diff options
| -rw-r--r-- | doc/man/partialator.1 | 6 | ||||
| -rw-r--r-- | src/partialator.c | 33 | ||||
| -rw-r--r-- | src/post-refinement.c | 7 |
3 files changed, 45 insertions, 1 deletions
diff --git a/doc/man/partialator.1 b/doc/man/partialator.1 index c9ef85a0..0a5b78ba 100644 --- a/doc/man/partialator.1 +++ b/doc/man/partialator.1 @@ -151,6 +151,12 @@ Specify the indexing ambiguity operator. Example: \fB--operator=k,h,-l\fR. .IP If you prefer, you can specify the ambiguity operator by specifying the apparent symmetry using \fB-w\fR. +.PD 0 +.IP \fB--force-bandwidth=\fIbw\fR +.IP \fB--force-radius=\fIR\fR +.PD +Set the X-ray bandwidth or initial profile radius for all crystals before proceeding. Bandwidth is given as a fraction, i.e. \fB--force-bandwidth=0.0013\fR means 0.13 percent (approximate FWHM). Radius is given in nm^-1. + .SH PARTIALITY MODELS The available partiality models are: diff --git a/src/partialator.c b/src/partialator.c index e9053841..0d5a8a84 100644 --- a/src/partialator.c +++ b/src/partialator.c @@ -329,7 +329,9 @@ static void show_help(const char *s) " --max-rel-B Maximum allowable relative |B| factor.\n" " --no-logs Do not write extensive log files.\n" " -w <pg> Apparent point group for resolving ambiguities.\n" -" --operator=<op> Indexing ambiguity operator for resolving.\n"); +" --operator=<op> Indexing ambiguity operator for resolving.\n" +" --force-bandwidth=<n> Set all bandwidths to <n> (fraction).\n" +" --force-radius=<n> Set all profile radii to <n> nm^-1.\n"); } @@ -858,6 +860,8 @@ int main(int argc, char *argv[]) int no_logs = 0; char *w_sym_str = NULL; char *operator = NULL; + double force_bandwidth = -1.0; + double force_radius = -1.0; /* Long options */ const struct option longopts[] = { @@ -882,6 +886,8 @@ int main(int argc, char *argv[]) {"max-rel-b", 1, NULL, 7}, /* compat */ {"reference", 1, NULL, 8}, /* ssshhh! */ {"operator", 1, NULL, 9}, + {"force-bandwidth", 1, NULL, 10}, + {"force-radius", 1, NULL, 11}, {"no-scale", 0, &no_scale, 1}, {"no-pr", 0, &no_pr, 1}, @@ -1020,6 +1026,25 @@ int main(int argc, char *argv[]) operator = strdup(optarg); break; + case 10 : + errno = 0; + force_bandwidth = strtod(optarg, &rval); + if ( *rval != '\0' ) { + ERROR("Invalid value for --force-bandwidth.\n"); + return 1; + } + break; + + case 11 : + errno = 0; + force_radius = strtod(optarg, &rval); + if ( *rval != '\0' ) { + ERROR("Invalid value for --force-radius.\n"); + return 1; + } + force_radius *= 1e9; + break; + case 0 : break; @@ -1278,6 +1303,12 @@ int main(int argc, char *argv[]) STATUS("Initial partiality calculation...\n"); for ( i=0; i<n_crystals; i++ ) { Crystal *cr = crystals[i]; + if ( force_bandwidth > 0.0 ) { + crystal_get_image(cr)->bw = force_bandwidth; + } + if ( force_radius > 0.0 ) { + crystal_set_profile_radius(cr, force_radius); + } update_predictions(cr); calculate_partialities(cr, pmodel); } diff --git a/src/post-refinement.c b/src/post-refinement.c index 60810349..acafb8aa 100644 --- a/src/post-refinement.c +++ b/src/post-refinement.c @@ -330,6 +330,13 @@ static double residual_f(const gsl_vector *v, void *pp) return GSL_NAN; } + /* Can happen with grid scans and certain --force-radius values */ + if ( fabs(crystal_get_profile_radius(cr)) < 0.0000001e9 ) { + crystal_free(cr); + if ( pv->verbose ) STATUS("radius very small\n"); + return GSL_NAN; + } + if ( im.lambda <= 0.0 ) { crystal_free(cr); if ( pv->verbose ) STATUS("lambda < 0\n"); |