applications/staticProps/P2OrderParameter.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/P2OrderParameter.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"

using namespace std;
namespace OpenMD {

  P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, 
                                     const string& sele1)
    : StaticAnalyser(info, filename), doVect_(true),
      selectionScript1_(sele1), evaluator1_(info), 
      evaluator2_(info), seleMan1_(info), seleMan2_(info) {
    
    setOutputName(getPrefix(filename) + ".p2");
    
    evaluator1_.loadScriptString(sele1);
    
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }
  }

  P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, 
                                     const string& sele1, const string& sele2)
    : StaticAnalyser(info, filename), doVect_(false),
      selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), 
      evaluator2_(info), seleMan1_(info), seleMan2_(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 = 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(make_pair(sd1, sd2));
    } 
  }

  void P2OrderParameter::process() {
    Molecule* mol;
    RigidBody* rb;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    StuntDouble* sd;
    int i, ii;
  
    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);

      if (doVect_) {
        
        if  (evaluator1_.isDynamic()) 
          seleMan1_.setSelectionSet(evaluator1_.evaluate());
        
        for (sd = seleMan1_.beginSelected(ii); sd != NULL; 
             sd = seleMan1_.nextSelected(ii)) {
          if (sd->isDirectional()) {
            Vector3d vec = sd->getA().getColumn(2);
            vec.normalize();
            orderTensor += outProduct(vec, vec);
          }
        }
  
        orderTensor /= seleMan1_.getSelectionCount();

      } else {
            
        for (vector<pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); 
             j != sdPairs_.end(); ++j) {
          Vector3d vec = j->first->getPos() - j->second->getPos();
          if (usePeriodicBoundaryConditions_)
            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;
      
      if (doVect_) {
        for (sd = seleMan1_.beginSelected(ii); sd != NULL; 
             sd = seleMan1_.nextSelected(ii)) {
          if (sd->isDirectional()) {
            Vector3d vec = sd->getA().getColumn(2);
            vec.normalize();
            angle += acos(dot(vec, director));
          }
        }
        angle = angle/(seleMan1_.getSelectionCount()*NumericConstant::PI)*180.0;
        
      } else {
        for (vector<pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
          Vector3d vec = j->first->getPos() - j->second->getPos();
          if (usePeriodicBoundaryConditions_)
            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 P2OrderParameter::writeP2() {

    ofstream os(getOutputFileName().c_str());
    os << "#radial distribution function\n";
    os<< "#selection1: (" << selectionScript1_ << ")\t";
    if (!doVect_) {
      os << "selection2: (" << selectionScript2_ << ")\n";
    }
    os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";    

    for (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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	8785 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	1078	/*
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	gezelter	1078	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	1078	* 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	gezelter	1078	*/
42
43			#include "applications/staticProps/P2OrderParameter.hpp"
44			#include "utils/simError.h"
45			#include "io/DumpReader.hpp"
46			#include "primitives/Molecule.hpp"
47			#include "utils/NumericConstant.hpp"
48	gezelter	1629
49			using namespace std;
50	gezelter	1390	namespace OpenMD {
51	gezelter	1078
52	gezelter	1629	P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename,
53			const string& sele1)
54			: StaticAnalyser(info, filename), doVect_(true),
55			selectionScript1_(sele1), evaluator1_(info),
56			evaluator2_(info), seleMan1_(info), seleMan2_(info) {
57
58			setOutputName(getPrefix(filename) + ".p2");
59
60			evaluator1_.loadScriptString(sele1);
61
62			if (!evaluator1_.isDynamic()) {
63			seleMan1_.setSelectionSet(evaluator1_.evaluate());
64			}
65			}
66	gezelter	1078
67	gezelter	1629	P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename,
68			const string& sele1, const string& sele2)
69			: StaticAnalyser(info, filename), doVect_(false),
70			selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info),
71			evaluator2_(info), seleMan1_(info), seleMan2_(info) {
72
73	gezelter	1078	setOutputName(getPrefix(filename) + ".p2");
74	gezelter	1629
75	gezelter	1078	evaluator1_.loadScriptString(sele1);
76			evaluator2_.loadScriptString(sele2);
77	gezelter	1629
78	gezelter	1078	if (!evaluator1_.isDynamic()) {
79			seleMan1_.setSelectionSet(evaluator1_.evaluate());
80			}else {
81			sprintf( painCave.errMsg,
82			"--sele1 must be static selection\n");
83	gezelter	1390	painCave.severity = OPENMD_ERROR;
84	gezelter	1078	painCave.isFatal = 1;
85			simError();
86			}
87	gezelter	1629
88	gezelter	1078	if (!evaluator2_.isDynamic()) {
89			seleMan2_.setSelectionSet(evaluator2_.evaluate());
90			}else {
91			sprintf( painCave.errMsg,
92			"--sele2 must be static selection\n");
93	gezelter	1390	painCave.severity = OPENMD_ERROR;
94	gezelter	1078	painCave.isFatal = 1;
95			simError();
96			}
97	gezelter	1629
98	gezelter	1078	if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
99			sprintf( painCave.errMsg,
100			"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n");
101	gezelter	1390	painCave.severity = OPENMD_ERROR;
102	gezelter	1078	painCave.isFatal = 1;
103			simError();
104	gezelter	1629
105	gezelter	1078	}
106	gezelter	1629
107	gezelter	1078	int i;
108			int j;
109			StuntDouble* sd1;
110			StuntDouble* sd2;
111			for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
112			sd1 != NULL && sd2 != NULL;
113			sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
114
115	gezelter	1629	sdPairs_.push_back(make_pair(sd1, sd2));
116			}
117	gezelter	1078	}
118
119			void P2OrderParameter::process() {
120			Molecule* mol;
121			RigidBody* rb;
122			SimInfo::MoleculeIterator mi;
123			Molecule::RigidBodyIterator rbIter;
124	gezelter	1629	StuntDouble* sd;
125			int i, ii;
126	gezelter	1078
127			DumpReader reader(info_, dumpFilename_);
128			int nFrames = reader.getNFrames();
129
130			for (int i = 0; i < nFrames; i += step_) {
131			reader.readFrame(i);
132			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
133	gezelter	1629
134			for (mol = info_->beginMolecule(mi); mol != NULL;
135			mol = info_->nextMolecule(mi)) {
136	gezelter	1078	//change the positions of atoms which belong to the rigidbodies
137	gezelter	1629	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
138			rb = mol->nextRigidBody(rbIter)) {
139	gezelter	1078	rb->updateAtoms();
140	gezelter	1629	}
141	gezelter	1078	}
142
143			Mat3x3d orderTensor(0.0);
144	gezelter	1629
145			if (doVect_) {
146
147			if (evaluator1_.isDynamic())
148			seleMan1_.setSelectionSet(evaluator1_.evaluate());
149
150			for (sd = seleMan1_.beginSelected(ii); sd != NULL;
151			sd = seleMan1_.nextSelected(ii)) {
152			if (sd->isDirectional()) {
153			Vector3d vec = sd->getA().getColumn(2);
154			vec.normalize();
155			orderTensor += outProduct(vec, vec);
156			}
157			}
158
159			orderTensor /= seleMan1_.getSelectionCount();
160
161			} else {
162
163			for (vector<pair<StuntDouble, StuntDouble> >::iterator j = sdPairs_.begin();
164			j != sdPairs_.end(); ++j) {
165			Vector3d vec = j->first->getPos() - j->second->getPos();
166			if (usePeriodicBoundaryConditions_)
167			currentSnapshot_->wrapVector(vec);
168			vec.normalize();
169			orderTensor +=outProduct(vec, vec);
170			}
171
172			orderTensor /= sdPairs_.size();
173	gezelter	1078	}
174
175	gezelter	1629
176	gezelter	1078	orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity();
177
178			Vector3d eigenvalues;
179			Mat3x3d eigenvectors;
180	gezelter	1629
181	gezelter	1078	Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors);
182
183			int which;
184			RealType maxEval = 0.0;
185			for(int k = 0; k< 3; k++){
186			if(fabs(eigenvalues[k]) > maxEval){
187			which = k;
188			maxEval = fabs(eigenvalues[k]);
189			}
190			}
191			RealType p2 = 1.5 * maxEval;
192
193			//the eigen vector is already normalized in SquareMatrix3::diagonalize
194			Vector3d director = eigenvectors.getColumn(which);
195			if (director[0] < 0) {
196			director.negate();
197			}
198
199			RealType angle = 0.0;
200	gezelter	1629
201			if (doVect_) {
202			for (sd = seleMan1_.beginSelected(ii); sd != NULL;
203			sd = seleMan1_.nextSelected(ii)) {
204			if (sd->isDirectional()) {
205			Vector3d vec = sd->getA().getColumn(2);
206			vec.normalize();
207			angle += acos(dot(vec, director));
208			}
209			}
210			angle = angle/(seleMan1_.getSelectionCount()NumericConstant::PI)180.0;
211
212			} else {
213			for (vector<pair<StuntDouble, StuntDouble> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
214			Vector3d vec = j->first->getPos() - j->second->getPos();
215			if (usePeriodicBoundaryConditions_)
216			currentSnapshot_->wrapVector(vec);
217			vec.normalize();
218			angle += acos(dot(vec, director)) ;
219			}
220			angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0;
221	gezelter	1078	}
222
223			OrderParam param;
224			param.p2 = p2;
225			param.director = director;
226			param.angle = angle;
227
228			orderParams_.push_back(param);
229
230			}
231	gezelter	1629
232	gezelter	1078	writeP2();
233	gezelter	1629
234	gezelter	1078	}
235
236			void P2OrderParameter::writeP2() {
237
238	gezelter	1629	ofstream os(getOutputFileName().c_str());
239	gezelter	1078	os << "#radial distribution function\n";
240			os<< "#selection1: (" << selectionScript1_ << ")\t";
241	gezelter	1629	if (!doVect_) {
242			os << "selection2: (" << selectionScript2_ << ")\n";
243			}
244	gezelter	1078	os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
245
246	gezelter	1629	for (size_t i = 0; i < orderParams_.size(); ++i) {
247	gezelter	1078	os << orderParams_[i].p2 << "\t"
248			<< orderParams_[i].director[0] << "\t"
249			<< orderParams_[i].director[1] << "\t"
250			<< orderParams_[i].director[2] << "\t"
251			<< orderParams_[i].angle << "\n";
252
253			}
254
255			}
256
257			}
258