// Calculate the RDF normalisation for the Box
bool Box::calculateRDFNormalisation(ProcessPool& procPool, Data2D& boxNorm, double rdfRange, double rdfBinWidth, int nPoints) const
{
// Setup array - we will use a nominal bin width of 0.1 Angstroms and then interpolate to the rdfBinWidth afterwards
const double binWidth = 0.1;
const double rBinWidth = 1.0/binWidth;
int bin, nBins = rdfRange / binWidth;
Data2D normData;
normData.initialise(nBins);
Array<double>& y = normData.arrayY();
for (int n=0; n<nBins; ++n) normData.arrayX()[n] = (n+0.5)*binWidth;
Vec3<double> centre = axes_*Vec3<double>(0.5,0.5,0.5);
// Divide points over processes
const int nPointsPerProcess = nPoints / procPool.nProcesses();
Messenger::print("--> Number of insertion points (per process) is %i\n", nPointsPerProcess);
y = 0.0;
for (int n=0; n<nPointsPerProcess; ++n)
{
bin = (randomCoordinate() - centre).magnitude() * rBinWidth;
if (bin < nBins) y[bin] += 1.0;
}
if (!procPool.allSum(y.array(), nBins)) return false;
// Normalise histogram data, and scale by volume and binWidth ratio
y /= double(nPointsPerProcess*procPool.nProcesses());
y *= volume_ * (rdfBinWidth / binWidth);
normData.interpolate();
// Write histogram data for random distribution
if (procPool.isMaster()) normData.save("duq.box.random");
// Now we have the interpolated data, create the proper interpolated data
nBins = rdfRange/rdfBinWidth;
boxNorm.clear();
// Rescale against expected volume for spherical shells
double shellVolume, r = 0.0, maxHalf = inscribedSphereRadius(), x = 0.5*rdfBinWidth;
for (int n=0; n<nBins; ++n)
{
// We know that up to the maximum (orthogonal) half-cell width the normalisation should be exactly 1.0...
if (x < maxHalf) boxNorm.addPoint(x, 1.0);
else
{
shellVolume = (4.0/3.0)*PI*(pow(r+rdfBinWidth,3.0) - pow(r,3.0));
boxNorm.addPoint(x, shellVolume / normData.interpolated(x));
// boxNorm[n] = normData.interpolated(r);
}
r += rdfBinWidth;
x += rdfBinWidth;
}
// Interpolate normalisation array
boxNorm.interpolate();
// Write final box normalisation file
if (procPool.isMaster()) boxNorm.save("duq.box.norm");
return true;
}
// Calculate total forces within the system
void DUQ::totalForces(ProcessPool& procPool, Configuration* cfg, double* fx, double* fy, double* fz, double cutoffSq)
{
/*
* Calculates the total forces within the system, arising from inter-Grain PairPotential interactions
* and intramolecular contributions.
*
* This is a serial routine (subroutines called from within are parallel).
*/
// Create a Timer
Timer timer;
// Calculate Grain forces
timer.start();
grainForces(procPool, cfg, fx, fy, fz, cutoffSq);
timer.stop();
Messenger::printVerbose("Time to do Grain forces was %s.\n", timer.timeString());
// Calculate intramolecular forces
timer.start();
intramolecularForces(procPool, cfg, fx, fy, fz);
timer.stop();
Messenger::printVerbose("Time to do intramolecular forces was %s.\n", timer.timeString());
// Gather forces together
if (!procPool.allSum(fx, cfg->nAtoms())) return;
if (!procPool.allSum(fy, cfg->nAtoms())) return;
if (!procPool.allSum(fz, cfg->nAtoms())) return;
}
int main(int argc, const char * argv[]) {
if(argc != 2){
printf("Usage: ./xxx port(port stands for the port wanna listen on.)\n");
exit(1);
}
signal(SIGCHLD, SIG_IGN);
if(!is_free()){
// exit(0);
}
int port = atoi(argv[1]);
struct sockaddr_in addr;
bzero(&addr, sizeof(addr));
addr.sin_family = AF_INET;
addr.sin_addr.s_addr = htonl(INADDR_ANY);
addr.sin_port = htons(port);
int server_socket = socket(AF_INET, SOCK_STREAM, 0);
bind(server_socket, (struct sockaddr *) &addr, sizeof(addr));
listen(server_socket, 0);
ProcessPool* pool = new ProcessPool(server_socket, 1, 10);
pool->init();
pool->addTask(print, NULL);
pool->start();
if(pool)
delete(pool);
exit(0);
}
windows_process::~windows_process()
{
ProcessPool *pp = ProcPool();
GeneratorWindows* winGen = static_cast<GeneratorWindows*>(GeneratorWindows::getDefaultGenerator());
pp->condvar()->lock();
winGen->removeProcess(this);
pp->condvar()->unlock();
// Do NOT close the process handle; that's handled by ContinueDebugEvent. Closing the file is okay.
::CloseHandle(hfile);
}
// Broadcast data from Master to all Slaves
bool Parameters::broadcast(ProcessPool& procPool)
{
#ifdef PARALLEL
if (!procPool.broadcast(name_)) return false;
if (!procPool.broadcast(description_)) return false;
if (!procPool.broadcast(&sigma_, 1)) return false;
if (!procPool.broadcast(&epsilon_, 1)) return false;
if (!procPool.broadcast(&charge_, 1)) return false;
#endif
return true;
}
// Execute Method
bool Export::process(DUQ& duq, ProcessPool& procPool)
{
/*
* Export data from the target Configuration(s)
*/
// Loop over target Configurations
for (RefListItem<Configuration,bool>* ri = targetConfigurations_.first(); ri != NULL; ri = ri->next)
{
// Grab Configuration pointer
Configuration* cfg = ri->item;
// Retrieve control parameters from Configuration
const char* saveTrajectory = variableAsChar(cfg, "SaveTrajectory");
/*
* Save XYZ Trajectory
*/
if (!DUQSys::isEmpty(saveTrajectory))
{
Messenger::print("Export: Appending to trajectory output file '%s'...\n", cfg->outputCoordinatesFile());
// Only the pool master saves the data
if (procPool.isMaster())
{
// Open the file
LineParser parser;
if (!parser.appendOutput(saveTrajectory))
{
parser.closeFiles();
procPool.stop();
return false;
}
else if (!writeConfigurationXYZ(parser, cfg, cfg->name()))
{
Messenger::print("Export: Failed to append to trajectory file.\n");
parser.closeFiles();
procPool.stop();
return false;
}
procPool.proceed();
}
else if (!procPool.decision()) return false;
Messenger::print("Export: Finished appending trajectory file.\n");
}
}
return true;
}
// Broadcast data
bool VariableValue::broadcast(ProcessPool& procPool)
{
#ifdef PARALLEL
// Broadcast type first, then value
int tempType = type_;
if (!procPool.broadcast(&tempType, 1)) return false;
type_ = (VariableValue::ValueType) tempType;
switch (type_)
{
case (VariableValue::BooleanType):
if (!procPool.broadcast(valueB_)) return false;
break;
case (VariableValue::IntegerType):
if (!procPool.broadcast(&valueI_, 1)) return false;
break;
case (VariableValue::DoubleType):
if (!procPool.broadcast(&valueD_, 1)) return false;
break;
case (VariableValue::CharType):
if (!procPool.broadcast(valueC_)) return false;
break;
case (VariableValue::IntegerArrayType):
if (!procPool.broadcast(arrayI_)) return false;
break;
case (VariableValue::DoubleArrayType):
if (!procPool.broadcast(arrayD_)) return false;
break;
default:
Messenger::error("Broadcast of VariableValue failed - type_ %s not accounted for.\n", VariableValue::valueType(type_));
return false;
}
#endif
return true;
}
// Broadcast data from Master to all Slaves
bool AtomType::broadcast(ProcessPool& procPool)
{
#ifdef PARALLEL
int index;
// Send name
procPool.broadcast(name_);
// Send element
procPool.broadcast(&element_, 1);
// Get index of Parameters,
if (procPool.isMaster()) index = PeriodicTable::element(element_).indexOfParameters(parameters_);
procPool.broadcast(&index, 1);
parameters_ = PeriodicTable::element(element_).parameters(index);
#endif
return true;
}
bool GeneratorMT::processWait(bool block)
{
ProcessPool *pp = ProcPool();
pp->condvar()->lock();
pthrd_printf("Checking for live processes\n");
while (!hasLiveProc() && !isExitingState()) {
pthrd_printf("Checked and found no live processes\n");
if (!block) {
pthrd_printf("Returning from non-blocking processWait\n");
pp->condvar()->broadcast();
pp->condvar()->unlock();
return false;
}
pp->condvar()->wait();
}
pp->condvar()->broadcast();
pp->condvar()->unlock();
pthrd_printf("processWait returning true\n");
return true;
}
// Calculate total intramolecular forces
void DUQ::intramolecularForces(ProcessPool& procPool, Configuration* cfg, double* fx, double* fy, double* fz)
{
/*
* Calculate the total intramolecular forces within the system, arising from Bond, Angle, and Torsion
* terms in all molecules.
*
* This is a parallel routine.
*/
double distance, angle, force, dp, magji, magjk;
int index, start, stride;
Atom* i, *j, *k;
Vec3<double> vecji, vecjk, forcei, forcek;
// Set start/skip for parallel loop
start = procPool.interleavedLoopStart(ProcessPool::OverPoolProcesses);
stride = procPool.interleavedLoopStride(ProcessPool::OverPoolProcesses);
// Main loop over molecules
for (Molecule* mol = cfg->molecules(); mol != NULL; mol = mol->next)
{
// Bonds
for (SpeciesBond* b = mol->species()->bonds(); b != NULL; b = b->next)
{
// Grab pointers to atoms involved in bond
i = mol->atom(b->indexI());
j = mol->atom(b->indexJ());
// Determine whether we need to apply minimum image to the vector calculation
if (cfg->useMim(i->grain()->cell(), j->grain()->cell())) vecji = cfg->box()->minimumVector(i, j);
else vecji = j->r() - i->r();
// Get distance and normalise vector ready for force calculation
distance = vecji.magAndNormalise();
// Determine final forces
vecji *= b->force(distance);
// Calculate forces
index = b->i()->index();
fx[index] -= vecji.x;
fy[index] -= vecji.y;
fz[index] -= vecji.z;
index = b->j()->index();
fx[index] += vecji.x;
fy[index] += vecji.y;
fz[index] += vecji.z;
}
// Angles
for (SpeciesAngle* a = mol->species()->angles(); a != NULL; a = a->next)
{
// Grab pointers to atoms involved in angle
i = mol->atom(a->indexI());
j = mol->atom(a->indexJ());
k = mol->atom(a->indexK());
// Determine whether we need to apply minimum image between 'j-i' and 'j-k'
if (cfg->useMim(j->grain()->cell(), i->grain()->cell())) vecji = cfg->box()->minimumVector(j, i);
else vecji = i->r() - j->r();
if (cfg->useMim(j->grain()->cell(), k->grain()->cell())) vecjk = cfg->box()->minimumVector(j, k);
else vecjk = k->r() - j->r();
// Calculate angle
magji = vecji.magAndNormalise();
magjk = vecjk.magAndNormalise();
angle = Box::angle(vecji, vecjk, dp);
// Determine Angle force vectors for atoms
force = a->force(angle);
forcei = vecjk - vecji * dp;
forcei *= force / magji;
forcek = vecji - vecjk * dp;
forcek *= force / magjk;
// Store forces
index = a->i()->index();
fx[index] += forcei.x;
fy[index] += forcei.y;
fz[index] += forcei.z;
index = a->j()->index();
fx[index] -= forcei.x + forcek.x;
fy[index] -= forcei.y + forcek.y;
fz[index] -= forcei.z + forcek.z;
index = a->k()->index();
fx[index] += forcek.x;
fy[index] += forcek.y;
fz[index] += forcek.z;
}
}
}
// Calculate Grain forces within the system
void DUQ::grainForces(ProcessPool& procPool, Configuration* cfg, double* fx, double* fy, double* fz, double cutoffSq)
{
/*
* Calculates the total Grain forces within the system, i.e. the energy contributions from PairPotential
* interactions between Grains. Any connections between Grains (which in reality correspond to proper chemical bonds
* between Atoms) are automatically excluded.
*
* This is a parallel routine.
*/
// Initialise the Cell distributor
const bool willBeModified = false, allowRepeats = false;
cfg->initialiseCellDistribution();
// Create a ForcesKernel
ForceKernel kernel(procPool, cfg->box(), potentialMap_);
int cellId, n, m, start, stride;
Cell* cell;
Grain* grainI, *grainJ;
// Set start/skip for parallel loop
start = procPool.interleavedLoopStart(ProcessPool::OverGroups);
stride = procPool.interleavedLoopStride(ProcessPool::OverGroups);
while (cellId = cfg->nextAvailableCell(procPool, willBeModified, allowRepeats), cellId != Cell::AllCellsComplete)
{
// Check for valid cell
if (cellId == Cell::NoCellsAvailable)
{
Messenger::printVerbose("Nothing for this process to do.\n");
cfg->finishedWithCell(procPool, willBeModified, cellId);
continue;
}
cell = cfg->cell(cellId);
Messenger::printVerbose("Cell %i now the target, containing %i Grains interacting with %i neighbours.\n", cellId, cell->nGrains(), cell->nTotalCellNeighbours());
/*
* Calculation Begins
*/
for (n=start; n<cell->nGrains(); n += stride)
{
grainI = cell->grain(n);
// Inter-Grain interactions in this Cell...
for (m=n+1; m<cell->nGrains(); ++m)
{
grainJ = cell->grain(m);
kernel.forces(grainI, grainJ, false, false, fx, fy, fz);
}
// Inter-Grain interactions between this Grain and those in Cell neighbours
kernel.forces(grainI, cell->nCellNeighbours(), cell->cellNeighbours(), false, true, fx, fy, fz, ProcessPool::Individual);
kernel.forces(grainI, cell->nMimCellNeighbours(), cell->mimCellNeighbours(), true, true, fx, fy, fz, ProcessPool::Individual);
}
/*
* Calculation End
*/
// Must unlock the Cell when we are done with it!
cfg->finishedWithCell(procPool, willBeModified, cellId);
}
}
