* Fix how the species fluxes are summed

* Modernize the loop (clang-tidy)

* fix species flux summing so final Dnp1 isnt double counted

* implement marc's suggestion and correct for 1 sdc iter case

Bumps [Submodules/PelePhysics](https://github.com/AMReX-Combustion/PelePhysics) from `60716de` to `d9c1335`.
- [Release notes](https://github.com/AMReX-Combustion/PelePhysics/releases)
- [Commits](AMReX-Combustion/PelePhysics@60716de...d9c1335)

---
updated-dependencies:
- dependency-name: Submodules/PelePhysics
  dependency-version: d9c1335db4be8d7f84db973e97e6a23f9093e5b2
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…e warning. (#611)

* give option to specify custom chemistry_model paths

* Add list of usefule GNUmakefile options

* Fix EOS entry

* Fix typo

* Remove text about full list

* remove rogue print statement

* clarify manifold compile flags

---------

Co-authored-by: Bruce Perry <[email protected]>

* Add max_iter since different from mac/nodal proj

* Fix space

* Use amrex max and min.

* Changes for single precision.

* Update PelePhysics.

* Actually test the single precision build.

* Use amrex clamp.

* Fix CI file.

* Formatting.

* Try to fix test_masscons.py.

* Fix clamp.

* Fix narrowing conversions.

* add stationary reference frame option for FlameSheet

* add moving constant velocity reference frame option

* add user suffix for chemistry model to FlameSheet gnumake

* change flamesheet executable name in ci

* first syncs

* fix

* remove random file

* missing prandtl

* better naming

* inv sc

* sc

* some more sync shifts

---------

Co-authored-by: Thomas Howarth <[email protected]>
Co-authored-by: Jon Rood <[email protected]>

#617)

* add capability option for single output prefix across all output types

* fix string initialization

Bumps [Submodules/AMReX-Hydro](https://github.com/AMReX-Fluids/AMReX-Hydro) from `756c76a` to `75da770`.
- [Commits](AMReX-Fluids/AMReX-Hydro@756c76a...75da770)

---
updated-dependencies:
- dependency-name: Submodules/AMReX-Hydro
  dependency-version: 75da770ea36e4064b5947d7e56baa19f5bc92263
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Initialize dt when restarting from plt

* Use AMREX_REAL_MAX

Tested with amr.dt_shrink and amr.dt_change_max

* initial changes

* included manifold variables for patch flux reporting

* changed initBpatch declaration

* clang tidyied