IMPORTANT: Refactored state vector indices

[arango]

• The state vector indices are used in various algorithms. The numeric order is essential in data assimilation because they are used to associate observations to the type of variables in the state vector:

        isFsur = 1                ! free-surface
        isUbar = 2                ! 2D U-velocity
        isVbar = 3                ! 2D V-velocity
        isUvel = 4                ! 3D U-velocity
        isVvel = 5                ! 3D V-velocity
        ic=5
  #ifdef SOLVE3D
        DO i=1,MT
          ic=ic+1
          isTvar(i)=ic            ! Active/Passive tracers
        END DO
  #endif
  #if defined ADJUST_WSTRESS || defined FORCING_SV     || \
      defined HESSIAN_FSV    || defined SO_SEMI        || \
      defined STOCHASTIC_OPT
        ic=ic+1
        isUstr=ic                 ! surface U-velocity stress
        ic=ic+1
        isVstr=ic                 ! surface V-velocity stress
  #endif
  #ifdef SOLVE3D
  # if defined ADJUST_STFLUX  || defined FORCING_SV     || \
       defined HESSIAN_FSV    || defined SO_SEMI        || \
       defined STOCHASTIC_OPT
        DO i=1,MT
          ic=ic+1
          isTsur(i)=ic            ! surface tracer flux      
        END DO
  # endif
  #endif
  #ifdef WEC
        ic=ic+1
        isU2Sd=ic                 ! 2D Stokes U-velocity 
        ic=ic+1
        isV2Sd=ic                 ! 2D Stokes V-velocity
  # if defined SOLVE3D
        ic=ic+1
        isU3Sd=ic                 ! 3D Stokes U-velocity
        ic=ic+1
        isV3Sd=ic                 ! 3D Stokes V-velocity
  # endif
  #endif
  #ifdef SOLVE3D
  # if defined GLS_MIXING || defined MY25_MIXING
        ic=ic+1
        isMtke=ic                 ! TKE
  # endif
        ic=ic+1
        isWvel=ic                 ! vertical velocity
  #endif
  

  Therefore, all the state indices from the zeta to the last Tvar(:) tracer variables cannot be changed.

• Updated the GNU make configuration (*.mk) files to include the environmental variable ESMFMKFILE. Thus, now we have:

  ifdef USE_ESMF
                       include $(ESMFMKFILE)
            ESMF_OS ?= $(OS)
        ESMF_SUBDIR := $(ESMF_OS).$(ESMF_COMPILER).$(ESMF_ABI).$(ESMF_COMM).$(ESMF_SITE)
        ESMF_MK_DIR ?= $(ESMF_DIR)/lib/lib$(ESMF_BOPT)/$(ESMF_SUBDIR)
             FFLAGS += $(ESMF_F90COMPILEPATHS)
               LIBS += $(ESMF_F90LINKPATHS) $(ESMF_F90ESMFLINKLIBS)
  endif
  

  Many thanks to Ufuk Turuncoglu for bringing this issue to my attention.

• Made tiny changes to NUOPC cap modules cmeps_roms.F and esmf_roms.F.