diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/detector.c | 8 | ||||
| -rw-r--r-- | src/diffraction.c | 43 | ||||
| -rw-r--r-- | src/diffraction.h | 1 |
3 files changed, 44 insertions, 8 deletions
diff --git a/src/detector.c b/src/detector.c index f4de05ff..dc378480 100644 --- a/src/detector.c +++ b/src/detector.c @@ -156,14 +156,16 @@ void record_image(struct image *image) for ( x=0; x<image->width; x++ ) { for ( y=0; y<image->height; y++ ) { - double counts; - double intensity; - double sa; + double counts, intensity, sa; double complex val; val = image->sfacs[x + image->width*y]; intensity = (double)(val * conj(val)); + /* Add intensity contribution from water */ + intensity += water_intensity(image->qvecs[x + image->width*y], + image->xray_energy); + /* What solid angle is subtended by this pixel? */ sa = sa_per_pixel * cos(image->twotheta[x + image->width*y]); diff --git a/src/diffraction.c b/src/diffraction.c index 9a9e31b6..07749ac7 100644 --- a/src/diffraction.c +++ b/src/diffraction.c @@ -99,9 +99,44 @@ static double complex molecule_factor(struct molecule *mol, struct threevec q, } -static double complex water_factor(struct threevec q, double en) +double water_intensity(struct threevec q, double en) { - return 0.0; + complex double fH, fO; + double s, modq; + double intensity; + + /* Interatomic distances in water molecule */ + const double rOH = 0.09584e-9; + const double rHH = 0.1515e-9; + + /* Dimensions of water column */ + const double water_r = 0.5e-6; + const double beam_r = 1.5e-6; + + /* Volume of water column */ + const double water_v = M_PI*pow(water_r, 2.0) * 2.0 * beam_r; + + /* 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 */ + intensity = 4.0*fH*fO * sin(modq*rOH)/(modq*rOH); + + /* Three H-H cross terms */ + intensity += 3.0*fH*fH * sin(modq*rHH)/(modq*rHH); + + /* Three diagonal terms */ + intensity += 2.0*fH*fH + fO*fO; + + return intensity * n_water; } @@ -137,7 +172,6 @@ void get_diffraction(struct image *image) double f_lattice; double complex f_molecule; - double complex f_water; struct threevec q; double complex val; @@ -147,8 +181,7 @@ void get_diffraction(struct image *image) f_molecule = molecule_factor(image->molecule, q, ax,ay,az,bx,by,bz,cx,cy,cz); - f_water = water_factor(q, image->xray_energy); - val = (f_molecule * f_lattice) + f_water; + val = f_molecule * f_lattice; image->sfacs[x + image->width*y] = val; } diff --git a/src/diffraction.h b/src/diffraction.h index 112818bc..e2994a0b 100644 --- a/src/diffraction.h +++ b/src/diffraction.h @@ -20,5 +20,6 @@ #include "cell.h" extern void get_diffraction(struct image *image); +extern double water_intensity(struct threevec q, double en); #endif /* DIFFRACTION_H */ |