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Comparing trunk/src/integrators/RNEMD.cpp (file contents):
Revision 1330 by skuang, Thu Mar 19 21:03:36 2009 UTC vs.
Revision 1341 by skuang, Fri May 8 19:47:05 2009 UTC

# Line 40 | Line 40
40   */
41  
42   #include "integrators/RNEMD.hpp"
43 + #include "math/Vector3.hpp"
44   #include "math/SquareMatrix3.hpp"
45   #include "primitives/Molecule.hpp"
46   #include "primitives/StuntDouble.hpp"
47 + #include "utils/OOPSEConstant.hpp"
48 + #include "utils/Tuple.hpp"
49  
50   #ifndef IS_MPI
51   #include "math/SeqRandNumGen.hpp"
# Line 50 | Line 53
53   #include "math/ParallelRandNumGen.hpp"
54   #endif
55  
53 – /* Remove me after testing*/
54 – /*
55 – #include <cstdio>
56 – #include <iostream>
57 – */
58 – /*End remove me*/
56  
57   namespace oopse {
58    
59 <  RNEMD::RNEMD(SimInfo* info) : info_(info) {
59 >  RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
60      
61      int seedValue;
62      Globals * simParams = info->getSimParams();
# Line 70 | Line 67 | namespace oopse {
67      stringToEnumMap_["Pz"] = rnemdPz;
68      stringToEnumMap_["Unknown"] = rnemdUnknown;
69  
70 +    rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
71 +    evaluator_.loadScriptString(rnemdObjectSelection_);
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  
98      std::map<std::string, RNEMDTypeEnum>::iterator i;
99      i = stringToEnumMap_.find(st);
100      rnemdType_  = (i == stringToEnumMap_.end()) ? RNEMD::rnemdUnknown : i->second;
101  
79 –
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 103 | Line 126 | namespace oopse {
126    }
127  
128    void RNEMD::doSwap() {
129 <    std::cerr << "in RNEMD!\n";  
130 <    std::cerr << "nBins = " << nBins_ << "\n";
131 <    std::cerr << "swapTime = " << swapTime_ << "\n";
132 <    std::cerr << "exchangeSum = " << exchangeSum_ << "\n";
133 <    std::cerr << "swapType = " << rnemdType_ << "\n";
134 <  }  
129 >    int midBin = nBins_ / 2;
130 >
131 >    Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
132 >    Mat3x3d hmat = currentSnap_->getHmat();
133 >
134 >    seleMan_.setSelectionSet(evaluator_.evaluate());
135 >
136 >    int selei;
137 >    StuntDouble* sd;
138 >    int idx;
139 >
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 >
151 >      idx = sd->getLocalIndex();
152 >
153 >      Vector3d pos = sd->getPos();
154 >
155 >      // wrap the stuntdouble's position back into the box:
156 >
157 >      if (usePeriodicBoundaryConditions_)
158 >        currentSnap_->wrapVector(pos);
159 >
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 = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
164 >
165 >
166 >      // if we're in bin 0 or the middleBin
167 >      if (binNo == 0 || binNo == midBin) {
168 >        
169 >        RealType mass = sd->getMass();
170 >        Vector3d vel = sd->getVel();
171 >        RealType value;
172 >
173 >        switch(rnemdType_) {
174 >        case rnemdKinetic :
175 >          
176 >          value = mass * (vel[0]*vel[0] + vel[1]*vel[1] +
177 >                          vel[2]*vel[2]);
178 >          if (sd->isDirectional()) {
179 >            Vector3d angMom = sd->getJ();
180 >            Mat3x3d I = sd->getI();
181 >            
182 >            if (sd->isLinear()) {
183 >              int i = sd->linearAxis();
184 >              int j = (i + 1) % 3;
185 >              int k = (i + 2) % 3;
186 >              value += angMom[j] * angMom[j] / I(j, j) +
187 >                angMom[k] * angMom[k] / I(k, k);
188 >            } else {                        
189 >              value += angMom[0]*angMom[0]/I(0, 0)
190 >                + angMom[1]*angMom[1]/I(1, 1)
191 >                + angMom[2]*angMom[2]/I(2, 2);
192 >            }
193 >          }
194 >          value = value * 0.5 / OOPSEConstant::energyConvert;
195 >          break;
196 >        case rnemdPx :
197 >          value = mass * vel[0];
198 >          break;
199 >        case rnemdPy :
200 >          value = mass * vel[1];
201 >          break;
202 >        case rnemdPz :
203 >          value = mass * vel[2];
204 >          break;
205 >        case rnemdUnknown :
206 >        default :
207 >          break;
208 >        }
209 >        
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 >    // 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   }

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