Example 1 with VCCMeshSequence
use of org.vcell.solver.comsol.model.VCCMeshSequence in project vcell by virtualcell.
the class ComsolServiceScripting method run.
// private String tojs(String[] a){
// StringBuffer buffer = new StringBuffer();
// buffer.append("[");
// for (int i=0;i<a.length;i++){
// buffer.append("'"+a[i]+"'");
// if (i<a.length-1){
// buffer.append(",");
// }
// }
// buffer.append("]");
// return buffer.toString();
// }
private void run(ScriptEngine engine, VCCModel vccModel, File reportFile, File javaFile, File mphFile, File jsFile) throws ScriptException, IOException {
StringBuffer buffer = new StringBuffer();
// ModelUtil.initStandalone(true);
buffer.append("com.comsol.model.util.ModelUtil.initStandalone(true);" + "\n");
// Model model = ModelUtil.create(vccModel.name);
buffer.append("model = com.comsol.model.util.ModelUtil.create('" + vccModel.name + "');" + "\n");
// // model.modelPath(vccModel.modelpath);
// buffer.append( "model.modelPath('"+vccModel.modelpath+"');" + "\n");
// model.comments(vccModel.comments);
buffer.append("model.comments('" + vccModel.comments.replaceAll("\n", " ") + "');" + "\n");
for (VCCModelNode modelNode : vccModel.modelnodes) {
// model.modelNode().create(modelNode.name);
buffer.append("model.modelNode().create('" + modelNode.name + "');" + "\n");
}
boolean bBeforeSelections = true;
for (VCCGeomSequence geomSequence : vccModel.geometrysequences) {
// model.geom().create(geomSequence.name, geomSequence.dim);
buffer.append("model.geom().create('" + geomSequence.name + "'," + geomSequence.dim + ");" + "\n");
for (VCCGeomFeature geomFeature : geomSequence.geomfeatures) {
switch(geomFeature.type) {
case Circle:
{
buffer.append("print('geomFeature Circle named " + geomFeature.name + "');" + "\n");
VCCCircle circle = (VCCCircle) geomFeature;
// model.geom(geomSequence.name) .create(circle.name, "Circle");
buffer.append("model.geom('" + geomSequence.name + "').create('" + circle.name + "','Circle');" + "\n");
// model.geom(geomSequence.name) .feature(circle.name) .set("selresult", "on");
buffer.append("model.geom('" + geomSequence.name + "').feature('" + circle.name + "').set('selresult','on');" + "\n");
// model.geom(geomSequence.name) .feature(circle.name) .set("pos", circle.pos);
buffer.append("model.geom('" + geomSequence.name + "').feature('" + circle.name + "').set('pos', " + tojs(circle.pos) + ");" + "\n");
// model.geom(geomSequence.name) .feature(circle.name) .set("r", circle.r);
buffer.append("model.geom('" + geomSequence.name + "').feature('" + circle.name + "').set('r', '" + circle.r + "');" + "\n");
break;
}
case Sphere:
{
buffer.append("print('geomFeature Sphere named " + geomFeature.name + "');" + "\n");
VCCSphere sphere = (VCCSphere) geomFeature;
// model.geom(geomSequence.name) .create(sphere.name, "Sphere");
buffer.append("model.geom('" + geomSequence.name + "').create('" + sphere.name + "','Sphere');" + "\n");
// model.geom(geomSequence.name) .feature(sphere.name) .set("pos", sphere.pos);
buffer.append("model.geom('" + geomSequence.name + "').feature('" + sphere.name + "').set('pos', " + tojs(sphere.pos) + ");" + "\n");
// model.geom(geomSequence.name) .feature(sphere.name) .set("r", sphere.r);
buffer.append("model.geom('" + geomSequence.name + "').feature('" + sphere.name + "').set('r', " + sphere.r + ");" + "\n");
break;
}
case Square:
{
VCCSquare square = (VCCSquare) geomFeature;
// model.geom(geomSequence.name) .create(square.name, "Square");
buffer.append("model.geom('" + geomSequence.name + "').create('" + square.name + "','Square');" + "\n");
// buffer.append( "model.geom('"+geomSequence.name+"').feature('"+square.name+"').set('selresult','on');" + "\n");
break;
}
case Block:
{
buffer.append("print('geomFeature Block named " + geomFeature.name + "');" + "\n");
VCCBlock block = (VCCBlock) geomFeature;
// model.geom(geomSequence.name) .create(block.name, "Block");
buffer.append("model.geom('" + geomSequence.name + "').create('" + block.name + "','Block');" + "\n");
// model.geom(geomSequence.name) .feature(block.name) .set("pos", block.pos);
buffer.append("model.geom('" + geomSequence.name + "').feature('" + block.name + "').set('pos', " + tojs(block.pos) + ");" + "\n");
// model.geom(geomSequence.name) .feature(block.name) .set("size", bock.size);
buffer.append("model.geom('" + geomSequence.name + "').feature('" + block.name + "').set('size', " + tojs(block.size) + ");" + "\n");
break;
}
case Difference:
{
buffer.append("print('geomFeature Difference named " + geomFeature.name + "');" + "\n");
VCCDifference diff = (VCCDifference) geomFeature;
// model.geom(geomSequence.name) .create(diff.name, "Difference");
buffer.append("model.geom('" + geomSequence.name + "').create('" + diff.name + "','Difference');" + "\n");
// model.geom(geomSequence.name) .feature(diff.name) .set("selresult", "on");
buffer.append("model.geom('" + geomSequence.name + "').feature('" + diff.name + "').set('selresult','on');" + "\n");
ArrayList<String> inputNames = new ArrayList<String>();
for (VCCGeomFeature feature : diff.input) {
inputNames.add(feature.name);
}
String[] inputSet = inputNames.toArray(new String[0]);
ArrayList<String> input2Names = new ArrayList<String>();
for (VCCGeomFeature feature : diff.input2) {
input2Names.add(feature.name);
}
String[] input2Set = input2Names.toArray(new String[0]);
// model.geom(geomSequence.name) .feature(diff.name) .selection("input").set(inputSet);
buffer.append("model.geom('" + geomSequence.name + "').feature('" + diff.name + "').selection('input').set(" + tojs(inputSet) + ");" + "\n");
// model.geom(geomSequence.name) .feature(diff.name) .selection("input2").set(input2Set);
buffer.append("model.geom('" + geomSequence.name + "').feature('" + diff.name + "').selection('input2').set(" + tojs(input2Set) + ");" + "\n");
if (diff.keep == Keep.on) {
// model.geom(geomSequence.name) .feature(diff.name) .set("keep", "on");
buffer.append("model.geom('" + geomSequence.name + "').feature('" + diff.name + "').set('keep', 'on');" + "\n");
} else if (diff.keep == Keep.off) {
// model.geom(geomSequence.name) .feature(diff.name) .set("keep", "off");
buffer.append("model.geom('" + geomSequence.name + "').feature('" + diff.name + "').set('keep', 'off');" + "\n");
}
break;
}
case Scale:
{
buffer.append("print('geomFeature Scale named " + geomFeature.name + "');" + "\n");
VCCScale scale = (VCCScale) geomFeature;
// model.geom(geomSequence.name) .create(diff.name, "Difference");
buffer.append("model.geom('" + geomSequence.name + "').create('" + scale.name + "','Scale');" + "\n");
ArrayList<String> inputNames = new ArrayList<String>();
for (VCCGeomFeature feature : scale.input) {
inputNames.add(feature.name);
}
String[] inputSet = inputNames.toArray(new String[0]);
// model.geom(geomSequence.name) .feature(scale.name) .selection("input").set(inputSet);
buffer.append("model.geom('" + geomSequence.name + "').feature('" + scale.name + "').selection('input').set(" + tojs(inputSet) + ");" + "\n");
// model.geom(geomSequence.name) .feature(scale.name) .set('factor', scale.factor);
buffer.append("model.geom('" + geomSequence.name + "').feature('" + scale.name + "').set('factor'," + tojs(scale.factor) + ");" + "\n");
break;
}
case Move:
{
buffer.append("print('geomFeature Move named " + geomFeature.name + "');" + "\n");
VCCMove move = (VCCMove) geomFeature;
// model.geom(geomSequence.name) .create(diff.name, "Difference");
buffer.append("model.geom('" + geomSequence.name + "').create('" + move.name + "','Move');" + "\n");
ArrayList<String> inputNames = new ArrayList<String>();
for (VCCGeomFeature feature : move.input) {
inputNames.add(feature.name);
}
String[] inputSet = inputNames.toArray(new String[0]);
// model.geom(geomSequence.name) .feature(move.name) .selection("input").set(inputSet);
buffer.append("model.geom('" + geomSequence.name + "').feature('" + move.name + "').selection('input').set(" + tojs(inputSet) + ");" + "\n");
// model.geom(geomSequence.name) .feature(move.name) .set("displ", move.displ);
buffer.append("model.geom('" + geomSequence.name + "').feature('" + move.name + "').set('displ'," + tojs(move.displ) + ");" + "\n");
break;
}
case IntersectionSelection:
{
buffer.append("print('geomFeature IntersectionSelection named " + geomFeature.name + "');" + "\n");
if (bBeforeSelections) {
bBeforeSelections = false;
// model.geom("geom1") .run("fin");
buffer.append("model.geom('" + geomSequence.name + "').run('fin');" + "\n");
}
VCCIntersectionSelection intersectionSelection = (VCCIntersectionSelection) geomFeature;
// model.geom("geom1") .create("intsel1", "IntersectionSelection");
buffer.append("model.geom('" + geomSequence.name + "').create('" + intersectionSelection.name + "', 'IntersectionSelection');" + "\n");
// model.geom("geom1") .feature("intsel1") .set("entitydim", "2");
buffer.append("model.geom('" + geomSequence.name + "').feature('" + intersectionSelection.name + "').set('entitydim', '" + intersectionSelection.entitydim + "');" + "\n");
ArrayList<String> inputNames = new ArrayList<String>();
for (VCCGeomFeature feature : intersectionSelection.input) {
inputNames.add(feature.name);
}
String[] inputSet = inputNames.toArray(new String[0]);
// model.geom("geom1") .feature("intsel1") .set("input", new String[]{"diffec", "celltranslation0"});
buffer.append("model.geom('" + geomSequence.name + "').feature('" + intersectionSelection.name + "').set('input'," + tojs(inputSet) + ");" + "\n");
break;
}
default:
{
throw new RuntimeException("unexpected Geometry Feature type " + geomFeature.type.name());
}
}
if (!(geomFeature instanceof VCCIntersectionSelection)) {
// model.geom(geomSequence.name) .feature(geomFeature.name) .set("selresult", "on");
buffer.append("model.geom('" + geomSequence.name + "').feature('" + geomFeature.name + "').set('selresult','on');" + "\n");
}
}
System.out.println("building geometry");
// long t_startGeomRun_ms = System.currentTimeMillis();
buffer.append("var t_startGeomRun_ms = Date.now();" + "\n");
// model.geom(geomSequence.name) .run();
buffer.append("model.geom('" + geomSequence.name + "').run();" + "\n");
// long t_endGeomRun_ms = System.currentTimeMillis();
buffer.append("var t_endGeomRun_ms = Date.now();" + "\n");
// System.out.println("geometry built in " + ((t_endGeomRun_ms - t_startGeomRun_ms) / 1000.0) + " seconds");
buffer.append("print('geometry built in ' + ((t_endGeomRun_ms - t_startGeomRun_ms) / 1000.0) + ' seconds');" + "\n");
}
for (VCCMeshSequence meshSequence : vccModel.meshes) {
// model.mesh().create(meshSequence.name, meshSequence.geom.name);
buffer.append("model.mesh().create('" + meshSequence.name + "','" + meshSequence.geom.name + "');" + "\n");
}
for (VCCPhysics physics : vccModel.physics) {
switch(physics.type) {
// }
case ConvectionDiffusionEquation:
{
VCCConvectionDiffusionEquation pde = (VCCConvectionDiffusionEquation) physics;
buffer.append("print('(0) physics ConvectionDiffusionEquation for field name " + pde.fieldName + "');" + "\n");
// model.physics().create(pde.name, "ConvectionDiffusionEquation", pde.geom.name);
buffer.append("model.physics().create('" + pde.name + "','ConvectionDiffusionEquation','" + pde.geom.name + "');" + "\n");
buffer.append("print('(1) physics ConvectionDiffusionEquation for field name " + pde.fieldName + "');" + "\n");
String c = pde.diffTerm_c;
if (c != null) {
if (vccModel.dim == 2) {
// model.physics(pde.name) .feature("cdeq1").setIndex("c", new String[] { c, "0", "0", c }, 0);
buffer.append("model.physics('" + pde.name + "').feature('cdeq1').setIndex('c', " + tojs(new String[] { c, "0", "0", c }) + ", 0);" + "\n");
} else if (vccModel.dim == 3) {
// model.physics(pde.name) .feature("cdeq1").setIndex("c", new String[] { c, "0", "0", c }, 0);
buffer.append("model.physics('" + pde.name + "').feature('cdeq1').setIndex('c', " + tojs(new String[] { c, "0", "0", "0", c, "0", "0", "0", c }) + ", 0);" + "\n");
}
}
if (pde.advection_be != null) {
// model.physics(pde.name) .feature("cdeq1").setIndex("be", pde.advection_be, 0);
buffer.append("model.physics('" + pde.name + "').feature('cdeq1').setIndex('be', " + tojs(pde.advection_be) + ", 0);" + "\n");
}
buffer.append("print('(2) physics ConvectionDiffusionEquation for field name " + pde.fieldName + "');" + "\n");
// model.physics(pde.name) .feature("cdeq1").setIndex("f", pde.sourceTerm_f, 0);
buffer.append("model.physics('" + pde.name + "').feature('cdeq1').setIndex('f', '" + pde.sourceTerm_f + "', 0);" + "\n");
buffer.append("print('(3) physics ConvectionDiffusionEquation for field name " + pde.fieldName + "');" + "\n");
// model.physics(pde.name) .field("dimensionless") .field(pde.fieldName);
buffer.append("model.physics('" + pde.name + "').field('dimensionless').field('" + pde.fieldName + "');" + "\n");
buffer.append("print('(4) physics ConvectionDiffusionEquation for field name " + pde.fieldName + "');" + "\n");
// model.physics(pde.name) .feature("init1").set(pde.fieldName, pde.initial);
buffer.append("model.physics('" + pde.name + "').feature('init1').set('" + pde.fieldName + "','" + pde.initial + "');" + "\n");
String selectionName = null;
if (pde.dim == vccModel.dim) {
selectionName = pde.geom.name + "_" + pde.geomFeature.name + "_dom";
} else if (pde.dim == vccModel.dim - 1) {
selectionName = pde.geom.name + "_" + pde.geomFeature.name + "_bnd";
}
buffer.append("print('(5) physics ConvectionDiffusionEquation for field name " + pde.fieldName + ", selection " + selectionName + "');" + "\n");
// model.physics(pde.name) .selection().named(selectionName);
buffer.append("model.physics('" + pde.name + "').selection().named('" + selectionName + "');" + "\n");
buffer.append("print('(6) physics ConvectionDiffusionEquation for field name " + pde.fieldName + ", selection " + selectionName + "');" + "\n");
for (VCCPhysicsFeature feature : pde.features) {
if (feature instanceof VCCFluxBoundary) {
VCCFluxBoundary fluxBoundary = (VCCFluxBoundary) feature;
String boundarySelectionName = pde.geom.name + "_" + fluxBoundary.selection.name;
buffer.append("print('(0) physics ConvectionDiffusionEquation for field name " + pde.fieldName + ", FluxBoundary name " + fluxBoundary.name + ", selection name " + boundarySelectionName + "');" + "\n");
// model.physics(pde.name) .create(fluxBoundary.name, "FluxBoundary", 2);
buffer.append("model.physics('" + pde.name + "').create('" + fluxBoundary.name + "','FluxBoundary'," + fluxBoundary.dim + ");" + "\n");
buffer.append("print('(1) physics ConvectionDiffusionEquation for field name " + pde.fieldName + ", FluxBoundary name " + fluxBoundary.name + ", selection name " + boundarySelectionName + "');" + "\n");
// model.physics(pde.name) .feature(fluxBoundary.name) .selection().named("geom1_intsel1");
buffer.append("model.physics('" + pde.name + "').feature('" + fluxBoundary.name + "').selection().named('" + boundarySelectionName + "');" + "\n");
buffer.append("print('(2) physics ConvectionDiffusionEquation for field name " + pde.fieldName + ", FluxBoundary name " + fluxBoundary.name + ", selection name " + boundarySelectionName + "');" + "\n");
// model.physics(pde.name) .feature(fluxBoundary.name) .set("g", "5-RanC_nuc");
buffer.append("model.physics('" + pde.name + "').feature('" + fluxBoundary.name + "').set('g', '" + fluxBoundary.flux_g + "');" + "\n");
buffer.append("print('(3) physics ConvectionDiffusionEquation for field name " + pde.fieldName + ", FluxBoundary name " + fluxBoundary.name + ", selection name " + boundarySelectionName + "');" + "\n");
}
}
break;
}
default:
{
throw new RuntimeException("unsupported physics type " + physics.type.name() + " in COMSOL script builder");
}
}
}
System.out.println("building mesh");
// long t_startMeshRun_ms = System.currentTimeMillis();
buffer.append("var t_startMeshRun_ms = Date.now();" + "\n");
// model.mesh("mesh1").run();
buffer.append("model.mesh('mesh1').run();" + "\n");
// long t_endMeshRun_ms = System.currentTimeMillis();
buffer.append("var t_endMeshRun_ms = Date.now();" + "\n");
// System.out.println("mesh built in " + ((t_endMeshRun_ms - t_startMeshRun_ms) / 1000.0) + " seconds");
buffer.append("print('mesh built in ' + ((t_endMeshRun_ms - t_startMeshRun_ms) / 1000.0) + ' seconds');" + "\n");
// model.study().create(vccModel.study.name);
buffer.append("model.study().create('" + vccModel.study.name + "');" + "\n");
for (VCCStudyFeature studyFeature : vccModel.study.features) {
switch(studyFeature.type) {
case Transient:
{
VCCTransientStudyFeature transientTime = (VCCTransientStudyFeature) studyFeature;
// model.study(vccModel.study.name) .create("time", "Transient");
buffer.append("model.study('" + vccModel.study.name + "').create('time', 'Transient');" + "\n");
String range = "range(" + transientTime.startingTime + "," + transientTime.timeStep + "," + transientTime.endTime + ")";
// model.study(vccModel.study.name) .feature("time").set("tlist", range);
buffer.append("model.study('" + vccModel.study.name + "').feature('time').set('tlist', '" + range + "');" + "\n");
break;
}
default:
{
throw new RuntimeException("unknown studyFeature type " + studyFeature.type.name());
}
}
// model.study(study.name).create(studyFeature.name,
// studyFeature.type.name());
// for (VCCPhysics activePhysics : studyFeature.activePhysics){
// model.study(study.name).feature(studyFeature.name).activate(activePhysics.name);
// }
}
// model.sol().create("sol1");
buffer.append("model.sol().create('sol1');" + "\n");
// model.sol("sol1").study(vccModel.study.name);
buffer.append("model.sol('sol1').study('" + vccModel.study.name + "');" + "\n");
// model.sol("sol1").attach(vccModel.study.name);
buffer.append("model.sol('sol1').attach('" + vccModel.study.name + "');" + "\n");
// model.sol("sol1").create("st1", "StudyStep");
buffer.append("model.sol('sol1').create('st1', 'StudyStep');" + "\n");
// model.sol("sol1").create("v1", "Variables");
buffer.append("model.sol('sol1').create('v1', 'Variables');" + "\n");
// model.sol("sol1").create("t1", "Time");
buffer.append("model.sol('sol1').create('t1', 'Time');" + "\n");
// model.sol("sol1").feature("t1").create("fc1", "FullyCoupled");
buffer.append("model.sol('sol1').feature('t1').create('fc1', 'FullyCoupled');" + "\n");
// model.sol("sol1").feature("t1").feature().remove("fcDef");
buffer.append("model.sol('sol1').feature('t1').feature().remove('fcDef');" + "\n");
// model.result().export().create("data1", "Data");
buffer.append("model.result().export().create('data1', 'Data');" + "\n");
// model.sol("sol1").attach(vccModel.study.name);
buffer.append("model.sol('sol1').attach('" + vccModel.study.name + "');" + "\n");
// long t_beginsolver_ms = System.currentTimeMillis();
buffer.append("var t_beginsolver_ms = Date.now();" + "\n");
// System.out.println("running solver");
buffer.append("print('running solver');" + "\n");
// model.sol("sol1").runAll();
buffer.append("model.sol('sol1').runAll();" + "\n");
// long t_endsolver_ms = System.currentTimeMillis();
buffer.append("var t_endsolver_ms = Date.now();" + "\n");
// System.out.println("solver finished in " + ((t_endsolver_ms - t_beginsolver_ms) / 1000.0) + " seconds");
buffer.append("print('solver finished in ' + ((t_endsolver_ms - t_beginsolver_ms) / 1000.0) + ' seconds');" + "\n");
// model.result().export("data1").label("Data 2");
buffer.append("model.result().export('data1').label('Data 2');" + "\n");
// model.result().export("data1").set("struct", "sectionwise");
buffer.append("model.result().export('data1').set('struct', 'sectionwise');" + "\n");
// model.result().export("data1").set("filename", reportFile.getAbsolutePath());
String reportFileName = StringEscapeUtils.escapeEcmaScript(reportFile.getAbsolutePath());
buffer.append("model.result().export('data1').set('filename', '" + reportFileName + "');" + "\n");
ArrayList<String> units = new ArrayList<String>();
ArrayList<String> descriptions = new ArrayList<String>();
ArrayList<String> expressions = new ArrayList<String>();
for (VCCPhysics physics : vccModel.physics) {
if (physics instanceof VCCConvectionDiffusionEquation) {
VCCConvectionDiffusionEquation pde = (VCCConvectionDiffusionEquation) physics;
units.add("1");
descriptions.add(pde.fieldName);
expressions.add(pde.fieldName);
}
}
// model.result().export("data1").set("unit", units.toArray(new String[0]));
buffer.append("model.result().export('data1').set('unit'," + tojs(units.toArray(new String[0])) + ");" + "\n");
// model.result().export("data1").set("descr", descriptions.toArray(new String[0]));
buffer.append("model.result().export('data1').set('descr'," + tojs(descriptions.toArray(new String[0])) + ");" + "\n");
// model.result().export("data1").set("expr", expressions.toArray(new String[0]));
buffer.append("model.result().export('data1').set('expr'," + tojs(expressions.toArray(new String[0])) + ");" + "\n");
System.out.println("about to run() report");
// model.result().export("data1").run();
buffer.append("model.result().export('data1').run();" + "\n");
// long t_endexport_ms = System.currentTimeMillis();
buffer.append("var t_endexport_ms = Date.now();" + "\n");
// System.out.println("export finshed in " + ((t_endexport_ms - t_endsolver_ms) / 1000.0) + " seconds");
buffer.append("print('export finshed in ' + ((t_endexport_ms - t_endsolver_ms) / 1000.0) + ' seconds');" + "\n");
// model.save(javaFile.getAbsolutePath(), "java");
String javaFileName = StringEscapeUtils.escapeEcmaScript(javaFile.getAbsolutePath());
buffer.append("model.save('" + javaFileName + "','java');" + "\n");
// model.save(mphFile.getAbsolutePath());
String mphFileName = StringEscapeUtils.escapeEcmaScript(mphFile.getAbsolutePath());
buffer.append("model.save('" + mphFileName + "');" + "\n");
// ModelUtil.disconnect();
buffer.append("com.comsol.model.util.ModelUtil.disconnect();" + "\n");
String script = buffer.toString();
System.out.println(script);
FileUtils.write(jsFile, script);
System.out.println("script written to " + jsFile.getAbsolutePath() + " prior to execution");
// RhinoScriptEngineFactory factory = new RhinoScriptEngineFactory();
// factory.
// ContextFactory factory = new ContextFactory();
// Main dbg = new Main("script");
// dbg.attachTo(factory);
// Context context = factory.
// .
// ScriptContext scriptContext = new ScriptContext
engine.eval(script);
}
Also used :
VCCDifference(org.vcell.solver.comsol.model.VCCGeomFeature.VCCDifference)
VCCGeomSequence(org.vcell.solver.comsol.model.VCCGeomSequence)
VCCPhysicsFeature(org.vcell.solver.comsol.model.VCCPhysicsFeature)
VCCMove(org.vcell.solver.comsol.model.VCCGeomFeature.VCCMove)
VCCIntersectionSelection(org.vcell.solver.comsol.model.VCCGeomFeature.VCCIntersectionSelection)
VCCBlock(org.vcell.solver.comsol.model.VCCGeomFeature.VCCBlock)
VCCConvectionDiffusionEquation(org.vcell.solver.comsol.model.VCCConvectionDiffusionEquation)
ArrayList(java.util.ArrayList)
VCCSphere(org.vcell.solver.comsol.model.VCCGeomFeature.VCCSphere)
VCCModelNode(org.vcell.solver.comsol.model.VCCModelNode)
VCCSquare(org.vcell.solver.comsol.model.VCCGeomFeature.VCCSquare)
VCCFluxBoundary(org.vcell.solver.comsol.model.VCCPhysicsFeature.VCCFluxBoundary)
VCCTransientStudyFeature(org.vcell.solver.comsol.model.VCCTransientStudyFeature)
VCCScale(org.vcell.solver.comsol.model.VCCGeomFeature.VCCScale)
VCCMeshSequence(org.vcell.solver.comsol.model.VCCMeshSequence)
VCCStudyFeature(org.vcell.solver.comsol.model.VCCStudyFeature)
VCCCircle(org.vcell.solver.comsol.model.VCCGeomFeature.VCCCircle)
VCCPhysics(org.vcell.solver.comsol.model.VCCPhysics)
VCCGeomFeature(org.vcell.solver.comsol.model.VCCGeomFeature)
Example 2 with VCCMeshSequence
use of org.vcell.solver.comsol.model.VCCMeshSequence in project vcell by virtualcell.
the class ComsolModelBuilder method getVCCModel.
public static VCCModel getVCCModel(SimulationJob vcellSimJob) throws ExpressionException {
MathDescription vcellMathDesc = vcellSimJob.getSimulation().getMathDescription();
Geometry vcellGeometry = vcellMathDesc.getGeometry();
GeometrySpec vcellGeometrySpec = vcellGeometry.getGeometrySpec();
int vcellDim = vcellGeometrySpec.getDimension();
VCCModel model = new VCCModel("Model", vcellDim);
model.modelpath = "D:\\Developer\\eclipse\\workspace_refactor\\comsol_java\\src";
model.comments = "Untitled\n\n";
VCCModelNode comp1 = new VCCModelNode("comp1");
model.modelnodes.add(comp1);
// if (vcellDim != 2){
// throw new RuntimeException("expecting 2D simulation");
// }
//
// assume initial geometry is circle centered at 0.5, 0.5 of radius 0.3
//
// String comsolOutsideDomainName = "dif1";
// String comsolInsideDomainName = "c1";
VCCGeomSequence geom1 = new VCCGeomSequence("geom1", vcellDim);
model.geometrysequences.add(geom1);
VCCMeshSequence mesh1 = new VCCMeshSequence("mesh1", geom1);
model.meshes.add(mesh1);
VCCStudy std1 = new VCCStudy("std1");
model.study = std1;
TimeBounds timeBounds = vcellSimJob.getSimulation().getSolverTaskDescription().getTimeBounds();
TimeStep timeStep = vcellSimJob.getSimulation().getSolverTaskDescription().getTimeStep();
String beginTime = Double.toString(timeBounds.getStartingTime());
String endTime = Double.toString(timeBounds.getEndingTime());
String step = Double.toString(timeStep.getDefaultTimeStep());
VCCStudyFeature time = new VCCTransientStudyFeature("time", beginTime, step, endTime);
std1.features.add(time);
if (vcellGeometrySpec.getImage() != null) {
throw new RuntimeException("image-based geometries not yet supported by VCell's COMSOL model builder");
}
if (vcellGeometrySpec.getNumSubVolumes() == 0) {
throw new RuntimeException("no subvolumes defined in geometry");
}
if (vcellGeometrySpec.getNumAnalyticOrCSGSubVolumes() != vcellGeometrySpec.getNumSubVolumes()) {
throw new RuntimeException("only analytic and CSG subvolumes currently supported by VCell's COMSOL model builder");
}
//
// add geometry for all subvolumes
//
HashMap<String, VCCGeomFeature> subvolumeNameFeatureMap = new HashMap<String, VCCGeomFeature>();
SubVolume[] subVolumes = vcellGeometrySpec.getSubVolumes();
for (int i = 0; i < subVolumes.length; i++) {
SubVolume subvolume = subVolumes[i];
if (subvolume instanceof CSGObject) {
CSGObject vcellCSGObject = (CSGObject) subvolume;
CSGNode vcellCSGNode = vcellCSGObject.getRoot();
ArrayList<VCCGeomFeature> geomFeatureList = new ArrayList<VCCGeomFeature>();
VCCGeomFeature feature = csgVisitor(vcellCSGNode, geomFeatureList, subvolume.getName());
geom1.geomfeatures.addAll(geomFeatureList);
if (i == 0) {
// first subvolume (on top in ordinals) doesn't need any differencing
subvolumeNameFeatureMap.put(subvolume.getName(), feature);
} else {
// have to subtract union of prior subvolumes
ArrayList<VCCGeomFeature> priorFeatures = new ArrayList<VCCGeomFeature>();
for (int j = 0; j < i; j++) {
CSGObject priorCSGObject = (CSGObject) subVolumes[j];
CSGNode priorCSGNode = priorCSGObject.getRoot();
geomFeatureList.clear();
VCCGeomFeature priorFeature = csgVisitor(priorCSGNode, geomFeatureList, subvolume.getName());
priorFeatures.add(priorFeature);
geom1.geomfeatures.addAll(geomFeatureList);
}
VCCDifference diff = new VCCDifference("diff" + subvolume.getName(), Keep.off);
diff.input.add(feature);
diff.input2.addAll(priorFeatures);
geom1.geomfeatures.add(diff);
subvolumeNameFeatureMap.put(subvolume.getName(), diff);
}
} else {
throw new RuntimeException("only CSG subvolumes currently supported by VCell's COMSOL model builder");
}
}
//
// add geometry for all surfaceClasses
//
HashMap<String, VCCGeomFeature> surfaceclassNameFeatureMap = new HashMap<String, VCCGeomFeature>();
SurfaceClass[] surfaceClasses = vcellGeometry.getGeometrySurfaceDescription().getSurfaceClasses();
for (int i = 0; i < surfaceClasses.length; i++) {
SurfaceClass surfaceClass = surfaceClasses[i];
Set<SubVolume> adjacentSubvolumes = surfaceClass.getAdjacentSubvolumes();
if (adjacentSubvolumes.size() != 2) {
throw new RuntimeException("expecting two adjacent subvolumes for surface " + surfaceClass.getName() + " in COMSOL model builder");
}
// find adjacent Geometry Features (for subvolumes)
Iterator<SubVolume> svIter = adjacentSubvolumes.iterator();
SubVolume subvolume0 = svIter.next();
SubVolume subvolume1 = svIter.next();
ArrayList<VCCGeomFeature> adjacentFeatures = new ArrayList<VCCGeomFeature>();
adjacentFeatures.add(subvolumeNameFeatureMap.get(subvolume0.getName()));
adjacentFeatures.add(subvolumeNameFeatureMap.get(subvolume1.getName()));
String name = "inter_" + subvolume0.getName() + "_" + subvolume1.getName();
// surfaces are dimension N-1
int entitydim = vcellDim - 1;
VCCIntersectionSelection intersect_subvolumes = new VCCIntersectionSelection(name, entitydim);
intersect_subvolumes.input.addAll(adjacentFeatures);
geom1.geomfeatures.add(intersect_subvolumes);
surfaceclassNameFeatureMap.put(surfaceClass.getName(), intersect_subvolumes);
}
SimulationSymbolTable symbolTable = new SimulationSymbolTable(vcellSimJob.getSimulation(), vcellSimJob.getJobIndex());
//
for (SubDomain subDomain : Collections.list(vcellMathDesc.getSubDomains())) {
for (Equation equ : subDomain.getEquationCollection()) {
if (equ instanceof PdeEquation || equ instanceof OdeEquation) {
VCCGeomFeature geomFeature = null;
final int dim;
if (subDomain instanceof CompartmentSubDomain) {
geomFeature = subvolumeNameFeatureMap.get(subDomain.getName());
dim = vcellDim;
} else if (subDomain instanceof MembraneSubDomain) {
geomFeature = surfaceclassNameFeatureMap.get(subDomain.getName());
dim = vcellDim - 1;
} else {
throw new RuntimeException("subdomains of type '" + subDomain.getClass().getSimpleName() + "' not yet supported in COMSOL model builder");
}
if (geomFeature == null) {
throw new RuntimeException("cannot find COMSOL geometry feature named " + subDomain.getName() + " in COMSOL model builder");
}
VCCConvectionDiffusionEquation cdeq = new VCCConvectionDiffusionEquation("cdeq_" + equ.getVariable().getName(), geom1, geomFeature, dim);
cdeq.fieldName = equ.getVariable().getName();
cdeq.initial = MathUtilities.substituteModelParameters(equ.getInitialExpression(), symbolTable).flatten().infix();
cdeq.sourceTerm_f = MathUtilities.substituteModelParameters(equ.getRateExpression(), symbolTable).flatten().infix();
if (equ instanceof PdeEquation) {
PdeEquation pde = (PdeEquation) equ;
cdeq.diffTerm_c = MathUtilities.substituteModelParameters(pde.getDiffusionExpression(), symbolTable).flatten().infix();
if (subDomain instanceof CompartmentSubDomain) {
CompartmentSubDomain compartmentSubdomain = (CompartmentSubDomain) subDomain;
ArrayList<String> be = new ArrayList<String>();
if (pde.getVelocityX() != null) {
be.add(MathUtilities.substituteModelParameters(pde.getVelocityX(), symbolTable).flatten().infix());
} else {
be.add("0");
}
if (vcellDim >= 2) {
if (pde.getVelocityY() != null) {
be.add(MathUtilities.substituteModelParameters(pde.getVelocityY(), symbolTable).flatten().infix());
} else {
be.add("0");
}
}
if (vcellDim == 3) {
if (pde.getVelocityY() != null) {
be.add(MathUtilities.substituteModelParameters(pde.getVelocityZ(), symbolTable).flatten().infix());
} else {
be.add("0");
}
}
cdeq.advection_be = be.toArray(new String[vcellDim]);
//
// look for membrane boundary conditions for this variable
//
MembraneSubDomain[] membraneSubdomains = vcellMathDesc.getMembraneSubDomains(compartmentSubdomain);
for (MembraneSubDomain membraneSubdomain : membraneSubdomains) {
JumpCondition jumpCondition = membraneSubdomain.getJumpCondition((VolVariable) pde.getVariable());
if (jumpCondition != null) {
Expression fluxExpr = null;
if (membraneSubdomain.getInsideCompartment() == compartmentSubdomain) {
fluxExpr = jumpCondition.getInFluxExpression();
} else if (membraneSubdomain.getOutsideCompartment() == compartmentSubdomain) {
fluxExpr = jumpCondition.getOutFluxExpression();
}
String name = equ.getVariable().getName() + "_flux_" + membraneSubdomain.getName();
VCCGeomFeature selection = surfaceclassNameFeatureMap.get(membraneSubdomain.getName());
VCCFluxBoundary fluxBoundary = new VCCFluxBoundary(name, selection, vcellDim - 1);
fluxBoundary.flux_g = MathUtilities.substituteModelParameters(fluxExpr, symbolTable).flatten().infix();
cdeq.features.add(fluxBoundary);
}
}
}
}
model.physics.add(cdeq);
}
}
}
//
return model;
}
Also used :
JumpCondition(cbit.vcell.math.JumpCondition)
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
MathDescription(cbit.vcell.math.MathDescription)
HashMap(java.util.HashMap)
SurfaceClass(cbit.vcell.geometry.SurfaceClass)
VCCConvectionDiffusionEquation(org.vcell.solver.comsol.model.VCCConvectionDiffusionEquation)
CSGNode(cbit.vcell.geometry.CSGNode)
ArrayList(java.util.ArrayList)
VCCFluxBoundary(org.vcell.solver.comsol.model.VCCPhysicsFeature.VCCFluxBoundary)
GeometrySpec(cbit.vcell.geometry.GeometrySpec)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
SubDomain(cbit.vcell.math.SubDomain)
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
PdeEquation(cbit.vcell.math.PdeEquation)
TimeBounds(cbit.vcell.solver.TimeBounds)
TimeStep(cbit.vcell.solver.TimeStep)
SubVolume(cbit.vcell.geometry.SubVolume)
VCCStudyFeature(org.vcell.solver.comsol.model.VCCStudyFeature)
CSGObject(cbit.vcell.geometry.CSGObject)
VCCGeomFeature(org.vcell.solver.comsol.model.VCCGeomFeature)
VCCDifference(org.vcell.solver.comsol.model.VCCGeomFeature.VCCDifference)
VCCGeomSequence(org.vcell.solver.comsol.model.VCCGeomSequence)
VCCIntersectionSelection(org.vcell.solver.comsol.model.VCCGeomFeature.VCCIntersectionSelection)
SimulationSymbolTable(cbit.vcell.solver.SimulationSymbolTable)
VCCConvectionDiffusionEquation(org.vcell.solver.comsol.model.VCCConvectionDiffusionEquation)
OdeEquation(cbit.vcell.math.OdeEquation)
PdeEquation(cbit.vcell.math.PdeEquation)
Equation(cbit.vcell.math.Equation)
VCCModelNode(org.vcell.solver.comsol.model.VCCModelNode)
VCCTransientStudyFeature(org.vcell.solver.comsol.model.VCCTransientStudyFeature)
VCCMeshSequence(org.vcell.solver.comsol.model.VCCMeshSequence)
Geometry(cbit.vcell.geometry.Geometry)
VCCStudy(org.vcell.solver.comsol.model.VCCStudy)
OdeEquation(cbit.vcell.math.OdeEquation)
Expression(cbit.vcell.parser.Expression)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
VCCModel(org.vcell.solver.comsol.model.VCCModel)
Aggregations
ArrayList (java.util.ArrayList)2
VCCConvectionDiffusionEquation (org.vcell.solver.comsol.model.VCCConvectionDiffusionEquation)2
VCCGeomFeature (org.vcell.solver.comsol.model.VCCGeomFeature)2
VCCDifference (org.vcell.solver.comsol.model.VCCGeomFeature.VCCDifference)2
VCCIntersectionSelection (org.vcell.solver.comsol.model.VCCGeomFeature.VCCIntersectionSelection)2
VCCGeomSequence (org.vcell.solver.comsol.model.VCCGeomSequence)2
VCCMeshSequence (org.vcell.solver.comsol.model.VCCMeshSequence)2
VCCModelNode (org.vcell.solver.comsol.model.VCCModelNode)2
VCCFluxBoundary (org.vcell.solver.comsol.model.VCCPhysicsFeature.VCCFluxBoundary)2
VCCStudyFeature (org.vcell.solver.comsol.model.VCCStudyFeature)2
VCCTransientStudyFeature (org.vcell.solver.comsol.model.VCCTransientStudyFeature)2
CSGNode (cbit.vcell.geometry.CSGNode)1
CSGObject (cbit.vcell.geometry.CSGObject)1
Geometry (cbit.vcell.geometry.Geometry)1
GeometrySpec (cbit.vcell.geometry.GeometrySpec)1
SubVolume (cbit.vcell.geometry.SubVolume)1
SurfaceClass (cbit.vcell.geometry.SurfaceClass)1
CompartmentSubDomain (cbit.vcell.math.CompartmentSubDomain)1
Equation (cbit.vcell.math.Equation)1
JumpCondition (cbit.vcell.math.JumpCondition)1
