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root/OpenMD/trunk/src/applications/staticProps/RNEMDStats.cpp
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Comparing trunk/src/applications/staticProps/RNEMDStats.cpp (file contents):
Revision 1888 by gezelter, Tue Jun 18 17:52:37 2013 UTC vs.
Revision 2026 by gezelter, Wed Oct 22 12:23:59 2014 UTC

# Line 104 | Line 104 | namespace OpenMD {
104      int i;
105  
106      vector<RealType> binMass(nBins_, 0.0);
107 <    vector<Vector3d> binVel(nBins_, V3Zero);
107 >    vector<Vector3d> binP(nBins_, V3Zero);
108      vector<RealType> binKE(nBins_, 0.0);
109      vector<unsigned int> binDof(nBins_, 0);
110 –    vector<unsigned int> binCount(nBins_, 0);
110      
112 –    
111      for (mol = info_->beginMolecule(mi); mol != NULL;
112           mol = info_->nextMolecule(mi)) {
113        
# Line 117 | Line 115 | namespace OpenMD {
115        
116        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
117             rb = mol->nextRigidBody(rbIter)) {
118 <        rb->updateAtoms();
118 >        rb->updateAtomVel();
119        }
120      }
121    
# Line 137 | Line 135 | namespace OpenMD {
135  
136        int bin = getBin(pos);
137  
140 –      binCount[bin] += 1;
141 –
138        binMass[bin] += m;
139 <      binVel[bin] += vel;
139 >      binP[bin] += m * vel;
140        binKE[bin] += 0.5 * (m * vel.lengthSquare());
141        binDof[bin] += 3;
142        
# Line 163 | Line 159 | namespace OpenMD {
159        }
160      }
161      
162 <    for (unsigned int i = 0; i < nBins_; i++) {
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 = binVel[i] / RealType(binCount[i]);
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);
# Line 201 | 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 231 | Line 228 | namespace OpenMD {
228      int i;
229  
230      vector<RealType> binMass(nBins_, 0.0);
231 <    vector<Vector3d> binaVel(nBins_, V3Zero);
231 >    vector<Mat3x3d>  binI(nBins_);
232 >    vector<Vector3d> binL(nBins_, V3Zero);
233      vector<RealType> binKE(nBins_, 0.0);
234 <    vector<unsigned int> binDof(nBins_, 0);
237 <    vector<unsigned int> binCount(nBins_, 0);
234 >    vector<int> binDof(nBins_, 0);
235      
236      for (mol = info_->beginMolecule(mi); mol != NULL;
237           mol = info_->nextMolecule(mi)) {
# Line 243 | Line 240 | namespace OpenMD {
240        
241        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
242             rb = mol->nextRigidBody(rbIter)) {
243 <        rb->updateAtoms();
243 >        rb->updateAtomVel();
244        }
245      }
246    
# Line 255 | Line 252 | namespace OpenMD {
252      
253      for (sd = seleMan_.beginSelected(i); sd != NULL;
254           sd = seleMan_.nextSelected(i)) {
255 <      
255 >
256        // figure out where that object is:
257 +      int bin = getBin( sd->getPos() );  
258  
259 <      Vector3d rPos = sd->getPos() - coordinateOrigin_;
262 <      Vector3d vel = sd->getVel();      
263 <      Vector3d aVel = cross(rPos, vel);
264 <      RealType m = sd->getMass();
259 >      if (bin >= 0 && bin < nBins_)  {
260  
261 <      int bin = getBin(rPos);
262 <
263 <      binCount[bin] += 1;
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 <      binaVel[bin] += aVel;
274 <      binKE[bin] += 0.5 * (m * vel.lengthSquare());
275 <      binDof[bin] += 3;
276 <      
277 <      if (sd->isDirectional()) {
278 <        Vector3d angMom = sd->getJ();
279 <        Mat3x3d I = sd->getI();
280 <        if (sd->isLinear()) {
281 <          int i = sd->linearAxis();
282 <          int j = (i + 1) % 3;
283 <          int k = (i + 2) % 3;
284 <          binKE[bin] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
285 <                               angMom[k] * angMom[k] / I(k, k));
286 <          binDof[bin] += 2;
287 <        } else {
288 <          binKE[bin] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
289 <                               angMom[1] * angMom[1] / I(1, 1) +
290 <                               angMom[2] * angMom[2] / I(2, 2));
291 <          binDof[bin] += 3;
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 (unsigned int i = 0; i < nBins_; i++) {
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 <        Vector3d aVel = binaVel[i] / RealType(binCount[i]);
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(aVel);
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        }
# Line 310 | Line 316 | namespace OpenMD {
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 +      std::vector<RealType> amf = rnemdParams->getAngularMomentumFluxVector();
331 +      if (amf.size() != 3) {
332 +        sprintf(painCave.errMsg,
333 +                "RNEMDRTheta: Incorrect number of parameters specified for angularMomentumFluxVector.\n"
334 +                "\tthere should be 3 parameters, but %lu were specified.\n",
335 +                amf.size());
336 +        painCave.isFatal = 1;
337 +        simError();      
338 +      }
339 +      fluxVector_.x() = amf[0];
340 +      fluxVector_.y() = amf[1];
341 +      fluxVector_.z() = amf[2];
342 +    } else {
343 +      
344 +      std::string fluxStr = rnemdParams->getFluxType();
345 +      if (fluxStr.find("Lx") != std::string::npos) {
346 +        fluxVector_ = V3X;
347 +      } else if (fluxStr.find("Ly") != std::string::npos) {
348 +        fluxVector_ = V3Y;
349 +      } else {
350 +        fluxVector_ = V3Z;
351 +      }
352 +    }
353 +    
354 +    fluxVector_.normalize();
355 +
356 +    setOutputName(getPrefix(filename) + ".rnemdRTheta");
357 +
358 +    angularVelocity = new OutputData;
359 +    angularVelocity->units = "angstroms^2/fs";
360 +    angularVelocity->title =  "Angular Velocity";  
361 +    angularVelocity->dataType = odtArray2d;
362 +    angularVelocity->dataHandling = odhAverage;
363 +    angularVelocity->accumulatorArray2d.reserve(nBins_);
364 +    for (int i = 0; i < nBins_; i++) {
365 +      angularVelocity->accumulatorArray2d[i].reserve(nAngleBins_);
366 +      for (int j = 0 ; j < nAngleBins_; j++) {      
367 +        angularVelocity->accumulatorArray2d[i][j] = new Accumulator();
368 +      }
369 +    }
370 +    data_.push_back(angularVelocity);
371 +
372    }
373 +
374 +
375 +  std::pair<int,int> RNEMDRTheta::getBins(Vector3d pos) {
376 +    std::pair<int,int> result;
377 +
378 +    Vector3d rPos = pos - coordinateOrigin_;
379 +    RealType cosAngle= dot(rPos, fluxVector_) / rPos.length();
380 +
381 +    result.first = int(rPos.length() / binWidth_);
382 +    result.second = int( (nAngleBins_ - 1) * 0.5 * (cosAngle + 1.0) );
383 +    return result;
384 +  }
385 +
386 +  void RNEMDRTheta::processStuntDouble(StuntDouble* sd, int bin) {
387 +  }
388 +
389 +  void RNEMDRTheta::processFrame(int istep) {
390 +
391 +    Molecule* mol;
392 +    RigidBody* rb;
393 +    StuntDouble* sd;
394 +    SimInfo::MoleculeIterator mi;
395 +    Molecule::RigidBodyIterator rbIter;
396 +    int i;
397 +
398 +    vector<vector<Mat3x3d> >  binI;
399 +    vector<vector<Vector3d> > binL;
400 +    vector<vector<int> > binCount;
401 +    
402 +    for (mol = info_->beginMolecule(mi); mol != NULL;
403 +         mol = info_->nextMolecule(mi)) {
404 +      
405 +      // change the positions of atoms which belong to the rigidbodies
406 +      
407 +      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
408 +           rb = mol->nextRigidBody(rbIter)) {
409 +        rb->updateAtomVel();
410 +      }
411 +    }
412 +  
413 +    if (evaluator_.isDynamic()) {
414 +      seleMan_.setSelectionSet(evaluator_.evaluate());
415 +    }
416 +    
417 +    // loop over the selected atoms:
418 +    
419 +    for (sd = seleMan_.beginSelected(i); sd != NULL;
420 +         sd = seleMan_.nextSelected(i)) {
421 +
422 +      // figure out where that object is:
423 +      std::pair<int,int> bins = getBins( sd->getPos() );  
424 +
425 +      if (bins.first >= 0 && bins.first < nBins_)  {
426 +        if (bins.second >= 0 && bins.second < nAngleBins_) {
427 +
428 +          Vector3d rPos = sd->getPos() - coordinateOrigin_;
429 +          Vector3d vel = sd->getVel();      
430 +          RealType m = sd->getMass();
431 +          Vector3d L = m * cross(rPos, vel);
432 +          Mat3x3d I(0.0);
433 +          I = outProduct(rPos, rPos) * m;
434 +          RealType r2 = rPos.lengthSquare();
435 +          I(0, 0) += m * r2;
436 +          I(1, 1) += m * r2;
437 +          I(2, 2) += m * r2;      
438 +
439 +          binI[bins.first][bins.second] += I;
440 +          binL[bins.first][bins.second] += L;
441 +          binCount[bins.first][bins.second]++;
442 +        }
443 +      }
444 +    }
445 +  
446 +    
447 +    for (int i = 0; i < nBins_; i++) {
448 +      for (int j = 0; j < nAngleBins_; j++) {
449 +
450 +        if (binCount[i][j] > 0) {
451 +          Vector3d omega = binI[i][j].inverse() * binL[i][j];
452 +          RealType omegaProj = dot(omega, fluxVector_);
453 +
454 +          dynamic_cast<Accumulator *>(angularVelocity->accumulatorArray2d[i][j])->add(omegaProj);
455 +        }
456 +      }
457 +    }
458 +  }
459 +
460 +  void RNEMDRTheta::writeOutput() {
461 +    
462 +    vector<OutputData*>::iterator i;
463 +    OutputData* outputData;
464 +    
465 +    ofstream outStream(outputFilename_.c_str());
466 +    if (outStream.is_open()) {
467 +      
468 +      //write title
469 +      outStream << "# SPATIAL STATISTICS\n";
470 +      outStream << "#";
471 +      
472 +      for(outputData = beginOutputData(i); outputData;
473 +          outputData = nextOutputData(i)) {
474 +        outStream << "\t" << outputData->title <<
475 +          "(" << outputData->units << ")";
476 +        // add some extra tabs for column alignment
477 +        if (outputData->dataType == odtVector3) outStream << "\t\t";
478 +      }
479 +      
480 +      outStream << std::endl;
481 +      
482 +      outStream.precision(8);
483 +      
484 +      for (int j = 0; j < nBins_; j++) {        
485 +        
486 +        int counts = counts_->accumulator[j]->count();
487 +
488 +        if (counts > 0) {
489 +          for(outputData = beginOutputData(i); outputData;
490 +              outputData = nextOutputData(i)) {
491 +            
492 +            int n = outputData->accumulator[j]->count();
493 +            if (n != 0) {
494 +              writeData( outStream, outputData, j );
495 +            }
496 +          }
497 +          outStream << std::endl;
498 +        }
499 +      }
500 +    }
501 +  }
502   }
503  

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