Specific water species handling from physics_update needs to be implemented

Inside of CAM's version of physics_update, there are two sections which impact water species, but have not been implemented in CAM-SIMA yet. These sections are:

``` ! now test for mixing ratios which are too small
! don't call qneg3 for number concentration variables
if (m /= ixnumice .and. m /= ixnumliq .and. &
m /= ixnumrain .and. m /= ixnumsnow ) then
call qneg3(trim(ptend%name), state%lchnk, ncol, state%psetcols, pver, m, m, qmin(m:m), state%q(:,1:pver,m:m))
else
do k = ptend%top_level, ptend%bot_level
! checks for number concentration
state%q(:ncol,k,m) = max(1.e-12_r8,state%q(:ncol,k,m))
state%q(:ncol,k,m) = min(1.e10_r8,state%q(:ncol,k,m))
end do
end if
```

``` ! Special tests for cloud liquid and ice:
! Enforce a minimum non-zero value.
if (ixcldliq > 1) then
if(ptend%lq(ixcldliq)) then
#ifdef PERGRO
if ( any(ptend%name == pergro_cldlim_names) ) &
call state_cnst_min_nz(1.e-12_r8, ixcldliq, ixnumliq)
#endif
if ( any(ptend%name == cldlim_names) ) &
call state_cnst_min_nz(1.e-36_r8, ixcldliq, ixnumliq)
end if
end if
```
```
if (ixcldice > 1) then
if(ptend%lq(ixcldice)) then
#ifdef PERGRO
if ( any(ptend%name == pergro_cldlim_names) ) &
call state_cnst_min_nz(1.e-12_r8, ixcldice, ixnumice)
#endif
if ( any(ptend%name == cldlim_names) ) &
call state_cnst_min_nz(1.e-36_r8, ixcldice, ixnumice)
end if
end if
```

Without these changes, a test run of ZM code using snapshots generated with the unaltered physics_update code gives the following differences:
```
Variable # Diffs Max Diff Max Diff loc (rank, col, lev)
-------- ------- -------- -----------------------------
air_temperature 1279 0.22E-15 (0,383,25)
geopotential_height_wrt_surface 1647 0.44E-15 (0,427,29)
geopotential_height_wrt_surface_at_interface 1612 0.43E-15 (0,429,31)
tendency_of_air_temperature_due_to_model_physics 2041 0.95E-15 (0,324,26)
cnst_NUMICE 6548 0.30E-11 (0,36,28)
cloud_ice_mixing_ratio_wrt_moist_air_and_condensed_water
660 0.96E-36 (0,134,32)
water_vapor_mixing_ratio_wrt_moist_air_and_condensed_water
790 0.30E-15 (0,146,29)
cnst_NUMLIQ 9700 0.11E-09 (0,126,29)
cnst_NUMSNO 5463 0.10E-11 (0,31,26)
cnst_NUMRAI 6023 0.32E-13 (0,141,21)
cloud_liquid_water_mixing_ratio_wrt_moist_air_and_condensed_water
7072 0.10E-35 (0,45,21)
********** End Physics Check Data Results **********

```

With the above three sections of code commented out in the CAM run which made the snapshot files, the identical ZM code gives the following differences:
```
Variable # Diffs Max Diff Max Diff loc (rank, col, lev)
-------- ------- -------- -----------------------------
air_temperature 1248 0.22E-15 (0,419,26)
geopotential_height_wrt_surface 1858 0.44E-15 (0,7,27)
geopotential_height_wrt_surface_at_interface 1813 0.44E-15 (0,440,31)
tendency_of_air_temperature_due_to_model_physics 2109 0.11E-14 (0,47,23)
water_vapor_mixing_ratio_wrt_moist_air_and_condensed_water
706 0.35E-15 (0,271,30)

```