applications/staticProps/RippleOP.cpp

/*
 * 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include "applications/staticProps/RippleOP.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
#include "types/MultipoleAdapter.hpp"
namespace OpenMD {


  RippleOP::RippleOP(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
    : StaticAnalyser(info, filename),
      selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), 
      seleMan1_(info), seleMan2_(info){
    
    setOutputName(getPrefix(filename) + ".rp2");
    
    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 = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();  
    }
    
    if (!evaluator2_.isDynamic()) {
      seleMan2_.setSelectionSet(evaluator2_.evaluate());
    }else {
      sprintf( painCave.errMsg,
               "--sele2 must be static selection\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();  
    }
    
    if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
      sprintf( painCave.errMsg,
               "The number of selected Stuntdoubles are not the same in --sele1 and sele2\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();  

    }
    
    int i;
    int j;
    StuntDouble* sd1;
    StuntDouble* sd2;
    for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
     sd1 != NULL && sd2 != NULL;
         sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
      
      sdPairs_.push_back(std::make_pair(sd1, sd2));
    }
    
  }
  
  void RippleOP::process() {
    Molecule* mol;
    RigidBody* rb;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;

    StuntDouble* j1;
    StuntDouble* j2;
    StuntDouble* sd3;
  
    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();

    for (int i = 0; i < nFrames; i += step_) {
      reader.readFrame(i);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      int nMolecules = info_->getNGlobalMolecules();
      int i1;
      int nUpper=0;
      int nLower=0;
      int nTail=0;
      RealType sumZ = 0.0;
      
      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();
        }
      }      

      for (sd3 = seleMan2_.beginSelected(i1); sd3 != NULL; sd3 = seleMan2_.nextSelected(i1)) {
        Vector3d pos1 = sd3->getPos();
        if (usePeriodicBoundaryConditions_)
          currentSnapshot_->wrapVector(pos1);
        sd3->setPos(pos1);
      }

      for (sd3 = seleMan2_.beginSelected(i1); sd3 != NULL; sd3 = seleMan2_.nextSelected(i1)) {
        Vector3d pos1 = sd3->getPos();
        sumZ += pos1.z();
      }
      RealType avgZ = sumZ / (RealType) nMolecules;
      
      Mat3x3d orderTensorHeadUpper(0.0), orderTensorTail(0.0), orderTensorHeadLower(0.0);
      //      for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
      for (j1 = seleMan1_.beginSelected(i1); j1 != NULL; j1 = seleMan1_.nextSelected(i1)) {
        Vector3d pos = j1->getPos();
        if (usePeriodicBoundaryConditions_)
          currentSnapshot_->wrapVector(pos);
        Vector3d vecHeadUpper;
        if (pos.z() >= avgZ){
          AtomType* atype1 = static_cast<Atom*>(j1)->getAtomType();          
          MultipoleAdapter ma1 = MultipoleAdapter(atype1);
          if (ma1.isDipole())
            vecHeadUpper = j1->getDipole();
          else
            vecHeadUpper = j1->getA().transpose()*V3Z;
          nUpper++;
        }
        Vector3d vecHeadLower;
        if (pos.z() <= avgZ){
          AtomType* atype1 = static_cast<Atom*>(j1)->getAtomType();          
          MultipoleAdapter ma1 = MultipoleAdapter(atype1);
          if (ma1.isDipole())
            vecHeadLower = j1->getDipole();
          else
            vecHeadLower = j1->getA().transpose() * V3Z;
          nLower++;
        }
        orderTensorHeadUpper +=outProduct(vecHeadUpper, vecHeadUpper);
        orderTensorHeadLower +=outProduct(vecHeadLower, vecHeadLower);
      }
      for (j2 = seleMan2_.beginSelected(i1); j2 != NULL; j2 = seleMan2_.nextSelected(i1)) {
        // The lab frame vector corresponding to the body-fixed 
        // z-axis is simply the second column of A.transpose()
        // or, identically, the second row of A itself.

        Vector3d vecTail = j2->getA().getRow(2);
        orderTensorTail +=outProduct(vecTail, vecTail);
        nTail++;
      }
      
      orderTensorHeadUpper /= (RealType) nUpper;
      orderTensorHeadLower /= (RealType) nLower;
      orderTensorHeadUpper -= (RealType)(1.0/3.0) * Mat3x3d::identity();  
      orderTensorHeadLower -= (RealType)(1.0/3.0) * Mat3x3d::identity();  
      
      orderTensorTail /= (RealType) nTail;
      orderTensorTail -= (RealType)(1.0/3.0) * Mat3x3d::identity();  
      
      Vector3d eigenvaluesHeadUpper, eigenvaluesHeadLower, eigenvaluesTail;
      Mat3x3d eigenvectorsHeadUpper, eigenvectorsHeadLower, eigenvectorsTail;    
      Mat3x3d::diagonalize(orderTensorHeadUpper, eigenvaluesHeadUpper, eigenvectorsHeadUpper);
      Mat3x3d::diagonalize(orderTensorHeadLower, eigenvaluesHeadLower, eigenvectorsHeadLower);
      Mat3x3d::diagonalize(orderTensorTail, eigenvaluesTail, eigenvectorsTail);
      
      int whichUpper, whichLower, whichTail;
      RealType maxEvalUpper = 0.0;
      RealType maxEvalLower = 0.0;
      RealType maxEvalTail = 0.0;
      for(int k = 0; k< 3; k++){
        if(fabs(eigenvaluesHeadUpper[k]) > maxEvalUpper){
          whichUpper = k;
          maxEvalUpper = fabs(eigenvaluesHeadUpper[k]);
        }
      }
      RealType p2HeadUpper = 1.5 * maxEvalUpper;
      for(int k = 0; k< 3; k++){
        if(fabs(eigenvaluesHeadLower[k]) > maxEvalLower){
          whichLower = k;
          maxEvalLower = fabs(eigenvaluesHeadLower[k]);
        }
      }
      RealType p2HeadLower = 1.5 * maxEvalLower;
      for(int k = 0; k< 3; k++){
        if(fabs(eigenvaluesTail[k]) > maxEvalTail){
          whichTail = k;
          maxEvalTail = fabs(eigenvaluesTail[k]);
        }
      }
      RealType p2Tail = 1.5 * maxEvalTail;
      
      //the eigen vector is already normalized in SquareMatrix3::diagonalize
      Vector3d directorHeadUpper = eigenvectorsHeadUpper.getColumn(whichUpper);
      if (directorHeadUpper[0] < 0) {
        directorHeadUpper.negate();
      }
      Vector3d directorHeadLower = eigenvectorsHeadLower.getColumn(whichLower);
      if (directorHeadLower[0] < 0) {
        directorHeadLower.negate();
      }
      Vector3d directorTail = eigenvectorsTail.getColumn(whichTail);
      if (directorTail[0] < 0) {
        directorTail.negate();
      }   

      OrderParam paramHeadUpper, paramHeadLower, paramTail;
      paramHeadUpper.p2 = p2HeadUpper;
      paramHeadUpper.director = directorHeadUpper;
      paramHeadLower.p2 = p2HeadLower;
      paramHeadLower.director = directorHeadLower;
      paramTail.p2 = p2Tail;
      paramTail.director = directorTail;
      
      orderParamsHeadUpper_.push_back(paramHeadUpper);
      orderParamsHeadLower_.push_back(paramHeadLower);
      orderParamsTail_.push_back(paramTail);       
      
    }

    OrderParam sumOPHeadUpper, errsumOPHeadUpper;
    OrderParam sumOPHeadLower, errsumOPHeadLower;
    OrderParam sumOPTail, errsumOPTail;

    sumOPHeadUpper.p2 = 0.0;
    errsumOPHeadUpper.p2 = 0.0;
    sumOPHeadLower.p2 = 0.0;
    errsumOPHeadLower.p2 = 0.0;
    for (std::size_t i = 0; i < orderParamsHeadUpper_.size(); ++i) {
      sumOPHeadUpper.p2 += orderParamsHeadUpper_[i].p2;
      sumOPHeadUpper.director[0] += orderParamsHeadUpper_[i].director[0];
      sumOPHeadUpper.director[1] += orderParamsHeadUpper_[i].director[1];
      sumOPHeadUpper.director[2] += orderParamsHeadUpper_[i].director[2];
    }

    avgOPHeadUpper.p2 = sumOPHeadUpper.p2 / (RealType)orderParamsHeadUpper_.size();
    avgOPHeadUpper.director[0] = sumOPHeadUpper.director[0] / (RealType)orderParamsHeadUpper_.size();
    avgOPHeadUpper.director[1] = sumOPHeadUpper.director[1] / (RealType)orderParamsHeadUpper_.size();
    avgOPHeadUpper.director[2] = sumOPHeadUpper.director[2] / (RealType)orderParamsHeadUpper_.size();
    for (std::size_t i = 0; i < orderParamsHeadUpper_.size(); ++i) {
      errsumOPHeadUpper.p2 += pow((orderParamsHeadUpper_[i].p2 - avgOPHeadUpper.p2), 2);
    }
    errOPHeadUpper.p2 = sqrt(errsumOPHeadUpper.p2 / (RealType)orderParamsHeadUpper_.size());
    for (std::size_t i = 0; i < orderParamsHeadLower_.size(); ++i) {
      sumOPHeadLower.p2 += orderParamsHeadLower_[i].p2;
      sumOPHeadLower.director[0] += orderParamsHeadLower_[i].director[0];
      sumOPHeadLower.director[1] += orderParamsHeadLower_[i].director[1];
      sumOPHeadLower.director[2] += orderParamsHeadLower_[i].director[2];
    }

    avgOPHeadLower.p2 = sumOPHeadLower.p2 / (RealType)orderParamsHeadLower_.size();
    avgOPHeadLower.director[0] = sumOPHeadLower.director[0] / (RealType)orderParamsHeadLower_.size();
    avgOPHeadLower.director[1] = sumOPHeadLower.director[1] / (RealType)orderParamsHeadLower_.size();
    avgOPHeadLower.director[2] = sumOPHeadLower.director[2] / (RealType)orderParamsHeadLower_.size();
    for (std::size_t i = 0; i < orderParamsHeadLower_.size(); ++i) {
      errsumOPHeadLower.p2 += pow((orderParamsHeadLower_[i].p2 - avgOPHeadLower.p2), 2);
    }
    errOPHeadLower.p2 = sqrt(errsumOPHeadLower.p2 / (RealType)orderParamsHeadLower_.size());

    sumOPTail.p2 = 0.0;
    errsumOPTail.p2 = 0.0;
    for (std::size_t i = 0; i < orderParamsTail_.size(); ++i) {
      sumOPTail.p2 += orderParamsTail_[i].p2;
      sumOPTail.director[0] += orderParamsTail_[i].director[0];
      sumOPTail.director[1] += orderParamsTail_[i].director[1];
      sumOPTail.director[2] += orderParamsTail_[i].director[2];
    }

    avgOPTail.p2 = sumOPTail.p2 / (RealType)orderParamsTail_.size();
    avgOPTail.director[0] = sumOPTail.director[0] / (RealType)orderParamsTail_.size();
    avgOPTail.director[1] = sumOPTail.director[1] / (RealType)orderParamsTail_.size();
    avgOPTail.director[2] = sumOPTail.director[2] / (RealType)orderParamsTail_.size();
    for (std::size_t i = 0; i < orderParamsTail_.size(); ++i) {
      errsumOPTail.p2 += pow((orderParamsTail_[i].p2 - avgOPTail.p2), 2);
    }
    errOPTail.p2 = sqrt(errsumOPTail.p2 / (RealType)orderParamsTail_.size());
    
    writeP2();
    
  }
  
  void RippleOP::writeP2() {
    
    std::ofstream os(getOutputFileName().c_str());
    os<< "#selection1: (" << selectionScript1_ << ")\n";
    os << "#p2\terror\tdirector_x\tdirector_y\tdiretor_z\n";    
    
    os <<  avgOPHeadUpper.p2 << "\t"
       <<  errOPHeadUpper.p2 << "\t"
       <<  avgOPHeadUpper.director[0] << "\t"
       <<  avgOPHeadUpper.director[1] << "\t"
       <<  avgOPHeadUpper.director[2] << "\n";

    os <<  avgOPHeadLower.p2 << "\t"
       <<  errOPHeadLower.p2 << "\t"
       <<  avgOPHeadLower.director[0] << "\t"
       <<  avgOPHeadLower.director[1] << "\t"
       <<  avgOPHeadLower.director[2] << "\n";
    
    os << "selection2: (" << selectionScript2_ << ")\n";
    os << "#p2\terror\tdirector_x\tdirector_y\tdiretor_z\n";
    
    os <<  avgOPTail.p2 << "\t"
       <<  errOPTail.p2 << "\t"
       <<  avgOPTail.director[0] << "\t"
       <<  avgOPTail.director[1] << "\t"
       <<  avgOPTail.director[2] << "\n";
  }
  
}

Revision:	1787
Committed:	Wed Aug 29 18:13:11 2012 UTC (12 years, 8 months ago) by gezelter
File size:	13816 byte(s)
Log Message:	Massive multipole rewrite
#	User	Rev	Content
1	xsun	980	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	xsun	980	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	xsun	980	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	xsun	980	*/
42
43			#include "applications/staticProps/RippleOP.hpp"
44			#include "utils/simError.h"
45			#include "io/DumpReader.hpp"
46			#include "primitives/Molecule.hpp"
47			#include "utils/NumericConstant.hpp"
48	gezelter	1787	#include "types/MultipoleAdapter.hpp"
49	gezelter	1390	namespace OpenMD {
50	xsun	980
51
52			RippleOP::RippleOP(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
53			: StaticAnalyser(info, filename),
54			selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info),
55			seleMan1_(info), seleMan2_(info){
56
57			setOutputName(getPrefix(filename) + ".rp2");
58
59			evaluator1_.loadScriptString(sele1);
60			evaluator2_.loadScriptString(sele2);
61
62			if (!evaluator1_.isDynamic()) {
63			seleMan1_.setSelectionSet(evaluator1_.evaluate());
64			}else {
65			sprintf( painCave.errMsg,
66			"--sele1 must be static selection\n");
67	gezelter	1390	painCave.severity = OPENMD_ERROR;
68	xsun	980	painCave.isFatal = 1;
69			simError();
70			}
71
72			if (!evaluator2_.isDynamic()) {
73			seleMan2_.setSelectionSet(evaluator2_.evaluate());
74			}else {
75			sprintf( painCave.errMsg,
76			"--sele2 must be static selection\n");
77	gezelter	1390	painCave.severity = OPENMD_ERROR;
78	xsun	980	painCave.isFatal = 1;
79			simError();
80			}
81
82			if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
83			sprintf( painCave.errMsg,
84			"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n");
85	gezelter	1390	painCave.severity = OPENMD_ERROR;
86	xsun	980	painCave.isFatal = 1;
87			simError();
88
89			}
90
91			int i;
92			int j;
93			StuntDouble* sd1;
94			StuntDouble* sd2;
95			for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
96			sd1 != NULL && sd2 != NULL;
97			sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
98
99			sdPairs_.push_back(std::make_pair(sd1, sd2));
100			}
101
102			}
103
104			void RippleOP::process() {
105			Molecule* mol;
106			RigidBody* rb;
107			SimInfo::MoleculeIterator mi;
108			Molecule::RigidBodyIterator rbIter;
109	xsun	1213
110			StuntDouble* j1;
111			StuntDouble* j2;
112			StuntDouble* sd3;
113	xsun	980
114			DumpReader reader(info_, dumpFilename_);
115			int nFrames = reader.getNFrames();
116	xsun	1213
117	xsun	980	for (int i = 0; i < nFrames; i += step_) {
118			reader.readFrame(i);
119			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
120	xsun	1213	int nMolecules = info_->getNGlobalMolecules();
121			int i1;
122			int nUpper=0;
123			int nLower=0;
124			int nTail=0;
125			RealType sumZ = 0.0;
126	xsun	980
127			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
128			//change the positions of atoms which belong to the rigidbodies
129			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
130			rb->updateAtoms();
131			}
132			}
133	xsun	1213
134			for (sd3 = seleMan2_.beginSelected(i1); sd3 != NULL; sd3 = seleMan2_.nextSelected(i1)) {
135			Vector3d pos1 = sd3->getPos();
136			if (usePeriodicBoundaryConditions_)
137			currentSnapshot_->wrapVector(pos1);
138			sd3->setPos(pos1);
139			}
140
141			for (sd3 = seleMan2_.beginSelected(i1); sd3 != NULL; sd3 = seleMan2_.nextSelected(i1)) {
142			Vector3d pos1 = sd3->getPos();
143			sumZ += pos1.z();
144			}
145			RealType avgZ = sumZ / (RealType) nMolecules;
146	xsun	980
147	xsun	1213	Mat3x3d orderTensorHeadUpper(0.0), orderTensorTail(0.0), orderTensorHeadLower(0.0);
148			// for (std::vector<std::pair<StuntDouble, StuntDouble> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
149			for (j1 = seleMan1_.beginSelected(i1); j1 != NULL; j1 = seleMan1_.nextSelected(i1)) {
150			Vector3d pos = j1->getPos();
151			if (usePeriodicBoundaryConditions_)
152			currentSnapshot_->wrapVector(pos);
153			Vector3d vecHeadUpper;
154			if (pos.z() >= avgZ){
155	gezelter	1787	AtomType* atype1 = static_cast<Atom*>(j1)->getAtomType();
156			MultipoleAdapter ma1 = MultipoleAdapter(atype1);
157			if (ma1.isDipole())
158			vecHeadUpper = j1->getDipole();
159			else
160			vecHeadUpper = j1->getA().transpose()*V3Z;
161	xsun	1213	nUpper++;
162			}
163			Vector3d vecHeadLower;
164			if (pos.z() <= avgZ){
165	gezelter	1787	AtomType* atype1 = static_cast<Atom*>(j1)->getAtomType();
166			MultipoleAdapter ma1 = MultipoleAdapter(atype1);
167			if (ma1.isDipole())
168			vecHeadLower = j1->getDipole();
169			else
170			vecHeadLower = j1->getA().transpose() * V3Z;
171	xsun	1213	nLower++;
172			}
173			orderTensorHeadUpper +=outProduct(vecHeadUpper, vecHeadUpper);
174			orderTensorHeadLower +=outProduct(vecHeadLower, vecHeadLower);
175			}
176			for (j2 = seleMan2_.beginSelected(i1); j2 != NULL; j2 = seleMan2_.nextSelected(i1)) {
177			// The lab frame vector corresponding to the body-fixed
178			// z-axis is simply the second column of A.transpose()
179			// or, identically, the second row of A itself.
180
181			Vector3d vecTail = j2->getA().getRow(2);
182	xsun	980	orderTensorTail +=outProduct(vecTail, vecTail);
183	xsun	1213	nTail++;
184	xsun	980	}
185
186	xsun	1213	orderTensorHeadUpper /= (RealType) nUpper;
187			orderTensorHeadLower /= (RealType) nLower;
188			orderTensorHeadUpper -= (RealType)(1.0/3.0) * Mat3x3d::identity();
189			orderTensorHeadLower -= (RealType)(1.0/3.0) * Mat3x3d::identity();
190
191			orderTensorTail /= (RealType) nTail;
192	xsun	980	orderTensorTail -= (RealType)(1.0/3.0) * Mat3x3d::identity();
193
194	xsun	1213	Vector3d eigenvaluesHeadUpper, eigenvaluesHeadLower, eigenvaluesTail;
195			Mat3x3d eigenvectorsHeadUpper, eigenvectorsHeadLower, eigenvectorsTail;
196			Mat3x3d::diagonalize(orderTensorHeadUpper, eigenvaluesHeadUpper, eigenvectorsHeadUpper);
197			Mat3x3d::diagonalize(orderTensorHeadLower, eigenvaluesHeadLower, eigenvectorsHeadLower);
198	xsun	980	Mat3x3d::diagonalize(orderTensorTail, eigenvaluesTail, eigenvectorsTail);
199
200	xsun	1213	int whichUpper, whichLower, whichTail;
201			RealType maxEvalUpper = 0.0;
202			RealType maxEvalLower = 0.0;
203			RealType maxEvalTail = 0.0;
204	xsun	980	for(int k = 0; k< 3; k++){
205	xsun	1213	if(fabs(eigenvaluesHeadUpper[k]) > maxEvalUpper){
206			whichUpper = k;
207			maxEvalUpper = fabs(eigenvaluesHeadUpper[k]);
208	xsun	980	}
209			}
210	xsun	1213	RealType p2HeadUpper = 1.5 * maxEvalUpper;
211	xsun	980	for(int k = 0; k< 3; k++){
212	xsun	1213	if(fabs(eigenvaluesHeadLower[k]) > maxEvalLower){
213			whichLower = k;
214			maxEvalLower = fabs(eigenvaluesHeadLower[k]);
215	xsun	980	}
216			}
217	xsun	1213	RealType p2HeadLower = 1.5 * maxEvalLower;
218			for(int k = 0; k< 3; k++){
219			if(fabs(eigenvaluesTail[k]) > maxEvalTail){
220			whichTail = k;
221			maxEvalTail = fabs(eigenvaluesTail[k]);
222			}
223			}
224			RealType p2Tail = 1.5 * maxEvalTail;
225	xsun	980
226			//the eigen vector is already normalized in SquareMatrix3::diagonalize
227	xsun	1213	Vector3d directorHeadUpper = eigenvectorsHeadUpper.getColumn(whichUpper);
228			if (directorHeadUpper[0] < 0) {
229			directorHeadUpper.negate();
230	xsun	980	}
231	xsun	1213	Vector3d directorHeadLower = eigenvectorsHeadLower.getColumn(whichLower);
232			if (directorHeadLower[0] < 0) {
233			directorHeadLower.negate();
234			}
235			Vector3d directorTail = eigenvectorsTail.getColumn(whichTail);
236	xsun	980	if (directorTail[0] < 0) {
237			directorTail.negate();
238			}
239
240	xsun	1213	OrderParam paramHeadUpper, paramHeadLower, paramTail;
241			paramHeadUpper.p2 = p2HeadUpper;
242			paramHeadUpper.director = directorHeadUpper;
243			paramHeadLower.p2 = p2HeadLower;
244			paramHeadLower.director = directorHeadLower;
245	xsun	980	paramTail.p2 = p2Tail;
246			paramTail.director = directorTail;
247
248	xsun	1213	orderParamsHeadUpper_.push_back(paramHeadUpper);
249			orderParamsHeadLower_.push_back(paramHeadLower);
250	xsun	980	orderParamsTail_.push_back(paramTail);
251
252			}
253
254	xsun	1213	OrderParam sumOPHeadUpper, errsumOPHeadUpper;
255			OrderParam sumOPHeadLower, errsumOPHeadLower;
256	xsun	980	OrderParam sumOPTail, errsumOPTail;
257
258	xsun	1213	sumOPHeadUpper.p2 = 0.0;
259			errsumOPHeadUpper.p2 = 0.0;
260			sumOPHeadLower.p2 = 0.0;
261			errsumOPHeadLower.p2 = 0.0;
262			for (std::size_t i = 0; i < orderParamsHeadUpper_.size(); ++i) {
263			sumOPHeadUpper.p2 += orderParamsHeadUpper_[i].p2;
264			sumOPHeadUpper.director[0] += orderParamsHeadUpper_[i].director[0];
265			sumOPHeadUpper.director[1] += orderParamsHeadUpper_[i].director[1];
266			sumOPHeadUpper.director[2] += orderParamsHeadUpper_[i].director[2];
267	xsun	980	}
268
269	xsun	1213	avgOPHeadUpper.p2 = sumOPHeadUpper.p2 / (RealType)orderParamsHeadUpper_.size();
270			avgOPHeadUpper.director[0] = sumOPHeadUpper.director[0] / (RealType)orderParamsHeadUpper_.size();
271			avgOPHeadUpper.director[1] = sumOPHeadUpper.director[1] / (RealType)orderParamsHeadUpper_.size();
272			avgOPHeadUpper.director[2] = sumOPHeadUpper.director[2] / (RealType)orderParamsHeadUpper_.size();
273			for (std::size_t i = 0; i < orderParamsHeadUpper_.size(); ++i) {
274			errsumOPHeadUpper.p2 += pow((orderParamsHeadUpper_[i].p2 - avgOPHeadUpper.p2), 2);
275	xsun	980	}
276	xsun	1213	errOPHeadUpper.p2 = sqrt(errsumOPHeadUpper.p2 / (RealType)orderParamsHeadUpper_.size());
277			for (std::size_t i = 0; i < orderParamsHeadLower_.size(); ++i) {
278			sumOPHeadLower.p2 += orderParamsHeadLower_[i].p2;
279			sumOPHeadLower.director[0] += orderParamsHeadLower_[i].director[0];
280			sumOPHeadLower.director[1] += orderParamsHeadLower_[i].director[1];
281			sumOPHeadLower.director[2] += orderParamsHeadLower_[i].director[2];
282			}
283	xsun	980
284	xsun	1213	avgOPHeadLower.p2 = sumOPHeadLower.p2 / (RealType)orderParamsHeadLower_.size();
285			avgOPHeadLower.director[0] = sumOPHeadLower.director[0] / (RealType)orderParamsHeadLower_.size();
286			avgOPHeadLower.director[1] = sumOPHeadLower.director[1] / (RealType)orderParamsHeadLower_.size();
287			avgOPHeadLower.director[2] = sumOPHeadLower.director[2] / (RealType)orderParamsHeadLower_.size();
288			for (std::size_t i = 0; i < orderParamsHeadLower_.size(); ++i) {
289			errsumOPHeadLower.p2 += pow((orderParamsHeadLower_[i].p2 - avgOPHeadLower.p2), 2);
290			}
291			errOPHeadLower.p2 = sqrt(errsumOPHeadLower.p2 / (RealType)orderParamsHeadLower_.size());
292
293	xsun	980	sumOPTail.p2 = 0.0;
294			errsumOPTail.p2 = 0.0;
295			for (std::size_t i = 0; i < orderParamsTail_.size(); ++i) {
296			sumOPTail.p2 += orderParamsTail_[i].p2;
297			sumOPTail.director[0] += orderParamsTail_[i].director[0];
298			sumOPTail.director[1] += orderParamsTail_[i].director[1];
299			sumOPTail.director[2] += orderParamsTail_[i].director[2];
300			}
301
302			avgOPTail.p2 = sumOPTail.p2 / (RealType)orderParamsTail_.size();
303			avgOPTail.director[0] = sumOPTail.director[0] / (RealType)orderParamsTail_.size();
304			avgOPTail.director[1] = sumOPTail.director[1] / (RealType)orderParamsTail_.size();
305			avgOPTail.director[2] = sumOPTail.director[2] / (RealType)orderParamsTail_.size();
306			for (std::size_t i = 0; i < orderParamsTail_.size(); ++i) {
307			errsumOPTail.p2 += pow((orderParamsTail_[i].p2 - avgOPTail.p2), 2);
308			}
309			errOPTail.p2 = sqrt(errsumOPTail.p2 / (RealType)orderParamsTail_.size());
310
311			writeP2();
312
313			}
314
315			void RippleOP::writeP2() {
316
317			std::ofstream os(getOutputFileName().c_str());
318			os<< "#selection1: (" << selectionScript1_ << ")\n";
319			os << "#p2\terror\tdirector_x\tdirector_y\tdiretor_z\n";
320
321	xsun	1213	os << avgOPHeadUpper.p2 << "\t"
322			<< errOPHeadUpper.p2 << "\t"
323			<< avgOPHeadUpper.director[0] << "\t"
324			<< avgOPHeadUpper.director[1] << "\t"
325			<< avgOPHeadUpper.director[2] << "\n";
326
327			os << avgOPHeadLower.p2 << "\t"
328			<< errOPHeadLower.p2 << "\t"
329			<< avgOPHeadLower.director[0] << "\t"
330			<< avgOPHeadLower.director[1] << "\t"
331			<< avgOPHeadLower.director[2] << "\n";
332	xsun	980
333			os << "selection2: (" << selectionScript2_ << ")\n";
334			os << "#p2\terror\tdirector_x\tdirector_y\tdiretor_z\n";
335
336			os << avgOPTail.p2 << "\t"
337			<< errOPTail.p2 << "\t"
338			<< avgOPTail.director[0] << "\t"
339			<< avgOPTail.director[1] << "\t"
340			<< avgOPTail.director[2] << "\n";
341			}
342
343			}
344