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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 784 by mmeineke, Wed Sep 24 19:34:39 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    }
32 <  
32 >
33    nAtoms = info->n_atoms;
34 +  integrableObjects = info->integrableObjects;
35  
36    // check for constraints
37  
# Line 64 | 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 110 | Line 116 | template<typename T> void Integrator<T>::checkConstrai
116      }
117    }
118  
119 +
120    if (nConstrained > 0){
121      isConstrained = 1;
122  
# Line 131 | 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 146 | Line 153 | template<typename T> void Integrator<T>::integrate(voi
153  
154  
155   template<typename T> void Integrator<T>::integrate(void){
149 –  int i, j;                         // loop counters
156  
157    double runTime = info->run_time;
158    double sampleTime = info->sampleTime;
# Line 159 | 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;
164 –  int isError;
170  
171    tStats = new Thermo(info);
172    statOut = new StatWriter(info);
173    dumpOut = new DumpWriter(info);
174  
175    atoms = info->atoms;
171 –  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 <
189 >  
190    if (nConstrained){
191      preMove();
192      constrainA();
193 <    calcForce(1, 1);    
193 >    calcForce(1, 1);
194      constrainB();
195    }
196    
# Line 201 | Line 209 | template<typename T> void Integrator<T>::integrate(voi
209    statOut->writeStat(info->getTime());
210  
211  
204 –
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 230 | 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 242 | 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 249 | Line 270 | template<typename T> void Integrator<T>::integrate(voi
270   #endif // is_mpi
271    }
272  
252 –  dumpOut->writeFinal(info->getTime());
253 –
273    delete dumpOut;
274    delete statOut;
275   }
# Line 258 | 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 <  moveA();
287 > #ifdef PROFILE
288 >  endProfile(pro3);
289  
290 +  startProfile(pro4);
291 + #endif // profile
292  
293 +  moveA();
294  
295 + #ifdef PROFILE
296 +  endProfile(pro4);
297 +  
298 +  startProfile(pro5);
299 + #endif//profile
300  
301 +
302   #ifdef IS_MPI
303    strcpy(checkPointMsg, "Succesful moveA\n");
304    MPIcheckPoint();
# Line 280 | 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 + #ifdef PROFILE
328 +  endProfile(pro6);
329 + #endif // profile
330  
289 –
331   #ifdef IS_MPI
332    strcpy(checkPointMsg, "Succesful moveB\n");
333    MPIcheckPoint();
# Line 295 | 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];
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);
307 <    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  
309 –    mass = atoms[i]->getMass();
310 –
354      for (j = 0; j < 3; j++){
355        // velocity half step
356        vel[j] += (dt2 * frc[j] / mass) * eConvert;
# Line 315 | 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()){
322 <      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 <      this->rotationPropagation( dAtom, ji );
378 >      this->rotationPropagation( integrableObjects[i], ji );
379  
380 <      dAtom->setJ(ji);
380 >      integrableObjects[i]->setJ(ji);
381      }
382    }
383  
# Line 347 | Line 389 | template<typename T> void Integrator<T>::moveB(void){
389  
390   template<typename T> void Integrator<T>::moveB(void){
391    int i, j;
350 –  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()){
368 <      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  
# Line 405 | 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 549 | Line 589 | template<typename T> void Integrator<T>::constrainB(vo
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 558 | 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;
562 <  double diffsq;
601 >  double rvab;
602    double gab;
603    int iteration;
604  
# Line 650 | Line 689 | template<typename T> void Integrator<T>::rotationPropa
689   }
690  
691   template<typename T> void Integrator<T>::rotationPropagation
692 < ( DirectionalAtom* dAtom, double ji[3] ){
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 <  dAtom->getA(A);
702 <  dAtom->getI(I);
703 <  
704 <  // rotate about the x-axis      
705 <  angle = dt2 * ji[0] / I[0][0];
706 <  this->rotate( 1, 2, angle, ji, A );
707 <  
708 <  // rotate about the y-axis
709 <  angle = dt2 * ji[1] / I[1][1];
710 <  this->rotate( 2, 0, angle, ji, A );
711 <  
712 <  // rotate about the z-axis
713 <  angle = dt * ji[2] / I[2][2];
714 <  this->rotate( 0, 1, angle, ji, A);
715 <  
716 <  // rotate about the y-axis
717 <  angle = dt2 * ji[1] / I[1][1];
718 <  this->rotate( 2, 0, angle, ji, A );
719 <  
720 <  // rotate about the x-axis
721 <  angle = dt2 * ji[0] / I[0][0];
722 <  this->rotate( 1, 2, angle, ji, A );
723 <  
724 <  dAtom->setA( A  );    
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 749 | 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 778 | Line 834 | template<typename T> double Integrator<T>::getConserve
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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