Diags with coarsening (#856)

* Start implementation of new averaging with staggering:

- face-to-cell-center and edge-to-cell-center replaced so far;
- TODO: node-to-cell-center and 1D behavior (AMREX_SPACEDIM=1).

* first implementation of Diags base classes

* add example, temporarily

* Continue implementation of new averaging with staggering:

- new function takes reference to single MultiFab (no vector);
- TODO: node-to-cell-center still in progress.

* Fix small bug and clean up

* Fix bug in loop over n=0,...,ncomp-1 and clean up

* add more functions

* Add Doxygen documentation and clean up

* Small clean-up in Doxygen documentation

* Compile in single precision: add _rt suffix to avoid unnecessary conversions

* Avoid accessing staggering index directly from IntVect in innermost loops

* Replace do-while loop with for loop (default ncomp=1)

* Remove temporary pointer and pass reference to MultiFab (instead of MultiFab*)

* Replace AMREX_LAUNCH_HOST_DEVICE_LAMBDA with ParallelFor

* cleaning and initialize output mf

* use general average routine

* move flush in new class, and implemented the Plotfile derived class

* add comments

* eol

* free memory in destructor

* typo

* typo

* no need to clear MF pointers there

* though shalt not break existing tests

* FlushRaw doesnt have to be virtual for now

* The importance of being constant

* Capability to select fields in output files

* EOL

* revert to old inputs

* const in right place

* avoid brace initializer there

* oops, fix logic error in is_in

* user can choose flush interval, same behavior as plot_int

* Add option to plot raw fields

* eol

* replace ter flush with dump to avoid confusion

* add options

* Diagnostics stores a vector of functors to compute diags on the fly

* eol

* Field gather from diags to sync particle quantities

* New diagnostics handle RZ with same behavior as old ones

* cleaning and doc

* const ref for string

* smarter for loop from Axel and typo fix from Reva

* Functors to compute some fields

* simplify code following Dave's comments

* Create subfolders and add more output options (divE etc.)

* eol

* rename mode_avg to convertRZmodes2cartesian

* Update CellCenterFunctor.H

* fill varnames and vector of functors at the same time

* output rho_new, not rho_old

* WarpX instance not needed here

* add const

* little bit more of reorganization

* Apply suggestions from code review

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* add a bunch of const

* Move average_down overload used in WarpX to Average::FineToCoarse

* Write Average::FineToCoarse for cell-centered and nodal data

* Clean up Average::FineToCoarse (WARNING: interface changed)

* Small clean-up

* Replace AMREX_LAUNCH_HOST_DEVICE_LAMBDA with ParallelFor

* parse input for diag_crse_ratio, mf_avg allocate, call FineToCoarse

* eol fix

* fix compilation error by adding bool variable

* Small clean-up

* er-organizing placement for diag_crse_ratio

* calling member function for crse_Ratio

* cleaning

* Change name from Average::FineToCoarse to Average::Coarsen

* Add dcomp to interface of Coarsen (different from scomp in general)

* fixing RZ build error by adding diag_crse_ratio

* Remove ASSERT (general input and output staggerings will be accepted)

* Fix averaging from fine nodal to coarse centered

* Clean up Doxygen in old Average::ToCellCenter (likely to be removed)

* Intermediate layers Average::CoarsenLoop and Average::CoarsenKernel

* Revert "Intermediate layers Average::CoarsenLoop and Average::CoarsenKernel"

This reverts commit 91f2beaa20617a3fb25df536472b74899942ffc5.

* Clean-up

* Implement interpolation with coarsening (remove averaging)

* Trigger failing source/style checks on Travis CI

* merged EZ's coarsen_branch added comments about ba.coarsen

* Add ASSERTS to check coarsening ratio and guard cells

* clarified a comment

* cleaning

* Input/output MultiFabs can have different number of components

* Call the correct coarsen and interpolate function

* adding comments for the input parameter

* Use AMReX built-in functions to check if MultiFab is coarsenable

* fixing assert

* EOL fix

* changes based on suggestions in the review

* EOL fix

* Add Doxygen documentation for new functions

* Copy starting from correct component in destination MultiFab

* making crse_ratio IntVect a protected variable

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* removing this function since crse_ratio is protected

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* removing assert since it is temporaty only for this PR

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* crse_ratio is protected and can be accessed directly

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Pass IntVect to BoxArray method 'coarsenable' directly

* Improve comments

* Rename 'ratio' as 'crse_ratio'

* Extending coarsening to divE and divB functors

* Add _rt suffix when necessary

* Improve comments

* Use method 'toIntVect' instead of 'ixType'

* New names: mf_src, arr_src, stag_src, mf_dst, arr_dst, stag_dst

* More clean-up

* adding coarsening capability to all diag_functors

* fixing compilation errors

* fix eol

* Replace calls to ToCellCenter and fix bug with staggering of temporary BoxArray

* Check if coarsenable on BoxArray with destination staggering

* clean up

* dix eol

* typo in comment

* Replace remaining calls to Average::ToCellCenter

* Remove Average::ToCellCenter

* Use amrex::Gpu::ManagedVector<int> to avoid issues on GPUs

* Add default value IntVect(1) for coarsening ratio

* Add ngrow to possibly fill guard cells too

* Add ngrow to Doxygen documentation

* Count number of points outside innermost loop

* added capability for different user-defined lo and hi for diags

* eol fix

* Add number of guard cells required to previous ASSERT and force ngrow=0 with coarsening

* cleaning up by moving multifab generation to a new function

* eol fix

* added a small description for function

* Update Source/Diagnostics/Diagnostics.H

incorporating comments for member variables

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Update Source/Diagnostics/Diagnostics.cpp

adding comments for a function

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* Apply suggestions from code review

Thanks to Maxence Thevenet for the suggestions from review

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* adding suggestion from code review directly

* Apply suggestions from code review

max to prevent negative values due to precision errors

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* incorporating suggestions and some comments from code review

* adding assert to ensure crse ratio is power of 2

* fix eol

* cleaned code and added refine,coarsen for ba definition

* fix eol

* minor fix

* Apply suggestions from code review

Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>

* constexpr instead of const

* add a comment clarifying ng=1 for tmp multifabs

* eol fix

Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

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