Merge pull request #66 from chrishavlin/low_hanging

Various small fixes and improvements

Projects/bayesian_fitting/functions/process_SeismicModels.m

@@ -23,9 +23,8 @@
 %           lon         longitude - assumed to be positive [degrees East]
 %           z_min       minimum depth for observation range [km]
 %           z_max       maximum depth for observation range [km]
-%          (smooth_rad) half-width of box size in which to average
-%                       observations - if this field is not in location,
-%                       a default value of 0.5 is assumed [degrees E and N]
+%           smooth_rad  half-width of box size in which to average
+%                       observations [degrees]
 %
 %       model_file  string with path to saved .mat file of observations
 %                   This .mat file is expected to contain a single variable

docs/_pages/vbrmethods/visc/xfit_premelt.md

@@ -9,7 +9,7 @@ Steady state flow law for pre-melting viscosity drop following Yamauchi and Take
 
 ## Requires
 
-In addition to the state variable arrays required by the other viscous methods (see [HK2003](/vbrmethods/visc/hk2003/), [HZK2011](/vbrmethods/visc/hzk2011/)), this method also requires a solidus:
+In addition to the state variable arrays required by the other viscous methods (see [HK2003](/vbr/vbrmethods/visc/hk2003/), [HZK2011](/vbr/vbrmethods/visc/hzk2011/)), this method also requires a solidus:
 
 ```matlab
 VBR.in.SV.Tsolidus_K % solidus in degrees K
@@ -43,9 +43,9 @@ VBR.in.viscous.xfit_premelt = Params_Viscous('xfit_premelt');
 disp(VBR.in.viscous.xfit_premelt)
 ```
 
-### eta_dry_method
+### eta_melt_free_method
 
-The parameter, `VBR.in.viscous.xfit_premelt.eta_dry_method`, controls what viscosity method to use to calculate the melt free viscosity. By default, this is set to `xfit_premelt`, in which case it uses the upper mantle fit directly from Yamauchi and Takei (2016). If set to one of the other viscosity mtehods, `HK2003` or `HZK2011`, then the melt free viscosity is calculated using those methods with melt fraction set to 0 and then the near-solidus pre-melting effect is then multiplied on.
+The parameter, `VBR.in.viscous.xfit_premelt.eta_melt_free_method`, controls what viscosity method is used to calculate the melt free viscosity. By default, this is set to `xfit_premelt`, in which case it uses the upper mantle fit directly from Yamauchi and Takei (2016). If set to one of the other viscosity mtehods, `HK2003` or `HZK2011`, then the melt free viscosity is calculated using those methods with melt fraction set to 0 and then the near-solidus pre-melting effect is then multiplied on.
 
 ## Output
 Output is stored in `VBR.out.viscous.xfit_premelt`. Unlike the other viscous methods, `xfit_premelt` only returns a diffusion creep viscosity sub-structure:

release_history.md

@@ -1,34 +1,42 @@
+# v1.0.1
+
+Bug fix release.
+
+## bug fixes
+
+- rename `Project/bayesian_fitting/run.m` to `run_bayes.m` to avoid name conflict.
+
 # v1.0.0
 
 This is the first series-1 release! It is backwards compatible.
 
-## new features 
+## new features
 
 - units metadata: `VBR.in.SV` as well as all output methods now contain a units structure that contains the units for each field. You can also call `SV_input_units()` to get a structure that lists the expected units for each `VBR.in.SV` field.
 - version tracking: after calling `VBR_spine`, all `VBR` structures will have a field, `VBR.version_used` with info on the VBR version that you used.
-- a new function for calculating density as a function of pressure, using an interpolation of experimental measurements on F90 San Carlos olivine, `san_carlos_density_from_pressure`, following Abramson et al., JGR, 1997. Useful for 
+- a new function for calculating density as a function of pressure, using an interpolation of experimental measurements on F90 San Carlos olivine, `san_carlos_density_from_pressure`, following Abramson et al., JGR, 1997. Useful for
 quickly calculating olivine density for a given pressure.
 
 ## bug fixes
 
 (add bug fixes)
 
-## changes 
+## changes
 
-- some of the functions related to non-seismic material properties used in the forward 
-models directory have been moved and renamed. No change in usage, but it is now easier 
+- some of the functions related to non-seismic material properties used in the forward
+models directory have been moved and renamed. No change in usage, but it is now easier
 to use those functions in a piecemeal fashion if desired. See functions in the `density`
-and `thermal_properties` subdirectories within `vbr/vbrCore/fucntions/` for available 
-functions. 
+and `thermal_properties` subdirectories within `vbr/vbrCore/fucntions/` for available
+functions.
 
-# v0.99.4 
+# v0.99.4
 
 maintenance updates (testing, github CI, documentation)
 
-## new features 
+## new features
 
 - `vbr_version()` function, returns the version of the VBRc that you are using
 
 # v <= 0.99.3
 
-release_history.md covers v>0.99.3. 
+release_history.md covers v>0.99.3.

release_notes.md

@@ -1,7 +1 @@
-# v1.0.1
-
-Bug fix release. 
-
-## bug fixes
-
-- rename `Project/bayesian_fitting/run.m` to `run_bayes.m` to avoid name conflict.
+# v1.1.0

vbr/support/is_octave.m

@@ -0,0 +1,8 @@
+function is_octave_bool = is_octave()
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    % is_octave()
+    %
+    % returns 1 if running in Octave, 0 if running in MATLAB 
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    is_octave_bool = exist('OCTAVE_VERSION', 'builtin') ~= 0;
+end

vbr/testing/run_tests.m

@@ -36,7 +36,7 @@
     end
 
     if numel(mfiles) > 0
-        [TestResults, failedCount, SkippedTests] = runTheMfiles(mfiles, test_config);
+        [TestResults, failedCount, SkippedTests, ErrorMessages] = runTheMfiles(mfiles, test_config);
         TestResults.failedCount = failedCount;
         TestResults.n_tests = numel(mfiles);
     else
@@ -49,61 +49,77 @@
     disp('Testing complete.')
     disp(' ')
     if TestResults.failedCount > 0
-        disp('Displaying failed test functions. Please run each one and debug:')
+        disp('Displaying failed test functions:')
         fldz=fieldnames(TestResults);
         for ifi = 1:numel(fldz)
             fld=TestResults.(fldz{ifi});
             if fld==0
                 disp(['    ',fldz{ifi}])
+                ei = ErrorMessages.(fldz{ifi});
+                disp(['        ', ei.identifier, ': ', ei.message])
+
             end
         end
     elseif TestResults.n_tests == 0
         disp('found no tests to run')
     else
-        skfields = fieldnames(SkippedTests);
-        if numel(skfields) > 0
-            for ifield = 1:numel(skfields)
-                reason = SkippedTests.(skfields{ifield});
-                disp('Displaying Skipped tests and reason for skipping:')
-                disp(['    ', skfields{ifield}, " : ", reason])
-            end
-        else
-            disp('all test functions ran successfully')
+        disp('Test functions ran successfully')
+    end
+
+    skfields = fieldnames(SkippedTests);
+    if numel(skfields) > 0
+        for ifield = 1:numel(skfields)
+            reason = SkippedTests.(skfields{ifield});
+            disp(' ')
+            disp('Displaying Skipped tests and reason for skipping:')
+            disp(['    ', skfields{ifield}, " : ", reason])
+            disp(' ')
         end
     end
 
+
 end
 
-function [TestResults,failedCount, SkippedTests] = runTheMfiles(mfiles, test_config)
+function [TestResults,failedCount, SkippedTests, ErrorMessages] = runTheMfiles(mfiles, test_config)
     TestResults=struct();
     SkippedTests = struct();
+    ErrorMessages = struct();
     failedCount=0;
     isOctave = exist('OCTAVE_VERSION', 'builtin') ~= 0;
 
     for ifile = 1:numel(mfiles)
         fname=mfiles(ifile).name;
         if ~strcmp('run_tests.m',fname)
-            [fdir,funcname,ext]=fileparts(fname);
 
+            [fdir,funcname,ext]=fileparts(fname);
+            disp(['    **** Running ', funcname, ' ****'])
             if any(strcmp(test_config.matlab_only, funcname)) && isOctave
                 SkippedTests.(funcname) = "MATLAB Only";
             else
 
                 try
                     testResult=feval(funcname);
-                    if testResult>0
+                    test_error.message = testResult.fail_message;
+                    test_error.identifier = 'VBRc_TEST_ERROR';
+                    if testResult.passed>0
                         disp('    test passed :D'); disp(' ')
                     else
                         failedCount=failedCount+1;
                         disp('    test failed :('); disp(' ')
                     end
-                catch
+                catch ME
+                    err_id = ME.identifier;
+                    err_msg = ME.message;
+                    test_error = ME;
                     disp(['    ',funcname,' failed :('])
-                    disp(['    please run ',funcname,'() and debug.']); disp(' ')
-                    testResult=false;
+                    disp(' ')
+                    disp(['        ', err_id, ': ', err_msg])
+                    disp(' ')
+                    testResult.passed=false;
                     failedCount=failedCount+1;
                 end
-                TestResults.(funcname)=testResult;
+                TestResults.(funcname)=testResult.passed;
+                ErrorMessages.(funcname) = test_error;
             end
         end
     end

vbr/testing/test_fm_plates_001.m

@@ -10,9 +10,10 @@
 %
 % Output
 % ------
-% TestResult   True if passed, False otherwise.
+% TestResult  struct with fields:
+%           .passed         True if passed, False otherwise.
+%           .fail_message   Message to display if false
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-  disp('    **** Running test_fm_plates_001 ****')
 
   %  Load Default Settings
   [settings]=init_settings;
@@ -42,5 +43,6 @@
   % Lithosphere temperature evolution
   [Vars,Info]=Thermal_Evolution(Info,settings);
 
-  TestResult=true;
+  TestResult.passed=true;
+  TestResult.fail_message = '';
 end

vbr/testing/test_fm_plates_002.m

@@ -10,11 +10,12 @@
 %
 % Output
 % ------
-% TestResult   True if passed, False otherwise.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-  disp('    **** Running test_fm_plates_002 ****')
-  disp('         (takes a few minutes)')
-  TestResult=true;
+% TestResult  struct with fields:
+%           .passed         True if passed, False otherwise.
+%           .fail_message   Message to display if false
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  
+  TestResult.passed=true;
+  TestResult.fail_message = '';
   %  Load Default Settings
   [settings]=init_settings;
 
@@ -53,8 +54,10 @@
   % get the diffusivity (make sure it's constant)
   kappa=Vars.Kc ./ (Vars.rho .* Vars.cp);
   if min(kappa(:))<max(kappa(:))
-    TestResult=false;
-    disp('    diffusivity is not constant!!!!!')
+    TestResult.passed=false;
+    msg = '    diffusivity is not constant!!!!!';
+    TestResult.fail_message = msg;
+    disp(msg)
   end
   kappa=min(kappa(:));
 
@@ -73,8 +76,10 @@
   t_cutoffs=[5,Info.tMyrs(end)]; % min/max for transient h space soln
   tmask=(Info.tMyrs>=t_cutoffs(1))&(Info.tMyrs<=t_cutoffs(2));
   if sum(max_err(tmask)>max_err_tol)
-    disp('     half space cooling solution incorrect!!!!!')
-    TestResult=false;
+    msg = '     half space cooling solution incorrect!!!!!';
+    TestResult.passed=false;
+    TestResult.fail_message = msg;
+    disp(msg)
   end
 
 end

vbr/testing/test_fm_plates_003.m

@@ -10,11 +10,12 @@
 %
 % Output
 % ------
-% TestResult   True if passed, False otherwise.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-  disp('    **** Running test_fm_plates_003 ****')
-  disp('         (takes <1 minute)')
-  TestResult=true;
+% TestResult  struct with fields:
+%           .passed         True if passed, False otherwise.
+%           .fail_message   Message to display if false
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  
+  TestResult.passed =true;
+  TestResult.fail_message = '';
   %  Load Default Settings
   [settings]=init_settings;
 
@@ -56,7 +57,9 @@
   % check if it passes
   max_err_tol=1e-5;
   if max_err_tol>max_err_tol
-    disp('     steady state plate solution incorrect!!!!!')
-    TestResult=false;
+    msg = '     steady state plate solution incorrect!!!!!'
+    disp(msg)
+    TestResult.passed=false;
+    TestResult.fail_message = msg;
   end
 end

vbr/testing/test_fm_plates_004_solidus.m

@@ -10,14 +10,16 @@
   %
   % Output
   % ------
-  % TestResult   True if passed, False otherwise.
-  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-  disp('    **** Running test_fm_plates_004_solidus ****')
-
+  % TestResult  struct with fields:
+  %           .passed         True if passed, False otherwise.
+  %           .fail_message   Message to display if false
+  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  
+
   % Note that the SoLiquidus function now lives in the vbrCore/functions/thermal_properties/
-  % directory. 
-
-  TestResult=true;
+  % directory.
+
+  TestResult.passed =true;
+  TestResult.fail_message = '';
 
   F = 0.05;
   z = linspace(0,200,100)*1e3;

vbr/testing/test_fm_plates_005_box.m

@@ -10,10 +10,13 @@
   %
   % Output
   % ------
-  % TestResult   True if passed, False otherwise.
+  % TestResult  struct with fields:
+  %           .passed         True if passed, False otherwise.
+  %           .fail_message   Message to display if false
   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-  disp('    **** Running test_fm_plates_005_box ****')
-  TestResult=true;
+
+  TestResult.passed =true;
+  TestResult.fail_message = '';
   % Parameter sweep settings
   %  define parameter sweep here. var1name must match EXACTLY a field in
   %  settings structure. var1 must be defined, var2 lines can be

vbr/testing/test_fm_plates_006_thermoprops.m

@@ -10,10 +10,13 @@
   %
   % Output
   % ------
-  % TestResult   True if passed, False otherwise.
+  % TestResult  struct with fields:
+  %           .passed         True if passed, False otherwise.
+  %           .fail_message   Message to display if false
   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-  disp('    **** Running test_fm_plates_006_thermoprops ****')
-  TestResult=true;
+
+  TestResult.passed =true;
+  TestResult.fail_message = '';
 
   z=transpose(linspace(0,400,100)*1e3);
   P0=1e5;
@@ -25,7 +28,7 @@
   T=1400*z/z_L;
   T(z>z_L)=(z(z>z_L)-z_L) * dTdz_ad + max(T(z<=z_L));
   T=T+273;
-  PropTypes= {'con';'P_dep';'T_dep';'PT_dep'};  
+  PropTypes= {'con';'P_dep';'T_dep';'PT_dep'};
   P1=zeros(numel(z),4);
   P2=zeros(numel(z),4);
 
@@ -37,14 +40,20 @@
 % [Rho,Cp,Kc,P]
     diff=sum(abs(P1(:)-P2(:))./P1(:));
     if diff > 0
-      TestResult=false;
-      disp('        ThermodynamicProps not matching MaterialProperties')
+      TestResult.passed=false;
+      msg = '        ThermodynamicProps not matching MaterialProperties';
+      TestResult.fail_message = msg;
+      disp(msg)
     elseif sum(isnan(P1))>0
-      TestResult=false;
-      disp('        ThermodynamicProps solution contains nans')
+      TestResult.passed=false;
+      msg = '        ThermodynamicProps solution contains nans';
+      disp(msg)
+      TestResult.fail_message = msg;
     elseif sum(isnan(P2))>0
-      TestResult=false;
-      disp('        MaterialProperties solution contains nans')
+      TestResult.passed=false;
+      msg = '        MaterialProperties solution contains nans';
+      disp(msg)
+      TestResult.fail_message = msg;
     end
   end