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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 726 by tim, Tue Aug 26 20:37:30 2003 UTC vs.
Revision 1268 by tim, Fri Jun 11 17:16:21 2004 UTC

# Line 1 | Line 1
1   #include <iostream>
2 < #include <cstdlib>
3 < #include <cmath>
4 <
2 > #include <stdlib.h>
3 > #include <math.h>
4 > #include "Rattle.hpp"
5 > #include "Roll.hpp"
6   #ifdef IS_MPI
7   #include "mpiSimulation.hpp"
8   #include <unistd.h>
9   #endif //is_mpi
10  
11 + #ifdef PROFILE
12 + #include "mdProfile.hpp"
13 + #endif // profile
14 +
15   #include "Integrator.hpp"
16   #include "simError.h"
17  
# Line 25 | Line 30 | template<typename T> Integrator<T>::Integrator(SimInfo
30    if (info->the_integrator != NULL){
31      delete info->the_integrator;
32    }
28 –  info->the_integrator = this;
33  
34    nAtoms = info->n_atoms;
35 +  integrableObjects = info->integrableObjects;
36  
37 +  consFramework = new RattleFramework(info);
38 +
39 +  if(consFramework == NULL){
40 +    sprintf(painCave.errMsg,
41 +      "Integrator::Intergrator() Error: Memory allocation error for RattleFramework" );
42 +    painCave.isFatal = 1;
43 +    simError();
44 +  }
45 +  
46 + /*
47    // check for constraints
48  
49    constrainedA = NULL;
# Line 41 | Line 56 | template<typename T> Integrator<T>::Integrator(SimInfo
56    nConstrained = 0;
57  
58    checkConstraints();
59 + */
60   }
61  
62   template<typename T> Integrator<T>::~Integrator(){
63 +  if (consFramework != NULL)
64 +    delete consFramework;
65 + /*
66    if (nConstrained){
67      delete[] constrainedA;
68      delete[] constrainedB;
# Line 52 | Line 71 | template<typename T> Integrator<T>::~Integrator(){
71      delete[] moved;
72      delete[] oldPos;
73    }
74 + */
75   }
76  
77 + /*
78   template<typename T> void Integrator<T>::checkConstraints(void){
79    isConstrained = 0;
80  
# Line 65 | Line 86 | template<typename T> void Integrator<T>::checkConstrai
86  
87    SRI** theArray;
88    for (int i = 0; i < nMols; i++){
89 <    theArray = (SRI * *) molecules[i].getMyBonds();
89 >
90 >          theArray = (SRI * *) molecules[i].getMyBonds();
91      for (int j = 0; j < molecules[i].getNBonds(); j++){
92        constrained = theArray[j]->is_constrained();
93  
# Line 87 | Line 109 | template<typename T> void Integrator<T>::checkConstrai
109        if (constrained){
110          dummy_plug = theArray[j]->get_constraint();
111          temp_con[nConstrained].set_a(dummy_plug->get_a());
112 <        temp_con[nConstrained].set_b(dummy_plug->get_b());
112 >        temp_con[nConstrained].set_b(Dummy_plug->get_b());
113          temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
114  
115          nConstrained++;
# Line 111 | Line 133 | template<typename T> void Integrator<T>::checkConstrai
133      }
134    }
135  
136 +
137    if (nConstrained > 0){
138      isConstrained = 1;
139  
# Line 132 | Line 155 | template<typename T> void Integrator<T>::checkConstrai
155      }
156  
157  
158 <    // save oldAtoms to check for lode balanceing later on.
158 >    // save oldAtoms to check for lode balancing later on.
159  
160      oldAtoms = nAtoms;
161  
# Line 144 | Line 167 | template<typename T> void Integrator<T>::checkConstrai
167  
168    delete[] temp_con;
169   }
170 + */
171  
148 –
172   template<typename T> void Integrator<T>::integrate(void){
150 –  int i, j;                         // loop counters
173  
174    double runTime = info->run_time;
175    double sampleTime = info->sampleTime;
176    double statusTime = info->statusTime;
177    double thermalTime = info->thermalTime;
178 +  double resetTime = info->resetTime;
179  
180 +  double difference;
181    double currSample;
182    double currThermal;
183    double currStatus;
184 +  double currReset;
185  
186    int calcPot, calcStress;
162 –  int isError;
187  
188    tStats = new Thermo(info);
189    statOut = new StatWriter(info);
190    dumpOut = new DumpWriter(info);
191  
192    atoms = info->atoms;
169 –  DirectionalAtom* dAtom;
193  
194    dt = info->dt;
195    dt2 = 0.5 * dt;
196  
197 +  readyCheck();
198 +
199 +  // remove center of mass drift velocity (in case we passed in a configuration
200 +  // that was drifting
201 +  tStats->removeCOMdrift();
202 +
203 +  // initialize the retraints if necessary
204 +  if (info->useSolidThermInt && !info->useLiquidThermInt) {
205 +    myFF->initRestraints();
206 +  }
207 +
208    // initialize the forces before the first step
209  
210    calcForce(1, 1);
177 –  // myFF->doForces(1,1);
211  
212 +  //execute constraint algorithm to make sure at the very beginning the system is constrained  
213 +  consFramework->doPreConstraint();
214 +  consFramework->doConstrainA();
215 +  calcForce(1, 1);
216 +  consFramework->doConstrainB();
217 +  
218    if (info->setTemp){
219      thermalize();
220    }
221  
183 –  calcPot = 0;
184 –  calcStress = 0;
185 –  currSample = sampleTime;
186 –  currThermal = thermalTime;
187 –  currStatus = statusTime;
188 –  
222    calcPot     = 0;
223    calcStress  = 0;
224    currSample  = sampleTime + info->getTime();
225    currThermal = thermalTime+ info->getTime();
226    currStatus  = statusTime + info->getTime();
227 +  currReset   = resetTime  + info->getTime();
228  
229    dumpOut->writeDump(info->getTime());
230    statOut->writeStat(info->getTime());
231  
198 –  readyCheck();
232  
233   #ifdef IS_MPI
234    strcpy(checkPointMsg, "The integrator is ready to go.");
235    MPIcheckPoint();
236   #endif // is_mpi
237  
238 <  while (info->getTime() < runTime){
239 <    if ((info->getTime() + dt) >= currStatus){
238 >  while (info->getTime() < runTime && !stopIntegrator()){
239 >    difference = info->getTime() + dt - currStatus;
240 >    if (difference > 0 || fabs(difference) < 1e-4 ){
241        calcPot = 1;
242        calcStress = 1;
243      }
244  
245 + #ifdef PROFILE
246 +    startProfile( pro1 );
247 + #endif
248 +    
249      integrateStep(calcPot, calcStress);
250  
251 + #ifdef PROFILE
252 +    endProfile( pro1 );
253 +
254 +    startProfile( pro2 );
255 + #endif // profile
256 +
257      info->incrTime(dt);
258  
259      if (info->setTemp){
# Line 225 | Line 269 | template<typename T> void Integrator<T>::integrate(voi
269      }
270  
271      if (info->getTime() >= currStatus){
272 <      statOut->writeStat(info->getTime());
273 <      calcPot = 0;
272 >      statOut->writeStat(info->getTime());
273 >      calcPot = 0;
274        calcStress = 0;
275        currStatus += statusTime;
276 <    }
276 >    }
277  
278 +    if (info->resetIntegrator){
279 +      if (info->getTime() >= currReset){
280 +        this->resetIntegrator();
281 +        currReset += resetTime;
282 +      }
283 +    }
284 +    
285 + #ifdef PROFILE
286 +    endProfile( pro2 );
287 + #endif //profile
288 +
289   #ifdef IS_MPI
290      strcpy(checkPointMsg, "successfully took a time step.");
291      MPIcheckPoint();
292   #endif // is_mpi
293    }
294  
295 <  dumpOut->writeFinal(info->getTime());
295 >  // dump out a file containing the omega values for the final configuration
296 >  if (info->useSolidThermInt && !info->useLiquidThermInt)
297 >    myFF->dumpzAngle();
298 >  
299  
300    delete dumpOut;
301    delete statOut;
# Line 246 | Line 304 | template<typename T> void Integrator<T>::integrateStep
304   template<typename T> void Integrator<T>::integrateStep(int calcPot,
305                                                         int calcStress){
306    // Position full step, and velocity half step
249 –  preMove();
307  
308 + #ifdef PROFILE
309 +  startProfile(pro3);
310 + #endif //profile
311 +
312 +  //save old state (position, velocity etc)
313 +  consFramework->doPreConstraint();
314 +
315 + #ifdef PROFILE
316 +  endProfile(pro3);
317 +
318 +  startProfile(pro4);
319 + #endif // profile
320 +
321    moveA();
322  
323 <  if (nConstrained){
324 <    constrainA();
325 <  }
323 > #ifdef PROFILE
324 >  endProfile(pro4);
325 >  
326 >  startProfile(pro5);
327 > #endif//profile
328  
329  
330   #ifdef IS_MPI
# Line 260 | Line 332 | template<typename T> void Integrator<T>::integrateStep
332    MPIcheckPoint();
333   #endif // is_mpi
334  
263 –
335    // calc forces
265 –
336    calcForce(calcPot, calcStress);
337  
338   #ifdef IS_MPI
# Line 270 | Line 340 | template<typename T> void Integrator<T>::integrateStep
340    MPIcheckPoint();
341   #endif // is_mpi
342  
343 + #ifdef PROFILE
344 +  endProfile( pro5 );
345  
346 +  startProfile( pro6 );
347 + #endif //profile
348 +
349    // finish the velocity  half step
350  
351    moveB();
352  
353 <  if (nConstrained){
354 <    constrainB();
355 <  }
353 > #ifdef PROFILE
354 >  endProfile(pro6);
355 > #endif // profile
356  
357   #ifdef IS_MPI
358    strcpy(checkPointMsg, "Succesful moveB\n");
# Line 287 | Line 362 | template<typename T> void Integrator<T>::moveA(void){
362  
363  
364   template<typename T> void Integrator<T>::moveA(void){
365 <  int i, j;
365 >  size_t i, j;
366    DirectionalAtom* dAtom;
367    double Tb[3], ji[3];
293 –  double A[3][3], I[3][3];
294 –  double angle;
368    double vel[3], pos[3], frc[3];
369    double mass;
370 <
371 <  for (i = 0; i < nAtoms; i++){
372 <    atoms[i]->getVel(vel);
373 <    atoms[i]->getPos(pos);
374 <    atoms[i]->getFrc(frc);
375 <
376 <    mass = atoms[i]->getMass();
370 >  double omega;
371 >
372 >  for (i = 0; i < integrableObjects.size() ; i++){
373 >    integrableObjects[i]->getVel(vel);
374 >    integrableObjects[i]->getPos(pos);
375 >    integrableObjects[i]->getFrc(frc);
376 >    
377 >    mass = integrableObjects[i]->getMass();
378  
379      for (j = 0; j < 3; j++){
380        // velocity half step
# Line 309 | Line 383 | template<typename T> void Integrator<T>::moveA(void){
383        pos[j] += dt * vel[j];
384      }
385  
386 <    atoms[i]->setVel(vel);
387 <    atoms[i]->setPos(pos);
386 >    integrableObjects[i]->setVel(vel);
387 >    integrableObjects[i]->setPos(pos);
388  
389 <    if (atoms[i]->isDirectional()){
316 <      dAtom = (DirectionalAtom *) atoms[i];
389 >    if (integrableObjects[i]->isDirectional()){
390  
391        // get and convert the torque to body frame
392  
393 <      dAtom->getTrq(Tb);
394 <      dAtom->lab2Body(Tb);
393 >      integrableObjects[i]->getTrq(Tb);
394 >      integrableObjects[i]->lab2Body(Tb);
395  
396        // get the angular momentum, and propagate a half step
397  
398 <      dAtom->getJ(ji);
398 >      integrableObjects[i]->getJ(ji);
399  
400        for (j = 0; j < 3; j++)
401          ji[j] += (dt2 * Tb[j]) * eConvert;
402  
403 <      // use the angular velocities to propagate the rotation matrix a
331 <      // full time step
403 >      this->rotationPropagation( integrableObjects[i], ji );
404  
405 <      dAtom->getA(A);
334 <      dAtom->getI(I);
335 <
336 <      // rotate about the x-axis      
337 <      angle = dt2 * ji[0] / I[0][0];
338 <      this->rotate(1, 2, angle, ji, A);
339 <
340 <      // rotate about the y-axis
341 <      angle = dt2 * ji[1] / I[1][1];
342 <      this->rotate(2, 0, angle, ji, A);
343 <
344 <      // rotate about the z-axis
345 <      angle = dt * ji[2] / I[2][2];
346 <      this->rotate(0, 1, angle, ji, A);
347 <
348 <      // rotate about the y-axis
349 <      angle = dt2 * ji[1] / I[1][1];
350 <      this->rotate(2, 0, angle, ji, A);
351 <
352 <      // rotate about the x-axis
353 <      angle = dt2 * ji[0] / I[0][0];
354 <      this->rotate(1, 2, angle, ji, A);
355 <
356 <
357 <      dAtom->setJ(ji);
358 <      dAtom->setA(A);
405 >      integrableObjects[i]->setJ(ji);
406      }
407    }
408 +
409 +  consFramework->doConstrainA();
410   }
411  
412  
413   template<typename T> void Integrator<T>::moveB(void){
414    int i, j;
366 –  DirectionalAtom* dAtom;
415    double Tb[3], ji[3];
416    double vel[3], frc[3];
417    double mass;
418  
419 <  for (i = 0; i < nAtoms; i++){
420 <    atoms[i]->getVel(vel);
421 <    atoms[i]->getFrc(frc);
419 >  for (i = 0; i < integrableObjects.size(); i++){
420 >    integrableObjects[i]->getVel(vel);
421 >    integrableObjects[i]->getFrc(frc);
422  
423 <    mass = atoms[i]->getMass();
423 >    mass = integrableObjects[i]->getMass();
424  
425      // velocity half step
426      for (j = 0; j < 3; j++)
427        vel[j] += (dt2 * frc[j] / mass) * eConvert;
428  
429 <    atoms[i]->setVel(vel);
429 >    integrableObjects[i]->setVel(vel);
430  
431 <    if (atoms[i]->isDirectional()){
384 <      dAtom = (DirectionalAtom *) atoms[i];
431 >    if (integrableObjects[i]->isDirectional()){
432  
433 <      // get and convert the torque to body frame      
433 >      // get and convert the torque to body frame
434  
435 <      dAtom->getTrq(Tb);
436 <      dAtom->lab2Body(Tb);
435 >      integrableObjects[i]->getTrq(Tb);
436 >      integrableObjects[i]->lab2Body(Tb);
437  
438        // get the angular momentum, and propagate a half step
439  
440 <      dAtom->getJ(ji);
440 >      integrableObjects[i]->getJ(ji);
441  
442        for (j = 0; j < 3; j++)
443          ji[j] += (dt2 * Tb[j]) * eConvert;
444  
445  
446 <      dAtom->setJ(ji);
446 >      integrableObjects[i]->setJ(ji);
447      }
448    }
449 +
450 +  consFramework->doConstrainB();
451   }
452  
453 + /*
454   template<typename T> void Integrator<T>::preMove(void){
455    int i, j;
456    double pos[3];
# Line 417 | Line 467 | template<typename T> void Integrator<T>::constrainA(){
467   }
468  
469   template<typename T> void Integrator<T>::constrainA(){
470 <  int i, j, k;
470 >  int i, j;
471    int done;
472    double posA[3], posB[3];
473    double velA[3], velB[3];
# Line 557 | Line 607 | template<typename T> void Integrator<T>::constrainA(){
607      painCave.isFatal = 1;
608      simError();
609    }
610 +
611   }
612  
613   template<typename T> void Integrator<T>::constrainB(void){
614 <  int i, j, k;
614 >  int i, j;
615    int done;
616    double posA[3], posB[3];
617    double velA[3], velB[3];
# Line 569 | Line 620 | template<typename T> void Integrator<T>::constrainB(vo
620    int a, b, ax, ay, az, bx, by, bz;
621    double rma, rmb;
622    double dx, dy, dz;
623 <  double rabsq, pabsq, rvab;
573 <  double diffsq;
623 >  double rvab;
624    double gab;
625    int iteration;
626  
# Line 657 | Line 707 | template<typename T> void Integrator<T>::constrainB(vo
707              iteration);
708      painCave.isFatal = 1;
709      simError();
710 +  }
711 + }
712 + */
713 + template<typename T> void Integrator<T>::rotationPropagation
714 + ( StuntDouble* sd, double ji[3] ){
715 +
716 +  double angle;
717 +  double A[3][3], I[3][3];
718 +  int i, j, k;
719 +
720 +  // use the angular velocities to propagate the rotation matrix a
721 +  // full time step
722 +
723 +  sd->getA(A);
724 +  sd->getI(I);
725 +
726 +  if (sd->isLinear()) {
727 +    i = sd->linearAxis();
728 +    j = (i+1)%3;
729 +    k = (i+2)%3;
730 +    
731 +    angle = dt2 * ji[j] / I[j][j];
732 +    this->rotate( k, i, angle, ji, A );
733 +
734 +    angle = dt * ji[k] / I[k][k];
735 +    this->rotate( i, j, angle, ji, A);
736 +
737 +    angle = dt2 * ji[j] / I[j][j];
738 +    this->rotate( k, i, angle, ji, A );
739 +
740 +  } else {
741 +    // rotate about the x-axis
742 +    angle = dt2 * ji[0] / I[0][0];
743 +    this->rotate( 1, 2, angle, ji, A );
744 +    
745 +    // rotate about the y-axis
746 +    angle = dt2 * ji[1] / I[1][1];
747 +    this->rotate( 2, 0, angle, ji, A );
748 +    
749 +    // rotate about the z-axis
750 +    angle = dt * ji[2] / I[2][2];
751 +    sd->addZangle(angle);
752 +    this->rotate( 0, 1, angle, ji, A);
753 +    
754 +    // rotate about the y-axis
755 +    angle = dt2 * ji[1] / I[1][1];
756 +    this->rotate( 2, 0, angle, ji, A );
757 +    
758 +    // rotate about the x-axis
759 +    angle = dt2 * ji[0] / I[0][0];
760 +    this->rotate( 1, 2, angle, ji, A );
761 +    
762    }
763 +  sd->setA( A  );
764   }
765  
766   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
# Line 725 | Line 828 | template<typename T> void Integrator<T>::rotate(int ax
828      }
829    }
830  
831 <  // rotate the Rotation matrix acording to:
831 >  // rotate the Rotation matrix acording to:
832    //            A[][] = A[][] * transpose(rot[][])
833  
834  
# Line 750 | Line 853 | template<typename T> void Integrator<T>::thermalize(){
853   template<typename T> void Integrator<T>::thermalize(){
854    tStats->velocitize();
855   }
856 +
857 + template<typename T> double Integrator<T>::getConservedQuantity(void){
858 +  return tStats->getTotalE();
859 + }
860 + template<typename T> string Integrator<T>::getAdditionalParameters(void){
861 +  //By default, return a null string
862 +  //The reason we use string instead of char* is that if we use char*, we will
863 +  //return a pointer point to local variable which might cause problem
864 +  return string();
865 + }

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