--- trunk/src/applications/staticProps/BondOrderParameter.cpp 2006/06/27 16:36:25 995 +++ trunk/src/applications/staticProps/BondOrderParameter.cpp 2009/11/25 20:02:06 1390 @@ -1,182 +1,432 @@ -/* - * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. - * - * The University of Notre Dame grants you ("Licensee") a - * non-exclusive, royalty free, license to use, modify and - * redistribute this software in source and binary code form, provided - * that the following conditions are met: - * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright - * notice, this list of conditions and the following disclaimer. - * - * 3. Redistributions in binary form must reproduce the above copyright - * notice, this list of conditions and the following disclaimer in the - * documentation and/or other materials provided with the - * distribution. - * - * This software is provided "AS IS," without a warranty of any - * kind. All express or implied conditions, representations and - * warranties, including any implied warranty of merchantability, - * fitness for a particular purpose or non-infringement, are hereby - * excluded. The University of Notre Dame and its licensors shall not - * be liable for any damages suffered by licensee as a result of - * using, modifying or distributing the software or its - * derivatives. In no event will the University of Notre Dame or its - * licensors be liable for any lost revenue, profit or data, or for - * direct, indirect, special, consequential, incidental or punitive - * damages, however caused and regardless of the theory of liability, - * arising out of the use of or inability to use software, even if the - * University of Notre Dame has been advised of the possibility of - * such damages. - */ - -#include "applications/staticProps/BondOrderParameter.hpp" -#include "utils/simError.h" -#include "io/DumpReader.hpp" -#include "primitives/Molecule.hpp" -#include "utils/NumericConstant.hpp" -namespace oopse { - - -BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, - const std::string& sele2, double rCut, int lNumber) - : StaticAnalyser(info, filename), - selectionScript1_(sele1), evaluator1_(info), - seleMan1_(info){ - - setOutputName(getPrefix(filename) + ".p2"); - - evaluator1_.loadScriptString(sele1); - evaluator2_.loadScriptString(sele2); - - if (!evaluator1_.isDynamic()) { - seleMan1_.setSelectionSet(evaluator1_.evaluate()); - }else { - sprintf( painCave.errMsg, - "--sele1 must be static selection\n"); - painCave.severity = OOPSE_ERROR; - painCave.isFatal = 1; - simError(); - } - - - int i; - int j; - StuntDouble* sd1; - StuntDouble* sd2; - for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan1_.beginSelected(j); - sd1 != NULL && sd2 != NULL; - sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) { - - sdPairs_.push_back(std::make_pair(sd1, sd2)); - } - - - } - -void BondOrderParameter::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(); - } - - } - - Mat3x3d orderTensor(0.0); - for (std::vector >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { - Vector3d vec = j->first->getPos() - j->second->getPos(); - currentSnapshot_->wrapVector(vec); - vec.normalize(); - orderTensor +=outProduct(vec, vec); - } - - orderTensor /= sdPairs_.size(); - orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity(); - - Vector3d eigenvalues; - Mat3x3d eigenvectors; - Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors); - - int which; - RealType maxEval = 0.0; - for(int k = 0; k< 3; k++){ - if(fabs(eigenvalues[k]) > maxEval){ - which = k; - maxEval = fabs(eigenvalues[k]); - } - } - RealType p2 = 1.5 * maxEval; - - //the eigen vector is already normalized in SquareMatrix3::diagonalize - Vector3d director = eigenvectors.getColumn(which); - if (director[0] < 0) { - director.negate(); - } - - RealType angle = 0.0; - for (std::vector >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { - Vector3d vec = j->first->getPos() - j->second->getPos(); - currentSnapshot_->wrapVector(vec); - vec.normalize(); - - angle += acos(dot(vec, director)) ; - } - angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0; - - OrderParam param; - param.p2 = p2; - param.director = director; - param.angle = angle; - - orderParams_.push_back(param); - - } - - writeP2(); - -} - -void BondOrderParameter::writeOrderParameter() { - - std::ofstream os(getOutputFileName().c_str()); - os << "#radial distribution function\n"; - os<< "#selection1: (" << selectionScript1_ << ")\t"; - os << "selection2: (" << selectionScript2_ << ")\n"; - os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; - - for (std::size_t i = 0; i < orderParams_.size(); ++i) { - os << orderParams_[i].p2 << "\t" - << orderParams_[i].director[0] << "\t" - << orderParams_[i].director[1] << "\t" - << orderParams_[i].director[2] << "\t" - << orderParams_[i].angle << "\n"; - - } - -} - -} - +/* + * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. + * + * The University of Notre Dame grants you ("Licensee") a + * non-exclusive, royalty free, license to use, modify and + * redistribute this software in source and binary code form, provided + * that the following conditions are met: + * + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * + * 2. Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the + * distribution. + * + * This software is provided "AS IS," without a warranty of any + * kind. All express or implied conditions, representations and + * warranties, including any implied warranty of merchantability, + * fitness for a particular purpose or non-infringement, are hereby + * excluded. The University of Notre Dame and its licensors shall not + * be liable for any damages suffered by licensee as a result of + * using, modifying or distributing the software or its + * derivatives. In no event will the University of Notre Dame or its + * licensors be liable for any lost revenue, profit or data, or for + * direct, indirect, special, consequential, incidental or punitive + * damages, however caused and regardless of the theory of liability, + * arising out of the use of or inability to use software, even if the + * University of Notre Dame has been advised of the possibility of + * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Vardeman & Gezelter, in progress (2009). + * + * Created by J. Daniel Gezelter on 09/26/06. + * @author J. Daniel Gezelter + * @version $Id: BondOrderParameter.cpp,v 1.23 2009-11-25 20:01:59 gezelter Exp $ + * + */ + +#include "applications/staticProps/BondOrderParameter.hpp" +#include "utils/simError.h" +#include "io/DumpReader.hpp" +#include "primitives/Molecule.hpp" +#include "utils/NumericConstant.hpp" + +namespace OpenMD { + + BondOrderParameter::BondOrderParameter(SimInfo* info, + const std::string& filename, + const std::string& sele, + double rCut, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ + + setOutputName(getPrefix(filename) + ".bo"); + + evaluator_.loadScriptString(sele); + if (!evaluator_.isDynamic()) { + seleMan_.setSelectionSet(evaluator_.evaluate()); + } + + // Set up cutoff radius and order of the Legendre Polynomial: + + rCut_ = rCut; + nBins_ = nbins; + Qcount_.resize(lMax_+1); + Wcount_.resize(lMax_+1); + + // Q can take values from 0 to 1 + + MinQ_ = 0.0; + MaxQ_ = 1.1; + deltaQ_ = (MaxQ_ - MinQ_) / nbins; + + // W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll + // use values for MinW_ and MaxW_ that are slightly larger than this: + + MinW_ = -1.1; + MaxW_ = 1.1; + deltaW_ = (MaxW_ - MinW_) / nbins; + + // Make arrays for Wigner3jm + double* THRCOF = new double[2*lMax_+1]; + // Variables for Wigner routine + double lPass, m1Pass, m2m, m2M; + int error, mSize; + mSize = 2*lMax_+1; + + for (int l = 0; l <= lMax_; l++) { + lPass = (double)l; + for (int m1 = -l; m1 <= l; m1++) { + m1Pass = (double)m1; + + std::pair lm = std::make_pair(l, m1); + + // Zero work array + for (int ii = 0; ii < 2*l + 1; ii++){ + THRCOF[ii] = 0.0; + } + + // Get Wigner coefficients + Wigner3jm(&lPass, &lPass, &lPass, + &m1Pass, &m2m, &m2M, + THRCOF, &mSize, &error); + + m2Min[lm] = (int)floor(m2m); + m2Max[lm] = (int)floor(m2M); + + for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) { + w3j[lm].push_back(THRCOF[mmm]); + } + } + } + delete [] THRCOF; + THRCOF = NULL; + } + + BondOrderParameter::~BondOrderParameter() { + Q_histogram_.clear(); + W_histogram_.clear(); + for (int l = 0; l <= lMax_; l++) { + for (int m = -l; m <= l; m++) { + w3j[std::make_pair(l,m)].clear(); + } + } + w3j.clear(); + m2Min.clear(); + m2Max.clear(); + } + + void BondOrderParameter::initalizeHistogram() { + for (int bin = 0; bin < nBins_; bin++) { + for (int l = 0; l <= lMax_; l++) { + Q_histogram_[std::make_pair(bin,l)] = 0; + W_histogram_[std::make_pair(bin,l)] = 0; + } + } + } + + void BondOrderParameter::process() { + Molecule* mol; + Atom* atom; + RigidBody* rb; + int myIndex; + SimInfo::MoleculeIterator mi; + Molecule::RigidBodyIterator rbIter; + Molecule::AtomIterator ai; + StuntDouble* sd; + Vector3d vec; + RealType costheta; + RealType phi; + RealType r; + RealType dist; + std::map,ComplexType> q; + std::vector q_l; + std::vector q2; + std::vector w; + std::vector w_hat; + std::map,ComplexType> QBar; + std::vector Q2; + std::vector Q; + std::vector W; + std::vector W_hat; + int nBonds, Nbonds; + SphericalHarmonic sphericalHarmonic; + int i, j; + + DumpReader reader(info_, dumpFilename_); + int nFrames = reader.getNFrames(); + frameCounter_ = 0; + + q_l.resize(lMax_+1); + q2.resize(lMax_+1); + w.resize(lMax_+1); + w_hat.resize(lMax_+1); + + Q2.resize(lMax_+1); + Q.resize(lMax_+1); + W.resize(lMax_+1); + W_hat.resize(lMax_+1); + Nbonds = 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; + + for (int l = 0; l <= lMax_; l++) { + for (int m = -l; m <= l; m++) { + q[std::make_pair(l,m)] = 0.0; + } + } + + // 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 build Q_lm(r) where + // Q_lm = Y_lm(theta(r),phi(r)) + // The spherical harmonics are wrt any arbitrary coordinate + // system, we choose standard spherical coordinates + + r = vec.length(); + + // Check to see if neighbor is in bond cutoff + + if (r < rCut_) { + costheta = vec.z() / r; + phi = atan2(vec.y(), vec.x()); + + for (int l = 0; l <= lMax_; l++) { + sphericalHarmonic.setL(l); + for(int m = -l; m <= l; m++){ + sphericalHarmonic.setM(m); + q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); + } + } + nBonds++; + } + } + } + } + + + for (int l = 0; l <= lMax_; l++) { + q2[l] = 0.0; + for (int m = -l; m <= l; m++){ + q[std::make_pair(l,m)] /= (RealType)nBonds; + q2[l] += norm(q[std::make_pair(l,m)]); + } + q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); + } + + // Find Third Order Invariant W_l + + for (int l = 0; l <= lMax_; l++) { + w[l] = 0.0; + for (int m1 = -l; m1 <= l; m1++) { + std::pair lm = std::make_pair(l, m1); + for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { + int m2 = m2Min[lm] + mmm; + int m3 = -m1-m2; + w[l] += w3j[lm][mmm] * q[lm] * + q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)]; + } + } + + w_hat[l] = w[l] / pow(q2[l], 1.5); + } + + collectHistogram(q_l, w_hat); + + Nbonds += nBonds; + for (int l = 0; l <= lMax_; l++) { + for (int m = -l; m <= l; m++) { + QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)]; + } + } + } + } + + // Normalize Qbar2 + for (int l = 0; l <= lMax_; l++) { + for (int m = -l; m <= l; m++){ + QBar[std::make_pair(l,m)] /= Nbonds; + } + } + + // Find second order invariant Q_l + + for (int l = 0; l <= lMax_; l++) { + Q2[l] = 0.0; + for (int m = -l; m <= l; m++){ + Q2[l] += norm(QBar[std::make_pair(l,m)]); + } + Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); + } + + // Find Third Order Invariant W_l + + for (int l = 0; l <= lMax_; l++) { + W[l] = 0.0; + for (int m1 = -l; m1 <= l; m1++) { + std::pair lm = std::make_pair(l, m1); + for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { + int m2 = m2Min[lm] + mmm; + int m3 = -m1-m2; + W[l] += w3j[lm][mmm] * QBar[lm] * + QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)]; + } + } + + W_hat[l] = W[l] / pow(Q2[l], 1.5); + } + + writeOrderParameter(Q, W_hat); + } + + void BondOrderParameter::collectHistogram(std::vector q, + std::vector what) { + + for (int l = 0; l <= lMax_; l++) { + if (q[l] >= MinQ_ && q[l] < MaxQ_) { + int qbin = (q[l] - MinQ_) / deltaQ_; + Q_histogram_[std::make_pair(qbin,l)] += 1; + Qcount_[l]++; + } else { + sprintf( painCave.errMsg, + "q_l value outside reasonable range\n"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + } + + for (int l = 0; l <= lMax_; l++) { + if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) { + int wbin = (real(what[l]) - MinW_) / deltaW_; + W_histogram_[std::make_pair(wbin,l)] += 1; + Wcount_[l]++; + } else { + sprintf( painCave.errMsg, + "Re[w_hat] value (%lf) outside reasonable range\n", real(what[l])); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + } + + } + + + void BondOrderParameter::writeOrderParameter(std::vector Q, + std::vector What) { + + std::ofstream osq((getOutputFileName() + "q").c_str()); + + if (osq.is_open()) { + + osq << "# Bond Order Parameters\n"; + osq << "# selection: (" << selectionScript_ << ")\n"; + osq << "# \n"; + for (int l = 0; l <= lMax_; l++) { + osq << "# : " << Q[l] << "\n"; + } + // Normalize by number of frames and write it out: + for (int i = 0; i < nBins_; ++i) { + RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; + osq << Qval; + for (int l = 0; l <= lMax_; l++) { + + osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_; + } + osq << "\n"; + } + + osq.close(); + + } else { + sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", + (getOutputFileName() + "q").c_str()); + painCave.isFatal = 1; + simError(); + } + + std::ofstream osw((getOutputFileName() + "w").c_str()); + + if (osw.is_open()) { + osw << "# Bond Order Parameters\n"; + osw << "# selection: (" << selectionScript_ << ")\n"; + osw << "# \n"; + for (int l = 0; l <= lMax_; l++) { + osw << "# : " << real(What[l]) << "\t" << imag(What[l]) << "\n"; + } + // Normalize by number of frames and write it out: + for (int i = 0; i < nBins_; ++i) { + RealType Wval = MinW_ + (i + 0.5) * deltaW_; + osw << Wval; + for (int l = 0; l <= lMax_; l++) { + + osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_; + } + osw << "\n"; + } + + osw.close(); + } else { + sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", + (getOutputFileName() + "w").c_str()); + painCave.isFatal = 1; + simError(); + } + + } +}