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root/OpenMD/trunk/src/restraints/RestraintForceManager.cpp
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Comparing trunk/src/restraints/RestraintForceManager.cpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 1973 by gezelter, Thu Mar 6 19:34:22 2014 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43 + #ifdef IS_MPI
44 + #include <mpi.h>
45 + #endif
46 +
47   #include "config.h"
48   #include <cmath>
49  
# Line 52 | Line 56
56   #include "utils/StringUtils.hpp"
57   #include "selection/SelectionEvaluator.hpp"
58   #include "selection/SelectionManager.hpp"
55 – #ifdef IS_MPI
56 – #include <mpi.h>
57 – #endif
59  
59 –
60   namespace OpenMD {
61  
62    RestraintForceManager::RestraintForceManager(SimInfo* info): ForceManager(info) {
# Line 101 | Line 101 | namespace OpenMD {
101        if (myType.compare("MOLECULAR")==0){
102  
103          int molIndex;
104 –        std::vector<Vector3d> ref;
104          Vector3d refCom;
105  
106          if (!stamp[i]->haveMolIndex()) {
# Line 137 | Line 136 | namespace OpenMD {
136            // this proc doesn't have the molecule.  Do a quick check to
137            // make sure another processor is supposed to have it.
138          
139 <          int myrank = MPI::COMM_WORLD.Get_rank();
139 >          int myrank;
140 >          MPI_Comm_rank( MPI_COMM_WORLD, &myrank);
141 >
142            if (info_->getMolToProc(molIndex) == myrank) {
143          
144              // If we were supposed to have it but got a null, then freak out.
# Line 159 | Line 160 | namespace OpenMD {
160   #ifdef IS_MPI
161          // only handle this molecular restraint if this processor owns the
162          // molecule
163 <        int myrank = MPI::COMM_WORLD.Get_rank();
163 >        int myrank;
164 >        MPI_Comm_rank( MPI_COMM_WORLD, &myrank);
165          if (info_->getMolToProc(molIndex) == myrank) {
166  
167   #endif
# Line 229 | Line 231 | namespace OpenMD {
231                  "\t\t%s\n"
232                  "\twill result in %d integrable objects being\n"
233                  "\trestrained.\n", objectSelection.c_str(), selectionCount);
234 +        painCave.severity = OPENMD_INFO;
235          painCave.isFatal = 0;
236          simError();                    
237  
# Line 316 | Line 319 | namespace OpenMD {
319      restPot_local = doRestraints(1.0);
320  
321   #ifdef IS_MPI    
322 <    MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1,
323 <                              MPI::REALTYPE, MPI::SUM);
322 >    MPI_Allreduce(&restPot_local, &restPot, 1,
323 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
324   #else
325      restPot = restPot_local;
326   #endif
# Line 389 | Line 392 | namespace OpenMD {
392  
393        std::vector<Vector3d> struc;
394        std::vector<Vector3d> forces;
395 +
396        
397        for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL;
398            sd = (*rm)->nextIntegrableObject(ioi)) {
# Line 449 | Line 453 | namespace OpenMD {
453        
454        // phew.  At this point, we should have the pointer to the
455        // correct Object restraint in the variable oRest.
452 –
456        oRest->setScaleFactor(scalingFactor);
457        
458        Vector3d pos = (*ro)->getPos();

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