Examples with Membrane cbit.vcell.model.Membrane used on opensource projects

Example 11 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class SpeciesContextSpec method initializeForSpatial.

public void initializeForSpatial() {
    if (getDiffusionParameter() != null && getDiffusionParameter().getExpression() != null && getDiffusionParameter().getExpression().isZero()) {
        Expression e = null;
        ModelUnitSystem modelUnitSystem = getSimulationContext().getModel().getUnitSystem();
        VCUnitDefinition micronsqpersecond = modelUnitSystem.getInstance("um2.s-1");
        if (speciesContext.getStructure() instanceof Feature) {
            RationalNumber rn = RationalNumber.getApproximateFraction(micronsqpersecond.convertTo(10, getDiffusionParameter().getUnitDefinition()));
            e = new Expression(rn.doubleValue());
        } else if (speciesContext.getStructure() instanceof Membrane) {
            RationalNumber rn = RationalNumber.getApproximateFraction(micronsqpersecond.convertTo(0.1, getDiffusionParameter().getUnitDefinition()));
            e = new Expression(rn.doubleValue());
        } else {
            RationalNumber rn = RationalNumber.getApproximateFraction(micronsqpersecond.convertTo(1.0, getDiffusionParameter().getUnitDefinition()));
            e = new Expression(rn.doubleValue());
        }
        try {
            getDiffusionParameter().setExpression(e);
        } catch (ExpressionBindingException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Error while initializing diffusion rate, " + e1.getMessage());
        }
    }
}

Example 12 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class SpeciesContextSpec method hasTransport.

public boolean hasTransport() {
    if (isConstant() || isWellMixed() || simulationContext == null || simulationContext.getGeometry() == null || simulationContext.getGeometry().getDimension() == 0) {
        return false;
    }
    int dimension = simulationContext.getGeometry().getDimension();
    SpeciesContext speciesContext = getSpeciesContext();
    if (speciesContext.getStructure() instanceof Membrane) {
        if (dimension > 1 && !getDiffusionParameter().getExpression().isZero()) {
            return true;
        }
    } else if (speciesContext.getStructure() instanceof Feature) {
        if (!getDiffusionParameter().getExpression().isZero()) {
            return true;
        }
        if (getVelocityXParameter().getExpression() != null && !getVelocityXParameter().getExpression().isZero()) {
            return true;
        }
        SpatialQuantity[] velX_quantities = getVelocityQuantities(QuantityComponent.X);
        if (velX_quantities.length > 0) {
            return true;
        }
        if (dimension > 1) {
            if (getVelocityYParameter().getExpression() != null && !getVelocityYParameter().getExpression().isZero()) {
                return true;
            }
            if (dimension > 2) {
                if (getVelocityZParameter().getExpression() != null && !getVelocityZParameter().getExpression().isZero()) {
                    return true;
                }
            }
        }
    }
    return false;
}

Example 13 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class SpeciesContextSpec method computeApplicableParameterList.

public List<SpeciesContextSpecParameter> computeApplicableParameterList() {
    List<SpeciesContextSpecParameter> speciesContextSpecParameterList = new ArrayList<SpeciesContextSpecParameter>();
    speciesContextSpecParameterList.add(getInitialConditionParameter());
    int dimension = simulationContext.getGeometry().getDimension();
    if (!isConstant() && !isWellMixed() && dimension > 0) {
        // diffusion
        speciesContextSpecParameterList.add(getDiffusionParameter());
    }
    if (hasTransport()) {
        SpeciesContext speciesContext = getSpeciesContext();
        if (speciesContext.getStructure() instanceof Membrane) {
            // boundary condition
            speciesContextSpecParameterList.add(getBoundaryXmParameter());
            speciesContextSpecParameterList.add(getBoundaryXpParameter());
            speciesContextSpecParameterList.add(getBoundaryYmParameter());
            speciesContextSpecParameterList.add(getBoundaryYpParameter());
            if (dimension > 2) {
                speciesContextSpecParameterList.add(getBoundaryZmParameter());
                speciesContextSpecParameterList.add(getBoundaryZpParameter());
            }
        } else if (speciesContext.getStructure() instanceof Feature) {
            // boundary condition
            speciesContextSpecParameterList.add(getBoundaryXmParameter());
            speciesContextSpecParameterList.add(getBoundaryXpParameter());
            if (dimension > 1) {
                speciesContextSpecParameterList.add(getBoundaryYmParameter());
                speciesContextSpecParameterList.add(getBoundaryYpParameter());
                if (dimension > 2) {
                    speciesContextSpecParameterList.add(getBoundaryZmParameter());
                    speciesContextSpecParameterList.add(getBoundaryZpParameter());
                }
            }
            // velocity
            speciesContextSpecParameterList.add(getVelocityXParameter());
            if (dimension > 1) {
                speciesContextSpecParameterList.add(getVelocityYParameter());
                if (dimension > 2) {
                    speciesContextSpecParameterList.add(getVelocityZParameter());
                }
            }
        }
    }
    return speciesContextSpecParameterList;
}

Example 14 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class ElectricalCircuitGraph method getCircuitGraph.

/**
 * Insert the method's description here.
 * Creation date: (2/19/2002 11:24:04 AM)
 * @return cbit.vcell.mapping.potential.Graph
 * @param simContext cbit.vcell.mapping.SimulationContext
 */
public static Graph getCircuitGraph(SimulationContext simContext, AbstractMathMapping mathMapping) throws ExpressionException {
    Graph graph = new Graph();
    Model model = simContext.getModel();
    // 
    // add nodes to the graph (one for each Feature)
    // 
    Structure[] structures = model.getStructures();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Feature) {
            graph.addNode(new Node(structures[i].getName(), structures[i]));
        }
    }
    // 
    // add edges for all current clamp electrodes (always have dependent voltages)
    // 
    ElectricalStimulus[] stimuli = simContext.getElectricalStimuli();
    Electrode groundElectrode = simContext.getGroundElectrode();
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof CurrentDensityClampStimulus) {
            CurrentDensityClampStimulus ccStimulus = (CurrentDensityClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        } else if (stimulus instanceof TotalCurrentClampStimulus) {
            TotalCurrentClampStimulus ccStimulus = (TotalCurrentClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // 
    // add edges for all membranes
    // 
    ElectricalTopology electricalTopology = simContext.getModel().getElectricalTopology();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Membrane) {
            Membrane membrane = (Membrane) structures[i];
            MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
            Feature positiveFeature = electricalTopology.getPositiveFeature(membrane);
            Feature negativeFeature = electricalTopology.getNegativeFeature(membrane);
            if (positiveFeature != null && negativeFeature != null) {
                Node insideNode = graph.getNode(positiveFeature.getName());
                Node outsideNode = graph.getNode(negativeFeature.getName());
                // 
                // getTotalMembraneCurrent() already converts to "outwardCurrent" so that same convention as voltage
                // 
                Expression currentSource = getTotalMembraneCurrent(simContext, membrane, mathMapping);
                MembraneElectricalDevice device = new MembraneElectricalDevice(membraneMapping, mathMapping);
                device.getParameterFromRole(ElectricalDevice.ROLE_TransmembraneCurrent).setExpression(currentSource);
                Edge edge = new Edge(insideNode, outsideNode, device);
                graph.addEdge(edge);
            }
        }
    }
    // 
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof VoltageClampStimulus) {
            VoltageClampStimulus vcStimulus = (VoltageClampStimulus) stimulus;
            ElectricalDevice device = new VoltageClampElectricalDevice(vcStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // System.out.println(graph);
    return graph;
}

Example 15 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class MathMapping_4_8 method getResidualVolumeFraction.

public Expression getResidualVolumeFraction(FeatureMapping featureMapping) throws ExpressionException {
    Expression exp = new Expression(1.0);
    Structure[] structures = simContext.getGeometryContext().getModel().getStructures();
    StructureTopology structTopology = simContext.getModel().getStructureTopology();
    for (int i = 0; i < structures.length; i++) {
        // 
        // for each membrane that is distributed within this feature, subtract that volume fraction
        // ????? beware, 1 - v1 - v2 ... can result in a negative number if we're not careful.
        // 
        Structure struct = structures[i];
        if (struct instanceof Membrane) {
            if ((structTopology.getOutsideFeature((Membrane) struct)) == featureMapping.getFeature()) {
                MembraneMapping mm = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(struct);
                if (getResolved(mm) == false) {
                    exp = Expression.add(exp, Expression.negate(new Expression(mm.getVolumeFractionParameter(), simContext.getNameScope())));
                }
            }
        }
    }
    return exp;
}