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Comparing trunk/src/brains/Thermo.cpp (file contents):
Revision 1604 by jmichalk, Mon Aug 8 18:53:40 2011 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

# Line 36 | Line 36
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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
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   #include <math.h>
# Line 50 | Line 51
51   #include "primitives/Molecule.hpp"
52   #include "utils/simError.h"
53   #include "utils/PhysicalConstants.hpp"
54 + #include "types/FixedChargeAdapter.hpp"
55 + #include "types/FluctuatingChargeAdapter.hpp"
56 + #include "types/MultipoleAdapter.hpp"
57 + #ifdef HAVE_QHULL
58 + #include "math/ConvexHull.hpp"
59 + #include "math/AlphaHull.hpp"
60 + #endif
61  
62 + using namespace std;
63   namespace OpenMD {
64  
65 <  RealType Thermo::getKinetic() {
66 <    SimInfo::MoleculeIterator miter;
67 <    std::vector<StuntDouble*>::iterator iiter;
68 <    Molecule* mol;
69 <    StuntDouble* integrableObject;    
70 <    Vector3d vel;
71 <    Vector3d angMom;
72 <    Mat3x3d I;
73 <    int i;
74 <    int j;
75 <    int k;
76 <    RealType mass;
77 <    RealType kinetic = 0.0;
78 <    RealType kinetic_global = 0.0;
70 <    
71 <    for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
72 <      for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
73 <           integrableObject = mol->nextIntegrableObject(iiter)) {
65 >  RealType Thermo::getTranslationalKinetic() {
66 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
67 >
68 >    if (!snap->hasTranslationalKineticEnergy) {
69 >      SimInfo::MoleculeIterator miter;
70 >      vector<StuntDouble*>::iterator iiter;
71 >      Molecule* mol;
72 >      StuntDouble* sd;    
73 >      Vector3d vel;
74 >      RealType mass;
75 >      RealType kinetic(0.0);
76 >      
77 >      for (mol = info_->beginMolecule(miter); mol != NULL;
78 >           mol = info_->nextMolecule(miter)) {
79          
80 <        mass = integrableObject->getMass();
81 <        vel = integrableObject->getVel();
82 <        
83 <        kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
84 <        
85 <        if (integrableObject->isDirectional()) {
86 <          angMom = integrableObject->getJ();
87 <          I = integrableObject->getI();
80 >        for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
81 >             sd = mol->nextIntegrableObject(iiter)) {
82 >          
83 >          mass = sd->getMass();
84 >          vel = sd->getVel();
85 >          
86 >          kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
87 >          
88 >        }
89 >      }
90 >      
91 > #ifdef IS_MPI
92 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
93 >                                MPI::SUM);
94 > #endif
95 >      
96 >      kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
97 >      
98 >      
99 >      snap->setTranslationalKineticEnergy(kinetic);
100 >    }
101 >    return snap->getTranslationalKineticEnergy();
102 >  }
103  
104 <          if (integrableObject->isLinear()) {
105 <            i = integrableObject->linearAxis();
106 <            j = (i + 1) % 3;
107 <            k = (i + 2) % 3;
108 <            kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
109 <          } else {                        
110 <            kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
111 <              + angMom[2]*angMom[2]/I(2, 2);
112 <          }
113 <        }
104 >  RealType Thermo::getRotationalKinetic() {
105 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
106 >
107 >    if (!snap->hasRotationalKineticEnergy) {
108 >      SimInfo::MoleculeIterator miter;
109 >      vector<StuntDouble*>::iterator iiter;
110 >      Molecule* mol;
111 >      StuntDouble* sd;    
112 >      Vector3d angMom;
113 >      Mat3x3d I;
114 >      int i, j, k;
115 >      RealType kinetic(0.0);
116 >      
117 >      for (mol = info_->beginMolecule(miter); mol != NULL;
118 >           mol = info_->nextMolecule(miter)) {
119 >        
120 >        for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
121 >             sd = mol->nextIntegrableObject(iiter)) {
122 >          
123 >          if (sd->isDirectional()) {
124 >            angMom = sd->getJ();
125 >            I = sd->getI();
126              
127 +            if (sd->isLinear()) {
128 +              i = sd->linearAxis();
129 +              j = (i + 1) % 3;
130 +              k = (i + 2) % 3;
131 +              kinetic += angMom[j] * angMom[j] / I(j, j)
132 +                + angMom[k] * angMom[k] / I(k, k);
133 +            } else {                        
134 +              kinetic += angMom[0]*angMom[0]/I(0, 0)
135 +                + angMom[1]*angMom[1]/I(1, 1)
136 +                + angMom[2]*angMom[2]/I(2, 2);
137 +            }
138 +          }          
139 +        }
140        }
141 <    }
97 <    
141 >      
142   #ifdef IS_MPI
143 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
144 +                                MPI::SUM);
145 + #endif
146 +      
147 +      kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
148 +          
149 +      snap->setRotationalKineticEnergy(kinetic);
150 +    }
151 +    return snap->getRotationalKineticEnergy();
152 +  }
153  
154 <    MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
101 <                  MPI_COMM_WORLD);
102 <    kinetic = kinetic_global;
154 >      
155  
156 < #endif //is_mpi
156 >  RealType Thermo::getKinetic() {
157 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
158  
159 <    kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
160 <
161 <    return kinetic;
159 >    if (!snap->hasKineticEnergy) {
160 >      RealType ke = getTranslationalKinetic() + getRotationalKinetic();
161 >      snap->setKineticEnergy(ke);
162 >    }
163 >    return snap->getKineticEnergy();
164    }
165  
166    RealType Thermo::getPotential() {
112 –    RealType potential = 0.0;
113 –    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
114 –    RealType shortRangePot_local =  curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
167  
168 <    // Get total potential for entire system from MPI.
168 >    // ForceManager computes the potential and stores it in the
169 >    // Snapshot.  All we have to do is report it.
170  
171 < #ifdef IS_MPI
171 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
172 >    return snap->getPotentialEnergy();
173 >  }
174  
175 <    MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
121 <                  MPI_COMM_WORLD);
122 <    potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
175 >  RealType Thermo::getTotalEnergy() {
176  
177 < #else
177 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
178  
179 <    potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
179 >    if (!snap->hasTotalEnergy) {
180 >      snap->setTotalEnergy(this->getKinetic() + this->getPotential());
181 >    }
182  
183 < #endif // is_mpi
129 <
130 <    return potential;
183 >    return snap->getTotalEnergy();
184    }
185  
133 –  RealType Thermo::getTotalE() {
134 –    RealType total;
135 –
136 –    total = this->getKinetic() + this->getPotential();
137 –    return total;
138 –  }
139 –
186    RealType Thermo::getTemperature() {
141 –    
142 –    RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
143 –    return temperature;
144 –  }
187  
188 <  RealType Thermo::getVolume() {
147 <    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
148 <    return curSnapshot->getVolume();
149 <  }
188 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
189  
190 <  RealType Thermo::getPressure() {
190 >    if (!snap->hasTemperature) {
191  
192 <    // Relies on the calculation of the full molecular pressure tensor
192 >      RealType temperature = ( 2.0 * this->getKinetic() )
193 >        / (info_->getNdf()* PhysicalConstants::kb );
194  
195 +      snap->setTemperature(temperature);
196 +    }
197 +    
198 +    return snap->getTemperature();
199 +  }
200  
201 <    Mat3x3d tensor;
202 <    RealType pressure;
201 >  RealType Thermo::getElectronicTemperature() {
202 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
203  
204 <    tensor = getPressureTensor();
204 >    if (!snap->hasElectronicTemperature) {
205 >      
206 >      SimInfo::MoleculeIterator miter;
207 >      vector<Atom*>::iterator iiter;
208 >      Molecule* mol;
209 >      Atom* atom;    
210 >      RealType cvel;
211 >      RealType cmass;
212 >      RealType kinetic(0.0);
213 >      RealType eTemp;
214 >      
215 >      for (mol = info_->beginMolecule(miter); mol != NULL;
216 >           mol = info_->nextMolecule(miter)) {
217 >        
218 >        for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL;
219 >             atom = mol->nextFluctuatingCharge(iiter)) {
220 >          
221 >          cmass = atom->getChargeMass();
222 >          cvel = atom->getFlucQVel();
223 >          
224 >          kinetic += cmass * cvel * cvel;
225 >          
226 >        }
227 >      }
228 >    
229 > #ifdef IS_MPI
230 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &kinetic, 1, MPI::REALTYPE,
231 >                                MPI::SUM);
232 > #endif
233  
234 <    pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
234 >      kinetic *= 0.5;
235 >      eTemp =  (2.0 * kinetic) /
236 >        (info_->getNFluctuatingCharges() * PhysicalConstants::kb );
237 >    
238 >      snap->setElectronicTemperature(eTemp);
239 >    }
240  
241 <    return pressure;
241 >    return snap->getElectronicTemperature();
242    }
243  
166 –  RealType Thermo::getPressure(int direction) {
244  
245 <    // Relies on the calculation of the full molecular pressure tensor
245 >  RealType Thermo::getVolume() {
246 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
247 >    return snap->getVolume();
248 >  }
249  
250 <          
251 <    Mat3x3d tensor;
172 <    RealType pressure;
250 >  RealType Thermo::getPressure() {
251 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
252  
253 <    tensor = getPressureTensor();
254 <
255 <    pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
256 <
257 <    return pressure;
253 >    if (!snap->hasPressure) {
254 >      // Relies on the calculation of the full molecular pressure tensor
255 >      
256 >      Mat3x3d tensor;
257 >      RealType pressure;
258 >      
259 >      tensor = getPressureTensor();
260 >      
261 >      pressure = PhysicalConstants::pressureConvert *
262 >        (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
263 >      
264 >      snap->setPressure(pressure);
265 >    }
266 >    
267 >    return snap->getPressure();    
268    }
269  
270    Mat3x3d Thermo::getPressureTensor() {
271      // returns pressure tensor in units amu*fs^-2*Ang^-1
272      // routine derived via viral theorem description in:
273      // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
274 <    Mat3x3d pressureTensor;
186 <    Mat3x3d p_local(0.0);
187 <    Mat3x3d p_global(0.0);
274 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
275  
276 <    SimInfo::MoleculeIterator i;
190 <    std::vector<StuntDouble*>::iterator j;
191 <    Molecule* mol;
192 <    StuntDouble* integrableObject;    
193 <    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
194 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
195 <           integrableObject = mol->nextIntegrableObject(j)) {
276 >    if (!snap->hasPressureTensor) {
277  
278 <        RealType mass = integrableObject->getMass();
279 <        Vector3d vcom = integrableObject->getVel();
280 <        p_local += mass * outProduct(vcom, vcom);        
278 >      Mat3x3d pressureTensor;
279 >      Mat3x3d p_tens(0.0);
280 >      RealType mass;
281 >      Vector3d vcom;
282 >      
283 >      SimInfo::MoleculeIterator i;
284 >      vector<StuntDouble*>::iterator j;
285 >      Molecule* mol;
286 >      StuntDouble* sd;    
287 >      for (mol = info_->beginMolecule(i); mol != NULL;
288 >           mol = info_->nextMolecule(i)) {
289 >        
290 >        for (sd = mol->beginIntegrableObject(j); sd != NULL;
291 >             sd = mol->nextIntegrableObject(j)) {
292 >          
293 >          mass = sd->getMass();
294 >          vcom = sd->getVel();
295 >          p_tens += mass * outProduct(vcom, vcom);        
296 >        }
297        }
298 +      
299 + #ifdef IS_MPI
300 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, p_tens.getArrayPointer(), 9,
301 +                                MPI::REALTYPE, MPI::SUM);
302 + #endif
303 +      
304 +      RealType volume = this->getVolume();
305 +      Mat3x3d stressTensor = snap->getStressTensor();
306 +      
307 +      pressureTensor =  (p_tens +
308 +                         PhysicalConstants::energyConvert * stressTensor)/volume;
309 +      
310 +      snap->setPressureTensor(pressureTensor);
311      }
312 <    
312 >    return snap->getPressureTensor();
313 >  }
314 >
315 >
316 >
317 >
318 >  Vector3d Thermo::getSystemDipole() {
319 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
320 >
321 >    if (!snap->hasSystemDipole) {
322 >      SimInfo::MoleculeIterator miter;
323 >      vector<Atom*>::iterator aiter;
324 >      Molecule* mol;
325 >      Atom* atom;
326 >      RealType charge;
327 >      RealType moment(0.0);
328 >      Vector3d ri(0.0);
329 >      Vector3d dipoleVector(0.0);
330 >      Vector3d nPos(0.0);
331 >      Vector3d pPos(0.0);
332 >      RealType nChg(0.0);
333 >      RealType pChg(0.0);
334 >      int nCount = 0;
335 >      int pCount = 0;
336 >      
337 >      RealType chargeToC = 1.60217733e-19;
338 >      RealType angstromToM = 1.0e-10;
339 >      RealType debyeToCm = 3.33564095198e-30;
340 >      
341 >      for (mol = info_->beginMolecule(miter); mol != NULL;
342 >           mol = info_->nextMolecule(miter)) {
343 >        
344 >        for (atom = mol->beginAtom(aiter); atom != NULL;
345 >             atom = mol->nextAtom(aiter)) {
346 >          
347 >          charge = 0.0;
348 >          
349 >          FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType());
350 >          if ( fca.isFixedCharge() ) {
351 >            charge = fca.getCharge();
352 >          }
353 >          
354 >          FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType());
355 >          if ( fqa.isFluctuatingCharge() ) {
356 >            charge += atom->getFlucQPos();
357 >          }
358 >          
359 >          charge *= chargeToC;
360 >          
361 >          ri = atom->getPos();
362 >          snap->wrapVector(ri);
363 >          ri *= angstromToM;
364 >          
365 >          if (charge < 0.0) {
366 >            nPos += ri;
367 >            nChg -= charge;
368 >            nCount++;
369 >          } else if (charge > 0.0) {
370 >            pPos += ri;
371 >            pChg += charge;
372 >            pCount++;
373 >          }
374 >          
375 >          MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
376 >          if (ma.isDipole() ) {
377 >            Vector3d u_i = atom->getElectroFrame().getColumn(2);
378 >            moment = ma.getDipoleMoment();
379 >            moment *= debyeToCm;
380 >            dipoleVector += u_i * moment;
381 >          }
382 >        }
383 >      }
384 >      
385 >      
386   #ifdef IS_MPI
387 <    MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
388 < #else
389 <    p_global = p_local;
390 < #endif // is_mpi
387 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pChg, 1, MPI::REALTYPE,
388 >                                MPI::SUM);
389 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nChg, 1, MPI::REALTYPE,
390 >                                MPI::SUM);
391  
392 <    RealType volume = this->getVolume();
393 <    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
394 <    Mat3x3d tau = curSnapshot->statData.getTau();
392 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pCount, 1, MPI::INTEGER,
393 >                                MPI::SUM);
394 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nCount, 1, MPI::INTEGER,
395 >                                MPI::SUM);
396  
397 <    pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;
398 <    
399 <    return pressureTensor;
400 <  }
397 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, pPos.getArrayPointer(), 3,
398 >                                MPI::REALTYPE, MPI::SUM);
399 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, nPos.getArrayPointer(), 3,
400 >                                MPI::REALTYPE, MPI::SUM);
401  
402 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, dipoleVector.getArrayPointer(),
403 +                                3, MPI::REALTYPE, MPI::SUM);
404 + #endif
405 +      
406 +      // first load the accumulated dipole moment (if dipoles were present)
407 +      Vector3d boxDipole = dipoleVector;
408 +      // now include the dipole moment due to charges
409 +      // use the lesser of the positive and negative charge totals
410 +      RealType chg_value = nChg <= pChg ? nChg : pChg;
411 +      
412 +      // find the average positions
413 +      if (pCount > 0 && nCount > 0 ) {
414 +        pPos /= pCount;
415 +        nPos /= nCount;
416 +      }
417 +      
418 +      // dipole is from the negative to the positive (physics notation)
419 +      boxDipole += (pPos - nPos) * chg_value;
420 +      snap->setSystemDipole(boxDipole);
421 +    }
422  
423 <  void Thermo::saveStat(){
423 >    return snap->getSystemDipole();
424 >  }
425 >
426 >  // Returns the Heat Flux Vector for the system
427 >  Vector3d Thermo::getHeatFlux(){
428      Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
429 <    Stats& stat = currSnapshot->statData;
430 <    
431 <    stat[Stats::KINETIC_ENERGY] = getKinetic();
432 <    stat[Stats::POTENTIAL_ENERGY] = getPotential();
433 <    stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
434 <    stat[Stats::TEMPERATURE] = getTemperature();
435 <    stat[Stats::PRESSURE] = getPressure();
436 <    stat[Stats::VOLUME] = getVolume();      
429 >    SimInfo::MoleculeIterator miter;
430 >    vector<StuntDouble*>::iterator iiter;
431 >    Molecule* mol;
432 >    StuntDouble* sd;    
433 >    RigidBody::AtomIterator ai;
434 >    Atom* atom;      
435 >    Vector3d vel;
436 >    Vector3d angMom;
437 >    Mat3x3d I;
438 >    int i;
439 >    int j;
440 >    int k;
441 >    RealType mass;
442  
443 <    Mat3x3d tensor =getPressureTensor();
444 <    stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);      
445 <    stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);      
446 <    stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);      
447 <    stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);      
448 <    stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);      
449 <    stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);      
237 <    stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);      
238 <    stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);      
239 <    stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);      
443 >    Vector3d x_a;
444 >    RealType kinetic;
445 >    RealType potential;
446 >    RealType eatom;
447 >    RealType AvgE_a_ = 0;
448 >    // Convective portion of the heat flux
449 >    Vector3d heatFluxJc = V3Zero;
450  
451 +    /* Calculate convective portion of the heat flux */
452 +    for (mol = info_->beginMolecule(miter); mol != NULL;
453 +         mol = info_->nextMolecule(miter)) {
454 +      
455 +      for (sd = mol->beginIntegrableObject(iiter);
456 +           sd != NULL;
457 +           sd = mol->nextIntegrableObject(iiter)) {
458 +        
459 +        mass = sd->getMass();
460 +        vel = sd->getVel();
461  
462 <    Globals* simParams = info_->getSimParams();
462 >        kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
463 >        
464 >        if (sd->isDirectional()) {
465 >          angMom = sd->getJ();
466 >          I = sd->getI();
467 >
468 >          if (sd->isLinear()) {
469 >            i = sd->linearAxis();
470 >            j = (i + 1) % 3;
471 >            k = (i + 2) % 3;
472 >            kinetic += angMom[j] * angMom[j] / I(j, j)
473 >              + angMom[k] * angMom[k] / I(k, k);
474 >          } else {                        
475 >            kinetic += angMom[0]*angMom[0]/I(0, 0)
476 >              + angMom[1]*angMom[1]/I(1, 1)
477 >              + angMom[2]*angMom[2]/I(2, 2);
478 >          }
479 >        }
480 >
481 >        potential = 0.0;
482  
483 +        if (sd->isRigidBody()) {
484 +          RigidBody* rb = dynamic_cast<RigidBody*>(sd);
485 +          for (atom = rb->beginAtom(ai); atom != NULL;
486 +               atom = rb->nextAtom(ai)) {
487 +            potential +=  atom->getParticlePot();
488 +          }          
489 +        } else {
490 +          potential = sd->getParticlePot();
491 +        }
492 +
493 +        potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
494 +        // The potential may not be a 1/2 factor
495 +        eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
496 +        heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
497 +        heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
498 +        heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
499 +      }
500 +    }
501 +
502 +    /* The J_v vector is reduced in the forceManager so everyone has
503 +     *  the global Jv. Jc is computed over the local atoms and must be
504 +     *  reduced among all processors.
505 +     */
506 + #ifdef IS_MPI
507 +    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
508 +                              MPI::SUM);
509 + #endif
510 +    
511 +    // (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
512 +
513 +    Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
514 +      PhysicalConstants::energyConvert;
515 +        
516 +    // Correct for the fact the flux is 1/V (Jc + Jv)
517 +    return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
518 +  }
519 +
520 +
521 +  Vector3d Thermo::getComVel(){
522 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
523 +
524 +    if (!snap->hasCOMvel) {
525 +
526 +      SimInfo::MoleculeIterator i;
527 +      Molecule* mol;
528 +      
529 +      Vector3d comVel(0.0);
530 +      RealType totalMass(0.0);
531 +      
532 +      for (mol = info_->beginMolecule(i); mol != NULL;
533 +           mol = info_->nextMolecule(i)) {
534 +        RealType mass = mol->getMass();
535 +        totalMass += mass;
536 +        comVel += mass * mol->getComVel();
537 +      }  
538 +      
539 + #ifdef IS_MPI
540 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
541 +                                MPI::SUM);
542 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
543 +                                MPI::REALTYPE, MPI::SUM);
544 + #endif
545 +      
546 +      comVel /= totalMass;
547 +      snap->setCOMvel(comVel);
548 +    }
549 +    return snap->getCOMvel();
550 +  }
551 +
552 +  Vector3d Thermo::getCom(){
553 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
554 +
555 +    if (!snap->hasCOM) {
556 +      
557 +      SimInfo::MoleculeIterator i;
558 +      Molecule* mol;
559 +      
560 +      Vector3d com(0.0);
561 +      RealType totalMass(0.0);
562 +      
563 +      for (mol = info_->beginMolecule(i); mol != NULL;
564 +           mol = info_->nextMolecule(i)) {
565 +        RealType mass = mol->getMass();
566 +        totalMass += mass;
567 +        com += mass * mol->getCom();
568 +      }  
569 +      
570 + #ifdef IS_MPI
571 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
572 +                                MPI::SUM);
573 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
574 +                                MPI::REALTYPE, MPI::SUM);
575 + #endif
576 +      
577 +      com /= totalMass;
578 +      snap->setCOM(com);
579 +    }
580 +    return snap->getCOM();
581 +  }        
582 +
583 +  /**
584 +   * Returns center of mass and center of mass velocity in one
585 +   * function call.
586 +   */  
587 +  void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
588 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
589 +
590 +    if (!(snap->hasCOM && snap->hasCOMvel)) {
591 +
592 +      SimInfo::MoleculeIterator i;
593 +      Molecule* mol;
594 +      
595 +      RealType totalMass(0.0);
596 +      
597 +      com = 0.0;
598 +      comVel = 0.0;
599 +      
600 +      for (mol = info_->beginMolecule(i); mol != NULL;
601 +           mol = info_->nextMolecule(i)) {
602 +        RealType mass = mol->getMass();
603 +        totalMass += mass;
604 +        com += mass * mol->getCom();
605 +        comVel += mass * mol->getComVel();          
606 +      }  
607 +      
608 + #ifdef IS_MPI
609 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
610 +                                MPI::SUM);
611 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
612 +                                MPI::REALTYPE, MPI::SUM);
613 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
614 +                                MPI::REALTYPE, MPI::SUM);
615 + #endif
616 +      
617 +      com /= totalMass;
618 +      comVel /= totalMass;
619 +      snap->setCOM(com);
620 +      snap->setCOMvel(comVel);
621 +    }    
622 +    com = snap->getCOM();
623 +    comVel = snap->getCOMvel();
624 +    return;
625 +  }        
626 +  
627 +  /**
628 +   * Return intertia tensor for entire system and angular momentum
629 +   * Vector.
630 +   *
631 +   *
632 +   *
633 +   *    [  Ixx -Ixy  -Ixz ]
634 +   * I =| -Iyx  Iyy  -Iyz |
635 +   *    [ -Izx -Iyz   Izz ]
636 +   */
637 +  void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
638 +                                Vector3d &angularMomentum){
639 +
640 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
641 +    
642 +    if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
643 +      
644 +      RealType xx = 0.0;
645 +      RealType yy = 0.0;
646 +      RealType zz = 0.0;
647 +      RealType xy = 0.0;
648 +      RealType xz = 0.0;
649 +      RealType yz = 0.0;
650 +      Vector3d com(0.0);
651 +      Vector3d comVel(0.0);
652 +      
653 +      getComAll(com, comVel);
654 +      
655 +      SimInfo::MoleculeIterator i;
656 +      Molecule* mol;
657 +      
658 +      Vector3d thisq(0.0);
659 +      Vector3d thisv(0.0);
660 +      
661 +      RealType thisMass = 0.0;
662 +      
663 +      for (mol = info_->beginMolecule(i); mol != NULL;
664 +           mol = info_->nextMolecule(i)) {
665 +        
666 +        thisq = mol->getCom()-com;
667 +        thisv = mol->getComVel()-comVel;
668 +        thisMass = mol->getMass();
669 +        // Compute moment of intertia coefficients.
670 +        xx += thisq[0]*thisq[0]*thisMass;
671 +        yy += thisq[1]*thisq[1]*thisMass;
672 +        zz += thisq[2]*thisq[2]*thisMass;
673 +        
674 +        // compute products of intertia
675 +        xy += thisq[0]*thisq[1]*thisMass;
676 +        xz += thisq[0]*thisq[2]*thisMass;
677 +        yz += thisq[1]*thisq[2]*thisMass;
678 +        
679 +        angularMomentum += cross( thisq, thisv ) * thisMass;            
680 +      }
681 +      
682 +      inertiaTensor(0,0) = yy + zz;
683 +      inertiaTensor(0,1) = -xy;
684 +      inertiaTensor(0,2) = -xz;
685 +      inertiaTensor(1,0) = -xy;
686 +      inertiaTensor(1,1) = xx + zz;
687 +      inertiaTensor(1,2) = -yz;
688 +      inertiaTensor(2,0) = -xz;
689 +      inertiaTensor(2,1) = -yz;
690 +      inertiaTensor(2,2) = xx + yy;
691 +      
692 + #ifdef IS_MPI
693 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, inertiaTensor.getArrayPointer(),
694 +                                9, MPI::REALTYPE, MPI::SUM);
695 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
696 +                                angularMomentum.getArrayPointer(), 3,
697 +                                MPI::REALTYPE, MPI::SUM);
698 + #endif
699 +      
700 +      snap->setCOMw(angularMomentum);
701 +      snap->setInertiaTensor(inertiaTensor);
702 +    }
703 +    
704 +    angularMomentum = snap->getCOMw();
705 +    inertiaTensor = snap->getInertiaTensor();
706 +    
707 +    return;
708 +  }
709 +
710 +  // Returns the angular momentum of the system
711 +  Vector3d Thermo::getAngularMomentum(){
712 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
713 +    
714 +    if (!snap->hasCOMw) {
715 +      
716 +      Vector3d com(0.0);
717 +      Vector3d comVel(0.0);
718 +      Vector3d angularMomentum(0.0);
719 +      
720 +      getComAll(com, comVel);
721 +      
722 +      SimInfo::MoleculeIterator i;
723 +      Molecule* mol;
724 +      
725 +      Vector3d thisr(0.0);
726 +      Vector3d thisp(0.0);
727 +      
728 +      RealType thisMass;
729 +      
730 +      for (mol = info_->beginMolecule(i); mol != NULL;
731 +           mol = info_->nextMolecule(i)) {
732 +        thisMass = mol->getMass();
733 +        thisr = mol->getCom() - com;
734 +        thisp = (mol->getComVel() - comVel) * thisMass;
735 +        
736 +        angularMomentum += cross( thisr, thisp );      
737 +      }  
738 +      
739 + #ifdef IS_MPI
740 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
741 +                                angularMomentum.getArrayPointer(), 3,
742 +                                MPI::REALTYPE, MPI::SUM);
743 + #endif
744 +      
745 +      snap->setCOMw(angularMomentum);
746 +    }
747 +    
748 +    return snap->getCOMw();
749 +  }
750 +  
751 +  
752 +  /**
753 +   * Returns the Volume of the system based on a ellipsoid with
754 +   * semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
755 +   * where R_i are related to the principle inertia moments
756 +   *  R_i = sqrt(C*I_i/N), this reduces to
757 +   *  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
758 +   * See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
759 +   */
760 +  RealType Thermo::getGyrationalVolume(){
761 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
762 +    
763 +    if (!snap->hasGyrationalVolume) {
764 +      
765 +      Mat3x3d intTensor;
766 +      RealType det;
767 +      Vector3d dummyAngMom;
768 +      RealType sysconstants;
769 +      RealType geomCnst;
770 +      RealType volume;
771 +      
772 +      geomCnst = 3.0/2.0;
773 +      /* Get the inertial tensor and angular momentum for free*/
774 +      getInertiaTensor(intTensor, dummyAngMom);
775 +      
776 +      det = intTensor.determinant();
777 +      sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
778 +      volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
779 +
780 +      snap->setGyrationalVolume(volume);
781 +    }
782 +    return snap->getGyrationalVolume();
783 +  }
784 +  
785 +  void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
786 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
787 +
788 +    if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
789 +    
790 +      Mat3x3d intTensor;
791 +      Vector3d dummyAngMom;
792 +      RealType sysconstants;
793 +      RealType geomCnst;
794 +      
795 +      geomCnst = 3.0/2.0;
796 +      /* Get the inertia tensor and angular momentum for free*/
797 +      this->getInertiaTensor(intTensor, dummyAngMom);
798 +      
799 +      detI = intTensor.determinant();
800 +      sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
801 +      volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
802 +      snap->setGyrationalVolume(volume);
803 +    } else {
804 +      volume = snap->getGyrationalVolume();
805 +      detI = snap->getInertiaTensor().determinant();
806 +    }
807 +    return;
808 +  }
809 +  
810 +  RealType Thermo::getTaggedAtomPairDistance(){
811 +    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
812 +    Globals* simParams = info_->getSimParams();
813 +    
814      if (simParams->haveTaggedAtomPair() &&
815          simParams->havePrintTaggedPairDistance()) {
816        if ( simParams->getPrintTaggedPairDistance()) {
817          
818 <        std::pair<int, int> tap = simParams->getTaggedAtomPair();
818 >        pair<int, int> tap = simParams->getTaggedAtomPair();
819          Vector3d pos1, pos2, rab;
820 <
820 >        
821   #ifdef IS_MPI        
252 –        std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
253 –
822          int mol1 = info_->getGlobalMolMembership(tap.first);
823          int mol2 = info_->getGlobalMolMembership(tap.second);
256 –        std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
824  
825          int proc1 = info_->getMolToProc(mol1);
826          int proc2 = info_->getMolToProc(mol2);
827  
261 –        std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
262 –
828          RealType data[3];
829          if (proc1 == worldRank) {
830            StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
266 –          std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
831            pos1 = sd1->getPos();
832            data[0] = pos1.x();
833            data[1] = pos1.y();
# Line 274 | Line 838 | namespace OpenMD {
838            pos1 = Vector3d(data);
839          }
840  
277 –
841          if (proc2 == worldRank) {
842            StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
280 –          std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
843            pos2 = sd2->getPos();
844            data[0] = pos2.x();
845            data[1] = pos2.y();
# Line 295 | Line 857 | namespace OpenMD {
857   #endif        
858          rab = pos2 - pos1;
859          currSnapshot->wrapVector(rab);
860 <        stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
860 >        return rab.length();
861        }
862 +      return 0.0;    
863      }
864 <      
302 <    /**@todo need refactorying*/
303 <    //Conserved Quantity is set by integrator and time is set by setTime
304 <    
864 >    return 0.0;
865    }
866  
867 +  RealType Thermo::getHullVolume(){
868 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
869  
870 + #ifdef HAVE_QHULL    
871 +    if (!snap->hasHullVolume) {
872 +      Hull* surfaceMesh_;
873  
874 < Vector3d Thermo::getBoxDipole() {
875 <    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
876 <    SimInfo::MoleculeIterator miter;
877 <    std::vector<Atom*>::iterator aiter;
878 <    Molecule* mol;
879 <    Atom* atom;
880 <    RealType charge;
881 <    RealType moment(0.0);
882 <    Vector3d ri(0.0);
318 <    Vector3d dipoleVector(0.0);
319 <    Vector3d nPos(0.0);
320 <    Vector3d pPos(0.0);
321 <    RealType nChg(0.0);
322 <    RealType pChg(0.0);
323 <    int nCount = 0;
324 <    int pCount = 0;
325 <
326 <    RealType chargeToC = 1.60217733e-19;
327 <    RealType angstromToM = 1.0e-10;    RealType debyeToCm = 3.33564095198e-30;
328 <
329 <    for (mol = info_->beginMolecule(miter); mol != NULL;
330 <         mol = info_->nextMolecule(miter)) {
331 <
332 <      for (atom = mol->beginAtom(aiter); atom != NULL;
333 <           atom = mol->nextAtom(aiter)) {
334 <
335 <        if (atom->isCharge() ) {
336 <          charge = 0.0;
337 <          GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
338 <          if (data != NULL) {
339 <
340 <            charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
341 <            charge *= chargeToC;
342 <
343 <            ri = atom->getPos();
344 <            currSnapshot->wrapVector(ri);
345 <            ri *= angstromToM;
346 <
347 <            if (charge < 0.0) {
348 <              nPos += ri;
349 <              nChg -= charge;
350 <              nCount++;
351 <            } else if (charge > 0.0) {
352 <              pPos += ri;
353 <              pChg += charge;
354 <              pCount++;
355 <            }
356 <          }
357 <        }
358 <
359 <        if (atom->isDipole() ) {
360 <          Vector3d u_i = atom->getElectroFrame().getColumn(2);
361 <          GenericData* data = dynamic_cast<DirectionalAtomType*>(atom->getAtomType())->getPropertyByName("Dipole");
362 <          if (data != NULL) {
363 <            moment = (dynamic_cast<DoubleGenericData*>(data))->getData();
364 <
365 <            moment *= debyeToCm;
366 <            dipoleVector += u_i * moment;
367 <          }
368 <        }
874 >      Globals* simParams = info_->getSimParams();
875 >      const std::string ht = simParams->getHULL_Method();
876 >      
877 >      if (ht == "Convex") {
878 >        surfaceMesh_ = new ConvexHull();
879 >      } else if (ht == "AlphaShape") {
880 >        surfaceMesh_ = new AlphaHull(simParams->getAlpha());
881 >      } else {
882 >        return 0.0;
883        }
884 +      
885 +      // Build a vector of stunt doubles to determine if they are
886 +      // surface atoms
887 +      std::vector<StuntDouble*> localSites_;
888 +      Molecule* mol;
889 +      StuntDouble* sd;
890 +      SimInfo::MoleculeIterator i;
891 +      Molecule::IntegrableObjectIterator  j;
892 +      
893 +      for (mol = info_->beginMolecule(i); mol != NULL;
894 +           mol = info_->nextMolecule(i)) {          
895 +        for (sd = mol->beginIntegrableObject(j);
896 +             sd != NULL;
897 +             sd = mol->nextIntegrableObject(j)) {  
898 +          localSites_.push_back(sd);
899 +        }
900 +      }  
901 +      
902 +      // Compute surface Mesh
903 +      surfaceMesh_->computeHull(localSites_);
904 +      snap->setHullVolume(surfaceMesh_->getVolume());
905      }
906 <
907 <
908 < #ifdef IS_MPI
909 <    RealType pChg_global, nChg_global;
375 <    int pCount_global, nCount_global;
376 <    Vector3d pPos_global, nPos_global, dipVec_global;
377 <
378 <    MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
379 <                  MPI_COMM_WORLD);
380 <    pChg = pChg_global;
381 <    MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
382 <                  MPI_COMM_WORLD);
383 <    nChg = nChg_global;
384 <    MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
385 <                  MPI_COMM_WORLD);
386 <    pCount = pCount_global;
387 <    MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
388 <                  MPI_COMM_WORLD);
389 <    nCount = nCount_global;
390 <    MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
391 <                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
392 <    pPos = pPos_global;
393 <    MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
394 <                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
395 <    nPos = nPos_global;
396 <    MPI_Allreduce(dipoleVector.getArrayPointer(),
397 <                  dipVec_global.getArrayPointer(), 3,
398 <                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
399 <    dipoleVector = dipVec_global;
400 < #endif //is_mpi
401 <
402 <    // first load the accumulated dipole moment (if dipoles were present)
403 <    Vector3d boxDipole = dipoleVector;
404 <    // now include the dipole moment due to charges
405 <    // use the lesser of the positive and negative charge totals
406 <    RealType chg_value = nChg <= pChg ? nChg : pChg;
407 <
408 <    // find the average positions
409 <    if (pCount > 0 && nCount > 0 ) {
410 <      pPos /= pCount;
411 <      nPos /= nCount;
412 <    }
413 <
414 <    // dipole is from the negative to the positive (physics notation)
415 <    boxDipole += (pPos - nPos) * chg_value;
416 <
417 <    return boxDipole;
906 >    return snap->getHullVolume();
907 > #else
908 >    return 0.0;
909 > #endif
910    }
911 <
420 <
421 < } //end namespace OpenMD
911 > }

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