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/*
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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*
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* The University of Notre Dame grants you ("Licensee") a
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* non-exclusive, royalty free, license to use, modify and
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* redistribute this software in source and binary code form, provided
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* that the following conditions are met:
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*
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* 1. Acknowledgement of the program authors must be made in any
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* publication of scientific results based in part on use of the
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* program. An acceptable form of acknowledgement is citation of
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* the article in which the program was described (Matthew
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
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* Parallel Simulation Engine for Molecular Dynamics,"
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* J. Comput. Chem. 26, pp. 252-271 (2005))
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*
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* 2. Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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*
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* 3. Redistributions in binary form must reproduce the above copyright
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* notice, this list of conditions and the following disclaimer in the
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* documentation and/or other materials provided with the
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* distribution.
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*
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* This software is provided "AS IS," without a warranty of any
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* kind. All express or implied conditions, representations and
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* warranties, including any implied warranty of merchantability,
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* fitness for a particular purpose or non-infringement, are hereby
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* excluded. The University of Notre Dame and its licensors shall not
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* be liable for any damages suffered by licensee as a result of
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* using, modifying or distributing the software or its
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* derivatives. In no event will the University of Notre Dame or its
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* licensors be liable for any lost revenue, profit or data, or for
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* direct, indirect, special, consequential, incidental or punitive
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* damages, however caused and regardless of the theory of liability,
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* arising out of the use of or inability to use software, even if the
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* University of Notre Dame has been advised of the possibility of
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* such damages.
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*/
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/* Creates orientational bond order parameters as outlined by
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* Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti
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* Phys Rev B, 28,784,1983
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*
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*/
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#include "applications/staticProps/BondOrderParameter.hpp"
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#include "utils/simError.h"
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#include "io/DumpReader.hpp"
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#include "primitives/Molecule.hpp"
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#include "utils/NumericConstant.hpp"
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#include "math/RealSphericalHarmonic.hpp"
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namespace oopse {
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BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1,
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const std::string& sele2, double rCut, int lNumber)
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: StaticAnalyser(info, filename),
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selectionScript1_(sele1), evaluator1_(info),
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seleMan1_(info){
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setOutputName(getPrefix(filename) + ".obo");
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evaluator1_.loadScriptString(sele1);
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evaluator2_.loadScriptString(sele2);
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if (!evaluator1_.isDynamic()) {
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seleMan1_.setSelectionSet(evaluator1_.evaluate());
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}else {
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sprintf( painCave.errMsg,
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"--sele1 must be static selection\n");
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painCave.severity = OOPSE_ERROR;
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painCave.isFatal = 1;
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simError();
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}
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/* Set up cutoff radius and type of order parameter we are calcuating*/
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lNumber_ = lNumber;
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rCut_ = rCut;
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mSize_ = 2*lNumber_+1;
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int i;
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int j;
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StuntDouble* sd1;
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StuntDouble* sd2;
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for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan1_.beginSelected(j);
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sd1 != NULL && sd2 != NULL;
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sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
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sdPairs_.push_back(std::make_pair(sd1, sd2));
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}
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}
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void BondOrderParameter::process() {
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Molecule* mol;
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RigidBody* rb;
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SimInfo::MoleculeIterator mi;
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Molecule::RigidBodyIterator rbIter;
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RealType theta;
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RealType phi;
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RealType r;
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RealType dist;
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RealType* QBar_lm;
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int nBonds;
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RealSphericalHarmonic sphericalHarmonic;
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DumpReader reader(info_, dumpFilename_);
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int nFrames = reader.getNFrames();
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/*Set the l for the spherical harmonic, it doesn't change*/
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sphericalHarmonic.setL(lNumber_);
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for (int i = 0; i < nFrames; i += step_) {
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reader.readFrame(i);
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
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nBonds = 0;
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
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//change the positions of atoms which belong to the rigidbodies
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
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rb->updateAtoms();
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}
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}
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/* Calculate "bonds" and build Q_lm(r) where Q_lm = Y_lm(theta(r),phi(r)) */
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for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
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Vector3d vec = j->first->getPos() - j->second->getPos();
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currentSnapshot_->wrapVector(vec);
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/* The spherical harmonics are wrt any arbitray coordiate sysetm,
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* we choose standard spherical coordinates */
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r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2));
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/* Check to see if neighbor is in bond cuttoff*/
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if (r<rCut_){
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theta = atan(vec.y()/vec.x());
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phi = acos(vec.z()/r);
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for(int m = -lNumber_; m <= lNumber_; m++){
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sphericalHarmonic.setM(m);
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QBar_lm(m) += sphericalHarmonic.getValueAt(theta,phi);
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}
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nBonds++;
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}
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}
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/*Normalize Qbar*/
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for (int m = -lNumber_;m <= lNumber_; m++){
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QBar_lm(m) = QBar_lm(m)/nBonds;
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}
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}
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/*Normalize by number of frames*/
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for (int m = -lNumber_;m <= lNumber_; m++){
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QBar_lm(m) = QBar_lm(m)/nFrames;
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}
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/* Find second order invariant Q_l*/
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for (int m = -lNumber_;m <= lNumber_; m++){
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QSq_l += pow(QBar_lm(m),2);
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}
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Q_l = sqrt((4*NumericConstant::PI/lNumber_+1)*QSq_l);
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/* Find Third Order Invariant W_l*/
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for (int m = -lNumber_;m<= lNumber_;m++){
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}
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writeOrderParameter();
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}
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void BondOrderParameter::initalizeHistogram() {
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std::fill(histogram_.begin(), histogram_.end(), 0);
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}
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void BondOrderParameter::processHistogram() {
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int nPairs = getNPairs();
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RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
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RealType pairDensity = nPairs /volume * 2.0;
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RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
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for(int i = 0 ; i < histogram_.size(); ++i){
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RealType rLower = i * deltaR_;
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RealType rUpper = rLower + deltaR_;
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RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
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RealType nIdeal = volSlice * pairConstant;
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avgGofr_[i] += histogram_[i] / nIdeal;
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}
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}
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void BondOrderParameter::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
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if (sd1 == sd2) {
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return;
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}
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Vector3d pos1 = sd1->getPos();
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Vector3d pos2 = sd2->getPos();
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Vector3d r12 = pos2 - pos1;
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currentSnapshot_->wrapVector(r12);
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RealType distance = r12.length();
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if (distance < len_) {
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int whichBin = distance / deltaR_;
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histogram_[whichBin] += 2;
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}
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}
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void BondOrderParameter::writeOrderParameter() {
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std::ofstream os(getOutputFileName().c_str());
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os << "#radial distribution function\n";
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os<< "#selection1: (" << selectionScript1_ << ")\t";
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os << "selection2: (" << selectionScript2_ << ")\n";
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os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
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for (std::size_t i = 0; i < orderParams_.size(); ++i) {
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os << orderParams_[i].p2 << "\t"
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<< orderParams_[i].director[0] << "\t"
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<< orderParams_[i].director[1] << "\t"
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<< orderParams_[i].director[2] << "\t"
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<< orderParams_[i].angle << "\n";
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}
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}
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}
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|
