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Example 6 with PointSubDomain

use of cbit.vcell.math.PointSubDomain in project vcell by virtualcell.

the class MovingBoundaryFileWriter method manageCompartment.

private void manageCompartment(Element e, SubDomain sd) {
    try {
        if (!sd.getEquationCollection().isEmpty()) {
            Element se = getXMLSubdomain(sd);
            if (sd instanceof CompartmentSubDomain || sd instanceof PointSubDomain) {
                for (Equation equation : sd.getEquationCollection()) {
                    System.out.println("add this: " + equation.getVariable().getName());
                    se.addContent(getSpecies(equation));
                }
                e.addContent(se);
            }
        }
    } catch (Exception exc) {
        throw new RuntimeException("error managing compartment", exc);
    }
}
Also used : CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) Element(org.jdom.Element) PointSubDomain(cbit.vcell.math.PointSubDomain) PdeEquation(cbit.vcell.math.PdeEquation) Equation(cbit.vcell.math.Equation) SolverException(cbit.vcell.solver.SolverException) ExpressionException(cbit.vcell.parser.ExpressionException) MathException(cbit.vcell.math.MathException)

Aggregations

PointSubDomain (cbit.vcell.math.PointSubDomain)6 CompartmentSubDomain (cbit.vcell.math.CompartmentSubDomain)5 Element (org.jdom.Element)4 MathException (cbit.vcell.math.MathException)3 MembraneSubDomain (cbit.vcell.math.MembraneSubDomain)3 FilamentSubDomain (cbit.vcell.math.FilamentSubDomain)2 SubDomain (cbit.vcell.math.SubDomain)2 Domain (cbit.vcell.math.Variable.Domain)2 VolVariable (cbit.vcell.math.VolVariable)2 ExpressionException (cbit.vcell.parser.ExpressionException)2 GeometryClass (cbit.vcell.geometry.GeometryClass)1 SubVolume (cbit.vcell.geometry.SubVolume)1 SurfaceClass (cbit.vcell.geometry.SurfaceClass)1 LocalParameter (cbit.vcell.mapping.ParameterContext.LocalParameter)1 PointObject (cbit.vcell.mapping.spatial.PointObject)1 SpatialObject (cbit.vcell.mapping.spatial.SpatialObject)1 SpatialQuantity (cbit.vcell.mapping.spatial.SpatialObject.SpatialQuantity)1 SurfaceRegionObject (cbit.vcell.mapping.spatial.SurfaceRegionObject)1 VolumeRegionObject (cbit.vcell.mapping.spatial.VolumeRegionObject)1 PointKinematics (cbit.vcell.mapping.spatial.processes.PointKinematics)1