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root/OpenMD/trunk/src/integrators/NPTf.cpp
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Comparing trunk/src/integrators/NPTf.cpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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1 < #include <math.h>
2 <
3 < #include "math/MatVec3.h"
4 < #include "primitives/Atom.hpp"
5 < #include "primitives/SRI.hpp"
6 < #include "primitives/AbstractClasses.hpp"
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 "brains/SimInfo.hpp"
8 #include "UseTheForce/ForceFields.hpp"
44   #include "brains/Thermo.hpp"
45 < #include "io/ReadWrite.hpp"
46 < #include "integrators/Integrator.hpp"
45 > #include "integrators/IntegratorCreator.hpp"
46 > #include "integrators/NPTf.hpp"
47 > #include "primitives/Molecule.hpp"
48 > #include "utils/PhysicalConstants.hpp"
49   #include "utils/simError.h"
50  
51 < #ifdef IS_MPI
15 < #include "brains/mpiSimulation.hpp"
16 < #endif
51 > namespace OpenMD {
52  
53 < // Basic non-isotropic thermostating and barostating via the Melchionna
54 < // modification of the Hoover algorithm:
55 < //
56 < //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
57 < //       Molec. Phys., 78, 533.
58 < //
59 < //           and
60 < //
61 < //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
53 >  // Basic non-isotropic thermostating and barostating via the Melchionna
54 >  // modification of the Hoover algorithm:
55 >  //
56 >  //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
57 >  //       Molec. Phys., 78, 533.
58 >  //
59 >  //           and
60 >  //
61 >  //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
62  
63 < template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
29 <  T( theInfo, the_ff )
30 < {
31 <  GenericData* data;
32 <  DoubleArrayData * etaValue;
33 <  vector<double> etaArray;
34 <  int i,j;
63 >  void NPTf::evolveEtaA() {
64  
65 <  for(i = 0; i < 3; i++){
37 <    for (j = 0; j < 3; j++){
65 >    int i, j;
66  
67 <      eta[i][j] = 0.0;
68 <      oldEta[i][j] = 0.0;
69 <    }
70 <  }
71 <
72 <
45 <  if( theInfo->useInitXSstate ){
46 <    // retrieve eta array from simInfo if it exists
47 <    data = info->getProperty(ETAVALUE_ID);
48 <    if(data){
49 <      etaValue = dynamic_cast<DoubleArrayData*>(data);
50 <      
51 <      if(etaValue){
52 <        etaArray = etaValue->getData();
53 <        
54 <        for(i = 0; i < 3; i++){
55 <          for (j = 0; j < 3; j++){
56 <            eta[i][j] = etaArray[3*i+j];
57 <            oldEta[i][j] = eta[i][j];
58 <          }
67 >    for(i = 0; i < 3; i ++){
68 >      for(j = 0; j < 3; j++){
69 >        if( i == j) {
70 >          eta(i, j) += dt2 *  instaVol * (press(i, j) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
71 >        } else {
72 >          eta(i, j) += dt2 * instaVol * press(i, j) / (NkBT*tb2);
73          }
74        }
75      }
76 +  
77 +    for(i = 0; i < 3; i++) {
78 +      for (j = 0; j < 3; j++) {
79 +        oldEta(i, j) = eta(i, j);
80 +      }
81 +    }
82 +  
83    }
84  
85 < }
85 >  void NPTf::evolveEtaB() {
86  
87 < template<typename T> NPTf<T>::~NPTf() {
87 >    int i;
88 >    int j;
89  
90 <  // empty for now
91 < }
92 <
93 < template<typename T> void NPTf<T>::resetIntegrator() {
72 <
73 <  int i, j;
74 <
75 <  for(i = 0; i < 3; i++)
76 <    for (j = 0; j < 3; j++)
77 <      eta[i][j] = 0.0;
78 <
79 <  T::resetIntegrator();
80 < }
81 <
82 < template<typename T> void NPTf<T>::evolveEtaA() {
83 <
84 <  int i, j;
85 <
86 <  for(i = 0; i < 3; i ++){
87 <    for(j = 0; j < 3; j++){
88 <      if( i == j)
89 <        eta[i][j] += dt2 *  instaVol *
90 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
91 <      else
92 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
90 >    for(i = 0; i < 3; i++) {
91 >      for (j = 0; j < 3; j++) {
92 >        prevEta(i, j) = eta(i, j);
93 >      }
94      }
94  }
95  
96  for(i = 0; i < 3; i++)
97    for (j = 0; j < 3; j++)
98      oldEta[i][j] = eta[i][j];
99 }
95  
96 < template<typename T> void NPTf<T>::evolveEtaB() {
97 <
98 <  int i,j;
99 <
100 <  for(i = 0; i < 3; i++)
101 <    for (j = 0; j < 3; j++)
102 <      prevEta[i][j] = eta[i][j];
103 <
109 <  for(i = 0; i < 3; i ++){
110 <    for(j = 0; j < 3; j++){
111 <      if( i == j) {
112 <        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
113 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
114 <      } else {
115 <        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
96 >    for(i = 0; i < 3; i ++){
97 >      for(j = 0; j < 3; j++){
98 >        if( i == j) {
99 >          eta(i, j) = oldEta(i, j) + dt2 *  instaVol *
100 >            (press(i, j) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
101 >        } else {
102 >          eta(i, j) = oldEta(i, j) + dt2 * instaVol * press(i, j) / (NkBT*tb2);
103 >        }
104        }
105      }
106 +
107 +  
108    }
119 }
109  
110 < template<typename T> void NPTf<T>::calcVelScale(void){
122 <  int i,j;
110 >  void NPTf::calcVelScale(){
111  
112 <  for (i = 0; i < 3; i++ ) {
113 <    for (j = 0; j < 3; j++ ) {
114 <      vScale[i][j] = eta[i][j];
112 >    for (int i = 0; i < 3; i++ ) {
113 >      for (int j = 0; j < 3; j++ ) {
114 >        vScale(i, j) = eta(i, j);
115  
116 <      if (i == j) {
117 <        vScale[i][j] += chi;
116 >        if (i == j) {
117 >          vScale(i, j) += thermostat.first;
118 >        }
119        }
120      }
121    }
133 }
122  
123 < template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
124 <
125 <  matVecMul3( vScale, vel, sc );
138 < }
123 >  void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel){
124 >    sc = vScale * vel;
125 >  }
126  
127 < template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
128 <  int j;
129 <  double myVel[3];
127 >  void NPTf::getVelScaleB(Vector3d& sc, int index ) {
128 >    sc = vScale * oldVel[index];
129 >  }
130  
131 <  for (j = 0; j < 3; j++)
145 <    myVel[j] = oldVel[3*index + j];
146 <  
147 <  matVecMul3( vScale, myVel, sc );
148 < }
131 >  void NPTf::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {
132  
133 < template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
134 <                                               int index, double sc[3]){
135 <  int j;
136 <  double rj[3];
133 >    /**@todo */
134 >    Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
135 >    sc = eta * rj;
136 >  }
137  
138 <  for(j=0; j<3; j++)
156 <    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
138 >  void NPTf::scaleSimBox(){
139  
140 <  matVecMul3( eta, rj, sc );
141 < }
140 >    int i;
141 >    int j;
142 >    int k;
143 >    Mat3x3d scaleMat;
144 >    RealType eta2ij;
145 >    RealType bigScale, smallScale, offDiagMax;
146 >    Mat3x3d hm;
147 >    Mat3x3d hmnew;
148  
161 template<typename T> void NPTf<T>::scaleSimBox( void ){
149  
163  int i,j,k;
164  double scaleMat[3][3];
165  double eta2ij;
166  double bigScale, smallScale, offDiagMax;
167  double hm[3][3], hmnew[3][3];
150  
151 +    // Scale the box after all the positions have been moved:
152  
153 +    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
154 +    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
155  
156 <  // Scale the box after all the positions have been moved:
156 >    bigScale = 1.0;
157 >    smallScale = 1.0;
158 >    offDiagMax = 0.0;
159  
160 <  // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
161 <  //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
175 <
176 <  bigScale = 1.0;
177 <  smallScale = 1.0;
178 <  offDiagMax = 0.0;
160 >    for(i=0; i<3; i++){
161 >      for(j=0; j<3; j++){
162  
163 <  for(i=0; i<3; i++){
164 <    for(j=0; j<3; j++){
163 >        // Calculate the matrix Product of the eta array (we only need
164 >        // the ij element right now):
165  
166 <      // Calculate the matrix Product of the eta array (we only need
167 <      // the ij element right now):
166 >        eta2ij = 0.0;
167 >        for(k=0; k<3; k++){
168 >          eta2ij += eta(i, k) * eta(k, j);
169 >        }
170  
171 <      eta2ij = 0.0;
172 <      for(k=0; k<3; k++){
173 <        eta2ij += eta[i][k] * eta[k][j];
174 <      }
175 <
191 <      scaleMat[i][j] = 0.0;
192 <      // identity matrix (see above):
193 <      if (i == j) scaleMat[i][j] = 1.0;
194 <      // Taylor expansion for the exponential truncated at second order:
195 <      scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
171 >        scaleMat(i, j) = 0.0;
172 >        // identity matrix (see above):
173 >        if (i == j) scaleMat(i, j) = 1.0;
174 >        // Taylor expansion for the exponential truncated at second order:
175 >        scaleMat(i, j) += dt*eta(i, j)  + 0.5*dt*dt*eta2ij;
176        
177  
178 <      if (i != j)
179 <        if (fabs(scaleMat[i][j]) > offDiagMax)
180 <          offDiagMax = fabs(scaleMat[i][j]);
178 >        if (i != j)
179 >          if (fabs(scaleMat(i, j)) > offDiagMax)
180 >            offDiagMax = fabs(scaleMat(i, j));
181 >      }
182 >
183 >      if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i);
184 >      if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i);
185      }
186  
187 <    if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
188 <    if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
189 <  }
187 >    if ((bigScale > 1.01) || (smallScale < 0.99)) {
188 >      sprintf( painCave.errMsg,
189 >               "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
190 >               " Check your tauBarostat, as it is probably too small!\n\n"
191 >               " scaleMat = [%lf\t%lf\t%lf]\n"
192 >               "            [%lf\t%lf\t%lf]\n"
193 >               "            [%lf\t%lf\t%lf]\n"
194 >               "      eta = [%lf\t%lf\t%lf]\n"
195 >               "            [%lf\t%lf\t%lf]\n"
196 >               "            [%lf\t%lf\t%lf]\n",
197 >               scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
198 >               scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
199 >               scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
200 >               eta(0, 0),eta(0, 1),eta(0, 2),
201 >               eta(1, 0),eta(1, 1),eta(1, 2),
202 >               eta(2, 0),eta(2, 1),eta(2, 2));
203 >      painCave.isFatal = 1;
204 >      simError();
205 >    } else if (offDiagMax > 0.01) {
206 >      sprintf( painCave.errMsg,
207 >               "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
208 >               " Check your tauBarostat, as it is probably too small!\n\n"
209 >               " scaleMat = [%lf\t%lf\t%lf]\n"
210 >               "            [%lf\t%lf\t%lf]\n"
211 >               "            [%lf\t%lf\t%lf]\n"
212 >               "      eta = [%lf\t%lf\t%lf]\n"
213 >               "            [%lf\t%lf\t%lf]\n"
214 >               "            [%lf\t%lf\t%lf]\n",
215 >               scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
216 >               scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
217 >               scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
218 >               eta(0, 0),eta(0, 1),eta(0, 2),
219 >               eta(1, 0),eta(1, 1),eta(1, 2),
220 >               eta(2, 0),eta(2, 1),eta(2, 2));
221 >      painCave.isFatal = 1;
222 >      simError();
223 >    } else {
224  
225 <  if ((bigScale > 1.01) || (smallScale < 0.99)) {
226 <    sprintf( painCave.errMsg,
227 <             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
228 <             " Check your tauBarostat, as it is probably too small!\n\n"
229 <             " scaleMat = [%lf\t%lf\t%lf]\n"
212 <             "            [%lf\t%lf\t%lf]\n"
213 <             "            [%lf\t%lf\t%lf]\n"
214 <             "      eta = [%lf\t%lf\t%lf]\n"
215 <             "            [%lf\t%lf\t%lf]\n"
216 <             "            [%lf\t%lf\t%lf]\n",
217 <             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
218 <             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
219 <             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2],
220 <             eta[0][0],eta[0][1],eta[0][2],
221 <             eta[1][0],eta[1][1],eta[1][2],
222 <             eta[2][0],eta[2][1],eta[2][2]);
223 <    painCave.isFatal = 1;
224 <    simError();
225 <  } else if (offDiagMax > 0.01) {
226 <    sprintf( painCave.errMsg,
227 <             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
228 <             " Check your tauBarostat, as it is probably too small!\n\n"
229 <             " scaleMat = [%lf\t%lf\t%lf]\n"
230 <             "            [%lf\t%lf\t%lf]\n"
231 <             "            [%lf\t%lf\t%lf]\n"
232 <             "      eta = [%lf\t%lf\t%lf]\n"
233 <             "            [%lf\t%lf\t%lf]\n"
234 <             "            [%lf\t%lf\t%lf]\n",
235 <             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
236 <             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
237 <             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2],
238 <             eta[0][0],eta[0][1],eta[0][2],
239 <             eta[1][0],eta[1][1],eta[1][2],
240 <             eta[2][0],eta[2][1],eta[2][2]);
241 <    painCave.isFatal = 1;
242 <    simError();
243 <  } else {
244 <    info->getBoxM(hm);
245 <    matMul3(hm, scaleMat, hmnew);
246 <    info->setBoxM(hmnew);
225 >      Mat3x3d hmat = snap->getHmat();
226 >      hmat = hmat *scaleMat;
227 >      snap->setHmat(hmat);
228 >        
229 >    }
230    }
248 }
231  
232 < template<typename T> bool NPTf<T>::etaConverged() {
233 <  int i;
234 <  double diffEta, sumEta;
232 >  bool NPTf::etaConverged() {
233 >    int i;
234 >    RealType diffEta, sumEta;
235  
236 <  sumEta = 0;
237 <  for(i = 0; i < 3; i++)
238 <    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
236 >    sumEta = 0;
237 >    for(i = 0; i < 3; i++) {
238 >      sumEta += pow(prevEta(i, i) - eta(i, i), 2);
239 >    }
240 >    
241 >    diffEta = sqrt( sumEta / 3.0 );
242  
243 <  diffEta = sqrt( sumEta / 3.0 );
243 >    return ( diffEta <= etaTolerance );
244 >  }
245  
246 <  return ( diffEta <= etaTolerance );
247 < }
246 >  RealType NPTf::calcConservedQuantity(){
247 >    
248 >    thermostat = snap->getThermostat();
249 >    loadEta();
250 >    
251 >    // We need NkBT a lot, so just set it here: This is the RAW number
252 >    // of integrableObjects, so no subtraction or addition of constraints or
253 >    // orientational degrees of freedom:
254 >    NkBT = info_->getNGlobalIntegrableObjects()*PhysicalConstants::kB *targetTemp;
255  
256 < template<typename T> double NPTf<T>::getConservedQuantity(void){
256 >    // fkBT is used because the thermostat operates on more degrees of freedom
257 >    // than the barostat (when there are particles with orientational degrees
258 >    // of freedom).  
259 >    fkBT = info_->getNdf()*PhysicalConstants::kB *targetTemp;    
260 >    
261 >    RealType conservedQuantity;
262 >    RealType totalEnergy;
263 >    RealType thermostat_kinetic;
264 >    RealType thermostat_potential;
265 >    RealType barostat_kinetic;
266 >    RealType barostat_potential;
267 >    RealType trEta;
268  
269 <  double conservedQuantity;
270 <  double totalEnergy;
271 <  double thermostat_kinetic;
272 <  double thermostat_potential;
269 <  double barostat_kinetic;
270 <  double barostat_potential;
271 <  double trEta;
272 <  double a[3][3], b[3][3];
269 >    totalEnergy = thermo.getTotalEnergy();
270 >    
271 >    thermostat_kinetic = fkBT * tt2 * thermostat.first *
272 >      thermostat.first /(2.0 * PhysicalConstants::energyConvert);
273  
274 <  totalEnergy = tStats->getTotalE();
274 >    thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert;
275  
276 <  thermostat_kinetic = fkBT * tt2 * chi * chi /
277 <    (2.0 * eConvert);
276 >    SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
277 >    trEta = tmp.trace();
278 >    
279 >    barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);
280  
281 <  thermostat_potential = fkBT* integralOfChidt / eConvert;
281 >    barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
282  
283 <  transposeMat3(eta, a);
284 <  matMul3(a, eta, b);
283 <  trEta = matTrace3(b);
283 >    conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
284 >      barostat_kinetic + barostat_potential;
285  
286 <  barostat_kinetic = NkBT * tb2 * trEta /
286 <    (2.0 * eConvert);
286 >    return conservedQuantity;
287  
288 <  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
289 <    eConvert;
288 >  }
289  
290 <  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
291 <    barostat_kinetic + barostat_potential;
290 >  void NPTf::loadEta() {
291 >    eta= snap->getBarostat();
292  
293 <  return conservedQuantity;
293 >    //if (!eta.isDiagonal()) {
294 >    //    sprintf( painCave.errMsg,
295 >    //             "NPTf error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
296 >    //    painCave.isFatal = 1;
297 >    //    simError();
298 >    //}
299 >  }
300  
301 < }
302 <
298 < template<typename T> string NPTf<T>::getAdditionalParameters(void){
299 <  string parameters;
300 <  const int BUFFERSIZE = 2000; // size of the read buffer
301 <  char buffer[BUFFERSIZE];
302 <
303 <  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
304 <  parameters += buffer;
305 <
306 <  for(int i = 0; i < 3; i++){
307 <    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
308 <    parameters += buffer;
301 >  void NPTf::saveEta() {
302 >    snap->setBarostat(eta);
303    }
304  
311  return parameters;
312
305   }

Comparing trunk/src/integrators/NPTf.cpp (property svn:keywords):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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