Important: Corrected the state indices counters

[arango]

• Corrected conflict with the state variables counters for isMtke and isWvel. In mod_ncparam.F, we now have:

  !
  !  Set IDs for state some state variables.
  !
        ic=5
  #ifdef SOLVE3D
        DO i=1,MT
          ic=ic+1
          isTvar(i)=ic
        END DO
  # if defined GLS_MIXING || defined MY25_MIXING
        ic=ic+1
        isMtke=ic
  # endif
        ic=ic+1
        isWvel=ic
  #endif
  #if defined ADJUST_WSTRESS || defined FORCING_SV     || \
      defined HESSIAN_FSV    || defined SO_SEMI        || \
      defined STOCHASTIC_OPT
        isUstr=ic+1
        isVstr=ic+2
        ic=ic+2
  #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
        END DO
  # endif
  #endif
  

  The state variables indices (order is necessary). Currently, the maximum number of state variables in 3D applications is 9+2*MT. If MT=2 (temperature and salinity), the state variables have the following order:

       1,   2,    3,4,5,      6,      7,  8,9,  10,  11,     12,     13
    zeta,ubar, vbar,u,v,Tvar(1),Tvar(2),TKE,W,Ustr,Vstr,Tsur(1),Tsur(2)
  

  Many thanks to John Warner for bringing this issue to my attention.

• Provided more information in mod_param.F for state variables lateral boundary conditions indices to the LBC structure:

#ifdef SOLVE3D
      nLBCvar=5+MT                 ! zeta, ubar, vbar, u, v, Tvar(1:MT)
# if defined GLS_MIXING || defined MY25_MIXING
      nLBCvar=nLBCvar+1            ! TKE
# endif
#else
      nLBCvar=3                    ! zeta, ubar, vbar
#endif

• The state variables in mod_scalars.F are allocated as vectors of size 9+2*MT.