applications/staticProps/BondOrderParameter.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. 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<std::pair<StuntDouble*, StuntDouble*> >::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<std::pair<StuntDouble*, StuntDouble*> >::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";

    }

}

}

Revision:	2902
Committed:	Tue Jun 27 16:36:25 2006 UTC (18 years ago) by chuckv
File size:	6479 byte(s)
Log Message:	Beginnings of a order parameter.
#	User	Rev	Content
1	chuckv	2901	/*
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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42	chuckv	2902	#include "applications/staticProps/BondOrderParameter.hpp"
43	chuckv	2901	#include "utils/simError.h"
44			#include "io/DumpReader.hpp"
45			#include "primitives/Molecule.hpp"
46			#include "utils/NumericConstant.hpp"
47			namespace oopse {
48
49
50	chuckv	2902	BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1,
51			const std::string& sele2, double rCut, int lNumber)
52	chuckv	2901	: StaticAnalyser(info, filename),
53	chuckv	2902	selectionScript1_(sele1), evaluator1_(info),
54			seleMan1_(info){
55	chuckv	2901
56			setOutputName(getPrefix(filename) + ".p2");
57
58			evaluator1_.loadScriptString(sele1);
59			evaluator2_.loadScriptString(sele2);
60
61			if (!evaluator1_.isDynamic()) {
62			seleMan1_.setSelectionSet(evaluator1_.evaluate());
63			}else {
64			sprintf( painCave.errMsg,
65			"--sele1 must be static selection\n");
66			painCave.severity = OOPSE_ERROR;
67			painCave.isFatal = 1;
68			simError();
69			}
70
71
72			int i;
73			int j;
74			StuntDouble* sd1;
75			StuntDouble* sd2;
76	chuckv	2902	for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan1_.beginSelected(j);
77	chuckv	2901	sd1 != NULL && sd2 != NULL;
78			sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
79
80			sdPairs_.push_back(std::make_pair(sd1, sd2));
81			}
82
83
84			}
85
86	chuckv	2902	void BondOrderParameter::process() {
87	chuckv	2901	Molecule* mol;
88			RigidBody* rb;
89			SimInfo::MoleculeIterator mi;
90			Molecule::RigidBodyIterator rbIter;
91
92			DumpReader reader(info_, dumpFilename_);
93			int nFrames = reader.getNFrames();
94
95			for (int i = 0; i < nFrames; i += step_) {
96			reader.readFrame(i);
97			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
98
99
100			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
101			//change the positions of atoms which belong to the rigidbodies
102			for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
103			rb->updateAtoms();
104			}
105
106			}
107
108			Mat3x3d orderTensor(0.0);
109			for (std::vector<std::pair<StuntDouble, StuntDouble> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
110			Vector3d vec = j->first->getPos() - j->second->getPos();
111			currentSnapshot_->wrapVector(vec);
112			vec.normalize();
113			orderTensor +=outProduct(vec, vec);
114			}
115
116			orderTensor /= sdPairs_.size();
117			orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity();
118
119			Vector3d eigenvalues;
120			Mat3x3d eigenvectors;
121			Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors);
122
123			int which;
124			RealType maxEval = 0.0;
125			for(int k = 0; k< 3; k++){
126			if(fabs(eigenvalues[k]) > maxEval){
127			which = k;
128			maxEval = fabs(eigenvalues[k]);
129			}
130			}
131			RealType p2 = 1.5 * maxEval;
132
133			//the eigen vector is already normalized in SquareMatrix3::diagonalize
134			Vector3d director = eigenvectors.getColumn(which);
135			if (director[0] < 0) {
136			director.negate();
137			}
138
139			RealType angle = 0.0;
140			for (std::vector<std::pair<StuntDouble, StuntDouble> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
141			Vector3d vec = j->first->getPos() - j->second->getPos();
142			currentSnapshot_->wrapVector(vec);
143			vec.normalize();
144
145			angle += acos(dot(vec, director)) ;
146			}
147			angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0;
148
149			OrderParam param;
150			param.p2 = p2;
151			param.director = director;
152			param.angle = angle;
153
154			orderParams_.push_back(param);
155
156			}
157
158			writeP2();
159
160			}
161
162	chuckv	2902	void BondOrderParameter::writeOrderParameter() {
163	chuckv	2901
164			std::ofstream os(getOutputFileName().c_str());
165			os << "#radial distribution function\n";
166			os<< "#selection1: (" << selectionScript1_ << ")\t";
167			os << "selection2: (" << selectionScript2_ << ")\n";
168			os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
169
170			for (std::size_t i = 0; i < orderParams_.size(); ++i) {
171			os << orderParams_[i].p2 << "\t"
172			<< orderParams_[i].director[0] << "\t"
173			<< orderParams_[i].director[1] << "\t"
174			<< orderParams_[i].director[2] << "\t"
175			<< orderParams_[i].angle << "\n";
176
177			}
178
179			}
180
181			}
182