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Comparing trunk/OOPSE/libmdtools/NPTf.cpp (file contents):
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC vs.
Revision 857 by mmeineke, Fri Nov 7 17:09:48 2003 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <math.h>
2 >
3   #include "Atom.hpp"
4   #include "SRI.hpp"
5   #include "AbstractClasses.hpp"
# Line 7 | Line 8
8   #include "Thermo.hpp"
9   #include "ReadWrite.hpp"
10   #include "Integrator.hpp"
11 < #include "simError.h"
11 > #include "simError.h"
12  
13 + #ifdef IS_MPI
14 + #include "mpiSimulation.hpp"
15 + #endif
16  
17   // Basic non-isotropic thermostating and barostating via the Melchionna
18   // modification of the Hoover algorithm:
19   //
20   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
21 < //       Molec. Phys., 78, 533.
21 > //       Molec. Phys., 78, 533.
22   //
23   //           and
24 < //
24 > //
25   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
26  
27   template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
28    T( theInfo, the_ff )
29   {
30 <  int i, j;
31 <  chi = 0.0;
30 >  GenericData* data;
31 >  DoubleArrayData * etaValue;
32 >  vector<double> etaArray;
33 >  int i,j;
34  
35 <  for(i = 0; i < 3; i++)
36 <    for (j = 0; j < 3; j++)
35 >  for(i = 0; i < 3; i++){
36 >    for (j = 0; j < 3; j++){
37 >
38        eta[i][j] = 0.0;
39 +      oldEta[i][j] = 0.0;
40 +    }
41 +  }
42  
43 <  have_tau_thermostat = 0;
44 <  have_tau_barostat = 0;
45 <  have_target_temp = 0;
46 <  have_target_pressure = 0;
43 >
44 >  if( theInfo->useInitXSstate ){
45 >    // retrieve eta array from simInfo if it exists
46 >    data = info->getProperty(ETAVALUE_ID);
47 >    if(data){
48 >      etaValue = dynamic_cast<DoubleArrayData*>(data);
49 >      
50 >      if(etaValue){
51 >        etaArray = etaValue->getData();
52 >        
53 >        for(i = 0; i < 3; i++){
54 >          for (j = 0; j < 3; j++){
55 >            eta[i][j] = etaArray[3*i+j];
56 >            oldEta[i][j] = eta[i][j];
57 >          }
58 >        }
59 >      }
60 >    }
61 >  }
62 >
63   }
64  
65 < template<typename T> void NPTf<T>::moveA() {
40 <  
41 <  int i, j, k;
42 <  DirectionalAtom* dAtom;
43 <  double Tb[3], ji[3];
44 <  double A[3][3], I[3][3];
45 <  double angle, mass;
46 <  double vel[3], pos[3], frc[3];
65 > template<typename T> NPTf<T>::~NPTf() {
66  
67 <  double rj[3];
68 <  double instaTemp, instaPress, instaVol;
50 <  double tt2, tb2;
51 <  double sc[3];
52 <  double eta2ij;
53 <  double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3];
54 <  double bigScale, smallScale, offDiagMax;
67 >  // empty for now
68 > }
69  
70 <  tt2 = tauThermostat * tauThermostat;
57 <  tb2 = tauBarostat * tauBarostat;
70 > template<typename T> void NPTf<T>::resetIntegrator() {
71  
72 <  instaTemp = tStats->getTemperature();
60 <  tStats->getPressureTensor(press);
61 <  instaVol = tStats->getVolume();
62 <  
63 <  // first evolve chi a half step
64 <  
65 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
72 >  int i, j;
73  
74 <  for (i = 0; i < 3; i++ ) {
75 <    for (j = 0; j < 3; j++ ) {
76 <      if (i == j) {
77 <        
78 <        eta[i][j] += dt2 * instaVol *
79 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
80 <        
81 <        vScale[i][j] = eta[i][j] + chi;
82 <        
83 <      } else {
84 <        
74 >  for(i = 0; i < 3; i++)
75 >    for (j = 0; j < 3; j++)
76 >      eta[i][j] = 0.0;
77 >
78 >  T::resetIntegrator();
79 > }
80 >
81 > template<typename T> void NPTf<T>::evolveEtaA() {
82 >
83 >  int i, j;
84 >
85 >  for(i = 0; i < 3; i ++){
86 >    for(j = 0; j < 3; j++){
87 >      if( i == j)
88 >        eta[i][j] += dt2 *  instaVol *
89 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
90 >      else
91          eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
92 +    }
93 +  }
94  
95 <        vScale[i][j] = eta[i][j];
96 <        
95 >  for(i = 0; i < 3; i++)
96 >    for (j = 0; j < 3; j++)
97 >      oldEta[i][j] = eta[i][j];
98 > }
99 >
100 > template<typename T> void NPTf<T>::evolveEtaB() {
101 >
102 >  int i,j;
103 >
104 >  for(i = 0; i < 3; i++)
105 >    for (j = 0; j < 3; j++)
106 >      prevEta[i][j] = eta[i][j];
107 >
108 >  for(i = 0; i < 3; i ++){
109 >    for(j = 0; j < 3; j++){
110 >      if( i == j) {
111 >        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
112 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
113 >      } else {
114 >        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
115        }
116      }
117    }
118 + }
119  
120 <  for( i=0; i<nAtoms; i++ ){
120 > template<typename T> void NPTf<T>::calcVelScale(void){
121 >  int i,j;
122  
123 <    atoms[i]->getVel( vel );
124 <    atoms[i]->getPos( pos );
125 <    atoms[i]->getFrc( frc );
123 >  for (i = 0; i < 3; i++ ) {
124 >    for (j = 0; j < 3; j++ ) {
125 >      vScale[i][j] = eta[i][j];
126  
127 <    mass = atoms[i]->getMass();
128 <    
129 <    // velocity half step
95 <        
96 <    info->matVecMul3( vScale, vel, sc );
97 <    
98 <    for (j = 0; j < 3; j++) {
99 <      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
100 <      rj[j] = pos[j];
127 >      if (i == j) {
128 >        vScale[i][j] += chi;
129 >      }
130      }
131 +  }
132 + }
133  
134 <    atoms[i]->setVel( vel );
134 > template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
135 >
136 >  info->matVecMul3( vScale, vel, sc );
137 > }
138  
139 <    // position whole step    
139 > template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
140 >  int j;
141 >  double myVel[3];
142 >  double vScale[3][3];
143  
144 <    info->wrapVector(rj);
144 >  for (j = 0; j < 3; j++)
145 >    myVel[j] = oldVel[3*index + j];
146  
147 <    info->matVecMul3( eta, rj, sc );
147 >  info->matVecMul3( vScale, myVel, sc );
148 > }
149  
150 <    for (j = 0; j < 3; j++ )
151 <      pos[j] += dt * (vel[j] + sc[j]);
150 > template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
151 >                                               int index, double sc[3]){
152 >  int j;
153 >  double rj[3];
154  
155 <    atoms[i]->setPos( pos );
156 <  
116 <    if( atoms[i]->isDirectional() ){
155 >  for(j=0; j<3; j++)
156 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
157  
158 <      dAtom = (DirectionalAtom *)atoms[i];
159 <          
120 <      // get and convert the torque to body frame
121 <      
122 <      dAtom->getTrq( Tb );
123 <      dAtom->lab2Body( Tb );
124 <      
125 <      // get the angular momentum, and propagate a half step
158 >  info->matVecMul3( eta, rj, sc );
159 > }
160  
161 <      dAtom->getJ( ji );
161 > template<typename T> void NPTf<T>::scaleSimBox( void ){
162  
163 <      for (j=0; j < 3; j++)
164 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
165 <      
166 <      // use the angular velocities to propagate the rotation matrix a
167 <      // full time step
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];
168  
135 –      dAtom->getA(A);
136 –      dAtom->getI(I);
137 –    
138 –      // rotate about the x-axis      
139 –      angle = dt2 * ji[0] / I[0][0];
140 –      this->rotate( 1, 2, angle, ji, A );
169  
170 <      // rotate about the y-axis
143 <      angle = dt2 * ji[1] / I[1][1];
144 <      this->rotate( 2, 0, angle, ji, A );
145 <      
146 <      // rotate about the z-axis
147 <      angle = dt * ji[2] / I[2][2];
148 <      this->rotate( 0, 1, angle, ji, A);
149 <      
150 <      // rotate about the y-axis
151 <      angle = dt2 * ji[1] / I[1][1];
152 <      this->rotate( 2, 0, angle, ji, A );
153 <      
154 <       // rotate about the x-axis
155 <      angle = dt2 * ji[0] / I[0][0];
156 <      this->rotate( 1, 2, angle, ji, A );
157 <      
158 <      dAtom->setJ( ji );
159 <      dAtom->setA( A  );    
160 <    }                    
161 <  }
162 <  
170 >
171    // Scale the box after all the positions have been moved:
172 <  
172 >
173    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
174    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
175 <  
175 >
176    bigScale = 1.0;
177    smallScale = 1.0;
178    offDiagMax = 0.0;
179 <  
179 >
180    for(i=0; i<3; i++){
181      for(j=0; j<3; j++){
182 <      
182 >
183        // Calculate the matrix Product of the eta array (we only need
184        // the ij element right now):
185 <      
185 >
186        eta2ij = 0.0;
187        for(k=0; k<3; k++){
188          eta2ij += eta[i][k] * eta[k][j];
189        }
190 <      
190 >
191        scaleMat[i][j] = 0.0;
192        // identity matrix (see above):
193        if (i == j) scaleMat[i][j] = 1.0;
# Line 187 | Line 195 | template<typename T> void NPTf<T>::moveA() {
195        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
196  
197        if (i != j)
198 <        if (fabs(scaleMat[i][j]) > offDiagMax)
198 >        if (fabs(scaleMat[i][j]) > offDiagMax)
199            offDiagMax = fabs(scaleMat[i][j]);
192 –      
200      }
201  
202      if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
203      if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
204    }
205 <  
206 <  if ((bigScale > 1.1) || (smallScale < 0.9)) {
205 >
206 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
207      sprintf( painCave.errMsg,
208 <             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
208 >             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
209               " Check your tauBarostat, as it is probably too small!\n\n"
210               " scaleMat = [%lf\t%lf\t%lf]\n"
211               "            [%lf\t%lf\t%lf]\n"
# Line 208 | Line 215 | template<typename T> void NPTf<T>::moveA() {
215               scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
216      painCave.isFatal = 1;
217      simError();
218 <  } else if (offDiagMax > 0.1) {
218 >  } else if (offDiagMax > 0.01) {
219      sprintf( painCave.errMsg,
220 <             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
220 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
221               " Check your tauBarostat, as it is probably too small!\n\n"
222               " scaleMat = [%lf\t%lf\t%lf]\n"
223               "            [%lf\t%lf\t%lf]\n"
# Line 225 | Line 232 | template<typename T> void NPTf<T>::moveA() {
232      info->matMul3(hm, scaleMat, hmnew);
233      info->setBoxM(hmnew);
234    }
228 –  
235   }
236  
237 < template<typename T> void NPTf<T>::moveB( void ){
237 > template<typename T> bool NPTf<T>::etaConverged() {
238 >  int i;
239 >  double diffEta, sumEta;
240  
241 <  int i, j;
242 <  DirectionalAtom* dAtom;
243 <  double Tb[3], ji[3];
236 <  double vel[3], frc[3];
237 <  double mass;
241 >  sumEta = 0;
242 >  for(i = 0; i < 3; i++)
243 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
244  
245 <  double instaTemp, instaPress, instaVol;
240 <  double tt2, tb2;
241 <  double sc[3];
242 <  double press[3][3], vScale[3][3];
243 <  
244 <  tt2 = tauThermostat * tauThermostat;
245 <  tb2 = tauBarostat * tauBarostat;
245 >  diffEta = sqrt( sumEta / 3.0 );
246  
247 <  instaTemp = tStats->getTemperature();
248 <  tStats->getPressureTensor(press);
249 <  instaVol = tStats->getVolume();
250 <  
251 <  // first evolve chi a half step
252 <  
253 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
254 <  
255 <  for (i = 0; i < 3; i++ ) {
256 <    for (j = 0; j < 3; j++ ) {
257 <      if (i == j) {
247 >  return ( diffEta <= etaTolerance );
248 > }
249  
250 <        eta[i][j] += dt2 * instaVol *
260 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
250 > template<typename T> double NPTf<T>::getConservedQuantity(void){
251  
252 <        vScale[i][j] = eta[i][j] + chi;
253 <        
254 <      } else {
255 <        
256 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
252 >  double conservedQuantity;
253 >  double totalEnergy;
254 >  double thermostat_kinetic;
255 >  double thermostat_potential;
256 >  double barostat_kinetic;
257 >  double barostat_potential;
258 >  double trEta;
259 >  double a[3][3], b[3][3];
260  
261 <        vScale[i][j] = eta[i][j];
269 <        
270 <      }
271 <    }
272 <  }
261 >  totalEnergy = tStats->getTotalE();
262  
263 <  for( i=0; i<nAtoms; i++ ){
263 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
264 >    (2.0 * eConvert);
265  
266 <    atoms[i]->getVel( vel );
277 <    atoms[i]->getFrc( frc );
266 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
267  
268 <    mass = atoms[i]->getMass();
269 <    
270 <    // velocity half step
282 <        
283 <    info->matVecMul3( vScale, vel, sc );
284 <    
285 <    for (j = 0; j < 3; j++) {
286 <      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
287 <    }
268 >  info->transposeMat3(eta, a);
269 >  info->matMul3(a, eta, b);
270 >  trEta = info->matTrace3(b);
271  
272 <    atoms[i]->setVel( vel );
273 <    
291 <    if( atoms[i]->isDirectional() ){
272 >  barostat_kinetic = NkBT * tb2 * trEta /
273 >    (2.0 * eConvert);
274  
275 <      dAtom = (DirectionalAtom *)atoms[i];
276 <          
295 <      // get and convert the torque to body frame
296 <      
297 <      dAtom->getTrq( Tb );
298 <      dAtom->lab2Body( Tb );
299 <      
300 <      // get the angular momentum, and propagate a half step
301 <      
302 <      dAtom->getJ( ji );
303 <      
304 <      for (j=0; j < 3; j++)
305 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
306 <      
307 <      dAtom->setJ( ji );
275 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
276 >    eConvert;
277  
278 <    }                    
279 <  }
278 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
279 >    barostat_kinetic + barostat_potential;
280 >
281 >  return conservedQuantity;
282 >
283   }
284  
285 < template<typename T> int NPTf<T>::readyCheck() {
285 > template<typename T> string NPTf<T>::getAdditionalParameters(void){
286 >  string parameters;
287 >  const int BUFFERSIZE = 2000; // size of the read buffer
288 >  char buffer[BUFFERSIZE];
289  
290 <  //check parent's readyCheck() first
291 <  if (T::readyCheck() == -1)
317 <    return -1;
318 <
319 <  // First check to see if we have a target temperature.
320 <  // Not having one is fatal.
321 <  
322 <  if (!have_target_temp) {
323 <    sprintf( painCave.errMsg,
324 <             "NPTf error: You can't use the NPTf integrator\n"
325 <             "   without a targetTemp!\n"
326 <             );
327 <    painCave.isFatal = 1;
328 <    simError();
329 <    return -1;
330 <  }
290 >  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
291 >  parameters += buffer;
292  
293 <  if (!have_target_pressure) {
294 <    sprintf( painCave.errMsg,
295 <             "NPTf error: You can't use the NPTf integrator\n"
335 <             "   without a targetPressure!\n"
336 <             );
337 <    painCave.isFatal = 1;
338 <    simError();
339 <    return -1;
293 >  for(int i = 0; i < 3; i++){
294 >    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
295 >    parameters += buffer;
296    }
341 –  
342 –  // We must set tauThermostat.
343 –  
344 –  if (!have_tau_thermostat) {
345 –    sprintf( painCave.errMsg,
346 –             "NPTf error: If you use the NPTf\n"
347 –             "   integrator, you must set tauThermostat.\n");
348 –    painCave.isFatal = 1;
349 –    simError();
350 –    return -1;
351 –  }    
297  
298 <  // We must set tauBarostat.
354 <  
355 <  if (!have_tau_barostat) {
356 <    sprintf( painCave.errMsg,
357 <             "NPTf error: If you use the NPTf\n"
358 <             "   integrator, you must set tauBarostat.\n");
359 <    painCave.isFatal = 1;
360 <    simError();
361 <    return -1;
362 <  }    
298 >  return parameters;
299  
364 –  // We need NkBT a lot, so just set it here:
365 –
366 –  NkBT = (double)info->ndf * kB * targetTemp;
367 –
368 –  return 1;
300   }

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