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root/OpenMD/trunk/src/brains/Stats.cpp
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Comparing trunk/src/brains/Stats.cpp (file contents):
Revision 1834 by gezelter, Tue Jan 15 16:28:42 2013 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 200 | Line 200 | namespace OpenMD {
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 463 | Line 498 | namespace OpenMD {
498          case HYDROGENBONDING_POTENTIAL:
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            dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getShortRangePotential());
506            break;
# Line 487 | Line 525 | namespace OpenMD {
525          case TAGGED_PAIR_DISTANCE:
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            dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getShadowHamiltionian());
# Line 495 | Line 545 | namespace OpenMD {
545            dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getHelfandMoment());
546            break;
547            */
498 –        case ELECTRONIC_TEMPERATURE:
499 –          dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getElectronicTemperature());
500 –          break;
548          }
549        }
550      }

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