void PolymerizationProcess::initSubunits(Species* aSpecies)
{
if(aSpecies->getIsPolymer() && !aSpecies->getIsSubunitInitialized())
{
std::vector<Voxel*>& molecules(aSpecies->getMolecules());
for(std::vector<Voxel*>::iterator i(molecules.begin());
i != molecules.end(); ++i)
{
initSubunit(*i, aSpecies);
}
aSpecies->setIsSubunitInitialized();
}
}
int main(int argc, char *argv[])
{
# include "setRootCase.H"
# include "createTime.H"
# include "createMesh.H"
potential pot(mesh);
moleculeCloud molecules(mesh, pot);
# include "temperatureAndPressureVariables.H"
# include "readmdEquilibrationDict.H"
label nAveragingSteps = 0;
Info << "\nStarting time loop\n" << endl;
while (runTime.loop())
{
nAveragingSteps++;
Info << "Time = " << runTime.timeName() << endl;
molecules.evolve();
# include "meanMomentumEnergyAndNMols.H"
# include "temperatureAndPressure.H"
# include "temperatureEquilibration.H"
runTime.write();
if (runTime.outputTime())
{
nAveragingSteps = 0;
}
Info << "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
<< " ClockTime = " << runTime.elapsedClockTime() << " s"
<< nl << endl;
}
Info << "End\n" << endl;
return 0;
}
void MainWindow::reindexAtoms()
{
bool all(false); // we only want the visible molecules;
MoleculeList molecules(m_viewerModel.moleculeList(all));
if (molecules.size() == 0) return;
if (molecules.size() > 1) {
QString msg("Only one molecule can be visible when reindexing atoms.");
QMsgBox::warning(0, "IQmol", msg);
return;
}
QList<QAction*>::iterator iter;
for (iter = m_labelActions.begin(); iter != m_labelActions.end(); ++iter) {
(*iter)->setChecked(false);
}
m_viewer.reindexAtoms(molecules.first());
}
int main(int argc, char *argv[])
{
# include "setRootCase.H"
# include "createTime.H"
# include "createMesh.H"
# include "createRandom.H"
reducedUnits rU(runTime, mesh);
constantMoleculeProperties cP (mesh, rU);
polyMoleculeCloud molecules
(
runTime,
mesh,
rU,
cP,
rndGen,
"mdInitialise",
true
);
IOstream::defaultPrecision(15);
if (!mesh.write())
{
FatalErrorIn(args.executable())
<< "Failed writing moleculeCloud."
<< nl << exit(FatalError);
}
Info<< nl << "ClockTime = " << runTime.elapsedClockTime() << " s"
<< nl << endl;
Info << nl << "End\n" << endl;
return 0;
}
void BuildAtom::leftMouseMoveEvent(QMouseEvent* e)
{
m_viewer->clearSelection();
m_viewer->QGLViewer::select(e);
// Remove from the selection any objects we may have created during
// the current mouse action. (I think this is redundant now)
m_viewer->m_selectedObjects.removeAll(m_endAtom);
m_viewer->m_selectedObjects.removeAll(m_bond);
// Any atom left over must be an existing one
m_existingAtom = 0;
for (int i = 0; i < m_viewer->m_selectedObjects.size(); ++i) {
m_existingAtom = qobject_cast<Layer::Atom*>(m_viewer->m_selectedObjects[i]);
if (m_existingAtom) break;
}
Vec startingMousePosition(m_beginAtom->getPosition());
Vec currentMousePosition(m_viewer->worldCoordinatesOf(e, startingMousePosition));
double shift((startingMousePosition-currentMousePosition).norm());
if (shift < 0.2) {
// We haven't moved far enough from where we started to create
// a second atom or bond.
if (m_endAtom) {
m_buildObjects.removeAll(m_endAtom);
delete m_endAtom;
m_endAtom = 0;
}
if (m_bond) {
m_buildObjects.removeAll(m_bond);
delete m_bond;
m_bond = 0;
}
}else if (m_existingAtom ) {
// We have landed on an existing atom so we do not need either
// m_endAtom or m_bond;
if (m_endAtom) {
m_buildObjects.removeAll(m_endAtom);
delete m_endAtom;
m_endAtom = 0;
}
if (m_bond) {
m_buildObjects.removeAll(m_bond);
delete m_bond;
m_bond = 0;
}
if (m_existingAtom != m_beginAtom) {
if (!m_molecule->getBond(m_existingAtom, m_beginAtom)) {
// bond does not already exist
MoleculeList molecules(m_existingAtom->findLayers<Layer::Molecule>(Layer::Parents));
if (!molecules.isEmpty() && molecules.first() == m_molecule) {
m_bond = m_molecule->createBond(m_beginAtom, m_existingAtom);
m_buildObjects.append(m_bond);
}
}
}
}else {
// We are floating out in space, create a
// new atom if we haven't already done so
if (!m_endAtom) {
// take care of any bond we may have formed
if (m_bond) {
m_buildObjects.removeAll(m_bond);
delete m_bond;
m_bond = 0;
}
Vec pos(m_viewer->worldCoordinatesOf(e, m_beginAtom->getPosition()));
m_endAtom = m_molecule->createAtom(m_buildElement, pos);
m_bond = m_molecule->createBond(m_beginAtom, m_endAtom);
m_buildObjects.append(m_endAtom);
m_buildObjects.append(m_bond);
}
// Move the atom to where the mouse is
m_endAtom->setPosition(m_viewer->worldCoordinatesOf(e, m_beginAtom->getPosition()));
}
m_viewer->updateGL();
e->accept();
}
int main(int argc, char *argv[])
{
# include "setRootCase.H"
# include "createTime.H"
# include "createMesh.H"
IOdictionary mdInitialiseDict
(
IOobject
(
"mdInitialiseDict",
runTime.system(),
runTime,
IOobject::MUST_READ_IF_MODIFIED,
IOobject::NO_WRITE,
false
)
);
IOdictionary idListDict
(
IOobject
(
"idList",
mesh.time().constant(),
mesh,
IOobject::NO_READ,
IOobject::AUTO_WRITE
)
);
potential pot(mesh, mdInitialiseDict, idListDict);
moleculeCloud molecules(mesh, pot, mdInitialiseDict);
label totalMolecules = molecules.size();
if (Pstream::parRun())
{
reduce(totalMolecules, sumOp<label>());
}
Info<< nl << "Total number of molecules added: " << totalMolecules
<< nl << endl;
IOstream::defaultPrecision(15);
if (!mesh.write())
{
FatalErrorIn(args.executable())
<< "Failed writing moleculeCloud."
<< nl << exit(FatalError);
}
Info<< nl << "ClockTime = " << runTime.elapsedClockTime() << " s"
<< nl << endl;
Info<< "\nEnd\n" << endl;
return 0;
}
int main(){
molecules();
}
int main(int argc, char *argv[])
{
#include "setRootCaseLists.H"
#include "createTime.H"
#include "createMesh.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Info<< "\nReading field U\n" << endl;
volVectorField U
(
IOobject
(
"U",
runTime.timeName(),
mesh,
IOobject::MUST_READ,
IOobject::AUTO_WRITE
),
mesh
);
potential pot(mesh);
moleculeCloud molecules(mesh, pot);
#include "temperatureAndPressureVariables.H"
#include "readmdEquilibrationDict.H"
label nAveragingSteps = 0;
Info<< "\nStarting time loop\n" << endl;
while (runTime.loop())
{
nAveragingSteps++;
Info<< "Time = " << runTime.timeName() << endl;
molecules.evolve();
#include "meanMomentumEnergyAndNMols.H"
#include "temperatureAndPressure.H"
#include "temperatureEquilibration.H"
runTime.write();
if (runTime.writeTime())
{
nAveragingSteps = 0;
}
Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
<< " ClockTime = " << runTime.elapsedClockTime() << " s"
<< nl << endl;
}
Info<< "End\n" << endl;
return 0;
}
