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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

/* 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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	5400 byte(s)
Log Message:	updated copyright notices
#	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	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	1629	*/
42
43			/* Calculates Angle(R) for DirectionalAtoms*/
44			#include <algorithm>
45			#include <fstream>
46			#include "applications/staticProps/AngleR.hpp"
47			#include "utils/simError.h"
48			#include "utils/NumericConstant.hpp"
49			#include "io/DumpReader.hpp"
50			#include "primitives/Molecule.hpp"
51			#include <math.h>
52
53			namespace OpenMD {
54
55
56			AngleR::AngleR(SimInfo* info, const std::string& filename, const std::string& sele, RealType len, int nrbins)
57			: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), len_(len), nRBins_(nrbins){
58
59
60			evaluator_.loadScriptString(sele);
61			if (!evaluator_.isDynamic()) {
62			seleMan_.setSelectionSet(evaluator_.evaluate());
63			}
64
65
66			deltaR_ = len_ /nRBins_;
67
68			histogram_.resize(nRBins_);
69			count_.resize(nRBins_);
70			avgAngleR_.resize(nRBins_);
71			setOutputName(getPrefix(filename) + ".AngleR");
72			}
73
74
75			void AngleR::process() {
76
77			DumpReader reader(info_, dumpFilename_);
78			int nFrames = reader.getNFrames();
79			nProcessed_ = nFrames/step_;
80
81			std::fill(avgAngleR_.begin(), avgAngleR_.end(), 0.0);
82			std::fill(histogram_.begin(), histogram_.end(), 0.0);
83			std::fill(count_.begin(), count_.end(), 0);
84
85			for (int istep = 0; istep < nFrames; istep += step_) {
86
87			int i;
88			StuntDouble* sd;
89			reader.readFrame(istep);
90			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
91			Vector3d CenterOfMass = info_->getCom();
92
93
94			if (evaluator_.isDynamic()) {
95			seleMan_.setSelectionSet(evaluator_.evaluate());
96			}
97
98			//determine which atom belongs to which slice
99			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
100			Vector3d pos = sd->getPos();
101			Vector3d r1 = CenterOfMass - pos;
102			// only do this if the stunt double actually has a vector associated
103			// with it
104			if (sd->isDirectional()) {
105			Vector3d dipole = sd->getA().getColumn(2);
106			// std::cerr << "pos = " << pos << " dipole = " << dipole << "\n";
107			RealType distance = r1.length();
108
109			dipole.normalize();
110			r1.normalize();
111			RealType cosangle = dot(r1, dipole);
112
113			if (distance < len_) {
114			int whichBin = distance / deltaR_;
115			histogram_[whichBin] += cosangle;
116			count_[whichBin] += 1;
117			}
118			}
119
120			}
121
122			}
123
124			processHistogram();
125			writeAngleR();
126			}
127
128
129
130			void AngleR::processHistogram() {
131
132			for(int i = 0 ; i < histogram_.size(); ++i){
133
134			if (count_[i] > 0)
135			avgAngleR_[i] += histogram_[i] / count_[i];
136			else
137			avgAngleR_[i] = 0.0;
138
139			std::cerr << " count = " << count_[i] << " avgAngle = " << avgAngleR_[i] << "\n";
140			}
141
142			}
143
144
145
146			void AngleR::writeAngleR() {
147			std::ofstream rdfStream(outputFilename_.c_str());
148			if (rdfStream.is_open()) {
149			rdfStream << "#radial density function Angle(r)\n";
150			rdfStream << "#r\tcorrValue\n";
151			for (int i = 0; i < avgAngleR_.size(); ++i) {
152			RealType r = deltaR_ * (i + 0.5);
153			rdfStream << r << "\t" << avgAngleR_[i] << "\n";
154			}
155
156			} else {
157
158			sprintf(painCave.errMsg, "AngleR: unable to open %s\n", outputFilename_.c_str());
159			painCave.isFatal = 1;
160			simError();
161			}
162
163			rdfStream.close();
164			}
165
166			}
167