void StatisticsWriter::initOutput(ParticleContainer* particleContainer,
DomainDecompBase* domainDecomp, Domain* domain) {
#ifndef NDEBUG
if (static_cast<const void*>(&_container) != static_cast<const void*>(particleContainer)) {
global_log->error() << "VTKGridWriter works only with PlottableLinkCells!" << std::endl;
exit(1);
}
#endif
std::stringstream fileNameStream;
fileNameStream << _outputPrefix << "_LC" << ".stat";
ofstream outfile(fileNameStream.str().c_str());
outfile << "Number of Cells (including halo): [" << _container._cellsPerDimension[0]
<< "," << _container._cellsPerDimension[1] << "," << _container._cellsPerDimension[2] << "]" << endl;
outfile << "HaloWidth in num cells: [" << _container._haloWidthInNumCells[0]
<< "," << _container._haloWidthInNumCells[1] << "," << _container._haloWidthInNumCells[2] << "]" << endl;
outfile << "Cell Width: [" << _container._cellLength[0] << "," << _container._cellLength[1] << "," << _container._cellLength[2] << "]" << endl;
outfile << endl;
outfile << "SizeOf(Molecule) = " << sizeof(Molecule) << endl;
std::vector<bool> count;
Molecule* tmpMolecule = particleContainer->begin();
while (tmpMolecule != particleContainer->end()) {
if (tmpMolecule->componentid() >= count.size()) {
count.resize(tmpMolecule->componentid()+1, false);
}
if (count[tmpMolecule->componentid()] == false) {
outfile << "Molecule(cid=" << tmpMolecule->componentid() << ") " << tmpMolecule->totalMemsize() << endl;
count[tmpMolecule->componentid()] = true;
}
tmpMolecule = particleContainer->next();
}
outfile.close();
}
unsigned long DomainDecompDummy::countMolecules(ParticleContainer* moleculeContainer, vector<unsigned long> &compCount) {
for (unsigned i = 0; i < compCount.size(); i++) {
compCount[i] = 0;
}
Molecule* tempMolecule;
for (tempMolecule = moleculeContainer->begin(); tempMolecule != moleculeContainer->end(); tempMolecule = moleculeContainer->next()) {
compCount[tempMolecule->componentid()] += 1;
}
int numMolecules = 0;
for (unsigned i = 0; i < compCount.size(); i++) {
numMolecules += compCount[i];
}
return numMolecules;
}
Molecule ChemicalPotential::loadMolecule()
{
assert(!this->reservoir.empty());
Molecule tmp = this->reservoir.front();
this->reservoir.pop_front();
if(this->reservoir.empty())
{
tmp.scale_v(-1.0);
this->reservoir.push_back( tmp );
}
assert(tmp.componentid() == componentid);
#ifndef NDEBUG
tmp.check(tmp.id());
#endif
return tmp;
}
bool ChemicalPotential::getDeletion(TMoleculeContainer* cell, double* minco, double* maxco)
{
if(this->remainingDeletions.empty()) return false;
if(cell->getNumberOfParticles() == 0) return false;
unsigned idx = *this->remainingDeletions.begin();
this->remainingDeletions.erase(this->remainingDeletions.begin());
double tminco[3];
double tmaxco[3];
if(restrictedControlVolume) for(int d=0; d < 3; d++)
{
tminco[d] = (minco[d] > control_bottom[d])? minco[d]
: control_bottom[d];
tmaxco[d] = (maxco[d] < control_top[d])? maxco[d]
: control_top[d];
}
else for(int d=0; d < 3; d++)
{
tminco[d] = minco[d];
tmaxco[d] = maxco[d];
}
Molecule* m = cell->begin();
int j=0;
for(unsigned i=0; (i < idx); i++)
{
while(( (m->r(0) > tmaxco[0]) || (m->r(1) > tmaxco[1]) ||
(m->r(2) > tmaxco[2]) || (m->r(0) < tminco[0]) ||
(m->r(1) < tminco[1]) || (m->r(2) < tminco[2]) ||
(m->componentid() != this->componentid) )
&& (m != cell->end()))
{
m = cell->next();
if(m == cell->end())
{
if(j == 0) return false;
m = cell->begin();
j = 0;
}
}
m = cell->next();
j++;
if(m == cell->end())
{
if(j == 0) return false;
m = cell->begin();
j = 0;
}
}
while( (m->r(0) > tmaxco[0]) || (m->r(1) > tmaxco[1]) ||
(m->r(2) > tmaxco[2]) || (m->r(0) < tminco[0]) ||
(m->r(1) < tminco[1]) || (m->r(2) < tminco[2]) ||
(m->componentid() != this->componentid) )
{
m = cell->next();
if(m == cell->end())
{
if(j == 0) return false;
m = cell->begin();
}
}
#ifndef NDEBUG
global_log->debug() << "ID " << m->id() << " selected for deletion (index " << idx << ")." << std::endl;
#endif
assert(m->id() < nextid);
return true;
}
/*
* diese Version beschleunigt in alle Raumrichtungen
*/
void PressureGradient::determineAdditionalAcceleration
(
DomainDecompBase* domainDecomp,
ParticleContainer* molCont, double dtConstantAcc )
{
for( map<unsigned int, double>::iterator uAAit = _universalAdditionalAcceleration[0].begin();
uAAit != _universalAdditionalAcceleration[0].end();
uAAit++ )
{
this->_localN[uAAit->first] = 0;
for(unsigned short int d = 0; d < 3; d++)
this->_localVelocitySum[d][uAAit->first] = 0.0;
}
for(Molecule* thismol = molCont->begin(); thismol != molCont->end(); thismol = molCont->next())
{
unsigned int cid = thismol->componentid();
map<unsigned int, unsigned int>::iterator uCSIDit = this->_universalComponentSetID.find(cid);
if(uCSIDit == _universalComponentSetID.end()) continue;
unsigned cosetid = uCSIDit->second;
this->_localN[cosetid]++;
for(unsigned short int d = 0; d < 3; d++)
this->_localVelocitySum[d][cosetid] += thismol->v(d);
}
// domainDecomp->collectCosetVelocity(&_localN, _localVelocitySum, &_globalN, _globalVelocitySum);
//
domainDecomp->collCommInit( 4 * _localN.size() );
for( map<unsigned int, unsigned int long>::iterator lNit = _localN.begin(); lNit != _localN.end(); lNit++ )
{
domainDecomp->collCommAppendUnsLong(lNit->second);
for(int d = 0; d < 3; d++)
domainDecomp->collCommAppendDouble( this->_localVelocitySum[d][lNit->first]);
}
domainDecomp->collCommAllreduceSum();
for( map<unsigned int, unsigned long>::iterator lNit = _localN.begin(); lNit != _localN.end(); lNit++ )
{
_globalN[lNit->first] = domainDecomp->collCommGetUnsLong();
for(int d = 0; d < 3; d++)
_globalVelocitySum[d][lNit->first] = domainDecomp->collCommGetDouble();
}
domainDecomp->collCommFinalize();
map<unsigned int, long double>::iterator gVSit;
if(!this->_localRank)
{
for(gVSit = _globalVelocitySum[0].begin(); gVSit != _globalVelocitySum[0].end(); gVSit++)
{
#ifndef NDEBUG
global_log->debug() << "required entries in velocity queue: " << _globalVelocityQueuelength[gVSit->first] << endl;
global_log->debug() << "entries in velocity queue: " << _globalPriorVelocitySums[0][gVSit->first].size() << endl;
#endif
for(unsigned short int d = 0; d < 3; d++)
{
while(_globalPriorVelocitySums[d][gVSit->first].size() < _globalVelocityQueuelength[gVSit->first])
_globalPriorVelocitySums[d][gVSit->first].push_back(_globalVelocitySum[d][gVSit->first]);
}
}
}
if(!this->_localRank)
{
for(gVSit = _globalVelocitySum[0].begin(); gVSit != _globalVelocitySum[0].end(); gVSit++)
{
double invgN = 1.0 / this->_globalN[gVSit->first];
double invgtau = 1.0 / this->_universalTau[gVSit->first];
double invgtau2 = invgtau * invgtau;
double previousVelocity[3];
for(unsigned short int d = 0; d < 3; d++)
{
previousVelocity[d] = invgN * _globalPriorVelocitySums[d][gVSit->first].front();
this->_globalPriorVelocitySums[d][gVSit->first].pop_front();
this->_universalAdditionalAcceleration[d][gVSit->first]
+= dtConstantAcc * invgtau2 *
( this->_globalTargetVelocity[d][gVSit->first]
- 2.0*this->_globalVelocitySum[d][gVSit->first]*invgN
+ previousVelocity[d] );
}
#ifndef NDEBUG
global_log->debug() << "accelerator no. " << gVSit->first
<< "previous vz: " << previousVelocity[2]
<< "current vz: " << _globalVelocitySum[2][gVSit->first]*invgN << endl;
#endif
}
}
domainDecomp->collCommInit(7*this->_localN.size());
for( map<unsigned int, unsigned long>::iterator lNit = _localN.begin();
lNit != this->_localN.end();
lNit++ )
{
domainDecomp->collCommAppendUnsLong(_globalN[lNit->first]);
for(int d=0; d < 3; d++)
{
domainDecomp->collCommAppendDouble(
this->_universalAdditionalAcceleration[d][lNit->first]
);
domainDecomp->collCommAppendDouble(
this->_globalVelocitySum[d][lNit->first]
);
}
}
domainDecomp->collCommBroadcast();
for( map<unsigned int, unsigned long>::iterator lNit = _localN.begin();
lNit != this->_localN.end();
lNit++ )
{
_globalN[lNit->first] = domainDecomp->collCommGetUnsLong();
for(int d=0; d < 3; d++)
{
this->_universalAdditionalAcceleration[d][lNit->first]
= domainDecomp->collCommGetDouble();
this->_globalVelocitySum[d][lNit->first]
= domainDecomp->collCommGetDouble();
}
}
domainDecomp->collCommFinalize();
}
void PovWriter::doOutput(ParticleContainer* particleContainer,
DomainDecompBase* domainDecomp, Domain* domain,
unsigned long simstep, list<ChemicalPotential>* lmu) {
if (simstep % _writeFrequency == 0) {
stringstream filenamestream;
if (_filenameisdate) {
filenamestream << "mardyn" << gettimestring();
}
else {
filenamestream << _filename;
}
if (_incremental) {
filenamestream << "-";
/* align file numbers with preceding '0's in the required range from 0 to _numberOfTimesteps. */
int num_digits = ceil(log(double(_numberOfTimesteps / _writeFrequency)) / log(10.));
filenamestream << aligned_number(simstep / _writeFrequency, num_digits, '0');
}
filenamestream << ".pov";
ofstream ostrm(filenamestream.str().c_str());
ostrm << "// " << filenamestream.str() << endl;
ostrm << "// moldy" << endl;
time_t now;
now = time(NULL);
ostrm << "// " << ctime(&now) << endl;
ostrm << "// bb: [0," << domain->getGlobalLength(0) << "]^3" << endl;
ostrm << "//*PMRawBegin" << endl;
ostrm << "background {rgb <1,1,1>}" << endl;
ostrm << "//*PMRawEnd" << endl;
vector<Component> dcomponents = domain->getComponents();
for (unsigned int i = 0; i < dcomponents.size(); ++i) {
ostringstream osstrm;
osstrm.clear();
osstrm.str("");
osstrm << " pigment {color rgb <" << (i + 1) % 2 << "," << (i + 1) / 2 % 2 << "," << (i + 1) / 4 % 2 << ">}";
osstrm << " finish{ambient 0.5 diffuse 0.4 phong 0.3 phong_size 3}";
ostrm << "#declare T" << i << " = ";
//ostrm << "sphere {<0,0,0>,0.5 pigment {color rgb<1,0,0>} finish{ambient 0.5 diffuse 0.4 phong 0.3 phong_size 3} scale 1.}";
dcomponents.at(i).writePOVobjs(ostrm, osstrm.str());
ostrm << endl;
}
ostrm << endl;
ostrm << "camera { perspective" << endl;
float xloc = -.1 * domain->getGlobalLength(0);
float yloc = 1.1 * domain->getGlobalLength(1);
float zloc = -1.5 * domain->getGlobalLength(2);
ostrm << " location <" << xloc << ", " << yloc << ", " << zloc << ">" << endl;
//ostrm << " direction <0, 0, 1>" << endl;
//ostrm << " right <1.33333, 0, 0>" << endl;
//ostrm << " up <0, 1, 0>" << endl;
//ostrm << " sky <0, 1, 0>" << endl;
ostrm << " look_at <" << .5 * domain->getGlobalLength(0) << ", " << .5 * domain->getGlobalLength(1) << ", " << .5 * domain->getGlobalLength(2) << ">" << endl;
ostrm << "}" << endl;
ostrm << endl;
ostrm << "light_source { <" << xloc << ", " << yloc << ", " << zloc << ">, color rgb <1,1,1> }" << endl;
ostrm << "light_source { <0,0,0>, color rgb <1,1,1> }" << endl;
ostrm << "light_source { <0,0," << domain->getGlobalLength(2) << ">, color rgb <1,1,1> }" << endl;
ostrm << "light_source { <0," << domain->getGlobalLength(1) << ",0>, color rgb <1,1,1> }" << endl;
ostrm << "light_source { <0," << domain->getGlobalLength(1) << "," << domain->getGlobalLength(2) << ">, color rgb <1,1,1> }" << endl;
ostrm << "light_source { <" << domain->getGlobalLength(0) << ",0,0>, color rgb <1,1,1> }" << endl;
ostrm << "light_source { <" << domain->getGlobalLength(0) << ",0," << domain->getGlobalLength(2) << ">, color rgb <1,1,1> }" << endl;
ostrm << "light_source { <" << domain->getGlobalLength(0) << "," << domain->getGlobalLength(1) << ",0>, color rgb <1,1,1> }" << endl;
ostrm << "light_source { <" << domain->getGlobalLength(0) << "," << domain->getGlobalLength(1) << "," << domain->getGlobalLength(2) << ">, color rgb <1,1,1> }" << endl;
ostrm << endl;
ostrm << "// " << dcomponents.size() << " objects for the atoms following..." << endl;
double mrot[3][3];
for (Molecule* pos = particleContainer->begin(); pos != particleContainer->end(); pos = particleContainer->next()) {
(pos->q()).getRotinvMatrix(mrot);
//cout << "object { T0 rotate <0,0,0> translate <0,0,0>}" << endl;
ostrm << "object { T" << pos->componentid();
ostrm << " matrix <"
<< mrot[0][0] << "," << mrot[0][1] << "," << mrot[0][2] << ","
<< mrot[1][0] << "," << mrot[1][1] << "," << mrot[1][2] << ","
<< mrot[2][0] << "," << mrot[2][1] << "," << mrot[2][2] << ","
<< pos->r(0) << "," << pos->r(1) << "," << pos->r(2)
<< ">";
ostrm << "}" << endl;
}
// RK
/* map cluster ID to color */
//if ((pos->clusterid() != -1) && (m_clusters.find(pos->clusterid())->second > MINCLUSTERSIZE)) {
// ostrm << " pigment {color rgb<" <<
// (0.25*(pos->clusterid()%5)) << "," <<
// (0.25*((pos->clusterid()/5)%5)) << "," <<
// (0.25*((pos->clusterid()/125)%5)) << "," <<
// ">}";
//}
//else {
// ostrm << " pigment {color rgb<0.9,0.9,0.9>}";
//}
// /RK
ostrm.close();
}
}
void DomainDecompDummy::exchangeMolecules(ParticleContainer* moleculeContainer, const vector<Component>& components, Domain* domain) {
double rmin[3]; // lower corner of the process-specific domain //ENABLE_MPI
double rmax[3];
double halo_L[3]; // width of the halo strip //ENABLE_MPI
for (int i = 0; i < 3; i++) {
rmin[i] = moleculeContainer->getBoundingBoxMin(i);
rmax[i] = moleculeContainer->getBoundingBoxMax(i);
halo_L[i] = moleculeContainer->get_halo_L(i);
}
Molecule* currentMolecule;
// molecules that have to be copied (because of halo), get a new position
double new_position[3];
double phaseSpaceSize[3];
double low_limit; // particles below this limit have to be copied or moved to the lower process
double high_limit; // particles above(or equal) this limit have to be copied or moved to the higher process
for (unsigned short d = 0; d < 3; ++d) {
phaseSpaceSize[d] = rmax[d] - rmin[d];
// set limits (outside "inner" region)
low_limit = rmin[d] + halo_L[d];
high_limit = rmax[d] - halo_L[d];
currentMolecule = moleculeContainer->begin();
//cout << "low_limit: " << low_limit << " / high_limit: " << high_limit << endl;
//cout << "halo_L: " << halo_L[0] << " / " << halo_L[1] << " / " << halo_L[2] << endl;
//cout << "proc_domain_L: " << proc_domain_L[0] << " / " << proc_domain_L[1] << " / " << proc_domain_L[2] << endl;
while (currentMolecule != moleculeContainer->end()) {
const double& rd = currentMolecule->r(d);
if (rd < low_limit) {
#ifdef MADPAC_LBMD_COUPLING
if(madpac::PeanoCouplingService::getInstance().bEnabled() && d < madpac::PeanoCouplingService::getInstance().getDim())
{
madpac::PeanoCouplingService::getInstance().getDataContainer()->incNumInsertMolecules();
}
else
{
#endif
// determine the position for the copy of the molecule
for (unsigned short d2 = 0; d2 < 3; d2++) {
// when moving parallel to the coordinate d2 to another process, the
// local coordinates in d2 change
if (d2 == d)
new_position[d2] = rd + phaseSpaceSize[d2];
else
new_position[d2] = currentMolecule->r(d2);
}
Molecule m1 = Molecule(currentMolecule->id(),currentMolecule->componentid(),
new_position[0], new_position[1], new_position[2],
currentMolecule->v(0),currentMolecule->v(1),currentMolecule->v(2),
currentMolecule->q().qw(),currentMolecule->q().qx(),currentMolecule->q().qy(),currentMolecule->q().qz(),
currentMolecule->D(0),currentMolecule->D(1),currentMolecule->D(2), &components);
moleculeContainer->addParticle(m1);
currentMolecule = moleculeContainer->next();
#ifdef MADPAC_LBMD_COUPLING
}
#endif
}
else if (rd >= high_limit) {
#ifdef MADPAC_LBMD_COUPLING
if(madpac::PeanoCouplingService::getInstance().bEnabled() && d < madpac::PeanoCouplingService::getInstance().getDim())
{
madpac::PeanoCouplingService::getInstance().getDataContainer()->incNumInsertMolecules();
}
else
{
#endif
// determine the position for the copy of the molecule
for (unsigned short d2 = 0; d2 < 3; d2++) {
// when moving parallel to the coordinate d2 to another process, the
// local coordinates in d2 change
if (d2 == d)
new_position[d2] = rd - phaseSpaceSize[d2];
else
new_position[d2] = currentMolecule->r(d2);
}
Molecule m1 = Molecule(currentMolecule->id(),currentMolecule->componentid(),
new_position[0], new_position[1], new_position[2],
currentMolecule->v(0),currentMolecule->v(1),currentMolecule->v(2),
currentMolecule->q().qw(),currentMolecule->q().qx(),currentMolecule->q().qy(),currentMolecule->q().qz(),
currentMolecule->D(0),currentMolecule->D(1),currentMolecule->D(2), &components);
moleculeContainer->addParticle(m1);
currentMolecule = moleculeContainer->next();
#ifdef MADPAC_LBMD_COUPLING
}
#endif
}
else
currentMolecule = moleculeContainer->next();
}
}
}
