Removed the IDAS solver (closes #1515).

CMakeLists.txt

@@ -861,7 +861,6 @@ SET(PLUGINS
     solver/ForwardEulerSolver
     solver/FourthOrderRungeKuttaSolver
     solver/HeunSolver
-    solver/IDASSolver
     solver/KINSOLSolver
     solver/SecondOrderRungeKuttaSolver
 

doc/downloads/index.js

@@ -38,7 +38,7 @@ var jsonData = { "versions": [
                      ],
                      "changes": [
                        { "change": "<strong>General:</strong> improved our support for <a href=\"https://en.wikipedia.org/wiki/Differential_algebraic_equation\">DAE</a> models (see issues <a href=\"https://github.com/opencor/opencor/issues/188\">#188</a> and <a href=\"https://github.com/opencor/opencor/issues/536\">#536</a>)." },
-                       { "change": "<strong>Solvers:</strong> can now parameterise the <a href=\"https://computation.llnl.gov/projects/sundials/kinsol\">KINSOL</a> solver (see issue <a href=\"https://github.com/opencor/opencor/issues/1510\">#1510</a>). Don't reset the <a href=\"https://computation.llnl.gov/projects/sundials/kinsol\">KINSOL</a> solver on consecutive runs and improved its implementation (see issue <a href=\"https://github.com/opencor/opencor/issues/1512\">#1512</a>)." },
+                       { "change": "<strong>Solvers:</strong> can now parameterise the <a href=\"https://computation.llnl.gov/projects/sundials/kinsol\">KINSOL</a> solver (see issue <a href=\"https://github.com/opencor/opencor/issues/1510\">#1510</a>). Don't reset the <a href=\"https://computation.llnl.gov/projects/sundials/kinsol\">KINSOL</a> solver on consecutive runs and improved its implementation (see issue <a href=\"https://github.com/opencor/opencor/issues/1512\">#1512</a>). Removed the <a href=\"https://computation.llnl.gov/projects/sundials/idas\">IDAS</a> solver (see issue <a href=\"https://github.com/opencor/opencor/issues/1515\">#1515</a>)." },
                        { "change": "<strong>Simulation Experiment view:</strong> don’t incorrectly mark a CellML file as modified (see issue <a href=\"https://github.com/opencor/opencor/issues/1513\">#1513</a>)." },
                        { "change": "<strong>Third-party libraries:</strong> upgraded the <a href=\"http://computation.llnl.gov/projects/sundials\">SUNDIALS</a> library to version 3.1.0 (see issue <a href=\"https://github.com/opencor/opencor/issues/1507\">#1507</a>)." }
                      ]

doc/user/index.html

@@ -94,7 +94,6 @@
                             <li><a href="plugins/solver/ForwardEulerSolver.html">ForwardEulerSolver</a></li>
                             <li><a href="plugins/solver/FourthOrderRungeKuttaSolver.html">FourthOrderRungeKuttaSolver</a></li>
                             <li><a href="plugins/solver/HeunSolver.html">HeunSolver</a></li>
-                            <li><a href="plugins/solver/IDASSolver.html">IDASSolver</a></li>
                             <li><a href="plugins/solver/KINSOLSolver.html">KINSOLSolver</a></li>
                             <li><a href="plugins/solver/SecondOrderRungeKuttaSolver.html">SecondOrderRungeKuttaSolver</a></li>
                         </ul>

doc/user/knownLimitations.html

@@ -35,7 +35,6 @@
                     <li>It may incorrectly (in)validate certain <a href="https://www.cellml.org/">CellML</a> files.</li>
                 </ul>
             </li>
-            <li>Ideally, models consisting of <a href="https://en.wikipedia.org/wiki/Differential_algebraic_equation">differential algebraic equations</a> (DAEs) would be run using a DAE solver, but this is not currently supported. However, a DAE model is nothing more than a system of <a href="https://en.wikipedia.org/wiki/Ordinary_differential_equation">ordinary differential equations</a> (ODEs) and <a href="https://en.wikipedia.org/wiki/Nonlinear_system#Nonlinear_algebraic_equations">non-linear algebraic (NLA) equations</a>. So, for now, DAE models can be run using both an ODE and an NLA solver.</li>
         </ul>
 
         <div class="section">

doc/user/plugins/index.html

@@ -160,7 +160,6 @@
             <li><strong><a href="solver/ForwardEulerSolver.html">ForwardEulerSolver</a>:</strong> a plugin that implements the <a href="https://en.wikipedia.org/wiki/Euler_method">Forward Euler method</a> to solve ODEs.</li>
             <li><strong><a href="solver/FourthOrderRungeKuttaSolver.html">FourthOrderRungeKuttaSolver</a>:</strong> a plugin that implements the fourth-order <a href="https://en.wikipedia.org/wiki/Runge–Kutta_methods">Runge-Kutta method</a> to solve ODEs.</li>
             <li><strong><a href="solver/HeunSolver.html">HeunSolver</a>:</strong> a plugin that implements the <a href="https://en.wikipedia.org/wiki/Heun's_method">Heun's method</a> to solve ODEs.</li>
-            <li><strong><a href="solver/IDASSolver.html">IDASSolver</a>:</strong> a plugin that uses <a href="http://computation.llnl.gov/projects/sundials/idas">IDAS</a> to solve DAEs.</li>
             <li><strong><a href="solver/KINSOLSolver.html">KINSOLSolver</a>:</strong> a plugin that uses <a href="http://computation.llnl.gov/projects/sundials/kinsol">KINSOL</a> to solve non-linear algebraic systems.</li>
             <li><strong><a href="solver/SecondOrderRungeKuttaSolver.html">SecondOrderRungeKuttaSolver</a>:</strong> a plugin that implements the second-order <a href="https://en.wikipedia.org/wiki/Runge–Kutta_methods">Runge-Kutta method</a> to solve ODEs.</li>
         </ul>

doc/user/plugins/simulation/SimulationExperimentView.html

@@ -24,7 +24,7 @@
         </p>
 
         <p>
-            A CellML file describes either a system of <a href = "https://en.wikipedia.org/wiki/Ordinary_differential_equation">ordinary differential equations</a> (ODEs) or <a href="https://en.wikipedia.org/wiki/Differential_algebraic_equation">differential algebraic equations</a> (DAEs). That system may be <a href="https://en.wikipedia.org/wiki/Nonlinear_system">non-linear</a>.
+            A CellML file describes either a system of <a href = "https://en.wikipedia.org/wiki/Ordinary_differential_equation">ordinary differential equations</a> (ODEs) or <a href="https://en.wikipedia.org/wiki/Differential_algebraic_equation">differential algebraic equations</a> (DAEs).
         </p>
 
         <div class="section">
@@ -217,7 +217,7 @@
         </div>
 
         <p>
-            To simulate a <a href="https://en.wikipedia.org/wiki/Differential_algebraic_equation">DAE</a> model is similar to simulating an <a href = "https://en.wikipedia.org/wiki/Ordinary_differential_equation">ODE</a> model, except that OpenCOR only offers one DAE solver (<a href="http://computation.llnl.gov/projects/sundials/idas">IDAS</a>) at this stage:
+            To simulate a <a href="https://en.wikipedia.org/wiki/Differential_algebraic_equation">DAE</a> model is similar to simulating an <a href = "https://en.wikipedia.org/wiki/Ordinary_differential_equation">ODE</a> model, except that OpenCOR will also need to solve one or several systems of <a href="https://en.wikipedia.org/wiki/Nonlinear_system#Nonlinear_algebraic_equations">non-linear algebraic</a> (NLA) equations:
         </p>
 
         <p class="center">

doc/user/plugins/solver/KINSOLSolver.html

@@ -19,9 +19,48 @@
         </script>
 
         <p>
-            The KINSOLSolver plugin uses <a href="http://computation.llnl.gov/projects/sundials/kinsol">KINSOL</a> to solve non-linear systems. It does not require any kind of customisation.
+            The KINSOLSolver plugin uses <a href="http://computation.llnl.gov/projects/sundials/kinsol">KINSOL</a> to solve systems of NLA equations and it can be customised through the following properties:
         </p>
 
+        <ul>
+            <li>
+                <strong>Maximum number of iterations:</strong> the maximum number of iterations used by the solver to solve the system (default: <code>200</code>).
+            </li>
+        </ul>
+
+        <ul>
+            <li>
+                <strong>Linear solver:</strong> the linear solver used by the solver (default: <code>Dense</code>).
+
+                <p class="nomargins note note1">
+                    <code>Dense</code>, <code>Banded</code>, <code>GMRES</code>, <code>BiCGStab</code> or <code>TFQMR</code> can be used.
+                </p>
+                <p class="nomargins note note2">
+                    <code>Banded</code> requires specifying both an upper and a lower half-bandwidth value.
+                </p>
+            </li>
+        </ul>
+
+        <ul>
+            <li>
+                <strong>Upper half-bandwidth:</strong> the upper half-bandwidth value used by the <code>Banded</code> linear solver (default: <code>0</code>).
+
+                <p class="nomargins note">
+                    the upper half-bandwidth value must be between <code>0</code> and <code>n-1</code> with <code>n</code> the number of NLA equations in the system.
+                </p>
+            </li>
+        </ul>
+
+        <ul>
+            <li>
+                <strong>Lower half-bandwidth:</strong> the lower half-bandwidth value used by the <code>Banded</code> linear solver (default: <code>0</code>).
+
+                <p class="nomargins note">
+                    the lower half-bandwidth value must be between <code>0</code> and <code>n-1</code> with <code>n</code> the number of NLA equations in the system.
+                </p>
+            </li>
+        </ul>
+
         <script type="text/javascript">
             copyright("../../..");
         </script>

doc/user/res/menu.js

@@ -36,7 +36,6 @@ function headerAndContentsMenu(pageName, relativePath) {
                                 { "level": 2, "label": "ForwardEulerSolver", "link": "user/plugins/solver/ForwardEulerSolver.html", "subMenuItem": true },
                                 { "level": 2, "label": "FourthOrderRungeKuttaSolver", "link": "user/plugins/solver/FourthOrderRungeKuttaSolver.html", "subMenuItem": true },
                                 { "level": 2, "label": "HeunSolver", "link": "user/plugins/solver/HeunSolver.html", "subMenuItem": true },
-                                { "level": 2, "label": "IDASSolver", "link": "user/plugins/solver/IDASSolver.html", "subMenuItem": true },
                                 { "level": 2, "label": "KINSOLSolver", "link": "user/plugins/solver/KINSOLSolver.html", "subMenuItem": true },
                                 { "level": 2, "label": "SecondOrderRungeKuttaSolver", "link": "user/plugins/solver/SecondOrderRungeKuttaSolver.html", "subMenuItem": true },
                                 { "level": 1, "label": "Tools", "subMenuHeader": true },

doc/user/whatIsNew.html

@@ -19,7 +19,7 @@
             headerAndContentsMenu("What Is New?", "..");
 
             var versions = jsonData.versions;
-            var typeWidths = { "Added": 37, "Improved": 51, "Fixed": 31 };
+            var typeWidths = { "added": 37, "improved": 51, "fixed": 31 };
 
             for (var versionIndex = 0; versionIndex < versions.length; ++versionIndex) {
                 var version = versions[versionIndex];
@@ -73,13 +73,15 @@
                                 for (var subEntryIndex = 0; subEntryIndex < subEntries.length; ++subEntryIndex) {
                                     var subEntry = subEntries[subEntryIndex];
 
-                                    document.write("                    <li><img src=\"res/pics/"+subEntry.type.toLowerCase()+".png\" class=\"vcenter\" width="+typeWidths[subEntry.type]+" height=15> "+subEntry.description+"</li>\n");
+                                    document.write("                    <li><img src=\"res/pics/"+subEntry.type+".png\" class=\"vcenter\" width="+typeWidths[subEntry.type]+" height=15> "+subEntry.description+"</li>\n");
                                 }
 
                                 document.write("                </ul>\n");
                                 document.write("            </li>\n");
+                            } else if (entry.type === "comment") {
+                                document.write("            <li>"+entry.description+"</li>\n");
                             } else {
-                                document.write("            <li><img src=\"res/pics/"+entry.type.toLowerCase()+".png\" class=\"vcenter\" width="+typeWidths[entry.type]+" height=15> "+entry.description+"</li>\n");
+                                document.write("            <li><img src=\"res/pics/"+entry.type+".png\" class=\"vcenter\" width="+typeWidths[entry.type]+" height=15> "+entry.description+"</li>\n");
                             }
                         }