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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 784 by mmeineke, Wed Sep 24 19:34:39 2003 UTC vs.
Revision 1284 by tim, Mon Jun 21 18:52:21 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    }
33 <  
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 40 | 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 51 | 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 64 | 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 86 | 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 110 | Line 133 | template<typename T> void Integrator<T>::checkConstrai
133      }
134    }
135  
136 +
137    if (nConstrained > 0){
138      isConstrained = 1;
139  
# Line 131 | 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 143 | Line 167 | template<typename T> void Integrator<T>::checkConstrai
167  
168    delete[] temp_con;
169   }
170 + */
171  
147 –
172   template<typename T> void Integrator<T>::integrate(void){
149 –  int i, j;                         // loop counters
173  
174    double runTime = info->run_time;
175    double sampleTime = info->sampleTime;
# Line 154 | Line 177 | template<typename T> void Integrator<T>::integrate(voi
177    double thermalTime = info->thermalTime;
178    double resetTime = info->resetTime;
179  
180 <
180 >  double difference;
181    double currSample;
182    double currThermal;
183    double currStatus;
184    double currReset;
185 <  
185 >
186    int calcPot, calcStress;
164 –  int isError;
187  
188    tStats = new Thermo(info);
189    statOut = new StatWriter(info);
190    dumpOut = new DumpWriter(info);
191  
192    atoms = info->atoms;
171 –  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);
211  
212 <  if (nConstrained){
213 <    preMove();
214 <    constrainA();
215 <    calcForce(1, 1);    
216 <    constrainB();
187 <  }
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();
# Line 201 | Line 230 | template<typename T> void Integrator<T>::integrate(voi
230    statOut->writeStat(info->getTime());
231  
232  
204 –
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 230 | 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){
# Line 242 | Line 281 | template<typename T> void Integrator<T>::integrate(voi
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.");
# Line 249 | Line 292 | template<typename T> void Integrator<T>::integrate(voi
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 258 | 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
261 –  preMove();
307  
308 <  moveA();
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 + #ifdef PROFILE
324 +  endProfile(pro4);
325 +  
326 +  startProfile(pro5);
327 + #endif//profile
328 +
329 +
330   #ifdef IS_MPI
331    strcpy(checkPointMsg, "Succesful moveA\n");
332    MPIcheckPoint();
333   #endif // is_mpi
334  
273 –
335    // calc forces
275 –
336    calcForce(calcPot, calcStress);
337  
338   #ifdef IS_MPI
# Line 280 | 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 + #ifdef PROFILE
354 +  endProfile(pro6);
355 + #endif // profile
356  
289 –
357   #ifdef IS_MPI
358    strcpy(checkPointMsg, "Succesful moveB\n");
359    MPIcheckPoint();
# Line 295 | 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];
368    double vel[3], pos[3], frc[3];
369    double mass;
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  
304 –  for (i = 0; i < nAtoms; i++){
305 –    atoms[i]->getVel(vel);
306 –    atoms[i]->getPos(pos);
307 –    atoms[i]->getFrc(frc);
308 –
309 –    mass = atoms[i]->getMass();
310 –
379      for (j = 0; j < 3; j++){
380        // velocity half step
381        vel[j] += (dt2 * frc[j] / mass) * eConvert;
# Line 315 | 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()){
322 <      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 <      this->rotationPropagation( dAtom, ji );
403 >      this->rotationPropagation( integrableObjects[i], ji );
404  
405 <      dAtom->setJ(ji);
405 >      integrableObjects[i]->setJ(ji);
406      }
407    }
408  
409 <  if (nConstrained){
343 <    constrainA();
344 <  }
409 >  consFramework->doConstrainA();
410   }
411  
412  
413   template<typename T> void Integrator<T>::moveB(void){
414    int i, j;
350 –  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()){
368 <      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 <  if (nConstrained){
388 <    constrainB();
389 <  }
450 >  consFramework->doConstrainB();
451   }
452  
453 + /*
454   template<typename T> void Integrator<T>::preMove(void){
455    int i, j;
456    double pos[3];
# Line 405 | 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 549 | Line 611 | template<typename T> void Integrator<T>::constrainB(vo
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 558 | 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;
562 <  double diffsq;
623 >  double rvab;
624    double gab;
625    int iteration;
626  
# Line 648 | Line 709 | template<typename T> void Integrator<T>::constrainB(vo
709      simError();
710    }
711   }
712 <
712 > */
713   template<typename T> void Integrator<T>::rotationPropagation
714 < ( DirectionalAtom* dAtom, double ji[3] ){
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 <  dAtom->getA(A);
724 <  dAtom->getI(I);
725 <  
726 <  // rotate about the x-axis      
727 <  angle = dt2 * ji[0] / I[0][0];
728 <  this->rotate( 1, 2, angle, ji, A );
729 <  
730 <  // rotate about the y-axis
731 <  angle = dt2 * ji[1] / I[1][1];
732 <  this->rotate( 2, 0, angle, ji, A );
733 <  
734 <  // rotate about the z-axis
735 <  angle = dt * ji[2] / I[2][2];
736 <  this->rotate( 0, 1, angle, ji, A);
737 <  
738 <  // rotate about the y-axis
739 <  angle = dt2 * ji[1] / I[1][1];
740 <  this->rotate( 2, 0, angle, ji, A );
741 <  
742 <  // rotate about the x-axis
743 <  angle = dt2 * ji[0] / I[0][0];
744 <  this->rotate( 1, 2, angle, ji, A );
745 <  
746 <  dAtom->setA( A  );    
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 749 | 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 778 | Line 857 | template<typename T> double Integrator<T>::getConserve
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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