applications/staticProps/GofR.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.
 */

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

namespace oopse {

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

      deltaR_ = len_ /nRBins_;
    
      histogram_.resize(nRBins_);
      avgGofr_.resize(nRBins_);

      setOutputName(getPrefix(filename) + ".gofr");
    }


  void GofR::preProcess() {
    std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0);    
  }

  void GofR::initalizeHistogram() {
    std::fill(histogram_.begin(), histogram_.end(), 0);
  }


  void GofR::processHistogram() {

    int nPairs = getNPairs();
    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    RealType pairDensity = nPairs /volume * 2.0;
    RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;

    for(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;

      avgGofr_[i] += histogram_[i] / nIdeal;    
    }

  }

  void GofR::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();

    if (distance < len_) {
      int whichBin = distance / deltaR_;
      histogram_[whichBin] += 2;
    }
  }


  void GofR::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 < avgGofr_.size(); ++i) {
        RealType r = deltaR_ * (i + 0.5);
        rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n";
      }
        
    } else {

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

    rdfStream.close();
  }

}

Revision:	3054
Committed:	Wed Oct 18 21:58:48 2006 UTC (17 years, 9 months ago) by gezelter
File size:	4520 byte(s)
Log Message:	fixing a wrapVector problem in staticProps, also making Shifted force and electrostatic damping the default behavior
#	User	Rev	Content
1	tim	1990	/*
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			#include <algorithm>
43			#include <fstream>
44			#include "applications/staticProps/GofR.hpp"
45	tim	1991	#include "utils/simError.h"
46	tim	1990
47			namespace oopse {
48
49	tim	2759	GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins)
50	tim	2038	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){
51	tim	1990
52	gezelter	2204	deltaR_ = len_ /nRBins_;
53	tim	1994
54	gezelter	2204	histogram_.resize(nRBins_);
55			avgGofr_.resize(nRBins_);
56	tim	1995
57	gezelter	2204	setOutputName(getPrefix(filename) + ".gofr");
58			}
59	tim	1990
60
61	gezelter	2204	void GofR::preProcess() {
62	tim	1990	std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0);
63	gezelter	2204	}
64	tim	1990
65	gezelter	2204	void GofR::initalizeHistogram() {
66	tim	1990	std::fill(histogram_.begin(), histogram_.end(), 0);
67	gezelter	2204	}
68	tim	1990
69
70	gezelter	2204	void GofR::processHistogram() {
71	tim	1990
72	tim	2037	int nPairs = getNPairs();
73	tim	2759	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
74			RealType pairDensity = nPairs /volume * 2.0;
75			RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
76	tim	1990
77			for(int i = 0 ; i < histogram_.size(); ++i){
78
79	tim	2759	RealType rLower = i * deltaR_;
80			RealType rUpper = rLower + deltaR_;
81			RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
82			RealType nIdeal = volSlice * pairConstant;
83	tim	1990
84	gezelter	2204	avgGofr_[i] += histogram_[i] / nIdeal;
85	tim	1990	}
86
87	gezelter	2204	}
88	tim	1990
89	gezelter	2204	void GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
90	tim	1990
91			if (sd1 == sd2) {
92	gezelter	2204	return;
93	tim	1990	}
94
95			Vector3d pos1 = sd1->getPos();
96			Vector3d pos2 = sd2->getPos();
97	tim	2045	Vector3d r12 = pos2 - pos1;
98	gezelter	3054	if (usePeriodicBoundaryConditions_)
99			currentSnapshot_->wrapVector(r12);
100	tim	1990
101	tim	2759	RealType distance = r12.length();
102	tim	1991
103	tim	2012	if (distance < len_) {
104	gezelter	2204	int whichBin = distance / deltaR_;
105			histogram_[whichBin] += 2;
106	tim	2012	}
107	gezelter	2204	}
108	tim	1990
109
110	gezelter	2204	void GofR::writeRdf() {
111	tim	1990	std::ofstream rdfStream(outputFilename_.c_str());
112			if (rdfStream.is_open()) {
113	gezelter	2204	rdfStream << "#radial distribution function\n";
114			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
115			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
116			rdfStream << "#r\tcorrValue\n";
117			for (int i = 0; i < avgGofr_.size(); ++i) {
118	tim	2759	RealType r = deltaR_ * (i + 0.5);
119	gezelter	2204	rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n";
120			}
121	tim	1990
122			} else {
123
124	gezelter	2204	sprintf(painCave.errMsg, "GofR: unable to open %s\n", outputFilename_.c_str());
125			painCave.isFatal = 1;
126			simError();
127	tim	1990	}
128	tim	1991
129			rdfStream.close();
130	gezelter	2204	}
131	tim	1990
132			}
133