Xiaowen Tang of Nanjing University, China

modified:   Registry/registry.var
modified:   var/build/depend.txt
modified:   var/da/da_define_structures/da_define_structures.f90
new file:   var/da/da_dynamics/da_divergence_constraint.inc
new file:   var/da/da_dynamics/da_divergence_constraint_adj.inc
modified:   var/da/da_dynamics/da_dynamics.f90
modified:   var/da/da_minimisation/da_calculate_gradj.inc
modified:   var/da/da_minimisation/da_calculate_j.inc
modified:   var/da/da_minimisation/da_get_var_diagnostics.inc
modified:   var/da/da_minimisation/da_minimisation.f90
modified:   var/da/da_test/da_check.inc
new file:   var/da/da_test/da_check_dynamics_adjoint.inc
modified:   var/da/da_test/da_test.f90

Xiaowen Tang of Nanjing University, China

modified:   Registry/registry.var
modified:   var/build/depend.txt
modified:   var/da/da_obs/da_fill_obs_structures.inc
modified:   var/da/da_obs_io/da_obs_io.f90
new file:   var/da/da_obs_io/da_read_lsac_util.inc
new file:   var/da/da_obs_io/da_read_obs_lsac.inc
new file:   var/da/da_obs_io/da_scan_obs_lsac.inc
modified:   var/da/da_setup_structures/da_setup_obs_structures.inc
modified:   var/da/da_setup_structures/da_setup_obs_structures_ascii.inc
modified:   var/da/da_setup_structures/da_setup_structures.f90

Shibo Gao of Nanjing University of Information Science & Technology, China.

MPI re-coded by Jamie Bresch of NCAR.

modified:   Registry/registry.var
modified:   var/da/da_minimisation/da_get_innov_vector.inc
modified:   var/da/da_minimisation/da_minimisation.f90
modified:   var/da/da_radar/da_get_innov_vector_radar.inc
modified:   var/da/da_radar/da_radar.f90

new file:   README.CWB_v39a

git cherry-pick -n 070d870 96fb5f3

------
Merge 2016's MRI-4DVAR code changes into WRFDA V3.9.
Tested on NCAR HPC cheyenne and obtained similar result to previous V3.8-based
code ran on yellowstone.
------

modified:   Registry/registry.var
modified:   var/build/depend.txt
modified:   var/da/da_main/da_solve.inc
modified:   var/da/da_main/da_wrfvar_top.f90
modified:   var/da/da_recursive_filter/da_recursive_filter.f90
new file:   var/da/da_recursive_filter/da_recursive_filter_1d_inv.inc
modified:   var/da/da_recursive_filter/da_transform_through_rf.inc
new file:   var/da/da_recursive_filter/da_transform_through_rf_inv.inc
modified:   var/da/da_setup_structures/da_setup_structures.f90
new file:   var/da/da_setup_structures/da_write_vp.inc
modified:   var/da/da_vtox_transforms/da_transform_vptox.inc
new file:   var/da/da_vtox_transforms/da_transform_vptox_inv.inc
new file:   var/da/da_vtox_transforms/da_transform_vtovv_inv.inc
new file:   var/da/da_vtox_transforms/da_transform_vtox_inv.inc
modified:   var/da/da_vtox_transforms/da_transform_vvtovp.inc
modified:   var/da/da_vtox_transforms/da_transform_vvtovp_adj.inc
new file:   var/da/da_vtox_transforms/da_transform_vvtovp_inv.inc
modified:   var/da/da_vtox_transforms/da_vertical_transform.inc
modified:   var/da/da_vtox_transforms/da_vtox_transforms.f90

…ecip_opt=1 bug fix.

modified:   README.CWB_v39a

DIVC works fine with the CWB_v381a code.

CWB_v39a (CWB_v39f2a) includes the new 4DEnsVar capability that
requires "call da_zero_vp_type (vp)" to be removed from
subroutine da_transform_vtox_adj. Therefore, da_zero_vp_type
must now be called before "call da_transform_vtox_adj".

modified:   README.CWB_v39a
modified:   var/da/da_minimisation/da_calculate_gradj.inc
modified:   var/da/da_minimisation/da_calculate_j.inc

The original gen_be_ep2.f90 is renamed to gen_be_ep2_serial.f90 and
its executable is gen_be_ep2_serial.exe.

The new gen_be_ep2.f90 is a lot faster than the original one
even when running in serial mode.
The main improvements are in:
(1) using WRF netCDF ioapi to replace inefficient reading in 2D slices.
(2) eliminating large temporary outputs.

The compilation mode for the new gen_be_ep2.f90 is decided by
the option chosen when 'configure wrfda', either serial or dmpar.

modified:   README.CWB_v39a
modified:   var/build/depend.txt
modified:   var/build/gen_be.make
modified:   var/gen_be/Makefile
modified:   var/gen_be/gen_be_ep2.f90
copied:     var/gen_be/gen_be_ep2.f90 -> var/gen_be/gen_be_ep2_serial.f90

lsac_nvstart:  index of starting vertical grid point
lsac_use_u:    switch for large scale u analysis constraint
lsac_use_v:    switch for large scale v analysis constraint
lsac_use_t:    switch for large scale t analysis constraint
lsac_use_q:    switch for large scale q analysis constraint

modified:   Registry/registry.var
modified:   var/da/da_obs_io/da_obs_io.f90
modified:   var/da/da_obs_io/da_read_lsac_util.inc

…n repository for the coming V3.9.1 release.

(git cherry-pick -n db7841c 49ec556 3e3c4ce ee3fd4a c4eeff5 81ca2ff d21f0db c7405bb)
 1. Bug fix and clean-up for WRFDA pseudo ob capability.
 2. Bug fix for ZTD with 4DVAR when there are ZTD obs in non-first time slots.
 3. Fix incorrect calculation of an unused variable cv_size_domain_jb.
 4. WRFDA registry.var fixes for packaging moist variables and for non-4DVAR.
    This reduces non-4DVAR memory usage by ~35%.
 5. Add packaging in registry.var for WRFDA derived type variables.
    This reduces 3DVAR memory usage by another ~15-20%.

modified:   README.CWB_v39a
modified:   Registry/registry.var
modified:   tools/gen_allocs.c
modified:   tools/gen_scalar_indices.c
modified:   tools/protos.h
modified:   var/build/da_name_space.pl
modified:   var/da/da_gpspw/da_transform_xtoy_gpsztd.inc
modified:   var/da/da_main/da_med_initialdata_input.inc
modified:   var/da/da_main/da_solve.inc
modified:   var/da/da_main/da_update_firstguess.inc
modified:   var/da/da_main/da_wrfvar_init2.inc
modified:   var/da/da_main/da_wrfvar_io.f90
modified:   var/da/da_minimisation/da_calculate_gradj.inc
modified:   var/da/da_minimisation/da_calculate_j.inc
modified:   var/da/da_minimisation/da_sensitivity.inc
modified:   var/da/da_minimisation/da_transform_vtoy.inc
modified:   var/da/da_minimisation/da_transform_vtoy_adj.inc
modified:   var/da/da_radar/da_radar.f90
modified:   var/da/da_radar/da_transform_xtoy_radar.inc
modified:   var/da/da_radar/da_transform_xtoy_radar_adj.inc
modified:   var/da/da_radiance/da_crtm.f90
modified:   var/da/da_radiance/da_transform_xtoy_crtm.inc
modified:   var/da/da_radiance/da_transform_xtoy_crtm_adj.inc
modified:   var/da/da_setup_structures/da_setup_cv.inc
modified:   var/da/da_setup_structures/da_setup_obs_structures.inc
modified:   var/da/da_setup_structures/da_setup_pseudo_obs.inc
modified:   var/da/da_setup_structures/da_setup_structures.f90
modified:   var/da/da_test/da_check_dynamics_adjoint.inc (this is in CWB_v39a branch only)
modified:   var/da/da_test/da_check_vtoy_adjoint.inc
modified:   var/da/da_test/da_check_xtoy_adjoint.inc
modified:   var/da/da_transfer_model/da_transfer_model.f90
modified:   var/da/da_transfer_model/da_transfer_wrftltoxa.inc
modified:   var/da/da_transfer_model/da_transfer_wrftltoxa_adj.inc
modified:   var/da/da_transfer_model/da_transfer_xatowrftl.inc
modified:   var/da/da_transfer_model/da_transfer_xatowrftl_adj.inc

Contributed by Siou-Ying Jiang.
Fix the calculation of Vt component of Vr by adding density
term in the Vt calculation and making qrain unit consistent.

modified:   var/da/da_radar/da_get_innov_vector_radar.inc
modified:   var/da/da_radar/da_radial_velocity.inc
modified:   var/da/da_radar/da_radial_velocity_adj.inc
modified:   var/da/da_radar/da_radial_velocity_lin.inc
modified:   var/da/da_radar/da_transform_xtoy_radar.inc
modified:   var/da/da_radar/da_transform_xtoy_radar_adj.inc

1. Implement obs-model height difference check
2. Write out ZTD innov info properly

modified:   README.CWB_v39a
modified:   Registry/registry.var
modified:   var/da/da_gpspw/da_get_innov_vector_gpsztd.inc
modified:   var/da/da_gpspw/da_gpspw.f90
modified:   var/da/da_physics/da_physics.f90
modified:   var/da/da_physics/da_transform_xtoztd_adj.inc
modified:   var/da/da_physics/da_transform_xtoztd_lin.inc

1. fix the staggering variable problem
2. update namelists
lsac_calcerr is removed, some names are changed and some optinos are added.
The current LSAC namelist options and the defaults are:
  use_lsac            .false.
  lsac_nh_step        1
  lsac_nv_step        1
  lsac_nv_start       1
  lsac_use_u          .true.
  lsac_use_v          .true.
  lsac_use_t          .true.
  lsac_use_q          .true.
  lsac_u_error        2.5 (m/s)
  lsac_v_error        2.5 (m/s)
  lsac_t_error        2.0 (C)
  lsac_q_error        0.002 (kg/kg)
  lsac_print_details  .false.

modified:   Registry/registry.var
modified:   var/da/da_obs_io/da_obs_io.f90
modified:   var/da/da_obs_io/da_read_lsac_util.inc

git cherry-pick -n 5e94060 606ac0e 4cc9707 85e4d11 baa3fe6

1. add offline programs and scripts for MRI-4DVAR
2. add w and cloud control variables for MRI-4DVAR
3. allow properly reading of BE file with cloud/w variables generated by stand-alone GEN_BE
4. bug fix for radar data OMB file I/O for MRI-4DVAR

modified:   var/da/da_main/da_solve.inc
modified:   var/da/da_obs_io/da_search_obs.inc
modified:   var/da/da_recursive_filter/da_transform_through_rf_inv.inc
modified:   var/da/da_setup_structures/da_setup_be_regional.inc
modified:   var/da/da_setup_structures/da_write_vp.inc
modified:   var/da/da_vtox_transforms/da_transform_vptox_inv.inc
modified:   var/da/da_vtox_transforms/da_transform_vtovv_inv.inc
modified:   var/da/da_vtox_transforms/da_transform_vtox_inv.inc
new file:   var/mri4dvar/Makefile
new file:   var/mri4dvar/README.Multi_inc
new file:   var/mri4dvar/da_bdy.f90
new file:   var/mri4dvar/da_bilin.f90
new file:   var/mri4dvar/da_thin.f90
new file:   var/mri4dvar/da_vp_bilin.f90
new file:   var/mri4dvar/da_vp_split.f90
new file:   var/mri4dvar/nc_increment.ncl
new file:   var/mri4dvar/nc_vpglobal.ncl
new file:   var/mri4dvar/nc_vphires.ncl
new file:   var/mri4dvar/nc_vpinput.ncl
new file:   var/mri4dvar/nc_vplocal.ncl
new file:   var/mri4dvar/rsl_lite.h
new file:   var/mri4dvar/run_mri3d4dvar.csh_lsf
new file:   var/mri4dvar/run_mri3d4dvar.csh_pbs
new file:   var/mri4dvar/task_for_point.c
new file:   var/mri4dvar/wraper_mri3d4dvar.csh

…mosaic data.

For CWB's radar data assimilation, the radar data are pre-processed
to be on mass points of the model grid.
When WRFDA reads in the radar mosaic data on model mass points,
it prints out a lot of "Report is outside of domain" messages when
print_detail_radar=.true.

Those "outside of domain" obs appear to be along the domain boundaries.

When calculating grid x/y from lat/lon (by calling da_llxy),
the output x/y are floating numbers and they do not match exactly the grid index.
For example, by giving the lat/lon of (450,1),
the calculated x is 450.000183 and y is 0.999511719.
A few more examples are listed below:
  (450,   2) :  (450.000183,    2.00000000)
  (450,   3) :  (450.000153,    3.00000000)
  (450,   4) :  (450.000153,    3.99951172)
  (450,   5) :  (450.000092,    5.00048828)
  (450,   6) :  (450.000061,    6.00000000)
  (446, 450) :  (446.000580,  450.000000)
  (447, 450) :  (446.999146,  449.999512)
  (448, 450) :  (448.000671,  449.999512)
  (449, 450) :  (448.999268,  450.000000)
  (450, 450) :  (450.000793,  450.000000)

By removing the "=" sign in line 52 and line 53 of var/da/da_tools/da_llxy.inc,
the "outside of domain" prints can be reduced.

Another solution to reducing run-time output is to set print_detail_radar=.false.
for operational runs.

modified:   var/da/da_tools/da_llxy.inc

…ound in obsproc.

modified:   var/obsproc/src/module_qc.F90

…om different sources.

ccv_be_inp_opt=0 (default), original hard-coded values used by cloud_cv_options=3.
ccv_be_inp_opt=1, user-specified values in be_ccv.txt and be_w.txt to be used by cloud_cv_options=3.
ccv_be_inp_opt=2, the same behavior as used in mri4dvar for cloud_cv_options=2.
ccv_be_inp_opt=3, univariate cloud and w BES in independent files for cloud_cv_options=2.

Note that the code compiles but has not yet been tested.

modified:   Registry/registry.var
modified:   var/da/da_setup_structures/da_setup_be_regional.inc
modified:   var/da/da_setup_structures/da_setup_structures.f90

But note that for now use_cv_w also uses the same ccv_be_inp_opt intended for cloud cv.
A new namelist, wcv_be_inp_opt, can be added in the future if desired.

modified:   var/da/da_setup_structures/da_setup_be_regional.inc

Set retrieved qr, qs, qg to zero when echo is non-precip.

modified:   var/da/da_radar/da_get_innov_vector_radar.inc

Also set the default Max_StHeight_Diff_ztd a large value for backward compatibility
when users do not explicitly set Max_StHeight_Diff_ztd.

The same code has been in the master repository as of commit bc60b4c.

modified:   Registry/registry.var
modified:   var/da/da_gpspw/da_get_innov_vector_gpsztd.inc
modified:   var/da/da_gpspw/da_gpspw.f90

…error_options=2.

Add checks for missing Q obs to set proper Q qc flags.

I-Han Chen reported the problem and helped with the test.

modified:   var/da/da_synop/da_get_innov_vector_synop.inc

…tion.

The same code has been in the master repository as of commit bd9a460.

modified:   external/RSL_LITE/module_dm.F

modified:   var/da/da_define_structures/da_allocate_y.inc
modified:   var/da/da_define_structures/da_allocate_y_radar.inc
modified:   var/da/da_define_structures/da_deallocate_observations.inc
modified:   var/da/da_define_structures/da_define_structures.f90
modified:   var/da/da_obs_io/da_obs_io.f90
modified:   var/da/da_obs_io/da_read_obs_radar.inc
modified:   var/da/da_radar/da_ao_stats_radar.inc
modified:   var/da/da_radar/da_get_innov_vector_radar.inc
modified:   var/da/da_radar/da_jo_and_grady_radar.inc
modified:   var/da/da_radar/da_oi_stats_radar.inc
modified:   var/da/da_radar/da_radar.f90
modified:   var/da/da_radar/da_transform_xtoy_radar.inc
modified:   var/da/da_radar/da_transform_xtoy_radar_adj.inc
modified:   var/da/da_setup_structures/da_setup_obs_structures_radar.inc

This fixes the unreasonable 4DVAR QICE and QGRAUP increments when
only surface observations are assimilated with cloud_cv_options=3
and mp_physics=99, a case reported by Ihan.
This should also fix other subtle 4DVAR moist problems.
However, there are probably more fixes needed for rainfall DA.

modified:   Registry/registry.var
modified:   var/da/da_main/da_update_firstguess.inc
modified:   var/da/da_main/da_wrfvar_init2.inc
modified:   var/da/da_transfer_model/da_transfer_model.f90
modified:   var/da/da_transfer_model/da_transfer_wrftltoxa.inc
modified:   var/da/da_transfer_model/da_transfer_wrftltoxa_adj.inc
modified:   var/da/da_transfer_model/da_transfer_xatowrftl.inc
modified:   var/da/da_transfer_model/da_transfer_xatowrftl_adj.inc

To be consistent with what had been committed to the master repository.
1. Change default of mp_physics_ad to 99
2. Remove some unused variables
3. Fix a couple typos (g_->a_)

modified:   Registry/registry.var

modified:   var/da/da_setup_structures/da_setup_be_regional.inc

… sfc wind correction.

As in figure 2 of Stauffer et al. 1991, MWR,
0<z0<0.2 : u40/u10=1.000+0.320*z0**0.2
z0>=0.2 : u40/u10=1.169+0.315*z0

modified:   var/da/da_tools/da_mo_correction.inc

modified:   Registry/registry.var
modified:   var/build/depend.txt
modified:   var/da/da_minimisation/da_get_innov_vector.inc
modified:   var/da/da_minimisation/da_minimisation.f90
modified:   var/da/da_obs_io/da_obs_io.f90
new file:   var/da/da_obs_io/da_read_iv_for_multi_inc_opt2.inc
new file:   var/da/da_obs_io/da_write_iv_for_multi_inc_opt2.inc

…k_max_iv prints.

modified:   var/da/da_obs_io/da_read_obs_radar.inc
modified:   var/da/da_radar/da_get_innov_vector_radar.inc

Missing rv are set incorrectly as no-rain rf in NCAR-processed radar data.
The fix is to set qc to missing_data for -999.99 rv in var/da/da_radar/da_get_innov_vector_radar.inc

NCAR-processed radar data sample
FM-128 RADAR   2017-06-02_03:06:00        22.961       117.830      38.0       1
         5158.0    -999.990   0       0.500      -999.990   0       0.000     -8888.880

Missing rv/rf has error of missing_r in CWB-processed radar data.
The fix is to set a default error value in var/da/da_obs_io/da_read_obs_radar.inc.

CWB-processed radar data sample 1
FM-128 RADAR   2017-07-06_06:00:00        19.570       117.335       0.0       1
        12000.0 -888888.000 -88 -888888.000      -999.990   0       0.000

CWB-processed radar data sample 2
FM-128 RADAR   2017-07-06_06:02:00        24.134       122.223      63.0       1
          946.0       1.300   0       2.000   -888888.000 -88 -888888.000

radar_rhv_err_opt:
 1 (original; errors calculated in da_get_innov_vector_radar)
 2 (new; use error settings from new namelists radar_rhv_rrn_err, radar_rhv_rsn_err, radar_rhv_rgr_err)

modified:   Registry/registry.var
modified:   var/da/da_radar/da_get_innov_vector_radar.inc
modified:   var/da/da_radar/da_radar.f90

Add in &wrfvar1 a new namelist option, multi_inc_io_opt = 2, to use the new code for radar rv/rf/rhv/rqv.
The innovation output in binary format is called radar_innov_t00*.

The code for other observation types are not touched/changed in this initial implementation.

modified:   Registry/registry.var
modified:   var/build/depend.txt
modified:   var/da/da_minimisation/da_get_innov_vector.inc
modified:   var/da/da_minimisation/da_minimisation.f90
modified:   var/da/da_obs_io/da_obs_io.f90
new file:   var/da/da_obs_io/da_read_iv_for_multi_inc_opt2.inc
new file:   var/da/da_obs_io/da_write_iv_for_multi_inc_opt2.inc

modified:   Registry/registry.var
modified:   var/da/da_main/da_solve.inc

&wrfvar1
write_gts_omb_oma  = .true.  !(default)
write_rej_obs_conv = .false. !(default), the information is not too helpful
write_unpert_obs   = .false. !(default), the information is not usually used

modified:   Registry/registry.var
modified:   var/da/da_airep/da_airep.f90
modified:   var/da/da_airep/da_check_max_iv_airep.inc
modified:   var/da/da_airsr/da_airsr.f90
modified:   var/da/da_airsr/da_check_max_iv_airsr.inc
modified:   var/da/da_bogus/da_bogus.f90
modified:   var/da/da_bogus/da_check_max_iv_bogus.inc
modified:   var/da/da_buoy/da_buoy.f90
modified:   var/da/da_buoy/da_check_max_iv_buoy.inc
modified:   var/da/da_geoamv/da_check_max_iv_geoamv.inc
modified:   var/da/da_geoamv/da_geoamv.f90
modified:   var/da/da_gpspw/da_check_max_iv_gpspw.inc
modified:   var/da/da_gpspw/da_gpspw.f90
modified:   var/da/da_gpsref/da_check_max_iv_gpsref.inc
modified:   var/da/da_gpsref/da_gpsref.f90
modified:   var/da/da_metar/da_check_max_iv_metar.inc
modified:   var/da/da_metar/da_metar.f90
modified:   var/da/da_minimisation/da_get_innov_vector.inc
modified:   var/da/da_minimisation/da_minimisation.f90
modified:   var/da/da_minimisation/da_write_diagnostics.inc
modified:   var/da/da_mtgirs/da_check_max_iv_mtgirs.inc
modified:   var/da/da_mtgirs/da_mtgirs.f90
modified:   var/da/da_pilot/da_check_max_iv_pilot.inc
modified:   var/da/da_pilot/da_pilot.f90
modified:   var/da/da_polaramv/da_check_max_iv_polaramv.inc
modified:   var/da/da_polaramv/da_polaramv.f90
modified:   var/da/da_profiler/da_check_max_iv_profiler.inc
modified:   var/da/da_profiler/da_profiler.f90
modified:   var/da/da_qscat/da_check_max_iv_qscat.inc
modified:   var/da/da_qscat/da_qscat.f90
modified:   var/da/da_rain/da_check_max_iv_rain.inc
modified:   var/da/da_rain/da_rain.f90
modified:   var/da/da_satem/da_check_max_iv_satem.inc
modified:   var/da/da_satem/da_satem.f90
modified:   var/da/da_ships/da_check_max_iv_ships.inc
modified:   var/da/da_ships/da_ships.f90
modified:   var/da/da_sound/da_check_max_iv_sonde_sfc.inc
modified:   var/da/da_sound/da_check_max_iv_sound.inc
modified:   var/da/da_sound/da_sound.f90
modified:   var/da/da_ssmi/da_check_max_iv_ssmi_rv.inc
modified:   var/da/da_ssmi/da_check_max_iv_ssmt1.inc
modified:   var/da/da_ssmi/da_check_max_iv_ssmt2.inc
modified:   var/da/da_ssmi/da_ssmi.f90
modified:   var/da/da_synop/da_check_max_iv_synop.inc
modified:   var/da/da_synop/da_synop.f90
modified:   var/da/da_tamdar/da_check_max_iv_tamdar.inc
modified:   var/da/da_tamdar/da_check_max_iv_tamdar_sfc.inc
modified:   var/da/da_tamdar/da_tamdar.f90

Remove mistakenly added check condition to make non-radar data types
work for both multi_inc_io_opt = 1 and 2.

modified:   var/da/da_minimisation/da_get_innov_vector.inc

…eck_max_iv prints.

The previous fix in commit 1d39c22 did not have correct checking logic
for missing_r values.

modified:   var/da/da_obs_io/da_read_obs_radar.inc

modified:   var/da/da_radar/da_write_oa_radar_ascii.inc
modified:   var/mri4dvar/da_thin.f90

In addition to adding cloud and w control variables that were not
included in the original rescaling code, a couple other changes
are also made in the commit.
1. Only root processor writes out the intermediate file.
2. Change the log message from Jb factor used() to var_scaling used().

modified:   var/da/da_minimisation/da_get_var_diagnostics.inc
modified:   var/da/da_minimisation/da_minimisation.f90
modified:   var/da/da_setup_structures/da_scale_background_errors.inc
modified:   var/da/da_setup_structures/da_setup_be_regional.inc

modified:   var/da/da_obs_io/da_obs_io.f90
modified:   var/da/da_obs_io/da_read_obs_radar.inc
modified:   var/da/da_obs_io/da_scan_obs_radar.inc

git cherry-pick -n 070d870 96fb5f3 5e94060 606ac0e 4cc9707 85e4d11 baa3fe6
excluding offline programs and scripts in var/mri4dvar directory.

On branch mri4dvar
Changes to be committed:
modified:   Registry/registry.var
modified:   var/build/depend.txt
modified:   var/da/da_main/da_solve.inc
modified:   var/da/da_main/da_wrfvar_top.f90
modified:   var/da/da_obs_io/da_search_obs.inc
modified:   var/da/da_recursive_filter/da_recursive_filter.f90
new file:   var/da/da_recursive_filter/da_recursive_filter_1d_inv.inc
modified:   var/da/da_recursive_filter/da_transform_through_rf.inc
new file:   var/da/da_recursive_filter/da_transform_through_rf_inv.inc
modified:   var/da/da_setup_structures/da_setup_be_regional.inc
modified:   var/da/da_setup_structures/da_setup_structures.f90
new file:   var/da/da_setup_structures/da_write_vp.inc
modified:   var/da/da_vtox_transforms/da_transform_vptox.inc
new file:   var/da/da_vtox_transforms/da_transform_vptox_inv.inc
new file:   var/da/da_vtox_transforms/da_transform_vtovv_inv.inc
new file:   var/da/da_vtox_transforms/da_transform_vtox_inv.inc
modified:   var/da/da_vtox_transforms/da_transform_vvtovp.inc
modified:   var/da/da_vtox_transforms/da_transform_vvtovp_adj.inc
new file:   var/da/da_vtox_transforms/da_transform_vvtovp_inv.inc
modified:   var/da/da_vtox_transforms/da_vertical_transform.inc
modified:   var/da/da_vtox_transforms/da_vtox_transforms.f90

Note that the code for non-radar observation types are not changed.

On branch mri4dvar
Changes to be committed:
modified:   Registry/registry.var
modified:   var/build/depend.txt
modified:   var/da/da_minimisation/da_get_innov_vector.inc
modified:   var/da/da_minimisation/da_minimisation.f90
modified:   var/da/da_obs_io/da_obs_io.f90
new file:   var/da/da_obs_io/da_read_iv_for_multi_inc_opt2.inc
modified:   var/da/da_obs_io/da_read_obs_radar.inc
modified:   var/da/da_obs_io/da_scan_obs_radar.inc
new file:   var/da/da_obs_io/da_write_iv_for_multi_inc_opt2.inc

TYPE: text only

KEYWORDS: version_decl, v4.1-alpha

SOURCE: internal

DESCRIPTION OF CHANGES: 
Update the character string inside the WRF system from 4.0.3 to 4.1-alpha.

LIST OF MODIFIED FILES: 
M inc/version_decl

TESTS CONDUCTED: 
 - [x] Code runs and v4.1-alpha is the version printed from the WRF system programs.
```
> ncdump -h wrfinput_d01 | grep TITLE
		:TITLE = " OUTPUT FROM REAL_EM V4.1-alpha PREPROCESSOR" ;
> ncdump -h wrfinput_initialized_d01  | grep TITLE
		:TITLE = " OUTPUT FROM WRF V4.1-alpha MODEL" ;
> ncdump -h met_em.d01.2019-02-15_12:00:00.nc  | grep TITLE
		:TITLE = "OUTPUT FROM METGRID V4.1" ;
> ncdump -h wrfout_d01_2019-02-16_12:00:00  | grep TITLE
		:TITLE = " OUTPUT FROM WRF V4.1-alpha MODEL" ;
```

	deleted:    .gitignore
	modified:   Registry/registry.var
	modified:   var/da/da_define_structures/da_define_structures.f90
	modified:   var/da/da_minimisation/da_get_innov_vector.inc
	modified:   var/da/da_minimisation/da_minimisation.f90
	modified:   var/da/da_obs_io/da_final_write_obs.inc
	modified:   var/da/da_obs_io/da_obs_io.f90
	modified:   var/da/da_obs_io/da_read_iv_for_multi_inc_opt2.inc
	modified:   var/da/da_obs_io/da_read_obs_radar.inc
	modified:   var/da/da_obs_io/da_scan_obs_radar.inc
	new file:   var/da/da_obs_io/log
	modified:   var/da/da_radiance/da_allocate_rad_iv.inc
	modified:   var/da/da_radiance/da_crtm.f90
	modified:   var/da/da_radiance/da_deallocate_radiance.inc
	modified:   var/da/da_radiance/da_get_innov_vector_radiance.inc
	modified:   var/da/da_radiance/da_initialize_rad_iv.inc
	new file:   var/da/da_radiance/da_qc_ahi.inc
	new file:   var/da/da_radiance/da_qc_ahi.inc.bak
	new file:   var/da/da_radiance/da_qc_ahi_zou.inc
	modified:   var/da/da_radiance/da_qc_rad.inc
	modified:   var/da/da_radiance/da_radiance.f90
	modified:   var/da/da_radiance/da_radiance1.f90
	modified:   var/da/da_radiance/da_radiance_init.inc
	new file:   var/da/da_radiance/da_read_iv_rad_ascii.inc
	new file:   var/da/da_radiance/da_read_iv_rad_for_multi_inc.inc
	new file:   var/da/da_radiance/da_read_iv_rad_for_multi_inc.inc.ok
	new file:   var/da/da_radiance/da_read_obs_AHI.inc
	new file:   var/da/da_radiance/da_read_obs_AHI.inc.1
	modified:   var/da/da_radiance/da_read_obs_fy3.inc
	new file:   var/da/da_radiance/da_read_obs_hdf5ahi.inc
	new file:   var/da/da_radiance/da_read_obs_netcdf4ahi_geocat.inc
	new file:   var/da/da_radiance/da_read_obs_netcdf4ahi_jaxa.inc
	new file:   var/da/da_radiance/da_read_obs_netcdf4ahi_zou.inc
	modified:   var/da/da_radiance/da_setup_radiance_structures.inc
	modified:   var/da/da_radiance/da_transform_xtoy_crtm.inc
	modified:   var/da/da_radiance/da_transform_xtoy_crtm_adj.inc
	modified:   var/da/da_radiance/da_write_filtered_rad.inc
	modified:   var/da/da_radiance/da_write_iv_rad_ascii.inc
	new file:   var/da/da_radiance/da_write_iv_rad_for_multi_inc.inc
	modified:   var/da/da_radiance/da_write_oa_rad_ascii.inc
	new file:   var/da/da_radiance/log
	modified:   var/da/da_radiance/module_radiance.f90
	modified:   var/da/da_setup_structures/da_setup_obs_structures.inc
	modified:   var/da/da_setup_structures/da_setup_structures.f90
	modified:   var/da/da_tools/da_get_time_slots.inc
	modified:   var/da/da_transfer_model/da_transfer_xatowrf.inc
	typechange: var/run/VARBC.in
	new file:   var/run/ahi_info
	new file:   var/run/radiance_info/himawari-8-ahi.info
	modified:   var/test/4dvar/namelist.input

 Changes to be committed:
	deleted:    .gitignore
new file:   README.CWB_v39a
	modified:   Registry/registry.var
	modified:   var/build/depend.txt
	modified:   var/build/gen_be.make
	modified:   var/da/da_define_structures/da_define_structures.f90
	modified:   var/da/da_minimisation/da_get_innov_vector.inc
	modified:   var/da/da_minimisation/da_minimisation.f90
	modified:   var/da/da_obs_io/da_final_write_obs.inc
	modified:   var/da/da_obs_io/da_read_iv_for_multi_inc_opt2.inc
	new file:   var/da/da_obs_io/log
	modified:   var/da/da_radar/da_get_innov_vector_radar.inc
	modified:   var/da/da_radar/da_radar.f90
	modified:   var/da/da_radar/da_write_oa_radar_ascii.inc
	modified:   var/da/da_radiance/da_allocate_rad_iv.inc
	modified:   var/da/da_radiance/da_crtm.f90
	modified:   var/da/da_radiance/da_deallocate_radiance.inc
	modified:   var/da/da_radiance/da_get_innov_vector_radiance.inc
	modified:   var/da/da_radiance/da_initialize_rad_iv.inc
	new file:   var/da/da_radiance/da_qc_ahi.inc
	new file:   var/da/da_radiance/da_qc_ahi.inc.bak
	new file:   var/da/da_radiance/da_qc_ahi_zou.inc
	modified:   var/da/da_radiance/da_qc_rad.inc
	modified:   var/da/da_radiance/da_radiance.f90
	modified:   var/da/da_radiance/da_radiance1.f90
	modified:   var/da/da_radiance/da_radiance_init.inc
	new file:   var/da/da_radiance/da_read_iv_rad_ascii.inc
	new file:   var/da/da_radiance/da_read_iv_rad_for_multi_inc.inc
	new file:   var/da/da_radiance/da_read_iv_rad_for_multi_inc.inc.ok
	new file:   var/da/da_radiance/da_read_obs_AHI.inc
	new file:   var/da/da_radiance/da_read_obs_AHI.inc.1
	modified:   var/da/da_radiance/da_read_obs_fy3.inc
	new file:   var/da/da_radiance/da_read_obs_hdf5ahi.inc
	new file:   var/da/da_radiance/da_read_obs_netcdf4ahi_geocat.inc
	new file:   var/da/da_radiance/da_read_obs_netcdf4ahi_jaxa.inc
	new file:   var/da/da_radiance/da_read_obs_netcdf4ahi_zou.inc
	modified:   var/da/da_radiance/da_setup_radiance_structures.inc
	modified:   var/da/da_radiance/da_transform_xtoy_crtm.inc
	modified:   var/da/da_radiance/da_transform_xtoy_crtm_adj.inc
	modified:   var/da/da_radiance/da_write_filtered_rad.inc
	modified:   var/da/da_radiance/da_write_iv_rad_ascii.inc
	new file:   var/da/da_radiance/da_write_iv_rad_for_multi_inc.inc
	modified:   var/da/da_radiance/da_write_oa_rad_ascii.inc
	new file:   var/da/da_radiance/log
	modified:   var/da/da_radiance/module_radiance.f90
	modified:   var/da/da_setup_structures/da_scale_background_errors.inc
	modified:   var/da/da_setup_structures/da_setup_be_regional.inc
	modified:   var/da/da_setup_structures/da_setup_obs_structures.inc
	modified:   var/da/da_setup_structures/da_setup_structures.f90
	modified:   var/da/da_tools/da_get_time_slots.inc
	modified:   var/da/da_tools/da_llxy.inc
	modified:   var/gen_be/Makefile
	modified:   var/gen_be/gen_be_ep2.f90
	copied:     var/gen_be/gen_be_ep2.f90 -> var/gen_be/gen_be_ep2_serial.f90
	new file:   var/mri4dvar/Makefile
	new file:   var/mri4dvar/README.Multi_inc
	new file:   var/mri4dvar/da_bdy.f90
	new file:   var/mri4dvar/da_bilin.f90
	new file:   var/mri4dvar/da_thin.f90
	new file:   var/mri4dvar/da_vp_bilin.f90
	new file:   var/mri4dvar/da_vp_split.f90
	new file:   var/mri4dvar/nc_increment.ncl
	new file:   var/mri4dvar/nc_vpglobal.ncl
	new file:   var/mri4dvar/nc_vphires.ncl
	new file:   var/mri4dvar/nc_vpinput.ncl
	new file:   var/mri4dvar/nc_vplocal.ncl
	new file:   var/mri4dvar/rsl_lite.h
	new file:   var/mri4dvar/run_mri3d4dvar.csh_lsf
	new file:   var/mri4dvar/run_mri3d4dvar.csh_pbs
	new file:   var/mri4dvar/task_for_point.c
	new file:   var/mri4dvar/wraper_mri3d4dvar.csh
	new file:   var/run/ahi_info
	new file:   var/run/radiance_info/himawari-8-ahi.info
	modified:   var/test/4dvar/namelist.input

…write_iv_rad_for_multi_inc.inc

 Conflicts:
	var/da/da_define_structures/da_define_structures.f90
	var/da/da_radiance/da_allocate_rad_iv.inc
	var/da/da_radiance/da_deallocate_radiance.inc
	var/da/da_radiance/da_initialize_rad_iv.inc
	var/da/da_radiance/da_qc_ahi.inc
	var/da/da_radiance/da_qc_rad.inc
	var/da/da_radiance/da_radiance1.f90
	var/da/da_radiance/da_read_obs_hdf5ahi.inc
	var/da/da_radiance/da_read_obs_netcdf4ahi_geocat.inc
	var/da/da_radiance/da_setup_radiance_structures.inc
	var/da/da_setup_structures/da_setup_obs_structures.inc
	var/run/radiance_info/himawari-8-ahi.info

… rather than da_qc_ahi.inc)

	modified:   var/da/da_radiance/da_read_obs_netcdf4ahi_geocat.inc
	modified:   var/da/da_varbc/da_varbc_pred.inc

 Junmei Ban's additional changes
	modified:   var/build/depend.txt
	modified:   var/da/da_minimisation/da_get_innov_vector.inc
	modified:   var/da/da_obs_io/da_final_write_obs.inc
	modified:   var/da/da_radiance/da_get_innov_vector_crtm.inc
	modified:   var/da/da_radiance/da_get_innov_vector_radiance.inc
	modified:   var/da/da_radiance/da_read_iv_rad_for_multi_inc.inc
	modified:   var/da/da_radiance/da_write_iv_rad_for_multi_inc.inc

 Conflicts:
	.gitignore
	inc/version_decl
	var/build/depend.txt
	var/da/da_main/da_solve.inc
	var/da/da_minimisation/da_get_innov_vector.inc
	var/da/da_minimisation/da_minimisation.f90
	var/da/da_radar/da_get_innov_vector_radar.inc
	var/da/da_radiance/da_crtm.f90
	var/da/da_radiance/da_get_innov_vector_crtm.inc
	var/da/da_radiance/da_get_innov_vector_radiance.inc
	var/da/da_setup_structures/da_setup_be_regional.inc
	var/da/da_setup_structures/da_setup_obs_structures.inc
	var/da/da_setup_structures/da_setup_structures.f90

 On branch latest_develop_mri4dvar
 All conflicts fixed but you are still merging.
 Changes to be committed:

 Changes to be committed:
	deleted:    README.CWB_v39a
	deleted:    var/da/da_obs_io/log
	deleted:    var/da/da_radiance/da_qc_ahi.inc.bak
	deleted:    var/da/da_radiance/da_qc_ahi_zou.inc
	deleted:    var/da/da_radiance/da_read_iv_rad_for_multi_inc.inc.ok
	deleted:    var/da/da_radiance/da_read_obs_AHI.inc.1
	deleted:    var/da/da_radiance/da_read_obs_netcdf4ahi_zou.inc
	deleted:    var/da/da_radiance/log

	modified:   var/build/gen_be.make
	modified:   var/gen_be/Makefile
	renamed:    var/gen_be/gen_be_ep2_serial.f90 -> var/gen_be/gen_be_ep2.f90

	modified:   var/build/depend.txt

 Recover 4dvar namelist
	modified:   var/test/4dvar/namelist.input

 Remove the code changes for neighborhood non-rain radar DA scheme
	modified:   var/da/da_radar/da_get_innov_vector_radar.inc
	modified:   var/da/da_radar/da_radar.f90
	modified:   var/da/da_radar/da_write_oa_radar_ascii.inc

 Remove Changes of be reading for hydrometeor variables
	modified:   Registry/registry.var
	modified:   var/da/da_setup_structures/da_scale_background_errors.inc
	modified:   var/da/da_setup_structures/da_setup_be_regional.inc

 remove duplicate ahiobs
	modified:   Registry/registry.var

 remove duplicate 'tropt' defination
	modified:   var/da/da_define_structures/da_define_structures.f90

 Remove 'old' varbc bugfix as this was already merged earlier in develop
	modified:   var/da/da_minimisation/da_get_innov_vector.inc

 remove duplicate varbc_scan
	modified:   Registry/registry.var

  remove duplicate 'tropt' allocate/deallocate
	modified:   var/da/da_radiance/da_allocate_rad_iv.inc
	modified:   var/da/da_radiance/da_deallocate_radiance.inc

 Recover unnecessary changes. make it consistent with new code.
	modified:   var/da/da_radiance/da_get_innov_vector_crtm.inc
	modified:   var/da/da_radiance/da_get_innov_vector_radiance.inc
	modified:   var/da/da_radiance/da_qc_ahi.inc
	modified:   var/da/da_radiance/da_qc_rad.inc
	modified:   var/da/da_radiance/da_radiance.f90
	deleted:    var/da/da_radiance/da_read_obs_AHI.inc

 Recover varbc_scan change
	modified:   var/da/da_varbc/da_varbc_pred.inc

  recover undeeded change
	modified:   var/da/da_radiance/da_read_obs_fy3.inc

 recover unneeded change
	modified:   var/da/da_radiance/da_read_obs_hdf5ahi.inc

  recover unneeded change
	modified:   var/da/da_radiance/da_read_obs_netcdf4ahi_geocat.inc

  remove unneeded change
	modified:   var/da/da_radiance/da_setup_radiance_structures.inc

  recover unneeded change
	modified:   var/da/da_radiance/da_transform_xtoy_crtm.inc
	modified:   var/da/da_radiance/da_transform_xtoy_crtm_adj.inc

  recover change
	modified:   var/da/da_radiance/da_radiance1.f90
	modified:   var/da/da_radiance/da_radiance_init.inc

  Remove ca_mean and SDob of all-sky ahi
	modified:   var/da/da_define_structures/da_define_structures.f90
	modified:   var/da/da_radiance/da_allocate_rad_iv.inc
	modified:   var/da/da_radiance/da_deallocate_radiance.inc
	modified:   var/da/da_radiance/da_radiance1.f90

 remove gmi/agri and ahi all-sky
	modified:   var/da/da_radiance/da_allocate_rad_iv.inc
	modified:   var/da/da_radiance/da_deallocate_radiance.inc

	modified:   var/da/da_radiance/da_allocate_rad_iv.inc
	modified:   var/da/da_radiance/da_deallocate_radiance.inc

	modified:   var/da/da_obs_io/da_search_obs.inc
	modified:   var/da/da_radiance/da_radiance1.f90
	modified:   var/da/da_radiance/da_read_iv_rad_for_multi_inc.inc

	modified:   var/run/radiance_info/himawari-8-ahi.info

  Fixes so that code compiles Ok.
	modified:   Registry/registry.var
	modified:   var/da/da_main/da_solve.inc
	modified:   var/da/da_main/da_wrfvar_top.f90
	modified:   var/da/da_radiance/da_radiance1.f90

  remove obsolete da_read_iv_rad_ascii.inc
	modified:   var/da/da_main/da_solve.inc
	deleted:    var/da/da_radiance/da_read_iv_rad_ascii.inc

	modified:   var/mri4dvar/run_mri3d4dvar.csh_lsf
	modified:   var/mri4dvar/run_mri3d4dvar.csh_pbs
	modified:   var/mri4dvar/wraper_mri3d4dvar.csh

…th versions.

	modified:   Registry/registry.var
	modified:   var/da/da_minimisation/da_get_innov_vector.inc
	modified:   var/da/da_minimisation/da_minimisation.f90
	modified:   var/da/da_obs_io/da_obs_io.f90
	modified:   var/da/da_obs_io/da_read_iv_for_multi_inc.inc
	modified:   var/da/da_obs_io/da_write_iv_for_multi_inc.inc

 into latest_develop_mri4dvar

	deleted:    var/da/da_obs_io/da_write_iv_for_multi_inc_opt2.inc

	modified:   var/build/depend.txt

	modified:   var/da/da_radiance/da_write_filtered_rad.inc
	modified:   var/da/da_radiance/da_write_iv_rad_ascii.inc
	modified:   var/da/da_radiance/da_write_oa_rad_ascii.inc
	modified:   var/da/da_setup_structures/da_setup_structures.f90
	modified:   var/da/da_tools/da_get_time_slots.inc

	modified:   var/da/da_radiance/da_radiance1.f90
	modified:   var/da/da_radiance/da_read_iv_rad_for_multi_inc.inc
	modified:   var/da/da_radiance/da_write_iv_rad_for_multi_inc.inc

	modified:   var/da/da_main/da_solve.inc