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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 733 by tim, Wed Aug 27 19:23:29 2003 UTC vs.
Revision 1035 by tim, Fri Feb 6 21:37:59 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  
# Line 132 | Line 135 | template<typename T> void Integrator<T>::checkConstrai
135      }
136  
137  
138 <    // save oldAtoms to check for lode balanceing later on.
138 >    // save oldAtoms to check for lode balancing later on.
139  
140      oldAtoms = nAtoms;
141  
# 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;
156    double statusTime = info->statusTime;
157    double thermalTime = info->thermalTime;
158 +  double resetTime = info->resetTime;
159  
160 +
161    double currSample;
162    double currThermal;
163    double currStatus;
164 +  double currReset;
165  
166    int calcPot, calcStress;
162 –  int isError;
167  
168    tStats = new Thermo(info);
169    statOut = new StatWriter(info);
170    dumpOut = new DumpWriter(info);
171  
172    atoms = info->atoms;
169 –  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 +  //temp test
184 +  tStats->getPotential();
185    
186 +  if (nConstrained){
187 +    preMove();
188 +    constrainA();
189 +    calcForce(1, 1);
190 +    constrainB();
191 +  }
192 +  
193    if (info->setTemp){
194      thermalize();
195    }
196  
182 –  calcPot = 0;
183 –  calcStress = 0;
184 –  currSample = sampleTime;
185 –  currThermal = thermalTime;
186 –  currStatus = statusTime;
187 –  
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  
197 –  readyCheck();
207  
208   #ifdef IS_MPI
209    strcpy(checkPointMsg, "The integrator is ready to go.");
# Line 207 | Line 216 | template<typename T> void Integrator<T>::integrate(voi
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 224 | 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.");
265      MPIcheckPoint();
266   #endif // is_mpi
267    }
268  
239 –  dumpOut->writeFinal(info->getTime());
240 –
269    delete dumpOut;
270    delete statOut;
271   }
# Line 245 | 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 269 | 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 289 | Line 335 | template<typename T> void Integrator<T>::moveA(void){
335    int i, j;
336    DirectionalAtom* dAtom;
337    double Tb[3], ji[3];
292 –  double A[3][3], I[3][3];
293 –  double angle;
338    double vel[3], pos[3], frc[3];
339    double mass;
340  
# Line 326 | Line 370 | template<typename T> void Integrator<T>::moveA(void){
370        for (j = 0; j < 3; j++)
371          ji[j] += (dt2 * Tb[j]) * eConvert;
372  
373 <      // use the angular velocities to propagate the rotation matrix a
330 <      // full time step
331 <
332 <      dAtom->getA(A);
333 <      dAtom->getI(I);
334 <
335 <      // rotate about the x-axis      
336 <      angle = dt2 * ji[0] / I[0][0];
337 <      this->rotate(1, 2, angle, ji, A);
338 <
339 <      // rotate about the y-axis
340 <      angle = dt2 * ji[1] / I[1][1];
341 <      this->rotate(2, 0, angle, ji, A);
342 <
343 <      // rotate about the z-axis
344 <      angle = dt * ji[2] / I[2][2];
345 <      this->rotate(0, 1, angle, ji, A);
346 <
347 <      // rotate about the y-axis
348 <      angle = dt2 * ji[1] / I[1][1];
349 <      this->rotate(2, 0, angle, ji, A);
350 <
351 <      // rotate about the x-axis
352 <      angle = dt2 * ji[0] / I[0][0];
353 <      this->rotate(1, 2, angle, ji, A);
373 >      this->rotationPropagation( dAtom, ji );
374  
355 –
375        dAtom->setJ(ji);
357 –      dAtom->setA(A);
376      }
377    }
378 +
379 +  if (nConstrained){
380 +    constrainA();
381 +  }
382   }
383  
384  
# Line 382 | Line 404 | template<typename T> void Integrator<T>::moveB(void){
404      if (atoms[i]->isDirectional()){
405        dAtom = (DirectionalAtom *) atoms[i];
406  
407 <      // get and convert the torque to body frame      
407 >      // get and convert the torque to body frame
408  
409        dAtom->getTrq(Tb);
410        dAtom->lab2Body(Tb);
# Line 398 | Line 420 | template<typename T> void Integrator<T>::moveB(void){
420        dAtom->setJ(ji);
421      }
422    }
423 +
424 +  if (nConstrained){
425 +    constrainB();
426 +  }
427   }
428  
429   template<typename T> void Integrator<T>::preMove(void){
# Line 416 | Line 442 | template<typename T> void Integrator<T>::constrainA(){
442   }
443  
444   template<typename T> void Integrator<T>::constrainA(){
445 <  int i, j, k;
445 >  int i, j;
446    int done;
447    double posA[3], posB[3];
448    double velA[3], velB[3];
# Line 556 | Line 582 | template<typename T> void Integrator<T>::constrainA(){
582      painCave.isFatal = 1;
583      simError();
584    }
585 +
586   }
587  
588   template<typename T> void Integrator<T>::constrainB(void){
589 <  int i, j, k;
589 >  int i, j;
590    int done;
591    double posA[3], posB[3];
592    double velA[3], velB[3];
# Line 568 | Line 595 | template<typename T> void Integrator<T>::constrainB(vo
595    int a, b, ax, ay, az, bx, by, bz;
596    double rma, rmb;
597    double dx, dy, dz;
598 <  double rabsq, pabsq, rvab;
572 <  double diffsq;
598 >  double rvab;
599    double gab;
600    int iteration;
601  
# Line 657 | Line 683 | template<typename T> void Integrator<T>::constrainB(vo
683      painCave.isFatal = 1;
684      simError();
685    }
686 + }
687 +
688 + template<typename T> void Integrator<T>::rotationPropagation
689 + ( DirectionalAtom* dAtom, double ji[3] ){
690 +
691 +  double angle;
692 +  double A[3][3], I[3][3];
693 +
694 +  // use the angular velocities to propagate the rotation matrix a
695 +  // full time step
696 +
697 +  dAtom->getA(A);
698 +  dAtom->getI(I);
699 +
700 +  // rotate about the x-axis
701 +  angle = dt2 * ji[0] / I[0][0];
702 +  this->rotate( 1, 2, angle, ji, A );
703 +
704 +  // rotate about the y-axis
705 +  angle = dt2 * ji[1] / I[1][1];
706 +  this->rotate( 2, 0, angle, ji, A );
707 +
708 +  // rotate about the z-axis
709 +  angle = dt * ji[2] / I[2][2];
710 +  this->rotate( 0, 1, angle, ji, A);
711 +
712 +  // rotate about the y-axis
713 +  angle = dt2 * ji[1] / I[1][1];
714 +  this->rotate( 2, 0, angle, ji, A );
715 +
716 +  // rotate about the x-axis
717 +  angle = dt2 * ji[0] / I[0][0];
718 +  this->rotate( 1, 2, angle, ji, A );
719 +
720 +  dAtom->setA( A  );
721   }
722  
723   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
# Line 724 | Line 785 | template<typename T> void Integrator<T>::rotate(int ax
785      }
786    }
787  
788 <  // rotate the Rotation matrix acording to:
788 >  // rotate the Rotation matrix acording to:
789    //            A[][] = A[][] * transpose(rot[][])
790  
791  
# Line 749 | Line 810 | template<typename T> void Integrator<T>::thermalize(){
810   template<typename T> void Integrator<T>::thermalize(){
811    tStats->velocitize();
812   }
813 +
814 + template<typename T> double Integrator<T>::getConservedQuantity(void){
815 +  return tStats->getTotalE();
816 + }
817 + template<typename T> string Integrator<T>::getAdditionalParameters(void){
818 +  //By default, return a null string
819 +  //The reason we use string instead of char* is that if we use char*, we will
820 +  //return a pointer point to local variable which might cause problem
821 +  return string();
822 + }

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