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root/group/trunk/OOPSE/libmdtools/NPTf.cpp
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Comparing trunk/OOPSE/libmdtools/NPTf.cpp (file contents):
Revision 590 by mmeineke, Thu Jul 10 22:15:53 2003 UTC vs.
Revision 853 by mmeineke, Thu Nov 6 19:11:38 2003 UTC

# Line 1 | Line 1
1 + #include <math.h>
2   #include "Atom.hpp"
3   #include "SRI.hpp"
4   #include "AbstractClasses.hpp"
# Line 6 | 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 < 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 +  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 +    // retrieve eta array from simInfo if it exists
43 +    data = info->getProperty(ETAVALUE_ID);
44 +    if(data){
45 +      etaValue = dynamic_cast<DoubleArrayData*>(data);
46 +
47 +      if(etaValue){
48 +        etaArray = etaValue->getData();
49 +
50 +        for(i = 0; i < 3; i++){
51 +          for (j = 0; j < 3; j++){
52 +            eta[i][j] = etaArray[3*i+j];
53 +            oldEta[i][j] = eta[i][j];
54 +          }
55 +        }
56 +
57 +      }
58 +    }
59 +
60 + }
61 +
62 + template<typename T> NPTf<T>::~NPTf() {
63 +
64 +  // empty for now
65 + }
66 +
67 + template<typename T> void NPTf<T>::resetIntegrator() {
68 +
69    int i, j;
26 –  chi = 0.0;
70  
71 <  for(i = 0; i < 3; i++)
72 <    for (j = 0; j < 3; j++)
71 >  for(i = 0; i < 3; i++)
72 >    for (j = 0; j < 3; j++)
73        eta[i][j] = 0.0;
74  
75 <  have_tau_thermostat = 0;
33 <  have_tau_barostat = 0;
34 <  have_target_temp = 0;
35 <  have_target_pressure = 0;
75 >  T::resetIntegrator();
76   }
77  
78 < void NPTf::moveA() {
39 <  
40 <  int i,j,k;
41 <  int atomIndex, aMatIndex;
42 <  DirectionalAtom* dAtom;
43 <  double Tb[3];
44 <  double ji[3];
45 <  double ri[3], vi[3], sc[3];
46 <  double instaTemp, instaVol;
47 <  double tt2, tb2, eta2ij;
48 <  double angle;
49 <  double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3];
78 > template<typename T> void NPTf<T>::evolveEtaA() {
79  
80 <  tt2 = tauThermostat * tauThermostat;
52 <  tb2 = tauBarostat * tauBarostat;
80 >  int i, j;
81  
82 <  instaTemp = tStats->getTemperature();
83 <  tStats->getPressureTensor(press);
84 <  instaVol = tStats->getVolume();
85 <  
86 <  // first evolve chi a half step
87 <  
88 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
82 >  for(i = 0; i < 3; i ++){
83 >    for(j = 0; j < 3; j++){
84 >      if( i == j)
85 >        eta[i][j] += dt2 *  instaVol *
86 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
87 >      else
88 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
89 >    }
90 >  }
91  
92 +  for(i = 0; i < 3; i++)
93 +    for (j = 0; j < 3; j++)
94 +      oldEta[i][j] = eta[i][j];
95 + }
96 +
97 + template<typename T> void NPTf<T>::evolveEtaB() {
98 +
99 +  int i,j;
100 +
101 +  for(i = 0; i < 3; i++)
102 +    for (j = 0; j < 3; j++)
103 +      prevEta[i][j] = eta[i][j];
104 +
105 +  for(i = 0; i < 3; i ++){
106 +    for(j = 0; j < 3; j++){
107 +      if( i == j) {
108 +        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
109 +          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
110 +      } else {
111 +        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
112 +      }
113 +    }
114 +  }
115 + }
116 +
117 + template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
118 +  int i,j;
119 +  double vScale[3][3];
120 +
121    for (i = 0; i < 3; i++ ) {
122      for (j = 0; j < 3; j++ ) {
123 +      vScale[i][j] = eta[i][j];
124 +
125        if (i == j) {
126 +        vScale[i][j] += chi;
127 +      }
128 +    }
129 +  }
130  
131 <        eta[i][j] += dt2 * instaVol *
132 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
131 >  info->matVecMul3( vScale, vel, sc );
132 > }
133  
134 <        vScale[i][j] = eta[i][j] + chi;
135 <        
136 <      } else {
137 <        
73 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
134 > template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
135 >  int i,j;
136 >  double myVel[3];
137 >  double vScale[3][3];
138  
139 <        vScale[i][j] = eta[i][j];
140 <        
139 >  for (i = 0; i < 3; i++ ) {
140 >    for (j = 0; j < 3; j++ ) {
141 >      vScale[i][j] = eta[i][j];
142 >
143 >      if (i == j) {
144 >        vScale[i][j] += chi;
145        }
146      }
147    }
148  
149 <  for( i=0; i<nAtoms; i++ ){
150 <    atomIndex = i * 3;
83 <    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]);
149 >  for (j = 0; j < 3; j++)
150 >    myVel[j] = oldVel[3*index + j];
151  
152 <    vel[atomIndex]   = vi[0];
153 <    vel[atomIndex+1] = vi[1];
99 <    vel[atomIndex+2] = vi[2];
152 >  info->matVecMul3( vScale, myVel, sc );
153 > }
154  
155 <    // position whole step    
155 > template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
156 >                                               int index, double sc[3]){
157 >  int j;
158 >  double rj[3];
159  
160 <    ri[0] = pos[atomIndex];
161 <    ri[1] = pos[atomIndex+1];
105 <    ri[2] = pos[atomIndex+2];
160 >  for(j=0; j<3; j++)
161 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
162  
163 <    info->wrapVector(ri);
163 >  info->matVecMul3( eta, rj, sc );
164 > }
165  
166 <    info->matVecMul3( eta, ri, sc );
166 > template<typename T> void NPTf<T>::scaleSimBox( void ){
167  
168 <    pos[atomIndex]   += dt * (vel[atomIndex] + sc[0]);
169 <    pos[atomIndex+1] += dt * (vel[atomIndex+1] + sc[1]);
170 <    pos[atomIndex+2] += dt * (vel[atomIndex+2] + sc[2]);
171 <  
172 <    if( atoms[i]->isDirectional() ){
168 >  int i,j,k;
169 >  double scaleMat[3][3];
170 >  double eta2ij;
171 >  double bigScale, smallScale, offDiagMax;
172 >  double hm[3][3], hmnew[3][3];
173  
117 –      dAtom = (DirectionalAtom *)atoms[i];
118 –          
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
174  
129 –      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 –  }
175  
176    // Scale the box after all the positions have been moved:
177  
178    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
179    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
180  
181 +  bigScale = 1.0;
182 +  smallScale = 1.0;
183 +  offDiagMax = 0.0;
184  
185    for(i=0; i<3; i++){
186      for(j=0; j<3; j++){
# Line 180 | Line 192 | void NPTf::moveA() {
192        for(k=0; k<3; k++){
193          eta2ij += eta[i][k] * eta[k][j];
194        }
195 <      
195 >
196        scaleMat[i][j] = 0.0;
197        // identity matrix (see above):
198        if (i == j) scaleMat[i][j] = 1.0;
199        // Taylor expansion for the exponential truncated at second order:
200        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
201  
202 +      if (i != j)
203 +        if (fabs(scaleMat[i][j]) > offDiagMax)
204 +          offDiagMax = fabs(scaleMat[i][j]);
205      }
206 +
207 +    if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
208 +    if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
209    }
210 <  
211 <  info->getBoxM(hm);
212 <  info->matMul3(hm, scaleMat, hmnew);
213 <  info->setBoxM(hmnew);
214 <  
210 >
211 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
212 >    sprintf( painCave.errMsg,
213 >             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
214 >             " Check your tauBarostat, as it is probably too small!\n\n"
215 >             " scaleMat = [%lf\t%lf\t%lf]\n"
216 >             "            [%lf\t%lf\t%lf]\n"
217 >             "            [%lf\t%lf\t%lf]\n",
218 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
219 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
220 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
221 >    painCave.isFatal = 1;
222 >    simError();
223 >  } else if (offDiagMax > 0.01) {
224 >    sprintf( painCave.errMsg,
225 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
226 >             " Check your tauBarostat, as it is probably too small!\n\n"
227 >             " scaleMat = [%lf\t%lf\t%lf]\n"
228 >             "            [%lf\t%lf\t%lf]\n"
229 >             "            [%lf\t%lf\t%lf]\n",
230 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
231 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
232 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
233 >    painCave.isFatal = 1;
234 >    simError();
235 >  } else {
236 >    info->getBoxM(hm);
237 >    info->matMul3(hm, scaleMat, hmnew);
238 >    info->setBoxM(hmnew);
239 >  }
240   }
241  
242 < void NPTf::moveB( void ){
243 <  int i,j, k;
244 <  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;
242 > template<typename T> bool NPTf<T>::etaConverged() {
243 >  int i;
244 >  double diffEta, sumEta;
245  
246 <  instaTemp = tStats->getTemperature();
247 <  tStats->getPressureTensor(press);
248 <  instaVol = tStats->getVolume();
216 <  
217 <  // first evolve chi a half step
218 <  
219 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
220 <  
221 <  for (i = 0; i < 3; i++ ) {
222 <    for (j = 0; j < 3; j++ ) {
223 <      if (i == j) {
246 >  sumEta = 0;
247 >  for(i = 0; i < 3; i++)
248 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
249  
250 <        eta[i][j] += dt2 * instaVol *
226 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
250 >  diffEta = sqrt( sumEta / 3.0 );
251  
252 <        vScale[i][j] = eta[i][j] + chi;
253 <        
230 <      } else {
231 <        
232 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
252 >  return ( diffEta <= etaTolerance );
253 > }
254  
255 <        vScale[i][j] = eta[i][j];
235 <        
236 <      }
237 <    }
238 <  }
255 > template<typename T> double NPTf<T>::getConservedQuantity(void){
256  
257 <  for( i=0; i<nAtoms; i++ ){
258 <    atomIndex = i * 3;
257 >  double conservedQuantity;
258 >  double totalEnergy;
259 >  double thermostat_kinetic;
260 >  double thermostat_potential;
261 >  double barostat_kinetic;
262 >  double barostat_potential;
263 >  double trEta;
264 >  double a[3][3], b[3][3];
265  
266 <    // velocity half step
244 <    
245 <    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]);
266 >  totalEnergy = tStats->getTotalE();
267  
268 <    vel[atomIndex]   = vi[0];
269 <    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 < }
268 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
269 >    (2.0 * eConvert);
270  
271 < int NPTf::readyCheck() {
290 <
291 <  // First check to see if we have a target temperature.
292 <  // Not having one is fatal.
293 <  
294 <  if (!have_target_temp) {
295 <    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 <  }
271 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
272  
273 <  if (!have_target_pressure) {
274 <    sprintf( painCave.errMsg,
275 <             "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 <  }
313 <  
314 <  // We must set tauThermostat.
315 <  
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 <  }    
273 >  info->transposeMat3(eta, a);
274 >  info->matMul3(a, eta, b);
275 >  trEta = info->matTrace3(b);
276  
277 <  // We must set tauBarostat.
278 <  
327 <  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 <  }    
277 >  barostat_kinetic = NkBT * tb2 * trEta /
278 >    (2.0 * eConvert);
279  
280 <  // We need NkBT a lot, so just set it here:
280 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
281 >    eConvert;
282  
283 <  NkBT = (double)info->ndf * kB * targetTemp;
283 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
284 >    barostat_kinetic + barostat_potential;
285  
286 <  return 1;
286 >  return conservedQuantity;
287 >
288   }
289 +
290 + template<typename T> string NPTf<T>::getAdditionalParameters(void){
291 +  string parameters;
292 +  const int BUFFERSIZE = 2000; // size of the read buffer
293 +  char buffer[BUFFERSIZE];
294 +
295 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
296 +  parameters += buffer;
297 +
298 +  for(int i = 0; i < 3; i++){
299 +    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
300 +    parameters += buffer;
301 +  }
302 +
303 +  return parameters;
304 +
305 + }

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