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, 234107 (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 "primitives/Atom.hpp"
#include "types/MultipoleAdapter.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 = int(distance / deltaR_);

    if (distance <= len_) {

      RealType cosAngle = evaluateAngle(sd1, sd2);
      RealType halfBin = (nAngleBins_ - 1) * 0.5;
      int whichThetaBin = int(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 vec;    
    
    if (sd1->isAtom()) {
      AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
      MultipoleAdapter ma1 = MultipoleAdapter(atype1);
      
      if (ma1.isDipole() )
        vec = sd1->getDipole();
      else 
        vec = sd1->getA().transpose() * V3Z;
    } else {
      vec = sd1->getA().transpose() * V3Z;
    }

    vec.normalize();    
      
    return dot(r12, vec);
  }

  RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
    Vector3d v1, v2;

    if (sd1->isAtom()){
      AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
      MultipoleAdapter ma1 = MultipoleAdapter(atype1);
      if (ma1.isDipole() )
        v1 = sd1->getDipole();
      else 
        v1 = sd1->getA().transpose() * V3Z;
    } else {
      v1 = sd1->getA().transpose() * V3Z;
    }
    
    if (sd2->isAtom()) {
      AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
      MultipoleAdapter ma2 = MultipoleAdapter(atype2);
           
      if (ma2.isDipole() )
        v2 = sd2->getDipole();
      else 
        v2 = sd2->getA().transpose() * V3Z;
    } else {
      v2 = sd2->getA().transpose() * V3Z;
    }
      
    v1.normalize();
    v2.normalize();
    return dot(v1, v2);
  }


}


Revision:	1968
Committed:	Thu Feb 20 16:27:30 2014 UTC (11 years, 2 months ago) by gezelter
File size:	7202 byte(s)
Log Message:	Fixed a bug in g(r,theta) and g(r,omega) that assumed all StuntDoubles were atoms.
#	User	Rev	Content
1	tim	309	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	309	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	309	* 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	gezelter	1390	*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	309	*/
42
43			#include <algorithm>
44			#include <fstream>
45			#include "applications/staticProps/GofRAngle.hpp"
46	gezelter	1879	#include "primitives/Atom.hpp"
47			#include "types/MultipoleAdapter.hpp"
48	tim	309	#include "utils/simError.h"
49
50	gezelter	1390	namespace OpenMD {
51	tim	309
52	gezelter	507	GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1,
53	tim	963	const std::string& sele2, RealType len, int nrbins, int nangleBins)
54	tim	354	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){
55	tim	309
56	xsun	1213	deltaR_ = len_ /(double) nRBins_;
57			deltaCosAngle_ = 2.0 / (double)nAngleBins_;
58	gezelter	507	histogram_.resize(nRBins_);
59			avgGofr_.resize(nRBins_);
60			for (int i = 0 ; i < nRBins_; ++i) {
61	tim	354	histogram_[i].resize(nAngleBins_);
62			avgGofr_[i].resize(nAngleBins_);
63	gezelter	507	}
64	tim	354	}
65	tim	309
66
67	gezelter	507	void GofRAngle::preProcess() {
68	gezelter	1782	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
69	gezelter	507	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
70	tim	310	}
71	gezelter	507	}
72	tim	309
73	jmichalk	1785	void GofRAngle::initializeHistogram() {
74	tim	309	npairs_ = 0;
75	gezelter	1782	for (unsigned int i = 0; i < histogram_.size(); ++i){
76	gezelter	507	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
77	xsun	1213	}
78	gezelter	507	}
79	tim	309
80	gezelter	507	void GofRAngle::processHistogram() {
81	tim	353	int nPairs = getNPairs();
82	tim	963	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
83			RealType pairDensity = nPairs /volume;
84			RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
85	tim	309
86	gezelter	1782	for(unsigned int i = 0 ; i < histogram_.size(); ++i){
87	tim	309
88	tim	963	RealType rLower = i * deltaR_;
89			RealType rUpper = rLower + deltaR_;
90			RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
91			RealType nIdeal = volSlice * pairConstant;
92	tim	309
93	gezelter	1782	for (unsigned int j = 0; j < histogram_[i].size(); ++j){
94	gezelter	507	avgGofr_[i][j] += histogram_[i][j] / nIdeal;
95			}
96	tim	309	}
97
98	gezelter	507	}
99	tim	309
100	gezelter	507	void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
101	tim	309
102			if (sd1 == sd2) {
103	gezelter	507	return;
104	tim	309	}
105			Vector3d pos1 = sd1->getPos();
106			Vector3d pos2 = sd2->getPos();
107	tim	361	Vector3d r12 = pos2 - pos1;
108	gezelter	1078	if (usePeriodicBoundaryConditions_)
109			currentSnapshot_->wrapVector(r12);
110	tim	309
111	tim	963	RealType distance = r12.length();
112	gezelter	1790	int whichRBin = int(distance / deltaR_);
113	tim	309
114	tim	328	if (distance <= len_) {
115	xsun	1213
116	tim	963	RealType cosAngle = evaluateAngle(sd1, sd2);
117			RealType halfBin = (nAngleBins_ - 1) * 0.5;
118	gezelter	1790	int whichThetaBin = int(halfBin * (cosAngle + 1.0));
119	gezelter	507	++histogram_[whichRBin][whichThetaBin];
120	tim	328
121	gezelter	507	++npairs_;
122	tim	328	}
123	gezelter	507	}
124	tim	309
125	gezelter	507	void GofRAngle::writeRdf() {
126	tim	309	std::ofstream rdfStream(outputFilename_.c_str());
127			if (rdfStream.is_open()) {
128	gezelter	507	rdfStream << "#radial distribution function\n";
129			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
130			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
131			rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
132			rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
133	gezelter	1782	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
134	gezelter	1796	// RealType r = deltaR_ * (i + 0.5);
135	tim	309
136	gezelter	1782	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
137	gezelter	1796	// RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
138	gezelter	507	rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
139			}
140	tim	360
141	gezelter	507	rdfStream << "\n";
142			}
143	tim	309
144			} else {
145	gezelter	507	sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str());
146			painCave.isFatal = 1;
147			simError();
148	tim	309	}
149
150			rdfStream.close();
151	gezelter	507	}
152	tim	309
153	tim	963	RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
154	tim	309	Vector3d pos1 = sd1->getPos();
155			Vector3d pos2 = sd2->getPos();
156	tim	361	Vector3d r12 = pos2 - pos1;
157	xsun	1213
158	gezelter	1078	if (usePeriodicBoundaryConditions_)
159			currentSnapshot_->wrapVector(r12);
160
161	tim	309	r12.normalize();
162	gezelter	1879
163	gezelter	1968	Vector3d vec;
164
165			if (sd1->isAtom()) {
166			AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
167			MultipoleAdapter ma1 = MultipoleAdapter(atype1);
168
169			if (ma1.isDipole() )
170			vec = sd1->getDipole();
171			else
172			vec = sd1->getA().transpose() * V3Z;
173			} else {
174	gezelter	1879	vec = sd1->getA().transpose() * V3Z;
175	gezelter	1968	}
176
177	gezelter	1879	vec.normalize();
178	gezelter	1968
179	gezelter	1879	return dot(r12, vec);
180	gezelter	507	}
181	tim	309
182	tim	963	RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
183	gezelter	1879	Vector3d v1, v2;
184
185	gezelter	1968	if (sd1->isAtom()){
186			AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
187			MultipoleAdapter ma1 = MultipoleAdapter(atype1);
188			if (ma1.isDipole() )
189			v1 = sd1->getDipole();
190			else
191			v1 = sd1->getA().transpose() * V3Z;
192			} else {
193	gezelter	1879	v1 = sd1->getA().transpose() * V3Z;
194	gezelter	1968	}
195
196			if (sd2->isAtom()) {
197			AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
198			MultipoleAdapter ma2 = MultipoleAdapter(atype2);
199
200			if (ma2.isDipole() )
201			v2 = sd2->getDipole();
202			else
203			v2 = sd2->getA().transpose() * V3Z;
204			} else {
205	gezelter	1879	v2 = sd2->getA().transpose() * V3Z;
206	gezelter	1968	}
207
208	tim	311	v1.normalize();
209			v2.normalize();
210			return dot(v1, v2);
211	gezelter	507	}
212	tim	309
213
214			}
215
216