Select "File|Export|MODFLOW 6 Input Files" to run the model. The percent discrepancy in the first few stress periods can be high because there is no flow in the first few stress periods. You can check the energy budget in the list file to verify that the budget really is not a problem.
For comparison with the original model described in mf6examples.pdf, import the temperatures at the following times: 210, 340 520, and 1270.
Plot of simulated temperature at 210 days
Plot of simulated temperature at 340 days
Plot of simulated temperature at 520 days
Plot of simulated temperature at 1270 days
