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-rw-r--r--src/indexamajig.c35
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,