bool Engine::setFunction(QString n, ELAM::Function p)
{
if(p==0)return false;
if(!d->cclass.isName(n))return false;
if(hasConstant(n))return false;
if(hasVariable(n))return false;
d->funcs.insert(n,p);
return true;
}
void Programme::setVariable(Variable& var) {
if(hasArgument(var.getNom())) {
arguments[indexOfVar(arguments, var.getNom())] = var;
}
else if(hasVariable(var.getNom())) {
variables[indexOfVar(variables, var.getNom())] = var;
}
else {
throw "La variable \""+var.getNom()+"\" n'existe pas dans le programme \""+nom+"\".";
}
}
Variable Programme::getVariable(std::string var) const {
if(hasArgument(var)) {
return arguments[indexOfVar(arguments, var)];
}
else if(hasVariable(var)) {
return variables[indexOfVar(variables, var)];
}
else {
throw "Le programme \""+nom+"\" ne dispose d'aucune variable \""+var+"\".";
}
}
bool planning_models::KinematicModel::RevoluteJointModel::isValueWithinVariableBounds(const std::string& variable,
const double& value,
bool& within_bounds) const
{
if(!continuous_) {
return JointModel::isValueWithinVariableBounds(variable, value, within_bounds);
}
if(!hasVariable(variable)) {
return false;
}
within_bounds = true;
return true;
}
void RMemoryStorage::setVariable(const QString& key, const QVariant& value, bool overwrite) {
if (!overwrite && hasVariable(key)) {
return;
}
if (variables.contains(key) && variables[key]==value) {
// no change:
return;
}
// remove existing variable with same name (case insensitive comparison):
if (variableCaseMap.contains(key.toLower()) && variableCaseMap[key.toLower()]!=key) {
variables.remove(variableCaseMap[key.toLower()]);
}
variableCaseMap[key.toLower()] = key;
variables[key] = value;
setModified(true);
}
vTrimGain::vTrimGain(sCurveAnalysis &anAnalysis) : sCurveAnalysis(anAnalysis)
{
for (std::map<QString, std::map<std::string, TH2F*> >::iterator hIt = histogramSum2D.begin(); hIt != histogramSum2D.end(); ++ hIt)
{
gainPoint_ [hIt->first] = new TGraph();
gainPointX_[hIt->first] = new TGraph();
gainPointY_[hIt->first] = new TGraph();
}
if (!hasVariable("25. Vcal vs 11. Vtrim"))
{
std::cout << "No plot available for finding the VTrim gain: VTrim vs VCal needed!" << std::endl;
isGainAnalysisPossible_ = false;
return;
}
isGainAnalysisPossible_ = true;
minThreashold_ = 0;
std::cout << "Be sure that TrimBit is 15 now!\n";
}
void gkDebugPropertyPage::addVariable(gkVariable* prop)
{
if (hasVariable(prop))
return;
m_props.push_back(prop);
gkScalar strWidth = PROP_SIZE * prop->getName().size();
gkScalar nh = m_cont->getHeight() + PROP_SIZE;
m_cont->setHeight(nh);
if (m_key->getWidth() < strWidth || m_props.size() == 1)
{
gkScalar diffw = strWidth - m_key->getWidth();
m_cont->setWidth(m_cont->getWidth() + diffw);
gkScalar half = m_cont->getWidth() / 2.f;
m_key->setWidth(half);
m_val->setWidth(half);
m_val->setPosition(m_props.size() == 1 ? strWidth : half, 0);
}
}
bool Potential1210::extractSection
(ForceFieldParameters& parameters, const String& section_name)
{
// clear the fields first
clear();
// check whether the parameters are valid
if (!parameters.isValid())
{
return false;
}
// extract the basis information
ParameterSection::extractSection(parameters, section_name);
// check whether all variables we need are defined, terminate otherwise
if (!hasVariable("A") || !hasVariable("B"))
{
return false;
}
// build a two dimensional array of the atom types
// loop variable
Size i;
AtomTypes& atom_types = parameters.getAtomTypes();
number_of_atom_types_ = atom_types.getNumberOfTypes();
// allocate two onedimensional fields for the two parameters
A_.resize(number_of_atom_types_ * number_of_atom_types_);
B_.resize(number_of_atom_types_ * number_of_atom_types_);
is_defined_.resize(number_of_atom_types_ * number_of_atom_types_);
for (i = 0; i < number_of_atom_types_ * number_of_atom_types_; i++)
{
is_defined_[i] = false;
}
StringHashMap<Index>::Iterator it;
// determine the factor to convert the parameters to the standard units used
// as a default, energies are assumend to be in kJ/mol and distances in Angstrom
double factor_A = 1.0;
double factor_B = 1.0;
if (options.has("unit_A"))
{
if (options["unit_A"] == "kcal/mol*A^12")
{
factor_A = Constants::JOULE_PER_CAL;
}
else
{
Log.warn() << "unknown unit for parameter A: " << options["unit_A"] << endl;
}
}
if (options.has("unit_B"))
{
if (options["unit_B"] == "kcal/mol*A^10")
{
factor_B = Constants::JOULE_PER_CAL;
}
else
{
Log.warn() << "unknown unit for parameter B: " << options["unit_B"] << endl;
}
}
Atom::Type type_I;
Atom::Type type_J;
String type_name_I;
String type_name_J;
String key;
Index index = 0;
for (it = section_entries_.begin(); !(it == section_entries_.end()); ++it)
{
key = (*it).first;
if ((key.size() > 0) && (key.find_first_of(" ", 0) > 0))
{
type_name_I = key.before(" ", 0);
type_name_J = key.after(" ", 0);
if ((atom_types.hasType(type_name_I)) && (atom_types.hasType(type_name_J)))
{
type_I = atom_types.getType(type_name_I);
type_J = atom_types.getType(type_name_J);
index = (Index)(type_I * number_of_atom_types_ + type_J);
is_defined_[index] = true;
A_ [index] = getValue(key, "A").toFloat() * factor_A;
B_ [index] = getValue(key, "B").toFloat() * factor_B;
index = (Index)(type_I + number_of_atom_types_ * type_J);
is_defined_[index] = true;
A_ [index] = getValue(key, "A").toFloat() * factor_A;
B_ [index] = getValue(key, "B").toFloat() * factor_B;
}
}
}
return true;
}
bool QgsExpressionContextScope::isReadOnly( const QString &name ) const
{
return hasVariable( name ) ? mVariables.value( name ).readOnly : false;
}
QVariant QgsExpressionContextScope::variable( const QString &name ) const
{
return hasVariable( name ) ? mVariables.value( name ).value : QVariant();
}
bool Engine::hasValue(QString n) const
{
return hasVariable(n) || hasConstant(n);
}
QVariant Engine::getValue(QString n) const
{
if(hasConstant(n))return getConstant(n);
if(hasVariable(n))return getVariable(n);
return QVariant();
}
QString QgsExpressionContextScope::description( const QString &name ) const
{
return hasVariable( name ) ? mVariables.value( name ).description : QString();
}
bool QgsExpressionContextScope::isStatic( const QString &name ) const
{
return hasVariable( name ) ? mVariables.value( name ).isStatic : false;
}
bool CosineTorsion::extractSection(ForceFieldParameters& parameters, const String& section_name)
{
// check whether the parameters are valid
if (!parameters.isValid())
{
return false;
}
// extract the section information
if (!ParameterSection::extractSection(parameters, section_name))
{
Log.error() << "CosineTorison::extractSection: Could not find section "
<< section_name << " in parameter file!" << std::endl;
return false;
}
// check whether all variables we need are defined, terminate otherwise
if (!hasVariable("div") || !hasVariable("V")
|| !hasVariable("phi0") || !hasVariable("f"))
{
Log.error() << "CosineTorsion::extractSection: CosineTorsion section (" << section_name
<< ") needs columns div, V, phi0, and f!" << std::endl;
return false;
}
// build a two dimensional array of the atom types
// loop variable
Size i;
const AtomTypes& atom_types = parameters.getAtomTypes();
number_of_atom_types_ = atom_types.getNumberOfTypes();
// clear all old torsions
// - torsions_ is a vector containing Values objects
// - torsion_hash_map_ hashes the product of the atom types (I + number_of_atom_types_ * J +...)
// to a the index in torsions_
torsions_.clear();
torsion_hash_map_.clear();
// determine the units of the phase and potential wall
// (if given in options)
float factor_phase = 1.0;
if (options.has("unit_phase"))
{
if (options["unit_phase"] == "rad")
{
factor_phase = 180.0 / Constants::PI;
}
}
float factor_V = 1.0;
if (options.has("unit_V"))
{
if (options["unit_V"] == "kcal/mol")
{
factor_V = Constants::JOULE_PER_CAL;
}
}
Atom::Type type_I;
Atom::Type type_J;
Atom::Type type_K;
Atom::Type type_L;
String key;
String fields[5];
StringHashMap<Index>::Iterator it;
for (it = section_entries_.begin(); it != section_entries_.end(); ++it)
{
key = it->first;
if (key.split(fields, 5) == 5)
{
// the first of line for each torsion has to contain N as last part of the key.
// this line only contains the number of torsion terms in "div"
if (fields[4] == "N")
{
// determine all atom types
type_I = atom_types.getType(fields[0]);
type_J = atom_types.getType(fields[1]);
type_K = atom_types.getType(fields[2]);
type_L = atom_types.getType(fields[3]);
// retrieve the number of torsion terms
Size n = getValue(key, "div").toUnsignedInt();
if ((n < 1) || (n > 4))
{
Log.error() << "CosineTorsion::extractSection: wrong number of torsion terms for "
<< key << ": " << n << std::endl;
}
else
{
// create a new torsion and store
// it in the vector of torsions
Size array_idx = (Size)torsions_.size();
torsions_.push_back(Values(n));
// try to find the torsion terms
for (i = 0; i < n; i++)
{
// calculate the correct key: "I J K L <number>"
String term_key(key, 0, (Size)key.size() - 1);
term_key += (String)(i + 1);
// lookup the corresponding entry
torsions_[array_idx].values[i].n = getValue(term_key, "div").toFloat();
torsions_[array_idx].values[i].phase = getValue(term_key, "phi0").toFloat() * factor_phase;
torsions_[array_idx].values[i].f = getValue(term_key, "f").toFloat();
torsions_[array_idx].values[i].V = getValue(term_key, "V").toFloat() * factor_V;
}
// insert the array index and the atom type key into the
// hash map
// calculate a unique number for each possible combination of
// atom types and use it to hash the torsion parameters
Size index = type_I + type_J * number_of_atom_types_
+ type_K * number_of_atom_types_ * number_of_atom_types_
+ type_L * number_of_atom_types_ * number_of_atom_types_ * number_of_atom_types_;
torsion_hash_map_.insert(pair<Size, Size>(index, array_idx));
}
}
}
else
{
Log.error() << "CosineTorsion::extractSection: could not interpret key " << key << std::endl;
}
}
return true;
}
