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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 855 by mmeineke, Thu Nov 6 22:01:37 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 +
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;
26 –  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;
33 <  have_tau_barostat = 0;
34 <  have_target_temp = 0;
35 <  have_target_pressure = 0;
77 >  T::resetIntegrator();
78   }
79  
80 < 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];
80 > template<typename T> void NPTf<T>::evolveEtaA() {
81  
82 <  tt2 = tauThermostat * tauThermostat;
52 <  tb2 = tauBarostat * tauBarostat;
82 >  int i, j;
83  
84 <  instaTemp = tStats->getTemperature();
85 <  tStats->getPressureTensor(press);
86 <  instaVol = tStats->getVolume();
87 <  
88 <  // first evolve chi a half step
89 <  
90 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
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 +  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 +      vScale[i][j] = eta[i][j];
126 +
127        if (i == j) {
128 +        vScale[i][j] += chi;
129 +      }
130 +    }
131 +  }
132  
133 <        eta[i][j] += dt2 * instaVol *
134 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
133 >  info->matVecMul3( vScale, vel, sc );
134 > }
135  
136 <        vScale[i][j] = eta[i][j] + chi;
137 <        
138 <      } else {
139 <        
73 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
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 <        vScale[i][j] = eta[i][j];
142 <        
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 <  for( i=0; i<nAtoms; i++ ){
152 <    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]);
151 >  for (j = 0; j < 3; j++)
152 >    myVel[j] = oldVel[3*index + j];
153  
154 <    vel[atomIndex]   = vi[0];
155 <    vel[atomIndex+1] = vi[1];
99 <    vel[atomIndex+2] = vi[2];
154 >  info->matVecMul3( vScale, myVel, sc );
155 > }
156  
157 <    // position whole step    
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 <    ri[0] = pos[atomIndex];
163 <    ri[1] = pos[atomIndex+1];
105 <    ri[2] = pos[atomIndex+2];
162 >  for(j=0; j<3; j++)
163 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
164  
165 <    info->wrapVector(ri);
165 >  info->matVecMul3( eta, rj, sc );
166 > }
167  
168 <    info->matVecMul3( eta, ri, sc );
168 > template<typename T> void NPTf<T>::scaleSimBox( void ){
169  
170 <    pos[atomIndex]   += dt * (vel[atomIndex] + sc[0]);
171 <    pos[atomIndex+1] += dt * (vel[atomIndex+1] + sc[1]);
172 <    pos[atomIndex+2] += dt * (vel[atomIndex+2] + sc[2]);
173 <  
174 <    if( atoms[i]->isDirectional() ){
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  
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
176  
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 –  }
177  
178    // Scale the box after all the positions have been moved:
179  
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  
183 +  bigScale = 1.0;
184 +  smallScale = 1.0;
185 +  offDiagMax = 0.0;
186  
187    for(i=0; i<3; i++){
188      for(j=0; j<3; j++){
# Line 180 | Line 194 | void NPTf::moveA() {
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;
201        // Taylor expansion for the exponential truncated at second order:
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)
206 +          offDiagMax = fabs(scaleMat[i][j]);
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 <  info->getBoxM(hm);
214 <  info->matMul3(hm, scaleMat, hmnew);
215 <  info->setBoxM(hmnew);
216 <  
212 >
213 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
214 >    sprintf( painCave.errMsg,
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"
219 >             "            [%lf\t%lf\t%lf]\n",
220 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
221 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
222 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
223 >    painCave.isFatal = 1;
224 >    simError();
225 >  } else if (offDiagMax > 0.01) {
226 >    sprintf( painCave.errMsg,
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"
231 >             "            [%lf\t%lf\t%lf]\n",
232 >             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
233 >             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
234 >             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
235 >    painCave.isFatal = 1;
236 >    simError();
237 >  } else {
238 >    info->getBoxM(hm);
239 >    info->matMul3(hm, scaleMat, hmnew);
240 >    info->setBoxM(hmnew);
241 >  }
242   }
243  
244 < void NPTf::moveB( void ){
245 <  int i,j, k;
246 <  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;
244 > template<typename T> bool NPTf<T>::etaConverged() {
245 >  int i;
246 >  double diffEta, sumEta;
247  
248 <  instaTemp = tStats->getTemperature();
249 <  tStats->getPressureTensor(press);
250 <  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) {
248 >  sumEta = 0;
249 >  for(i = 0; i < 3; i++)
250 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
251  
252 <        eta[i][j] += dt2 * instaVol *
226 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
252 >  diffEta = sqrt( sumEta / 3.0 );
253  
254 <        vScale[i][j] = eta[i][j] + chi;
255 <        
230 <      } else {
231 <        
232 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
254 >  return ( diffEta <= etaTolerance );
255 > }
256  
257 <        vScale[i][j] = eta[i][j];
235 <        
236 <      }
237 <    }
238 <  }
257 > template<typename T> double NPTf<T>::getConservedQuantity(void){
258  
259 <  for( i=0; i<nAtoms; i++ ){
260 <    atomIndex = i * 3;
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 <    // 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]);
268 >  totalEnergy = tStats->getTotalE();
269  
270 <    vel[atomIndex]   = vi[0];
271 <    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 < }
270 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
271 >    (2.0 * eConvert);
272  
273 < 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 <  }
273 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
274  
275 <  if (!have_target_pressure) {
276 <    sprintf( painCave.errMsg,
277 <             "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 <  }    
275 >  info->transposeMat3(eta, a);
276 >  info->matMul3(a, eta, b);
277 >  trEta = info->matTrace3(b);
278  
279 <  // We must set tauBarostat.
280 <  
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 <  }    
279 >  barostat_kinetic = NkBT * tb2 * trEta /
280 >    (2.0 * eConvert);
281  
282 <  // We need NkBT a lot, so just set it here:
282 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
283 >    eConvert;
284  
285 <  NkBT = (double)info->ndf * kB * targetTemp;
285 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
286 >    barostat_kinetic + barostat_potential;
287  
288 <  return 1;
288 >  return conservedQuantity;
289 >
290   }
291 +
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 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
298 +  parameters += buffer;
299 +
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 +  }
304 +
305 +  return parameters;
306 +
307 + }

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