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;
}