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, 234107 (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), 
      seleMan1_(info), seleMan2_(info), evaluator1_(info), evaluator2_(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);
      Mat3x3d orderTensorTail(0.0);
      Mat3x3d orderTensorHeadLower(0.0);
      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(-1), whichLower(-1), whichTail(-1);
      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 eigenvector 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:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 7 months ago) by gezelter
File size:	13780 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [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	1879	#include "types/MultipoleAdapter.hpp"
49	gezelter	1390	namespace OpenMD {
50	xsun	980
51	gezelter	2071
52			RippleOP::RippleOP(SimInfo* info, const std::string& filename,
53			const std::string& sele1, const std::string& sele2)
54			: StaticAnalyser(info, filename),
55			selectionScript1_(sele1), selectionScript2_(sele2),
56			seleMan1_(info), seleMan2_(info), evaluator1_(info), evaluator2_(info) {
57	xsun	980
58			setOutputName(getPrefix(filename) + ".rp2");
59
60			evaluator1_.loadScriptString(sele1);
61			evaluator2_.loadScriptString(sele2);
62
63			if (!evaluator1_.isDynamic()) {
64			seleMan1_.setSelectionSet(evaluator1_.evaluate());
65			}else {
66			sprintf( painCave.errMsg,
67			"--sele1 must be static selection\n");
68	gezelter	1390	painCave.severity = OPENMD_ERROR;
69	xsun	980	painCave.isFatal = 1;
70			simError();
71			}
72
73			if (!evaluator2_.isDynamic()) {
74			seleMan2_.setSelectionSet(evaluator2_.evaluate());
75			}else {
76			sprintf( painCave.errMsg,
77			"--sele2 must be static selection\n");
78	gezelter	1390	painCave.severity = OPENMD_ERROR;
79	xsun	980	painCave.isFatal = 1;
80			simError();
81			}
82
83			if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
84			sprintf( painCave.errMsg,
85			"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n");
86	gezelter	1390	painCave.severity = OPENMD_ERROR;
87	xsun	980	painCave.isFatal = 1;
88			simError();
89
90			}
91
92			int i;
93			int j;
94			StuntDouble* sd1;
95			StuntDouble* sd2;
96			for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
97			sd1 != NULL && sd2 != NULL;
98			sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
99
100			sdPairs_.push_back(std::make_pair(sd1, sd2));
101			}
102
103			}
104
105			void RippleOP::process() {
106			Molecule* mol;
107			RigidBody* rb;
108			SimInfo::MoleculeIterator mi;
109			Molecule::RigidBodyIterator rbIter;
110	xsun	1213
111			StuntDouble* j1;
112			StuntDouble* j2;
113			StuntDouble* sd3;
114	xsun	980
115			DumpReader reader(info_, dumpFilename_);
116			int nFrames = reader.getNFrames();
117	xsun	1213
118	xsun	980	for (int i = 0; i < nFrames; i += step_) {
119			reader.readFrame(i);
120			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
121	xsun	1213	int nMolecules = info_->getNGlobalMolecules();
122			int i1;
123			int nUpper=0;
124			int nLower=0;
125			int nTail=0;
126			RealType sumZ = 0.0;
127	xsun	980
128	gezelter	2071	for (mol = info_->beginMolecule(mi); mol != NULL;
129			mol = info_->nextMolecule(mi)) {
130	xsun	980	//change the positions of atoms which belong to the rigidbodies
131	gezelter	2071	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
132			rb = mol->nextRigidBody(rbIter)) {
133	xsun	980	rb->updateAtoms();
134			}
135			}
136	xsun	1213
137	gezelter	2071	for (sd3 = seleMan2_.beginSelected(i1); sd3 != NULL;
138			sd3 = seleMan2_.nextSelected(i1)) {
139	xsun	1213	Vector3d pos1 = sd3->getPos();
140			if (usePeriodicBoundaryConditions_)
141			currentSnapshot_->wrapVector(pos1);
142			sd3->setPos(pos1);
143			}
144
145	gezelter	2071	for (sd3 = seleMan2_.beginSelected(i1); sd3 != NULL;
146			sd3 = seleMan2_.nextSelected(i1)) {
147	xsun	1213	Vector3d pos1 = sd3->getPos();
148			sumZ += pos1.z();
149			}
150			RealType avgZ = sumZ / (RealType) nMolecules;
151	xsun	980
152	gezelter	2071	Mat3x3d orderTensorHeadUpper(0.0);
153			Mat3x3d orderTensorTail(0.0);
154			Mat3x3d orderTensorHeadLower(0.0);
155			for (j1 = seleMan1_.beginSelected(i1); j1 != NULL;
156			j1 = seleMan1_.nextSelected(i1)) {
157	xsun	1213	Vector3d pos = j1->getPos();
158			if (usePeriodicBoundaryConditions_)
159			currentSnapshot_->wrapVector(pos);
160			Vector3d vecHeadUpper;
161			if (pos.z() >= avgZ){
162	gezelter	1879	AtomType* atype1 = static_cast<Atom*>(j1)->getAtomType();
163			MultipoleAdapter ma1 = MultipoleAdapter(atype1);
164			if (ma1.isDipole())
165			vecHeadUpper = j1->getDipole();
166			else
167			vecHeadUpper = j1->getA().transpose()*V3Z;
168	xsun	1213	nUpper++;
169			}
170			Vector3d vecHeadLower;
171			if (pos.z() <= avgZ){
172	gezelter	1879	AtomType* atype1 = static_cast<Atom*>(j1)->getAtomType();
173			MultipoleAdapter ma1 = MultipoleAdapter(atype1);
174			if (ma1.isDipole())
175			vecHeadLower = j1->getDipole();
176			else
177			vecHeadLower = j1->getA().transpose() * V3Z;
178	xsun	1213	nLower++;
179			}
180			orderTensorHeadUpper +=outProduct(vecHeadUpper, vecHeadUpper);
181			orderTensorHeadLower +=outProduct(vecHeadLower, vecHeadLower);
182			}
183	gezelter	2071	for (j2 = seleMan2_.beginSelected(i1); j2 != NULL;
184			j2 = seleMan2_.nextSelected(i1)) {
185	xsun	1213	// The lab frame vector corresponding to the body-fixed
186			// z-axis is simply the second column of A.transpose()
187			// or, identically, the second row of A itself.
188
189			Vector3d vecTail = j2->getA().getRow(2);
190	xsun	980	orderTensorTail +=outProduct(vecTail, vecTail);
191	xsun	1213	nTail++;
192	xsun	980	}
193
194	xsun	1213	orderTensorHeadUpper /= (RealType) nUpper;
195			orderTensorHeadLower /= (RealType) nLower;
196			orderTensorHeadUpper -= (RealType)(1.0/3.0) * Mat3x3d::identity();
197			orderTensorHeadLower -= (RealType)(1.0/3.0) * Mat3x3d::identity();
198
199			orderTensorTail /= (RealType) nTail;
200	xsun	980	orderTensorTail -= (RealType)(1.0/3.0) * Mat3x3d::identity();
201
202	xsun	1213	Vector3d eigenvaluesHeadUpper, eigenvaluesHeadLower, eigenvaluesTail;
203	gezelter	2071	Mat3x3d eigenvectorsHeadUpper, eigenvectorsHeadLower, eigenvectorsTail;
204			Mat3x3d::diagonalize(orderTensorHeadUpper, eigenvaluesHeadUpper,
205			eigenvectorsHeadUpper);
206			Mat3x3d::diagonalize(orderTensorHeadLower, eigenvaluesHeadLower,
207			eigenvectorsHeadLower);
208	xsun	980	Mat3x3d::diagonalize(orderTensorTail, eigenvaluesTail, eigenvectorsTail);
209
210	gezelter	2071	int whichUpper(-1), whichLower(-1), whichTail(-1);
211	xsun	1213	RealType maxEvalUpper = 0.0;
212			RealType maxEvalLower = 0.0;
213			RealType maxEvalTail = 0.0;
214	xsun	980	for(int k = 0; k< 3; k++){
215	xsun	1213	if(fabs(eigenvaluesHeadUpper[k]) > maxEvalUpper){
216			whichUpper = k;
217			maxEvalUpper = fabs(eigenvaluesHeadUpper[k]);
218	xsun	980	}
219			}
220	xsun	1213	RealType p2HeadUpper = 1.5 * maxEvalUpper;
221	xsun	980	for(int k = 0; k< 3; k++){
222	xsun	1213	if(fabs(eigenvaluesHeadLower[k]) > maxEvalLower){
223			whichLower = k;
224			maxEvalLower = fabs(eigenvaluesHeadLower[k]);
225	xsun	980	}
226			}
227	xsun	1213	RealType p2HeadLower = 1.5 * maxEvalLower;
228			for(int k = 0; k< 3; k++){
229			if(fabs(eigenvaluesTail[k]) > maxEvalTail){
230			whichTail = k;
231			maxEvalTail = fabs(eigenvaluesTail[k]);
232			}
233			}
234			RealType p2Tail = 1.5 * maxEvalTail;
235	xsun	980
236	gezelter	2071	//the eigenvector is already normalized in SquareMatrix3::diagonalize
237	xsun	1213	Vector3d directorHeadUpper = eigenvectorsHeadUpper.getColumn(whichUpper);
238			if (directorHeadUpper[0] < 0) {
239			directorHeadUpper.negate();
240	xsun	980	}
241	xsun	1213	Vector3d directorHeadLower = eigenvectorsHeadLower.getColumn(whichLower);
242			if (directorHeadLower[0] < 0) {
243			directorHeadLower.negate();
244			}
245			Vector3d directorTail = eigenvectorsTail.getColumn(whichTail);
246	xsun	980	if (directorTail[0] < 0) {
247			directorTail.negate();
248			}
249
250	xsun	1213	OrderParam paramHeadUpper, paramHeadLower, paramTail;
251			paramHeadUpper.p2 = p2HeadUpper;
252			paramHeadUpper.director = directorHeadUpper;
253			paramHeadLower.p2 = p2HeadLower;
254			paramHeadLower.director = directorHeadLower;
255	xsun	980	paramTail.p2 = p2Tail;
256			paramTail.director = directorTail;
257
258	xsun	1213	orderParamsHeadUpper_.push_back(paramHeadUpper);
259			orderParamsHeadLower_.push_back(paramHeadLower);
260	xsun	980	orderParamsTail_.push_back(paramTail);
261
262			}
263
264	xsun	1213	OrderParam sumOPHeadUpper, errsumOPHeadUpper;
265			OrderParam sumOPHeadLower, errsumOPHeadLower;
266	xsun	980	OrderParam sumOPTail, errsumOPTail;
267
268	xsun	1213	sumOPHeadUpper.p2 = 0.0;
269			errsumOPHeadUpper.p2 = 0.0;
270			sumOPHeadLower.p2 = 0.0;
271			errsumOPHeadLower.p2 = 0.0;
272			for (std::size_t i = 0; i < orderParamsHeadUpper_.size(); ++i) {
273			sumOPHeadUpper.p2 += orderParamsHeadUpper_[i].p2;
274			sumOPHeadUpper.director[0] += orderParamsHeadUpper_[i].director[0];
275			sumOPHeadUpper.director[1] += orderParamsHeadUpper_[i].director[1];
276			sumOPHeadUpper.director[2] += orderParamsHeadUpper_[i].director[2];
277	xsun	980	}
278
279	xsun	1213	avgOPHeadUpper.p2 = sumOPHeadUpper.p2 / (RealType)orderParamsHeadUpper_.size();
280			avgOPHeadUpper.director[0] = sumOPHeadUpper.director[0] / (RealType)orderParamsHeadUpper_.size();
281			avgOPHeadUpper.director[1] = sumOPHeadUpper.director[1] / (RealType)orderParamsHeadUpper_.size();
282			avgOPHeadUpper.director[2] = sumOPHeadUpper.director[2] / (RealType)orderParamsHeadUpper_.size();
283			for (std::size_t i = 0; i < orderParamsHeadUpper_.size(); ++i) {
284			errsumOPHeadUpper.p2 += pow((orderParamsHeadUpper_[i].p2 - avgOPHeadUpper.p2), 2);
285	xsun	980	}
286	xsun	1213	errOPHeadUpper.p2 = sqrt(errsumOPHeadUpper.p2 / (RealType)orderParamsHeadUpper_.size());
287			for (std::size_t i = 0; i < orderParamsHeadLower_.size(); ++i) {
288			sumOPHeadLower.p2 += orderParamsHeadLower_[i].p2;
289			sumOPHeadLower.director[0] += orderParamsHeadLower_[i].director[0];
290			sumOPHeadLower.director[1] += orderParamsHeadLower_[i].director[1];
291			sumOPHeadLower.director[2] += orderParamsHeadLower_[i].director[2];
292			}
293	xsun	980
294	xsun	1213	avgOPHeadLower.p2 = sumOPHeadLower.p2 / (RealType)orderParamsHeadLower_.size();
295			avgOPHeadLower.director[0] = sumOPHeadLower.director[0] / (RealType)orderParamsHeadLower_.size();
296			avgOPHeadLower.director[1] = sumOPHeadLower.director[1] / (RealType)orderParamsHeadLower_.size();
297			avgOPHeadLower.director[2] = sumOPHeadLower.director[2] / (RealType)orderParamsHeadLower_.size();
298			for (std::size_t i = 0; i < orderParamsHeadLower_.size(); ++i) {
299			errsumOPHeadLower.p2 += pow((orderParamsHeadLower_[i].p2 - avgOPHeadLower.p2), 2);
300			}
301			errOPHeadLower.p2 = sqrt(errsumOPHeadLower.p2 / (RealType)orderParamsHeadLower_.size());
302
303	xsun	980	sumOPTail.p2 = 0.0;
304			errsumOPTail.p2 = 0.0;
305			for (std::size_t i = 0; i < orderParamsTail_.size(); ++i) {
306			sumOPTail.p2 += orderParamsTail_[i].p2;
307			sumOPTail.director[0] += orderParamsTail_[i].director[0];
308			sumOPTail.director[1] += orderParamsTail_[i].director[1];
309			sumOPTail.director[2] += orderParamsTail_[i].director[2];
310			}
311
312			avgOPTail.p2 = sumOPTail.p2 / (RealType)orderParamsTail_.size();
313			avgOPTail.director[0] = sumOPTail.director[0] / (RealType)orderParamsTail_.size();
314			avgOPTail.director[1] = sumOPTail.director[1] / (RealType)orderParamsTail_.size();
315			avgOPTail.director[2] = sumOPTail.director[2] / (RealType)orderParamsTail_.size();
316			for (std::size_t i = 0; i < orderParamsTail_.size(); ++i) {
317			errsumOPTail.p2 += pow((orderParamsTail_[i].p2 - avgOPTail.p2), 2);
318			}
319			errOPTail.p2 = sqrt(errsumOPTail.p2 / (RealType)orderParamsTail_.size());
320
321			writeP2();
322
323			}
324
325			void RippleOP::writeP2() {
326
327			std::ofstream os(getOutputFileName().c_str());
328			os<< "#selection1: (" << selectionScript1_ << ")\n";
329			os << "#p2\terror\tdirector_x\tdirector_y\tdiretor_z\n";
330
331	xsun	1213	os << avgOPHeadUpper.p2 << "\t"
332			<< errOPHeadUpper.p2 << "\t"
333			<< avgOPHeadUpper.director[0] << "\t"
334			<< avgOPHeadUpper.director[1] << "\t"
335			<< avgOPHeadUpper.director[2] << "\n";
336
337			os << avgOPHeadLower.p2 << "\t"
338			<< errOPHeadLower.p2 << "\t"
339			<< avgOPHeadLower.director[0] << "\t"
340			<< avgOPHeadLower.director[1] << "\t"
341			<< avgOPHeadLower.director[2] << "\n";
342	xsun	980
343			os << "selection2: (" << selectionScript2_ << ")\n";
344			os << "#p2\terror\tdirector_x\tdirector_y\tdiretor_z\n";
345
346			os << avgOPTail.p2 << "\t"
347			<< errOPTail.p2 << "\t"
348			<< avgOPTail.director[0] << "\t"
349			<< avgOPTail.director[1] << "\t"
350			<< avgOPTail.director[2] << "\n";
351			}
352
353			}
354