set up alternative inner patch example.

...ain_with_inner_patch/TP-R-multi-patch-with-inner-patch.py

...i-patch/five_patch_domain_with_inner_patch/run-simulation

...-layered_soil_with_inner_patch-all-params-one-finer-dt.py

...ner_patch/TP-R-layered_soil_with_inner_patch-realistic.py