use FillPatcher class for ghost cell filling when using AMR

[BenWibking]

Reduces the communication needed when filling ghost cells on fine levels when multi-stage integrators such as RK2 are used.

Closes #124.

[BenWibking]

/azp run

[azure-pipelines]

Azure Pipelines successfully started running 4 pipeline(s).

[BenWibking]

The ShockCloud problem fails on level 1 with the error:

[Level 1 step 1] ADVANCE with time = 0 dt = 5999266175
        Computing first-half source terms on level 1.
terminate called after throwing an instance of 'std::runtime_error'
terminate called after throwing an instance of 'std::runtime_error'
  what():  Assertion `false' failed, file "/home/benwibking.linux/quokka/src/root_finding.hpp", line 308, Msg: "Parameters a and b out of order!"

It looks like this is caused by bogus values of Egas input to the temperature root-finding function.

Edit: Fixed with update to AMReX.

[BenWibking]

This can also fail when extra subcycling happens:

[Level 3 step 430988] Advanced 64454656 cells
	Minimum cooling time on level 1: 1.945905783e+10
	Minimum cooling time on level 2: 1.620309593e+10
	Minimum cooling time on level 3: 2.8119675e+10
	Subcycling --- maxFactorSublevels: 64
		Level 1: factor: 64 (1), dt: 12677207.36
		Level 2: factor: 1 (64), dt: 6338603.682
		Level 3: factor: 1 (64), dt: 3169301.841
[Level 1 step 107923] ADVANCE with time = 1.420028215e+14 dt = 12677207.36
	Computing first-half source terms on level 1.
	Computing second-half source terms on level 1.
[Level 1 step 107923] Advanced 14155776 cells
[Level 2 step 215581] ADVANCE with time = 1.420028215e+14 dt = 6338603.682
	Computing first-half source terms on level 2.
	Computing second-half source terms on level 2.
[Level 2 step 215581] Advanced 31817728 cells
[Level 3 step 430989] ADVANCE with time = 1.420028215e+14 dt = 3169301.841
	Computing first-half source terms on level 3.
terminate called after throwing an instance of 'std::runtime_error'
terminate called after throwing an instance of 'std::runtime_error'
terminate called after throwing an instance of 'std::runtime_error'
terminate called after throwing an instance of 'std::runtime_error'
  what():  FillPatcher: High order interpolation in time not supported.  Or FillPatcher was not properly deleted.
  what():  FillPatcher: High order interpolation in time not supported.  Or FillPatcher was not properly deleted.
  what():  FillPatcher: High order interpolation in time not supported.  Or FillPatcher was not properly deleted.
  what():  FillPatcher: High order interpolation in time not supported.  Or FillPatcher was not properly deleted.

[BenWibking]

/azp run

[azure-pipelines]

Azure Pipelines successfully started running 4 pipeline(s).

[BenWibking]

/azp run

[azure-pipelines]

Azure Pipelines successfully started running 4 pipeline(s).