Simplify test input files using AMReX FILE directive - #1

Closed

baperry2 with Copilot wants to merge 560 commits into

mainfrom

copilot/simplify-test-input-files

This pull request is big! We're only showing the most recent 250 commits

Commits on Jan 16, 2025

Update anelastic to define and use a reference temperature field (#1446)
marchdf
authored
2dd8805
add tolerance to boundary file write time check (#1447)
mbkuhn
authored
6583842
Enable optional coupling to openfast 4.0 (#1441)
marchdf
authored
9fee431

Commits on Jan 17, 2025

Commits on Jan 22, 2025

Commits on Jan 24, 2025

Create transport model before the physics (#1458)
marchdf
authored
d7046e1
Fix MOST documentation (#1460)
moprak-nrel
authored
3e9ef95

Commits on Jan 27, 2025

Reduce size of some reg tests (#1461)
hgopalan
authored
9ce018c
Terrain blanking informed by ocean waves (#1369)
mbkuhn
authored
7353631

Commits on Jan 28, 2025

Reg test speedup (#1464)
mbkuhn
authored
0eb2687
Unit test - Periodic multilevel fillpatch (#1465)
mbkuhn
authored
d08789d

Commits on Jan 29, 2025

Pin python to v3.12 for the CI docs (#1467)
marchdf
authored
bf7e55d
Fix potential null pointer dereference in new test (#1468)
marchdf
authored
e5f5083

Commits on Jan 30, 2025

w2a fields - replace fillpatch with FillBoundary (#1470)
mbkuhn
authored
2d2394e
Decrease fixed point iters for abl regtest (#1471)
marchdf
authored
6080de5
terrain are waves only if vof is not a field (#1472)
mbkuhn
authored
1f9ea0e
Meso-Micro Coupling with no precursor for Terrain (#1426)

authored
82f64d2

Commits on Jan 31, 2025

Speedup some regression test (#1473)
marchdf
authored
4f11d0b

Commits on Feb 3, 2025

Underwater terrain-aware wave forcing (#1475)
mbkuhn
authored
38d1b9f

Commits on Feb 10, 2025

Changes for coupling with ERF using MultiBlock (#1478)

authored
b3cf40a

Commits on Feb 12, 2025

Update amrex and amrex-hydro submodules (#1483)
marchdf
authored
c6a54a7

Commits on Feb 13, 2025

Initialize anelastic with isentropic hydrostatic equilibrium (#1484)
marchdf
authored
d2b200d

Commits on Feb 14, 2025

fix dangling reference bug (#1486)
mukul1992
authored
a09d3e7

Commits on Feb 17, 2025

Fix warning extra ';' (#1490)
marchdf
authored
4081d83

Commits on Feb 19, 2025

Initialize density to reference density for anelastic (#1492)
marchdf
authored
dc3ef9e

Commits on Feb 20, 2025

Add clarification documentation for TurbineFastLine (#1497)
marchdf
authored
e9cbd29

Commits on Feb 24, 2025

Remove gpu stream syncs (#1499)
marchdf
authored
b785b7d
MF parallelfor loops for the unit tests (#1500)
marchdf
authored
458878e

Commits on Feb 25, 2025

Commits on Feb 26, 2025

Update the bottom solver default absolute tolerance (#1506)
marchdf
authored
f42c0cf

Commits on Feb 27, 2025

Commits on Feb 28, 2025

Update amrex and amrex-hydro submods (#1509)
marchdf
authored
41253bc

Commits on Mar 3, 2025

Enforce solvability AFTER multiplying rho0 for anelastic (#1513)
mukul1992
authored
2606327

Commits on Mar 5, 2025

Turn on CMAKE_VERBOSE_MAKEFILE in CI. (#1491)
jrood-nrel
authored
f4133ea
Remove duplicate line in CI (#1517)
jrood-nrel
authored
3ce49a9

Commits on Mar 7, 2025

Update CI (#1518)
jrood-nrel
authored
da7c546
Update cache cleanup scripts. (#1521)
jrood-nrel
authored
4c8dff3
Simplify cache cleanup. (#1522)
jrood-nrel
authored
9ac42c5
Fix clang-tidy job. (#1523)
jrood-nrel
authored
1a71b88

Commits on Mar 12, 2025

Adjust sampling particles tolerance bounds (#1527)
marchdf
authored
5a4e231

Commits on Mar 19, 2025

Fix the DTU spinner check (#1533)
marchdf
authored
659f5fe

Commits on Mar 26, 2025

Add amr-wind journal article reference (#1503)

marchdf
and
moprak-nrel
authored
d9eae71
ABL Boundary Plane: convert some asserts to aborts (#1537)
mbkuhn
authored
273edc8

Commits on Mar 27, 2025

Check density bounds upon initialization - for constant density single-phase and two-phase (#1538)

mbkuhn
and
marchdf
authored
bbee024

Commits on Mar 28, 2025

Update docker CI (#1540)
jrood-nrel
authored
071a055
more advice for initial density check failures (#1543)
mbkuhn
authored
6ea51eb

Commits on Mar 31, 2025

Simplify Docker CI. (#1545)
jrood-nrel
authored
fe3799a

Commits on Apr 2, 2025

Fix issues with multiply_rho (#1541)

authored
ef30de9

Commits on Apr 4, 2025

Correcting ConvectingTaylorVortex error calculation for the hybrid solver (#1539)

itopcuoglu
and
marchdf
authored
1df202e

Commits on Apr 10, 2025

Commits on Apr 11, 2025

avoid dividing by 0 for dx1; quantity doesn't actually get used when n1_sp = 1 (#1557)
mbkuhn
authored
1035404

Commits on Apr 14, 2025

Commits on Apr 15, 2025

Commits on Apr 16, 2025

Remove mention of deprecated GNUmake path (#1570)
marchdf
authored
9f4b619
Remote deprecated MOL section (#1571)
moprak-nrel
authored
0659e48
Add inviscid to documentation spellist (#1573)
moprak-nrel
authored
e811d0d
Update dev docs and some typo fixes (#1572)
marchdf
authored
c7946ad
Multiphase inputs for input file reference (#1575)
mbkuhn
authored
e50dc97
Split theory.rst into individual sections (#1576)
moprak-nrel
authored
8c7c64c
Restructuring walkthrough with addition of getting started section (#1574)
mpolimeno
authored
637276f
Add documentation for turbine models (#1577)
marchdf
authored
71a0e2c
Include FAQ, common errors for documentation (#1579)
mbkuhn
authored
d5659e3
deleting dollar signs from doc dev manual in code snippets (#1578)
mpolimeno
authored
da68352
Doc FLLC (#1580)

authored
9f7458a

Commits on Apr 17, 2025

Update governing equations in documentation (#1581)
moprak-nrel
authored
280379f
Use fcompare in CI (#1569)
jrood-nrel
authored
a1d52e0
fix FLLC note (#1582)
mbkuhn
authored
92bbb92
Fllc doc edits (#1583)
mbkuhn
authored
08a52b5

Commits on Apr 21, 2025

Fix RK2 approach for explicit diffusion (#1584)
mbkuhn
authored
473dde9
Modify density check at initialization - bug fix (#1586)
mbkuhn
authored
9c0d6fb

Commits on Apr 22, 2025

Document boundary condition options (#1589)
marchdf
authored
9463276
Specified Monin-Obukhov Length (#1418)

authored
f9f1eeb
Use multiply_rho true for potential temperature evolution (#1498)

marchdf
and
Michael Kuhn
authored
25cdac5

Commits on Apr 23, 2025

Refactor to allow adaptive timestepping for overset; improve adaptive timestepping (#1542)
mbkuhn
authored
691aba5

Commits on Apr 28, 2025

Commits on Apr 29, 2025

Improve VOF BC defaults and density BC with VOF (#1596)
mbkuhn
authored
802bd67
Update OF 40 API (#1595)
marchdf
authored
aa1c63a

Commits on May 1, 2025

Document IO compression (#1563)
marchdf
authored
6ac1ca4

Commits on May 6, 2025

Fix mask-value-specific field extrema calculation (#1594)
mbkuhn
authored
15ee1cd

Commits on May 16, 2025

Fix typos (#1610)
omahs
authored
a691ea1

Commits on May 19, 2025

Update amrex and amrex-hydro submods (#1613)
marchdf
authored
0b1359c

Commits on May 20, 2025

overset MAC projection: changes to avoid diffs (#1614)
mbkuhn
authored
eee722c
Improve FreeSurfaceSampler (#1615)
mbkuhn
authored
359b310

Commits on May 21, 2025

Terrain Aligned Profile (#1611)

hgopalan
and
marchdf
authored
ae231ed

Commits on May 22, 2025

More default verbosity for Waves2AMR interface (#1619)
mbkuhn
authored
8d8080c
Improve time interpolation of Waves2AMR approach (#1620)

mbkuhn
and
mpolimeno
authored
2fc3ae3

Commits on May 23, 2025

Ability to Specify a Time-Table of Surface Temperature (#1618)

authored
f956642
documentation of ABL surface temp arguments (#1623)
mbkuhn
authored
ed79282
remove hard-coded inflow-on-outflow flag (#1624)
mbkuhn
authored
f319384

Commits on May 27, 2025

Waves2AMR usage: remove postprocess_velocity_*_liquid() (#1626)
mbkuhn
authored
e23ba10

Commits on May 28, 2025

Commits on May 29, 2025

Ability to Have Multiple Instances of Time Averaging and Specify an Averaging Interval (#1616)

authored
cad9238

Commits on May 30, 2025

Post processing output upgrade (#1592)

mbkuhn
and
moprak-nrel
authored
eb7c106
Revert "Improve FreeSurfaceSampler" (#1627)
mbkuhn
authored
23cf02b

Commits on Jun 2, 2025

Post-processing: adding default back (#1635)
mbkuhn
authored
b855e6c

Commits on Jun 3, 2025

Commits on Jun 4, 2025

Time averaging modifications: use of offset, remove step-based, add unit tests (#1642)
mbkuhn
authored
412f015

Commits on Jun 12, 2025

Make initial iterations compatible with boundary planes (#1651)
mbkuhn
authored
744ab4f

Commits on Jun 13, 2025

Ignore max steps and max time during overset simulation (#1653)
mbkuhn
authored
b0e9396

Commits on Jun 18, 2025

Clarify running the amr_wind exec (#1663)
moprak-nrel
authored
3a6030f
Add sanity check for read_flat_grid_file (#1655)
marchdf
authored
c1c4bf0

Commits on Jun 25, 2025

User specified tagging criteria (#1673)
marchdf
authored
e3595fa

Commits on Jun 26, 2025

Try simple spec in docker CI. (#1675)
jrood-nrel
authored
1775012
adding weto stack at readme (#1666)
Garrett Barter
authored
69224b8

Commits on Jul 8, 2025

Add links to amrex documentation (#1682)
marchdf
authored
56d19d0
Use native Spack commands in container CI (#1681)
jrood-nrel
authored
fd44654

Commits on Jul 9, 2025

OpenFAST 4.1.0: changes to ExtInfw (#1665)

mbkuhn
and
marchdf
authored
56f79ad
Post processing logic fix (#1683)
mbkuhn
authored
547b24a
replace "output_frequency" with "output_interval" for post-processing in tests (#1686)
mbkuhn
authored
7346fd2

Commits on Jul 11, 2025

Commits on Jul 16, 2025

Initialize pressure for sloshing tank, waves cases (overset purposes) (#1687)
mbkuhn
authored
79bb29a

Commits on Jul 17, 2025

Update max_level documentation (#1698)
marchdf
authored
f84ed57

Commits on Jul 18, 2025

Document tools; add tools for converting native sampler outputs (#1670)
mbkuhn
authored
4f76d51

Commits on Jul 21, 2025

make w2a initialization more accurate, especially for low resolutions (#1669)
mbkuhn
authored
66a70ff

Commits on Jul 23, 2025

Commits on Jul 24, 2025

field norms output: switching to scientific, correct width (#1705)
mbkuhn
authored
501c711

Commits on Jul 25, 2025

Commits on Jul 30, 2025

Output better timing information with each step (#1714)
marchdf
authored
7baa889

Commits on Aug 11, 2025

Remove assert in meso forcing (#1720)
marchdf
authored
bb9646e
Ocean Waves: relaxation zones in y (#1715)
mbkuhn
authored
97349ae
Remove deprecated docs in meso forcing (#1721)
marchdf
authored
f3e85e6

Commits on Aug 15, 2025

FreeSurface sampler: avoid issues when sampling within numerical beach (#1678)
mbkuhn
authored
5a79177

Commits on Aug 25, 2025

update max_cfl default to match current methods (#1725)
mbkuhn
authored
4e452e3

Commits on Aug 26, 2025

correct input argument on FLLC docs page (#1727)
mbkuhn
authored
621696d

Commits on Sep 8, 2025

Add active wake control to Joukowsky Disk models (#1733)
moprak-nrel
authored
243e620

Commits on Sep 12, 2025

Update openfast version doc (#1739)
marchdf
authored
4e50422

Commits on Sep 24, 2025

Update amrex submodule (#1749)
marchdf
authored
567a4e2
Fix dependabot (#1750)
marchdf
authored
6c47e7f

Commits on Sep 30, 2025

create a smooth buffer between y relaxation zones and numerical beach (#1753)
mbkuhn
authored
767752b

Commits on Oct 8, 2025

Skip stats frequency output if the frequency is negative (#1762)
marchdf
authored
0c83e4b

Commits on Oct 14, 2025

add underscore to make docs link work (#1766)
mbkuhn
authored
34006ad
add numpy to ignored spellcheck list (#1767)
mbkuhn
authored
15e3fc5
change the correct spelling list (#1769)
mbkuhn
authored
0963c24

Commits on Oct 28, 2025

Fix variable length arrays warning in waves2amr (#1774)
marchdf
authored
41c6f2e
Update waves2amr submod (#1777)
marchdf
authored
ad22df5

Commits on Oct 30, 2025

Update wave2amr submodule (#1779)
marchdf
authored
9f14537

Commits on Oct 31, 2025

Update waves2amr (#1780)
marchdf
authored
32a4a58

Commits on Nov 3, 2025

Commits on Nov 4, 2025

Speedup ABLStats (#1726)
marchdf
authored
33f8996
Make ocean waves boundary compatible with relaxation zones in y (#1784)
mbkuhn
authored
35d6375

Commits on Nov 8, 2025

CMake updates to coincide with Waves2AMR updates (#1786)
jrood-nrel
authored
a1c9c4a

Commits on Nov 10, 2025

Revert "Make ocean waves boundary compatible with relaxation zones in y (#1784)" (#1787)
mbkuhn
authored
464ce08

Commits on Nov 11, 2025

Commits on Nov 17, 2025

Improve FieldPlaneAveragingFine using interpolation where coarse (#1792)

mbkuhn
and
moprak-nrel
authored
0c17511

Commits on Dec 4, 2025

Couple to Kynema for ALM and templatize existing OpenFAST interface (#1759)
mbkuhn
authored
02102eb

Commits on Dec 5, 2025

harmonize 2d for initialize waves2amr (#1800)
mbkuhn
authored
ffe2b52
Relax zones y + beach bugfix (#1801)
mbkuhn
authored
cb22bb9
Enable initial iterations for overset wave problems (#1802)
mbkuhn
authored
a258b10

Commits on Dec 9, 2025

Fix FPE in waves2amr initialization that incorporates y relax zones (#1804)
mbkuhn
authored
0677e1f

Commits on Dec 10, 2025

Commits on Dec 16, 2025

Improve time-based outputs (#1810)
mbkuhn
authored
c85a91c

Commits on Dec 17, 2025

modifications to kynema interface and setup + docs (#1803)
mbkuhn
authored
567b064

Commits on Jan 8, 2026

Bump submods/amrex from `3c1f1c7` to `53dc0a4` (#1816)
dependabot[bot]
authored
5278fd7

Commits on Jan 9, 2026

Write out sampling time in yaml file with more precision (#1822)

mchurchf
and
Matt Churchfield
authored
689a891
Add deterministic GPU option to MLMG. (#1821)
jrood-nrel
authored
8c25d80

Commits on Jan 13, 2026

Fail if OpenMP is enabled in the compiler but not the build system (#1824)
jrood-nrel
authored
71cbd06

Commits on Jan 15, 2026

Commits on Jan 26, 2026

Fix reversed arguments in amrex::Vector. (#1831)
jrood-nrel
authored
b1ee63c

Commits on Jan 28, 2026

Fix docker CI. (#1833)
jrood-nrel
authored
ed39e43
Update ccache. (#1834)
jrood-nrel
authored
29bbba6

Commits on Feb 2, 2026

Changes for building with single precision. (#1830)
jrood-nrel
authored
9d96344

Commits on Feb 3, 2026

Bump submods/AMReX-Hydro from `99d6acd` to `75da770` (#1836)
dependabot[bot]
authored
30dfc27
Update AMReX. (#1837)
jrood-nrel
authored
82053e2

Commits on Feb 6, 2026

Commits on Feb 9, 2026

Commits on Feb 10, 2026

Revert to scaling LOW_NUM. (#1842)
jrood-nrel
authored
8bd1680

Commits on Feb 11, 2026

Use different default MLMG tolerances depending on precision (#1843)
jrood-nrel
authored
752c3e7

Commits on Feb 12, 2026

Fix casting in amrex::min. (#1844)
jrood-nrel
authored
d9dc4ac
Use initial arena size of 0 for GPU tests. (#1845)
jrood-nrel
authored
caf6a4f

Commits on Feb 18, 2026

Use https when cloning OpenFAST. (#1847)
jrood-nrel
authored
37b94dd

Commits on Feb 19, 2026

Update to c++20 standard (#1848)
jrood-nrel
authored
241240a

Commits on Feb 20, 2026

Require CUDA 12 or newer. (#1849)
jrood-nrel
authored
190cee3
Add explicit parentheses. (#1850)
jrood-nrel
authored
8c56e88

Commits on Feb 21, 2026

Commits on Feb 23, 2026

Use std ranges (#1854)
jrood-nrel
authored
18eb062
Fix some warnings. (#1855)
jrood-nrel
authored
3e72fd8

Commits on Feb 24, 2026

Fix more static analysis warnings and make NOLINT more specific (#1856)
jrood-nrel
authored
4523405
Avoid use of std::endl (#1857)
jrood-nrel
authored
70b0f52
Use smaller int type for enums. (#1858)
jrood-nrel
authored
857f898

Commits on Feb 25, 2026

Commits on Feb 26, 2026

Make headers consistent (#1863)
jrood-nrel
authored
2f6c787
Remove noexcept and add check. (#1864)
jrood-nrel
authored
cfe0428

Commits on Mar 4, 2026

fix broken nrel urls in README (#1869)
baperry2
authored
12ba29f

Commits on Mar 6, 2026

Check that MPI is enabled when using Kynema or OpenFAST. (#1870)
jrood-nrel
authored
42b6ce1

Commits on Mar 9, 2026

fix erroneous parentheses in Rankine definition (#1872)
mbkuhn
authored
52809f5
Delay time fix (#1874)
mbkuhn
authored
8611911
fix github CI - reference test (#1875)
mbkuhn
authored
edf199e

Commits on Mar 11, 2026

Commits on Mar 12, 2026

Precision based tests (#1873)
mbkuhn
authored
bd8740f

Commits on Mar 13, 2026

Update GitHub Actions to Node.js 24 runtime versions (#1880)

Copilot
and
baperry2
authored
9cf67d2
Attach backtrace in nightly tests when the test fails. (#1881)
jrood-nrel
authored
2cfeff8

Commits on Mar 16, 2026

add mpi commands to fcompare command (#1882)

mbkuhn
and
Michael Kuhn
authored
982532f
Fix errors with single precision on GPUs (#1879)

mbkuhn
and
Michael Kuhn
authored
acecf1e
Run more tests in Debug (#1878)
jrood-nrel
authored
c944073
Bug fix: subvolume post-processing utility (#1883)
mbkuhn
authored
37d1aab

Commits on Mar 17, 2026

Commits on Mar 18, 2026

Commits on Mar 19, 2026

Removing overset two-phase reinitialization (#1815)
mbkuhn
authored
fb972bd

Commits on Mar 20, 2026

Commits on Mar 25, 2026

Fix typo: "checkpoint_inteval" → "checkpoint_interval" in CheckAndSetUpDryRun() (#1895)

Copilot
and
jrood-nrel
authored
496f089

Commits on Mar 26, 2026

Commits on Mar 27, 2026

Initial plan
Copilot
authored
89d590b
Simplify test input files using AMReX FILE directive

Copilot
and
baperry2
authored
a6f9192
Simplify test input files using AMReX FILE directive

Copilot
and
baperry2
authored
011de4b
Merge remote-tracking branch 'origin/copilot/simplify-test-input-files' into copilot/simplify-test-input-files

Copilot
and
baperry2
authored
87c392a
add documentation on FILE directive in input files
baperry2
committed
f83e00e