void Molecule::moveCom(const Vetor3d& delta) { StuntDouble* sd; std::vector<StuntDouble*>::iterator i; for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ s->setPos(sd->getPos() + delta); } }
void NVE::moveA(){ SimInfo::MoleculeIterator i; Molecule::IntegrableObjectIterator j; Molecule* mol; StuntDouble* sd; Vector3d vel; Vector3d pos; Vector3d frc; Vector3d Tb; Vector3d ji; RealType mass; for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { for (sd = mol->beginIntegrableObject(j); sd != NULL; sd = mol->nextIntegrableObject(j)) { vel = sd->getVel(); pos = sd->getPos(); frc = sd->getFrc(); mass = sd->getMass(); // velocity half step vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; // position whole step pos += dt * vel; sd->setVel(vel); sd->setPos(pos); if (sd->isDirectional()){ // get and convert the torque to body frame Tb = sd->lab2Body(sd->getTrq()); // get the angular momentum, and propagate a half step ji = sd->getJ(); ji += (dt2 * PhysicalConstants::energyConvert) * Tb; rotAlgo_->rotate(sd, ji, dt); sd->setJ(ji); } } } flucQ_->moveA(); rattle_->constraintA(); }
Vector3d DensityPlot::calcNewOrigin() { int i; Vector3d newOrigin(0.0); RealType totalMass = 0.0; for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { RealType mass = sd->getMass(); totalMass += mass; newOrigin += sd->getPos() * mass; } newOrigin /= totalMass; return newOrigin; }
Vector3d Molecule::getCom() { StuntDouble* sd; std::vector<StuntDouble*>::iterator i; Vector3d com; double totalMass = 0; double mass; for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ mass = sd->getMass(); totalMass += mass; com += sd->getPos() * mass; } com /= totalMass; return com; }
void NPT::moveA() { SimInfo::MoleculeIterator i; Molecule::IntegrableObjectIterator j; Molecule* mol; StuntDouble* sd; Vector3d Tb, ji; RealType mass; Vector3d vel; Vector3d pos; Vector3d frc; Vector3d sc; int index; thermostat = snap->getThermostat(); loadEta(); instaTemp =thermo.getTemperature(); press = thermo.getPressureTensor(); instaPress = PhysicalConstants::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0; instaVol =thermo.getVolume(); Vector3d COM = thermo.getCom(); //evolve velocity half step calcVelScale(); for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { for (sd = mol->beginIntegrableObject(j); sd != NULL; sd = mol->nextIntegrableObject(j)) { vel = sd->getVel(); frc = sd->getFrc(); mass = sd->getMass(); getVelScaleA(sc, vel); // velocity half step (use chi from previous step here): vel += dt2*PhysicalConstants::energyConvert/mass* frc - dt2*sc; sd->setVel(vel); if (sd->isDirectional()) { // get and convert the torque to body frame Tb = sd->lab2Body(sd->getTrq()); // get the angular momentum, and propagate a half step ji = sd->getJ(); ji += dt2*PhysicalConstants::energyConvert * Tb - dt2*thermostat.first* ji; rotAlgo_->rotate(sd, ji, dt); sd->setJ(ji); } } } // evolve chi and eta half step thermostat.first += dt2 * (instaTemp / targetTemp - 1.0) / tt2; evolveEtaA(); //calculate the integral of chidt thermostat.second += dt2 * thermostat.first; flucQ_->moveA(); index = 0; for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { for (sd = mol->beginIntegrableObject(j); sd != NULL; sd = mol->nextIntegrableObject(j)) { oldPos[index++] = sd->getPos(); } } //the first estimation of r(t+dt) is equal to r(t) for(int k = 0; k < maxIterNum_; k++) { index = 0; for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { for (sd = mol->beginIntegrableObject(j); sd != NULL; sd = mol->nextIntegrableObject(j)) { vel = sd->getVel(); pos = sd->getPos(); this->getPosScale(pos, COM, index, sc); pos = oldPos[index] + dt * (vel + sc); sd->setPos(pos); ++index; } } rattle_->constraintA(); } // Scale the box after all the positions have been moved: this->scaleSimBox(); snap->setThermostat(thermostat); saveEta(); }
void DensityPlot::process() { Molecule* mol; RigidBody* rb; SimInfo::MoleculeIterator mi; Molecule::RigidBodyIterator rbIter; DumpReader reader(info_, dumpFilename_); int nFrames = reader.getNFrames(); for (int i = 0; i < nFrames; i += step_) { reader.readFrame(i); currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { //change the positions of atoms which belong to the rigidbodies for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { rb->updateAtoms(); } } if (evaluator_.isDynamic()) { seleMan_.setSelectionSet(evaluator_.evaluate()); } if (cmEvaluator_.isDynamic()) { cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate()); } Vector3d origin = calcNewOrigin(); Mat3x3d hmat = currentSnapshot_->getHmat(); RealType slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1); int k; for (StuntDouble* sd = seleMan_.beginSelected(k); sd != NULL; sd = seleMan_.nextSelected(k)) { if (!sd->isAtom()) { sprintf( painCave.errMsg, "Can not calculate electron density if it is not atom\n"); painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } Atom* atom = static_cast<Atom*>(sd); GenericData* data = atom->getAtomType()->getPropertyByName("nelectron"); if (data == NULL) { sprintf( painCave.errMsg, "Can not find Parameters for nelectron\n"); painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data); if (doubleData == NULL) { sprintf( painCave.errMsg, "Can not cast GenericData to DoubleGenericData\n"); painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } RealType nelectron = doubleData->getData(); LennardJonesAdapter lja = LennardJonesAdapter(atom->getAtomType()); RealType sigma = lja.getSigma() * 0.5; RealType sigma2 = sigma * sigma; Vector3d pos = sd->getPos() - origin; for (int j =0; j < nRBins_; ++j) { Vector3d tmp(pos); RealType zdist =j * deltaR_ - halfLen_; tmp[2] += zdist; if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(tmp); RealType wrappedZdist = tmp.z() + halfLen_; if (wrappedZdist < 0.0 || wrappedZdist > len_) { continue; } int which = int(wrappedZdist / deltaR_); density_[which] += nelectron * exp(-zdist*zdist/(sigma2*2.0)) /(slabVolume* sqrt(2*NumericConstant::PI*sigma*sigma)); } } } int nProcessed = nFrames /step_; std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<RealType>(), nProcessed)); writeDensity(); }
SelectionSet DistanceFinder::find(const SelectionSet& bs, RealType distance, int frame ) { StuntDouble * center; Vector3d centerPos; Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame); SelectionSet bsResult(nObjects_); assert(bsResult.size() == bs.size()); #ifdef IS_MPI int mol; int proc; RealType data[3]; int worldRank = MPI::COMM_WORLD.Get_rank(); #endif for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) { if (stuntdoubles_[j]->isRigidBody()) { RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]); rb->updateAtoms(frame); } } SelectionSet bsTemp(nObjects_); bsTemp = bs; bsTemp.parallelReduce(); for (int i = bsTemp.bitsets_[STUNTDOUBLE].firstOnBit(); i != -1; i = bsTemp.bitsets_[STUNTDOUBLE].nextOnBit(i)) { // Now, if we own stuntdouble i, we can use the position, but in // parallel, we'll need to let everyone else know what that // position is! #ifdef IS_MPI mol = info_->getGlobalMolMembership(i); proc = info_->getMolToProc(mol); if (proc == worldRank) { center = stuntdoubles_[i]; centerPos = center->getPos(frame); data[0] = centerPos.x(); data[1] = centerPos.y(); data[2] = centerPos.z(); MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc); } else { MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc); centerPos = Vector3d(data); } #else center = stuntdoubles_[i]; centerPos = center->getPos(frame); #endif for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) { Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame); currSnapshot->wrapVector(r); if (r.length() <= distance) { bsResult.bitsets_[STUNTDOUBLE].setBitOn(j); } } for (unsigned int j = 0; j < bonds_.size(); ++j) { Vector3d loc = bonds_[j]->getAtomA()->getPos(frame); loc += bonds_[j]->getAtomB()->getPos(frame); loc = loc / 2.0; Vector3d r = centerPos - loc; currSnapshot->wrapVector(r); if (r.length() <= distance) { bsResult.bitsets_[BOND].setBitOn(j); } } for (unsigned int j = 0; j < bends_.size(); ++j) { Vector3d loc = bends_[j]->getAtomA()->getPos(frame); loc += bends_[j]->getAtomB()->getPos(frame); loc += bends_[j]->getAtomC()->getPos(frame); loc = loc / 3.0; Vector3d r = centerPos - loc; currSnapshot->wrapVector(r); if (r.length() <= distance) { bsResult.bitsets_[BEND].setBitOn(j); } } for (unsigned int j = 0; j < torsions_.size(); ++j) { Vector3d loc = torsions_[j]->getAtomA()->getPos(frame); loc += torsions_[j]->getAtomB()->getPos(frame); loc += torsions_[j]->getAtomC()->getPos(frame); loc += torsions_[j]->getAtomD()->getPos(frame); loc = loc / 4.0; Vector3d r = centerPos - loc; currSnapshot->wrapVector(r); if (r.length() <= distance) { bsResult.bitsets_[TORSION].setBitOn(j); } } for (unsigned int j = 0; j < inversions_.size(); ++j) { Vector3d loc = inversions_[j]->getAtomA()->getPos(frame); loc += inversions_[j]->getAtomB()->getPos(frame); loc += inversions_[j]->getAtomC()->getPos(frame); loc += inversions_[j]->getAtomD()->getPos(frame); loc = loc / 4.0; Vector3d r = centerPos - loc; currSnapshot->wrapVector(r); if (r.length() <= distance) { bsResult.bitsets_[INVERSION].setBitOn(j); } } } return bsResult; }
void BondAngleDistribution::process() { Molecule* mol; Atom* atom; RigidBody* rb; int myIndex; SimInfo::MoleculeIterator mi; Molecule::RigidBodyIterator rbIter; Molecule::AtomIterator ai; StuntDouble* sd; Vector3d vec; std::vector<Vector3d> bondvec; RealType r; int nBonds; int i; bool usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions(); DumpReader reader(info_, dumpFilename_); int nFrames = reader.getNFrames(); frameCounter_ = 0; nTotBonds_ = 0; for (int istep = 0; istep < nFrames; istep += step_) { reader.readFrame(istep); frameCounter_++; currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); if (evaluator_.isDynamic()) { seleMan_.setSelectionSet(evaluator_.evaluate()); } // update the positions of atoms which belong to the rigidbodies for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { rb->updateAtoms(); } } // outer loop is over the selected StuntDoubles: for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { myIndex = sd->getGlobalIndex(); nBonds = 0; bondvec.clear(); // inner loop is over all other atoms in the system: for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { if (atom->getGlobalIndex() != myIndex) { vec = sd->getPos() - atom->getPos(); if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(vec); // Calculate "bonds" and make a pair list r = vec.length(); // Check to see if neighbor is in bond cutoff if (r < rCut_) { // Add neighbor to bond list's bondvec.push_back(vec); nBonds++; nTotBonds_++; } } } for (int i = 0; i < nBonds-1; i++ ){ Vector3d vec1 = bondvec[i]; vec1.normalize(); for(int j = i+1; j < nBonds; j++){ Vector3d vec2 = bondvec[j]; vec2.normalize(); RealType theta = acos(dot(vec1,vec2))*180.0/NumericConstant::PI; if (theta > 180.0){ theta = 360.0 - theta; } int whichBin = int(theta/deltaTheta_); histogram_[whichBin] += 2; } } } } } writeBondAngleDistribution(); }
void ContactAngle1::doFrame(int frame) { StuntDouble* sd; int i; if (evaluator1_.isDynamic()) { seleMan1_.setSelectionSet(evaluator1_.evaluate()); } RealType mtot = 0.0; Vector3d com(V3Zero); RealType mass; for (sd = seleMan1_.beginSelected(i); sd != NULL; sd = seleMan1_.nextSelected(i)) { mass = sd->getMass(); mtot += mass; com += sd->getPos() * mass; } com /= mtot; RealType dz = com.z() - solidZ_; if (dz < 0.0) { sprintf(painCave.errMsg, "ContactAngle1: Z-center of mass of selection, %lf, was\n" "\tlocated below the solid reference plane, %lf\n", com.z(), solidZ_); painCave.isFatal = 1; painCave.severity = OPENMD_ERROR; simError(); } if (dz > dropletRadius_) { values_.push_back(180.0); } else { RealType k = pow(2.0, -4.0/3.0) * dropletRadius_; RealType z2 = dz*dz; RealType z3 = z2 * dz; RealType k2 = k*k; RealType k3 = k2*k; Polynomial<RealType> poly; poly.setCoefficient(4, z3 + k3); poly.setCoefficient(3, 8.0*z3 + 8.0*k3); poly.setCoefficient(2, 24.0*z3 + 18.0*k3); poly.setCoefficient(1, 32.0*z3 ); poly.setCoefficient(0, 16.0*z3 - 27.0*k3); vector<RealType> realRoots = poly.FindRealRoots(); RealType ct; vector<RealType>::iterator ri; RealType maxct = -1.0; for (ri = realRoots.begin(); ri !=realRoots.end(); ++ri) { ct = *ri; if (ct > 1.0) ct = 1.0; if (ct < -1.0) ct = -1.0; // use the largest magnitude of ct that it finds: if (ct > maxct) { maxct = ct; } } values_.push_back( acos(maxct)*(180.0/M_PI) ); } }
void TetrahedralityParamXYZ::process() { Molecule* mol; StuntDouble* sd; StuntDouble* sd2; StuntDouble* sdi; StuntDouble* sdj; RigidBody* rb; int myIndex; SimInfo::MoleculeIterator mi; Molecule::RigidBodyIterator rbIter; Vector3d vec; Vector3d ri, rj, rk, rik, rkj; RealType r; RealType cospsi; RealType Qk; std::vector<std::pair<RealType,StuntDouble*> > myNeighbors; //std::vector<std::pair<Vector3d, RealType> > qvals; //std::vector<std::pair<Vector3d, RealType> >::iterator qiter; int isd1; int isd2; int kMax = int(5.0 * gaussWidth_ / voxelSize_); int kSqLim = kMax*kMax; cerr << "gw = " << gaussWidth_ << " vS = " << voxelSize_ << " kMax = " << kMax << " kSqLim = " << kSqLim << "\n"; DumpReader reader(info_, dumpFilename_); int nFrames = reader.getNFrames(); for (int istep = 0; istep < nFrames; istep += step_) { reader.readFrame(istep); currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); Mat3x3d hmat = currentSnapshot_->getHmat(); Vector3d halfBox = Vector3d(hmat(0,0), hmat(1,1), hmat(2,2)) / 2.0; if (evaluator1_.isDynamic()) { seleMan1_.setSelectionSet(evaluator1_.evaluate()); } if (evaluator2_.isDynamic()) { seleMan2_.setSelectionSet(evaluator2_.evaluate()); } // update the positions of atoms which belong to the rigidbodies for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { rb->updateAtoms(); } } //qvals.clear(); // outer loop is over the selected StuntDoubles: for (sd = seleMan1_.beginSelected(isd1); sd != NULL; sd = seleMan1_.nextSelected(isd1)) { myIndex = sd->getGlobalIndex(); Qk = 1.0; myNeighbors.clear(); for (sd2 = seleMan2_.beginSelected(isd2); sd2 != NULL; sd2 = seleMan2_.nextSelected(isd2)) { if (sd2->getGlobalIndex() != myIndex) { vec = sd->getPos() - sd2->getPos(); if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(vec); r = vec.length(); // Check to see if neighbor is in bond cutoff if (r < rCut_) { myNeighbors.push_back(std::make_pair(r,sd2)); } } } // Sort the vector using predicate and std::sort std::sort(myNeighbors.begin(), myNeighbors.end()); // Use only the 4 closest neighbors to do the rest of the work: int nbors = myNeighbors.size()> 4 ? 4 : myNeighbors.size(); int nang = int (0.5 * (nbors * (nbors - 1))); rk = sd->getPos(); for (int i = 0; i < nbors-1; i++) { sdi = myNeighbors[i].second; ri = sdi->getPos(); rik = rk - ri; if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(rik); rik.normalize(); for (int j = i+1; j < nbors; j++) { sdj = myNeighbors[j].second; rj = sdj->getPos(); rkj = rk - rj; if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(rkj); rkj.normalize(); cospsi = dot(rik,rkj); // Calculates scaled Qk for each molecule using calculated // angles from 4 or fewer nearest neighbors. Qk -= (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang); } } if (nang > 0) { if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(rk); //qvals.push_back(std::make_pair(rk, Qk)); Vector3d pos = rk + halfBox; Vector3i whichVoxel(int(pos[0] / voxelSize_), int(pos[1] / voxelSize_), int(pos[2] / voxelSize_)); for (int l = -kMax; l <= kMax; l++) { for (int m = -kMax; m <= kMax; m++) { for (int n = -kMax; n <= kMax; n++) { int kk = l*l + m*m + n*n; if(kk <= kSqLim) { int ll = (whichVoxel[0] + l) % nBins_(0); ll = ll < 0 ? nBins_(0) + ll : ll; int mm = (whichVoxel[1] + m) % nBins_(1); mm = mm < 0 ? nBins_(1) + mm : mm; int nn = (whichVoxel[2] + n) % nBins_(2); nn = nn < 0 ? nBins_(2) + nn : nn; Vector3d bPos = Vector3d(ll,mm,nn) * voxelSize_ - halfBox; Vector3d d = bPos - rk; currentSnapshot_->wrapVector(d); RealType denom = pow(2.0 * sqrt(M_PI) * gaussWidth_, 3); RealType exponent = -dot(d,d) / pow(2.0*gaussWidth_, 2); RealType weight = exp(exponent) / denom; count_[ll][mm][nn] += weight; hist_[ll][mm][nn] += weight * Qk; } } } } } } // for (int i = 0; i < nBins_(0); ++i) { // for(int j = 0; j < nBins_(1); ++j) { // for(int k = 0; k < nBins_(2); ++k) { // Vector3d pos = Vector3d(i, j, k) * voxelSize_ - halfBox; // for(qiter = qvals.begin(); qiter != qvals.end(); ++qiter) { // Vector3d d = pos - (*qiter).first; // currentSnapshot_->wrapVector(d); // RealType denom = pow(2.0 * sqrt(M_PI) * gaussWidth_, 3); // RealType exponent = -dot(d,d) / pow(2.0*gaussWidth_, 2); // RealType weight = exp(exponent) / denom; // count_[i][j][k] += weight; // hist_[i][j][k] += weight * (*qiter).second; // } // } // } // } } writeQxyz(); }
void TetrahedralityParam::process() { Molecule* mol; StuntDouble* sd; StuntDouble* sd2; StuntDouble* sdi; StuntDouble* sdj; RigidBody* rb; int myIndex; SimInfo::MoleculeIterator mi; Molecule::RigidBodyIterator rbIter; Molecule::IntegrableObjectIterator ioi; Vector3d vec; Vector3d ri, rj, rk, rik, rkj, dposition, tposition; RealType r; RealType cospsi; RealType Qk; std::vector<std::pair<RealType,StuntDouble*> > myNeighbors; int isd; bool usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions(); DumpReader reader(info_, dumpFilename_); int nFrames = reader.getNFrames(); frameCounter_ = 0; Distorted_.clear(); Tetrahedral_.clear(); for (int istep = 0; istep < nFrames; istep += step_) { reader.readFrame(istep); frameCounter_++; currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); if (evaluator_.isDynamic()) { seleMan_.setSelectionSet(evaluator_.evaluate()); } // update the positions of atoms which belong to the rigidbodies for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { rb->updateAtoms(); } } // outer loop is over the selected StuntDoubles: for (sd = seleMan_.beginSelected(isd); sd != NULL; sd = seleMan_.nextSelected(isd)) { myIndex = sd->getGlobalIndex(); Qk = 1.0; myNeighbors.clear(); // inner loop is over all StuntDoubles in the system: for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { for (sd2 = mol->beginIntegrableObject(ioi); sd2 != NULL; sd2 = mol->nextIntegrableObject(ioi)) { if (sd2->getGlobalIndex() != myIndex) { vec = sd->getPos() - sd2->getPos(); if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(vec); r = vec.length(); // Check to see if neighbor is in bond cutoff if (r < rCut_) { myNeighbors.push_back(std::make_pair(r,sd2)); } } } } // Sort the vector using predicate and std::sort std::sort(myNeighbors.begin(), myNeighbors.end()); //std::cerr << myNeighbors.size() << " neighbors within " // << rCut_ << " A" << " \n"; // Use only the 4 closest neighbors to do the rest of the work: int nbors = myNeighbors.size()> 4 ? 4 : myNeighbors.size(); int nang = int (0.5 * (nbors * (nbors - 1))); rk = sd->getPos(); //std::cerr<<nbors<<endl; for (int i = 0; i < nbors-1; i++) { sdi = myNeighbors[i].second; ri = sdi->getPos(); rik = rk - ri; if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(rik); rik.normalize(); for (int j = i+1; j < nbors; j++) { sdj = myNeighbors[j].second; rj = sdj->getPos(); rkj = rk - rj; if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(rkj); rkj.normalize(); cospsi = dot(rik,rkj); //std::cerr << "cos(psi) = " << cospsi << " \n"; // Calculates scaled Qk for each molecule using calculated // angles from 4 or fewer nearest neighbors. Qk = Qk - (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang); //std::cerr<<Qk<<"\t"<<nang<<endl; } } //std::cerr<<nang<<endl; if (nang > 0) { collectHistogram(Qk); // Saves positions of StuntDoubles & neighbors with distorted // coordination (low Qk value) if ((Qk < 0.55) && (Qk > 0.45)) { //std::cerr<<Distorted_.size()<<endl; Distorted_.push_back(sd); //std::cerr<<Distorted_.size()<<endl; dposition = sd->getPos(); //std::cerr << "distorted position \t" << dposition << "\n"; } // Saves positions of StuntDoubles & neighbors with // tetrahedral coordination (high Qk value) if (Qk > 0.05) { Tetrahedral_.push_back(sd); tposition = sd->getPos(); //std::cerr << "tetrahedral position \t" << tposition << "\n"; } //std::cerr<<Tetrahedral_.size()<<endl; } } } writeOrderParameter(); std::cerr << "number of distorted StuntDoubles = " << Distorted_.size() << "\n"; std::cerr << "number of tetrahedral StuntDoubles = " << Tetrahedral_.size() << "\n"; }
void ContactAngle2::doFrame(int frame) { StuntDouble* sd; int i; // set up the bins for density analysis Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat(); RealType len = std::min(hmat(0, 0), hmat(1, 1)); RealType zLen = hmat(2,2); RealType dr = len / (RealType) nRBins_; RealType dz = zLen / (RealType) nZBins_; std::vector<std::vector<RealType> > histo; histo.resize(nRBins_); for (unsigned int i = 0; i < histo.size(); ++i){ histo[i].resize(nZBins_); std::fill(histo[i].begin(), histo[i].end(), 0.0); } if (evaluator1_.isDynamic()) { seleMan1_.setSelectionSet(evaluator1_.evaluate()); } Vector3d com(centroidX_, centroidY_, solidZ_); // now that we have the centroid, we can make cylindrical density maps Vector3d pos; RealType r; RealType z; for (sd = seleMan1_.beginSelected(i); sd != NULL; sd = seleMan1_.nextSelected(i)) { pos = sd->getPos() - com; // r goes from zero upwards r = sqrt(pow(pos.x(), 2) + pow(pos.y(), 2)); // z is possibly symmetric around 0 z = pos.z(); int whichRBin = int(r / dr); int whichZBin = int( (zLen/2.0 + z) / dz); if ((whichRBin < int(nRBins_)) && (whichZBin >= 0) && (whichZBin < int(nZBins_))) { histo[whichRBin][whichZBin] += sd->getMass(); } } for(unsigned int i = 0 ; i < histo.size(); ++i){ RealType rL = i * dr; RealType rU = rL + dr; RealType volSlice = NumericConstant::PI * dz * (( rU*rU ) - ( rL*rL )); for (unsigned int j = 0; j < histo[i].size(); ++j) { histo[i][j] *= PhysicalConstants::densityConvert / volSlice; } } std::vector<Vector<RealType, 2> > points; points.clear(); for (unsigned int j = 0; j < nZBins_; ++j) { // The z coordinates were measured relative to the selection // center of mass. However, we're interested in the elevation // above the solid surface. Also, the binning was done around // zero with enough bins to cover the zLength of the box: RealType thez = com.z() - solidZ_ - zLen/2.0 + dz * (j + 0.5); bool aboveThresh = false; bool foundThresh = false; int rloc = 0; for (std::size_t i = 0; i < nRBins_; ++i) { if (histo[i][j] >= threshDens_) aboveThresh = true; if (aboveThresh && (histo[i][j] <= threshDens_)) { rloc = i; foundThresh = true; aboveThresh = false; } } if (foundThresh) { Vector<RealType,2> point; point[0] = dr*(rloc+0.5); point[1] = thez; if (thez > bufferLength_) { points.push_back( point ); } } } int numPoints = points.size(); // Compute the average of the data points. Vector<RealType, 2> average = points[0]; int i0; for (i0 = 1; i0 < numPoints; ++i0) { average += points[i0]; } RealType invNumPoints = ((RealType)1)/(RealType)numPoints; average *= invNumPoints; DynamicRectMatrix<RealType> mat(4, 4); int row, col; for (row = 0; row < 4; ++row) { for (col = 0; col < 4; ++col){ mat(row,col) = 0.0; } } for (int i = 0; i < numPoints; ++i) { RealType x = points[i][0]; RealType y = points[i][1]; RealType x2 = x*x; RealType y2 = y*y; RealType xy = x*y; RealType r2 = x2+y2; RealType xr2 = x*r2; RealType yr2 = y*r2; RealType r4 = r2*r2; mat(0,1) += x; mat(0,2) += y; mat(0,3) += r2; mat(1,1) += x2; mat(1,2) += xy; mat(1,3) += xr2; mat(2,2) += y2; mat(2,3) += yr2; mat(3,3) += r4; } mat(0,0) = (RealType)numPoints; for (row = 0; row < 4; ++row) { for (col = 0; col < row; ++col) { mat(row,col) = mat(col,row); } } for (row = 0; row < 4; ++row) { for (col = 0; col < 4; ++col) { mat(row,col) *= invNumPoints; } } JAMA::Eigenvalue<RealType> eigensystem(mat); DynamicRectMatrix<RealType> evects(4, 4); DynamicVector<RealType> evals(4); eigensystem.getRealEigenvalues(evals); eigensystem.getV(evects); DynamicVector<RealType> evector = evects.getColumn(0); RealType inv = ((RealType)1)/evector[3]; // beware zero divide RealType coeff[3]; for (row = 0; row < 3; ++row) { coeff[row] = inv*evector[row]; } Vector<RealType, 2> center; center[0] = -((RealType)0.5)*coeff[1]; center[1] = -((RealType)0.5)*coeff[2]; RealType radius = sqrt(fabs(center[0]*center[0] + center[1]*center[1] - coeff[0])); int i1; for (i1 = 0; i1 < 100; ++i1) { // Update the iterates. Vector<RealType, 2> current = center; // Compute average L, dL/da, dL/db. RealType lenAverage = (RealType)0; Vector<RealType, 2> derLenAverage = Vector<RealType, 2>(0.0); for (i0 = 0; i0 < numPoints; ++i0) { Vector<RealType, 2> diff = points[i0] - center; RealType length = diff.length(); if (length > 1e-6) { lenAverage += length; RealType invLength = ((RealType)1)/length; derLenAverage -= invLength*diff; } } lenAverage *= invNumPoints; derLenAverage *= invNumPoints; center = average + lenAverage*derLenAverage; radius = lenAverage; Vector<RealType, 2> diff = center - current; if (fabs(diff[0]) <= 1e-6 && fabs(diff[1]) <= 1e-6) { break; } } RealType zCen = center[1]; RealType rDrop = radius; RealType ca; if (fabs(zCen) > rDrop) { ca = 180.0; } else { ca = 90.0 + asin(zCen/rDrop)*(180.0/M_PI); } values_.push_back( ca ); }
void TetrahedralityParamZ::process() { Molecule* mol; StuntDouble* sd; StuntDouble* sd2; StuntDouble* sdi; StuntDouble* sdj; RigidBody* rb; int myIndex; SimInfo::MoleculeIterator mi; Molecule::RigidBodyIterator rbIter; Vector3d vec; Vector3d ri, rj, rk, rik, rkj; RealType r; RealType cospsi; RealType Qk; std::vector<std::pair<RealType,StuntDouble*> > myNeighbors; int isd1; int isd2; DumpReader reader(info_, dumpFilename_); int nFrames = reader.getNFrames(); for (int istep = 0; istep < nFrames; istep += step_) { reader.readFrame(istep); currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); Mat3x3d hmat = currentSnapshot_->getHmat(); zBox_.push_back(hmat(2,2)); RealType halfBoxZ_ = hmat(2,2) / 2.0; if (evaluator1_.isDynamic()) { seleMan1_.setSelectionSet(evaluator1_.evaluate()); } if (evaluator2_.isDynamic()) { seleMan2_.setSelectionSet(evaluator2_.evaluate()); } // update the positions of atoms which belong to the rigidbodies for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { rb->updateAtoms(); } } // outer loop is over the selected StuntDoubles: for (sd = seleMan1_.beginSelected(isd1); sd != NULL; sd = seleMan1_.nextSelected(isd1)) { myIndex = sd->getGlobalIndex(); Qk = 1.0; myNeighbors.clear(); for (sd2 = seleMan2_.beginSelected(isd2); sd2 != NULL; sd2 = seleMan2_.nextSelected(isd2)) { if (sd2->getGlobalIndex() != myIndex) { vec = sd->getPos() - sd2->getPos(); if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(vec); r = vec.length(); // Check to see if neighbor is in bond cutoff if (r < rCut_) { myNeighbors.push_back(std::make_pair(r,sd2)); } } } // Sort the vector using predicate and std::sort std::sort(myNeighbors.begin(), myNeighbors.end()); // Use only the 4 closest neighbors to do the rest of the work: int nbors = myNeighbors.size()> 4 ? 4 : myNeighbors.size(); int nang = int (0.5 * (nbors * (nbors - 1))); rk = sd->getPos(); for (int i = 0; i < nbors-1; i++) { sdi = myNeighbors[i].second; ri = sdi->getPos(); rik = rk - ri; if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(rik); rik.normalize(); for (int j = i+1; j < nbors; j++) { sdj = myNeighbors[j].second; rj = sdj->getPos(); rkj = rk - rj; if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(rkj); rkj.normalize(); cospsi = dot(rik,rkj); // Calculates scaled Qk for each molecule using calculated // angles from 4 or fewer nearest neighbors. Qk -= (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang); } } if (nang > 0) { if (usePeriodicBoundaryConditions_) currentSnapshot_->wrapVector(rk); int binNo = int(nZBins_ * (halfBoxZ_ + rk.z()) / hmat(2,2)); sliceQ_[binNo] += Qk; sliceCount_[binNo] += 1; } } } writeQz(); }
int main(int argc, char* argv[]){ gengetopt_args_info args_info; string dumpFileName; string outFileName; //parse the command line option if (cmdline_parser (argc, argv, &args_info) != 0) { exit(1) ; } //get the dumpfile name and meta-data file name if (args_info.input_given){ dumpFileName = args_info.input_arg; } else { strcpy( painCave.errMsg, "No input file name was specified.\n" ); painCave.isFatal = 1; simError(); } if (args_info.output_given){ outFileName = args_info.output_arg; } else { strcpy( painCave.errMsg, "No output file name was specified.\n" ); painCave.isFatal = 1; simError(); } Vector3i repeat = Vector3i(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg); Mat3x3d repeatD = Mat3x3d(0.0); repeatD(0,0) = repeat.x(); repeatD(1,1) = repeat.y(); repeatD(2,2) = repeat.z(); Vector3d translate = Vector3d(args_info.translateX_arg, args_info.translateY_arg, args_info.translateZ_arg); //parse md file and set up the system SimCreator oldCreator; SimInfo* oldInfo = oldCreator.createSim(dumpFileName, false); Globals* simParams = oldInfo->getSimParams(); std::vector<Component*> components = simParams->getComponents(); std::vector<int> nMol; for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) { int nMolOld = (*i)->getNMol(); int nMolNew = nMolOld * repeat.x() * repeat.y() * repeat.z(); nMol.push_back(nMolNew); } createMdFile(dumpFileName, outFileName, nMol); SimCreator newCreator; SimInfo* newInfo = newCreator.createSim(outFileName, false); DumpReader* dumpReader = new DumpReader(oldInfo, dumpFileName); int nframes = dumpReader->getNFrames(); DumpWriter* writer = new DumpWriter(newInfo, outFileName); if (writer == NULL) { sprintf(painCave.errMsg, "error in creating DumpWriter"); painCave.isFatal = 1; simError(); } SimInfo::MoleculeIterator miter; Molecule::IntegrableObjectIterator iiter; Molecule::RigidBodyIterator rbIter; Molecule* mol; StuntDouble* sd; StuntDouble* sdNew; RigidBody* rb; Mat3x3d oldHmat; Mat3x3d newHmat; Snapshot* oldSnap; Snapshot* newSnap; Vector3d oldPos; Vector3d newPos; for (int i = 0; i < nframes; i++){ cerr << "frame = " << i << "\n"; dumpReader->readFrame(i); oldSnap = oldInfo->getSnapshotManager()->getCurrentSnapshot(); newSnap = newInfo->getSnapshotManager()->getCurrentSnapshot(); newSnap->setID( oldSnap->getID() ); newSnap->setTime( oldSnap->getTime() ); oldHmat = oldSnap->getHmat(); newHmat = repeatD*oldHmat; newSnap->setHmat(newHmat); newSnap->setThermostat( oldSnap->getThermostat() ); newSnap->setBarostat( oldSnap->getBarostat() ); int newIndex = 0; for (mol = oldInfo->beginMolecule(miter); mol != NULL; mol = oldInfo->nextMolecule(miter)) { for (int ii = 0; ii < repeat.x(); ii++) { for (int jj = 0; jj < repeat.y(); jj++) { for (int kk = 0; kk < repeat.z(); kk++) { Vector3d trans = Vector3d(ii, jj, kk); for (sd = mol->beginIntegrableObject(iiter); sd != NULL; sd = mol->nextIntegrableObject(iiter)) { oldPos = sd->getPos() + translate; oldSnap->wrapVector(oldPos); newPos = oldPos + trans * oldHmat; sdNew = newInfo->getIOIndexToIntegrableObject(newIndex); sdNew->setPos( newPos ); sdNew->setVel( sd->getVel() ); if (sd->isDirectional()) { sdNew->setA( sd->getA() ); sdNew->setJ( sd->getJ() ); } newIndex++; } } } } } //update atoms of rigidbody for (mol = newInfo->beginMolecule(miter); mol != NULL; mol = newInfo->nextMolecule(miter)) { //change the positions of atoms which belong to the rigidbodies for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { rb->updateAtoms(); rb->updateAtomVel(); } } writer->writeDump(); } // deleting the writer will put the closing at the end of the dump file. delete writer; delete oldInfo; }