void moveAtom(simflat_t *s, int iId, int iBox, int jBox) {
int nj,ni;
nj = s->natoms[jBox];
copyAtom(s,iId, iBox, nj, jBox);
s->natoms[jBox]++;
if(s->natoms[jBox]>= MAXATOMS) simulationAbort(-11,"Increase maxatoms");
s->natoms[iBox]--;
ni = s->natoms[iBox];
if(ni) copyAtom(s,ni,iBox,iId,iBox);
return;
}
// Copy selection
void Clipboard::copySelection(Model* m, bool quiet)
{
Messenger::enter("Clipboard::copySelection");
if (m->nSelected() == 0)
{
Messenger::print("Nothing selected to copy.");
Messenger::exit("Clipboard::copySelection");
return;
}
// Clear the clipboard first and make sure atom ids are valid
clear();
// Copy atoms
if (!quiet) Messenger::print("Copying %i atoms from model '%s'...", m->nSelected(), qPrintable(m->name()));
for (RefListItem<Atom,int>* ri = m->selection(); ri != NULL; ri = ri->next) copyAtom(ri->item);
renumberAtoms();
// Copy bonds
if (!quiet) Messenger::print("bonds...");
copyBonds();
if (!quiet) Messenger::print(" Done.");
Messenger::exit("Clipboard::copySelection");
}
/// Move an atom from one link cell to another.
/// \param iId [in] The index with box iBox of the atom to be moved.
/// \param iBox [in] The index of the link cell the particle is moving from.
/// \param jBox [in] The index of the link cell the particle is moving to.
void moveAtom(LinkCell* boxes, Atoms* atoms, int iId, int iBox, int jBox)
{
int nj = boxes->nAtoms[jBox];
copyAtom(boxes, atoms, iId, iBox, nj, jBox);
boxes->nAtoms[jBox]++;
assert(boxes->nAtoms[jBox] < MAXATOMS);
boxes->nAtoms[iBox]--;
int ni = boxes->nAtoms[iBox];
if (ni) copyAtom(boxes, atoms, ni, iBox, iId, iBox);
if (jBox > boxes->nLocalBoxes)
--atoms->nLocal;
return;
}
// Copy model
void Clipboard::copyAll(Model* m, bool quiet)
{
Messenger::enter("Clipboard::copyAll");
// Clear the clipboard first and make sure atom ids are valid
clear();
// Copy atoms
if (!quiet) Messenger::print("Copying all atoms from model '%s'...", qPrintable(m->name()));
for (Atom* i = m->atoms(); i != NULL; i = i->next) copyAtom(i);
renumberAtoms();
if (!quiet) Messenger::print("bonds...");
// Copy bonds
copyBonds();
if (!quiet) Messenger::print(" Done.");
Messenger::exit("Clipboard::copyAll");
}
//This copies a cell from one box buffer to another and sorts it in the process.
void copySortedCell(LinkCell *sourceBoxes, LinkCell *destBoxes, Atoms *sourceAtoms, Atoms *destAtoms, int iBox)
{
const int numAtoms = sourceBoxes->nAtoms[iBox];
int highestGID, lowestGID;
int atomOffset = MAXATOMS * iBox;
highestGID = lowestGID = sourceAtoms->gid[atomOffset];
for(int i = atomOffset; i < atomOffset + numAtoms; i++) {
if(sourceAtoms->gid[i] < lowestGID) {
lowestGID = sourceAtoms->gid[i];
}
if(sourceAtoms->gid[i] > highestGID) {
highestGID = sourceAtoms->gid[i];
}
}
int targetAtom = nextHighestAtom(sourceAtoms, atomOffset, numAtoms, highestGID, lowestGID - 1);
for(int atomNum = 0; atomNum < numAtoms; atomNum++) {
copyAtom(sourceAtoms, destAtoms, atomNum, iBox, targetAtom, iBox);
targetAtom = nextHighestAtom(sourceAtoms, atomOffset, numAtoms, highestGID, sourceAtoms->gid[atomOffset + targetAtom]);
}
destBoxes->nAtoms[iBox] = sourceBoxes->nAtoms[iBox];
}
// Copy selection
void Clipboard::copyMarked(Model* m)
{
Messenger::enter("Clipboard::copyMarked");
if (m->nMarked() == 0)
{
Messenger::print("Nothing marked to copy.");
Messenger::exit("Clipboard::copyMarked");
return;
}
// Clear the clipboard first and make sure atom ids are valid
clear();
// Copy atoms
for (RefListItem<Atom,int>* ri = m->selection(true); ri != NULL; ri = ri->next) copyAtom(ri->item);
renumberAtoms();
// Copy bonds
copyBonds();
Messenger::exit("Clipboard::copyMarked");
}
//The correctness of the task dependencies here depends on the assumption that there are no
//dependencies between this function and the function that last wrote the position
void updateLinkCells(LinkCell* boxes, LinkCell* boxesBuffer, Atoms* atoms, Atoms* atomsBuffer)
{
real3 *atomF = atoms->f;
real3 *atomR = atoms->r;
real3 *atomP = atoms->p;
real3 *atomsBufferR = atomsBuffer->r;
int dep[9];
for(int z=0; z < sim->boxes->gridSize[2]; z++) {
for(int y=0; y < sim->boxes->gridSize[1]; y++) {
int rowBox = z*sim->boxes->gridSize[1]*sim->boxes->gridSize[0]+y*sim->boxes->gridSize[0];
getNeighborRows(boxes, y, z, dep);
#pragma omp task depend(out: atomsBufferR[rowBox*MAXATOMS]) \
depend( in: atomR[dep[0]*MAXATOMS], atomR[dep[1]*MAXATOMS], atomR[dep[2]*MAXATOMS], \
atomR[dep[3]*MAXATOMS], atomR[dep[4]*MAXATOMS], atomR[dep[5]*MAXATOMS], \
atomR[dep[6]*MAXATOMS], atomR[dep[7]*MAXATOMS], atomR[dep[8]*MAXATOMS] )
{ //This task pulls all atoms that belong in cell iBox from multiple cells in the main buffer to cell iBox in the secondary buffer
startTimer(redistributeTimer);
for(int iBox=rowBox; iBox < rowBox + sim->boxes->gridSize[0]; iBox++) {
boxesBuffer->nAtoms[iBox] = 0;
int firstCopy = 0;
for(int i=0; i<27; i++) {
int neighborBox = boxes->nbrBoxes[iBox][i];
if(neighborBox != iBox || firstCopy == 0) {
if(neighborBox == iBox)
firstCopy = 1;
for(int atomNum = 0; atomNum < boxes->nAtoms[neighborBox]; atomNum++) {
real3 tempPosition;
for(int i=0; i<3; i++) {
tempPosition[i] = atoms->r[neighborBox*MAXATOMS + atomNum][i];
if(tempPosition[i] >= boxes->localMax[i]) {
tempPosition[i] -= boxes->localMax[i];
} else if(tempPosition[i] <= boxes->localMin[i]) {
tempPosition[i] += boxes->localMax[i];
}
}
if(iBox == getBoxFromCoord(boxes, tempPosition)) {
copyAtom(atoms, atomsBuffer, atomNum, neighborBox, boxesBuffer->nAtoms[iBox], iBox);
for(int i=0; i<3; i++) {
atomsBuffer->r[iBox*MAXATOMS + boxesBuffer->nAtoms[iBox]][i] = tempPosition[i];
}
boxesBuffer->nAtoms[iBox]++;
}
}
}
}
}
stopTimer(redistributeTimer);
}
}
}
//This loop copies the cells from the buffer back to the main buffer while sorting them.
for(int z=0; z < sim->boxes->gridSize[2]; z++) {
for(int y=0; y < sim->boxes->gridSize[1]; y++) {
int rowBox = z*sim->boxes->gridSize[1]*sim->boxes->gridSize[0]+y*sim->boxes->gridSize[0];
int *nAtoms = &sim->boxes->nAtoms[rowBox];
#pragma omp task depend(in : atomsBufferR[rowBox*MAXATOMS]) \
depend(out: nAtoms, \
atomF[rowBox*MAXATOMS], atomR[rowBox*MAXATOMS],\
atomP[rowBox*MAXATOMS] )
{
startTimer(redistributeSortTimer);
for(int iBox=rowBox; iBox < rowBox + sim->boxes->gridSize[0]; iBox++) {
copySortedCell(boxesBuffer, boxes, atomsBuffer, atoms, iBox);
}
stopTimer(redistributeSortTimer);
}
}
}
}