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.
#	Content
1	/*
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	#include "applications/staticProps/BondOrderParameter.hpp"
43	#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	BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1,
51	const std::string& sele2, double rCut, int lNumber)
52	: StaticAnalyser(info, filename),
53	selectionScript1_(sele1), evaluator1_(info),
54	seleMan1_(info){
55
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	for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan1_.beginSelected(j);
77	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	void BondOrderParameter::process() {
87	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	void BondOrderParameter::writeOrderParameter() {
163
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