feature/rm_nemsutils: Merge branch 'develop' into feature/rm_nemsutils

Issue ufs-community#104.

driver_scripts/driver_grid.cray.sh

@@ -49,7 +49,7 @@
 #   7) For "regional_esg" grids, set center lat/lon of grid,
 #      - "target_lat/lon" - the i/j dimensions - "i/jdim", the
 #      x/y grid spacing - "delx/y", and halo.
-#   8) Set working directory - TMPDIR - and path to the repository
+#   8) Set working directory - TEMP_DIR - and path to the repository
 #      clone - home_dir.
 #   9) Submit script: "cat $script | bsub".
 #  10) All files will be placed in "out_dir".
@@ -106,12 +106,12 @@ fi
 #-----------------------------------------------------------------------
 # Check paths.
 #   home_dir - location of repository.
-#   TMPDIR   - working directory.
+#   TEMP_DIR - working directory.
 #   out_dir  - where files will be placed upon completion.
 #-----------------------------------------------------------------------
 
 export home_dir=$LS_SUBCWD/..
-export TMPDIR=/gpfs/hps3/stmp/$LOGNAME/fv3_grid.$gtype
+export TEMP_DIR=/gpfs/hps3/stmp/$LOGNAME/fv3_grid.$gtype
 export out_dir=/gpfs/hps3/stmp/$LOGNAME/my_grids
 
 #-----------------------------------------------------------------------

driver_scripts/driver_grid.dell.sh

@@ -51,7 +51,7 @@
 #   7) For "regional_esg" grids, set center lat/lon of grid,
 #      - "target_lat/lon" - the i/j dimensions - "i/jdim", the 
 #      x/y grid spacing - "delx/y", and halo.
-#   8) Set working directory - TMPDIR - and path to the repository
+#   8) Set working directory - TEMP_DIR - and path to the repository
 #      clone - home_dir.
 #   9) Submit script: "cat $script | bsub".
 #  10) All files will be placed in "out_dir".
@@ -108,12 +108,12 @@ fi
 #-----------------------------------------------------------------------
 # Check paths.
 #   home_dir - location of repository.
-#   TMPDIR   - working directory.
+#   TEMP_DIR   - working directory.
 #   out_dir  - where files will be placed upon completion.
 #-----------------------------------------------------------------------
 
 export home_dir=$LS_SUBCWD/..
-export TMPDIR=/gpfs/dell1/stmp/$LOGNAME/fv3_grid.$gtype
+export TEMP_DIR=/gpfs/dell1/stmp/$LOGNAME/fv3_grid.$gtype
 export out_dir=/gpfs/dell1/stmp/$LOGNAME/my_grids
 
 #-----------------------------------------------------------------------

driver_scripts/driver_grid.hera.sh

@@ -49,7 +49,7 @@
 #   7) For "regional_esg" grids, set center lat/lon of grid,
 #      - "target_lat/lon" - the i/j dimensions - "i/jdim", the
 #      x/y grid spacing - "delx/y", and halo.
-#   8) Set working directory - TMPDIR - and path to the repository
+#   8) Set working directory - TEMP_DIR - and path to the repository
 #      clone - home_dir.
 #   9) Submit script: "sbatch $script".
 #  10) All files will be placed in "out_dir".
@@ -108,12 +108,12 @@ fi
 #-----------------------------------------------------------------------
 # Check paths.  
 #   home_dir - location of repository.
-#   TMPDIR   - working directory.
+#   TEMP_DIR   - working directory.
 #   out_dir  - where files will be placed upon completion. 
 #-----------------------------------------------------------------------
 
 export home_dir=$SLURM_SUBMIT_DIR/..
-export TMPDIR=/scratch2/NCEPDEV/stmp1/$LOGNAME/fv3_grid.$gtype
+export TEMP_DIR=/scratch2/NCEPDEV/stmp1/$LOGNAME/fv3_grid.$gtype
 export out_dir=/scratch2/NCEPDEV/stmp1/$LOGNAME/my_grids
 
 #-----------------------------------------------------------------------

driver_scripts/driver_grid.jet.sh

@@ -50,7 +50,7 @@
 #   7) For "regional_esg" grids, set center lat/lon of grid,
 #      - "target_lat/lon" - the i/j dimensions - "i/jdim", the
 #      x/y grid spacing - "delx/y", and halo.
-#   8) Set working directory - TMPDIR - and path to the repository
+#   8) Set working directory - TEMP_DIR - and path to the repository
 #      clone - home_dir.
 #   9) Submit script: "sbatch $script".
 #  10) All files will be placed in "out_dir".
@@ -109,12 +109,12 @@ fi
 #-----------------------------------------------------------------------
 # Check paths.  
 #   home_dir - location of repository.
-#   TMPDIR   - working directory.
+#   TEMP_DIR   - working directory.
 #   out_dir  - where files will be placed upon completion. 
 #-----------------------------------------------------------------------
 
 export home_dir=$SLURM_SUBMIT_DIR/..
-export TMPDIR=/lfs4/HFIP/emcda/$LOGNAME/stmp/fv3_grid.$gtype
+export TEMP_DIR=/lfs4/HFIP/emcda/$LOGNAME/stmp/fv3_grid.$gtype
 export out_dir=/lfs4/HFIP/emcda/$LOGNAME/stmp/my_grids
 
 #-----------------------------------------------------------------------

driver_scripts/driver_grid.orion.sh

@@ -49,7 +49,7 @@
 #   7) For "regional_esg" grids, set center lat/lon of grid,
 #      - "target_lat/lon" - the i/j dimensions - "i/jdim", the
 #      x/y grid spacing - "delx/y", and halo.
-#   8) Set working directory - TMPDIR - and path to the repository
+#   8) Set working directory - TEMP_DIR - and path to the repository
 #      clone - home_dir.
 #   9) Submit script: "sbatch $script".
 #  10) All files will be placed in "out_dir".
@@ -108,12 +108,12 @@ fi
 #-----------------------------------------------------------------------
 # Check paths.  
 #   home_dir - location of repository.
-#   TMPDIR   - working directory.
+#   TEMP_DIR   - working directory.
 #   out_dir  - where files will be placed upon completion. 
 #-----------------------------------------------------------------------
 
 export home_dir=$SLURM_SUBMIT_DIR/..
-export TMPDIR=/work/noaa/stmp/$LOGNAME/fv3_grid.$gtype
+export TEMP_DIR=/work/noaa/stmp/$LOGNAME/fv3_grid.$gtype
 export out_dir=/work/noaa/stmp/$LOGNAME/my_grids
 
 #-----------------------------------------------------------------------

modulefiles/build.hera

@@ -24,6 +24,6 @@ module load landsfcutil/2.4.1
 module load wgrib2/2.0.8
 
 module use /scratch1/NCEPDEV/nems/emc.nemspara/soft/modulefiles
-module load hdf5_parallel/1.10.6
-module load netcdf_parallel/4.7.4
+module load hdf5_parallel/1.10.6.release
+module load netcdf_parallel/4.7.4.release
 module load esmf/8.0.0_ParallelNetCDF

reg_tests/chgres_cube/driver.hera.sh

@@ -123,7 +123,7 @@ TEST8=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_C
 
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE -d afterok:$TEST8 << EOF
-#!/bin/sh
+#!/bin/bash
 grep -a '<<<' $LOG_FILE  > $SUM_FILE
 EOF
 

reg_tests/chgres_cube/driver.jet.sh

@@ -123,7 +123,7 @@ TEST8=$(sbatch --parsable --partition=xjet --nodes=1 --ntasks-per-node=6 -t 0:05
 
 sbatch --partition=xjet --nodes=1  -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE -d afterok:$TEST8 << EOF
-#!/bin/sh
+#!/bin/bash
 grep -a '<<<' $LOG_FILE  > $SUM_FILE
 EOF
 

reg_tests/chgres_cube/driver.orion.sh

@@ -126,7 +126,7 @@ TEST8=$(sbatch --parsable --ntasks-per-node=6 --nodes=2 -t 0:10:00 -A $PROJECT_C
 
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE -d afterok:$TEST8 << EOF
-#!/bin/sh
+#!/bin/bash
 grep -a '<<<' $LOG_FILE  > $SUM_FILE
 EOF
 

reg_tests/grid_gen/c96.uniform.sh

@@ -8,7 +8,7 @@
 
 set -x
 
-export TMPDIR=${WORK_DIR}/c96.uniform.work
+export TEMP_DIR=${WORK_DIR}/c96.uniform.work
 export out_dir=${WORK_DIR}/c96.uniform
 
 export res=96

reg_tests/grid_gen/driver.hera.sh

@@ -71,6 +71,6 @@ TEST2=$(sbatch --parsable --ntasks-per-node=24 --nodes=1 -t 0:10:00 -A $PROJECT_
 
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J grid_summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE -d afterok:$TEST2 << EOF
-#!/bin/sh
+#!/bin/bash
 grep -a '<<<' $LOG_FILE  > $SUM_FILE
 EOF

reg_tests/grid_gen/driver.jet.sh

@@ -71,6 +71,6 @@ TEST2=$(sbatch --parsable --ntasks-per-node=24 --nodes=1 -t 0:10:00 -A $PROJECT_
 
 sbatch --partition=xjet --nodes=1  -t 0:01:00 -A $PROJECT_CODE -J grid_summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE -d afterok:$TEST2 << EOF
-#!/bin/sh
+#!/bin/bash
 grep -a '<<<' $LOG_FILE  > $SUM_FILE
 EOF

reg_tests/grid_gen/driver.orion.sh

@@ -67,6 +67,6 @@ TEST2=$(sbatch --parsable --ntasks-per-node=24 --nodes=1 -t 0:10:00 -A $PROJECT_
 
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J grid_summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE -d afterok:$TEST2 << EOF
-#!/bin/sh
+#!/bin/bash
 grep -a '<<<' $LOG_FILE  > $SUM_FILE
 EOF

reg_tests/grid_gen/gfdl.regional.sh

@@ -8,7 +8,7 @@
 
 set -x
 
-export TMPDIR=${WORK_DIR}/gfdl.regional.work
+export TEMP_DIR=${WORK_DIR}/gfdl.regional.work
 export out_dir=${WORK_DIR}/gfdl.regional
 
 export res=96                # global resolution in which grid is embedded.

scripts/exemcsfc_global_sfc_prep.sh.ecf

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 
 ####  UNIX Script Documentation Block ###################################
 #                      .                                             .

sorc/CMakeLists.txt

@@ -13,3 +13,4 @@ add_subdirectory(grid_tools.fd)
 add_subdirectory(chgres_cube.fd)
 add_subdirectory(orog_mask_tools.fd)
 add_subdirectory(sfc_climo_gen.fd)
+add_subdirectory(vcoord_gen.fd)

sorc/vcoord_gen.fd/CMakeLists.txt

@@ -0,0 +1,15 @@
+set(fortran_src
+    driver.f90
+    matrix_utils.f90
+    vcoord_gen.f90)
+
+if(CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel)$")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -r8")
+elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU)$")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fdefault-real-8")
+endif()
+
+set(exe_name vcoord_gen)
+add_executable(${exe_name} ${fortran_src})
+
+install(TARGETS ${exe_name} RUNTIME DESTINATION ${exec_dir})

sorc/vcoord_gen.fd/driver.f90

@@ -0,0 +1,13 @@
+program driver
+  implicit none
+  integer levs,lupp,k
+  real pbot,psig,ppre,pupp,ptop,dpbot,dpsig,dppre,dpupp,dptop,pmin
+  real,allocatable:: ak(:),bk(:)
+  write(0,*) 'Enter levs,lupp,pbot,psig,ppre,pupp,ptop,dpbot,dpsig,dppre,dpupp,dptop'
+  read *,levs,lupp,pbot,psig,ppre,pupp,ptop,dpbot,dpsig,dppre,dpupp,dptop
+  allocate(ak(0:levs),bk(0:levs))
+  call vcoord_gen(levs,lupp,pbot,psig,ppre,pupp,ptop,dpbot,dpsig,dppre,dpupp,dptop,pmin,ak,bk)
+  write(0,*) 'pmin=',pmin
+  print '(2i6)',2,levs
+  print '(f12.3,f12.8)',(ak(k),bk(k),k=0,levs)
+end program

sorc/vcoord_gen.fd/matrix_utils.f90

@@ -0,0 +1,158 @@
+!-------------------------------------------------------------------------------
+!$$$  Subprogram documentation block
+!
+! Subprogram:    ludcmp      lower and upper triangular decomposition
+!   Prgmmr: Iredell    Org: W/NP23      Date: 2008-08-01
+!
+! Abstract: This subprogram decomposes a matrix into a product of
+!   lower and upper triangular matrices.
+!
+! Program history log:
+!   2008-08-01  Mark Iredell
+!
+! Usage:    call ludcmp(a,n,np,indx,d)
+!   Input argument list:
+!     a        real(np,np) matrix (will be overwritten)
+!     n        integer order of matrix
+!     np       integer dimension of matrix
+!
+!   Output argument list:
+!     a        real(np,np) LU-decomposed matrix
+!              (U is upper part of A, including diagonal;
+!               L is lower part of A, with 1 as diagonal;
+!               L*U equals original A after permuting)
+!     indx     integer(n) pivot indices
+!              (original A rows are permuted in order i with indx(i))
+!     d        real determinant permutation (1 or -1, or 0 if singular)
+!              (determinant is output diagonal product times d)
+!
+! Attributes:
+!   Language: Fortran 90
+!
+!$$$
+subroutine ludcmp(a,n,np,indx,d)
+  implicit none
+  integer,intent(in):: n,np
+  real,intent(inout):: a(np,np)
+  integer,intent(out):: indx(n)
+  real,intent(out):: d
+  integer i,j,k,imax
+  real aamax,sum,dum
+  real vv(n)
+! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+  d=1
+  do i=1,n
+    aamax=0
+    do j=1,n
+      if(abs(a(i,j))>aamax) aamax=abs(a(i,j))
+    enddo
+    if(aamax==0) then
+      d=0
+      return
+    endif
+    vv(i)=1/aamax
+  enddo
+  do j=1,n
+    do i=1,j-1
+      sum=a(i,j)
+      do k=1,i-1
+        sum=sum-a(i,k)*a(k,j)
+      enddo
+      a(i,j)=sum
+    enddo
+    aamax=0.
+    do i=j,n
+      sum=a(i,j)
+      do k=1,j-1
+        sum=sum-a(i,k)*a(k,j)
+      enddo
+      a(i,j)=sum
+      dum=vv(i)*abs(sum)
+      if(dum>=aamax) then
+        imax=i
+        aamax=dum
+      endif
+    enddo
+    if (j/=imax)then
+      do k=1,n
+        dum=a(imax,k)
+        a(imax,k)=a(j,k)
+        a(j,k)=dum
+      enddo
+      d=-d
+      vv(imax)=vv(j)
+    endif
+    indx(j)=imax
+    if(a(j,j)==0) then
+      d=0
+      return
+    endif
+    if(j/=n)then
+      dum=1/a(j,j)
+      do i=j+1,n
+        a(i,j)=a(i,j)*dum
+      enddo
+    endif
+  enddo
+end subroutine
+!-------------------------------------------------------------------------------
+!$$$  Subprogram documentation block
+!
+! Subprogram:    lubksb      lower and upper triangular back substitution
+!   Prgmmr: Iredell    Org: W/NP23      Date: 2008-08-01
+!
+! Abstract: This subprogram back substitutes to solve decomposed
+!   lower and upper triangular matrices as outputted by ludcmp.
+!
+! Program history log:
+!   2008-08-01  Mark Iredell
+!
+! Usage:    call lubksb(a,n,np,indx,b)
+!   Input argument list:
+!     a        real(np,np) LU-decomposed matrix
+!              (from ludcmp)
+!     n        integer order of matrix
+!     np       integer dimension of matrix
+!     indx     integer(n) pivot indices
+!              (from ludcmp)
+!     b        real(n) rhs vector of linear problem (will be overwritten)
+!
+!   Output argument list:
+!     b        real(n) solution of linear problem 
+!              (original A times output B equals original B)
+!
+! Attributes:
+!   Language: Fortran 90
+!
+!$$$
+subroutine lubksb(a,n,np,indx,b)
+  implicit none
+  integer,intent(in):: n,np
+  real,intent(in):: a(np,np)
+  integer,intent(in):: indx(n)
+  real,intent(inout):: b(n)
+  integer i,j,ii,ll
+  real sum
+! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+  ii=0
+  do i=1,n
+    ll=indx(i)
+    sum=b(ll)
+    b(ll)=b(i)
+    if (ii/=0)then
+      do j=ii,i-1
+        sum=sum-a(i,j)*b(j)
+      enddo
+    elseif(sum/=0) then
+      ii=i
+    endif
+    b(i)=sum
+  enddo
+  do i=n,1,-1
+    sum=b(i)
+    do j=i+1,n
+      sum=sum-a(i,j)*b(j)
+    enddo
+    b(i)=sum/a(i,i)
+  enddo
+end subroutine