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root/group/trunk/OOPSE/libmdtools/NPTf.cpp
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Comparing trunk/OOPSE/libmdtools/NPTf.cpp (file contents):
Revision 617 by gezelter, Tue Jul 15 19:56:08 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <math.h>
2 >
3 > #include "MatVec3.h"
4   #include "Atom.hpp"
5   #include "SRI.hpp"
6   #include "AbstractClasses.hpp"
# Line 7 | 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 <  int i, j;
32 <  chi = 0.0;
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++)
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 <  have_tau_thermostat = 0;
45 <  have_tau_barostat = 0;
46 <  have_target_temp = 0;
47 <  have_target_pressure = 0;
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 < void NPTf::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];
66 > template<typename T> NPTf<T>::~NPTf() {
67  
68 <  double rj[3];
69 <  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;
68 >  // empty for now
69 > }
70  
71 <  tt2 = tauThermostat * tauThermostat;
57 <  tb2 = tauBarostat * tauBarostat;
71 > template<typename T> void NPTf<T>::resetIntegrator() {
72  
73 <  instaTemp = tStats->getTemperature();
60 <  tStats->getPressureTensor(press);
61 <  instaVol = tStats->getVolume();
62 <  
63 <  // first evolve chi a half step
64 <  
65 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
73 >  int i, j;
74  
75 <  for (i = 0; i < 3; i++ ) {
76 <    for (j = 0; j < 3; j++ ) {
77 <      if (i == j) {
78 <        
79 <        eta[i][j] += dt2 * instaVol *
80 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
81 <        
82 <        vScale[i][j] = eta[i][j] + chi;
83 <        
84 <      } else {
85 <        
75 >  for(i = 0; i < 3; i++)
76 >    for (j = 0; j < 3; j++)
77 >      eta[i][j] = 0.0;
78 >
79 >  T::resetIntegrator();
80 > }
81 >
82 > template<typename T> void NPTf<T>::evolveEtaA() {
83 >
84 >  int i, j;
85 >
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 <        vScale[i][j] = eta[i][j];
97 <        
96 >  for(i = 0; i < 3; i++)
97 >    for (j = 0; j < 3; j++)
98 >      oldEta[i][j] = eta[i][j];
99 > }
100 >
101 > template<typename T> void NPTf<T>::evolveEtaB() {
102 >
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 >        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
116        }
117      }
118    }
119 + }
120  
121 <  for( i=0; i<nAtoms; i++ ){
121 > template<typename T> void NPTf<T>::calcVelScale(void){
122 >  int i,j;
123  
124 <    atoms[i]->getVel( vel );
125 <    atoms[i]->getPos( pos );
126 <    atoms[i]->getFrc( frc );
124 >  for (i = 0; i < 3; i++ ) {
125 >    for (j = 0; j < 3; j++ ) {
126 >      vScale[i][j] = eta[i][j];
127  
128 <    mass = atoms[i]->getMass();
129 <    
130 <    // velocity half step
95 <        
96 <    info->matVecMul3( vScale, vel, sc );
97 <    
98 <    for (j = 0; j < 3; j++) {
99 <      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
100 <      rj[j] = pos[j];
128 >      if (i == j) {
129 >        vScale[i][j] += chi;
130 >      }
131      }
132 +  }
133 + }
134  
135 <    atoms[i]->setVel( vel );
135 > template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
136 >
137 >  matVecMul3( vScale, vel, sc );
138 > }
139  
140 <    // position whole step    
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 <    info->wrapVector(rj);
145 >  for (j = 0; j < 3; j++)
146 >    myVel[j] = oldVel[3*index + j];
147  
148 <    info->matVecMul3( eta, rj, sc );
148 >  matVecMul3( vScale, myVel, sc );
149 > }
150  
151 <    for (j = 0; j < 3; j++ )
152 <      pos[j] += dt * (vel[j] + sc[j]);
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 <    atoms[i]->setPos( pos );
157 <  
116 <    if( atoms[i]->isDirectional() ){
156 >  for(j=0; j<3; j++)
157 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
158  
159 <      dAtom = (DirectionalAtom *)atoms[i];
160 <          
120 <      // get and convert the torque to body frame
121 <      
122 <      dAtom->getTrq( Tb );
123 <      dAtom->lab2Body( Tb );
124 <      
125 <      // get the angular momentum, and propagate a half step
159 >  matVecMul3( eta, rj, sc );
160 > }
161  
162 <      dAtom->getJ( ji );
162 > template<typename T> void NPTf<T>::scaleSimBox( void ){
163  
164 <      for (j=0; j < 3; j++)
165 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
166 <      
167 <      // use the angular velocities to propagate the rotation matrix a
168 <      // full time step
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  
135 –      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 );
170  
171 <      // 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 <  
171 >
172    // Scale the box after all the positions have been moved:
173 <  
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 <  
176 >
177    bigScale = 1.0;
178    smallScale = 1.0;
179    offDiagMax = 0.0;
180 <  
180 >
181    for(i=0; i<3; i++){
182      for(j=0; j<3; j++){
183 <      
183 >
184        // Calculate the matrix Product of the eta array (we only need
185        // the ij element right now):
186 <      
186 >
187        eta2ij = 0.0;
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;
# Line 187 | Line 196 | void NPTf::moveA() {
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)
199 >        if (fabs(scaleMat[i][j]) > offDiagMax)
200            offDiagMax = fabs(scaleMat[i][j]);
192 –      
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 <  if ((bigScale > 1.1) || (smallScale < 0.9)) {
206 >
207 >  if ((bigScale > 1.01) || (smallScale < 0.99)) {
208      sprintf( painCave.errMsg,
209 <             "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
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"
# Line 208 | Line 216 | void NPTf::moveA() {
216               scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
217      painCave.isFatal = 1;
218      simError();
219 <  } else if (offDiagMax > 0.1) {
219 >  } else if (offDiagMax > 0.01) {
220      sprintf( painCave.errMsg,
221 <             "NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
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"
# Line 222 | Line 230 | void NPTf::moveA() {
230      simError();
231    } else {
232      info->getBoxM(hm);
233 <    info->matMul3(hm, scaleMat, hmnew);
233 >    matMul3(hm, scaleMat, hmnew);
234      info->setBoxM(hmnew);
235    }
228 –  
236   }
237  
238 < void NPTf::moveB( void ){
238 > template<typename T> bool NPTf<T>::etaConverged() {
239 >  int i;
240 >  double diffEta, sumEta;
241  
242 <  int i, j;
243 <  DirectionalAtom* dAtom;
244 <  double Tb[3], ji[3];
236 <  double vel[3], frc[3];
237 <  double mass;
242 >  sumEta = 0;
243 >  for(i = 0; i < 3; i++)
244 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
245  
246 <  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;
246 >  diffEta = sqrt( sumEta / 3.0 );
247  
248 <  instaTemp = tStats->getTemperature();
249 <  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) {
248 >  return ( diffEta <= etaTolerance );
249 > }
250  
251 <        eta[i][j] += dt2 * instaVol *
260 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
251 > template<typename T> double NPTf<T>::getConservedQuantity(void){
252  
253 <        vScale[i][j] = eta[i][j] + chi;
254 <        
255 <      } else {
256 <        
257 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
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 <        vScale[i][j] = eta[i][j];
269 <        
270 <      }
271 <    }
272 <  }
262 >  totalEnergy = tStats->getTotalE();
263  
264 <  for( i=0; i<nAtoms; i++ ){
264 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
265 >    (2.0 * eConvert);
266  
267 <    atoms[i]->getVel( vel );
277 <    atoms[i]->getFrc( frc );
267 >  thermostat_potential = fkBT* integralOfChidt / eConvert;
268  
269 <    mass = atoms[i]->getMass();
270 <    
271 <    // 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 <    }
269 >  transposeMat3(eta, a);
270 >  matMul3(a, eta, b);
271 >  trEta = matTrace3(b);
272  
273 <    atoms[i]->setVel( vel );
274 <    
291 <    if( atoms[i]->isDirectional() ){
273 >  barostat_kinetic = NkBT * tb2 * trEta /
274 >    (2.0 * eConvert);
275  
276 <      dAtom = (DirectionalAtom *)atoms[i];
277 <          
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 );
276 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
277 >    eConvert;
278  
279 <    }                    
280 <  }
311 < }
279 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
280 >    barostat_kinetic + barostat_potential;
281  
282 < int NPTf::readyCheck() {
314 <
315 <  // First check to see if we have a target temperature.
316 <  // Not having one is fatal.
317 <  
318 <  if (!have_target_temp) {
319 <    sprintf( painCave.errMsg,
320 <             "NPTf error: You can't use the NPTf integrator\n"
321 <             "   without a targetTemp!\n"
322 <             );
323 <    painCave.isFatal = 1;
324 <    simError();
325 <    return -1;
326 <  }
282 >  return conservedQuantity;
283  
284 <  if (!have_target_pressure) {
329 <    sprintf( painCave.errMsg,
330 <             "NPTf error: You can't use the NPTf integrator\n"
331 <             "   without a targetPressure!\n"
332 <             );
333 <    painCave.isFatal = 1;
334 <    simError();
335 <    return -1;
336 <  }
337 <  
338 <  // We must set tauThermostat.
339 <  
340 <  if (!have_tau_thermostat) {
341 <    sprintf( painCave.errMsg,
342 <             "NPTf error: If you use the NPTf\n"
343 <             "   integrator, you must set tauThermostat.\n");
344 <    painCave.isFatal = 1;
345 <    simError();
346 <    return -1;
347 <  }    
284 > }
285  
286 <  // We must set tauBarostat.
287 <  
288 <  if (!have_tau_barostat) {
289 <    sprintf( painCave.errMsg,
353 <             "NPTf error: If you use the NPTf\n"
354 <             "   integrator, you must set tauBarostat.\n");
355 <    painCave.isFatal = 1;
356 <    simError();
357 <    return -1;
358 <  }    
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 <  // We need NkBT a lot, so just set it here:
291 >  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
292 >  parameters += buffer;
293  
294 <  NkBT = (double)info->ndf * kB * targetTemp;
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 1;
299 >  return parameters;
300 >
301   }

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