described above.
\n
"
"
\n
"
"Polarisation is not currently included in pattern_sim, although it is included
\n
"
"in the analysis of Bragg peaks by 'indexamajig'.
\n
"
"
\n
"
"Poisson counts are generated from the expected intensities using Knuth's
\n
"
"algorithm. When the intensity is sufficiently high that Knuth's algorithm
\n
"
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment