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root/group/branches/new-templateless/OOPSE/libmdtools/NPTf.cpp
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Comparing:
trunk/OOPSE/libmdtools/NPTf.cpp (file contents), Revision 778 by mmeineke, Fri Sep 19 20:00:27 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/NPTf.cpp (file contents), Revision 851 by mmeineke, Wed Nov 5 19:18:17 2003 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <stdlib.h>
2 > #include <math.h>
3 > #include <string.h>
4 >
5   #include "Atom.hpp"
6   #include "SRI.hpp"
7   #include "AbstractClasses.hpp"
# Line 7 | Line 10
10   #include "Thermo.hpp"
11   #include "ReadWrite.hpp"
12   #include "Integrator.hpp"
13 < #include "simError.h"
13 > #include "simError.h"
14  
15   #ifdef IS_MPI
16   #include "mpiSimulation.hpp"
# Line 17 | Line 20
20   // modification of the Hoover algorithm:
21   //
22   //    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
23 < //       Molec. Phys., 78, 533.
23 > //       Molec. Phys., 78, 533.
24   //
25   //           and
26 < //
26 > //
27   //    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
28  
29 < template<typename T> NPTf<T>::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
30 <  T( theInfo, the_ff )
29 > NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
30 >  NPT( theInfo, the_ff )
31   {
32 <  int i, j;
33 <  chi = 0.0;
34 <  integralOfChidt = 0.0;
32 >  GenericData* data;
33 >  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 >  // retrieve eta array from simInfo if it exists
45 >  data = info->getProperty(ETAVALUE_ID);
46 >  if(data != NULL){
47 >    
48 >    int test = data->getDarray(etaArray);
49 >    
50 >    if( test == 9 ){
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 >      delete[] etaArray;
59 >    }
60 >    else
61 >      std::cerr << "NPTf error: etaArray is not length 9 (actual = " << test
62 >                << ").\n"
63 >                << "            Simulation wil proceed with eta = 0;\n";
64 >  }
65 > }
66  
67 <  have_chi_tolerance = 0;
43 <  have_eta_tolerance = 0;
44 <  have_pos_iter_tolerance = 0;
67 > NPTf::~NPTf() {
68  
69 <  oldPos = new double[3*nAtoms];
47 <  oldVel = new double[3*nAtoms];
48 <  oldJi = new double[3*nAtoms];
49 < #ifdef IS_MPI
50 <  Nparticles = mpiSim->getTotAtoms();
51 < #else
52 <  Nparticles = theInfo->n_atoms;
53 < #endif
54 <
69 >  // empty for now
70   }
71  
72 < template<typename T> NPTf<T>::~NPTf() {
73 <  delete[] oldPos;
74 <  delete[] oldVel;
75 <  delete[] oldJi;
72 > void NPTf::resetIntegrator() {
73 >
74 >  int i, j;
75 >
76 >  for(i = 0; i < 3; i++)
77 >    for (j = 0; j < 3; j++)
78 >      eta[i][j] = 0.0;
79 >
80 >  NPT::resetIntegrator();
81   }
82  
83 < template<typename T> void NPTf<T>::moveA() {
83 > void NPTf::evolveEtaA() {
84  
85 <  // new version of NPTf
66 <  int i, j, k;
67 <  DirectionalAtom* dAtom;
68 <  double Tb[3], ji[3];
85 >  int i, j;
86  
87 <  double mass;
88 <  double vel[3], pos[3], frc[3];
87 >  for(i = 0; i < 3; i ++){
88 >    for(j = 0; j < 3; j++){
89 >      if( i == j)
90 >        eta[i][j] += dt2 *  instaVol *
91 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
92 >      else
93 >        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
94 >    }
95 >  }
96  
97 <  double rj[3];
98 <  double instaTemp, instaPress, instaVol;
99 <  double tt2, tb2;
100 <  double sc[3];
77 <  double eta2ij;
78 <  double press[3][3], vScale[3][3], hm[3][3], hmnew[3][3], scaleMat[3][3];
79 <  double bigScale, smallScale, offDiagMax;
80 <  double COM[3];
97 >  for(i = 0; i < 3; i++)
98 >    for (j = 0; j < 3; j++)
99 >      oldEta[i][j] = eta[i][j];
100 > }
101  
102 <  tt2 = tauThermostat * tauThermostat;
83 <  tb2 = tauBarostat * tauBarostat;
102 > void NPTf::evolveEtaB() {
103  
104 <  instaTemp = tStats->getTemperature();
86 <  tStats->getPressureTensor(press);
87 <  instaVol = tStats->getVolume();
88 <  
89 <  tStats->getCOM(COM);
104 >  int i,j;
105  
106 <  //calculate scale factor of veloity
106 >  for(i = 0; i < 3; i++)
107 >    for (j = 0; j < 3; j++)
108 >      prevEta[i][j] = eta[i][j];
109 >
110 >  for(i = 0; i < 3; i ++){
111 >    for(j = 0; j < 3; j++){
112 >      if( i == j) {
113 >        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
114 >          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
115 >      } else {
116 >        eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
117 >      }
118 >    }
119 >  }
120 > }
121 >
122 > void NPTf::getVelScaleA(double sc[3], double vel[3]) {
123 >  int i,j;
124 >  double vScale[3][3];
125 >
126    for (i = 0; i < 3; i++ ) {
127      for (j = 0; j < 3; j++ ) {
128        vScale[i][j] = eta[i][j];
129 <      
129 >
130        if (i == j) {
131 <        vScale[i][j] += chi;          
132 <      }              
131 >        vScale[i][j] += chi;
132 >      }
133      }
134    }
101  
102  //evolve velocity half step
103  for( i=0; i<nAtoms; i++ ){
135  
136 <    atoms[i]->getVel( vel );
137 <    atoms[i]->getFrc( frc );
136 >  info->matVecMul3( vScale, vel, sc );
137 > }
138  
139 <    mass = atoms[i]->getMass();
140 <    
141 <    info->matVecMul3( vScale, vel, sc );
139 > void NPTf::getVelScaleB(double sc[3], int index ){
140 >  int i,j;
141 >  double myVel[3];
142 >  double vScale[3][3];
143  
144 <    for (j=0; j < 3; j++) {
113 <      // velocity half step
114 <      vel[j] += dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
115 <    }
144 > //   std::cerr << "velScaleB chi = " << chi << "\n";
145  
146 <    atoms[i]->setVel( vel );
147 <  
148 <    if( atoms[i]->isDirectional() ){
146 >  for (i = 0; i < 3; i++ ) {
147 >    for (j = 0; j < 3; j++ ) {
148 >      vScale[i][j] = eta[i][j];
149  
150 <      dAtom = (DirectionalAtom *)atoms[i];
150 >      if (i == j) {
151 >        vScale[i][j] += chi;
152 >      }
153 >    }
154 >  }
155  
156 <      // get and convert the torque to body frame
157 <      
125 <      dAtom->getTrq( Tb );
126 <      dAtom->lab2Body( Tb );
127 <      
128 <      // get the angular momentum, and propagate a half step
156 >  for (j = 0; j < 3; j++)
157 >    myVel[j] = oldVel[3*index + j];
158  
159 <      dAtom->getJ( ji );
159 > //   std::cerr << "velScaleB = \n"
160 > //          << "[ " << vScale[0][0] << " , " << vScale[0][1] << " , " << vScale[0][2] << "]\n"
161 > //          << "[ " << vScale[1][0] << " , " << vScale[1][1] << " , " << vScale[1][2] << "]\n"
162 > //          << "[ " << vScale[2][0] << " , " << vScale[2][1] << " , " << vScale[2][2] << "]\n\n";
163  
132      for (j=0; j < 3; j++)
133        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
134      
135      this->rotationPropagation( dAtom, ji );
136  
137      dAtom->setJ( ji );
138    }    
139  }
164  
165 <  // advance chi half step
166 <  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
165 > //  std::cerr << "myVel " << index << " in => "
166 > //          << myVel[0] << ", " << myVel[1] << ", " << myVel[2] << "\n";
167  
168 <  // calculate the integral of chidt
145 <  integralOfChidt += dt2*chi;
168 >  info->matVecMul3( vScale, myVel, sc );
169  
170 <  // advance eta half step
170 > //  std::cerr << "sc " << index << " out => "
171 > //          << sc[0] << ", " << sc[1] << ", " << sc[2] << "\n";
172 > }
173  
174 <  for(i = 0; i < 3; i ++)
175 <    for(j = 0; j < 3; j++){
176 <      if( i == j)
177 <        eta[i][j] += dt2 *  instaVol *
153 <          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
154 <      else
155 <        eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
156 <    }
157 <    
158 <  //save the old positions
159 <  for(i = 0; i < nAtoms; i++){
160 <    atoms[i]->getPos(pos);
161 <    for(j = 0; j < 3; j++)
162 <      oldPos[i*3 + j] = pos[j];
163 <  }
164 <  
165 <  //the first estimation of r(t+dt) is equal to  r(t)
166 <    
167 <  for(k = 0; k < 4; k ++){
174 > void NPTf::getPosScale(double pos[3], double COM[3],
175 >                                               int index, double sc[3]){
176 >  int j;
177 >  double rj[3];
178  
179 <    for(i =0 ; i < nAtoms; i++){
179 >  for(j=0; j<3; j++)
180 >    rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
181  
182 <      atoms[i]->getVel(vel);
183 <      atoms[i]->getPos(pos);
182 >  info->matVecMul3( eta, rj, sc );
183 > }
184  
185 <      for(j = 0; j < 3; j++)
175 <        rj[j] = (oldPos[i*3 + j] + pos[j])/2 - COM[j];
176 <      
177 <      info->matVecMul3( eta, rj, sc );
178 <      
179 <      for(j = 0; j < 3; j++)
180 <        pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]);
185 > void NPTf::scaleSimBox( void ){
186  
187 <      atoms[i]->setPos( pos );
187 >  int i,j,k;
188 >  double scaleMat[3][3];
189 >  double eta2ij;
190 >  double bigScale, smallScale, offDiagMax;
191 >  double hm[3][3], hmnew[3][3];
192  
184    }
193  
186    if (nConstrained) {
187      constrainA();
188    }
189  }  
194  
191
195    // Scale the box after all the positions have been moved:
196 <  
196 >
197    // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
198    //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)
199 <  
199 >
200    bigScale = 1.0;
201    smallScale = 1.0;
202    offDiagMax = 0.0;
203 <  
203 >
204    for(i=0; i<3; i++){
205      for(j=0; j<3; j++){
206 <      
206 >
207        // Calculate the matrix Product of the eta array (we only need
208        // the ij element right now):
209 <      
209 >
210        eta2ij = 0.0;
211        for(k=0; k<3; k++){
212          eta2ij += eta[i][k] * eta[k][j];
213        }
214 <      
214 >
215        scaleMat[i][j] = 0.0;
216        // identity matrix (see above):
217        if (i == j) scaleMat[i][j] = 1.0;
# Line 216 | Line 219 | template<typename T> void NPTf<T>::moveA() {
219        scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;
220  
221        if (i != j)
222 <        if (fabs(scaleMat[i][j]) > offDiagMax)
222 >        if (fabs(scaleMat[i][j]) > offDiagMax)
223            offDiagMax = fabs(scaleMat[i][j]);
224      }
225  
226      if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
227      if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
228    }
229 <  
229 >
230    if ((bigScale > 1.1) || (smallScale < 0.9)) {
231      sprintf( painCave.errMsg,
232               "NPTf error: Attempting a Box scaling of more than 10 percent.\n"
# Line 253 | Line 256 | template<typename T> void NPTf<T>::moveA() {
256      info->matMul3(hm, scaleMat, hmnew);
257      info->setBoxM(hmnew);
258    }
256  
259   }
260  
261 < template<typename T> void NPTf<T>::moveB( void ){
261 > bool NPTf::etaConverged() {
262 >  int i;
263 >  double diffEta, sumEta;
264  
265 <  //new version of NPTf
262 <  int i, j, k;
263 <  DirectionalAtom* dAtom;
264 <  double Tb[3], ji[3];
265 <  double vel[3], myVel[3], frc[3];
266 <  double mass;
267 <
268 <  double instaTemp, instaPress, instaVol;
269 <  double tt2, tb2;
270 <  double sc[3];
271 <  double press[3][3], vScale[3][3];
272 <  double oldChi, prevChi;
273 <  double oldEta[3][3], prevEta[3][3], diffEta;
274 <  
275 <  tt2 = tauThermostat * tauThermostat;
276 <  tb2 = tauBarostat * tauBarostat;
277 <
278 <  // Set things up for the iteration:
279 <
280 <  oldChi = chi;
281 <  
265 >  sumEta = 0;
266    for(i = 0; i < 3; i++)
267 <    for(j = 0; j < 3; j++)
284 <      oldEta[i][j] = eta[i][j];
267 >    sumEta += pow(prevEta[i][i] - eta[i][i], 2);
268  
269 <  for( i=0; i<nAtoms; i++ ){
269 >  diffEta = sqrt( sumEta / 3.0 );
270  
271 <    atoms[i]->getVel( vel );
289 <
290 <    for (j=0; j < 3; j++)
291 <      oldVel[3*i + j]  = vel[j];
292 <
293 <    if( atoms[i]->isDirectional() ){
294 <
295 <      dAtom = (DirectionalAtom *)atoms[i];
296 <
297 <      dAtom->getJ( ji );
298 <
299 <      for (j=0; j < 3; j++)
300 <        oldJi[3*i + j] = ji[j];
301 <
302 <    }
303 <  }
304 <
305 <  // do the iteration:
306 <
307 <  instaVol = tStats->getVolume();
308 <  
309 <  for (k=0; k < 4; k++) {
310 <    
311 <    instaTemp = tStats->getTemperature();
312 <    tStats->getPressureTensor(press);
313 <
314 <    // evolve chi another half step using the temperature at t + dt/2
315 <
316 <    prevChi = chi;
317 <    chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
318 <    
319 <    for(i = 0; i < 3; i++)
320 <      for(j = 0; j < 3; j++)
321 <        prevEta[i][j] = eta[i][j];
322 <
323 <    //advance eta half step and calculate scale factor for velocity
324 <
325 <    for(i = 0; i < 3; i ++)
326 <      for(j = 0; j < 3; j++){
327 <        if( i == j) {
328 <          eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
329 <            (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
330 <          vScale[i][j] = eta[i][j] + chi;
331 <        } else {
332 <          eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
333 <          vScale[i][j] = eta[i][j];
334 <        }
335 <      }  
336 <    
337 <    for( i=0; i<nAtoms; i++ ){
338 <
339 <      atoms[i]->getFrc( frc );
340 <      atoms[i]->getVel(vel);
341 <      
342 <      mass = atoms[i]->getMass();
343 <    
344 <      for (j = 0; j < 3; j++)
345 <        myVel[j] = oldVel[3*i + j];
346 <      
347 <      info->matVecMul3( vScale, myVel, sc );
348 <      
349 <      // velocity half step
350 <      for (j=0; j < 3; j++) {
351 <        // velocity half step  (use chi from previous step here):
352 <        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j]  / mass) * eConvert - sc[j]);
353 <      }
354 <      
355 <      atoms[i]->setVel( vel );
356 <      
357 <      if( atoms[i]->isDirectional() ){
358 <
359 <        dAtom = (DirectionalAtom *)atoms[i];
360 <  
361 <        // get and convert the torque to body frame      
362 <  
363 <        dAtom->getTrq( Tb );
364 <        dAtom->lab2Body( Tb );      
365 <            
366 <        for (j=0; j < 3; j++)
367 <          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
368 <      
369 <          dAtom->setJ( ji );
370 <      }
371 <    }
372 <
373 <    if (nConstrained) {
374 <      constrainB();
375 <    }
376 <    
377 <    diffEta = 0;
378 <    for(i = 0; i < 3; i++)
379 <      diffEta += pow(prevEta[i][i] - eta[i][i], 2);    
380 <    
381 <    if (fabs(prevChi - chi) <= chiTolerance && sqrt(diffEta / 3) <= etaTolerance)
382 <      break;
383 <  }
384 <
385 <  //calculate integral of chidt
386 <  integralOfChidt += dt2*chi;
387 <  
271 >  return ( diffEta <= etaTolerance );
272   }
273  
274 < template<typename T> void NPTf<T>::resetIntegrator() {
391 <  int i,j;
392 <  
393 <  chi = 0.0;
274 > double NPTf::getConservedQuantity(void){
275  
395  for(i = 0; i < 3; i++)
396    for (j = 0; j < 3; j++)
397      eta[i][j] = 0.0;
398
399 }
400
401 template<typename T> int NPTf<T>::readyCheck() {
402
403  //check parent's readyCheck() first
404  if (T::readyCheck() == -1)
405    return -1;
406
407  // First check to see if we have a target temperature.
408  // Not having one is fatal.
409  
410  if (!have_target_temp) {
411    sprintf( painCave.errMsg,
412             "NPTf error: You can't use the NPTf integrator\n"
413             "   without a targetTemp!\n"
414             );
415    painCave.isFatal = 1;
416    simError();
417    return -1;
418  }
419
420  if (!have_target_pressure) {
421    sprintf( painCave.errMsg,
422             "NPTf error: You can't use the NPTf integrator\n"
423             "   without a targetPressure!\n"
424             );
425    painCave.isFatal = 1;
426    simError();
427    return -1;
428  }
429  
430  // We must set tauThermostat.
431  
432  if (!have_tau_thermostat) {
433    sprintf( painCave.errMsg,
434             "NPTf error: If you use the NPTf\n"
435             "   integrator, you must set tauThermostat.\n");
436    painCave.isFatal = 1;
437    simError();
438    return -1;
439  }    
440
441  // We must set tauBarostat.
442  
443  if (!have_tau_barostat) {
444    sprintf( painCave.errMsg,
445             "NPTf error: If you use the NPTf\n"
446             "   integrator, you must set tauBarostat.\n");
447    painCave.isFatal = 1;
448    simError();
449    return -1;
450  }    
451
452  
453  // We need NkBT a lot, so just set it here: This is the RAW number
454  // of particles, so no subtraction or addition of constraints or
455  // orientational degrees of freedom:
456  
457  NkBT = (double)Nparticles * kB * targetTemp;
458  
459  // fkBT is used because the thermostat operates on more degrees of freedom
460  // than the barostat (when there are particles with orientational degrees
461  // of freedom).  ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons
462  
463  fkBT = (double)info->ndf * kB * targetTemp;
464
465  return 1;
466 }
467
468 template<typename T> double NPTf<T>::getConservedQuantity(void){
469
276    double conservedQuantity;
277 <  double Energy;
277 >  double totalEnergy;
278    double thermostat_kinetic;
279    double thermostat_potential;
280    double barostat_kinetic;
# Line 476 | Line 282 | template<typename T> double NPTf<T>::getConservedQuant
282    double trEta;
283    double a[3][3], b[3][3];
284  
285 <  Energy = tStats->getTotalE();
285 >  totalEnergy = tStats->getTotalE();
286  
287 <  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
287 >  thermostat_kinetic = fkBT * tt2 * chi * chi /
288      (2.0 * eConvert);
289  
290    thermostat_potential = fkBT* integralOfChidt / eConvert;
# Line 487 | Line 293 | template<typename T> double NPTf<T>::getConservedQuant
293    info->matMul3(a, eta, b);
294    trEta = info->matTrace3(b);
295  
296 <  barostat_kinetic = NkBT * tauBarostat * tauBarostat * trEta /
296 >  barostat_kinetic = NkBT * tb2 * trEta /
297      (2.0 * eConvert);
298 <  
299 <  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
298 >
299 >  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
300      eConvert;
301  
302 <  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
302 >  conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
303      barostat_kinetic + barostat_potential;
498  
499  cout.width(8);
500  cout.precision(8);
304  
305 <  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
306 <      "\t" << thermostat_potential << "\t" << barostat_kinetic <<
504 <      "\t" << barostat_potential << "\t" << conservedQuantity << endl;
305 > //   cout.width(8);
306 > //   cout.precision(8);
307  
308 <  return conservedQuantity;
308 > //   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
309 > //       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
310 > //       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
311 >
312 >  return conservedQuantity;
313 >
314   }
315 +
316 + char* NPTf::getAdditionalParameters(void){
317 +
318 +  sprintf(addParamBuffer,
319 +          "\t%G\t%G;"
320 +          "\t%G\t%G\t%G;"
321 +          "\t%G\t%G\t%G;"
322 +          "\t%G\t%G\t%G;",
323 +          chi, integralOfChidt,
324 +          eta[0][0], eta[0][1], eta[0][2],
325 +          eta[1][0], eta[1][1], eta[1][2],
326 +          eta[2][0], eta[2][1], eta[2][2]
327 +          );
328 +
329 +  return addParamBuffer;
330 + }

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