bug fixes

jalessandri · Oct 18, 2019 · 4a27d85 · 4a27d85
1 parent 58fab1d
commit 4a27d85
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Showing 14 changed files with 61 additions and 117 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,12 @@
+
+#-----------------------------------------------
+
 .DS_Store
+
 #-----------------------------------------------
 
+fembfm1
+
 arc
 test
 tmp
@@ -10,11 +16,9 @@ private
 
 /lib
 /bin
-#fem3d/bin
 bugs
 
 femmpi
-#rules
 stable
 femdoc/old/
 
@@ -245,6 +249,10 @@ fembin/mesh
 fembin/exgrd
 
 #-----------------------------------------------
-
 # compiled examples
+#-----------------------------------------------
+
 Output
+
+#-----------------------------------------------
+
diff --git a/COMMIT b/COMMIT
@@ -1,5 +1,24 @@
 ============================================================
 
+Fri Oct 18 18:19:26 CEST 2019
+
+bug fixes
+
+ .gitignore                | 14 +++++++++---
+ Rules.make                |  2 ++
+ fem3d/Makefile            |  8 ++++---
+ fem3d/newbfm.f            |  4 ++--
+ fem3d/subfind.f           | 42 +++-------------------------------
+ fem3d/submask.f           | 58 +----------------------------------------------
+ fem3d/subsys.f            |  2 +-
+ femcheck/rules/Rules.dist |  2 ++
+ femcheck/test_compile.sh  |  2 ++
+ femplot/mod_hydro_plot.f  |  4 ++--
+ femplot/supano.f          | 15 ++++++------
+ 11 files changed, 38 insertions(+), 115 deletions(-)
+
+============================================================
+
 Thu Oct 17 16:36:54 CEST 2019
 
 several small changes

diff --git a/Rules.make b/Rules.make
@@ -192,6 +192,8 @@ ECOLOGICAL = NONE
 #
 # BFM model - how to
 #
+# this feature is still experimental - no support
+#
 # to integrate the BFM model the following has to be done:
 #   1) set "NETCDF = true" in the lines above (BFM needs NETCDF)
 #   2) set "ECOLOGICAL = BFM" in the lines above

diff --git a/VERSION b/VERSION
@@ -1,3 +1,5 @@
+version  7_5_64    19-07-2019    VERS_7_5_64   commit_2019-10-18
+
 version  7_5_64    19-07-2019    VERS_7_5_64   commit_2019-10-17
 
 version  7_5_64    19-07-2019    VERS_7_5_64   commit_2019-10-17

diff --git a/fem3d/Makefile b/fem3d/Makefile
@@ -156,10 +156,11 @@ ECOLOGICAL_OBJ = ecological_dummy.o newbfm_dummy.o
 ifeq ($(ECOLOGICAL),EUTRO)
   ECOLOGICAL_OBJ = bio3d.o bio3d_util.o \
 		weutro.o weutro_sedim.o weutro_light.o \
-		weutro_seed.o weutro_shell.o weutro_ulva.o
+		weutro_seed.o weutro_shell.o weutro_ulva.o \
+		newbfm_dummy.o
 endif
 ifeq ($(ECOLOGICAL),ERSEM)
-  ECOLOGICAL_OBJ = subbfm.o
+  ECOLOGICAL_OBJ = subbfm.o newbfm_dummy.o
   LIBG_ERSEM     = -l$(LIBERSEM)
   LIBF_ERSEM     = $(DIRLIB)/lib$(LIBERSEM).a
 endif
@@ -168,7 +169,8 @@ ifeq ($(ECOLOGICAL),AQUABC)
 		aquabc_II_co2sys.o aquabc_II_apara.o aquabc_II_util.o \
 		aquabc_II_sediment_model_1.o aquabc_II_sediment_lib.o \
 		aquabc_II_pelagic_model.o aquabc_II.o \
-		aquabc_II_ini.o aquabc_II_svindex.o
+		aquabc_II_ini.o aquabc_II_svindex.o \
+		newbfm_dummy.o
 endif
 ifeq ($(ECOLOGICAL),BFM)
   LIBBFM =     bfm

diff --git a/fem3d/newbfm.f b/fem3d/newbfm.f
@@ -234,8 +234,8 @@ subroutine bfm_compute
 
 	do i=1,nvar
 
-!$OMP TASK FIRSTPRIVATE(i,rkpar,wsink,difhv,difv,difmol,idbfm,what,
-!$OMP&     dt,nlvdi) SHARED(bfmv)  DEFAULT(NONE)
+!$OMP TASK FIRSTPRIVATE(i,rkpar,wsink,difhv,difv,difmol,idbfm,what
+!$OMP&     ,nlvdi) SHARED(bfmv)  DEFAULT(NONE)
 
 ! use scal_adv_fact to pass wsink matrix into advection
 

diff --git a/fem3d/subfind.f b/fem3d/subfind.f
@@ -27,51 +27,14 @@
 c
 c contents :
 c
-c subroutine setgeo(x0,y0,dx,dy,flag)
-c		sets grid values for interpolation
-c subroutine getgeo(x0,y0,dx,dy,flag)
-c		gets grid values for interpolation
-c subroutine getgeoflag(flag)
-c		gets flag value for interpolation
-c
-c subroutine av2am(av,am,ip,jp)
-c		interpolation of av onto a regular net
-c subroutine av2amk(bwater,av,am,ip,jp)
-c		interpolation of av onto a regular net
-c function intri(x,y,xp,yp)
-c		point in triangle or not
-c function intrid(x,y,xp,yp)
-c		point in triangle or not (double precision version)
-c subroutine am2av(am,av,ip,jp)
-c		interpolation of am onto finite element mesh
-c function am2val(am,ip,jp,xx,yy)
-c		interpolation of am onto finite element mesh
-c subroutine ave2am(av,am,ip,jp)
-c		interpolation of av (elementwise) onto a regular net
-c
-c subroutine mkmask(bwater,zv,href,hzoff)
-c		makes mask in element
-c
-c subroutine mimareg(am,ip,jp,amin,amax)
-c		computes min/max of regular matrix (without flag values)
-c subroutine a2char(am,ac,ip,jp)
-c		creates 1 char representation of matrix
-c subroutine prchar(ac,ip,jp)
-c		prints 1 char representation of matrix
-c
-c subroutine femintp(ie,z,xp,yp,zp)
-c               interpolation in element (with ev)
-c subroutine elemintp(x,y,z,xp,yp,zp)
-c               interpolation in element (no ev)
-c
+c subroutine find_close_elem(ieold,xp,yp,ielem)
+c		finds element for point (xp,yp) starting from ieold
 c subroutine find_elem_from_old(ieold,xp,yp,ielem)
 c		finds element for point (xp,yp) starting from ieold
 c subroutine find_element(xp,yp,ielem)
 c		finds element for point (xp,yp)
 c function in_element(ie,xp,yp)
 c		checks if point (xp,yp) is in element ie
-c subroutine get_xy_elem(ie,x,y)
-c		returns x,y of vertices of element ie
 c
 c revision log :
 c
@@ -102,6 +65,7 @@
 c 25.05.2017	ggu	changed VERS_7_5_28
 c 16.02.2019	ggu	changed VERS_7_5_60
 c 13.03.2019	ggu	changed VERS_7_5_61
+c 18.10.2019	ggu	cleaned contents
 c
 c notes :
 c

diff --git a/fem3d/submask.f b/fem3d/submask.f
@@ -27,52 +27,6 @@
 c
 c contents :
 c
-c subroutine setgeo(x0,y0,dx,dy,flag)
-c		sets grid values for interpolation
-c subroutine getgeo(x0,y0,dx,dy,flag)
-c		gets grid values for interpolation
-c subroutine getgeoflag(flag)
-c		gets flag value for interpolation
-c
-c subroutine av2am(av,am,ip,jp)
-c		interpolation of av onto a regular net
-c subroutine av2amk(bwater,av,am,ip,jp)
-c		interpolation of av onto a regular net
-c function intri(x,y,xp,yp)
-c		point in triangle or not
-c function intrid(x,y,xp,yp)
-c		point in triangle or not (double precision version)
-c subroutine am2av(am,av,ip,jp)
-c		interpolation of am onto finite element mesh
-c function am2val(am,ip,jp,xx,yy)
-c		interpolation of am onto finite element mesh
-c subroutine ave2am(av,am,ip,jp)
-c		interpolation of av (elementwise) onto a regular net
-c
-c subroutine mkmask(bwater,zv,href,hzoff)
-c		makes mask in element
-c
-c subroutine mimareg(am,ip,jp,amin,amax)
-c		computes min/max of regular matrix (without flag values)
-c subroutine a2char(am,ac,ip,jp)
-c		creates 1 char representation of matrix
-c subroutine prchar(ac,ip,jp)
-c		prints 1 char representation of matrix
-c
-c subroutine femintp(ie,z,xp,yp,zp)
-c               interpolation in element (with ev)
-c subroutine elemintp(x,y,z,xp,yp,zp)
-c               interpolation in element (no ev)
-c
-c subroutine find_elem_from_old(ieold,xp,yp,ielem)
-c		finds element for point (xp,yp) starting from ieold
-c subroutine find_element(xp,yp,ielem)
-c		finds element for point (xp,yp)
-c function in_element(ie,xp,yp)
-c		checks if point (xp,yp) is in element ie
-c subroutine get_xy_elem(ie,x,y)
-c		returns x,y of vertices of element ie
-c
 c revision log :
 c
 c 18.11.1998	ggu	routine commented
@@ -103,12 +57,7 @@
 c 11.07.2017	ggu	changed VERS_7_5_30
 c 16.02.2019	ggu	changed VERS_7_5_60
 c 13.03.2019	ggu	changed VERS_7_5_61
-c
-c notes :
-c
-c pxareg,pyareg         coordinates of lower left point of matrix
-c pxdreg,pydreg         grid size of matrix
-c pzlreg                value of z for land points
+c 18.10.2019	ggu	cleaned contents
 c
 c******************************************************
 c******************************************************
@@ -175,18 +124,13 @@ subroutine set_level_mask(bwater,ilhv,level)
 
 	nedry = 0
 
-	!write(6,*) 'set_level_mask: ',level
-	!write(6,*) (ilhv(ie),ie=1,nel,nel/10)
-
 	do ie=1,nel
 	  if( level .gt. ilhv(ie) ) then
 	    bwater(ie) = .false.
 	    nedry = nedry + 1
 	  end if
 	end do
 
-	!write(6,*) 'level exist  (dry/wet/total): ',nedry,nel-nedry,nel
-
 	end
 
 c******************************************************

diff --git a/fem3d/subsys.f b/fem3d/subsys.f
@@ -324,7 +324,7 @@ subroutine nlsinh_general
 c			value of 2 will guarantee that the program will not
 c			abort and continue running, but it might not
 c			be doing what you intended. (Default 0)
-c |flgrst|		This variable indicateswhich variables are read
+c |flgrst|		This variable indicates which variables are read
 c			from the restart file. By default all available
 c			variables are read and used. If some variables
 c			are not wanted (because, e.g., you want to restart

diff --git a/fem3d/subver.f b/fem3d/subver.f
@@ -375,14 +375,14 @@ module shyfem_version
 c
 c \newcommand{\VERSION}{7.5.64}
 c \newcommand{\version}{7\_5\_64}
-c \newcommand{\COMMIT}{2019-10-17}
+c \newcommand{\COMMIT}{2019-10-18}
 c
 c DOCS	END
 
         implicit none
 
         character*10, parameter :: version = '7.5.64'
-        character*10, parameter :: commit  = '2019-10-17'
+        character*10, parameter :: commit  = '2019-10-18'
         character*17, parameter :: text    = 'SHYFEM VERSION = '
 
         character*40, parameter :: string = text//version//'  '//commit

diff --git a/femcheck/rules/Rules.dist b/femcheck/rules/Rules.dist
@@ -192,6 +192,8 @@ ECOLOGICAL = NONE
 #
 # BFM model - how to
 #
+# this feature is still experimental - no support
+#
 # to integrate the BFM model the following has to be done:
 #   1) set "NETCDF = true" in the lines above (BFM needs NETCDF)
 #   2) set "ECOLOGICAL = BFM" in the lines above

diff --git a/femcheck/test_compile.sh b/femcheck/test_compile.sh
@@ -44,6 +44,7 @@ Clean_before()
   cp $rules_dist ./Rules.make
   [ -f allstdout.txt ] && rm allstdout.txt
   [ -f allstderr.txt ] && rm allstderr.txt
+  make cleanall
 }
 
 Clean_after()
@@ -54,6 +55,7 @@ Clean_after()
   mv -f $rules_save ./Rules.make
   [ -f allstdout.txt ] && mv allstdout.txt allstdout.tmp
   [ -f allstderr.txt ] && mv allstderr.txt allstderr.tmp
+  make cleanall
 }
 
 SetUp()

diff --git a/femplot/mod_hydro_plot.f b/femplot/mod_hydro_plot.f
@@ -79,8 +79,8 @@ module mod_hydro_plot
 
         logical, allocatable, save :: bwater(:)
         logical, allocatable, save :: bkwater(:)
-        logical, allocatable, save :: bplot(:)
-        logical, allocatable, save :: bkplot(:)
+        logical, allocatable, save :: bplot(:)	!.false. if iarv(ie) == ianopl
+        logical, allocatable, save :: bkplot(:)	!.false. if iarv(ie) == ianopl
 
         real, allocatable, save :: fvlv(:,:)
         real, allocatable, save :: wauxv(:,:)

diff --git a/femplot/supano.f b/femplot/supano.f
@@ -2104,7 +2104,7 @@ subroutine occupy(iquad)
 
 	integer iqc(4)
 
-	logical bplot
+	logical bwrite
 	character*80 line
 	integer i,j,k,n
 	integer iq,jq,ip
@@ -2116,8 +2116,8 @@ subroutine occupy(iquad)
 	save ijq
 	data ijq /1,2,4,3/
 
-	bplot = bbverb
-	bplot = .false.
+	bwrite = bbverb
+	bwrite = .false.
 
 	do j=1,ndim
 	  do i=1,ndim
@@ -2144,10 +2144,9 @@ subroutine occupy(iquad)
 
 	n = min(ndim,80)
 
-	if( bplot ) write(6,*) 'occupy... ',n,ndim,x0,y0,x1,y1
-
-	if( bplot ) then
-	do j=n,1,-1
+	if( bwrite ) then
+	 write(6,*) 'occupy... ',n,ndim,x0,y0,x1,y1
+	 do j=n,1,-1
 	  do i=1,n
 	    if( ia(i,j) .ne. 0 ) then
 	      line(i:i) = '*'
@@ -2156,7 +2155,7 @@ subroutine occupy(iquad)
 	    end if
 	  end do
 	  write(6,*) line(1:n)
-	end do
+	 end do
 	end if
 
 	do i=1,4