/* NOTE: provisional steady state finding! */
SBML_ODESOLVER_API int IntegratorInstance_checkSteadyState(integratorInstance_t *engine)
{
int i;
double dy_mean, dy_var, dy_std;
cvodeData_t *data = engine->data;
odeModel_t *om = engine->om;
/* calculate the mean and standard deviation of rates of change and
store in cvodeData_t * */
dy_mean = 0.0;
dy_var = 0.0;
dy_std = 0.0;
for ( i=0; i<om->neq; i++ ) {
dy_mean += fabs(evaluateAST(om->ode[i],data));
}
dy_mean = dy_mean / om->neq;
for ( i=0; i<om->neq; i++ ) {
dy_var += MySQR(evaluateAST(om->ode[i],data) - dy_mean);
}
dy_var = dy_var / (om->neq -1);
dy_std = MySQRT(dy_var);
/* stop integrator if mean + std of rates of change are lower than
1e-11 */
if ( (dy_mean + dy_std) < 1e-11 ) {
data->steadystate = 1;
SolverError_error(WARNING_ERROR_TYPE,
SOLVER_MESSAGE_STEADYSTATE_FOUND,
"Steady state found. "
"Simulation aborted at %g seconds. "
"Mean of rates: %g, std %g",
data->currenttime, dy_mean, dy_std);
return(1) ;
}
else {
data->steadystate = 0;
return(0);
}
}
double SolverData::evaluate(const ASTNode* node)
{
double result{0};
if ( !node )
{
m_Errors.add(new SimError(SIM_ERROR_EMPTY_AST, "Empy ASTNode"));
return 0;
}
if ( node->isUnknown() )
{
m_Errors.add(new SimError(SIM_ERROR_UNKNOWN_AST, "Unknown ASTNode"));
return 0;
}
int childnum = node->getNumChildren();
int isTrue{};
int i{};
ASTNodeType_t type = node->getType();
switch(type)
{
case AST_INTEGER:
result = (double) node->getInteger();
break;
case AST_REAL:
result = node->getReal();
break;
case AST_REAL_E:
result = node->getReal();
break;
case AST_RATIONAL:
result = node->getReal() ;
break;
case AST_NAME:
{
const OdeVariable* variable = (const OdeVariable*) node->getUserData();
if (variable)
{
int index = variable->getIndex();
switch (m_EvalStatus[index])
{
case EVAL_DOING:
{
std::ostringstream strstr;
strstr << "Cyclic AST evaluation at " << node->getName();
m_Errors.add(new SimError(SIM_ERROR_CYCLIC_AST, strstr.str()));
break;
}
case EVAL_DONE:
result = m_Values[index];
break;
default: // EVAL_WAIT
m_EvalStatus[index] = EVAL_DOING;
if (variable->getType() == ODE_ASSIGNMENT_VARIABLE)
{
result=evaluate(m_Model->getAssignment(variable->getEqIndex()));
} else if (variable->getInitEqIndex()>=0)
{
result=evaluate(m_Model->getInitAssignment(variable->getInitEqIndex()));
} else
{
//should never happen
m_Errors.add(new SimError(SIM_UNKNOWN_ERROR, LEVEL_FATAL));
}
m_Values[index] = result;
m_EvalStatus[index] = EVAL_DONE;
break;
}
} else
{
const char* name = node->getName();
if ( strcmp(name, "t") == 0
|| strcmp(name,"T") == 0
|| strcmp(name,"time") == 0
|| strcmp(name, "Time") == 0
|| strcmp(name, "TIME") == 0 )
{
result = (double) m_Time;
} else
{
std::ostringstream strstr;
strstr << node->getName() << " has not beed defined";
m_Errors.add(new SimError(SIM_ERROR_CYCLIC_AST, strstr.str()));
result = 0.0;
}
}
break;
}
case AST_FUNCTION_DELAY:
m_Errors.add(new SimError(SIM_WARNING_DELAY_ODE
, "Solving ODEs with Delay is not implemented. "
"Defaults to 0 to avoid program crash", LEVEL_WARNING));
result = 0.0;
break;
case AST_NAME_TIME:
result = (double) m_Time;
break;
case AST_CONSTANT_E:
/** exp(1) is used to adjust exponentiale to machine precision */
result = (double)exp(1.0);
break;
case AST_CONSTANT_FALSE:
result = 0.0;
break;
case AST_CONSTANT_PI:
/** pi = 4 * atan 1 is used to adjust Pi to machine precision */
result = 4.*atan(1.);
break;
case AST_CONSTANT_TRUE:
result = 1.0;
break;
case AST_PLUS:
result = 0.0;
for(i=0; i<childnum; ++i)
result += evaluate(node->getChild(i));
break;
case AST_MINUS:
if(childnum<2)
result = - (evaluate(node->getChild(0)));
else
result = evaluate(node->getChild(0)) - evaluate(node->getChild(1));
break;
case AST_TIMES:
result = 1.0;
for( i=0; i<childnum; ++i)
result *= evaluate(node->getChild(i));
break;
case AST_DIVIDE:
result = evaluate(node->getChild(0)) / evaluate(node->getChild(1));
break;
case AST_POWER:
result = pow(evaluate(node->getChild(0)),evaluate(node->getChild(1)));
break;
case AST_LAMBDA:
m_Errors.add(new SimError(SIM_WARNING_LAMBDA_USING,
"Lambda can only be used in function definitions."
" Defaults to 0 to avoid program crash", LEVEL_WARNING));
result = 0.0;
break;
/** FUNCTIONS: */
case AST_FUNCTION:
{
std::ostringstream strstr;
strstr << "The function " << node->getName() << "() has not been defined "
<< "in the SBML input model or as an externally "
<< "supplied function. Defaults to 0 to avoid "
<< "program crash";
m_Errors.add(new SimError(SIM_WARNING_UNDEFINED_FUNCTION, strstr.str(), LEVEL_WARNING));
result = 0.0;
break;
}
case AST_FUNCTION_ABS:
result = (double) fabs(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_ARCCOS:
result = acos(evaluate(node->getChild(0))) ;
break;
case AST_FUNCTION_ARCCOSH:
result = acosh(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_ARCCOT:
/** arccot x = arctan (1 / x) */
result = atan(1./ evaluate(node->getChild(0)));
break;
case AST_FUNCTION_ARCCOTH:
/** arccoth x = 1/2 * ln((x+1)/(x-1)) */
result = ((1./2.)*log((evaluate(node->getChild(0))+1.)/
(evaluate(node->getChild(0))-1.)) );
break;
case AST_FUNCTION_ARCCSC:
/** arccsc(x) = Arctan(1 / sqrt((x - 1)(x + 1))) */
result = atan( 1. / sqrt( (evaluate(node->getChild(0))-1.)*
(evaluate(node->getChild(0))+1.) ) );
break;
case AST_FUNCTION_ARCCSCH:
/** arccsch(x) = ln((1 + sqrt(1 + x^2)) / x) */
result = log((1.+sqrt((1+MySQR(evaluate(node->getChild(0)))))) /
evaluate(node->getChild(0)));
break;
case AST_FUNCTION_ARCSEC:
/** arcsec(x) = arctan(sqrt((x - 1)(x + 1))) */
result = atan( sqrt( (evaluate(node->getChild(0))-1.)*
(evaluate(node->getChild(0))+1.) ) );
break;
case AST_FUNCTION_ARCSECH:
/** arcsech(x) = ln((1 + sqrt(1 - x^2)) / x) */
result = log((1.+sqrt((1-MySQR(evaluate(node->getChild(0))))))/
evaluate(node->getChild(0)));
break;
case AST_FUNCTION_ARCSIN:
result = asin(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_ARCSINH:
result = asinh(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_ARCTAN:
result = atan(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_ARCTANH:
result = atanh(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_CEILING:
result = ceil(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_COS:
result = cos(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_COSH:
result = cosh(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_COT:
/** cot x = 1 / tan x */
result = (1./tan(evaluate(node->getChild(0))));
break;
case AST_FUNCTION_COTH:
/** coth x = cosh x / sinh x */
result = cosh(evaluate(node->getChild(0))) /
sinh(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_CSC:
/** csc x = 1 / sin x */
result = (1./sin(evaluate(node->getChild(0))));
break;
case AST_FUNCTION_CSCH:
/** csch x = 1 / sinh x */
result = (1./sinh(evaluate(node->getChild(0))));
break;
case AST_FUNCTION_EXP:
result = exp(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_FACTORIAL:
{
double floam_Timek = evaluate(node->getChild(0));
int k = (int) floor(floam_Timek);
if ( floam_Timek != k )
{
m_Errors.add(new SimError(SIM_WARNING_FACTORIAL_USING
, "The factorial is only implemented "
"for integer values. The floor value of the "
"passed float is used for calculation!", LEVEL_WARNING));
}
for(result=1; k>1; --k)
result *= k;
}
break;
case AST_FUNCTION_FLOOR:
result = floor(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_LN:
result = log(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_LOG:
/** log(x,y) = log10(y)/log10(x) (where x is the base) */
result = log10(evaluate(node->getChild(1))) /
log10(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_PIECEWISE:
if ( evaluate(node->getChild(0)) ) {
result = evaluate(node->getChild(1));
}
else {
result = evaluate(node->getChild(2));
}
break;
case AST_FUNCTION_POWER:
result = pow(evaluate(node->getChild(0)),evaluate(node->getChild(1)));
break;
case AST_FUNCTION_ROOT:
result = pow(evaluate(node->getChild(1)),
(1./evaluate(node->getChild(0))));
break;
case AST_FUNCTION_SEC:
/** sec x = 1 / cos x */
result = 1./cos(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_SECH:
/** sech x = 1 / cosh x */
result = 1./cosh(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_SIN:
result = sin(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_SINH:
result = sinh(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_TAN:
result = tan(evaluate(node->getChild(0)));
break;
case AST_FUNCTION_TANH:
result = tanh(evaluate(node->getChild(0)));
break;
case AST_LOGICAL_AND:
isTrue = 0;
for ( i=0; i<childnum; ++i )
{
isTrue += (int)evaluate(node->getChild(i));
}
if ( isTrue == childnum )
{
result = 1.0;
} else
{
result = 0.0;
}
break;
case AST_LOGICAL_NOT:
result = (double) (!(evaluate(node->getChild(0))));
break;
case AST_LOGICAL_OR:
isTrue = 0;
for (i=0; i<childnum; ++i )
{
isTrue += (int)evaluate(node->getChild(i));
}
if ( isTrue > 0 )
{
result = 1.0;
}
else
{
result = 0.0;
}
break;
case AST_LOGICAL_XOR:
/* n-ary: true if an odd number of children is true */
isTrue = 0;
for ( i=0; i<childnum; ++i )
{
isTrue += (int)evaluate(node->getChild(i));
}
if ( isTrue % 2 != 0 )
{
result = 1.0;
} else
{
result = 0.0;
}
break;
/* !!! check n-ary definitions for relational operators !!! */
case AST_RELATIONAL_EQ:
/* n-ary: all children must be equal */
result = 1.0;
for ( i=1; i<childnum; ++i )
{
if ( (evaluate(node->getChild(0))) !=
(evaluate(node->getChild(i))) )
{
result = 0.0;
}
}
break;
case AST_RELATIONAL_GEQ:
/* n-ary: each child must be greater than or equal to the following */
result = 1.0;
for ( i=0; i < childnum-1; ++i )
{
if ( (evaluate(node->getChild(i))) <
(evaluate(node->getChild(i+1))) )
{
result = 0.0;
}
}
break;
case AST_RELATIONAL_GT:
/* n-ary: each child must be greater than the following */
result = 1.0;
for ( i=0; i<childnum-1; ++i )
{
if ( (evaluate(node->getChild(i))) <=
(evaluate(node->getChild(i+1))) )
{
result = 0.0;
}
}
break;
case AST_RELATIONAL_LEQ:
/* n-ary: each child must be lower than or equal to the following */
result = 1.0;
for ( i=0; i<childnum-1; ++i )
{
if ( (evaluate(node->getChild(i))) >
(evaluate(node->getChild(i+1))) )
{
result = 0.0;
}
}
break;
case AST_RELATIONAL_LT :
/* n-ary: each child must be lower the following */
result = 1.0;
for ( i=0; i<childnum-1; ++i )
{
if ( (evaluate(node->getChild(i))) >=
(evaluate(node->getChild(i+1))) )
{
result = 0.0;
}
}
break;
default:
result = 0;
break;
}
return result;
}