Remove water simulation stuff

It's not really useful - our dominant background is from elsewhere

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 ------------------------------- */