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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 763 by tim, Mon Sep 15 16:52:02 2003 UTC vs.
Revision 1207 by chrisfen, Thu May 27 20:06:38 2004 UTC

# Line 1 | Line 1
1   #include <iostream>
2 < #include <cstdlib>
3 < #include <cmath>
2 > #include <stdlib.h>
3 > #include <math.h>
4  
5   #ifdef IS_MPI
6   #include "mpiSimulation.hpp"
7   #include <unistd.h>
8   #endif //is_mpi
9  
10 + #ifdef PROFILE
11 + #include "mdProfile.hpp"
12 + #endif // profile
13 +
14   #include "Integrator.hpp"
15   #include "simError.h"
16  
# Line 25 | Line 29 | template<typename T> Integrator<T>::Integrator(SimInfo
29    if (info->the_integrator != NULL){
30      delete info->the_integrator;
31    }
28 –  info->the_integrator = this;
32  
33    nAtoms = info->n_atoms;
34 <
34 >  integrableObjects = info->integrableObjects;
35 >
36    // check for constraints
37  
38    constrainedA = NULL;
# Line 41 | Line 45 | template<typename T> Integrator<T>::Integrator(SimInfo
45    nConstrained = 0;
46  
47    checkConstraints();
48 +
49   }
50  
51   template<typename T> Integrator<T>::~Integrator(){
# Line 65 | Line 70 | template<typename T> void Integrator<T>::checkConstrai
70  
71    SRI** theArray;
72    for (int i = 0; i < nMols; i++){
73 <    theArray = (SRI * *) molecules[i].getMyBonds();
73 >
74 >          theArray = (SRI * *) molecules[i].getMyBonds();
75      for (int j = 0; j < molecules[i].getNBonds(); j++){
76        constrained = theArray[j]->is_constrained();
77  
# Line 111 | Line 117 | template<typename T> void Integrator<T>::checkConstrai
117      }
118    }
119  
120 +
121    if (nConstrained > 0){
122      isConstrained = 1;
123  
# Line 132 | Line 139 | template<typename T> void Integrator<T>::checkConstrai
139      }
140  
141  
142 <    // save oldAtoms to check for lode balanceing later on.
142 >    // save oldAtoms to check for lode balancing later on.
143  
144      oldAtoms = nAtoms;
145  
# Line 147 | Line 154 | template<typename T> void Integrator<T>::integrate(voi
154  
155  
156   template<typename T> void Integrator<T>::integrate(void){
150 –  int i, j;                         // loop counters
157  
158    double runTime = info->run_time;
159    double sampleTime = info->sampleTime;
# Line 155 | Line 161 | template<typename T> void Integrator<T>::integrate(voi
161    double thermalTime = info->thermalTime;
162    double resetTime = info->resetTime;
163  
164 <
164 >  double difference;
165    double currSample;
166    double currThermal;
167    double currStatus;
168    double currReset;
169 <  
169 >
170    int calcPot, calcStress;
165 –  int isError;
171  
172    tStats = new Thermo(info);
173    statOut = new StatWriter(info);
174    dumpOut = new DumpWriter(info);
175  
176    atoms = info->atoms;
172 –  DirectionalAtom* dAtom;
177  
178    dt = info->dt;
179    dt2 = 0.5 * dt;
180  
181 +  readyCheck();
182 +
183 +  // remove center of mass drift velocity (in case we passed in a configuration
184 +  // that was drifting
185 +  tStats->removeCOMdrift();
186 +
187 +  // initialize the retraints if necessary
188 +  if (info->useThermInt) {
189 +    myFF->initRestraints();
190 +  }
191 +
192    // initialize the forces before the first step
193  
194    calcForce(1, 1);
195    
196 +  if (nConstrained){
197 +    preMove();
198 +    constrainA();
199 +    calcForce(1, 1);
200 +    constrainB();
201 +  }
202 +  
203    if (info->setTemp){
204      thermalize();
205    }
# Line 192 | Line 214 | template<typename T> void Integrator<T>::integrate(voi
214    dumpOut->writeDump(info->getTime());
215    statOut->writeStat(info->getTime());
216  
195 –  readyCheck();
217  
218   #ifdef IS_MPI
219    strcpy(checkPointMsg, "The integrator is ready to go.");
220    MPIcheckPoint();
221   #endif // is_mpi
222  
223 <  while (info->getTime() < runTime){
224 <    if ((info->getTime() + dt) >= currStatus){
223 >  while (info->getTime() < runTime && !stopIntegrator()){
224 >    difference = info->getTime() + dt - currStatus;
225 >    if (difference > 0 || fabs(difference) < 1e-4 ){
226        calcPot = 1;
227        calcStress = 1;
228      }
229  
230 + #ifdef PROFILE
231 +    startProfile( pro1 );
232 + #endif
233 +    
234      integrateStep(calcPot, calcStress);
235  
236 + #ifdef PROFILE
237 +    endProfile( pro1 );
238 +
239 +    startProfile( pro2 );
240 + #endif // profile
241 +
242      info->incrTime(dt);
243  
244      if (info->setTemp){
# Line 222 | Line 254 | template<typename T> void Integrator<T>::integrate(voi
254      }
255  
256      if (info->getTime() >= currStatus){
257 <      statOut->writeStat(info->getTime());
258 <      calcPot = 0;
257 >      statOut->writeStat(info->getTime());
258 >      if (info->useThermInt)
259 >        statOut->writeRaw(info->getTime());
260 >      calcPot = 0;
261        calcStress = 0;
262        currStatus += statusTime;
263 <    }
263 >    }
264  
265      if (info->resetIntegrator){
266        if (info->getTime() >= currReset){
# Line 234 | Line 268 | template<typename T> void Integrator<T>::integrate(voi
268          currReset += resetTime;
269        }
270      }
271 +    
272 + #ifdef PROFILE
273 +    endProfile( pro2 );
274 + #endif //profile
275  
276   #ifdef IS_MPI
277      strcpy(checkPointMsg, "successfully took a time step.");
# Line 241 | Line 279 | template<typename T> void Integrator<T>::integrate(voi
279   #endif // is_mpi
280    }
281  
282 <  dumpOut->writeFinal(info->getTime());
282 >  // dump out a file containing the omega values for the final configuration
283 >  if (info->useThermInt)
284 >    myFF->dumpzAngle();
285 >  
286  
287    delete dumpOut;
288    delete statOut;
# Line 250 | Line 291 | template<typename T> void Integrator<T>::integrateStep
291   template<typename T> void Integrator<T>::integrateStep(int calcPot,
292                                                         int calcStress){
293    // Position full step, and velocity half step
294 +
295 + #ifdef PROFILE
296 +  startProfile(pro3);
297 + #endif //profile
298 +
299    preMove();
300  
301 + #ifdef PROFILE
302 +  endProfile(pro3);
303 +
304 +  startProfile(pro4);
305 + #endif // profile
306 +
307    moveA();
308  
309 <  if (nConstrained){
310 <    constrainA();
311 <  }
309 > #ifdef PROFILE
310 >  endProfile(pro4);
311 >  
312 >  startProfile(pro5);
313 > #endif//profile
314  
315  
316   #ifdef IS_MPI
# Line 264 | Line 318 | template<typename T> void Integrator<T>::integrateStep
318    MPIcheckPoint();
319   #endif // is_mpi
320  
267 –
321    // calc forces
269 –
322    calcForce(calcPot, calcStress);
323  
324   #ifdef IS_MPI
# Line 274 | Line 326 | template<typename T> void Integrator<T>::integrateStep
326    MPIcheckPoint();
327   #endif // is_mpi
328  
329 + #ifdef PROFILE
330 +  endProfile( pro5 );
331  
332 +  startProfile( pro6 );
333 + #endif //profile
334 +
335    // finish the velocity  half step
336  
337    moveB();
338  
339 <  if (nConstrained){
340 <    constrainB();
341 <  }
339 > #ifdef PROFILE
340 >  endProfile(pro6);
341 > #endif // profile
342  
343   #ifdef IS_MPI
344    strcpy(checkPointMsg, "Succesful moveB\n");
# Line 291 | Line 348 | template<typename T> void Integrator<T>::moveA(void){
348  
349  
350   template<typename T> void Integrator<T>::moveA(void){
351 <  int i, j;
351 >  size_t i, j;
352    DirectionalAtom* dAtom;
353    double Tb[3], ji[3];
297 –  double A[3][3], I[3][3];
298 –  double angle;
354    double vel[3], pos[3], frc[3];
355    double mass;
356 +  double omega;
357 +
358 +  for (i = 0; i < integrableObjects.size() ; i++){
359 +    integrableObjects[i]->getVel(vel);
360 +    integrableObjects[i]->getPos(pos);
361 +    integrableObjects[i]->getFrc(frc);
362 +    
363 +    mass = integrableObjects[i]->getMass();
364  
302 –  for (i = 0; i < nAtoms; i++){
303 –    atoms[i]->getVel(vel);
304 –    atoms[i]->getPos(pos);
305 –    atoms[i]->getFrc(frc);
306 –
307 –    mass = atoms[i]->getMass();
308 –
365      for (j = 0; j < 3; j++){
366        // velocity half step
367        vel[j] += (dt2 * frc[j] / mass) * eConvert;
# Line 313 | Line 369 | template<typename T> void Integrator<T>::moveA(void){
369        pos[j] += dt * vel[j];
370      }
371  
372 <    atoms[i]->setVel(vel);
373 <    atoms[i]->setPos(pos);
372 >    integrableObjects[i]->setVel(vel);
373 >    integrableObjects[i]->setPos(pos);
374  
375 <    if (atoms[i]->isDirectional()){
320 <      dAtom = (DirectionalAtom *) atoms[i];
375 >    if (integrableObjects[i]->isDirectional()){
376  
377        // get and convert the torque to body frame
378  
379 <      dAtom->getTrq(Tb);
380 <      dAtom->lab2Body(Tb);
379 >      integrableObjects[i]->getTrq(Tb);
380 >      integrableObjects[i]->lab2Body(Tb);
381  
382        // get the angular momentum, and propagate a half step
383  
384 <      dAtom->getJ(ji);
384 >      integrableObjects[i]->getJ(ji);
385  
386        for (j = 0; j < 3; j++)
387          ji[j] += (dt2 * Tb[j]) * eConvert;
388  
389 <      // use the angular velocities to propagate the rotation matrix a
335 <      // full time step
389 >      this->rotationPropagation( integrableObjects[i], ji );
390  
391 <      dAtom->getA(A);
338 <      dAtom->getI(I);
339 <
340 <      // rotate about the x-axis      
341 <      angle = dt2 * ji[0] / I[0][0];
342 <      this->rotate(1, 2, angle, ji, A);
343 <
344 <      // rotate about the y-axis
345 <      angle = dt2 * ji[1] / I[1][1];
346 <      this->rotate(2, 0, angle, ji, A);
347 <
348 <      // rotate about the z-axis
349 <      angle = dt * ji[2] / I[2][2];
350 <      this->rotate(0, 1, angle, ji, A);
351 <
352 <      // rotate about the y-axis
353 <      angle = dt2 * ji[1] / I[1][1];
354 <      this->rotate(2, 0, angle, ji, A);
355 <
356 <      // rotate about the x-axis
357 <      angle = dt2 * ji[0] / I[0][0];
358 <      this->rotate(1, 2, angle, ji, A);
359 <
360 <      dAtom->setJ(ji);
361 <      dAtom->setA(A);
391 >      integrableObjects[i]->setJ(ji);
392      }
393    }
394 +
395 +  if (nConstrained){
396 +    constrainA();
397 +  }
398   }
399  
400  
401   template<typename T> void Integrator<T>::moveB(void){
402    int i, j;
369 –  DirectionalAtom* dAtom;
403    double Tb[3], ji[3];
404    double vel[3], frc[3];
405    double mass;
406  
407 <  for (i = 0; i < nAtoms; i++){
408 <    atoms[i]->getVel(vel);
409 <    atoms[i]->getFrc(frc);
407 >  for (i = 0; i < integrableObjects.size(); i++){
408 >    integrableObjects[i]->getVel(vel);
409 >    integrableObjects[i]->getFrc(frc);
410  
411 <    mass = atoms[i]->getMass();
411 >    mass = integrableObjects[i]->getMass();
412  
413      // velocity half step
414      for (j = 0; j < 3; j++)
415        vel[j] += (dt2 * frc[j] / mass) * eConvert;
416  
417 <    atoms[i]->setVel(vel);
417 >    integrableObjects[i]->setVel(vel);
418  
419 <    if (atoms[i]->isDirectional()){
387 <      dAtom = (DirectionalAtom *) atoms[i];
419 >    if (integrableObjects[i]->isDirectional()){
420  
421 <      // get and convert the torque to body frame      
421 >      // get and convert the torque to body frame
422  
423 <      dAtom->getTrq(Tb);
424 <      dAtom->lab2Body(Tb);
423 >      integrableObjects[i]->getTrq(Tb);
424 >      integrableObjects[i]->lab2Body(Tb);
425  
426        // get the angular momentum, and propagate a half step
427  
428 <      dAtom->getJ(ji);
428 >      integrableObjects[i]->getJ(ji);
429  
430        for (j = 0; j < 3; j++)
431          ji[j] += (dt2 * Tb[j]) * eConvert;
432  
433  
434 <      dAtom->setJ(ji);
434 >      integrableObjects[i]->setJ(ji);
435      }
436    }
437 +
438 +  if (nConstrained){
439 +    constrainB();
440 +  }
441   }
442  
443   template<typename T> void Integrator<T>::preMove(void){
# Line 420 | Line 456 | template<typename T> void Integrator<T>::constrainA(){
456   }
457  
458   template<typename T> void Integrator<T>::constrainA(){
459 <  int i, j, k;
459 >  int i, j;
460    int done;
461    double posA[3], posB[3];
462    double velA[3], velB[3];
# Line 560 | Line 596 | template<typename T> void Integrator<T>::constrainA(){
596      painCave.isFatal = 1;
597      simError();
598    }
599 +
600   }
601  
602   template<typename T> void Integrator<T>::constrainB(void){
603 <  int i, j, k;
603 >  int i, j;
604    int done;
605    double posA[3], posB[3];
606    double velA[3], velB[3];
# Line 572 | Line 609 | template<typename T> void Integrator<T>::constrainB(vo
609    int a, b, ax, ay, az, bx, by, bz;
610    double rma, rmb;
611    double dx, dy, dz;
612 <  double rabsq, pabsq, rvab;
576 <  double diffsq;
612 >  double rvab;
613    double gab;
614    int iteration;
615  
# Line 663 | Line 699 | template<typename T> void Integrator<T>::constrainB(vo
699    }
700   }
701  
702 + template<typename T> void Integrator<T>::rotationPropagation
703 + ( StuntDouble* sd, double ji[3] ){
704 +
705 +  double angle;
706 +  double A[3][3], I[3][3];
707 +  int i, j, k;
708 +
709 +  // use the angular velocities to propagate the rotation matrix a
710 +  // full time step
711 +
712 +  sd->getA(A);
713 +  sd->getI(I);
714 +
715 +  if (sd->isLinear()) {
716 +    i = sd->linearAxis();
717 +    j = (i+1)%3;
718 +    k = (i+2)%3;
719 +    
720 +    angle = dt2 * ji[j] / I[j][j];
721 +    this->rotate( k, i, angle, ji, A );
722 +
723 +    angle = dt * ji[k] / I[k][k];
724 +    this->rotate( i, j, angle, ji, A);
725 +
726 +    angle = dt2 * ji[j] / I[j][j];
727 +    this->rotate( k, i, angle, ji, A );
728 +
729 +  } else {
730 +    // rotate about the x-axis
731 +    angle = dt2 * ji[0] / I[0][0];
732 +    this->rotate( 1, 2, angle, ji, A );
733 +    
734 +    // rotate about the y-axis
735 +    angle = dt2 * ji[1] / I[1][1];
736 +    this->rotate( 2, 0, angle, ji, A );
737 +    
738 +    // rotate about the z-axis
739 +    angle = dt * ji[2] / I[2][2];
740 +    sd->addZangle(angle);
741 +    this->rotate( 0, 1, angle, ji, A);
742 +    
743 +    // rotate about the y-axis
744 +    angle = dt2 * ji[1] / I[1][1];
745 +    this->rotate( 2, 0, angle, ji, A );
746 +    
747 +    // rotate about the x-axis
748 +    angle = dt2 * ji[0] / I[0][0];
749 +    this->rotate( 1, 2, angle, ji, A );
750 +    
751 +  }
752 +  sd->setA( A  );
753 + }
754 +
755   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
756                                                  double angle, double ji[3],
757                                                  double A[3][3]){
# Line 728 | Line 817 | template<typename T> void Integrator<T>::rotate(int ax
817      }
818    }
819  
820 <  // rotate the Rotation matrix acording to:
820 >  // rotate the Rotation matrix acording to:
821    //            A[][] = A[][] * transpose(rot[][])
822  
823  
# Line 756 | Line 845 | template<typename T> double Integrator<T>::getConserve
845  
846   template<typename T> double Integrator<T>::getConservedQuantity(void){
847    return tStats->getTotalE();
848 < }
848 > }
849 > template<typename T> string Integrator<T>::getAdditionalParameters(void){
850 >  //By default, return a null string
851 >  //The reason we use string instead of char* is that if we use char*, we will
852 >  //return a pointer point to local variable which might cause problem
853 >  return string();
854 > }

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