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Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC vs.
Revision 1850 by gezelter, Wed Feb 20 15:39:39 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 51 | 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;
72 <    
73 <    for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
74 <      for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
75 <           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 <    }
99 <    
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,
103 <                  MPI_COMM_WORLD);
104 <    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() {
114 –    RealType potential = 0.0;
115 –    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
116 –    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,
123 <                  MPI_COMM_WORLD);
124 <    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
131 <
132 <    return potential;
183 >    return snap->getTotalEnergy();
184    }
185  
135 –  RealType Thermo::getTotalE() {
136 –    RealType total;
137 –
138 –    total = this->getKinetic() + this->getPotential();
139 –    return total;
140 –  }
141 –
186    RealType Thermo::getTemperature() {
143 –    
144 –    RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
145 –    return temperature;
146 –  }
187  
188 <  RealType Thermo::getVolume() {
149 <    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
150 <    return curSnapshot->getVolume();
151 <  }
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  
168 –  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;
174 <    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;
188 <    Mat3x3d p_local(0.0);
189 <    Mat3x3d p_global(0.0);
274 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
275  
276 <    SimInfo::MoleculeIterator i;
192 <    std::vector<StuntDouble*>::iterator j;
193 <    Molecule* mol;
194 <    StuntDouble* integrableObject;    
195 <    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
196 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
197 <           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 >      Vector3d ri(0.0);
328 >      Vector3d dipoleVector(0.0);
329 >      Vector3d nPos(0.0);
330 >      Vector3d pPos(0.0);
331 >      RealType nChg(0.0);
332 >      RealType pChg(0.0);
333 >      int nCount = 0;
334 >      int pCount = 0;
335 >      
336 >      RealType chargeToC = 1.60217733e-19;
337 >      RealType angstromToM = 1.0e-10;
338 >      RealType debyeToCm = 3.33564095198e-30;
339 >      
340 >      for (mol = info_->beginMolecule(miter); mol != NULL;
341 >           mol = info_->nextMolecule(miter)) {
342 >        
343 >        for (atom = mol->beginAtom(aiter); atom != NULL;
344 >             atom = mol->nextAtom(aiter)) {
345 >          
346 >          charge = 0.0;
347 >          
348 >          FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType());
349 >          if ( fca.isFixedCharge() ) {
350 >            charge = fca.getCharge();
351 >          }
352 >          
353 >          FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType());
354 >          if ( fqa.isFluctuatingCharge() ) {
355 >            charge += atom->getFlucQPos();
356 >          }
357 >          
358 >          charge *= chargeToC;
359 >          
360 >          ri = atom->getPos();
361 >          snap->wrapVector(ri);
362 >          ri *= angstromToM;
363 >          
364 >          if (charge < 0.0) {
365 >            nPos += ri;
366 >            nChg -= charge;
367 >            nCount++;
368 >          } else if (charge > 0.0) {
369 >            pPos += ri;
370 >            pChg += charge;
371 >            pCount++;
372 >          }
373 >          
374 >          if (atom->isDipole()) {
375 >            dipoleVector += atom->getDipole() * debyeToCm;
376 >          }
377 >        }
378 >      }
379 >      
380 >      
381   #ifdef IS_MPI
382 <    MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
383 < #else
384 <    p_global = p_local;
385 < #endif // is_mpi
382 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pChg, 1, MPI::REALTYPE,
383 >                                MPI::SUM);
384 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nChg, 1, MPI::REALTYPE,
385 >                                MPI::SUM);
386  
387 <    RealType volume = this->getVolume();
388 <    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
389 <    Mat3x3d tau = curSnapshot->getTau();
387 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &pCount, 1, MPI::INTEGER,
388 >                                MPI::SUM);
389 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &nCount, 1, MPI::INTEGER,
390 >                                MPI::SUM);
391  
392 <    pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;
393 <    
394 <    return pressureTensor;
395 <  }
392 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, pPos.getArrayPointer(), 3,
393 >                                MPI::REALTYPE, MPI::SUM);
394 >      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, nPos.getArrayPointer(), 3,
395 >                                MPI::REALTYPE, MPI::SUM);
396  
397 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, dipoleVector.getArrayPointer(),
398 +                                3, MPI::REALTYPE, MPI::SUM);
399 + #endif
400 +      
401 +      // first load the accumulated dipole moment (if dipoles were present)
402 +      Vector3d boxDipole = dipoleVector;
403 +      // now include the dipole moment due to charges
404 +      // use the lesser of the positive and negative charge totals
405 +      RealType chg_value = nChg <= pChg ? nChg : pChg;
406 +      
407 +      // find the average positions
408 +      if (pCount > 0 && nCount > 0 ) {
409 +        pPos /= pCount;
410 +        nPos /= nCount;
411 +      }
412 +      
413 +      // dipole is from the negative to the positive (physics notation)
414 +      boxDipole += (pPos - nPos) * chg_value;
415 +      snap->setSystemDipole(boxDipole);
416 +    }
417  
418 <  void Thermo::saveStat(){
418 >    return snap->getSystemDipole();
419 >  }
420 >
421 >  // Returns the Heat Flux Vector for the system
422 >  Vector3d Thermo::getHeatFlux(){
423      Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
424 <    Stats& stat = currSnapshot->statData;
425 <    
426 <    stat[Stats::KINETIC_ENERGY] = getKinetic();
427 <    stat[Stats::POTENTIAL_ENERGY] = getPotential();
428 <    stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
429 <    stat[Stats::TEMPERATURE] = getTemperature();
430 <    stat[Stats::PRESSURE] = getPressure();
431 <    stat[Stats::VOLUME] = getVolume();      
424 >    SimInfo::MoleculeIterator miter;
425 >    vector<StuntDouble*>::iterator iiter;
426 >    Molecule* mol;
427 >    StuntDouble* sd;    
428 >    RigidBody::AtomIterator ai;
429 >    Atom* atom;      
430 >    Vector3d vel;
431 >    Vector3d angMom;
432 >    Mat3x3d I;
433 >    int i;
434 >    int j;
435 >    int k;
436 >    RealType mass;
437  
438 <    Mat3x3d tensor =getPressureTensor();
439 <    stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);      
440 <    stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);      
441 <    stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);      
442 <    stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);      
443 <    stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);      
238 <    stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);      
239 <    stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);      
240 <    stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);      
241 <    stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);      
438 >    Vector3d x_a;
439 >    RealType kinetic;
440 >    RealType potential;
441 >    RealType eatom;
442 >    // Convective portion of the heat flux
443 >    Vector3d heatFluxJc = V3Zero;
444  
445 <    // grab the simulation box dipole moment if specified
446 <    if (info_->getCalcBoxDipole()){
447 <      Vector3d totalDipole = getBoxDipole();
448 <      stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
449 <      stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
450 <      stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
445 >    /* Calculate convective portion of the heat flux */
446 >    for (mol = info_->beginMolecule(miter); mol != NULL;
447 >         mol = info_->nextMolecule(miter)) {
448 >      
449 >      for (sd = mol->beginIntegrableObject(iiter);
450 >           sd != NULL;
451 >           sd = mol->nextIntegrableObject(iiter)) {
452 >        
453 >        mass = sd->getMass();
454 >        vel = sd->getVel();
455 >
456 >        kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
457 >        
458 >        if (sd->isDirectional()) {
459 >          angMom = sd->getJ();
460 >          I = sd->getI();
461 >
462 >          if (sd->isLinear()) {
463 >            i = sd->linearAxis();
464 >            j = (i + 1) % 3;
465 >            k = (i + 2) % 3;
466 >            kinetic += angMom[j] * angMom[j] / I(j, j)
467 >              + angMom[k] * angMom[k] / I(k, k);
468 >          } else {                        
469 >            kinetic += angMom[0]*angMom[0]/I(0, 0)
470 >              + angMom[1]*angMom[1]/I(1, 1)
471 >              + angMom[2]*angMom[2]/I(2, 2);
472 >          }
473 >        }
474 >
475 >        potential = 0.0;
476 >
477 >        if (sd->isRigidBody()) {
478 >          RigidBody* rb = dynamic_cast<RigidBody*>(sd);
479 >          for (atom = rb->beginAtom(ai); atom != NULL;
480 >               atom = rb->nextAtom(ai)) {
481 >            potential +=  atom->getParticlePot();
482 >          }          
483 >        } else {
484 >          potential = sd->getParticlePot();
485 >        }
486 >
487 >        potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
488 >        // The potential may not be a 1/2 factor
489 >        eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
490 >        heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
491 >        heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
492 >        heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
493 >      }
494      }
495  
496 <    Globals* simParams = info_->getSimParams();
496 >    /* The J_v vector is reduced in the forceManager so everyone has
497 >     *  the global Jv. Jc is computed over the local atoms and must be
498 >     *  reduced among all processors.
499 >     */
500 > #ifdef IS_MPI
501 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
502 >                              MPI::SUM);
503 > #endif
504 >    
505 >    // (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
506  
507 +    Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
508 +      PhysicalConstants::energyConvert;
509 +        
510 +    // Correct for the fact the flux is 1/V (Jc + Jv)
511 +    return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
512 +  }
513 +
514 +
515 +  Vector3d Thermo::getComVel(){
516 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
517 +
518 +    if (!snap->hasCOMvel) {
519 +
520 +      SimInfo::MoleculeIterator i;
521 +      Molecule* mol;
522 +      
523 +      Vector3d comVel(0.0);
524 +      RealType totalMass(0.0);
525 +      
526 +      for (mol = info_->beginMolecule(i); mol != NULL;
527 +           mol = info_->nextMolecule(i)) {
528 +        RealType mass = mol->getMass();
529 +        totalMass += mass;
530 +        comVel += mass * mol->getComVel();
531 +      }  
532 +      
533 + #ifdef IS_MPI
534 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
535 +                                MPI::SUM);
536 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
537 +                                MPI::REALTYPE, MPI::SUM);
538 + #endif
539 +      
540 +      comVel /= totalMass;
541 +      snap->setCOMvel(comVel);
542 +    }
543 +    return snap->getCOMvel();
544 +  }
545 +
546 +  Vector3d Thermo::getCom(){
547 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
548 +
549 +    if (!snap->hasCOM) {
550 +      
551 +      SimInfo::MoleculeIterator i;
552 +      Molecule* mol;
553 +      
554 +      Vector3d com(0.0);
555 +      RealType totalMass(0.0);
556 +      
557 +      for (mol = info_->beginMolecule(i); mol != NULL;
558 +           mol = info_->nextMolecule(i)) {
559 +        RealType mass = mol->getMass();
560 +        totalMass += mass;
561 +        com += mass * mol->getCom();
562 +      }  
563 +      
564 + #ifdef IS_MPI
565 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
566 +                                MPI::SUM);
567 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
568 +                                MPI::REALTYPE, MPI::SUM);
569 + #endif
570 +      
571 +      com /= totalMass;
572 +      snap->setCOM(com);
573 +    }
574 +    return snap->getCOM();
575 +  }        
576 +
577 +  /**
578 +   * Returns center of mass and center of mass velocity in one
579 +   * function call.
580 +   */  
581 +  void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
582 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
583 +
584 +    if (!(snap->hasCOM && snap->hasCOMvel)) {
585 +
586 +      SimInfo::MoleculeIterator i;
587 +      Molecule* mol;
588 +      
589 +      RealType totalMass(0.0);
590 +      
591 +      com = 0.0;
592 +      comVel = 0.0;
593 +      
594 +      for (mol = info_->beginMolecule(i); mol != NULL;
595 +           mol = info_->nextMolecule(i)) {
596 +        RealType mass = mol->getMass();
597 +        totalMass += mass;
598 +        com += mass * mol->getCom();
599 +        comVel += mass * mol->getComVel();          
600 +      }  
601 +      
602 + #ifdef IS_MPI
603 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &totalMass, 1, MPI::REALTYPE,
604 +                                MPI::SUM);
605 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, com.getArrayPointer(), 3,
606 +                                MPI::REALTYPE, MPI::SUM);
607 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, comVel.getArrayPointer(), 3,
608 +                                MPI::REALTYPE, MPI::SUM);
609 + #endif
610 +      
611 +      com /= totalMass;
612 +      comVel /= totalMass;
613 +      snap->setCOM(com);
614 +      snap->setCOMvel(comVel);
615 +    }    
616 +    com = snap->getCOM();
617 +    comVel = snap->getCOMvel();
618 +    return;
619 +  }        
620 +  
621 +  /**
622 +   * Return intertia tensor for entire system and angular momentum
623 +   * Vector.
624 +   *
625 +   *
626 +   *
627 +   *    [  Ixx -Ixy  -Ixz ]
628 +   * I =| -Iyx  Iyy  -Iyz |
629 +   *    [ -Izx -Iyz   Izz ]
630 +   */
631 +  void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
632 +                                Vector3d &angularMomentum){
633 +
634 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
635 +    
636 +    if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
637 +      
638 +      RealType xx = 0.0;
639 +      RealType yy = 0.0;
640 +      RealType zz = 0.0;
641 +      RealType xy = 0.0;
642 +      RealType xz = 0.0;
643 +      RealType yz = 0.0;
644 +      Vector3d com(0.0);
645 +      Vector3d comVel(0.0);
646 +      
647 +      getComAll(com, comVel);
648 +      
649 +      SimInfo::MoleculeIterator i;
650 +      Molecule* mol;
651 +      
652 +      Vector3d thisq(0.0);
653 +      Vector3d thisv(0.0);
654 +      
655 +      RealType thisMass = 0.0;
656 +      
657 +      for (mol = info_->beginMolecule(i); mol != NULL;
658 +           mol = info_->nextMolecule(i)) {
659 +        
660 +        thisq = mol->getCom()-com;
661 +        thisv = mol->getComVel()-comVel;
662 +        thisMass = mol->getMass();
663 +        // Compute moment of intertia coefficients.
664 +        xx += thisq[0]*thisq[0]*thisMass;
665 +        yy += thisq[1]*thisq[1]*thisMass;
666 +        zz += thisq[2]*thisq[2]*thisMass;
667 +        
668 +        // compute products of intertia
669 +        xy += thisq[0]*thisq[1]*thisMass;
670 +        xz += thisq[0]*thisq[2]*thisMass;
671 +        yz += thisq[1]*thisq[2]*thisMass;
672 +        
673 +        angularMomentum += cross( thisq, thisv ) * thisMass;            
674 +      }
675 +      
676 +      inertiaTensor(0,0) = yy + zz;
677 +      inertiaTensor(0,1) = -xy;
678 +      inertiaTensor(0,2) = -xz;
679 +      inertiaTensor(1,0) = -xy;
680 +      inertiaTensor(1,1) = xx + zz;
681 +      inertiaTensor(1,2) = -yz;
682 +      inertiaTensor(2,0) = -xz;
683 +      inertiaTensor(2,1) = -yz;
684 +      inertiaTensor(2,2) = xx + yy;
685 +      
686 + #ifdef IS_MPI
687 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, inertiaTensor.getArrayPointer(),
688 +                                9, MPI::REALTYPE, MPI::SUM);
689 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
690 +                                angularMomentum.getArrayPointer(), 3,
691 +                                MPI::REALTYPE, MPI::SUM);
692 + #endif
693 +      
694 +      snap->setCOMw(angularMomentum);
695 +      snap->setInertiaTensor(inertiaTensor);
696 +    }
697 +    
698 +    angularMomentum = snap->getCOMw();
699 +    inertiaTensor = snap->getInertiaTensor();
700 +    
701 +    return;
702 +  }
703 +
704 +  // Returns the angular momentum of the system
705 +  Vector3d Thermo::getAngularMomentum(){
706 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
707 +    
708 +    if (!snap->hasCOMw) {
709 +      
710 +      Vector3d com(0.0);
711 +      Vector3d comVel(0.0);
712 +      Vector3d angularMomentum(0.0);
713 +      
714 +      getComAll(com, comVel);
715 +      
716 +      SimInfo::MoleculeIterator i;
717 +      Molecule* mol;
718 +      
719 +      Vector3d thisr(0.0);
720 +      Vector3d thisp(0.0);
721 +      
722 +      RealType thisMass;
723 +      
724 +      for (mol = info_->beginMolecule(i); mol != NULL;
725 +           mol = info_->nextMolecule(i)) {
726 +        thisMass = mol->getMass();
727 +        thisr = mol->getCom() - com;
728 +        thisp = (mol->getComVel() - comVel) * thisMass;
729 +        
730 +        angularMomentum += cross( thisr, thisp );      
731 +      }  
732 +      
733 + #ifdef IS_MPI
734 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
735 +                                angularMomentum.getArrayPointer(), 3,
736 +                                MPI::REALTYPE, MPI::SUM);
737 + #endif
738 +      
739 +      snap->setCOMw(angularMomentum);
740 +    }
741 +    
742 +    return snap->getCOMw();
743 +  }
744 +  
745 +  
746 +  /**
747 +   * Returns the Volume of the system based on a ellipsoid with
748 +   * semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
749 +   * where R_i are related to the principle inertia moments
750 +   *  R_i = sqrt(C*I_i/N), this reduces to
751 +   *  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
752 +   * See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
753 +   */
754 +  RealType Thermo::getGyrationalVolume(){
755 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
756 +    
757 +    if (!snap->hasGyrationalVolume) {
758 +      
759 +      Mat3x3d intTensor;
760 +      RealType det;
761 +      Vector3d dummyAngMom;
762 +      RealType sysconstants;
763 +      RealType geomCnst;
764 +      RealType volume;
765 +      
766 +      geomCnst = 3.0/2.0;
767 +      /* Get the inertial tensor and angular momentum for free*/
768 +      getInertiaTensor(intTensor, dummyAngMom);
769 +      
770 +      det = intTensor.determinant();
771 +      sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
772 +      volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
773 +
774 +      snap->setGyrationalVolume(volume);
775 +    }
776 +    return snap->getGyrationalVolume();
777 +  }
778 +  
779 +  void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
780 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
781 +
782 +    if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
783 +    
784 +      Mat3x3d intTensor;
785 +      Vector3d dummyAngMom;
786 +      RealType sysconstants;
787 +      RealType geomCnst;
788 +      
789 +      geomCnst = 3.0/2.0;
790 +      /* Get the inertia tensor and angular momentum for free*/
791 +      this->getInertiaTensor(intTensor, dummyAngMom);
792 +      
793 +      detI = intTensor.determinant();
794 +      sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
795 +      volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
796 +      snap->setGyrationalVolume(volume);
797 +    } else {
798 +      volume = snap->getGyrationalVolume();
799 +      detI = snap->getInertiaTensor().determinant();
800 +    }
801 +    return;
802 +  }
803 +  
804 +  RealType Thermo::getTaggedAtomPairDistance(){
805 +    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
806 +    Globals* simParams = info_->getSimParams();
807 +    
808      if (simParams->haveTaggedAtomPair() &&
809          simParams->havePrintTaggedPairDistance()) {
810        if ( simParams->getPrintTaggedPairDistance()) {
811          
812 <        std::pair<int, int> tap = simParams->getTaggedAtomPair();
812 >        pair<int, int> tap = simParams->getTaggedAtomPair();
813          Vector3d pos1, pos2, rab;
814 <
814 >        
815   #ifdef IS_MPI        
261 –        std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
262 –
816          int mol1 = info_->getGlobalMolMembership(tap.first);
817          int mol2 = info_->getGlobalMolMembership(tap.second);
265 –        std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
818  
819          int proc1 = info_->getMolToProc(mol1);
820          int proc2 = info_->getMolToProc(mol2);
821  
270 –        std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
271 –
822          RealType data[3];
823          if (proc1 == worldRank) {
824            StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
275 –          std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
825            pos1 = sd1->getPos();
826            data[0] = pos1.x();
827            data[1] = pos1.y();
828            data[2] = pos1.z();          
829 <          MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
829 >          MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1);
830          } else {
831 <          MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
831 >          MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1);
832            pos1 = Vector3d(data);
833          }
834  
286 –
835          if (proc2 == worldRank) {
836            StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
289 –          std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
837            pos2 = sd2->getPos();
838            data[0] = pos2.x();
839            data[1] = pos2.y();
840 <          data[2] = pos2.z();          
841 <          MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
840 >          data[2] = pos2.z();  
841 >          MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2);
842          } else {
843 <          MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
843 >          MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2);
844            pos2 = Vector3d(data);
845          }
846   #else
# Line 304 | Line 851 | namespace OpenMD {
851   #endif        
852          rab = pos2 - pos1;
853          currSnapshot->wrapVector(rab);
854 <        stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
854 >        return rab.length();
855        }
856 +      return 0.0;    
857      }
858 <      
311 <    /**@todo need refactorying*/
312 <    //Conserved Quantity is set by integrator and time is set by setTime
313 <    
858 >    return 0.0;
859    }
860  
861 +  RealType Thermo::getHullVolume(){
862 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
863  
864 <  Vector3d Thermo::getBoxDipole() {
865 <    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
866 <    SimInfo::MoleculeIterator miter;
320 <    std::vector<Atom*>::iterator aiter;
321 <    Molecule* mol;
322 <    Atom* atom;
323 <    RealType charge;
324 <    RealType moment(0.0);
325 <    Vector3d ri(0.0);
326 <    Vector3d dipoleVector(0.0);
327 <    Vector3d nPos(0.0);
328 <    Vector3d pPos(0.0);
329 <    RealType nChg(0.0);
330 <    RealType pChg(0.0);
331 <    int nCount = 0;
332 <    int pCount = 0;
864 > #ifdef HAVE_QHULL    
865 >    if (!snap->hasHullVolume) {
866 >      Hull* surfaceMesh_;
867  
868 <    RealType chargeToC = 1.60217733e-19;
869 <    RealType angstromToM = 1.0e-10;
870 <    RealType debyeToCm = 3.33564095198e-30;
871 <    
872 <    for (mol = info_->beginMolecule(miter); mol != NULL;
873 <         mol = info_->nextMolecule(miter)) {
874 <
875 <      for (atom = mol->beginAtom(aiter); atom != NULL;
876 <           atom = mol->nextAtom(aiter)) {
343 <        
344 <        if (atom->isCharge() ) {
345 <          charge = 0.0;
346 <          GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
347 <          if (data != NULL) {
348 <
349 <            charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
350 <            charge *= chargeToC;
351 <
352 <            ri = atom->getPos();
353 <            currSnapshot->wrapVector(ri);
354 <            ri *= angstromToM;
355 <
356 <            if (charge < 0.0) {
357 <              nPos += ri;
358 <              nChg -= charge;
359 <              nCount++;
360 <            } else if (charge > 0.0) {
361 <              pPos += ri;
362 <              pChg += charge;
363 <              pCount++;
364 <            }                      
365 <          }
366 <        }
367 <        
368 <        MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
369 <        if (ma.isDipole() ) {
370 <          Vector3d u_i = atom->getElectroFrame().getColumn(2);
371 <          moment = ma.getDipoleMoment();
372 <          moment *= debyeToCm;
373 <          dipoleVector += u_i * moment;
374 <        }
868 >      Globals* simParams = info_->getSimParams();
869 >      const std::string ht = simParams->getHULL_Method();
870 >      
871 >      if (ht == "Convex") {
872 >        surfaceMesh_ = new ConvexHull();
873 >      } else if (ht == "AlphaShape") {
874 >        surfaceMesh_ = new AlphaHull(simParams->getAlpha());
875 >      } else {
876 >        return 0.0;
877        }
878 +      
879 +      // Build a vector of stunt doubles to determine if they are
880 +      // surface atoms
881 +      std::vector<StuntDouble*> localSites_;
882 +      Molecule* mol;
883 +      StuntDouble* sd;
884 +      SimInfo::MoleculeIterator i;
885 +      Molecule::IntegrableObjectIterator  j;
886 +      
887 +      for (mol = info_->beginMolecule(i); mol != NULL;
888 +           mol = info_->nextMolecule(i)) {          
889 +        for (sd = mol->beginIntegrableObject(j);
890 +             sd != NULL;
891 +             sd = mol->nextIntegrableObject(j)) {  
892 +          localSites_.push_back(sd);
893 +        }
894 +      }  
895 +      
896 +      // Compute surface Mesh
897 +      surfaceMesh_->computeHull(localSites_);
898 +      snap->setHullVolume(surfaceMesh_->getVolume());
899      }
900 <    
901 <                      
902 < #ifdef IS_MPI
903 <    RealType pChg_global, nChg_global;
381 <    int pCount_global, nCount_global;
382 <    Vector3d pPos_global, nPos_global, dipVec_global;
383 <
384 <    MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
385 <                  MPI_COMM_WORLD);
386 <    pChg = pChg_global;
387 <    MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
388 <                  MPI_COMM_WORLD);
389 <    nChg = nChg_global;
390 <    MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
391 <                  MPI_COMM_WORLD);
392 <    pCount = pCount_global;
393 <    MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
394 <                  MPI_COMM_WORLD);
395 <    nCount = nCount_global;
396 <    MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
397 <                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
398 <    pPos = pPos_global;
399 <    MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
400 <                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
401 <    nPos = nPos_global;
402 <    MPI_Allreduce(dipoleVector.getArrayPointer(),
403 <                  dipVec_global.getArrayPointer(), 3,
404 <                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
405 <    dipoleVector = dipVec_global;
406 < #endif //is_mpi
407 <
408 <    // first load the accumulated dipole moment (if dipoles were present)
409 <    Vector3d boxDipole = dipoleVector;
410 <    // now include the dipole moment due to charges
411 <    // use the lesser of the positive and negative charge totals
412 <    RealType chg_value = nChg <= pChg ? nChg : pChg;
413 <      
414 <    // find the average positions
415 <    if (pCount > 0 && nCount > 0 ) {
416 <      pPos /= pCount;
417 <      nPos /= nCount;
418 <    }
419 <
420 <    // dipole is from the negative to the positive (physics notation)
421 <    boxDipole += (pPos - nPos) * chg_value;
422 <
423 <    return boxDipole;
900 >    return snap->getHullVolume();
901 > #else
902 >    return 0.0;
903 > #endif
904    }
905 < } //end namespace OpenMD
905 > }

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