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Fix style issues.
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@BSchilperoort
BSchilperoort committed Nov 28, 2023
1 parent f23ad62 commit 515a232
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Showing 2 changed files with 27 additions and 29 deletions.
32 changes: 15 additions & 17 deletions src/STEMMUS_SCOPE.m
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Original file line number Diff line number Diff line change
Expand Up @@ -83,9 +83,9 @@
X = X(j, 1:end);

F = struct('FileID', {'Simulation_Name', 'soil_file', 'leaf_file', 'atmos_file'...
'Dataset_dir', 't_file', 'year_file', 'Rin_file', 'Rli_file' ...
, 'p_file', 'Ta_file', 'ea_file', 'u_file', 'CO2_file', 'z_file', 'tts_file' ...
, 'LAI_file', 'hc_file', 'SMC_file', 'Vcmax_file', 'Cab_file', 'LIDF_file'});
'Dataset_dir', 't_file', 'year_file', 'Rin_file', 'Rli_file' ...
'p_file', 'Ta_file', 'ea_file', 'u_file', 'CO2_file', 'z_file', 'tts_file' ...
'LAI_file', 'hc_file', 'SMC_file', 'Vcmax_file', 'Cab_file', 'LIDF_file'});
for i = 1:length(F)
k = find(strcmp(F(i).FileID, strtok(X(:, 1))));
if ~isempty(k)
Expand Down Expand Up @@ -286,7 +286,7 @@
%% soil layer information
SoilLayer.thickness = ModelSettings.DeltZ_R;
SoilLayer.depth = Ztot'; % used in Initial_root_biomass

% NOTE: workspace will be saved, this code block is after the update step.
% (this is to not repeat the save-workspace code).
disp('Finished model initialization');
Expand Down Expand Up @@ -433,10 +433,10 @@

switch options.calc_ebal
case 1
[iter, fluxes, rad, thermal, profiles, soil, RWU, frac] ...
= ebal(iter, options, spectral, rad, gap, ...
leafopt, angles, meteo, soil, canopy, leafbio, xyt, k, profiles, Delt_t, ...
Rl, SoilVariables, VanGenuchten, InitialValues);
[iter, fluxes, rad, thermal, profiles, soil, RWU, frac] ...
= ebal(iter, options, spectral, rad, gap, ...
leafopt, angles, meteo, soil, canopy, leafbio, xyt, k, profiles, Delt_t, ...
Rl, SoilVariables, VanGenuchten, InitialValues);
if options.calc_fluor
if options.calc_vert_profiles
[rad, profiles] = RTMf(spectral, rad, soil, leafopt, canopy, gap, angles, profiles);
Expand Down Expand Up @@ -590,8 +590,7 @@
GasDispersivity = conductivity.calculateGasDispersivity(InitialValues, SoilVariables, P_gg, k_g);

% Srt is both input and output
[SoilVariables, HeatMatrices, HeatVariables, HBoundaryFlux, Rn_SOIL, Evap, EVAP, Trap, r_a_SOIL, Srt, CHK, AVAIL0, Precip] = soilmoisture.solveSoilMoistureBalance(SoilVariables, InitialValues, ForcingData, VaporVariables, GasDispersivity, TimeProperties, SoilProperties, ...
BoundaryCondition, Delt_t, RHOV, DRHOVh, DRHOVT, D_Ta, hN, RWU, fluxes, KT, hOLD, Srt, P_gg);
[SoilVariables, HeatMatrices, HeatVariables, HBoundaryFlux, Rn_SOIL, Evap, EVAP, Trap, r_a_SOIL, Srt, CHK, AVAIL0, Precip] = soilmoisture.solveSoilMoistureBalance(SoilVariables, InitialValues, ForcingData, VaporVariables, GasDispersivity, TimeProperties, SoilProperties, BoundaryCondition, Delt_t, RHOV, DRHOVh, DRHOVT, D_Ta, hN, RWU, fluxes, KT, hOLD, Srt, P_gg);

if BoundaryCondition.NBCh == 1
DSTOR = 0;
Expand All @@ -616,7 +615,7 @@

if ModelSettings.Soilairefc == 1
[AirVariabes, RHS, SAVE, P_gg] = dryair.solveDryAirEquations(SoilVariables, GasDispersivity, TransportCoefficient, InitialValues, VaporVariables, ...
BoundaryCondition, ForcingData, P_gg, P_g, Xah, XaT, Xaa, RHODA, KT, Delt_t);
BoundaryCondition, ForcingData, P_gg, P_g, Xah, XaT, Xaa, RHODA, KT, Delt_t);
else
AirVariabes.KLhBAR = InitialValues.KLhBAR;
AirVariabes.KLTBAR = InitialValues.KLTBAR;
Expand All @@ -631,10 +630,10 @@
if ModelSettings.Thmrlefc == 1
% CHK will be updated
[RHS, SAVE, CHK, SoilVariables] = energy.solveEnergyBalanceEquations(InitialValues, SoilVariables, HeatVariables, TransportCoefficient, ...
AirVariabes, VaporVariables, GasDispersivity, ThermalConductivityCapacity, ...
HBoundaryFlux, BoundaryCondition, ForcingData, DRHOVh, DRHOVT, KL_T, ...
Xah, XaT, Xaa, Srt, L_f, RHOV, RHODA, DRHODAz, L, Delt_t, P_g, P_gg, ...
TOLD, Precip, EVAP, r_a_SOIL, Rn_SOIL, KT, CHK);
AirVariabes, VaporVariables, GasDispersivity, ThermalConductivityCapacity, ...
HBoundaryFlux, BoundaryCondition, ForcingData, DRHOVh, DRHOVT, KL_T, ...
Xah, XaT, Xaa, Srt, L_f, RHOV, RHODA, DRHODAz, L, Delt_t, P_g, P_gg, ...
TOLD, Precip, EVAP, r_a_SOIL, Rn_SOIL, KT, CHK);
end

if max(CHK) < 0.1
Expand Down Expand Up @@ -716,10 +715,9 @@
save([Output_dir, 'STEMMUS_SCOPE_state.mat'], bmiVarNames{:}, "-v7.3", "-nocompression");
end


if strcmp(runMode, 'finalize')
% Load the workspace to be able to finalize the model.
load([OutputPath, 'STEMMUS_SCOPE_state.mat']);
load([OutputPath, 'STEMMUS_SCOPE_state.mat']);
end

if strcmp(runMode, 'finalize') || strcmp(runMode, 'full')
Expand Down
24 changes: 12 additions & 12 deletions src/STEMMUS_SCOPE_exe.m
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
%%%%%%% A function to run STEMMUS_SCOPE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function STEMMUS_SCOPE_exe(config_file, run_mode)
if ~exist('run_mode','var')
if ~exist('run_mode', 'var')
runMode = "full";
else
runMode = run_mode;
Expand All @@ -15,23 +15,23 @@ function STEMMUS_SCOPE_exe(config_file, run_mode)
% If the runMode is "full" or was not provided, the model will run as normal
if strcmp(runMode, "full")
run STEMMUS_SCOPE;

% In interactive mode MATLAB stays open and waits for a new command...

elseif strcmp(runMode, "interactive")
% In interactive mode MATLAB stays open and waits for a new command...

% Define BMI required variable names:
bmiVarNames = {...
'ModelSettings', ... % Model settings struct
'TimeStep', ... % Time step size (in seconds)
'KT', ... % Index of current time step
'SiteProperties', ... % Site properties (e.g. lat, lon)
'fluxes', ... % Atmospheric fluxes
'TT', ... % Soil temperature over depth
}; %#ok
bmiVarNames = {'ModelSettings', ... % Model settings struct
'TimeStep', ... % Time step size (in seconds)
'KT', ... % Index of current time step
'SiteProperties', ... % Site properties (e.g. lat, lon)
'fluxes', ... % Atmospheric fluxes
'TT' ... % Soil temperature over depth
}; %#ok

% ...until finalize has been run, at which point it quits.
while ~strcmp(runMode, "finalize")
runMode = input("\nFinished command. Select run mode: ", "s");

if strcmp(runMode, "initialize") || strcmp(runMode, "update") || strcmp(runMode, "finalize")
% The 'initialize', 'update' and 'finalize' run modes are dispatched to the model.
run STEMMUS_SCOPE;
Expand Down

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