Skip to content

Commit

Permalink
Merge pull request #640 from chrislxj/cn-matrix_v3
Browse files Browse the repository at this point in the history 
use_matrixcn and use_soil_matrixcn are coming in as default .false.
  • Loading branch information
@slevis-lmwg
slevis-lmwg authored Jul 19, 2024
2 parents a784f41 + 5aeb618 commit d020439
Show file tree
Hide file tree
Showing 78 changed files with 13,550 additions and 908 deletions.
2 changes: 2 additions & 0 deletions .git-blame-ignore-revs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@ e096358c832ab292ddfd22dd5878826c7c788968
6fccf682eaf718615407d9bacdd3903b8786a03d
2500534eb0a83cc3aff94b30fb62e915054030bf
78d05967c2b027dc9776a884716597db6ef7f57c
47839a77229c61555e3b8932927bb54cdc511b27
a0d014fae9550dd9ffbc934abd29ef16176f8208
c7b7ca1d94ac19abb9ecea9fb5b712ddbdd6645d
b565b55ce7a9f8d812a573d716a5fd3d78cfea81
Expand All @@ -46,4 +47,5 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
6c6f57e948bfa31e60b383536cc21663fedb8b70
9660667b1267dcd4150889f5f39db540158be74a
665cf86102e09b4c4c5a140700676dca23bc55a9
1a49e547ba3c48fa483f9ae81a8f05adcd6b888c
045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
209 changes: 191 additions & 18 deletions bld/CLMBuildNamelist.pm
View file
Original file line number Diff line number Diff line change
Expand Up @@ -101,18 +101,22 @@ OPTIONS
(Only for CLM4.5/CLM5.0)
-[no-]chk_res Also check [do NOT check] to make sure the resolution and
land-mask is valid.
-clm_accelerated_spinup "on|off" Setup in a configuration to run as fast as possible for doing a throw-away
-clm_accelerated_spinup "on|sasu|off" Setup in a configuration to run as fast as possible for doing a throw-away
simulation in order to get the model to a spun-up state. So do things like
turn off expensive options and setup for a low level of history output.
If CLM4.5/CLM5.0 and bgc it also includes a prognostic Carbon model (cn or bgc)
, also by default turn on Accelerated Decomposition mode which
is controlled by the namelist variable spinup_state.
is controlled by the namelist variable spinup_state (when soil matrix CN is off).
Turn on given spinup mode for BGC setting of CN
Turn on given spinup mode for BGC setting of CN (soil matrix CN off)
on : Turn on Accelerated Decomposition (spinup_state = 1 or 2)
off : run in normal mode (spinup_state = 0)
To spinup using the CN soil matrix method use "sasu" SemiAnalytic Spin-Up (SASU)
sasu: Turn on matrix spinup (spinup_matrixcn=T)
Normal spinup sequence is: on, sasu, off
Default is set by clm_accelerated_spinup mode.
Spinup is now a two step procedure. First, run the model
Expand Down Expand Up @@ -895,6 +899,7 @@ sub setup_cmdl_bgc {
'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fates'=>$nl_flags->{'use_fates'},
'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
my $soil_decomp_method = remove_leading_and_trailing_quotes( $nl->get_value( $var ) );
$nl_flags->{$var} = $soil_decomp_method;

if ( &value_is_true($nl_flags->{'use_cn'}) ) {
if ( $soil_decomp_method eq "None" ) {
Expand Down Expand Up @@ -953,6 +958,30 @@ sub setup_cmdl_bgc {
if ( (! &value_is_true($nl_flags->{'use_nitrif_denitrif'}) ) && &value_is_true($nl->get_value('use_fun')) ) {
$log->fatal_error("When FUN is on, use_nitrif_denitrif MUST also be on!");
}
#
# Make sure clm_accelerate_spinup is set correctly
#
$var = "clm_accelerated_spinup";
if ( $opts->{$var} ne "default" ) {
$val = $opts->{$var};
} else {
$val = $defaults->get_value($var);
}
$nl_flags->{$var} = $val;
# Set soil matrix (which is needed later for spinup)
$var = "use_soil_matrixcn";
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
, 'use_fates'=>$nl_flags->{'use_fates'},
, 'soil_decomp_method'=>$nl_flags->{'soil_decomp_method'},
, 'phys'=>$nl_flags->{'phys'}, clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'} );
if ( &value_is_true($nl->get_value($var)) ) {
$nl_flags->{$var} = ".true.";
} else {
$nl_flags->{$var} = ".false.";
}
if ( &value_is_true($nl->get_value($var)) && $nl_flags->{'soil_decomp_method'} ne "CENTURYKoven2013" ) {
$log->fatal_error("$var can only be on with CENTURYKoven2013 soil decomposition");
}
} # end bgc


Expand Down Expand Up @@ -1157,32 +1186,40 @@ sub setup_cmdl_spinup {
my $val;
my $var;
$nl_flags->{'spinup'} = undef;
# clm_accelerated_spinup will already have been set in setup_cmdl_bgc
$var = "clm_accelerated_spinup";
if ( $opts->{$var} ne "default" ) {
$val = $opts->{$var};
} else {
$val = $defaults->get_value($var);
}
$nl_flags->{$var} = $val;
$val = $nl_flags->{'clm_accelerated_spinup'};
my $group = $definition->get_group_name($var);
$nl->set_variable_value($group, $var, quote_string($val) );
if ( ! $definition->is_valid_value( $var, $val , 'noquotes' => 1) ) {
my @valid_values = $definition->get_valid_values( $var );
$log->fatal_error("$var has an invalid value ($val). Valid values are: @valid_values");
}
if ( $nl_flags->{'clm_accelerated_spinup'} eq "sasu" ) {
if ( ! &value_is_true($nl_flags->{'use_cn'}) ) {
$log->fatal_error("If clm_accelerated_spinup is sasu, use_cn MUST be on" );
}
if ( ! &value_is_true($nl_flags->{'use_soil_matrixcn'}) ) {
$log->fatal_error("If clm_accelerated_spinup is sasu, use_soil_matrixcn MUST be on" );
}
}
$log->verbose_message("CLM accelerated spinup mode is $val");
if ( &value_is_true($nl_flags->{'use_cn'}) ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition,
$defaults, $nl, "spinup_state", clm_accelerated_spinup=>$nl_flags->{$var},
use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'} );
$defaults, $nl, "spinup_state", clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'},
use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'},
use_soil_matrixcn=>$nl_flags->{"use_soil_matrixcn"} );
if ( $nl->get_value("spinup_state") ne 0 ) {
$nl_flags->{'bgc_spinup'} = "on";
if ( &value_is_true($nl_flags->{'use_soil_matrixcn'}) ) {
$log->fatal_error("spinup_state is accelerated (=1 or 2), but use_soil_matrixcn is also true" .
", change one or the other");
}
if ( $nl_flags->{'clm_accelerated_spinup'} eq "off" ) {
$log->fatal_error("spinup_state is accelerated, but clm_accelerated_spinup is off, change one or the other");
}
} else {
$nl_flags->{'bgc_spinup'} = "off";
$val = $defaults->get_value($var);
}
# For AD spinup mode by default reseed dead plants
if ( $nl_flags->{$var} ne "off" ) {
Expand All @@ -1197,6 +1234,27 @@ sub setup_cmdl_spinup {
}
}
$nl_flags->{$var} = $val;
if ( &value_is_true($nl_flags->{'use_soil_matrixcn'}) ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "spinup_matrixcn",
, 'use_fates'=>$nl_flags->{'use_fates'}, 'bgc_mode'=>$nl_flags->{'bgc_mode'}
, 'phys'=>$nl_flags->{'phys'}, 'use_soil_matrixcn'=>$nl_flags->{'use_soil_matrixcn'},
, clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'} );
my $spinup;
if ( &value_is_true($nl->get_value("spinup_matrixcn") ) ) {
$spinup = ".true.";
} else {
$spinup = ".false.";
}
$nl_flags->{'spinup_matrixcn'} = $spinup;
if ( &value_is_true($nl_flags->{'spinup_matrixcn'}) ) {
$nl_flags->{'bgc_spinup'} = "on";
if ( $nl_flags->{'clm_accelerated_spinup'} eq "off" ) {
$log->fatal_error("matrix spinup (spinup_matrixcn) is True, but clm_accelerated_spinup is off, change one or the other");
}
} else {
$nl_flags->{'bgc_spinup'} = "off";
}
}
my $group = $definition->get_group_name($var);
$nl->set_variable_value($group, $var, quote_string($val) );
if ( ! $definition->is_valid_value( $var, $val , 'noquotes' => 1) ) {
Expand All @@ -1206,11 +1264,13 @@ sub setup_cmdl_spinup {
if ( $nl_flags->{'bgc_spinup'} eq "on" && (not &value_is_true( $nl_flags->{'use_cn'} )) && (not &value_is_true($nl_flags->{'use_fates'})) ) {
$log->fatal_error("$var can not be '$nl_flags->{'bgc_spinup'}' if neither CN nor FATES is turned on (use_cn=$nl_flags->{'use_cn'}, use_fates=$nl_flags->{'use_fates'}).");
}
if ( $nl->get_value("spinup_state") eq 0 && $nl_flags->{'bgc_spinup'} eq "on" ) {
$log->fatal_error("Namelist spinup_state contradicts the command line option bgc_spinup" );
}
if ( $nl->get_value("spinup_state") eq 1 && $nl_flags->{'bgc_spinup'} eq "off" ) {
$log->fatal_error("Namelist spinup_state contradicts the command line option bgc_spinup" );
if ( ! &value_is_true($nl_flags->{'use_soil_matrixcn'}) ) {
if ( $nl->get_value("spinup_state") eq 0 && $nl_flags->{'bgc_spinup'} eq "on" ) {
$log->fatal_error("Namelist spinup_state contradicts the command line option bgc_spinup" );
}
if ( $nl->get_value("spinup_state") eq 1 && $nl_flags->{'bgc_spinup'} eq "off" ) {
$log->fatal_error("Namelist spinup_state contradicts the command line option bgc_spinup" );
}
}

$val = $nl_flags->{'bgc_spinup'};
Expand Down Expand Up @@ -1595,6 +1655,7 @@ sub process_namelist_inline_logic {
if ( remove_leading_and_trailing_quotes($nl_flags->{'clm_start_type'}) ne "branch" ) {
setup_logic_initial_conditions($opts, $nl_flags, $definition, $defaults, $nl, $physv);
}
setup_logic_cnmatrix($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref);
setup_logic_spinup($opts, $nl_flags, $definition, $defaults, $nl);
setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl);
setup_logic_snowpack($opts, $nl_flags, $definition, $defaults, $nl);
Expand Down Expand Up @@ -3103,7 +3164,7 @@ sub setup_logic_spinup {
if ( $nl_flags->{'bgc_mode'} eq "sp" && defined($nl->get_value('override_bgc_restart_mismatch_dump'))) {
$log->fatal_error("CN must be on if override_bgc_restart_mismatch_dump is set.");
}
if ( $nl_flags->{'clm_accelerated_spinup'} eq "on" ) {
if ( $nl_flags->{'clm_accelerated_spinup'} =~ /on|sasu/ ) {
foreach my $var ( "hist_nhtfrq", "hist_fincl1", "hist_empty_htapes", "hist_mfilt" ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
$var, use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'},
Expand Down Expand Up @@ -4651,6 +4712,118 @@ sub setup_logic_fates {
}
}


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

sub setup_logic_cnmatrix {
#
# Set some default options related to the CN Matrix options
#
my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref) = @_;

my @matrixlist = ( "use_matrixcn", "hist_wrt_matrixcn_diag" );
foreach my $var ( @matrixlist ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var
, 'use_fates'=>$nl_flags->{'use_fates'}, 'bgc_mode'=>$nl_flags->{'bgc_mode'}
, 'phys'=>$nl_flags->{'phys'}, 'use_soil_matrixcn'=>$nl_flags->{'use_soil_matrixcn'},
, 'spinup_matrixcn'=>$nl_flags->{'spinup_matrixcn'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} );
}
@matrixlist = ( "use_matrixcn", "use_soil_matrixcn", "hist_wrt_matrixcn_diag", "spinup_matrixcn" );
# Matrix items can't be on for OMP_NUM_THREADS (also known as NTHRDS_LND) > 1
my $var_xml = "OMP_NUM_THREADS";
my $val_xml = $ENV{$var_xml};
if ( $val_xml > 1) {
foreach my $var ( @matrixlist ) {
if ( &value_is_true($nl->get_value($var)) ) {
$log->warning("$var and $var_xml > 1 (in this case $val_xml) causes a clm threading test to FAIL (as of 2024/7/10), so use at your own risk." );
}
}
}

# Matrix items can't be on for transient
if (not string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) {
foreach my $var ( @matrixlist ) {
if ( &value_is_true($nl->get_value($var)) ) {
$log->warning("$var may FAIL with balance error in transient mode" );
}
}
}
# Matrix items can't be on for SP mode
if ( $nl_flags->{'bgc_mode'} eq "sp" ) {
foreach my $var ( @matrixlist ) {
if ( &value_is_true($nl->get_value($var)) ) {
$log->fatal_error("$var can NOT be on for SP mode" );
}
}
# Matrix items can't be on for FATES
} elsif ( $nl_flags->{'bgc_mode'} eq "fates" ) {
foreach my $var ( @matrixlist ) {
if ( &value_is_true($nl->get_value($var)) ) {
$log->fatal_error("$var can NOT be on with FATES" );
}
}
# Otherwise for CN or BGC mode
} else {
# TODO (slevis 2023/12/1) The next two if statements do nothing. Erik K and Sam L found that
# for_testing_use_second_grain_pool and for_testing_use_repr_structure_pool
# are empty rather than .true. or .false., but we did not get to the bottom
# of why, yet. The same error-check in the code does get triggered at run-time,
# so we will not pursue fixing this right now.
# If matrixcn is on, for_testing_use_second_grain_pool and for_testing_use_repr_structure_pool must be off
if ( &value_is_true($nl->get_value("use_matrixcn")) && &value_is_true($nl_flags->{"for_testing_use_second_grain_pool"}) ) {
$log->fatal_error("for_testing_use_second_grain_pool can NOT be on when use_matrixcn is on" );
}
if ( &value_is_true($nl->get_value("use_matrixcn")) && &value_is_true($nl_flags->{"for_testing_use_repr_structure_pool"}) ) {
$log->fatal_error("for_testing_use_repr_structure_pool can NOT be on when use_matrixcn is on" );
}
# If both matrixcn and soil_matrix are off hist_wrt_matrixcn_diag can't be on
if ( ! &value_is_true($nl->get_value("use_matrixcn")) && ! &value_is_true($nl_flags->{"use_soil_matrixcn"}) ) {
my $var = "hist_wrt_matrixcn_diag";
if ( &value_is_true($nl->get_value($var)) ) {
$log->fatal_error("$var can NOT be on when both use_matrixcn and use_soil_matrixcn are off" );
}
}
# If soil_matrix is off spinup_matrixcn can't be on
if ( ! &value_is_true($nl_flags->{"use_soil_matrixcn"}) ) {
my $var = "spinup_matrixcn";
if ( &value_is_true($nl->get_value($var)) ) {
$log->fatal_error("$var can NOT be on when use_soil_matrixcn is off" );
}
}
}
# if soil matrix is on and spinup is on, set spinup specific variables
my @spinup_vars = ( "nyr_forcing", "nyr_sasu", "iloop_avg" );
foreach my $var ( @spinup_vars ) {
if ( &value_is_true($nl_flags->{"use_soil_matrixcn"}) && &value_is_true($nl_flags->{'spinup_matrixcn'}) ) {
if ( $var ne "nyr_sasu" ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
, 'phys'=>$nl_flags->{'phys'}, 'spinup_matrixcn'=>$nl_flags->{'spinup_matrixcn'} );
} else {
# Set SASU spinup period to nyr_forcing (slow mode) by default
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
, 'val'=>$nl->get_value("nyr_forcing") );
}
my $val = $nl->get_value($var);
if ( $val == -999 && ($var eq "iloop_avg") ) { next; } # iloop_avg can be special flag value
if ( $val < 1 ) {
$log->fatal_error("$var can NOT be negative or zero" );
}
} else {
my $val = $nl->get_value($var);
if ( defined($val) ) {
$log->fatal_error("$var can NOT be set when use_soil_matrixcn and isspsinup are off" );
}
}
}
if ( &value_is_true($nl_flags->{"use_soil_matrixcn"}) && &value_is_true($nl_flags->{'spinup_matrixcn'}) ) {
my $nyr_forcing = $nl->get_value('nyr_forcing');
my $nyr_sasu = $nl->get_value('nyr_sasu');
if ( $nyr_sasu > $nyr_forcing ) {
$log->fatal_error("nyr_sasu can NOT be greater than nyr_forcing" );
}
}
}

#-------------------------------------------------------------------------------
sub setup_logic_exice {
#
Expand Down
Loading

0 comments on commit d020439

Please sign in to comment.