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Comparing trunk/src/brains/Thermo.cpp (file contents):
Revision 1638 by chuckv, Fri Sep 23 20:52:24 2011 UTC vs.
Revision 2046 by gezelter, Tue Dec 2 22:11:04 2014 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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
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   */
41 –
42 – #include <math.h>
43 – #include <iostream>
42  
43   #ifdef IS_MPI
44   #include <mpi.h>
45   #endif //is_mpi
46 +
47 + #include <math.h>
48 + #include <iostream>
49  
50   #include "brains/Thermo.hpp"
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_Allreduce(MPI_IN_PLACE, &kinetic, 1, MPI_REALTYPE,
93 >                    MPI_SUM, MPI_COMM_WORLD);
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_Allreduce(MPI_IN_PLACE, &kinetic, 1, MPI_REALTYPE,
144 +                    MPI_SUM, MPI_COMM_WORLD);
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_Allreduce(MPI_IN_PLACE, &kinetic, 1, MPI_REALTYPE,
231 >                    MPI_SUM, MPI_COMM_WORLD);
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_Allreduce(MPI_IN_PLACE, p_tens.getArrayPointer(), 9,
301 +                    MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
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_Allreduce(MPI_IN_PLACE, &pChg, 1, MPI_REALTYPE,
383 >                    MPI_SUM, MPI_COMM_WORLD);
384 >      MPI_Allreduce(MPI_IN_PLACE, &nChg, 1, MPI_REALTYPE,
385 >                    MPI_SUM, MPI_COMM_WORLD);
386 >      
387 >      MPI_Allreduce(MPI_IN_PLACE, &pCount, 1, MPI_INTEGER,
388 >                    MPI_SUM, MPI_COMM_WORLD);
389 >      MPI_Allreduce(MPI_IN_PLACE, &nCount, 1, MPI_INTEGER,
390 >                    MPI_SUM, MPI_COMM_WORLD);
391 >      
392 >      MPI_Allreduce(MPI_IN_PLACE, pPos.getArrayPointer(), 3,
393 >                    MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
394 >      MPI_Allreduce(MPI_IN_PLACE, nPos.getArrayPointer(), 3,
395 >                    MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
396  
397 <    RealType volume = this->getVolume();
398 <    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
399 <    Mat3x3d tau = curSnapshot->statData.getTau();
397 >      MPI_Allreduce(MPI_IN_PLACE, dipoleVector.getArrayPointer(),
398 >                    3, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
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 <    pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;
214 <    
215 <    return pressureTensor;
418 >    return snap->getSystemDipole();
419    }
420  
421  
422 <  void Thermo::saveStat(){
422 >  Mat3x3d Thermo::getSystemQuadrupole() {
423 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
424 >
425 >    if (!snap->hasSystemQuadrupole) {
426 >      SimInfo::MoleculeIterator miter;
427 >      vector<Atom*>::iterator aiter;
428 >      Molecule* mol;
429 >      Atom* atom;
430 >      RealType charge;
431 >      Vector3d ri(0.0);
432 >      Vector3d dipole(0.0);
433 >      Mat3x3d qpole(0.0);
434 >      
435 >      RealType chargeToC = 1.60217733e-19;
436 >      RealType angstromToM = 1.0e-10;
437 >      RealType debyeToCm = 3.33564095198e-30;
438 >      
439 >      for (mol = info_->beginMolecule(miter); mol != NULL;
440 >           mol = info_->nextMolecule(miter)) {
441 >        
442 >        for (atom = mol->beginAtom(aiter); atom != NULL;
443 >             atom = mol->nextAtom(aiter)) {
444 >
445 >          ri = atom->getPos();
446 >          snap->wrapVector(ri);
447 >          ri *= angstromToM;
448 >          
449 >          charge = 0.0;
450 >          
451 >          FixedChargeAdapter fca = FixedChargeAdapter(atom->getAtomType());
452 >          if ( fca.isFixedCharge() ) {
453 >            charge = fca.getCharge();
454 >          }
455 >          
456 >          FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atom->getAtomType());
457 >          if ( fqa.isFluctuatingCharge() ) {
458 >            charge += atom->getFlucQPos();
459 >          }
460 >          
461 >          charge *= chargeToC;
462 >          
463 >          qpole += 0.5 * charge * outProduct(ri, ri);
464 >
465 >          MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
466 >          
467 >          if ( ma.isDipole() ) {
468 >            dipole = atom->getDipole() * debyeToCm;
469 >            qpole += 0.5 * outProduct( dipole, ri );
470 >            qpole += 0.5 * outProduct( ri, dipole );
471 >          }
472 >
473 >          if ( ma.isQuadrupole() ) {
474 >            qpole += atom->getQuadrupole() * debyeToCm * angstromToM;          
475 >          }
476 >        }
477 >      }
478 >        
479 > #ifdef IS_MPI
480 >      MPI_Allreduce(MPI_IN_PLACE, qpole.getArrayPointer(),
481 >                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
482 > #endif
483 >      
484 >      snap->setSystemQuadrupole(qpole);
485 >    }
486 >    
487 >    return snap->getSystemQuadrupole();
488 >  }
489 >
490 >  // Returns the Heat Flux Vector for the system
491 >  Vector3d Thermo::getHeatFlux(){
492      Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
493 <    Stats& stat = currSnapshot->statData;
493 >    SimInfo::MoleculeIterator miter;
494 >    vector<StuntDouble*>::iterator iiter;
495 >    Molecule* mol;
496 >    StuntDouble* sd;    
497 >    RigidBody::AtomIterator ai;
498 >    Atom* atom;      
499 >    Vector3d vel;
500 >    Vector3d angMom;
501 >    Mat3x3d I;
502 >    int i;
503 >    int j;
504 >    int k;
505 >    RealType mass;
506 >
507 >    Vector3d x_a;
508 >    RealType kinetic;
509 >    RealType potential;
510 >    RealType eatom;
511 >    // Convective portion of the heat flux
512 >    Vector3d heatFluxJc = V3Zero;
513 >
514 >    /* Calculate convective portion of the heat flux */
515 >    for (mol = info_->beginMolecule(miter); mol != NULL;
516 >         mol = info_->nextMolecule(miter)) {
517 >      
518 >      for (sd = mol->beginIntegrableObject(iiter);
519 >           sd != NULL;
520 >           sd = mol->nextIntegrableObject(iiter)) {
521 >        
522 >        mass = sd->getMass();
523 >        vel = sd->getVel();
524 >
525 >        kinetic = mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
526 >        
527 >        if (sd->isDirectional()) {
528 >          angMom = sd->getJ();
529 >          I = sd->getI();
530 >
531 >          if (sd->isLinear()) {
532 >            i = sd->linearAxis();
533 >            j = (i + 1) % 3;
534 >            k = (i + 2) % 3;
535 >            kinetic += angMom[j] * angMom[j] / I(j, j)
536 >              + angMom[k] * angMom[k] / I(k, k);
537 >          } else {                        
538 >            kinetic += angMom[0]*angMom[0]/I(0, 0)
539 >              + angMom[1]*angMom[1]/I(1, 1)
540 >              + angMom[2]*angMom[2]/I(2, 2);
541 >          }
542 >        }
543 >
544 >        potential = 0.0;
545 >
546 >        if (sd->isRigidBody()) {
547 >          RigidBody* rb = dynamic_cast<RigidBody*>(sd);
548 >          for (atom = rb->beginAtom(ai); atom != NULL;
549 >               atom = rb->nextAtom(ai)) {
550 >            potential +=  atom->getParticlePot();
551 >          }          
552 >        } else {
553 >          potential = sd->getParticlePot();
554 >        }
555 >
556 >        potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
557 >        // The potential may not be a 1/2 factor
558 >        eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
559 >        heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
560 >        heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
561 >        heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
562 >      }
563 >    }
564 >
565 >    /* The J_v vector is reduced in the forceManager so everyone has
566 >     *  the global Jv. Jc is computed over the local atoms and must be
567 >     *  reduced among all processors.
568 >     */
569 > #ifdef IS_MPI
570 >    MPI_Allreduce(MPI_IN_PLACE, &heatFluxJc[0], 3, MPI_REALTYPE,
571 >                  MPI_SUM, MPI_COMM_WORLD);
572 > #endif
573      
574 <    stat[Stats::KINETIC_ENERGY] = getKinetic();
224 <    stat[Stats::POTENTIAL_ENERGY] = getPotential();
225 <    stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
226 <    stat[Stats::TEMPERATURE] = getTemperature();
227 <    stat[Stats::PRESSURE] = getPressure();
228 <    stat[Stats::VOLUME] = getVolume();      
574 >    // (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
575  
576 <    Mat3x3d tensor =getPressureTensor();
577 <    stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);      
578 <    stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);      
579 <    stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);      
580 <    stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);      
581 <    stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);      
582 <    stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);      
583 <    stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);      
584 <    stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);      
585 <    stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);      
586 <    Vector3d GKappa_t = getThermalHelfand();
587 <    stat[Stats::THERMAL_HELFANDMOMENT_X] = GKappa_t.x();
242 <    stat[Stats::THERMAL_HELFANDMOMENT_Y] = GKappa_t.y();
243 <    stat[Stats::THERMAL_HELFANDMOMENT_Z] = GKappa_t.z();
576 >    Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
577 >      PhysicalConstants::energyConvert;
578 >        
579 >    // Correct for the fact the flux is 1/V (Jc + Jv)
580 >    return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
581 >  }
582 >
583 >
584 >  Vector3d Thermo::getComVel(){
585 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
586 >
587 >    if (!snap->hasCOMvel) {
588  
589 <    Globals* simParams = info_->getSimParams();
589 >      SimInfo::MoleculeIterator i;
590 >      Molecule* mol;
591 >      
592 >      Vector3d comVel(0.0);
593 >      RealType totalMass(0.0);
594 >      
595 >      for (mol = info_->beginMolecule(i); mol != NULL;
596 >           mol = info_->nextMolecule(i)) {
597 >        RealType mass = mol->getMass();
598 >        totalMass += mass;
599 >        comVel += mass * mol->getComVel();
600 >      }  
601 >      
602 > #ifdef IS_MPI
603 >      MPI_Allreduce(MPI_IN_PLACE, &totalMass, 1, MPI_REALTYPE,
604 >                    MPI_SUM, MPI_COMM_WORLD);
605 >      MPI_Allreduce(MPI_IN_PLACE, comVel.getArrayPointer(), 3,
606 >                    MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
607 > #endif
608 >      
609 >      comVel /= totalMass;
610 >      snap->setCOMvel(comVel);
611 >    }
612 >    return snap->getCOMvel();
613 >  }
614  
615 +  Vector3d Thermo::getCom(){
616 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
617 +
618 +    if (!snap->hasCOM) {
619 +      
620 +      SimInfo::MoleculeIterator i;
621 +      Molecule* mol;
622 +      
623 +      Vector3d com(0.0);
624 +      RealType totalMass(0.0);
625 +      
626 +      for (mol = info_->beginMolecule(i); mol != NULL;
627 +           mol = info_->nextMolecule(i)) {
628 +        RealType mass = mol->getMass();
629 +        totalMass += mass;
630 +        com += mass * mol->getCom();
631 +      }  
632 +      
633 + #ifdef IS_MPI
634 +      MPI_Allreduce(MPI_IN_PLACE, &totalMass, 1, MPI_REALTYPE,
635 +                    MPI_SUM, MPI_COMM_WORLD);
636 +      MPI_Allreduce(MPI_IN_PLACE, com.getArrayPointer(), 3,
637 +                    MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
638 + #endif
639 +      
640 +      com /= totalMass;
641 +      snap->setCOM(com);
642 +    }
643 +    return snap->getCOM();
644 +  }        
645 +
646 +  /**
647 +   * Returns center of mass and center of mass velocity in one
648 +   * function call.
649 +   */  
650 +  void Thermo::getComAll(Vector3d &com, Vector3d &comVel){
651 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
652 +
653 +    if (!(snap->hasCOM && snap->hasCOMvel)) {
654 +
655 +      SimInfo::MoleculeIterator i;
656 +      Molecule* mol;
657 +      
658 +      RealType totalMass(0.0);
659 +      
660 +      com = 0.0;
661 +      comVel = 0.0;
662 +      
663 +      for (mol = info_->beginMolecule(i); mol != NULL;
664 +           mol = info_->nextMolecule(i)) {
665 +        RealType mass = mol->getMass();
666 +        totalMass += mass;
667 +        com += mass * mol->getCom();
668 +        comVel += mass * mol->getComVel();          
669 +      }  
670 +      
671 + #ifdef IS_MPI
672 +      MPI_Allreduce(MPI_IN_PLACE, &totalMass, 1, MPI_REALTYPE,
673 +                    MPI_SUM, MPI_COMM_WORLD);
674 +      MPI_Allreduce(MPI_IN_PLACE, com.getArrayPointer(), 3,
675 +                    MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
676 +      MPI_Allreduce(MPI_IN_PLACE, comVel.getArrayPointer(), 3,
677 +                    MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
678 + #endif
679 +      
680 +      com /= totalMass;
681 +      comVel /= totalMass;
682 +      snap->setCOM(com);
683 +      snap->setCOMvel(comVel);
684 +    }    
685 +    com = snap->getCOM();
686 +    comVel = snap->getCOMvel();
687 +    return;
688 +  }        
689 +  
690 +  /**
691 +   * \brief Return inertia tensor for entire system and angular momentum
692 +   *  Vector.
693 +   *
694 +   *
695 +   *
696 +   *    [  Ixx -Ixy  -Ixz ]
697 +   * I =| -Iyx  Iyy  -Iyz |
698 +   *    [ -Izx -Iyz   Izz ]
699 +   */
700 +  void Thermo::getInertiaTensor(Mat3x3d &inertiaTensor,
701 +                                Vector3d &angularMomentum){
702 +
703 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
704 +    
705 +    if (!(snap->hasInertiaTensor && snap->hasCOMw)) {
706 +      
707 +      RealType xx = 0.0;
708 +      RealType yy = 0.0;
709 +      RealType zz = 0.0;
710 +      RealType xy = 0.0;
711 +      RealType xz = 0.0;
712 +      RealType yz = 0.0;
713 +      Vector3d com(0.0);
714 +      Vector3d comVel(0.0);
715 +      
716 +      getComAll(com, comVel);
717 +      
718 +      SimInfo::MoleculeIterator i;
719 +      Molecule* mol;
720 +      
721 +      Vector3d thisq(0.0);
722 +      Vector3d thisv(0.0);
723 +      
724 +      RealType thisMass = 0.0;
725 +      
726 +      for (mol = info_->beginMolecule(i); mol != NULL;
727 +           mol = info_->nextMolecule(i)) {
728 +        
729 +        thisq = mol->getCom()-com;
730 +        thisv = mol->getComVel()-comVel;
731 +        thisMass = mol->getMass();
732 +        // Compute moment of intertia coefficients.
733 +        xx += thisq[0]*thisq[0]*thisMass;
734 +        yy += thisq[1]*thisq[1]*thisMass;
735 +        zz += thisq[2]*thisq[2]*thisMass;
736 +        
737 +        // compute products of intertia
738 +        xy += thisq[0]*thisq[1]*thisMass;
739 +        xz += thisq[0]*thisq[2]*thisMass;
740 +        yz += thisq[1]*thisq[2]*thisMass;
741 +        
742 +        angularMomentum += cross( thisq, thisv ) * thisMass;            
743 +      }
744 +      
745 +      inertiaTensor(0,0) = yy + zz;
746 +      inertiaTensor(0,1) = -xy;
747 +      inertiaTensor(0,2) = -xz;
748 +      inertiaTensor(1,0) = -xy;
749 +      inertiaTensor(1,1) = xx + zz;
750 +      inertiaTensor(1,2) = -yz;
751 +      inertiaTensor(2,0) = -xz;
752 +      inertiaTensor(2,1) = -yz;
753 +      inertiaTensor(2,2) = xx + yy;
754 +      
755 + #ifdef IS_MPI
756 +      MPI_Allreduce(MPI_IN_PLACE, inertiaTensor.getArrayPointer(),
757 +                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
758 +      MPI_Allreduce(MPI_IN_PLACE,
759 +                    angularMomentum.getArrayPointer(), 3,
760 +                    MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
761 + #endif
762 +      
763 +      snap->setCOMw(angularMomentum);
764 +      snap->setInertiaTensor(inertiaTensor);
765 +    }
766 +    
767 +    angularMomentum = snap->getCOMw();
768 +    inertiaTensor = snap->getInertiaTensor();
769 +    
770 +    return;
771 +  }
772 +
773 +
774 +  Mat3x3d Thermo::getBoundingBox(){
775 +    
776 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
777 +    
778 +    if (!(snap->hasBoundingBox)) {
779 +      
780 +      SimInfo::MoleculeIterator i;
781 +      Molecule::RigidBodyIterator ri;
782 +      Molecule::AtomIterator ai;
783 +      Molecule* mol;
784 +      RigidBody* rb;
785 +      Atom* atom;
786 +      Vector3d pos, bMax, bMin;
787 +      int index = 0;
788 +      
789 +      for (mol = info_->beginMolecule(i); mol != NULL;
790 +           mol = info_->nextMolecule(i)) {
791 +        
792 +        //change the positions of atoms which belong to the rigidbodies
793 +        for (rb = mol->beginRigidBody(ri); rb != NULL;
794 +             rb = mol->nextRigidBody(ri)) {          
795 +          rb->updateAtoms();
796 +        }
797 +        
798 +        for(atom = mol->beginAtom(ai); atom != NULL;
799 +            atom = mol->nextAtom(ai)) {
800 +          
801 +          pos = atom->getPos();
802 +
803 +          if (index == 0) {
804 +            bMax = pos;
805 +            bMin = pos;
806 +          } else {
807 +            for (int i = 0; i < 3; i++) {
808 +              bMax[i] = max(bMax[i], pos[i]);
809 +              bMin[i] = min(bMin[i], pos[i]);
810 +            }
811 +          }
812 +          index++;
813 +        }
814 +      }
815 +      
816 + #ifdef IS_MPI
817 +      MPI_Allreduce(MPI_IN_PLACE, &bMax[0], 3, MPI_REALTYPE,
818 +                    MPI_MAX, MPI_COMM_WORLD);
819 +
820 +      MPI_Allreduce(MPI_IN_PLACE, &bMin[0], 3, MPI_REALTYPE,
821 +                    MPI_MIN, MPI_COMM_WORLD);
822 + #endif
823 +      Mat3x3d bBox = Mat3x3d(0.0);
824 +      for (int i = 0; i < 3; i++) {          
825 +        bBox(i,i) = bMax[i] - bMin[i];
826 +      }
827 +      snap->setBoundingBox(bBox);
828 +    }
829 +    
830 +    return snap->getBoundingBox();    
831 +  }
832 +  
833 +  
834 +  // Returns the angular momentum of the system
835 +  Vector3d Thermo::getAngularMomentum(){
836 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
837 +    
838 +    if (!snap->hasCOMw) {
839 +      
840 +      Vector3d com(0.0);
841 +      Vector3d comVel(0.0);
842 +      Vector3d angularMomentum(0.0);
843 +      
844 +      getComAll(com, comVel);
845 +      
846 +      SimInfo::MoleculeIterator i;
847 +      Molecule* mol;
848 +      
849 +      Vector3d thisr(0.0);
850 +      Vector3d thisp(0.0);
851 +      
852 +      RealType thisMass;
853 +      
854 +      for (mol = info_->beginMolecule(i); mol != NULL;
855 +           mol = info_->nextMolecule(i)) {
856 +        thisMass = mol->getMass();
857 +        thisr = mol->getCom() - com;
858 +        thisp = (mol->getComVel() - comVel) * thisMass;
859 +        
860 +        angularMomentum += cross( thisr, thisp );      
861 +      }  
862 +      
863 + #ifdef IS_MPI
864 +      MPI_Allreduce(MPI_IN_PLACE,
865 +                    angularMomentum.getArrayPointer(), 3,
866 +                    MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
867 + #endif
868 +      
869 +      snap->setCOMw(angularMomentum);
870 +    }
871 +    
872 +    return snap->getCOMw();
873 +  }
874 +  
875 +  
876 +  /**
877 +   * Returns the Volume of the system based on a ellipsoid with
878 +   * semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
879 +   * where R_i are related to the principle inertia moments
880 +   *  R_i = sqrt(C*I_i/N), this reduces to
881 +   *  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
882 +   * See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
883 +   */
884 +  RealType Thermo::getGyrationalVolume(){
885 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
886 +    
887 +    if (!snap->hasGyrationalVolume) {
888 +      
889 +      Mat3x3d intTensor;
890 +      RealType det;
891 +      Vector3d dummyAngMom;
892 +      RealType sysconstants;
893 +      RealType geomCnst;
894 +      RealType volume;
895 +      
896 +      geomCnst = 3.0/2.0;
897 +      /* Get the inertial tensor and angular momentum for free*/
898 +      getInertiaTensor(intTensor, dummyAngMom);
899 +      
900 +      det = intTensor.determinant();
901 +      sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
902 +      volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
903 +
904 +      snap->setGyrationalVolume(volume);
905 +    }
906 +    return snap->getGyrationalVolume();
907 +  }
908 +  
909 +  void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
910 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
911 +
912 +    if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
913 +    
914 +      Mat3x3d intTensor;
915 +      Vector3d dummyAngMom;
916 +      RealType sysconstants;
917 +      RealType geomCnst;
918 +      
919 +      geomCnst = 3.0/2.0;
920 +      /* Get the inertia tensor and angular momentum for free*/
921 +      this->getInertiaTensor(intTensor, dummyAngMom);
922 +      
923 +      detI = intTensor.determinant();
924 +      sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
925 +      volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
926 +      snap->setGyrationalVolume(volume);
927 +    } else {
928 +      volume = snap->getGyrationalVolume();
929 +      detI = snap->getInertiaTensor().determinant();
930 +    }
931 +    return;
932 +  }
933 +  
934 +  RealType Thermo::getTaggedAtomPairDistance(){
935 +    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
936 +    Globals* simParams = info_->getSimParams();
937 +    
938      if (simParams->haveTaggedAtomPair() &&
939          simParams->havePrintTaggedPairDistance()) {
940        if ( simParams->getPrintTaggedPairDistance()) {
941          
942 <        std::pair<int, int> tap = simParams->getTaggedAtomPair();
942 >        pair<int, int> tap = simParams->getTaggedAtomPair();
943          Vector3d pos1, pos2, rab;
944 <
944 >        
945   #ifdef IS_MPI        
255 –        std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
256 –
946          int mol1 = info_->getGlobalMolMembership(tap.first);
947          int mol2 = info_->getGlobalMolMembership(tap.second);
259 –        std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
948  
949          int proc1 = info_->getMolToProc(mol1);
950          int proc2 = info_->getMolToProc(mol2);
951  
264 –        std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
265 –
952          RealType data[3];
953          if (proc1 == worldRank) {
954            StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
269 –          std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
955            pos1 = sd1->getPos();
956            data[0] = pos1.x();
957            data[1] = pos1.y();
# Line 277 | Line 962 | namespace OpenMD {
962            pos1 = Vector3d(data);
963          }
964  
280 –
965          if (proc2 == worldRank) {
966            StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
283 –          std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
967            pos2 = sd2->getPos();
968            data[0] = pos2.x();
969            data[1] = pos2.y();
970 <          data[2] = pos2.z();          
970 >          data[2] = pos2.z();  
971            MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
972          } else {
973            MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
# Line 298 | Line 981 | namespace OpenMD {
981   #endif        
982          rab = pos2 - pos1;
983          currSnapshot->wrapVector(rab);
984 <        stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
984 >        return rab.length();
985        }
986 +      return 0.0;    
987      }
988 <      
305 <    /**@todo need refactorying*/
306 <    //Conserved Quantity is set by integrator and time is set by setTime
307 <    
988 >    return 0.0;
989    }
990  
991 <
992 <
993 < Vector3d Thermo::getBoxDipole() {
994 <    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
995 <    SimInfo::MoleculeIterator miter;
996 <    std::vector<Atom*>::iterator aiter;
997 <    Molecule* mol;
998 <    Atom* atom;
999 <    RealType charge;
1000 <    RealType moment(0.0);
1001 <    Vector3d ri(0.0);
1002 <    Vector3d dipoleVector(0.0);
1003 <    Vector3d nPos(0.0);
1004 <    Vector3d pPos(0.0);
1005 <    RealType nChg(0.0);
325 <    RealType pChg(0.0);
326 <    int nCount = 0;
327 <    int pCount = 0;
328 <
329 <    RealType chargeToC = 1.60217733e-19;
330 <    RealType angstromToM = 1.0e-10;    RealType debyeToCm = 3.33564095198e-30;
331 <
332 <    for (mol = info_->beginMolecule(miter); mol != NULL;
333 <         mol = info_->nextMolecule(miter)) {
334 <
335 <      for (atom = mol->beginAtom(aiter); atom != NULL;
336 <           atom = mol->nextAtom(aiter)) {
337 <
338 <        if (atom->isCharge() ) {
339 <          charge = 0.0;
340 <          GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
341 <          if (data != NULL) {
342 <
343 <            charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
344 <            charge *= chargeToC;
345 <
346 <            ri = atom->getPos();
347 <            currSnapshot->wrapVector(ri);
348 <            ri *= angstromToM;
349 <
350 <            if (charge < 0.0) {
351 <              nPos += ri;
352 <              nChg -= charge;
353 <              nCount++;
354 <            } else if (charge > 0.0) {
355 <              pPos += ri;
356 <              pChg += charge;
357 <              pCount++;
358 <            }
359 <          }
360 <        }
361 <
362 <        if (atom->isDipole() ) {
363 <          Vector3d u_i = atom->getElectroFrame().getColumn(2);
364 <          GenericData* data = dynamic_cast<DirectionalAtomType*>(atom->getAtomType())->getPropertyByName("Dipole");
365 <          if (data != NULL) {
366 <            moment = (dynamic_cast<DoubleGenericData*>(data))->getData();
367 <
368 <            moment *= debyeToCm;
369 <            dipoleVector += u_i * moment;
370 <          }
371 <        }
991 >  RealType Thermo::getHullVolume(){
992 > #ifdef HAVE_QHULL    
993 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
994 >    if (!snap->hasHullVolume) {
995 >      Hull* surfaceMesh_;
996 >      
997 >      Globals* simParams = info_->getSimParams();
998 >      const std::string ht = simParams->getHULL_Method();
999 >      
1000 >      if (ht == "Convex") {
1001 >        surfaceMesh_ = new ConvexHull();
1002 >      } else if (ht == "AlphaShape") {
1003 >        surfaceMesh_ = new AlphaHull(simParams->getAlpha());
1004 >      } else {
1005 >        return 0.0;
1006        }
1007 +      
1008 +      // Build a vector of stunt doubles to determine if they are
1009 +      // surface atoms
1010 +      std::vector<StuntDouble*> localSites_;
1011 +      Molecule* mol;
1012 +      StuntDouble* sd;
1013 +      SimInfo::MoleculeIterator i;
1014 +      Molecule::IntegrableObjectIterator  j;
1015 +      
1016 +      for (mol = info_->beginMolecule(i); mol != NULL;
1017 +           mol = info_->nextMolecule(i)) {          
1018 +        for (sd = mol->beginIntegrableObject(j);
1019 +             sd != NULL;
1020 +             sd = mol->nextIntegrableObject(j)) {  
1021 +          localSites_.push_back(sd);
1022 +        }
1023 +      }  
1024 +      
1025 +      // Compute surface Mesh
1026 +      surfaceMesh_->computeHull(localSites_);
1027 +      snap->setHullVolume(surfaceMesh_->getVolume());
1028 +      
1029 +      delete surfaceMesh_;
1030      }
374 –
375 –
376 – #ifdef IS_MPI
377 –    RealType pChg_global, nChg_global;
378 –    int pCount_global, nCount_global;
379 –    Vector3d pPos_global, nPos_global, dipVec_global;
380 –
381 –    MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
382 –                  MPI_COMM_WORLD);
383 –    pChg = pChg_global;
384 –    MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
385 –                  MPI_COMM_WORLD);
386 –    nChg = nChg_global;
387 –    MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
388 –                  MPI_COMM_WORLD);
389 –    pCount = pCount_global;
390 –    MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
391 –                  MPI_COMM_WORLD);
392 –    nCount = nCount_global;
393 –    MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
394 –                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
395 –    pPos = pPos_global;
396 –    MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
397 –                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
398 –    nPos = nPos_global;
399 –    MPI_Allreduce(dipoleVector.getArrayPointer(),
400 –                  dipVec_global.getArrayPointer(), 3,
401 –                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
402 –    dipoleVector = dipVec_global;
403 – #endif //is_mpi
404 –
405 –    // first load the accumulated dipole moment (if dipoles were present)
406 –    Vector3d boxDipole = dipoleVector;
407 –    // now include the dipole moment due to charges
408 –    // use the lesser of the positive and negative charge totals
409 –    RealType chg_value = nChg <= pChg ? nChg : pChg;
410 –
411 –    // find the average positions
412 –    if (pCount > 0 && nCount > 0 ) {
413 –      pPos /= pCount;
414 –      nPos /= nCount;
415 –    }
416 –
417 –    // dipole is from the negative to the positive (physics notation)
418 –    boxDipole += (pPos - nPos) * chg_value;
419 –
420 –    return boxDipole;
421 –  }
422 –
423 – Vector3d Thermo::getThermalHelfand() {
424 –    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
425 –    SimInfo::MoleculeIterator miter;
426 –    std::vector<Atom*>::iterator aiter;
427 –    Molecule* mol;
428 –    Atom* atom;
429 –    RealType mass;
430 –    Vector3d velocity;
431 –    Vector3d x_a;
432 –    RealType kinetic;
433 –    RealType potential;
434 –    RealType eatom;
435 –    RealType AvgE_a_ = 0;
436 –    Vector3d GKappa_t = V3Zero;
437 –    Vector3d ThermalHelfandMoment;
1031      
1032 <    for (mol = info_->beginMolecule(miter); mol != NULL;
1033 <         mol = info_->nextMolecule(miter)) {
1034 <
442 <      for (atom = mol->beginAtom(aiter); atom != NULL;
443 <           atom = mol->nextAtom(aiter)) {
444 <
445 <        mass = atom->getMass();
446 <        velocity = atom->getVel();
447 <        kinetic = mass * (velocity[0]*velocity[0] + velocity[1]*velocity[1] +
448 <                                   velocity[2]*velocity[2]) / PhysicalConstants::energyConvert;
449 <        potential =  atom->getParticlePot();
450 <        eatom += (kinetic + potential)/2.0;
451 <      }
452 <    }
453 <
454 <   int natoms = info_->getNGlobalAtoms();
455 < #ifdef IS_MPI
456 <    
457 <    MPI_Allreduce(&eatom, &AvgE_a_, 1, MPI_REALTYPE, MPI_SUM,
458 <                  MPI_COMM_WORLD);
459 < #else    
460 <    AvgE_a_ = eatom;
1032 >    return snap->getHullVolume();
1033 > #else
1034 >    return 0.0;
1035   #endif
1036 <    AvgE_a_ = AvgE_a_/RealType(natoms);
463 <    
464 <    for (mol = info_->beginMolecule(miter); mol != NULL;
465 <         mol = info_->nextMolecule(miter)) {
466 <      
467 <      for (atom = mol->beginAtom(aiter); atom != NULL;
468 <           atom = mol->nextAtom(aiter)) {
469 <        
470 <        /* We think that x_a is relative to the total box and should be a wrapped coordinate */
471 <        x_a = atom->getPos();
472 <        currSnapshot->wrapVector(x_a);
473 <        potential =  atom->getParticlePot();
1036 >  }
1037  
475 –        GKappa_t += x_a*(potential-AvgE_a_);
476 –        }
477 –      }
478 – #ifdef IS_MPI
479 –     MPI_Allreduce(GKappa_t.getArrayPointer(), ThermalHelfandMoment.getArrayPointer(), 3,
480 –                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
481 – #else    
482 –     ThermalHelfandMoment = GKappa_t;
483 – #endif  
484 –     return ThermalHelfandMoment;
485 –    
486 – }
1038  
1039 <
489 <
490 < } //end namespace OpenMD
1039 > }

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