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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 1127 by tim, Tue Apr 20 16:56:40 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 +  // 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 <  // myFF->doForces(1,1);
190 <
189 >  
190 >  if (nConstrained){
191 >    preMove();
192 >    constrainA();
193 >    calcForce(1, 1);
194 >    constrainB();
195 >  }
196 >  
197    if (info->setTemp){
198      thermalize();
199    }
200  
183 –  calcPot = 0;
184 –  calcStress = 0;
185 –  currSample = sampleTime;
186 –  currThermal = thermalTime;
187 –  currStatus = statusTime;
188 –  
201    calcPot     = 0;
202    calcStress  = 0;
203    currSample  = sampleTime + info->getTime();
204    currThermal = thermalTime+ info->getTime();
205    currStatus  = statusTime + info->getTime();
206 +  currReset   = resetTime  + info->getTime();
207  
208    dumpOut->writeDump(info->getTime());
209    statOut->writeStat(info->getTime());
210  
198 –  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 225 | 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){
258 >        this->resetIntegrator();
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 237 | Line 270 | template<typename T> void Integrator<T>::integrate(voi
270   #endif // is_mpi
271    }
272  
240 –  dumpOut->writeFinal(info->getTime());
241 –
273    delete dumpOut;
274    delete statOut;
275   }
# Line 246 | 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 270 | 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 287 | 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];
293 –  double A[3][3], I[3][3];
294 –  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 +    mass = integrableObjects[i]->getMass();
351  
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 –
352      for (j = 0; j < 3; j++){
353        // velocity half step
354        vel[j] += (dt2 * frc[j] / mass) * eConvert;
# Line 309 | Line 356 | template<typename T> void Integrator<T>::moveA(void){
356        pos[j] += dt * vel[j];
357      }
358  
359 <    atoms[i]->setVel(vel);
360 <    atoms[i]->setPos(pos);
359 >    integrableObjects[i]->setVel(vel);
360 >    integrableObjects[i]->setPos(pos);
361  
362 <    if (atoms[i]->isDirectional()){
316 <      dAtom = (DirectionalAtom *) atoms[i];
362 >    if (integrableObjects[i]->isDirectional()){
363  
364        // get and convert the torque to body frame
365  
366 <      dAtom->getTrq(Tb);
367 <      dAtom->lab2Body(Tb);
366 >      integrableObjects[i]->getTrq(Tb);
367 >      integrableObjects[i]->lab2Body(Tb);
368  
369        // get the angular momentum, and propagate a half step
370  
371 <      dAtom->getJ(ji);
371 >      integrableObjects[i]->getJ(ji);
372  
373        for (j = 0; j < 3; j++)
374          ji[j] += (dt2 * Tb[j]) * eConvert;
375  
376 <      // use the angular velocities to propagate the rotation matrix a
331 <      // full time step
376 >      this->rotationPropagation( integrableObjects[i], ji );
377  
378 <      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);
378 >      integrableObjects[i]->setJ(ji);
379      }
380    }
381 +
382 +  if (nConstrained){
383 +    constrainA();
384 +  }
385   }
386  
387  
388   template<typename T> void Integrator<T>::moveB(void){
389    int i, j;
366 –  DirectionalAtom* dAtom;
390    double Tb[3], ji[3];
391    double vel[3], frc[3];
392    double mass;
393  
394 <  for (i = 0; i < nAtoms; i++){
395 <    atoms[i]->getVel(vel);
396 <    atoms[i]->getFrc(frc);
394 >  for (i = 0; i < integrableObjects.size(); i++){
395 >    integrableObjects[i]->getVel(vel);
396 >    integrableObjects[i]->getFrc(frc);
397  
398 <    mass = atoms[i]->getMass();
398 >    mass = integrableObjects[i]->getMass();
399  
400      // velocity half step
401      for (j = 0; j < 3; j++)
402        vel[j] += (dt2 * frc[j] / mass) * eConvert;
403  
404 <    atoms[i]->setVel(vel);
404 >    integrableObjects[i]->setVel(vel);
405  
406 <    if (atoms[i]->isDirectional()){
384 <      dAtom = (DirectionalAtom *) atoms[i];
406 >    if (integrableObjects[i]->isDirectional()){
407  
408 <      // get and convert the torque to body frame      
408 >      // get and convert the torque to body frame
409  
410 <      dAtom->getTrq(Tb);
411 <      dAtom->lab2Body(Tb);
410 >      integrableObjects[i]->getTrq(Tb);
411 >      integrableObjects[i]->lab2Body(Tb);
412  
413        // get the angular momentum, and propagate a half step
414  
415 <      dAtom->getJ(ji);
415 >      integrableObjects[i]->getJ(ji);
416  
417        for (j = 0; j < 3; j++)
418          ji[j] += (dt2 * Tb[j]) * eConvert;
419  
420  
421 <      dAtom->setJ(ji);
421 >      integrableObjects[i]->setJ(ji);
422      }
423    }
424 +
425 +  if (nConstrained){
426 +    constrainB();
427 +  }
428   }
429  
430   template<typename T> void Integrator<T>::preMove(void){
# Line 417 | Line 443 | template<typename T> void Integrator<T>::constrainA(){
443   }
444  
445   template<typename T> void Integrator<T>::constrainA(){
446 <  int i, j, k;
446 >  int i, j;
447    int done;
448    double posA[3], posB[3];
449    double velA[3], velB[3];
# Line 557 | Line 583 | template<typename T> void Integrator<T>::constrainA(){
583      painCave.isFatal = 1;
584      simError();
585    }
586 +
587   }
588  
589   template<typename T> void Integrator<T>::constrainB(void){
590 <  int i, j, k;
590 >  int i, j;
591    int done;
592    double posA[3], posB[3];
593    double velA[3], velB[3];
# Line 569 | Line 596 | template<typename T> void Integrator<T>::constrainB(vo
596    int a, b, ax, ay, az, bx, by, bz;
597    double rma, rmb;
598    double dx, dy, dz;
599 <  double rabsq, pabsq, rvab;
573 <  double diffsq;
599 >  double rvab;
600    double gab;
601    int iteration;
602  
# Line 660 | Line 686 | template<typename T> void Integrator<T>::constrainB(vo
686    }
687   }
688  
689 + template<typename T> void Integrator<T>::rotationPropagation
690 + ( StuntDouble* sd, double ji[3] ){
691 +
692 +  double angle;
693 +  double A[3][3], I[3][3];
694 +  int i, j, k;
695 +
696 +  // use the angular velocities to propagate the rotation matrix a
697 +  // full time step
698 +
699 +  sd->getA(A);
700 +  sd->getI(I);
701 +
702 +  if (sd->isLinear()) {
703 +    i = sd->linearAxis();
704 +    j = (i+1)%3;
705 +    k = (i+2)%3;
706 +    
707 +    angle = dt2 * ji[j] / I[j][j];
708 +    this->rotate( k, i, angle, ji, A );
709 +
710 +    angle = dt * ji[k] / I[k][k];
711 +    this->rotate( i, j, angle, ji, A);
712 +
713 +    angle = dt2 * ji[j] / I[j][j];
714 +    this->rotate( k, i, angle, ji, A );
715 +
716 +  } else {
717 +    // rotate about the x-axis
718 +    angle = dt2 * ji[0] / I[0][0];
719 +    this->rotate( 1, 2, angle, ji, A );
720 +    
721 +    // rotate about the y-axis
722 +    angle = dt2 * ji[1] / I[1][1];
723 +    this->rotate( 2, 0, angle, ji, A );
724 +    
725 +    // rotate about the z-axis
726 +    angle = dt * ji[2] / I[2][2];
727 +    this->rotate( 0, 1, angle, ji, A);
728 +    
729 +    // rotate about the y-axis
730 +    angle = dt2 * ji[1] / I[1][1];
731 +    this->rotate( 2, 0, angle, ji, A );
732 +    
733 +    // rotate about the x-axis
734 +    angle = dt2 * ji[0] / I[0][0];
735 +    this->rotate( 1, 2, angle, ji, A );
736 +    
737 +  }
738 +  sd->setA( A  );
739 + }
740 +
741   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
742                                                  double angle, double ji[3],
743                                                  double A[3][3]){
# Line 725 | Line 803 | template<typename T> void Integrator<T>::rotate(int ax
803      }
804    }
805  
806 <  // rotate the Rotation matrix acording to:
806 >  // rotate the Rotation matrix acording to:
807    //            A[][] = A[][] * transpose(rot[][])
808  
809  
# Line 750 | Line 828 | template<typename T> void Integrator<T>::thermalize(){
828   template<typename T> void Integrator<T>::thermalize(){
829    tStats->velocitize();
830   }
831 +
832 + template<typename T> double Integrator<T>::getConservedQuantity(void){
833 +  return tStats->getTotalE();
834 + }
835 + template<typename T> string Integrator<T>::getAdditionalParameters(void){
836 +  //By default, return a null string
837 +  //The reason we use string instead of char* is that if we use char*, we will
838 +  //return a pointer point to local variable which might cause problem
839 +  return string();
840 + }

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