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Comparing trunk/src/applications/staticProps/RhoZ.cpp (file contents):
Revision 769 by chuckv, Wed Nov 30 21:00:39 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
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
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
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.
# Line 38 | Line 29
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   *
42 – *  RhoZ.cpp
43 – *  OOPSE-2.0
44 – *
41   *  Created by Charles F. Vardeman II on 11/26/05.
42   *  @author  Charles F. Vardeman II
43 < *  @version $Id: RhoZ.cpp,v 1.1 2005-11-30 21:00:39 chuckv Exp $
43 > *  @version $Id: RhoZ.cpp,v 1.8 2009-11-25 20:01:59 gezelter Exp $
44   *
45   */
46  
# Line 54 | Line 50
50   #include <fstream>
51   #include "applications/staticProps/RhoZ.hpp"
52   #include "utils/simError.h"
53 <
54 < namespace oopse {
53 > #include "io/DumpReader.hpp"
54 > #include "primitives/Molecule.hpp"
55 > namespace OpenMD {
56    
57 <  RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins)
58 <  : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){
57 >  RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, int nzbins)
58 >    : StaticAnalyser(info, filename), selectionScript_(sele),  evaluator_(info), seleMan_(info), nZBins_(nzbins){
59 >
60 >    evaluator_.loadScriptString(sele);
61 >    if (!evaluator_.isDynamic()) {
62 >      seleMan_.setSelectionSet(evaluator_.evaluate());
63 >    }      
64      
65 <    deltaR_ = len_ /nRBins_;
65 >    // fixed number of bins
66 >
67 >    sliceSDLists_.resize(nZBins_);
68 >    density_.resize(nZBins_);
69      
65 –    histogram_.resize(nRBins_);
66 –    avgRhoZ_.resize(nRBins_);
67 –    
70      setOutputName(getPrefix(filename) + ".RhoZ");
71    }
72 <  
73 <  
74 <  void RhoZ::preProcess() {
75 <    std::fill(avgRhoZ_.begin(), avgRhoZ_.end(), 0.0);    
76 <  }
77 <  
78 <  void RhoZ::initalizeHistogram() {
79 <    std::fill(histogram_.begin(), histogram_.end(), 0);
80 <  }
81 <  
82 <  
83 <  void RhoZ::processHistogram() {
84 <    
85 <    int nPairs = getNPairs();
86 <    double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
87 <    double pairDensity = nPairs /volume * 2.0;
88 <    double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
89 <    
90 <    for(int i = 0 ; i < histogram_.size(); ++i){
72 >
73 >  void RhoZ::process() {
74 >    Molecule* mol;
75 >    RigidBody* rb;
76 >    StuntDouble* sd;
77 >    SimInfo::MoleculeIterator mi;
78 >    Molecule::RigidBodyIterator rbIter;
79 >
80 >    DumpReader reader(info_, dumpFilename_);    
81 >    int nFrames = reader.getNFrames();
82 >    nProcessed_ = nFrames/step_;
83 >
84 >    for (int istep = 0; istep < nFrames; istep += step_) {
85 >      reader.readFrame(istep);
86 >      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
87 >
88 >      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
89 >        //change the positions of atoms which belong to the rigidbodies
90 >        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
91 >          rb->updateAtoms();
92 >        }
93 >      }
94 >
95 >      int i;    
96 >      for (i=0; i < nZBins_; i++) {
97 >        sliceSDLists_[i].clear();
98 >      }
99 >
100 >      RealType sliceVolume = currentSnapshot_->getVolume() /nZBins_;
101 >      Mat3x3d hmat = currentSnapshot_->getHmat();
102 >      zBox_.push_back(hmat(2,2));
103        
104 <      double rLower = i * deltaR_;
105 <      double rUpper = rLower + deltaR_;
106 <      double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
107 <      double nIdeal = volSlice * pairConstant;
104 >      RealType halfBoxZ_ = hmat(2,2) / 2.0;      
105 >
106 >      if (evaluator_.isDynamic()) {
107 >        seleMan_.setSelectionSet(evaluator_.evaluate());
108 >      }
109        
110 <      avgRhoZ_[i] += histogram_[i] / nIdeal;    
110 >      //wrap the stuntdoubles into a cell      
111 >      for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
112 >        Vector3d pos = sd->getPos();
113 >        if (usePeriodicBoundaryConditions_)
114 >          currentSnapshot_->wrapVector(pos);
115 >        sd->setPos(pos);
116 >      }
117 >      
118 >      //determine which atom belongs to which slice
119 >      for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
120 >        Vector3d pos = sd->getPos();
121 >        // shift molecules by half a box to have bins start at 0
122 >        int binNo = int(nZBins_ * (halfBoxZ_ + pos.z()) / hmat(2,2));
123 >        sliceSDLists_[binNo].push_back(sd);
124 >      }
125 >
126 >      //loop over the slices to calculate the densities
127 >      for (i = 0; i < nZBins_; i++) {
128 >        RealType totalMass = 0;
129 >        for (int k = 0; k < sliceSDLists_[i].size(); ++k) {
130 >          totalMass += sliceSDLists_[i][k]->getMass();
131 >        }
132 >        density_[i] += totalMass/sliceVolume;
133 >      }
134      }
135      
136 +    writeDensity();
137 +
138    }
139    
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 –  }
140    
141    
142 <  void RhoZ::writeRdf() {
142 >  void RhoZ::writeDensity() {
143 >
144 >    // compute average box length:
145 >    std::vector<RealType>::iterator j;
146 >    RealType zSum = 0.0;
147 >    for (j = zBox_.begin(); j != zBox_.end(); ++j) {
148 >      zSum += *j;      
149 >    }
150 >    RealType zAve = zSum / zBox_.size();
151 >
152      std::ofstream rdfStream(outputFilename_.c_str());
153      if (rdfStream.is_open()) {
154 <      rdfStream << "#radial distribution function\n";
155 <      rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
156 <      rdfStream << "selection2: (" << selectionScript2_ << ")\n";
157 <      rdfStream << "#r\tcorrValue\n";
158 <      for (int i = 0; i < avgRhoZ_.size(); ++i) {
159 <        double r = deltaR_ * (i + 0.5);
160 <        rdfStream << r << "\t" << avgRhoZ_[i]/nProcessed_ << "\n";
154 >      rdfStream << "#RhoZ\n";
155 >      rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
156 >      rdfStream << "#selection: (" << selectionScript_ << ")\n";
157 >      rdfStream << "#z\tdensity\n";
158 >      for (int i = 0; i < density_.size(); ++i) {
159 >        RealType z = zAve * (i+0.5)/density_.size();
160 >        rdfStream << z << "\t" << 1.660535*density_[i]/nProcessed_ << "\n";
161        }
162        
163      } else {

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