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root/group/trunk/OOPSE/libmdtools/NPTf.cpp
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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 857 by mmeineke, Fri Nov 7 17:09:48 2003 UTC

# Line 1 | Line 1
1 + #include <math.h>
2 +
3   #include "Atom.hpp"
4   #include "SRI.hpp"
5   #include "AbstractClasses.hpp"
# Line 6 | 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 < NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
28 <  Integrator( theInfo, the_ff )
27 > template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
28 >  T( theInfo, the_ff )
29   {
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++){
37 +
38 +      eta[i][j] = 0.0;
39 +      oldEta[i][j] = 0.0;
40 +    }
41 +  }
42 +
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> NPTf<T>::~NPTf() {
66 +
67 +  // empty for now
68 + }
69 +
70 + template<typename T> void NPTf<T>::resetIntegrator() {
71 +
72    int i, j;
26 –  chi = 0.0;
73  
74 <  for(i = 0; i < 3; i++)
75 <    for (j = 0; j < 3; j_++)
74 >  for(i = 0; i < 3; i++)
75 >    for (j = 0; j < 3; j++)
76        eta[i][j] = 0.0;
77  
78 <  have_tau_thermostat = 0;
33 <  have_tau_barostat = 0;
34 <  have_target_temp = 0;
35 <  have_target_pressure = 0;
78 >  T::resetIntegrator();
79   }
80  
81 < 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];
81 > template<typename T> void NPTf<T>::evolveEtaA() {
82  
83 <  tt2 = tauThermostat * tauThermostat;
52 <  tb2 = tauBarostat * tauBarostat;
83 >  int i, j;
84  
85 <  instaTemp = tStats->getTemperature();
86 <  tStats->getPressureTensor(press);
87 <  instaVol = tStats->getVolume();
88 <  
89 <  // first evolve chi a half step
90 <  
91 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
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 <  for (i = 0; i < 3; i++ ) {
96 <    for (j = 0; j < 3; j++ ) {
97 <      if (i == j) {
95 >  for(i = 0; i < 3; i++)
96 >    for (j = 0; j < 3; j++)
97 >      oldEta[i][j] = eta[i][j];
98 > }
99  
100 <        eta[i][j] += dt2 * instaVol *
67 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
100 > template<typename T> void NPTf<T>::evolveEtaB() {
101  
102 <        vScale[i][j] = eta[i][j] + chi;
103 <        
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 <        
115 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
114 >        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
115 >      }
116 >    }
117 >  }
118 > }
119  
120 <        vScale[i][j] = eta[i][j];
121 <        
120 > template<typename T> void NPTf<T>::calcVelScale(void){
121 >  int i,j;
122 >
123 >  for (i = 0; i < 3; i++ ) {
124 >    for (j = 0; j < 3; j++ ) {
125 >      vScale[i][j] = eta[i][j];
126 >
127 >      if (i == j) {
128 >        vScale[i][j] += chi;
129        }
130      }
131    }
132 + }
133  
134 <  for( i=0; i<nAtoms; i++ ){
135 <    atomIndex = i * 3;
136 <    aMatIndex = i * 9;
137 <    
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]);
134 > template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
135 >
136 >  info->matVecMul3( vScale, vel, sc );
137 > }
138  
139 <    vel[atomIndex] = vi[0]
140 <    vel[atomIndex+1] = vi[1];
141 <    vel[atomIndex+2] = vi[2];
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 <    // position whole step    
144 >  for (j = 0; j < 3; j++)
145 >    myVel[j] = oldVel[3*index + j];
146  
147 <    ri[0] = pos[atomIndex];
148 <    ri[1] = pos[atomIndex+1];
105 <    ri[2] = pos[atomIndex+2];
147 >  info->matVecMul3( vScale, myVel, sc );
148 > }
149  
150 <    info->wrapVector(ri);
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 <    info->matVecMul3( eta, ri, sc );
155 >  for(j=0; j<3; j++)
156 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
157  
158 <    pos[atomIndex] += dt * (vel[atomIndex] + sc[0]);
159 <    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() ){
158 >  info->matVecMul3( eta, rj, sc );
159 > }
160  
161 <      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
161 > template<typename T> void NPTf<T>::scaleSimBox( void ){
162  
163 <      ji[0] = dAtom->getJx();
164 <      ji[1] = dAtom->getJy();
165 <      ji[2] = dAtom->getJz();
166 <      
167 <      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 <  }
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  
169 +
170 +
171    // Scale the box after all the positions have been moved:
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  
176 +  bigScale = 1.0;
177 +  smallScale = 1.0;
178 +  offDiagMax = 0.0;
179  
180    for(i=0; i<3; i++){
181      for(j=0; j<3; j++){
# Line 180 | Line 187 | void NPTf::moveA() {
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;
194        // Taylor expansion for the exponential truncated at second order:
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)
199 +          offDiagMax = fabs(scaleMat[i][j]);
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 <  info->getBoxM(hm);
207 <  info->matMul3(hm, scaleMat, hmnew);
208 <  info->setBoxM(hmnew);
209 <  
205 >
206 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
207 >    sprintf( painCave.errMsg,
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"
212 >             "            [%lf\t%lf\t%lf]\n",
213 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
214 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
215 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
216 >    painCave.isFatal = 1;
217 >    simError();
218 >  } else if (offDiagMax > 0.01) {
219 >    sprintf( painCave.errMsg,
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"
224 >             "            [%lf\t%lf\t%lf]\n",
225 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
226 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
227 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
228 >    painCave.isFatal = 1;
229 >    simError();
230 >  } else {
231 >    info->getBoxM(hm);
232 >    info->matMul3(hm, scaleMat, hmnew);
233 >    info->setBoxM(hmnew);
234 >  }
235   }
236  
237 < void NPTf::moveB( void ){
238 <  int i,j, k;
239 <  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;
237 > template<typename T> bool NPTf<T>::etaConverged() {
238 >  int i;
239 >  double diffEta, sumEta;
240  
241 <  instaTemp = tStats->getTemperature();
242 <  tStats->getPressureTensor(press);
243 <  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) {
241 >  sumEta = 0;
242 >  for(i = 0; i < 3; i++)
243 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
244  
245 <        eta[i][j] += dt2 * instaVol *
226 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
245 >  diffEta = sqrt( sumEta / 3.0 );
246  
247 <        vScale[i][j] = eta[i][j] + chi;
248 <        
230 <      } else {
231 <        
232 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
247 >  return ( diffEta <= etaTolerance );
248 > }
249  
250 <        vScale[i][j] = eta[i][j];
235 <        
236 <      }
237 <    }
238 <  }
250 > template<typename T> double NPTf<T>::getConservedQuantity(void){
251  
252 <  for( i=0; i<nAtoms; i++ ){
253 <    atomIndex = i * 3;
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 <    // 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]);
261 >  totalEnergy = tStats->getTotalE();
262  
263 <    vel[atomIndex] = vi[0]
264 <    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 < }
263 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
264 >    (2.0 * eConvert);
265  
266 < 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 <  }
266 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
267  
268 <  if (!have_target_pressure) {
269 <    sprintf( painCave.errMsg,
270 <             "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 <  }    
268 >  info->transposeMat3(eta, a);
269 >  info->matMul3(a, eta, b);
270 >  trEta = info->matTrace3(b);
271  
272 <  // We must set tauBarostat.
273 <  
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 <  }    
272 >  barostat_kinetic = NkBT * tb2 * trEta /
273 >    (2.0 * eConvert);
274  
275 <  // We need NkBT a lot, so just set it here:
275 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
276 >    eConvert;
277  
278 <  NkBT = (double)info->ndf * kB * targetTemp;
278 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
279 >    barostat_kinetic + barostat_potential;
280  
281 <  return 1;
281 >  return conservedQuantity;
282 >
283   }
284 +
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 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
291 +  parameters += buffer;
292 +
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 +  }
297 +
298 +  return parameters;
299 +
300 + }

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