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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 755 by mmeineke, Tue Sep 9 20:35:25 2003 UTC vs.
Revision 1187 by chrisfen, Sat May 22 18:16:18 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 >      statOut->writeRaw(info->getTime());
259 >      calcPot = 0;
260        calcStress = 0;
261        currStatus += statusTime;
262 <    }
262 >    }
263  
264      if (info->resetIntegrator){
265        if (info->getTime() >= currReset){
# Line 234 | Line 267 | template<typename T> void Integrator<T>::integrate(voi
267          currReset += resetTime;
268        }
269      }
270 +    
271 + #ifdef PROFILE
272 +    endProfile( pro2 );
273 + #endif //profile
274  
275   #ifdef IS_MPI
276      strcpy(checkPointMsg, "successfully took a time step.");
# Line 241 | Line 278 | template<typename T> void Integrator<T>::integrate(voi
278   #endif // is_mpi
279    }
280  
281 <  dumpOut->writeFinal(info->getTime());
281 >  // dump out a file containing the omega values for the final configuration
282 >  if (info->useThermInt)
283 >    myFF->dumpzAngle();
284 >  
285  
286    delete dumpOut;
287    delete statOut;
# Line 250 | Line 290 | template<typename T> void Integrator<T>::integrateStep
290   template<typename T> void Integrator<T>::integrateStep(int calcPot,
291                                                         int calcStress){
292    // Position full step, and velocity half step
293 +
294 + #ifdef PROFILE
295 +  startProfile(pro3);
296 + #endif //profile
297 +
298    preMove();
299  
300 + #ifdef PROFILE
301 +  endProfile(pro3);
302 +
303 +  startProfile(pro4);
304 + #endif // profile
305 +
306    moveA();
307  
308 <  if (nConstrained){
309 <    constrainA();
310 <  }
308 > #ifdef PROFILE
309 >  endProfile(pro4);
310 >  
311 >  startProfile(pro5);
312 > #endif//profile
313  
314  
315   #ifdef IS_MPI
# Line 264 | Line 317 | template<typename T> void Integrator<T>::integrateStep
317    MPIcheckPoint();
318   #endif // is_mpi
319  
267 –
320    // calc forces
269 –
321    calcForce(calcPot, calcStress);
322  
323   #ifdef IS_MPI
# Line 274 | Line 325 | template<typename T> void Integrator<T>::integrateStep
325    MPIcheckPoint();
326   #endif // is_mpi
327  
328 + #ifdef PROFILE
329 +  endProfile( pro5 );
330  
331 +  startProfile( pro6 );
332 + #endif //profile
333 +
334    // finish the velocity  half step
335  
336    moveB();
337  
338 <  if (nConstrained){
339 <    constrainB();
340 <  }
338 > #ifdef PROFILE
339 >  endProfile(pro6);
340 > #endif // profile
341  
342   #ifdef IS_MPI
343    strcpy(checkPointMsg, "Succesful moveB\n");
# Line 291 | Line 347 | template<typename T> void Integrator<T>::moveA(void){
347  
348  
349   template<typename T> void Integrator<T>::moveA(void){
350 <  int i, j;
350 >  size_t i, j;
351    DirectionalAtom* dAtom;
352    double Tb[3], ji[3];
297 –  double A[3][3], I[3][3];
298 –  double angle;
353    double vel[3], pos[3], frc[3];
354    double mass;
355 +  double omega;
356 +
357 +  for (i = 0; i < integrableObjects.size() ; i++){
358 +    integrableObjects[i]->getVel(vel);
359 +    integrableObjects[i]->getPos(pos);
360 +    integrableObjects[i]->getFrc(frc);
361 +    
362 +    mass = integrableObjects[i]->getMass();
363  
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 –
364      for (j = 0; j < 3; j++){
365        // velocity half step
366        vel[j] += (dt2 * frc[j] / mass) * eConvert;
# Line 313 | Line 368 | template<typename T> void Integrator<T>::moveA(void){
368        pos[j] += dt * vel[j];
369      }
370  
371 <    atoms[i]->setVel(vel);
372 <    atoms[i]->setPos(pos);
371 >    integrableObjects[i]->setVel(vel);
372 >    integrableObjects[i]->setPos(pos);
373  
374 <    if (atoms[i]->isDirectional()){
320 <      dAtom = (DirectionalAtom *) atoms[i];
374 >    if (integrableObjects[i]->isDirectional()){
375  
376        // get and convert the torque to body frame
377  
378 <      dAtom->getTrq(Tb);
379 <      dAtom->lab2Body(Tb);
378 >      integrableObjects[i]->getTrq(Tb);
379 >      integrableObjects[i]->lab2Body(Tb);
380  
381        // get the angular momentum, and propagate a half step
382  
383 <      dAtom->getJ(ji);
383 >      integrableObjects[i]->getJ(ji);
384  
385        for (j = 0; j < 3; j++)
386          ji[j] += (dt2 * Tb[j]) * eConvert;
387  
388 <      // use the angular velocities to propagate the rotation matrix a
389 <      // full time step
390 <
337 <      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);
388 >      this->rotationPropagation( integrableObjects[i], ji );
389 >
390 >      integrableObjects[i]->setJ(ji);
391      }
392    }
393 +
394 +  if (nConstrained){
395 +    constrainA();
396 +  }
397   }
398  
399  
400   template<typename T> void Integrator<T>::moveB(void){
401    int i, j;
369 –  DirectionalAtom* dAtom;
402    double Tb[3], ji[3];
403    double vel[3], frc[3];
404    double mass;
405  
406 <  for (i = 0; i < nAtoms; i++){
407 <    atoms[i]->getVel(vel);
408 <    atoms[i]->getFrc(frc);
406 >  for (i = 0; i < integrableObjects.size(); i++){
407 >    integrableObjects[i]->getVel(vel);
408 >    integrableObjects[i]->getFrc(frc);
409  
410 <    mass = atoms[i]->getMass();
410 >    mass = integrableObjects[i]->getMass();
411  
412      // velocity half step
413      for (j = 0; j < 3; j++)
414        vel[j] += (dt2 * frc[j] / mass) * eConvert;
415  
416 <    atoms[i]->setVel(vel);
416 >    integrableObjects[i]->setVel(vel);
417  
418 <    if (atoms[i]->isDirectional()){
387 <      dAtom = (DirectionalAtom *) atoms[i];
418 >    if (integrableObjects[i]->isDirectional()){
419  
420 <      // get and convert the torque to body frame      
420 >      // get and convert the torque to body frame
421  
422 <      dAtom->getTrq(Tb);
423 <      dAtom->lab2Body(Tb);
422 >      integrableObjects[i]->getTrq(Tb);
423 >      integrableObjects[i]->lab2Body(Tb);
424  
425        // get the angular momentum, and propagate a half step
426  
427 <      dAtom->getJ(ji);
427 >      integrableObjects[i]->getJ(ji);
428  
429        for (j = 0; j < 3; j++)
430          ji[j] += (dt2 * Tb[j]) * eConvert;
431  
432  
433 <      dAtom->setJ(ji);
433 >      integrableObjects[i]->setJ(ji);
434      }
435    }
436 +
437 +  if (nConstrained){
438 +    constrainB();
439 +  }
440   }
441  
442   template<typename T> void Integrator<T>::preMove(void){
# Line 420 | Line 455 | template<typename T> void Integrator<T>::constrainA(){
455   }
456  
457   template<typename T> void Integrator<T>::constrainA(){
458 <  int i, j, k;
458 >  int i, j;
459    int done;
460    double posA[3], posB[3];
461    double velA[3], velB[3];
# Line 560 | Line 595 | template<typename T> void Integrator<T>::constrainA(){
595      painCave.isFatal = 1;
596      simError();
597    }
598 +
599   }
600  
601   template<typename T> void Integrator<T>::constrainB(void){
602 <  int i, j, k;
602 >  int i, j;
603    int done;
604    double posA[3], posB[3];
605    double velA[3], velB[3];
# Line 572 | Line 608 | template<typename T> void Integrator<T>::constrainB(vo
608    int a, b, ax, ay, az, bx, by, bz;
609    double rma, rmb;
610    double dx, dy, dz;
611 <  double rabsq, pabsq, rvab;
576 <  double diffsq;
611 >  double rvab;
612    double gab;
613    int iteration;
614  
# Line 663 | Line 698 | template<typename T> void Integrator<T>::rotate(int ax
698    }
699   }
700  
701 + template<typename T> void Integrator<T>::rotationPropagation
702 + ( StuntDouble* sd, double ji[3] ){
703 +
704 +  double angle;
705 +  double A[3][3], I[3][3];
706 +  int i, j, k;
707 +
708 +  // use the angular velocities to propagate the rotation matrix a
709 +  // full time step
710 +
711 +  sd->getA(A);
712 +  sd->getI(I);
713 +
714 +  if (sd->isLinear()) {
715 +    i = sd->linearAxis();
716 +    j = (i+1)%3;
717 +    k = (i+2)%3;
718 +    
719 +    angle = dt2 * ji[j] / I[j][j];
720 +    this->rotate( k, i, angle, ji, A );
721 +
722 +    angle = dt * ji[k] / I[k][k];
723 +    this->rotate( i, j, angle, ji, A);
724 +
725 +    angle = dt2 * ji[j] / I[j][j];
726 +    this->rotate( k, i, angle, ji, A );
727 +
728 +  } else {
729 +    // rotate about the x-axis
730 +    angle = dt2 * ji[0] / I[0][0];
731 +    this->rotate( 1, 2, angle, ji, A );
732 +    
733 +    // rotate about the y-axis
734 +    angle = dt2 * ji[1] / I[1][1];
735 +    this->rotate( 2, 0, angle, ji, A );
736 +    
737 +    // rotate about the z-axis
738 +    angle = dt * ji[2] / I[2][2];
739 +    sd->addZangle(angle);
740 +    this->rotate( 0, 1, angle, ji, A);
741 +    
742 +    // rotate about the y-axis
743 +    angle = dt2 * ji[1] / I[1][1];
744 +    this->rotate( 2, 0, angle, ji, A );
745 +    
746 +    // rotate about the x-axis
747 +    angle = dt2 * ji[0] / I[0][0];
748 +    this->rotate( 1, 2, angle, ji, A );
749 +    
750 +  }
751 +  sd->setA( A  );
752 + }
753 +
754   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
755                                                  double angle, double ji[3],
756                                                  double A[3][3]){
# Line 728 | Line 816 | template<typename T> void Integrator<T>::rotate(int ax
816      }
817    }
818  
819 <  // rotate the Rotation matrix acording to:
819 >  // rotate the Rotation matrix acording to:
820    //            A[][] = A[][] * transpose(rot[][])
821  
822  
# Line 753 | Line 841 | template<typename T> void Integrator<T>::thermalize(){
841   template<typename T> void Integrator<T>::thermalize(){
842    tStats->velocitize();
843   }
844 +
845 + template<typename T> double Integrator<T>::getConservedQuantity(void){
846 +  return tStats->getTotalE();
847 + }
848 + template<typename T> string Integrator<T>::getAdditionalParameters(void){
849 +  //By default, return a null string
850 +  //The reason we use string instead of char* is that if we use char*, we will
851 +  //return a pointer point to local variable which might cause problem
852 +  return string();
853 + }

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