Nyx

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Documentation is about Sundials 6, but in the sidebar it still says "Sundials 5". This PR fixes that.

n8xm

Extended the `.gitignore` with some common files that should be ignored: 1. ctags file 2. [JSON compilation database](https://clang.llvm.org/docs/JSONCompilationDatabase.html) 3. `runlog` file 1) and 2) are often generated during C++ development...

n8xm

On [Line 308 of Nyx.cpp](https://github.com/AMReX-Astro/Nyx/blob/05ccb5950c4fc9979dec253b89319ae5ae58bac8/Source/Driver/Nyx.cpp#L308), the value of `do_hydro` is used in the following if statement : ``` if (DefaultGeometry().isAnyPeriodic() || (!do_dm_particles && !do_hydro)) ``` However, this if statement comes...

n8xm

We should adopt a code of conduct for our project. I adapted the Astropy code of conduct (which is CC licensed). My intention is for this code of conduct to...

zingale

Currently, the `Amr-density` regression test [assumes the chk00300_for_rt checkpoint file exists](https://github.com/AMReX-Astro/Nyx/blob/a91f4b05bcc262e4a280b6e8f075d3c69f659aae/Util/regression_testing/Nyx-tests.ini#L258). But there is currently no such checkpoint file under the [Exec/Amr-density directory](https://github.com/AMReX-Astro/Nyx/tree/development/Exec/AMR-density). The test will fail as a result.

n8xm

Fix compile error when Reeber is enabled

1

Fix #96.

n8xm

Compile with Reeber fails: "no matching function for call to FabComponentBlock"

2

When I attempt to compile the `LyA` project with Reeber enabled on the Nyx development branch, GCC gives me the following error: ``` ../../Util/reeber/src/reeber.cpp:433:98: error: no matching function for call...

n8xm

Documentation for #101

n8xm

Add ability to pass `reeber.negate` and `reeber.halo_component_threshold` via input file. (Despite appearing in the documentation and in several input files, prior to this commit these values are not read by...

n8xm

In this PR 1. parameters `halo_component_threshold` and `halo_extrema_threshold` are now being read in, and passed into Reeber. 2. includes changes to Reeber required for the halo finder. ie. changes to...

nataraj2