void CellmlFileRuntime::update()
{
// Reset the runtime's properties
reset(true, true);
// Check that the model is either a 'simple' ODE model or a DAE model
// Note #1: we don't check whether a model is valid, since all we want is to
// update its runtime (which has nothing to do with editing or even
// validating a model), so if it can be done then great otherwise
// tough luck (so to speak)...
// Note #2: in order to do so, we need to get a 'normal' code generator (as
// opposed to an IDA, i.e. DAE, code generator) since if the model
// is correctly constrained, then we can check whether some of its
// equations were flagged as needing a Newton-Raphson evaluation,
// in which case we would be dealing with a DAE model...
// Note #3: ideally, there would be a more convenient way to determine the
// type of a model, but there isn't...
iface::cellml_api::Model *model = mCellmlFile->model();
if (!model)
return;
// Retrieve the model's type
// Note: this can be done by checking whether some equations were flagged
// as needing a Newton-Raphson evaluation...
retrieveOdeCodeInformation(model);
if (!mOdeCodeInformation)
return;
ObjRef<iface::mathml_dom::MathMLNodeList> flaggedEquations = mOdeCodeInformation->flaggedEquations();
mModelType = flaggedEquations->length()?CellmlFileRuntime::Dae:CellmlFileRuntime::Ode;
// If the model is of DAE type, then we don't want the ODE-specific code
// information, but the DAE-specific code one
ObjRef<iface::cellml_services::CodeInformation> genericCodeInformation;
if (mModelType == CellmlFileRuntime::Ode) {
genericCodeInformation = mOdeCodeInformation;
} else {
retrieveDaeCodeInformation(model);
if (!mDaeCodeInformation)
return;
genericCodeInformation = mDaeCodeInformation;
}
// Retrieve the number of constants, states/rates, algebraic and conditional
// variables in the model
// Note: this is to avoid having to go through the ODE/DAE code information
// an unnecessary number of times when we want to retrieve either of
// those numbers (e.g. see
// SingleCellViewSimulationResults::addPoint())...
if (mModelType == CellmlFileRuntime::Ode) {
mConstantsCount = mOdeCodeInformation->constantIndexCount();
mStatesRatesCount = mOdeCodeInformation->rateIndexCount();
mAlgebraicCount = mOdeCodeInformation->algebraicIndexCount();
mCondVarCount = 0;
} else {
mConstantsCount = mDaeCodeInformation->constantIndexCount();
mStatesRatesCount = mDaeCodeInformation->rateIndexCount();
mAlgebraicCount = mDaeCodeInformation->algebraicIndexCount();
mCondVarCount = mDaeCodeInformation->conditionVariableCount();
}
// Determine whether the model imports some components
// Note #1: a model that only imports units will clearly not affect our
// model's variables, hence such a model won't be relevant for our
// mapping below...
// Note #2: a model cannot be fully instantiated if it imports an empty
// component or a component with unmapped variables, so we don't
// need to worry about this type of model...
ObjRef<iface::cellml_api::CellMLImportSet> imports = model->imports();
ObjRef<iface::cellml_api::CellMLImportIterator> importsIter = imports->iterateImports();
bool hasComponentImports = false;
for (ObjRef<iface::cellml_api::CellMLImport> import = importsIter->nextImport();
import; import = importsIter->nextImport()) {
ObjRef<iface::cellml_api::ImportComponentSet> importComponents = import->components();
if (importComponents->length()) {
hasComponentImports = true;
break;
}
}
// If the model contains some imports then we want to to go through the
// variables defined or referenced in our main CellML file and do a mapping
// between the source of a variable and a variable in the main CellML file
// Note: indeed, when it comes to CellML 1.1 files, we only want to list the
// parameters that are either defined or referenced in our main CellML
// file. Not only does it make sense, but also only the parameters
// listed in a main CellML file can be referenced in SED-ML...
QMap<iface::cellml_api::CellMLVariable *, iface::cellml_api::CellMLVariable *> mainVariables = QMap<iface::cellml_api::CellMLVariable *, iface::cellml_api::CellMLVariable *>();
ObjRef<iface::cellml_api::CellMLComponentSet> localComponents = model->localComponents();
ObjRef<iface::cellml_api::CellMLComponentIterator> localComponentsIter = localComponents->iterateComponents();
if (hasComponentImports) {
for (ObjRef<iface::cellml_api::CellMLComponent> component = localComponentsIter->nextComponent();
component; component = localComponentsIter->nextComponent()) {
ObjRef<iface::cellml_api::CellMLVariableSet> variables = component->variables();
ObjRef<iface::cellml_api::CellMLVariableIterator> variablesIter = variables->iterateVariables();
for (ObjRef<iface::cellml_api::CellMLVariable> variable = variablesIter->nextVariable();
variable; variable = variablesIter->nextVariable()) {
ObjRef<iface::cellml_api::CellMLVariable> sourceVariable = variable->sourceVariable();
mainVariables.insert(sourceVariable, variable);
}
}
}
// Go through all our computation targets and determine which ones are
// referenced in our main CellML file, and sort them by component and
// variable name
ObjRef<iface::cellml_services::ComputationTargetIterator> computationTargetIter = genericCodeInformation->iterateTargets();
for (ObjRef<iface::cellml_services::ComputationTarget> computationTarget = computationTargetIter->nextComputationTarget();
computationTarget; computationTarget = computationTargetIter->nextComputationTarget()) {
// Make sure that our computation target is defined or referenced in our
// main CellML file, if it has imports
ObjRef<iface::cellml_api::CellMLVariable> variable = computationTarget->variable();
iface::cellml_api::CellMLVariable *mainVariable = mainVariables.value(variable);
iface::cellml_api::CellMLVariable *realVariable = mainVariable?mainVariable:variable.getPointer();
if ( hasComponentImports && !mainVariable
&& (computationTarget->type() != iface::cellml_services::VARIABLE_OF_INTEGRATION)) {
continue;
}
// Determine the type of our computation target
CellmlFileRuntimeParameter::ParameterType parameterType;
switch (computationTarget->type()) {
case iface::cellml_services::VARIABLE_OF_INTEGRATION:
parameterType = CellmlFileRuntimeParameter::Voi;
break;
case iface::cellml_services::CONSTANT:
// We are dealing with a constant, but the question is whether that
// constant is a 'proper' constant, a 'computed' constant or even a
// rate, and this can be determined by checking whether the computed
// target has an initial value or even a degree
// Note: a state variable that is initialised using the initial
// value of another variable will have its rate considered as
// a constant. However, when it comes to the GUI, we really
// want it to be seen as a rate hence we check for the degree
// of the computed target...
if (QString::fromStdWString(variable->initialValue()).isEmpty()) {
// The computed target doesn't have an initial value, so it must
// be a 'computed' constant
parameterType = CellmlFileRuntimeParameter::ComputedConstant;
} else if (computationTarget->degree()) {
// The computed target has a degree, so it is effectively a rate
parameterType = CellmlFileRuntimeParameter::Rate;
} else {
// The computed target has an initial value, so it must be a
// 'proper' constant
parameterType = CellmlFileRuntimeParameter::Constant;
}
break;
case iface::cellml_services::STATE_VARIABLE:
case iface::cellml_services::PSEUDOSTATE_VARIABLE:
parameterType = CellmlFileRuntimeParameter::State;
break;
case iface::cellml_services::ALGEBRAIC:
// We are dealing with either a 'proper' algebraic variable or a
// rate variable
// Note: if the variable's degree is equal to zero, then we are
// dealing with a 'proper' algebraic variable otherwise we
// are dealing with a rate variable...
if (computationTarget->degree())
parameterType = CellmlFileRuntimeParameter::Rate;
else
parameterType = CellmlFileRuntimeParameter::Algebraic;
break;
case iface::cellml_services::FLOATING:
parameterType = CellmlFileRuntimeParameter::Floating;
break;
case iface::cellml_services::LOCALLY_BOUND:
parameterType = CellmlFileRuntimeParameter::LocallyBound;
break;
}
// Keep track of our computation target, should its type be of interest
if ( (parameterType != CellmlFileRuntimeParameter::Floating)
&& (parameterType != CellmlFileRuntimeParameter::LocallyBound)) {
CellmlFileRuntimeParameter *parameter = new CellmlFileRuntimeParameter(QString::fromStdWString(realVariable->name()),
computationTarget->degree(),
QString::fromStdWString(realVariable->unitsName()),
componentHierarchy(realVariable),
parameterType,
computationTarget->assignedIndex());
if (parameterType == CellmlFileRuntimeParameter::Voi)
mVariableOfIntegration = parameter;
if (!hasComponentImports || (realVariable == mainVariable))
mParameters << parameter;
}
}
std::sort(mParameters.begin(), mParameters.end(), sortParameters);
// Generate the model code
QString modelCode = QString();
QString functionsString = QString::fromStdWString(genericCodeInformation->functionsString());
if (!functionsString.isEmpty()) {
// We will need to solve at least one NLA system
mAtLeastOneNlaSystem = true;
modelCode += "struct rootfind_info\n"
"{\n"
" double aVOI;\n"
"\n"
" double *aCONSTANTS;\n"
" double *aRATES;\n"
" double *aSTATES;\n"
" double *aALGEBRAIC;\n"
"\n"
" int *aPRET;\n"
"};\n"
"\n"
"extern void doNonLinearSolve(char *, void (*)(double *, double *, void*), double *, int *, int, void *);\n"
"\n"
+functionsString.replace("do_nonlinearsolve(", QString("doNonLinearSolve(\"%1\", ").arg(address()))
+"\n";
// Note: we rename do_nonlinearsolve() to doNonLinearSolve() because
// CellML's CIS service already defines do_nonlinearsolve(), yet
// we want to use our own non-linear solve routine defined in our
// Compiler plugin. Also, we add a new parameter to all our calls
// to doNonLinearSolve() so that doNonLinearSolve() can retrieve
// the correct instance of our NLA solver...
}
// Retrieve the body of the function that initialises constants and extract
// the statements that are related to computed variables (since we want to
// be able to recompute those whenever the user modifies a parameter)
// Note: ideally, we wouldn't have to do that, but the CellML API doesn't
// distinguish between 'proper' and 'computed' constants...
// (See https://tracker.physiomeproject.org/show_bug.cgi?id=3499)
static const QRegularExpression InitializationStatementRegEx = QRegularExpression("^(CONSTANTS|RATES|STATES)\\[\\d*\\] = [+-]?\\d*\\.?\\d+([eE][+-]?\\d+)?;$");
QStringList initConstsList = cleanCode(genericCodeInformation->initConstsString()).split("\n");
QString initConsts = QString();
QString compCompConsts = QString();
foreach (const QString &initConst, initConstsList) {
// Add the statement either to our list of 'proper' constants or
// 'computed' constants
if (InitializationStatementRegEx.match(initConst).hasMatch())
initConsts += (initConsts.isEmpty()?QString():"\n")+initConst;
else
compCompConsts += (compCompConsts.isEmpty()?QString():"\n")+initConst;
}
modelCode += functionCode("int initializeConstants(double *CONSTANTS, double *RATES, double *STATES)",
initConsts, true);
modelCode += "\n";
modelCode += functionCode("int computeComputedConstants(double *CONSTANTS, double *RATES, double *STATES)",
compCompConsts, true);
modelCode += "\n";
// Retrieve the body of the remaining functions
if (mModelType == CellmlFileRuntime::Ode) {
modelCode += functionCode("int computeOdeRates(double VOI, double *CONSTANTS, double *RATES, double *STATES, double *ALGEBRAIC)",
cleanCode(mOdeCodeInformation->ratesString()));
modelCode += "\n";
modelCode += functionCode("int computeOdeVariables(double VOI, double *CONSTANTS, double *RATES, double *STATES, double *ALGEBRAIC)",
cleanCode(genericCodeInformation->variablesString()));
} else {
modelCode += functionCode("int computeDaeEssentialVariables(double VOI, double *CONSTANTS, double *RATES, double *OLDRATES, double *STATES, double *OLDSTATES, double *ALGEBRAIC, double *CONDVAR)",
cleanCode(mDaeCodeInformation->essentialVariablesString()));
modelCode += "\n";
modelCode += functionCode("int computeDaeResiduals(double VOI, double *CONSTANTS, double *RATES, double *OLDRATES, double *STATES, double *OLDSTATES, double *ALGEBRAIC, double *CONDVAR, double *resid)",
cleanCode(mDaeCodeInformation->ratesString()));
modelCode += "\n";
modelCode += functionCode("int computeDaeRootInformation(double VOI, double *CONSTANTS, double *RATES, double *OLDRATES, double *STATES, double *OLDSTATES, double *ALGEBRAIC, double *CONDVAR)",
cleanCode(mDaeCodeInformation->rootInformationString()));
modelCode += functionCode("int computeDaeStateInformation(double *SI)",
cleanCode(mDaeCodeInformation->stateInformationString()));
modelCode += "\n";
modelCode += functionCode("int computeDaeVariables(double VOI, double *CONSTANTS, double *RATES, double *STATES, double *ALGEBRAIC, double *CONDVAR)",
cleanCode(genericCodeInformation->variablesString()));
}
// Check whether the model code contains a definite integral, otherwise
// compute it and check that everything went fine
if (modelCode.contains("defint(func")) {
mIssues << CellmlFileIssue(CellmlFileIssue::Error,
QObject::tr("definite integrals are not yet supported"));
} else if (!mCompilerEngine->compileCode(modelCode)) {
mIssues << CellmlFileIssue(CellmlFileIssue::Error,
mCompilerEngine->error());
}
// Keep track of the ODE/DAE functions, but only if no issues were reported
if (mIssues.count()) {
reset(true, false);
} else {
// Add the symbol of any required external function, if any
if (mAtLeastOneNlaSystem)
llvm::sys::DynamicLibrary::AddSymbol("doNonLinearSolve",
(void *) (intptr_t) doNonLinearSolve);
// Retrieve the ODE/DAE functions
mInitializeConstants = (InitializeConstantsFunction) (intptr_t) mCompilerEngine->getFunction("initializeConstants");
mComputeComputedConstants = (ComputeComputedConstantsFunction) (intptr_t) mCompilerEngine->getFunction("computeComputedConstants");
if (mModelType == CellmlFileRuntime::Ode) {
mComputeOdeRates = (ComputeOdeRatesFunction) (intptr_t) mCompilerEngine->getFunction("computeOdeRates");
mComputeOdeVariables = (ComputeOdeVariablesFunction) (intptr_t) mCompilerEngine->getFunction("computeOdeVariables");
} else {
mComputeDaeEssentialVariables = (ComputeDaeEssentialVariablesFunction) (intptr_t) mCompilerEngine->getFunction("computeDaeEssentialVariables");
mComputeDaeResiduals = (ComputeDaeResidualsFunction) (intptr_t) mCompilerEngine->getFunction("computeDaeResiduals");
mComputeDaeRootInformation = (ComputeDaeRootInformationFunction) (intptr_t) mCompilerEngine->getFunction("computeDaeRootInformation");
mComputeDaeStateInformation = (ComputeDaeStateInformationFunction) (intptr_t) mCompilerEngine->getFunction("computeDaeStateInformation");
mComputeDaeVariables = (ComputeDaeVariablesFunction) (intptr_t) mCompilerEngine->getFunction("computeDaeVariables");
}
// Make sure that we managed to retrieve all the ODE/DAE functions
bool functionsOk = mInitializeConstants
&& mComputeComputedConstants;
if (mModelType == CellmlFileRuntime::Ode) {
functionsOk = functionsOk
&& mComputeOdeRates
&& mComputeOdeVariables;
} else {
functionsOk = functionsOk
&& mComputeDaeEssentialVariables
&& mComputeDaeResiduals
&& mComputeDaeRootInformation
&& mComputeDaeStateInformation
&& mComputeDaeVariables;
}
if (!functionsOk) {
mIssues << CellmlFileIssue(CellmlFileIssue::Error,
QObject::tr("an unexpected problem occurred while trying to retrieve the model functions"));
reset(true, false);
}
}
}
std::string generateCodeForModel(CellmlApiObjects* capi,
std::map<std::string, unsigned char>& variableTypes,
std::map<std::string, std::map<unsigned char, int> >& variableIndices,
int numberOfInputs, int numberOfStates)
{
std::stringstream code;
std::string codeString;
if (! (capi && capi->codeInformation))
{
std::cerr << "CellML Model Definition::generateCodeForModel: missing model implementation?" << std::endl;
return "";
}
// We need to regenerate the code information to make use of the flagged variables.
ObjRef<iface::cellml_services::CodeGeneratorBootstrap> cgb = CreateCodeGeneratorBootstrap();
ObjRef<iface::cellml_services::CodeGenerator> cg = cgb->createCodeGenerator();
// catch any exceptions from the CellML API
try
{
// annotate the source variables in the model with the code-names based on existing annotations
for (unsigned int i=0; i < capi->cevas->length(); i++)
{
ObjRef<iface::cellml_services::ConnectedVariableSet> cvs = capi->cevas->getVariableSet(i);
ObjRef<iface::cellml_api::CellMLVariable> sv = cvs->sourceVariable();
std::string currentId = getVariableUniqueId(sv);
std::map<std::string, unsigned char>::iterator typeit(variableTypes.find(currentId));
if (typeit != variableTypes.end())
{
std::wstringstream ename;
// here we assign an array and index based on the "primary" purpose of the variable. Later
// we will add in secondary purposes.
unsigned char vType = typeit->second;
if (vType & csim::StateType)
{
ename << L"CSIM_STATE[" << variableIndices[currentId][csim::StateType] << L"]";
}
else if (vType & csim::IndependentType)
{
// do nothing, but stop input and output annotations
}
else if (vType & csim::InputType)
{
ename << L"CSIM_INPUT[" << variableIndices[currentId][csim::InputType] << L"]";
}
else if (vType & csim::OutputType)
{
ename << L"CSIM_OUTPUT[" << variableIndices[currentId][csim::OutputType] << L"]";
}
capi->annotations->setStringAnnotation(sv, L"expression", ename.str());
if (vType & csim::StateType)
{
ename.str(L"");
ename.clear();
ename << L"CSIM_RATE[" << variableIndices[currentId][csim::StateType] << L"]";
capi->annotations->setStringAnnotation(sv, L"expression_d1", ename.str());
}
}
}
cg->useCeVAS(capi->cevas);
cg->useAnnoSet(capi->annotations);
ObjRef<iface::cellml_services::CodeInformation> cci = cg->generateCode(capi->model);
std::wstring m = cci->errorMessage();
if (m != L"")
{
std::cerr << "CellML Model Definition::generateCodeForModel: error generating code?" << std::endl;
return "";
}
iface::cellml_services::ModelConstraintLevel mcl = cci->constraintLevel();
if (mcl == iface::cellml_services::UNDERCONSTRAINED)
{
std::cerr << "Model is underconstrained" << std::endl;
return "";
}
else if (mcl == iface::cellml_services::OVERCONSTRAINED)
{
std::cerr << "Model is overconstrained" << std::endl;
return "";
}
else if (mcl == iface::cellml_services::UNSUITABLY_CONSTRAINED)
{
std::cerr << "Model is unsuitably constrained" << std::endl;
return "";
}
std::cout << "Model is correctly constrained" << std::endl;
// create the code in the format we know how to handle
code << "//#include <math.h>\n"
/* required functions */
<< "double fabs(double x);\n"
<< "double acos(double x);\n"
<< "double acosh(double x);\n"
<< "double atan(double x);\n"
<< "double atanh(double x);\n"
<< "double asin(double x);\n"
<< "double asinh(double x);\n"
<< "double acos(double x);\n"
<< "double acosh(double x);\n"
<< "double asin(double x);\n"
<< "double asinh(double x);\n"
<< "double atan(double x);\n"
<< "double atanh(double x);\n"
<< "double ceil(double x);\n"
<< "double cos(double x);\n"
<< "double cosh(double x);\n"
<< "double tan(double x);\n"
<< "double tanh(double x);\n"
<< "double sin(double x);\n"
<< "double sinh(double x);\n"
<< "double exp(double x);\n"
<< "double floor(double x);\n"
<< "double pow(double x, double y);\n"
<< "double factorial(double x);\n"
<< "double log(double x);\n"
<< "double arbitrary_log(double x, double base);\n"
<< "double gcd_pair(double a, double b);\n"
<< "double lcm_pair(double a, double b);\n"
<< "double gcd_multi(unsigned int size, ...);\n"
<< "double lcm_multi(unsigned int size, ...);\n"
<< "double multi_min(unsigned int size, ...);\n"
<< "double multi_max(unsigned int size, ...);\n"
<< "void NR_MINIMISE(double(*func)"
"(double VOI, double *C, double *R, double *S, double *A),"
"double VOI, double *C, double *R, double *S, double *A, "
"double *V);\n";
std::wstring frag = cci->functionsString();
code << ws2s(frag);
int nAlgebraic = cci->algebraicIndexCount();
int nConstants = cci->constantIndexCount();
code << "\n\nvoid csim_rhs_routine(double VOI, double* CSIM_STATE, double* CSIM_RATE, double* CSIM_OUTPUT, "
<< "double* CSIM_INPUT)\n{\n\n"
<< "double DUMMY_ASSIGNMENT;\n"
<< "double CONSTANTS["
<< nConstants
<< "], ALGEBRAIC["
<< nAlgebraic
<< "];\n\n";
/* initConsts - all variables which aren't state variables but have
* an initial_value attribute, and any variables & rates
* which follow.
*/
code << ws2s(cci->initConstsString());
/* rates - All rates which are not static.
*/
code << ws2s(cci->ratesString());
/* variables - All variables not computed by initConsts or rates
* (i.e., these are not required for the integration of the model and
* thus only need to be called for output or presentation or similar
* purposes)
*/
code << ws2s(cci->variablesString());
// add in the setting of any outputs that are not already defined
for (unsigned int i=0; i < capi->cevas->length(); i++)
{
ObjRef<iface::cellml_services::ConnectedVariableSet> cvs = capi->cevas->getVariableSet(i);
ObjRef<iface::cellml_api::CellMLVariable> sv = cvs->sourceVariable();
std::string currentId = getVariableUniqueId(sv);
std::map<std::string, unsigned char>::iterator typeit(variableTypes.find(currentId));
if (typeit != variableTypes.end())
{
unsigned char vType = typeit->second;
if (vType & csim::OutputType)
{
if (vType & csim::StateType)
code << "CSIM_OUTPUT[" << variableIndices[currentId][csim::OutputType]
<< "] = CSIM_STATE[" << variableIndices[currentId][csim::StateType]
<< "];\n";
else if (vType & csim::InputType)
code << "CSIM_OUTPUT[" << variableIndices[currentId][csim::OutputType]
<< "] = CSIM_INPUT[" << variableIndices[currentId][csim::InputType]
<< "];\n";
else if (vType & csim::IndependentType)
code << "CSIM_OUTPUT[" << variableIndices[currentId][csim::OutputType]
<< "] = VOI;\n";
}
}
}
// close the subroutine
code << "\n\n}//csim_rhs_routine()\n\n";
// and now clear out initialisation of state variables and known variables from
// the RHS routine.
codeString = clearCodeAssignments(code.str(), "CSIM_STATE", numberOfStates);
codeString = clearCodeAssignments(codeString, "CSIM_INPUT", numberOfInputs);
// and finally create the initialisation routine
std::stringstream initRoutine;
initRoutine << "\nvoid csim_initialise_routine(double* CSIM_STATE, double* CSIM_OUTPUT, double* CSIM_INPUT)\n{\n";
// FIXME: this doesn't need to be in the interface?
initRoutine << "double CSIM_RATES[" << numberOfStates << "];\n";
initRoutine << "double CONSTANTS[" << nConstants << "];\n";
initRoutine << ws2s(cci->initConstsString());
initRoutine << "\n}\n";
codeString += initRoutine.str();
}
catch (...)
{
std::cerr << "CellML Model Definition::generateCodeForModel: something went wrong generating code?" << std::endl;
return "";
}
return codeString;
}