applications/staticProps/GofRAngle.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).
 */

#include <algorithm>
#include <fstream>
#include "applications/staticProps/GofRAngle.hpp"
#include "utils/simError.h"

namespace OpenMD {

  GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, 
                       const std::string& sele2, RealType len, int nrbins, int nangleBins)
    : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){

      deltaR_ = len_ /(double) nRBins_;
      deltaCosAngle_ = 2.0 / (double)nAngleBins_;    
      histogram_.resize(nRBins_);
      avgGofr_.resize(nRBins_);
      for (int i = 0 ; i < nRBins_; ++i) {
        histogram_[i].resize(nAngleBins_);
        avgGofr_[i].resize(nAngleBins_);
      }
    }


  void GofRAngle::preProcess() {
    for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
      std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
    }
  }

  void GofRAngle::initializeHistogram() {
    npairs_ = 0;
    for (unsigned int i = 0; i < histogram_.size(); ++i){
      std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
    }
  }

  void GofRAngle::processHistogram() {
    int nPairs = getNPairs();
    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    RealType pairDensity = nPairs /volume;
    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;

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

      RealType rLower = i * deltaR_;
      RealType rUpper = rLower + deltaR_;
      RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
      RealType nIdeal = volSlice * pairConstant;

      for (unsigned int j = 0; j < histogram_[i].size(); ++j){
        avgGofr_[i][j] += histogram_[i][j] / nIdeal;    
      }
    }

  }

  void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {

    if (sd1 == sd2) {
      return;
    }
    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12 = pos2 - pos1;
    if (usePeriodicBoundaryConditions_)
      currentSnapshot_->wrapVector(r12);

    RealType distance = r12.length();
    int whichRBin = distance / deltaR_;

    if (distance <= len_) {

      RealType cosAngle = evaluateAngle(sd1, sd2);
      RealType halfBin = (nAngleBins_ - 1) * 0.5;
      int whichThetaBin = halfBin * (cosAngle + 1.0);
      ++histogram_[whichRBin][whichThetaBin];
        
      ++npairs_;
    }
  }

  void GofRAngle::writeRdf() {
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#radial distribution function\n";
      rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
      rdfStream << "selection2: (" << selectionScript2_ << ")\n";
      rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
      rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
      for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
        RealType r = deltaR_ * (i + 0.5);

        for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
          RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
          rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
        }

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

    rdfStream.close();
  }

  RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12 = pos2 - pos1;
  
    if (usePeriodicBoundaryConditions_)
      currentSnapshot_->wrapVector(r12);

    r12.normalize();
    Vector3d dipole = sd1->getElectroFrame().getColumn(2);
    dipole.normalize();    
    return dot(r12, dipole);
  }

  RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
    Vector3d v1 = sd1->getElectroFrame().getColumn(2);
    Vector3d v2 = sd2->getElectroFrame().getColumn(2);    
    v1.normalize();
    v2.normalize();
    return dot(v1, v2);
  }


}


Revision:	1785
Committed:	Wed Aug 22 18:43:27 2012 UTC (12 years, 8 months ago) by jmichalk
File size:	6244 byte(s)
Log Message:	Trunk: The changes in this commit are confined to applications/staticProps and for the most part deal with a misspelling of initialize. The one other change took place in StaticProps.cpp and deals with the default treatment of sele2. It had previously been set to 'select all' which seems to go against what would be desired by not specifying it with regard to proper operations of many of the analysis programs ( g of r's especially)
#	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	#include <algorithm>
44	#include <fstream>
45	#include "applications/staticProps/GofRAngle.hpp"
46	#include "utils/simError.h"
47
48	namespace OpenMD {
49
50	GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1,
51	const std::string& sele2, RealType len, int nrbins, int nangleBins)
52	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){
53
54	deltaR_ = len_ /(double) nRBins_;
55	deltaCosAngle_ = 2.0 / (double)nAngleBins_;
56	histogram_.resize(nRBins_);
57	avgGofr_.resize(nRBins_);
58	for (int i = 0 ; i < nRBins_; ++i) {
59	histogram_[i].resize(nAngleBins_);
60	avgGofr_[i].resize(nAngleBins_);
61	}
62	}
63
64
65	void GofRAngle::preProcess() {
66	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
67	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
68	}
69	}
70
71	void GofRAngle::initializeHistogram() {
72	npairs_ = 0;
73	for (unsigned int i = 0; i < histogram_.size(); ++i){
74	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
75	}
76	}
77
78	void GofRAngle::processHistogram() {
79	int nPairs = getNPairs();
80	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
81	RealType pairDensity = nPairs /volume;
82	RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
83
84	for(unsigned int i = 0 ; i < histogram_.size(); ++i){
85
86	RealType rLower = i * deltaR_;
87	RealType rUpper = rLower + deltaR_;
88	RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
89	RealType nIdeal = volSlice * pairConstant;
90
91	for (unsigned int j = 0; j < histogram_[i].size(); ++j){
92	avgGofr_[i][j] += histogram_[i][j] / nIdeal;
93	}
94	}
95
96	}
97
98	void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
99
100	if (sd1 == sd2) {
101	return;
102	}
103	Vector3d pos1 = sd1->getPos();
104	Vector3d pos2 = sd2->getPos();
105	Vector3d r12 = pos2 - pos1;
106	if (usePeriodicBoundaryConditions_)
107	currentSnapshot_->wrapVector(r12);
108
109	RealType distance = r12.length();
110	int whichRBin = distance / deltaR_;
111
112	if (distance <= len_) {
113
114	RealType cosAngle = evaluateAngle(sd1, sd2);
115	RealType halfBin = (nAngleBins_ - 1) * 0.5;
116	int whichThetaBin = halfBin * (cosAngle + 1.0);
117	++histogram_[whichRBin][whichThetaBin];
118
119	++npairs_;
120	}
121	}
122
123	void GofRAngle::writeRdf() {
124	std::ofstream rdfStream(outputFilename_.c_str());
125	if (rdfStream.is_open()) {
126	rdfStream << "#radial distribution function\n";
127	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
128	rdfStream << "selection2: (" << selectionScript2_ << ")\n";
129	rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
130	rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
131	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
132	RealType r = deltaR_ * (i + 0.5);
133
134	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
135	RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
136	rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
137	}
138
139	rdfStream << "\n";
140	}
141
142	} else {
143	sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str());
144	painCave.isFatal = 1;
145	simError();
146	}
147
148	rdfStream.close();
149	}
150
151	RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
152	Vector3d pos1 = sd1->getPos();
153	Vector3d pos2 = sd2->getPos();
154	Vector3d r12 = pos2 - pos1;
155
156	if (usePeriodicBoundaryConditions_)
157	currentSnapshot_->wrapVector(r12);
158
159	r12.normalize();
160	Vector3d dipole = sd1->getElectroFrame().getColumn(2);
161	dipole.normalize();
162	return dot(r12, dipole);
163	}
164
165	RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
166	Vector3d v1 = sd1->getElectroFrame().getColumn(2);
167	Vector3d v2 = sd2->getElectroFrame().getColumn(2);
168	v1.normalize();
169	v2.normalize();
170	return dot(v1, v2);
171	}
172
173
174	}
175
176