replace "output_frequency" with "output_interval" for post-processing…

… in tests (#1686)

Time averaging modifications: use of offset, remove step-based, add u…

…nit tests (#1642)

* start of unit test

* test for every step

* test output value in comparison unit test

* add start time offset

* two new unit tests: one passing, one failing

* strip out timestep-based phase averaging

* docs update

* convert window to query, update docs, address CI

* fix unit test

* unit test cleanup

* more CI

* remove deprecated input file option

* codeQL this time

* clang-tidy

Modify density check at initialization - bug fix (#1586)

HOS-NWT capability (#1536)

* compiling with these changes, Waves2AMR commit a033db8

* fix rmodes initialization

* differentiate between dimensions for fft and for interpolations, goes with Waves2AMR commit 8a55cd1

* adapting to Waves2AMR ed0aba8, something is off with the 3d case

* update Waves2AMR submodule

* correct dimensions of additional mode pointers

* correct offset arguments

* correct readmodes type

* correct dx

* add vertical shift to ow_w2a case

* NWT cases for 2D and 3D data

* update Waves2AMR module

* update Waves2AMR module again

* formatting

* skip .dat files for spellcheck

* Update test/test_files/ow_w2a_nwt_3d/ow_w2a_nwt_3d.inp

* keep y offset for 3d case, remove from 2d case

* document offset arguments

Underwater terrain-aware wave forcing (#1475)

* turn off apply_relaxation_zones where terrain blanking (or terrain drag forcing) happens

* modify ow boundary for underwater terrain

* add regression test

fix multiple errors in eta for stokes waves (#1392)

* fix parenthesis error in eta for stokes waves

* divide eta terms by wavenumber

Forest Canopy Model (#1324)



Co-authored-by: Marc T. Henry de Frahan <marchdf@gmail.com>
Co-authored-by: Jon Rood <jon.rood@nrel.gov>
Co-authored-by: Marc T. Henry de Frahan <marc.henrydefrahan@nrel.gov>
Co-authored-by: prakash <120606615+moprak-nrel@users.noreply.github.com>

Alter fillpatch and boundary plane calls for overset simulations (#1358)

* introduce bool to CFDSim to know which part of overset step we're in & make fillpatch time smart in TiogaInterface
* change when pre_advance_work happens for boundary planes with overset

Adding a dynamic stress (wave model) to wall_models (#1233)



---------

Co-authored-by: Manuel Ayala <mayalag@kl2.head.cm.kestrel.hpc.nrel.gov>
Co-authored-by: mayala5 <mayala5@login01.cm.cluster>
Co-authored-by: mayala5 <mayala5@login02.cm.cluster>
Co-authored-by: Manuel Ayala <mayalag@kl3.head.cm.kestrel.hpc.nrel.gov>
Co-authored-by: Manuel Ayala <manuelayala@Manuels-MacBook-Pro.local>
Co-authored-by: mayala5 <mayala5@login03.cm.cluster>
Co-authored-by: Marc T. Henry de Frahan <marc.henrydefrahan@nrel.gov>
Co-authored-by: prakash <prakash.mohan@nrel.gov>
Co-authored-by: prakash <120606615+moprak-nrel@users.noreply.github.com>

Clipped outflow made default for momentum equation (#1340)

* Clipped outflow made default for momentum equation
* update docs and README about pressure_outflow
* inputs documentation
* docs correction