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

Comparing branches/development/src/brains/Thermo.cpp (file contents):
Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC vs.
Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

# 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 >      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->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);      
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);      
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 <    // grab the simulation box dipole moment if specified
452 <    if (info_->getCalcBoxDipole()){
453 <      Vector3d totalDipole = getBoxDipole();
454 <      stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
455 <      stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
456 <      stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
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 >        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 <    Globals* simParams = info_->getSimParams();
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        
261 –        std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
262 –
822          int mol1 = info_->getGlobalMolMembership(tap.first);
823          int mol2 = info_->getGlobalMolMembership(tap.second);
265 –        std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
824  
825          int proc1 = info_->getMolToProc(mol1);
826          int proc2 = info_->getMolToProc(mol2);
827  
270 –        std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
271 –
828          RealType data[3];
829          if (proc1 == worldRank) {
830            StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
275 –          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 283 | Line 838 | namespace OpenMD {
838            pos1 = Vector3d(data);
839          }
840  
286 –
841          if (proc2 == worldRank) {
842            StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
289 –          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 304 | 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 <      
311 <    /**@todo need refactorying*/
312 <    //Conserved Quantity is set by integrator and time is set by setTime
313 <    
864 >    return 0.0;
865    }
866  
867 +  RealType Thermo::getHullVolume(){
868 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
869  
870 <  Vector3d Thermo::getBoxDipole() {
871 <    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
872 <    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;
870 > #ifdef HAVE_QHULL    
871 >    if (!snap->hasHullVolume) {
872 >      Hull* surfaceMesh_;
873  
874 <    RealType chargeToC = 1.60217733e-19;
875 <    RealType angstromToM = 1.0e-10;
876 <    RealType debyeToCm = 3.33564095198e-30;
877 <    
878 <    for (mol = info_->beginMolecule(miter); mol != NULL;
879 <         mol = info_->nextMolecule(miter)) {
880 <
881 <      for (atom = mol->beginAtom(aiter); atom != NULL;
882 <           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 <        }
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;
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;
906 >    return snap->getHullVolume();
907 > #else
908 >    return 0.0;
909 > #endif
910    }
911 < } //end namespace OpenMD
911 > }

Diff Legend

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