applications/staticProps/AngleR.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]  Vardeman & Gezelter, in progress (2009).                        
 */

/* Calculates Angle(R) for DirectionalAtoms*/
#include <algorithm>
#include <fstream>
#include "applications/staticProps/AngleR.hpp"
#include "utils/simError.h"
#include "utils/NumericConstant.hpp"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include <math.h>

namespace OpenMD {

     
  AngleR::AngleR(SimInfo* info, const std::string& filename, const std::string& sele, RealType len, int nrbins)
    : StaticAnalyser(info, filename), selectionScript_(sele),  evaluator_(info), seleMan_(info), len_(len), nRBins_(nrbins){
    
    
    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
    
    
    deltaR_ = len_ /nRBins_;
    
    histogram_.resize(nRBins_);
    count_.resize(nRBins_);
    avgAngleR_.resize(nRBins_);
    setOutputName(getPrefix(filename) + ".AngleR");
  }
  

  void AngleR::process() {
    
    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();
    nProcessed_ = nFrames/step_;
    
    std::fill(avgAngleR_.begin(), avgAngleR_.end(), 0.0);     
    std::fill(histogram_.begin(), histogram_.end(), 0.0);
    std::fill(count_.begin(), count_.end(), 0);
    
    for (int istep = 0; istep < nFrames; istep += step_) {
      
      int i;    
      StuntDouble* sd;
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      Vector3d CenterOfMass = info_->getCom();      
      
      
      if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
      }
      
      //determine which atom belongs to which slice
      for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
        Vector3d pos = sd->getPos();
        Vector3d r1 = CenterOfMass - pos;
        // only do this if the stunt double actually has a vector associated
        // with it
        if (sd->isDirectional()) {
          Vector3d dipole = sd->getA().getColumn(2);
          // std::cerr << "pos = " << pos << " dipole = " << dipole << "\n";
          RealType distance = r1.length();
          
          dipole.normalize();
          r1.normalize();
          RealType cosangle = dot(r1, dipole);
          
          if (distance < len_) {
            int whichBin = distance / deltaR_;
            histogram_[whichBin] += cosangle;
            count_[whichBin] += 1;
          }
        }
        
      }

    }

    processHistogram(); 
    writeAngleR();
  }


  void AngleR::processHistogram() {

    for(int i = 0 ; i < histogram_.size(); ++i){

      if (count_[i] > 0)
        avgAngleR_[i] += histogram_[i] / count_[i];    
      else 
        avgAngleR_[i] = 0.0;

    std::cerr << " count = " << count_[i] << " avgAngle = " << avgAngleR_[i] << "\n";  
    }

  }

 
  void AngleR::writeAngleR() {
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#radial density function Angle(r)\n";
      rdfStream << "#r\tcorrValue\n";
      for (int i = 0; i < avgAngleR_.size(); ++i) {
        RealType r = deltaR_ * (i + 0.5);
        rdfStream << r << "\t" << avgAngleR_[i] << "\n";
      }
        
    } else {

      sprintf(painCave.errMsg, "AngleR: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }

    rdfStream.close();
  }

}

Revision:	1629
Committed:	Wed Sep 14 21:15:17 2011 UTC (13 years, 7 months ago) by gezelter
File size:	5334 byte(s)
Log Message:	Merging changes from old branch into development branch
#	User	Rev	Content
1	gezelter	1629	/*
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] Vardeman & Gezelter, in progress (2009).
40			*/
41
42			/* Calculates Angle(R) for DirectionalAtoms*/
43			#include <algorithm>
44			#include <fstream>
45			#include "applications/staticProps/AngleR.hpp"
46			#include "utils/simError.h"
47			#include "utils/NumericConstant.hpp"
48			#include "io/DumpReader.hpp"
49			#include "primitives/Molecule.hpp"
50			#include <math.h>
51
52			namespace OpenMD {
53
54
55			AngleR::AngleR(SimInfo* info, const std::string& filename, const std::string& sele, RealType len, int nrbins)
56			: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), len_(len), nRBins_(nrbins){
57
58
59			evaluator_.loadScriptString(sele);
60			if (!evaluator_.isDynamic()) {
61			seleMan_.setSelectionSet(evaluator_.evaluate());
62			}
63
64
65			deltaR_ = len_ /nRBins_;
66
67			histogram_.resize(nRBins_);
68			count_.resize(nRBins_);
69			avgAngleR_.resize(nRBins_);
70			setOutputName(getPrefix(filename) + ".AngleR");
71			}
72
73
74			void AngleR::process() {
75
76			DumpReader reader(info_, dumpFilename_);
77			int nFrames = reader.getNFrames();
78			nProcessed_ = nFrames/step_;
79
80			std::fill(avgAngleR_.begin(), avgAngleR_.end(), 0.0);
81			std::fill(histogram_.begin(), histogram_.end(), 0.0);
82			std::fill(count_.begin(), count_.end(), 0);
83
84			for (int istep = 0; istep < nFrames; istep += step_) {
85
86			int i;
87			StuntDouble* sd;
88			reader.readFrame(istep);
89			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
90			Vector3d CenterOfMass = info_->getCom();
91
92
93			if (evaluator_.isDynamic()) {
94			seleMan_.setSelectionSet(evaluator_.evaluate());
95			}
96
97			//determine which atom belongs to which slice
98			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
99			Vector3d pos = sd->getPos();
100			Vector3d r1 = CenterOfMass - pos;
101			// only do this if the stunt double actually has a vector associated
102			// with it
103			if (sd->isDirectional()) {
104			Vector3d dipole = sd->getA().getColumn(2);
105			// std::cerr << "pos = " << pos << " dipole = " << dipole << "\n";
106			RealType distance = r1.length();
107
108			dipole.normalize();
109			r1.normalize();
110			RealType cosangle = dot(r1, dipole);
111
112			if (distance < len_) {
113			int whichBin = distance / deltaR_;
114			histogram_[whichBin] += cosangle;
115			count_[whichBin] += 1;
116			}
117			}
118
119			}
120
121			}
122
123			processHistogram();
124			writeAngleR();
125			}
126
127
128
129			void AngleR::processHistogram() {
130
131			for(int i = 0 ; i < histogram_.size(); ++i){
132
133			if (count_[i] > 0)
134			avgAngleR_[i] += histogram_[i] / count_[i];
135			else
136			avgAngleR_[i] = 0.0;
137
138			std::cerr << " count = " << count_[i] << " avgAngle = " << avgAngleR_[i] << "\n";
139			}
140
141			}
142
143
144
145			void AngleR::writeAngleR() {
146			std::ofstream rdfStream(outputFilename_.c_str());
147			if (rdfStream.is_open()) {
148			rdfStream << "#radial density function Angle(r)\n";
149			rdfStream << "#r\tcorrValue\n";
150			for (int i = 0; i < avgAngleR_.size(); ++i) {
151			RealType r = deltaR_ * (i + 0.5);
152			rdfStream << r << "\t" << avgAngleR_[i] << "\n";
153			}
154
155			} else {
156
157			sprintf(painCave.errMsg, "AngleR: unable to open %s\n", outputFilename_.c_str());
158			painCave.isFatal = 1;
159			simError();
160			}
161
162			rdfStream.close();
163			}
164
165			}
166