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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 1452 by tim, Mon Aug 23 15:11:36 2004 UTC

# Line 1 | Line 1
1   #include <iostream>
2 < #include <cstdlib>
3 < #include <cmath>
4 <
2 > #include <stdlib.h>
3 > #include <math.h>
4 > #include "Rattle.hpp"
5 > #include "Roll.hpp"
6   #ifdef IS_MPI
7   #include "mpiSimulation.hpp"
8   #include <unistd.h>
9   #endif //is_mpi
10  
11 + #ifdef PROFILE
12 + #include "mdProfile.hpp"
13 + #endif // profile
14 +
15   #include "Integrator.hpp"
16   #include "simError.h"
17  
# Line 25 | Line 30 | template<typename T> Integrator<T>::Integrator(SimInfo
30    if (info->the_integrator != NULL){
31      delete info->the_integrator;
32    }
33 <  
33 >
34    nAtoms = info->n_atoms;
35 +  integrableObjects = info->integrableObjects;
36  
37 +  consFramework = new RollFramework(info);
38 +
39 +  if(consFramework == NULL){
40 +    sprintf(painCave.errMsg,
41 +      "Integrator::Intergrator() Error: Memory allocation error for RattleFramework" );
42 +    painCave.isFatal = 1;
43 +    simError();
44 +  }
45 +  
46 + /*
47    // check for constraints
48  
49    constrainedA = NULL;
# Line 40 | Line 56 | template<typename T> Integrator<T>::Integrator(SimInfo
56    nConstrained = 0;
57  
58    checkConstraints();
59 + */
60   }
61  
62   template<typename T> Integrator<T>::~Integrator(){
63 +  if (consFramework != NULL)
64 +    delete consFramework;
65 + /*
66    if (nConstrained){
67      delete[] constrainedA;
68      delete[] constrainedB;
# Line 51 | Line 71 | template<typename T> Integrator<T>::~Integrator(){
71      delete[] moved;
72      delete[] oldPos;
73    }
74 + */
75   }
76  
77 + /*
78   template<typename T> void Integrator<T>::checkConstraints(void){
79    isConstrained = 0;
80  
# Line 64 | Line 86 | template<typename T> void Integrator<T>::checkConstrai
86  
87    SRI** theArray;
88    for (int i = 0; i < nMols; i++){
89 <    theArray = (SRI * *) molecules[i].getMyBonds();
89 >
90 >          theArray = (SRI * *) molecules[i].getMyBonds();
91      for (int j = 0; j < molecules[i].getNBonds(); j++){
92        constrained = theArray[j]->is_constrained();
93  
# Line 86 | Line 109 | template<typename T> void Integrator<T>::checkConstrai
109        if (constrained){
110          dummy_plug = theArray[j]->get_constraint();
111          temp_con[nConstrained].set_a(dummy_plug->get_a());
112 <        temp_con[nConstrained].set_b(dummy_plug->get_b());
112 >        temp_con[nConstrained].set_b(Dummy_plug->get_b());
113          temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
114  
115          nConstrained++;
# Line 110 | Line 133 | template<typename T> void Integrator<T>::checkConstrai
133      }
134    }
135  
136 +
137    if (nConstrained > 0){
138      isConstrained = 1;
139  
# Line 131 | Line 155 | template<typename T> void Integrator<T>::checkConstrai
155      }
156  
157  
158 <    // save oldAtoms to check for lode balanceing later on.
158 >    // save oldAtoms to check for lode balancing later on.
159  
160      oldAtoms = nAtoms;
161  
# Line 143 | Line 167 | template<typename T> void Integrator<T>::checkConstrai
167  
168    delete[] temp_con;
169   }
170 + */
171  
147 –
172   template<typename T> void Integrator<T>::integrate(void){
149 –  int i, j;                         // loop counters
173  
174    double runTime = info->run_time;
175    double sampleTime = info->sampleTime;
# Line 154 | Line 177 | template<typename T> void Integrator<T>::integrate(voi
177    double thermalTime = info->thermalTime;
178    double resetTime = info->resetTime;
179  
180 <
180 >  double difference;
181    double currSample;
182    double currThermal;
183    double currStatus;
184    double currReset;
185 <  
185 >
186    int calcPot, calcStress;
164 –  int isError;
187  
188    tStats = new Thermo(info);
189    statOut = new StatWriter(info);
190    dumpOut = new DumpWriter(info);
191  
192    atoms = info->atoms;
171 –  DirectionalAtom* dAtom;
193  
194    dt = info->dt;
195    dt2 = 0.5 * dt;
196  
197    readyCheck();
198  
199 +  // remove center of mass drift velocity (in case we passed in a configuration
200 +  // that was drifting
201 +  tStats->removeCOMdrift();
202 +  //tStats->removeAngularMomentum();
203 +  
204 +  // initialize the retraints if necessary
205 +  if (info->useSolidThermInt && !info->useLiquidThermInt) {
206 +    myFF->initRestraints();
207 +  }
208 +
209    // initialize the forces before the first step
210  
211    calcForce(1, 1);
212  
213 <  if (nConstrained){
214 <    preMove();
215 <    constrainA();
216 <    calcForce(1, 1);    
217 <    constrainB();
187 <  }
213 >  //execute constraint algorithm to make sure at the very beginning the system is constrained  
214 >  //consFramework->doPreConstraint();
215 >  //consFramework->doConstrainA();
216 >  //calcForce(1, 1);
217 >  //consFramework->doConstrainB();
218    
219    if (info->setTemp){
220      thermalize();
# Line 201 | Line 231 | template<typename T> void Integrator<T>::integrate(voi
231    statOut->writeStat(info->getTime());
232  
233  
204 –
234   #ifdef IS_MPI
235    strcpy(checkPointMsg, "The integrator is ready to go.");
236    MPIcheckPoint();
237   #endif // is_mpi
238  
239 <  while (info->getTime() < runTime){
240 <    if ((info->getTime() + dt) >= currStatus){
239 >  while (info->getTime() < runTime && !stopIntegrator()){
240 >    difference = info->getTime() + dt - currStatus;
241 >    if (difference > 0 || fabs(difference) < 1e-4 ){
242        calcPot = 1;
243        calcStress = 1;
244      }
245  
246 + #ifdef PROFILE
247 +    startProfile( pro1 );
248 + #endif
249 +    
250      integrateStep(calcPot, calcStress);
251  
252 + #ifdef PROFILE
253 +    endProfile( pro1 );
254 +
255 +    startProfile( pro2 );
256 + #endif // profile
257 +
258      info->incrTime(dt);
259  
260      if (info->setTemp){
# Line 230 | Line 270 | template<typename T> void Integrator<T>::integrate(voi
270      }
271  
272      if (info->getTime() >= currStatus){
273 <      statOut->writeStat(info->getTime());
274 <      calcPot = 0;
273 >      statOut->writeStat(info->getTime());
274 >      calcPot = 0;
275        calcStress = 0;
276        currStatus += statusTime;
277 <    }
277 >    }
278  
279      if (info->resetIntegrator){
280        if (info->getTime() >= currReset){
# Line 242 | Line 282 | template<typename T> void Integrator<T>::integrate(voi
282          currReset += resetTime;
283        }
284      }
285 +    
286 + #ifdef PROFILE
287 +    endProfile( pro2 );
288 + #endif //profile
289  
290   #ifdef IS_MPI
291      strcpy(checkPointMsg, "successfully took a time step.");
# Line 249 | Line 293 | template<typename T> void Integrator<T>::integrate(voi
293   #endif // is_mpi
294    }
295  
296 <  dumpOut->writeFinal(info->getTime());
296 >  // dump out a file containing the omega values for the final configuration
297 >  if (info->useSolidThermInt && !info->useLiquidThermInt)
298 >    myFF->dumpzAngle();
299 >  
300  
301    delete dumpOut;
302    delete statOut;
# Line 258 | Line 305 | template<typename T> void Integrator<T>::integrateStep
305   template<typename T> void Integrator<T>::integrateStep(int calcPot,
306                                                         int calcStress){
307    // Position full step, and velocity half step
261 –  preMove();
308  
309 <  moveA();
309 > #ifdef PROFILE
310 >  startProfile(pro3);
311 > #endif //profile
312  
313 +  //save old state (position, velocity etc)
314 +  consFramework->doPreConstraint();
315  
316 + #ifdef PROFILE
317 +  endProfile(pro3);
318  
319 +  startProfile(pro4);
320 + #endif // profile
321  
322 +  moveA();
323 +
324 + #ifdef PROFILE
325 +  endProfile(pro4);
326 +  
327 +  startProfile(pro5);
328 + #endif//profile
329 +
330 +
331   #ifdef IS_MPI
332    strcpy(checkPointMsg, "Succesful moveA\n");
333    MPIcheckPoint();
334   #endif // is_mpi
335  
273 –
336    // calc forces
275 –
337    calcForce(calcPot, calcStress);
338  
339   #ifdef IS_MPI
# Line 280 | Line 341 | template<typename T> void Integrator<T>::integrateStep
341    MPIcheckPoint();
342   #endif // is_mpi
343  
344 + #ifdef PROFILE
345 +  endProfile( pro5 );
346  
347 +  startProfile( pro6 );
348 + #endif //profile
349 +
350 +  consFramework->doPreConstraint();
351 +
352    // finish the velocity  half step
353  
354    moveB();
355  
356 + #ifdef PROFILE
357 +  endProfile(pro6);
358 + #endif // profile
359  
289 –
360   #ifdef IS_MPI
361    strcpy(checkPointMsg, "Succesful moveB\n");
362    MPIcheckPoint();
# Line 295 | Line 365 | template<typename T> void Integrator<T>::moveA(void){
365  
366  
367   template<typename T> void Integrator<T>::moveA(void){
368 <  int i, j;
368 >  size_t i, j;
369    DirectionalAtom* dAtom;
370    double Tb[3], ji[3];
371    double vel[3], pos[3], frc[3];
372    double mass;
373 +  double omega;
374 +
375 +  for (i = 0; i < integrableObjects.size() ; i++){
376 +    integrableObjects[i]->getVel(vel);
377 +    integrableObjects[i]->getPos(pos);
378 +    integrableObjects[i]->getFrc(frc);
379 +    
380 +    mass = integrableObjects[i]->getMass();
381  
304 –  for (i = 0; i < nAtoms; i++){
305 –    atoms[i]->getVel(vel);
306 –    atoms[i]->getPos(pos);
307 –    atoms[i]->getFrc(frc);
308 –
309 –    mass = atoms[i]->getMass();
310 –
382      for (j = 0; j < 3; j++){
383        // velocity half step
384        vel[j] += (dt2 * frc[j] / mass) * eConvert;
# Line 315 | Line 386 | template<typename T> void Integrator<T>::moveA(void){
386        pos[j] += dt * vel[j];
387      }
388  
389 <    atoms[i]->setVel(vel);
390 <    atoms[i]->setPos(pos);
389 >    integrableObjects[i]->setVel(vel);
390 >    integrableObjects[i]->setPos(pos);
391  
392 <    if (atoms[i]->isDirectional()){
322 <      dAtom = (DirectionalAtom *) atoms[i];
392 >    if (integrableObjects[i]->isDirectional()){
393  
394        // get and convert the torque to body frame
395  
396 <      dAtom->getTrq(Tb);
397 <      dAtom->lab2Body(Tb);
396 >      integrableObjects[i]->getTrq(Tb);
397 >      integrableObjects[i]->lab2Body(Tb);
398  
399        // get the angular momentum, and propagate a half step
400  
401 <      dAtom->getJ(ji);
401 >      integrableObjects[i]->getJ(ji);
402  
403        for (j = 0; j < 3; j++)
404          ji[j] += (dt2 * Tb[j]) * eConvert;
405  
406 <      this->rotationPropagation( dAtom, ji );
406 >      this->rotationPropagation( integrableObjects[i], ji );
407  
408 <      dAtom->setJ(ji);
408 >      integrableObjects[i]->setJ(ji);
409 >
410      }
411    }
412  
413 <  if (nConstrained){
343 <    constrainA();
344 <  }
413 >  consFramework->doConstrainA();
414   }
415  
416  
417   template<typename T> void Integrator<T>::moveB(void){
418    int i, j;
350 –  DirectionalAtom* dAtom;
419    double Tb[3], ji[3];
420    double vel[3], frc[3];
421    double mass;
422  
423 <  for (i = 0; i < nAtoms; i++){
424 <    atoms[i]->getVel(vel);
425 <    atoms[i]->getFrc(frc);
423 >  for (i = 0; i < integrableObjects.size(); i++){
424 >    integrableObjects[i]->getVel(vel);
425 >    integrableObjects[i]->getFrc(frc);
426  
427 <    mass = atoms[i]->getMass();
427 >    mass = integrableObjects[i]->getMass();
428  
429      // velocity half step
430      for (j = 0; j < 3; j++)
431        vel[j] += (dt2 * frc[j] / mass) * eConvert;
432  
433 <    atoms[i]->setVel(vel);
433 >    integrableObjects[i]->setVel(vel);
434  
435 <    if (atoms[i]->isDirectional()){
368 <      dAtom = (DirectionalAtom *) atoms[i];
369 <
370 <      // get and convert the torque to body frame      
435 >    if (integrableObjects[i]->isDirectional()){
436  
437 <      dAtom->getTrq(Tb);
373 <      dAtom->lab2Body(Tb);
437 >      // get and convert the torque to body frame
438  
439 +      integrableObjects[i]->getTrq(Tb);
440 +      integrableObjects[i]->lab2Body(Tb);
441 +
442        // get the angular momentum, and propagate a half step
443  
444 <      dAtom->getJ(ji);
444 >      integrableObjects[i]->getJ(ji);
445  
446        for (j = 0; j < 3; j++)
447          ji[j] += (dt2 * Tb[j]) * eConvert;
448  
449  
450 <      dAtom->setJ(ji);
450 >      integrableObjects[i]->setJ(ji);
451      }
385 –  }
452  
387 –  if (nConstrained){
388 –    constrainB();
453    }
454 +
455 +  consFramework->doConstrainB();
456   }
457  
458 + /*
459   template<typename T> void Integrator<T>::preMove(void){
460    int i, j;
461    double pos[3];
# Line 405 | Line 472 | template<typename T> void Integrator<T>::constrainA(){
472   }
473  
474   template<typename T> void Integrator<T>::constrainA(){
475 <  int i, j, k;
475 >  int i, j;
476    int done;
477    double posA[3], posB[3];
478    double velA[3], velB[3];
# Line 549 | Line 616 | template<typename T> void Integrator<T>::constrainB(vo
616   }
617  
618   template<typename T> void Integrator<T>::constrainB(void){
619 <  int i, j, k;
619 >  int i, j;
620    int done;
621    double posA[3], posB[3];
622    double velA[3], velB[3];
# Line 558 | Line 625 | template<typename T> void Integrator<T>::constrainB(vo
625    int a, b, ax, ay, az, bx, by, bz;
626    double rma, rmb;
627    double dx, dy, dz;
628 <  double rabsq, pabsq, rvab;
562 <  double diffsq;
628 >  double rvab;
629    double gab;
630    int iteration;
631  
# Line 648 | Line 714 | template<typename T> void Integrator<T>::constrainB(vo
714      simError();
715    }
716   }
717 <
717 > */
718   template<typename T> void Integrator<T>::rotationPropagation
719 < ( DirectionalAtom* dAtom, double ji[3] ){
719 > ( StuntDouble* sd, double ji[3] ){
720  
721    double angle;
722    double A[3][3], I[3][3];
723 +  int i, j, k;
724  
725    // use the angular velocities to propagate the rotation matrix a
726    // full time step
727  
728 <  dAtom->getA(A);
729 <  dAtom->getI(I);
730 <  
731 <  // rotate about the x-axis      
732 <  angle = dt2 * ji[0] / I[0][0];
733 <  this->rotate( 1, 2, angle, ji, A );
734 <  
735 <  // rotate about the y-axis
736 <  angle = dt2 * ji[1] / I[1][1];
737 <  this->rotate( 2, 0, angle, ji, A );
738 <  
739 <  // rotate about the z-axis
740 <  angle = dt * ji[2] / I[2][2];
741 <  this->rotate( 0, 1, angle, ji, A);
742 <  
743 <  // rotate about the y-axis
744 <  angle = dt2 * ji[1] / I[1][1];
745 <  this->rotate( 2, 0, angle, ji, A );
746 <  
747 <  // rotate about the x-axis
748 <  angle = dt2 * ji[0] / I[0][0];
749 <  this->rotate( 1, 2, angle, ji, A );
750 <  
751 <  dAtom->setA( A  );    
728 >  sd->getA(A);
729 >  sd->getI(I);
730 >
731 >  if (sd->isLinear()) {
732 >    i = sd->linearAxis();
733 >    j = (i+1)%3;
734 >    k = (i+2)%3;
735 >    
736 >    angle = dt2 * ji[j] / I[j][j];
737 >    this->rotate( k, i, angle, ji, A );
738 >
739 >    angle = dt * ji[k] / I[k][k];
740 >    this->rotate( i, j, angle, ji, A);
741 >
742 >    angle = dt2 * ji[j] / I[j][j];
743 >    this->rotate( k, i, angle, ji, A );
744 >
745 >  } else {
746 >    // rotate about the x-axis
747 >    angle = dt2 * ji[0] / I[0][0];
748 >    this->rotate( 1, 2, angle, ji, A );
749 >    
750 >    // rotate about the y-axis
751 >    angle = dt2 * ji[1] / I[1][1];
752 >    this->rotate( 2, 0, angle, ji, A );
753 >    
754 >    // rotate about the z-axis
755 >    angle = dt * ji[2] / I[2][2];
756 >    sd->addZangle(angle);
757 >    this->rotate( 0, 1, angle, ji, A);
758 >    
759 >    // rotate about the y-axis
760 >    angle = dt2 * ji[1] / I[1][1];
761 >    this->rotate( 2, 0, angle, ji, A );
762 >    
763 >    // rotate about the x-axis
764 >    angle = dt2 * ji[0] / I[0][0];
765 >    this->rotate( 1, 2, angle, ji, A );
766 >    
767 >  }
768 >  sd->setA( A  );
769   }
770  
771   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
# Line 749 | Line 833 | template<typename T> void Integrator<T>::rotate(int ax
833      }
834    }
835  
836 <  // rotate the Rotation matrix acording to:
836 >  // rotate the Rotation matrix acording to:
837    //            A[][] = A[][] * transpose(rot[][])
838  
839  
# Line 778 | Line 862 | template<typename T> double Integrator<T>::getConserve
862   template<typename T> double Integrator<T>::getConservedQuantity(void){
863    return tStats->getTotalE();
864   }
865 + template<typename T> string Integrator<T>::getAdditionalParameters(void){
866 +  //By default, return a null string
867 +  //The reason we use string instead of char* is that if we use char*, we will
868 +  //return a pointer point to local variable which might cause problem
869 +  return string();
870 + }
871 +
872 +
873 + template<typename T>  void Integrator<T>::printQuaternion(StuntDouble* sd){
874 +  Mat4x4d S;
875 +  double I[3][3];
876 +  Vector4d j4;
877 +  Vector3d j;
878 +  Vector3d tempJ;
879 +  Vector4d qdot;
880 +  Vector4d omega4;
881 +  Mat4x4d I4;
882 +  Quaternion q;
883 +  double I0;
884 +  Vector4d p_qua;
885 +  
886 +  if (sd->isDirectional()){
887 +    sd->getQ(q.vec);
888 +    sd->getI(I);
889 +    sd->getJ(j.vec);
890 +
891 +    //omega4[0] = 0.0;
892 +    //omega4[1] = j[0]/I[0][0];
893 +    //omega4[2] = j[1]/I[1][1];
894 +    //omega4[3] = j[2]/I[2][2];
895 +
896 +    //S = getS(q);
897 +    //qdot = 0.5 * S * omega4;
898 +
899 +    //I0 = (qdot[1] * q[1] * I[0][0] + qdot[2] * q[2] * I[1][1] + qdot[3] * q[3] * I[2][2])/(qdot[1] * q[1]+ qdot[2] * q[2] + qdot[3] * q[3]);
900 +
901 +    //I4.element[0][0] = I0;
902 +    //I4.element[1][1] = I[0][0];
903 +    //I4.element[2][2] = I[1][1];
904 +    //I4.element[3][3] = I[2][2];
905 +
906 +    S = getS(q);
907 +    j4[0] = 0.0;
908 +    j4[1] = j[0];
909 +    j4[2] = j[1];
910 +    j4[3] = j[2];
911 +    
912 +    p_qua = 2 * S * j4;
913 +
914 +    j4 = 0.5 * S.transpose() * p_qua;
915 +    //cout << "q0^2 + q1^2 + q2^2 + q3^2 = " << q[0]*q[0] + q[1]*q[1] + q[2]*q[2] + q[3]*q[3] << endl;
916 +    //cout << "q0*q0dot + q1*q1dot + q2 *q2dot + q3*q3dot = " <<q[0]*qdot[0] + q[1]*qdot[1] + q[2]*qdot[2] + q[3]*qdot[3] << endl;
917 +    //cout << "q1*q1dot* Ixx + q2*q2dot* Iyy + q3 *q3dot* Izz = " << qdot[1] * q[1] * I[0][0] + qdot[2] * q[2] * I[1][1] + qdot[3] * q[3] * I[2][2] << endl;
918 +    //cout << "q1*q1dot + q2 *q2dot + q3*q3dot = "  << qdot[1] * q[1]+ qdot[2] * q[2] + qdot[3] * q[3] << endl;
919 +    //cout << "I0 = " << I0 << endl;
920 +    cout << "p_qua[0] = " << p_qua[0] << endl;
921 +  }    
922 + }
923 +
924 + template<typename T> Mat4x4d Integrator<T>::getS(const Quaternion& q){
925 +  Mat4x4d result;
926 +
927 +  result.element[0][0] = q.x;
928 +  result.element[0][1] = -q.y;
929 +  result.element[0][2] = -q.z;
930 +  result.element[0][3] = -q.w;
931 +
932 +  result.element[1][0] = q.y;
933 +  result.element[1][1] = q.x;
934 +  result.element[1][2] = -q.w;
935 +  result.element[1][3] = q.z;
936 +
937 +  result.element[2][0] = q.z;
938 +  result.element[2][1] = q.w;
939 +  result.element[2][2] = q.x;
940 +  result.element[2][3] = -q.y;
941 +
942 +  result.element[3][0] = q.w;
943 +  result.element[3][1] = -q.z;
944 +  result.element[3][2] = q.y;
945 +  result.element[3][3] = q.x;
946 +
947 +  return result;  
948 + }
949 +

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