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root/group/trunk/OOPSE/libmdtools/NPTf.cpp
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Comparing trunk/OOPSE/libmdtools/NPTf.cpp (file contents):
Revision 586 by mmeineke, Wed Jul 9 22:14:06 2003 UTC vs.
Revision 778 by mmeineke, Fri Sep 19 20:00:27 2003 UTC

# Line 1 | Line 1
1 + #include <cmath>
2   #include "Atom.hpp"
3   #include "SRI.hpp"
4   #include "AbstractClasses.hpp"
# Line 8 | Line 9
9   #include "Integrator.hpp"
10   #include "simError.h"
11  
12 + #ifdef IS_MPI
13 + #include "mpiSimulation.hpp"
14 + #endif
15  
16   // Basic non-isotropic thermostating and barostating via the Melchionna
17   // modification of the Hoover algorithm:
# Line 19 | Line 23 | NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
23   //
24   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
25  
26 < NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
27 <  Integrator( theInfo, the_ff )
26 > template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
27 >  T( theInfo, the_ff )
28   {
29 <  int i;
29 >  int i, j;
30    chi = 0.0;
31 <  for(i = 0; i < 9; i++) eta[i] = 0.0;
31 >  integralOfChidt = 0.0;
32 >
33 >  for(i = 0; i < 3; i++)
34 >    for (j = 0; j < 3; j++)
35 >      eta[i][j] = 0.0;
36 >
37    have_tau_thermostat = 0;
38    have_tau_barostat = 0;
39    have_target_temp = 0;
40    have_target_pressure = 0;
41 +
42 +  have_chi_tolerance = 0;
43 +  have_eta_tolerance = 0;
44 +  have_pos_iter_tolerance = 0;
45 +
46 +  oldPos = new double[3*nAtoms];
47 +  oldVel = new double[3*nAtoms];
48 +  oldJi = new double[3*nAtoms];
49 + #ifdef IS_MPI
50 +  Nparticles = mpiSim->getTotAtoms();
51 + #else
52 +  Nparticles = theInfo->n_atoms;
53 + #endif
54 +
55   }
56  
57 < void NPTf::moveA() {
58 <  
59 <  int i,j,k;
60 <  int atomIndex, aMatIndex;
57 > template<typename T> NPTf<T>::~NPTf() {
58 >  delete[] oldPos;
59 >  delete[] oldVel;
60 >  delete[] oldJi;
61 > }
62 >
63 > template<typename T> void NPTf<T>::moveA() {
64 >
65 >  // new version of NPTf
66 >  int i, j, k;
67    DirectionalAtom* dAtom;
68 <  double Tb[3];
69 <  double ji[3];
68 >  double Tb[3], ji[3];
69 >
70 >  double mass;
71 >  double vel[3], pos[3], frc[3];
72 >
73    double rj[3];
42 –  double ident[3][3], eta1[3][3], eta2[3][3], hmnew[3][3];
43 –  double hm[9];
44 –  double vx, vy, vz;
45 –  double scx, scy, scz;
74    double instaTemp, instaPress, instaVol;
75    double tt2, tb2;
76 <  double angle;
77 <  double press[9];
76 >  double sc[3];
77 >  double eta2ij;
78 >  double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3];
79 >  double bigScale, smallScale, offDiagMax;
80 >  double COM[3];
81  
82    tt2 = tauThermostat * tauThermostat;
83    tb2 = tauBarostat * tauBarostat;
# Line 54 | Line 85 | void NPTf::moveA() {
85    instaTemp = tStats->getTemperature();
86    tStats->getPressureTensor(press);
87    instaVol = tStats->getVolume();
57 –  
58 –  // first evolve chi a half step
88    
89 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
89 >  tStats->getCOM(COM);
90 >
91 >  //calculate scale factor of veloity
92 >  for (i = 0; i < 3; i++ ) {
93 >    for (j = 0; j < 3; j++ ) {
94 >      vScale[i][j] = eta[i][j];
95 >      
96 >      if (i == j) {
97 >        vScale[i][j] += chi;          
98 >      }              
99 >    }
100 >  }
101    
102 <  eta[0] += dt2 * instaVol * (press[0] - targetPressure/p_convert) /
63 <    (NkBT*tb2);
64 <  eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2);
65 <  eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2);
66 <  eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2);
67 <  eta[4] += dt2 * instaVol * (press[4] - targetPressure/p_convert) /
68 <    (NkBT*tb2);
69 <  eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2);
70 <  eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2);
71 <  eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2);
72 <  eta[8] += dt2 * instaVol * (press[8] - targetPressure/p_convert) /
73 <    (NkBT*tb2);
74 <  
102 >  //evolve velocity half step
103    for( i=0; i<nAtoms; i++ ){
76 –    atomIndex = i * 3;
77 –    aMatIndex = i * 9;
78 –    
79 –    // velocity half step
80 –    
81 –    vx = vel[atomIndex];
82 –    vy = vel[atomIndex+1];
83 –    vz = vel[atomIndex+2];
84 –    
85 –    scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz;
86 –    scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz;
87 –    scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz;
88 –    
89 –    vx += dt2 * ((frc[atomIndex]  /atoms[i]->getMass())*eConvert - scx);
90 –    vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy);
91 –    vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz);
104  
105 <    vel[atomIndex] = vx;
106 <    vel[atomIndex+1] = vy;
95 <    vel[atomIndex+2] = vz;
105 >    atoms[i]->getVel( vel );
106 >    atoms[i]->getFrc( frc );
107  
108 <    // position whole step    
108 >    mass = atoms[i]->getMass();
109 >    
110 >    info->matVecMul3( vScale, vel, sc );
111  
112 <    rj[0] = pos[atomIndex];
113 <    rj[1] = pos[atomIndex+1];
114 <    rj[2] = pos[atomIndex+2];
112 >    for (j=0; j < 3; j++) {
113 >      // velocity half step
114 >      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
115 >    }
116  
117 <    info->wrapVector(rj);
104 <
105 <    scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2];
106 <    scy = eta[3]*rj[0] + eta[4]*rj[1] + eta[5]*rj[2];
107 <    scz = eta[6]*rj[0] + eta[7]*rj[1] + eta[8]*rj[2];
108 <
109 <    pos[atomIndex] += dt * (vel[atomIndex] + scx);
110 <    pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy);
111 <    pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz);
117 >    atoms[i]->setVel( vel );
118    
119      if( atoms[i]->isDirectional() ){
120  
121        dAtom = (DirectionalAtom *)atoms[i];
122 <          
122 >
123        // get and convert the torque to body frame
124        
125 <      Tb[0] = dAtom->getTx();
120 <      Tb[1] = dAtom->getTy();
121 <      Tb[2] = dAtom->getTz();
122 <      
125 >      dAtom->getTrq( Tb );
126        dAtom->lab2Body( Tb );
127        
128        // get the angular momentum, and propagate a half step
129  
130 <      ji[0] = dAtom->getJx();
131 <      ji[1] = dAtom->getJy();
132 <      ji[2] = dAtom->getJz();
130 >      dAtom->getJ( ji );
131 >
132 >      for (j=0; j < 3; j++)
133 >        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
134        
135 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
136 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
137 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
138 <      
139 <      // use the angular velocities to propagate the rotation matrix a
140 <      // full time step
141 <      
142 <      // rotate about the x-axis      
143 <      angle = dt2 * ji[0] / dAtom->getIxx();
144 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
145 <      
146 <      // rotate about the y-axis
147 <      angle = dt2 * ji[1] / dAtom->getIyy();
148 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
149 <      
150 <      // rotate about the z-axis
151 <      angle = dt * ji[2] / dAtom->getIzz();
152 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
153 <      
154 <      // rotate about the y-axis
155 <      angle = dt2 * ji[1] / dAtom->getIyy();
152 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
153 <      
154 <       // rotate about the x-axis
155 <      angle = dt2 * ji[0] / dAtom->getIxx();
156 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
157 <      
158 <      dAtom->setJx( ji[0] );
159 <      dAtom->setJy( ji[1] );
160 <      dAtom->setJz( ji[2] );
135 >      this->rotationPropagation( dAtom, ji );
136 >  
137 >      dAtom->setJ( ji );
138 >    }    
139 >  }
140 >
141 >  // advance chi half step
142 >  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
143 >
144 >  // calculate the integral of chidt
145 >  integralOfChidt += dt2*chi;
146 >
147 >  // advance eta half step
148 >
149 >  for(i = 0; i < 3; i ++)
150 >    for(j = 0; j < 3; j++){
151 >      if( i == j)
152 >        eta[i][j] += dt2 *  instaVol *
153 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
154 >      else
155 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
156      }
157      
158 +  //save the old positions
159 +  for(i = 0; i < nAtoms; i++){
160 +    atoms[i]->getPos(pos);
161 +    for(j = 0; j < 3; j++)
162 +      oldPos[i*3 + j] = pos[j];
163    }
164 +  
165 +  //the first estimation of r(t+dt) is equal to  r(t)
166 +    
167 +  for(k = 0; k < 4; k ++){
168  
169 <  // Scale the box after all the positions have been moved:
169 >    for(i =0 ; i < nAtoms; i++){
170  
171 <  // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
172 <  //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
171 >      atoms[i]->getVel(vel);
172 >      atoms[i]->getPos(pos);
173  
174 +      for(j = 0; j < 3; j++)
175 +        rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j];
176 +      
177 +      info->matVecMul3( eta, rj, sc );
178 +      
179 +      for(j = 0; j < 3; j++)
180 +        pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]);
181  
182 <  for(i=0; i<3; i++){
183 <    for(j=0; j<3; j++){
173 <      ident[i][j] = 0.0;
174 <      eta1[i][j] = eta[3*i+j];
175 <      eta2[i][j] = 0.0;
176 <      for(k=0; k<3; k++){
177 <        eta2[i][j] += eta[3*i+k] * eta[3*k+j];
178 <      }
182 >      atoms[i]->setPos( pos );
183 >
184      }
180 –    ident[i][i] = 1.0;
181 –  }
185  
186 <  
187 <  info->getBoxM(hm);
186 >    if (nConstrained) {
187 >      constrainA();
188 >    }
189 >  }  
190 >
191  
192 +  // Scale the box after all the positions have been moved:
193 +  
194 +  // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
195 +  //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
196 +  
197 +  bigScale = 1.0;
198 +  smallScale = 1.0;
199 +  offDiagMax = 0.0;
200 +  
201    for(i=0; i<3; i++){
202 <    for(j=0; j<3; j++){      
203 <      hmnew[i][j] = 0.0;
202 >    for(j=0; j<3; j++){
203 >      
204 >      // Calculate the matrix Product of the eta array (we only need
205 >      // the ij element right now):
206 >      
207 >      eta2ij = 0.0;
208        for(k=0; k<3; k++){
209 <        // remember that hmat has transpose ordering for Fortran compat:
191 <        hmnew[i][j] += hm[3*k+i] * (ident[k][j]
192 <                                    + dt * eta1[k][j]
193 <                                    + 0.5 * dt * dt * eta2[k][j]);
209 >        eta2ij += eta[i][k] * eta[k][j];
210        }
211 +      
212 +      scaleMat[i][j] = 0.0;
213 +      // identity matrix (see above):
214 +      if (i == j) scaleMat[i][j] = 1.0;
215 +      // Taylor expansion for the exponential truncated at second order:
216 +      scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
217 +
218 +      if (i != j)
219 +        if (fabs(scaleMat[i][j]) > offDiagMax)
220 +          offDiagMax = fabs(scaleMat[i][j]);
221      }
222 +
223 +    if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
224 +    if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
225    }
226    
227 <  for (i = 0; i < 3; i++) {
228 <    for (j = 0; j < 3; j++) {
229 <      // remember that hmat has transpose ordering for Fortran compat:
230 <      hm[3*j + i] = hmnew[i][j];
231 <    }
227 >  if ((bigScale > 1.1) || (smallScale < 0.9)) {
228 >    sprintf( painCave.errMsg,
229 >             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
230 >             " Check your tauBarostat, as it is probably too small!\n\n"
231 >             " scaleMat = [%lf\t%lf\t%lf]\n"
232 >             "            [%lf\t%lf\t%lf]\n"
233 >             "            [%lf\t%lf\t%lf]\n",
234 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
235 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
236 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
237 >    painCave.isFatal = 1;
238 >    simError();
239 >  } else if (offDiagMax > 0.1) {
240 >    sprintf( painCave.errMsg,
241 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
242 >             " Check your tauBarostat, as it is probably too small!\n\n"
243 >             " scaleMat = [%lf\t%lf\t%lf]\n"
244 >             "            [%lf\t%lf\t%lf]\n"
245 >             "            [%lf\t%lf\t%lf]\n",
246 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
247 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
248 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
249 >    painCave.isFatal = 1;
250 >    simError();
251 >  } else {
252 >    info->getBoxM(hm);
253 >    info->matMul3(hm, scaleMat, hmnew);
254 >    info->setBoxM(hmnew);
255    }
204 –
205 –  info->setBoxM(hm);
256    
257   }
258  
259 < void NPTf::moveB( void ){
260 <  int i,j,k;
261 <  int atomIndex;
259 > template<typename T> void NPTf<T>::moveB( void ){
260 >
261 >  //new version of NPTf
262 >  int i, j, k;
263    DirectionalAtom* dAtom;
264 <  double Tb[3];
265 <  double ji[3];
266 <  double press[9];
267 <  double instaTemp, instaVol;
264 >  double Tb[3], ji[3];
265 >  double vel[3], myVel[3], frc[3];
266 >  double mass;
267 >
268 >  double instaTemp, instaPress, instaVol;
269    double tt2, tb2;
270 <  double vx, vy, vz;
271 <  double scx, scy, scz;
272 <  const double p_convert = 1.63882576e8;
270 >  double sc[3];
271 >  double press[3][3], vScale[3][3];
272 >  double oldChi, prevChi;
273 >  double oldEta[3][3], prevEta[3][3], diffEta;
274    
275    tt2 = tauThermostat * tauThermostat;
276    tb2 = tauBarostat * tauBarostat;
277  
278 <  instaTemp = tStats->getTemperature();
279 <  tStats->getPressureTensor(press);
280 <  instaVol = tStats->getVolume();
228 <  
229 <  // first evolve chi a half step
278 >  // Set things up for the iteration:
279 >
280 >  oldChi = chi;
281    
282 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
283 <  
284 <  eta[0] += dt2 * instaVol * (press[0] - targetPressure/p_convert) /
234 <    (NkBT*tb2);
235 <  eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2);
236 <  eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2);
237 <  eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2);
238 <  eta[4] += dt2 * instaVol * (press[4] - targetPressure/p_convert) /
239 <    (NkBT*tb2);
240 <  eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2);
241 <  eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2);
242 <  eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2);
243 <  eta[8] += dt2 * instaVol * (press[8] - targetPressure/p_convert) /
244 <    (NkBT*tb2);
282 >  for(i = 0; i < 3; i++)
283 >    for(j = 0; j < 3; j++)
284 >      oldEta[i][j] = eta[i][j];
285  
286    for( i=0; i<nAtoms; i++ ){
247 –    atomIndex = i * 3;
287  
288 <    // velocity half step
288 >    atoms[i]->getVel( vel );
289 >
290 >    for (j=0; j < 3; j++)
291 >      oldVel[3*i + j]  = vel[j];
292 >
293 >    if( atoms[i]->isDirectional() ){
294 >
295 >      dAtom = (DirectionalAtom *)atoms[i];
296 >
297 >      dAtom->getJ( ji );
298 >
299 >      for (j=0; j < 3; j++)
300 >        oldJi[3*i + j] = ji[j];
301 >
302 >    }
303 >  }
304 >
305 >  // do the iteration:
306 >
307 >  instaVol = tStats->getVolume();
308 >  
309 >  for (k=0; k < 4; k++) {
310      
311 <    vx = vel[atomIndex];
312 <    vy = vel[atomIndex+1];
313 <    vz = vel[atomIndex+2];
311 >    instaTemp = tStats->getTemperature();
312 >    tStats->getPressureTensor(press);
313 >
314 >    // evolve chi another half step using the temperature at t + dt/2
315 >
316 >    prevChi = chi;
317 >    chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
318      
319 <    scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz;
320 <    scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz;
321 <    scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz;
258 <    
259 <    vx += dt2 * ((frc[atomIndex]  /atoms[i]->getMass())*eConvert - scx);
260 <    vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy);
261 <    vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz);
319 >    for(i = 0; i < 3; i++)
320 >      for(j = 0; j < 3; j++)
321 >        prevEta[i][j] = eta[i][j];
322  
323 <    vel[atomIndex] = vx;
324 <    vel[atomIndex+1] = vy;
325 <    vel[atomIndex+2] = vz;
323 >    //advance eta half step and calculate scale factor for velocity
324 >
325 >    for(i = 0; i < 3; i ++)
326 >      for(j = 0; j < 3; j++){
327 >        if( i == j) {
328 >          eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
329 >            (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
330 >          vScale[i][j] = eta[i][j] + chi;
331 >        } else {
332 >          eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
333 >          vScale[i][j] = eta[i][j];
334 >        }
335 >      }  
336      
337 <    if( atoms[i]->isDirectional() ){
337 >    for( i=0; i<nAtoms; i++ ){
338 >
339 >      atoms[i]->getFrc( frc );
340 >      atoms[i]->getVel(vel);
341        
342 <      dAtom = (DirectionalAtom *)atoms[i];
342 >      mass = atoms[i]->getMass();
343 >    
344 >      for (j = 0; j < 3; j++)
345 >        myVel[j] = oldVel[3*i + j];
346        
347 <      // get and convert the torque to body frame
347 >      info->matVecMul3( vScale, myVel, sc );
348        
349 <      Tb[0] = dAtom->getTx();
350 <      Tb[1] = dAtom->getTy();
351 <      Tb[2] = dAtom->getTz();
349 >      // velocity half step
350 >      for (j=0; j < 3; j++) {
351 >        // velocity half step  (use chi from previous step here):
352 >        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
353 >      }
354        
355 <      dAtom->lab2Body( Tb );
355 >      atoms[i]->setVel( vel );
356        
357 <      // get the angular momentum, and complete the angular momentum
358 <      // half step
357 >      if( atoms[i]->isDirectional() ){
358 >
359 >        dAtom = (DirectionalAtom *)atoms[i];
360 >  
361 >        // get and convert the torque to body frame      
362 >  
363 >        dAtom->getTrq( Tb );
364 >        dAtom->lab2Body( Tb );      
365 >            
366 >        for (j=0; j < 3; j++)
367 >          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
368        
369 <      ji[0] = dAtom->getJx();
370 <      ji[1] = dAtom->getJy();
284 <      ji[2] = dAtom->getJz();
285 <      
286 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
287 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
288 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
289 <      
290 <      dAtom->setJx( ji[0] );
291 <      dAtom->setJy( ji[1] );
292 <      dAtom->setJz( ji[2] );
369 >          dAtom->setJ( ji );
370 >      }
371      }
372 +
373 +    if (nConstrained) {
374 +      constrainB();
375 +    }
376 +    
377 +    diffEta = 0;
378 +    for(i = 0; i < 3; i++)
379 +      diffEta += pow(prevEta[i][i] - eta[i][i], 2);    
380 +    
381 +    if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance)
382 +      break;
383    }
384 +
385 +  //calculate integral of chidt
386 +  integralOfChidt += dt2*chi;
387 +  
388   }
389  
390 < int NPTf::readyCheck() {
390 > template<typename T> void NPTf<T>::resetIntegrator() {
391 >  int i,j;
392 >  
393 >  chi = 0.0;
394 >
395 >  for(i = 0; i < 3; i++)
396 >    for (j = 0; j < 3; j++)
397 >      eta[i][j] = 0.0;
398 >
399 > }
400 >
401 > template<typename T> int NPTf<T>::readyCheck() {
402 >
403 >  //check parent's readyCheck() first
404 >  if (T::readyCheck() == -1)
405 >    return -1;
406  
407    // First check to see if we have a target temperature.
408    // Not having one is fatal.
# Line 341 | Line 449 | int NPTf::readyCheck() {
449      return -1;
450    }    
451  
452 <  // We need NkBT a lot, so just set it here:
452 >  
453 >  // We need NkBT a lot, so just set it here: This is the RAW number
454 >  // of particles, so no subtraction or addition of constraints or
455 >  // orientational degrees of freedom:
456 >  
457 >  NkBT = (double)Nparticles * kB * targetTemp;
458 >  
459 >  // fkBT is used because the thermostat operates on more degrees of freedom
460 >  // than the barostat (when there are particles with orientational degrees
461 >  // of freedom).  ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons
462 >  
463 >  fkBT = (double)info->ndf * kB * targetTemp;
464  
346 –  NkBT = (double)info->ndf * kB * targetTemp;
347 –
465    return 1;
466   }
467 +
468 + template<typename T> double NPTf<T>::getConservedQuantity(void){
469 +
470 +  double conservedQuantity;
471 +  double Energy;
472 +  double thermostat_kinetic;
473 +  double thermostat_potential;
474 +  double barostat_kinetic;
475 +  double barostat_potential;
476 +  double trEta;
477 +  double a[3][3], b[3][3];
478 +
479 +  Energy = tStats->getTotalE();
480 +
481 +  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
482 +    (2.0 * eConvert);
483 +
484 +  thermostat_potential = fkBT* integralOfChidt / eConvert;
485 +
486 +  info->transposeMat3(eta, a);
487 +  info->matMul3(a, eta, b);
488 +  trEta = info->matTrace3(b);
489 +
490 +  barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta /
491 +    (2.0 * eConvert);
492 +  
493 +  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
494 +    eConvert;
495 +
496 +  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
497 +    barostat_kinetic + barostat_potential;
498 +  
499 +  cout.width(8);
500 +  cout.precision(8);
501 +
502 +  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
503 +      "\t" << thermostat_potential << "\t" << barostat_kinetic <<
504 +      "\t" << barostat_potential << "\t" << conservedQuantity << endl;
505 +
506 +  return conservedQuantity;
507 + }

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