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root/OpenMD/trunk/src/applications/staticProps/RNEMDStats.cpp
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Comparing:
branches/development/src/applications/staticProps/RNEMDStats.cpp (file contents), Revision 1865 by gezelter, Wed Apr 17 18:24:08 2013 UTC vs.
trunk/src/applications/staticProps/RNEMDStats.cpp (file contents), Revision 1892 by gezelter, Wed Jun 19 14:14:56 2013 UTC

# Line 43 | Line 43
43   #include <algorithm>
44   #include <fstream>
45   #include "applications/staticProps/RNEMDStats.hpp"
46 + #include "primitives/Molecule.hpp"
47   #include "utils/PhysicalConstants.hpp"
48  
49   namespace OpenMD {
# Line 84 | Line 85 | namespace OpenMD {
85      data_.push_back(density);
86    }
87  
88 <  void RNEMDZ::processStuntDouble(StuntDouble* sd, int bin) {
89 <    RealType mass = sd->getMass();
89 <    Vector3d pos = sd->getPos();    
90 <    Vector3d vel = sd->getVel();
91 <    RealType KE = 0.5 * (mass * vel.lengthSquare());
92 <    int dof = 3;
88 >  void RNEMDZ::processFrame(int istep) {
89 >    RealType z;
90  
91 <    if (sd->isDirectional()) {
92 <      Vector3d angMom = sd->getJ();
93 <      Mat3x3d I = sd->getI();
94 <      if (sd->isLinear()) {
95 <        int i = sd->linearAxis();
96 <        int j = (i + 1) % 3;
97 <        int k = (i + 2) % 3;
98 <        KE += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
99 <                     angMom[k] * angMom[k] / I(k, k));
100 <        dof += 2;
101 <      } else {
102 <        KE += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
103 <                     angMom[1] * angMom[1] / I(1, 1) +
104 <                     angMom[2] * angMom[2] / I(2, 2));
105 <        dof += 3;
91 >    hmat_ = currentSnapshot_->getHmat();
92 >    for (int i = 0; i < nBins_; i++) {
93 >      z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat_(2,2);
94 >      dynamic_cast<Accumulator*>(z_->accumulator[i])->add(z);
95 >    }
96 >    volume_ = currentSnapshot_->getVolume();
97 >
98 >
99 >    Molecule* mol;
100 >    RigidBody* rb;
101 >    StuntDouble* sd;
102 >    SimInfo::MoleculeIterator mi;
103 >    Molecule::RigidBodyIterator rbIter;
104 >    int i;
105 >
106 >    vector<RealType> binMass(nBins_, 0.0);
107 >    vector<RealType> binPx(nBins_, 0.0);
108 >    vector<RealType> binPy(nBins_, 0.0);
109 >    vector<RealType> binPz(nBins_, 0.0);
110 >    vector<RealType> binKE(nBins_, 0.0);
111 >    vector<unsigned int> binDof(nBins_, 0);
112 >    vector<unsigned int> binCount(nBins_, 0);
113 >    
114 >    
115 >    for (mol = info_->beginMolecule(mi); mol != NULL;
116 >         mol = info_->nextMolecule(mi)) {
117 >      
118 >      // change the positions of atoms which belong to the rigidbodies
119 >      
120 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
121 >           rb = mol->nextRigidBody(rbIter)) {
122 >        rb->updateAtomVel();
123        }
124      }
125 +  
126 +    if (evaluator_.isDynamic()) {
127 +      seleMan_.setSelectionSet(evaluator_.evaluate());
128 +    }
129      
130 <    RealType temp = 2.0 * KE / (dof * PhysicalConstants::kb *
113 <                                PhysicalConstants::energyConvert);
114 <    RealType den = mass * nBins_ * PhysicalConstants::densityConvert / volume_;
130 >    // loop over the selected atoms:
131      
132 <    dynamic_cast<Accumulator *>(temperature->accumulator[bin])->add(temp);
133 <    dynamic_cast<VectorAccumulator *>(velocity->accumulator[bin])->add(vel);
134 <    dynamic_cast<Accumulator *>(density->accumulator[bin])->add(den);
132 >    for (sd = seleMan_.beginSelected(i); sd != NULL;
133 >         sd = seleMan_.nextSelected(i)) {
134 >      
135 >      // figure out where that object is:
136 >      Vector3d pos = sd->getPos();
137 >      Vector3d vel = sd->getVel();
138 >      RealType m = sd->getMass();
139  
140 +      int bin = getBin(pos);
141 +
142 +      binCount[bin] += 1;
143 +
144 +      binMass[bin] += m;
145 +      binPx[bin] += m * vel.x();
146 +      binPy[bin] += m * vel.y();
147 +      binPz[bin] += m * vel.z();
148 +      binKE[bin] += 0.5 * (m * vel.lengthSquare());
149 +      binDof[bin] += 3;
150 +      
151 +      if (sd->isDirectional()) {
152 +        Vector3d angMom = sd->getJ();
153 +        Mat3x3d I = sd->getI();
154 +        if (sd->isLinear()) {
155 +          int i = sd->linearAxis();
156 +          int j = (i + 1) % 3;
157 +          int k = (i + 2) % 3;
158 +          binKE[bin] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
159 +                               angMom[k] * angMom[k] / I(k, k));
160 +          binDof[bin] += 2;
161 +        } else {
162 +          binKE[bin] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
163 +                               angMom[1] * angMom[1] / I(1, 1) +
164 +                               angMom[2] * angMom[2] / I(2, 2));
165 +          binDof[bin] += 3;
166 +        }
167 +      }
168 +    }
169 +    
170 +    for (unsigned int i = 0; i < nBins_; i++) {
171 +
172 +      if (binDof[i] > 0) {
173 +        RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb *
174 +                                          PhysicalConstants::energyConvert);
175 +        RealType den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
176 +          / volume_;
177 +        Vector3d vel;
178 +        vel.x() = binPx[i] / binMass[i];
179 +        vel.y() = binPy[i] / binMass[i];
180 +        vel.z() = binPz[i] / binMass[i];
181 +
182 +        dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp);
183 +        dynamic_cast<VectorAccumulator *>(velocity->accumulator[i])->add(vel);
184 +        dynamic_cast<Accumulator *>(density->accumulator[i])->add(den);
185 +        dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1);
186 +      }
187 +    }
188    }
189 +  
190 +  void RNEMDZ::processStuntDouble(StuntDouble* sd, int bin) {
191 +  }
192  
193    RNEMDR::RNEMDR(SimInfo* info, const std::string& filename,
194                   const std::string& sele, int nrbins)
# Line 155 | Line 226 | namespace OpenMD {
226      for (int i = 0; i < nBins_; i++)
227        density->accumulator.push_back( new Accumulator() );
228      data_.push_back(density);
229 <  }
229 >  }
230 >
231  
232 <  void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) {
161 <    RealType mass = sd->getMass();
162 <    Vector3d vel = sd->getVel();
163 <    Vector3d rPos = sd->getPos() - coordinateOrigin_;
164 <    Vector3d aVel = cross(rPos, vel);
232 >  void RNEMDR::processFrame(int istep) {
233  
234 <    RealType KE = 0.5 * (mass * vel.lengthSquare());
235 <    int dof = 3;
234 >    Molecule* mol;
235 >    RigidBody* rb;
236 >    StuntDouble* sd;
237 >    SimInfo::MoleculeIterator mi;
238 >    Molecule::RigidBodyIterator rbIter;
239 >    int i;
240  
241 <    if (sd->isDirectional()) {
242 <      Vector3d angMom = sd->getJ();
243 <      Mat3x3d I = sd->getI();
244 <      if (sd->isLinear()) {
245 <        int i = sd->linearAxis();
246 <        int j = (i + 1) % 3;
247 <        int k = (i + 2) % 3;
248 <        KE += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
249 <                     angMom[k] * angMom[k] / I(k, k));
250 <        dof += 2;
251 <      } else {
252 <        KE += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
253 <                     angMom[1] * angMom[1] / I(1, 1) +
254 <                     angMom[2] * angMom[2] / I(2, 2));
183 <        dof += 3;
241 >    vector<RealType> binMass(nBins_, 0.0);
242 >    vector<Vector3d> binaVel(nBins_, V3Zero);
243 >    vector<RealType> binKE(nBins_, 0.0);
244 >    vector<unsigned int> binDof(nBins_, 0);
245 >    vector<unsigned int> binCount(nBins_, 0);
246 >    
247 >    for (mol = info_->beginMolecule(mi); mol != NULL;
248 >         mol = info_->nextMolecule(mi)) {
249 >      
250 >      // change the positions of atoms which belong to the rigidbodies
251 >      
252 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
253 >           rb = mol->nextRigidBody(rbIter)) {
254 >        rb->updateAtomVel();
255        }
256      }
257 +  
258 +    if (evaluator_.isDynamic()) {
259 +      seleMan_.setSelectionSet(evaluator_.evaluate());
260 +    }
261      
262 <    RealType temp = 2.0 * KE / (dof * PhysicalConstants::kb *
263 <                                PhysicalConstants::energyConvert);
262 >    // loop over the selected atoms:
263 >    
264 >    for (sd = seleMan_.beginSelected(i); sd != NULL;
265 >         sd = seleMan_.nextSelected(i)) {
266 >      
267 >      // figure out where that object is:
268  
269 <    RealType rinner = (RealType)bin * binWidth_;
270 <    RealType router = (RealType)(bin+1) * binWidth_;
271 <    RealType den = mass * 3.0 * PhysicalConstants::densityConvert
272 <      / (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));  
269 >      Vector3d rPos = sd->getPos() - coordinateOrigin_;
270 >      Vector3d vel = sd->getVel();      
271 >      Vector3d aVel = cross(rPos, vel);
272 >      RealType m = sd->getMass();
273 >
274 >      int bin = getBin(rPos);
275 >
276 >      binCount[bin] += 1;
277 >
278 >      binMass[bin] += m;
279 >      binaVel[bin] += aVel;
280 >      binKE[bin] += 0.5 * (m * vel.lengthSquare());
281 >      binDof[bin] += 3;
282 >      
283 >      if (sd->isDirectional()) {
284 >        Vector3d angMom = sd->getJ();
285 >        Mat3x3d I = sd->getI();
286 >        if (sd->isLinear()) {
287 >          int i = sd->linearAxis();
288 >          int j = (i + 1) % 3;
289 >          int k = (i + 2) % 3;
290 >          binKE[bin] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
291 >                               angMom[k] * angMom[k] / I(k, k));
292 >          binDof[bin] += 2;
293 >        } else {
294 >          binKE[bin] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
295 >                               angMom[1] * angMom[1] / I(1, 1) +
296 >                               angMom[2] * angMom[2] / I(2, 2));
297 >          binDof[bin] += 3;
298 >        }
299 >      }
300 >    }
301      
302 <    dynamic_cast<Accumulator *>(temperature->accumulator[bin])->add(temp);
303 <    dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[bin])->add(aVel);
304 <    dynamic_cast<Accumulator *>(density->accumulator[bin])->add(den);
302 >    for (unsigned int i = 0; i < nBins_; i++) {
303 >      RealType rinner = (RealType)i * binWidth_;
304 >      RealType router = (RealType)(i+1) * binWidth_;
305 >      if (binDof[i] > 0) {
306 >        RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb *
307 >                                          PhysicalConstants::energyConvert);
308 >        RealType den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
309 >          / (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));  
310 >        Vector3d aVel = binaVel[i] / RealType(binCount[i]);
311 >        dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp);
312 >        dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[i])->add(aVel);
313 >        dynamic_cast<Accumulator *>(density->accumulator[i])->add(den);
314 >        dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1);
315 >      }
316 >    }
317 >  }
318  
319 +
320 +  void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) {
321    }
322   }
323  

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