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root/OpenMD/branches/development/src/rnemd/RNEMD.cpp
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Comparing:
branches/development/src/integrators/RNEMD.cpp (file contents), Revision 1730 by jmarr, Wed May 30 16:07:03 2012 UTC vs.
branches/development/src/rnemd/RNEMD.cpp (file contents), Revision 1731 by gezelter, Thu May 31 12:25:30 2012 UTC

# Line 40 | Line 40
40   */
41  
42   #include <cmath>
43 < #include "integrators/RNEMD.hpp"
43 > #include "rnemd/RNEMD.hpp"
44   #include "math/Vector3.hpp"
45   #include "math/Vector.hpp"
46   #include "math/SquareMatrix3.hpp"
# Line 70 | Line 70 | namespace OpenMD {
70  
71      int seedValue;
72      Globals * simParams = info->getSimParams();
73 +    RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
74  
75      stringToEnumMap_["KineticSwap"] = rnemdKineticSwap;
76      stringToEnumMap_["KineticScale"] = rnemdKineticScale;
# Line 88 | Line 89 | namespace OpenMD {
89      runTime_ = simParams->getRunTime();
90      statusTime_ = simParams->getStatusTime();
91  
92 <    rnemdObjectSelection_ = simParams->getRNEMD_objectSelection();
92 >    rnemdObjectSelection_ = rnemdParams->getObjectSelection();
93      evaluator_.loadScriptString(rnemdObjectSelection_);
94      seleMan_.setSelectionSet(evaluator_.evaluate());
95  
# Line 113 | Line 114 | namespace OpenMD {
114        simError();
115      }
116      
117 <    const string st = simParams->getRNEMD_exchangeType();
117 >    const string st = rnemdParams->getExchangeType();
118  
119      map<string, RNEMDTypeEnum>::iterator i;
120      i = stringToEnumMap_.find(st);
# Line 130 | Line 131 | namespace OpenMD {
131      }
132      
133      outputTemp_ = false;
134 <    if (simParams->haveRNEMD_outputTemperature()) {
135 <      outputTemp_ = simParams->getRNEMD_outputTemperature();
134 >    if (rnemdParams->haveOutputTemperature()) {
135 >      outputTemp_ = rnemdParams->getOutputTemperature();
136      } else if ((rnemdType_ == rnemdKineticSwap) ||
137                 (rnemdType_ == rnemdKineticScale) ||
138                 (rnemdType_ == rnemdKineticScaleVAM) ||
# Line 139 | Line 140 | namespace OpenMD {
140        outputTemp_ = true;
141      }
142      outputVx_ = false;
143 <    if (simParams->haveRNEMD_outputVx()) {
144 <      outputVx_ = simParams->getRNEMD_outputVx();
143 >    if (rnemdParams->haveOutputVx()) {
144 >      outputVx_ = rnemdParams->getOutputVx();
145      } else if ((rnemdType_ == rnemdPx) || (rnemdType_ == rnemdPxScale)) {
146        outputVx_ = true;
147      }
148      outputVy_ = false;
149 <    if (simParams->haveRNEMD_outputVy()) {
150 <      outputVy_ = simParams->getRNEMD_outputVy();
149 >    if (rnemdParams->haveOutputVy()) {
150 >      outputVy_ = rnemdParams->getOutputVy();
151      } else if ((rnemdType_ == rnemdPy) || (rnemdType_ == rnemdPyScale)) {
152        outputVy_ = true;
153      }
154      output3DTemp_ = false;
155 <    if (simParams->haveRNEMD_outputXyzTemperature()) {
156 <      output3DTemp_ = simParams->getRNEMD_outputXyzTemperature();
155 >    if (rnemdParams->haveOutputXyzTemperature()) {
156 >      output3DTemp_ = rnemdParams->getOutputXyzTemperature();
157      }
158      outputRotTemp_ = false;
159 <    if (simParams->haveRNEMD_outputRotTemperature()) {
160 <      outputRotTemp_ = simParams->getRNEMD_outputRotTemperature();
159 >    if (rnemdParams->haveOutputRotTemperature()) {
160 >      outputRotTemp_ = rnemdParams->getOutputRotTemperature();
161      }
162      // James put this in.
163      outputDen_ = false;
164 <    if (simParams->haveRNEMD_outputDen()) {
165 <      outputDen_ = simParams->getRNEMD_outputDen();
164 >    if (rnemdParams->haveOutputDen()) {
165 >      outputDen_ = rnemdParams->getOutputDen();
166      }
167      outputAh_ = false;
168 <    if (simParams->haveRNEMD_outputAh()) {
169 <      outputAh_ = simParams->getRNEMD_outputAh();
168 >    if (rnemdParams->haveOutputAh()) {
169 >      outputAh_ = rnemdParams->getOutputAh();
170      }    
171      outputVz_ = false;
172 <    if (simParams->haveRNEMD_outputVz()) {
173 <      outputVz_ = simParams->getRNEMD_outputVz();
172 >    if (rnemdParams->haveOutputVz()) {
173 >      outputVz_ = rnemdParams->getOutputVz();
174      } else if ((rnemdType_ == rnemdPz) || (rnemdType_ == rnemdPzScale)) {
175        outputVz_ = true;
176      }
# Line 226 | Line 227 | namespace OpenMD {
227      }
228   #endif
229  
230 <    set_RNEMD_exchange_time(simParams->getRNEMD_exchangeTime());
231 <    set_RNEMD_nBins(simParams->getRNEMD_nBins());
230 >    set_RNEMD_exchange_time(rnemdParams->getExchangeTime());
231 >    set_RNEMD_nBins(rnemdParams->getNbins());
232      midBin_ = nBins_ / 2;
233 <    if (simParams->haveRNEMD_binShift()) {
234 <      if (simParams->getRNEMD_binShift()) {
233 >    if (rnemdParams->haveBinShift()) {
234 >      if (rnemdParams->getBinShift()) {
235          zShift_ = 0.5 / (RealType)(nBins_);
236        } else {
237          zShift_ = 0.0;
# Line 241 | Line 242 | namespace OpenMD {
242      //cerr << "I shift slabs by " << zShift_ << " Lz\n";
243      //shift slabs by half slab width, maybe useful in heterogeneous systems
244      //set to 0.0 if not using it; N/A in status output yet
245 <    if (simParams->haveRNEMD_logWidth()) {
246 <      set_RNEMD_logWidth(simParams->getRNEMD_logWidth());
245 >    if (rnemdParams->haveLogWidth()) {
246 >      set_RNEMD_logWidth(rnemdParams->getLogWidth());
247        /*arbitary rnemdLogWidth_, no checking;
248        if (rnemdLogWidth_ != nBins_ && rnemdLogWidth_ != midBin_ + 1) {
249          cerr << "WARNING! RNEMD_logWidth has abnormal value!\n";
# Line 271 | Line 272 | namespace OpenMD {
272      pzzHist_.resize(rnemdLogWidth_, 0.0);
273  
274      set_RNEMD_exchange_total(0.0);
275 <    if (simParams->haveRNEMD_targetFlux()) {
276 <      set_RNEMD_target_flux(simParams->getRNEMD_targetFlux());
275 >    if (rnemdParams->haveTargetFlux()) {
276 >      set_RNEMD_target_flux(rnemdParams->getTargetFlux());
277      } else {
278        set_RNEMD_target_flux(0.0);
279      }
280 <    if (simParams->haveRNEMD_targetJzKE()) {
281 <      set_RNEMD_target_JzKE(simParams->getRNEMD_targetJzKE());
280 >    if (rnemdParams->haveTargetJzKE()) {
281 >      set_RNEMD_target_JzKE(rnemdParams->getTargetJzKE());
282      } else {
283        set_RNEMD_target_JzKE(0.0);
284      }
285 <    if (simParams->haveRNEMD_targetJzpx()) {
286 <      set_RNEMD_target_jzpx(simParams->getRNEMD_targetJzpx());
285 >    if (rnemdParams->haveTargetJzpx()) {
286 >      set_RNEMD_target_jzpx(rnemdParams->getTargetJzpx());
287      } else {
288        set_RNEMD_target_jzpx(0.0);
289      }
290      jzp_.x() = targetJzpx_;
291      njzp_.x() = -targetJzpx_;
292 <    if (simParams->haveRNEMD_targetJzpy()) {
293 <      set_RNEMD_target_jzpy(simParams->getRNEMD_targetJzpy());
292 >    if (rnemdParams->haveTargetJzpy()) {
293 >      set_RNEMD_target_jzpy(rnemdParams->getTargetJzpy());
294      } else {
295        set_RNEMD_target_jzpy(0.0);
296      }
297      jzp_.y() = targetJzpy_;
298      njzp_.y() = -targetJzpy_;
299 <    if (simParams->haveRNEMD_targetJzpz()) {
300 <      set_RNEMD_target_jzpz(simParams->getRNEMD_targetJzpz());
299 >    if (rnemdParams->haveTargetJzpz()) {
300 >      set_RNEMD_target_jzpz(rnemdParams->getTargetJzpz());
301      } else {
302        set_RNEMD_target_jzpz(0.0);
303      }

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