private BatchProblemNoDiffusion CreateExampleOne()
{
//components
var componentList = new List <Component>();
componentList.Add(new Component("A", "A"));
componentList.Add(new Component("B", "B"));
// define partial reactions
var ListReaction1LHS = new List <ReactionElement>();
var ListReaction1RHS = new List <ReactionElement>();
ListReaction1LHS.Add(new ReactionElement(componentList[0], 1));
ListReaction1RHS.Add(new ReactionElement(componentList[1], 1));
var Reaction1 = new ElementaryReaction(ListReaction1LHS, ListReaction1RHS, 250000, 50000, 125000, 52000);
//make globalreaction
List <ElementaryReaction> reactionList = new List <ElementaryReaction> {
Reaction1
};
var GlobalReaction = new GlobalReaction(reactionList);
var returnproblem = new BatchProblemNoDiffusion(1000.0, 10, GlobalReaction);
returnproblem.InitialConcentration = new Dictionary <Component, double>(new Component.EqualityComparer());
return(returnproblem);
}
private static BatchProblemNoDiffusion CreateProblem()
{
var componentList = MakeComponents();
// define partial reactions
//B + E -> P
var ListReaction1LHS = new List <ReactionElement>();
var ListReaction1RHS = new List <ReactionElement>();
ListReaction1LHS.Add(new ReactionElement(componentList[1].Copy(), 1));
ListReaction1LHS.Add(new ReactionElement(componentList[4].Copy(), 1));
ListReaction1RHS.Add(new ReactionElement(componentList[5].Copy(), 1));
var Reaction1 = new ElementaryReaction(ListReaction1LHS, ListReaction1RHS, 250000, 60000, 62500, 76000);
//B + A -> BA
var ListReaction2LHS = new List <ReactionElement>();
var ListReaction2RHS = new List <ReactionElement>();
ListReaction2LHS.Add(new ReactionElement(componentList[1].Copy(), 1));
ListReaction2LHS.Add(new ReactionElement(componentList[0].Copy(), 1));
ListReaction2RHS.Add(new ReactionElement(componentList[6].Copy(), 1));
var Reaction2 = new ElementaryReaction(ListReaction2LHS, ListReaction2RHS, 250000, 50000, 125000, 22000);
//BA + E => P + A
var ListReaction3LHS = new List <ReactionElement>();
var ListReaction3RHS = new List <ReactionElement>();
ListReaction3LHS.Add(new ReactionElement(componentList[6].Copy(), 1));
ListReaction3LHS.Add(new ReactionElement(componentList[4].Copy(), 1));
ListReaction3RHS.Add(new ReactionElement(componentList[5].Copy(), 1));
ListReaction3RHS.Add(new ReactionElement(componentList[0].Copy(), 1));
var Reaction3 = new ElementaryReaction(ListReaction3LHS, ListReaction3RHS, 300000, 18000, 150000, 64000);
//dummy reaction C + D => P
var ListReaction4LHS = new List <ReactionElement>();
var ListReaction4RHS = new List <ReactionElement>();
ListReaction4LHS.Add(new ReactionElement(componentList[2].Copy(), 1));
ListReaction4LHS.Add(new ReactionElement(componentList[3].Copy(), 1));
ListReaction4RHS.Add(new ReactionElement(componentList[5].Copy(), 1));
var Reaction4 = new ElementaryReaction(ListReaction4LHS, ListReaction4RHS, 0, 1000000, 0, 1000000);
//make globalreaction
List <ElementaryReaction> reactionList = new List <ElementaryReaction> {
Reaction1, Reaction2, Reaction3, Reaction4
};
var GlobalReaction = new GlobalReaction(reactionList);
return(new BatchProblemNoDiffusion(1000.0, 10, GlobalReaction));
}
public Dictionary <Component, double> UpdateConcentration(ElementaryReaction reaction, Dictionary <Component, double> currentConcentration, double currentTemperature, double timestep)
{
var returnDictionary = new Dictionary <Component, double>(new Component.EqualityComparer());
//calculate rate
double prodConcentration = 1.0;
foreach (var reactionElement in reaction.LeftHandSide)
{
prodConcentration = prodConcentration * Math.Pow(currentConcentration[reactionElement.ReactionComponent], reactionElement.Power);
}
var forwardRate = reaction.ForwardRateCoefficient(currentTemperature) * prodConcentration * timestep;
prodConcentration = 1.0;
foreach (var reactionElement in reaction.RightHandSide)
{
prodConcentration = prodConcentration * Math.Pow(currentConcentration[reactionElement.ReactionComponent], reactionElement.Power);
}
var backwardRate = reaction.BackwardRateCoefficient(currentTemperature) * prodConcentration * timestep;
//calculate concentration changes associated to rates
foreach (var element in reaction.LeftHandSide)
{
if (!returnDictionary.ContainsKey(element.ReactionComponent))
{
returnDictionary.Add(element.ReactionComponent.Copy(), (backwardRate - forwardRate) * element.Power);
}
else
{
returnDictionary[element.ReactionComponent] += (backwardRate - forwardRate) * element.Power;
}
}
foreach (var element in reaction.RightHandSide)
{
if (!returnDictionary.ContainsKey(element.ReactionComponent))
{
returnDictionary.Add(element.ReactionComponent.Copy(), (-backwardRate + forwardRate) * element.Power);
}
else
{
returnDictionary[element.ReactionComponent] += (-backwardRate + forwardRate) * element.Power;
}
}
return(returnDictionary);
}
public static BatchProblemNoDiffusion CreateExample()
{
var componentList = MakeComponents();
// define partial reactions
var ListReaction1LHS = new List <ReactionElement>();
var ListReaction1RHS = new List <ReactionElement>();
ListReaction1LHS.Add(new ReactionElement(componentList[0], 1));
ListReaction1RHS.Add(new ReactionElement(componentList[1], 1));
var Reaction1 = new ElementaryReaction(ListReaction1LHS, ListReaction1RHS, 250000, 50000, 125000, 52000);
//make globalreaction
List <ElementaryReaction> reactionList = new List <ElementaryReaction> {
Reaction1
};
var GlobalReaction = new GlobalReaction(reactionList);
return(new BatchProblemNoDiffusion(1000.0, 10, GlobalReaction));
}
private BatchProblemNoDiffusion CreateExampleTwo()
{
//components
var componentList = new List <Component>();
componentList.Add(new Component("A", "A"));
componentList.Add(new Component("B", "B"));
componentList.Add(new Component("C", "C"));
// define partial reactions
var ListReaction1LHS = new List <ReactionElement>();
var ListReaction1RHS = new List <ReactionElement>();
ListReaction1LHS.Add(new ReactionElement(componentList[0], 1));
ListReaction1RHS.Add(new ReactionElement(componentList[1], 1));
var Reaction1 = new ElementaryReaction(ListReaction1LHS, ListReaction1RHS, 250000, 40000, 125000, 42000);
var ListReaction2LHS = new List <ReactionElement>();
var ListReaction2RHS = new List <ReactionElement>();
ListReaction2LHS.Add(new ReactionElement(componentList[1], 1));
ListReaction2RHS.Add(new ReactionElement(componentList[2], 1));
var Reaction2 = new ElementaryReaction(ListReaction2LHS, ListReaction2RHS, 220000, 51000, 0, 52000);
//make globalreaction
List <ElementaryReaction> reactionList = new List <ElementaryReaction> {
Reaction1, Reaction2
};
var GlobalReaction = new GlobalReaction(reactionList);
var returnproblem = new BatchProblemNoDiffusion(1000.0, 10, GlobalReaction);
return(returnproblem);
}