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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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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 1113 by tim, Thu Apr 15 16:18:26 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;
159    double statusTime = info->statusTime;
160    double thermalTime = info->thermalTime;
161 +  double resetTime = info->resetTime;
162  
163 +
164    double currSample;
165    double currThermal;
166    double currStatus;
167 +  double currReset;
168  
169    int calcPot, calcStress;
162 –  int isError;
170  
171    tStats = new Thermo(info);
172    statOut = new StatWriter(info);
173    dumpOut = new DumpWriter(info);
174  
175    atoms = info->atoms;
169 –  DirectionalAtom* dAtom;
176  
177    dt = info->dt;
178    dt2 = 0.5 * dt;
179  
180 +  readyCheck();
181 +
182    // initialize the forces before the first step
183  
184    calcForce(1, 1);
185 <  // myFF->doForces(1,1);
186 <
185 >  
186 >  if (nConstrained){
187 >    preMove();
188 >    constrainA();
189 >    calcForce(1, 1);
190 >    constrainB();
191 >  }
192 >  
193    if (info->setTemp){
194      thermalize();
195    }
196  
183 –  calcPot = 0;
184 –  calcStress = 0;
185 –  currSample = sampleTime;
186 –  currThermal = thermalTime;
187 –  currStatus = statusTime;
188 –  
197    calcPot     = 0;
198    calcStress  = 0;
199    currSample  = sampleTime + info->getTime();
200    currThermal = thermalTime+ info->getTime();
201    currStatus  = statusTime + info->getTime();
202 +  currReset   = resetTime  + info->getTime();
203  
204    dumpOut->writeDump(info->getTime());
205    statOut->writeStat(info->getTime());
206  
198 –  readyCheck();
207  
208   #ifdef IS_MPI
209    strcpy(checkPointMsg, "The integrator is ready to go.");
210    MPIcheckPoint();
211   #endif // is_mpi
212  
213 <  while (info->getTime() < runTime){
213 >  while (info->getTime() < runTime && !stopIntegrator()){
214      if ((info->getTime() + dt) >= currStatus){
215        calcPot = 1;
216        calcStress = 1;
217      }
218  
219 + #ifdef PROFILE
220 +    startProfile( pro1 );
221 + #endif
222 +    
223      integrateStep(calcPot, calcStress);
224  
225 + #ifdef PROFILE
226 +    endProfile( pro1 );
227 +
228 +    startProfile( pro2 );
229 + #endif // profile
230 +
231      info->incrTime(dt);
232  
233      if (info->setTemp){
# Line 225 | Line 243 | template<typename T> void Integrator<T>::integrate(voi
243      }
244  
245      if (info->getTime() >= currStatus){
246 <      statOut->writeStat(info->getTime());
247 <      calcPot = 0;
246 >      statOut->writeStat(info->getTime());
247 >      calcPot = 0;
248        calcStress = 0;
249        currStatus += statusTime;
250 <    }
250 >    }
251 >
252 >    if (info->resetIntegrator){
253 >      if (info->getTime() >= currReset){
254 >        this->resetIntegrator();
255 >        currReset += resetTime;
256 >      }
257 >    }
258 >    
259 > #ifdef PROFILE
260 >    endProfile( pro2 );
261 > #endif //profile
262  
263   #ifdef IS_MPI
264      strcpy(checkPointMsg, "successfully took a time step.");
# Line 237 | Line 266 | template<typename T> void Integrator<T>::integrate(voi
266   #endif // is_mpi
267    }
268  
240 –  dumpOut->writeFinal(info->getTime());
241 –
269    delete dumpOut;
270    delete statOut;
271   }
# Line 246 | Line 273 | template<typename T> void Integrator<T>::integrateStep
273   template<typename T> void Integrator<T>::integrateStep(int calcPot,
274                                                         int calcStress){
275    // Position full step, and velocity half step
276 +
277 + #ifdef PROFILE
278 +  startProfile(pro3);
279 + #endif //profile
280 +
281    preMove();
282  
283 + #ifdef PROFILE
284 +  endProfile(pro3);
285 +
286 +  startProfile(pro4);
287 + #endif // profile
288 +
289    moveA();
290  
291 <  if (nConstrained){
292 <    constrainA();
293 <  }
291 > #ifdef PROFILE
292 >  endProfile(pro4);
293 >  
294 >  startProfile(pro5);
295 > #endif//profile
296  
297  
298   #ifdef IS_MPI
# Line 270 | Line 310 | template<typename T> void Integrator<T>::integrateStep
310    MPIcheckPoint();
311   #endif // is_mpi
312  
313 + #ifdef PROFILE
314 +  endProfile( pro5 );
315  
316 +  startProfile( pro6 );
317 + #endif //profile
318 +
319    // finish the velocity  half step
320  
321    moveB();
322  
323 <  if (nConstrained){
324 <    constrainB();
325 <  }
323 > #ifdef PROFILE
324 >  endProfile(pro6);
325 > #endif // profile
326  
327   #ifdef IS_MPI
328    strcpy(checkPointMsg, "Succesful moveB\n");
# Line 287 | Line 332 | template<typename T> void Integrator<T>::moveA(void){
332  
333  
334   template<typename T> void Integrator<T>::moveA(void){
335 <  int i, j;
335 >  size_t i, j;
336    DirectionalAtom* dAtom;
337    double Tb[3], ji[3];
293 –  double A[3][3], I[3][3];
294 –  double angle;
338    double vel[3], pos[3], frc[3];
339    double mass;
340 +
341 +  for (i = 0; i < integrableObjects.size() ; i++){
342 +    integrableObjects[i]->getVel(vel);
343 +    integrableObjects[i]->getPos(pos);
344 +    integrableObjects[i]->getFrc(frc);
345 +    
346 +    mass = integrableObjects[i]->getMass();
347  
298 –  for (i = 0; i < nAtoms; i++){
299 –    atoms[i]->getVel(vel);
300 –    atoms[i]->getPos(pos);
301 –    atoms[i]->getFrc(frc);
302 –
303 –    mass = atoms[i]->getMass();
304 –
348      for (j = 0; j < 3; j++){
349        // velocity half step
350        vel[j] += (dt2 * frc[j] / mass) * eConvert;
# Line 309 | Line 352 | template<typename T> void Integrator<T>::moveA(void){
352        pos[j] += dt * vel[j];
353      }
354  
355 <    atoms[i]->setVel(vel);
356 <    atoms[i]->setPos(pos);
355 >    integrableObjects[i]->setVel(vel);
356 >    integrableObjects[i]->setPos(pos);
357  
358 <    if (atoms[i]->isDirectional()){
316 <      dAtom = (DirectionalAtom *) atoms[i];
358 >    if (integrableObjects[i]->isDirectional()){
359  
360        // get and convert the torque to body frame
361  
362 <      dAtom->getTrq(Tb);
363 <      dAtom->lab2Body(Tb);
362 >      integrableObjects[i]->getTrq(Tb);
363 >      integrableObjects[i]->lab2Body(Tb);
364  
365        // get the angular momentum, and propagate a half step
366  
367 <      dAtom->getJ(ji);
367 >      integrableObjects[i]->getJ(ji);
368  
369        for (j = 0; j < 3; j++)
370          ji[j] += (dt2 * Tb[j]) * eConvert;
371  
372 <      // use the angular velocities to propagate the rotation matrix a
331 <      // full time step
372 >      this->rotationPropagation( integrableObjects[i], ji );
373  
374 <      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);
374 >      integrableObjects[i]->setJ(ji);
375      }
376    }
377 +
378 +  if (nConstrained){
379 +    constrainA();
380 +  }
381   }
382  
383  
384   template<typename T> void Integrator<T>::moveB(void){
385    int i, j;
366 –  DirectionalAtom* dAtom;
386    double Tb[3], ji[3];
387    double vel[3], frc[3];
388    double mass;
389  
390 <  for (i = 0; i < nAtoms; i++){
391 <    atoms[i]->getVel(vel);
392 <    atoms[i]->getFrc(frc);
390 >  for (i = 0; i < integrableObjects.size(); i++){
391 >    integrableObjects[i]->getVel(vel);
392 >    integrableObjects[i]->getFrc(frc);
393  
394 <    mass = atoms[i]->getMass();
394 >    mass = integrableObjects[i]->getMass();
395  
396      // velocity half step
397      for (j = 0; j < 3; j++)
398        vel[j] += (dt2 * frc[j] / mass) * eConvert;
399  
400 <    atoms[i]->setVel(vel);
400 >    integrableObjects[i]->setVel(vel);
401  
402 <    if (atoms[i]->isDirectional()){
384 <      dAtom = (DirectionalAtom *) atoms[i];
402 >    if (integrableObjects[i]->isDirectional()){
403  
404 <      // get and convert the torque to body frame      
404 >      // get and convert the torque to body frame
405  
406 <      dAtom->getTrq(Tb);
407 <      dAtom->lab2Body(Tb);
406 >      integrableObjects[i]->getTrq(Tb);
407 >      integrableObjects[i]->lab2Body(Tb);
408  
409        // get the angular momentum, and propagate a half step
410  
411 <      dAtom->getJ(ji);
411 >      integrableObjects[i]->getJ(ji);
412  
413        for (j = 0; j < 3; j++)
414          ji[j] += (dt2 * Tb[j]) * eConvert;
415  
416  
417 <      dAtom->setJ(ji);
417 >      integrableObjects[i]->setJ(ji);
418      }
419    }
420 +
421 +  if (nConstrained){
422 +    constrainB();
423 +  }
424   }
425  
426   template<typename T> void Integrator<T>::preMove(void){
# Line 417 | Line 439 | template<typename T> void Integrator<T>::constrainA(){
439   }
440  
441   template<typename T> void Integrator<T>::constrainA(){
442 <  int i, j, k;
442 >  int i, j;
443    int done;
444    double posA[3], posB[3];
445    double velA[3], velB[3];
# Line 557 | Line 579 | template<typename T> void Integrator<T>::constrainA(){
579      painCave.isFatal = 1;
580      simError();
581    }
582 +
583   }
584  
585   template<typename T> void Integrator<T>::constrainB(void){
586 <  int i, j, k;
586 >  int i, j;
587    int done;
588    double posA[3], posB[3];
589    double velA[3], velB[3];
# Line 569 | Line 592 | template<typename T> void Integrator<T>::constrainB(vo
592    int a, b, ax, ay, az, bx, by, bz;
593    double rma, rmb;
594    double dx, dy, dz;
595 <  double rabsq, pabsq, rvab;
573 <  double diffsq;
595 >  double rvab;
596    double gab;
597    int iteration;
598  
# Line 660 | Line 682 | template<typename T> void Integrator<T>::constrainB(vo
682    }
683   }
684  
685 + template<typename T> void Integrator<T>::rotationPropagation
686 + ( StuntDouble* sd, double ji[3] ){
687 +
688 +  double angle;
689 +  double A[3][3], I[3][3];
690 +
691 +  // use the angular velocities to propagate the rotation matrix a
692 +  // full time step
693 +
694 +  sd->getA(A);
695 +  sd->getI(I);
696 +
697 +  // rotate about the x-axis
698 +  angle = dt2 * ji[0] / I[0][0];
699 +  this->rotate( 1, 2, angle, ji, A );
700 +
701 +  // rotate about the y-axis
702 +  angle = dt2 * ji[1] / I[1][1];
703 +  this->rotate( 2, 0, angle, ji, A );
704 +
705 +  // rotate about the z-axis
706 +  angle = dt * ji[2] / I[2][2];
707 +  this->rotate( 0, 1, angle, ji, A);
708 +
709 +  // rotate about the y-axis
710 +  angle = dt2 * ji[1] / I[1][1];
711 +  this->rotate( 2, 0, angle, ji, A );
712 +
713 +  // rotate about the x-axis
714 +  angle = dt2 * ji[0] / I[0][0];
715 +  this->rotate( 1, 2, angle, ji, A );
716 +
717 +  sd->setA( A  );
718 + }
719 +
720   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
721                                                  double angle, double ji[3],
722                                                  double A[3][3]){
# Line 725 | Line 782 | template<typename T> void Integrator<T>::rotate(int ax
782      }
783    }
784  
785 <  // rotate the Rotation matrix acording to:
785 >  // rotate the Rotation matrix acording to:
786    //            A[][] = A[][] * transpose(rot[][])
787  
788  
# Line 750 | Line 807 | template<typename T> void Integrator<T>::thermalize(){
807   template<typename T> void Integrator<T>::thermalize(){
808    tStats->velocitize();
809   }
810 +
811 + template<typename T> double Integrator<T>::getConservedQuantity(void){
812 +  return tStats->getTotalE();
813 + }
814 + template<typename T> string Integrator<T>::getAdditionalParameters(void){
815 +  //By default, return a null string
816 +  //The reason we use string instead of char* is that if we use char*, we will
817 +  //return a pointer point to local variable which might cause problem
818 +  return string();
819 + }

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