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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 746 by mmeineke, Thu Sep 4 21:48:35 2003 UTC vs.
Revision 1144 by tim, Sat May 1 18:52:38 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 +  integrableObjects = info->integrableObjects;
35  
36    // check for constraints
37  
# Line 65 | Line 69 | template<typename T> void Integrator<T>::checkConstrai
69  
70    SRI** theArray;
71    for (int i = 0; i < nMols; i++){
72 <    theArray = (SRI * *) molecules[i].getMyBonds();
72 >
73 >          theArray = (SRI * *) molecules[i].getMyBonds();
74      for (int j = 0; j < molecules[i].getNBonds(); j++){
75        constrained = theArray[j]->is_constrained();
76  
# Line 111 | Line 116 | template<typename T> void Integrator<T>::checkConstrai
116      }
117    }
118  
119 +
120    if (nConstrained > 0){
121      isConstrained = 1;
122  
# Line 132 | Line 138 | template<typename T> void Integrator<T>::checkConstrai
138      }
139  
140  
141 <    // save oldAtoms to check for lode balanceing later on.
141 >    // save oldAtoms to check for lode balancing later on.
142  
143      oldAtoms = nAtoms;
144  
# Line 147 | Line 153 | template<typename T> void Integrator<T>::integrate(voi
153  
154  
155   template<typename T> void Integrator<T>::integrate(void){
150 –  int i, j;                         // loop counters
156  
157    double runTime = info->run_time;
158    double sampleTime = info->sampleTime;
# Line 160 | Line 165 | template<typename T> void Integrator<T>::integrate(voi
165    double currThermal;
166    double currStatus;
167    double currReset;
168 <  
168 >
169    int calcPot, calcStress;
165 –  int isError;
170  
171    tStats = new Thermo(info);
172    statOut = new StatWriter(info);
173    dumpOut = new DumpWriter(info);
174  
175    atoms = info->atoms;
172 –  DirectionalAtom* dAtom;
176  
177    dt = info->dt;
178    dt2 = 0.5 * dt;
179  
180 +  readyCheck();
181 +
182 +  // remove center of mass drift velocity (in case we passed in a configuration
183 +  // that was drifting
184 +  tStats->removeCOMdrift();
185 +
186    // initialize the forces before the first step
187  
188    calcForce(1, 1);
189 +  
190 +  if (nConstrained){
191 +    preMove();
192 +    constrainA();
193 +    calcForce(1, 1);
194 +    constrainB();
195 +  }
196    
197    if (info->setTemp){
198      thermalize();
# Line 192 | Line 208 | template<typename T> void Integrator<T>::integrate(voi
208    dumpOut->writeDump(info->getTime());
209    statOut->writeStat(info->getTime());
210  
195 –  readyCheck();
211  
212   #ifdef IS_MPI
213    strcpy(checkPointMsg, "The integrator is ready to go.");
214    MPIcheckPoint();
215   #endif // is_mpi
216  
217 <  while (info->getTime() < runTime){
217 >  while (info->getTime() < runTime && !stopIntegrator()){
218      if ((info->getTime() + dt) >= currStatus){
219        calcPot = 1;
220        calcStress = 1;
221      }
222  
223 + #ifdef PROFILE
224 +    startProfile( pro1 );
225 + #endif
226 +    
227      integrateStep(calcPot, calcStress);
228  
229 + #ifdef PROFILE
230 +    endProfile( pro1 );
231 +
232 +    startProfile( pro2 );
233 + #endif // profile
234 +
235      info->incrTime(dt);
236  
237      if (info->setTemp){
# Line 222 | Line 247 | template<typename T> void Integrator<T>::integrate(voi
247      }
248  
249      if (info->getTime() >= currStatus){
250 <      statOut->writeStat(info->getTime());
251 <      calcPot = 0;
250 >      statOut->writeStat(info->getTime());
251 >      calcPot = 0;
252        calcStress = 0;
253        currStatus += statusTime;
254 <    }
254 >    }
255  
256      if (info->resetIntegrator){
257        if (info->getTime() >= currReset){
# Line 234 | Line 259 | template<typename T> void Integrator<T>::integrate(voi
259          currReset += resetTime;
260        }
261      }
262 +    
263 + #ifdef PROFILE
264 +    endProfile( pro2 );
265 + #endif //profile
266  
267   #ifdef IS_MPI
268      strcpy(checkPointMsg, "successfully took a time step.");
# Line 241 | Line 270 | template<typename T> void Integrator<T>::integrate(voi
270   #endif // is_mpi
271    }
272  
244 –  dumpOut->writeFinal(info->getTime());
245 –
273    delete dumpOut;
274    delete statOut;
275   }
# Line 250 | Line 277 | template<typename T> void Integrator<T>::integrateStep
277   template<typename T> void Integrator<T>::integrateStep(int calcPot,
278                                                         int calcStress){
279    // Position full step, and velocity half step
280 +
281 + #ifdef PROFILE
282 +  startProfile(pro3);
283 + #endif //profile
284 +
285    preMove();
286 +
287 + #ifdef PROFILE
288 +  endProfile(pro3);
289 +
290 +  startProfile(pro4);
291 + #endif // profile
292  
293    moveA();
294  
295 <  if (nConstrained){
296 <    constrainA();
297 <  }
295 > #ifdef PROFILE
296 >  endProfile(pro4);
297 >  
298 >  startProfile(pro5);
299 > #endif//profile
300  
301  
302   #ifdef IS_MPI
# Line 274 | Line 314 | template<typename T> void Integrator<T>::integrateStep
314    MPIcheckPoint();
315   #endif // is_mpi
316  
317 + #ifdef PROFILE
318 +  endProfile( pro5 );
319  
320 +  startProfile( pro6 );
321 + #endif //profile
322 +
323    // finish the velocity  half step
324  
325    moveB();
326  
327 <  if (nConstrained){
328 <    constrainB();
329 <  }
327 > #ifdef PROFILE
328 >  endProfile(pro6);
329 > #endif // profile
330  
331   #ifdef IS_MPI
332    strcpy(checkPointMsg, "Succesful moveB\n");
# Line 291 | Line 336 | template<typename T> void Integrator<T>::moveA(void){
336  
337  
338   template<typename T> void Integrator<T>::moveA(void){
339 <  int i, j;
339 >  size_t i, j;
340    DirectionalAtom* dAtom;
341    double Tb[3], ji[3];
297 –  double A[3][3], I[3][3];
298 –  double angle;
342    double vel[3], pos[3], frc[3];
343    double mass;
344 +
345 +  for (i = 0; i < integrableObjects.size() ; i++){
346 +    integrableObjects[i]->getVel(vel);
347 +    integrableObjects[i]->getPos(pos);
348 +    integrableObjects[i]->getFrc(frc);
349  
350 <  for (i = 0; i < nAtoms; i++){
351 <    atoms[i]->getVel(vel);
352 <    atoms[i]->getPos(pos);
305 <    atoms[i]->getFrc(frc);
350 >    std::cerr << "i =\t" << i << "\t" << frc[0] << "\t" << frc[1]<< "\t" << frc[2] << "\n";
351 >    
352 >    mass = integrableObjects[i]->getMass();
353  
307 –    mass = atoms[i]->getMass();
308 –
354      for (j = 0; j < 3; j++){
355        // velocity half step
356        vel[j] += (dt2 * frc[j] / mass) * eConvert;
# Line 313 | Line 358 | template<typename T> void Integrator<T>::moveA(void){
358        pos[j] += dt * vel[j];
359      }
360  
361 <    atoms[i]->setVel(vel);
362 <    atoms[i]->setPos(pos);
361 >    integrableObjects[i]->setVel(vel);
362 >    integrableObjects[i]->setPos(pos);
363  
364 <    if (atoms[i]->isDirectional()){
320 <      dAtom = (DirectionalAtom *) atoms[i];
364 >    if (integrableObjects[i]->isDirectional()){
365  
366        // get and convert the torque to body frame
367  
368 <      dAtom->getTrq(Tb);
369 <      dAtom->lab2Body(Tb);
368 >      integrableObjects[i]->getTrq(Tb);
369 >      integrableObjects[i]->lab2Body(Tb);
370  
371        // get the angular momentum, and propagate a half step
372  
373 <      dAtom->getJ(ji);
373 >      integrableObjects[i]->getJ(ji);
374  
375        for (j = 0; j < 3; j++)
376          ji[j] += (dt2 * Tb[j]) * eConvert;
377  
378 <      // use the angular velocities to propagate the rotation matrix a
335 <      // full time step
378 >      this->rotationPropagation( integrableObjects[i], ji );
379  
380 <      dAtom->getA(A);
381 <      dAtom->getI(I);
382 <
340 <      // rotate about the x-axis      
341 <      angle = dt2 * ji[0] / I[0][0];
342 <      this->rotate(1, 2, angle, ji, A);
380 >      integrableObjects[i]->setJ(ji);
381 >    }
382 >  }
383  
384 <      // rotate about the y-axis
385 <      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 <
361 <      dAtom->setJ(ji);
362 <      dAtom->setA(A);
363 <    }
384 >  if (nConstrained){
385 >    constrainA();
386    }
387   }
388  
389  
390   template<typename T> void Integrator<T>::moveB(void){
391    int i, j;
370 –  DirectionalAtom* dAtom;
392    double Tb[3], ji[3];
393    double vel[3], frc[3];
394    double mass;
395  
396 <  for (i = 0; i < nAtoms; i++){
397 <    atoms[i]->getVel(vel);
398 <    atoms[i]->getFrc(frc);
396 >  for (i = 0; i < integrableObjects.size(); i++){
397 >    integrableObjects[i]->getVel(vel);
398 >    integrableObjects[i]->getFrc(frc);
399  
400 <    mass = atoms[i]->getMass();
400 >    mass = integrableObjects[i]->getMass();
401  
402      // velocity half step
403      for (j = 0; j < 3; j++)
404        vel[j] += (dt2 * frc[j] / mass) * eConvert;
405  
406 <    atoms[i]->setVel(vel);
406 >    integrableObjects[i]->setVel(vel);
407  
408 <    if (atoms[i]->isDirectional()){
388 <      dAtom = (DirectionalAtom *) atoms[i];
408 >    if (integrableObjects[i]->isDirectional()){
409  
410 <      // get and convert the torque to body frame      
410 >      // get and convert the torque to body frame
411  
412 <      dAtom->getTrq(Tb);
413 <      dAtom->lab2Body(Tb);
412 >      integrableObjects[i]->getTrq(Tb);
413 >      integrableObjects[i]->lab2Body(Tb);
414  
415        // get the angular momentum, and propagate a half step
416  
417 <      dAtom->getJ(ji);
417 >      integrableObjects[i]->getJ(ji);
418  
419        for (j = 0; j < 3; j++)
420          ji[j] += (dt2 * Tb[j]) * eConvert;
421  
422  
423 <      dAtom->setJ(ji);
423 >      integrableObjects[i]->setJ(ji);
424      }
425    }
426 +
427 +  if (nConstrained){
428 +    constrainB();
429 +  }
430   }
431  
432   template<typename T> void Integrator<T>::preMove(void){
# Line 421 | Line 445 | template<typename T> void Integrator<T>::constrainA(){
445   }
446  
447   template<typename T> void Integrator<T>::constrainA(){
448 <  int i, j, k;
448 >  int i, j;
449    int done;
450    double posA[3], posB[3];
451    double velA[3], velB[3];
# Line 561 | Line 585 | template<typename T> void Integrator<T>::constrainA(){
585      painCave.isFatal = 1;
586      simError();
587    }
588 +
589   }
590  
591   template<typename T> void Integrator<T>::constrainB(void){
592 <  int i, j, k;
592 >  int i, j;
593    int done;
594    double posA[3], posB[3];
595    double velA[3], velB[3];
# Line 573 | Line 598 | template<typename T> void Integrator<T>::constrainB(vo
598    int a, b, ax, ay, az, bx, by, bz;
599    double rma, rmb;
600    double dx, dy, dz;
601 <  double rabsq, pabsq, rvab;
577 <  double diffsq;
601 >  double rvab;
602    double gab;
603    int iteration;
604  
# Line 661 | Line 685 | template<typename T> void Integrator<T>::constrainB(vo
685              iteration);
686      painCave.isFatal = 1;
687      simError();
688 +  }
689 + }
690 +
691 + template<typename T> void Integrator<T>::rotationPropagation
692 + ( StuntDouble* sd, double ji[3] ){
693 +
694 +  double angle;
695 +  double A[3][3], I[3][3];
696 +  int i, j, k;
697 +
698 +  // use the angular velocities to propagate the rotation matrix a
699 +  // full time step
700 +
701 +  sd->getA(A);
702 +  sd->getI(I);
703 +
704 +  if (sd->isLinear()) {
705 +    i = sd->linearAxis();
706 +    j = (i+1)%3;
707 +    k = (i+2)%3;
708 +    
709 +    angle = dt2 * ji[j] / I[j][j];
710 +    this->rotate( k, i, angle, ji, A );
711 +
712 +    angle = dt * ji[k] / I[k][k];
713 +    this->rotate( i, j, angle, ji, A);
714 +
715 +    angle = dt2 * ji[j] / I[j][j];
716 +    this->rotate( k, i, angle, ji, A );
717 +
718 +  } else {
719 +    // rotate about the x-axis
720 +    angle = dt2 * ji[0] / I[0][0];
721 +    this->rotate( 1, 2, angle, ji, A );
722 +    
723 +    // rotate about the y-axis
724 +    angle = dt2 * ji[1] / I[1][1];
725 +    this->rotate( 2, 0, angle, ji, A );
726 +    
727 +    // rotate about the z-axis
728 +    angle = dt * ji[2] / I[2][2];
729 +    this->rotate( 0, 1, angle, ji, A);
730 +    
731 +    // rotate about the y-axis
732 +    angle = dt2 * ji[1] / I[1][1];
733 +    this->rotate( 2, 0, angle, ji, A );
734 +    
735 +    // rotate about the x-axis
736 +    angle = dt2 * ji[0] / I[0][0];
737 +    this->rotate( 1, 2, angle, ji, A );
738 +    
739    }
740 +  sd->setA( A  );
741   }
742  
743   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
# Line 729 | Line 805 | template<typename T> void Integrator<T>::rotate(int ax
805      }
806    }
807  
808 <  // rotate the Rotation matrix acording to:
808 >  // rotate the Rotation matrix acording to:
809    //            A[][] = A[][] * transpose(rot[][])
810  
811  
# Line 754 | Line 830 | template<typename T> void Integrator<T>::thermalize(){
830   template<typename T> void Integrator<T>::thermalize(){
831    tStats->velocitize();
832   }
833 +
834 + template<typename T> double Integrator<T>::getConservedQuantity(void){
835 +  return tStats->getTotalE();
836 + }
837 + template<typename T> string Integrator<T>::getAdditionalParameters(void){
838 +  //By default, return a null string
839 +  //The reason we use string instead of char* is that if we use char*, we will
840 +  //return a pointer point to local variable which might cause problem
841 +  return string();
842 + }

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