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);
  }

  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);    
  }

  void P2OrderParameter::process() {
    Molecule* mol;
    RigidBody* rb;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    StuntDouble* sd1;
    StuntDouble* sd2;
    int ii; 
    int jj;
    int vecCount;
 
    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);
      vecCount = 0;

      seleMan1_.setSelectionSet(evaluator1_.evaluate());
      
      if (doVect_) {
        
        for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; 
             sd1 = seleMan1_.nextSelected(ii)) {
          if (sd1->isDirectional()) {
            Vector3d vec = sd1->getA().getColumn(2);
            vec.normalize();
            orderTensor += outProduct(vec, vec);
            vecCount++;
          }
        }
  
        orderTensor /= vecCount;

      } else {

        seleMan2_.setSelectionSet(evaluator2_.evaluate());
            
        if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
          sprintf( painCave.errMsg,
                   "In frame %d, the number of selected StuntDoubles are not\n"
                   "\tthe same in --sele1 and sele2\n", i);
          painCave.severity = OPENMD_INFO;
          painCave.isFatal = 0;
          simError();            
        }
        
        for (sd1 = seleMan1_.beginSelected(ii), 
               sd2 = seleMan2_.beginSelected(jj);
             sd1 != NULL && sd2 != NULL;
             sd1 = seleMan1_.nextSelected(ii), 
               sd2 = seleMan2_.nextSelected(jj)) {

          Vector3d vec = sd1->getPos() - sd2->getPos();

          if (usePeriodicBoundaryConditions_)
            currentSnapshot_->wrapVector(vec);

          vec.normalize();

          orderTensor +=outProduct(vec, vec);
          vecCount++;
        }
      
        orderTensor /= vecCount;
      }
      
      if (vecCount == 0) {
          sprintf( painCave.errMsg,
                   "In frame %d, the number of selected vectors was zero.\n"
                   "\tThis will not give a meaningful order parameter.", i);
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();        
      }

      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;
      vecCount = 0;
      
      if (doVect_) {
        for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; 
             sd1 = seleMan1_.nextSelected(ii)) {
          if (sd1->isDirectional()) {
            Vector3d vec = sd1->getA().getColumn(2);
            vec.normalize();
            angle += acos(dot(vec, director));
            vecCount++;
          }
        }
        angle = angle/(vecCount*NumericConstant::PI)*180.0;
        
      } else {
        for (sd1 = seleMan1_.beginSelected(ii), 
               sd2 = seleMan2_.beginSelected(jj);
             sd1 != NULL && sd2 != NULL;
             sd1 = seleMan1_.nextSelected(ii), 
               sd2 = seleMan2_.nextSelected(jj)) {
          
          Vector3d vec = sd1->getPos() - sd2->getPos();
          if (usePeriodicBoundaryConditions_)
            currentSnapshot_->wrapVector(vec);
          vec.normalize();          
          angle += acos(dot(vec, director)) ;
          vecCount++;
        }
        angle = angle / (vecCount * 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:	1818
Committed:	Wed Dec 12 20:37:29 2012 UTC (12 years, 4 months ago) by gezelter
File size:	8572 byte(s)
Log Message:	Fixed a dynamic selection problem.
#	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	1782	* [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	1542
49			using namespace std;
50	gezelter	1390	namespace OpenMD {
51	gezelter	1078
52	gezelter	1542	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	gezelter	1078
63	gezelter	1542	P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename,
64			const string& sele1, const string& sele2)
65			: StaticAnalyser(info, filename), doVect_(false),
66			selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info),
67			evaluator2_(info), seleMan1_(info), seleMan2_(info) {
68
69	gezelter	1078	setOutputName(getPrefix(filename) + ".p2");
70	gezelter	1542
71	gezelter	1078	evaluator1_.loadScriptString(sele1);
72	gezelter	1817	evaluator2_.loadScriptString(sele2);
73	gezelter	1078	}
74
75			void P2OrderParameter::process() {
76			Molecule* mol;
77			RigidBody* rb;
78			SimInfo::MoleculeIterator mi;
79			Molecule::RigidBodyIterator rbIter;
80	gezelter	1817	StuntDouble* sd1;
81			StuntDouble* sd2;
82			int ii;
83			int jj;
84			int vecCount;
85
86	gezelter	1078	DumpReader reader(info_, dumpFilename_);
87			int nFrames = reader.getNFrames();
88
89			for (int i = 0; i < nFrames; i += step_) {
90			reader.readFrame(i);
91			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
92	gezelter	1543
93	gezelter	1542	for (mol = info_->beginMolecule(mi); mol != NULL;
94			mol = info_->nextMolecule(mi)) {
95	gezelter	1078	//change the positions of atoms which belong to the rigidbodies
96	gezelter	1542	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
97			rb = mol->nextRigidBody(rbIter)) {
98	gezelter	1078	rb->updateAtoms();
99	gezelter	1542	}
100	gezelter	1078	}
101
102			Mat3x3d orderTensor(0.0);
103	gezelter	1817	vecCount = 0;
104	gezelter	1542
105	gezelter	1818	seleMan1_.setSelectionSet(evaluator1_.evaluate());
106	gezelter	1817
107	gezelter	1542	if (doVect_) {
108
109	gezelter	1817	for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
110			sd1 = seleMan1_.nextSelected(ii)) {
111			if (sd1->isDirectional()) {
112			Vector3d vec = sd1->getA().getColumn(2);
113	gezelter	1542	vec.normalize();
114			orderTensor += outProduct(vec, vec);
115	gezelter	1817	vecCount++;
116	gezelter	1542	}
117			}
118
119	gezelter	1817	orderTensor /= vecCount;
120	gezelter	1542
121			} else {
122	gezelter	1817
123	gezelter	1818	seleMan2_.setSelectionSet(evaluator2_.evaluate());
124	gezelter	1542
125	gezelter	1817	if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
126			sprintf( painCave.errMsg,
127			"In frame %d, the number of selected StuntDoubles are not\n"
128			"\tthe same in --sele1 and sele2\n", i);
129			painCave.severity = OPENMD_INFO;
130			painCave.isFatal = 0;
131			simError();
132			}
133
134			for (sd1 = seleMan1_.beginSelected(ii),
135			sd2 = seleMan2_.beginSelected(jj);
136			sd1 != NULL && sd2 != NULL;
137			sd1 = seleMan1_.nextSelected(ii),
138			sd2 = seleMan2_.nextSelected(jj)) {
139
140			Vector3d vec = sd1->getPos() - sd2->getPos();
141
142	gezelter	1542	if (usePeriodicBoundaryConditions_)
143			currentSnapshot_->wrapVector(vec);
144	gezelter	1817
145	gezelter	1542	vec.normalize();
146	gezelter	1817
147	gezelter	1542	orderTensor +=outProduct(vec, vec);
148	gezelter	1817	vecCount++;
149	gezelter	1542	}
150
151	gezelter	1817	orderTensor /= vecCount;
152	gezelter	1078	}
153
154	gezelter	1817	if (vecCount == 0) {
155			sprintf( painCave.errMsg,
156			"In frame %d, the number of selected vectors was zero.\n"
157			"\tThis will not give a meaningful order parameter.", i);
158			painCave.severity = OPENMD_ERROR;
159			painCave.isFatal = 1;
160			simError();
161			}
162	gezelter	1543
163	gezelter	1078	orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity();
164
165			Vector3d eigenvalues;
166			Mat3x3d eigenvectors;
167	gezelter	1543
168	gezelter	1078	Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors);
169
170			int which;
171			RealType maxEval = 0.0;
172			for(int k = 0; k< 3; k++){
173			if(fabs(eigenvalues[k]) > maxEval){
174			which = k;
175			maxEval = fabs(eigenvalues[k]);
176			}
177			}
178			RealType p2 = 1.5 * maxEval;
179
180			//the eigen vector is already normalized in SquareMatrix3::diagonalize
181			Vector3d director = eigenvectors.getColumn(which);
182			if (director[0] < 0) {
183			director.negate();
184			}
185
186			RealType angle = 0.0;
187	gezelter	1817	vecCount = 0;
188	gezelter	1542
189			if (doVect_) {
190	gezelter	1817	for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
191			sd1 = seleMan1_.nextSelected(ii)) {
192			if (sd1->isDirectional()) {
193			Vector3d vec = sd1->getA().getColumn(2);
194	gezelter	1542	vec.normalize();
195	gezelter	1782	angle += acos(dot(vec, director));
196	gezelter	1817	vecCount++;
197	gezelter	1542	}
198			}
199	gezelter	1817	angle = angle/(vecCountNumericConstant::PI)180.0;
200	gezelter	1782
201	gezelter	1542	} else {
202	gezelter	1817	for (sd1 = seleMan1_.beginSelected(ii),
203			sd2 = seleMan2_.beginSelected(jj);
204			sd1 != NULL && sd2 != NULL;
205			sd1 = seleMan1_.nextSelected(ii),
206			sd2 = seleMan2_.nextSelected(jj)) {
207
208			Vector3d vec = sd1->getPos() - sd2->getPos();
209	gezelter	1542	if (usePeriodicBoundaryConditions_)
210			currentSnapshot_->wrapVector(vec);
211	gezelter	1558	vec.normalize();
212	gezelter	1782	angle += acos(dot(vec, director)) ;
213	gezelter	1817	vecCount++;
214	gezelter	1542	}
215	gezelter	1817	angle = angle / (vecCount * NumericConstant::PI) * 180.0;
216	gezelter	1078	}
217
218			OrderParam param;
219			param.p2 = p2;
220			param.director = director;
221			param.angle = angle;
222
223			orderParams_.push_back(param);
224
225			}
226	gezelter	1542
227	gezelter	1078	writeP2();
228	gezelter	1542
229	gezelter	1078	}
230
231			void P2OrderParameter::writeP2() {
232
233	gezelter	1542	ofstream os(getOutputFileName().c_str());
234	gezelter	1078	os << "#radial distribution function\n";
235			os<< "#selection1: (" << selectionScript1_ << ")\t";
236	gezelter	1542	if (!doVect_) {
237			os << "selection2: (" << selectionScript2_ << ")\n";
238			}
239	gezelter	1782	os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
240	gezelter	1078
241	gezelter	1542	for (size_t i = 0; i < orderParams_.size(); ++i) {
242	gezelter	1078	os << orderParams_[i].p2 << "\t"
243			<< orderParams_[i].director[0] << "\t"
244			<< orderParams_[i].director[1] << "\t"
245			<< orderParams_[i].director[2] << "\t"
246	gezelter	1782	<< orderParams_[i].angle << "\n";
247	gezelter	1078
248			}
249
250			}
251
252			}
253