// PairList::SetupPairList()
int PairList::SetupPairList(Box::BoxType typeIn, Vec3 const& recipLengthsIn) {
Timer t_setup;
t_setup.Start();
if (typeIn == Box::NOBOX) {
mprinterr("Error: Pair list code currently requires box coordinates.\n");
return 1;
}
// Allocate/reallocate memory
if (SetupGrids(recipLengthsIn)) return 1;
t_setup.Stop();
t_setup.WriteTiming(1, "Pair List Setup:");
mprintf("\tGrid dimensions: %i %i %i (%zu total).\n", nGridX_, nGridY_, nGridZ_, cells_.size());
return 0;
}
// PairList::CreatePairList()
int PairList::CreatePairList(Frame const& frmIn, Matrix_3x3 const& ucell,
Matrix_3x3 const& recip, AtomMask const& maskIn)
{
t_total_.Start();
// Calculate translation vectors based on current unit cell.
FillTranslateVec(ucell);
// If box size has changed a lot this will reallocate grid
t_gridpointers_.Start();
if (SetupGrids(frmIn.BoxCrd().RecipLengths(recip))) return 1;
t_gridpointers_.Stop();
// Place atoms in grid cells
t_map_.Start();
GridUnitCell(frmIn, ucell, recip, maskIn);
t_map_.Stop();
t_total_.Stop();
return 0;
}
///////////////////////////////////////////////////////////////////////////////
// GetData
/////////////////////////////////////////////////////////////////////////////
void clSubstrateDepSeedSurvival::GetData(xercesc::DOMDocument * p_oDoc) {
try {
GetParameterFileData(p_oDoc);
//Set up the grids
SetupGrids();
} catch (modelErr& err) {
throw(err);
} catch (modelMsg & msg) {
throw(msg);
} //non-fatal error
catch (...) {
modelErr stcErr;
stcErr.iErrorCode = UNKNOWN;
stcErr.sFunction = "clSubstrateDepSeedSurvival::GetData";
throw(stcErr);
}
}
