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;

      if  (evaluator1_.isDynamic()) 
        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 (evaluator2_.isDynamic())
          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:	1817
Committed:	Wed Dec 12 19:05:43 2012 UTC (12 years, 10 months ago) by gezelter
File size:	8650 byte(s)
Log Message:	Updating P2 to handle dynamic selections
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
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
49	using namespace std;
50	namespace OpenMD {
51
52	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
63	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	setOutputName(getPrefix(filename) + ".p2");
70
71	evaluator1_.loadScriptString(sele1);
72	evaluator2_.loadScriptString(sele2);
73	}
74
75	void P2OrderParameter::process() {
76	Molecule* mol;
77	RigidBody* rb;
78	SimInfo::MoleculeIterator mi;
79	Molecule::RigidBodyIterator rbIter;
80	StuntDouble* sd1;
81	StuntDouble* sd2;
82	int ii;
83	int jj;
84	int vecCount;
85
86	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
93	for (mol = info_->beginMolecule(mi); mol != NULL;
94	mol = info_->nextMolecule(mi)) {
95	//change the positions of atoms which belong to the rigidbodies
96	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
97	rb = mol->nextRigidBody(rbIter)) {
98	rb->updateAtoms();
99	}
100	}
101
102	Mat3x3d orderTensor(0.0);
103	vecCount = 0;
104
105	if (evaluator1_.isDynamic())
106	seleMan1_.setSelectionSet(evaluator1_.evaluate());
107
108	if (doVect_) {
109
110	for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
111	sd1 = seleMan1_.nextSelected(ii)) {
112	if (sd1->isDirectional()) {
113	Vector3d vec = sd1->getA().getColumn(2);
114	vec.normalize();
115	orderTensor += outProduct(vec, vec);
116	vecCount++;
117	}
118	}
119
120	orderTensor /= vecCount;
121
122	} else {
123
124	if (evaluator2_.isDynamic())
125	seleMan2_.setSelectionSet(evaluator2_.evaluate());
126
127	if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
128	sprintf( painCave.errMsg,
129	"In frame %d, the number of selected StuntDoubles are not\n"
130	"\tthe same in --sele1 and sele2\n", i);
131	painCave.severity = OPENMD_INFO;
132	painCave.isFatal = 0;
133	simError();
134	}
135
136	for (sd1 = seleMan1_.beginSelected(ii),
137	sd2 = seleMan2_.beginSelected(jj);
138	sd1 != NULL && sd2 != NULL;
139	sd1 = seleMan1_.nextSelected(ii),
140	sd2 = seleMan2_.nextSelected(jj)) {
141
142	Vector3d vec = sd1->getPos() - sd2->getPos();
143
144	if (usePeriodicBoundaryConditions_)
145	currentSnapshot_->wrapVector(vec);
146
147	vec.normalize();
148
149	orderTensor +=outProduct(vec, vec);
150	vecCount++;
151	}
152
153	orderTensor /= vecCount;
154	}
155
156	if (vecCount == 0) {
157	sprintf( painCave.errMsg,
158	"In frame %d, the number of selected vectors was zero.\n"
159	"\tThis will not give a meaningful order parameter.", i);
160	painCave.severity = OPENMD_ERROR;
161	painCave.isFatal = 1;
162	simError();
163	}
164
165	orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity();
166
167	Vector3d eigenvalues;
168	Mat3x3d eigenvectors;
169
170	Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors);
171
172	int which;
173	RealType maxEval = 0.0;
174	for(int k = 0; k< 3; k++){
175	if(fabs(eigenvalues[k]) > maxEval){
176	which = k;
177	maxEval = fabs(eigenvalues[k]);
178	}
179	}
180	RealType p2 = 1.5 * maxEval;
181
182	//the eigen vector is already normalized in SquareMatrix3::diagonalize
183	Vector3d director = eigenvectors.getColumn(which);
184	if (director[0] < 0) {
185	director.negate();
186	}
187
188	RealType angle = 0.0;
189	vecCount = 0;
190
191	if (doVect_) {
192	for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
193	sd1 = seleMan1_.nextSelected(ii)) {
194	if (sd1->isDirectional()) {
195	Vector3d vec = sd1->getA().getColumn(2);
196	vec.normalize();
197	angle += acos(dot(vec, director));
198	vecCount++;
199	}
200	}
201	angle = angle/(vecCountNumericConstant::PI)180.0;
202
203	} else {
204	for (sd1 = seleMan1_.beginSelected(ii),
205	sd2 = seleMan2_.beginSelected(jj);
206	sd1 != NULL && sd2 != NULL;
207	sd1 = seleMan1_.nextSelected(ii),
208	sd2 = seleMan2_.nextSelected(jj)) {
209
210	Vector3d vec = sd1->getPos() - sd2->getPos();
211	if (usePeriodicBoundaryConditions_)
212	currentSnapshot_->wrapVector(vec);
213	vec.normalize();
214	angle += acos(dot(vec, director)) ;
215	vecCount++;
216	}
217	angle = angle / (vecCount * NumericConstant::PI) * 180.0;
218	}
219
220	OrderParam param;
221	param.p2 = p2;
222	param.director = director;
223	param.angle = angle;
224
225	orderParams_.push_back(param);
226
227	}
228
229	writeP2();
230
231	}
232
233	void P2OrderParameter::writeP2() {
234
235	ofstream os(getOutputFileName().c_str());
236	os << "#radial distribution function\n";
237	os<< "#selection1: (" << selectionScript1_ << ")\t";
238	if (!doVect_) {
239	os << "selection2: (" << selectionScript2_ << ")\n";
240	}
241	os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
242
243	for (size_t i = 0; i < orderParams_.size(); ++i) {
244	os << orderParams_[i].p2 << "\t"
245	<< orderParams_[i].director[0] << "\t"
246	<< orderParams_[i].director[1] << "\t"
247	<< orderParams_[i].director[2] << "\t"
248	<< orderParams_[i].angle << "\n";
249
250	}
251
252	}
253
254	}
255