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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 *
 *  BondAngleDistribution.cpp
 *  OOPSE-4
 *
 *  Created by J. Daniel Gezelter on 07/27/07.
 *  @author  J. Daniel Gezelter
 *  @version $Id: BondAngleDistribution.cpp,v 1.1 2007-09-17 20:05:51 chuckv Exp $
 *
 */
 
#include "applications/staticProps/BondAngleDistribution.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"

namespace oopse {

  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:	1180
Committed:	Mon Sep 17 20:05:51 2007 UTC (17 years, 7 months ago) by chuckv
Original Path:	*trunk/src/applications/staticProps/BondAngleDistribution.cpp*
File size:	7501 byte(s)
Log Message:	Added code to compute bond angle distributions.
#	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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*
41			* BondAngleDistribution.cpp
42			* OOPSE-4
43			*
44			* Created by J. Daniel Gezelter on 07/27/07.
45			* @author J. Daniel Gezelter
46			* @version $Id: BondAngleDistribution.cpp,v 1.1 2007-09-17 20:05:51 chuckv Exp $
47			*
48			*/
49
50			#include "applications/staticProps/BondAngleDistribution.hpp"
51			#include "utils/simError.h"
52			#include "io/DumpReader.hpp"
53			#include "primitives/Molecule.hpp"
54			#include "utils/NumericConstant.hpp"
55
56			namespace oopse {
57
58			BondAngleDistribution::BondAngleDistribution(SimInfo* info,
59			const std::string& filename,
60			const std::string& sele,
61			double rCut, int nbins) : StaticAnalyser(info, filename),
62			selectionScript_(sele),
63			evaluator_(info), seleMan_(info){
64
65			setOutputName(getPrefix(filename) + ".bad");
66
67			evaluator_.loadScriptString(sele);
68			if (!evaluator_.isDynamic()) {
69			seleMan_.setSelectionSet(evaluator_.evaluate());
70			}
71
72			// Set up cutoff radius and order of the Legendre Polynomial:
73
74			rCut_ = rCut;
75			nBins_ = nbins;
76
77
78			// Theta can take values from 0 to 180
79			deltaTheta_ = (180.0) / nBins_;
80			histogram_.resize(nBins_);
81			}
82
83			BondAngleDistribution::~BondAngleDistribution() {
84			histogram_.clear();
85			}
86
87			void BondAngleDistribution::initalizeHistogram() {
88			for (int bin = 0; bin < nBins_; bin++) {
89			histogram_[bin] = 0;
90			}
91			}
92
93			void BondAngleDistribution::process() {
94			Molecule* mol;
95			Atom* atom;
96			RigidBody* rb;
97			int myIndex;
98			SimInfo::MoleculeIterator mi;
99			Molecule::RigidBodyIterator rbIter;
100			Molecule::AtomIterator ai;
101			StuntDouble* sd;
102			Vector3d vec;
103			std::vector<Vector3d> bondvec;
104			std::vector<RealType> bonddist;
105			RealType costheta;
106			RealType r;
107			RealType dist;
108
109			int nBonds;
110
111			int i, j;
112
113			DumpReader reader(info_, dumpFilename_);
114			int nFrames = reader.getNFrames();
115			frameCounter_ = 0;
116
117			nTotBonds_ = 0;
118
119			for (int istep = 0; istep < nFrames; istep += step_) {
120			reader.readFrame(istep);
121			frameCounter_++;
122			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
123
124			if (evaluator_.isDynamic()) {
125			seleMan_.setSelectionSet(evaluator_.evaluate());
126			}
127
128			// update the positions of atoms which belong to the rigidbodies
129
130			for (mol = info_->beginMolecule(mi); mol != NULL;
131			mol = info_->nextMolecule(mi)) {
132			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
133			rb = mol->nextRigidBody(rbIter)) {
134			rb->updateAtoms();
135			}
136			}
137
138			// outer loop is over the selected StuntDoubles:
139
140			for (sd = seleMan_.beginSelected(i); sd != NULL;
141			sd = seleMan_.nextSelected(i)) {
142
143			myIndex = sd->getGlobalIndex();
144			nBonds = 0;
145			bondvec.clear();
146
147			// inner loop is over all other atoms in the system:
148
149			for (mol = info_->beginMolecule(mi); mol != NULL;
150			mol = info_->nextMolecule(mi)) {
151			for (atom = mol->beginAtom(ai); atom != NULL;
152			atom = mol->nextAtom(ai)) {
153
154			if (atom->getGlobalIndex() != myIndex) {
155
156			vec = sd->getPos() - atom->getPos();
157
158			if (usePeriodicBoundaryConditions_)
159			currentSnapshot_->wrapVector(vec);
160
161			// Calculate "bonds" and make a pair list
162
163			r = vec.length();
164
165			// Check to see if neighbor is in bond cutoff
166
167			if (r < rCut_) {
168			// Add neighbor to bond list's
169			bondvec.push_back(vec);
170			nBonds++;
171			nTotBonds_++;
172			}
173			}
174			}
175
176
177			for (int i = 0; i < nBonds-1; i++ ){
178			Vector3d vec1 = bondvec[i];
179			vec1.normalize();
180			for(int j = i+1; j < nBonds; j++){
181			Vector3d vec2 = bondvec[j];
182
183			vec2.normalize();
184
185			RealType theta = acos(dot(vec1,vec2))*180.0/NumericConstant::PI;
186
187
188			if (theta > 180.0){
189			theta = 360.0 - theta;
190			}
191			int whichBin = theta/deltaTheta_;
192
193			histogram_[whichBin] += 2;
194			}
195			}
196			}
197			}
198			}
199
200
201			writeBondAngleDistribution();
202			}
203
204
205			void BondAngleDistribution::writeBondAngleDistribution() {
206
207			std::ofstream osbad(getOutputFileName().c_str());
208
209
210			RealType norm = (RealType)nTotBonds_*((RealType)nTotBonds_-1.0)/2.0;
211			if (osbad.is_open()) {
212
213			// Normalize by number of frames and write it out:
214			for (int i = 0; i < nBins_; ++i) {
215			RealType Thetaval = i * deltaTheta_;
216			osbad << Thetaval;
217			osbad << "\t" << (RealType)histogram_[i]/norm/frameCounter_;
218
219			osbad << "\n";
220			}
221
222			osbad.close();
223
224			} else {
225			sprintf(painCave.errMsg, "BondAngleDistribution: unable to open %s\n",
226			(getOutputFileName() + "q").c_str());
227			painCave.isFatal = 1;
228			simError();
229			}
230
231			}
232			}