Examples with VCCMove org.vcell.solver.comsol.model.VCCGeomFeature.VCCMove used on opensource projects

Example 1 with VCCMove

use of org.vcell.solver.comsol.model.VCCGeomFeature.VCCMove in project vcell by virtualcell.

the class ComsolModelBuilder method csgVisitor.

private static VCCGeomFeature csgVisitor(CSGNode node, ArrayList<VCCGeomFeature> geomFeatureList, String namePrefix) {
    final VCCGeomFeature newFeature;
    if (node instanceof CSGPrimitive) {
        CSGPrimitive csg = (CSGPrimitive) node;
        switch(csg.getType()) {
            case CONE:
                {
                    newFeature = new VCCCone(namePrefix + csg.getName());
                    break;
                }
            case CUBE:
                {
                    String[] size = new String[] { "2", "2", "2" };
                    String[] pos = new String[] { "-1", "-1", "-1" };
                    VCCBlock vccblock = new VCCBlock(namePrefix + csg.getName(), size, pos);
                    newFeature = vccblock;
                    break;
                }
            case CYLINDER:
                {
                    newFeature = new VCCCylinder(namePrefix + csg.getName());
                    break;
                }
            case SPHERE:
                {
                    String r = "1";
                    String[] pos = new String[] { "0", "0", "0" };
                    newFeature = new VCCSphere(namePrefix + csg.getName(), pos, r);
                    break;
                }
            default:
                {
                    throw new RuntimeException("csg primative type '" + csg.getType().name() + "' not yet supported in COMSOL model builder");
                }
        }
    } else if (node instanceof CSGSetOperator) {
        CSGSetOperator setOp = (CSGSetOperator) node;
        ArrayList<VCCGeomFeature> childSubtrees = new ArrayList<VCCGeomFeature>();
        for (CSGNode child : setOp.getChildren()) {
            VCCGeomFeature vccChild = csgVisitor(child, geomFeatureList, namePrefix);
            childSubtrees.add(vccChild);
        }
        switch(setOp.getOpType()) {
            case DIFFERENCE:
                {
                    if (childSubtrees.size() != 2) {
                        throw new RuntimeException("expecting exactly two children for CSG difference operator");
                    }
                    VCCDifference diff = new VCCDifference(namePrefix + setOp.getName(), Keep.off);
                    diff.input.add(childSubtrees.get(0));
                    diff.input2.add(childSubtrees.get(1));
                    newFeature = diff;
                    break;
                }
            case INTERSECTION:
                {
                    if (childSubtrees.size() < 2) {
                        throw new RuntimeException("expecting two or more children for CSG intersection operator");
                    }
                    VCCIntersection intersection = new VCCIntersection(namePrefix + setOp.getName(), Keep.off);
                    intersection.input.add(childSubtrees.get(0));
                    newFeature = intersection;
                    break;
                }
            case UNION:
                {
                    if (childSubtrees.size() < 2) {
                        throw new RuntimeException("expecting two or more children for CSG union operator");
                    }
                    VCCUnion union = new VCCUnion(namePrefix + setOp.getName(), Keep.off);
                    union.input.add(childSubtrees.get(0));
                    newFeature = union;
                    break;
                }
            default:
                {
                    throw new RuntimeException("csg set operator '" + setOp.getOpType().name() + "' not yet supported in COMSOL model builder");
                }
        }
    } else if (node instanceof CSGTransformation) {
        CSGTransformation transformation = (CSGTransformation) node;
        VCCGeomFeature vccChild = csgVisitor(transformation.getChild(), geomFeatureList, namePrefix);
        if (transformation instanceof CSGHomogeneousTransformation) {
            throw new RuntimeException("unsupported CSG transformation type Homogeneous transformation");
        } else if (transformation instanceof CSGRotation) {
            CSGRotation rotation = (CSGRotation) transformation;
            String[] axis = new String[] { Double.toString(rotation.getAxis().getX()), Double.toString(rotation.getAxis().getY()), Double.toString(rotation.getAxis().getZ()) };
            String[] pos = new String[] { "0.0", "0.0", "0.0" };
            String rot = Double.toString(rotation.getRotationRadians());
            VCCRotate vccrotate = new VCCRotate(namePrefix + rotation.getName(), axis, pos, rot, Keep.off);
            vccrotate.input.add(vccChild);
            newFeature = vccrotate;
        } else if (transformation instanceof CSGScale) {
            CSGScale scale = (CSGScale) transformation;
            String[] factor = new String[] { Double.toString(scale.getScale().getX()), Double.toString(scale.getScale().getY()), Double.toString(scale.getScale().getZ()) };
            String[] pos = new String[] { "0.0", "0.0", "0.0" };
            VCCScale vccscale = new VCCScale(namePrefix + scale.getName(), pos, factor, Keep.off);
            vccscale.input.add(vccChild);
            newFeature = vccscale;
        } else if (transformation instanceof CSGTranslation) {
            CSGTranslation translation = (CSGTranslation) transformation;
            String[] displ = new String[] { Double.toString(translation.getTranslation().getX()), Double.toString(translation.getTranslation().getY()), Double.toString(translation.getTranslation().getZ()) };
            VCCMove vccmove = new VCCMove(namePrefix + translation.getName(), displ, Keep.off);
            vccmove.input.add(vccChild);
            newFeature = vccmove;
        } else {
            throw new RuntimeException("unsupported CSG transformation type '" + transformation.getClass().getSimpleName() + "'");
        }
    } else {
        throw new RuntimeException("unsupported CSGNode type '" + node.getClass().getSimpleName() + "'");
    }
    geomFeatureList.add(newFeature);
    return newFeature;
}

Example 2 with VCCMove

use of org.vcell.solver.comsol.model.VCCGeomFeature.VCCMove 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);
}