applications/staticProps/GofRZ.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]  Vardeman & Gezelter, in progress (2009).                        
 */

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

namespace OpenMD {

  GofRZ::GofRZ(SimInfo* info, const std::string& filename, const std::string& sele1, 
                       const std::string& sele2, RealType len, int nrbins, int nZBins)
    : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nZBins_(nZBins){

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


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

  void GofRZ::initalizeHistogram() {
    npairs_ = 0;
    for (int i = 0; i < histogram_.size(); ++i){
      std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
    }
  }
  
  void GofRZ::processHistogram() {
    int nPairs = getNPairs();
    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    RealType pairDensity = nPairs / volume;

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

      RealType rLower = i * deltaR_;
      RealType rUpper = rLower + deltaR_;
      RealType volSlice = NumericConstant::PI * deltaZ_ * (( rUpper * rUpper ) - ( rLower * rLower ));
      RealType nIdeal = volSlice * pairDensity;

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

  }

  void GofRZ::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 = sqrt(pow(r12.x(), 2) + pow(r12.y(), 2));

    int whichRBin = distance / deltaR_;

    if (distance <= len_) {
     
      RealType Z = abs(r12.z());

      if (Z <= len_) {
        int whichZBin = Z / deltaZ_;
        ++histogram_[whichRBin][whichZBin];        
        ++npairs_;
      }
    }
  }

  void GofRZ::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 << "#nZBins =" << nZBins_ << "deltaZ = " << deltaZ_ << "\n";
      for (int i = 0; i < avgGofr_.size(); ++i) {
        RealType r = deltaR_ * (i + 0.5);

        for(int j = 0; j < avgGofr_[i].size(); ++j) {
          RealType z = deltaZ_ * (j + 0.5);
          rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
        }

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

    rdfStream.close();
  }

}


Revision:	1440
Committed:	Thu Apr 29 14:41:48 2010 UTC (15 years ago) by gezelter
File size:	5281 byte(s)
Log Message:	Adding a new correlation function to do slab-segregated g(r) calculations. This computes at g(r) for pairs while requiring the z coordinates of the two sites to be at fixed separations. The data is output in: r, z, g(r,z)
#	User	Rev	Content
1	gezelter	1440	/*
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] Vardeman & Gezelter, in progress (2009).
40			*/
41
42			#include <algorithm>
43			#include <fstream>
44			#include "applications/staticProps/GofRZ.hpp"
45			#include "utils/simError.h"
46
47			namespace OpenMD {
48
49			GofRZ::GofRZ(SimInfo* info, const std::string& filename, const std::string& sele1,
50			const std::string& sele2, RealType len, int nrbins, int nZBins)
51			: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nZBins_(nZBins){
52
53			deltaR_ = len_ / (double) nRBins_;
54			deltaZ_ = len_ / (double)nZBins_;
55			histogram_.resize(nRBins_);
56			avgGofr_.resize(nRBins_);
57			for (int i = 0 ; i < nRBins_; ++i) {
58			histogram_[i].resize(nZBins_);
59			avgGofr_[i].resize(nZBins_);
60			}
61			}
62
63
64			void GofRZ::preProcess() {
65			for (int i = 0; i < avgGofr_.size(); ++i) {
66			std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
67			}
68			}
69
70			void GofRZ::initalizeHistogram() {
71			npairs_ = 0;
72			for (int i = 0; i < histogram_.size(); ++i){
73			std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
74			}
75			}
76
77			void GofRZ::processHistogram() {
78			int nPairs = getNPairs();
79			RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
80			RealType pairDensity = nPairs / volume;
81
82			for(int i = 0 ; i < histogram_.size(); ++i){
83
84			RealType rLower = i * deltaR_;
85			RealType rUpper = rLower + deltaR_;
86			RealType volSlice = NumericConstant::PI * deltaZ_ * (( rUpper * rUpper ) - ( rLower * rLower ));
87			RealType nIdeal = volSlice * pairDensity;
88
89			for (int j = 0; j < histogram_[i].size(); ++j){
90			avgGofr_[i][j] += histogram_[i][j] / nIdeal;
91			}
92			}
93
94			}
95
96			void GofRZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
97
98			if (sd1 == sd2) {
99			return;
100			}
101			Vector3d pos1 = sd1->getPos();
102			Vector3d pos2 = sd2->getPos();
103			Vector3d r12 = pos2 - pos1;
104			if (usePeriodicBoundaryConditions_)
105			currentSnapshot_->wrapVector(r12);
106
107			RealType distance = sqrt(pow(r12.x(), 2) + pow(r12.y(), 2));
108
109			int whichRBin = distance / deltaR_;
110
111			if (distance <= len_) {
112
113			RealType Z = abs(r12.z());
114
115			if (Z <= len_) {
116			int whichZBin = Z / deltaZ_;
117			++histogram_[whichRBin][whichZBin];
118			++npairs_;
119			}
120			}
121			}
122
123			void GofRZ::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 << "#nZBins =" << nZBins_ << "deltaZ = " << deltaZ_ << "\n";
131			for (int i = 0; i < avgGofr_.size(); ++i) {
132			RealType r = deltaR_ * (i + 0.5);
133
134			for(int j = 0; j < avgGofr_[i].size(); ++j) {
135			RealType z = deltaZ_ * (j + 0.5);
136			rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
137			}
138
139			rdfStream << "\n";
140			}
141
142			} else {
143			sprintf(painCave.errMsg, "GofRZ: unable to open %s\n", outputFilename_.c_str());
144			painCave.isFatal = 1;
145			simError();
146			}
147
148			rdfStream.close();
149			}
150
151			}
152
153