# | 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); | |
# | Line 199 | Line 197 | template<typename T> void Integrator<T>::integrate(voi | |
197 | dumpOut->writeDump(info->getTime()); | |
198 | statOut->writeStat(info->getTime()); | |
199 | ||
202 | – | readyCheck(); |
200 | ||
201 | + | |
202 | #ifdef IS_MPI | |
203 | strcpy(checkPointMsg, "The integrator is ready to go."); | |
204 | MPIcheckPoint(); | |
# | Line 248 | Line 246 | template<typename T> void Integrator<T>::integrate(voi | |
246 | #endif // is_mpi | |
247 | } | |
248 | ||
251 | – | dumpOut->writeFinal(info->getTime()); |
249 | ||
250 | + | // write the last frame |
251 | + | dumpOut->writeDump(info->getTime()); |
252 | + | |
253 | delete dumpOut; | |
254 | delete statOut; | |
255 | } | |
# | Line 404 | 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 548 | 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 557 | 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; |
561 | < | double diffsq; |
560 | > | double rvab; |
561 | double gab; | |
562 | int iteration; | |
563 |
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