Adding &probit_transform_nml to remaining model input.nml files

NCAR · Oct 4, 2023 · 5f41368 · 5f41368
1 parent f2d20b7
commit 5f41368
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Showing 36 changed files with 248 additions and 7 deletions.
diff --git a/models/FESOM/work/input.nml b/models/FESOM/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.
+   use_logit_instead_of_probit = .false.
+   do_inverse_check            = .true.
+   /
+
 &perfect_model_obs_nml
    read_input_state_from_file = .true.
    input_state_files          = "ENS01.2009.oce.nc"
@@ -31,6 +37,7 @@
 # state by specifying the 'input' stage.
 
 &filter_nml
+   qcf_table_filename       = ''
    async                    = 5
    adv_ens_command          = "advance_model_script.die"
    ens_size                 = 3

diff --git a/models/LMDZ/work/input.nml b/models/LMDZ/work/input.nml
@@ -1,4 +1,11 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.,
+   use_logit_instead_of_probit = .false.,
+   do_inverse_check            = .true.,
+   /
+
 &filter_nml
+   qcf_table_filename       = '',
    async                    = 2,
    adv_ens_command          = "./advance_model.csh",
    ens_size                 = 40, 

diff --git a/models/MITgcm_annulus/work/input.nml b/models/MITgcm_annulus/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.,
+   use_logit_instead_of_probit = .false.,
+   do_inverse_check            = .true.,
+   /
+
 &perfect_model_obs_nml
    start_from_restart    = .false.,
    output_restart        = .true.,
@@ -22,6 +28,7 @@
   /
 
 &filter_nml
+   qcf_table_filename       = '',
    async                    = 0,
    adv_ens_command          = "../shell_scripts/advance_model.csh",
    ens_size                 = 20,

diff --git a/models/MOM6/work/input.nml b/models/MOM6/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.,
+   use_logit_instead_of_probit = .false.,
+   do_inverse_check            = .true.,
+   /
+
 &perfect_model_obs_nml
    read_input_state_from_file = .true.,
    single_file_in             = .true.
@@ -28,6 +34,7 @@
    /
 
 &filter_nml
+   qcf_table_filename           = '',
    single_file_in               = .false.,
    input_state_files            = ''
    input_state_file_list        = 'filter_input_list.txt'

diff --git a/models/NAAPS/work/input.nml b/models/NAAPS/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.
+   use_logit_instead_of_probit = .false.
+   do_inverse_check            = .true.
+   /
+
 &assim_tools_nml
    filter_kind                     = 1
    cutoff                          = 0.03
@@ -123,6 +129,7 @@
 
 
 &filter_nml
+   qcf_table_filename       = ''
    async                    = 0
    adv_ens_command          = "./advance_model.csh"
    ens_size                 = 20

diff --git a/models/NCOMMAS/work/input.nml b/models/NCOMMAS/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.,
+   use_logit_instead_of_probit = .false.,
+   do_inverse_check            = .true.,
+   /
+
 &perfect_model_obs_nml
    start_from_restart    = .true.,
    output_restart        = .true.,
@@ -24,6 +30,7 @@
 
 
 &filter_nml
+   qcf_table_filename       = '',
    async                    = 4,
    adv_ens_command          = "../shell_scripts/advance_model.csh",
    ens_size                 =  20,

diff --git a/models/POP/work/input.nml b/models/POP/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.
+   use_logit_instead_of_probit = .false.
+   do_inverse_check            = .true.
+   /
+
 &perfect_model_obs_nml
    read_input_state_from_file = .true.
    single_file_in             = .false.
@@ -28,6 +34,7 @@
   /
 
 &filter_nml
+   qcf_table_filename       = ''
    async                    = 0
    adv_ens_command          = 'no_CESM_advance_script'
    ens_size                 =  3

diff --git a/models/ROMS/work/input.nml b/models/ROMS/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.
+   use_logit_instead_of_probit = .false.
+   do_inverse_check            = .true.
+   /
+
 &perfect_model_obs_nml
    read_input_state_from_file = .true.
    single_file_in             = .false.
@@ -29,6 +35,7 @@
 
 
 &filter_nml
+   qcf_table_filename       = ''
    async                    = 0
    adv_ens_command          = "DART_trying_to_advance_ROMS_not_supported"
    ens_size                 = 3

diff --git a/models/cam-fv/work/input.nml b/models/cam-fv/work/input.nml
@@ -33,14 +33,14 @@
 !    inf_sd_from_restart      inflation restart files from the values in inf*_initial
 !                             if needed.
 
-&quantile_distributions_nml
-   fix_bound_violations = .true.,
+&probit_transform_nml
+   fix_bound_violations        = .false.
    use_logit_instead_of_probit = .false.
-   do_inverse_check = .false.
+   do_inverse_check            = .true.
    /
 
 &filter_nml
-   use_algorithm_info_mod       = .true.
+   qcf_table_filename           = ''
    input_state_file_list        = 'cam_init_files'
    input_state_files            = ''
    single_file_in               = .false.
@@ -360,7 +360,6 @@
 
 
 &assim_tools_nml
-   use_algorithm_info_mod            = .true.
    filter_kind                       = 1
    cutoff                            = 0.15
    sort_obs_inc                      = .false.

diff --git a/models/cam-se/work/input.nml b/models/cam-se/work/input.nml
@@ -28,7 +28,14 @@
 !    inf_sd_from_restart      inflation restart files from the values in inf*_initial
 !                             if needed.
 
+&probit_transform_nml
+   fix_bound_violations        = .false.
+   use_logit_instead_of_probit = .false.
+   do_inverse_check            = .true.
+   /
+
 &filter_nml
+   qcf_table_filename           = ''
    input_state_files            = ''
    input_state_file_list        = 'cam_init_files'
    single_file_in               = .false.

diff --git a/models/cice/work/input.nml b/models/cice/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.
+   use_logit_instead_of_probit = .false.
+   do_inverse_check            = .true.
+   /
+
 &perfect_model_obs_nml
    read_input_state_from_file = .true.
    write_output_state_to_file = .true.
@@ -22,6 +28,7 @@
    /
 
 &filter_nml
+   qcf_table_filename       = ''
    async                    = 0
    adv_ens_command          = "no_advance_script"
    ens_size                 =  6

diff --git a/models/clm/work/input.nml b/models/clm/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.
+   use_logit_instead_of_probit = .false.
+   do_inverse_check            = .true.
+   /
+
 &perfect_model_obs_nml
    read_input_state_from_file = .true.
    write_output_state_to_file = .false.
@@ -25,6 +31,7 @@
 
 
 &filter_nml
+   qcf_table_filename           = ''
    allow_missing_clm = .true.
    perturb_from_single_instance = .FALSE.
    perturbation_amplitude       = 0.2

diff --git a/models/cm1/work/input.nml b/models/cm1/work/input.nml
@@ -2,7 +2,14 @@
 ! For high-resolution models with large DART states, 
 ! use 'distributed_state = .true.'
 
+&probit_transform_nml
+   fix_bound_violations        = .false.
+   use_logit_instead_of_probit = .false.
+   do_inverse_check            = .true.
+   /
+
 &filter_nml
+  qcf_table_filename          = ''
   async                       = 2
   adv_ens_command             = 'advance_model.csh'
   input_state_file_list       = 'input_filelist.txt'

diff --git a/models/coamps_nest/templates/EXPERIMENT_EXAMPLE/input.nml b/models/coamps_nest/templates/EXPERIMENT_EXAMPLE/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.
+   use_logit_instead_of_probit = .false.
+   do_inverse_check            = .true.
+   /
+
 &perfect_model_obs_nml
    start_from_restart    = .true.,
    output_restart        = .true.,
@@ -17,6 +23,7 @@
    /
 
 &filter_nml
+   qcf_table_filename       = ''
    async                    = 4,
    adv_ens_command          = "./advance_wrapper.sh",
    ens_size                 = 16,

diff --git a/models/dynamo/work/input.nml b/models/dynamo/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.,
+   use_logit_instead_of_probit = .false.,
+   do_inverse_check            = .true.,
+   /
+
 &perfect_model_obs_nml
    start_from_restart    = .false.,
    output_restart        = .true.,
@@ -22,6 +28,7 @@
    /
 
 &filter_nml
+   qcf_table_filename       = '',
    async                    = 2,
    adv_ens_command          = "./advance_model.ksh",
    ens_size                 = 20,

diff --git a/models/forced_barot/work/input.nml b/models/forced_barot/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.,
+   use_logit_instead_of_probit = .false.,
+   do_inverse_check            = .true.,
+   /
+
 &perfect_model_obs_nml
    start_from_restart       = .true.,
    output_restart           = .true.,
@@ -22,6 +28,7 @@
    /
 
 &filter_nml
+   qcf_table_filename       = '',
    async                    = 0,
    adv_ens_command          = "./advance_model.csh",
    ens_size                 = 20,

diff --git a/models/forced_lorenz_96/work/input.nml b/models/forced_lorenz_96/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.,
+   use_logit_instead_of_probit = .false.,
+   do_inverse_check            = .true.,
+   /
+
 &perfect_model_obs_nml
    read_input_state_from_file = .true.,
    single_file_in             = .true.
@@ -30,6 +36,7 @@
    # stages_to_write  = 'preassim', 'postassim', 'output'
 
 &filter_nml
+   qcf_table_filename           = '',
    single_file_in               = .true.,
    input_state_files            = ''
    input_state_file_list        = 'filter_input_list.txt'

diff --git a/models/gitm/work/input.nml b/models/gitm/work/input.nml
@@ -1,5 +1,11 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.
+   use_logit_instead_of_probit = .false.
+   do_inverse_check            = .true.
+   /
 
 &filter_nml
+   qcf_table_filename           = ''
    input_state_files            = ''
    input_state_file_list        = 'gitm_input_files.txt'
    single_file_in               = .false.

diff --git a/models/ikeda/work/input.nml b/models/ikeda/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.,
+   use_logit_instead_of_probit = .false.,
+   do_inverse_check            = .true.,
+   /
+
 &perfect_model_obs_nml
    read_input_state_from_file = .false.,
    single_file_in             = .true.
@@ -28,6 +34,7 @@
    /
 
 &filter_nml
+   qcf_table_filename           = '',
    single_file_in               = .true.,
    input_state_files            = 'filter_input.nc'
    input_state_file_list        = ''

diff --git a/models/lorenz_04/work/input.nml b/models/lorenz_04/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.,
+   use_logit_instead_of_probit = .false.,
+   do_inverse_check            = .true.,
+   /
+
 &perfect_model_obs_nml
    read_input_state_from_file = .true.,
    single_file_in             = .true.
@@ -32,6 +38,7 @@
 #   output_state_files            = 'filter_output.nc'
 
 &filter_nml
+   qcf_table_filename           = '',
    single_file_in               = .true.,
    input_state_files            = ''
    input_state_file_list        = 'filter_input_list.txt'

diff --git a/models/lorenz_84/work/input.nml b/models/lorenz_84/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.,
+   use_logit_instead_of_probit = .false.,
+   do_inverse_check            = .true.,
+   /
+
 &perfect_model_obs_nml
    read_input_state_from_file = .true.,
    single_file_in             = .true.
@@ -32,6 +38,7 @@
 #   output_state_files            = 'filter_output.nc'
 
 &filter_nml
+   qcf_table_filename           = '',
    single_file_in               = .true.,
    input_state_files            = ''
    input_state_file_list        = 'filter_input_list.txt'

diff --git a/models/lorenz_96_2scale/work/input.nml b/models/lorenz_96_2scale/work/input.nml
@@ -1,3 +1,9 @@
+&probit_transform_nml
+   fix_bound_violations        = .false.,
+   use_logit_instead_of_probit = .false.,
+   do_inverse_check            = .true.,
+   /
+
 &perfect_model_obs_nml
    read_input_state_from_file = .true.,
    single_file_in             = .true.
@@ -32,6 +38,7 @@
 #   output_state_files            = 'filter_output.nc'
 
 &filter_nml
+   qcf_table_filename           = '',
    single_file_in               = .true.,
    input_state_files            = ''
    input_state_file_list        = 'filter_input_list.txt'