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Comparing trunk/src/brains/Thermo.cpp (file contents):
Revision 1667 by chuckv, Wed Dec 14 20:24:39 2011 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

# Line 32 | Line 32
32   * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33   * research, please cite the appropriate papers when you publish your
34   * work.  Good starting points are:
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).
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, 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   */
42  
42 – #include <math.h>
43 – #include <iostream>
44 –
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;
58 <    std::vector<StuntDouble*>::iterator iiter;
59 <    Molecule* mol;
60 <    StuntDouble* integrableObject;
61 <    Vector3d vel;
62 <    Vector3d angMom;
63 <    Mat3x3d I;
64 <    int i;
65 <    int j;
66 <    int k;
67 <    RealType mass;
68 <    RealType kinetic = 0.0;
69 <    RealType kinetic_global = 0.0;
65 >  RealType Thermo::getTranslationalKinetic() {
66 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
67  
68 <    for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
69 <      for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
70 <     integrableObject = mol->nextIntegrableObject(iiter)) {
71 <
72 <  mass = integrableObject->getMass();
73 <  vel = integrableObject->getVel();
74 <
75 <  kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
76 <
77 <  if (integrableObject->isDirectional()) {
78 <    angMom = integrableObject->getJ();
79 <    I = integrableObject->getI();
80 <
81 <    if (integrableObject->isLinear()) {
82 <      i = integrableObject->linearAxis();
83 <      j = (i + 1) % 3;
84 <      k = (i + 2) % 3;
85 <      kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
86 <    } else {
87 <      kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
88 <        + angMom[2]*angMom[2]/I(2, 2);
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 >        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 +  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 +      
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 < #ifdef IS_MPI
154 >      
155  
156 <    MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
157 <                  MPI_COMM_WORLD);
102 <    kinetic = kinetic_global;
156 >  RealType Thermo::getKinetic() {
157 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
158  
159 < #endif //is_mpi
160 <
161 <    kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
162 <
163 <    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  
186 <  RealType Thermo::getTotalE() {
134 <    RealType total;
186 >  RealType Thermo::getTemperature() {
187  
188 <    total = this->getKinetic() + this->getPotential();
137 <    return total;
138 <  }
188 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
189  
190 <  RealType Thermo::getTemperature() {
190 >    if (!snap->hasTemperature) {
191  
192 <    RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
193 <    return temperature;
144 <  }
192 >      RealType temperature = ( 2.0 * this->getKinetic() )
193 >        / (info_->getNdf()* PhysicalConstants::kb );
194  
195 <  RealType Thermo::getVolume() {
196 <    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
197 <    return curSnapshot->getVolume();
195 >      snap->setTemperature(temperature);
196 >    }
197 >    
198 >    return snap->getTemperature();
199    }
200  
201 <  RealType Thermo::getPressure() {
201 >  RealType Thermo::getElectronicTemperature() {
202 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
203  
204 <    // Relies on the calculation of the full molecular pressure tensor
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 +      kinetic *= 0.5;
235 +      eTemp =  (2.0 * kinetic) /
236 +        (info_->getNFluctuatingCharges() * PhysicalConstants::kb );            
237 +    
238 +      snap->setElectronicTemperature(eTemp);
239 +    }
240  
241 <    Mat3x3d tensor;
242 <    RealType pressure;
241 >    return snap->getElectronicTemperature();
242 >  }
243  
159 –    tensor = getPressureTensor();
244  
245 <    pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
246 <
247 <    return pressure;
245 >  RealType Thermo::getVolume() {
246 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
247 >    return snap->getVolume();
248    }
249  
250 <  RealType Thermo::getPressure(int direction) {
250 >  RealType Thermo::getPressure() {
251 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
252  
253 <    // Relies on the calculation of the full molecular pressure tensor
254 <
255 <
256 <    Mat3x3d tensor;
257 <    RealType pressure;
258 <
259 <    tensor = getPressureTensor();
260 <
261 <    pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
262 <
263 <    return pressure;
253 >    if (!snap->hasPressure) {
254 >      // Relies on the calculation of the full molecular pressure tensor
255 >      
256 >      Mat3x3d tensor;
257 >      RealType pressure;
258 >      
259 >      tensor = getPressureTensor();
260 >      
261 >      pressure = PhysicalConstants::pressureConvert *
262 >        (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
263 >      
264 >      snap->setPressure(pressure);
265 >    }
266 >    
267 >    return snap->getPressure();    
268    }
269  
270    Mat3x3d Thermo::getPressureTensor() {
271      // returns pressure tensor in units amu*fs^-2*Ang^-1
272      // routine derived via viral theorem description in:
273      // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
274 <    Mat3x3d pressureTensor;
186 <    Mat3x3d p_local(0.0);
187 <    Mat3x3d p_global(0.0);
274 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
275  
276 <    SimInfo::MoleculeIterator i;
190 <    std::vector<StuntDouble*>::iterator j;
191 <    Molecule* mol;
192 <    StuntDouble* integrableObject;
193 <    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
194 <      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
195 <     integrableObject = mol->nextIntegrableObject(j)) {
276 >    if (!snap->hasPressureTensor) {
277  
278 <  RealType mass = integrableObject->getMass();
279 <  Vector3d vcom = integrableObject->getVel();
280 <  p_local += mass * outProduct(vcom, vcom);
278 >      Mat3x3d pressureTensor;
279 >      Mat3x3d p_tens(0.0);
280 >      RealType mass;
281 >      Vector3d vcom;
282 >      
283 >      SimInfo::MoleculeIterator i;
284 >      vector<StuntDouble*>::iterator j;
285 >      Molecule* mol;
286 >      StuntDouble* sd;    
287 >      for (mol = info_->beginMolecule(i); mol != NULL;
288 >           mol = info_->nextMolecule(i)) {
289 >        
290 >        for (sd = mol->beginIntegrableObject(j); sd != NULL;
291 >             sd = mol->nextIntegrableObject(j)) {
292 >          
293 >          mass = sd->getMass();
294 >          vcom = sd->getVel();
295 >          p_tens += mass * outProduct(vcom, vcom);        
296 >        }
297        }
298 +      
299 + #ifdef IS_MPI
300 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, p_tens.getArrayPointer(), 9,
301 +                                MPI::REALTYPE, MPI::SUM);
302 + #endif
303 +      
304 +      RealType volume = this->getVolume();
305 +      Mat3x3d stressTensor = snap->getStressTensor();
306 +      
307 +      pressureTensor =  (p_tens +
308 +                         PhysicalConstants::energyConvert * stressTensor)/volume;
309 +      
310 +      snap->setPressureTensor(pressureTensor);
311      }
312 +    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->statData.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;
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 <    return pressureTensor;
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 >    return snap->getSystemDipole();
419    }
420  
421 <
422 <  void Thermo::saveStat(){
421 >  // Returns the Heat Flux Vector for the system
422 >  Vector3d Thermo::getHeatFlux(){
423      Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
424 <    Stats& stat = currSnapshot->statData;
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 <    stat[Stats::KINETIC_ENERGY] = getKinetic();
439 <    stat[Stats::POTENTIAL_ENERGY] = getPotential();
440 <    stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
441 <    stat[Stats::TEMPERATURE] = getTemperature();
442 <    stat[Stats::PRESSURE] = getPressure();
443 <    stat[Stats::VOLUME] = getVolume();
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 <    Mat3x3d tensor =getPressureTensor();
446 <    stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
447 <    stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
448 <    stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
449 <    stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
450 <    stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
451 <    stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
452 <    stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
453 <    stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
454 <    stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
455 <    Vector3d GKappa_t = getThermalHelfand();
456 <    stat[Stats::THERMAL_HELFANDMOMENT_X] = GKappa_t.x();
457 <    stat[Stats::THERMAL_HELFANDMOMENT_Y] = GKappa_t.y();
458 <    stat[Stats::THERMAL_HELFANDMOMENT_Z] = GKappa_t.z();
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 >    /* 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 <    Globals* simParams = info_->getSimParams();
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 (simParams->haveTaggedAtomPair() &&
248 <        simParams->havePrintTaggedPairDistance()) {
249 <      if ( simParams->getPrintTaggedPairDistance()) {
584 >    if (!(snap->hasCOM && snap->hasCOMvel)) {
585  
586 <        std::pair<int, int> tap = simParams->getTaggedAtomPair();
587 <        Vector3d pos1, pos2, rab;
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 >   * \brief Return inertia 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 <        std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;
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  
257 –  int mol1 = info_->getGlobalMolMembership(tap.first);
258 –  int mol2 = info_->getGlobalMolMembership(tap.second);
259 –        std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
704  
705 +  Mat3x3d Thermo::getBoundingBox(){
706 +    
707 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
708 +    
709 +    if (!(snap->hasBoundingBox)) {
710 +      
711 +      SimInfo::MoleculeIterator i;
712 +      Molecule::RigidBodyIterator ri;
713 +      Molecule::AtomIterator ai;
714 +      Molecule* mol;
715 +      RigidBody* rb;
716 +      Atom* atom;
717 +      Vector3d pos, bMax, bMin;
718 +      int index = 0;
719 +      
720 +      for (mol = info_->beginMolecule(i); mol != NULL;
721 +           mol = info_->nextMolecule(i)) {
722 +        
723 +        //change the positions of atoms which belong to the rigidbodies
724 +        for (rb = mol->beginRigidBody(ri); rb != NULL;
725 +             rb = mol->nextRigidBody(ri)) {          
726 +          rb->updateAtoms();
727 +        }
728 +        
729 +        for(atom = mol->beginAtom(ai); atom != NULL;
730 +            atom = mol->nextAtom(ai)) {
731 +          
732 +          pos = atom->getPos();
733 +
734 +          if (index == 0) {
735 +            bMax = pos;
736 +            bMin = pos;
737 +          } else {
738 +            for (int i = 0; i < 3; i++) {
739 +              bMax[i] = max(bMax[i], pos[i]);
740 +              bMin[i] = min(bMin[i], pos[i]);
741 +            }
742 +          }
743 +          index++;
744 +        }
745 +      }
746 +      
747 + #ifdef IS_MPI
748 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bMax[0], 3, MPI::REALTYPE,
749 +                                MPI::MAX);
750 +
751 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bMin[0], 3, MPI::REALTYPE,
752 +                                MPI::MIN);
753 + #endif
754 +      Mat3x3d bBox = Mat3x3d(0.0);
755 +      for (int i = 0; i < 3; i++) {          
756 +        bBox(i,i) = bMax[i] - bMin[i];
757 +      }
758 +      snap->setBoundingBox(bBox);
759 +    }
760 +    
761 +    return snap->getBoundingBox();    
762 +  }
763 +  
764 +  
765 +  // Returns the angular momentum of the system
766 +  Vector3d Thermo::getAngularMomentum(){
767 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
768 +    
769 +    if (!snap->hasCOMw) {
770 +      
771 +      Vector3d com(0.0);
772 +      Vector3d comVel(0.0);
773 +      Vector3d angularMomentum(0.0);
774 +      
775 +      getComAll(com, comVel);
776 +      
777 +      SimInfo::MoleculeIterator i;
778 +      Molecule* mol;
779 +      
780 +      Vector3d thisr(0.0);
781 +      Vector3d thisp(0.0);
782 +      
783 +      RealType thisMass;
784 +      
785 +      for (mol = info_->beginMolecule(i); mol != NULL;
786 +           mol = info_->nextMolecule(i)) {
787 +        thisMass = mol->getMass();
788 +        thisr = mol->getCom() - com;
789 +        thisp = (mol->getComVel() - comVel) * thisMass;
790 +        
791 +        angularMomentum += cross( thisr, thisp );      
792 +      }  
793 +      
794 + #ifdef IS_MPI
795 +      MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE,
796 +                                angularMomentum.getArrayPointer(), 3,
797 +                                MPI::REALTYPE, MPI::SUM);
798 + #endif
799 +      
800 +      snap->setCOMw(angularMomentum);
801 +    }
802 +    
803 +    return snap->getCOMw();
804 +  }
805 +  
806 +  
807 +  /**
808 +   * Returns the Volume of the system based on a ellipsoid with
809 +   * semi-axes based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
810 +   * where R_i are related to the principle inertia moments
811 +   *  R_i = sqrt(C*I_i/N), this reduces to
812 +   *  V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)).
813 +   * See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
814 +   */
815 +  RealType Thermo::getGyrationalVolume(){
816 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
817 +    
818 +    if (!snap->hasGyrationalVolume) {
819 +      
820 +      Mat3x3d intTensor;
821 +      RealType det;
822 +      Vector3d dummyAngMom;
823 +      RealType sysconstants;
824 +      RealType geomCnst;
825 +      RealType volume;
826 +      
827 +      geomCnst = 3.0/2.0;
828 +      /* Get the inertial tensor and angular momentum for free*/
829 +      getInertiaTensor(intTensor, dummyAngMom);
830 +      
831 +      det = intTensor.determinant();
832 +      sysconstants = geomCnst / (RealType)(info_->getNGlobalIntegrableObjects());
833 +      volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
834 +
835 +      snap->setGyrationalVolume(volume);
836 +    }
837 +    return snap->getGyrationalVolume();
838 +  }
839 +  
840 +  void Thermo::getGyrationalVolume(RealType &volume, RealType &detI){
841 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
842 +
843 +    if (!(snap->hasInertiaTensor && snap->hasGyrationalVolume)) {
844 +    
845 +      Mat3x3d intTensor;
846 +      Vector3d dummyAngMom;
847 +      RealType sysconstants;
848 +      RealType geomCnst;
849 +      
850 +      geomCnst = 3.0/2.0;
851 +      /* Get the inertia tensor and angular momentum for free*/
852 +      this->getInertiaTensor(intTensor, dummyAngMom);
853 +      
854 +      detI = intTensor.determinant();
855 +      sysconstants = geomCnst/(RealType)(info_->getNGlobalIntegrableObjects());
856 +      volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
857 +      snap->setGyrationalVolume(volume);
858 +    } else {
859 +      volume = snap->getGyrationalVolume();
860 +      detI = snap->getInertiaTensor().determinant();
861 +    }
862 +    return;
863 +  }
864 +  
865 +  RealType Thermo::getTaggedAtomPairDistance(){
866 +    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
867 +    Globals* simParams = info_->getSimParams();
868 +    
869 +    if (simParams->haveTaggedAtomPair() &&
870 +        simParams->havePrintTaggedPairDistance()) {
871 +      if ( simParams->getPrintTaggedPairDistance()) {
872 +        
873 +        pair<int, int> tap = simParams->getTaggedAtomPair();
874 +        Vector3d pos1, pos2, rab;
875 +        
876 + #ifdef IS_MPI        
877 +        int mol1 = info_->getGlobalMolMembership(tap.first);
878 +        int mol2 = info_->getGlobalMolMembership(tap.second);
879 +
880          int proc1 = info_->getMolToProc(mol1);
881          int proc2 = info_->getMolToProc(mol2);
882  
883 <        std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
265 <
266 <  RealType data[3];
883 >        RealType data[3];
884          if (proc1 == worldRank) {
885            StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
269 –          std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
886            pos1 = sd1->getPos();
887            data[0] = pos1.x();
888            data[1] = pos1.y();
889 <          data[2] = pos1.z();
890 <          MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
889 >          data[2] = pos1.z();          
890 >          MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1);
891          } else {
892 <          MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
892 >          MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1);
893            pos1 = Vector3d(data);
894          }
895  
280 –
896          if (proc2 == worldRank) {
897            StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
283 –          std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
898            pos2 = sd2->getPos();
899            data[0] = pos2.x();
900            data[1] = pos2.y();
901 <          data[2] = pos2.z();
902 <          MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
901 >          data[2] = pos2.z();  
902 >          MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2);
903          } else {
904 <          MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
904 >          MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2);
905            pos2 = Vector3d(data);
906          }
907   #else
# Line 295 | Line 909 | namespace OpenMD {
909          StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
910          pos1 = at1->getPos();
911          pos2 = at2->getPos();
912 < #endif
912 > #endif        
913          rab = pos2 - pos1;
914          currSnapshot->wrapVector(rab);
915 <        stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
915 >        return rab.length();
916        }
917 +      return 0.0;    
918      }
919 <
305 <    /**@todo need refactorying*/
306 <    //Conserved Quantity is set by integrator and time is set by setTime
307 <
919 >    return 0.0;
920    }
921  
922 <
923 <
924 < Vector3d Thermo::getBoxDipole() {
925 <    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
926 <    SimInfo::MoleculeIterator miter;
927 <    std::vector<Atom*>::iterator aiter;
928 <    Molecule* mol;
929 <    Atom* atom;
930 <    RealType charge;
931 <    RealType moment(0.0);
932 <    Vector3d ri(0.0);
933 <    Vector3d dipoleVector(0.0);
934 <    Vector3d nPos(0.0);
935 <    Vector3d pPos(0.0);
936 <    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 <        }
922 >  RealType Thermo::getHullVolume(){
923 > #ifdef HAVE_QHULL    
924 >    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
925 >    if (!snap->hasHullVolume) {
926 >      Hull* surfaceMesh_;
927 >      
928 >      Globals* simParams = info_->getSimParams();
929 >      const std::string ht = simParams->getHULL_Method();
930 >      
931 >      if (ht == "Convex") {
932 >        surfaceMesh_ = new ConvexHull();
933 >      } else if (ht == "AlphaShape") {
934 >        surfaceMesh_ = new AlphaHull(simParams->getAlpha());
935 >      } else {
936 >        return 0.0;
937        }
938 +      
939 +      // Build a vector of stunt doubles to determine if they are
940 +      // surface atoms
941 +      std::vector<StuntDouble*> localSites_;
942 +      Molecule* mol;
943 +      StuntDouble* sd;
944 +      SimInfo::MoleculeIterator i;
945 +      Molecule::IntegrableObjectIterator  j;
946 +      
947 +      for (mol = info_->beginMolecule(i); mol != NULL;
948 +           mol = info_->nextMolecule(i)) {          
949 +        for (sd = mol->beginIntegrableObject(j);
950 +             sd != NULL;
951 +             sd = mol->nextIntegrableObject(j)) {  
952 +          localSites_.push_back(sd);
953 +        }
954 +      }  
955 +      
956 +      // Compute surface Mesh
957 +      surfaceMesh_->computeHull(localSites_);
958 +      snap->setHullVolume(surfaceMesh_->getVolume());
959 +      
960 +      delete surfaceMesh_;
961      }
962 <
963 <
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;
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 <        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);
962 >    
963 >    return snap->getHullVolume();
964   #else
965 <    AvgE_a_ = eatom;
965 >    return 0.0;
966   #endif
967 <    AvgE_a_ = AvgE_a_/RealType(natoms);
967 >  }
968  
464 –    for (mol = info_->beginMolecule(miter); mol != NULL;
465 –         mol = info_->nextMolecule(miter)) {
969  
970 <      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();
474 <        velocity = atom->getVel();
475 <        kinetic = mass * (velocity[0]*velocity[0] + velocity[1]*velocity[1] +
476 <                           velocity[2]*velocity[2]) / PhysicalConstants::energyConvert;
477 <        eatom += (kinetic + potential)/2.0;
478 <        GKappa_t += x_a*(eatom-AvgE_a_);
479 <        }
480 <      }
481 < #ifdef IS_MPI
482 <     MPI_Allreduce(GKappa_t.getArrayPointer(), ThermalHelfandMoment.getArrayPointer(), 3,
483 <                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
484 < #else
485 <     ThermalHelfandMoment = GKappa_t;
486 < #endif
487 <     return ThermalHelfandMoment;
488 <
489 < }
490 <
491 <
492 <
493 < } //end namespace OpenMD
970 > }

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