ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/brains/Stats.cpp
(Generate patch)

Comparing trunk/src/brains/Stats.cpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 1925 by gezelter, Wed Aug 7 15:24:16 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;
202      statsMap_["HYDROGENBONDING_POTENTIAL"] =  HYDROGENBONDING_POTENTIAL;
203 +
204 +    StatsData reciprocal_potential;
205 +    reciprocal_potential.units =  "kcal/mol";
206 +    reciprocal_potential.title =  "Reciprocal Space Potential";    
207 +    reciprocal_potential.dataType = "RealType";
208 +    reciprocal_potential.accumulator = new Accumulator();
209 +    data_[RECIPROCAL_POTENTIAL] = reciprocal_potential;
210 +    statsMap_["RECIPROCAL_POTENTIAL"] =  RECIPROCAL_POTENTIAL;
211  
212      StatsData short_range_potential;
213      short_range_potential.units =  "kcal/mol";
# 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  
350      Globals* simParams = info_->getSimParams();
# Line 379 | Line 411 | namespace OpenMD {
411      }  
412    }
413  
414 +  Stats::~Stats() {
415 +    data_.clear();
416 +    statsMap_.clear();
417 +  }
418  
419    std::string Stats::getTitle(int index) {
420      assert(index >=0 && index < ENDINDEX);
# Line 396 | Line 432 | namespace OpenMD {
432    }
433  
434    void Stats::collectStats(){
399 –    Globals* simParams = info_->getSimParams();
435      Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
436      Thermo thermo(info_);
437    
# Line 404 | Line 439 | namespace OpenMD {
439        if (statsMask_[i]) {
440          switch (i) {
441          case TIME:
442 <          data_[i].accumulator->add(snap->getTime());
442 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getTime());
443            break;
444          case KINETIC_ENERGY:
445 <          data_[i].accumulator->add(thermo.getKinetic());
445 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getKinetic());
446            break;
447          case POTENTIAL_ENERGY:
448 <          data_[i].accumulator->add(thermo.getPotential());
448 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getPotential());
449            break;
450          case TOTAL_ENERGY:
451 <          data_[i].accumulator->add(thermo.getTotalEnergy());
451 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTotalEnergy());
452            break;
453          case TEMPERATURE:
454 <          data_[i].accumulator->add(thermo.getTemperature());
454 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTemperature());
455            break;
456          case PRESSURE:
457 <          data_[i].accumulator->add(thermo.getPressure());
457 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getPressure());
458            break;
459          case VOLUME:
460 <          data_[i].accumulator->add(thermo.getVolume());
460 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getVolume());
461            break;
462          case CONSERVED_QUANTITY:
463 <          data_[i].accumulator->add(snap->getConservedQuantity());
463 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getConservedQuantity());
464            break;
465          case PRESSURE_TENSOR:
466            dynamic_cast<MatrixAccumulator *>(data_[i].accumulator)->add(thermo.getPressureTensor());
# Line 437 | Line 472 | namespace OpenMD {
472            dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getHeatFlux());
473            break;
474          case HULLVOLUME:
475 <          data_[i].accumulator->add(thermo.getHullVolume());
475 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getHullVolume());
476            break;
477          case GYRVOLUME:
478 <          data_[i].accumulator->add(thermo.getGyrationalVolume());
478 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getGyrationalVolume());
479            break;
480          case TRANSLATIONAL_KINETIC:
481 <          data_[i].accumulator->add(thermo.getTranslationalKinetic());
481 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTranslationalKinetic());
482            break;
483          case ROTATIONAL_KINETIC:
484 <          data_[i].accumulator->add(thermo.getRotationalKinetic());
484 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getRotationalKinetic());
485            break;
486          case LONG_RANGE_POTENTIAL:
487 <          data_[i].accumulator->add(snap->getLongRangePotential());
487 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotential());
488            break;
489          case VANDERWAALS_POTENTIAL:
490 <          data_[i].accumulator->add(snap->getLongRangePotentials()[VANDERWAALS_FAMILY]);
490 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[VANDERWAALS_FAMILY]);
491            break;
492          case ELECTROSTATIC_POTENTIAL:
493 <          data_[i].accumulator->add(snap->getLongRangePotentials()[ELECTROSTATIC_FAMILY]);
493 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[ELECTROSTATIC_FAMILY]);
494            break;
495          case METALLIC_POTENTIAL:
496 <          data_[i].accumulator->add(snap->getLongRangePotentials()[METALLIC_FAMILY]);
496 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[METALLIC_FAMILY]);
497            break;
498          case HYDROGENBONDING_POTENTIAL:
499 <          data_[i].accumulator->add(snap->getLongRangePotentials()[HYDROGENBONDING_FAMILY]);
499 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[HYDROGENBONDING_FAMILY]);
500            break;
501 +        case RECIPROCAL_POTENTIAL:
502 +          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getReciprocalPotential());
503 +          break;
504          case SHORT_RANGE_POTENTIAL:
505 <          data_[i].accumulator->add(snap->getShortRangePotential());
505 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getShortRangePotential());
506            break;
507          case BOND_POTENTIAL:
508 <          data_[i].accumulator->add(snap->getBondPotential());
508 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getBondPotential());
509            break;
510          case BEND_POTENTIAL:
511 <          data_[i].accumulator->add(snap->getBendPotential());
511 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getBendPotential());
512            break;
513          case DIHEDRAL_POTENTIAL:
514 <          data_[i].accumulator->add(snap->getTorsionPotential());
514 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getTorsionPotential());
515            break;
516          case INVERSION_POTENTIAL:
517 <          data_[i].accumulator->add(snap->getInversionPotential());
517 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getInversionPotential());
518            break;
519          case RAW_POTENTIAL:
520 <          data_[i].accumulator->add(snap->getRawPotential());
520 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getRawPotential());
521            break;
522          case RESTRAINT_POTENTIAL:
523 <          data_[i].accumulator->add(snap->getRestraintPotential());
523 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getRestraintPotential());
524            break;
525          case TAGGED_PAIR_DISTANCE:
526 <          data_[i].accumulator->add(thermo.getTaggedAtomPairDistance());
526 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTaggedAtomPairDistance());
527            break;
528 +        case ELECTRONIC_TEMPERATURE:
529 +          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getElectronicTemperature());
530 +          break;
531 +        case COM:
532 +          dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getCom());
533 +          break;
534 +        case COM_VELOCITY:
535 +          dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getComVel());
536 +          break;
537 +        case ANGULAR_MOMENTUM:
538 +          dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getAngularMomentum());
539 +          break;
540            /*
541          case SHADOWH:
542 <          data_[i].accumulator->add(thermo.getShadowHamiltionian());
542 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getShadowHamiltionian());
543            break;
544          case HELFANDMOMENT:
545 <          data_[i].accumulator->add(thermo.getHelfandMoment());
545 >          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getHelfandMoment());
546            break;
547            */
498 –        case ELECTRONIC_TEMPERATURE:
499 –          data_[i].accumulator->add(thermo.getElectronicTemperature());
500 –          break;
548          }
549        }
550      }
# Line 506 | Line 553 | namespace OpenMD {
553    int Stats::getIntData(int index) {
554      assert(index >=0 && index < ENDINDEX);
555      RealType value;
556 <    data_[index].accumulator->getLastValue(value);
556 >    dynamic_cast<Accumulator *>(data_[index].accumulator)->getLastValue(value);
557      return (int) value;
558    }
559    RealType Stats::getRealData(int index) {
560      assert(index >=0 && index < ENDINDEX);
561      RealType value(0.0);
562 <    data_[index].accumulator->getLastValue(value);
562 >    dynamic_cast<Accumulator *>(data_[index].accumulator)->getLastValue(value);
563      return value;
564    }
565    Vector3d Stats::getVectorData(int index) {

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines