applications/staticProps/RhoZ.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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 *
 *
 *  RhoZ.cpp
 *  OOPSE-2.0
 *
 *  Created by Charles F. Vardeman II on 11/26/05.
 *  @author  Charles F. Vardeman II 
 *  @version $Id: RhoZ.cpp,v 1.1 2005-11-30 21:00:39 chuckv Exp $
 *
 */

/* Calculates Rho(Z) for density profile of liquid slab. */

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

namespace oopse {
  
  RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins)
  : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){
    
    deltaR_ = len_ /nRBins_;
    
    histogram_.resize(nRBins_);
    avgRhoZ_.resize(nRBins_);
    
    setOutputName(getPrefix(filename) + ".RhoZ");
  }
  
  
  void RhoZ::preProcess() {
    std::fill(avgRhoZ_.begin(), avgRhoZ_.end(), 0.0);    
  }
  
  void RhoZ::initalizeHistogram() {
    std::fill(histogram_.begin(), histogram_.end(), 0);
  }
  
  
  void RhoZ::processHistogram() {
    
    int nPairs = getNPairs();
    double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    double pairDensity = nPairs /volume * 2.0;
    double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
    
    for(int i = 0 ; i < histogram_.size(); ++i){
      
      double rLower = i * deltaR_;
      double rUpper = rLower + deltaR_;
      double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
      double nIdeal = volSlice * pairConstant;
      
      avgRhoZ_[i] += histogram_[i] / nIdeal;    
    }
    
  }
  
  void RhoZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
    
    if (sd1 == sd2) {
      return;
    }
    
    Vector3d pos1 = sd1->getPosZ();
    Vector3d pos2 = sd2->getPosZ();
    Vector3d r12 = pos2 - pos1;
    currentSnapshot_->wrapVector(r12);
    
    double distance = r12.length();
    
    if (distance < len_) {
      int whichBin = distance / deltaR_;
      histogram_[whichBin] += 2;
    }
  }
  
  
  void RhoZ::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 << "#r\tcorrValue\n";
      for (int i = 0; i < avgRhoZ_.size(); ++i) {
        double r = deltaR_ * (i + 0.5);
        rdfStream << r << "\t" << avgRhoZ_[i]/nProcessed_ << "\n";
      }
      
    } else {
      
      sprintf(painCave.errMsg, "RhoZ: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }
    
    rdfStream.close();
  }
  
}

Revision:	769
Committed:	Wed Nov 30 21:00:39 2005 UTC (19 years, 5 months ago) by chuckv
File size:	4788 byte(s)
Log Message:	Code to calculate rho(Z) to calculate density profiles for water slabs.
#	User	Rev	Content
1	chuckv	769	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*
41			*
42			* RhoZ.cpp
43			* OOPSE-2.0
44			*
45			* Created by Charles F. Vardeman II on 11/26/05.
46			* @author Charles F. Vardeman II
47			* @version $Id: RhoZ.cpp,v 1.1 2005-11-30 21:00:39 chuckv Exp $
48			*
49			*/
50
51			/* Calculates Rho(Z) for density profile of liquid slab. */
52
53			#include <algorithm>
54			#include <fstream>
55			#include "applications/staticProps/RhoZ.hpp"
56			#include "utils/simError.h"
57
58			namespace oopse {
59
60			RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins)
61			: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){
62
63			deltaR_ = len_ /nRBins_;
64
65			histogram_.resize(nRBins_);
66			avgRhoZ_.resize(nRBins_);
67
68			setOutputName(getPrefix(filename) + ".RhoZ");
69			}
70
71
72			void RhoZ::preProcess() {
73			std::fill(avgRhoZ_.begin(), avgRhoZ_.end(), 0.0);
74			}
75
76			void RhoZ::initalizeHistogram() {
77			std::fill(histogram_.begin(), histogram_.end(), 0);
78			}
79
80
81			void RhoZ::processHistogram() {
82
83			int nPairs = getNPairs();
84			double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
85			double pairDensity = nPairs /volume * 2.0;
86			double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
87
88			for(int i = 0 ; i < histogram_.size(); ++i){
89
90			double rLower = i * deltaR_;
91			double rUpper = rLower + deltaR_;
92			double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
93			double nIdeal = volSlice * pairConstant;
94
95			avgRhoZ_[i] += histogram_[i] / nIdeal;
96			}
97
98			}
99
100			void RhoZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
101
102			if (sd1 == sd2) {
103			return;
104			}
105
106			Vector3d pos1 = sd1->getPosZ();
107			Vector3d pos2 = sd2->getPosZ();
108			Vector3d r12 = pos2 - pos1;
109			currentSnapshot_->wrapVector(r12);
110
111			double distance = r12.length();
112
113			if (distance < len_) {
114			int whichBin = distance / deltaR_;
115			histogram_[whichBin] += 2;
116			}
117			}
118
119
120			void RhoZ::writeRdf() {
121			std::ofstream rdfStream(outputFilename_.c_str());
122			if (rdfStream.is_open()) {
123			rdfStream << "#radial distribution function\n";
124			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
125			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
126			rdfStream << "#r\tcorrValue\n";
127			for (int i = 0; i < avgRhoZ_.size(); ++i) {
128			double r = deltaR_ * (i + 0.5);
129			rdfStream << r << "\t" << avgRhoZ_[i]/nProcessed_ << "\n";
130			}
131
132			} else {
133
134			sprintf(painCave.errMsg, "RhoZ: unable to open %s\n", outputFilename_.c_str());
135			painCave.isFatal = 1;
136			simError();
137			}
138
139			rdfStream.close();
140			}
141
142			}
143