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){

      setOutputName(getPrefix(filename) + ".gofrz");

      deltaR_ = len_ / (double) nRBins_;
      deltaZ_ = 86.52361692 / (double)nZBins_;    // for solvated_NVT.md4

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

  void GofRZ::initalizeHistogram() {
    npairs_ = 0;
    for (int i = 0; i < histogram_[i].size(); ++i){
      histogram_[i].resize(nRBins_);
      for (int j = 0; j < histogram_[i][j].size(); ++j){
      std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
      }
    }
  }
  
  void GofRZ::processHistogram() {
    int nPairs = getNPairs();
    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    RealType pairDensity = nPairs / volume * 2.0;

    for(int i = 0 ; i < histogram_[i].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][j].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 = fabs(r12.z());

      if (Z <= 86.52361692) {
        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_ << "\t deltaZ = " << deltaZ_ << "\n";
      for (int i = 0; i < avgGofr_[i].size(); ++i) {
        RealType r = deltaR_ * (i + 0.5);

        for(int j = 0; j < avgGofr_[i][j].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:	1444
Committed:	Tue Jun 8 18:35:22 2010 UTC (14 years, 10 months ago) by chuckv
File size:	5746 byte(s)
Log Message:	More changes to gofrz.
#	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	gezelter	1441	setOutputName(getPrefix(filename) + ".gofrz");
54
55	gezelter	1440	deltaR_ = len_ / (double) nRBins_;
56	chuckv	1444	deltaZ_ = 86.52361692 / (double)nZBins_; // for solvated_NVT.md4
57
58	gezelter	1440	histogram_.resize(nRBins_);
59			avgGofr_.resize(nRBins_);
60			for (int i = 0 ; i < nRBins_; ++i) {
61	chuckv	1444	histogram_[i].resize(nRBins_);
62			avgGofr_[i].resize(nRBins_);
63			for (int j = 0 ; j < nZBins_; ++j) {
64			histogram_[i][j].resize(nZBins_);
65			avgGofr_[i][j].resize(nZBins_);
66	gezelter	1440	}
67			}
68	chuckv	1444
69			}
70	gezelter	1440	void GofRZ::preProcess() {
71	chuckv	1444	for (int i = 0; i < avgGofr_[i].size(); ++i) {
72			avgGofr_[i].resize(nRBins_);
73			for (int j = 0; j < avgGofr_[i][j].size(); ++j) {
74			std::fill(avgGofr_[i][j].begin(), avgGofr_[i][j].end(), 0);
75			}
76	gezelter	1440	}
77			}
78
79			void GofRZ::initalizeHistogram() {
80			npairs_ = 0;
81	chuckv	1444	for (int i = 0; i < histogram_[i].size(); ++i){
82			histogram_[i].resize(nRBins_);
83			for (int j = 0; j < histogram_[i][j].size(); ++j){
84			std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
85			}
86	gezelter	1440	}
87			}
88
89			void GofRZ::processHistogram() {
90			int nPairs = getNPairs();
91			RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
92	chuckv	1444	RealType pairDensity = nPairs / volume * 2.0;
93	gezelter	1440
94	chuckv	1444	for(int i = 0 ; i < histogram_[i].size(); ++i){
95	gezelter	1440
96			RealType rLower = i * deltaR_;
97			RealType rUpper = rLower + deltaR_;
98			RealType volSlice = NumericConstant::PI * deltaZ_ * (( rUpper * rUpper ) - ( rLower * rLower ));
99			RealType nIdeal = volSlice * pairDensity;
100
101	chuckv	1444	for (int j = 0; j < histogram_[i][j].size(); ++j){
102	gezelter	1440	avgGofr_[i][j] += histogram_[i][j] / nIdeal;
103			}
104			}
105
106			}
107
108			void GofRZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
109
110			if (sd1 == sd2) {
111			return;
112			}
113			Vector3d pos1 = sd1->getPos();
114			Vector3d pos2 = sd2->getPos();
115			Vector3d r12 = pos2 - pos1;
116			if (usePeriodicBoundaryConditions_)
117			currentSnapshot_->wrapVector(r12);
118
119			RealType distance = sqrt(pow(r12.x(), 2) + pow(r12.y(), 2));
120
121			int whichRBin = distance / deltaR_;
122
123			if (distance <= len_) {
124
125	chuckv	1444	RealType Z = fabs(r12.z());
126	gezelter	1440
127	chuckv	1444	if (Z <= 86.52361692) {
128	gezelter	1440	int whichZBin = Z / deltaZ_;
129	chuckv	1444
130	gezelter	1440	++histogram_[whichRBin][whichZBin];
131			++npairs_;
132			}
133			}
134			}
135
136			void GofRZ::writeRdf() {
137			std::ofstream rdfStream(outputFilename_.c_str());
138			if (rdfStream.is_open()) {
139			rdfStream << "#radial distribution function\n";
140			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
141			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
142			rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
143	chuckv	1444	rdfStream << "#nZBins =" << nZBins_ << "\t deltaZ = " << deltaZ_ << "\n";
144			for (int i = 0; i < avgGofr_[i].size(); ++i) {
145	gezelter	1440	RealType r = deltaR_ * (i + 0.5);
146
147	chuckv	1444	for(int j = 0; j < avgGofr_[i][j].size(); ++j) {
148	gezelter	1440	RealType z = deltaZ_ * (j + 0.5);
149			rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
150			}
151
152			rdfStream << "\n";
153			}
154
155			} else {
156			sprintf(painCave.errMsg, "GofRZ: unable to open %s\n", outputFilename_.c_str());
157			painCave.isFatal = 1;
158			simError();
159			}
160
161			rdfStream.close();
162			}
163
164			}
165
166
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