Matlab interface (new) test suite

.github/workflows/main.yml

@@ -19,6 +19,46 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  matlab-test:
+    name: Run MATLAB Test Script
+    runs-on: ubuntu-latest
+    env:
+      LD_PRELOAD: /usr/lib/x86_64-linux-gnu/libstdc++.so.6
+      CANTERA_ROOT: /home/runner/work/cantera/cantera
+      CANTERA_DATA: /home/runner/work/cantera/cantera/data
+    steps:
+      - uses: actions/checkout@v3
+        name: Checkout the repository
+        with:
+          submodules: recursive
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          architecture: x64
+      - name: Install Apt dependencies
+        run: |
+          sudo apt update
+          sudo apt install libboost-dev gfortran libopenmpi-dev libpython3-dev \
+          libblas-dev liblapack-dev libhdf5-dev
+          gcc --version
+      - name: Upgrade pip
+        run: python3 -m pip install -U pip setuptools wheel
+      - name: Install Python dependencies
+        run: |
+          python3 -m pip install ruamel.yaml scons==3.1.2
+      - name: Build Cantera
+        run: |
+          python3 `which scons` build env_vars=all -j2 debug=n --debug=time \
+          cc_flags=-D_GLIBCXX_ASSERTIONS
+      - name: Set up MATLAB
+        uses: matlab-actions/setup-matlab@v1
+      - name: Run tests
+        uses: matlab-actions/run-tests@v1
+        with:
+          select-by-folder: /home/runner/work/cantera/cantera/test/matlab_experimental
+
+
   ubuntu-multiple-pythons:
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}

.gitignore

@@ -16,6 +16,7 @@ include/cantera/base/system.h.gch
 include/cantera/ext/
 interfaces/matlab/ctpath.m
 interfaces/matlab/Contents.m
+interfaces/matlab_experimental/ctRoot.m
 src/extensions/delegator.h
 stage/
 .sconsign.dblite

interfaces/matlab_experimental/Base/Solution.m

@@ -90,7 +90,6 @@
         function delete(s)
             % Delete :mat:class:`Solution` object.
             ctFunc('soln_del', s.phaseID);
-            disp('Solution class object has been deleted');
         end
 
     end

test/matlab_experimental/ctTestKinetics.m

@@ -0,0 +1,162 @@
+classdef ctTestKinetics < matlab.unittest.TestCase
+
+    properties
+        phase
+        rtol = 1e-6;
+        atol = 1e-8;
+    end
+
+    methods (TestClassSetup)
+
+        function testSetUp(self)
+            ctTestSetUp
+        end
+
+    end
+
+    methods (TestClassTeardown)
+
+        function testTearDown(self)
+            ctCleanUp
+            ctTestTearDown
+        end
+
+    end
+
+    methods (TestMethodSetup)
+
+        function createPhase(self)
+            src = 'h2o2.yaml';
+            id = 'ohmech';
+            transport = 'none';
+            self.phase = Solution(src, id, transport);
+            self.phase.TPX = {800, 2 * OneAtm, ...
+                              [0.1, 1e-4, 1e-5, 0.2, 2e-4, 0.3, 1e-6, 5e-5, 0.4, 0]};
+        end
+
+    end
+
+    methods (TestMethodTeardown)
+
+        function deleteSolution(self)
+            clear self.phase;
+        end
+
+    end
+
+    methods (Test)
+
+        function testCounts(self)
+            self.verifyEqual(self.phase.nReactions, 29);
+            self.verifyEqual(self.phase.nTotalSpecies, 10);
+            self.verifyEqual(self.phase.nPhases, 1);
+
+            self.assumeFail('Fails because Kinetics.reactionPhaseIndex is missing')
+            self.verifyEqual(self.phase.reactionPhaseIndex, 0);
+        end
+
+        function testIsReversible(self)
+            self.assumeFail('Fails because of incorrect reaction indexing');
+
+            for i = 1:self.phase.nReactions
+                self.verifyTrue(self.phase.isReversible(i));
+            end
+            % To do: test on a mechanism where not all reactions are
+            % reversible
+
+        end
+
+        function testMultipler(self)
+
+            f0 = self.phase.forwardRatesOfProgress;
+            r0 = self.phase.reverseRatesOfProgress;
+
+            self.phase.setMultiplier(1, 2.0);
+            self.phase.setMultiplier(7, 0.1);
+
+            f1 = self.phase.forwardRatesOfProgress;
+            r1 = self.phase.reverseRatesOfProgress;
+
+            self.verifyEqual(2 .* f0(1), f1(1), 'AbsTol', self.atol);
+            self.verifyEqual(0.1 .* f0(7), f1(7), 'AbsTol', self.atol);
+            self.verifyEqual(2 .* r0(1), r1(1), 'AbsTol', self.atol);
+            self.verifyEqual(0.1 .* r0(7), r1(7), 'AbsTol', self.atol);
+
+            for i = 1:self.phase.nReactions
+
+                if i ~= 1 && i ~= 7
+                    self.verifyEqual(f0(i), f1(i), 'AbsTol', self.atol);
+                    self.verifyEqual(r0(i), r1(i), 'AbsTol', self.atol);
+                end
+
+            end
+
+            self.phase.setMultiplier(0.5);
+            f2 = self.phase.forwardRatesOfProgress;
+            r2 = self.phase.reverseRatesOfProgress;
+            tol = ones(1, self.phase.nReactions) .* self.atol;
+            self.verifyEqual(0.5 .* f0, f2, 'AbsTol', tol);
+            self.verifyEqual(0.5 .* r0, r2, 'AbsTol', tol);
+
+        end
+
+        function testReactionEquations(self)
+            self.verifyEqual(self.phase.nReactions, ...
+                             length(self.phase.reactionEquations));
+            s = strsplit(self.phase.reactionEquation(19), '<=>');
+            r = s{1};
+            p = s{2};
+            self.verifySubstring(r, 'H');
+            self.verifySubstring(r, 'H2O2');
+            self.verifySubstring(p, 'HO2');
+            self.verifySubstring(p, 'H2');
+
+        end
+
+        function testStoichCoeffs(self)
+            self.assumeFail(['Fails because StoichCoeffs methods do not', ...
+                             ' convert species names to species indices']);
+
+            nu_r = self.phase.reactantStoichCoeffs;
+            nu_p = self.phase.productStoichCoeffs;
+
+            function checkReactant(s, i, val)
+                k = self.phase.kineticsSpeciesIndex(s);
+                self.verifyEqual(self.phase.reactantStoichCoeffs(s, i), ...
+                                 val);
+                self.verifyEqual(self.phase.reactantStoichCoeffs(k, i), ...
+                                 val);
+                self.verifyEqual(nu_r(k, i), val);
+            end
+
+            function checkProduct(s, i, val)
+                k = self.phase.kineticsSpeciesIndex(s);
+                self.verifyEqual(self.phase.productStoichCoeffs(s, i), ...
+                                 val);
+                self.verifyEqual(self.phase.productStoichCoeffs(k, i), ...
+                                 val);
+                self.verifyEqual(nu_p(k, i), val);
+            end
+
+            % H + H2O2 <=> HO2 + H2
+            checkReactant('H', 19, 1)
+            checkReactant('H2O2', 19, 1)
+            checkReactant('HO2', 19, 0)
+            checkReactant('H2', 19, 0)
+
+            checkProduct('H', 19, 0)
+            checkProduct('H2O2', 19, 0)
+            checkProduct('HO2', 19, 1)
+            checkProduct('H2', 19, 1)
+
+            % 2 O + M <=> O2 + M
+            checkReactant('O', 1, 2)
+            checkReactant('O2', 1, 0)
+            checkProduct('O', 1, 0)
+            checkProduct('O2', 1, 1)
+
+        end
+
+    end
+
+end

test/matlab_experimental/ctTestPath.m

@@ -0,0 +1,23 @@
+% ctTestPath.m
+% Set up environment for testing the Cantera Matlab interface
+% from within the Cantera source tree. Run this file from the
+% root of the Cantera source tree, for example:
+%
+%    cd ~/src/cantera
+%    run interfaces/matlab_experimental/testpath.m
+
+% get the list of directories on the Matlab path
+dirs = split(path, pathsep);
+
+% if 'cantera' is already in the path, remove it
+for i = 1:length(dirs)
+    if contains(dirs{i}, 'CANTERA', 'IgnoreCase', true)
+        rmpath(dirs{i});
+    end
+end
+
+cantera_root = getenv('CANTERA_ROOT');
+
+% Add the Cantera toolbox to the Matlab path
+addpath(genpath([cantera_root, '/interfaces/matlab_experimental']));
+addpath(genpath([cantera_root, '/test/matlab_experimental']));

test/matlab_experimental/ctTestSetUp.m

@@ -0,0 +1,27 @@
+clear all
+
+% Copy library to test folder
+ctTestPath;
+
+% Load Cantera
+rootDir = getenv('CANTERA_ROOT');
+
+if ispc
+    ctName = '/build/lib/cantera_shared.dll';
+elseif ismac
+    ctName = '/build/lib/libcantera_shared.dylib';
+elseif isunix
+    ctName = '/build/lib/libcantera_shared.so';
+end
+% Load Cantera
+if ~libisloaded('libcantera_shared')
+    [~, warnings] = loadlibrary([rootDir, ctName], ...
+                                [rootDir, '/include/cantera/clib/ctmatlab.h'], ...
+                                'includepath', [rootDir, '/include'], ...
+                                'addheader', 'ct', 'addheader', 'ctfunc', ...
+                                'addheader', 'ctmultiphase', 'addheader', ...
+                                'ctonedim', 'addheader', 'ctreactor', ...
+                                'addheader', 'ctrpath', 'addheader', 'ctsurf');
+end
+
+disp('Cantera is loaded for test');

test/matlab_experimental/ctTestTearDown.m

@@ -0,0 +1,4 @@
+clear all
+% Unload Cantera
+unloadlibrary('libcantera_shared');
+disp('Cantera has been unloaded');