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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 UTC vs.
Revision 2069 by gezelter, Thu Mar 5 16:30:23 2015 UTC

# Line 228 | 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 253 | Line 253 | namespace OpenMD {
253      std::string mdRawData;
254      int metaDataBlockStart = -1;
255      int metaDataBlockEnd = -1;
256 –    int i, j;
256      streamoff mdOffset;
257      int mdFileVersion;
258  
# Line 294 | 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 335 | 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 374 | 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 785 | 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 825 | 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:

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