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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 755 by mmeineke, Tue Sep 9 20:35:25 2003 UTC vs.
Revision 837 by tim, Wed Oct 29 00:19:10 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"
# Line 25 | Line 25 | template<typename T> Integrator<T>::Integrator(SimInfo
25    if (info->the_integrator != NULL){
26      delete info->the_integrator;
27    }
28 –  info->the_integrator = this;
28  
29    nAtoms = info->n_atoms;
30  
# Line 147 | Line 146 | template<typename T> void Integrator<T>::integrate(voi
146  
147  
148   template<typename T> void Integrator<T>::integrate(void){
150 –  int i, j;                         // loop counters
149  
150    double runTime = info->run_time;
151    double sampleTime = info->sampleTime;
# Line 160 | Line 158 | template<typename T> void Integrator<T>::integrate(voi
158    double currThermal;
159    double currStatus;
160    double currReset;
161 <  
161 >
162    int calcPot, calcStress;
165 –  int isError;
163  
164    tStats = new Thermo(info);
165    statOut = new StatWriter(info);
166    dumpOut = new DumpWriter(info);
167  
168    atoms = info->atoms;
172 –  DirectionalAtom* dAtom;
169  
170    dt = info->dt;
171    dt2 = 0.5 * dt;
172  
173 +  readyCheck();
174 +
175    // initialize the forces before the first step
176  
177    calcForce(1, 1);
178 <  
178 >
179 >  if (nConstrained){
180 >    preMove();
181 >    constrainA();
182 >    calcForce(1, 1);
183 >    constrainB();
184 >  }
185 >
186    if (info->setTemp){
187      thermalize();
188    }
# Line 192 | Line 197 | template<typename T> void Integrator<T>::integrate(voi
197    dumpOut->writeDump(info->getTime());
198    statOut->writeStat(info->getTime());
199  
195 –  readyCheck();
200  
201 +
202   #ifdef IS_MPI
203    strcpy(checkPointMsg, "The integrator is ready to go.");
204    MPIcheckPoint();
# Line 222 | Line 227 | template<typename T> void Integrator<T>::integrate(voi
227      }
228  
229      if (info->getTime() >= currStatus){
230 <      statOut->writeStat(info->getTime());
231 <      calcPot = 0;
230 >      statOut->writeStat(info->getTime());
231 >      calcPot = 0;
232        calcStress = 0;
233        currStatus += statusTime;
234 <    }
234 >    }
235  
236      if (info->resetIntegrator){
237        if (info->getTime() >= currReset){
# Line 241 | Line 246 | template<typename T> void Integrator<T>::integrate(voi
246   #endif // is_mpi
247    }
248  
244 –  dumpOut->writeFinal(info->getTime());
249  
250 +  // write the last frame
251 +  dumpOut->writeDump(info->getTime());
252 +
253    delete dumpOut;
254    delete statOut;
255   }
# Line 254 | Line 261 | template<typename T> void Integrator<T>::integrateStep
261  
262    moveA();
263  
257 –  if (nConstrained){
258 –    constrainA();
259 –  }
264  
265  
266 +
267   #ifdef IS_MPI
268    strcpy(checkPointMsg, "Succesful moveA\n");
269    MPIcheckPoint();
# Line 279 | Line 284 | template<typename T> void Integrator<T>::integrateStep
284  
285    moveB();
286  
282 –  if (nConstrained){
283 –    constrainB();
284 –  }
287  
288 +
289   #ifdef IS_MPI
290    strcpy(checkPointMsg, "Succesful moveB\n");
291    MPIcheckPoint();
# Line 294 | Line 297 | template<typename T> void Integrator<T>::moveA(void){
297    int i, j;
298    DirectionalAtom* dAtom;
299    double Tb[3], ji[3];
297 –  double A[3][3], I[3][3];
298 –  double angle;
300    double vel[3], pos[3], frc[3];
301    double mass;
302  
# Line 331 | Line 332 | template<typename T> void Integrator<T>::moveA(void){
332        for (j = 0; j < 3; j++)
333          ji[j] += (dt2 * Tb[j]) * eConvert;
334  
335 <      // use the angular velocities to propagate the rotation matrix a
335 <      // full time step
335 >      this->rotationPropagation( dAtom, ji );
336  
337 –      dAtom->getA(A);
338 –      dAtom->getI(I);
339 –
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);
359 –
337        dAtom->setJ(ji);
361 –      dAtom->setA(A);
338      }
339    }
340 +
341 +  if (nConstrained){
342 +    constrainA();
343 +  }
344   }
345  
346  
# Line 386 | Line 366 | template<typename T> void Integrator<T>::moveB(void){
366      if (atoms[i]->isDirectional()){
367        dAtom = (DirectionalAtom *) atoms[i];
368  
369 <      // get and convert the torque to body frame      
369 >      // get and convert the torque to body frame
370  
371        dAtom->getTrq(Tb);
372        dAtom->lab2Body(Tb);
# Line 402 | Line 382 | template<typename T> void Integrator<T>::moveB(void){
382        dAtom->setJ(ji);
383      }
384    }
385 +
386 +  if (nConstrained){
387 +    constrainB();
388 +  }
389   }
390  
391   template<typename T> void Integrator<T>::preMove(void){
# Line 420 | Line 404 | template<typename T> void Integrator<T>::constrainA(){
404   }
405  
406   template<typename T> void Integrator<T>::constrainA(){
407 <  int i, j, k;
407 >  int i, j;
408    int done;
409    double posA[3], posB[3];
410    double velA[3], velB[3];
# Line 560 | Line 544 | template<typename T> void Integrator<T>::constrainA(){
544      painCave.isFatal = 1;
545      simError();
546    }
547 +
548   }
549  
550   template<typename T> void Integrator<T>::constrainB(void){
551 <  int i, j, k;
551 >  int i, j;
552    int done;
553    double posA[3], posB[3];
554    double velA[3], velB[3];
# Line 572 | Line 557 | template<typename T> void Integrator<T>::constrainB(vo
557    int a, b, ax, ay, az, bx, by, bz;
558    double rma, rmb;
559    double dx, dy, dz;
560 <  double rabsq, pabsq, rvab;
576 <  double diffsq;
560 >  double rvab;
561    double gab;
562    int iteration;
563  
# Line 661 | Line 645 | template<typename T> void Integrator<T>::constrainB(vo
645      painCave.isFatal = 1;
646      simError();
647    }
648 + }
649 +
650 + template<typename T> void Integrator<T>::rotationPropagation
651 + ( DirectionalAtom* dAtom, double ji[3] ){
652 +
653 +  double angle;
654 +  double A[3][3], I[3][3];
655 +
656 +  // use the angular velocities to propagate the rotation matrix a
657 +  // full time step
658 +
659 +  dAtom->getA(A);
660 +  dAtom->getI(I);
661 +
662 +  // rotate about the x-axis
663 +  angle = dt2 * ji[0] / I[0][0];
664 +  this->rotate( 1, 2, angle, ji, A );
665 +
666 +  // rotate about the y-axis
667 +  angle = dt2 * ji[1] / I[1][1];
668 +  this->rotate( 2, 0, angle, ji, A );
669 +
670 +  // rotate about the z-axis
671 +  angle = dt * ji[2] / I[2][2];
672 +  this->rotate( 0, 1, angle, ji, A);
673 +
674 +  // rotate about the y-axis
675 +  angle = dt2 * ji[1] / I[1][1];
676 +  this->rotate( 2, 0, angle, ji, A );
677 +
678 +  // rotate about the x-axis
679 +  angle = dt2 * ji[0] / I[0][0];
680 +  this->rotate( 1, 2, angle, ji, A );
681 +
682 +  dAtom->setA( A  );
683   }
684  
685   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
# Line 728 | Line 747 | template<typename T> void Integrator<T>::rotate(int ax
747      }
748    }
749  
750 <  // rotate the Rotation matrix acording to:
750 >  // rotate the Rotation matrix acording to:
751    //            A[][] = A[][] * transpose(rot[][])
752  
753  
# Line 753 | Line 772 | template<typename T> void Integrator<T>::thermalize(){
772   template<typename T> void Integrator<T>::thermalize(){
773    tStats->velocitize();
774   }
775 +
776 + template<typename T> double Integrator<T>::getConservedQuantity(void){
777 +  return tStats->getTotalE();
778 + }
779 + template<typename T> string Integrator<T>::getAdditionalParameters(void){
780 +  //By default, return a null string
781 +  //The reason we use string instead of char* is that if we use char*, we will
782 +  //return a pointer point to local variable which might cause problem
783 +  return string();
784 + }

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