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root/OpenMD/trunk/src/applications/staticProps/RNEMDStats.cpp
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Comparing trunk/src/applications/staticProps/RNEMDStats.cpp (file contents):
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC vs.
Revision 1944 by gezelter, Wed Nov 6 18:30:25 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<Vector3d> binP(nBins_, V3Zero);
108 >    vector<RealType> binKE(nBins_, 0.0);
109 >    vector<unsigned int> binDof(nBins_, 0);
110 >    
111 >    for (mol = info_->beginMolecule(mi); mol != NULL;
112 >         mol = info_->nextMolecule(mi)) {
113 >      
114 >      // change the positions of atoms which belong to the rigidbodies
115 >      
116 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
117 >           rb = mol->nextRigidBody(rbIter)) {
118 >        rb->updateAtomVel();
119        }
120      }
121 +  
122 +    if (evaluator_.isDynamic()) {
123 +      seleMan_.setSelectionSet(evaluator_.evaluate());
124 +    }
125      
126 <    RealType temp = 2.0 * KE / (dof * PhysicalConstants::kb *
113 <                                PhysicalConstants::energyConvert);
114 <    RealType den = mass * nBins_ * PhysicalConstants::densityConvert / volume_;
126 >    // loop over the selected atoms:
127      
128 <    dynamic_cast<Accumulator *>(temperature->accumulator[bin])->add(temp);
129 <    dynamic_cast<VectorAccumulator *>(velocity->accumulator[bin])->add(vel);
130 <    dynamic_cast<Accumulator *>(density->accumulator[bin])->add(den);
128 >    for (sd = seleMan_.beginSelected(i); sd != NULL;
129 >         sd = seleMan_.nextSelected(i)) {
130 >      
131 >      // figure out where that object is:
132 >      Vector3d pos = sd->getPos();
133 >      Vector3d vel = sd->getVel();
134 >      RealType m = sd->getMass();
135  
136 +      int bin = getBin(pos);
137 +
138 +      binMass[bin] += m;
139 +      binP[bin] += m * vel;
140 +      binKE[bin] += 0.5 * (m * vel.lengthSquare());
141 +      binDof[bin] += 3;
142 +      
143 +      if (sd->isDirectional()) {
144 +        Vector3d angMom = sd->getJ();
145 +        Mat3x3d I = sd->getI();
146 +        if (sd->isLinear()) {
147 +          int i = sd->linearAxis();
148 +          int j = (i + 1) % 3;
149 +          int k = (i + 2) % 3;
150 +          binKE[bin] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
151 +                               angMom[k] * angMom[k] / I(k, k));
152 +          binDof[bin] += 2;
153 +        } else {
154 +          binKE[bin] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
155 +                               angMom[1] * angMom[1] / I(1, 1) +
156 +                               angMom[2] * angMom[2] / I(2, 2));
157 +          binDof[bin] += 3;
158 +        }
159 +      }
160 +    }
161 +    
162 +    for (unsigned int i = 0; i < nBins_; i++) {
163 +
164 +      if (binDof[i] > 0) {
165 +        RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb *
166 +                                          PhysicalConstants::energyConvert);
167 +        RealType den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
168 +          / volume_;
169 +        Vector3d vel = binP[i] / binMass[i];
170 +
171 +        dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp);
172 +        dynamic_cast<VectorAccumulator *>(velocity->accumulator[i])->add(vel);
173 +        dynamic_cast<Accumulator *>(density->accumulator[i])->add(den);
174 +        dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1);
175 +      }
176 +    }
177    }
178 +  
179 +  void RNEMDZ::processStuntDouble(StuntDouble* sd, int bin) {
180 +  }
181  
182    RNEMDR::RNEMDR(SimInfo* info, const std::string& filename,
183                   const std::string& sele, int nrbins)
# Line 157 | Line 217 | namespace OpenMD {
217      data_.push_back(density);
218    }
219  
160 –  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);
220  
221 <    RealType KE = 0.5 * (mass * vel.lengthSquare());
222 <    int dof = 3;
221 >  void RNEMDR::processFrame(int istep) {
222 >
223 >    Molecule* mol;
224 >    RigidBody* rb;
225 >    StuntDouble* sd;
226 >    SimInfo::MoleculeIterator mi;
227 >    Molecule::RigidBodyIterator rbIter;
228 >    int i;
229  
230 <    if (sd->isDirectional()) {
231 <      Vector3d angMom = sd->getJ();
232 <      Mat3x3d I = sd->getI();
233 <      if (sd->isLinear()) {
234 <        int i = sd->linearAxis();
235 <        int j = (i + 1) % 3;
236 <        int k = (i + 2) % 3;
237 <        KE += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
238 <                     angMom[k] * angMom[k] / I(k, k));
239 <        dof += 2;
240 <      } else {
241 <        KE += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
242 <                     angMom[1] * angMom[1] / I(1, 1) +
243 <                     angMom[2] * angMom[2] / I(2, 2));
183 <        dof += 3;
230 >    vector<RealType> binMass(nBins_, 0.0);
231 >    vector<Mat3x3d>  binI(nBins_);
232 >    vector<Vector3d> binL(nBins_, V3Zero);
233 >    vector<RealType> binKE(nBins_, 0.0);
234 >    vector<int> binDof(nBins_, 0);
235 >    
236 >    for (mol = info_->beginMolecule(mi); mol != NULL;
237 >         mol = info_->nextMolecule(mi)) {
238 >      
239 >      // change the positions of atoms which belong to the rigidbodies
240 >      
241 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
242 >           rb = mol->nextRigidBody(rbIter)) {
243 >        rb->updateAtomVel();
244        }
245      }
246 +  
247 +    if (evaluator_.isDynamic()) {
248 +      seleMan_.setSelectionSet(evaluator_.evaluate());
249 +    }
250      
251 <    RealType temp = 2.0 * KE / (dof * PhysicalConstants::kb *
252 <                                PhysicalConstants::energyConvert);
251 >    // loop over the selected atoms:
252 >    
253 >    for (sd = seleMan_.beginSelected(i); sd != NULL;
254 >         sd = seleMan_.nextSelected(i)) {
255  
256 <    RealType rinner = (RealType)bin * binWidth_;
257 <    RealType router = (RealType)(bin+1) * binWidth_;
258 <    RealType den = mass * 3.0 * PhysicalConstants::densityConvert
259 <      / (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));  
256 >      // figure out where that object is:
257 >      int bin = getBin(sd->getPos() );      
258 >
259 >      if (bin >= 0 && bin < nBins_)  {
260 >
261 >        Vector3d rPos = sd->getPos() - coordinateOrigin_;
262 >        Vector3d vel = sd->getVel();      
263 >        RealType m = sd->getMass();
264 >        Vector3d L = m * cross(rPos, vel);
265 >        Mat3x3d I(0.0);
266 >        I = outProduct(rPos, rPos) * m;
267 >        RealType r2 = rPos.lengthSquare();
268 >        I(0, 0) += m * r2;
269 >        I(1, 1) += m * r2;
270 >        I(2, 2) += m * r2;      
271 >
272 >        binMass[bin] += m;
273 >        binI[bin] += I;
274 >        binL[bin] += L;
275 >        binKE[bin] += 0.5 * (m * vel.lengthSquare());
276 >        binDof[bin] += 3;
277 >        
278 >        if (sd->isDirectional()) {
279 >          Vector3d angMom = sd->getJ();
280 >          Mat3x3d Ia = sd->getI();
281 >          if (sd->isLinear()) {
282 >            int i = sd->linearAxis();
283 >            int j = (i + 1) % 3;
284 >            int k = (i + 2) % 3;
285 >            binKE[bin] += 0.5 * (angMom[j] * angMom[j] / Ia(j, j) +
286 >                                 angMom[k] * angMom[k] / Ia(k, k));
287 >            binDof[bin] += 2;
288 >          } else {
289 >            binKE[bin] += 0.5 * (angMom[0] * angMom[0] / Ia(0, 0) +
290 >                                 angMom[1] * angMom[1] / Ia(1, 1) +
291 >                                 angMom[2] * angMom[2] / Ia(2, 2));
292 >            binDof[bin] += 3;
293 >          }
294 >        }
295 >      }
296 >    }
297      
298 <    dynamic_cast<Accumulator *>(temperature->accumulator[bin])->add(temp);
299 <    dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[bin])->add(aVel);
300 <    dynamic_cast<Accumulator *>(density->accumulator[bin])->add(den);
298 >    for (unsigned int i = 0; i < nBins_; i++) {
299 >      RealType rinner = (RealType)i * binWidth_;
300 >      RealType router = (RealType)(i+1) * binWidth_;
301 >      if (binDof[i] > 0) {
302 >        RealType temp = 2.0 * binKE[i] / (binDof[i] * PhysicalConstants::kb *
303 >                                          PhysicalConstants::energyConvert);
304 >        RealType den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
305 >          / (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
306  
307 +        Vector3d omega = binI[i].inverse() * binL[i];
308 +
309 +        dynamic_cast<Accumulator *>(temperature->accumulator[i])->add(temp);
310 +        dynamic_cast<VectorAccumulator *>(angularVelocity->accumulator[i])->add(omega);
311 +        dynamic_cast<Accumulator *>(density->accumulator[i])->add(den);
312 +        dynamic_cast<Accumulator *>(counts_->accumulator[i])->add(1);
313 +      }
314 +    }
315    }
316 +
317 +
318 +  void RNEMDR::processStuntDouble(StuntDouble* sd, int bin) {
319 +  }
320   }
321  

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