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authorThomas White <taw@physics.org>2009-11-20 15:15:02 +0100
committerThomas White <taw@physics.org>2009-11-20 15:15:02 +0100
commitfb42533ca6f9077c6b1a03ad9cc76d73a53fb9f1 (patch)
tree45e50ffa8afec07c00b8cfb6ec740d53d85a242c
parentc72fcf4bc2a9f46daf6cbcb14ac2fc388696de09 (diff)
Tidy up and fix
-rw-r--r--src/diffraction.c9
-rw-r--r--src/ewald.c23
-rw-r--r--src/main.c40
3 files changed, 42 insertions, 30 deletions
diff --git a/src/diffraction.c b/src/diffraction.c
index 87f2a5f7..6bb48332 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -129,7 +129,7 @@ static double complex water_factor(struct threevec q, double en)
/* Density of water molecules */
molecules_per_m3 = WATER_DENSITY * (AVOGADRO / WATER_MOLAR_MASS);
-
+
/* Number of water molecules per slice */
molecules_per_m = (2*rb*2*rc) * molecules_per_m3 / N_WATER_SLICES;
@@ -168,8 +168,11 @@ void get_diffraction(struct image *image, UnitCell *cell)
/* Generate the array of reciprocal space vectors in image->qvecs */
get_ewald(image);
- image->molecule = load_molecule();
- if ( image->molecule == NULL ) return;
+
+ if ( image->molecule == NULL ) {
+ image->molecule = load_molecule();
+ if ( image->molecule == NULL ) return;
+ }
cell_get_cartesian(cell, &ax, &ay, &az,
&bx, &by, &bz,
diff --git a/src/ewald.c b/src/ewald.c
index 7a620c42..d1f47da7 100644
--- a/src/ewald.c
+++ b/src/ewald.c
@@ -55,32 +55,32 @@ void get_ewald(struct image *image)
{
int x, y;
double k; /* Wavenumber */
-
+
k = 1/image->lambda;
-
+
image->qvecs = malloc(image->width * image->height
* sizeof(struct threevec));
-
+
image->twotheta = malloc(image->width * image->height
* sizeof(double));
-
+
for ( x=0; x<image->width; x++ ) {
for ( y=0; y<image->height; y++ ) {
-
+
double rx, ry, r;
double twothetax, twothetay, twotheta;
double qx, qy, qz;
struct threevec q;
-
+
/* Calculate q vectors for Ewald sphere */
rx = ((double)x - image->x_centre) / image->resolution;
ry = ((double)y - image->y_centre) / image->resolution;
r = sqrt(pow(rx, 2.0) + pow(ry, 2.0));
-
+
twothetax = atan2(rx, image->camera_len);
- twothetay = atan2(ry, image->camera_len);
+ twothetay = atan2(ry, image->camera_len);
twotheta = atan2(r, image->camera_len);
-
+
qx = k * sin(twothetax);
qy = k * sin(twothetay);
qz = k - k * cos(twotheta);
@@ -89,11 +89,8 @@ void get_ewald(struct image *image)
image->qvecs[x + image->width*y] = quat_rot(q,
image->orientation);
- image->qvecs[x + image->width*y].u = qx;
- image->qvecs[x + image->width*y].v = qy;
- image->qvecs[x + image->width*y].w = qz;
image->twotheta[x + image->width*y] = twotheta;
-
+
}
}
}
diff --git a/src/main.c b/src/main.c
index d26bea7c..54876718 100644
--- a/src/main.c
+++ b/src/main.c
@@ -67,6 +67,21 @@ int main(int argc, char *argv[])
deg2rad(90.0),
deg2rad(120.0));
+ /* Define image parameters */
+ image.width = 512;
+ image.height = 512;
+ image.fmode = FORMULATION_CLEN;
+ image.x_centre = 255.5;
+ image.y_centre = 255.5;
+ image.camera_len = 0.2; /* 20 cm */
+ image.resolution = 5120; /* 512 pixels in 10 cm */
+ image.xray_energy = eV_to_J(2.0e3); /* 2 keV energy */
+ image.lambda = ph_en_to_lambda(image.xray_energy); /* Wavelength */
+ image.molecule = NULL;
+
+ /* Splurge a few useful numbers */
+ printf("Wavelength is %f nm\n", image.lambda/1.0e-9);
+
again:
/* Read quaternion from stdin */
@@ -102,23 +117,12 @@ again:
} while ( !done );
- /* Define image parameters */
- image.width = 512;
- image.height = 512;
- image.fmode = FORMULATION_CLEN;
- image.x_centre = 255.5;
- image.y_centre = 255.5;
- image.camera_len = 0.2; /* 20 cm */
- image.resolution = 5120; /* 512 pixels in 10 cm */
- image.xray_energy = eV_to_J(2.0e3); /* 2 keV energy */
- image.lambda = ph_en_to_lambda(image.xray_energy); /* Wavelength */
+ /* Ensure no residual information */
image.qvecs = NULL;
image.sfacs = NULL;
image.data = NULL;
image.twotheta = NULL;
-
- /* Splurge a few useful numbers */
- printf("Wavelength is %f nm\n", image.lambda/1.0e-9);
+ image.hdr = NULL;
get_diffraction(&image, cell);
record_image(&image);
@@ -128,6 +132,14 @@ again:
/* Write the output file */
hdf5_write(filename, image.data, image.width, image.height);
- printf("Mock write: %i\n", number-1);
+
+ /* Clean up */
+ free(image.data);
+ free(image.qvecs);
+ free(image.hdr);
+ free(image.sfacs);
+ free(image.twotheta);
+
+ /* Do it all again */
goto again;
}