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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 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 1 | Line 1
1 + #include <math.h>
2 +
3 + #include "MatVec3.h"
4   #include "Atom.hpp"
5   #include "SRI.hpp"
6   #include "AbstractClasses.hpp"
# Line 6 | Line 9
9   #include "Thermo.hpp"
10   #include "ReadWrite.hpp"
11   #include "Integrator.hpp"
12 < #include "simError.h"
12 > #include "simError.h"
13  
14 + #ifdef IS_MPI
15 + #include "mpiSimulation.hpp"
16 + #endif
17  
18   // Basic non-isotropic thermostating and barostating via the Melchionna
19   // modification of the Hoover algorithm:
20   //
21   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
22 < //       Molec. Phys., 78, 533.
22 > //       Molec. Phys., 78, 533.
23   //
24   //           and
25 < //
25 > //
26   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
27  
28 < NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
29 <  Integrator( theInfo, the_ff )
28 > template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
29 >  T( theInfo, the_ff )
30   {
31 +  GenericData* data;
32 +  DoubleArrayData * etaValue;
33 +  vector<double> etaArray;
34 +  int i,j;
35 +
36 +  for(i = 0; i < 3; i++){
37 +    for (j = 0; j < 3; j++){
38 +
39 +      eta[i][j] = 0.0;
40 +      oldEta[i][j] = 0.0;
41 +    }
42 +  }
43 +
44 +
45 +  if( theInfo->useInitXSstate ){
46 +    // retrieve eta array from simInfo if it exists
47 +    data = info->getProperty(ETAVALUE_ID);
48 +    if(data){
49 +      etaValue = dynamic_cast<DoubleArrayData*>(data);
50 +      
51 +      if(etaValue){
52 +        etaArray = etaValue->getData();
53 +        
54 +        for(i = 0; i < 3; i++){
55 +          for (j = 0; j < 3; j++){
56 +            eta[i][j] = etaArray[3*i+j];
57 +            oldEta[i][j] = eta[i][j];
58 +          }
59 +        }
60 +      }
61 +    }
62 +  }
63 +
64 + }
65 +
66 + template<typename T> NPTf<T>::~NPTf() {
67 +
68 +  // empty for now
69 + }
70 +
71 + template<typename T> void NPTf<T>::resetIntegrator() {
72 +
73    int i, j;
26 –  chi = 0.0;
74  
75 <  for(i = 0; i < 3; i++)
76 <    for (j = 0; j < 3; j_++)
75 >  for(i = 0; i < 3; i++)
76 >    for (j = 0; j < 3; j++)
77        eta[i][j] = 0.0;
78  
79 <  have_tau_thermostat = 0;
33 <  have_tau_barostat = 0;
34 <  have_target_temp = 0;
35 <  have_target_pressure = 0;
79 >  T::resetIntegrator();
80   }
81  
82 < 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];
82 > template<typename T> void NPTf<T>::evolveEtaA() {
83  
84 <  tt2 = tauThermostat * tauThermostat;
52 <  tb2 = tauBarostat * tauBarostat;
84 >  int i, j;
85  
86 <  instaTemp = tStats->getTemperature();
87 <  tStats->getPressureTensor(press);
88 <  instaVol = tStats->getVolume();
89 <  
90 <  // first evolve chi a half step
91 <  
92 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
86 >  for(i = 0; i < 3; i ++){
87 >    for(j = 0; j < 3; j++){
88 >      if( i == j)
89 >        eta[i][j] += dt2 *  instaVol *
90 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
91 >      else
92 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
93 >    }
94 >  }
95  
96 <  for (i = 0; i < 3; i++ ) {
97 <    for (j = 0; j < 3; j++ ) {
98 <      if (i == j) {
96 >  for(i = 0; i < 3; i++)
97 >    for (j = 0; j < 3; j++)
98 >      oldEta[i][j] = eta[i][j];
99 > }
100  
101 <        eta[i][j] += dt2 * instaVol *
67 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
101 > template<typename T> void NPTf<T>::evolveEtaB() {
102  
103 <        vScale[i][j] = eta[i][j] + chi;
104 <        
103 >  int i,j;
104 >
105 >  for(i = 0; i < 3; i++)
106 >    for (j = 0; j < 3; j++)
107 >      prevEta[i][j] = eta[i][j];
108 >
109 >  for(i = 0; i < 3; i ++){
110 >    for(j = 0; j < 3; j++){
111 >      if( i == j) {
112 >        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
113 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
114        } else {
115 <        
116 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
115 >        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
116 >      }
117 >    }
118 >  }
119 > }
120  
121 <        vScale[i][j] = eta[i][j];
122 <        
121 > template<typename T> void NPTf<T>::calcVelScale(void){
122 >  int i,j;
123 >
124 >  for (i = 0; i < 3; i++ ) {
125 >    for (j = 0; j < 3; j++ ) {
126 >      vScale[i][j] = eta[i][j];
127 >
128 >      if (i == j) {
129 >        vScale[i][j] += chi;
130        }
131      }
132    }
133 + }
134  
135 <  for( i=0; i<nAtoms; i++ ){
136 <    atomIndex = i * 3;
137 <    aMatIndex = i * 9;
138 <    
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]);
135 > template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
136 >
137 >  matVecMul3( vScale, vel, sc );
138 > }
139  
140 <    vel[atomIndex] = vi[0]
141 <    vel[atomIndex+1] = vi[1];
142 <    vel[atomIndex+2] = vi[2];
140 > template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
141 >  int j;
142 >  double myVel[3];
143 >  double vScale[3][3];
144  
145 <    // position whole step    
145 >  for (j = 0; j < 3; j++)
146 >    myVel[j] = oldVel[3*index + j];
147  
148 <    ri[0] = pos[atomIndex];
149 <    ri[1] = pos[atomIndex+1];
105 <    ri[2] = pos[atomIndex+2];
148 >  matVecMul3( vScale, myVel, sc );
149 > }
150  
151 <    info->wrapVector(ri);
151 > template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
152 >                                               int index, double sc[3]){
153 >  int j;
154 >  double rj[3];
155  
156 <    info->matVecMul3( eta, ri, sc );
156 >  for(j=0; j<3; j++)
157 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
158  
159 <    pos[atomIndex] += dt * (vel[atomIndex] + sc[0]);
160 <    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() ){
159 >  matVecMul3( eta, rj, sc );
160 > }
161  
162 <      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
162 > template<typename T> void NPTf<T>::scaleSimBox( void ){
163  
164 <      ji[0] = dAtom->getJx();
165 <      ji[1] = dAtom->getJy();
166 <      ji[2] = dAtom->getJz();
167 <      
168 <      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 <  }
164 >  int i,j,k;
165 >  double scaleMat[3][3];
166 >  double eta2ij;
167 >  double bigScale, smallScale, offDiagMax;
168 >  double hm[3][3], hmnew[3][3];
169  
170 +
171 +
172    // Scale the box after all the positions have been moved:
173  
174    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
175    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
176  
177 +  bigScale = 1.0;
178 +  smallScale = 1.0;
179 +  offDiagMax = 0.0;
180  
181    for(i=0; i<3; i++){
182      for(j=0; j<3; j++){
# Line 180 | Line 188 | void NPTf::moveA() {
188        for(k=0; k<3; k++){
189          eta2ij += eta[i][k] * eta[k][j];
190        }
191 <      
191 >
192        scaleMat[i][j] = 0.0;
193        // identity matrix (see above):
194        if (i == j) scaleMat[i][j] = 1.0;
195        // Taylor expansion for the exponential truncated at second order:
196        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
197  
198 +      if (i != j)
199 +        if (fabs(scaleMat[i][j]) > offDiagMax)
200 +          offDiagMax = fabs(scaleMat[i][j]);
201      }
202 +
203 +    if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
204 +    if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
205    }
206 <  
207 <  info->getBoxM(hm);
208 <  info->matMul3(hm, scaleMat, hmnew);
209 <  info->setBoxM(hmnew);
210 <  
206 >
207 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
208 >    sprintf( painCave.errMsg,
209 >             "NPTf error: Attempting a Box scaling of more than 1 percent.\n"
210 >             " Check your tauBarostat, as it is probably too small!\n\n"
211 >             " scaleMat = [%lf\t%lf\t%lf]\n"
212 >             "            [%lf\t%lf\t%lf]\n"
213 >             "            [%lf\t%lf\t%lf]\n",
214 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
215 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
216 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
217 >    painCave.isFatal = 1;
218 >    simError();
219 >  } else if (offDiagMax > 0.01) {
220 >    sprintf( painCave.errMsg,
221 >             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
222 >             " Check your tauBarostat, as it is probably too small!\n\n"
223 >             " scaleMat = [%lf\t%lf\t%lf]\n"
224 >             "            [%lf\t%lf\t%lf]\n"
225 >             "            [%lf\t%lf\t%lf]\n",
226 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
227 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
228 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
229 >    painCave.isFatal = 1;
230 >    simError();
231 >  } else {
232 >    info->getBoxM(hm);
233 >    matMul3(hm, scaleMat, hmnew);
234 >    info->setBoxM(hmnew);
235 >  }
236   }
237  
238 < void NPTf::moveB( void ){
239 <  int i,j, k;
240 <  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;
238 > template<typename T> bool NPTf<T>::etaConverged() {
239 >  int i;
240 >  double diffEta, sumEta;
241  
242 <  instaTemp = tStats->getTemperature();
243 <  tStats->getPressureTensor(press);
244 <  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) {
242 >  sumEta = 0;
243 >  for(i = 0; i < 3; i++)
244 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
245  
246 <        eta[i][j] += dt2 * instaVol *
226 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
246 >  diffEta = sqrt( sumEta / 3.0 );
247  
248 <        vScale[i][j] = eta[i][j] + chi;
249 <        
230 <      } else {
231 <        
232 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
248 >  return ( diffEta <= etaTolerance );
249 > }
250  
251 <        vScale[i][j] = eta[i][j];
235 <        
236 <      }
237 <    }
238 <  }
251 > template<typename T> double NPTf<T>::getConservedQuantity(void){
252  
253 <  for( i=0; i<nAtoms; i++ ){
254 <    atomIndex = i * 3;
253 >  double conservedQuantity;
254 >  double totalEnergy;
255 >  double thermostat_kinetic;
256 >  double thermostat_potential;
257 >  double barostat_kinetic;
258 >  double barostat_potential;
259 >  double trEta;
260 >  double a[3][3], b[3][3];
261  
262 <    // 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]);
262 >  totalEnergy = tStats->getTotalE();
263  
264 <    vel[atomIndex] = vi[0]
265 <    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 < }
264 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
265 >    (2.0 * eConvert);
266  
267 < 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 <  }
267 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
268  
269 <  if (!have_target_pressure) {
270 <    sprintf( painCave.errMsg,
271 <             "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 <  }    
269 >  transposeMat3(eta, a);
270 >  matMul3(a, eta, b);
271 >  trEta = matTrace3(b);
272  
273 <  // We must set tauBarostat.
274 <  
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 <  }    
273 >  barostat_kinetic = NkBT * tb2 * trEta /
274 >    (2.0 * eConvert);
275  
276 <  // We need NkBT a lot, so just set it here:
276 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
277 >    eConvert;
278  
279 <  NkBT = (double)info->ndf * kB * targetTemp;
279 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
280 >    barostat_kinetic + barostat_potential;
281  
282 <  return 1;
282 >  return conservedQuantity;
283 >
284   }
285 +
286 + template<typename T> string NPTf<T>::getAdditionalParameters(void){
287 +  string parameters;
288 +  const int BUFFERSIZE = 2000; // size of the read buffer
289 +  char buffer[BUFFERSIZE];
290 +
291 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
292 +  parameters += buffer;
293 +
294 +  for(int i = 0; i < 3; i++){
295 +    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
296 +    parameters += buffer;
297 +  }
298 +
299 +  return parameters;
300 +
301 + }

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