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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC vs.
Revision 2069 by gezelter, Thu Mar 5 16:30:23 2015 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 113 | Line 113 | namespace OpenMD {
113   #ifdef IS_MPI            
114          //broadcasting the stream size
115          streamSize = ppStream.str().size() +1;
116 <        MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
117 <        MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
116 >        MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
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_LONG, masterNode, MPI_COMM_WORLD);
131 <        // MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
124 >        MPI_Bcast(&streamSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
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 236 | Line 228 | namespace OpenMD {
228      catch (OpenMDException& e) {
229        sprintf(painCave.errMsg,
230                "%s\n",
231 <              e.getMessage().c_str());
231 >              e.what());
232        painCave.isFatal = 1;
233        simError();
234      }
# Line 261 | Line 253 | namespace OpenMD {
253      std::string mdRawData;
254      int metaDataBlockStart = -1;
255      int metaDataBlockEnd = -1;
264 –    int i, j;
256      streamoff mdOffset;
257      int mdFileVersion;
258  
# Line 272 | Line 263 | namespace OpenMD {
263      version.append(".");
264      version.append(OPENMD_VERSION_MINOR);
265  
266 <    std::string svnrev;
266 >    std::string svnrev(g_REVISION, strnlen(g_REVISION, 20));
267      //convert a macro from compiler to a string in c++
268 <    STR_DEFINE(svnrev, SVN_REV );
268 >    // STR_DEFINE(svnrev, SVN_REV );
269      version.append(" Revision: ");
270      // If there's no SVN revision, just call this the RELEASE revision.
271      if (!svnrev.empty()) {
# Line 302 | Line 293 | namespace OpenMD {
293        mdFile_.getline(buffer, bufferSize);
294        ++lineNo;
295        std::string line = trimLeftCopy(buffer);
296 <      i = CaseInsensitiveFind(line, "<OpenMD");
297 <      if (static_cast<size_t>(i) == string::npos) {
296 >      std::size_t i = CaseInsensitiveFind(line, "<OpenMD");
297 >      if (i == string::npos) {
298          // try the older file strings to see if that works:
299          i = CaseInsensitiveFind(line, "<OOPSE");
300        }
301        
302 <      if (static_cast<size_t>(i) == string::npos) {
302 >      if (i == string::npos) {
303          // still no luck!
304          sprintf(painCave.errMsg,
305                  "SimCreator: File: %s is not a valid OpenMD file!\n",
# Line 343 | Line 334 | namespace OpenMD {
334          
335          std::string line = trimLeftCopy(buffer);
336          if (metaDataBlockStart == -1) {
337 <          i = CaseInsensitiveFind(line, "<MetaData>");
337 >          std::size_t i = CaseInsensitiveFind(line, "<MetaData>");
338            if (i != string::npos) {
339              metaDataBlockStart = lineNo;
340              mdOffset = mdFile_.tellg();
341            }
342          } else {
343 <          i = CaseInsensitiveFind(line, "</MetaData>");
343 >          std::size_t i = CaseInsensitiveFind(line, "</MetaData>");
344            if (i != string::npos) {
345              metaDataBlockEnd = lineNo;
346            }
# Line 382 | Line 373 | namespace OpenMD {
373        for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
374          mdFile_.getline(buffer, bufferSize);
375          std::string line = trimLeftCopy(buffer);
376 <        j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
377 <        if (static_cast<size_t>(j) != string::npos) {
376 >        std::size_t j = CaseInsensitiveFind(line,
377 >                                            "## Last run using OpenMD Version");
378 >        if (j != string::npos) {
379            foundVersion = true;
380            mdRawData += version;
381          } else {
# 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 795 | Line 785 | namespace OpenMD {
785        }
786      }
787  
788 <    if (simParams->getOutputElectricField() | simParams->haveElectricField()) {
788 >    if (simParams->getOutputElectricField() |
789 >        simParams->haveElectricField() | simParams->haveUniformField() |
790 >        simParams->haveUniformGradientStrength() |
791 >        simParams->haveUniformGradientDirection1() |
792 >        simParams->haveUniformGradientDirection2() ) {
793        storageLayout |= DataStorage::dslElectricField;
794      }
795  
796 +    if (simParams->getOutputSitePotential() ) {
797 +      storageLayout |= DataStorage::dslSitePotential;
798 +    }
799 +
800      if (simParams->getOutputFluctuatingCharges()) {
801        storageLayout |= DataStorage::dslFlucQPosition;
802        storageLayout |= DataStorage::dslFlucQVelocity;
# Line 835 | Line 833 | namespace OpenMD {
833      int beginBendIndex;
834      int beginTorsionIndex;
835      int beginInversionIndex;
836 + #ifdef IS_MPI
837      int nGlobalAtoms = info->getNGlobalAtoms();
838      int nGlobalRigidBodies = info->getNGlobalRigidBodies();
839 + #endif
840      
841      beginAtomIndex = 0;
842      // The rigid body indices begin immediately after the atom indices:
# Line 932 | Line 932 | namespace OpenMD {
932      MPI_Allreduce(&globalGroupMembership[0],
933                    &tmpGroupMembership[0], nGlobalAtoms,
934                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
935 <    // MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
936 <    //                           &tmpGroupMembership[0], nGlobalAtoms,
937 <    //                           MPI::INT, MPI::SUM);
935 >
936      info->setGlobalGroupMembership(tmpGroupMembership);
937   #else
938      info->setGlobalGroupMembership(globalGroupMembership);
# Line 961 | Line 959 | namespace OpenMD {
959      MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
960                    nGlobalAtoms + nGlobalRigidBodies,
961                    MPI_INT, MPI_SUM, MPI_COMM_WORLD);
964 –    // MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
965 –    //                           nGlobalAtoms + nGlobalRigidBodies,
966 –    //                           MPI::INT, MPI::SUM);
962      
963      info->setGlobalMolMembership(tmpMolMembership);
964   #else
# Line 983 | Line 978 | namespace OpenMD {
978      std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
979      MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
980        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);
981   #else
982      std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
983   #endif    

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