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 = 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 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:	1796
Committed:	Mon Sep 10 18:38:44 2012 UTC (12 years, 7 months ago) by gezelter
File size:	6260 byte(s)
Log Message:	Updating MPI calls to C++, fixing a DumpWriter bug, cleaning cruft
#	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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (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			#include "utils/simError.h"
47
48	gezelter	1390	namespace OpenMD {
49	tim	309
50	gezelter	507	GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1,
51	tim	963	const std::string& sele2, RealType len, int nrbins, int nangleBins)
52	tim	354	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){
53	tim	309
54	xsun	1213	deltaR_ = len_ /(double) nRBins_;
55			deltaCosAngle_ = 2.0 / (double)nAngleBins_;
56	gezelter	507	histogram_.resize(nRBins_);
57			avgGofr_.resize(nRBins_);
58			for (int i = 0 ; i < nRBins_; ++i) {
59	tim	354	histogram_[i].resize(nAngleBins_);
60			avgGofr_[i].resize(nAngleBins_);
61	gezelter	507	}
62	tim	354	}
63	tim	309
64
65	gezelter	507	void GofRAngle::preProcess() {
66	gezelter	1782	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
67	gezelter	507	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
68	tim	310	}
69	gezelter	507	}
70	tim	309
71	jmichalk	1785	void GofRAngle::initializeHistogram() {
72	tim	309	npairs_ = 0;
73	gezelter	1782	for (unsigned int i = 0; i < histogram_.size(); ++i){
74	gezelter	507	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
75	xsun	1213	}
76	gezelter	507	}
77	tim	309
78	gezelter	507	void GofRAngle::processHistogram() {
79	tim	353	int nPairs = getNPairs();
80	tim	963	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
81			RealType pairDensity = nPairs /volume;
82			RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
83	tim	309
84	gezelter	1782	for(unsigned int i = 0 ; i < histogram_.size(); ++i){
85	tim	309
86	tim	963	RealType rLower = i * deltaR_;
87			RealType rUpper = rLower + deltaR_;
88			RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
89			RealType nIdeal = volSlice * pairConstant;
90	tim	309
91	gezelter	1782	for (unsigned int j = 0; j < histogram_[i].size(); ++j){
92	gezelter	507	avgGofr_[i][j] += histogram_[i][j] / nIdeal;
93			}
94	tim	309	}
95
96	gezelter	507	}
97	tim	309
98	gezelter	507	void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
99	tim	309
100			if (sd1 == sd2) {
101	gezelter	507	return;
102	tim	309	}
103			Vector3d pos1 = sd1->getPos();
104			Vector3d pos2 = sd2->getPos();
105	tim	361	Vector3d r12 = pos2 - pos1;
106	gezelter	1078	if (usePeriodicBoundaryConditions_)
107			currentSnapshot_->wrapVector(r12);
108	tim	309
109	tim	963	RealType distance = r12.length();
110	gezelter	1790	int whichRBin = int(distance / deltaR_);
111	tim	309
112	tim	328	if (distance <= len_) {
113	xsun	1213
114	tim	963	RealType cosAngle = evaluateAngle(sd1, sd2);
115			RealType halfBin = (nAngleBins_ - 1) * 0.5;
116	gezelter	1790	int whichThetaBin = int(halfBin * (cosAngle + 1.0));
117	gezelter	507	++histogram_[whichRBin][whichThetaBin];
118	tim	328
119	gezelter	507	++npairs_;
120	tim	328	}
121	gezelter	507	}
122	tim	309
123	gezelter	507	void GofRAngle::writeRdf() {
124	tim	309	std::ofstream rdfStream(outputFilename_.c_str());
125			if (rdfStream.is_open()) {
126	gezelter	507	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	gezelter	1782	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
132	gezelter	1796	// RealType r = deltaR_ * (i + 0.5);
133	tim	309
134	gezelter	1782	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
135	gezelter	1796	// RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
136	gezelter	507	rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
137			}
138	tim	360
139	gezelter	507	rdfStream << "\n";
140			}
141	tim	309
142			} else {
143	gezelter	507	sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str());
144			painCave.isFatal = 1;
145			simError();
146	tim	309	}
147
148			rdfStream.close();
149	gezelter	507	}
150	tim	309
151	tim	963	RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
152	tim	309	Vector3d pos1 = sd1->getPos();
153			Vector3d pos2 = sd2->getPos();
154	tim	361	Vector3d r12 = pos2 - pos1;
155	xsun	1213
156	gezelter	1078	if (usePeriodicBoundaryConditions_)
157			currentSnapshot_->wrapVector(r12);
158
159	tim	309	r12.normalize();
160	tim	311	Vector3d dipole = sd1->getElectroFrame().getColumn(2);
161	tim	309	dipole.normalize();
162	tim	311	return dot(r12, dipole);
163	gezelter	507	}
164	tim	309
165	tim	963	RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
166	tim	309	Vector3d v1 = sd1->getElectroFrame().getColumn(2);
167	tim	373	Vector3d v2 = sd2->getElectroFrame().getColumn(2);
168	tim	311	v1.normalize();
169			v2.normalize();
170			return dot(v1, v2);
171	gezelter	507	}
172	tim	309
173
174			}
175
176