Grounded answers on MODFLOW, PEST, FloPy, and PyEMU.

How do I set up a heat transport model in MODFLOW 6 using the GWE (energy) package?

A GWE model couples to a GWF flow simulation and adds packages specific to thermal energy. In FloPy you instantiate ModflowGwe with an EST package for thermal storage, a CND package for conduction and mechanical dispersion, and boundary conditions through CTP or the advanced packages (SFE for streams, LKE for lakes, MWE for multi-aquifer wells). A GwfGweExchange block wires the two models together so heads from GWF drive temperature in GWE.

How do I assign a time-varying pumping rate to a well in ModelMuse?

Draw or select the object that represents the well, open Object Properties, and activate WEL on the MODFLOW Features tab. Add rows with a starting time, ending time, and pumping rate. Use a negative rate for extraction and a positive rate for injection. ModelMuse converts those time ranges into the required stress-period entries, so you do not need to edit each stress period manually.

What does PyEMU's PstFrom do, and how do I use it to build a PEST interface from a MODFLOW model?

PstFrom is a builder class in pyemu.utils that generates the full PEST(++) interface from your MODFLOW inputs. It produces a control file, template files, instruction files, and a forward run script. Parameters are set up as multipliers over existing arrays and list file values, so the original model stays the prior mean while PEST scales them during calibration.