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]  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/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, RealType zlen, int nrbins, int nZBins)
    : RadialDistrFunc(info, filename, sele1, sele2), len_(len), zLen_(zlen), nRBins_(nrbins), nZBins_(nZBins){

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

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

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

  void GofRZ::initializeHistogram() {
    npairs_ = 0;
    for (unsigned 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 * 2.0;

    for(unsigned 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 (unsigned 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 = fabs(r12.z());

      if (Z <= zLen_) {
        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 (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 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:	1785
Committed:	Wed Aug 22 18:43:27 2012 UTC (12 years, 8 months ago) by jmichalk
File size:	5563 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)
#	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	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1440	*/
42
43			#include <algorithm>
44			#include <fstream>
45			#include "applications/staticProps/GofRZ.hpp"
46			#include "utils/simError.h"
47
48			namespace OpenMD {
49
50	gezelter	1782	GofRZ::GofRZ(SimInfo* info, const std::string& filename, const std::string& sele1,
51			const std::string& sele2, RealType len, RealType zlen, int nrbins, int nZBins)
52			: RadialDistrFunc(info, filename, sele1, sele2), len_(len), zLen_(zlen), nRBins_(nrbins), nZBins_(nZBins){
53	gezelter	1440
54	gezelter	1782	setOutputName(getPrefix(filename) + ".gofrz");
55	gezelter	1441
56	gezelter	1782	deltaR_ = len_ / (double) nRBins_;
57			deltaZ_ = zLen_ / (double)nZBins_; // for solvated_NVT.md4
58	chuckv	1444
59	gezelter	1782	histogram_.resize(nRBins_);
60			avgGofr_.resize(nRBins_);
61			for (int i = 0 ; i < nRBins_; ++i) {
62			histogram_[i].resize(nZBins_);
63			avgGofr_[i].resize(nZBins_);
64			}
65			}
66	chuckv	1445
67	gezelter	1782	void GofRZ::preProcess() {
68			for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
69			std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
70	gezelter	1440	}
71	gezelter	1782	}
72	gezelter	1440
73	jmichalk	1785	void GofRZ::initializeHistogram() {
74	gezelter	1782	npairs_ = 0;
75			for (unsigned int i = 0; i < histogram_.size(); ++i){
76			std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
77	gezelter	1440	}
78	gezelter	1782	}
79	gezelter	1440
80	gezelter	1782	void GofRZ::processHistogram() {
81			int nPairs = getNPairs();
82			RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
83			RealType pairDensity = nPairs / volume * 2.0;
84	gezelter	1440
85	gezelter	1782	for(unsigned int i = 0 ; i < histogram_.size(); ++i){
86	gezelter	1440
87	gezelter	1782	RealType rLower = i * deltaR_;
88			RealType rUpper = rLower + deltaR_;
89			RealType volSlice = NumericConstant::PI * deltaZ_ * (( rUpper * rUpper ) - ( rLower * rLower ));
90			RealType nIdeal = volSlice * pairDensity;
91	gezelter	1440
92	gezelter	1782	for (unsigned int j = 0; j < histogram_[i].size(); ++j){
93			avgGofr_[i][j] += histogram_[i][j] / nIdeal;
94			}
95	gezelter	1440	}
96
97	gezelter	1782	}
98	gezelter	1440
99	gezelter	1782	void GofRZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
100	gezelter	1440
101	gezelter	1782	if (sd1 == sd2) {
102			return;
103			}
104			Vector3d pos1 = sd1->getPos();
105			Vector3d pos2 = sd2->getPos();
106			Vector3d r12 = pos2 - pos1;
107			if (usePeriodicBoundaryConditions_)
108			currentSnapshot_->wrapVector(r12);
109	gezelter	1440
110	gezelter	1782	RealType distance = sqrt(pow(r12.x(), 2) + pow(r12.y(), 2));
111	gezelter	1440
112	gezelter	1782	int whichRBin = distance / deltaR_;
113
114			if (distance <= len_) {
115	gezelter	1440
116	gezelter	1782	RealType Z = fabs(r12.z());
117	gezelter	1440
118	gezelter	1782	if (Z <= zLen_) {
119			int whichZBin = Z / deltaZ_;
120
121			++histogram_[whichRBin][whichZBin];
122			++npairs_;
123			}
124	gezelter	1440	}
125	gezelter	1782	}
126	gezelter	1440
127	gezelter	1782	void GofRZ::writeRdf() {
128			std::ofstream rdfStream(outputFilename_.c_str());
129			if (rdfStream.is_open()) {
130			rdfStream << "#radial distribution function\n";
131			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
132			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
133			rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
134			rdfStream << "#nZBins =" << nZBins_ << "\t deltaZ = " << deltaZ_ << "\n";
135			for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
136			RealType r = deltaR_ * (i + 0.5);
137	gezelter	1440
138	gezelter	1782	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
139			RealType z = deltaZ_ * (j + 0.5);
140			rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
141			}
142	chuckv	1445
143	gezelter	1782	rdfStream << "\n";
144			}
145	chuckv	1445
146	gezelter	1782	} else {
147			sprintf(painCave.errMsg, "GofRZ: unable to open %s\n", outputFilename_.c_str());
148			painCave.isFatal = 1;
149			simError();
150	gezelter	1440	}
151
152	gezelter	1782	rdfStream.close();
153			}
154
155	gezelter	1440	}
156
157
Name	Value
svn:eol-style	native
svn:keywords	Author Id Revision Date