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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 781 by tim, Mon Sep 22 23:07:57 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);
# 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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