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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 1127 by tim, Tue Apr 20 16:56:40 2004 UTC vs.
Revision 1452 by tim, Mon Aug 23 15:11:36 2004 UTC

# Line 1 | Line 1
1   #include <iostream>
2   #include <stdlib.h>
3   #include <math.h>
4 <
4 > #include "Rattle.hpp"
5 > #include "Roll.hpp"
6   #ifdef IS_MPI
7   #include "mpiSimulation.hpp"
8   #include <unistd.h>
# Line 33 | Line 34 | template<typename T> Integrator<T>::Integrator(SimInfo
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 45 | 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 56 | 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 92 | 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 150 | Line 167 | template<typename T> void Integrator<T>::checkConstrai
167  
168    delete[] temp_con;
169   }
170 + */
171  
154 –
172   template<typename T> void Integrator<T>::integrate(void){
173  
174    double runTime = info->run_time;
# Line 160 | 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;
# Line 182 | Line 199 | template<typename T> void Integrator<T>::integrate(voi
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();
195 <  }
212 >
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 215 | Line 237 | template<typename T> void Integrator<T>::integrate(voi
237   #endif // is_mpi
238  
239    while (info->getTime() < runTime && !stopIntegrator()){
240 <    if ((info->getTime() + dt) >= currStatus){
240 >    difference = info->getTime() + dt - currStatus;
241 >    if (difference > 0 || fabs(difference) < 1e-4 ){
242        calcPot = 1;
243        calcStress = 1;
244      }
# Line 270 | Line 293 | template<typename T> void Integrator<T>::integrate(voi
293   #endif // is_mpi
294    }
295  
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;
303   }
# Line 282 | Line 310 | template<typename T> void Integrator<T>::integrateStep
310    startProfile(pro3);
311   #endif //profile
312  
313 <  preMove();
313 >  //save old state (position, velocity etc)
314 >  consFramework->doPreConstraint();
315  
316   #ifdef PROFILE
317    endProfile(pro3);
# Line 304 | Line 333 | template<typename T> void Integrator<T>::integrateStep
333    MPIcheckPoint();
334   #endif // is_mpi
335  
307 –
336    // calc forces
309 –
337    calcForce(calcPot, calcStress);
338  
339   #ifdef IS_MPI
# Line 320 | Line 347 | template<typename T> void Integrator<T>::integrateStep
347    startProfile( pro6 );
348   #endif //profile
349  
350 +  consFramework->doPreConstraint();
351 +
352    // finish the velocity  half step
353  
354    moveB();
# Line 341 | Line 370 | template<typename T> void Integrator<T>::moveA(void){
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);
# Line 376 | Line 406 | template<typename T> void Integrator<T>::moveA(void){
406        this->rotationPropagation( integrableObjects[i], ji );
407  
408        integrableObjects[i]->setJ(ji);
409 +
410      }
411    }
412  
413 <  if (nConstrained){
383 <    constrainA();
384 <  }
413 >  consFramework->doConstrainA();
414   }
415  
416  
# Line 420 | Line 449 | template<typename T> void Integrator<T>::moveB(void){
449  
450        integrableObjects[i]->setJ(ji);
451      }
452 +
453    }
454  
455 <  if (nConstrained){
426 <    constrainB();
427 <  }
455 >  consFramework->doConstrainB();
456   }
457  
458 + /*
459   template<typename T> void Integrator<T>::preMove(void){
460    int i, j;
461    double pos[3];
# Line 685 | 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   ( StuntDouble* sd, double ji[3] ){
720  
# Line 724 | Line 753 | template<typename T> void Integrator<T>::rotationPropa
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
# Line 838 | Line 868 | template<typename T> string Integrator<T>::getAddition
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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