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-rw-r--r--src/beam-parameters.c7
-rw-r--r--src/beam-parameters.h2
-rw-r--r--src/diffraction.c62
-rw-r--r--src/diffraction.h2
-rw-r--r--src/pattern_sim.c16
-rw-r--r--src/sfac.c2
-rw-r--r--src/sfac.h4
-rw-r--r--src/utils.h9
8 files changed, 4 insertions, 100 deletions
diff --git a/src/beam-parameters.c b/src/beam-parameters.c
index 8d34eacf..ac30ad04 100644
--- a/src/beam-parameters.c
+++ b/src/beam-parameters.c
@@ -41,7 +41,6 @@ struct beam_params *get_beam_parameters(const char *filename)
b->divergence = -1.0;
b->dqe = -1.0;
b->adu_per_photon = -1.0;
- b->water_radius = -1.0;
do {
@@ -81,8 +80,6 @@ struct beam_params *get_beam_parameters(const char *filename)
b->dqe = atof(bits[2]);
} else if ( strcmp(bits[0], "detector/adu_per_photon") == 0 ) {
b->adu_per_photon = atof(bits[2]);
- } else if ( strcmp(bits[0], "jet/radius") == 0 ) {
- b->water_radius = atof(bits[2]);
} else {
ERROR("Unrecognised field '%s'\n", bits[0]);
}
@@ -125,10 +122,6 @@ struct beam_params *get_beam_parameters(const char *filename)
" 'detector/adu_per_photon'.\n");
reject = 1;
}
- if ( b->water_radius < 0.0 ) {
- ERROR("Invalid or unspecified value for 'jet/radius'.\n");
- reject = 1;
- }
if ( reject ) {
ERROR("Please fix the above problems with the beam"
diff --git a/src/beam-parameters.h b/src/beam-parameters.h
index 1fadc3f8..411ab449 100644
--- a/src/beam-parameters.h
+++ b/src/beam-parameters.h
@@ -31,8 +31,6 @@ struct beam_params
double dqe; /* Detector DQE (fraction) */
double adu_per_photon; /* Detector "gain" */
-
- double water_radius; /* metres */
};
diff --git a/src/diffraction.c b/src/diffraction.c
index aa06c44b..5b949594 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -319,55 +319,10 @@ static double molecule_factor(const double *intensities, const double *phases,
}
-double water_diffraction(struct rvec q, double en,
- double beam_r, double water_r)
-{
- double complex fH, fO;
- double s, modq;
- double width;
- double complex ifac;
-
- /* Interatomic distances in water molecule */
- const double rOH = 0.09584e-9;
- const double rHH = 0.1515e-9;
-
- /* Volume of water column, approximated as:
- * (2water_r) * (2beam_r) * smallest(2beam_r, 2water_r)
- * neglecting the curvature of the faces of the volume */
- if ( beam_r > water_r ) {
- width = 2.0 * water_r;
- } else {
- width = 2.0 * beam_r;
- }
- const double water_v = 2.0*beam_r * 2.0*water_r * width;
-
- /* Number of water molecules */
- const double n_water = water_v * WATER_DENSITY
- * (AVOGADRO / WATER_MOLAR_MASS);
-
- /* s = sin(theta)/lambda = 1/2d = |q|/2 */
- modq = modulus(q.u, q.v, q.w);
- s = modq / 2.0;
-
- fH = get_sfac("H", s, en);
- fO = get_sfac("O", s, en);
-
- /* Four O-H cross terms */
- ifac = 4.0*fH*fO * sin(2.0*M_PI*modq*rOH)/(2.0*M_PI*modq*rOH);
-
- /* Three H-H cross terms */
- ifac += 3.0*fH*fH * sin(2.0*M_PI*modq*rHH)/(2.0*M_PI*modq*rHH);
-
- /* Three diagonal terms */
- ifac += 2.0*fH*fH + fO*fO;
-
- return cabs(ifac) * n_water;
-}
-
void get_diffraction(struct image *image, int na, int nb, int nc,
const double *intensities, const double *phases,
- const unsigned char *flags, UnitCell *cell, int do_water,
+ const unsigned char *flags, UnitCell *cell,
GradientMethod m, const char *sym)
{
unsigned int xs, ys;
@@ -436,21 +391,6 @@ void get_diffraction(struct image *image, int na, int nb, int nc,
}
- if ( do_water ) {
-
- /* Bandwidth not simulated for water */
- struct rvec q;
-
- q = get_q(image, x, y, 1, NULL, 1.0/image->lambda);
-
- /* Add intensity contribution from water */
- image->data[x + image->width*y] += water_diffraction(q,
- ph_lambda_to_en(image->lambda),
- image->beam->beam_radius,
- image->beam->water_radius) * sw;
-
- }
-
}
progress_bar(xs, SAMPLING*image->width-1, "Calculating diffraction");
diff --git a/src/diffraction.h b/src/diffraction.h
index 607b066e..f21147b9 100644
--- a/src/diffraction.h
+++ b/src/diffraction.h
@@ -28,6 +28,6 @@ typedef enum {
extern void get_diffraction(struct image *image, int na, int nb, int nc,
const double *intensities, const double *phases,
const unsigned char *flags, UnitCell *cell,
- int do_water, GradientMethod m, const char *sym);
+ GradientMethod m, const char *sym);
#endif /* DIFFRACTION_H */
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index fe6a8f0d..29e1b263 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -97,7 +97,6 @@ static void show_help(const char *s)
"speed, or for testing, you can choose to disable certain things using the\n"
"following options.\n"
"\n"
-" --no-water Do not simulate water background.\n"
" --no-noise Do not calculate Poisson noise.\n"
);
}
@@ -124,10 +123,6 @@ static void show_details()
"This can be approximated to varying levels of accuracy by the methods given by\n"
"the '--gradients' option.\n"
"\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 * I_latt(q) * I_mol(q) * S\n"
@@ -208,7 +203,6 @@ int main(int argc, char *argv[])
int config_nearbragg = 0;
int config_randomquat = 0;
int config_noimages = 0;
- int config_nowater = 0;
int config_nonoise = 0;
int config_nosfac = 0;
int config_gpu = 0;
@@ -241,7 +235,6 @@ int main(int argc, char *argv[])
{"random-orientation", 0, NULL, 'r'},
{"number", 1, NULL, 'n'},
{"no-images", 0, &config_noimages, 1},
- {"no-water", 0, &config_nowater, 1},
{"no-noise", 0, &config_nonoise, 1},
{"intensities", 1, NULL, 'i'},
{"symmetry", 1, NULL, 'y'},
@@ -375,12 +368,6 @@ int main(int argc, char *argv[])
return 0;
}
- if ( (!config_nowater) && config_gpu ) {
- ERROR("Cannot simulate water scattering on the GPU.\n");
- ERROR("Please try again with the --no-water option.\n");
- return 1;
- }
-
if ( grad_str == NULL ) {
STATUS("You didn't specify a gradient calculation method, so"
" I'm using the 'mosaic' method, which is fastest.\n");
@@ -553,8 +540,7 @@ int main(int argc, char *argv[])
get_diffraction_gpu(gctx, &image, na, nb, nc, cell);
} else {
get_diffraction(&image, na, nb, nc, intensities, phases,
- flags, cell, !config_nowater, grad,
- sym);
+ flags, cell, grad, sym);
}
if ( image.data == NULL ) {
ERROR("Diffraction calculation failed.\n");
diff --git a/src/sfac.c b/src/sfac.c
index 436544c8..8b69f2e3 100644
--- a/src/sfac.c
+++ b/src/sfac.c
@@ -240,7 +240,7 @@ static double get_waas_kirf(const char *n, double s)
/* Get complex scattering factors for element 'n' at energy 'en' (J/photon),
* at resolution 's' = sin(theta)/lambda (in m^-1) */
-double complex get_sfac(const char *n, double s, double en)
+static double complex get_sfac(const char *n, double s, double en)
{
double complex f1f2;
double fq;
diff --git a/src/sfac.h b/src/sfac.h
index 115dcb5f..e05b3ddf 100644
--- a/src/sfac.h
+++ b/src/sfac.h
@@ -55,10 +55,6 @@ struct molecule
double zc;
};
-
-/* This is so that the water background calculation can use it */
-extern double complex get_sfac(const char *n, double s, double en);
-
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,
diff --git a/src/utils.h b/src/utils.h
index ff8a613b..169892d4 100644
--- a/src/utils.h
+++ b/src/utils.h
@@ -42,15 +42,6 @@
/* Thomson scattering length (m) */
#define THOMSON_LENGTH (2.81794e-15)
-/* Density of water in kg/m^3 */
-#define WATER_DENSITY (1.0e6)
-
-/* Molar mass of water, in kg/mol */
-#define WATER_MOLAR_MASS (18.01528e3)
-
-/* Avogadro's number */
-#define AVOGADRO (6.022e23)
-
/* ------------------------------ Quaternions ------------------------------- */
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-15 03:26:12 +0000