diff options
Diffstat (limited to 'src/indexamajig.c')
-rw-r--r-- | src/indexamajig.c | 35 |
1 files changed, 20 insertions, 15 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index bac1ee04..38d83d58 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -123,11 +123,11 @@ static void show_help(const char *s) " --no-check-cell Don't check lattice parameters against input cell\n" " --no-cell-combinations\n" " Don't use axis combinations when checking cell\n" -" --no-multi Don't repeat indexing to index multiple hits\n" +" --multi Repeat indexing to index multiple hits\n" " --no-retry Don't repeat indexing to increase indexing rate\n" " --no-refine Skip the prediction refinement step\n" -" --check-peaks Check that most of the peaks can be accounted for\n" -" by the indexing solution\n" +" --no-check-peaks Don't check that most of the peaks can be accounted\n" +" for by the indexing solution\n" "\n" " --taketwo-member-threshold\n" " Minimum number of members in network\n" @@ -238,8 +238,8 @@ int main(int argc, char *argv[]) int if_refine = 1; int if_nocomb = 0; int if_nocheck = 0; - int if_peaks = 0; - int if_multi = 1; + int if_peaks = 1; + int if_multi = 0; int if_retry = 1; int serial_start = 1; @@ -342,8 +342,11 @@ int main(int argc, char *argv[]) {"no-check-cell", 0, &if_nocheck, 1}, {"no-cell-check", 0, &if_nocheck, 1}, {"check-peaks", 0, &if_peaks, 1}, + {"no-check-peaks", 0, &if_peaks, 0}, {"no-retry", 0, &if_retry, 0}, + {"retry", 0, &if_retry, 1}, {"no-multi", 0, &if_multi, 0}, + {"multi", 0, &if_multi, 1}, {"overpredict", 0, &iargs.overpredict, 1}, /* Long-only options which don't actually do anything */ @@ -851,6 +854,8 @@ int main(int argc, char *argv[]) if ( have_push_res && !(iargs.int_meth & INTEGRATION_RESCUT) ) { ERROR("WARNING: You used --push-res, but not -rescut, " "therefore --push-res will have no effect.\n"); + ERROR("WARNING: Add --integration=rings-rescut or " + "--integration=prof2d-rescut.\n"); } /* Parse unit cell tolerance */ @@ -955,15 +960,6 @@ int main(int argc, char *argv[]) } - /* Open output stream */ - st = open_stream_for_write_3(outfile, geom_filename, iargs.cell, - argc, argv); - if ( st == NULL ) { - ERROR("Failed to open stream '%s'\n", outfile); - return 1; - } - free(outfile); - if ( indm_str == NULL ) { STATUS("No indexing methods specified. I will try to "); @@ -1035,10 +1031,19 @@ int main(int argc, char *argv[]) ERROR("Failed to set up indexing system\n"); return 1; } - free(indm_str); } + /* Open output stream */ + st = open_stream_for_write_4(outfile, geom_filename, iargs.cell, + argc, argv, indm_str); + if ( st == NULL ) { + ERROR("Failed to open stream '%s'\n", outfile); + return 1; + } + free(outfile); + free(indm_str); + gsl_set_error_handler_off(); create_sandbox(&iargs, n_proc, prefix, config_basename, fh, |