Merge pull request #30 from ltrotter/master

v2.1
wknoben · Apr 25, 2022 · f71aec4 · f71aec4
2 parents ee6524c + e8b6807
commit f71aec4
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Showing 74 changed files with 9,759 additions and 6,252 deletions.
diff --git a/.gitignore b/.gitignore
diff --git a/.zenodo.json b/.zenodo.json
@@ -10,5 +10,6 @@
             "affiliation": "University of Saskatchewan",
             "name": "Knoben, Wouter"
         }
-    ]
+    ],
+    "title": "MARRMoT"
 }
diff --git a/BMI/Config/BMI_testcase_m01_BuffaloRiver_TN_USA.mat b/BMI/Config/BMI_testcase_m01_BuffaloRiver_TN_USA.mat
diff --git a/BMI/Runners/marrmotRunner_testCase.m b/BMI/Runners/marrmotRunner_testCase.m
@@ -16,7 +16,7 @@
 forcing.precip       = data_MARRMoT_examples.precipitation;
 forcing.temp         = data_MARRMoT_examples.temperature;
 forcing.pet          = data_MARRMoT_examples.potential_evapotranspiration;
-forcing.delta_t_days = 1;   % 1 [d]
+forcing.delta_t      = 1;   % 1 [d]
 forcing.time_unit    = 'day';
 
 % 'time_start' & 'time_end' are a vector with starting/end date

diff --git a/BMI/lib/marrmotBMI.m b/BMI/lib/marrmotBMI.m
@@ -1,4 +1,4 @@
-classdef m01BMI < BMI
+classdef marrmotBMI < BMI
     % MARRMoT m01 implemented as a BMI model
 
 
@@ -18,8 +18,7 @@
                          'pet',0,...                % time series of potential evapotranspiration
                          'delta_t',0,...            % time step size in [days]
                          'time_unit','str');        % string with time units
-        solver = struct('name','str',...            % string with solver function name
-                        'resnorm_tolerance',0,...   % approximation accuracy
+        solver = struct('resnorm_tolerance',0,...   % approximation accuracy
                         'resnorm_maxiter',0);       % max number of re-runs
 
             % Output storage for a single time-step
@@ -64,7 +63,7 @@ function initialize(obj,path)
             obj.model_name = model_name;
             obj.startTime  = time_start;
             obj.endTime    = time_end;
-            obj.dt         = forcing.delta_t_days;
+            obj.dt         = forcing.delta_t;
             obj.time_unit  = forcing.time_unit;
             obj.forcing    = forcing;
             obj.solver     = solver;
@@ -83,15 +82,15 @@ function update(obj)
             input_forcing.precip       = obj.forcing.precip(obj.time);
             input_forcing.temp         = obj.forcing.temp(obj.time);
             input_forcing.pet          = obj.forcing.pet(obj.time);
-            input_forcing.delta_t_days = obj.forcing.delta_t;
-                
+            input_forcing.delta_t      = obj.forcing.delta_t;
+
            % Run model for 1 time step
+            m = feval(obj.model_name);
             [output_ex,...                                                  % Fluxes leaving the model: simulated flow (Q) and evaporation (Ea)
              output_in,...                                                  % Internal model fluxes
              output_ss,...                                                  % Internal storages
              output_wb] = ...                                               % Water balance check
-                                feval(obj.model_name,...                    % Model function name
-                                      input_forcing,...                     % Time series of climatic fluxes in simulation period
+                         m.get_output(input_forcing,...                     % Time series of climatic fluxes in simulation period
                                       obj.store_cur,...                     % Initial storages
                                       obj.parameters,...                    % Parameter values
                                       obj.solver);                          % Solver settings

diff --git a/Changelog.txt b/Changelog.txt
@@ -1,11 +1,15 @@
 This file highlights the most important changes made during version updates. The changes listed here are limited to those changes that directly impact model code. Changes to comments or workflow example files are not included.
 
+=== v2.1 ===
+Updated from v2.0 to v2.1 to incorporate changes in the root-finding method.
+
+- Inclusion of NewtonRaphson solver before fsolve to speeed up the framework
 
 === v2.0 ===
-Updated from v1 to v2 to incorporate the new object-oriented structure
+Updated from v1.- to v2.- to incorporate the new object-oriented structure
 
 === v1.4 ===
-Updated from v1.3 to v1.4 to incorporate bug fixes in a few models and to publish m_47. Main changes:
+Updated from v1.2 to v1.3 to incorporate bug fixes in a few models and to publish m_47. Main changes:
 
 - Added m_47 and necessary additional flux files.
 
@@ -17,8 +21,6 @@ Updated from v1.3 to v1.4 to incorporate bug fixes in a few models and to publis
 
 - Fixed error in m_37: added costraint that Smax>0, this otherwise causes numerical instability to the logistic smoother.
 
-- Fixed a typo in the sign of the exponent of 'percolation_3', affecting m_07
-
 === v1.3 ===
 Updated from v1.2 to v1.3 to incorporate a bug fix in 'interflow_9'. Main changes:
 

diff --git a/MARRMoT/Functions/Flux smoothing/smoothThreshold_storage_logistic.m b/MARRMoT/Functions/Flux smoothing/smoothThreshold_storage_logistic.m
@@ -39,6 +39,7 @@
 end
 
 % Calculate multiplier
+Smax = max(Smax,0);   % this avoids numerical instabilities when Smax<0
 if r*Smax == 0
     out = 1 ./ (1+exp((S-Smax+r*e*Smax)/(r)));
 else