id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc
955	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 with 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**.

* Corrected issue in **esmf_esm.F** (routine **ESM_SetRunSequence**) that used **LocalPET** before being assigned. "	upgrade	closed	major	Release ROMS/TOMS 4.2	Nonlinear	4.1	Done