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Comparing trunk/OOPSE/libmdtools/NPTf.cpp (file contents):
Revision 588 by gezelter, Thu Jul 10 17:10:56 2003 UTC vs.
Revision 829 by gezelter, Tue Oct 28 16:03:37 2003 UTC

# Line 1 | Line 1
1 + #include <math.h>
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
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, j;
30 <  chi = 0.0;
31 <
32 <  for(i = 0; i < 3; i++)
33 <    for (j = 0; j < 3; j_++)
29 >  
30 >  int i,j;
31 >  
32 >  for(i = 0; i < 3; i++){
33 >    for (j = 0; j < 3; j++){
34 >      
35        eta[i][j] = 0.0;
36 +      oldEta[i][j] = 0.0;
37 +    }
38 +  }
39 + }
40  
41 <  have_tau_thermostat = 0;
42 <  have_tau_barostat = 0;
43 <  have_target_temp = 0;
35 <  have_target_pressure = 0;
41 > template<typename T> NPTf<T>::~NPTf() {
42 >
43 >  // empty for now
44   }
45  
46 < void NPTf::moveA() {
46 > template<typename T> void NPTf<T>::resetIntegrator() {
47    
48 <  int i,j,k;
49 <  int atomIndex, aMatIndex;
50 <  DirectionalAtom* dAtom;
51 <  double Tb[3];
52 <  double ji[3];
53 <  double ri[3], vi[3], sc[3];
54 <  double instaTemp, instaVol;
55 <  double tt2, tb2, eta2ij;
48 <  double angle;
49 <  double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3];
48 >  int i, j;
49 >  
50 >  for(i = 0; i < 3; i++)
51 >    for (j = 0; j < 3; j++)
52 >      eta[i][j] = 0.0;
53 >  
54 >  T::resetIntegrator();
55 > }
56  
57 <  tt2 = tauThermostat * tauThermostat;
58 <  tb2 = tauBarostat * tauBarostat;
57 > template<typename T> void NPTf<T>::evolveEtaA() {
58 >  
59 >  int i, j;
60 >  
61 >  for(i = 0; i < 3; i ++){
62 >    for(j = 0; j < 3; j++){
63 >      if( i == j)
64 >        eta[i][j] += dt2 *  instaVol *
65 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
66 >      else
67 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
68 >    }
69 >  }
70 >  
71 >  for(i = 0; i < 3; i++)
72 >    for (j = 0; j < 3; j++)
73 >      oldEta[i][j] = eta[i][j];
74 > }
75  
76 <  instaTemp = tStats->getTemperature();
55 <  tStats->getPressureTensor(press);
56 <  instaVol = tStats->getVolume();
57 <  
58 <  // first evolve chi a half step
76 > template<typename T> void NPTf<T>::evolveEtaB() {
77    
78 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
78 >  int i,j;
79  
80 <  for (i = 0; i < 3; i++ ) {
81 <    for (j = 0; j < 3; j++ ) {
82 <      if (i == j) {
80 >  for(i = 0; i < 3; i++)
81 >    for (j = 0; j < 3; j++)
82 >      prevEta[i][j] = eta[i][j];
83  
84 <        eta[i][j] += dt2 * instaVol *
85 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
86 <
87 <        vScale[i][j] = eta[i][j] + chi;
88 <        
84 >  for(i = 0; i < 3; i ++){
85 >    for(j = 0; j < 3; j++){
86 >      if( i == j) {
87 >        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
88 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
89        } else {
90 <        
73 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
74 <
75 <        vScale[i][j] = eta[i][j];
76 <        
90 >        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
91        }
92      }
93    }
94 + }
95  
96 <  for( i=0; i<nAtoms; i++ ){
97 <    atomIndex = i * 3;
98 <    aMatIndex = i * 9;
84 <    
85 <    // velocity half step
86 <    
87 <    vi[0] = vel[atomIndex];
88 <    vi[1] = vel[atomIndex+1];
89 <    vi[2] = vel[atomIndex+2];
90 <    
91 <    info->matVecMul3( vScale, vi, sc );
92 <    
93 <    vi[0] += dt2 * ((frc[atomIndex]  /atoms[i]->getMass())*eConvert - sc[0]);
94 <    vi[1] += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - sc[1]);
95 <    vi[2] += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - sc[2]);
96 > template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
97 >  int i,j;
98 >  double vScale[3][3];
99  
100 <    vel[atomIndex] = vi[0]
101 <    vel[atomIndex+1] = vi[1];
102 <    vel[atomIndex+2] = vi[2];
100 >  for (i = 0; i < 3; i++ ) {
101 >    for (j = 0; j < 3; j++ ) {
102 >      vScale[i][j] = eta[i][j];
103 >      
104 >      if (i == j) {
105 >        vScale[i][j] += chi;          
106 >      }              
107 >    }
108 >  }
109 >  
110 >  info->matVecMul3( vScale, vel, sc );
111 > }
112  
113 <    // position whole step    
113 > template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
114 >  int i,j;
115 >  double myVel[3];
116 >  double vScale[3][3];
117  
118 <    ri[0] = pos[atomIndex];
119 <    ri[1] = pos[atomIndex+1];
120 <    ri[2] = pos[atomIndex+2];
118 >  for (i = 0; i < 3; i++ ) {
119 >    for (j = 0; j < 3; j++ ) {
120 >      vScale[i][j] = eta[i][j];
121 >      
122 >      if (i == j) {
123 >        vScale[i][j] += chi;          
124 >      }              
125 >    }
126 >  }
127 >  
128 >  for (j = 0; j < 3; j++)
129 >    myVel[j] = oldVel[3*index + j];
130  
131 <    info->wrapVector(ri);
131 >  info->matVecMul3( vScale, myVel, sc );
132 > }
133  
134 <    info->matVecMul3( eta, ri, sc );
134 > template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
135 >                                               int index, double sc[3]){
136 >  int j;
137 >  double rj[3];
138  
139 <    pos[atomIndex] += dt * (vel[atomIndex] + sc[0]);
140 <    pos[atomIndex+1] += dt * (vel[atomIndex+1] + sc[1]);
113 <    pos[atomIndex+2] += dt * (vel[atomIndex+2] + sc[2]);
114 <  
115 <    if( atoms[i]->isDirectional() ){
139 >  for(j=0; j<3; j++)
140 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
141  
142 <      dAtom = (DirectionalAtom *)atoms[i];
143 <          
119 <      // get and convert the torque to body frame
120 <      
121 <      Tb[0] = dAtom->getTx();
122 <      Tb[1] = dAtom->getTy();
123 <      Tb[2] = dAtom->getTz();
124 <      
125 <      dAtom->lab2Body( Tb );
126 <      
127 <      // get the angular momentum, and propagate a half step
142 >  info->matVecMul3( eta, rj, sc );
143 > }
144  
145 <      ji[0] = dAtom->getJx();
130 <      ji[1] = dAtom->getJy();
131 <      ji[2] = dAtom->getJz();
132 <      
133 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
134 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
135 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
136 <      
137 <      // use the angular velocities to propagate the rotation matrix a
138 <      // full time step
139 <      
140 <      // rotate about the x-axis      
141 <      angle = dt2 * ji[0] / dAtom->getIxx();
142 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
143 <      
144 <      // rotate about the y-axis
145 <      angle = dt2 * ji[1] / dAtom->getIyy();
146 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
147 <      
148 <      // rotate about the z-axis
149 <      angle = dt * ji[2] / dAtom->getIzz();
150 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
151 <      
152 <      // rotate about the y-axis
153 <      angle = dt2 * ji[1] / dAtom->getIyy();
154 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
155 <      
156 <       // rotate about the x-axis
157 <      angle = dt2 * ji[0] / dAtom->getIxx();
158 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
159 <      
160 <      dAtom->setJx( ji[0] );
161 <      dAtom->setJy( ji[1] );
162 <      dAtom->setJz( ji[2] );
163 <    }
164 <    
165 <  }
145 > template<typename T> void NPTf<T>::scaleSimBox( void ){
146  
147 <  // Scale the box after all the positions have been moved:
147 >  int i,j,k;
148 >  double scaleMat[3][3];
149 >  double eta2ij;
150 >  double bigScale, smallScale, offDiagMax;
151 >  double hm[3][3], hmnew[3][3];
152 >  
153  
154 +
155 +  // Scale the box after all the positions have been moved:
156 +  
157    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
158    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
159 <
160 <
159 >  
160 >  bigScale = 1.0;
161 >  smallScale = 1.0;
162 >  offDiagMax = 0.0;
163 >  
164    for(i=0; i<3; i++){
165      for(j=0; j<3; j++){
166 <
166 >      
167        // Calculate the matrix Product of the eta array (we only need
168        // the ij element right now):
169 <
169 >      
170        eta2ij = 0.0;
171        for(k=0; k<3; k++){
172          eta2ij += eta[i][k] * eta[k][j];
# Line 187 | Line 178 | void NPTf::moveA() {
178        // Taylor expansion for the exponential truncated at second order:
179        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
180  
181 +      if (i != j)
182 +        if (fabs(scaleMat[i][j]) > offDiagMax)
183 +          offDiagMax = fabs(scaleMat[i][j]);
184      }
185 +
186 +    if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
187 +    if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
188    }
192 –  
193 –  info->getBoxM(hm);
194 –  info->matMul3(hm, scaleMat, hmnew);
195 –  info->setBoxM(hmnew);
189    
190 +  if ((bigScale > 1.1) || (smallScale < 0.9)) {
191 +    sprintf( painCave.errMsg,
192 +             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
193 +             " Check your tauBarostat, as it is probably too small!\n\n"
194 +             " scaleMat = [%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 +    painCave.isFatal = 1;
201 +    simError();
202 +  } else if (offDiagMax > 0.1) {
203 +    sprintf( painCave.errMsg,
204 +             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
205 +             " Check your tauBarostat, as it is probably too small!\n\n"
206 +             " scaleMat = [%lf\t%lf\t%lf]\n"
207 +             "            [%lf\t%lf\t%lf]\n"
208 +             "            [%lf\t%lf\t%lf]\n",
209 +             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
210 +             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
211 +             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
212 +    painCave.isFatal = 1;
213 +    simError();
214 +  } else {
215 +    info->getBoxM(hm);
216 +    info->matMul3(hm, scaleMat, hmnew);
217 +    info->setBoxM(hmnew);
218 +  }
219   }
220  
221 < void NPTf::moveB( void ){
222 <  int i,j, k;
223 <  int atomIndex;
202 <  DirectionalAtom* dAtom;
203 <  double Tb[3];
204 <  double ji[3];
205 <  double vi[3], sc[3];
206 <  double instaTemp, instaVol;
207 <  double tt2, tb2;
208 <  double press[3][3], vScale[3][3];
209 <  
210 <  tt2 = tauThermostat * tauThermostat;
211 <  tb2 = tauBarostat * tauBarostat;
221 > template<typename T> bool NPTf<T>::etaConverged() {
222 >  int i;
223 >  double diffEta, sumEta;
224  
225 <  instaTemp = tStats->getTemperature();
226 <  tStats->getPressureTensor(press);
227 <  instaVol = tStats->getVolume();
216 <  
217 <  // first evolve chi a half step
225 >  sumEta = 0;
226 >  for(i = 0; i < 3; i++)
227 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);    
228    
229 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
229 >  diffEta = sqrt( sumEta / 3.0 );
230    
231 <  for (i = 0; i < 3; i++ ) {
232 <    for (j = 0; j < 3; j++ ) {
223 <      if (i == j) {
231 >  return ( diffEta <= etaTolerance );
232 > }
233  
234 <        eta[i][j] += dt2 * instaVol *
235 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
234 > template<typename T> double NPTf<T>::getConservedQuantity(void){
235 >  
236 >  double conservedQuantity;
237 >  double totalEnergy;
238 >  double thermostat_kinetic;
239 >  double thermostat_potential;
240 >  double barostat_kinetic;
241 >  double barostat_potential;
242 >  double trEta;
243 >  double a[3][3], b[3][3];
244  
245 <        vScale[i][j] = eta[i][j] + chi;
229 <        
230 <      } else {
231 <        
232 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
245 >  totalEnergy = tStats->getTotalE();
246  
247 <        vScale[i][j] = eta[i][j];
248 <        
236 <      }
237 <    }
238 <  }
247 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
248 >    (2.0 * eConvert);
249  
250 <  for( i=0; i<nAtoms; i++ ){
241 <    atomIndex = i * 3;
250 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
251  
252 <    // velocity half step
253 <    
254 <    vi[0] = vel[atomIndex];
246 <    vi[1] = vel[atomIndex+1];
247 <    vi[2] = vel[atomIndex+2];
248 <    
249 <    info->matVecMul3( vScale, vi, sc );
250 <    
251 <    vi[0] += dt2 * ((frc[atomIndex]  /atoms[i]->getMass())*eConvert - sc[0]);
252 <    vi[1] += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - sc[1]);
253 <    vi[2] += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - sc[2]);
252 >  info->transposeMat3(eta, a);
253 >  info->matMul3(a, eta, b);
254 >  trEta = info->matTrace3(b);
255  
256 <    vel[atomIndex] = vi[0]
257 <    vel[atomIndex+1] = vi[1];
257 <    vel[atomIndex+2] = vi[2];
258 <    
259 <    if( atoms[i]->isDirectional() ){
260 <      
261 <      dAtom = (DirectionalAtom *)atoms[i];
262 <      
263 <      // get and convert the torque to body frame
264 <      
265 <      Tb[0] = dAtom->getTx();
266 <      Tb[1] = dAtom->getTy();
267 <      Tb[2] = dAtom->getTz();
268 <      
269 <      dAtom->lab2Body( Tb );
270 <      
271 <      // get the angular momentum, and complete the angular momentum
272 <      // half step
273 <      
274 <      ji[0] = dAtom->getJx();
275 <      ji[1] = dAtom->getJy();
276 <      ji[2] = dAtom->getJz();
277 <      
278 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
279 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
280 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
281 <      
282 <      dAtom->setJx( ji[0] );
283 <      dAtom->setJy( ji[1] );
284 <      dAtom->setJz( ji[2] );
285 <    }
286 <  }
287 < }
288 <
289 < int NPTf::readyCheck() {
290 <
291 <  // First check to see if we have a target temperature.
292 <  // Not having one is fatal.
256 >  barostat_kinetic = NkBT * tb2 * trEta /
257 >    (2.0 * eConvert);
258    
259 <  if (!have_target_temp) {
260 <    sprintf( painCave.errMsg,
296 <             "NPTf error: You can't use the NPTf integrator\n"
297 <             "   without a targetTemp!\n"
298 <             );
299 <    painCave.isFatal = 1;
300 <    simError();
301 <    return -1;
302 <  }
259 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
260 >    eConvert;
261  
262 <  if (!have_target_pressure) {
263 <    sprintf( painCave.errMsg,
306 <             "NPTf error: You can't use the NPTf integrator\n"
307 <             "   without a targetPressure!\n"
308 <             );
309 <    painCave.isFatal = 1;
310 <    simError();
311 <    return -1;
312 <  }
262 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
263 >    barostat_kinetic + barostat_potential;
264    
265 <  // We must set tauThermostat.
266 <  
316 <  if (!have_tau_thermostat) {
317 <    sprintf( painCave.errMsg,
318 <             "NPTf error: If you use the NPTf\n"
319 <             "   integrator, you must set tauThermostat.\n");
320 <    painCave.isFatal = 1;
321 <    simError();
322 <    return -1;
323 <  }    
265 > //   cout.width(8);
266 > //   cout.precision(8);
267  
268 <  // We must set tauBarostat.
269 <  
270 <  if (!have_tau_barostat) {
328 <    sprintf( painCave.errMsg,
329 <             "NPTf error: If you use the NPTf\n"
330 <             "   integrator, you must set tauBarostat.\n");
331 <    painCave.isFatal = 1;
332 <    simError();
333 <    return -1;
334 <  }    
268 > //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
269 > //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
270 > //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
271  
272 <  // We need NkBT a lot, so just set it here:
273 <
338 <  NkBT = (double)info->ndf * kB * targetTemp;
339 <
340 <  return 1;
272 >  return conservedQuantity;
273 >  
274   }

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