applications/staticProps/BondAngleDistribution.cpp

/*
 * Copyright (c) 2007 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]  Vardeman & Gezelter, in progress (2009).                        
 *
 *  Created by J. Daniel Gezelter on 07/27/07.
 *  @author  J. Daniel Gezelter
 *  @version $Id: BondAngleDistribution.cpp,v 1.2 2009-11-25 20:01:59 gezelter Exp $
 *
 */
 
#include "applications/staticProps/BondAngleDistribution.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"

namespace OpenMD {

  BondAngleDistribution::BondAngleDistribution(SimInfo* info, 
                                              const std::string& filename, 
                                              const std::string& sele,
                                              double rCut, int nbins) : StaticAnalyser(info, filename), 
                                              selectionScript_(sele), 
                                                                evaluator_(info), seleMan_(info){
    
    setOutputName(getPrefix(filename) + ".bad");
    
    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
    
    // Set up cutoff radius and order of the Legendre Polynomial:

    rCut_ = rCut;
    nBins_ = nbins;


    // Theta can take values from 0 to 180    
    deltaTheta_ = (180.0) / nBins_;
    histogram_.resize(nBins_);
  }
  
  BondAngleDistribution::~BondAngleDistribution() {
    histogram_.clear();
  }
  
  void BondAngleDistribution::initalizeHistogram() {
    for (int bin = 0; bin < nBins_; bin++) {      
      histogram_[bin] = 0;
    }
  }
  
  void BondAngleDistribution::process() {
    Molecule* mol;
    Atom* atom;
    RigidBody* rb;
    int myIndex;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Molecule::AtomIterator ai;
    StuntDouble* sd;
    Vector3d vec;
    std::vector<Vector3d> bondvec;
    std::vector<RealType> bonddist;
    RealType costheta;
    RealType r;
    RealType dist;
    
    int nBonds;
    
    int i, j;
    
    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();
    frameCounter_ = 0;
    
    nTotBonds_ = 0;
    
    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      frameCounter_++;
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      
      if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
      }

      // update the positions of atoms which belong to the rigidbodies
      
      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
             rb = mol->nextRigidBody(rbIter)) {
          rb->updateAtoms();
        }        
      }           
            
      // outer loop is over the selected StuntDoubles:

      for (sd = seleMan_.beginSelected(i); sd != NULL; 
           sd = seleMan_.nextSelected(i)) {

        myIndex = sd->getGlobalIndex();
        nBonds = 0;
        bondvec.clear();
        
        // inner loop is over all other atoms in the system:
        
        for (mol = info_->beginMolecule(mi); mol != NULL; 
             mol = info_->nextMolecule(mi)) {
          for (atom = mol->beginAtom(ai); atom != NULL; 
               atom = mol->nextAtom(ai)) {

            if (atom->getGlobalIndex() != myIndex) {

              vec = sd->getPos() - atom->getPos();       

              if (usePeriodicBoundaryConditions_) 
                currentSnapshot_->wrapVector(vec);
              
              // Calculate "bonds" and make a pair list 
              
              r = vec.length();
              
              // Check to see if neighbor is in bond cutoff 
              
              if (r < rCut_) { 
                // Add neighbor to bond list's
                bondvec.push_back(vec);
                nBonds++;
                nTotBonds_++;
              }  
            }
          }
          
          
          for (int i = 0; i < nBonds-1; i++ ){
            Vector3d vec1 = bondvec[i];
            vec1.normalize();
            for(int j = i+1; j < nBonds; j++){
              Vector3d vec2 = bondvec[j];
              
              vec2.normalize();
             
              RealType theta = acos(dot(vec1,vec2))*180.0/NumericConstant::PI;
               
              
              if (theta > 180.0){
                theta = 360.0 - theta;
              }
              int whichBin = theta/deltaTheta_;
              
              histogram_[whichBin] += 2;
            }
          }           
              }
      }
    }
    
    
    writeBondAngleDistribution();    
  }
  

  void BondAngleDistribution::writeBondAngleDistribution() {
    
    std::ofstream osbad(getOutputFileName().c_str());


    RealType norm = (RealType)nTotBonds_*((RealType)nTotBonds_-1.0)/2.0;
    if (osbad.is_open()) {
      
      // Normalize by number of frames and write it out:
      for (int i = 0; i < nBins_; ++i) {
        RealType Thetaval = i * deltaTheta_;               
        osbad << Thetaval;        
        osbad << "\t" << (RealType)histogram_[i]/norm/frameCounter_;
        
        osbad << "\n";
      }

      osbad.close();

    } else {
      sprintf(painCave.errMsg, "BondAngleDistribution: unable to open %s\n", 
              (getOutputFileName() + "q").c_str());
      painCave.isFatal = 1;
      simError();  
    }
       
  }
    }
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/applications/staticProps/BondAngleDistribution.cpp*
File size:	7500 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	chuckv	1180	/*
2			* Copyright (c) 2007 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	chuckv	1180	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	1180	* 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	gezelter	1390	* 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] Vardeman & Gezelter, in progress (2009).
40	chuckv	1180	*
41			* Created by J. Daniel Gezelter on 07/27/07.
42			* @author J. Daniel Gezelter
43	gezelter	1390	* @version $Id: BondAngleDistribution.cpp,v 1.2 2009-11-25 20:01:59 gezelter Exp $
44	chuckv	1180	*
45			*/
46
47			#include "applications/staticProps/BondAngleDistribution.hpp"
48			#include "utils/simError.h"
49			#include "io/DumpReader.hpp"
50			#include "primitives/Molecule.hpp"
51			#include "utils/NumericConstant.hpp"
52
53	gezelter	1390	namespace OpenMD {
54	chuckv	1180
55			BondAngleDistribution::BondAngleDistribution(SimInfo* info,
56			const std::string& filename,
57			const std::string& sele,
58			double rCut, int nbins) : StaticAnalyser(info, filename),
59			selectionScript_(sele),
60			evaluator_(info), seleMan_(info){
61
62			setOutputName(getPrefix(filename) + ".bad");
63
64			evaluator_.loadScriptString(sele);
65			if (!evaluator_.isDynamic()) {
66			seleMan_.setSelectionSet(evaluator_.evaluate());
67			}
68
69			// Set up cutoff radius and order of the Legendre Polynomial:
70
71			rCut_ = rCut;
72			nBins_ = nbins;
73
74
75			// Theta can take values from 0 to 180
76			deltaTheta_ = (180.0) / nBins_;
77			histogram_.resize(nBins_);
78			}
79
80			BondAngleDistribution::~BondAngleDistribution() {
81			histogram_.clear();
82			}
83
84			void BondAngleDistribution::initalizeHistogram() {
85			for (int bin = 0; bin < nBins_; bin++) {
86			histogram_[bin] = 0;
87			}
88			}
89
90			void BondAngleDistribution::process() {
91			Molecule* mol;
92			Atom* atom;
93			RigidBody* rb;
94			int myIndex;
95			SimInfo::MoleculeIterator mi;
96			Molecule::RigidBodyIterator rbIter;
97			Molecule::AtomIterator ai;
98			StuntDouble* sd;
99			Vector3d vec;
100			std::vector<Vector3d> bondvec;
101			std::vector<RealType> bonddist;
102			RealType costheta;
103			RealType r;
104			RealType dist;
105
106			int nBonds;
107
108			int i, j;
109
110			DumpReader reader(info_, dumpFilename_);
111			int nFrames = reader.getNFrames();
112			frameCounter_ = 0;
113
114			nTotBonds_ = 0;
115
116			for (int istep = 0; istep < nFrames; istep += step_) {
117			reader.readFrame(istep);
118			frameCounter_++;
119			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
120
121			if (evaluator_.isDynamic()) {
122			seleMan_.setSelectionSet(evaluator_.evaluate());
123			}
124
125			// update the positions of atoms which belong to the rigidbodies
126
127			for (mol = info_->beginMolecule(mi); mol != NULL;
128			mol = info_->nextMolecule(mi)) {
129			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
130			rb = mol->nextRigidBody(rbIter)) {
131			rb->updateAtoms();
132			}
133			}
134
135			// outer loop is over the selected StuntDoubles:
136
137			for (sd = seleMan_.beginSelected(i); sd != NULL;
138			sd = seleMan_.nextSelected(i)) {
139
140			myIndex = sd->getGlobalIndex();
141			nBonds = 0;
142			bondvec.clear();
143
144			// inner loop is over all other atoms in the system:
145
146			for (mol = info_->beginMolecule(mi); mol != NULL;
147			mol = info_->nextMolecule(mi)) {
148			for (atom = mol->beginAtom(ai); atom != NULL;
149			atom = mol->nextAtom(ai)) {
150
151			if (atom->getGlobalIndex() != myIndex) {
152
153			vec = sd->getPos() - atom->getPos();
154
155			if (usePeriodicBoundaryConditions_)
156			currentSnapshot_->wrapVector(vec);
157
158			// Calculate "bonds" and make a pair list
159
160			r = vec.length();
161
162			// Check to see if neighbor is in bond cutoff
163
164			if (r < rCut_) {
165			// Add neighbor to bond list's
166			bondvec.push_back(vec);
167			nBonds++;
168			nTotBonds_++;
169			}
170			}
171			}
172
173
174			for (int i = 0; i < nBonds-1; i++ ){
175			Vector3d vec1 = bondvec[i];
176			vec1.normalize();
177			for(int j = i+1; j < nBonds; j++){
178			Vector3d vec2 = bondvec[j];
179
180			vec2.normalize();
181
182			RealType theta = acos(dot(vec1,vec2))*180.0/NumericConstant::PI;
183
184
185			if (theta > 180.0){
186			theta = 360.0 - theta;
187			}
188			int whichBin = theta/deltaTheta_;
189
190			histogram_[whichBin] += 2;
191			}
192			}
193			}
194			}
195			}
196
197
198			writeBondAngleDistribution();
199			}
200
201
202			void BondAngleDistribution::writeBondAngleDistribution() {
203
204			std::ofstream osbad(getOutputFileName().c_str());
205
206
207			RealType norm = (RealType)nTotBonds_*((RealType)nTotBonds_-1.0)/2.0;
208			if (osbad.is_open()) {
209
210			// Normalize by number of frames and write it out:
211			for (int i = 0; i < nBins_; ++i) {
212			RealType Thetaval = i * deltaTheta_;
213			osbad << Thetaval;
214			osbad << "\t" << (RealType)histogram_[i]/norm/frameCounter_;
215
216			osbad << "\n";
217			}
218
219			osbad.close();
220
221			} else {
222			sprintf(painCave.errMsg, "BondAngleDistribution: unable to open %s\n",
223			(getOutputFileName() + "q").c_str());
224			painCave.isFatal = 1;
225			simError();
226			}
227
228			}
229			}