/**
* SPHSaverへのセーブ
* @param filename セーブファイル名
* @retval true セーブ成功
* @retval false セーブ失敗
*/
bool SPHSaver::Save(const char* filename){
// @todo { double precision. }
SphHeaderTop headerTop;
SphHeaderSingle headerSingle;
assert(m_volumeData->Component() == 1 || m_volumeData->Component() == 3);
headerTop.svType = m_volumeData->Component() == 1 ? 1 : 2;
headerTop.dType = 1; // float
headerSingle.size[0] = static_cast<int>(m_volumeData->Width());
headerSingle.size[1] = static_cast<int>(m_volumeData->Height());
headerSingle.size[2] = static_cast<int>(m_volumeData->Depth());
headerSingle.org[0] = 0.0f;
headerSingle.org[1] = 0.0f;
headerSingle.org[2] = 0.0f;
headerSingle.pitch[0] = 1.0f;
headerSingle.pitch[1] = 1.0f;
headerSingle.pitch[2] = 1.0f;
headerSingle.step = 0;
headerSingle.time = 0.0f;
SphData sph(headerTop, headerSingle, m_volumeData->Buffer()->GetBuffer());
std::string fname(filename);
bool byteSwap = IsBigEndian();
bool ret = SaveSphFile(&sph, fname, byteSwap);
return ret;
}
//--------------------------------------------------------------------------------------------------
// MAIN
int main(int argc, char* argv[])
{
// Validate arguments
if (argc != 2)
{
std::cout << "Usage: " << argv[0] << " OutputDirectory" << std::endl;
return -1;
}
std::string outputPath(argv[1]);
// Init simulator
std::cout << "Initializing simulator..." << std::endl;
const Vec3d volumeMin(-3, 0, -1);
const Vec3d volumeMax( 3, 3, 1);
const double mass = 1.0;
const double restDensity = 998.23;
const double h = 0.2;
const double k = 100.0;
const double dt = 0.001;
BasicSPH sph(volumeMin, volumeMax, mass, restDensity, h, k, dt);
sph.enableAdaptiveTimeStep();
// Init particles
std::cout << "Initializing particles" << std::endl;
Vec3d boxMin(-3, 0, -1);
Vec3d boxMax(-1, 2, 1);
initParticlesBox(boxMin, boxMax, 0.1, sph.particles());
// Output first frame (initial frames)
const std::string filePrefix("particles_");
SPHParticleHoudiniIO::outputParticles(sph.particles(), outputPath, filePrefix, 1);
// Run simulation and output a frame every 1/24 second
std::cout << "Running simulation!" << std::endl;
const double frameTime = 1.0/24.0;
const double totalSimulationTime = 10.0;
double time = 0.0;
int currentFrame = 2;
while (time < totalSimulationTime)
{
std::cout << "Simulating frame " << currentFrame << " (" << (frameTime+time) << "s)";
std::cout << std::endl;
// Run simulation
sph.run(frameTime);
// Output particles
SPHParticleHoudiniIO::outputParticles(sph.particles(), outputPath, filePrefix, currentFrame);
// Update simulation time
time += frameTime;
++currentFrame;
}
std::cout << "Done!" << std::endl;
return 0;
}
void
nsChromeRegistryContent::RegisterSubstitution(const SubstitutionMapping& aSubstitution)
{
nsCOMPtr<nsIIOService> io (do_GetIOService());
if (!io)
return;
nsCOMPtr<nsIProtocolHandler> ph;
nsresult rv = io->GetProtocolHandler(aSubstitution.scheme.get(), getter_AddRefs(ph));
if (NS_FAILED(rv))
return;
nsCOMPtr<nsISubstitutingProtocolHandler> sph (do_QueryInterface(ph));
if (!sph)
return;
nsCOMPtr<nsIURI> resolvedURI;
if (aSubstitution.resolvedURI.spec.Length()) {
rv = NS_NewURI(getter_AddRefs(resolvedURI),
aSubstitution.resolvedURI.spec,
aSubstitution.resolvedURI.charset.get(),
nullptr, io);
if (NS_FAILED(rv))
return;
}
rv = sph->SetSubstitution(aSubstitution.path, resolvedURI);
if (NS_FAILED(rv))
return;
}
void AABoxContainTest::testMakeVolumeSphere()
{
gmtl::Spheref sph(gmtl::Point3f(1,1,1), 2);
gmtl::AABoxf box;
gmtl::Point3f expected_min(-1,-1,-1);
gmtl::Point3f expected_max( 3, 3, 3);
gmtl::makeVolume(box, sph);
CPPUNIT_ASSERT(box.getMin() == expected_min);
CPPUNIT_ASSERT(box.getMax() == expected_max);
CPPUNIT_ASSERT(! box.isEmpty());
}
///Randomly rotate sgrid_m
void NonLocalECPComponent::randomize_grid(ParticleSet::ParticlePos_t& sphere, bool randomize)
{
if(randomize) {
//const RealType twopi(6.28318530718);
//RealType phi(twopi*Random()),psi(twopi*Random()),cth(Random()-0.5),
RealType phi(TWOPI*((*myRNG)())), psi(TWOPI*((*myRNG)())), cth(((*myRNG)())-0.5);
RealType sph(std::sin(phi)),cph(std::cos(phi)),
sth(std::sqrt(1.0-cth*cth)),sps(std::sin(psi)),
cps(std::cos(psi));
TensorType rmat( cph*cth*cps-sph*sps, sph*cth*cps+cph*sps,-sth*cps,
-cph*cth*sps-sph*cps,-sph*cth*sps+cph*cps, sth*sps,
cph*sth, sph*sth, cth );
SpherGridType::iterator it(sgridxyz_m.begin());
SpherGridType::iterator it_end(sgridxyz_m.end());
SpherGridType::iterator jt(rrotsgrid_m.begin());
int ic=0;
while(it != it_end) {*jt = dot(rmat,*it); ++it; ++jt;}
//copy the radomized grid to sphere
std::copy(rrotsgrid_m.begin(), rrotsgrid_m.end(), sphere.begin());
} else {
//copy sphere to the radomized grid
std::copy(sphere.begin(), sphere.end(), rrotsgrid_m.begin());
}
}
int main()
{
vector v1,v2,v3;
vec(&v1,0,-10004,-20);
vec(&v2,0.20,0.20,0.20);
vec(&v3,0,0,0);
sph(v1,10000,v2,0,0,v3,sp);
vec(&v1,0,0,-20);
vec(&v2,1,0.32,0.36);
sph(v1,4,v2,1,0.5,v3,sp+1);
vec(&v1,5,-1,-15);
vec(&v2,0.90,0.76,0.46);
sph(v1,2,v2,1,0,v3,sp+2);
vec(&v1,5,0,-25);
vec(&v2,0.65,0.77,0.97);
sph(v1,3,v2,1,0,v3,sp+3);
vec(&v1,-5.5,0,-15);
vec(&v2,0.90,0.90,0.90);
sph(v1,3,v2,1,0,v3,sp+4);
vec(&v1,0,20,-30);
vec(&v2,0,0,0);
vec(&v3,3,3,3);
sph(v1,3,v2,0,0,v3,sp+5);
rendering();
}
bool CollisionTester::FrustumCircleXZTest( const Frustum& frus, const Circle& cirXZ )
{
Sphere sph( CVector3( cirXZ.mCenter.GetX(), frus.mCenter.GetY(), cirXZ.mCenter.GetY() ), cirXZ.mRadius );
return FrustumSphereTest( frus, sph );
}
void Input::reader(const std::string & filename) {
Getkw input_ = Getkw(filename, false, true);
units_ = input_.getStr("UNITS");
CODATAyear_ = input_.getInt("CODATA");
initBohrToAngstrom(bohrToAngstrom, CODATAyear_);
const Section & mol = input_.getSect("MOLECULE");
MEPfromMolecule_ = true;
if (mol.isDefined()) {
geometry_ = mol.getDblVec("GEOMETRY");
MEPfromMolecule_ = mol.getBool("MEP");
}
const Section & cavity = input_.getSect("CAVITY");
cavityType_ = cavity.getStr("TYPE");
area_ = cavity.getDbl("AREA");
if (cavityType_ == "RESTART") {
cavFilename_ = cavity.getStr("NPZFILE");
}
scaling_ = cavity.getBool("SCALING");
radiiSet_ = detail::uppercase(cavity.getStr("RADIISET"));
minimalRadius_ = cavity.getDbl("MINRADIUS");
mode_ = detail::uppercase(cavity.getStr("MODE"));
if (mode_ == "EXPLICIT") {
std::vector<double> spheresInput = cavity.getDblVec("SPHERES");
int j = 0;
int nAtoms = int(spheresInput.size() / 4);
for (int i = 0; i < nAtoms; ++i) {
Eigen::Vector3d center;
center = (Eigen::Vector3d() << spheresInput[j],
spheresInput[j + 1],
spheresInput[j + 2])
.finished();
Sphere sph(center, spheresInput[j + 3]);
spheres_.push_back(sph);
j += 4;
}
// Initialize molecule from spheres only when molecule section is absent
if (!mol.isDefined())
molecule_ = Molecule(spheres_);
} else if (mode_ == "ATOMS") {
atoms_ = cavity.getIntVec("ATOMS");
radii_ = cavity.getDblVec("RADII");
}
// Get the contents of the Medium section
const Section & medium = input_.getSect("MEDIUM");
// Get the name of the solvent
std::string name = medium.getStr("SOLVENT");
if (name == "EXPLICIT") {
hasSolvent_ = false;
// Get the probe radius
probeRadius_ = medium.getDbl("PROBERADIUS");
// Get the contents of the Green<inside> section...
const Section & inside = medium.getSect("GREEN<INSIDE>");
// ...and initialize the data members
greenInsideType_ = inside.getStr("TYPE") + "_" + inside.getStr("DER");
epsilonInside_ = inside.getDbl("EPS");
// Get the contents of the Green<outside> section...
const Section & outside = medium.getSect("GREEN<OUTSIDE>");
// ...and initialize the data members
greenOutsideType_ = outside.getStr("TYPE") + "_" + outside.getStr("DER");
epsilonStaticOutside_ = outside.getDbl("EPS");
epsilonDynamicOutside_ = outside.getDbl("EPSDYN");
epsilonStatic1_ = outside.getDbl("EPS1");
epsilonDynamic1_ = outside.getDbl("EPSDYN1");
epsilonStatic2_ = outside.getDbl("EPS2");
epsilonDynamic2_ = outside.getDbl("EPSDYN2");
center_ = outside.getDbl("CENTER");
width_ = outside.getDbl("WIDTH");
origin_ = outside.getDblVec("INTERFACEORIGIN");
if (outside.getStr("TYPE") == "SPHERICALDIFFUSE") {
greenOutsideType_ += "_" + outside.getStr("PROFILE");
}
maxL_ = outside.getInt("MAXL");
} else { // This part must be reviewed!! Some data members are not initialized...
// Just initialize the solvent object in this class
hasSolvent_ = true;
if (solvents().find(name) == solvents().end()) {
PCMSOLVER_ERROR("Solvent " + name + " NOT found!");
} else {
solvent_ = solvents()[name];
}
probeRadius_ = solvent_.probeRadius * angstromToBohr();
// Specification of the solvent by name means isotropic PCM
// We have to initialize the Green's functions data here, Solvent class
// is an helper class and should not be used in the core classes.
greenInsideType_ = "VACUUM_DERIVATIVE";
epsilonInside_ = 1.0;
greenOutsideType_ = "UNIFORMDIELECTRIC_DERIVATIVE";
epsilonStaticOutside_ = solvent_.epsStatic;
epsilonDynamicOutside_ = solvent_.epsDynamic;
}
integratorType_ = medium.getStr("DIAGONALINTEGRATOR");
integratorScaling_ = medium.getDbl("DIAGONALSCALING");
solverType_ = medium.getStr("SOLVERTYPE");
correction_ = medium.getDbl("CORRECTION");
hermitivitize_ = medium.getBool("MATRIXSYMM");
isDynamic_ = medium.getBool("NONEQUILIBRIUM");
const Section & chgdist = input_.getSect("CHARGEDISTRIBUTION");
if (chgdist.isDefined()) {
// Set monopoles
if (chgdist.getKey<std::vector<double> >("MONOPOLES").isDefined()) {
std::vector<double> mono = chgdist.getDblVec("MONOPOLES");
int j = 0;
int n = int(mono.size() / 4);
multipoles_.monopoles = Eigen::VectorXd::Zero(n);
multipoles_.monopolesSites = Eigen::Matrix3Xd::Zero(3, n);
for (int i = 0; i < n; ++i) {
multipoles_.monopolesSites.col(i) =
(Eigen::Vector3d() << mono[j], mono[j + 1], mono[j + 2]).finished();
multipoles_.monopoles(i) = mono[j + 3];
j += 4;
}
}
// Set dipoles
if (chgdist.getKey<std::vector<double> >("DIPOLES").isDefined()) {
std::vector<double> dipo = chgdist.getDblVec("DIPOLES");
int j = 0;
int n = int(dipo.size() / 6);
multipoles_.dipoles = Eigen::Matrix3Xd::Zero(3, n);
multipoles_.dipolesSites = Eigen::Matrix3Xd::Zero(3, n);
for (int i = 0; i < n; ++i) {
multipoles_.dipolesSites.col(i) =
(Eigen::Vector3d() << dipo[j], dipo[j + 1], dipo[j + 2]).finished();
multipoles_.dipoles.col(i) =
(Eigen::Vector3d() << dipo[j + 3], dipo[j + 4], dipo[j + 5]).finished();
j += 6;
}
}
}
providedBy_ = std::string("API-side");
}
GridMolecularOrbitals::BasisSetType*
GridMolecularOrbitals::addBasisSet(xmlNodePtr cur)
{
if(!BasisSet)
BasisSet = new BasisSetType(IonSys.getSpeciesSet().getTotalNum());
QuantumNumberType nlms;
string rnl;
//current number of centers
int ncenters = CenterID.size();
int activeCenter;
int gridmode = -1;
bool addsignforM = false;
string sph("default"), Morder("gaussian");
//go thru the tree
cur = cur->xmlChildrenNode;
map<string,RGFBuilderBase*> rbuilderlist;
while(cur!=NULL)
{
string cname((const char*)(cur->name));
if(cname == basis_tag || cname == "atomicBasisSet")
{
int expandlm = GAUSSIAN_EXPAND;
string abasis("invalid"), btype("Numerical");
//Register valid attributes attributes
OhmmsAttributeSet aAttrib;
aAttrib.add(abasis,"elementType");
aAttrib.add(abasis,"species");
aAttrib.add(btype,"type");
aAttrib.add(sph,"angular");
aAttrib.add(addsignforM,"expM");
aAttrib.add(Morder,"expandYlm");
aAttrib.put(cur);
if(abasis == "invalid")
continue;
if(sph == "spherical")
addsignforM=1; //include (-1)^m
if(Morder == "gaussian")
{
expandlm = GAUSSIAN_EXPAND;
}
else
if(Morder == "natural")
{
expandlm = NATURAL_EXPAND;
}
else
if(Morder == "no")
{
expandlm = DONOT_EXPAND;
}
if(addsignforM)
LOGMSG("Spherical Harmonics contain (-1)^m factor")
else
LOGMSG("Spherical Harmonics DO NOT contain (-1)^m factor")
//search the species name
map<string,int>::iterator it = CenterID.find(abasis);
if(it == CenterID.end())
//add the name to the map CenterID
{
if(btype == "Numerical" || btype == "NG" || btype == "HFNG")
{
rbuilder = new NumericalRGFBuilder(cur);
}
else
{
rbuilder = new Any2GridBuilder(cur);
}
//CenterID[abasis] = activeCenter = ncenters++;
CenterID[abasis]=activeCenter=IonSys.getSpeciesSet().findSpecies(abasis);
int Lmax(0); //maxmimum angular momentum of this center
int num(0);//the number of localized basis functions of this center
//process the basic property: maximun angular momentum, the number of basis functions to be added
vector<xmlNodePtr> radGroup;
xmlNodePtr cur1 = cur->xmlChildrenNode;
xmlNodePtr gptr=0;
while(cur1 != NULL)
{
string cname1((const char*)(cur1->name));
if(cname1 == basisfunc_tag || cname1 == "basisGroup")
{
radGroup.push_back(cur1);
int l=atoi((const char*)(xmlGetProp(cur1, (const xmlChar *)"l")));
Lmax = max(Lmax,l);
//expect that only Rnl is given
if(expandlm)
num += 2*l+1;
else
num++;
}
else
if(cname1 == "grid")
{
gptr = cur1;
}
cur1 = cur1->next;
}
XMLReport("Adding a center " << abasis << " centerid "<< CenterID[abasis])
XMLReport("Maximum angular momentum = " << Lmax)
XMLReport("Number of centered orbitals = " << num)
//create a new set of atomic orbitals sharing a center with (Lmax, num)
//if(addsignforM) the basis function has (-1)^m sqrt(2)Re(Ylm)
CenteredOrbitalType* aos = new CenteredOrbitalType(Lmax,addsignforM);
aos->LM.resize(num);
aos->NL.resize(num);
//Now, add distinct Radial Orbitals and (l,m) channels
num=0;
rbuilder->setOrbitalSet(aos,abasis); //assign radial orbitals for the new center
rbuilder->addGrid(gptr); //assign a radial grid for the new center
vector<xmlNodePtr>::iterator it(radGroup.begin());
vector<xmlNodePtr>::iterator it_end(radGroup.end());
while(it != it_end)
{
cur1 = (*it);
xmlAttrPtr att = cur1->properties;
while(att != NULL)
{
string aname((const char*)(att->name));
if(aname == "rid" || aname == "id")
//accept id/rid
{
rnl = (const char*)(att->children->content);
}
else
{
map<string,int>::iterator iit = nlms_id.find(aname);
if(iit != nlms_id.end())
//valid for n,l,m,s
{
nlms[(*iit).second] = atoi((const char*)(att->children->content));
}
}
att = att->next;
}
XMLReport("\n(n,l,m,s) " << nlms[0] << " " << nlms[1] << " " << nlms[2] << " " << nlms[3])
//add Ylm channels
num = expandYlm(rnl,nlms,num,aos,cur1,expandlm);
++it;
}
//add the new atomic basis to the basis set
BasisSet->add(aos,activeCenter);
#if !defined(HAVE_MPI)
rbuilder->print(abasis,1);
#endif
if(rbuilder)
{
delete rbuilder;
rbuilder=0;
}
}
else
{
WARNMSG("Species " << abasis << " is already initialized. Ignore the input.")
}
}
cur = cur->next;
}
GTOMolecularOrbitals::BasisSetType*
GTOMolecularOrbitals::addBasisSet(xmlNodePtr cur) {
if(!BasisSet)
BasisSet = new BasisSetType(IonSys.getSpeciesSet().getTotalNum());
QuantumNumberType nlms;
string rnl;
//current number of centers
int ncenters = CenterID.size();
int activeCenter;
int gridmode = -1;
bool addsignforM = true;
string sph("spherical"), Morder("gaussian");
//go thru the tree
cur = cur->xmlChildrenNode;
while(cur!=NULL) {
string cname((const char*)(cur->name));
if(cname == basis_tag || cname == "atomicBasisSet") {
int expandlm = GAUSSIAN_EXPAND;
string abasis("invalid"), norm("no");
//Register valid attributes attributes
OhmmsAttributeSet aAttrib;
aAttrib.add(abasis,"elementType"); aAttrib.add(abasis,"species");
aAttrib.add(sph,"angular"); aAttrib.add(addsignforM,"expM");
aAttrib.add(Morder,"expandYlm");
aAttrib.add(norm,"normalized");
aAttrib.put(cur);
if(norm == "yes") Normalized=true;
else Normalized=false;
if(abasis == "invalid") continue;
if(sph == "spherical") addsignforM=true; //include (-1)^m
if(sph == "cartesian") addsignforM=false;
if(Morder == "gaussian") {
expandlm = GAUSSIAN_EXPAND;
} else if(Morder == "natural"){
expandlm = NATURAL_EXPAND;
} else if(Morder == "no") {
expandlm = DONOT_EXPAND;
}
if(addsignforM)
LOGMSG("Spherical Harmonics contain (-1)^m factor")
else
LOGMSG("Spherical Harmonics DO NOT contain (-1)^m factor")
map<string,int>::iterator it = CenterID.find(abasis); //search the species name
if(it == CenterID.end()) {//add the name to the map CenterID
//CenterID[abasis] = activeCenter = ncenters++;
CenterID[abasis]=activeCenter=IonSys.getSpeciesSet().findSpecies(abasis);
int Lmax(0); //maxmimum angular momentum of this center
int num(0);//the number of localized basis functions of this center
//process the basic property: maximun angular momentum, the number of basis functions to be added
vector<xmlNodePtr> radGroup;
xmlNodePtr cur1 = cur->xmlChildrenNode;
xmlNodePtr gptr=0;
while(cur1 != NULL) {
string cname1((const char*)(cur1->name));
if(cname1 == basisfunc_tag || cname1 == "basisGroup") {
radGroup.push_back(cur1);
int l=atoi((const char*)(xmlGetProp(cur1, (const xmlChar *)"l")));
Lmax = max(Lmax,l);
if(expandlm)
num += 2*l+1;
else
num++;
}
cur1 = cur1->next;
}
LOGMSG("Adding a center " << abasis << " centerid "<< CenterID[abasis])
LOGMSG("Maximum angular momentum = " << Lmax)
LOGMSG("Number of centered orbitals = " << num)
//create a new set of atomic orbitals sharing a center with (Lmax, num)
//if(addsignforM) the basis function has (-1)^m sqrt(2)Re(Ylm)
CenteredOrbitalType* aos = new CenteredOrbitalType(Lmax,addsignforM);
aos->LM.resize(num);
aos->NL.resize(num);
//Now, add distinct Radial Orbitals and (l,m) channels
num=0;
vector<xmlNodePtr>::iterator it(radGroup.begin());
vector<xmlNodePtr>::iterator it_end(radGroup.end());
while(it != it_end) {
cur1 = (*it);
xmlAttrPtr att = cur1->properties;
while(att != NULL) {
string aname((const char*)(att->name));
if(aname == "rid" || aname == "id") { //accept id/rid
rnl = (const char*)(att->children->content);
} else {
map<string,int>::iterator iit = nlms_id.find(aname);
if(iit != nlms_id.end()) { //valid for n,l,m,s
nlms[(*iit).second] = atoi((const char*)(att->children->content));
}
}
att = att->next;
}
LOGMSG("\n(n,l,m,s) " << nlms[0] << " " << nlms[1] << " " << nlms[2] << " " << nlms[3])
//add Ylm channels
num = expandYlm(rnl,nlms,num,aos,cur1,expandlm);
++it;
}
LOGMSG("Checking the order of angular momentum ")
std::copy(aos->LM.begin(), aos->LM.end(), ostream_iterator<int>(app_log()," "));
app_log() << endl;
//add the new atomic basis to the basis set
BasisSet->add(aos,activeCenter);
}else {
WARNMSG("Species " << abasis << " is already initialized. Ignore the input.")
}
}
cur = cur->next;
}
int main(int argc, char *argv[]) {
if (argc != 4) {
cout << "Usage: run infilename intimestep outfilename" << endl;
return(-1);
}
cout << "Ran program with argv = ";
for (int i=0;i<argc;i++) {
cout << argv[i];
}
cout << endl;
CglobalVars globals;
particleContainer ps;
//get rank and init all MPI stuff. Put rank in globals
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &(globals.mpiSize));
MPI_Comm_rank(MPI_COMM_WORLD, &(globals.mpiRank));
if (globals.mpiRank==0) cout << "Reading input file..." <<endl;
string filename = argv[1];
Cio_data_vtk io_data(filename,&globals);
io_data.readDomain(atoi(argv[2]),&globals);
io_data.readGlobals(atoi(argv[2]),&globals);
io_data.readRestart(atoi(argv[2]),&ps,&globals);
if (globals.mpiRank==0) cout << "after read, n = "<<ps.size()<<endl;
int outstep = atoi(argv[2]);
if (TIME_OVERIDE) {
if (globals.mpiRank==0) cout << "time was set to time = "<<globals.time<<endl;
globals.time = START_TIME;
if (globals.mpiRank==0) cout << "Overiding time, time = "<<globals.time<<endl;
}
if (NSTEP_OVERIDE) {
outstep = START_NSTEP;
if (globals.mpiRank==0) cout << "Overiding output timestep = "<<outstep<<endl;
}
string outFilename = argv[3];
if (globals.mpiRank==0) cout << "Setting output filename as: "<<outFilename<<endl;
io_data.setFilename(outFilename,&globals);
if (globals.mpiRank==0) cout << "1time was set to time = "<<globals.time<<endl;
if (globals.mpiRank==0) cout << "Creating data structure..." <<endl;
/*
CdataLL<sphParticle> *data = new CdataLL<sphParticle>(ps,globals,true);
#ifdef LIQ_DEM
CdataLL<demParticle> *dataDem = new CdataLL<demParticle>(ps,globals,true);
CsphLiqDem sph(data,dataDem);
CcustomSim customSim(data,dataDem,globals.time);
CcustomOutput customOutput(data,dataDem);
#else
CsphIncompress sph(data);
CcustomSim customSim(data,globals.time);
CcustomOutput customOutput(data);
#endif
*/
CdataLL *data = new CdataLL(ps,globals,true);
CsphIncompress sph(data);
CcustomSim customSim(data,globals.time);
CcustomOutput customOutput(data);
if (globals.mpiRank==0) cout << "2time was set to time = "<<globals.time<<endl;
globals.maxdt = MAXTIME/OUTSTEP;
if (globals.mpiRank==0) cout << "Starting simulation..."<<endl;
#ifndef START_WRITE_TIME
double nextWriteTime = globals.time+MAXTIME/OUTSTEP;
#else
double nextWriteTime = START_WRITE_TIME
#endif
timeval wtStartSphStep,wtStartOutStep,wtStartSim,wtCurrTime;
gettimeofday(&wtStartSim,NULL);
wtStartOutStep = wtStartSim;
wtStartSphStep = wtStartSim;
globals.startOutStep();
while ((globals.time <= MAXTIME) && (outstep <= OUTSTEP)) {
globals.sphStep++;
gettimeofday(&wtCurrTime,NULL);
double simTimeSPHStep = wtCurrTime.tv_sec-wtStartSim.tv_sec+(wtCurrTime.tv_usec-wtStartSim.tv_usec)/1000000.0;
//if (globals.mpiRank==0) cout << "\r#"<<globals.sphStep<<". Time = "<<globals.time<<". Simulation "<<globals.time/MAXTIME*100<<"\% complete. "<<wtCurrTime.tv_sec-wtStartSphStep.tv_sec+(wtCurrTime.tv_usec-wtStartSphStep.tv_usec)/1000000.0<<" sec per SPH step. Time taken = "<<simTimeSPHStep/(60*60)<<flush;
wtStartSphStep = wtCurrTime;
customSim.beforeStart(globals.time);
sph.start();
customSim.beforeMiddle(globals.time);
sph.middle();
customSim.beforeEnd(globals.time);
sph.end();
customSim.afterEnd(globals.time);
if (globals.time>= nextWriteTime) {
//if(globals.sphStep%10==0){
//if (1) {
cout << endl;
outstep++;
globals.outstep = outstep;
globals.endOutStep();
if (globals.mpiRank==0) cout << "\tWriting output at time = "<<globals.time<<". Simulation is "<<globals.time/MAXTIME*100<<"\% complete"<<endl;
sph.calcOutputVars();
customOutput.calcOutput(outstep,&customSim,&io_data);
io_data.writeOutput(outstep,ps,&globals);
io_data.writeGlobals(outstep,&globals);
if (outstep%RESTART_EVERY_N_STEPS==0) {
io_data.writeRestart(outstep,ps,&globals);
io_data.writeDomain(outstep,&globals);
}
data->calcTraverseOrder(); //arrange traverse order spatially
nextWriteTime = globals.time+MAXTIME/OUTSTEP;
globals.maxdt = MAXTIME/OUTSTEP;
gettimeofday(&wtCurrTime,NULL);
double oSTime = wtCurrTime.tv_sec-wtStartOutStep.tv_sec+(wtCurrTime.tv_usec-wtStartOutStep.tv_usec)/1000000.0;
double simTime = wtCurrTime.tv_sec-wtStartSim.tv_sec+(wtCurrTime.tv_usec-wtStartSim.tv_usec)/1000000.0;
if (globals.mpiRank==0) cout <<'\t'<<oSTime<< " seconds per output timestep, "<<oSTime*(OUTSTEP-outstep)/(60.0*60.0)<<" hours remaining. "<<simTime/(60.0*60.0)<<" hours since start"<<endl;
wtStartOutStep = wtCurrTime;
if (globals.mpiRank==0) cout <<'\t'<<"Step profile: Total time = "<<globals.wtTotalOutStep.tv_sec+globals.wtTotalOutStep.tv_usec/1000000.0<<" Force = "<<globals.wtTotalForceCalc.tv_sec+globals.wtTotalForceCalc.tv_usec/1000000.0<<" dddt = "<<globals.wtTotalDddtCalc.tv_sec+globals.wtTotalDddtCalc.tv_usec/1000000.0<<" reset = "<<globals.wtTotalReset.tv_sec+globals.wtTotalReset.tv_usec/1000000.0<<" update domain = "<<globals.wtTotalUpdateDomain.tv_sec+globals.wtTotalUpdateDomain.tv_usec/1000000.0<<" MPI = "<<globals.wtTotalMPI.tv_sec+globals.wtTotalMPI.tv_usec/1000000.0;
#ifdef SMOOTHING
if (globals.mpiRank==0) cout <<" Smooth = "<<globals.wtTotalSmooth.tv_sec+globals.wtTotalSmooth.tv_usec/1000000.0<<" SmoothMPI = "<<globals.wtTotalSmoothMPI.tv_sec+globals.wtTotalSmoothMPI.tv_usec/1000000.0<<endl;
#else
if (globals.mpiRank==0) cout <<endl;
#endif
globals.startOutStep();
//exit(-1);
}
}
MPI_Finalize();
}
class timingData {
timingData() {
gettimeofday(&wtStartSim,NULL);
wtStartOutStep = wtStartSim;
wtStartSphStep = wtStartSim;
}
outputStartTimestep() {
gettimeofday(&wtCurrTime,NULL);
double simTimeSPHStep = wtCurrTime.tv_sec-wtStartSim.tv_sec+(wtCurrTime.tv_usec-wtStartSim.tv_usec)/1000000.0;
//if (globals.mpiRank==0) cout << "\r#"<<globals.sphStep<<". Time = "<<globals.time<<". Simulation "<<globals.time/MAXTIME*100<<"\% complete. "<<wtCurrTime.tv_sec-wtStartSphStep.tv_sec+(wtCurrTime.tv_usec-wtStartSphStep.tv_usec)/1000000.0<<" sec per SPH step. Time taken = "<<simTimeSPHStep/(60*60)<<flush;
wtStartSphStep = wtCurrTime;
}
outputStartOutputstep() {
cout << endl;
}
private:
timeval wtStartSphStep,wtStartOutStep,wtStartSim,wtCurrTime;
}
int main(int argc, char *argv[]) {
CglobalVars globalsSPH;
vector<sphParticles> psSPH;
init(argc,argv,globalsSPH);
Cio_data_vtk<sphParticles> io_dataSPH(atoi(argv[2]),argv[1],&psSPH,&globalsSPH);
if (globals.mpiRank==0) cout << "Creating data structure..." <<endl;
CdataLL *dataSPH = new CdataLL(psSPH,globalsSPH,true);
CsphIncompress sph(dataSPH);
CcustomSim customSim(data,globals.time);
CcustomOutput customOutput(data);
if (globals.mpiRank==0) cout << "Starting simulation..."<<endl;
runUntilOutput(sph
double nextWriteTime = globals.time+MAXTIME/OUTSTEP;
globals.startOutStep();
timingData timing;
while ((globals.time <= MAXTIME) && (outstep <= OUTSTEP)) {
globals.sphStep++;
timing.outputStartTimestep();
customSim.beforeStart(globals.time);
sph.start();
customSim.beforeMiddle(globals.time);
sph.middle();
customSim.beforeEnd(globals.time);
sph.end();
customSim.afterEnd(globals.time);
if (globals.time>= nextWriteTime) {
//if(globals.sphStep%10==0){
//if (1) {
cout << endl;
outstep++;
globals.outstep = outstep;
globals.endOutStep();
if (globals.mpiRank==0) cout << "\tWriting output at time = "<<globals.time<<". Simulation is "<<globals.time/MAXTIME*100<<"\% complete"<<endl;
sph.calcOutputVars();
customOutput.calcOutput(outstep,&customSim,&io_data);
io_data.writeOutput(outstep,ps,customSim,&globals);
io_data.writeGlobals(outstep,&globals);
if (outstep%RESTART_EVERY_N_STEPS==0) {
io_data.writeRestart(outstep,ps,&globals);
io_data.writeDomain(outstep,&globals);
}
data->calcTraverseOrder(); //arrange traverse order spatially
//vector<Cparticle> psGrid;
//vectInt gridDims;
//sph.renderToGrid(psGrid,gridDims);
//io_data.writeGrid(outstep,psGrid,gridDims);
nextWriteTime = globals.time+MAXTIME/OUTSTEP;
globals.maxdt = MAXTIME/OUTSTEP;
gettimeofday(&wtCurrTime,NULL);
double oSTime = wtCurrTime.tv_sec-wtStartOutStep.tv_sec+(wtCurrTime.tv_usec-wtStartOutStep.tv_usec)/1000000.0;
double simTime = wtCurrTime.tv_sec-wtStartSim.tv_sec+(wtCurrTime.tv_usec-wtStartSim.tv_usec)/1000000.0;
if (globals.mpiRank==0) cout <<'\t'<<oSTime<< " seconds per output timestep, "<<oSTime*(OUTSTEP-outstep)/(60.0*60.0)<<" hours remaining. "<<simTime/(60.0*60.0)<<" hours since start"<<endl;
wtStartOutStep = wtCurrTime;
if (globals.mpiRank==0) cout <<'\t'<<"Step profile: Total time = "<<globals.wtTotalOutStep.tv_sec+globals.wtTotalOutStep.tv_usec/1000000.0<<" Force = "<<globals.wtTotalForceCalc.tv_sec+globals.wtTotalForceCalc.tv_usec/1000000.0<<" dddt = "<<globals.wtTotalDddtCalc.tv_sec+globals.wtTotalDddtCalc.tv_usec/1000000.0<<" reset = "<<globals.wtTotalReset.tv_sec+globals.wtTotalReset.tv_usec/1000000.0<<" update domain = "<<globals.wtTotalUpdateDomain.tv_sec+globals.wtTotalUpdateDomain.tv_usec/1000000.0<<" MPI = "<<globals.wtTotalMPI.tv_sec+globals.wtTotalMPI.tv_usec/1000000.0;
#ifdef SMOOTHING
if (globals.mpiRank==0) cout <<" Smooth = "<<globals.wtTotalSmooth.tv_sec+globals.wtTotalSmooth.tv_usec/1000000.0<<" SmoothMPI = "<<globals.wtTotalSmoothMPI.tv_sec+globals.wtTotalSmoothMPI.tv_usec/1000000.0<<endl;
#else
if (globals.mpiRank==0) cout <<endl;
#endif
globals.startOutStep();
//exit(-1);
}
}
MPI_Finalize();
}