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Comparing trunk/src/integrators/NPT.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

# Line 1 | Line 1
1 + /*
2 + * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 + *
4 + * The University of Notre Dame grants you ("Licensee") a
5 + * non-exclusive, royalty free, license to use, modify and
6 + * redistribute this software in source and binary code form, provided
7 + * that the following conditions are met:
8 + *
9 + * 1. Redistributions of source code must retain the above copyright
10 + *    notice, this list of conditions and the following disclaimer.
11 + *
12 + * 2. Redistributions in binary form must reproduce the above copyright
13 + *    notice, this list of conditions and the following disclaimer in the
14 + *    documentation and/or other materials provided with the
15 + *    distribution.
16 + *
17 + * This software is provided "AS IS," without a warranty of any
18 + * kind. All express or implied conditions, representations and
19 + * warranties, including any implied warranty of merchantability,
20 + * fitness for a particular purpose or non-infringement, are hereby
21 + * excluded.  The University of Notre Dame and its licensors shall not
22 + * be liable for any damages suffered by licensee as a result of
23 + * using, modifying or distributing the software or its
24 + * derivatives. In no event will the University of Notre Dame or its
25 + * licensors be liable for any lost revenue, profit or data, or for
26 + * direct, indirect, special, consequential, incidental or punitive
27 + * damages, however caused and regardless of the theory of liability,
28 + * arising out of the use of or inability to use software, even if the
29 + * University of Notre Dame has been advised of the possibility of
30 + * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39 + * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41 + */
42 +
43   #include <math.h>
44  
45 < #include "Atom.hpp"
46 < #include "SRI.hpp"
47 < #include "AbstractClasses.hpp"
48 < #include "SimInfo.hpp"
49 < #include "ForceFields.hpp"
50 < #include "Thermo.hpp"
51 < #include "ReadWrite.hpp"
10 < #include "Integrator.hpp"
11 < #include "simError.h"
45 > #include "brains/SimInfo.hpp"
46 > #include "brains/Thermo.hpp"
47 > #include "integrators/NPT.hpp"
48 > #include "math/SquareMatrix3.hpp"
49 > #include "primitives/Molecule.hpp"
50 > #include "utils/PhysicalConstants.hpp"
51 > #include "utils/simError.h"
52  
13 #ifdef IS_MPI
14 #include "mpiSimulation.hpp"
15 #endif
16
17
53   // Basic isotropic thermostating and barostating via the Melchionna
54   // modification of the Hoover algorithm:
55   //
# Line 25 | Line 60
60   //
61   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
62  
63 < template<typename T> NPT<T>::NPT ( SimInfo *theInfo, ForceFields* the_ff):
29 <  T( theInfo, the_ff )
30 < {
31 <  GenericData* data;
32 <  DoubleData * chiValue;
33 <  DoubleData * integralOfChidtValue;
63 > namespace OpenMD {
64  
65 <  chiValue = NULL;
66 <  integralOfChidtValue = NULL;
65 >  NPT::NPT(SimInfo* info) :
66 >    VelocityVerletIntegrator(info), etaTolerance(1e-6), chiTolerance(1e-6),
67 >    maxIterNum_(4) {
68  
69 <  chi = 0.0;
70 <  integralOfChidt = 0.0;
71 <  have_tau_thermostat = 0;
72 <  have_tau_barostat = 0;
73 <  have_target_temp = 0;
74 <  have_target_pressure = 0;
75 <  have_chi_tolerance = 0;
76 <  have_eta_tolerance = 0;
77 <  have_pos_iter_tolerance = 0;
69 >      Globals* simParams = info_->getSimParams();
70 >    
71 >      if (!simParams->getUseIntialExtendedSystemState()) {
72 >        Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
73 >        currSnapshot->setThermostat(make_pair(0.0, 0.0));
74 >        currSnapshot->setBarostat(Mat3x3d(0.0));
75 >      }
76 >    
77 >      if (!simParams->haveTargetTemp()) {
78 >        sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp!\n");
79 >        painCave.isFatal = 1;
80 >        painCave.severity = OPENMD_ERROR;
81 >        simError();
82 >      } else {
83 >        targetTemp = simParams->getTargetTemp();
84 >      }
85  
86 <  // retrieve chi and integralOfChidt from simInfo
87 <  data = info->getProperty(CHIVALUE_ID);
88 <  if(data){
89 <    chiValue = dynamic_cast<DoubleData*>(data);
52 <  }
86 >      // We must set tauThermostat
87 >      if (!simParams->haveTauThermostat()) {
88 >        sprintf(painCave.errMsg, "If you use the constant temperature\n"
89 >                "\tintegrator, you must set tauThermostat.\n");
90  
91 <  data = info->getProperty(INTEGRALOFCHIDT_ID);
92 <  if(data){
93 <    integralOfChidtValue = dynamic_cast<DoubleData*>(data);
94 <  }
91 >        painCave.severity = OPENMD_ERROR;
92 >        painCave.isFatal = 1;
93 >        simError();
94 >      } else {
95 >        tauThermostat = simParams->getTauThermostat();
96 >      }
97  
98 <  // chi and integralOfChidt should appear by pair
99 <  if(chiValue && integralOfChidtValue){
100 <    chi = chiValue->getData();
62 <    integralOfChidt = integralOfChidtValue->getData();
63 <  }
98 >      if (!simParams->haveTargetPressure()) {
99 >        sprintf(painCave.errMsg, "NPT error: You can't use the NPT integrator\n"
100 >                "   without a targetPressure!\n");
101  
102 <  oldPos = new double[3*integrableObjects.size()];
103 <  oldVel = new double[3*integrableObjects.size()];
104 <  oldJi = new double[3*integrableObjects.size()];
102 >        painCave.isFatal = 1;
103 >        simError();
104 >      } else {
105 >        targetPressure = simParams->getTargetPressure();
106 >      }
107 >    
108 >      if (!simParams->haveTauBarostat()) {
109 >        sprintf(painCave.errMsg,
110 >                "If you use the NPT integrator, you must set tauBarostat.\n");
111 >        painCave.severity = OPENMD_ERROR;
112 >        painCave.isFatal = 1;
113 >        simError();
114 >      } else {
115 >        tauBarostat = simParams->getTauBarostat();
116 >      }
117 >    
118 >      tt2 = tauThermostat * tauThermostat;
119 >      tb2 = tauBarostat * tauBarostat;
120  
121 < }
121 >      updateSizes();
122 >    }
123  
124 < template<typename T> NPT<T>::~NPT() {
125 <  delete[] oldPos;
73 <  delete[] oldVel;
74 <  delete[] oldJi;
75 < }
124 >  NPT::~NPT() {
125 >  }
126  
127 < template<typename T> void NPT<T>::moveA() {
127 >  void NPT::doUpdateSizes() {
128  
129 <  //new version of NPT
130 <  int i, j, k;
131 <  double Tb[3], ji[3];
82 <  double mass;
83 <  double vel[3], pos[3], frc[3];
84 <  double sc[3];
85 <  double COM[3];
129 >    oldPos.resize(info_->getNIntegrableObjects());
130 >    oldVel.resize(info_->getNIntegrableObjects());
131 >    oldJi.resize(info_->getNIntegrableObjects());
132  
133 <  instaTemp = tStats->getTemperature();
88 <  tStats->getPressureTensor( press );
89 <  instaPress = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
90 <  instaVol = tStats->getVolume();
133 >  }
134  
135 <  tStats->getCOM(COM);
135 >  void NPT::moveA() {
136 >    SimInfo::MoleculeIterator i;
137 >    Molecule::IntegrableObjectIterator  j;
138 >    Molecule* mol;
139 >    StuntDouble* sd;
140 >    Vector3d Tb, ji;
141 >    RealType mass;
142 >    Vector3d vel;
143 >    Vector3d pos;
144 >    Vector3d frc;
145 >    Vector3d sc;
146 >    int index;
147  
148 <  //evolve velocity half step
148 >    thermostat = snap->getThermostat();
149 >    loadEta();
150 >    
151 >    instaTemp =thermo.getTemperature();
152 >    press = thermo.getPressureTensor();
153 >    instaPress = PhysicalConstants::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0;
154 >    instaVol =thermo.getVolume();
155  
156 <  calcVelScale();
97 <  
98 <  for( i=0; i<integrableObjects.size(); i++ ){
156 >    Vector3d  COM = thermo.getCom();
157  
158 <    integrableObjects[i]->getVel( vel );
101 <    integrableObjects[i]->getFrc( frc );
158 >    //evolve velocity half step
159  
160 <    mass = integrableObjects[i]->getMass();
160 >    calcVelScale();
161  
162 <    getVelScaleA( sc, vel );
162 >    for (mol = info_->beginMolecule(i); mol != NULL;
163 >         mol = info_->nextMolecule(i)) {
164  
165 <    for (j=0; j < 3; j++) {
165 >      for (sd = mol->beginIntegrableObject(j); sd != NULL;
166 >           sd = mol->nextIntegrableObject(j)) {
167 >                
168 >        vel = sd->getVel();
169 >        frc = sd->getFrc();
170  
171 <      // velocity half step  (use chi from previous step here):
110 <      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - sc[j]);
171 >        mass = sd->getMass();
172  
173 <    }
173 >        getVelScaleA(sc, vel);
174  
175 <    integrableObjects[i]->setVel( vel );
175 >        // velocity half step  (use chi from previous step here):
176  
177 <    if( integrableObjects[i]->isDirectional() ){
177 >        vel += dt2*PhysicalConstants::energyConvert/mass* frc - dt2*sc;
178 >        sd->setVel(vel);
179  
180 <      // get and convert the torque to body frame
180 >        if (sd->isDirectional()) {
181  
182 <      integrableObjects[i]->getTrq( Tb );
121 <      integrableObjects[i]->lab2Body( Tb );
182 >          // get and convert the torque to body frame
183  
184 <      // get the angular momentum, and propagate a half step
184 >          Tb = sd->lab2Body(sd->getTrq());
185  
186 <      integrableObjects[i]->getJ( ji );
186 >          // get the angular momentum, and propagate a half step
187  
188 <      for (j=0; j < 3; j++)
128 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
188 >          ji = sd->getJ();
189  
190 <      this->rotationPropagation( integrableObjects[i], ji );
190 >          ji += dt2*PhysicalConstants::energyConvert * Tb
191 >            - dt2*thermostat.first* ji;
192 >                
193 >          rotAlgo_->rotate(sd, ji, dt);
194  
195 <      integrableObjects[i]->setJ( ji );
195 >          sd->setJ(ji);
196 >        }
197 >            
198 >      }
199      }
200 <  }
200 >    // evolve chi and eta  half step
201  
202 <  // evolve chi and eta  half step
202 >    thermostat.first += dt2 * (instaTemp / targetTemp - 1.0) / tt2;
203 >    
204 >    evolveEtaA();
205  
206 <  evolveChiA();
207 <  evolveEtaA();
206 >    //calculate the integral of chidt
207 >    thermostat.second += dt2 * thermostat.first;
208 >    
209 >    flucQ_->moveA();
210  
141  //calculate the integral of chidt
142  integralOfChidt += dt2*chi;
211  
212 <  //save the old positions
213 <  for(i = 0; i < integrableObjects.size(); i++){
214 <    integrableObjects[i]->getPos(pos);
147 <    for(j = 0; j < 3; j++)
148 <      oldPos[i*3 + j] = pos[j];
149 <  }
212 >    index = 0;
213 >    for (mol = info_->beginMolecule(i); mol != NULL;
214 >         mol = info_->nextMolecule(i)) {
215  
216 <  //the first estimation of r(t+dt) is equal to  r(t)
216 >      for (sd = mol->beginIntegrableObject(j); sd != NULL;
217 >           sd = mol->nextIntegrableObject(j)) {
218  
219 <  for(k = 0; k < 5; k ++){
219 >        oldPos[index++] = sd->getPos();            
220  
221 <    for(i =0 ; i < integrableObjects.size(); i++){
221 >      }
222 >    }
223 >    
224 >    //the first estimation of r(t+dt) is equal to  r(t)
225  
226 <      integrableObjects[i]->getVel(vel);
227 <      integrableObjects[i]->getPos(pos);
226 >    for(int k = 0; k < maxIterNum_; k++) {
227 >      index = 0;
228 >      for (mol = info_->beginMolecule(i); mol != NULL;
229 >           mol = info_->nextMolecule(i)) {
230  
231 <      this->getPosScale( pos, COM, i, sc );
231 >        for (sd = mol->beginIntegrableObject(j); sd != NULL;
232 >             sd = mol->nextIntegrableObject(j)) {
233  
234 <      for(j = 0; j < 3; j++)
235 <        pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]);
234 >          vel = sd->getVel();
235 >          pos = sd->getPos();
236  
237 <      integrableObjects[i]->setPos( pos );
237 >          this->getPosScale(pos, COM, index, sc);
238 >
239 >          pos = oldPos[index] + dt * (vel + sc);
240 >          sd->setPos(pos);    
241 >
242 >          ++index;
243 >        }
244 >      }
245 >
246 >      rattle_->constraintA();
247      }
167    
168    if(nConstrained)
169      constrainA();
170  }
248  
249 +    // Scale the box after all the positions have been moved:
250  
251 <  // Scale the box after all the positions have been moved:
251 >    this->scaleSimBox();
252  
253 <  this->scaleSimBox();
176 < }
253 >    snap->setThermostat(thermostat);
254  
255 < template<typename T> void NPT<T>::moveB( void ){
179 <
180 <  //new version of NPT
181 <  int i, j, k;
182 <  double Tb[3], ji[3], sc[3];
183 <  double vel[3], frc[3];
184 <  double mass;
185 <
186 <  // Set things up for the iteration:
187 <
188 <  for( i=0; i<integrableObjects.size(); i++ ){
189 <
190 <    integrableObjects[i]->getVel( vel );
191 <
192 <    for (j=0; j < 3; j++)
193 <      oldVel[3*i + j]  = vel[j];
194 <
195 <    if( integrableObjects[i]->isDirectional() ){
196 <
197 <      integrableObjects[i]->getJ( ji );
198 <
199 <      for (j=0; j < 3; j++)
200 <        oldJi[3*i + j] = ji[j];
201 <
202 <    }
255 >    saveEta();
256    }
257  
258 <  // do the iteration:
258 >  void NPT::moveB(void) {
259 >    SimInfo::MoleculeIterator i;
260 >    Molecule::IntegrableObjectIterator  j;
261 >    Molecule* mol;
262 >    StuntDouble* sd;
263 >    int index;
264 >    Vector3d Tb;
265 >    Vector3d ji;
266 >    Vector3d sc;
267 >    Vector3d vel;
268 >    Vector3d frc;
269 >    RealType mass;
270  
271 <  instaVol = tStats->getVolume();
271 >    thermostat = snap->getThermostat();
272 >    RealType oldChi  = thermostat.first;
273 >    RealType prevChi;
274  
275 <  for (k=0; k < 4; k++) {
275 >    loadEta();
276 >    
277 >    //save velocity and angular momentum
278 >    index = 0;
279 >    for (mol = info_->beginMolecule(i); mol != NULL;
280 >         mol = info_->nextMolecule(i)) {
281  
282 <    instaTemp = tStats->getTemperature();
283 <    instaPress = tStats->getPressure();
282 >      for (sd = mol->beginIntegrableObject(j); sd != NULL;
283 >           sd = mol->nextIntegrableObject(j)) {
284 >                
285 >        oldVel[index] = sd->getVel();
286  
287 <    // evolve chi another half step using the temperature at t + dt/2
287 >        if (sd->isDirectional())
288 >           oldJi[index] = sd->getJ();
289  
290 <    this->evolveChiB();
217 <    this->evolveEtaB();
218 <    this->calcVelScale();
219 <
220 <    for( i=0; i<integrableObjects.size(); i++ ){
221 <
222 <      integrableObjects[i]->getFrc( frc );
223 <      integrableObjects[i]->getVel(vel);
224 <
225 <      mass = integrableObjects[i]->getMass();
226 <
227 <      getVelScaleB( sc, i );
228 <
229 <      // velocity half step
230 <      for (j=0; j < 3; j++)
231 <        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - sc[j]);
232 <
233 <      integrableObjects[i]->setVel( vel );
234 <
235 <      if( integrableObjects[i]->isDirectional() ){
236 <
237 <        // get and convert the torque to body frame
238 <
239 <        integrableObjects[i]->getTrq( Tb );
240 <        integrableObjects[i]->lab2Body( Tb );
241 <
242 <        for (j=0; j < 3; j++)
243 <          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
244 <
245 <          integrableObjects[i]->setJ( ji );
290 >        ++index;
291        }
292      }
293  
294 <    if(nConstrained)
295 <      constrainB();
294 >    // do the iteration:
295 >    instaVol =thermo.getVolume();
296  
297 <    if ( this->chiConverged() && this->etaConverged() ) break;
298 <  }
297 >    for(int k = 0; k < maxIterNum_; k++) {
298 >      instaTemp =thermo.getTemperature();
299 >      instaPress =thermo.getPressure();
300  
301 <  //calculate integral of chida
302 <  integralOfChidt += dt2*chi;
301 >      // evolve chi another half step using the temperature at t + dt/2
302 >      prevChi = thermostat.first;
303 >      thermostat.first = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2;
304  
305 +      //evolve eta
306 +      this->evolveEtaB();
307 +      this->calcVelScale();
308  
309 < }
309 >      index = 0;
310 >      for (mol = info_->beginMolecule(i); mol != NULL;
311 >           mol = info_->nextMolecule(i)) {
312  
313 < template<typename T> void NPT<T>::resetIntegrator() {
314 <  chi = 0.0;
263 <  T::resetIntegrator();
264 < }
313 >        for (sd = mol->beginIntegrableObject(j); sd != NULL;
314 >             sd = mol->nextIntegrableObject(j)) {            
315  
316 < template<typename T> void NPT<T>::evolveChiA() {
317 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
268 <  oldChi = chi;
269 < }
316 >          frc = sd->getFrc();
317 >          mass = sd->getMass();
318  
319 < template<typename T> void NPT<T>::evolveChiB() {
319 >          getVelScaleB(sc, index);
320  
321 <  prevChi = chi;
322 <  chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
323 < }
321 >          // velocity half step
322 >          vel = oldVel[index]
323 >            + dt2*PhysicalConstants::energyConvert/mass* frc
324 >            - dt2*sc;
325  
326 < template<typename T> bool NPT<T>::chiConverged() {
326 >          sd->setVel(vel);
327  
328 <  return ( fabs( prevChi - chi ) <= chiTolerance );
329 < }
328 >          if (sd->isDirectional()) {
329 >            // get and convert the torque to body frame
330 >            Tb = sd->lab2Body(sd->getTrq());
331  
332 < template<typename T> int NPT<T>::readyCheck() {
332 >            ji = oldJi[index]
333 >              + dt2*PhysicalConstants::energyConvert*Tb
334 >              - dt2*thermostat.first*oldJi[index];
335  
336 <  //check parent's readyCheck() first
337 <  if (T::readyCheck() == -1)
286 <    return -1;
336 >            sd->setJ(ji);
337 >          }
338  
339 <  // First check to see if we have a target temperature.
340 <  // Not having one is fatal.
339 >          ++index;
340 >        }
341 >      }
342 >        
343 >      rattle_->constraintB();
344  
345 <  if (!have_target_temp) {
346 <    sprintf( painCave.errMsg,
347 <             "NPT error: You can't use the NPT integrator\n"
348 <             "   without a targetTemp!\n"
295 <             );
296 <    painCave.isFatal = 1;
297 <    simError();
298 <    return -1;
299 <  }
345 >      if ((fabs(prevChi - thermostat.first) <= chiTolerance) &&
346 >          this->etaConverged())
347 >        break;
348 >    }
349  
350 <  if (!have_target_pressure) {
351 <    sprintf( painCave.errMsg,
303 <             "NPT error: You can't use the NPT integrator\n"
304 <             "   without a targetPressure!\n"
305 <             );
306 <    painCave.isFatal = 1;
307 <    simError();
308 <    return -1;
309 <  }
350 >    //calculate integral of chidt
351 >    thermostat.second += dt2 * thermostat.first;
352  
353 <  // We must set tauThermostat.
353 >    snap->setThermostat(thermostat);
354  
355 <  if (!have_tau_thermostat) {
356 <    sprintf( painCave.errMsg,
315 <             "NPT error: If you use the NPT\n"
316 <             "   integrator, you must set tauThermostat.\n");
317 <    painCave.isFatal = 1;
318 <    simError();
319 <    return -1;
355 >    flucQ_->moveB();
356 >    saveEta();
357    }
358  
359 <  // We must set tauBarostat.
360 <
361 <  if (!have_tau_barostat) {
325 <    sprintf( painCave.errMsg,
326 <             "If you use the NPT integrator, you must set tauBarostat.\n");
327 <    painCave.severity = OOPSE_ERROR;
328 <    painCave.isFatal = 1;
329 <    simError();
330 <    return -1;
359 >  void NPT::resetIntegrator(){
360 >    snap->setThermostat(make_pair(0.0, 0.0));
361 >    resetEta();
362    }
363  
364 <  if (!have_chi_tolerance) {
365 <    sprintf( painCave.errMsg,
366 <             "Setting chi tolerance to 1e-6 in NPT integrator\n");
336 <    chiTolerance = 1e-6;
337 <    have_chi_tolerance = 1;
338 <    painCave.severity = OOPSE_INFO;
339 <    painCave.isFatal = 0;
340 <    simError();
364 >  void NPT::resetEta() {
365 >    Mat3x3d etaMat(0.0);
366 >    snap->setBarostat(etaMat);    
367    }
342
343  if (!have_eta_tolerance) {
344    sprintf( painCave.errMsg,
345             "Setting eta tolerance to 1e-6 in NPT integrator");
346    etaTolerance = 1e-6;
347    have_eta_tolerance = 1;
348    painCave.severity = OOPSE_INFO;
349    painCave.isFatal = 0;
350    simError();
351  }
352
353  // We need NkBT a lot, so just set it here: This is the RAW number
354  // of integrableObjects, so no subtraction or addition of constraints or
355  // orientational degrees of freedom:
356
357  NkBT = (double)(info->getTotIntegrableObjects()) * kB * targetTemp;
358
359  // fkBT is used because the thermostat operates on more degrees of freedom
360  // than the barostat (when there are particles with orientational degrees
361  // of freedom).  
362
363  fkBT = (double)(info->getNDF()) * kB * targetTemp;
364
365  tt2 = tauThermostat * tauThermostat;
366  tb2 = tauBarostat * tauBarostat;
367
368  return 1;
368   }

Comparing trunk/src/integrators/NPT.cpp (property svn:keywords):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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