SanderHulst · SanderHulst · May 6, 2022 · Jun 8, 2020 · Jul 16, 2020 · Jul 28, 2020
diff --git a/.github/ISSUE_TEMPLATE/add-development-request.md b/.github/ISSUE_TEMPLATE/add-development-request.md
@@ -0,0 +1,10 @@
+---
+name: Add Development Request
+about: Request that a new development be added to WW3
+title: ''
+labels: 'enhancement'
+assignees: ''
+
+---
+
+
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -0,0 +1,23 @@
+---
+name: Bug report
+about: Create a report to help us improve WW3
+title: ''
+labels: 'bug'
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+Add any other context about the problem here.
diff --git a/.github/ISSUE_TEMPLATE/documentation.md b/.github/ISSUE_TEMPLATE/documentation.md
@@ -0,0 +1,15 @@
+---
+name: Documentation request/update
+about: Add new section in the documentation or report a type/mistake in the documentation
+title: ''
+labels: 'documentation'
+assignees: ''
+
+---
+
+**Describe the section in the documentation that is missing or requires an update?**
+
+**Report a bug/typo in the documentation**
+
+**Link the issue(s) associated with this documentation update**
+
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for WW3
+title: ''
+labels: 'enhancement'
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. 
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -0,0 +1,43 @@
+# Pull Request Summary
+(Instructions: this, and all subsequent sections of text should be removed and filled in as appropriate.)   
+Please describe the PR summary
+
+## Description
+Provide a detailed description of what this PR does.
+What bug does it fix, or what feature does it add?
+Is a change of answers expected from this PR?
+
+### Issue(s) addressed
+* Is there an issue associated with this development (bug fix, enhancement, new feature)?    
+Please add a reference to a related issue(s) in WW3 repository (Follow [link](https://docs.github.com/en/github/managing-your-work-on-github/linking-a-pull-request-to-an-issue)).
+Link the issues to be closed with this PR, whether in this repository, or in another repository.
+(Remember, issues should always be created before starting work on a PR branch!).  
+Note that properly "linked issues" (either automatic links, or manual ones using the correct keywords) will be automatically closed when the PR is merged.
+
+- fixes #<issue_number>
+- fixes noaa-emc/ww3/issues/<issue_number>
+
+### Check list  
+* Is your feature branch up to date with the authoritative repository (NOAA/develop)?
+* Make sure you have checked the [checklist for a developer submitting to develop](https://github.com/NOAA-EMC/WW3/wiki/Code-Management#checklist-for-a-developer-submitting-to-develop), [checklist for a developer submitting to develop](https://github.com/NOAA-EMC/WW3/wiki/Code-Management#checklist-for-a-developer-submitting-to-develop) and [updating version number](https://github.com/NOAA-EMC/WW3/wiki/Code-Management#checklist-for-updating-version-number)
+* Reviewers: @mentions of suggested reviewers of the proposed changes.
+
+
+### Testing
+* How were these changes tested?
+* Are the changes covered by regression tests? (If not, why? Do new tests need to be added?)
+* If a new feature was added, was a new regression test added?
+* Have regression tests been run?
+* Which compiler / HPC you used to run the regression tests in the PR? 
+* Please provide the summary output of matrix.comp (_matrix.Diff.out_, _matrixCompFull.out_ and _matrixCompSummary.out_):    
+Please indicate the expected changes in the outputs ([excluding the known list of non-identical tests](https://github.com/NOAA-EMC/WW3/wiki/How-to-use-matrix.comp-to-compare-regtests-with-master#4-look-at-results)).
+
+
+
+
+
+
+
+
+
+
diff --git a/.gitignore b/.gitignore
@@ -45,6 +45,10 @@ manual/*.toc
 manual/*.out
 manual/*.dvi
 manual/*.pdf
+model?
+model??
+regtests/list*
+regtests/before
 regtests/matrix*
 regtests/*/work*
 regtests/*/input*/*.nc

diff --git a/model/bin/comp.tmpl b/model/bin/comp.tmpl
@@ -82,7 +82,8 @@
     case $WWATCH3_NETCDF in
       NC3) opt="$opt -I$NETCDF_INCDIR" ;;
       NC4) if [ "$mpi_mod" = 'no' ]; then comp="`$NETCDF_CONFIG --fc`"; fi
-           opt="$opt -I`$NETCDF_CONFIG --includedir`" ;;
+           #opt="$opt -I`$NETCDF_CONFIG --includedir`" ;;
+           opt="$opt `$NETCDF_CONFIG --cflags`" ;;
     esac
   fi
 

diff --git a/model/bin/link.tmpl b/model/bin/link.tmpl
@@ -116,7 +116,7 @@
     case $WWATCH3_NETCDF in
       NC3) libs="$libs -L$NETCDF_LIBDIR -lnetcdf" ;;
       NC4) if [ "$mpi_mod" = 'no' ]; then comp="`$NETCDF_CONFIG --fc`"; fi
-           libs="$libs `$NETCDF_CONFIG --flibs`" ;;
+           libs="$libs `$NETCDF_CONFIG --flibs` `$NETCDF_CONFIG --libs`" ;;
     esac
   fi
 

diff --git a/model/bin/make_makefile.sh b/model/bin/make_makefile.sh
@@ -887,7 +887,17 @@
                prop=
              source="w3parall w3triamd $stx $nlx $btx $is $uostmd"
                  IO='w3iogrmd'
-                aux="constants w3servmd w3arrymd w3dispmd w3gsrumd w3timemd w3nmlgridmd $pdlibyow $memcode" ;;
+                aux="constants w3servmd w3arrymd w3dispmd w3gsrumd w3timemd w3nmlgridmd $pdlibyow $memcode"
+                if [ "$scrip" = 'SCRIP' ]
+                then
+                  aux="$aux scrip_constants scrip_grids scrip_iounitsmod"
+                  aux="$aux scrip_remap_vars scrip_timers scrip_errormod scrip_interface"
+                  aux="$aux scrip_kindsmod scrip_remap_conservative wmscrpmd" 
+                fi 
+                if [ "$scripnc" = 'SCRIPNC' ]
+                then
+                  aux="$aux scrip_netcdfmod scrip_remap_write scrip_remap_read"
+                fi ;;
      ww3_strt) IDstring='Initial conditions program'
                core=
                data="$memcode w3gdatmd w3wdatmd w3adatmd w3idatmd w3odatmd"

diff --git a/model/bin/w3_make b/model/bin/w3_make
@@ -135,8 +135,7 @@
 
 # GRID STRT BOUND OUTF OUTP TRCK GRIB GINT GX* UPRSTR LIBWW3
 #  reg_programs = non-NetCDF programs
-  reg_programs="ww3_grid" 
-  reg_programs="$reg_programs ww3_strt"
+  reg_programs="ww3_strt"
   reg_programs="$reg_programs ww3_bound"
   reg_programs="$reg_programs ww3_outf"
   reg_programs="$reg_programs ww3_outp"
@@ -171,6 +170,7 @@
   # MULTI MULTI_ESMF SBS1
   if [ -n "`grep SCRIPNC $switch_file`" ] || [ -n "`grep OASIS $switch_file`" ]  || [ -n "`grep PDLIB $switch_file`" ]
   then
+    cdf_programs="$cdf_programs ww3_grid"
     cdf_programs="$cdf_programs ww3_multi"
     cdf_programs="$cdf_programs ww3_sbs1"
     cdf_programs="$cdf_programs libww3"
@@ -179,6 +179,7 @@
       cdf_programs="$cdf_programs ww3_multi_esmf"
     fi
   else
+    reg_programs="$reg_programs ww3_grid"
     reg_programs="$reg_programs ww3_multi"
     reg_programs="$reg_programs ww3_sbs1"
     reg_programs="$reg_programs libww3"

diff --git a/model/bin/ww3_from_ftp.sh b/model/bin/ww3_from_ftp.sh
@@ -8,7 +8,7 @@
 curr_dir=`pwd`
 
 # Set WW3 code version
-ww3ver=v7.07
+ww3ver=v7.12.1
 
 #Get top level directory of ww3 from user: 
 echo -e "\n\n This script will download data from the ftp for WAVEWATCH III "
@@ -51,7 +51,7 @@ cp -r data_regtests/ww3_tp2.14/input/toy/toy_coupled_field.nc.OASACM regtests/ww
 cp -r data_regtests/ww3_tp2.14/input/toy/toy_coupled_field.nc.OASACM regtests/ww3_tp2.14/input/toy/toy_coupled_field.nc.OASACM6
 cp -r data_regtests/ww3_tp2.14/input/toy/*.nc regtests/ww3_tp2.14/input/toy/
 cp -r data_regtests/ww3_tp2.17/input/*     regtests/ww3_tp2.17/input/
-
+cp -r data_regtests/ww3_tp2.21/input/*     regtests/ww3_tp2.21/input/
 
 #Do you want to clean up (aka delete tar file, delete the data_regtests directory) 
 echo -e "\n\n Do you want to delete the tar file ww3_from_ftp.${ww3ver}.tar.gz [y|n]: "

diff --git a/model/ftn/PDLIB/yowpdlibmain.ftn b/model/ftn/PDLIB/yowpdlibmain.ftn
@@ -1145,6 +1145,7 @@ module yowpdlibMain
     implicit none
     integer I1, I2, I3, stat, IE, NI(3)
     real(rkind) :: DXP1, DXP2, DXP3, DYP1, DYP2, DYP3, DBLTMP, TRIA03
+    logical     :: CROSSES_DATELINE
 
     allocate(PDLIB_SI(npa), PDLIB_CCON(npa), PDLIB_IEN(6,ne), PDLIB_TRIA(ne), stat=stat)
     if(stat/=0) call parallel_abort('SI allocation failure')
@@ -1163,6 +1164,12 @@ module yowpdlibMain
       DYP2=y(I3) - y(I2)
       DXP3=x(I1) - x(I3)
       DYP3=y(I1) - y(I3)
+      CALL ELEMENT_CROSSES_DATELINE(DXP1, DXP2, DXP3, CROSSES_DATELINE)
+      IF (CROSSES_DATELINE) THEN
+        CALL CORRECT_DX_GT180(DXP1)
+        CALL CORRECT_DX_GT180(DXP2)
+        CALL CORRECT_DX_GT180(DXP3)
+      ENDIF
 
       PDLIB_IEN(1,IE) = - DYP2
       PDLIB_IEN(2,IE) =   DXP2
@@ -1185,6 +1192,41 @@ module yowpdlibMain
   end subroutine
 !**********************************************************************
 !*                                                                    *
+!**********************************************************************
+  subroutine ELEMENT_CROSSES_DATELINE(RX1, RX2, RX3, CROSSES_DATELINE)
+!   Purpose: understanding if an element crosses the dateline.
+!   An element crossing the dateline has, e.g. a node with lon < 180
+!   and another 2 with lon > -180
+    IMPLICIT NONE
+    REAL(rkind),  INTENT(IN)  :: RX1, RX2, RX3
+    LOGICAL, INTENT(OUT) :: CROSSES_DATELINE
+    INTEGER :: R1GT180, R2GT180, R3GT180
+    R1GT180 = MERGE(1, 0, ABS(RX1).GT.180)
+    R2GT180 = MERGE(1, 0, ABS(RX2).GT.180)
+    R3GT180 = MERGE(1, 0, ABS(RX3).GT.180)
+! if R1GT180+R2GT180+R3GT180 .eq. 0 the element does not cross the dateline
+! if R1GT180+R2GT180+R3GT180 .eq. 1 the element contains the pole
+! if R1GT180+R2GT180+R3GT180 .eq. 2 the element crosses the dateline
+    CROSSES_DATELINE = R1GT180+R2GT180+R3GT180 .EQ. 2
+  end subroutine
+!**********************************************************************
+!*                                                                    *
+!**********************************************************************
+  subroutine CORRECT_DX_GT180(DXP)
+!   Purpose: the absolute zonal distance between 2 points is always <= 180
+!            This subroutine corrects the zonal distance to satifsy
+!            this requirement
+    IMPLICIT NONE
+    REAL(rkind), INTENT(INOUT) :: DXP
+    IF (DXP .le. -180) THEN
+      DXP=DXP + 360
+    END IF
+    IF (DXP .ge. 180) THEN
+      DXP=DXP - 360
+    END IF
+  end subroutine
+!**********************************************************************
+!*                                                                    *
 !**********************************************************************
   subroutine ComputeIA_JA_POSI_NNZ
     use yowElementpool, only: ne, ne_global, INE, ielg

diff --git a/model/ftn/SCRIP/scrip_grids.f b/model/ftn/SCRIP/scrip_grids.f
@@ -96,6 +96,10 @@ module scrip_grids
      &     special_polar_cell1,       ! cell with only 1 corner at pole
      &     special_polar_cell2        !
 
+      integer (SCRIP_i4), dimension(:), allocatable, target,save ::
+     &             grid1_imask,        ! flag which cells participate
+     &             grid2_imask         ! flag which cells participate
+
       real (SCRIP_r8), dimension(:), allocatable, target, save ::
      &             grid1_center_lat,  ! lat/lon coordinates for
      &             grid1_center_lon,  ! each grid center in radians

diff --git a/model/ftn/w3gsrumd.ftn b/model/ftn/w3gsrumd.ftn
@@ -3726,10 +3726,14 @@
                   IF ( K .EQ. 1 ) THEN
                       SIGN1 = SIGN(ONE,CROSS)
                     ELSE
-                      IF ( SIGN(ONE,CROSS) .NE. SIGN1 ) THEN
+                      ! If point lies along a border, the cross product
+                      ! is zero and its sign is not well defined
+                      IF ( ABS(CROSS) .GT. LEPS ) THEN
+                        IF ( SIGN(ONE,CROSS) .NE. SIGN1 ) THEN
                           LSBC = .FALSE.
                           CYCLE SUBCELL_LOOP
                         END IF
+                      END IF
                     END IF
                 END DO !K
                 IF ( LSBC ) RETURN

diff --git a/model/ftn/w3iopomd.ftn b/model/ftn/w3iopomd.ftn
@@ -242,7 +242,7 @@
       INTEGER                 :: IX1, IY1, IXS, IYS
 !/S      INTEGER, SAVE           :: IENT = 0
 !/O7a      INTEGER                 :: IX0, IXN, IY0, IYN, NNX,         &
-!/O7a                                 KX, KY, JX, IIX
+!/O7a                                 KX, KY, JX, IIX, IX2, IY2, IS1
       INTEGER                 :: IX(4), IY(4)   ! Indices of points used in interp.
       REAL                    :: RD(4)          ! Interpolation coefficient 
 !/O7a      REAL                    :: RD1, RD2, RDTOT, ZBOX(4), DEPTH
@@ -392,7 +392,7 @@
 !/O7a                         RD(4)*ZBOX(4) ) / RDTOT
 !/O7a            WRITE (SCREEN,943) DEPTH
 !
-!/O7a       *** implementation of O7a option with curvilinear grids is incomplete ***
+!/O7a      ! *** implementation of O7a option with curvilinear grids is incomplete ***
 !
 !/O7a            IF ( RD1 .LT. 0.05 ) IX2 = IX1
 !/O7a            IF ( RD1 .GT. 0.95 ) IX1 = IX2

diff --git a/model/ftn/w3odatmd.ftn b/model/ftn/w3odatmd.ftn
@@ -1591,9 +1591,9 @@
 !/MPI      RSBLKS => OUTPTS(IMOD)%OUT4%RSBLKS
 !/MPI      IF ( NRQRS .NE. 0 ) THEN
 !/MPI          IRQRS  => OUTPTS(IMOD)%OUT4%IRQRS
-!/MPI          IRQRSS => OUTPTS(IMOD)%OUT4%IRQRSS
-!/MPI          VAAUX  => OUTPTS(IMOD)%OUT4%VAAUX
 !/MPI        END IF
+!/MPI      IRQRSS => OUTPTS(IMOD)%OUT4%IRQRSS
+!/MPI      VAAUX  => OUTPTS(IMOD)%OUT4%VAAUX
 !
       NBI    => OUTPTS(IMOD)%OUT5%NBI
       NBI2   => OUTPTS(IMOD)%OUT5%NBI2

diff --git a/model/ftn/w3tidemd.ftn b/model/ftn/w3tidemd.ftn
@@ -531,10 +531,20 @@
       REAL(KIND=4), PARAMETER   :: PI=3.1415926536
       REAL(KIND=4), PARAMETER   :: TWOPI=2.*3.1415926536
 
-      REAL                      :: SLAT, VDBL, RR, SUMC, SUMS, UUDBL, UU
+      REAL                      :: SLAT, VDBL, RR, SUMC, SUMS, UUDBL, UU, CXLAT
       INTEGER                   :: IUU, IV
-
-      SLAT=SIN(PI*XLAT/180.)
+      ! This comment was taken from t_tide, a matlab tidal prediction suite
+      !
+      ! Apparently the second-order terms in the tidal potential go to zero
+      ! at the equator, but the third-order terms do not. Hence when trying
+      ! to infer the third-order terms from the second-order terms, the
+      ! nodal correction factors blow up. In order to prevent this, it is
+      ! assumed that the equatorial forcing is due to second-order forcing
+      ! OFF the equator, from about the 5 degree location. Latitudes are
+      ! hence (somewhat arbitrarily) forced to be no closer than 5 deg to
+      ! the equator, as per note in Foreman.
+      CXLAT = MAX(ABS(XLAT), 5.)
+      SLAT=SIN(PI*CXLAT/180.)
 
       JBASE=0
 ! All 
@@ -1869,12 +1879,13 @@
       REAL(KIND=4), PARAMETER   :: TWOPI=2.*3.1415926536
 !
       REAL                      :: SLAT, VDBL, VV, SUMC, SUMS, RR, &
-                                   UUDBL, UU
+                                   UUDBL, UU, CXLAT
       REAL(KIND=8)              :: d1,h,pp,s,p,enp,dh,dpp,ds,dp,dnp,hh,tau
 
       INTEGER                   :: indx(170)
 
-      SLAT=SIN(PI*XLAT/180.)
+      CXLAT = MAX(ABS(XLAT), 5.)
+      SLAT=SIN(PI*CXLAT/180.)
 !
 !***********************************************************************
 !*  THE ASTRONOMICAL ARGUMENTS ARE CALCULATED BY LINEAR APPROXIMATION