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Tracer advection siparcs #322

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merged 18 commits into from
Mar 10, 2022
Merged

Tracer advection siparcs #322

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3ce7a74
lorenz_96_tracer_advection model
fairaque1999 Jan 6, 2022
de83106
bug-fix for model interpolate tracer advection
jlaucar Jan 6, 2022
f470cad
cdl file rather than netcdf
hkershaw-brown Jan 6, 2022
6c54f84
Documentation for lorenz_96_tracer_advection
hkershaw-brown Jan 7, 2022
8fc5b91
reanmed target to target_loc to avoid using fortran keyword target
hkershaw-brown Jan 7, 2022
6d39e0a
fix link to model documentation, remove old add_dommain
hkershaw-brown Jan 7, 2022
33ccd01
bug-fix for state_loc. Was using integer division so elements
hkershaw-brown Jan 7, 2022
f13b23b
removed print statements and early exit left in from last commit
hkershaw-brown Jan 7, 2022
2a2d773
removed var_offset, conc_offset, source_offset from namelist.
hkershaw-brown Jan 7, 2022
79b1959
Merge branch 'main' into tracer_advection_siparcs
hkershaw-brown Jan 18, 2022
1448134
Merge branch 'main' into tracer_advection_siparcs
hkershaw-brown Feb 3, 2022
300fb54
replace hardcoded 1:40 and /3 with grid_size
hkershaw-brown Feb 3, 2022
d794dcf
Merge branch 'main' into tracer_advection_siparcs
hkershaw-brown Feb 7, 2022
309beb1
fix rst formatting and description of model size
hkershaw-brown Feb 11, 2022
953293e
Merge branch 'main' into tracer_advection_siparcs
hkershaw-brown Feb 14, 2022
7350f08
add lorenz_96_tracer_advection to plot_bins
hkershaw-brown Feb 17, 2022
461bfdc
Merge branch 'main' into tracer_advection_siparcs
hkershaw-brown Mar 10, 2022
d4d0192
bump version and changlog for release
hkershaw-brown Mar 10, 2022
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1 change: 1 addition & 0 deletions README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -390,6 +390,7 @@ References
models/lorenz_84/readme
models/lorenz_96/readme
models/lorenz_96_2scale/readme
models/lorenz_96_tracer_advection/readme
models/forced_lorenz_96/readme
models/MITgcm_ocean/readme
models/mpas_atm/readme
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2 changes: 2 additions & 0 deletions assimilation_code/modules/observations/oned_quantities_mod.f90
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Expand Up @@ -27,5 +27,7 @@
! QTY_LARGE_SCALE_STATE desc="state varies with large time/space scale"
! QTY_SMALL_SCALE_STATE desc="state varies with small time/space scale"
! QTY_1D_PARAMETER
! QTY_TRACER_CONCENTRATION
! QTY_TRACER_SOURCE
!
! END DART PREPROCESS QUANTITY DEFINITIONS
2 changes: 1 addition & 1 deletion diagnostics/matlab/plot_correl.m
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Expand Up @@ -91,7 +91,7 @@ function plot_correl(diagn_file)
fprintf('Correlating variable %s index %d at time %d.\n', ...
pinfo.base_var,pinfo.base_var_index, pinfo.base_time)

case {'simple_advection'}
case {'simple_advection', 'lorenz_96_tracer_advection'}

disp('Your choice of variables are:')
disp(pinfo.vars)
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2 changes: 1 addition & 1 deletion diagnostics/matlab/plot_ens_err_spread.m
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Expand Up @@ -71,7 +71,7 @@ function plot_ens_err_spread(input_file)
switch lower(pinfo.model)

case {'9var','lorenz_63','lorenz_84','lorenz_96','lorenz_96_2scale', ...
'forced_lorenz_96','lorenz_04','ikeda','simple_advection', 'null'}
'forced_lorenz_96','lorenz_04','ikeda','simple_advection','lorenz_96_tracer_advection', 'null'}

varid = SetVariableID(pinfo);
pinfo.var = varid.var;
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2 changes: 1 addition & 1 deletion diagnostics/matlab/plot_ens_mean_time_series.m
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Expand Up @@ -80,7 +80,7 @@ function plot_ens_mean_time_series(input_file)
switch lower(pinfo.model)

case {'9var','lorenz_63','lorenz_84','lorenz_96','lorenz_96_2scale', ...
'forced_lorenz_96','lorenz_04','ikeda','simple_advection', 'null'}
'forced_lorenz_96','lorenz_04','ikeda','simple_advection','lorenz_96_tracer_advection', 'null'}

varid = SetVariableID(pinfo);
pinfo.var = varid.var;
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2 changes: 1 addition & 1 deletion diagnostics/matlab/plot_ens_time_series.m
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Expand Up @@ -81,7 +81,7 @@ function plot_ens_time_series(input_file)

switch lower(pinfo.model)

case {'9var','lorenz_63','lorenz_84','lorenz_96','lorenz_96_2scale', ...
case {'9var','lorenz_63','lorenz_84','lorenz_96','lorenz_96_2scale','lorenz_96_tracer_advection' ...
'forced_lorenz_96','lorenz_04','ikeda','simple_advection', 'null'}

varid = SetVariableID(pinfo);
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2 changes: 1 addition & 1 deletion diagnostics/matlab/plot_jeff_correl.m
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Expand Up @@ -75,7 +75,7 @@ function plot_jeff_correl(fname)
inputstring = input('Input variable and index for correlation \n','s');
[pinfo.state_var, pinfo.state_var_index] = ParseAlphaNumerics(inputstring);

case {'simple_advection'}
case {'simple_advection', 'lorenz_96_tracer_advection'}

disp('Your choice of variables are:')
disp(pinfo.vars)
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2 changes: 1 addition & 1 deletion diagnostics/matlab/plot_phase_space.m
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Expand Up @@ -159,7 +159,7 @@ function plot_phase_space(fname)
'ens_mem' , ens_mem , ...
'ltype' , ltype );

case {'simple_advection'}
case {'simple_advection','lorenz_96_tracer_advection'}
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Member Author

@hkershaw-brown hkershaw-brown Feb 17, 2022 •
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I can't get this to run.

>> plot_phase_space
Input name of netCDF file:
<cr> for true_state.nc

Your choice of variables are:
    {'state_variable'      }
    {'tracer_concentration'}
    {'source'              }

the indices (locations) can range from 1 to 40
Input variable and index for axis 1 <cr> for state_variable 1
state_variable 1
Input variable and index for axis 2 <cr> for state_variable 13
tracer_concentration 1
Input variable and index for axis 2 <cr> for state_variable 27
source 1
Error using internal.matlab.imagesci.nc/getGroupAndVarid (line 2096)
Could not find variable or group 'CopyMetaData' in file.

Error in internal.matlab.imagesci.nc/read (line 593)
            [gid, varid] = getGroupAndVarid(this, location);

Error in ncread (line 66)
vardata = ncObj.read(varName, varargin{:});

Error in plot_phase_space (line 204)
         metadata = ncread(fname,'CopyMetaData');


if (ishold), clear var1 var2 var3 ens_mem ltype; end

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2 changes: 1 addition & 1 deletion diagnostics/matlab/plot_sawtooth.m
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Expand Up @@ -60,7 +60,7 @@ function plot_sawtooth(posterior_file,prior_file)
switch lower(pinfo.model)

case {'9var','lorenz_63','lorenz_84','lorenz_96','lorenz_96_2scale', ...
'lorenz_04','forced_lorenz_96','ikeda','simple_advection', 'null'}
'lorenz_04','forced_lorenz_96','ikeda','simple_advection','lorenz_96_tracer_advection','null'}

% determine which variable ['state','X','Y' ...] and
% determine which variable IDs (locations), as well as
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2 changes: 1 addition & 1 deletion diagnostics/matlab/plot_total_err.m
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Expand Up @@ -62,7 +62,7 @@ function plot_total_err(input_file)
pinfo = CheckModelCompatibility(truth_file,input_file);

switch lower(pinfo.model)
case{'9var','lorenz_63','lorenz_84','lorenz_96','lorenz_96_2scale', ...
case{'9var','lorenz_63','lorenz_84','lorenz_96','lorenz_96_2scale','lorenz_96_tracer_advection', ...
'lorenz_04', 'forced_lorenz_96','ikeda','simple_advection', 'null'}

case{'fms_bgrid'}
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2 changes: 1 addition & 1 deletion diagnostics/matlab/plot_var_var_correl.m
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Expand Up @@ -85,7 +85,7 @@ function plot_var_var_correl(fname)
inputstring = input('Input variable and index for correlation \n','s');
[pinfo.state_var, pinfo.state_var_index] = ParseAlphaNumerics(inputstring);

case {'simple_advection'}
case {'simple_advection', 'lorenz_96_tracer_advection'}

disp('Your choice of variables are:')
disp(pinfo.vars)
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2 changes: 1 addition & 1 deletion diagnostics/matlab/private/CheckModel.m
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Expand Up @@ -139,7 +139,7 @@

vars.fname = fname;

case {'simple_advection'}
case {'simple_advection', 'lorenz_96_tracer_advection'}

num_locs = dim_length(fname,'location'); % # of X variables
loc1d = ncread(fname,'location');
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2 changes: 1 addition & 1 deletion diagnostics/matlab/private/PlotBins.m
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Expand Up @@ -102,7 +102,7 @@ function PlotBins(pinfo)
axis tight
end

case {'lorenz_96_2scale','simple_advection'}
case {'lorenz_96_2scale','simple_advection', 'lorenz_96_tracer_advection'}

clf; iplot = 0;
for ivar = pinfo.var_inds,
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2 changes: 1 addition & 1 deletion diagnostics/matlab/private/PlotCorrel.m
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Expand Up @@ -38,7 +38,7 @@ function PlotCorrel( pinfo )
switch(lower(pinfo.model))

case {'9var','lorenz_63','lorenz_84','lorenz_96', 'lorenz_96_2scale', ...
'lorenz_04','forced_lorenz_96','ikeda','simple_advection', 'null'}
'lorenz_04','forced_lorenz_96','ikeda','simple_advection', 'lorenz_96_tracer_advection', 'null'}

% The Base Variable Index must be a valid state variable
if ( pinfo.base_var_index > pinfo.num_state_vars )
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2 changes: 1 addition & 1 deletion diagnostics/matlab/private/PlotEnsErrSpread.m
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Expand Up @@ -104,7 +104,7 @@ function PlotEnsErrSpread( pinfo )
end

case {'lorenz_63','lorenz_84','lorenz_96', 'lorenz_96_2scale', ...
'lorenz_04','forced_lorenz_96','ikeda','simple_advection', 'null'}
'lorenz_04','forced_lorenz_96','ikeda','simple_advection','lorenz_96_tracer_advection','null'}

truth = get_hyperslab('fname',pinfo.truth_file, ...
'varname',pinfo.var, ...
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2 changes: 1 addition & 1 deletion diagnostics/matlab/private/PlotEnsMeanTimeSeries.m
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Expand Up @@ -167,7 +167,7 @@ function PlotEnsMeanTimeSeries( pinfo )
legend boxoff

case {'lorenz_96', 'lorenz_96_2scale', 'forced_lorenz_96', 'lorenz_04', ...
'ikeda', 'simple_advection', 'null'}
'ikeda', 'simple_advection', 'lorenz_96_tracer_advection','null'}

%% Plot all variables in own subplot ... might get cluttered.
figure(1); clf; iplot = 0;
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2 changes: 1 addition & 1 deletion diagnostics/matlab/private/PlotEnsTimeSeries.m
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Expand Up @@ -181,7 +181,7 @@ function PlotEnsTimeSeries( pinfo )
legend boxoff

case {'lorenz_96', 'lorenz_96_2scale', 'forced_lorenz_96', 'lorenz_04', ...
'ikeda', 'simple_advection', 'null'}
'ikeda', 'simple_advection', 'lorenz_96_tracer_advection', 'null'}

% Use one figure with subplots
figure(1); clf; iplot = 0;
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2 changes: 1 addition & 1 deletion diagnostics/matlab/private/PlotPhaseSpace.m
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Expand Up @@ -113,7 +113,7 @@ function PlotPhaseSpace( pinfo )
legend boxoff

case {'9var', 'lorenz_63', 'lorenz_84', 'lorenz_96', 'lorenz_96_2scale', ...
'lorenz_04', 'forced_lorenz_96', 'simple_advection', 'null'}
'lorenz_04', 'forced_lorenz_96', 'simple_advection', 'lorenz_96_tracer_advection', 'null'}

BulletProof(pinfo, X, Y, Z) % rudimentary bulletproofing

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52 changes: 52 additions & 0 deletions diagnostics/matlab/private/PlotTotalErr.m
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Expand Up @@ -282,7 +282,59 @@ function PlotTotalErr( pinfo )
title({string1,string2},'interpreter','none','fontweight','bold')
xlabel(sprintf('model "days" (%d timesteps)',pinfo.time_series_length))
ylabel('Total Error')
end


case {'lorenz_96_tracer_advection'}

varlist = {'state_variable','tracer_concentration','source'};

for ivar = 1:length(varlist)

% Get the appropriate netcdf variables

truth = get_hyperslab('fname', pinfo.truth_file, ...
'varname', varlist{ivar}, ...
'permute', 'T', ...
'squeeze', 'T', ...
'tindex1', pinfo.truth_time(1), ...
'tcount', pinfo.truth_time(2));

varname = sprintf('%s_mean',varlist{ivar});
ens = get_hyperslab('fname', pinfo.diagn_file, ...
'varname', varname, ...
'permute', 'T', ...
'tindex1', pinfo.diagn_time(1), ...
'tcount', pinfo.diagn_time(2));

varname = sprintf('%s_sd',varlist{ivar});
spread = get_hyperslab('fname', pinfo.diagn_file, ...
'varname', varname, ...
'permute', 'T', ...
'tindex1', pinfo.diagn_time(1), ...
'tcount', pinfo.diagn_time(2));

[~,num_vars] = size(spread);

% Also need to compute the spread; zero truth for this and
% compute distance from 0
err = total_err(truth, ens);
err_spread = total_err(zeros(size(spread)), spread);
errTotal = sum(err)/pinfo.time_series_length;
spreadTotal= sum(err_spread)/pinfo.time_series_length;
string1 = ['time-mean Ensemble Mean Total Error = ' num2str(errTotal)];
string2 = ['time-mean Ensemble Spread = ' num2str(spreadTotal)];

figure(ivar); clf(ivar);
plot(pinfo.time,err, 'b', pinfo.time,err_spread, 'r','LineWidth',figdata.linewidth);
set(gca,'FontSize',figdata.fontsize)
legend(string1,string2,'Location','NorthEast','FontSize',figdata.fontsize)
legend boxoff
string1 = sprintf('%s Total Error over all %d variables', pinfo.model, num_vars);
string2 = sprintf('''%s'' %s', varlist{ivar}, pinfo.diagn_file);
title({string1,string2},'interpreter','none','fontweight','bold')
xlabel(sprintf('model "days" (%d timesteps)',pinfo.time_series_length))
ylabel('Total Error')
end

case 'fms_bgrid'
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2 changes: 1 addition & 1 deletion diagnostics/matlab/private/SetVariableID.m
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Expand Up @@ -73,7 +73,7 @@
varid.var_inds = vrbl_inds;
end

case 'simple_advection'
case {'simple_advection','lorenz_96_tracer_advection'}

% query to see if the defaults are OK ...

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1 change: 1 addition & 0 deletions models/README.rst
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Expand Up @@ -23,6 +23,7 @@ DART supported models:
- :doc:`lorenz_84/readme`
- :doc:`lorenz_96/readme`
- :doc:`lorenz_96_2scale/readme`
- :doc:`lorenz_96_tracer_advection/readme`
- :doc:`forced_lorenz_96/readme`
- :doc:`MITgcm_ocean/readme`
- :doc:`mpas_atm/readme`
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Binary file added models/lorenz_96_tracer_advection/images/Semi_lag.png
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40 changes: 40 additions & 0 deletions models/lorenz_96_tracer_advection/images/lorenz_96_cyclic_chain.svg
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