Examples with PointVariable cbit.vcell.math.PointVariable used on opensource projects

Example 1 with PointVariable

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

the class DiffEquMathMapping method addSpatialProcesses.

private void addSpatialProcesses(VariableHash varHash, ArrayList<CompartmentSubdomainContext> compartmentSubdomainContexts, ArrayList<MembraneSubdomainContext> membraneSubdomainContexts) throws MathException, MappingException, ExpressionException {
    if (simContext.getGeometry().getDimension() == 0) {
        return;
    }
    // 
    for (SpatialObject spatialObject : simContext.getSpatialObjects()) {
        if (spatialObject instanceof PointObject) {
            PointObject pointObject = (PointObject) spatialObject;
            // 
            // if true, have to solve for this category
            // 
            boolean bPosition = pointObject.isQuantityCategoryEnabled(QuantityCategory.PointPosition);
            boolean bVelocity = pointObject.isQuantityCategoryEnabled(QuantityCategory.PointVelocity);
            boolean bDirection = pointObject.isQuantityCategoryEnabled(QuantityCategory.DirectionToPoint);
            boolean bDistance = pointObject.isQuantityCategoryEnabled(QuantityCategory.PointDistanceMap);
            // 
            // either make a point subdomain, or just define functions.
            // 
            ArrayList<PointLocation> pointLocationProcesses = new ArrayList<PointLocation>();
            ArrayList<PointKinematics> pointKinematicsProcesses = new ArrayList<PointKinematics>();
            for (SpatialProcess spatialProcess : simContext.getSpatialProcesses()) {
                if (spatialProcess instanceof PointLocation && ((PointLocation) spatialProcess).getPointObject() == pointObject) {
                    pointLocationProcesses.add((PointLocation) spatialProcess);
                }
                if (spatialProcess instanceof PointKinematics && ((PointKinematics) spatialProcess).getPointObject() == pointObject) {
                    pointKinematicsProcesses.add((PointKinematics) spatialProcess);
                }
            }
            if (pointLocationProcesses.size() == 1 && pointKinematicsProcesses.size() == 0 && !bVelocity) {
                GeometryClass gc = null;
                PointLocation pointLocation = pointLocationProcesses.get(0);
                if (bPosition) {
                    if (simContext.getGeometry().getDimension() == 1) {
                        SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
                        LocalParameter posXParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionX);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXParam, gc), getIdentifierSubstitutions(posXParam.getExpression(), posXParam.getUnitDefinition(), gc), gc));
                        Expression posXExp = new Expression(posXParam, pointLocation.getNameScope());
                        Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXQuantity, gc), getIdentifierSubstitutions(posXExp, posXQuantity.getUnitDefinition(), gc), gc));
                        Expression posX_minus_X = Expression.add(posXExp, Expression.negate(xExp));
                        Expression signum_posX_minus_X = Expression.function(FunctionType.MIN, new Expression(1.0), Expression.function(FunctionType.MAX, Expression.mult(new Expression(1e10), posX_minus_X), new Expression(-1)));
                        if (bDirection) {
                            SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(signum_posX_minus_X, dirXQuantity.getUnitDefinition(), gc), gc));
                        }
                        if (bDistance) {
                            Expression abs_X_minux_posX = Expression.function(FunctionType.ABS, posX_minus_X);
                            SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(abs_X_minux_posX, distanceQuantity.getUnitDefinition(), gc), gc));
                        }
                    }
                    if (simContext.getGeometry().getDimension() == 2) {
                        SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
                        LocalParameter posXParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionX);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXParam, gc), getIdentifierSubstitutions(posXParam.getExpression(), posXParam.getUnitDefinition(), gc), gc));
                        Expression posXExp = new Expression(posXParam, pointLocation.getNameScope());
                        Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXQuantity, gc), getIdentifierSubstitutions(new Expression(posXParam, pointLocation.getNameScope()), posXQuantity.getUnitDefinition(), gc), gc));
                        SpatialQuantity posYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Y);
                        LocalParameter posYParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionY);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYParam, gc), getIdentifierSubstitutions(posYParam.getExpression(), posYParam.getUnitDefinition(), gc), gc));
                        Expression posYExp = new Expression(posYParam, pointLocation.getNameScope());
                        Expression yExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Y), simContext.getModel().getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYQuantity, gc), getIdentifierSubstitutions(new Expression(posYParam, pointLocation.getNameScope()), posYQuantity.getUnitDefinition(), gc), gc));
                        Expression posX_minux_X = Expression.add(posXExp, Expression.negate(xExp));
                        Expression posY_minux_Y = Expression.add(posYExp, Expression.negate(yExp));
                        Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
                        Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
                        Expression sqrt_DX2_DY2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2));
                        Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
                        Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
                        if (bDirection) {
                            SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
                            SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
                        }
                        if (bDistance) {
                            SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2, distanceQuantity.getUnitDefinition(), gc), gc));
                        }
                    }
                    if (simContext.getGeometry().getDimension() == 3) {
                        SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
                        LocalParameter posXParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionX);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXParam, gc), getIdentifierSubstitutions(posXParam.getExpression(), posXParam.getUnitDefinition(), gc), gc));
                        Expression posXExp = new Expression(posXParam, pointLocation.getNameScope());
                        Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posXQuantity, gc), getIdentifierSubstitutions(new Expression(posXParam, pointLocation.getNameScope()), posXQuantity.getUnitDefinition(), gc), gc));
                        SpatialQuantity posYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Y);
                        LocalParameter posYParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionY);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYParam, gc), getIdentifierSubstitutions(posYParam.getExpression(), posYParam.getUnitDefinition(), gc), gc));
                        Expression posYExp = new Expression(posYParam, pointLocation.getNameScope());
                        Expression yExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Y), simContext.getModel().getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posYQuantity, gc), getIdentifierSubstitutions(new Expression(posYParam, pointLocation.getNameScope()), posYQuantity.getUnitDefinition(), gc), gc));
                        SpatialQuantity posZQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Z);
                        LocalParameter posZParam = pointLocation.getParameter(SpatialProcessParameterType.PointPositionZ);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posZParam, gc), getIdentifierSubstitutions(posZParam.getExpression(), posZParam.getUnitDefinition(), gc), gc));
                        Expression posZExp = new Expression(posZParam, pointLocation.getNameScope());
                        Expression zExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Z), simContext.getModel().getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(posZQuantity, gc), getIdentifierSubstitutions(new Expression(posZParam, pointLocation.getNameScope()), posZQuantity.getUnitDefinition(), gc), gc));
                        Expression posX_minux_X = Expression.add(posXExp, Expression.negate(xExp));
                        Expression posY_minux_Y = Expression.add(posYExp, Expression.negate(yExp));
                        Expression posZ_minux_Z = Expression.add(posZExp, Expression.negate(zExp));
                        Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
                        Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
                        Expression DZ2 = Expression.mult(posZ_minux_Z, posZ_minux_Z);
                        Expression sqrt_DX2_DY2_DZ2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2, DZ2));
                        Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
                        Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
                        Expression dirZ = Expression.div(posZ_minux_Z, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
                        if (bDirection) {
                            SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
                            SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
                            SpatialQuantity dirZQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Z);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirZQuantity, gc), getIdentifierSubstitutions(dirZ, dirZQuantity.getUnitDefinition(), gc), gc));
                        }
                        if (bDistance) {
                            SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2_DZ2, distanceQuantity.getUnitDefinition(), gc), gc));
                        }
                    }
                } else {
                    throw new MappingException("PointLocation process defined for pointObject '" + pointObject.getName() + "' but Position not enabled");
                }
            } else if (pointLocationProcesses.size() == 0 && pointKinematicsProcesses.size() == 1) {
                GeometryClass gc = null;
                PointKinematics pointKinematics = pointKinematicsProcesses.get(0);
                if (bPosition && bVelocity) {
                    LocalParameter velXParam = pointKinematics.getParameter(SpatialProcessParameterType.PointVelocityX);
                    LocalParameter iniPosXParam = pointKinematics.getParameter(SpatialProcessParameterType.PointInitialPositionX);
                    SpatialQuantity posXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.X);
                    SpatialQuantity velXQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointVelocity, QuantityComponent.X);
                    Expression posXExp = new Expression(posXQuantity, simContext.getNameScope());
                    Expression xExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.X), simContext.getModel().getNameScope());
                    Expression posX_minux_X = Expression.add(posXExp, Expression.negate(xExp));
                    LocalParameter velYParam = pointKinematics.getParameter(SpatialProcessParameterType.PointVelocityY);
                    LocalParameter iniPosYParam = pointKinematics.getParameter(SpatialProcessParameterType.PointInitialPositionY);
                    SpatialQuantity posYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Y);
                    SpatialQuantity velYQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointVelocity, QuantityComponent.Y);
                    Expression posYExp = new Expression(posYQuantity, simContext.getNameScope());
                    Expression yExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Y), simContext.getModel().getNameScope());
                    Expression posY_minux_Y = Expression.add(posYExp, Expression.negate(yExp));
                    LocalParameter velZParam = pointKinematics.getParameter(SpatialProcessParameterType.PointVelocityZ);
                    LocalParameter iniPosZParam = pointKinematics.getParameter(SpatialProcessParameterType.PointInitialPositionZ);
                    SpatialQuantity posZQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointPosition, QuantityComponent.Z);
                    SpatialQuantity velZQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointVelocity, QuantityComponent.Z);
                    Expression posZExp = new Expression(posZQuantity, simContext.getNameScope());
                    Expression zExp = new Expression(simContext.getModel().getReservedSymbolByRole(ReservedSymbolRole.Z), simContext.getModel().getNameScope());
                    Expression posZ_minux_Z = Expression.add(posZExp, Expression.negate(zExp));
                    String pointSubdomainName = pointObject.getName();
                    Domain domain = new Domain(pointSubdomainName);
                    PointSubDomain pointSubdomain = new PointSubDomain(pointSubdomainName);
                    mathDesc.addSubDomain(pointSubdomain);
                    if (simContext.getGeometry().getDimension() >= 1) {
                        PointVariable posXVar = new PointVariable(getMathSymbol(posXQuantity, gc), domain);
                        varHash.addVariable(posXVar);
                        Expression initXExp = getIdentifierSubstitutions(new Expression(iniPosXParam, pointKinematics.getNameScope()), iniPosXParam.getUnitDefinition(), gc);
                        Expression rateXExp = getIdentifierSubstitutions(new Expression(velXParam, pointKinematics.getNameScope()), velXParam.getUnitDefinition(), gc);
                        OdeEquation odeX = new OdeEquation(posXVar, initXExp, rateXExp);
                        pointSubdomain.addEquation(odeX);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(iniPosXParam, gc), getIdentifierSubstitutions(new Expression(iniPosXParam.getExpression()), iniPosXParam.getUnitDefinition(), gc), gc));
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXParam, gc), getIdentifierSubstitutions(new Expression(velXParam.getExpression()), velXParam.getUnitDefinition(), gc), gc));
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXQuantity, gc), getIdentifierSubstitutions(new Expression(velXParam, pointKinematics.getNameScope()), velXQuantity.getUnitDefinition(), gc), gc));
                        pointSubdomain.setPositionX(getIdentifierSubstitutions(new Expression(posXQuantity, simContext.getNameScope()), posXQuantity.getUnitDefinition(), gc));
                    }
                    if (simContext.getGeometry().getDimension() >= 2) {
                        PointVariable posYVar = new PointVariable(getMathSymbol(posYQuantity, gc), domain);
                        varHash.addVariable(posYVar);
                        Expression initYExp = getIdentifierSubstitutions(new Expression(iniPosYParam, pointKinematics.getNameScope()), iniPosYParam.getUnitDefinition(), gc);
                        Expression rateYExp = getIdentifierSubstitutions(new Expression(velYParam, pointKinematics.getNameScope()), velYParam.getUnitDefinition(), gc);
                        OdeEquation odeY = new OdeEquation(posYVar, initYExp, rateYExp);
                        pointSubdomain.addEquation(odeY);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(iniPosYParam, gc), getIdentifierSubstitutions(new Expression(iniPosYParam.getExpression()), iniPosYParam.getUnitDefinition(), gc), gc));
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYParam, gc), getIdentifierSubstitutions(new Expression(velYParam.getExpression()), velYParam.getUnitDefinition(), gc), gc));
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYQuantity, gc), getIdentifierSubstitutions(new Expression(velYParam, pointKinematics.getNameScope()), velYQuantity.getUnitDefinition(), gc), gc));
                        pointSubdomain.setPositionY(getIdentifierSubstitutions(new Expression(posYQuantity, simContext.getNameScope()), posYQuantity.getUnitDefinition(), gc));
                    }
                    if (simContext.getGeometry().getDimension() == 3) {
                        PointVariable posZVar = new PointVariable(getMathSymbol(posZQuantity, gc), domain);
                        varHash.addVariable(posZVar);
                        Expression initZExp = getIdentifierSubstitutions(new Expression(iniPosZParam, pointKinematics.getNameScope()), iniPosZParam.getUnitDefinition(), gc);
                        Expression rateZExp = getIdentifierSubstitutions(new Expression(velZParam, pointKinematics.getNameScope()), velZParam.getUnitDefinition(), gc);
                        OdeEquation odeZ = new OdeEquation(posZVar, initZExp, rateZExp);
                        pointSubdomain.addEquation(odeZ);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(iniPosZParam, gc), getIdentifierSubstitutions(new Expression(iniPosZParam.getExpression()), iniPosZParam.getUnitDefinition(), gc), gc));
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZParam, gc), getIdentifierSubstitutions(new Expression(velZParam.getExpression()), velZParam.getUnitDefinition(), gc), gc));
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZQuantity, gc), getIdentifierSubstitutions(new Expression(velZParam, pointKinematics.getNameScope()), velZQuantity.getUnitDefinition(), gc), gc));
                        pointSubdomain.setPositionZ(getIdentifierSubstitutions(new Expression(posZQuantity, simContext.getNameScope()), posZQuantity.getUnitDefinition(), gc));
                    }
                    if (simContext.getGeometry().getDimension() == 1) {
                        Expression signum_posX_minus_X = Expression.function(FunctionType.MIN, new Expression(1.0), Expression.function(FunctionType.MAX, Expression.mult(new Expression(1e10), posX_minux_X), new Expression(-1)));
                        if (bDirection) {
                            SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(signum_posX_minus_X, dirXQuantity.getUnitDefinition(), gc), gc));
                        }
                        if (bDistance) {
                            Expression abs_X_minux_posX = Expression.function(FunctionType.ABS, posX_minux_X);
                            SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(abs_X_minux_posX, distanceQuantity.getUnitDefinition(), gc), gc));
                        }
                    }
                    if (simContext.getGeometry().getDimension() == 2) {
                        Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
                        Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
                        Expression sqrt_DX2_DY2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2));
                        Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
                        Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2, new Expression(1e-8)));
                        if (bDirection) {
                            SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
                            SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
                        }
                        if (bDistance) {
                            SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2, distanceQuantity.getUnitDefinition(), gc), gc));
                        }
                    }
                    if (simContext.getGeometry().getDimension() == 3) {
                        Expression DX2 = Expression.mult(posX_minux_X, posX_minux_X);
                        Expression DY2 = Expression.mult(posY_minux_Y, posY_minux_Y);
                        Expression DZ2 = Expression.mult(posZ_minux_Z, posZ_minux_Z);
                        Expression sqrt_DX2_DY2_DZ2 = Expression.function(FunctionType.SQRT, Expression.add(DX2, DY2, DZ2));
                        Expression dirX = Expression.div(posX_minux_X, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
                        Expression dirY = Expression.div(posY_minux_Y, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
                        Expression dirZ = Expression.div(posZ_minux_Z, Expression.add(sqrt_DX2_DY2_DZ2, new Expression(1e-8)));
                        if (bDirection) {
                            SpatialQuantity dirXQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.X);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirXQuantity, gc), getIdentifierSubstitutions(dirX, dirXQuantity.getUnitDefinition(), gc), gc));
                            SpatialQuantity dirYQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Y);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirYQuantity, gc), getIdentifierSubstitutions(dirY, dirYQuantity.getUnitDefinition(), gc), gc));
                            SpatialQuantity dirZQuantity = pointObject.getSpatialQuantity(QuantityCategory.DirectionToPoint, QuantityComponent.Z);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(dirZQuantity, gc), getIdentifierSubstitutions(dirZ, dirZQuantity.getUnitDefinition(), gc), gc));
                        }
                        if (bDistance) {
                            SpatialQuantity distanceQuantity = pointObject.getSpatialQuantity(QuantityCategory.PointDistanceMap, QuantityComponent.Scalar);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(distanceQuantity, gc), getIdentifierSubstitutions(sqrt_DX2_DY2_DZ2, distanceQuantity.getUnitDefinition(), gc), gc));
                        }
                    }
                } else {
                    throw new MappingException(pointKinematics.getDescription() + " process defined for pointObject '" + pointObject.getName() + "' but Position and Velocity not enabled");
                }
            } else {
                throw new MappingException("expecting 1 location or kinematics process for point '" + pointObject.getName() + "'");
            }
        } else if (spatialObject instanceof SurfaceRegionObject) {
            SurfaceRegionObject surfaceRegionObject = (SurfaceRegionObject) spatialObject;
            SubVolume insideSubvolume = surfaceRegionObject.getInsideSubVolume();
            SubVolume outsideSubvolume = surfaceRegionObject.getOutsideSubVolume();
            SurfaceClass surfaceClass = simContext.getGeometry().getGeometrySurfaceDescription().getSurfaceClass(insideSubvolume, outsideSubvolume);
            MembraneSubdomainContext memSubdomainContext = null;
            for (MembraneSubdomainContext context : membraneSubdomainContexts) {
                if (context.surfaceClass == surfaceClass) {
                    memSubdomainContext = context;
                }
            }
            // 
            // if true, have to solve for this category
            // 
            boolean bNormal = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.Normal);
            boolean bVelocity = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceVelocity);
            boolean bDistance = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceDistanceMap);
            boolean bDirection = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.DirectionToSurface);
            boolean bSize = surfaceRegionObject.isQuantityCategoryEnabled(QuantityCategory.SurfaceSize);
            if (bVelocity) {
                ArrayList<SurfaceKinematics> surfaceKinematicsList = new ArrayList<SurfaceKinematics>();
                for (SpatialProcess spatialProcess : simContext.getSpatialProcesses()) {
                    if (spatialProcess instanceof SurfaceKinematics && ((SurfaceKinematics) spatialProcess).getSurfaceRegionObject() == surfaceRegionObject) {
                        surfaceKinematicsList.add((SurfaceKinematics) spatialProcess);
                    }
                }
                if (surfaceKinematicsList.size() == 1) {
                    SurfaceKinematics surfaceKinematics = surfaceKinematicsList.get(0);
                    if (simContext.getGeometry().getDimension() >= 1) {
                        SpatialQuantity velXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.X);
                        LocalParameter velXParam = surfaceKinematics.getParameter(SpatialProcessParameterType.SurfaceVelocityX);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXParam, surfaceClass), getIdentifierSubstitutions(velXParam.getExpression(), velXParam.getUnitDefinition(), surfaceClass), surfaceClass));
                        Expression velXExp = new Expression(velXParam, surfaceKinematics.getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXQuantity, surfaceClass), getIdentifierSubstitutions(velXExp, velXQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
                        if (bNormal) {
                            SpatialQuantity normXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.Normal, QuantityComponent.X);
                            Expression normXExp = new Expression(MathFunctionDefinitions.FUNCTION_normalX);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(normXQuantity, surfaceClass), getIdentifierSubstitutions(normXExp, normXQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
                        }
                    }
                    if (simContext.getGeometry().getDimension() >= 2) {
                        SpatialQuantity velYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.Y);
                        LocalParameter velYParam = surfaceKinematics.getParameter(SpatialProcessParameterType.SurfaceVelocityY);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYParam, surfaceClass), getIdentifierSubstitutions(velYParam.getExpression(), velYParam.getUnitDefinition(), surfaceClass), surfaceClass));
                        Expression velYExp = new Expression(velYParam, surfaceKinematics.getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYQuantity, surfaceClass), getIdentifierSubstitutions(velYExp, velYQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
                        if (bNormal) {
                            SpatialQuantity normYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.Normal, QuantityComponent.Y);
                            Expression normYExp = new Expression(MathFunctionDefinitions.FUNCTION_normalY);
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(normYQuantity, surfaceClass), getIdentifierSubstitutions(normYExp, normYQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
                        }
                    }
                    if (simContext.getGeometry().getDimension() >= 3) {
                        SpatialQuantity velZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceVelocity, QuantityComponent.Z);
                        LocalParameter velZParam = surfaceKinematics.getParameter(SpatialProcessParameterType.SurfaceVelocityZ);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZParam, surfaceClass), getIdentifierSubstitutions(velZParam.getExpression(), velZParam.getUnitDefinition(), surfaceClass), surfaceClass));
                        Expression velYExp = new Expression(velZParam, surfaceKinematics.getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZQuantity, surfaceClass), getIdentifierSubstitutions(velYExp, velZQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
                        if (bNormal) {
                            SpatialQuantity normZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.Normal, QuantityComponent.Z);
                            // MathFunctionDefinitions.FUNCTION_normalZ);
                            Expression normZExp = new Expression("normalZ_not_implemented()");
                            varHash.addVariable(newFunctionOrConstant(getMathSymbol(normZQuantity, surfaceClass), getIdentifierSubstitutions(normZExp, normZQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
                        }
                    }
                } else {
                    throw new MappingException("expecting 1 Surface Kinematics process for Surface Object '" + surfaceRegionObject.getName() + "'");
                }
            }
            if (bSize) {
                SpatialQuantity sizeQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceSize, QuantityComponent.Scalar);
                String funcName = MathFunctionDefinitions.Function_regionArea_current.getFunctionName();
                Expression sizeExp = Expression.function(funcName, new Expression[] { new Expression("'" + surfaceClass.getName() + "'") });
                varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeQuantity, surfaceClass), getIdentifierSubstitutions(sizeExp, sizeQuantity.getUnitDefinition(), surfaceClass), surfaceClass));
            }
            if (bDirection) {
                SpatialQuantity directionXQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.DirectionToSurface, QuantityComponent.X);
                SpatialQuantity directionYQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.DirectionToSurface, QuantityComponent.Y);
                SpatialQuantity directionZQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.DirectionToSurface, QuantityComponent.Z);
                for (SubVolume adjacentSubvolume : surfaceClass.getAdjacentSubvolumes()) {
                    Domain domain = new Domain(adjacentSubvolume);
                    CompartmentSubDomain compSubdomain = mathDesc.getCompartmentSubDomain(adjacentSubvolume.getName());
                    if (simContext.getGeometry().getDimension() >= 1) {
                        String name = adjacentSubvolume.getName() + "_dirX_" + memSubdomainContext.membraneSubdomain.getName();
                        LocalizedDirectionToMembraneQuantity localDirectionXQuantity = addLocalizedDirectionToMembraneQuantity(name, surfaceClass, adjacentSubvolume, QuantityComponent.X);
                        VolVariable distanceVar = new VolVariable(getMathSymbol(localDirectionXQuantity, adjacentSubvolume), domain);
                        varHash.addVariable(distanceVar);
                        ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.directionToMembraneX);
                        membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
                        compSubdomain.addEquation(membraneMetricEquation);
                    }
                    if (simContext.getGeometry().getDimension() >= 2) {
                        String name = adjacentSubvolume.getName() + "_dirY_" + memSubdomainContext.membraneSubdomain.getName();
                        LocalizedDirectionToMembraneQuantity localDirectionYQuantity = addLocalizedDirectionToMembraneQuantity(name, surfaceClass, adjacentSubvolume, QuantityComponent.Y);
                        VolVariable distanceVar = new VolVariable(getMathSymbol(localDirectionYQuantity, adjacentSubvolume), domain);
                        varHash.addVariable(distanceVar);
                        ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.directionToMembraneY);
                        membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
                        compSubdomain.addEquation(membraneMetricEquation);
                    }
                    if (simContext.getGeometry().getDimension() == 3) {
                        String name = adjacentSubvolume.getName() + "_dirZ_" + memSubdomainContext.membraneSubdomain.getName();
                        LocalizedDirectionToMembraneQuantity localDirectionZQuantity = addLocalizedDirectionToMembraneQuantity(name, surfaceClass, adjacentSubvolume, QuantityComponent.Z);
                        VolVariable distanceVar = new VolVariable(getMathSymbol(localDirectionZQuantity, adjacentSubvolume), domain);
                        varHash.addVariable(distanceVar);
                        ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.directionToMembraneZ);
                        membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
                        compSubdomain.addEquation(membraneMetricEquation);
                    }
                }
            }
            if (bDistance) {
                SpatialQuantity distanceQuantity = surfaceRegionObject.getSpatialQuantity(QuantityCategory.SurfaceDistanceMap, QuantityComponent.Scalar);
                for (SubVolume adjacentSubvolume : surfaceClass.getAdjacentSubvolumes()) {
                    String name = adjacentSubvolume.getName() + "_distanceTo_" + memSubdomainContext.membraneSubdomain.getName();
                    LocalizedDistanceToMembraneQuantity localDistanceQuantity = addLocalizedDistanceToMembraneQuantity(name, surfaceClass, adjacentSubvolume);
                    CompartmentSubDomain compSubdomain = mathDesc.getCompartmentSubDomain(adjacentSubvolume.getName());
                    Domain domain = new Domain(adjacentSubvolume);
                    VolVariable distanceVar = new VolVariable(getMathSymbol(localDistanceQuantity, adjacentSubvolume), domain);
                    varHash.addVariable(distanceVar);
                    ComputeMembraneMetricEquation membraneMetricEquation = new ComputeMembraneMetricEquation(distanceVar, MembraneMetricComponent.distanceToMembrane);
                    membraneMetricEquation.setTargetMembraneName(memSubdomainContext.membraneSubdomain.getName());
                    compSubdomain.addEquation(membraneMetricEquation);
                }
            }
        } else if (spatialObject instanceof VolumeRegionObject) {
            VolumeRegionObject volumeRegionObject = (VolumeRegionObject) spatialObject;
            SubVolume subvolume = volumeRegionObject.getSubVolume();
            boolean bCentroid = volumeRegionObject.isQuantityCategoryEnabled(QuantityCategory.DirectionToSurface);
            boolean bSize = volumeRegionObject.isQuantityCategoryEnabled(QuantityCategory.VolumeSize);
            boolean bVelocity = volumeRegionObject.isQuantityCategoryEnabled(QuantityCategory.InteriorVelocity);
            if (bVelocity) {
                ArrayList<VolumeKinematics> volumeKinematicsList = new ArrayList<VolumeKinematics>();
                for (SpatialProcess spatialProcess : simContext.getSpatialProcesses()) {
                    if (spatialProcess instanceof VolumeKinematics && ((VolumeKinematics) spatialProcess).getVolumeRegionObject() == volumeRegionObject) {
                        volumeKinematicsList.add((VolumeKinematics) spatialProcess);
                    }
                }
                if (volumeKinematicsList.size() == 1) {
                    VolumeKinematics volumeKinematics = volumeKinematicsList.get(0);
                    if (simContext.getGeometry().getDimension() >= 1) {
                        SpatialQuantity velXQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.InteriorVelocity, QuantityComponent.X);
                        LocalParameter velXParam = volumeKinematics.getParameter(SpatialProcessParameterType.InternalVelocityX);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXParam, subvolume), getIdentifierSubstitutions(velXParam.getExpression(), velXParam.getUnitDefinition(), subvolume), subvolume));
                        Expression velXExp = new Expression(velXParam, volumeKinematics.getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velXQuantity, subvolume), getIdentifierSubstitutions(velXExp, velXQuantity.getUnitDefinition(), subvolume), subvolume));
                    }
                    if (simContext.getGeometry().getDimension() >= 2) {
                        SpatialQuantity velYQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.InteriorVelocity, QuantityComponent.Y);
                        LocalParameter velYParam = volumeKinematics.getParameter(SpatialProcessParameterType.InternalVelocityY);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYParam, subvolume), getIdentifierSubstitutions(velYParam.getExpression(), velYParam.getUnitDefinition(), subvolume), subvolume));
                        Expression velYExp = new Expression(velYParam, volumeKinematics.getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velYQuantity, subvolume), getIdentifierSubstitutions(velYExp, velYQuantity.getUnitDefinition(), subvolume), subvolume));
                    }
                    if (simContext.getGeometry().getDimension() == 3) {
                        SpatialQuantity velZQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.InteriorVelocity, QuantityComponent.Z);
                        LocalParameter velZParam = volumeKinematics.getParameter(SpatialProcessParameterType.InternalVelocityZ);
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZParam, subvolume), getIdentifierSubstitutions(velZParam.getExpression(), velZParam.getUnitDefinition(), subvolume), subvolume));
                        Expression velZExp = new Expression(velZParam, volumeKinematics.getNameScope());
                        varHash.addVariable(newFunctionOrConstant(getMathSymbol(velZQuantity, subvolume), getIdentifierSubstitutions(velZExp, velZQuantity.getUnitDefinition(), subvolume), subvolume));
                    }
                } else {
                    throw new MappingException("expecting 1 Volume Kinematics process for Volume Object '" + volumeRegionObject.getName() + "'");
                }
            }
            if (bSize) {
                SpatialQuantity sizeQuantity = volumeRegionObject.getSpatialQuantity(QuantityCategory.VolumeSize, QuantityComponent.Scalar);
                String funcName = MathFunctionDefinitions.Function_regionVolume_current.getFunctionName();
                Expression sizeExp = Expression.function(funcName, new Expression[] { new Expression("'" + subvolume.getName() + "'") });
                varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeQuantity, subvolume), getIdentifierSubstitutions(sizeExp, sizeQuantity.getUnitDefinition(), subvolume), subvolume));
            }
            if (bCentroid) {
                throw new MappingException(QuantityCategory.Centroid.description + " not yet implemented in math generation");
            }
        }
    }
}

Example 2 with PointVariable

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

the class SimulationSymbolTable method createAnnotatedFunctionsList.

public Vector<AnnotatedFunction> createAnnotatedFunctionsList(MathDescription mathDescription) throws InconsistentDomainException {
    // Get the list of (volVariables) in the simulation. Needed to determine 'type' of  functions
    boolean bSpatial = getSimulation().isSpatial();
    String[] variableNames = null;
    VariableType[] variableTypes = null;
    if (bSpatial) {
        Variable[] allVariables = getVariables();
        Vector<Variable> varVector = new Vector<Variable>();
        for (int i = 0; i < allVariables.length; i++) {
            if ((allVariables[i] instanceof VolVariable) || (allVariables[i] instanceof VolumeRegionVariable) || (allVariables[i] instanceof MemVariable) || (allVariables[i] instanceof MembraneRegionVariable) || (allVariables[i] instanceof FilamentVariable) || (allVariables[i] instanceof FilamentRegionVariable) || (allVariables[i] instanceof PointVariable) || (allVariables[i] instanceof ParticleVariable) || (allVariables[i] instanceof InsideVariable) || (allVariables[i] instanceof OutsideVariable)) {
                varVector.addElement(allVariables[i]);
            } else if (allVariables[i] instanceof Constant || (allVariables[i] instanceof Function)) {
            } else {
                System.err.println("SimulationSymbolTable.createAnnotatedFunctionsList() found unexpected variable type " + allVariables[i].getClass().getSimpleName() + " in spatial simulation");
            }
        }
        variableNames = new String[varVector.size()];
        for (int i = 0; i < variableNames.length; i++) {
            variableNames[i] = varVector.get(i).getName();
        }
        // Lookup table for variableType for each variable in 'variables' array.
        variableTypes = new VariableType[variableNames.length];
        for (int i = 0; i < variableNames.length; i++) {
            variableTypes[i] = VariableType.getVariableType(varVector.get(i));
        }
    }
    // 
    // Bind and substitute functions to simulation before storing them in the '.functions' file
    // 
    Function[] functions = getFunctions();
    Vector<AnnotatedFunction> annotatedFunctionVector = new Vector<AnnotatedFunction>();
    for (int i = 0; i < functions.length; i++) {
        if (isFunctionSaved(functions[i])) {
            String errString = "";
            VariableType funcType = null;
            try {
                Expression substitutedExp = substituteFunctions(functions[i].getExpression());
                substitutedExp.bindExpression(this);
                functions[i].setExpression(substitutedExp.flatten());
            } catch (MathException e) {
                e.printStackTrace(System.out);
                errString = errString + ", " + e.getMessage();
            // throw new RuntimeException(e.getMessage());
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                errString = errString + ", " + e.getMessage();
            // throw new RuntimeException(e.getMessage());
            }
            // 
            // get function's data type from the types of it's identifiers
            // 
            funcType = bSpatial ? getFunctionVariableType(functions[i], mathDescription, variableNames, variableTypes, bSpatial) : VariableType.NONSPATIAL;
            AnnotatedFunction annotatedFunc = new AnnotatedFunction(functions[i].getName(), functions[i].getExpression(), functions[i].getDomain(), errString, funcType, FunctionCategory.PREDEFINED);
            annotatedFunctionVector.addElement(annotatedFunc);
        }
    }
    return annotatedFunctionVector;
}

Example 3 with PointVariable

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

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a MathDescription object.
 * Creation date: (3/2/2001 10:57:25 AM)
 * @return Element
 * @param mathdes cbit.vcell.math.MathDescription
 */
Element getXML(MathDescription mathdes) throws XmlParseException {
    Element math = new Element(XMLTags.MathDescriptionTag);
    // Add attributes
    math.setAttribute(XMLTags.NameAttrTag, mangle(mathdes.getName()));
    // Add annotation
    if (mathdes.getDescription() != null && mathdes.getDescription().length() > 0) {
        Element annotationElem = new Element(XMLTags.AnnotationTag);
        annotationElem.setText(mangle(mathdes.getDescription()));
        math.addContent(annotationElem);
    }
    List<ParticleMolecularType> particleMolecularTypes = mathdes.getParticleMolecularTypes();
    for (ParticleMolecularType particleMolecularType : particleMolecularTypes) {
        math.addContent(getXML(particleMolecularType));
    }
    // Add Constant subelements
    Enumeration<Variable> enum1 = mathdes.getVariables();
    /*java.util.Iterator k;
    try {
    	VariableHash varHash = new VariableHash();
    	while (enum1.hasMoreElements()) 
    	 	varHash.addVariable((Variable)enum1.nextElement());
    	Variable vars [] = varHash.getReorderedVariables();
    	k = new ArrayList(java.util.Arrays.asList(vars)).iterator();
    } catch (cbit.vcell.mapping.MappingException e) {
		e.printStackTrace();
		return null;
    }*/
    while (enum1.hasMoreElements()) {
        Variable var = enum1.nextElement();
        Element element = null;
        if (var instanceof Constant) {
            element = getXML((Constant) var);
        } else if (var instanceof FilamentRegionVariable) {
            element = getXML((FilamentRegionVariable) var);
        } else if (var instanceof FilamentVariable) {
            element = getXML((FilamentVariable) var);
        } else if (var instanceof PointVariable) {
            element = getXML((PointVariable) var);
        } else if (var instanceof Function) {
            element = getXML((Function) var);
        } else if (var instanceof RandomVariable) {
            element = getXML((RandomVariable) var);
        } else if (var instanceof InsideVariable) {
            // *** for internal use! Ignore it ***
            continue;
        } else if (var instanceof MembraneRegionVariable) {
            element = getXML((MembraneRegionVariable) var);
        } else if (var instanceof MemVariable) {
            element = getXML((MemVariable) var);
        } else if (var instanceof OutsideVariable) {
            // *** for internal use! Ignore it ****
            continue;
        } else if (var instanceof VolumeRegionVariable) {
            element = getXML((VolumeRegionVariable) var);
        } else if (var instanceof VolVariable) {
            element = getXML((VolVariable) var);
        } else if (var instanceof StochVolVariable) {
            // added for stochastic volumn variables
            element = getXML((StochVolVariable) var);
        } else if (var instanceof ParticleVariable) {
            element = getXML((ParticleVariable) var);
        } else if (var instanceof ParticleObservable) {
            element = getXML((ParticleObservable) var);
        } else {
            throw new XmlParseException("An unknown variable type " + var.getClass().getName() + " was found when parsing the mathdescription " + mathdes.getName() + "!");
        }
        transcribeComments(var, element);
        math.addContent(element);
    }
    // this was moved to the simspec!
    /*	buffer.append("\n");
    	if (geometry != null){
    		buffer.append(geometry.getXML());
    	}	
    	buffer.append("\n");*/
    // Add subdomains
    Enumeration<SubDomain> enum2 = mathdes.getSubDomains();
    while (enum2.hasMoreElements()) {
        SubDomain subDomain = enum2.nextElement();
        math.addContent(getXML(subDomain));
    }
    // Add Metadata (Version) if there is!
    if (mathdes.getVersion() != null) {
        math.addContent(getXML(mathdes.getVersion(), mathdes));
    }
    Iterator<Event> iter = mathdes.getEvents();
    while (iter.hasNext()) {
        math.addContent(getXML(iter.next()));
    }
    PostProcessingBlock postProcessingBlock = mathdes.getPostProcessingBlock();
    if (postProcessingBlock.getNumDataGenerators() > 0) {
        math.addContent(getXML(postProcessingBlock));
    }
    return math;
}

Example 4 with PointVariable

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

the class XmlReader method getPointVariable.

private PointVariable getPointVariable(Element param) {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    // Create new memVariable
    PointVariable pointVariable = new PointVariable(name, domain);
    transcribeComments(param, pointVariable);
    return pointVariable;
}

Example 5 with PointVariable

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

the class MovingBoundaryFileWriter method getSpecies.

// TODO: flatten here
private Element getSpecies(Equation eq) throws ExpressionException, MathException {
    Element e = new Element(MBTags.species);
    e.setAttribute(MBTags.name, eq.getVariable().getName());
    VariableDomain varDomain = null;
    if (eq.getVariable() instanceof VolVariable) {
        e.setAttribute(MBXmlTags.type.name(), MBXmlTags.volume.name());
        varDomain = VariableDomain.VARIABLEDOMAIN_VOLUME;
    } else if (eq.getVariable() instanceof PointVariable) {
        e.setAttribute(MBXmlTags.type.name(), MBXmlTags.point.name());
        varDomain = VariableDomain.VARIABLEDOMAIN_POINT;
    }
    Element e1 = null;
    e1 = new Element(MBTags.initial);
    Expression ex = eq.getInitialExpression();
    setExpression(e1, ex, varDomain);
    e.addContent(e1);
    e1 = new Element(MBTags.source);
    ex = eq.getRateExpression();
    setExpression(e1, ex, varDomain);
    e.addContent(e1);
    if (eq instanceof PdeEquation) {
        e1 = new Element(MBTags.diffusion);
        ex = ((PdeEquation) eq).getDiffusionExpression();
        setExpression(e1, ex, varDomain);
        e.addContent(e1);
        ex = ((PdeEquation) eq).getVelocityX();
        if (ex != null) {
            e1 = new Element(MBTags.advectVelocityFunctionX);
            setExpression(e1, ex, varDomain);
            e.addContent(e1);
        }
        ex = ((PdeEquation) eq).getVelocityY();
        if (ex != null) {
            e1 = new Element(MBTags.advectVelocityFunctionY);
            setExpression(e1, ex, varDomain);
            e.addContent(e1);
        }
    }
    return e;
}