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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 2046 by gezelter, Tue Dec 2 22:11:04 2014 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   */
42    
43 – /**
44 – * @file Stats.cpp
45 – * @author tlin
46 – * @date 11/04/2004
47 – * @time 14:26am
48 – * @version 1.0
49 – */
50 –
43   #include "brains/Stats.hpp"
44   #include "brains/Thermo.hpp"
45  
# Line 195 | Line 187 | namespace OpenMD {
187  
188      StatsData hydrogenbonding_potential;
189      hydrogenbonding_potential.units =  "kcal/mol";
190 <    hydrogenbonding_potential.title =  "Metallic Potential";    
190 >    hydrogenbonding_potential.title =  "Hydrogen Bonding Potential";    
191      hydrogenbonding_potential.dataType = "RealType";
192      hydrogenbonding_potential.accumulator = new Accumulator();
193      data_[HYDROGENBONDING_POTENTIAL] = hydrogenbonding_potential;
194      statsMap_["HYDROGENBONDING_POTENTIAL"] =  HYDROGENBONDING_POTENTIAL;
195  
196 +    StatsData reciprocal_potential;
197 +    reciprocal_potential.units =  "kcal/mol";
198 +    reciprocal_potential.title =  "Reciprocal Space Potential";    
199 +    reciprocal_potential.dataType = "RealType";
200 +    reciprocal_potential.accumulator = new Accumulator();
201 +    data_[RECIPROCAL_POTENTIAL] = reciprocal_potential;
202 +    statsMap_["RECIPROCAL_POTENTIAL"] =  RECIPROCAL_POTENTIAL;
203 +
204      StatsData short_range_potential;
205      short_range_potential.units =  "kcal/mol";
206      short_range_potential.title =  "Short Range Potential";
# Line 273 | Line 273 | namespace OpenMD {
273      data_[SYSTEM_DIPOLE] = system_dipole;
274      statsMap_["SYSTEM_DIPOLE"] =  SYSTEM_DIPOLE;
275  
276 +    StatsData system_quadrupole;
277 +    system_quadrupole.units =  "C*m*m";
278 +    system_quadrupole.title =  "System Quadrupole";
279 +    system_quadrupole.dataType = "Mat3x3d";
280 +    system_quadrupole.accumulator = new MatrixAccumulator();
281 +    data_[SYSTEM_QUADRUPOLE] = system_quadrupole;
282 +    statsMap_["SYSTEM_QUADRUPOLE"] =  SYSTEM_QUADRUPOLE;
283 +
284      StatsData tagged_pair_distance;
285      tagged_pair_distance.units =  "Ang";
286      tagged_pair_distance.title =  "Tagged_Pair_Distance";
# Line 312 | Line 320 | namespace OpenMD {
320      electronic_temperature.accumulator = new Accumulator();
321      data_[ELECTRONIC_TEMPERATURE] = electronic_temperature;
322      statsMap_["ELECTRONIC_TEMPERATURE"] = ELECTRONIC_TEMPERATURE;
323 +
324 +    StatsData com;
325 +    com.units =  "A";
326 +    com.title =  "Center of Mass";
327 +    com.dataType = "Vector3d";
328 +    com.accumulator = new VectorAccumulator();
329 +    data_[COM] = com;
330 +    statsMap_["COM"] =  COM;
331 +
332 +    StatsData comVel;
333 +    comVel.units =  "A/fs";
334 +    comVel.title =  "Center of Mass Velocity";
335 +    comVel.dataType = "Vector3d";
336 +    comVel.accumulator = new VectorAccumulator();
337 +    data_[COM_VELOCITY] = comVel;
338 +    statsMap_["COM_VELOCITY"] =  COM_VELOCITY;
339 +
340 +    StatsData angMom;
341 +    angMom.units =  "amu A^2/fs";
342 +    angMom.title =  "Angular Momentum";
343 +    angMom.dataType = "Vector3d";
344 +    angMom.accumulator = new VectorAccumulator();
345 +    data_[ANGULAR_MOMENTUM] = angMom;
346 +    statsMap_["ANGULAR_MOMENTUM"] =  ANGULAR_MOMENTUM;
347  
348      // Now, set some defaults in the mask:
349  
# Line 344 | Line 376 | namespace OpenMD {
376        statsMask_.set(SYSTEM_DIPOLE);
377      }
378  
379 +    // Why do we have both of these?
380 +    if (simParams->getAccumulateBoxQuadrupole()) {
381 +      statsMask_.set(SYSTEM_QUADRUPOLE);
382 +    }
383 +    if (info_->getCalcBoxQuadrupole()){
384 +      statsMask_.set(SYSTEM_QUADRUPOLE);
385 +    }
386 +
387      if (simParams->havePrintHeatFlux()) {
388        if (simParams->getPrintHeatFlux()){
389          statsMask_.set(HEATFLUX);
# Line 379 | Line 419 | namespace OpenMD {
419      }  
420    }
421  
422 +  Stats::~Stats() {
423 +    data_.clear();
424 +    statsMap_.clear();
425 +  }
426  
427    std::string Stats::getTitle(int index) {
428      assert(index >=0 && index < ENDINDEX);
# Line 396 | Line 440 | namespace OpenMD {
440    }
441  
442    void Stats::collectStats(){
399 –    Globals* simParams = info_->getSimParams();
443      Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
444      Thermo thermo(info_);
445    
# Line 404 | Line 447 | namespace OpenMD {
447        if (statsMask_[i]) {
448          switch (i) {
449          case TIME:
450 <          data_[i].accumulator->add(snap->getTime());
450 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getTime());
451            break;
452          case KINETIC_ENERGY:
453 <          data_[i].accumulator->add(thermo.getKinetic());
453 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getKinetic());
454            break;
455          case POTENTIAL_ENERGY:
456 <          data_[i].accumulator->add(thermo.getPotential());
456 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getPotential());
457            break;
458          case TOTAL_ENERGY:
459 <          data_[i].accumulator->add(thermo.getTotalEnergy());
459 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTotalEnergy());
460            break;
461          case TEMPERATURE:
462 <          data_[i].accumulator->add(thermo.getTemperature());
462 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTemperature());
463            break;
464          case PRESSURE:
465 <          data_[i].accumulator->add(thermo.getPressure());
465 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getPressure());
466            break;
467          case VOLUME:
468 <          data_[i].accumulator->add(thermo.getVolume());
468 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getVolume());
469            break;
470          case CONSERVED_QUANTITY:
471 <          data_[i].accumulator->add(snap->getConservedQuantity());
471 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getConservedQuantity());
472            break;
473          case PRESSURE_TENSOR:
474            dynamic_cast<MatrixAccumulator *>(data_[i].accumulator)->add(thermo.getPressureTensor());
# Line 433 | Line 476 | namespace OpenMD {
476          case SYSTEM_DIPOLE:
477            dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getSystemDipole());
478            break;
479 +        case SYSTEM_QUADRUPOLE:
480 +          dynamic_cast<MatrixAccumulator *>(data_[i].accumulator)->add(thermo.getSystemQuadrupole());
481 +          break;
482          case HEATFLUX:
483            dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getHeatFlux());
484            break;
485          case HULLVOLUME:
486 <          data_[i].accumulator->add(thermo.getHullVolume());
486 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getHullVolume());
487            break;
488          case GYRVOLUME:
489 <          data_[i].accumulator->add(thermo.getGyrationalVolume());
489 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getGyrationalVolume());
490            break;
491          case TRANSLATIONAL_KINETIC:
492 <          data_[i].accumulator->add(thermo.getTranslationalKinetic());
492 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTranslationalKinetic());
493            break;
494          case ROTATIONAL_KINETIC:
495 <          data_[i].accumulator->add(thermo.getRotationalKinetic());
495 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getRotationalKinetic());
496            break;
497          case LONG_RANGE_POTENTIAL:
498 <          data_[i].accumulator->add(snap->getLongRangePotential());
498 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotential());
499            break;
500          case VANDERWAALS_POTENTIAL:
501 <          data_[i].accumulator->add(snap->getLongRangePotentials()[VANDERWAALS_FAMILY]);
501 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[VANDERWAALS_FAMILY]);
502            break;
503          case ELECTROSTATIC_POTENTIAL:
504 <          data_[i].accumulator->add(snap->getLongRangePotentials()[ELECTROSTATIC_FAMILY]);
504 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[ELECTROSTATIC_FAMILY]);
505            break;
506          case METALLIC_POTENTIAL:
507 <          data_[i].accumulator->add(snap->getLongRangePotentials()[METALLIC_FAMILY]);
507 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[METALLIC_FAMILY]);
508            break;
509          case HYDROGENBONDING_POTENTIAL:
510 <          data_[i].accumulator->add(snap->getLongRangePotentials()[HYDROGENBONDING_FAMILY]);
510 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[HYDROGENBONDING_FAMILY]);
511            break;
512 +        case RECIPROCAL_POTENTIAL:
513 +          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getReciprocalPotential());
514 +          break;
515          case SHORT_RANGE_POTENTIAL:
516 <          data_[i].accumulator->add(snap->getShortRangePotential());
516 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getShortRangePotential());
517            break;
518          case BOND_POTENTIAL:
519 <          data_[i].accumulator->add(snap->getBondPotential());
519 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getBondPotential());
520            break;
521          case BEND_POTENTIAL:
522 <          data_[i].accumulator->add(snap->getBendPotential());
522 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getBendPotential());
523            break;
524          case DIHEDRAL_POTENTIAL:
525 <          data_[i].accumulator->add(snap->getTorsionPotential());
525 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getTorsionPotential());
526            break;
527          case INVERSION_POTENTIAL:
528 <          data_[i].accumulator->add(snap->getInversionPotential());
528 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getInversionPotential());
529            break;
530          case RAW_POTENTIAL:
531 <          data_[i].accumulator->add(snap->getRawPotential());
531 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getRawPotential());
532            break;
533          case RESTRAINT_POTENTIAL:
534 <          data_[i].accumulator->add(snap->getRestraintPotential());
534 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getRestraintPotential());
535            break;
536          case TAGGED_PAIR_DISTANCE:
537 <          data_[i].accumulator->add(thermo.getTaggedAtomPairDistance());
537 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTaggedAtomPairDistance());
538            break;
539 +        case ELECTRONIC_TEMPERATURE:
540 +          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getElectronicTemperature());
541 +          break;
542 +        case COM:
543 +          dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getCom());
544 +          break;
545 +        case COM_VELOCITY:
546 +          dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getComVel());
547 +          break;
548 +        case ANGULAR_MOMENTUM:
549 +          dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getAngularMomentum());
550 +          break;
551            /*
552          case SHADOWH:
553 <          data_[i].accumulator->add(thermo.getShadowHamiltionian());
553 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getShadowHamiltionian());
554            break;
555          case HELFANDMOMENT:
556 <          data_[i].accumulator->add(thermo.getHelfandMoment());
556 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getHelfandMoment());
557            break;
558            */
498 –        case ELECTRONIC_TEMPERATURE:
499 –          data_[i].accumulator->add(thermo.getElectronicTemperature());
500 –          break;
559          }
560        }
561      }
# Line 506 | Line 564 | namespace OpenMD {
564    int Stats::getIntData(int index) {
565      assert(index >=0 && index < ENDINDEX);
566      RealType value;
567 <    data_[index].accumulator->getLastValue(value);
567 >    dynamic_cast<Accumulator *>(data_[index].accumulator)->getLastValue(value);
568      return (int) value;
569    }
570    RealType Stats::getRealData(int index) {
571      assert(index >=0 && index < ENDINDEX);
572      RealType value(0.0);
573 <    data_[index].accumulator->getLastValue(value);
573 >    dynamic_cast<Accumulator *>(data_[index].accumulator)->getLastValue(value);
574      return value;
575    }
576    Vector3d Stats::getVectorData(int index) {

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