Guard CREGEN against empty conformer groups

[PhelanShao]

Reproduction

crest struc.xyz \
  --qcg water.xyz --nsolv 6 \
  --gfnff --T 12 --alpb water \
  --ensemble --md --mdtime 10 --wscal 1.0

Example command taken from https://crest-lab.github.io/crest-docs/page/examples/qcg/example_5.html.

On master (c39758d) this workflow aborts during the first CREGEN pass with:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
#0  ... cregen_conffile_ at src/cregen.f90:2196

Any pure GFN‑FF QCG run that skips the RMSD/rotamer grouping step exhibits the same crash: degen is never populated, yet cregen_conffile dereferences xyz(:,:,degen(2,i)), so a zero index triggers the SIGSEGV.

Summary

• Provide a trivial 1:1 group mapping whenever sortRMSD is false.
• Guard cregen_conffile against invalid group indices so we never read outside [1, nall].

Details

1. If the RMSD branch is bypassed, allocate degen(:,i) = i (or a single zeroed entry when the ensemble is empty).
2. In the writer, skip any group whose degen(2,i) falls outside the valid index range before calling wrc0.

Testing

• CREST 3.0.2 (c39758d) + xtb 6.6.1
• The command above now completes the CREGEN stage without errors.