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root/OpenMD/trunk/src/applications/staticProps/RNEMDStats.cpp
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Comparing:
branches/development/src/applications/staticProps/RNEMDStats.cpp (file contents), Revision 1865 by gezelter, Wed Apr 17 18:24:08 2013 UTC vs.
trunk/src/applications/staticProps/RNEMDStats.cpp (file contents), Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

# Line 43 | Line 43
43   #include <algorithm>
44   #include <fstream>
45   #include "applications/staticProps/RNEMDStats.hpp"
46 + #include "primitives/Molecule.hpp"
47   #include "utils/PhysicalConstants.hpp"
48  
49   namespace OpenMD {
# Line 84 | Line 85 | namespace OpenMD {
85      data_.push_back(density);
86    }
87  
88 <  void RNEMDZ::processStuntDouble(StuntDouble* sd, int bin) {
89 <    RealType mass = sd->getMass();
89 <    Vector3d pos = sd->getPos();    
90 <    Vector3d vel = sd->getVel();
91 <    RealType KE = 0.5 * (mass * vel.lengthSquare());
92 <    int dof = 3;
88 >  void RNEMDZ::processFrame(int istep) {
89 >    RealType z;
90  
91 <    if (sd->isDirectional()) {
92 <      Vector3d angMom = sd->getJ();
93 <      Mat3x3d I = sd->getI();
94 <      if (sd->isLinear()) {
95 <        int i = sd->linearAxis();
96 <        int j = (i + 1) % 3;
97 <        int k = (i + 2) % 3;
98 <        KE += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
99 <                     angMom[k] * angMom[k] / I(k, k));
100 <        dof += 2;
101 <      } else {
102 <        KE += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
103 <                     angMom[1] * angMom[1] / I(1, 1) +
104 <                     angMom[2] * angMom[2] / I(2, 2));
105 <        dof += 3;
91 >    hmat_ = currentSnapshot_->getHmat();
92 >    for (int i = 0; i < nBins_; i++) {
93 >      z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat_(2,2);
94 >      dynamic_cast<Accumulator*>(z_->accumulator[i])->add(z);
95 >    }
96 >    volume_ = currentSnapshot_->getVolume();
97 >
98 >
99 >    Molecule* mol;
100 >    RigidBody* rb;
101 >    StuntDouble* sd;
102 >    SimInfo::MoleculeIterator mi;
103 >    Molecule::RigidBodyIterator rbIter;
104 >    int i;
105 >
106 >    vector<RealType> binMass(nBins_, 0.0);
107 >    vector<Vector3d> binP(nBins_, V3Zero);
108 >    vector<RealType> binKE(nBins_, 0.0);
109 >    vector<unsigned int> binDof(nBins_, 0);
110 >    
111 >    for (mol = info_->beginMolecule(mi); mol != NULL;
112 >         mol = info_->nextMolecule(mi)) {
113 >      
114 >      // change the positions of atoms which belong to the rigidbodies
115 >      
116 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
117 >           rb = mol->nextRigidBody(rbIter)) {
118 >        rb->updateAtomVel();
119        }
120      }
121 +  
122 +    if (evaluator_.isDynamic()) {
123 +      seleMan_.setSelectionSet(evaluator_.evaluate());
124 +    }
125      
126 <    RealType temp = 2.0 * KE / (dof * PhysicalConstants::kb *
113 <                                PhysicalConstants::energyConvert);
114 <    RealType den = mass * nBins_ * PhysicalConstants::densityConvert / volume_;
126 >    // loop over the selected atoms:
127      
128 <    dynamic_cast<Accumulator *>(temperature->accumulator[bin])->add(temp);
129 <    dynamic_cast<VectorAccumulator *>(velocity->accumulator[bin])->add(vel);
130 <    dynamic_cast<Accumulator *>(density->accumulator[bin])->add(den);
128 >    for (sd = seleMan_.beginSelected(i); sd != NULL;
129 >         sd = seleMan_.nextSelected(i)) {
130 >      
131 >      // figure out where that object is:
132 >      Vector3d pos = sd->getPos();
133 >      Vector3d vel = sd->getVel();
134 >      RealType m = sd->getMass();
135  
136 +      int bin = getBin(pos);
137 +
138 +      binMass[bin] += m;
139 +      binP[bin] += m * vel;
140 +      binKE[bin] += 0.5 * (m * vel.lengthSquare());
141 +      binDof[bin] += 3;
142 +      
143 +      if (sd->isDirectional()) {
144 +        Vector3d angMom = sd->getJ();
145 +        Mat3x3d I = sd->getI();
146 +        if (sd->isLinear()) {
147 +          int i = sd->linearAxis();
148 +          int j = (i + 1) % 3;
149 +          int k = (i + 2) % 3;
150 +          binKE[bin] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
151 +                               angMom[k] * angMom[k] / I(k, k));
152 +          binDof[bin] += 2;
153 +        } else {
154 +          binKE[bin] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
155 +                               angMom[1] * angMom[1] / I(1, 1) +
156 +                               angMom[2] * angMom[2] / I(2, 2));
157 +          binDof[bin] += 3;
158 +        }
159 +      }
160 +    }
161 +    
162 +    for (int i = 0; i < nBins_; i++) {
163 +
164 +      if (binDof[i] > 0) {
165 +        RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb *
166 +                                          PhysicalConstants::energyConvert);
167 +        RealType den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
168 +          / volume_;
169 +        Vector3d vel = binP[i] / binMass[i];
170 +
171 +        dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp);
172 +        dynamic_cast<VectorAccumulator *>(velocity->accumulator[i])->add(vel);
173 +        dynamic_cast<Accumulator *>(density->accumulator[i])->add(den);
174 +        dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1);
175 +      }
176 +    }
177    }
178 +  
179 +  void RNEMDZ::processStuntDouble(StuntDouble* sd, int bin) {
180 +  }
181  
182    RNEMDR::RNEMDR(SimInfo* info, const std::string& filename,
183                   const std::string& sele, int nrbins)
# Line 138 | Line 198 | namespace OpenMD {
198      
199      angularVelocity = new OutputData;
200      angularVelocity->units = "angstroms^2/fs";
201 <    angularVelocity->title =  "Velocity";  
201 >    angularVelocity->title =  "Angular Velocity";  
202      angularVelocity->dataType = odtVector3;
203      angularVelocity->dataHandling = odhAverage;
204      angularVelocity->accumulator.reserve(nBins_);
# Line 157 | Line 217 | namespace OpenMD {
217      data_.push_back(density);
218    }
219  
160 –  void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) {
161 –    RealType mass = sd->getMass();
162 –    Vector3d vel = sd->getVel();
163 –    Vector3d rPos = sd->getPos() - coordinateOrigin_;
164 –    Vector3d aVel = cross(rPos, vel);
220  
221 <    RealType KE = 0.5 * (mass * vel.lengthSquare());
167 <    int dof = 3;
221 >  void RNEMDR::processFrame(int istep) {
222  
223 <    if (sd->isDirectional()) {
224 <      Vector3d angMom = sd->getJ();
225 <      Mat3x3d I = sd->getI();
226 <      if (sd->isLinear()) {
227 <        int i = sd->linearAxis();
228 <        int j = (i + 1) % 3;
229 <        int k = (i + 2) % 3;
230 <        KE += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
231 <                     angMom[k] * angMom[k] / I(k, k));
232 <        dof += 2;
233 <      } else {
234 <        KE += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
235 <                     angMom[1] * angMom[1] / I(1, 1) +
236 <                     angMom[2] * angMom[2] / I(2, 2));
237 <        dof += 3;
223 >    Molecule* mol;
224 >    RigidBody* rb;
225 >    StuntDouble* sd;
226 >    SimInfo::MoleculeIterator mi;
227 >    Molecule::RigidBodyIterator rbIter;
228 >    int i;
229 >
230 >    vector<RealType> binMass(nBins_, 0.0);
231 >    vector<Mat3x3d>  binI(nBins_);
232 >    vector<Vector3d> binL(nBins_, V3Zero);
233 >    vector<RealType> binKE(nBins_, 0.0);
234 >    vector<int> binDof(nBins_, 0);
235 >    
236 >    for (mol = info_->beginMolecule(mi); mol != NULL;
237 >         mol = info_->nextMolecule(mi)) {
238 >      
239 >      // change the positions of atoms which belong to the rigidbodies
240 >      
241 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
242 >           rb = mol->nextRigidBody(rbIter)) {
243 >        rb->updateAtomVel();
244        }
245      }
246 +  
247 +    if (evaluator_.isDynamic()) {
248 +      seleMan_.setSelectionSet(evaluator_.evaluate());
249 +    }
250      
251 <    RealType temp = 2.0 * KE / (dof * PhysicalConstants::kb *
188 <                                PhysicalConstants::energyConvert);
189 <
190 <    RealType rinner = (RealType)bin * binWidth_;
191 <    RealType router = (RealType)(bin+1) * binWidth_;
192 <    RealType den = mass * 3.0 * PhysicalConstants::densityConvert
193 <      / (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));  
251 >    // loop over the selected atoms:
252      
253 <    dynamic_cast<Accumulator *>(temperature->accumulator[bin])->add(temp);
254 <    dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[bin])->add(aVel);
197 <    dynamic_cast<Accumulator *>(density->accumulator[bin])->add(den);
253 >    for (sd = seleMan_.beginSelected(i); sd != NULL;
254 >         sd = seleMan_.nextSelected(i)) {
255  
256 +      // figure out where that object is:
257 +      int bin = getBin( sd->getPos() );  
258 +
259 +      if (bin >= 0 && bin < nBins_)  {
260 +
261 +        Vector3d rPos = sd->getPos() - coordinateOrigin_;
262 +        Vector3d vel = sd->getVel();      
263 +        RealType m = sd->getMass();
264 +        Vector3d L = m * cross(rPos, vel);
265 +        Mat3x3d I(0.0);
266 +        I = outProduct(rPos, rPos) * m;
267 +        RealType r2 = rPos.lengthSquare();
268 +        I(0, 0) += m * r2;
269 +        I(1, 1) += m * r2;
270 +        I(2, 2) += m * r2;      
271 +
272 +        binMass[bin] += m;
273 +        binI[bin] += I;
274 +        binL[bin] += L;
275 +        binKE[bin] += 0.5 * (m * vel.lengthSquare());
276 +        binDof[bin] += 3;
277 +        
278 +        if (sd->isDirectional()) {
279 +          Vector3d angMom = sd->getJ();
280 +          Mat3x3d Ia = sd->getI();
281 +          if (sd->isLinear()) {
282 +            int i = sd->linearAxis();
283 +            int j = (i + 1) % 3;
284 +            int k = (i + 2) % 3;
285 +            binKE[bin] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) +
286 +                                 angMom[k] * angMom[k] / Ia(k, k));
287 +            binDof[bin] += 2;
288 +          } else {
289 +            binKE[bin] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
290 +                                 angMom[1] * angMom[1] / Ia(1, 1) +
291 +                                 angMom[2] * angMom[2] / Ia(2, 2));
292 +            binDof[bin] += 3;
293 +          }
294 +        }
295 +      }
296 +    }
297 +    
298 +    for (int i = 0; i < nBins_; i++) {
299 +      RealType rinner = (RealType)i * binWidth_;
300 +      RealType router = (RealType)(i+1) * binWidth_;
301 +      if (binDof[i] > 0) {
302 +        RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb *
303 +                                          PhysicalConstants::energyConvert);
304 +        RealType den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
305 +          / (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
306 +
307 +        Vector3d omega = binI[i].inverse() * binL[i];
308 +
309 +        dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp);
310 +        dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[i])->add(omega);
311 +        dynamic_cast<Accumulator *>(density->accumulator[i])->add(den);
312 +        dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1);
313 +      }
314 +    }
315    }
316 +
317 +
318 +  void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) {
319 +  }
320 +  
321 +  RNEMDRTheta::RNEMDRTheta(SimInfo* info, const std::string& filename,
322 +                           const std::string& sele, int nrbins, int nangleBins)
323 +    : ShellStatistics(info, filename, sele, nrbins), nAngleBins_(nangleBins) {
324 +    
325 +    Globals* simParams = info->getSimParams();
326 +    RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
327 +    bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
328 +    
329 +    if (hasAngularMomentumFluxVector) {
330 +      fluxVector_ = rnemdParams->getAngularMomentumFluxVector();
331 +    } else {
332 +      
333 +      std::string fluxStr = rnemdParams->getFluxType();
334 +      if (fluxStr.find("Lx") != std::string::npos) {
335 +        fluxVector_ = V3X;
336 +      } else if (fluxStr.find("Ly") != std::string::npos) {
337 +        fluxVector_ = V3Y;
338 +      } else {
339 +        fluxVector_ = V3Z;
340 +      }
341 +    }
342 +    
343 +    fluxVector_.normalize();
344 +
345 +    setOutputName(getPrefix(filename) + ".rnemdRTheta");
346 +
347 +    angularVelocity = new OutputData;
348 +    angularVelocity->units = "angstroms^2/fs";
349 +    angularVelocity->title =  "Angular Velocity";  
350 +    angularVelocity->dataType = odtArray2d;
351 +    angularVelocity->dataHandling = odhAverage;
352 +    angularVelocity->accumulatorArray2d.reserve(nBins_);
353 +    for (int i = 0; i < nBins_; i++) {
354 +      angularVelocity->accumulatorArray2d[i].reserve(nAngleBins_);
355 +      for (int j = 0 ; j < nAngleBins_; j++) {      
356 +        angularVelocity->accumulatorArray2d[i][j] = new Accumulator();
357 +      }
358 +    }
359 +    data_.push_back(angularVelocity);
360 +
361 +  }
362 +
363 +
364 +  std::pair<int,int> RNEMDRTheta::getBins(Vector3d pos) {
365 +    std::pair<int,int> result;
366 +
367 +    Vector3d rPos = pos - coordinateOrigin_;
368 +    RealType cosAngle= dot(rPos, fluxVector_) / rPos.length();
369 +
370 +    result.first = int(rPos.length() / binWidth_);
371 +    result.second = int( (nAngleBins_ - 1) * 0.5 * (cosAngle + 1.0) );
372 +    return result;
373 +  }
374 +
375 +  void RNEMDRTheta::processStuntDouble(StuntDouble* sd, int bin) {
376 +  }
377 +
378 +  void RNEMDRTheta::processFrame(int istep) {
379 +
380 +    Molecule* mol;
381 +    RigidBody* rb;
382 +    StuntDouble* sd;
383 +    SimInfo::MoleculeIterator mi;
384 +    Molecule::RigidBodyIterator rbIter;
385 +    int i;
386 +
387 +    vector<vector<Mat3x3d> >  binI;
388 +    vector<vector<Vector3d> > binL;
389 +    vector<vector<int> > binCount;
390 +    
391 +    for (mol = info_->beginMolecule(mi); mol != NULL;
392 +         mol = info_->nextMolecule(mi)) {
393 +      
394 +      // change the positions of atoms which belong to the rigidbodies
395 +      
396 +      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
397 +           rb = mol->nextRigidBody(rbIter)) {
398 +        rb->updateAtomVel();
399 +      }
400 +    }
401 +  
402 +    if (evaluator_.isDynamic()) {
403 +      seleMan_.setSelectionSet(evaluator_.evaluate());
404 +    }
405 +    
406 +    // loop over the selected atoms:
407 +    
408 +    for (sd = seleMan_.beginSelected(i); sd != NULL;
409 +         sd = seleMan_.nextSelected(i)) {
410 +
411 +      // figure out where that object is:
412 +      std::pair<int,int> bins = getBins( sd->getPos() );  
413 +
414 +      if (bins.first >= 0 && bins.first < nBins_)  {
415 +        if (bins.second >= 0 && bins.second < nAngleBins_) {
416 +
417 +          Vector3d rPos = sd->getPos() - coordinateOrigin_;
418 +          Vector3d vel = sd->getVel();      
419 +          RealType m = sd->getMass();
420 +          Vector3d L = m * cross(rPos, vel);
421 +          Mat3x3d I(0.0);
422 +          I = outProduct(rPos, rPos) * m;
423 +          RealType r2 = rPos.lengthSquare();
424 +          I(0, 0) += m * r2;
425 +          I(1, 1) += m * r2;
426 +          I(2, 2) += m * r2;      
427 +
428 +          binI[bins.first][bins.second] += I;
429 +          binL[bins.first][bins.second] += L;
430 +          binCount[bins.first][bins.second]++;
431 +        }
432 +      }
433 +    }
434 +  
435 +    
436 +    for (int i = 0; i < nBins_; i++) {
437 +      for (int j = 0; j < nAngleBins_; j++) {
438 +
439 +        if (binCount[i][j] > 0) {
440 +          Vector3d omega = binI[i][j].inverse() * binL[i][j];
441 +          RealType omegaProj = dot(omega, fluxVector_);
442 +
443 +          dynamic_cast<Accumulator *>(angularVelocity->accumulatorArray2d[i][j])->add(omegaProj);
444 +        }
445 +      }
446 +    }
447 +  }
448 +
449 +  void RNEMDRTheta::writeOutput() {
450 +    
451 +    vector<OutputData*>::iterator i;
452 +    OutputData* outputData;
453 +    
454 +    ofstream outStream(outputFilename_.c_str());
455 +    if (outStream.is_open()) {
456 +      
457 +      //write title
458 +      outStream << "# SPATIAL STATISTICS\n";
459 +      outStream << "#";
460 +      
461 +      for(outputData = beginOutputData(i); outputData;
462 +          outputData = nextOutputData(i)) {
463 +        outStream << "\t" << outputData->title <<
464 +          "(" << outputData->units << ")";
465 +        // add some extra tabs for column alignment
466 +        if (outputData->dataType == odtVector3) outStream << "\t\t";
467 +      }
468 +      
469 +      outStream << std::endl;
470 +      
471 +      outStream.precision(8);
472 +      
473 +      for (int j = 0; j < nBins_; j++) {        
474 +        
475 +        int counts = counts_->accumulator[j]->count();
476 +
477 +        if (counts > 0) {
478 +          for(outputData = beginOutputData(i); outputData;
479 +              outputData = nextOutputData(i)) {
480 +            
481 +            int n = outputData->accumulator[j]->count();
482 +            if (n != 0) {
483 +              writeData( outStream, outputData, j );
484 +            }
485 +          }
486 +          outStream << std::endl;
487 +        }
488 +      }
489 +    }
490 +  }
491   }
492  

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