bool PropagateEqualities::searchTerm(const ASTNode& lhs, const ASTNode& rhs)
{
const unsigned width = lhs.GetValueWidth();
if (lhs == rhs)
return true;
if (lhs.GetKind() == SYMBOL)
return simp->UpdateSubstitutionMap(lhs, rhs); // checks whether it's been
// solved for, or if the RHS
// contains the LHS.
if (lhs.GetKind() == BVUMINUS)
return searchTerm(lhs[0], nf->CreateTerm(BVUMINUS, width, rhs));
if (lhs.GetKind() == BVNEG)
return searchTerm(lhs[0], nf->CreateTerm(BVNEG, width, rhs));
if (lhs.GetKind() == BVXOR || lhs.GetKind() == BVPLUS)
for (size_t i = 0; i < lhs.Degree(); i++)
{
ASTVec others;
for (size_t j = 0; j < lhs.Degree(); j++)
if (j != i)
others.push_back(lhs[j]);
ASTNode new_rhs;
if (lhs.GetKind() == BVXOR)
{
others.push_back(rhs);
assert(others.size() > 1);
new_rhs = nf->CreateTerm(lhs.GetKind(), width, others);
}
else if (lhs.GetKind() == BVPLUS)
{
if (others.size() > 1)
new_rhs = nf->CreateTerm(BVPLUS, width, others);
else
new_rhs = others[0];
new_rhs = nf->CreateTerm(BVUMINUS, width, new_rhs);
new_rhs = nf->CreateTerm(BVPLUS, width, new_rhs, rhs);
}
else
FatalError("sdafasfsdf2q3234423");
bool result = searchTerm(lhs[i], new_rhs);
if (result)
return true;
}
if (lhs.Degree() == 2 && lhs.GetKind() == BVMULT && lhs[0].isConstant() &&
simp->BVConstIsOdd(lhs[0]))
return searchTerm(lhs[1],
nf->CreateTerm(BVMULT, width,
simp->MultiplicativeInverse(lhs[0]), rhs));
return false;
}
int
ASTPiecewiseFunctionNode::addChild(ASTBase* child, bool inRead)
{
// now here what I want to do is just keep track of the number
// of children being added so the mNumPiece and mHasOtherwise
// variables can be given appropriate values
// but not if we are reading a stream because then we already know
if (inRead == false)
{
if (child->getType() != AST_CONSTRUCTOR_PIECE &&
child->getType() != AST_CONSTRUCTOR_OTHERWISE)
{
// this child does not have a piece/otherwise but if
// the rest of the function does then it needs to fit in with that
unsigned int currentNum = getNumChildren();
if (usingChildConstructors() == false)
{
if ((currentNum+1)%2 == 0)
{
setNumPiece(getNumPiece()+1);
setHasOtherwise(false);
}
else
{
setHasOtherwise(true);
}
return ASTFunctionBase::addChild(child);
}
else
{
ASTBase * lastChild =
ASTFunctionBase::getChild(ASTFunctionBase::getNumChildren()-1);
if (lastChild == NULL)
{ // we have a serious issue going on but may as well just
// add the child
return ASTFunctionBase::addChild(child);
}
else if (lastChild->getType() == AST_CONSTRUCTOR_PIECE)
{
ASTNode * piece = dynamic_cast<ASTNode*>(lastChild);
if (piece == NULL)
{
return LIBSBML_OPERATION_FAILED;
}
if (piece->getNumChildren() == 1)
{
return piece->addChild((ASTNode*)(child));
}
else
{
ASTNode * otherwise = new ASTNode(AST_CONSTRUCTOR_OTHERWISE);
if (otherwise->addChild((ASTNode*)(child)) == LIBSBML_OPERATION_SUCCESS)
{
setHasOtherwise(true);
return ASTFunctionBase::addChild(otherwise);
}
else
{
return LIBSBML_OPERATION_FAILED;
}
}
}
else
{
ASTNode * otherwise = dynamic_cast<ASTNode*>(lastChild);
if (otherwise == NULL || otherwise->getNumChildren() != 1)
{
return LIBSBML_OPERATION_FAILED;
}
ASTNode * piece = new ASTNode(AST_CONSTRUCTOR_PIECE);
// add teh child from teh otherwise
if (piece->addChild(otherwise->getChild(0)) != LIBSBML_OPERATION_SUCCESS)
{
return LIBSBML_OPERATION_FAILED;
}
else
{
if (piece->addChild((ASTNode*)(child)) == LIBSBML_OPERATION_SUCCESS)
{
this->removeChild(currentNum-1);
setHasOtherwise(false);
setNumPiece(getNumPiece() + 1);
return ASTFunctionBase::addChild(piece);
}
else
{
return LIBSBML_OPERATION_FAILED;
}
}
}
}
}
else
{
if (child->getType() == AST_CONSTRUCTOR_PIECE)
{
setNumPiece(getNumPiece()+1);
}
else
{
setHasOtherwise(true);
}
return ASTFunctionBase::addChild(child);
}
}
else
{
return ASTFunctionBase::addChild(child);
}
}
int
ASTPiecewiseFunctionNode::removeChild(unsigned int n)
{
int removed = LIBSBML_INDEX_EXCEEDS_SIZE;
/* HACK TO REPLICATE OLD AST */
/* do not return a node with teh piece or otherwise type
* return the correct child of the piece type
* or the child of the otherwise
*/
unsigned int numChildren = ASTFunctionBase::getNumChildren();
// determine index that we actually want
unsigned int childNo = (unsigned int)(n/2);
unsigned int pieceIndex = (unsigned int)(n%2);
unsigned int size = getNumChildren();
if (size == 0)
{
return LIBSBML_OPERATION_FAILED;
}
if (n < size)
{
if (getHasOtherwise() == true && childNo == numChildren - 1)
{
removed = ASTFunctionBase::removeChild(childNo);
mHasOtherwise = false;
}
else if (ASTFunctionBase::getChild(childNo)->getType()
== AST_CONSTRUCTOR_PIECE)
{
ASTBase * base = ASTFunctionBase::getChild(childNo);
ASTNode * piece = dynamic_cast<ASTNode*>(base);
if (piece != NULL)
{
if (piece->getNumChildren() > pieceIndex)
{
removed = piece->removeChild(pieceIndex);
if (removed == LIBSBML_OPERATION_SUCCESS &&
piece->getNumChildren() == 0)
{
removed = this->ASTFunctionBase::removeChild(childNo);
mNumPiece = mNumPiece - 1;
}
}
else
{
removed = LIBSBML_OPERATION_FAILED;
}
}
else
{
removed = LIBSBML_OPERATION_FAILED;
}
}
else if (n < numChildren)
{
removed = ASTFunctionBase::removeChild(n);
}
else
{
removed = LIBSBML_OPERATION_FAILED;
}
}
return removed;
}
ASTNode BeevMgr::BVConstEvaluator(const ASTNode& t) {
ASTNode OutputNode;
Kind k = t.GetKind();
if(CheckSolverMap(t,OutputNode))
return OutputNode;
OutputNode = t;
unsigned int inputwidth = t.GetValueWidth();
unsigned int outputwidth = inputwidth;
CBV output = NULL;
CBV tmp0 = NULL;
CBV tmp1 = NULL;
//saving some typing. BVPLUS does not use these variables. if the
//input BVPLUS has two nodes, then we want to avoid setting these
//variables.
if(1 == t.Degree() ){
tmp0 = BVConstEvaluator(t[0]).GetBVConst();
}else if(2 == t.Degree() && k != BVPLUS ) {
tmp0 = BVConstEvaluator(t[0]).GetBVConst();
tmp1 = BVConstEvaluator(t[1]).GetBVConst();
}
switch(k) {
case UNDEFINED:
case READ:
case WRITE:
case SYMBOL:
FatalError("BVConstEvaluator: term is not a constant-term",t);
break;
case BVCONST:
//FIXME Handle this special case better
OutputNode = t;
break;
case BVNEG:{
output = CONSTANTBV::BitVector_Create(inputwidth,true);
CONSTANTBV::Set_Complement(output,tmp0);
OutputNode = CreateBVConst(output,outputwidth);
break;
}
case BVSX: {
output = CONSTANTBV::BitVector_Create(inputwidth,true);
//unsigned * out0 = BVConstEvaluator(t[0]).GetBVConst();
unsigned t0_width = t[0].GetValueWidth();
if(inputwidth == t0_width) {
CONSTANTBV::BitVector_Copy(output, tmp0);
OutputNode = CreateBVConst(output, outputwidth);
}
else {
bool topbit_sign = (CONSTANTBV::BitVector_Sign(tmp0) < 0 );
if(topbit_sign){
CONSTANTBV::BitVector_Fill(output);
}
CONSTANTBV::BitVector_Interval_Copy(output, tmp0, 0, 0, t0_width);
OutputNode = CreateBVConst(output, outputwidth);
}
break;
}
case BVAND: {
output = CONSTANTBV::BitVector_Create(inputwidth,true);
CONSTANTBV::Set_Intersection(output,tmp0,tmp1);
OutputNode = CreateBVConst(output, outputwidth);
break;
}
case BVOR: {
output = CONSTANTBV::BitVector_Create(inputwidth,true);
CONSTANTBV::Set_Union(output,tmp0,tmp1);
OutputNode = CreateBVConst(output, outputwidth);
break;
}
case BVXOR: {
output = CONSTANTBV::BitVector_Create(inputwidth,true);
CONSTANTBV::Set_ExclusiveOr(output,tmp0,tmp1);
OutputNode = CreateBVConst(output, outputwidth);
break;
}
case BVSUB: {
output = CONSTANTBV::BitVector_Create(inputwidth,true);
bool carry = false;
CONSTANTBV::BitVector_sub(output,tmp0,tmp1,&carry);
OutputNode = CreateBVConst(output, outputwidth);
break;
}
case BVUMINUS: {
output = CONSTANTBV::BitVector_Create(inputwidth,true);
CONSTANTBV::BitVector_Negate(output, tmp0);
OutputNode = CreateBVConst(output, outputwidth);
break;
}
case BVEXTRACT: {
output = CONSTANTBV::BitVector_Create(inputwidth,true);
tmp0 = BVConstEvaluator(t[0]).GetBVConst();
unsigned int hi = GetUnsignedConst(BVConstEvaluator(t[1]));
unsigned int low = GetUnsignedConst(BVConstEvaluator(t[2]));
unsigned int len = hi-low+1;
CONSTANTBV::BitVector_Destroy(output);
output = CONSTANTBV::BitVector_Create(len, false);
CONSTANTBV::BitVector_Interval_Copy(output, tmp0, 0, low, len);
outputwidth = len;
OutputNode = CreateBVConst(output, outputwidth);
break;
}
//FIXME Only 2 inputs?
case BVCONCAT: {
output = CONSTANTBV::BitVector_Create(inputwidth,true);
unsigned t0_width = t[0].GetValueWidth();
unsigned t1_width = t[1].GetValueWidth();
CONSTANTBV::BitVector_Destroy(output);
output = CONSTANTBV::BitVector_Concat(tmp0, tmp1);
outputwidth = t0_width + t1_width;
OutputNode = CreateBVConst(output, outputwidth);
break;
}
case BVMULT: {
output = CONSTANTBV::BitVector_Create(inputwidth,true);
CBV tmp = CONSTANTBV::BitVector_Create(2*inputwidth,true);
CONSTANTBV::ErrCode e = CONSTANTBV::BitVector_Multiply(tmp,tmp0,tmp1);
if(0 != e) {
BVConstEvaluatorError(e,t);
}
//FIXME WHAT IS MY OUTPUT???? THE SECOND HALF of tmp?
//CONSTANTBV::BitVector_Interval_Copy(output, tmp, 0, inputwidth, inputwidth);
CONSTANTBV::BitVector_Interval_Copy(output, tmp, 0, 0, inputwidth);
OutputNode = CreateBVConst(output, outputwidth);
CONSTANTBV::BitVector_Destroy(tmp);
break;
}
case BVPLUS: {
output = CONSTANTBV::BitVector_Create(inputwidth,true);
bool carry = false;
ASTVec c = t.GetChildren();
for(ASTVec::iterator it=c.begin(),itend=c.end();it!=itend;it++) {
CBV kk = BVConstEvaluator(*it).GetBVConst();
CONSTANTBV::BitVector_add(output,output,kk,&carry);
carry = false;
//CONSTANTBV::BitVector_Destroy(kk);
}
OutputNode = CreateBVConst(output, outputwidth);
break;
}
//FIXME ANOTHER SPECIAL CASE
case SBVDIV:
case SBVMOD:{
OutputNode = BVConstEvaluator(TranslateSignedDivMod(t));
break;
}
case BVDIV:
case BVMOD: {
CBV quotient = CONSTANTBV::BitVector_Create(inputwidth,true);
CBV remainder = CONSTANTBV::BitVector_Create(inputwidth,true);
// tmp0 is dividend, tmp1 is the divisor
//All parameters to BitVector_Div_Pos must be distinct unlike BitVector_Divide
//FIXME the contents of the second parameter to Div_Pos is destroyed
//As tmp0 is currently the same as the copy belonging to an ASTNode t[0]
//this must be copied.
tmp0 = CONSTANTBV::BitVector_Clone(tmp0);
CONSTANTBV::ErrCode e= CONSTANTBV::BitVector_Div_Pos(quotient,tmp0,tmp1,remainder);
CONSTANTBV::BitVector_Destroy(tmp0);
if(0 != e) {
//error printing
if(counterexample_checking_during_refinement) {
output = CONSTANTBV::BitVector_Create(inputwidth,true);
OutputNode = CreateBVConst(output, outputwidth);
bvdiv_exception_occured = true;
// CONSTANTBV::BitVector_Destroy(output);
break;
}
else {
BVConstEvaluatorError(e,t);
}
} //end of error printing
//FIXME Not very standard in the current scheme
if(BVDIV == k){
OutputNode = CreateBVConst(quotient, outputwidth);
CONSTANTBV::BitVector_Destroy(remainder);
}else{
OutputNode = CreateBVConst(remainder, outputwidth);
CONSTANTBV::BitVector_Destroy(quotient);
}
break;
}
case ITE:
if(ASTTrue == t[0])
OutputNode = BVConstEvaluator(t[1]);
else if(ASTFalse == t[0])
OutputNode = BVConstEvaluator(t[2]);
else
FatalError("BVConstEvaluator: ITE condiional must be either TRUE or FALSE:",t);
break;
case EQ:
if(CONSTANTBV::BitVector_equal(tmp0,tmp1))
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
case NEQ:
if(!CONSTANTBV::BitVector_equal(tmp0,tmp1))
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
case BVLT:
if(-1 == CONSTANTBV::BitVector_Lexicompare(tmp0,tmp1))
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
case BVLE: {
int comp = CONSTANTBV::BitVector_Lexicompare(tmp0,tmp1);
if(comp <= 0)
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
}
case BVGT:
if(1 == CONSTANTBV::BitVector_Lexicompare(tmp0,tmp1))
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
case BVGE: {
int comp = CONSTANTBV::BitVector_Lexicompare(tmp0,tmp1);
if(comp >= 0)
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
}
case BVSLT:
if(-1 == CONSTANTBV::BitVector_Compare(tmp0,tmp1))
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
case BVSLE: {
signed int comp = CONSTANTBV::BitVector_Compare(tmp0,tmp1);
if(comp <= 0)
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
}
case BVSGT:
if(1 == CONSTANTBV::BitVector_Compare(tmp0,tmp1))
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
case BVSGE: {
int comp = CONSTANTBV::BitVector_Compare(tmp0,tmp1);
if(comp >= 0)
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
}
default:
FatalError("BVConstEvaluator: The input kind is not supported yet:",t);
break;
}
/*
if(BVCONST != k){
cerr<<inputwidth<<endl;
cerr<<"------------------------"<<endl;
t.LispPrint(cerr);
cerr<<endl;
OutputNode.LispPrint(cerr);
cerr<<endl<<"------------------------"<<endl;
}
*/
UpdateSolverMap(t,OutputNode);
//UpdateSimplifyMap(t,OutputNode,false);
return OutputNode;
}
bool
ASTNaryFunctionNode::isLog10() const
{
bool valid = false;
if (getType() == AST_FUNCTION_LOG)
{
// a log can have either one child that is not the logbase qualifier
// or two where teh first is the logbase of 10
if (getNumChildren() == 1)
{
ASTBase * base1 = ASTFunctionBase::getChild(0);
if (base1->isQualifier() == false)
{
valid = true;
}
}
else if (getNumChildren() == 2)
{
ASTBase * base1 = ASTFunctionBase::getChild(0);
ASTFunction* fun = dynamic_cast<ASTFunction*>(base1);
if (fun != NULL)
{
if (fun->getType() == AST_QUALIFIER_LOGBASE
&& fun->getNumChildren() == 1)
{
ASTBase *base2 = fun->getChild(0);
if (base2->getType() == AST_INTEGER)
{
ASTNumber *child = static_cast<ASTNumber*>(base2);
if (child->getInteger() == 10)
{
valid = true;
}
}
}
}
else
{
// here we are working the ASTNode so the casting
// is more difficult
ASTNode* newAST = dynamic_cast<ASTNode*>(base1);
if (newAST != NULL && newAST->getType() == AST_QUALIFIER_LOGBASE
&& newAST->getNumChildren() == 1 )
{
ASTNode* newAST1 = newAST->getChild(0);
if (newAST1->getType() == AST_INTEGER)
{
if (newAST1->getInteger() == 10)
{
valid = true;
}
}
}
else
{
if (newAST != NULL && newAST->getType() == AST_INTEGER)
{
if (newAST->getInteger() == 10)
{
valid = true;
}
}
}
}
}
}
return valid;
}
int Submodel::convertTimeAndExtentWith(const ASTNode* tcf, const ASTNode* xcf, const ASTNode* klmod)
{
if (tcf==NULL && xcf==NULL) return LIBSBML_OPERATION_SUCCESS;
Model* model = getInstantiation();
if (model==NULL) {
//getInstantiation sets its own error messages.
return LIBSBML_OPERATION_FAILED;
}
ASTNode* tcftimes = NULL;
ASTNode* tcfdiv = NULL;
if (tcf != NULL) {
tcftimes = new ASTNode(AST_TIMES);
tcftimes->addChild(tcf->deepCopy());
tcfdiv = new ASTNode(AST_DIVIDE);
tcfdiv->addChild(tcf->deepCopy());
}
ASTNode* rxndivide = NULL;
if (klmod != NULL) {
rxndivide = new ASTNode(AST_DIVIDE);
ASTNode rxnref(AST_NAME);
rxndivide->addChild(rxnref.deepCopy());
rxndivide->addChild(klmod->deepCopy());
}
List* allelements = model->getAllElements();
for (unsigned int el=0; el<allelements->getSize(); el++) {
SBase* element = static_cast<SBase*>(allelements->get(el));
assert(element != NULL);
ASTNode* ast1 = NULL;
ASTNode* ast2 = NULL;
Constraint* constraint = NULL;
Delay* delay = NULL;
EventAssignment* ea = NULL;
InitialAssignment* ia = NULL;
KineticLaw* kl = NULL;
Priority* priority = NULL;
RateRule* rrule = NULL;
Rule* rule = NULL;
Submodel* submodel = NULL;
Trigger* trigger = NULL;
string cf = "";
//Reaction math will be converted below, in the bits with the kinetic law. But because of that, we need to handle references *to* the reaction: even if it has no kinetic law, the units have changed, and this needs to be reflected by the flattening routine.
if (rxndivide != NULL && element->getTypeCode()==SBML_REACTION && element->isSetId()) {
rxndivide->getChild(0)->setName(element->getId().c_str());
for (unsigned int sube=0; sube<allelements->getSize(); sube++) {
SBase* subelement = static_cast<SBase*>(allelements->get(sube));
subelement->replaceSIDWithFunction(element->getId(), rxndivide);
}
}
//Submodels need their timeConversionFactor and extentConversionFactor attributes converted. We're moving top-down, so all we need to do here is fix the conversion factor attributes themselves, pointing them to new parameters if need be.
if ((tcf !=NULL || xcf != NULL) && element->getTypeCode()==SBML_COMP_SUBMODEL) {
submodel = static_cast<Submodel*>(element);
if (tcf != NULL) {
if (submodel->isSetTimeConversionFactor()) {
createNewConversionFactor(cf, tcf, submodel->getTimeConversionFactor(), model);
submodel->setTimeConversionFactor(cf);
}
else {
submodel->setTimeConversionFactor(tcf->getName());
}
}
if (xcf != NULL) {
if (submodel->isSetExtentConversionFactor()) {
createNewConversionFactor(cf, xcf, submodel->getExtentConversionFactor(), model);
submodel->setExtentConversionFactor(cf);
}
else {
submodel->setExtentConversionFactor(xcf->getName());
}
}
}
if (tcf==NULL) {
if (klmod !=NULL && element->getTypeCode()==SBML_KINETIC_LAW) {
kl = static_cast<KineticLaw*>(element);
if (kl->isSetMath()) {
ast1 = new ASTNode(AST_TIMES);
ast1->addChild(klmod->deepCopy());
ast1->addChild(kl->getMath()->deepCopy());
kl->setMath(ast1);
delete ast1;
}
}
}
else {
// All math 'time' and 'delay' csymbols must still be converted.
// Also, several constructs are modified directly.
switch(element->getTypeCode()) {
//This would be a WHOLE LOT SIMPLER if there was a 'hasMath' class in libsbml. But even so, it would have to
// handle the kinetic laws, rate rules, and delays separately.
case SBML_KINETIC_LAW:
//Kinetic laws are multiplied by 'klmod'.
kl = static_cast<KineticLaw*>(element);
ast1 = kl->getMath()->deepCopy();
convertCSymbols(ast1, tcfdiv, tcftimes);
if (klmod !=NULL) {
kl = static_cast<KineticLaw*>(element);
if (kl->isSetMath()) {
ast2 = new ASTNode(AST_TIMES);
ast2->addChild(klmod->deepCopy());
ast2->addChild(ast1);
kl->setMath(ast2);
delete ast2;
}
}
else {
kl->setMath(ast1);
delete ast1;
}
break;
case SBML_DELAY:
//Delays are multiplied by the time conversion factor.
delay = static_cast<Delay*>(element);
if (delay->isSetMath()) {
ast1 = delay->getMath()->deepCopy();
convertCSymbols(ast1, tcfdiv, tcftimes);
tcftimes->addChild(ast1);
delay->setMath(tcftimes);
tcftimes->removeChild(1);
}
break;
case SBML_RATE_RULE:
//Rate rules are divided by the time conversion factor.
rrule = static_cast<RateRule*>(element);
if (rrule->isSetMath()) {
ast1 = rrule->getMath()->deepCopy();
tcfdiv->insertChild(0, rrule->getMath()->deepCopy());
rrule->setMath(tcfdiv);
tcfdiv->removeChild(0);
}
//Fall through to:
case SBML_ASSIGNMENT_RULE:
case SBML_ALGEBRAIC_RULE:
//Rules in general need csymbols converted.
rule = static_cast<Rule*>(element);
if (rule->isSetMath()) {
ast1 = rule->getMath()->deepCopy();
convertCSymbols(ast1, tcfdiv, tcftimes);
rule->setMath(ast1);
delete ast1;
}
break;
case SBML_EVENT_ASSIGNMENT:
//Event assignments need csymbols converted.
ea = static_cast<EventAssignment*>(element);
if (ea->isSetMath()) {
ast1 = ea->getMath()->deepCopy();
convertCSymbols(ast1, tcfdiv, tcftimes);
ea->setMath(ast1);
delete ast1;
}
break;
case SBML_INITIAL_ASSIGNMENT:
//Initial assignments need csymbols converted.
ia = static_cast<InitialAssignment*>(element);
if (ia->isSetMath()) {
ast1 = ia->getMath()->deepCopy();
convertCSymbols(ast1, tcfdiv, tcftimes);
ia->setMath(ast1);
delete ast1;
}
break;
case SBML_CONSTRAINT:
//Constraints need csymbols converted.
constraint = static_cast<Constraint*>(element);
if (constraint->isSetMath()) {
ast1 = constraint->getMath()->deepCopy();
convertCSymbols(ast1, tcfdiv, tcftimes);
constraint->setMath(ast1);
delete ast1;
}
break;
case SBML_PRIORITY:
//Priorities need csymbols converted.
priority = static_cast<Priority*>(element);
if (priority->isSetMath()) {
ast1 = priority->getMath()->deepCopy();
convertCSymbols(ast1, tcfdiv, tcftimes);
priority->setMath(ast1);
delete ast1;
}
break;
case SBML_TRIGGER:
//Triggers need csymbols converted.
trigger = static_cast<Trigger*>(element);
if (trigger->isSetMath()) {
ast1 = trigger->getMath()->deepCopy();
convertCSymbols(ast1, tcfdiv, tcftimes);
trigger->setMath(ast1);
delete ast1;
}
break;
default:
//Do nothing! If we wanted to call a plugin routine, this would be the place. The only other alternative is to #ifdef some code in here that deals with the math-containing package objects explicitly. Which might be the best option, all told.
break;
}
}
}
delete allelements;
return LIBSBML_OPERATION_SUCCESS;
}
/* FUNCTION: Typechecker for terms and formulas
*
* TypeChecker: Assumes that the immediate Children of the input
* ASTNode have been typechecked. This function is suitable in
* scenarios like where you are building the ASTNode Tree, and you
* typecheck as you go along. It is not suitable as a general
* typechecker.
*
* If this returns, this ALWAYS returns true. If there is an error it
* will call FatalError() and abort.
*/
bool BVTypeCheck(const ASTNode& n)
{
Kind k = n.GetKind();
//The children of bitvector terms are in turn bitvectors.
const ASTVec& v = n.GetChildren();
if (is_Term_kind(k))
{
switch (k)
{
case BVCONST:
if (BITVECTOR_TYPE != n.GetType())
FatalError("BVTypeCheck: The term t does not typecheck, where t = \n", n);
break;
case SYMBOL:
return true;
case ITE:
if (n.Degree() != 3)
FatalError("BVTypeCheck: should have exactly 3 args\n", n);
if (BOOLEAN_TYPE != n[0].GetType() || (n[1].GetType() != n[2].GetType()))
FatalError("BVTypeCheck: The term t does not typecheck, where t = \n", n);
if (n[1].GetValueWidth() != n[2].GetValueWidth())
FatalError("BVTypeCheck: length of THENbranch != length of ELSEbranch in the term t = \n", n);
if (n[1].GetIndexWidth() != n[2].GetIndexWidth())
FatalError("BVTypeCheck: length of THENbranch != length of ELSEbranch in the term t = \n", n);
break;
case READ:
if (n.GetChildren().size() !=2)
FatalError("2 params to read.");
if (n[0].GetIndexWidth() != n[1].GetValueWidth())
{
cerr << "Length of indexwidth of array: " << n[0] << " is : " << n[0].GetIndexWidth() << endl;
cerr << "Length of the actual index is: " << n[1] << " is : " << n[1].GetValueWidth() << endl;
FatalError("BVTypeCheck: length of indexwidth of array != length of actual index in the term t = \n", n);
}
if (ARRAY_TYPE != n[0].GetType())
FatalError("First parameter to read should be an array", n[0]);
if (BITVECTOR_TYPE != n[1].GetType())
FatalError("Second parameter to read should be a bitvector", n[1]);
break;
case WRITE:
if (n.GetChildren().size() !=3)
FatalError("3 params to write.");
if (n[0].GetIndexWidth() != n[1].GetValueWidth())
FatalError("BVTypeCheck: length of indexwidth of array != length of actual index in the term t = \n", n);
if (n[0].GetValueWidth() != n[2].GetValueWidth())
FatalError("BVTypeCheck: valuewidth of array != length of actual value in the term t = \n", n);
if (ARRAY_TYPE != n[0].GetType())
FatalError("First parameter to read should be an array", n[0]);
if (BITVECTOR_TYPE != n[1].GetType())
FatalError("Second parameter to read should be a bitvector", n[1]);
if (BITVECTOR_TYPE != n[2].GetType())
FatalError("Third parameter to read should be a bitvector", n[2]);
break;
case BVDIV:
case BVMOD:
case BVSUB:
case SBVDIV:
case SBVREM:
case SBVMOD:
case BVLEFTSHIFT:
case BVRIGHTSHIFT:
case BVSRSHIFT:
case BVVARSHIFT:
if (n.Degree() != 2)
FatalError("BVTypeCheck: should have exactly 2 args\n", n);
// run on.
case BVOR:
case BVAND:
case BVXOR:
case BVNOR:
case BVNAND:
case BVXNOR:
case BVPLUS:
case BVMULT:
{
if (!(v.size() >= 2))
FatalError("BVTypeCheck:bitwise Booleans and BV arith operators must have at least two arguments\n", n);
unsigned int width = n.GetValueWidth();
for (ASTVec::const_iterator it = v.begin(), itend = v.end(); it != itend; it++)
{
if (width != it->GetValueWidth())
{
cerr << "BVTypeCheck:Operands of bitwise-Booleans and BV arith operators must be of equal length\n";
cerr << n << endl;
cerr << "width of term:" << width << endl;
cerr << "width of offending operand:" << it->GetValueWidth() << endl;
FatalError("BVTypeCheck:Offending operand:\n", *it);
}
if (BITVECTOR_TYPE != it->GetType())
FatalError("BVTypeCheck: ChildNodes of bitvector-terms must be bitvectors\n", n);
}
break;
}
case BVSX:
case BVZX:
//in BVSX(n[0],len), the length of the BVSX term must be
//greater than the length of n[0]
if (n[0].GetValueWidth() > n.GetValueWidth()) {
FatalError(
"BVTypeCheck: BV[SZ]X(t,bv[sz]x_len) : length of 't' must be <= bv[sz]x_len\n",
n);
}
if ((v.size() != 2))
FatalError(
"BVTypeCheck:BV[SZ]X must have two arguments. The second is the new width\n",
n);
break;
case BVCONCAT:
checkChildrenAreBV(v, n);
if (n.Degree() != 2)
FatalError("BVTypeCheck: should have exactly 2 args\n", n);
if (n.GetValueWidth() != n[0].GetValueWidth()
+ n[1].GetValueWidth())
FatalError("BVTypeCheck:BVCONCAT: lengths do not add up\n", n);
break;
case BVUMINUS:
case BVNEG:
checkChildrenAreBV(v, n);
if (n.Degree() != 1)
FatalError("BVTypeCheck: should have exactly 1 args\n", n);
break;
case BVEXTRACT:
checkChildrenAreBV(v, n);
if (n.Degree() != 3)
FatalError("BVTypeCheck: should have exactly 3 args\n", n);
if (!(BVCONST == n[1].GetKind() && BVCONST == n[2].GetKind()))
FatalError("BVTypeCheck: indices should be BVCONST\n", n);
if (n.GetValueWidth() != n[1].GetUnsignedConst()
- n[2].GetUnsignedConst() + 1)
FatalError("BVTypeCheck: length mismatch\n", n);
if (n[1].GetUnsignedConst() >= n[0].GetValueWidth())
FatalError(
"BVTypeCheck: Top index of select is greater or equal to the bitwidth.\n",
n);
break;
default:
cerr << _kind_names[k];
FatalError("No type checking for type");
break;
}
}
else
{
if (!(is_Form_kind(k) && BOOLEAN_TYPE == n.GetType()))
FatalError("BVTypeCheck: not a formula:", n);
switch (k)
{
case TRUE:
case FALSE:
case SYMBOL:
return true;
case PARAMBOOL:
if(2 != n.Degree())
FatalError("BVTypeCheck: PARAMBOOL formula can have exactly two childNodes", n);
break;
case EQ:
if (n.Degree() != 2)
FatalError("BVTypeCheck: should have exactly 2 args\n", n);
if (!(n[0].GetValueWidth() == n[1].GetValueWidth() && n[0].GetIndexWidth() == n[1].GetIndexWidth()))
{
cerr << "valuewidth of lhs of EQ: " << n[0].GetValueWidth() << endl;
cerr << "valuewidth of rhs of EQ: " << n[1].GetValueWidth() << endl;
cerr << "indexwidth of lhs of EQ: " << n[0].GetIndexWidth() << endl;
cerr << "indexwidth of rhs of EQ: " << n[1].GetIndexWidth() << endl;
FatalError("BVTypeCheck: terms in atomic formulas must be of equal length", n);
}
break;
case BVLT:
case BVLE:
case BVGT:
case BVGE:
case BVSLT:
case BVSLE:
case BVSGT:
case BVSGE:
if (n.Degree() != 2)
FatalError("BVTypeCheck: should have exactly 2 args\n", n);
if (BITVECTOR_TYPE != n[0].GetType() && BITVECTOR_TYPE != n[1].GetType())
FatalError("BVTypeCheck: terms in atomic formulas must be bitvectors", n);
if (n[0].GetValueWidth() != n[1].GetValueWidth())
FatalError("BVTypeCheck: terms in atomic formulas must be of equal length", n);
if (n[0].GetIndexWidth() != n[1].GetIndexWidth())
FatalError("BVTypeCheck: terms in atomic formulas must be of equal length", n);
break;
case NOT:
if (1 != n.Degree())
FatalError("BVTypeCheck: NOT formula can have exactly one childNode", n);
break;
case AND:
case OR:
case XOR:
case NAND:
case NOR:
if (2 > n.Degree())
FatalError("BVTypeCheck: AND/OR/XOR/NAND/NOR: must have atleast 2 ChildNodes", n);
break;
case IFF:
case IMPLIES:
if (2 != n.Degree())
FatalError("BVTypeCheck:IFF/IMPLIES must have exactly 2 ChildNodes", n);
break;
case ITE:
if (3 != n.Degree())
FatalError("BVTypeCheck:ITE must have exactly 3 ChildNodes", n);
break;
case FOR:
//FIXME: Todo
break;
default:
FatalError("BVTypeCheck: Unrecognized kind: ");
break;
}
}
return true;
} //End of TypeCheck function
/********************************************************
* TransformFormula()
*
* Get rid of DIV/MODs, ARRAY read/writes, FOR constructs
********************************************************/
ASTNode ArrayTransformer::TransformFormula(const ASTNode& simpleForm)
{
assert(TransformMap != NULL);
const Kind k = simpleForm.GetKind();
if (!(is_Form_kind(k) && BOOLEAN_TYPE == simpleForm.GetType()))
{
//FIXME: "You have inputted a NON-formula"?
FatalError("TransformFormula:"\
"You have input a NON-formula", simpleForm);
}
ASTNodeMap::const_iterator iter;
if ((iter = TransformMap->find(simpleForm)) != TransformMap->end())
return iter->second;
ASTNode result;
switch (k)
{
case TRUE:
case FALSE:
{
result = simpleForm;
break;
}
case NOT:
{
ASTVec c;
c.push_back(TransformFormula(simpleForm[0]));
result = nf->CreateNode(NOT, c);
break;
}
case BOOLEXTRACT:
{
ASTVec c;
c.push_back(TransformTerm(simpleForm[0]));
c.push_back(simpleForm[1]);
result = nf->CreateNode(BOOLEXTRACT, c);
break;
}
case BVLT:
case BVLE:
case BVGT:
case BVGE:
case BVSLT:
case BVSLE:
case BVSGT:
case BVSGE:
{
ASTVec c;
c.push_back(TransformTerm(simpleForm[0]));
c.push_back(TransformTerm(simpleForm[1]));
result = nf->CreateNode(k, c);
break;
}
case EQ:
{
ASTNode term1 = TransformTerm(simpleForm[0]);
ASTNode term2 = TransformTerm(simpleForm[1]);
if (bm->UserFlags.optimize_flag)
result = simp->CreateSimplifiedEQ(term1, term2);
else
result = nf->CreateNode(EQ,term1, term2);
break;
}
case AND: // These could shortcut. Not sure if the extra effort is justified.
case OR:
case NAND:
case NOR:
case IFF:
case XOR:
case ITE:
case IMPLIES:
{
ASTVec vec;
vec.reserve(simpleForm.Degree());
for (ASTVec::const_iterator
it = simpleForm.begin(),
itend = simpleForm.end(); it != itend; it++)
{
vec.push_back(TransformFormula(*it));
}
result = nf->CreateNode(k, vec);
break;
}
case PARAMBOOL:
{
//If the parameteric boolean variable is of the form
//VAR(const), then convert it into a Boolean variable of the
//form "VAR(const)".
//
//Else if the paramteric boolean variable is of the form
//VAR(expression), then simply return it
if(BVCONST == simpleForm[1].GetKind())
{
result =
bm->NewParameterized_BooleanVar(simpleForm[0],simpleForm[1]);
}
else
{
result = simpleForm;
}
break;
}
default:
{
if (k == SYMBOL && BOOLEAN_TYPE == simpleForm.GetType())
result = simpleForm;
else
{
FatalError("TransformFormula: Illegal kind: ",
ASTUndefined, k);
std::cerr << "The input is: " << simpleForm << std::endl;
std::cerr << "The valuewidth of input is : "
<< simpleForm.GetValueWidth() << std::endl;
}
break;
}
} //end of Switch
assert(!result.IsNull());
if (simpleForm.Degree() > 0)
(*TransformMap)[simpleForm] = result;
return result;
} //End of TransformFormula
ASTNode ArrayTransformer::TransformTerm(const ASTNode& term)
{
assert(TransformMap != NULL);
const Kind k = term.GetKind();
if (!is_Term_kind(k))
FatalError("TransformTerm: Illegal kind: You have input a nonterm:",
term, k);
ASTNodeMap::const_iterator iter;
if ((iter = TransformMap->find(term)) != TransformMap->end())
return iter->second;
ASTNode result;
switch (k)
{
case SYMBOL:
case BVCONST:
{
result = term;
break;
}
case WRITE:
FatalError("TransformTerm: this kind is not supported", term);
break;
case READ:
result = TransformArrayRead(term);
break;
case ITE:
{
ASTNode cond = term[0];
ASTNode thn = term[1];
ASTNode els = term[2];
cond = TransformFormula(cond);
if (ASTTrue == cond)
result = TransformTerm(thn);
else if (ASTFalse == cond)
result = TransformTerm(els);
else
{
thn = TransformTerm(thn);
els = TransformTerm(els);
if (bm->UserFlags.optimize_flag)
result = simp->CreateSimplifiedTermITE(cond, thn, els);
else
result = nf->CreateTerm(ITE, thn.GetValueWidth(), cond, thn, els);
}
assert(result.GetIndexWidth() ==term.GetIndexWidth());
break;
}
default:
{
const ASTVec& c = term.GetChildren();
ASTVec::const_iterator it = c.begin();
ASTVec::const_iterator itend = c.end();
const unsigned width = term.GetValueWidth();
const unsigned indexwidth = term.GetIndexWidth();
ASTVec o;
o.reserve(c.size());
for (; it != itend; it++)
{
o.push_back(TransformTerm(*it));
}
if (c!=o)
{
result = nf->CreateArrayTerm(k,indexwidth, width, o);
}
else
result = term;
}
break;
}
if (term.Degree() > 0)
(*TransformMap)[term] = result;
if (term.GetValueWidth() != result.GetValueWidth())
FatalError("TransformTerm: "\
"result and input terms are of different length", result);
if (term.GetIndexWidth() != result.GetIndexWidth())
{
std::cerr << "TransformTerm: input term is : " << term << std::endl;
FatalError("TransformTerm: "\
"result & input terms have different index length", result);
}
return result;
} //End of TransformTerm
/*
* Checks the MathML of the ASTnode
* is appropriate for the function being performed
*
* If an inconsistency is found, an error message is logged.
*/
void
NumericArgsMathCheck::checkMath (const Model& m, const ASTNode& node, const SBase & sb)
{
// does not apply in L3V2 for general consistency checking
// BUT we want to use it for telling a converter that this occurs in L3V2
if (this->mValidator.getCategory() == LIBSBML_CAT_MATHML_CONSISTENCY)
{
if (m.getLevel() == 3 && m.getVersion() > 1) return;
}
else
{
if (m.getLevel() != 3) return;
else if (m.getVersion() == 1) return;
}
ASTNodeType_t type = node.getType();
switch (type)
{
case AST_PLUS:
case AST_MINUS:
case AST_TIMES:
case AST_DIVIDE:
case AST_POWER:
case AST_FUNCTION_POWER:
case AST_FUNCTION_ROOT:
case AST_FUNCTION_ABS:
case AST_FUNCTION_EXP:
case AST_FUNCTION_LN:
case AST_FUNCTION_LOG:
case AST_FUNCTION_CEILING:
case AST_FUNCTION_FLOOR:
case AST_FUNCTION_FACTORIAL:
case AST_FUNCTION_COS:
case AST_FUNCTION_COT:
case AST_FUNCTION_CSC:
case AST_FUNCTION_SEC:
case AST_FUNCTION_SIN:
case AST_FUNCTION_TAN:
case AST_FUNCTION_COSH:
case AST_FUNCTION_COTH:
case AST_FUNCTION_CSCH:
case AST_FUNCTION_SECH:
case AST_FUNCTION_SINH:
case AST_FUNCTION_TANH:
case AST_FUNCTION_ARCCOSH:
case AST_FUNCTION_ARCCOTH:
case AST_FUNCTION_ARCCSCH:
case AST_FUNCTION_ARCSECH:
case AST_FUNCTION_ARCSINH:
case AST_FUNCTION_ARCTANH:
case AST_FUNCTION_ARCCOS:
case AST_FUNCTION_ARCCOT:
case AST_FUNCTION_ARCCSC:
case AST_FUNCTION_ARCSEC:
case AST_FUNCTION_ARCSIN:
case AST_FUNCTION_ARCTAN:
checkNumericArgs(m, node, sb);
break;
case AST_FUNCTION:
checkFunction(m, node, sb);
break;
default:
checkChildren(m, node, sb);
break;
}
}
//Translates signed BVDIV,BVMOD and BVREM into unsigned variety
ASTNode ArrayTransformer::TranslateSignedDivModRem(const ASTNode& in, NodeFactory* nf, STPMgr *bm)
{
assert(in.GetChildren().size() ==2);
const ASTNode& dividend = in[0];
const ASTNode& divisor = in[1];
const unsigned len = in.GetValueWidth();
ASTNode hi1 = bm->CreateBVConst(32, len - 1);
ASTNode one = bm->CreateOneConst(1);
ASTNode zero = bm->CreateZeroConst(1);
// create the condition for the dividend
ASTNode cond_dividend =
nf->CreateNode(EQ, one, nf->CreateTerm(BVEXTRACT, 1, dividend, hi1, hi1));
// create the condition for the divisor
ASTNode cond_divisor =
nf->CreateNode(EQ, one,
nf->CreateTerm(BVEXTRACT, 1, divisor, hi1, hi1));
if (SBVREM == in.GetKind())
{
//BVMOD is an expensive operation. So have the fewest bvmods
//possible. Just one.
//Take absolute value.
ASTNode pos_dividend =
nf->CreateTerm(ITE, len,
cond_dividend,
nf->CreateTerm(BVUMINUS, len, dividend),
dividend);
ASTNode pos_divisor =
nf->CreateTerm(ITE, len,
cond_divisor,
nf->CreateTerm(BVUMINUS, len, divisor),
divisor);
//create the modulus term
ASTNode modnode =
nf->CreateTerm(BVMOD, len,
pos_dividend, pos_divisor);
//If the dividend is <0 take the unary minus.
ASTNode n =
nf->CreateTerm(ITE, len,
cond_dividend,
nf->CreateTerm(BVUMINUS, len, modnode),
modnode);
return n;
}
// This is the modulus of dividing rounding to -infinity.
else if (SBVMOD == in.GetKind())
{
/*
(bvsmod s t) abbreviates
(let ((?msb_s ((_ extract |m-1| |m-1|) s))
(?msb_t ((_ extract |m-1| |m-1|) t)))
(let ((abs_s (ite (= ?msb_s #b0) s (bvneg s)))
(abs_t (ite (= ?msb_t #b0) t (bvneg t))))
(let ((u (bvurem abs_s abs_t)))
(ite (= u (_ bv0 m))
u
(ite (and (= ?msb_s #b0) (= ?msb_t #b0))
u
(ite (and (= ?msb_s #b1) (= ?msb_t #b0))
(bvadd (bvneg u) t)
(ite (and (= ?msb_s #b0) (= ?msb_t #b1))
(bvadd u t)
(bvneg u))))))))
*/
//Take absolute value.
ASTNode pos_dividend =
nf->CreateTerm(ITE, len,
cond_dividend,
nf->CreateTerm(BVUMINUS, len, dividend),
dividend);
ASTNode pos_divisor =
nf->CreateTerm(ITE, len,
cond_divisor,
nf->CreateTerm(BVUMINUS, len, divisor),
divisor);
ASTNode urem_node =
nf->CreateTerm(BVMOD, len,
pos_dividend, pos_divisor);
// If the dividend is <0, then we negate the whole thing.
ASTNode rev_node =
nf->CreateTerm(ITE, len,
cond_dividend,
nf->CreateTerm(BVUMINUS, len, urem_node),
urem_node);
// if It's XOR <0, and it doesn't perfectly divide, then add t (not its absolute value).
ASTNode xor_node =
nf->CreateNode(XOR, cond_dividend, cond_divisor);
ASTNode neZ = nf->CreateNode(NOT, nf->CreateNode(EQ, rev_node, bm->CreateZeroConst(divisor.GetValueWidth())));
ASTNode cond = nf->CreateNode(AND,xor_node ,neZ);
ASTNode n =
nf->CreateTerm(ITE, len,
cond,
nf->CreateTerm(BVPLUS, len, rev_node, divisor),
rev_node);
return n;
}
else if (SBVDIV == in.GetKind())
{
//now handle the BVDIV case
//if topBit(dividend) is 1 and topBit(divisor) is 0
//
//then output is -BVDIV(-dividend,divisor)
//
//elseif topBit(dividend) is 0 and topBit(divisor) is 1
//
//then output is -BVDIV(dividend,-divisor)
//
//elseif topBit(dividend) is 1 and topBit(divisor) is 1
//
// then output is BVDIV(-dividend,-divisor)
//
//else simply output BVDIV(dividend,divisor)
//Take absolute value.
ASTNode pos_dividend =
nf->CreateTerm(ITE, len,
cond_dividend,
nf->CreateTerm(BVUMINUS, len, dividend),
dividend);
ASTNode pos_divisor =
nf->CreateTerm(ITE, len,
cond_divisor,
nf->CreateTerm(BVUMINUS, len, divisor),
divisor);
ASTNode divnode =
nf->CreateTerm(BVDIV, len, pos_dividend, pos_divisor);
// A little confusing. Only negate the result if they are XOR <0.
ASTNode xor_node =
nf->CreateNode(XOR, cond_dividend, cond_divisor);
ASTNode n =
nf->CreateTerm(ITE, len,
xor_node,
nf->CreateTerm(BVUMINUS, len, divnode),
divnode);
return n;
}
FatalError("TranslateSignedDivModRem:"\
"input must be signed DIV/MOD/REM", in);
return bm->ASTUndefined;
}//end of TranslateSignedDivModRem()
void dealWithL1Stoichiometry(Model & m, bool l2)
{
unsigned int idCount = 0;
char newid[15];
std::string id;
for (unsigned int i = 0; i < m.getNumReactions(); i++)
{
Reaction *r = m.getReaction(i);
unsigned int j;
for (j = 0; j < r->getNumReactants(); j++)
{
SpeciesReference *sr = r->getReactant(j);
if (sr->getDenominator() != 1)
{
long stoich = static_cast<long>(sr->getStoichiometry());
int denom = sr->getDenominator();
ASTNode *node = new ASTNode();
node->setValue(stoich, denom);
if (l2 == true)
{
StoichiometryMath * sm = sr->createStoichiometryMath();
sm->setMath(node);
}
else
{
sprintf(newid, "speciesRefId_%u", idCount);
id.assign(newid);
idCount++;
sr->setId(id);
InitialAssignment * ar = m.createInitialAssignment();
ar->setSymbol(id);
ar->setMath(node);
sr->unsetStoichiometry();
}
}
}
for (j = 0; j < r->getNumProducts(); j++)
{
SpeciesReference *sr = r->getProduct(j);
if (sr->getDenominator() != 1)
{
long stoich = static_cast<long>(sr->getStoichiometry());
int denom = sr->getDenominator();
ASTNode *node = new ASTNode();
node->setValue(stoich, denom);
if (l2 == true)
{
StoichiometryMath * sm = sr->createStoichiometryMath();
sm->setMath(node);
}
else
{
sprintf(newid, "speciesRefId_%u", idCount);
id.assign(newid);
idCount++;
sr->setId(id);
InitialAssignment * ar = m.createInitialAssignment();
ar->setSymbol(id);
ar->setMath(node);
sr->unsetStoichiometry();
}
}
}
}
}
END_TEST
START_TEST(test_SBMLTransforms_evaluateAST)
{
double temp;
ASTNode * node = new ASTNode();
node->setValue((int)(2));
fail_unless(SBMLTransforms::evaluateASTNode(node) == 2);
node->setValue((double) (3.2));
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 3.2));
node->setValue((long)(1), (long)(4));
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 0.25));
node->setValue((double) (4.234), (int) (2));
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 423.4));
node->setType(AST_NAME_AVOGADRO);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 6.02214179e23));
node->setType(AST_NAME_TIME);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 0.0));
node->setType(AST_NAME);
fail_unless(isnan(SBMLTransforms::evaluateASTNode(node)));
node->setType(AST_CONSTANT_E);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), exp(1.0)));
node->setType(AST_CONSTANT_FALSE);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 0.0));
node->setType(AST_CONSTANT_PI);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 4.0*atan(1.0)));
node->setType(AST_CONSTANT_TRUE);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 1.0));
node = SBML_parseFormula("2.5 + 6.1");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 8.6));
node = SBML_parseFormula("-4.3");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), -4.3));
node = SBML_parseFormula("9.2-4.3");
temp = 9.2-4.3;
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("2*3");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 6));
node = SBML_parseFormula("1/5");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 0.2));
node = SBML_parseFormula("pow(2, 3)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 8));
node = SBML_parseFormula("3^3");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 27));
node = SBML_parseFormula("abs(-9.456)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 9.456));
node = SBML_parseFormula("ceil(9.456)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 10));
node = SBML_parseFormula("exp(2.0)");
temp = exp(2.0);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("floor(2.04567)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 2));
node = SBML_parseFormula("ln(2.0)");
temp = log(2.0);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("log10(100.0)");
temp = log10(100.0);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("sin(2.0)");
temp = sin(2.0);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("cos(4.1)");
temp = cos(4.1);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("tan(0.345)");
temp = tan(0.345);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("arcsin(0.456)");
temp = asin(0.456);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("arccos(0.41)");
temp = acos(0.41);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("arctan(0.345)");
temp = atan(0.345);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("sinh(2.0)");
temp = sinh(2.0);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("cosh(4.1)");
temp = cosh(4.1);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("tanh(0.345)");
temp = tanh(0.345);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("and(1, 0)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 0.0));
node = SBML_parseFormula("or(1, 0)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 1.0));
node = SBML_parseFormula("not(1)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 0.0));
node = SBML_parseFormula("xor(1, 0)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 1.0));
node = SBML_parseFormula("xor(1, 1)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 0.0));
node = SBML_parseFormula("eq(1, 2)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 0.0));
node = SBML_parseFormula("eq(1, 1)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 1.0));
node = SBML_parseFormula("geq(2,1)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 1.0));
node = SBML_parseFormula("geq(2,4)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 0.0));
node = SBML_parseFormula("geq(2,2)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 1.0));
node = SBML_parseFormula("gt(2,1)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 1.0));
node = SBML_parseFormula("gt(2,4)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 0.0));
node = SBML_parseFormula("leq(2,1)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 0.0));
node = SBML_parseFormula("leq(2,4)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 1.0));
node = SBML_parseFormula("leq(2,2)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 1.0));
node = SBML_parseFormula("lt(2,1)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 0.0));
node = SBML_parseFormula("lt(2,4)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 1.0));
node = SBML_parseFormula("neq(2,2)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 0.0));
node = SBML_parseFormula("neq(3,2)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 1.0));
node = SBML_parseFormula("cot(2.0)");
temp = 1.0/tan(2.0);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("csc(4.1)");
temp = 1.0/sin(4.1);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("sec(0.345)");
temp = 1.0/cos(0.345);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("coth(2.0)");
temp = cosh(2.0)/sinh(2.0);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("sech(2.0)");
temp = 1.0/cosh(2.0);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("csch(2.0)");
temp = 1.0/sinh(2.0);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("arccot(2.0)");
temp = atan(1/2.0);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("arccsc(2.0)");
temp = asin(1/2.0);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("arcsec(2.0)");
temp = acos(1/2.0);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("arccosh(2.0)");
temp = log(2.0 + pow(3.0, 0.5));
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("arccoth(2.0)");
temp = 0.5 * log(3.0);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("arcsech(0.2)");
temp = log(2*pow(6, 0.5)+5);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("arccsch(0.2)");
/* temp = log(5 +pow(26, 0.5));
* only matches to 15 dp and therefore fails !!
*/
temp = 2.312438341272753;
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("arcsinh(3.0)");
temp = log(3.0 +pow(10.0, 0.5));
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node = SBML_parseFormula("arctanh(0.2)");
temp = 0.5 * log(1.5);
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), temp));
node->setType(AST_FUNCTION_DELAY);
fail_unless(isnan(SBMLTransforms::evaluateASTNode(node)));
node = SBML_parseFormula("factorial(3)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 6));
node->setType(AST_FUNCTION_PIECEWISE);
fail_unless(isnan(SBMLTransforms::evaluateASTNode(node)));
node = SBML_parseFormula("root(2, 4)");
fail_unless(equalDouble(SBMLTransforms::evaluateASTNode(node), 2));
}
string Bench_Print1(ostream& os, const ASTNode& n,
map<ASTNode, string>* alreadyOutput)
{
assert(((n.GetKind() == SYMBOL) || (n.GetKind() == BVCONST) ||
n.GetValueWidth() <= 1));
assert(!n.IsNull());
map<ASTNode, string>::iterator it;
if ((it = alreadyOutput->find(n)) != alreadyOutput->end())
return it->second;
if (n.GetKind() == BVCONST)
{
(*alreadyOutput)[n] = bvconstToString(n);
return (*alreadyOutput)[n];
}
if (n.GetKind() == SYMBOL)
{
(*alreadyOutput)[n] = symbolToString(n);
return (*alreadyOutput)[n];
}
if (n.GetKind() == TRUE)
{
return "vdd";
}
if (n.GetKind() == FALSE)
{
return "gnd";
}
if (n.GetKind() == BOOLEXTRACT)
{
assert(n[1].GetKind() == BVCONST);
std::stringstream nn;
nn << Bench_Print1(os, n[0], alreadyOutput) << "_"
<< Bench_Print1(os, n[1], alreadyOutput);
(*alreadyOutput)[n] = nn.str();
return (*alreadyOutput)[n];
}
std::stringstream nodeNameSS;
nodeNameSS << "n" << n.GetNodeNum();
string thisNode = nodeNameSS.str();
(*alreadyOutput)[n] = thisNode;
assert(n.Degree() > 0);
std::stringstream output;
// The bench format doesn't accept propositional ITEs.
if (n.GetKind() == ITE)
{
assert(n.Degree() == 3);
string p = Bench_Print1(os, n[0], alreadyOutput);
string p1 = Bench_Print1(os, n[1], alreadyOutput);
string p2 = Bench_Print1(os, n[2], alreadyOutput);
os << thisNode << "_1 = AND(" << p << "," << p1 << ")" << endl;
os << thisNode << "_2"
<< " = NOT(" << p << ")," << endl;
os << thisNode << "_3"
<< " = AND(" << thisNode << "_2"
<< "," << p2 << ")" << endl;
os << thisNode << "="
<< "OR(," << thisNode << "_1"
<< "," << thisNode << "_3)" << endl;
}
else
{
if (n.Degree() > 2)
{
assert(n.GetKind() == AND || n.GetKind() == XOR ||
n.GetKind() == OR); // must be associative.
std::deque<string> names;
for (unsigned i = 0; i < n.Degree(); i++)
names.push_back(Bench_Print1(os, n[i], alreadyOutput));
int id = 0;
while (names.size() > 2)
{
string a = names.front();
names.pop_front();
string b = names.front();
names.pop_front();
std::stringstream thisName;
thisName << thisNode << "___" << id++;
output << thisName.str() << "=" << name(n.GetKind()) << "(" << a << ","
<< b << ")" << endl;
names.push_back(thisName.str());
}
assert(names.size() == 2);
// last two now.
string a = names.front();
names.pop_front();
string b = names.front();
names.pop_front();
output << thisNode << "=" << name(n.GetKind()) << "(" << a << "," << b
<< ")" << endl;
os << output.str();
}
else
{
output << thisNode << "=" << name(n.GetKind()) << "(";
for (unsigned i = 0; i < n.Degree(); i++)
{
if (i >= 1)
output << " , ";
output << Bench_Print1(os, n[i], alreadyOutput);
}
os << output.str() << ")" << endl;
}
}
return thisNode;
}
bool CodeGeneratorVisitor::performStep(ASTNode& node)
{
node.accept(*this);
return true;
}
/* This function transforms Array Reads, Read over Writes, Read over
* ITEs into flattened form.
*
* Transform1: Suppose there are two array reads in the input
* Read(A,i) and Read(A,j) over the same array. Then Read(A,i) is
* replaced with a symbolic constant, say v1, and Read(A,j) is
* replaced with the following ITE:
*
* ITE(i=j,v1,v2)
*
*/
ASTNode ArrayTransformer::TransformArrayRead(const ASTNode& term)
{
assert(TransformMap != NULL);
const unsigned int width = term.GetValueWidth();
if (READ != term.GetKind())
return term;
ASTNodeMap::const_iterator iter;
if ((iter = TransformMap->find(term)) != TransformMap->end())
return iter->second;
//'term' is of the form READ(arrName, readIndex)
const ASTNode & arrName = term[0];
const ASTNode & readIndex = TransformTerm(term[1]);
ASTNode result;
switch (arrName.GetKind())
{
case SYMBOL:
{
/* input is of the form: READ(A, readIndex)
*
* output is of the from: A1, if this is the first READ over A
*
* ITE(previous_readIndex=readIndex,A1,A2)
*
* .....
*/
{
ArrType::const_iterator it;
if ((it = arrayToIndexToRead.find(arrName)) != arrayToIndexToRead.end())
{
std::map<ASTNode, ArrayRead>::const_iterator it2;
if ((it2 = it->second.find(readIndex)) != it->second.end())
{
result = it2->second.ite;
break;
}
}
}
// Make up a new abstract variable. Build symbolic name
// corresponding to array read. The symbolic name has 2
// components: stringname, and a count
ASTNode CurrentSymbol = bm->CreateFreshVariable(
term.GetIndexWidth(),
term.GetValueWidth(),
"array_" + string(arrName.GetName()));
result = CurrentSymbol;
if (!bm->UserFlags.ackermannisation)
{
// result is a variable here; it is an ite in the
// else-branch
}
else if (bm->UserFlags.isSet("old_ack","0"))
{
/* oops.
* This version of ack. doesn't do what I thought it did. The STP 0.1 version of Ack. produces simpler
* expressions. I've put that in the next block. Trevor's thesis measures AckITE using this implementation,
* rather than the next one like it should have!!!!
*/
// Full Array transform if we're not doing read refinement.
//list of array-read indices corresponding to arrName, seen while
//traversing the AST tree. we need this list to construct the ITEs
const arrTypeMap& new_read_Indices = arrayToIndexToRead[arrName];
arrTypeMap::const_iterator it2 = new_read_Indices.begin();
arrTypeMap::const_iterator it2end = new_read_Indices.end();
for (; it2 != it2end; it2++)
{
ASTNode cond = simp->CreateSimplifiedEQ(readIndex, it2->first);
if (ASTFalse == cond)
continue;
if (ASTTrue == cond)
{
result = it2->second.ite;
break;
}
result =
simp->CreateSimplifiedTermITE(cond, it2->second.ite, result);
}
}
else
{
// Full Array transform if we're not doing read refinement.
//list of array-read indices corresponding to arrName, seen while
//traversing the AST tree. we need this list to construct the ITEs
vector<std::pair<ASTNode, ASTNode > > p = ack_pair[arrName];
vector<std::pair<ASTNode, ASTNode > >::const_reverse_iterator it2 = p.rbegin();
vector<std::pair<ASTNode, ASTNode > >::const_reverse_iterator it2end = p.rend();
for (; it2 != it2end; it2++)
{
ASTNode cond = simp->CreateSimplifiedEQ(readIndex, it2->first);
if (ASTFalse == cond)
continue;
if (ASTTrue == cond)
{
result = it2->second;
break;
}
result =
simp->CreateSimplifiedTermITE(cond, it2->second, result);
}
ack_pair[arrName].push_back(make_pair(readIndex,CurrentSymbol));
}
assert(arrName.GetType() == ARRAY_TYPE);
arrayToIndexToRead[arrName].insert(make_pair(readIndex,ArrayRead (result, CurrentSymbol)));
break;
} //end of READ over a SYMBOL
case WRITE:
{
/* The input to this case is: READ((WRITE A i val) j)
*
* The output of this case is: ITE( (= i j) val (READ A j))
*/
/* 1. arrName or term[0] is infact a WRITE(A,i,val) expression
*
* 2. term[1] is the read-index j
*
* 3. arrName[0] is the new arrName i.e. A. A can be either a
SYMBOL or a nested WRITE. no other possibility
*
* 4. arrName[1] is the WRITE index i.e. i
*
* 5. arrName[2] is the WRITE value i.e. val (val can inturn
* be an array read)
*/
ASTNode writeIndex = TransformTerm(arrName[1]);
ASTNode writeVal = TransformTerm(arrName[2]);
if (ARRAY_TYPE != arrName[0].GetType())
FatalError("TransformArray: "\
"An array write is being attempted on a non-array:",
term);
//if ((SYMBOL == arrName[0].GetKind()
//|| WRITE == arrName[0].GetKind()))
{
ASTNode cond =
simp->CreateSimplifiedEQ(writeIndex, readIndex);
assert(BVTypeCheck(cond));
// If the condition is true, it saves iteratively transforming through
// all the (possibly nested) arrays.
if (ASTTrue == cond)
{
result = writeVal;
}
else
{
ASTNode readTerm =
nf->CreateTerm(READ, width, arrName[0], readIndex);
assert(BVTypeCheck(readTerm));
// The simplifying node factory may have produced
// something that's not a READ.
ASTNode readPushedIn = TransformTerm(readTerm);
assert(BVTypeCheck(readPushedIn));
result =
simp->CreateSimplifiedTermITE(cond, writeVal, readPushedIn);
}
}
// Trevor: I've removed this code because I don't see the advantage in working
// inside out. i.e. transforming read(write(ite(p,A,B),i,j),k), into
// read(ite(p,write(A,i,j),write(B,i,j),k). That is bringing up the ite.
// Without this code it will become: ite(i=k, j, read(ite(p,A,B),k))
#if 0
else if (ITE == arrName[0].GetKind())
{
// pull out the ite from the write // pushes the write
// through.
ASTNode writeTrue =
nf->CreateNode(WRITE, (arrName[0][1]), writeIndex, writeVal);
writeTrue.SetIndexWidth(writeIndex.GetValueWidth());
writeTrue.SetValueWidth(writeVal.GetValueWidth());
assert(ARRAY_TYPE == writeTrue.GetType());
ASTNode writeFalse =
nf->CreateNode(WRITE, (arrName[0][2]), writeIndex, writeVal);
writeFalse.SetIndexWidth(writeIndex.GetValueWidth());
writeFalse.SetValueWidth(writeVal.GetValueWidth());
assert(ARRAY_TYPE == writeFalse.GetType());
result = (writeTrue == writeFalse) ?
writeTrue : simp->CreateSimplifiedTermITE(TransformFormula(arrName[0][0]),
writeTrue, writeFalse);
result.SetIndexWidth(writeIndex.GetValueWidth());
result.SetValueWidth(writeVal.GetValueWidth());
assert(ARRAY_TYPE == result.GetType());
result =
nf->CreateTerm(READ, writeVal.GetValueWidth(),
result, readIndex);
BVTypeCheck(result);
result = TransformArrayRead(result);
}
else
FatalError("TransformArray: Write over bad type.");
#endif
break;
} //end of READ over a WRITE
case ITE:
{
/* READ((ITE cond thn els) j)
*
* is transformed into
*
* (ITE cond (READ thn j) (READ els j))
*/
// pull out the ite from the read // pushes the read through.
//(ITE cond thn els)
ASTNode cond = arrName[0];
cond = TransformFormula(cond);
const ASTNode& thn = arrName[1];
const ASTNode& els = arrName[2];
//(READ thn j)
ASTNode thnRead = nf->CreateTerm(READ, width, thn, readIndex);
assert(BVTypeCheck(thnRead));
//(READ els j)
ASTNode elsRead = nf->CreateTerm(READ, width, els, readIndex);
assert(BVTypeCheck(elsRead));
/* We try to call TransformTerm only if necessary, because it
* introduces a new symbol for each read. The amount of work we
* need to do later is based on the square of the number of symbols.
*/
if (ASTTrue == cond)
{
result = TransformTerm(thnRead);
}
else if (ASTFalse == cond)
{
result = TransformTerm(elsRead);
}
else
{
thnRead = TransformTerm(thnRead);
elsRead = TransformTerm(elsRead);
//(ITE cond (READ thn j) (READ els j))
result = simp->CreateSimplifiedTermITE(cond, thnRead, elsRead);
}
break;
}
default:
FatalError("TransformArray: "\
"The READ is NOT over SYMBOL/WRITE/ITE", term);
break;
}
/*
* Checks that all variables referenced in FunctionDefinition bodies are
* bound variables (function arguments).
*/
void
FunctionDefinitionVars::check_ (const Model& m, const FunctionDefinition& fd)
{
if ( fd.getLevel() == 1 ) return;
if ( !fd.isSetMath() ) return;
if ( fd.getBody() == NULL ) return;
//if ( fd.getNumArguments() == 0 ) return;
List* variables = fd.getBody()->getListOfNodes( ASTNode_isName );
for (unsigned int n = 0; n < variables->getSize(); ++n)
{
ASTNode* node = static_cast<ASTNode*>( variables->get(n) );
string name = node->getName() ? node->getName() : "";
if ( fd.getArgument(name) == NULL )
{
/* if this is the csymbol time - technically it is allowed
* in L2v1 and L2v2
*/
if (node->getType() == AST_NAME_TIME)
{
if (fd.getLevel() > 2
|| (fd.getLevel() == 2 && fd.getVersion() > 2))
{
logUndefined(fd, name);
}
}
else
{
logUndefined(fd, name);
}
}
}
if ((m.getLevel() == 2 && m.getVersion() == 5)
|| (m.getLevel() == 3 && m.getVersion() > 1))
{ // check we dont use delay csymbol
delete variables;
variables = fd.getBody()->getListOfNodes( ASTNode_isFunction );
for (unsigned int n = 0; n < variables->getSize(); ++n)
{
ASTNode* node = static_cast<ASTNode*>( variables->get(n) );
if (node->getType() == AST_FUNCTION_DELAY)
{
logUndefined(fd, node->getName());
}
}
}
//Check we don't use a function defined in a plugin (like rateOf)
delete variables;
variables = fd.getBody()->getListOfNodes(ASTNode_isFunction);
for (unsigned int n = 0; n < variables->getSize(); ++n)
{
ASTNode* node = static_cast<ASTNode*>(variables->get(n));
const ASTBasePlugin* plugin = node->getASTPlugin(node->getType());
if (plugin != NULL)
{
if (plugin->allowedInFunctionDefinition(node->getType()) == 0)
{
logUndefined(fd, node->getName());
}
}
}
delete variables;
}
void
AssignmentCycles::checkForImplicitCompartmentReference(const Model& m)
{
mIdMap.clear();
unsigned int i, ns;
std::string id;
for (i = 0; i < m.getNumInitialAssignments(); i++)
{
if (m.getInitialAssignment(i)->isSetMath())
{
id = m.getInitialAssignment(i)->getSymbol();
if (m.getCompartment(id)
&& m.getCompartment(id)->getSpatialDimensions() > 0)
{
List* variables = m.getInitialAssignment(i)->getMath()
->getListOfNodes( ASTNode_isName );
for (ns = 0; ns < variables->getSize(); ns++)
{
ASTNode* node = static_cast<ASTNode*>( variables->get(ns) );
string name = node->getName() ? node->getName() : "";
if (!name.empty() && !alreadyExistsInMap(mIdMap, pair<const std::string, std::string>(id, name)))
mIdMap.insert(pair<const std::string, std::string>(id, name));
}
delete variables;
}
}
}
for (i = 0; i < m.getNumRules(); i++)
{
if (m.getRule(i)->isSetMath() && m.getRule(i)->isAssignment())
{
id = m.getRule(i)->getVariable();
if (m.getCompartment(id)
&& m.getCompartment(id)->getSpatialDimensions() > 0)
{
List* variables = m.getRule(i)->getMath()->getListOfNodes( ASTNode_isName );
for (ns = 0; ns < variables->getSize(); ns++)
{
ASTNode* node = static_cast<ASTNode*>( variables->get(ns) );
string name = node->getName() ? node->getName() : "";
if (!name.empty() && !alreadyExistsInMap(mIdMap, pair<const std::string, std::string>(id, name)))
mIdMap.insert(pair<const std::string, std::string>(id, name));
}
delete variables;
}
}
}
IdIter it;
IdRange range;
for (i = 0; i < m.getNumCompartments(); i++)
{
std::string id = m.getCompartment(i)->getId();
range = mIdMap.equal_range(id);
for (it = range.first; it != range.second; it++)
{
const Species *s = m.getSpecies((*it).second);
if (s && s->getCompartment() == id
&& s->getHasOnlySubstanceUnits() == false)
{
logImplicitReference(m, id, s);
}
}
}
}
/** @cond doxygenLibsbmlInternal */
int
Replacing::updateIDs(SBase* oldnames, SBase* newnames)
{
int ret = LIBSBML_OPERATION_SUCCESS;
SBMLDocument* doc = getSBMLDocument();
if (oldnames->isSetId() && !newnames->isSetId()) {
if (doc) {
string error = "Unable to transform IDs in Replacing::updateIDs during replacement: the '" + oldnames->getId() + "' element's replacement does not have an ID set.";
doc->getErrorLog()->logPackageError("comp", CompMustReplaceIDs, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
if (oldnames->isSetMetaId() && !newnames->isSetMetaId()) {
if (doc) {
string error = "Unable to transform IDs in Replacing::updateIDs during replacement: the replacement of the element with metaid '" + oldnames->getMetaId() + "' does not have a metaid.";
doc->getErrorLog()->logPackageError("comp", CompMustReplaceMetaIDs, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
//LS DEBUG Somehow we need to check identifiers from other packages here (like spatial id's). How, exactly, is anyone's guess.
Model* replacedmod = const_cast<Model*>(CompBase::getParentModel(oldnames));
KineticLaw* replacedkl;
ASTNode newkl;
if (replacedmod==NULL) {
if (doc) {
string error = "Unable to transform IDs in Replacing::updateIDs during replacement: the replacement of '" + oldnames->getId() + "' does not have a valid model.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
List* allElements = replacedmod->getAllElements();
string oldid = oldnames->getId();
string newid = newnames->getId();
if (!oldid.empty()) {
switch(oldnames->getTypeCode()) {
case SBML_UNIT_DEFINITION:
replacedmod->renameUnitSIdRefs(oldid, newid);
for (unsigned int e=0; e<allElements->getSize(); e++) {
SBase* element = static_cast<SBase*>(allElements->get(e));
element->renameUnitSIdRefs(oldid, newid);
}
break;
case SBML_LOCAL_PARAMETER:
replacedkl = static_cast<KineticLaw*>(oldnames->getAncestorOfType(SBML_KINETIC_LAW));
if (replacedkl->isSetMath()) {
newkl = *replacedkl->getMath();
newkl.renameSIdRefs(oldid, newid);
replacedkl->setMath(&newkl);
}
break;
case SBML_COMP_PORT:
break;
//LS DEBUG And here is where we would need some sort of way to check if the id wasn't an SId for some objects.
default:
replacedmod->renameSIdRefs(oldnames->getId(), newnames->getId());
for (unsigned int e=0; e<allElements->getSize(); e++) {
SBase* element = static_cast<SBase*>(allElements->get(e));
element->renameSIdRefs(oldid, newid);
}
}
}
string oldmetaid = oldnames->getMetaId();
string newmetaid = newnames->getMetaId();
if (oldnames->isSetMetaId()) {
replacedmod->renameMetaIdRefs(oldmetaid, newmetaid);
for (unsigned int e=0; e<allElements->getSize(); e++) {
SBase* element = static_cast<SBase*>(allElements->get(e));
element->renameMetaIdRefs(oldmetaid, newmetaid);
}
}
//LS DEBUG And here is where we would need some sort of way to check for ids that were not 'id' or 'metaid'.
delete allElements;
return ret;
}
/*
* Checks that the units of the piecewise function are consistent
*
* If inconsistent units are found, an error message is logged.
*/
void
ArgumentsUnitsCheck::checkUnitsFromPiecewise (const Model& m,
const ASTNode& node,
const SBase & sb, bool inKL, int reactNo)
{
/* check that node has children */
if (node.getNumChildren() == 0)
{
return;
}
/* piecewise(a0, a1, a2, a3, ...)
* a0 and a2, a(n_even) must have same units
* a1, a3, a(n_odd) must be dimensionless
*/
unsigned int n;
UnitDefinition *dim = new UnitDefinition(m.getSBMLNamespaces());
Unit *unit = new Unit(m.getSBMLNamespaces());
unit->setKind(UNIT_KIND_DIMENSIONLESS);
unit->initDefaults();
UnitDefinition * tempUD;
UnitDefinition * tempUD1 = NULL;
dim->addUnit(unit);
UnitFormulaFormatter *unitFormat = new UnitFormulaFormatter(&m);
tempUD = unitFormat->getUnitDefinition(node.getChild(0), inKL, reactNo);
for(n = 2; n < node.getNumChildren(); n+=2)
{
tempUD1 = unitFormat->getUnitDefinition(node.getChild(n), inKL, reactNo);
if (!unitFormat->getContainsUndeclaredUnits())
{
if (!UnitDefinition::areEquivalent(tempUD, tempUD1))
{
logInconsistentPiecewise(node, sb);
}
}
delete tempUD1;
}
delete tempUD;
for(n = 1; n < node.getNumChildren(); n+=2)
{
tempUD = unitFormat->getUnitDefinition(node.getChild(n), inKL, reactNo);
if (!UnitDefinition::areEquivalent(tempUD, dim))
{
logInconsistentPiecewiseCondition(node, sb);
}
delete tempUD;
}
delete dim;
delete unit;
delete unitFormat;
for(n = 0; n < node.getNumChildren(); n++)
{
checkUnits(m, *node.getChild(n), sb, inKL, reactNo);
}
}
// helper function for printing C code (copied from PL_Print1())
void C_Print1(ostream& os, const ASTNode n, int indentation, bool letize)
{
unsigned int upper, lower, num_bytes;
Kind LHSkind, RHSkind;
//os << spaces(indentation);
//os << endl << spaces(indentation);
if (!n.IsDefined())
{
os << "<undefined>";
return;
}
//if this node is present in the letvar Map, then print the letvar
STPMgr *bm = n.GetSTPMgr();
//this is to print letvars for shared subterms inside the printing
//of "(LET v0 = term1, v1=term1@term2,...
if ((bm->NodeLetVarMap1.find(n) != bm->NodeLetVarMap1.end()) && !letize)
{
C_Print1(os, (bm->NodeLetVarMap1[n]), indentation, letize);
return;
}
//this is to print letvars for shared subterms inside the actual
//term to be printed
if ((bm->NodeLetVarMap.find(n) != bm->NodeLetVarMap.end()) && letize)
{
C_Print1(os, (bm->NodeLetVarMap[n]), indentation, letize);
return;
}
//otherwise print it normally
Kind kind = n.GetKind();
const ASTVec &c = n.GetChildren();
switch (kind)
{
case BOOLEXTRACT:
FatalError("C_Print1: printing not implemented for this kind: ", n);
C_Print1(os, c[0], indentation, letize);
os << "{";
C_Print1(os, c[1], indentation, letize);
os << "}";
break;
case BITVECTOR:
FatalError("C_Print1: printing not implemented for this kind: ", n);
os << "BITVECTOR(";
unsigned char * str;
str = CONSTANTBV::BitVector_to_Hex(c[0].GetBVConst());
os << str << ")";
CONSTANTBV::BitVector_Dispose(str);
break;
case BOOLEAN:
FatalError("C_Print1: printing not implemented for this kind: ", n);
os << "BOOLEAN";
break;
case FALSE:
os << "0";
break;
case TRUE:
os << "1";
break;
case BVCONST:
case SYMBOL:
// print in C friendly format:
n.nodeprint(os, true);
break;
case READ:
C_Print1(os, c[0], indentation, letize);
os << "[";
C_Print1(os, c[1], indentation, letize);
os << "]";
break;
case WRITE:
os << "(";
C_Print1(os, c[0], indentation, letize);
os << " WITH [";
C_Print1(os, c[1], indentation, letize);
os << "] := ";
C_Print1(os, c[2], indentation, letize);
os << ")";
os << endl;
break;
case BVUMINUS:
os << kind << "( ";
C_Print1(os, c[0], indentation, letize);
os << ")";
break;
case NOT:
os << "!(";
C_Print1(os, c[0], indentation, letize);
os << ") " << endl;
break;
case BVNEG:
os << " ~(";
C_Print1(os, c[0], indentation, letize);
os << ")";
break;
case BVCONCAT:
// stopgap for un-implemented features
FatalError("C_Print1: printing not implemented for this kind: ", n);
os << "(";
C_Print1(os, c[0], indentation, letize);
os << " @ ";
C_Print1(os, c[1], indentation, letize);
os << ")" << endl;
break;
case BVOR:
os << "(";
C_Print1(os, c[0], indentation, letize);
os << " | ";
C_Print1(os, c[1], indentation, letize);
os << ")";
break;
case BVAND:
os << "(";
C_Print1(os, c[0], indentation, letize);
os << " & ";
C_Print1(os, c[1], indentation, letize);
os << ")";
break;
case BVEXTRACT:
// we only accept indices that are byte-aligned
// (e.g., [15:8], [23:16])
// and round down to byte indices rather than bit indices
upper = c[1].GetUnsignedConst();
lower = c[2].GetUnsignedConst();
assert(upper > lower);
assert(lower % 8 == 0);
assert((upper + 1) % 8 == 0);
num_bytes = (upper - lower + 1) / 8;
assert (num_bytes > 0);
// for multi-byte extraction, use the ADDRESS
if (num_bytes > 1)
{
os << "&";
C_Print1(os, c[0], indentation, letize);
os << "[" << lower / 8 << "]";
}
// for single-byte extraction, use the VALUE
else
{
C_Print1(os, c[0], indentation, letize);
os << "[" << lower / 8 << "]";
}
break;
case BVLEFTSHIFT:
// stopgap for un-implemented features
FatalError("C_Print1: printing not implemented for this kind: ", n);
os << "(";
C_Print1(os, c[0], indentation, letize);
os << " << ";
os << c[1].GetUnsignedConst();
os << ")";
break;
case BVRIGHTSHIFT:
// stopgap for un-implemented features
FatalError("C_Print1: printing not implemented for this kind: ", n);
os << "(";
C_Print1(os, c[0], indentation, letize);
os << " >> ";
os << c[1].GetUnsignedConst();
os << ")";
break;
case BVMULT:
case BVSUB:
case BVPLUS:
case SBVDIV:
case SBVREM:
case BVDIV:
case BVMOD:
os << kind << "(";
os << n.GetValueWidth();
for (ASTVec::const_iterator
it = c.begin(), itend = c.end(); it != itend; it++)
{
os << ", " << endl;
C_Print1(os, *it, indentation, letize);
}
os << ")" << endl;
break;
case ITE:
os << "if (";
C_Print1(os, c[0], indentation, letize);
os << ")" << endl;
os << "{";
C_Print1(os, c[1], indentation, letize);
os << endl << "} else {";
C_Print1(os, c[2], indentation, letize);
os << endl << "}";
break;
case BVLT:
// convert to UNSIGNED before doing comparison!
os << "((unsigned char)";
C_Print1(os, c[0], indentation, letize);
os << " < ";
os << "(unsigned char)";
C_Print1(os, c[1], indentation, letize);
os << ")";
break;
case BVLE:
// convert to UNSIGNED before doing comparison!
os << "((unsigned char)";
C_Print1(os, c[0], indentation, letize);
os << " <= ";
os << "(unsigned char)";
C_Print1(os, c[1], indentation, letize);
os << ")";
break;
case BVGT:
// convert to UNSIGNED before doing comparison!
os << "((unsigned char)";
C_Print1(os, c[0], indentation, letize);
os << " > ";
os << "(unsigned char)";
C_Print1(os, c[1], indentation, letize);
os << ")";
break;
case BVGE:
// convert to UNSIGNED before doing comparison!
os << "((unsigned char)";
C_Print1(os, c[0], indentation, letize);
os << " >= ";
os << "(unsigned char)";
C_Print1(os, c[1], indentation, letize);
os << ")";
break;
case BVXOR:
case BVNAND:
case BVNOR:
case BVXNOR:
// stopgap for un-implemented features
FatalError("C_Print1: printing not implemented for this kind: ", n);
break;
case BVSLT:
// convert to SIGNED before doing comparison!
os << "((signed char)";
C_Print1(os, c[0], indentation, letize);
os << " < ";
os << "(signed char)";
C_Print1(os, c[1], indentation, letize);
os << ")";
break;
case BVSLE:
// convert to SIGNED before doing comparison!
os << "((signed char)";
C_Print1(os, c[0], indentation, letize);
os << " <= ";
os << "(signed char)";
C_Print1(os, c[1], indentation, letize);
os << ")";
break;
case BVSGT:
// convert to SIGNED before doing comparison!
os << "((signed char)";
C_Print1(os, c[0], indentation, letize);
os << " > ";
os << "(signed char)";
C_Print1(os, c[1], indentation, letize);
os << ")";
break;
case BVSGE:
// convert to SIGNED before doing comparison!
os << "((signed char)";
C_Print1(os, c[0], indentation, letize);
os << " >= ";
os << "(signed char)";
C_Print1(os, c[1], indentation, letize);
os << ")";
break;
case EQ:
// tricky tricky ... if it's a single-byte comparison,
// simply do ==, but if it's multi-byte, must do memcmp
LHSkind = c[0].GetKind();
RHSkind = c[1].GetKind();
num_bytes = 0;
// try to figure out whether it's a single-byte or multi-byte
// comparison
if (LHSkind == BVEXTRACT)
{
upper = c[0].GetChildren()[1].GetUnsignedConst();
lower = c[0].GetChildren()[2].GetUnsignedConst();
num_bytes = (upper - lower + 1) / 8;
}
else if (RHSkind == BVEXTRACT)
{
upper = c[1].GetChildren()[1].GetUnsignedConst();
lower = c[1].GetChildren()[2].GetUnsignedConst();
num_bytes = (upper - lower + 1) / 8;
}
if (num_bytes > 1)
{
os << "(memcmp(";
C_Print1(os, c[0], indentation, letize);
os << ", ";
C_Print1(os, c[1], indentation, letize);
os << ", ";
os << num_bytes;
os << ") == 0)";
}
else if (num_bytes == 1)
{
os << "(";
C_Print1(os, c[0], indentation, letize);
os << " == ";
C_Print1(os, c[1], indentation, letize);
os << ")";
}
else
{
FatalError("C_Print1: ugh problem in implementing ==");
}
break;
case AND:
case OR:
case NAND:
case NOR:
case XOR:
{
os << "(";
C_Print1(os, c[0], indentation, letize);
ASTVec::const_iterator it = c.begin();
ASTVec::const_iterator itend = c.end();
it++;
for (; it != itend; it++)
{
switch (kind)
{
case AND:
os << " && ";
break;
case OR:
os << " || ";
break;
case NAND:
FatalError("unsupported boolean type in C_Print1");
break;
case NOR:
FatalError("unsupported boolean type in C_Print1");
break;
case XOR:
FatalError("unsupported boolean type in C_Print1");
break;
default:
FatalError("unsupported boolean type in C_Print1");
}
C_Print1(os, *it, indentation, letize);
}
os << ")";
break;
}
case IFF:
// stopgap for un-implemented features
FatalError("C_Print1: printing not implemented for this kind: ", n);
os << "(";
os << "(";
C_Print1(os, c[0], indentation, letize);
os << ")";
os << " <=> ";
os << "(";
C_Print1(os, c[1], indentation, letize);
os << ")";
os << ")";
os << endl;
break;
case IMPLIES:
// stopgap for un-implemented features
FatalError("C_Print1: printing not implemented for this kind: ", n);
os << "(";
os << "(";
C_Print1(os, c[0], indentation, letize);
os << ")";
os << " => ";
os << "(";
C_Print1(os, c[1], indentation, letize);
os << ")";
os << ")";
os << endl;
break;
case BVSX:
// stopgap for un-implemented features
FatalError("C_Print1: printing not implemented for this kind: ", n);
os << kind << "(";
C_Print1(os, c[0], indentation, letize);
os << ",";
os << n.GetValueWidth();
os << ")" << endl;
break;
default:
//remember to use LispPrinter here. Otherwise this function will
//go into an infinite loop. Recall that "<<" is overloaded to
//the lisp printer. FatalError uses lispprinter
FatalError("C_Print1: printing not implemented for this kind: ", n);
break;
}
} //end of C_Print1()
ASTNode* TestASTTraverser::buildTree()
{
ASTNode* assignNode = new ASTNode("", ASSIGN, 1);
ASTNode* plusNode = new ASTNode("", PLUS, 0);
ASTNode* minusNode = new ASTNode("", MINUS, 0);
ASTNode* varNodeA = new ASTNode("a", VARIABLE, 0);
ASTNode* varNodeB = new ASTNode("b", VARIABLE, 0);
ASTNode* varNodeC = new ASTNode("c", VARIABLE, 0);
ASTNode* constantNode = new ASTNode("1", CONSTANT, 0);
assignNode->joinChild(varNodeA);
varNodeA->joinNext(minusNode);
minusNode->joinChild(plusNode);
plusNode->joinChild(varNodeB);
varNodeB->joinNext(varNodeC);
plusNode->joinNext(constantNode);
return assignNode;
}
//FIXME: Ideally I would like the ASTNodes to be able to operate on
//themselves (add, sub, concat, etc.) rather than doing a
//GetBVConst() and then do the operation externally. For now,
//this is the fastest path to completion.
ASTNode BeevMgr::BVConstEvaluator(const ASTNode& t) {
//cerr << "inside begin bcconstevaluator: " << t << endl;
ASTNode OutputNode;
if(CheckSolverMap(t,OutputNode))
return OutputNode;
OutputNode = ASTUndefined;
Kind k = t.GetKind();
unsigned long long int output = 0;
unsigned inputwidth = t.GetValueWidth();
ASTNode t0 = ASTUndefined;
ASTNode t1 = ASTUndefined;
if(2 == t.Degree()) {
t0 = BVConstEvaluator(t[0]);
t1 = BVConstEvaluator(t[1]);
}
switch(k) {
case READ:
case UNDEFINED:
case WRITE:
case SYMBOL:
cerr << t;
FatalError("BVConstEvaluator: term is not a constant-term",t);
break;
case BVCONST:
return t;
break;
case BVNEG:
//compute bitwise negation in C
output = ~(BVConstEvaluator(t[0]).GetBVConst());
break;
case BVSX:
output = SXBVConst64(BVConstEvaluator(t[0]));
break;
case BVAND:
output = t0.GetBVConst() & t1.GetBVConst();
break;
case BVOR:
output = t0.GetBVConst() | t1.GetBVConst();
break;
case BVXOR:
output = t0.GetBVConst() ^ t1.GetBVConst();
break;
case BVSUB:
output = t0.GetBVConst() - t1.GetBVConst();
break;
case BVUMINUS:
output = ~(BVConstEvaluator(t[0]).GetBVConst()) + 1;
break;
case BVEXTRACT: {
unsigned long long int val = BVConstEvaluator(t[0]).GetBVConst();
unsigned int hi = GetUnsignedConst(BVConstEvaluator(t[1]));
unsigned int low = GetUnsignedConst(BVConstEvaluator(t[2]));
if(!(0 <= hi <= 64))
FatalError("ConstantEvaluator: hi bit in BVEXTRACT is > 32bits",t);
if(!(0 <= low <= hi <= 64))
FatalError("ConstantEvaluator: low bit in BVEXTRACT is > 32bits or hi",t);
//64 bit mask.
unsigned long long int mask1 = 0xffffffffffffffffLL;
mask1 >>= 64-(hi+1);
//extract val[hi:0]
val &= mask1;
//extract val[hi:low]
val >>= low;
output = val;
break;
}
case BVCONCAT: {
unsigned long long int q = BVConstEvaluator(t0).GetBVConst();
unsigned long long int r = BVConstEvaluator(t1).GetBVConst();
unsigned int qlen = t[0].GetValueWidth();
unsigned int rlen = t[1].GetValueWidth();
unsigned int slen = t.GetValueWidth();
if(!(0 < qlen + rlen <= 64))
FatalError("BVConstEvaluator:"
"lengths of childnodes of BVCONCAT are > 64:",t);
//64 bit mask for q
unsigned long long int qmask = 0xffffffffffffffffLL;
qmask >>= 64-qlen;
//zero the useless bits of q
q &= qmask;
//64 bit mask for r
unsigned long long int rmask = 0xffffffffffffffffLL;
rmask >>= 64-rlen;
//zero the useless bits of r
r &= rmask;
//concatenate
q <<= rlen;
q |= r;
//64 bit mask for output s
unsigned long long int smask = 0xffffffffffffffffLL;
smask >>= 64-slen;
//currently q has the output
output = q;
output &= smask;
break;
}
case BVMULT: {
output = t0.GetBVConst() * t1.GetBVConst();
//64 bit mask
unsigned long long int mask = 0xffffffffffffffffLL;
mask = mask >> (64 - inputwidth);
output &= mask;
break;
}
case BVPLUS: {
ASTVec c = t.GetChildren();
for(ASTVec::iterator it=c.begin(),itend=c.end();it!=itend;it++)
output += BVConstEvaluator(*it).GetBVConst();
//64 bit mask
unsigned long long int mask = 0xffffffffffffffffLL;
mask = mask >> (64 -inputwidth);
output &= mask;
break;
}
case SBVDIV:
case SBVMOD: {
output = BVConstEvaluator(TranslateSignedDivMod(t)).GetBVConst();
break;
}
case BVDIV: {
if(0 == t1.GetBVConst()) {
//if denominator is 0 then
// (if refinement is ON then output is set to 0)
// (else produce a fatal error)
if(counterexample_checking_during_refinement) {
output = 0;
bvdiv_exception_occured = true;
break;
}
else {
FatalError("BVConstEvaluator: divide by zero not allowed:",t);
}
}
output = t0.GetBVConst() / t1.GetBVConst();
//64 bit mask
unsigned long long int mask = 0xffffffffffffffffLL;
mask = mask >> (64 - inputwidth);
output &= mask;
break;
}
case BVMOD: {
if(0 == t1.GetBVConst()) {
//if denominator is 0 then
// (if refinement is ON then output is set to 0)
// (else produce a fatal error)
if(counterexample_checking_during_refinement) {
output = 0;
bvdiv_exception_occured = true;
break;
}
else {
FatalError("BVConstEvaluator: divide by zero not allowed:",t);
}
}
output = t0.GetBVConst() % t1.GetBVConst();
//64 bit mask
unsigned long long int mask = 0xffffffffffffffffLL;
mask = mask >> (64 - inputwidth);
output &= mask;
break;
}
case ITE:
if(ASTTrue == t[0])
OutputNode = BVConstEvaluator(t[1]);
else if(ASTFalse == t[0])
OutputNode = BVConstEvaluator(t[2]);
else
FatalError("BVConstEvaluator:"
"ITE condiional must be either TRUE or FALSE:",t);
break;
case EQ:
if(t0.GetBVConst() == t1.GetBVConst())
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
case NEQ:
if(t0.GetBVConst() != t1.GetBVConst())
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
break;
case BVLT: {
unsigned long long n0 = t0.GetBVConst();
unsigned long long n1 = t1.GetBVConst();
if(n0 < n1)
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
}
case BVLE:
if(t0.GetBVConst() <= t1.GetBVConst())
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
case BVGT:
if(t0.GetBVConst() > t1.GetBVConst())
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
case BVGE:
if(t0.GetBVConst() >= t1.GetBVConst())
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
case BVSLT: {
signed long long int n0 = SXBVConst64(t0);
signed long long int n1 = SXBVConst64(t1);
if(n0 < n1)
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
}
case BVSLE: {
signed long long int n0 = SXBVConst64(t0);
signed long long int n1 = SXBVConst64(t1);
if(n0 <= n1)
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
}
case BVSGT: {
signed long long int n0 = SXBVConst64(t0);
signed long long int n1 = SXBVConst64(t1);
if(n0 > n1)
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
}
case BVSGE: {
signed long long int n0 = SXBVConst64(t0);
signed long long int n1 = SXBVConst64(t1);
if(n0 >= n1)
OutputNode = ASTTrue;
else
OutputNode = ASTFalse;
break;
}
default:
FatalError("BVConstEvaluator: The input kind is not supported yet:",t);
break;
}
if(ASTTrue != OutputNode && ASTFalse != OutputNode)
OutputNode = CreateBVConst(inputwidth, output);
UpdateSolverMap(t,OutputNode);
//UpdateSimplifyMap(t,OutputNode,false);
return OutputNode;
} //End of BVConstEvaluator
bool
ASTBinaryFunctionNode::isSqrt() const
{
bool valid = false;
ASTBase * base1 = NULL;
if (getType() == AST_FUNCTION_ROOT)
{
if (getNumChildren() == 2)
{
base1 = getChild(0);
ASTFunction* fun = dynamic_cast<ASTFunction*>(base1);
if (fun != NULL)
{
if (fun->getType() == AST_QUALIFIER_DEGREE
&& fun->getNumChildren() == 1)
{
ASTBase *base2 = fun->getChild(0);
if (base2->getType() == AST_INTEGER)
{
ASTNumber *child = static_cast<ASTNumber*>(base2);
if (child->getInteger() == 2)
{
valid = true;
}
}
}
}
else
{
// here we are working the ASTNode so the casting
// is more difficult
ASTNode* newAST = dynamic_cast<ASTNode*>(base1);
if (newAST != NULL && newAST->getType() == AST_QUALIFIER_DEGREE
&& newAST->getNumChildren() == 1)
{
ASTNode* newAST1 = newAST->getChild(0);
if (newAST1->getType() == AST_INTEGER)
{
if (newAST1->getInteger() == 2)
{
valid = true;
}
}
}
else
{
if (newAST != NULL && newAST->getType() == AST_INTEGER)
{
if (newAST->getInteger() == 2)
{
valid = true;
}
}
}
}
}
}
return valid;
}
bool
ASTNaryFunctionNode::isSqrt() const
{
bool valid = false;
if (getType() == AST_FUNCTION_ROOT)
{
// a sqrt can have either one child that is not the degree qualifier
// or two where teh first is the degree of 2
if (getNumChildren() == 1)
{
/* HACK to replicate OLD AST whic says a sqrt must have two children*/
valid = false;
//ASTBase * base1 = getChild(0);
//if (base1->isQualifier() == false)
//{
// valid = true;
//}
}
else if (getNumChildren() == 2)
{
ASTBase * base1 = ASTFunctionBase::getChild(0);
ASTFunction* fun = dynamic_cast<ASTFunction*>(base1);
if (fun != NULL)
{
if (fun->getType() == AST_QUALIFIER_DEGREE
&& fun->getNumChildren() == 1)
{
ASTBase *base2 = fun->getChild(0);
if (base2->getType() == AST_INTEGER)
{
ASTNumber *child = static_cast<ASTNumber*>(base2);
if (child->getInteger() == 2)
{
valid = true;
}
}
}
}
else
{
// here we are working the ASTNode so the casting
// is more difficult
ASTNode* newAST = dynamic_cast<ASTNode*>(base1);
if (newAST != NULL && newAST->getType() == AST_QUALIFIER_DEGREE
&& newAST->getNumChildren() == 1)
{
ASTNode* newAST1 = newAST->getChild(0);
if (newAST1->getType() == AST_INTEGER)
{
if (newAST1->getInteger() == 2)
{
valid = true;
}
}
}
else
{
if (newAST != NULL && newAST->getType() == AST_INTEGER)
{
if (newAST->getInteger() == 2)
{
valid = true;
}
}
}
}
}
}
return valid;
}
ASTNode SubstitutionMap::replace(const ASTNode& n, ASTNodeMap& fromTo,
ASTNodeMap& cache, NodeFactory* nf,
bool stopAtArrays, bool preventInfinite)
{
const Kind k = n.GetKind();
if (k == BVCONST || k == TRUE || k == FALSE)
return n;
ASTNodeMap::const_iterator it;
if ((it = cache.find(n)) != cache.end())
return it->second;
if ((it = fromTo.find(n)) != fromTo.end())
{
const ASTNode& r = it->second;
assert(r.GetIndexWidth() == n.GetIndexWidth());
if (preventInfinite)
cache.insert(make_pair(n, r));
ASTNode replaced =
replace(r, fromTo, cache, nf, stopAtArrays, preventInfinite);
if (replaced != r)
{
fromTo.erase(n);
fromTo[n] = replaced;
}
if (preventInfinite)
cache.erase(n);
cache.insert(make_pair(n, replaced));
return replaced;
}
// These can't be created like regular nodes are
if (k == SYMBOL)
return n;
const unsigned int indexWidth = n.GetIndexWidth();
if (stopAtArrays && indexWidth > 0) // is an array.
{
return n;
}
const ASTVec& children = n.GetChildren();
assert(children.size() > 0);
// Should have no leaves left here.
ASTVec new_children;
new_children.reserve(children.size());
for (ASTVec::const_iterator it = children.begin(); it != children.end(); it++)
{
new_children.push_back(
replace(*it, fromTo, cache, nf, stopAtArrays, preventInfinite));
}
assert(new_children.size() == children.size());
// This code short-cuts if the children are the same. Nodes with the same
// children,
// won't have necessarily given the same node if the simplifyingNodeFactory is
// enabled
// now, but wasn't enabled when the node was created. Shortcutting saves lots
// of time.
if (new_children == children)
{
cache.insert(make_pair(n, n));
return n;
}
ASTNode result;
const unsigned int valueWidth = n.GetValueWidth();
if (valueWidth == 0) // n.GetType() == BOOLEAN_TYPE
{
result = nf->CreateNode(k, new_children);
}
else
{
// If the index and value width aren't saved, they are reset sometimes (??)
result = nf->CreateArrayTerm(k, indexWidth, valueWidth, new_children);
}
// We may have created something that should be mapped. For instance,
// if n is READ(A, x), and the fromTo is: {x==0, READ(A,0) == 1}, then
// by here the result will be READ(A,0). Which needs to be mapped again..
// I hope that this makes it idempotent.
if (fromTo.find(result) != fromTo.end())
{
// map n->result, if running replace() on result gives us 'n', it will not
// infinite loop.
// This is only currently required for the bitblast equivalence stuff.
if (preventInfinite)
cache.insert(make_pair(n, result));
result = replace(result, fromTo, cache, nf, stopAtArrays, preventInfinite);
}
assert(result.GetValueWidth() == valueWidth);
assert(result.GetIndexWidth() == indexWidth);
// If there is already an "n" element in the cache, the maps semantics are to
// ignore the next insertion.
if (preventInfinite)
cache.erase(n);
cache.insert(make_pair(n, result));
return result;
}
ASTBase*
ASTPiecewiseFunctionNode::getChild (unsigned int n) const
{
/* HACK TO REPLICATE OLD AST */
/* do not return a node with teh piece or otherwise type
* return the correct child of the piece type
* or the child of the otherwise
*/
unsigned int numChildren = ASTFunctionBase::getNumChildren();
if (numChildren == 0)
{
return NULL;
}
// determine index that we actually want
unsigned int childNo = (unsigned int)(n/2);
unsigned int pieceIndex = (unsigned int)(n%2);
ASTBase * base = NULL;
if (childNo < numChildren)
{
base = ASTFunctionBase::getChild(childNo);
}
if (getHasOtherwise() == true && childNo == numChildren - 1)
{
if (base == NULL)
{
return NULL;
}
if (base->getType() == AST_CONSTRUCTOR_OTHERWISE)
{
ASTNode * otherwise = dynamic_cast<ASTNode*>(base);
if (otherwise != NULL)
{
if (otherwise->getNumChildren() > 0)
{
return otherwise->getChild(0);
}
else
{
return NULL;
}
}
else
{
return NULL;
}
}
else
{
return base;
}
}
else if (base != NULL && base->getType() == AST_CONSTRUCTOR_PIECE)
{
ASTNode * piece = dynamic_cast<ASTNode*>(base);
if (piece != NULL)
{
if (piece->getNumChildren() > pieceIndex)
{
return piece->getChild(pieceIndex);
}
else
{
return NULL;
}
}
else
{
return NULL;
}
}
else if (n < numChildren)
{
return ASTFunctionBase::getChild(n);
}
else
{
return NULL;
}
}
bool SymbolCheckVisitor::performStep(ASTNode& node)
{
node.accept(*this);
return true;
}
int
ASTPiecewiseFunctionNode::insertChildForReplace(unsigned int n, ASTBase* newChild)
{
int inserted = LIBSBML_INDEX_EXCEEDS_SIZE;
unsigned int numChildren = ASTFunctionBase::getNumChildren();
unsigned int numChildrenForUser = getNumChildren();
// determine index that we actually want
unsigned int childNo = (unsigned int)(n/2);
unsigned int pieceIndex = (unsigned int)(n%2);
if (numChildren == numChildrenForUser)
{
// we have an old style piecewise function
childNo = n;
pieceIndex = n;
}
ASTBase * base = NULL;
if (childNo < numChildren)
{
base = ASTFunctionBase::getChild(childNo);
}
if (getHasOtherwise() == true && childNo == numChildren - 1)
{
if (base == NULL)
{
return inserted;
}
if (base->getType() == AST_CONSTRUCTOR_OTHERWISE)
{
ASTNode * otherwise = dynamic_cast<ASTNode*>(base);
if (otherwise != NULL)
{
inserted = otherwise->replaceChild(0,
static_cast<ASTNode*>(newChild));
}
else
{
return inserted;
}
}
else
{
inserted = ASTFunctionBase::replaceChild(childNo, newChild);
}
}
else if (base != NULL && base->getType() == AST_CONSTRUCTOR_PIECE)
{
ASTNode * piece = dynamic_cast<ASTNode*>(base);
if (piece != NULL)
{
if (piece->getNumChildren() > pieceIndex)
{
inserted = piece->replaceChild(pieceIndex, static_cast<ASTNode*>(newChild));
}
else
{
return inserted;
}
}
else
{
return inserted;
}
}
else if (n < numChildren)
{
return ASTFunctionBase::replaceChild(n, newChild);
}
else
{
return inserted;
}
return inserted;
//unsigned int numChildren = ASTFunctionBase::getNumChildren();
//vector < ASTBase *> copyChildren;
//unsigned int i;
//for (i = n; i < numChildren; i++)
//{
// ASTBase * child = getChild(i);
// // this might be NULL if we have deleted part of the piece function
// if (child != NULL)
// {
// copyChildren.push_back(getChild(i));
// }
//}
//for (i = numChildren; i > n; i--)
//{
// ASTFunctionBase::removeChild(i-1);
//}
//unsigned int success = addChild(newChild);
//i = 0;
//while (success == LIBSBML_OPERATION_SUCCESS && i < copyChildren.size())
//{
// success = addChild(copyChildren.at(i));
// i++;
//}
//inserted = success;
//return inserted;
}
// This doesn't rewrite changes through properly so needs to have a substitution
// applied to its output.
ASTNode PropagateEqualities::propagate(const ASTNode& a, ArrayTransformer* at)
{
ASTNode output;
// if the variable has been solved for, then simply return it
if (simp->CheckSubstitutionMap(a, output))
return output;
if (!alreadyVisited.insert(a.GetNodeNum()).second)
{
return a;
}
output = a;
// traverse a and populate the SubstitutionMap
const Kind k = a.GetKind();
if (SYMBOL == k && BOOLEAN_TYPE == a.GetType())
{
bool updated = simp->UpdateSubstitutionMap(a, ASTTrue);
output = updated ? ASTTrue : a;
}
else if (NOT == k)
{
bool updated = searchXOR(a[0], ASTFalse);
output = updated ? ASTTrue : a;
}
else if (IFF == k || EQ == k)
{
const ASTVec& c = a.GetChildren();
if (c[0] == c[1])
return ASTTrue;
bool updated = simp->UpdateSubstitutionMap(c[0], c[1]);
if (updated)
{
// fill the arrayname readindices vector if e0 is a
// READ(Arr,index) and index is a BVCONST
int to;
if ((to = TermOrder(c[0], c[1])) == 1 && c[0].GetKind() == READ)
at->FillUp_ArrReadIndex_Vec(c[0], c[1]);
else if (to == -1 && c[1].GetKind() == READ)
at->FillUp_ArrReadIndex_Vec(c[1], c[0]);
}
if (!updated)
updated = searchTerm(c[0], c[1]);
if (!updated)
updated = searchTerm(c[1], c[0]);
output = updated ? ASTTrue : a;
}
else if (XOR == k)
{
bool updated = searchXOR(a, ASTTrue);
output = updated ? ASTTrue : a;
if (updated)
return output;
// The below block should be subsumed by the searchXOR function which
// generalises it.
// So the below block should never do anything..
#ifndef NDEBUG
if (a.Degree() != 2)
return output;
int to = TermOrder(a[0], a[1]);
if (0 == to)
{
if (a[0].GetKind() == NOT && a[0][0].GetKind() == EQ &&
a[0][0][0].GetValueWidth() == 1 && a[0][0][1].GetKind() == SYMBOL)
{
// (XOR (NOT(= (1 v))) ... )
const ASTNode& symbol = a[0][0][1];
const ASTNode newN = nf->CreateTerm(
ITE, 1, a[1], a[0][0][0], nf->CreateTerm(BVNEG, 1, a[0][0][0]));
if (simp->UpdateSolverMap(symbol, newN))
{
assert(false);
output = ASTTrue;
}
}
else if (a[1].GetKind() == NOT && a[1][0].GetKind() == EQ &&
a[1][0][0].GetValueWidth() == 1 &&
a[1][0][1].GetKind() == SYMBOL)
{
const ASTNode& symbol = a[1][0][1];
const ASTNode newN = nf->CreateTerm(
ITE, 1, a[0], a[1][0][0], nf->CreateTerm(BVNEG, 1, a[1][0][0]));
if (simp->UpdateSolverMap(symbol, newN))
{
assert(false);
output = ASTTrue;
}
}
else if (a[0].GetKind() == EQ && a[0][0].GetValueWidth() == 1 &&
a[0][1].GetKind() == SYMBOL)
{
// XOR ((= 1 v) ... )
const ASTNode& symbol = a[0][1];
const ASTNode newN = nf->CreateTerm(
ITE, 1, a[1], nf->CreateTerm(BVNEG, 1, a[0][0]), a[0][0]);
if (simp->UpdateSolverMap(symbol, newN))
{
assert(false);
output = ASTTrue;
}
}
else if (a[1].GetKind() == EQ && a[1][0].GetValueWidth() == 1 &&
a[1][1].GetKind() == SYMBOL)
{
const ASTNode& symbol = a[1][1];
const ASTNode newN = nf->CreateTerm(
ITE, 1, a[0], nf->CreateTerm(BVNEG, 1, a[1][0]), a[1][0]);
if (simp->UpdateSolverMap(symbol, newN))
{
assert(false);
output = ASTTrue;
}
}
else
return output;
}
else
{
ASTNode symbol, rhs;
if (to == 1)
{
symbol = a[0];
rhs = a[1];
}
else
{
symbol = a[1];
rhs = a[0];
}
assert(symbol.GetKind() == SYMBOL);
if (simp->UpdateSolverMap(symbol, nf->CreateNode(NOT, rhs)))
{
assert(false);
output = ASTTrue;
}
}
#endif
}
else if (AND == k)
{
const ASTVec& c = a.GetChildren();
ASTVec o;
o.reserve(c.size());
for (ASTVec::const_iterator it = c.begin(), itend = c.end(); it != itend;
it++)
{
if (always_true)
simp->UpdateAlwaysTrueFormSet(*it);
ASTNode aaa = propagate(*it, at);
if (ASTTrue != aaa)
{
if (ASTFalse == aaa)
return ASTFalse;
else
o.push_back(aaa);
}
}
if (o.size() == 0)
output = ASTTrue;
else if (o.size() == 1)
output = o[0];
else if (o != c)
output = nf->CreateNode(AND, o);
else
output = a;
}
return output;
} // end of CreateSubstitutionMap()
