diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/sfac.c | 60 | ||||
| -rw-r--r-- | src/sfac.h | 4 |
2 files changed, 63 insertions, 1 deletions
@@ -203,6 +203,62 @@ double complex get_sfac(const char *n, double s, double en) } +static void centre_molecule(struct molecule *mol) +{ + int i; + double tx = 0.0; + double ty = 0.0; + double tz = 0.0; + double total = 0.0; + + /* Atoms are grouped by species for faster calculation */ + for ( i=0; i<mol->n_species; i++ ) { + + struct mol_species *spec; + int j; + + spec = mol->species[i]; + + for ( j=0; j<spec->n_atoms; j++ ) { + + double sfac = get_waas_kirf(spec->species, 0.0); + + tx += spec->x[j] * sfac; + ty += spec->y[j] * sfac; + tz += spec->z[j] * sfac; + total += sfac; + + } + + } + + mol->xc = tx / total; + mol->yc = ty / total; + mol->zc = tz / total; + + for ( i=0; i<mol->n_species; i++ ) { + + struct mol_species *spec; + int j; + + spec = mol->species[i]; + + for ( j=0; j<spec->n_atoms; j++ ) { + + spec->x[j] -= mol->xc; + spec->y[j] -= mol->yc; + spec->z[j] -= mol->zc; + + } + + } + + printf("Molecule was shifted by %f,%f,%f nm\n", + mol->xc*1e9, mol->yc*1e9, mol->zc*1e9); + +} + + /* Load PDB file into a memory format suitable for efficient(ish) structure * factor calculation */ struct molecule *load_molecule() @@ -268,7 +324,7 @@ struct molecule *load_molecule() n = mol->species[j]->n_atoms; - spec->x[n] = x*1.0e-10; /* Convert to nm */ + spec->x[n] = x*1.0e-10; /* Convert to m */ spec->y[n] = y*1.0e-10; spec->z[n] = z*1.0e-10; spec->occ[n] = occ; @@ -304,6 +360,8 @@ struct molecule *load_molecule() fclose(fh); + centre_molecule(mol); + printf("There are %i species\n", mol->n_species); for ( i=0; i<mol->n_species; i++ ) { printf("%3s : %6i\n", mol->species[i]->species, @@ -36,6 +36,10 @@ struct molecule { int n_species; struct mol_species *species[32]; + + double xc; + double yc; + double zc; }; |