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root/OpenMD/trunk/src/applications/staticProps/DensityPlot.cpp
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Comparing trunk/src/applications/staticProps/DensityPlot.cpp (file contents):
Revision 1790 by gezelter, Thu Aug 30 17:18:22 2012 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

# Line 35 | Line 35
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 51 | Line 51 | namespace OpenMD {
51  
52   namespace OpenMD {
53  
54 +  
55 +  DensityPlot::DensityPlot(SimInfo* info, const std::string& filename,
56 +                           const std::string& sele, const std::string& cmSele,
57 +                           RealType len, int nrbins)
58 +    : StaticAnalyser(info, filename),
59 +      len_(len), halfLen_(len/2), nRBins_(nrbins),
60 +      selectionScript_(sele), seleMan_(info), evaluator_(info),
61 +      cmSelectionScript_(cmSele), cmSeleMan_(info), cmEvaluator_(info) {
62  
55 –  DensityPlot::DensityPlot(SimInfo* info, const std::string& filename, const std::string& sele, const std::string& cmSele, RealType len, int nrbins)
56 –    : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info),
57 –      cmSelectionScript_(cmSele), cmEvaluator_(info), cmSeleMan_(info),    
58 –      len_(len), nRBins_(nrbins), halfLen_(len/2)     {
59 –
63      setOutputName(getPrefix(filename) + ".density");
64 <
64 >    
65      deltaR_ = len_ /nRBins_;  
66      histogram_.resize(nRBins_);
67      density_.resize(nRBins_);
# Line 74 | Line 77 | namespace OpenMD {
77      cmEvaluator_.loadScriptString(cmSele);
78      if (!cmEvaluator_.isDynamic()) {
79        cmSeleMan_.setSelectionSet(cmEvaluator_.evaluate());
80 <    }
78 <    
79 <    
80 >    }    
81    }
82  
83    void DensityPlot::process() {
# Line 91 | Line 92 | namespace OpenMD {
92        reader.readFrame(i);
93        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
94  
95 <      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
95 >      for (mol = info_->beginMolecule(mi); mol != NULL;
96 >           mol = info_->nextMolecule(mi)) {
97          //change the positions of atoms which belong to the rigidbodies
98 <        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
98 >        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
99 >             rb = mol->nextRigidBody(rbIter)) {
100            rb->updateAtoms();
101          }
102          
# Line 112 | Line 115 | namespace OpenMD {
115        Mat3x3d hmat = currentSnapshot_->getHmat();
116        RealType slabVolume = deltaR_ * hmat(0, 0) * hmat(1, 1);
117        int k;
118 <      for (StuntDouble* sd = seleMan_.beginSelected(k); sd != NULL; sd = seleMan_.nextSelected(k)) {
118 >      for (StuntDouble* sd = seleMan_.beginSelected(k); sd != NULL;
119 >           sd = seleMan_.nextSelected(k)) {
120  
121  
122          if (!sd->isAtom()) {
123 <          sprintf( painCave.errMsg, "Can not calculate electron density if it is not atom\n");
123 >          sprintf( painCave.errMsg,
124 >                   "Can not calculate electron density if it is not atom\n");
125            painCave.severity = OPENMD_ERROR;
126            painCave.isFatal = 1;
127            simError();
# Line 166 | Line 171 | namespace OpenMD {
171      }
172    
173      int nProcessed = nFrames /step_;
174 <    std::transform(density_.begin(), density_.end(), density_.begin(), std::bind2nd(std::divides<RealType>(), nProcessed));  
174 >    std::transform(density_.begin(), density_.end(), density_.begin(),
175 >                   std::bind2nd(std::divides<RealType>(), nProcessed));  
176      writeDensity();
177          
178  
# Line 178 | Line 184 | namespace OpenMD {
184      int i;
185      Vector3d newOrigin(0.0);
186      RealType totalMass = 0.0;
187 <    for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) {
187 >    for (StuntDouble* sd = seleMan_.beginSelected(i); sd != NULL;
188 >         sd = seleMan_.nextSelected(i)) {
189        RealType mass = sd->getMass();
190        totalMass += mass;
191        newOrigin += sd->getPos() * mass;        
# Line 193 | Line 200 | namespace OpenMD {
200        ofs << "#g(x, y, z)\n";
201        ofs << "#selection: (" << selectionScript_ << ")\n";
202        ofs << "#cmSelection:(" << cmSelectionScript_ << ")\n";
203 <      ofs << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "\tdeltaR = " << deltaR_ <<"\n";
203 >      ofs << "#nRBins = " << nRBins_ << "\t maxLen = "
204 >          << len_ << "\tdeltaR = " << deltaR_ <<"\n";
205        for (unsigned int i = 0; i < histogram_.size(); ++i) {
206          ofs << i*deltaR_ - halfLen_ <<"\t" << density_[i]<< std::endl;
207        }        
208      } else {
209  
210 <      sprintf(painCave.errMsg, "DensityPlot: unable to open %s\n", outputFilename_.c_str());
210 >      sprintf(painCave.errMsg, "DensityPlot: unable to open %s\n",
211 >              outputFilename_.c_str());
212        painCave.isFatal = 1;
213        simError();  
214      }

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