# | Line 1 | Line 1 | |
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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 32 | Line 33 | template<typename T> Integrator<T>::Integrator(SimInfo | |
33 | ||
34 | nAtoms = info->n_atoms; | |
35 | integrableObjects = info->integrableObjects; | |
36 | < | |
36 | > | |
37 | > | consFramework = new RattleFramework(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 | < | |
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 57 | 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 93 | 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 151 | Line 167 | template<typename T> void Integrator<T>::checkConstrai | |
167 | ||
168 | delete[] temp_con; | |
169 | } | |
170 | + | */ |
171 | ||
155 | – | |
172 | template<typename T> void Integrator<T>::integrate(void){ | |
173 | ||
174 | double runTime = info->run_time; | |
# | Line 185 | Line 201 | template<typename T> void Integrator<T>::integrate(voi | |
201 | tStats->removeCOMdrift(); | |
202 | ||
203 | // initialize the retraints if necessary | |
204 | < | if (info->useThermInt) { |
204 | > | if (info->useSolidThermInt && !info->useLiquidThermInt) { |
205 | myFF->initRestraints(); | |
206 | } | |
207 | ||
208 | // initialize the forces before the first step | |
209 | ||
210 | calcForce(1, 1); | |
211 | < | |
212 | < | if (nConstrained){ |
213 | < | preMove(); |
214 | < | constrainA(); |
215 | < | calcForce(1, 1); |
216 | < | constrainB(); |
201 | < | } |
211 | > | |
212 | > | //execute constraint algorithm to make sure at the very beginning the system is constrained |
213 | > | //consFramework->doPreConstraint(); |
214 | > | //consFramework->doConstrainA(); |
215 | > | //calcForce(1, 1); |
216 | > | //consFramework->doConstrainB(); |
217 | ||
218 | if (info->setTemp){ | |
219 | thermalize(); | |
# | Line 255 | Line 270 | template<typename T> void Integrator<T>::integrate(voi | |
270 | ||
271 | if (info->getTime() >= currStatus){ | |
272 | statOut->writeStat(info->getTime()); | |
258 | – | if (info->useThermInt) |
259 | – | statOut->writeRaw(info->getTime()); |
273 | calcPot = 0; | |
274 | calcStress = 0; | |
275 | currStatus += statusTime; | |
# | Line 280 | Line 293 | template<typename T> void Integrator<T>::integrate(voi | |
293 | } | |
294 | ||
295 | // dump out a file containing the omega values for the final configuration | |
296 | < | if (info->useThermInt) |
296 | > | if (info->useSolidThermInt && !info->useLiquidThermInt) |
297 | myFF->dumpzAngle(); | |
298 | ||
299 | ||
# | Line 296 | Line 309 | template<typename T> void Integrator<T>::integrateStep | |
309 | startProfile(pro3); | |
310 | #endif //profile | |
311 | ||
312 | < | preMove(); |
312 | > | //save old state (position, velocity etc) |
313 | > | consFramework->doPreConstraint(); |
314 | ||
315 | #ifdef PROFILE | |
316 | endProfile(pro3); | |
# | Line 392 | Line 406 | template<typename T> void Integrator<T>::moveA(void){ | |
406 | } | |
407 | } | |
408 | ||
409 | < | if (nConstrained){ |
396 | < | constrainA(); |
397 | < | } |
409 | > | consFramework->doConstrainA(); |
410 | } | |
411 | ||
412 | ||
# | Line 435 | Line 447 | template<typename T> void Integrator<T>::moveB(void){ | |
447 | } | |
448 | } | |
449 | ||
450 | < | if (nConstrained){ |
439 | < | constrainB(); |
440 | < | } |
450 | > | consFramework->doConstrainB(); |
451 | } | |
452 | ||
453 | + | /* |
454 | template<typename T> void Integrator<T>::preMove(void){ | |
455 | int i, j; | |
456 | double pos[3]; | |
# | Line 698 | Line 709 | template<typename T> void Integrator<T>::constrainB(vo | |
709 | simError(); | |
710 | } | |
711 | } | |
712 | < | |
712 | > | */ |
713 | template<typename T> void Integrator<T>::rotationPropagation | |
714 | ( StuntDouble* sd, double ji[3] ){ | |
715 |
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