applications/staticProps/RhoR.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).
 */

/* Calculates Rho(R) for nanoparticle with radius R*/
#include <algorithm>
#include <fstream>
#include "applications/staticProps/RhoR.hpp"
#include "utils/simError.h"
#include "utils/NumericConstant.hpp"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "brains/Thermo.hpp"
#include <math.h>

namespace OpenMD {

     
  RhoR::RhoR(SimInfo* info, const std::string& filename, const std::string& sele, RealType len, int nrbins, RealType particleR)
    : StaticAnalyser(info, filename), selectionScript_(sele),  evaluator_(info), seleMan_(info), len_(len), nRBins_(nrbins){
    
    
    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }
    
    
    deltaR_ = len_ /nRBins_;
    
    histogram_.resize(nRBins_);
    avgRhoR_.resize(nRBins_);
    particleR_ = particleR;
    setOutputName(getPrefix(filename) + ".RhoR");
  }
  

  void RhoR::process() {
   
    Thermo thermo(info_);
    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();
    nProcessed_ = nFrames/step_;
    
    std::fill(avgRhoR_.begin(), avgRhoR_.end(), 0.0);     
    std::fill(histogram_.begin(), histogram_.end(), 0);
    
    for (int istep = 0; istep < nFrames; istep += step_) {
      
      int i;    
      StuntDouble* sd;
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      Vector3d CenterOfMass = thermo.getCom();      
      
      if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
      }
      
      //determine which atom belongs to which slice
      for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
        Vector3d pos = sd->getPos();
        Vector3d r12 = CenterOfMass - pos;

        RealType distance = r12.length();
        
        if (distance < len_) {
          int whichBin = distance / deltaR_;
          histogram_[whichBin] += 1;
        }
        
      }

    }

    processHistogram(); 
    writeRhoR();
  }


  void RhoR::processHistogram() {

    RealType particleDensity =  3.0 * info_->getNGlobalMolecules() / (4.0 * NumericConstant::PI * pow(particleR_,3));
    RealType pairConstant = ( 4.0 * NumericConstant::PI * particleDensity ) / 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;

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

  }

 
  void RhoR::writeRhoR() {
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#radial density function rho(r)\n";
      rdfStream << "#r\tcorrValue\n";
      for (int i = 0; i < avgRhoR_.size(); ++i) {
        RealType r = deltaR_ * (i + 0.5);
        rdfStream << r << "\t" << avgRhoR_[i]/nProcessed_ << "\n";
      }
        
    } else {

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

    rdfStream.close();
  }

}

Revision:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (12 years, 10 months ago) by gezelter
File size:	5316 byte(s)
Log Message:	Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
#	User	Rev	Content
1	chuckv	1091	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	1091	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	1091	* 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	gezelter	1390	*
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	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	chuckv	1091	*/
42
43			/* Calculates Rho(R) for nanoparticle with radius R*/
44			#include <algorithm>
45			#include <fstream>
46			#include "applications/staticProps/RhoR.hpp"
47			#include "utils/simError.h"
48			#include "utils/NumericConstant.hpp"
49			#include "io/DumpReader.hpp"
50			#include "primitives/Molecule.hpp"
51	gezelter	1764	#include "brains/Thermo.hpp"
52	chuckv	1306	#include <math.h>
53	chuckv	1091
54	gezelter	1390	namespace OpenMD {
55	chuckv	1091
56
57			RhoR::RhoR(SimInfo* info, const std::string& filename, const std::string& sele, RealType len, int nrbins, RealType particleR)
58			: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info), len_(len), nRBins_(nrbins){
59
60
61			evaluator_.loadScriptString(sele);
62			if (!evaluator_.isDynamic()) {
63			seleMan_.setSelectionSet(evaluator_.evaluate());
64			}
65
66
67			deltaR_ = len_ /nRBins_;
68
69			histogram_.resize(nRBins_);
70			avgRhoR_.resize(nRBins_);
71			particleR_ = particleR;
72			setOutputName(getPrefix(filename) + ".RhoR");
73			}
74
75
76			void RhoR::process() {
77	gezelter	1764
78			Thermo thermo(info_);
79	chuckv	1091	DumpReader reader(info_, dumpFilename_);
80			int nFrames = reader.getNFrames();
81			nProcessed_ = nFrames/step_;
82
83			std::fill(avgRhoR_.begin(), avgRhoR_.end(), 0.0);
84			std::fill(histogram_.begin(), histogram_.end(), 0);
85
86			for (int istep = 0; istep < nFrames; istep += step_) {
87
88			int i;
89			StuntDouble* sd;
90			reader.readFrame(istep);
91			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
92	gezelter	1764	Vector3d CenterOfMass = thermo.getCom();
93	chuckv	1091
94			if (evaluator_.isDynamic()) {
95			seleMan_.setSelectionSet(evaluator_.evaluate());
96			}
97
98			//determine which atom belongs to which slice
99			for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
100			Vector3d pos = sd->getPos();
101			Vector3d r12 = CenterOfMass - pos;
102
103			RealType distance = r12.length();
104
105			if (distance < len_) {
106			int whichBin = distance / deltaR_;
107	chuckv	1092	histogram_[whichBin] += 1;
108	chuckv	1091	}
109
110			}
111
112			}
113
114			processHistogram();
115			writeRhoR();
116			}
117
118
119
120			void RhoR::processHistogram() {
121
122			RealType particleDensity = 3.0 * info_->getNGlobalMolecules() / (4.0 * NumericConstant::PI * pow(particleR_,3));
123			RealType pairConstant = ( 4.0 * NumericConstant::PI * particleDensity ) / 3.0;
124
125			for(int i = 0 ; i < histogram_.size(); ++i){
126
127			RealType rLower = i * deltaR_;
128			RealType rUpper = rLower + deltaR_;
129			RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
130			RealType nIdeal = volSlice * pairConstant;
131
132			avgRhoR_[i] += histogram_[i] / nIdeal;
133			}
134
135			}
136
137
138
139			void RhoR::writeRhoR() {
140			std::ofstream rdfStream(outputFilename_.c_str());
141			if (rdfStream.is_open()) {
142			rdfStream << "#radial density function rho(r)\n";
143			rdfStream << "#r\tcorrValue\n";
144			for (int i = 0; i < avgRhoR_.size(); ++i) {
145			RealType r = deltaR_ * (i + 0.5);
146			rdfStream << r << "\t" << avgRhoR_[i]/nProcessed_ << "\n";
147			}
148
149			} else {
150
151			sprintf(painCave.errMsg, "RhoR: unable to open %s\n", outputFilename_.c_str());
152			painCave.isFatal = 1;
153			simError();
154			}
155
156			rdfStream.close();
157			}
158
159			}
160