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root/OpenMD/branches/development/src/rnemd/RNEMD.cpp
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Comparing trunk/src/integrators/RNEMD.cpp (file contents):
Revision 1334 by gezelter, Thu Apr 2 19:55:37 2009 UTC vs.
Revision 1341 by skuang, Fri May 8 19:47:05 2009 UTC

# Line 53 | Line 53
53   #include "math/ParallelRandNumGen.hpp"
54   #endif
55  
56 – /* Remove me after testing*/
57 – /*
58 – #include <cstdio>
59 – #include <iostream>
60 – */
61 – /*End remove me*/
56  
57   namespace oopse {
58    
# Line 74 | Line 68 | namespace oopse {
68      stringToEnumMap_["Unknown"] = rnemdUnknown;
69  
70      rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
77 –
78 –    std::cerr << "calling  evaluator with " << rnemdObjectSelection_ << "\n";
71      evaluator_.loadScriptString(rnemdObjectSelection_);
72 <    std::cerr << "done";
72 >    seleMan_.setSelectionSet(evaluator_.evaluate());
73 >
74 >
75 >    // do some sanity checking
76 >
77 >    int selectionCount = seleMan_.getSelectionCount();
78 >    int nIntegrable = info->getNGlobalIntegrableObjects();
79 >
80 >    if (selectionCount > nIntegrable) {
81 >      sprintf(painCave.errMsg,
82 >              "RNEMD warning: The current RNEMD_objectSelection,\n"
83 >              "\t\t%s\n"
84 >              "\thas resulted in %d selected objects.  However,\n"
85 >              "\tthe total number of integrable objects in the system\n"
86 >              "\tis only %d.  This is almost certainly not what you want\n"
87 >              "\tto do.  A likely cause of this is forgetting the _RB_0\n"
88 >              "\tselector in the selection script!\n",
89 >              rnemdObjectSelection_.c_str(),
90 >              selectionCount, nIntegrable);
91 >      painCave.isFatal = 0;
92 >      simError();
93 >
94 >    }
95      
96      const std::string st = simParams->getRNEMD_swapType();
97  
# Line 88 | Line 102 | namespace oopse {
102      set_RNEMD_swapTime(simParams->getRNEMD_swapTime());
103      set_RNEMD_nBins(simParams->getRNEMD_nBins());
104      exchangeSum_ = 0.0;
105 <    
105 >    counter_ = 0; //added by shenyu
106 >
107   #ifndef IS_MPI
108      if (simParams->haveSeed()) {
109        seedValue = simParams->getSeed();
# Line 111 | Line 126 | namespace oopse {
126    }
127  
128    void RNEMD::doSwap() {
114 –    std::cerr << "in RNEMD!\n";  
115 –    std::cerr << "nBins = " << nBins_ << "\n";
129      int midBin = nBins_ / 2;
117 –    std::cerr << "midBin = " << midBin << "\n";
118 –    std::cerr << "swapTime = " << swapTime_ << "\n";
119 –    std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
120 –    std::cerr << "swapType = " << rnemdType_ << "\n";
121 –    std::cerr << "selection = " << rnemdObjectSelection_ << "\n";
130  
131      Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
132      Mat3x3d hmat = currentSnap_->getHmat();
133  
126 –    std::cerr << "hmat = " << hmat << "\n";
127 –
134      seleMan_.setSelectionSet(evaluator_.evaluate());
135  
130 –    std::cerr << "selectionCount = " << seleMan_.getSelectionCount() << "\n\n";
131 –
136      int selei;
137      StuntDouble* sd;
138      int idx;
139  
140 <    std::vector<tuple3<RealType, int, StuntDouble* > > endSlice;
141 <    std::vector<tuple3<RealType, int, StuntDouble* > > midSlice;
142 <    
140 >    RealType min_val;
141 >    bool min_found = false;  
142 >    StuntDouble* min_sd;
143 >
144 >    RealType max_val;
145 >    bool max_found = false;
146 >    StuntDouble* max_sd;
147 >
148      for (sd = seleMan_.beginSelected(selei); sd != NULL;
149           sd = seleMan_.nextSelected(selei)) {
150  
# Line 151 | Line 160 | namespace oopse {
160        // which bin is this stuntdouble in?
161        // wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
162  
163 <      int binNo = midBin + int(nBins_ * (pos.z()) / hmat(2,2));
163 >      int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
164  
156 –      std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
165  
166        // if we're in bin 0 or the middleBin
167        if (binNo == 0 || binNo == midBin) {
# Line 167 | Line 175 | namespace oopse {
175            
176            value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
177                            vel[2]*vel[2]);
170 –          
178            if (sd->isDirectional()) {
179              Vector3d angMom = sd->getJ();
180              Mat3x3d I = sd->getI();
# Line 200 | Line 207 | namespace oopse {
207            break;
208          }
209          
210 <        if (binNo == 0)
211 <          endSlice.push_back( make_tuple3(value, idx, sd));
212 <        
213 <        if (binNo == midBin)
214 <          midSlice.push_back( make_tuple3(value, idx, sd));              
210 >        if (binNo == 0) {
211 >          if (!min_found) {
212 >            min_val = value;
213 >            min_sd = sd;
214 >            min_found = true;
215 >          } else {
216 >            if (min_val > value) {
217 >              min_val = value;
218 >              min_sd = sd;
219 >            }
220 >          }
221 >        } else {
222 >          if (!max_found) {
223 >            max_val = value;
224 >            max_sd = sd;
225 >            max_found = true;
226 >          } else {
227 >            if (max_val < value) {
228 >              max_val = value;
229 >              max_sd = sd;
230 >            }
231 >          }      
232 >        }
233        }
234      }
235 <    
236 <    // find smallest value in endSlice:
237 <    std::sort(endSlice.begin(), endSlice.end());    
238 <    RealType min_val = endSlice[0].first;
239 <    int min_idx = endSlice[0].second;
240 <    StuntDouble* min_sd = endSlice[0].third;
241 <    
242 <    std::cerr << "smallest value = " << min_val << " idx = " << min_idx << "\n";
243 <    
244 <    // find largest value in midSlice:
245 <    std::sort(midSlice.rbegin(), midSlice.rend());
246 <    RealType max_val = midSlice[0].first;
247 <    int max_idx = midSlice[0].second;
248 <    StuntDouble* max_sd = midSlice[0].third;
249 <    
250 <    std::cerr << "largest value = " << max_val << " idx = " << max_idx << "\n";
235 >
236 >    // missing:  swap information in parallel
237 >
238 >    if (max_found && min_found) {
239 >      if (min_val< max_val) {
240 >
241 >        Vector3d min_vel = min_sd->getVel();
242 >        Vector3d max_vel = max_sd->getVel();
243 >        RealType temp_vel;
244 >
245 >        switch(rnemdType_) {
246 >        case rnemdKinetic :
247 >          min_sd->setVel(max_vel);
248 >          max_sd->setVel(min_vel);
249 >
250 >          if (min_sd->isDirectional() && max_sd->isDirectional()) {
251 >            Vector3d min_angMom = min_sd->getJ();
252 >            Vector3d max_angMom = max_sd->getJ();
253 >            min_sd->setJ(max_angMom);
254 >            max_sd->setJ(min_angMom);
255 >          }
256 >          break;
257 >        case rnemdPx :
258 >          temp_vel = min_vel.x();
259 >          min_vel.x() = max_vel.x();
260 >          max_vel.x() = temp_vel;
261 >          min_sd->setVel(min_vel);
262 >          max_sd->setVel(max_vel);
263 >          break;
264 >        case rnemdPy :
265 >          temp_vel = min_vel.y();
266 >          min_vel.y() = max_vel.y();
267 >          max_vel.y() = temp_vel;
268 >          min_sd->setVel(min_vel);
269 >          max_sd->setVel(max_vel);
270 >          break;
271 >        case rnemdPz :
272 >          temp_vel = min_vel.z();
273 >          min_vel.z() = max_vel.z();
274 >          max_vel.z() = temp_vel;
275 >          min_sd->setVel(min_vel);
276 >          max_sd->setVel(max_vel);
277 >          break;
278 >        case rnemdUnknown :
279 >        default :
280 >          break;
281 >        }
282 >      exchangeSum_ += max_val - min_val;
283 >      } else {
284 >        std::cerr << "exchange NOT performed.\nmin_val > max_val.\n";
285 >      }
286 >    } else {
287 >      std::cerr << "exchange NOT performed.\none of the two slabs empty.\n";
288 >    }
289 >  }
290 >
291 >  void RNEMD::getStatus() {
292 >
293 >    Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
294 >    Mat3x3d hmat = currentSnap_->getHmat();
295 >    Stats& stat = currentSnap_->statData;
296 >
297 >    stat[Stats::RNEMD_SWAP_TOTAL] = exchangeSum_;
298 >
299 >    seleMan_.setSelectionSet(evaluator_.evaluate());
300 >
301 >    int selei;
302 >    StuntDouble* sd;
303 >    int idx;
304 >
305 >    std::vector<RealType> valueHist;  // keeps track of what's being averaged
306 >    std::vector<int> valueCount; // keeps track of the number of degrees of
307 >                                 // freedom being averaged
308 >    valueHist.resize(nBins_);
309 >    valueCount.resize(nBins_);
310 >    //do they initialize themselves to zero automatically?
311 >    for (sd = seleMan_.beginSelected(selei); sd != NULL;
312 >         sd = seleMan_.nextSelected(selei)) {
313 >      
314 >      idx = sd->getLocalIndex();
315 >      
316 >      Vector3d pos = sd->getPos();
317 >
318 >      // wrap the stuntdouble's position back into the box:
319 >      
320 >      if (usePeriodicBoundaryConditions_)
321 >        currentSnap_->wrapVector(pos);
322 >      
323 >      // which bin is this stuntdouble in?
324 >      // wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
325 >      
326 >      int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
327 >      
328 >      //std::cerr << "pos.z() = " << pos.z() << " bin = " << binNo << "\n";
329 >      
330 >      RealType mass = sd->getMass();
331 >      Vector3d vel = sd->getVel();
332 >      //std::cerr << "mass = " << mass << " vel = " << vel << "\n";
333 >      RealType value;
334 >
335 >      switch(rnemdType_) {
336 >      case rnemdKinetic :
337 >        
338 >        value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
339 >                        vel[2]*vel[2]);
340 >        
341 >        valueCount[binNo] += 3;
342 >        //std::cerr <<"starting value = " << value << "\n";
343 >        if (sd->isDirectional()) {
344 >          //std::cerr << "angMom calculated.\n";
345 >          Vector3d angMom = sd->getJ();
346 >          //std::cerr << "current angMom: " << angMom << "\n";
347 >          Mat3x3d I = sd->getI();
348 >          
349 >          if (sd->isLinear()) {
350 >            int i = sd->linearAxis();
351 >            int j = (i + 1) % 3;
352 >            int k = (i + 2) % 3;
353 >            value += angMom[j] * angMom[j] / I(j, j) +
354 >              angMom[k] * angMom[k] / I(k, k);
355 >
356 >            valueCount[binNo] +=2;
357 >
358 >          } else {
359 >            //std::cerr << "non-linear molecule.\n";
360 >            value += angMom[0]*angMom[0]/I(0, 0)
361 >              + angMom[1]*angMom[1]/I(1, 1)
362 >              + angMom[2]*angMom[2]/I(2, 2);
363 >            valueCount[binNo] +=3;
364 >
365 >          }
366 >        }
367 >        //std::cerr <<"total value = " << value << "\n";
368 >        //value *= 0.5 / OOPSEConstant::energyConvert;  // get it in kcal / mol
369 >        //value *= 2.0 / OOPSEConstant::kb;            // convert to temperature
370 >        value = value / OOPSEConstant::energyConvert / OOPSEConstant::kb;
371 >        //std::cerr <<"value = " << value << "\n";
372 >        break;
373 >      case rnemdPx :
374 >        value = mass * vel[0];
375 >        valueCount[binNo]++;
376 >        break;
377 >      case rnemdPy :
378 >        value = mass * vel[1];
379 >        valueCount[binNo]++;
380 >        break;
381 >      case rnemdPz :
382 >        value = mass * vel[2];
383 >        valueCount[binNo]++;
384 >        break;
385 >      case rnemdUnknown :
386 >      default :
387 >        break;
388 >      }
389 >      //std::cerr << "bin = " << binNo << " value = " << value ;
390 >      valueHist[binNo] += value;
391 >      //std::cerr << " hist = " << valueHist[binNo] << " count = " << valueCount[binNo] << "\n";
392 >    }
393      
394 +    std::cout << counter_++;
395 +    for (int j = 0; j < nBins_; j++)
396 +      std::cout << "\t" << valueHist[j] / (RealType)valueCount[j];
397 +    std::cout << "\n";
398    }
399 < }  
399 > }

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