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Merge tag 'ctsm5.1.dev025' into lmbirch_wkattge
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Refactor ozone code, and misc. small fixes

(1) Restructure ozone code (ESCOMP#1276) in
    preparation for new ozone parameterization.

(2) Fix non-standard hexadecimal constant
    (ESCOMP#1271), needed for gfortran 10

(3) Remove support for CISM1 (ESCOMP#1226)

(4) Move final WaterGridcellBalance call out to clm_driver (resolves
    ESCOMP#1286)

(5) Only add WA and QCHARGE history fields if use_aquifer_layer is true
    (resolves ESCOMP#1281)

(6) Consolidate conditional structures for VIC initialization (resolves
    ESCOMP#1287)

 Conflicts:
	bld/namelist_files/namelist_defaults_ctsm.xml
	bld/unit_testers/build-namelist_test.pl
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@ekluzek
ekluzek committed Mar 6, 2021
2 parents e169812 + 2094348 commit 0f5472d
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ manage_externals.log
/tools/PTCLM/
/cime/
/components/
/doc/doc-builder/

# ignore svn directories
**/.svn/**
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36 changes: 28 additions & 8 deletions Externals.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -16,31 +16,51 @@ required = True
local_path = components/rtm
protocol = git
repo_url = https://github.com/ESCOMP/RTM
tag = rtm1_0_72
tag = rtm1_0_73
required = True

[mosart]
local_path = components/mosart
protocol = git
repo_url = https://github.com/ESCOMP/MOSART
tag = mosart1_0_37
tag = mosart1_0_38
required = True

[cdeps]
hash = 45b7a85
[mizuRoute]
local_path = components/mizuRoute
protocol = git
repo_url = https://github.com/ESCOMP/CDEPS.git
local_path = components/cdeps
repo_url = https://github.com/nmizukami/mizuRoute
hash = 34723c2
required = True

[cime]
local_path = cime
protocol = git
repo_url = https://github.com/ESMCI/cime
tag = cime5.8.32
externals = ../Externals_cime.cfg
tag = branch_tags/cime5.8.32_a02
required = True

[cmeps]
local_path = cime/src/drivers/nuopc/
protocol = git
repo_url = https://github.com/ESCOMP/CMEPS.git
hash = 7654038
required = True

[cdeps]
local_path = components/cdeps
protocol = git
repo_url = https://github.com/ESCOMP/CDEPS.git
hash = 45b7a85
required = True

[doc-builder]
local_path = doc/doc-builder
protocol = git
repo_url = https://github.com/ESMCI/doc-builder
tag = v1.0.5
required = False

[externals_description]
schema_version = 1.0.0

2 changes: 1 addition & 1 deletion Externals_CLM.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
local_path = src/fates
protocol = git
repo_url = https://github.com/NGEET/fates
tag = sci.1.30.0_api.8.0.0
tag = sci.1.43.2_api.14.2.0
required = True

[PTCLM]
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9 changes: 0 additions & 9 deletions Externals_cime.cfg
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This file was deleted.

155 changes: 82 additions & 73 deletions bld/CLMBuildNamelist.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -765,8 +765,9 @@ sub setup_cmdl_fates_mode {
}
} else {
# dis-allow fates specific namelist items with non-fates runs
my @list = ( "use_fates_spitfire", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
"use_fates_inventory_init", "fates_inventory_ctrl_filename","use_fates_logging","fates_parteh_mode" );
my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
"use_fates_cohort_age_tracking",
"use_fates_inventory_init","use_fates_fixed_biogeog", "fates_inventory_ctrl_filename","use_fates_logging","fates_parteh_mode" );
foreach my $var ( @list ) {
if ( defined($nl->get_value($var)) ) {
$log->fatal_error("$var is being set, but can ONLY be set when -bgc fates option is used.\n");
Expand Down Expand Up @@ -907,52 +908,58 @@ sub setup_cmdl_fire_light_res {
my $var = "light_res";
my $val = $opts->{$var};
if ( $val eq "default" ) {
$nl_flags->{$var} = remove_leading_and_trailing_quotes($defaults->get_value($var));
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'},
'fates_spitfire_mode'=>$nl->get_value('fates_spitfire_mode'),
'use_fates'=>$nl_flags->{'use_fates'}, fire_method=>$nl->get_value('fire_method') );
$val = remove_leading_and_trailing_quotes( $nl->get_value($var) );
$nl_flags->{$var} = $val;
} else {
my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') );
if ( defined($fire_method) && $val ne "none" ) {
if ( $fire_method eq "nofire" ) {
$log->fatal_error("-$var option used with fire_method='nofire'. -$var can ONLY be used without the nofire option");
}
}
my $stream_fldfilename_lightng = remove_leading_and_trailing_quotes( $nl->get_value('stream_fldfilename_lightng') );
if ( defined($stream_fldfilename_lightng) && $val ne "none" ) {
$log->fatal_error("-$var option used while also explicitly setting stream_fldfilename_lightng filename which is a contradiction. Use one or the other not both.");
}
if ( ! &value_is_true($nl->get_value('use_cn')) ) {
$log->fatal_error("-$var option used CN is NOT on. -$var can only be used when CN is on (with bgc: cn or bgc)");
}
if ( &value_is_true($nl->get_value('use_cn')) && $val eq "none" ) {
$log->fatal_error("-$var option is set to none, but CN is on (with bgc: cn or bgc) which is a contradiction");
}
$nl_flags->{$var} = $val;
}
my $group = $definition->get_group_name($var);
$nl->set_variable_value($group, $var, quote_string($nl_flags->{$var}) );
if ( ! $definition->is_valid_value( $var, $nl_flags->{$var}, 'noquotes'=>1 ) ) {
my @valid_values = $definition->get_valid_values( $var );
$log->fatal_error("$var has a value (".$nl_flags->{$var}.") that is NOT valid. Valid values are: @valid_values");
}
$log->verbose_message("Using $nl_flags->{$var} for $var.");
#
# Set flag if cn-fires are on or not
#
$var = "cnfireson";
if ( &value_is_true($nl->get_value('use_cn')) ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_method');
}
my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') );
if ( defined($fire_method) && ! &value_is_true($nl_flags->{'use_cn'}) ) {
$log->fatal_error("fire_method is being set even though bgc is NOT cn or bgc.");
}
if ( defined($fire_method) && $fire_method eq "nofire" ) {
$nl_flags->{$var} = ".false.";
} elsif ( &value_is_true($nl->get_value('use_cn')) ) {
$nl_flags->{$var} = ".true.";
} else {
$nl_flags->{$var} = ".false.";
}
}
my $stream_fldfilename_lightng = remove_leading_and_trailing_quotes( $nl->get_value('stream_fldfilename_lightng') );
if ( defined($stream_fldfilename_lightng) && $val ne "none" ) {
$log->fatal_error("-$var option used while also explicitly setting stream_fldfilename_lightng filename which is a contradiction. Use one or the other not both.");
}
if ( ! &value_is_true($nl->get_value('use_cn')) ) {
$log->fatal_error("-$var option used CN is NOT on. -$var can only be used when CN is on (with bgc: cn or bgc)");
}
if ( &value_is_true($nl->get_value('use_cn')) && $val eq "none" ) {
$log->fatal_error("-$var option is set to none, but CN is on (with bgc: cn or bgc) which is a contradiction");
}
$nl_flags->{$var} = $val;
}
my $group = $definition->get_group_name($var);
$nl->set_variable_value($group, $var, quote_string($nl_flags->{$var}) );
if ( ! $definition->is_valid_value( $var, $nl_flags->{$var}, 'noquotes'=>1 ) ) {
my @valid_values = $definition->get_valid_values( $var );
$log->fatal_error("$var has a value (".$nl_flags->{$var}.") that is NOT valid. Valid values are: @valid_values");
}
$log->verbose_message("Using $nl_flags->{$var} for $var.");
#
# Set flag if cn-fires are on or not
#
$var = "cnfireson";
if ( &value_is_true($nl->get_value('use_cn')) ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_method');
}
my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') );
if ( defined($fire_method) && ! &value_is_true($nl_flags->{'use_cn'}) && ! &value_is_true($nl_flags->{'use_fates'}) ) {
$log->fatal_error("fire_method is being set while use_cn and use_fates are both false.");
}
if ( defined($fire_method) && $fire_method eq "nofire" ) {
$nl_flags->{$var} = ".false.";
# } elsif ( &value_is_true($nl->get_value('use_cn')) || $nl_flags->{'fates_spitfire_mode'} > 1 ) {
} elsif ( &value_is_true($nl->get_value('use_cn')) || &value_is_true($nl->get_value('use_fates')) ) {
$nl_flags->{$var} = ".true.";
} else {
$nl_flags->{$var} = ".false.";
}
}
}

#-------------------------------------------------------------------------------

Expand Down Expand Up @@ -2068,7 +2075,6 @@ sub error_if_set {
}
}


#-------------------------------------------------------------------------------

sub setup_logic_soilstate {
Expand Down Expand Up @@ -2182,9 +2188,6 @@ sub setup_logic_surface_dataset {
if ($flanduse_timeseries ne "null" && &value_is_true($nl_flags->{'use_cndv'}) ) {
$log->fatal_error( "dynamic PFT's (setting flanduse_timeseries) are incompatible with dynamic vegetation (use_cndv=.true)." );
}
if ($flanduse_timeseries ne "null" && &value_is_true($nl_flags->{'use_fates'}) ) {
$log->fatal_error( "dynamic PFT's (setting flanduse_timeseries) are incompatible with ecosystem dynamics (use_fates=.true)." );
}
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsurdat',
'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'},
'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>$nl_flags->{'irrigate'},
Expand Down Expand Up @@ -2625,17 +2628,17 @@ sub setup_logic_do_harvest {
# in any of these cases, a fatal error will be generated
my $cannot_be_true = "";

if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) {
$cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)";
} elsif (!&value_is_true($nl->get_value('use_cn'))) {
$cannot_be_true = "$var can only be set to true when running with CN (use_cn = true)";
} elsif (&value_is_true($nl->get_value('use_fates'))) {
$cannot_be_true = "$var currently doesn't work with ED";
}
if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) {
$cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)";
}

if ($cannot_be_true) {
$default_val = ".false.";
}
elsif (!&value_is_true($nl->get_value('use_cn')) && !&value_is_true($nl->get_value('use_fates'))) {
$cannot_be_true = "$var can only be set to true when running with either CN or FATES";
}

if ($cannot_be_true) {
$default_val = ".false.";
}

if (!$cannot_be_true) {
# Note that, if the variable cannot be true, we don't call add_default
Expand Down Expand Up @@ -3394,23 +3397,23 @@ sub setup_logic_lightning_streams {
# lightning streams require CN/BGC
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;

if ( &value_is_true($nl_flags->{'cnfireson'}) ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lightngmapalgo', 'use_cn'=>$nl_flags->{'use_cn'},
'hgrid'=>$nl_flags->{'res'},
'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_lightng', 'use_cn'=>$nl_flags->{'use_cn'},
'sim_year'=>$nl_flags->{'sim_year'},
'sim_year_range'=>$nl_flags->{'sim_year_range'});
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_lightng', 'use_cn'=>$nl_flags->{'use_cn'},
'sim_year'=>$nl_flags->{'sim_year'},
'sim_year_range'=>$nl_flags->{'sim_year_range'});
# Set align year, if first and last years are different
if ( $nl->get_value('stream_year_first_lightng') !=
$nl->get_value('stream_year_last_lightng') ) {
if ( $nl_flags->{'light_res'} ne "none" ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lightngmapalgo',
'hgrid'=>$nl_flags->{'res'},
'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_lightng',
'sim_year'=>$nl_flags->{'sim_year'},
'sim_year_range'=>$nl_flags->{'sim_year_range'});
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_lightng',
'sim_year'=>$nl_flags->{'sim_year'},
'sim_year_range'=>$nl_flags->{'sim_year_range'});
# Set align year, if first and last years are different
if ( $nl->get_value('stream_year_first_lightng') !=
$nl->get_value('stream_year_last_lightng') ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'model_year_align_lightng', 'sim_year'=>$nl_flags->{'sim_year'},
'sim_year_range'=>$nl_flags->{'sim_year_range'});
}
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lightng', 'use_cn'=>$nl_flags->{'use_cn'},
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lightng',
'hgrid'=>$nl_flags->{'light_res'} );
} else {
# If bgc is NOT CN/CNDV then make sure none of the Lightng settings are set
Expand All @@ -3419,7 +3422,7 @@ sub setup_logic_lightning_streams {
defined($nl->get_value('model_year_align_lightng')) ||
defined($nl->get_value('lightng_tintalgo' )) ||
defined($nl->get_value('stream_fldfilename_lightng')) ) {
$log->fatal_error("When bgc is SP (NOT CN or BGC) or fire_method==nofire none of: stream_year_first_lightng,\n" .
$log->fatal_error("When bgc is SP (NOT CN or BGC or FATES) or fire is turned off none of: stream_year_first_lightng,\n" .
"stream_year_last_lightng, model_year_align_lightng, lightng_tintalgo nor\n" .
"stream_fldfilename_lightng can be set!");
}
Expand Down Expand Up @@ -3699,6 +3702,11 @@ sub setup_logic_canopyfluxes {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_undercanopy_stability' );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'itmax_canopy_fluxes',
'structure'=>$nl_flags->{'structure'});
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_biomass_heat_storage',
'use_fates'=>$nl_flags->{'use_fates'}, 'phys'=>$nl_flags->{'phys'} );
if ( &value_is_true($nl->get_value('use_biomass_heat_storage') ) && &value_is_true( $nl_flags->{'use_fates'}) ) {
$log->fatal_error('use_biomass_heat_storage can NOT be set to true when fates is on');
}
}

#-------------------------------------------------------------------------------
Expand Down Expand Up @@ -3885,8 +3893,8 @@ sub setup_logic_fates {

if (&value_is_true( $nl_flags->{'use_fates'}) ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
my @list = ( "use_fates_spitfire", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
"use_fates_inventory_init", "use_fates_logging","fates_parteh_mode" );
my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
"use_fates_inventory_init","use_fates_fixed_biogeog", "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking" );
foreach my $var ( @list ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'} );
}
Expand Down Expand Up @@ -3914,6 +3922,7 @@ sub setup_logic_misc {
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;

add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'for_testing_run_ncdiopio_tests');
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hist_master_list_file');
}

#-------------------------------------------------------------------------------
Expand Down
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