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root/OpenMD/trunk/src/brains/Stats.cpp
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Comparing trunk/src/brains/Stats.cpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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 195 | Line 195 | namespace OpenMD {
195  
196      StatsData hydrogenbonding_potential;
197      hydrogenbonding_potential.units =  "kcal/mol";
198 <    hydrogenbonding_potential.title =  "Metallic Potential";    
198 >    hydrogenbonding_potential.title =  "Hydrogen Bonding Potential";    
199      hydrogenbonding_potential.dataType = "RealType";
200      hydrogenbonding_potential.accumulator = new Accumulator();
201      data_[HYDROGENBONDING_POTENTIAL] = hydrogenbonding_potential;
# Line 312 | Line 312 | namespace OpenMD {
312      electronic_temperature.accumulator = new Accumulator();
313      data_[ELECTRONIC_TEMPERATURE] = electronic_temperature;
314      statsMap_["ELECTRONIC_TEMPERATURE"] = ELECTRONIC_TEMPERATURE;
315 +
316 +    StatsData com;
317 +    com.units =  "A";
318 +    com.title =  "Center of Mass";
319 +    com.dataType = "Vector3d";
320 +    com.accumulator = new VectorAccumulator();
321 +    data_[COM] = com;
322 +    statsMap_["COM"] =  COM;
323  
324 +    StatsData comVel;
325 +    comVel.units =  "A/fs";
326 +    comVel.title =  "Center of Mass Velocity";
327 +    comVel.dataType = "Vector3d";
328 +    comVel.accumulator = new VectorAccumulator();
329 +    data_[COM_VELOCITY] = comVel;
330 +    statsMap_["COM_VELOCITY"] =  COM_VELOCITY;
331 +
332 +    StatsData angMom;
333 +    angMom.units =  "amu A^2/fs";
334 +    angMom.title =  "Angular Momentum";
335 +    angMom.dataType = "Vector3d";
336 +    angMom.accumulator = new VectorAccumulator();
337 +    data_[ANGULAR_MOMENTUM] = angMom;
338 +    statsMap_["ANGULAR_MOMENTUM"] =  ANGULAR_MOMENTUM;
339 +
340      // Now, set some defaults in the mask:
341  
342      Globals* simParams = info_->getSimParams();
# Line 379 | Line 403 | namespace OpenMD {
403      }  
404    }
405  
406 +  Stats::~Stats() {
407 +    data_.clear();
408 +    statsMap_.clear();
409 +  }
410  
411    std::string Stats::getTitle(int index) {
412      assert(index >=0 && index < ENDINDEX);
# Line 396 | Line 424 | namespace OpenMD {
424    }
425  
426    void Stats::collectStats(){
399 –    Globals* simParams = info_->getSimParams();
427      Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
428      Thermo thermo(info_);
429    
# Line 404 | Line 431 | namespace OpenMD {
431        if (statsMask_[i]) {
432          switch (i) {
433          case TIME:
434 <          data_[i].accumulator->add(snap->getTime());
434 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getTime());
435            break;
436          case KINETIC_ENERGY:
437 <          data_[i].accumulator->add(thermo.getKinetic());
437 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getKinetic());
438            break;
439          case POTENTIAL_ENERGY:
440 <          data_[i].accumulator->add(thermo.getPotential());
440 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getPotential());
441            break;
442          case TOTAL_ENERGY:
443 <          data_[i].accumulator->add(thermo.getTotalEnergy());
443 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTotalEnergy());
444            break;
445          case TEMPERATURE:
446 <          data_[i].accumulator->add(thermo.getTemperature());
446 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTemperature());
447            break;
448          case PRESSURE:
449 <          data_[i].accumulator->add(thermo.getPressure());
449 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getPressure());
450            break;
451          case VOLUME:
452 <          data_[i].accumulator->add(thermo.getVolume());
452 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getVolume());
453            break;
454          case CONSERVED_QUANTITY:
455 <          data_[i].accumulator->add(snap->getConservedQuantity());
455 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getConservedQuantity());
456            break;
457          case PRESSURE_TENSOR:
458            dynamic_cast<MatrixAccumulator *>(data_[i].accumulator)->add(thermo.getPressureTensor());
# Line 437 | Line 464 | namespace OpenMD {
464            dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getHeatFlux());
465            break;
466          case HULLVOLUME:
467 <          data_[i].accumulator->add(thermo.getHullVolume());
467 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getHullVolume());
468            break;
469          case GYRVOLUME:
470 <          data_[i].accumulator->add(thermo.getGyrationalVolume());
470 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getGyrationalVolume());
471            break;
472          case TRANSLATIONAL_KINETIC:
473 <          data_[i].accumulator->add(thermo.getTranslationalKinetic());
473 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTranslationalKinetic());
474            break;
475          case ROTATIONAL_KINETIC:
476 <          data_[i].accumulator->add(thermo.getRotationalKinetic());
476 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getRotationalKinetic());
477            break;
478          case LONG_RANGE_POTENTIAL:
479 <          data_[i].accumulator->add(snap->getLongRangePotential());
479 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotential());
480            break;
481          case VANDERWAALS_POTENTIAL:
482 <          data_[i].accumulator->add(snap->getLongRangePotentials()[VANDERWAALS_FAMILY]);
482 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[VANDERWAALS_FAMILY]);
483            break;
484          case ELECTROSTATIC_POTENTIAL:
485 <          data_[i].accumulator->add(snap->getLongRangePotentials()[ELECTROSTATIC_FAMILY]);
485 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[ELECTROSTATIC_FAMILY]);
486            break;
487          case METALLIC_POTENTIAL:
488 <          data_[i].accumulator->add(snap->getLongRangePotentials()[METALLIC_FAMILY]);
488 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[METALLIC_FAMILY]);
489            break;
490          case HYDROGENBONDING_POTENTIAL:
491 <          data_[i].accumulator->add(snap->getLongRangePotentials()[HYDROGENBONDING_FAMILY]);
491 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[HYDROGENBONDING_FAMILY]);
492            break;
493          case SHORT_RANGE_POTENTIAL:
494 <          data_[i].accumulator->add(snap->getShortRangePotential());
494 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getShortRangePotential());
495            break;
496          case BOND_POTENTIAL:
497 <          data_[i].accumulator->add(snap->getBondPotential());
497 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getBondPotential());
498            break;
499          case BEND_POTENTIAL:
500 <          data_[i].accumulator->add(snap->getBendPotential());
500 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getBendPotential());
501            break;
502          case DIHEDRAL_POTENTIAL:
503 <          data_[i].accumulator->add(snap->getTorsionPotential());
503 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getTorsionPotential());
504            break;
505          case INVERSION_POTENTIAL:
506 <          data_[i].accumulator->add(snap->getInversionPotential());
506 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getInversionPotential());
507            break;
508          case RAW_POTENTIAL:
509 <          data_[i].accumulator->add(snap->getRawPotential());
509 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getRawPotential());
510            break;
511          case RESTRAINT_POTENTIAL:
512 <          data_[i].accumulator->add(snap->getRestraintPotential());
512 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getRestraintPotential());
513            break;
514          case TAGGED_PAIR_DISTANCE:
515 <          data_[i].accumulator->add(thermo.getTaggedAtomPairDistance());
515 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTaggedAtomPairDistance());
516            break;
517 +        case ELECTRONIC_TEMPERATURE:
518 +          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getElectronicTemperature());
519 +          break;
520 +        case COM:
521 +          dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getCom());
522 +          break;
523 +        case COM_VELOCITY:
524 +          dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getComVel());
525 +          break;
526 +        case ANGULAR_MOMENTUM:
527 +          dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getAngularMomentum());
528 +          break;
529            /*
530          case SHADOWH:
531 <          data_[i].accumulator->add(thermo.getShadowHamiltionian());
531 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getShadowHamiltionian());
532            break;
533          case HELFANDMOMENT:
534 <          data_[i].accumulator->add(thermo.getHelfandMoment());
534 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getHelfandMoment());
535            break;
536            */
498 –        case ELECTRONIC_TEMPERATURE:
499 –          data_[i].accumulator->add(thermo.getElectronicTemperature());
500 –          break;
537          }
538        }
539      }
# Line 506 | Line 542 | namespace OpenMD {
542    int Stats::getIntData(int index) {
543      assert(index >=0 && index < ENDINDEX);
544      RealType value;
545 <    data_[index].accumulator->getLastValue(value);
545 >    dynamic_cast<Accumulator *>(data_[index].accumulator)->getLastValue(value);
546      return (int) value;
547    }
548    RealType Stats::getRealData(int index) {
549      assert(index >=0 && index < ENDINDEX);
550      RealType value(0.0);
551 <    data_[index].accumulator->getLastValue(value);
551 >    dynamic_cast<Accumulator *>(data_[index].accumulator)->getLastValue(value);
552      return value;
553    }
554    Vector3d Stats::getVectorData(int index) {

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