int VectorField::ReadXML(string xmlfilename)
{
FILE *xmlfile;
mxml_node_t *tree;
mxml_node_t *node;
bool bad_attr;
xmlfile = fopen(xmlfilename.c_str(),"r");
if (xmlfile == NULL)
{
// Failed to open the file.
cerr << "Error: Unable to open " << xmlfilename << "\n";
exit(-1);
}
tree = mxmlLoadFile(NULL,xmlfile,MXML_NO_CALLBACK);
fclose(xmlfile);
if (tree == NULL)
{
cerr << "Error: Unable to load the vector field from the file " << xmlfilename << ".\n";
cerr << "There may be an error in the XML definition of the vector field.\n";
mxmlDelete(tree);
exit(-1);
}
node = mxmlFindElement(tree,tree,"VectorField",NULL,NULL,MXML_DESCEND);
if (node == NULL)
{
cerr << "Error: No VectorField element found in XML defintion.\n";
mxmlDelete(tree);
exit(-1);
}
else
{
bad_attr = false;
for (int i = 0; i < node->value.element.num_attrs; ++i)
{
string attr = node->value.element.attrs[i].name;
if (attr != "Name" && attr != "IndependentVariable" && attr != "Description")
{
cerr << "Error: The VectorField element has an unknown attribute: " << attr << endl;
bad_attr = true;
}
}
if (bad_attr)
exit(-1);
const char *attr;
attr = mxmlElementGetAttr(node,"Name");
if (attr == NULL)
{
cerr << "Error: The VectorField element has no Name attribute.\n";
mxmlDelete(tree);
exit(-1);
}
else
{
if (!isValidName(attr))
{
cerr << "Error: The VectorField Name \"" << attr << "\" is not valid.\n";
mxmlDelete(tree);
exit(-1);
}
string s(attr);
Name(s);
}
attr = mxmlElementGetAttr(node,"Description");
if (attr != NULL)
{
string s(attr);
Description(s);
}
attr = mxmlElementGetAttr(node,"IndependentVariable");
if (attr == NULL)
IndependentVariable = "t";
else
{
if (!isValidName(attr))
{
cerr << "Error: The VectorField IndependentVariable \"" << attr << "\" is not valid.\n";
mxmlDelete(tree);
exit(-1);
}
string s(attr);
IndependentVariable = s;
}
}
//
// Get the constants
//
for (node = mxmlFindElement(tree,tree,"Constant",NULL,NULL,MXML_DESCEND);
node != NULL;
node = mxmlFindElement(node,tree,"Constant",NULL,NULL,MXML_DESCEND))
{
bad_attr = false;
for (int i = 0; i < node->value.element.num_attrs; ++i)
{
string attr = node->value.element.attrs[i].name;
if (attr != "Name" && attr != "Value" && attr != "Description" && attr != "Latex")
{
cerr << "Error: A Constant element has an unknown attribute: " << attr << endl;
bad_attr = true;
}
}
if (bad_attr)
{
cerr << "Valid Constant attributes are: Name, Value, Description, Latex.\n";
exit(-1);
}
const char *attr;
attr = mxmlElementGetAttr(node,"Name");
if (attr == NULL)
{
cerr << "Error: A Constant element has no Name attribute.\n";
mxmlDelete(tree);
exit(-1);
}
else
{
if (!isValidName(attr))
{
cerr << "Error: The Constant Name \"" << attr << "\" is not valid.\n";
mxmlDelete(tree);
exit(-1);
}
string name(attr);
Constant *c = new Constant(name);
AddConstant(c);
attr = mxmlElementGetAttr(node,"Description");
if (attr != NULL)
{
string descr(attr);
c->Description(descr);
}
attr = mxmlElementGetAttr(node,"Value");
if (attr == NULL)
{
cerr << "Error: The Constant element with Name=\"" << c->Name() << "\" has no Value attribute.\n";
mxmlDelete(tree);
exit(-1);
}
else
{
string val(attr);
c->Value(val);
}
attr = mxmlElementGetAttr(node,"Latex");
if (attr != NULL)
{
string latex(attr);
c->Latex(latex);
}
}
}
//
// Get the parameters
//
for (node = mxmlFindElement(tree,tree,"Parameter",NULL,NULL,MXML_DESCEND);
node != NULL;
node = mxmlFindElement(node,tree,"Parameter",NULL,NULL,MXML_DESCEND))
{
bad_attr = false;
for (int i = 0; i < node->value.element.num_attrs; ++i)
{
string attr = node->value.element.attrs[i].name;
if (attr != "Name" && attr != "DefaultValue" && attr != "Description" && attr != "Latex")
{
cerr << "Error: A Parameter element has an unknown attribute: " << attr << endl;
bad_attr = true;
}
}
if (bad_attr)
{
cerr << "Valid Parameter attributes are: Name, DefaultValue, Description, Latex.\n";
exit(-1);
}
const char *attr;
attr = mxmlElementGetAttr(node,"Name");
if (attr == NULL)
{
cerr << "Error: A Parameter element has no Name attribute.\n";
mxmlDelete(tree);
exit(-1);
}
else
{
if (!isValidName(attr))
{
cerr << "Error: The Parameter Name \"" << attr << "\" is not valid.\n";
mxmlDelete(tree);
exit(-1);
}
string name(attr);
Parameter *p = new Parameter(name);
AddParameter(p);
attr = mxmlElementGetAttr(node,"Description");
if (attr != NULL)
{
string descr(attr);
p->Description(descr);
}
attr = mxmlElementGetAttr(node,"DefaultValue");
if (attr != NULL)
{
string defval(attr);
p->DefaultValue(defval);
}
attr = mxmlElementGetAttr(node,"Latex");
if (attr != NULL)
{
string latex(attr);
p->Latex(latex);
}
}
}
//
// Get the auxiliary expressions
//
for (node = mxmlFindElement(tree,tree,"Expression",NULL,NULL,MXML_DESCEND);
node != NULL;
node = mxmlFindElement(node,tree,"Expression",NULL,NULL,MXML_DESCEND))
{
bad_attr = false;
for (int i = 0; i < node->value.element.num_attrs; ++i)
{
string attr = node->value.element.attrs[i].name;
if (attr != "Name" && attr != "Formula" && attr != "Description" && attr != "Latex")
{
cerr << "Error: An Expression element has an unknown attribute: " << attr << endl;
bad_attr = true;
}
}
if (bad_attr)
{
cerr << "Valid Expression attributes are: Name, Formula, Description, Latex.\n";
exit(-1);
}
const char *attr;
attr = mxmlElementGetAttr(node,"Name");
if (attr == NULL)
{
cerr << "Error: An Expression element has no Name attribute.\n";
mxmlDelete(tree);
exit(-1);
}
else
{
if (!isValidName(attr))
{
cerr << "Error: The Expression Name \"" << attr << "\" is not valid.\n";
mxmlDelete(tree);
exit(-1);
}
string name(attr);
Expression *e = new Expression(name);
AddExpression(e);
attr = mxmlElementGetAttr(node,"Description");
if (attr != NULL)
{
string descr(attr);
e->Description(descr);
}
attr = mxmlElementGetAttr(node,"Formula");
if (attr == NULL)
{
cerr << "Error: The Expression with Name=\"" << e->Name() << "\" has no Formula attribute.\n";
mxmlDelete(tree);
exit(-1);
}
else
{
string f(attr);
e->Formula(f);
}
attr = mxmlElementGetAttr(node,"Latex");
if (attr != NULL)
{
string latex(attr);
e->Latex(latex);
}
}
}
//
// Get the state variables
//
for (node = mxmlFindElement(tree,tree,"StateVariable",NULL,NULL,MXML_DESCEND);
node != NULL;
node = mxmlFindElement(node,tree,"StateVariable",NULL,NULL,MXML_DESCEND))
{
bad_attr = false;
for (int i = 0; i < node->value.element.num_attrs; ++i)
{
string attr = node->value.element.attrs[i].name;
if (attr != "Name" && attr != "DefaultInitialCondition" && attr != "Description"
&& attr != "Formula" && attr != "PeriodFrom" && attr != "PeriodTo"
&& attr != "DefaultHistory" && attr != "Latex")
{
cerr << "Error: A StateVariable element has an unknown attribute: " << attr << endl;
bad_attr = true;
}
}
if (bad_attr)
{
cerr << "Valid StateVariable attributes are: Name, Formula, Description, DefaultInitialCondition, DefaultHistory, PeriodFrom, PeriodTo, Latex.\n";
exit(-1);
}
const char *attr;
attr = mxmlElementGetAttr(node,"Name");
if (attr == NULL)
{
cerr << "Error: A StateVariable element has no Name attribute.\n";
mxmlDelete(tree);
exit(-1);
}
else
{
if (!isValidName(attr))
{
cerr << "Error: The StateVariable Name \"" << attr << "\" is not valid.\n";
mxmlDelete(tree);
exit(-1);
}
string name(attr);
StateVariable *sv = new StateVariable(name);
AddStateVariable(sv);
attr = mxmlElementGetAttr(node,"Description");
if (attr != NULL)
{
string descr(attr);
sv->Description(descr);
}
attr = mxmlElementGetAttr(node,"Formula");
if (attr == NULL)
{
cerr << "Error: The StateVariable with Name=\"" << sv->Name() << "\" has no Formula attribute.\n";
mxmlDelete(tree);
exit(-1);
}
else
{
string f(attr);
sv->Formula(f);
}
attr = mxmlElementGetAttr(node,"PeriodFrom");
if (attr != NULL)
{
string pfrom(attr);
sv->PeriodicFrom(pfrom);
}
attr = mxmlElementGetAttr(node,"PeriodTo");
if (attr != NULL)
{
string pto(attr);
sv->PeriodicTo(pto);
}
if (sv->PeriodicFrom() != "" & sv->PeriodicTo() == "")
{
cerr << "Error: The StateVariable with Name=\"" << sv->Name() << "\" has a PeriodicFrom attribute but no PeriodicTo attribute.\n";
mxmlDelete(tree);
exit(-1);
}
if (sv->PeriodicFrom() == "" & sv->PeriodicTo() != "")
{
cerr << "Error: The StateVariable with Name=\"" << sv->Name() << "\" has a PeriodTo attribute but no PeriodicFrom attribute.\n";
mxmlDelete(tree);
exit(-1);
}
attr = mxmlElementGetAttr(node,"DefaultInitialCondition");
if (attr != NULL)
{
string ic(attr);
sv->DefaultInitialCondition(ic);
}
attr = mxmlElementGetAttr(node,"DefaultHistory");
if (attr != NULL)
{
string hist(attr);
sv->DefaultHistory(hist);
}
attr = mxmlElementGetAttr(node,"Latex");
if (attr != NULL)
{
string latex(attr);
sv->Latex(latex);
}
}
}
//
// Get the functions
//
for (node = mxmlFindElement(tree,tree,"Function",NULL,NULL,MXML_DESCEND);
node != NULL;
node = mxmlFindElement(node,tree,"Function",NULL,NULL,MXML_DESCEND))
{
bad_attr = false;
for (int i = 0; i < node->value.element.num_attrs; ++i)
{
string attr = node->value.element.attrs[i].name;
if (attr != "Name" && attr != "Formula" && attr != "Description")
{
cerr << "Error: A Function element has an unknown attribute: " << attr << endl;
bad_attr = true;
}
}
if (bad_attr)
{
cerr << "Valid Function attributes are: Name, Formula, Description.\n";
exit(-1);
}
const char *attr;
attr = mxmlElementGetAttr(node,"Name");
if (attr == NULL)
{
cerr << "Error: A Function element has no Name attribute.\n";
mxmlDelete(tree);
exit(-1);
}
else
{
if (!isValidName(attr))
{
cerr << "Error: The Function Name \"" << attr << "\" is not valid.\n";
mxmlDelete(tree);
exit(-1);
}
string name(attr);
Function *func = new Function(name);
AddFunction(func);
attr = mxmlElementGetAttr(node,"Description");
if (attr != NULL)
{
string descr(attr);
func->Description(descr);
}
attr = mxmlElementGetAttr(node,"Formula");
if (attr == NULL)
{
cerr << "Error: The Function element with Name=\"" << func->Name() << "\" has no Formula attibute.\n";
mxmlDelete(tree);
exit(-1);
}
else
{
string f(attr);
func->Formula(f);
}
}
}
mxmlDelete(tree);
return 0;
}
void VectorField::Delay2ODE_ConvertAndExtend(ex& f, int N, int p)
{
lst dlist;
f.find(delay(wild(1),wild(2)),dlist);
// dlist is now a ginac lst of expressions of the form delay(delayexpr,del)
for (lst::const_iterator diter = dlist.begin(); diter != dlist.end(); ++diter)
{
// diter points to a ginac expression of the form delay(delayexpr,del).
ex delayfunc = *diter;
symbol tmpsymbol;
ex lag = delayfunc.op(1);
ex hist = delayfunc.op(0);
Delay2ODE_ConvertExprToDefHist(hist);
string delayed_var_name;
ostringstream os_N_over_delta;
os_N_over_delta << "(" << N << "/(" << lag << "))";
string N_over_delta = os_N_over_delta.str();
for (int k = 0; k < N; ++k)
{
if (p == 1)
{
string vstr1, prev_vstr1;
ostringstream os;
os << k+1;
vstr1 = tmpsymbol.get_name() + "_1_" + os.str();
os.str("");
os << k;
prev_vstr1 = tmpsymbol.get_name() + "_1_" + os.str();
//
StateVariable *var = new StateVariable(vstr1);
ostringstream os_varformula;
os_varformula << N_over_delta << "*(";
if (k == 0)
os_varformula << delayfunc.op(0);
else
os_varformula << prev_vstr1;
os_varformula << " - " << vstr1 << ")";
var->Formula(os_varformula.str());
ostringstream os_vardefic;
os_vardefic << hist.subs(IndVar==-(k+1)*lag/N);
var->DefaultInitialCondition(os_vardefic.str());
AddStateVariable(var);
if (k == N-1)
delayed_var_name = var->Name();
}
else if (p == 2)
{
string vstr1,vstr2, prev_vstr1;
ostringstream os;
os << k+1;
vstr1 = tmpsymbol.get_name() + "_1_" + os.str();
vstr2 = tmpsymbol.get_name() + "_2_" + os.str();
os.str("");
os << k;
prev_vstr1 = tmpsymbol.get_name() + "_1_" + os.str();
//
StateVariable *var = new StateVariable(vstr1);
var->Formula(vstr2);
ostringstream os_vardefic;
os_vardefic << hist.subs(IndVar==-(k+1)*lag/N);
var->DefaultInitialCondition(os_vardefic.str());
AddStateVariable(var);
if (k == N-1)
delayed_var_name = var->Name();
//
var = new StateVariable(vstr2);
ostringstream os_varformula;
os_varformula << "2*" << N_over_delta << "*";
os_varformula << "( -" << vstr2 << " + " << N_over_delta << "*";
os_varformula << "(";
if (k == 0)
os_varformula << delayfunc.op(0);
else
os_varformula << prev_vstr1;
os_varformula << " - " << vstr1 << "))";
var->Formula(os_varformula.str());
ex icderiv = hist.diff(IndVar);
ostringstream os_vardefic_deriv;
os_vardefic_deriv << icderiv.subs(IndVar==-(k+1)*lag/N);
var->DefaultInitialCondition(os_vardefic_deriv.str());
AddStateVariable(var);
}
else // p == 3
{
string vstr1,vstr2,vstr3, prev_vstr1;
ostringstream os;
os << k+1;
vstr1 = tmpsymbol.get_name() + "_1_" + os.str();
vstr2 = tmpsymbol.get_name() + "_2_" + os.str();
vstr3 = tmpsymbol.get_name() + "_3_" + os.str();
os.str("");
os << k;
prev_vstr1 = tmpsymbol.get_name() + "_1_" + os.str();
//
StateVariable *var = new StateVariable(vstr1);
var->Formula(vstr2);
ostringstream os_vardefic;
os_vardefic << hist.subs(IndVar==-(k+1)*lag/N);
var->DefaultInitialCondition(os_vardefic.str());
AddStateVariable(var);
if (k == N-1)
delayed_var_name = var->Name();
//
var = new StateVariable(vstr2);
var->Formula(vstr3);
ex icderiv = hist.diff(IndVar);
ostringstream os_vardefic_deriv;
os_vardefic_deriv << icderiv.subs(IndVar==-(k+1)*lag/N);
var->DefaultInitialCondition(os_vardefic_deriv.str());
AddStateVariable(var);
//
var = new StateVariable(vstr3);
ostringstream os_varformula;
os_varformula << N_over_delta << "*";
os_varformula << "(-3*" << vstr3;
os_varformula << " - 6*" << N_over_delta << "*";
os_varformula << "(" << vstr2 << " - " << N_over_delta << "*";
os_varformula << "(";
if (k == 0)
os_varformula << delayfunc.op(0);
else
os_varformula << prev_vstr1;
os_varformula << " - " << vstr1 << ")))";
var->Formula(os_varformula.str());
ex icderiv2 = icderiv.diff(IndVar);
ostringstream os_vardefic_deriv2;
os_vardefic_deriv2 << icderiv2.subs(IndVar==-(k+1)*lag/N);
var->DefaultInitialCondition(os_vardefic_deriv2.str());
AddStateVariable(var);
}
} // end k loop
symbol s(delayed_var_name);
f = f.subs(delayfunc == s);
} // end dlist loop
}
void VectorField::PrintEVF(map<string,string> options)
{
//
// This function adds variables to the vector field.
// The vector field for the new variables is given by the
// variational equations.
// The code should probably check for a partial derivative being
// zero and not bother generating the corresponding output. Or it
// could create a ginac ex to hold the expression until all derivatives
// have been added to it, then create the string in the new state variable.
// Ginac would automatically drop the zero terms. I'll get around to
// this some time...
//
// Note that this function MODIFIES THE OBJECT!!!
// It then calls PrintXML to output the extended vector field to the
// standard output in XML format.
//
int kpar = -1;
symbol p;
if (options.find("par") != options.end()) {
// cerr << "The option par=" << options["par"] << " has been given.\n";
kpar = findpar(options["par"],Parameters);
if (kpar == -1) {
cerr << "Error: Unknown parameter \"" << options["par"] << "\"\n";
cerr << "The parameters are: ";
for (unsigned j = 0; j < parname_list.nops(); ++j) {
if (j != 0) {
cerr << ", ";
}
cerr << parname_list[j];
}
cerr << endl;
exit(-1);
}
}
if (kpar != -1) {
// cerr << "parname_list[" << kpar << "] = " << parname_list[kpar] << endl;
p = ex_to<symbol>(parname_list[kpar]);
}
ostringstream oss;
int nv = varname_list.nops();
for (int i = 0; i < nv; ++i) {
oss.str("");
ex f = iterated_subs(varvecfield_list[i],expreqn_list);
int num_terms_output = 0;
for (int j = 0; j < nv; ++j) {
symbol v = ex_to<symbol>(varname_list[j]);
ex df = f.diff(v);
if (df != 0) {
if (num_terms_output > 0) {
oss << " + ";
}
if (df == 1) {
oss << "d" << varname_list[j];
}
else {
oss << "(" << df << ")*d" << varname_list[j];
}
num_terms_output = num_terms_output + 1;
}
}
if (kpar != -1) {
ex dfdp = f.diff(p);
if (dfdp != 0) {
if (num_terms_output > 0) {
oss << " + ";
}
oss << "(" << dfdp << ")";
num_terms_output = num_terms_output + 1;
}
}
if (num_terms_output == 0) {
oss << "0";
}
StateVariable *var = new StateVariable("d"+StateVariables[i]->Name());
var->Formula(oss.str());
AddStateVariable(var);
}
Name(Name()+"_evf");
PrintXML("evf");
}