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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 768 by mmeineke, Wed Sep 17 14:22:15 2003 UTC vs.
Revision 829 by gezelter, Tue Oct 28 16:03:37 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;
29 <
28 >  
29    nAtoms = info->n_atoms;
30  
31    // check for constraints
# 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 162 | Line 160 | template<typename T> void Integrator<T>::integrate(voi
160    double currReset;
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 +
179 +  if (nConstrained){
180 +    preMove();
181 +    constrainA();
182 +    calcForce(1, 1);    
183 +    constrainB();
184 +  }
185    
186    if (info->setTemp){
187      thermalize();
# 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 241 | Line 246 | template<typename T> void Integrator<T>::integrate(voi
246   #endif // is_mpi
247    }
248  
249 <  dumpOut->writeFinal(info->getTime());
249 >
250 >  // write the last frame
251 >  dumpOut->writeDump(info->getTime());
252  
253    delete dumpOut;
254    delete statOut;
# Line 290 | Line 297 | template<typename T> void Integrator<T>::moveA(void){
297    int i, j;
298    DirectionalAtom* dAtom;
299    double Tb[3], ji[3];
293 –  double A[3][3], I[3][3];
294 –  double angle;
300    double vel[3], pos[3], frc[3];
301    double mass;
302  
# Line 327 | 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
331 <      // full time step
332 <
333 <      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);
335 >      this->rotationPropagation( dAtom, ji );
336  
352 –      // rotate about the x-axis
353 –      angle = dt2 * ji[0] / I[0][0];
354 –      this->rotate(1, 2, angle, ji, A);
355 –
337        dAtom->setJ(ji);
357 –      dAtom->setA(A);
338      }
339    }
340  
# Line 424 | 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 568 | Line 548 | template<typename T> void Integrator<T>::constrainB(vo
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 577 | 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;
581 <  double diffsq;
560 >  double rvab;
561    double gab;
562    int iteration;
563  
# Line 668 | Line 647 | template<typename T> void Integrator<T>::rotate(int ax
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,
686                                                  double angle, double ji[3],
687                                                  double A[3][3]){

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