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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1971 by gezelter, Fri Feb 28 13:25:13 2014 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

# Line 64 | Line 64
64   #include "brains/ForceField.hpp"
65   #include "utils/simError.h"
66   #include "utils/StringUtils.hpp"
67 + #include "utils/Revision.hpp"
68   #include "math/SeqRandNumGen.hpp"
69   #include "mdParser/MDLexer.hpp"
70   #include "mdParser/MDParser.hpp"
# Line 104 | Line 105 | namespace OpenMD {
105  
106        if (worldRank == masterNode) {
107          MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
107 –        // MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
108   #endif                
109          SimplePreprocessor preprocessor;
110          preprocessor.preprocess(rawMetaDataStream, filename,
# Line 114 | Line 114 | namespace OpenMD {
114          //broadcasting the stream size
115          streamSize = ppStream.str().size() +1;
116          MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
117 <        MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
117 >        MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
118                    streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
119 –
120 –        // MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
121 –        // MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
122 –        //                       streamSize, MPI::CHAR, masterNode);
123 –                          
119        } else {
120  
121          MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
127 –        // MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
122  
123          //get stream size
124          MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
131 –        // MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
125          char* buf = new char[streamSize];
126          assert(buf);
127                  
128          //receive file content
129          MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
137 –        // MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
130  
131          ppStream.str(buf);
132          delete [] buf;
# Line 272 | Line 264 | namespace OpenMD {
264      version.append(".");
265      version.append(OPENMD_VERSION_MINOR);
266  
267 <    std::string svnrev;
267 >    std::string svnrev(g_REVISION, strnlen(g_REVISION, 20));
268      //convert a macro from compiler to a string in c++
269 <    STR_DEFINE(svnrev, SVN_REV );
269 >    // STR_DEFINE(svnrev, SVN_REV );
270      version.append(" Revision: ");
271      // If there's no SVN revision, just call this the RELEASE revision.
272      if (!svnrev.empty()) {
# Line 530 | Line 522 | namespace OpenMD {
522                                                      // condition:
523      
524      MPI_Comm_size( MPI_COMM_WORLD, &nProcessors);    
533 –    //nProcessors = MPI::COMM_WORLD.Get_size();
525      
526      if (nProcessors > nGlobalMols) {
527        sprintf(painCave.errMsg,
# Line 650 | Line 641 | namespace OpenMD {
641  
642        // Spray out this nonsense to all other processors:
643        MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
644 <      // MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
644 >
645      } else {
646        
647        // Listen to your marching orders from processor 0:
648        MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
658 –      // MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
649  
650      }
651      
# Line 797 | Line 787 | namespace OpenMD {
787  
788      if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
789        storageLayout |= DataStorage::dslElectricField;
790 +    }
791 +
792 +    if (simParams->getOutputSitePotential() ) {
793 +      storageLayout |= DataStorage::dslSitePotential;
794      }
795  
796      if (simParams->getOutputFluctuatingCharges()) {
# Line 932 | Line 926 | namespace OpenMD {
926      MPI_Allreduce(&globalGroupMembership[0],
927                    &tmpGroupMembership[0], nGlobalAtoms,
928                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
929 <    // MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
936 <    //                           &tmpGroupMembership[0], nGlobalAtoms,
937 <    //                           MPI::INT, MPI::SUM);
929 >
930      info->setGlobalGroupMembership(tmpGroupMembership);
931   #else
932      info->setGlobalGroupMembership(globalGroupMembership);
# Line 961 | Line 953 | namespace OpenMD {
953      MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
954                    nGlobalAtoms + nGlobalRigidBodies,
955                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
964 –    // MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
965 –    //                           nGlobalAtoms + nGlobalRigidBodies,
966 –    //                           MPI::INT, MPI::SUM);
956      
957      info->setGlobalMolMembership(tmpMolMembership);
958   #else
# Line 983 | Line 972 | namespace OpenMD {
972      std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
973      MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
974        info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
986 –    // MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
987 –    //                           info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
975   #else
976      std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
977   #endif    

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