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), doOffset_(false),
    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), doOffset_(false),
    selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), 
    evaluator2_(info), seleMan1_(info), seleMan2_(info) {
    
    setOutputName(getPrefix(filename) + ".p2");
    
    evaluator1_.loadScriptString(sele1);
    evaluator2_.loadScriptString(sele2);    
  }

  P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, 
                                     const string& sele1, int seleOffset)
  : StaticAnalyser(info, filename), doVect_(false), doOffset_(true), 
    seleOffset_(seleOffset), selectionScript1_(sele1), evaluator1_(info), 
    evaluator2_(info), seleMan1_(info), seleMan2_(info) {
    
    setOutputName(getPrefix(filename) + ".p2");
    
    evaluator1_.loadScriptString(sele1);
  }

  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 {

        if (doOffset_) {

          for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
               sd1 = seleMan1_.nextSelected(ii)) {

            // This will require careful rewriting if StaticProps is
            // ever parallelized.  For an example, see
            // Thermo::getTaggedAtomPairDistance

            int sd2Index = sd1->getGlobalIndex() + seleOffset_;
            sd2 = info_->getIOIndexToIntegrableObject(sd2Index);
            
            Vector3d vec = sd1->getPos() - sd2->getPos();
            
            if (usePeriodicBoundaryConditions_)
              currentSnapshot_->wrapVector(vec);
            
            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\n"
                     "\tnot the 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 {
        if (doOffset_) {

          for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
               sd1 = seleMan1_.nextSelected(ii)) {
            
            // This will require careful rewriting if StaticProps is
            // ever parallelized.  For an example, see
            // Thermo::getTaggedAtomPairDistance
            
            int sd2Index = sd1->getGlobalIndex() + seleOffset_;
            sd2 = info_->getIOIndexToIntegrableObject(sd2Index);
            
            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;

        } 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:	1831
Committed:	Thu Jan 10 14:06:34 2013 UTC (12 years, 3 months ago) by gezelter
File size:	10870 byte(s)
Log Message:	Merging trunk changes 1812:1830 into development branch.
#	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	gezelter	1831	: StaticAnalyser(info, filename), doVect_(true), doOffset_(false),
55			selectionScript1_(sele1), evaluator1_(info),
56			evaluator2_(info), seleMan1_(info), seleMan2_(info) {
57	gezelter	1629
58			setOutputName(getPrefix(filename) + ".p2");
59
60			evaluator1_.loadScriptString(sele1);
61			}
62	gezelter	1078
63	gezelter	1629	P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename,
64			const string& sele1, const string& sele2)
65	gezelter	1831	: StaticAnalyser(info, filename), doVect_(false), doOffset_(false),
66			selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info),
67			evaluator2_(info), seleMan1_(info), seleMan2_(info) {
68	gezelter	1629
69	gezelter	1078	setOutputName(getPrefix(filename) + ".p2");
70	gezelter	1629
71	gezelter	1078	evaluator1_.loadScriptString(sele1);
72	gezelter	1831	evaluator2_.loadScriptString(sele2);
73			}
74
75			P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename,
76			const string& sele1, int seleOffset)
77			: StaticAnalyser(info, filename), doVect_(false), doOffset_(true),
78			seleOffset_(seleOffset), selectionScript1_(sele1), evaluator1_(info),
79			evaluator2_(info), seleMan1_(info), seleMan2_(info) {
80	gezelter	1629
81	gezelter	1831	setOutputName(getPrefix(filename) + ".p2");
82	gezelter	1629
83	gezelter	1831	evaluator1_.loadScriptString(sele1);
84	gezelter	1078	}
85
86			void P2OrderParameter::process() {
87			Molecule* mol;
88			RigidBody* rb;
89			SimInfo::MoleculeIterator mi;
90			Molecule::RigidBodyIterator rbIter;
91	gezelter	1831	StuntDouble* sd1;
92			StuntDouble* sd2;
93			int ii;
94			int jj;
95			int vecCount;
96
97	gezelter	1078	DumpReader reader(info_, dumpFilename_);
98			int nFrames = reader.getNFrames();
99
100			for (int i = 0; i < nFrames; i += step_) {
101			reader.readFrame(i);
102			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
103	gezelter	1629
104			for (mol = info_->beginMolecule(mi); mol != NULL;
105			mol = info_->nextMolecule(mi)) {
106	gezelter	1078	//change the positions of atoms which belong to the rigidbodies
107	gezelter	1629	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
108			rb = mol->nextRigidBody(rbIter)) {
109	gezelter	1078	rb->updateAtoms();
110	gezelter	1629	}
111	gezelter	1078	}
112
113			Mat3x3d orderTensor(0.0);
114	gezelter	1831	vecCount = 0;
115	gezelter	1629
116	gezelter	1831	seleMan1_.setSelectionSet(evaluator1_.evaluate());
117
118	gezelter	1629	if (doVect_) {
119
120	gezelter	1831	for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
121			sd1 = seleMan1_.nextSelected(ii)) {
122			if (sd1->isDirectional()) {
123			Vector3d vec = sd1->getA().getColumn(2);
124	gezelter	1629	vec.normalize();
125			orderTensor += outProduct(vec, vec);
126	gezelter	1831	vecCount++;
127	gezelter	1629	}
128			}
129
130	gezelter	1831	orderTensor /= vecCount;
131	gezelter	1629
132			} else {
133	gezelter	1831
134			if (doOffset_) {
135
136			for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
137			sd1 = seleMan1_.nextSelected(ii)) {
138
139			// This will require careful rewriting if StaticProps is
140			// ever parallelized. For an example, see
141			// Thermo::getTaggedAtomPairDistance
142
143			int sd2Index = sd1->getGlobalIndex() + seleOffset_;
144			sd2 = info_->getIOIndexToIntegrableObject(sd2Index);
145	gezelter	1629
146	gezelter	1831	Vector3d vec = sd1->getPos() - sd2->getPos();
147
148			if (usePeriodicBoundaryConditions_)
149			currentSnapshot_->wrapVector(vec);
150
151			vec.normalize();
152
153			orderTensor +=outProduct(vec, vec);
154			vecCount++;
155			}
156
157			orderTensor /= vecCount;
158			} else {
159
160			seleMan2_.setSelectionSet(evaluator2_.evaluate());
161
162			if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
163			sprintf( painCave.errMsg,
164			"In frame %d, the number of selected StuntDoubles are\n"
165			"\tnot the same in --sele1 and sele2\n", i);
166			painCave.severity = OPENMD_INFO;
167			painCave.isFatal = 0;
168			simError();
169			}
170
171			for (sd1 = seleMan1_.beginSelected(ii),
172			sd2 = seleMan2_.beginSelected(jj);
173			sd1 != NULL && sd2 != NULL;
174			sd1 = seleMan1_.nextSelected(ii),
175			sd2 = seleMan2_.nextSelected(jj)) {
176
177			Vector3d vec = sd1->getPos() - sd2->getPos();
178
179			if (usePeriodicBoundaryConditions_)
180			currentSnapshot_->wrapVector(vec);
181
182			vec.normalize();
183
184			orderTensor +=outProduct(vec, vec);
185			vecCount++;
186			}
187
188			orderTensor /= vecCount;
189	gezelter	1629	}
190	gezelter	1831	}
191	gezelter	1629
192	gezelter	1831	if (vecCount == 0) {
193			sprintf( painCave.errMsg,
194			"In frame %d, the number of selected vectors was zero.\n"
195			"\tThis will not give a meaningful order parameter.", i);
196			painCave.severity = OPENMD_ERROR;
197			painCave.isFatal = 1;
198			simError();
199	gezelter	1078	}
200	gezelter	1629
201	gezelter	1078	orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity();
202
203			Vector3d eigenvalues;
204			Mat3x3d eigenvectors;
205	gezelter	1629
206	gezelter	1078	Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors);
207
208			int which;
209			RealType maxEval = 0.0;
210			for(int k = 0; k< 3; k++){
211			if(fabs(eigenvalues[k]) > maxEval){
212			which = k;
213			maxEval = fabs(eigenvalues[k]);
214			}
215			}
216			RealType p2 = 1.5 * maxEval;
217
218			//the eigen vector is already normalized in SquareMatrix3::diagonalize
219			Vector3d director = eigenvectors.getColumn(which);
220			if (director[0] < 0) {
221			director.negate();
222			}
223
224			RealType angle = 0.0;
225	gezelter	1831	vecCount = 0;
226	gezelter	1629
227			if (doVect_) {
228	gezelter	1831	for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
229			sd1 = seleMan1_.nextSelected(ii)) {
230			if (sd1->isDirectional()) {
231			Vector3d vec = sd1->getA().getColumn(2);
232	gezelter	1629	vec.normalize();
233			angle += acos(dot(vec, director));
234	gezelter	1831	vecCount++;
235	gezelter	1629	}
236			}
237	gezelter	1831	angle = angle/(vecCountNumericConstant::PI)180.0;
238	gezelter	1629
239			} else {
240	gezelter	1831	if (doOffset_) {
241
242			for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
243			sd1 = seleMan1_.nextSelected(ii)) {
244
245			// This will require careful rewriting if StaticProps is
246			// ever parallelized. For an example, see
247			// Thermo::getTaggedAtomPairDistance
248
249			int sd2Index = sd1->getGlobalIndex() + seleOffset_;
250			sd2 = info_->getIOIndexToIntegrableObject(sd2Index);
251
252			Vector3d vec = sd1->getPos() - sd2->getPos();
253			if (usePeriodicBoundaryConditions_)
254			currentSnapshot_->wrapVector(vec);
255			vec.normalize();
256			angle += acos(dot(vec, director)) ;
257			vecCount++;
258			}
259			angle = angle / (vecCount * NumericConstant::PI) * 180.0;
260
261			} else {
262
263			for (sd1 = seleMan1_.beginSelected(ii),
264			sd2 = seleMan2_.beginSelected(jj);
265			sd1 != NULL && sd2 != NULL;
266			sd1 = seleMan1_.nextSelected(ii),
267			sd2 = seleMan2_.nextSelected(jj)) {
268
269			Vector3d vec = sd1->getPos() - sd2->getPos();
270			if (usePeriodicBoundaryConditions_)
271			currentSnapshot_->wrapVector(vec);
272			vec.normalize();
273			angle += acos(dot(vec, director)) ;
274			vecCount++;
275			}
276			angle = angle / (vecCount * NumericConstant::PI) * 180.0;
277	gezelter	1629	}
278	gezelter	1078	}
279
280			OrderParam param;
281			param.p2 = p2;
282			param.director = director;
283			param.angle = angle;
284
285			orderParams_.push_back(param);
286
287			}
288	gezelter	1629
289	gezelter	1078	writeP2();
290	gezelter	1629
291	gezelter	1078	}
292
293			void P2OrderParameter::writeP2() {
294
295	gezelter	1629	ofstream os(getOutputFileName().c_str());
296	gezelter	1078	os << "#radial distribution function\n";
297			os<< "#selection1: (" << selectionScript1_ << ")\t";
298	gezelter	1629	if (!doVect_) {
299			os << "selection2: (" << selectionScript2_ << ")\n";
300			}
301	gezelter	1078	os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
302
303	gezelter	1629	for (size_t i = 0; i < orderParams_.size(); ++i) {
304	gezelter	1078	os << orderParams_[i].p2 << "\t"
305			<< orderParams_[i].director[0] << "\t"
306			<< orderParams_[i].director[1] << "\t"
307			<< orderParams_[i].director[2] << "\t"
308			<< orderParams_[i].angle << "\n";
309
310			}
311
312			}
313
314			}
315