public void test_RunSteadyStateCalculation_Newton() {
HashMap<String, Object> problemParameters = new HashMap<String, Object>();
problemParameters.put("JacobianRequested", new Boolean(true));
problemParameters.put("StabilityAnalysisRequested", new Boolean(true));
// iteration limit
// tolerance
HashMap<String, Object> methodParameters = new HashMap<String, Object>();
methodParameters.put("Resolution", new Double(1e-9));
methodParameters.put("Derivation Factor", new Double(1e-3));
methodParameters.put("Use Newton", new Boolean(true));
methodParameters.put("Use Integration", new Boolean(false));
methodParameters.put("Use Back Integration", new Boolean(false));
methodParameters.put("Accept Negative Concentrations", new Boolean(false));
methodParameters.put("Iteration Limit", new Integer(50));
// objective function
CSteadyStateTask steadyStateTask =
runSteadyStateCalculation(mDataModel, problemParameters, methodParameters);
assertFalse(steadyStateTask == null);
assertTrue(steadyStateTask.getResult() == CSteadyStateMethod.foundEquilibrium);
CEigen eigenvalues = steadyStateTask.getEigenValues();
assertFalse(eigenvalues == null);
assertTrue(eigenvalues.getMaxrealpart() <= 0.0);
assertTrue(eigenvalues.getNnegreal() + eigenvalues.getNreal() == eigenvalues.getR().size());
}
public static CSteadyStateTask runSteadyStateCalculation(
CCopasiDataModel dataModel,
HashMap<String, Object> problemParameters,
HashMap<String, Object> methodParameters) {
CSteadyStateTask steadyStateTask =
(CSteadyStateTask) dataModel.addTask(CCopasiTask.steadyState);
if (steadyStateTask == null) return null;
CSteadyStateProblem steadyStateProblem = (CSteadyStateProblem) steadyStateTask.getProblem();
if (steadyStateProblem == null) return null;
Set<String> keySet = problemParameters.keySet();
for (Iterator<String> it = keySet.iterator(); it.hasNext(); ) {
String key = (String) it.next();
CCopasiParameter param = steadyStateProblem.getParameter(key);
if (param == null) {
return null;
}
Object o = problemParameters.get(key);
if (o instanceof Double) {
param.setDblValue(((Double) o).doubleValue());
} else if (o instanceof Integer) {
param.setIntValue(((Integer) o).intValue());
} else if (o instanceof Boolean) {
param.setBoolValue(((Boolean) o).booleanValue());
} else if (o instanceof String) {
param.setStringValue(((String) o));
} else {
System.err.println("Error. Unknown parameter type.");
}
}
CNewtonMethod newtonMethod = (CNewtonMethod) steadyStateTask.getMethod();
if (newtonMethod == null) {
return null;
}
keySet = methodParameters.keySet();
for (Iterator<String> it = keySet.iterator(); it.hasNext(); ) {
String key = (String) it.next();
CCopasiParameter param = newtonMethod.getParameter(key);
if (param == null) {
return null;
}
Object o = methodParameters.get(key);
if (o instanceof Double) {
param.setDblValue(((Double) o).doubleValue());
} else if (o instanceof Integer) {
param.setIntValue(((Integer) o).intValue());
} else if (o instanceof Boolean) {
param.setBoolValue(((Boolean) o).booleanValue());
} else if (o instanceof String) {
param.setStringValue(((String) o));
} else {
System.err.println("Error. Unknown parameter type.");
}
}
boolean result = false;
try {
result = steadyStateTask.process(true);
} catch (Exception e) {
System.err.println("ERROR: " + e.getMessage());
}
if (!result) {
return null;
}
return steadyStateTask;
}