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 "brains/Thermo.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();
      Thermo thermo(info_);
      Vector3d CenterOfMass = thermo.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:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (12 years, 9 months ago) by gezelter
File size:	5457 byte(s)
Log Message:	Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
#	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	/* 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 "brains/Thermo.hpp"
52	#include <math.h>
53
54	namespace OpenMD {
55
56
57	AngleR::AngleR(SimInfo* info, const std::string& filename, const std::string& sele, RealType len, int nrbins)
58	: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), len_(len), nRBins_(nrbins){
59
60
61	evaluator_.loadScriptString(sele);
62	if (!evaluator_.isDynamic()) {
63	seleMan_.setSelectionSet(evaluator_.evaluate());
64	}
65
66
67	deltaR_ = len_ /nRBins_;
68
69	histogram_.resize(nRBins_);
70	count_.resize(nRBins_);
71	avgAngleR_.resize(nRBins_);
72	setOutputName(getPrefix(filename) + ".AngleR");
73	}
74
75
76	void AngleR::process() {
77
78	DumpReader reader(info_, dumpFilename_);
79	int nFrames = reader.getNFrames();
80	nProcessed_ = nFrames/step_;
81
82	std::fill(avgAngleR_.begin(), avgAngleR_.end(), 0.0);
83	std::fill(histogram_.begin(), histogram_.end(), 0.0);
84	std::fill(count_.begin(), count_.end(), 0);
85
86	for (int istep = 0; istep < nFrames; istep += step_) {
87
88	int i;
89	StuntDouble* sd;
90	reader.readFrame(istep);
91	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
92	Thermo thermo(info_);
93	Vector3d CenterOfMass = thermo.getCom();
94
95
96	if (evaluator_.isDynamic()) {
97	seleMan_.setSelectionSet(evaluator_.evaluate());
98	}
99
100	//determine which atom belongs to which slice
101	for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
102	Vector3d pos = sd->getPos();
103	Vector3d r1 = CenterOfMass - pos;
104	// only do this if the stunt double actually has a vector associated
105	// with it
106	if (sd->isDirectional()) {
107	Vector3d dipole = sd->getA().getColumn(2);
108	// std::cerr << "pos = " << pos << " dipole = " << dipole << "\n";
109	RealType distance = r1.length();
110
111	dipole.normalize();
112	r1.normalize();
113	RealType cosangle = dot(r1, dipole);
114
115	if (distance < len_) {
116	int whichBin = distance / deltaR_;
117	histogram_[whichBin] += cosangle;
118	count_[whichBin] += 1;
119	}
120	}
121
122	}
123
124	}
125
126	processHistogram();
127	writeAngleR();
128	}
129
130
131
132	void AngleR::processHistogram() {
133
134	for(int i = 0 ; i < histogram_.size(); ++i){
135
136	if (count_[i] > 0)
137	avgAngleR_[i] += histogram_[i] / count_[i];
138	else
139	avgAngleR_[i] = 0.0;
140
141	std::cerr << " count = " << count_[i] << " avgAngle = " << avgAngleR_[i] << "\n";
142	}
143
144	}
145
146
147
148	void AngleR::writeAngleR() {
149	std::ofstream rdfStream(outputFilename_.c_str());
150	if (rdfStream.is_open()) {
151	rdfStream << "#radial density function Angle(r)\n";
152	rdfStream << "#r\tcorrValue\n";
153	for (int i = 0; i < avgAngleR_.size(); ++i) {
154	RealType r = deltaR_ * (i + 0.5);
155	rdfStream << r << "\t" << avgAngleR_[i] << "\n";
156	}
157
158	} else {
159
160	sprintf(painCave.errMsg, "AngleR: unable to open %s\n", outputFilename_.c_str());
161	painCave.isFatal = 1;
162	simError();
163	}
164
165	rdfStream.close();
166	}
167
168	}
169