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Comparing trunk/OOPSE/libmdtools/NPTf.cpp (file contents):
Revision 746 by mmeineke, Thu Sep 4 21:48:35 2003 UTC vs.
Revision 855 by mmeineke, Thu Nov 6 22:01:37 2003 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <math.h>
2   #include "Atom.hpp"
3   #include "SRI.hpp"
4   #include "AbstractClasses.hpp"
# Line 7 | Line 7
7   #include "Thermo.hpp"
8   #include "ReadWrite.hpp"
9   #include "Integrator.hpp"
10 < #include "simError.h"
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:
18   //
19   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
20 < //       Molec. Phys., 78, 533.
20 > //       Molec. Phys., 78, 533.
21   //
22   //           and
23 < //
23 > //
24   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
25  
26   template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
27    T( theInfo, the_ff )
28   {
29 +  GenericData* data;
30 +  DoubleArrayData * etaValue;
31 +  vector<double> etaArray;
32 +  int i,j;
33 +
34 +  for(i = 0; i < 3; i++){
35 +    for (j = 0; j < 3; j++){
36 +
37 +      eta[i][j] = 0.0;
38 +      oldEta[i][j] = 0.0;
39 +    }
40 +  }
41 +
42 +
43 +  if( theInfo->useInitXSstate ){
44 +    // retrieve eta array from simInfo if it exists
45 +    data = info->getProperty(ETAVALUE_ID);
46 +    if(data){
47 +      etaValue = dynamic_cast<DoubleArrayData*>(data);
48 +      
49 +      if(etaValue){
50 +        etaArray = etaValue->getData();
51 +        
52 +        for(i = 0; i < 3; i++){
53 +          for (j = 0; j < 3; j++){
54 +            eta[i][j] = etaArray[3*i+j];
55 +            oldEta[i][j] = eta[i][j];
56 +          }
57 +        }
58 +      }
59 +    }
60 +  }
61 +
62 + }
63 +
64 + template<typename T> NPTf<T>::~NPTf() {
65 +
66 +  // empty for now
67 + }
68 +
69 + template<typename T> void NPTf<T>::resetIntegrator() {
70 +
71    int i, j;
27 –  chi = 0.0;
72  
73 <  for(i = 0; i < 3; i++)
74 <    for (j = 0; j < 3; j++)
73 >  for(i = 0; i < 3; i++)
74 >    for (j = 0; j < 3; j++)
75        eta[i][j] = 0.0;
76  
77 <  have_tau_thermostat = 0;
34 <  have_tau_barostat = 0;
35 <  have_target_temp = 0;
36 <  have_target_pressure = 0;
77 >  T::resetIntegrator();
78   }
79  
80 < 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];
80 > template<typename T> void NPTf<T>::evolveEtaA() {
81  
82 <  double rj[3];
49 <  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;
82 >  int i, j;
83  
84 <  tt2 = tauThermostat * tauThermostat;
85 <  tb2 = tauBarostat * tauBarostat;
84 >  for(i = 0; i < 3; i ++){
85 >    for(j = 0; j < 3; j++){
86 >      if( i == j)
87 >        eta[i][j] += dt2 *  instaVol *
88 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
89 >      else
90 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
91 >    }
92 >  }
93  
94 <  instaTemp = tStats->getTemperature();
95 <  tStats->getPressureTensor(press);
96 <  instaVol = tStats->getVolume();
97 <  
63 <  // first evolve chi a half step
64 <  
65 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
94 >  for(i = 0; i < 3; i++)
95 >    for (j = 0; j < 3; j++)
96 >      oldEta[i][j] = eta[i][j];
97 > }
98  
99 + template<typename T> void NPTf<T>::evolveEtaB() {
100 +
101 +  int i,j;
102 +
103 +  for(i = 0; i < 3; i++)
104 +    for (j = 0; j < 3; j++)
105 +      prevEta[i][j] = eta[i][j];
106 +
107 +  for(i = 0; i < 3; i ++){
108 +    for(j = 0; j < 3; j++){
109 +      if( i == j) {
110 +        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
111 +          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
112 +      } else {
113 +        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
114 +      }
115 +    }
116 +  }
117 + }
118 +
119 + template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
120 +  int i,j;
121 +  double vScale[3][3];
122 +
123    for (i = 0; i < 3; i++ ) {
124      for (j = 0; j < 3; j++ ) {
125 <      if (i == j) {
70 <        
71 <        eta[i][j] += dt2 * instaVol *
72 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
73 <        
74 <        vScale[i][j] = eta[i][j] + chi;
75 <        
76 <      } else {
77 <        
78 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
125 >      vScale[i][j] = eta[i][j];
126  
127 <        vScale[i][j] = eta[i][j];
128 <        
127 >      if (i == j) {
128 >        vScale[i][j] += chi;
129        }
130      }
131    }
132  
133 <  for( i=0; i<nAtoms; i++ ){
133 >  info->matVecMul3( vScale, vel, sc );
134 > }
135  
136 <    atoms[i]->getVel( vel );
137 <    atoms[i]->getPos( pos );
138 <    atoms[i]->getFrc( frc );
136 > template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
137 >  int i,j;
138 >  double myVel[3];
139 >  double vScale[3][3];
140  
141 <    mass = atoms[i]->getMass();
142 <    
143 <    // velocity half step
144 <        
145 <    info->matVecMul3( vScale, vel, sc );
146 <    
147 <    for (j = 0; j < 3; j++) {
99 <      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
100 <      rj[j] = pos[j];
141 >  for (i = 0; i < 3; i++ ) {
142 >    for (j = 0; j < 3; j++ ) {
143 >      vScale[i][j] = eta[i][j];
144 >
145 >      if (i == j) {
146 >        vScale[i][j] += chi;
147 >      }
148      }
149 +  }
150  
151 <    atoms[i]->setVel( vel );
151 >  for (j = 0; j < 3; j++)
152 >    myVel[j] = oldVel[3*index + j];
153  
154 <    // position whole step    
154 >  info->matVecMul3( vScale, myVel, sc );
155 > }
156  
157 <    info->wrapVector(rj);
157 > template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
158 >                                               int index, double sc[3]){
159 >  int j;
160 >  double rj[3];
161  
162 <    info->matVecMul3( eta, rj, sc );
162 >  for(j=0; j<3; j++)
163 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
164  
165 <    for (j = 0; j < 3; j++ )
166 <      pos[j] += dt * (vel[j] + sc[j]);
165 >  info->matVecMul3( eta, rj, sc );
166 > }
167  
168 <    atoms[i]->setPos( pos );
115 <  
116 <    if( atoms[i]->isDirectional() ){
168 > template<typename T> void NPTf<T>::scaleSimBox( void ){
169  
170 <      dAtom = (DirectionalAtom *)atoms[i];
171 <          
172 <      // get and convert the torque to body frame
173 <      
174 <      dAtom->getTrq( Tb );
123 <      dAtom->lab2Body( Tb );
124 <      
125 <      // get the angular momentum, and propagate a half step
170 >  int i,j,k;
171 >  double scaleMat[3][3];
172 >  double eta2ij;
173 >  double bigScale, smallScale, offDiagMax;
174 >  double hm[3][3], hmnew[3][3];
175  
127 –      dAtom->getJ( ji );
176  
129 –      for (j=0; j < 3; j++)
130 –        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
131 –      
132 –      // use the angular velocities to propagate the rotation matrix a
133 –      // full time step
177  
178 <      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 );
178 >  // Scale the box after all the positions have been moved:
179  
142 –      // 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 –  
163 –  // Scale the box after all the positions have been moved:
164 –  
180    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
181    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
182 <  
182 >
183    bigScale = 1.0;
184    smallScale = 1.0;
185    offDiagMax = 0.0;
186 <  
186 >
187    for(i=0; i<3; i++){
188      for(j=0; j<3; j++){
189 <      
189 >
190        // Calculate the matrix Product of the eta array (we only need
191        // the ij element right now):
192 <      
192 >
193        eta2ij = 0.0;
194        for(k=0; k<3; k++){
195          eta2ij += eta[i][k] * eta[k][j];
196        }
197 <      
197 >
198        scaleMat[i][j] = 0.0;
199        // identity matrix (see above):
200        if (i == j) scaleMat[i][j] = 1.0;
# Line 187 | Line 202 | template<typename T> void NPTf<T>::moveA() {
202        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
203  
204        if (i != j)
205 <        if (fabs(scaleMat[i][j]) > offDiagMax)
205 >        if (fabs(scaleMat[i][j]) > offDiagMax)
206            offDiagMax = fabs(scaleMat[i][j]);
192 –      
207      }
208  
209      if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
210      if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
211    }
212 <  
213 <  if ((bigScale > 1.1) || (smallScale < 0.9)) {
212 >
213 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
214      sprintf( painCave.errMsg,
215 <             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
215 >             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
216               " Check your tauBarostat, as it is probably too small!\n\n"
217               " scaleMat = [%lf\t%lf\t%lf]\n"
218               "            [%lf\t%lf\t%lf]\n"
# Line 208 | Line 222 | template<typename T> void NPTf<T>::moveA() {
222               scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
223      painCave.isFatal = 1;
224      simError();
225 <  } else if (offDiagMax > 0.1) {
225 >  } else if (offDiagMax > 0.01) {
226      sprintf( painCave.errMsg,
227 <             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
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"
# Line 225 | Line 239 | template<typename T> void NPTf<T>::moveA() {
239      info->matMul3(hm, scaleMat, hmnew);
240      info->setBoxM(hmnew);
241    }
228 –  
242   }
243  
244 < template<typename T> void NPTf<T>::moveB( void ){
244 > template<typename T> bool NPTf<T>::etaConverged() {
245 >  int i;
246 >  double diffEta, sumEta;
247  
248 <  int i, j;
249 <  DirectionalAtom* dAtom;
250 <  double Tb[3], ji[3];
236 <  double vel[3], frc[3];
237 <  double mass;
248 >  sumEta = 0;
249 >  for(i = 0; i < 3; i++)
250 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
251  
252 <  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;
252 >  diffEta = sqrt( sumEta / 3.0 );
253  
254 <  instaTemp = tStats->getTemperature();
255 <  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) {
254 >  return ( diffEta <= etaTolerance );
255 > }
256  
257 <        eta[i][j] += dt2 * instaVol *
260 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
257 > template<typename T> double NPTf<T>::getConservedQuantity(void){
258  
259 <        vScale[i][j] = eta[i][j] + chi;
260 <        
261 <      } else {
262 <        
263 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
259 >  double conservedQuantity;
260 >  double totalEnergy;
261 >  double thermostat_kinetic;
262 >  double thermostat_potential;
263 >  double barostat_kinetic;
264 >  double barostat_potential;
265 >  double trEta;
266 >  double a[3][3], b[3][3];
267  
268 <        vScale[i][j] = eta[i][j];
269 <        
270 <      }
271 <    }
272 <  }
268 >  totalEnergy = tStats->getTotalE();
269  
270 <  for( i=0; i<nAtoms; i++ ){
270 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
271 >    (2.0 * eConvert);
272  
273 <    atoms[i]->getVel( vel );
277 <    atoms[i]->getFrc( frc );
273 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
274  
275 <    mass = atoms[i]->getMass();
276 <    
277 <    // 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 <    }
275 >  info->transposeMat3(eta, a);
276 >  info->matMul3(a, eta, b);
277 >  trEta = info->matTrace3(b);
278  
279 <    atoms[i]->setVel( vel );
280 <    
291 <    if( atoms[i]->isDirectional() ){
279 >  barostat_kinetic = NkBT * tb2 * trEta /
280 >    (2.0 * eConvert);
281  
282 <      dAtom = (DirectionalAtom *)atoms[i];
283 <          
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 );
282 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
283 >    eConvert;
284  
285 <    }                    
286 <  }
311 < }
285 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
286 >    barostat_kinetic + barostat_potential;
287  
288 < template<typename T> void NPTf<T>::resetIntegrator() {
314 <  int i,j;
315 <  
316 <  chi = 0.0;
288 >  return conservedQuantity;
289  
318 –  for(i = 0; i < 3; i++)
319 –    for (j = 0; j < 3; j++)
320 –      eta[i][j] = 0.0;
321 –
290   }
291  
292 < template<typename T> int NPTf<T>::readyCheck() {
292 > template<typename T> string NPTf<T>::getAdditionalParameters(void){
293 >  string parameters;
294 >  const int BUFFERSIZE = 2000; // size of the read buffer
295 >  char buffer[BUFFERSIZE];
296  
297 <  //check parent's readyCheck() first
298 <  if (T::readyCheck() == -1)
328 <    return -1;
329 <
330 <  // First check to see if we have a target temperature.
331 <  // Not having one is fatal.
332 <  
333 <  if (!have_target_temp) {
334 <    sprintf( painCave.errMsg,
335 <             "NPTf error: You can't use the NPTf integrator\n"
336 <             "   without a targetTemp!\n"
337 <             );
338 <    painCave.isFatal = 1;
339 <    simError();
340 <    return -1;
341 <  }
297 >  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
298 >  parameters += buffer;
299  
300 <  if (!have_target_pressure) {
301 <    sprintf( painCave.errMsg,
302 <             "NPTf error: You can't use the NPTf integrator\n"
346 <             "   without a targetPressure!\n"
347 <             );
348 <    painCave.isFatal = 1;
349 <    simError();
350 <    return -1;
300 >  for(int i = 0; i < 3; i++){
301 >    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
302 >    parameters += buffer;
303    }
352 –  
353 –  // We must set tauThermostat.
354 –  
355 –  if (!have_tau_thermostat) {
356 –    sprintf( painCave.errMsg,
357 –             "NPTf error: If you use the NPTf\n"
358 –             "   integrator, you must set tauThermostat.\n");
359 –    painCave.isFatal = 1;
360 –    simError();
361 –    return -1;
362 –  }    
304  
305 <  // We must set tauBarostat.
365 <  
366 <  if (!have_tau_barostat) {
367 <    sprintf( painCave.errMsg,
368 <             "NPTf error: If you use the NPTf\n"
369 <             "   integrator, you must set tauBarostat.\n");
370 <    painCave.isFatal = 1;
371 <    simError();
372 <    return -1;
373 <  }    
305 >  return parameters;
306  
375 –  // We need NkBT a lot, so just set it here:
376 –
377 –  NkBT = (double)info->ndf * kB * targetTemp;
378 –
379 –  return 1;
307   }

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