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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 763 by tim, Mon Sep 15 16:52:02 2003 UTC vs.
Revision 892 by chuckv, Mon Dec 22 21:27:04 2003 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  
# Line 147 | Line 150 | template<typename T> void Integrator<T>::integrate(voi
150  
151  
152   template<typename T> void Integrator<T>::integrate(void){
150 –  int i, j;                         // loop counters
153  
154    double runTime = info->run_time;
155    double sampleTime = info->sampleTime;
# Line 160 | Line 162 | template<typename T> void Integrator<T>::integrate(voi
162    double currThermal;
163    double currStatus;
164    double currReset;
165 <  
165 >
166    int calcPot, calcStress;
165 –  int isError;
167  
168    tStats = new Thermo(info);
169    statOut = new StatWriter(info);
170    dumpOut = new DumpWriter(info);
171  
172    atoms = info->atoms;
172 –  DirectionalAtom* dAtom;
173  
174    dt = info->dt;
175    dt2 = 0.5 * dt;
176  
177 +  readyCheck();
178 +
179    // initialize the forces before the first step
180  
181    calcForce(1, 1);
182 +
183 +  if (nConstrained){
184 +    preMove();
185 +    constrainA();
186 +    calcForce(1, 1);
187 +    constrainB();
188 +  }
189    
190    if (info->setTemp){
191      thermalize();
# Line 192 | Line 201 | template<typename T> void Integrator<T>::integrate(voi
201    dumpOut->writeDump(info->getTime());
202    statOut->writeStat(info->getTime());
203  
195 –  readyCheck();
204  
205   #ifdef IS_MPI
206    strcpy(checkPointMsg, "The integrator is ready to go.");
# Line 205 | Line 213 | template<typename T> void Integrator<T>::integrate(voi
213        calcStress = 1;
214      }
215  
216 + #ifdef PROFILE
217 +    startProfile( pro1 );
218 + #endif
219 +    
220      integrateStep(calcPot, calcStress);
221  
222 + #ifdef PROFILE
223 +    endProfile( pro1 );
224 +
225 +    startProfile( pro2 );
226 + #endif // profile
227 +
228      info->incrTime(dt);
229  
230      if (info->setTemp){
# Line 222 | Line 240 | template<typename T> void Integrator<T>::integrate(voi
240      }
241  
242      if (info->getTime() >= currStatus){
243 <      statOut->writeStat(info->getTime());
244 <      calcPot = 0;
243 >      statOut->writeStat(info->getTime());
244 >      calcPot = 0;
245        calcStress = 0;
246        currStatus += statusTime;
247 <    }
247 >    }
248  
249      if (info->resetIntegrator){
250        if (info->getTime() >= currReset){
# Line 234 | Line 252 | template<typename T> void Integrator<T>::integrate(voi
252          currReset += resetTime;
253        }
254      }
255 +    
256 + #ifdef PROFILE
257 +    endProfile( pro2 );
258 + #endif //profile
259  
260   #ifdef IS_MPI
261      strcpy(checkPointMsg, "successfully took a time step.");
# Line 241 | Line 263 | template<typename T> void Integrator<T>::integrate(voi
263   #endif // is_mpi
264    }
265  
244 –  dumpOut->writeFinal(info->getTime());
266  
267 +  // write the last frame
268 +  dumpOut->writeDump(info->getTime());
269 +
270    delete dumpOut;
271    delete statOut;
272   }
# Line 250 | Line 274 | template<typename T> void Integrator<T>::integrateStep
274   template<typename T> void Integrator<T>::integrateStep(int calcPot,
275                                                         int calcStress){
276    // Position full step, and velocity half step
277 +
278 + #ifdef PROFILE
279 +  startProfile(pro3);
280 + #endif //profile
281 +
282    preMove();
283  
284 + #ifdef PROFILE
285 +  endProfile(pro3);
286 +
287 +  startProfile(pro4);
288 + #endif // profile
289 +
290    moveA();
291  
292 <  if (nConstrained){
293 <    constrainA();
294 <  }
292 > #ifdef PROFILE
293 >  endProfile(pro4);
294 >  
295 >  startProfile(pro5);
296 > #endif//profile
297  
298  
299   #ifdef IS_MPI
# Line 274 | Line 311 | template<typename T> void Integrator<T>::integrateStep
311    MPIcheckPoint();
312   #endif // is_mpi
313  
314 + #ifdef PROFILE
315 +  endProfile( pro5 );
316  
317 +  startProfile( pro6 );
318 + #endif //profile
319 +
320    // finish the velocity  half step
321  
322    moveB();
323  
324 <  if (nConstrained){
325 <    constrainB();
326 <  }
324 > #ifdef PROFILE
325 >  endProfile(pro6);
326 > #endif // profile
327  
328   #ifdef IS_MPI
329    strcpy(checkPointMsg, "Succesful moveB\n");
# Line 294 | Line 336 | template<typename T> void Integrator<T>::moveA(void){
336    int i, j;
337    DirectionalAtom* dAtom;
338    double Tb[3], ji[3];
297 –  double A[3][3], I[3][3];
298 –  double angle;
339    double vel[3], pos[3], frc[3];
340    double mass;
341  
# Line 331 | Line 371 | template<typename T> void Integrator<T>::moveA(void){
371        for (j = 0; j < 3; j++)
372          ji[j] += (dt2 * Tb[j]) * eConvert;
373  
374 <      // use the angular velocities to propagate the rotation matrix a
335 <      // full time step
374 >      this->rotationPropagation( dAtom, ji );
375  
376 <      dAtom->getA(A);
377 <      dAtom->getI(I);
378 <
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);
376 >      dAtom->setJ(ji);
377 >    }
378 >  }
379  
380 <      dAtom->setJ(ji);
381 <      dAtom->setA(A);
362 <    }
380 >  if (nConstrained){
381 >    constrainA();
382    }
383   }
384  
# Line 386 | Line 405 | template<typename T> void Integrator<T>::moveB(void){
405      if (atoms[i]->isDirectional()){
406        dAtom = (DirectionalAtom *) atoms[i];
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);
# Line 402 | Line 421 | template<typename T> void Integrator<T>::moveB(void){
421        dAtom->setJ(ji);
422      }
423    }
424 +
425 +  if (nConstrained){
426 +    constrainB();
427 +  }
428   }
429  
430   template<typename T> void Integrator<T>::preMove(void){
# Line 420 | 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 560 | 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 572 | 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;
576 <  double diffsq;
599 >  double rvab;
600    double gab;
601    int iteration;
602  
# Line 663 | Line 686 | template<typename T> void Integrator<T>::rotate(int ax
686    }
687   }
688  
689 + template<typename T> void Integrator<T>::rotationPropagation
690 + ( DirectionalAtom* dAtom, double ji[3] ){
691 +
692 +  double angle;
693 +  double A[3][3], I[3][3];
694 +
695 +  // use the angular velocities to propagate the rotation matrix a
696 +  // full time step
697 +
698 +  dAtom->getA(A);
699 +  dAtom->getI(I);
700 +
701 +  // rotate about the x-axis
702 +  angle = dt2 * ji[0] / I[0][0];
703 +  this->rotate( 1, 2, angle, ji, A );
704 +
705 +  // rotate about the y-axis
706 +  angle = dt2 * ji[1] / I[1][1];
707 +  this->rotate( 2, 0, angle, ji, A );
708 +
709 +  // rotate about the z-axis
710 +  angle = dt * ji[2] / I[2][2];
711 +  this->rotate( 0, 1, angle, ji, A);
712 +
713 +  // rotate about the y-axis
714 +  angle = dt2 * ji[1] / I[1][1];
715 +  this->rotate( 2, 0, angle, ji, A );
716 +
717 +  // rotate about the x-axis
718 +  angle = dt2 * ji[0] / I[0][0];
719 +  this->rotate( 1, 2, angle, ji, A );
720 +
721 +  dAtom->setA( A  );
722 + }
723 +
724   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
725                                                  double angle, double ji[3],
726                                                  double A[3][3]){
# Line 728 | Line 786 | template<typename T> void Integrator<T>::rotate(int ax
786      }
787    }
788  
789 <  // rotate the Rotation matrix acording to:
789 >  // rotate the Rotation matrix acording to:
790    //            A[][] = A[][] * transpose(rot[][])
791  
792  
# Line 756 | Line 814 | template<typename T> double Integrator<T>::getConserve
814  
815   template<typename T> double Integrator<T>::getConservedQuantity(void){
816    return tStats->getTotalE();
817 < }
817 > }
818 > template<typename T> string Integrator<T>::getAdditionalParameters(void){
819 >  //By default, return a null string
820 >  //The reason we use string instead of char* is that if we use char*, we will
821 >  //return a pointer point to local variable which might cause problem
822 >  return string();
823 > }

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