// Print out details of Molecule, taking the form:
// ========
// MOLECULE
// ========
// No. of e- = nel, charge = q, singlet/doublet/triplet etc.
// Enuc = nuclear energy
// (if inertia = true then also prints the section:
// ............................
// Principal Moments of Inertia
// ............................
// Ia = ..., Ib = ..., Ic = ...
// Rotational type: ...
// ....................
// Rotational Constants
// ....................
// (the coordinate system is also transformed to inertial coords)
// =====
// ATOMS
// =====
// Atom z Mass (a.m.u) Coordinates
// ...............................................................
// C 6 12.014 (0.0, 3.53, -1.24)
// etc...
void Logger::print(Molecule& mol, bool inertia) const
{
title("Molecule");
// Print out basic details
outfile << "# electrons = " << mol.getNel() << ", ";
outfile << "charge = " << mol.getCharge() << ", ";
std::string temp;
// Get the state type
switch (mol.getMultiplicity()) {
case 1: { temp = "Singlet"; break; }
case 2: { temp = "Doublet"; break; }
case 3: { temp = "Triplet"; break; }
case 4: { temp = "Quartet"; break; }
case 5: { temp = "Quintet"; break; }
default: { temp = "Spintacular"; break; } // Are hextets even a thing?!
}
outfile << temp << "\n";
outfile << "ENUC = " << mol.getEnuc() << " Hartree\n";
// Print inertial details if needed, and rotate
// into the inertial coordinate system
if (inertia) {
// Get it
temp = mol.rType();
Vector rconsts(3);
rconsts = mol.rConsts(1); // MHz
Vector inert(3);
inert = mol.getInertia(true);
// Print it out
outfile << std::string(30, '.') << "\n";
outfile << "Principal Moments of Inertia\n";
outfile << std::string(30, '.') << "\n";
outfile << "Ia = " << std::setw(12) << inert(0);
outfile << ", Ib = " << std::setw(12) << inert(1);
outfile << ", Ic = " << std::setw(12) << inert(2) << "\n";
outfile << "Rotational type: " << temp << "\n";
outfile << std::string(29, '.') << "\n";
outfile << "Rotational Constants / GHz\n";
outfile << std::string(29, '.') << "\n";
outfile << "A = " << std::setw(12) << rconsts(0);
outfile << ", B = " << std::setw(12) << rconsts(1);
outfile << ", C = " << std::setw(12) << rconsts(2) << "\n";
}
// Finally, print out all the atoms
title("Atoms");
outfile << std::setw(10) << "Atom" << std::setw(10) << "z";
outfile << std::setw(10) << "Mass" << std::setw(10) << "#CGBFs";
outfile << std::setw(30) << "Coordinates" << "\n";
outfile << std::string(70, '.') << "\n";
for (int i = 0; i < mol.getNAtoms(); i++){
print(mol.getAtom(i));
}
}
RESULT
CHECK(const System* getSystem() const throw())
System s1("aya");
Molecule m("a");
s1.append(m);
const System s(s1);
TEST_EQUAL(m.getSystem()->getName(), "aya")
RESULT
CHECK(void prepend(Atom& atom) throw())
Molecule m;
Atom a1;
Atom a2;
m.insert(a1);
TEST_EQUAL(m.getAtom(0), &a1)
m.prepend(a2);
TEST_EQUAL(m.getAtom(0), &a2)
TEST_EQUAL(m.getAtom(1), &a1)
RESULT
CHECK(void append(Atom& atom) throw())
Molecule m;
Atom a1;
Atom a2;
m.insert(a1);
m.append(a2);
TEST_EQUAL(m.getAtom(0), &a1)
TEST_EQUAL(m.getAtom(1), &a2)
RESULT
const Molecule* LevelSet::readLevelMolecule(int levelNum) const
{
Molecule* mol = new Molecule();
KConfigGroup config = m_levelsFile->group("Level"+QString::number(levelNum));
QString key;
atom current;
int atom_index = 1;
QString value;
while (true) {
key.sprintf("atom_%c", int2atom(atom_index));
value = config.readEntry(key,QString());
if (value.isEmpty())
break;
current.obj = value.at(0).toLatin1();
value = value.mid(2);
strncpy(current.conn, value.toLatin1(), sizeof(current.conn));
if (mol->m_atoms.indexOf(current) != -1)
qWarning()
<< "OOOPS, duplicate atom definition in" << key;
mol->m_atoms.append(current);
atom_index++;
}
QString line;
mol->m_width = 0;
mol->m_height = 0;
mol->m_weight = 0.0;
int max_i = -1;
for (int j = 0; j < MOLECULE_SIZE; j++) {
key.sprintf("mole_%d", j);
line = config.readEntry(key,QString());
int max_non_null_i = -1;
for (int i = 0; i < MOLECULE_SIZE; i++)
{
if (i >= line.size())
mol->m_molek[i][j] = 0;
else
{
mol->m_molek[i][j] = atom2int(line.at(i).toLatin1());
mol->m_weight += mol->getAtom(mol->m_molek[i][j]).weight();
max_non_null_i = i;
}
}
if( max_non_null_i != -1 )
mol->m_height++;
max_i = qMax( max_i, max_non_null_i );
}
mol->m_width = max_i+1;
mol->m_name = i18n(config.readEntry("Name", I18N_NOOP("Noname")).toUtf8());
return mol;
}
