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Comparing trunk/src/applications/staticProps/RhoZ.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 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 1.5 2006-05-17 21:51:42 tim Exp $
43 > *  @version $Id: RhoZ.cpp,v 1.8 2009-11-25 20:01:59 gezelter Exp $
44   *
45   */
46  
# Line 56 | Line 52
52   #include "utils/simError.h"
53   #include "io/DumpReader.hpp"
54   #include "primitives/Molecule.hpp"
55 < namespace oopse {
55 > namespace OpenMD {
56    
57 <  RhoZ::RhoZ(SimInfo* info, const std::string& filename, const std::string& sele, RealType len, int nrbins)
58 <    : StaticAnalyser(info, filename), selectionScript_(sele),  evaluator_(info), seleMan_(info), 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 <    }
68 <      
63 >    }      
64      
65 <    deltaR_ = len_ /(nRBins_);
65 >    // fixed number of bins
66 >
67 >    sliceSDLists_.resize(nZBins_);
68 >    density_.resize(nZBins_);
69      
72 –    sliceSDLists_.resize(nRBins_);
73 –    density_.resize(nRBins_);
74 –    
70      setOutputName(getPrefix(filename) + ".RhoZ");
71    }
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 < nRBins_; i++) {
96 >      for (i=0; i < nZBins_; i++) {
97          sliceSDLists_[i].clear();
98        }
99  
100 <      StuntDouble* sd;
101 <      reader.readFrame(istep);
102 <      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
100 >      RealType sliceVolume = currentSnapshot_->getVolume() /nZBins_;
101 >      Mat3x3d hmat = currentSnapshot_->getHmat();
102 >      zBox_.push_back(hmat(2,2));
103        
104 <      RealType sliceVolume = currentSnapshot_->getVolume() /nRBins_;
95 <      //assume simulation box will never change
96 <      //Mat3x3d hmat = currentSnapshot_->getHmat();
97 <      RealType halfBoxZ_ = len_ / 2.0;      
98 <        
99 <        if (evaluator_.isDynamic()) {
100 <          seleMan_.setSelectionSet(evaluator_.evaluate());
101 <        }
104 >      RealType halfBoxZ_ = hmat(2,2) / 2.0;      
105  
106 <        //wrap the stuntdoubles into a cell      
107 <        for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
108 <            Vector3d pos = sd->getPos();
109 <            currentSnapshot_->wrapVector(pos);
110 <            sd->setPos(pos);
111 <        }
106 >      if (evaluator_.isDynamic()) {
107 >        seleMan_.setSelectionSet(evaluator_.evaluate());
108 >      }
109 >      
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 <        //determine which atom belongs to which slice
127 <        for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
128 <           Vector3d pos = sd->getPos();
129 <           //int binNo = (pos.z() /deltaR_) - 1;
130 <           int binNo = (pos.z() + halfBoxZ_) /deltaR_   ;
115 <           //std::cout << "pos.z = " << pos.z() << " halfBoxZ_ = " << halfBoxZ_ << " deltaR_ = "  << deltaR_ << " binNo = " << binNo << "\n";
116 <           sliceSDLists_[binNo].push_back(sd);
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 <
133 <        //loop over the slices to calculate the densities
120 <        for (i = 0; i < nRBins_; i++) {
121 <            RealType totalMass = 0;
122 <            for (int k = 0; k < sliceSDLists_[i].size(); ++k) {
123 <                totalMass += sliceSDLists_[i][k]->getMass();
124 <            }
125 <            density_[i] += totalMass/sliceVolume;
126 <        }
132 >        density_[i] += totalMass/sliceVolume;
133 >      }
134      }
135 <
135 >    
136      writeDensity();
137  
138    }
139 <
140 <
141 <    
139 >  
140 >  
141 >  
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 << "#RhoZ\n";
# Line 140 | Line 156 | namespace oopse {
156        rdfStream << "#selection: (" << selectionScript_ << ")\n";
157        rdfStream << "#z\tdensity\n";
158        for (int i = 0; i < density_.size(); ++i) {
159 <        RealType r = deltaR_ * (i + 0.5);
160 <        rdfStream << r << "\t" << 1.660535*density_[i]/nProcessed_ << "\n";
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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