Pull bug fixes from main into dev

* updated the intro

* fixes a bug with the QTF interpolation function (#1396)

* fix #1288, cleanup waveclass (main) (#1417)

* fix on pDis function call

* preliminary fix for issue #1288

* Update readAQWA.m (#1253)

* body mask fixes for #1346

* add warning when variable hydro turned on for drag or nonhydro bodies

* flex body - add missing mask lines, define h5 button callback

* fix #1288 cleanup waveClass

* adding bodyClass, should match

---------

Co-authored-by: jtgrasb <87095491+jtgrasb@users.noreply.github.com>
Co-authored-by: akeeste <akeeste@sandia.gov>

* Fix irregular wave elevation with multiple directions (#1403)

* Fix irregular wave elevation with multiple directions

* Updates the Ubuntu and Matlab versions (#1420)

* Updates the Ubuntu and Matlab versions

---------

Co-authored-by: Mohamed Shabara <84589678+MShabara@users.noreply.github.com>

* new body class constructor, no need for h5file

* removed disp used in debugging

* short check to ensure hydro struct provided is the right hydro struct

* cleaned up one comment

* rename hydrodata to hydroinput in body constructor

* move input checking to body.checkInputs()

* make body.hydroStruct a private variable

* make body.hydroStruct public and alphabetize

* clear body.hydroStruct once used

* brief documentation

* function to build body class hydro format struct from BEMIO format

* update hydro to hydroData function for other features

* fix bug in reading water depth, ex.irf.t and dofs

* make readH5ToStruct function identically to writeBEMIOH5 for GBM modes

* read GBM data and irf times correctly

* reference function in documentation

* update function docstring

---------

Co-authored-by: Shabara <mshabara@nrel.gov>
Co-authored-by: Mohamed Shabara <84589678+MShabara@users.noreply.github.com>
Co-authored-by: dforbush2 <dforbus@sandia.gov>
Co-authored-by: jtgrasb <87095491+jtgrasb@users.noreply.github.com>
Co-authored-by: akeeste <akeeste@sandia.gov>

* updated the intro

* fixes a bug with the QTF interpolation function (#1396)

* fix #1288, cleanup waveclass (main) (#1417)

* fix on pDis function call

* preliminary fix for issue #1288

* Update readAQWA.m (#1253)

* body mask fixes for #1346

* add warning when variable hydro turned on for drag or nonhydro bodies

* flex body - add missing mask lines, define h5 button callback

* fix #1288 cleanup waveClass

* adding bodyClass, should match

---------

Co-authored-by: jtgrasb <87095491+jtgrasb@users.noreply.github.com>
Co-authored-by: akeeste <akeeste@sandia.gov>

* Fix irregular wave elevation with multiple directions (#1403)

* Fix irregular wave elevation with multiple directions

* Updates the Ubuntu and Matlab versions (#1420)

* Updates the Ubuntu and Matlab versions

---------

Co-authored-by: Mohamed Shabara <84589678+MShabara@users.noreply.github.com>

* Enhances function flexibility

* Fix warnings

* change coercion for consistency with documentation

---------

Co-authored-by: Shabara <mshabara@nrel.gov>
Co-authored-by: Mohamed Shabara <84589678+MShabara@users.noreply.github.com>
Co-authored-by: dforbush2 <dforbus@sandia.gov>
Co-authored-by: jtgrasb <87095491+jtgrasb@users.noreply.github.com>
Co-authored-by: akeeste <akeeste@sandia.gov>

* fix waveClass and irregExc functions for #1288

* fix badBemioFix_fcn with warning messages and dynamic defaults

* excitationSpread fix for dev branch

* removing drafts to badBemiofix_fcn from PR

* fix waveClass and irregExc functions for #1288

* fix badBemioFix_fcn with warning messages and dynamic defaults

* end despiking on all but excitation

* now does excitation too

* refactor radiation CIC calculation

* add radiation conv integral surface calc for variable hydro

* add CIC surface tests

* increase time step to speed up cicTest.m

* add cicTest to wecSimTest.m

* update ci surface docstring

* rename new function to camelCase

* create IRF surfaces in the body class

* minor clean up

* add excitation IRF time to body.variableHydro

* clarify where simu.cicDt is used

* excitation convolution integral surface calc

* add surface calcs and variant subsystems to library

* update library tag

* remove check preventing VH with userDefinedExcitation

* add goto tags for excitation and total forces

* fix goto tag name and turn off a warning

* comment to explain why a warning is turned off

* update excitation CI surface calc to use persistent amplitude

* add test for excitationConvolutionIntegralSurface

* fix issue template typo

* add empty bodies.hydroForceIndex to responseClass

* move the adjusted mass used in simulation to body.hydroForce

* fix hydroForce.mass definition for all cases

* clear persistent functions before simulation

* progress on library

* working but fundamentally incorrect excitation IRF surface

* remove excitation IRF surface function

* fix one more bug removing the excitation irf surface

* library to r2020b

* update post processing added mass force with VH

* fix added mass force postprocessing again

* docs - comment on added mass treatment with variable hydro

* docs - explain IRF surface for variable hydro

* update explanation of our handling of added mass

* fix reference typo

* add figures of an irf surface

* library to 2020b and add QTFs=2 flag

* fix paraview output for multiple bodies

* Add post-processing for multiple MoorDyn connections

* fix paraview macro for multiple moordyn connections

* update docs

* Update mooring.rst

---------

Co-authored-by: jtgrasb <87095491+jtgrasb@users.noreply.github.com>

* minor fix to the mass reference for drag and nonhydro bodies

* magic fix for simulink logging error

* actual fix for simulink logging error

* Adds Newman Approx for the QTFs

* Bug Fix

* Bug Fix

* Adds user guide doc for the QTFs

* asserts that the QTFs are not enabled with the meanDrift

* Update docs/user/advanced_features.rst

Co-authored-by: Adam Keester <72414466+akeeste@users.noreply.github.com>

* Update docs/user/advanced_features.rst

Co-authored-by: Adam Keester <72414466+akeeste@users.noreply.github.com>

* Update docs/user/advanced_features.rst

Co-authored-by: Adam Keester <72414466+akeeste@users.noreply.github.com>

* Update docs/user/advanced_features.rst

Co-authored-by: Adam Keester <72414466+akeeste@users.noreply.github.com>

* Update docs/user/advanced_features.rst

Co-authored-by: Adam Keester <72414466+akeeste@users.noreply.github.com>

* Adds QTFs option 2 for the run from simulink feature

* fixes a bug with the QTF doc

* Pulled updated WECSim_Lib_Body_Elements.slx from dev branch to resolve conflicts

* Modifies the user doc

* Modifies lines in the Standing approx

* Modifies the user doc

---------

Co-authored-by: Adam Keester <72414466+akeeste@users.noreply.github.com>

* refactor radiation CIC calculation

* add radiation conv integral surface calc for variable hydro

* add CIC surface tests

* increase time step to speed up cicTest.m

* add cicTest to wecSimTest.m

* update ci surface docstring

* rename new function to camelCase

* create IRF surfaces in the body class

* minor clean up

* add excitation IRF time to body.variableHydro

* clarify where simu.cicDt is used

* excitation convolution integral surface calc

* add surface calcs and variant subsystems to library

* update library tag

* remove check preventing VH with userDefinedExcitation

* add goto tags for excitation and total forces

* fix goto tag name and turn off a warning

* comment to explain why a warning is turned off

* update excitation CI surface calc to use persistent amplitude

* add test for excitationConvolutionIntegralSurface

* fix issue template typo

* add empty bodies.hydroForceIndex to responseClass

* move the adjusted mass used in simulation to body.hydroForce

* fix hydroForce.mass definition for all cases

* clear persistent functions before simulation

* progress on library

* working but fundamentally incorrect excitation IRF surface

* remove excitation IRF surface function

* fix one more bug removing the excitation irf surface

* library to r2020b

* update post processing added mass force with VH

* fix added mass force postprocessing again

* docs - comment on added mass treatment with variable hydro

* docs - explain IRF surface for variable hydro

* update explanation of our handling of added mass

* fix reference typo

* add figures of an irf surface

* updates to bodyClass

* remove comments

* initialize inertialMass

* clarify gravity force in added mass dev docs

* resolve some issues

* update docs on use of mass vs adjustedMass

* updates

* Fix indexing

* add inertia products option and warning message

* amend warning

* revise warning

* remove extraneous moordyn readme

* clarifying comment in docs

* add docstring to body.variableHydro

* expand warning message

* add error to prevent variable hydro and elevationImport

* disable nonlinear hydro and variable hydro

* update docs and error message

* typo

* use hydroforce.mass for nonlinear hydro

* Revert "use hydroforce.mass for nonlinear hydro"

This reverts commit fa7ca47.

* storage.mass to mass

* fix typos

---------

Co-authored-by: akeeste <akeeste@sandia.gov>

* Radiation damping load extrapolation

* update convolutionIntegralInterp rename elsewhere

* update extrapFrad docstring

* update dimensions in docstring

* Simpler implementation of the extrapolation feature

* Simpler implementation of the extrapolation feature

* add extrapFrad to flex body, and library to R2020b

* update cicTest format

* update size of force output in CIC functions

---------

Co-authored-by: akeeste <akeeste@sandia.gov>

* Match PR 1478 on main (#1479)

* match PR 1478 changes on main

---------

Co-authored-by: jtgrasb <87095491+jtgrasb@users.noreply.github.com>
Co-authored-by: akeeste <akeeste@sandia.gov>

* Fixing Regression Tests for RM3 (#1473)

* Fixing Regression Tests for RM3

* Updating the correct _org.mat files

* resolving figure issues

---------

Co-authored-by: Ruehl <kmruehl@sandia.gov>

---------

Co-authored-by: dforbush2 <dforbus@sandia.gov>
Co-authored-by: jtgrasb <87095491+jtgrasb@users.noreply.github.com>
Co-authored-by: akeeste <akeeste@sandia.gov>
Co-authored-by: Jorge Leon <72461917+jleonqu@users.noreply.github.com>

* update body class and add documentation

* Doc updates

* Irregular CIC test for OSWEC - needs more work

* Update OSWEC tests

* changing fig size and legend defaults

---------

Co-authored-by: jtgrasb <87095491+jtgrasb@users.noreply.github.com>
Co-authored-by: Ruehl <kmruehl@sandia.gov>

* break out body library into 4 files

* remove nonhydro body library

* remove body type variant subsystems

* fix library formatting

* update mask initialization commands

* update forwarding table for old blocks

* working flex and drag bodies

* remove simulink GUI from flex body

* remove extraneous RM3FromSimulink example

* remove run from simulink test

* move top level mask init functions to .m files

* flex body - restore VH control link

* fully remove runFromSimTest

* update forwarding table, fix links aross flex body

* fix F_rad extrapolation rate transition

* updating library files

* restructure body library again

* refactor and readd run from simulink test

* add bodyClass deprecation warning and update instructions for body.nonHydro~=0

* update use of body.nonhydro flag

* update documentation on use of body.nonhydro

* remove wecsim gui docs

* remove wecsim gui functions

* revert body library separation and remove nonhydro body

* revert mask to m files

* remove WS GUI from body library again

* add drag body variant subsystem back in again

* update body library reference in docs

* remove WEC-Sim GUI from all library files

* minor revs towards required doc and initializeWecSim updates

* documentation fixes

* clean up initializeWecSim for no WS GUI and streamlined run from Simulink

* remove non-hydro body reference in rigid body mask

* minor fix

* remove docs note

* return to test directory after runFromSimTest

* fix body in Flex body CIC Outport naming

* remove outdated compilation test, close sim models after each test

* close simulink file after every regression test

* minor formatting

---------

Co-authored-by: Ruehl <kmruehl@sandia.gov>

* make logic easier to read

* major badBemiofix_fcn refactor

* rename BEM cleaning function

* old and new functions basically identical, bugs not withstanding

* fix a couple bugs, improve robustness

* minor function formatting

* back to skipping scattering and FK coefficients

* add citation

* add comment on despike.filter variables

* doc fix to resolve #1487

* minor change

---------

Co-authored-by: MShabara <mshabara@nrel.gov>

* add universal joint to PTO library

* allow [1 n] pto extension and hardstop parameters

* fix sign of forces and power

* minor doc update for new pto block

* Change waveClass constructor to use enumeration instead of string

* load new source folder

* bladepitch0 bug fixed

* revert extraneous changes to wec-sim source

* revert extraneous changes to wec-sim source 2

* rebase MOST changes on top of current wec-sim dev

* define MOST acronym before using

* camelCase and some space formatting

* combine redundant mooring set-up

* mooring class formatting and cleanup, re-add lookUpTableFlag

* minor formatting for source/lib/**/slBlocks.m

* remove duplicate mooring set-up

* fix error message typo

* initial release notes

* re-add new mooring block that akeeste accidentally removed

* review comment from @DavideIssoglio

* remove spreadfigures.m

* refactor new mooring method

* separate flags for mooring LUT and NLSD

* revert to more robust lookup table loading

* update windClass initialization

* misc formatting

* adds description for the nonLinearStaticData prop

* move pto, constraint, mooring setup after body setup

* fix a few bugs in mooring class pre-processing

* update parameter in mooring library initialization

* fix simulink bug in mooring library

* save most library to r2020b

* update release notes

---------

Co-authored-by: Davide  Issoglio <davide.issoglio@polito.it>
Co-authored-by: Shabara <mshabara@nrel.gov>
Co-authored-by: jtgrasb <jtgrasb@sandia.gov>

* Commenting line 221 in InitializeWecSim.m and adding V4.0 results for the OSWEC Test

* Update original data with proper phase

* Update org file and syntax

* fix orig data

* fix phase?

* Update spread comparison

* fix wave class in org mat

* fix spectral moment calculation

---------

Co-authored-by: jtgrasb <87095491+jtgrasb@users.noreply.github.com>

* Add back moordyn blocks

* Add MoorDyn Caller

)

* fix for the elevation plot when multiple wave classes are defined

* converts the types of waves to char

* Update source/functions/initializeWecSim.m

* update waves.plotSpectra() for multiple waves

---------

Co-authored-by: Adam Keester <72414466+akeeste@users.noreply.github.com>
Co-authored-by: akeeste <akeeste@sandia.gov>

* correct current velocity in noWave case

* correct current velocity in regular case

* correct current velocity in irregular case