| 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" |
| 104 |
|
const int masterNode = 0; |
| 105 |
|
|
| 106 |
|
if (worldRank == masterNode) { |
| 107 |
< |
MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); |
| 107 |
> |
MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 108 |
|
#endif |
| 109 |
|
SimplePreprocessor preprocessor; |
| 110 |
< |
preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream); |
| 110 |
> |
preprocessor.preprocess(rawMetaDataStream, filename, |
| 111 |
> |
startOfMetaDataBlock, ppStream); |
| 112 |
|
|
| 113 |
|
#ifdef IS_MPI |
| 114 |
< |
//brocasting the stream size |
| 114 |
> |
//broadcasting the stream size |
| 115 |
|
streamSize = ppStream.str().size() +1; |
| 116 |
< |
MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode); |
| 117 |
< |
MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI::CHAR, masterNode); |
| 118 |
< |
|
| 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 |
|
} else { |
| 118 |
– |
MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); |
| 120 |
|
|
| 121 |
< |
//get stream size |
| 121 |
< |
MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode); |
| 121 |
> |
MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 122 |
|
|
| 123 |
+ |
//get stream size |
| 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::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode); |
| 130 |
< |
|
| 129 |
> |
MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 130 |
> |
|
| 131 |
|
ppStream.str(buf); |
| 132 |
|
delete [] buf; |
| 133 |
|
} |
| 151 |
|
parser.initializeASTFactory(factory); |
| 152 |
|
parser.setASTFactory(&factory); |
| 153 |
|
parser.mdfile(); |
| 152 |
– |
|
| 154 |
|
// Create a tree parser that reads information into Globals |
| 155 |
|
MDTreeParser treeParser; |
| 156 |
|
treeParser.initializeASTFactory(factory); |
| 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()) { |
| 521 |
|
// error |
| 522 |
|
// condition: |
| 523 |
|
|
| 524 |
< |
nProcessors = MPI::COMM_WORLD.Get_size(); |
| 524 |
> |
MPI_Comm_size( MPI_COMM_WORLD, &nProcessors); |
| 525 |
|
|
| 526 |
|
if (nProcessors > nGlobalMols) { |
| 527 |
|
sprintf(painCave.errMsg, |
| 640 |
|
delete myRandom; |
| 641 |
|
|
| 642 |
|
// Spray out this nonsense to all other processors: |
| 643 |
< |
MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); |
| 643 |
> |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
| 644 |
> |
|
| 645 |
|
} else { |
| 646 |
|
|
| 647 |
|
// Listen to your marching orders from processor 0: |
| 648 |
< |
MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); |
| 648 |
> |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
| 649 |
|
|
| 650 |
|
} |
| 651 |
|
|
| 789 |
|
storageLayout |= DataStorage::dslElectricField; |
| 790 |
|
} |
| 791 |
|
|
| 792 |
+ |
if (simParams->getOutputSitePotential() ) { |
| 793 |
+ |
storageLayout |= DataStorage::dslSitePotential; |
| 794 |
+ |
} |
| 795 |
+ |
|
| 796 |
|
if (simParams->getOutputFluctuatingCharges()) { |
| 797 |
|
storageLayout |= DataStorage::dslFlucQPosition; |
| 798 |
|
storageLayout |= DataStorage::dslFlucQVelocity; |
| 923 |
|
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
| 924 |
|
// docs said we could. |
| 925 |
|
std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0); |
| 926 |
< |
MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0], |
| 927 |
< |
&tmpGroupMembership[0], nGlobalAtoms, |
| 928 |
< |
MPI::INT, MPI::SUM); |
| 926 |
> |
MPI_Allreduce(&globalGroupMembership[0], |
| 927 |
> |
&tmpGroupMembership[0], nGlobalAtoms, |
| 928 |
> |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 929 |
> |
|
| 930 |
|
info->setGlobalGroupMembership(tmpGroupMembership); |
| 931 |
|
#else |
| 932 |
|
info->setGlobalGroupMembership(globalGroupMembership); |
| 950 |
|
#ifdef IS_MPI |
| 951 |
|
std::vector<int> tmpMolMembership(info->getNGlobalAtoms() + |
| 952 |
|
info->getNGlobalRigidBodies(), 0); |
| 953 |
< |
MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0], |
| 954 |
< |
nGlobalAtoms + nGlobalRigidBodies, |
| 955 |
< |
MPI::INT, MPI::SUM); |
| 953 |
> |
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], |
| 954 |
> |
nGlobalAtoms + nGlobalRigidBodies, |
| 955 |
> |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 956 |
|
|
| 957 |
|
info->setGlobalMolMembership(tmpMolMembership); |
| 958 |
|
#else |
| 970 |
|
|
| 971 |
|
#ifdef IS_MPI |
| 972 |
|
std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0); |
| 973 |
< |
MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
| 974 |
< |
info->getNGlobalMolecules(), MPI::INT, MPI::SUM); |
| 973 |
> |
MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
| 974 |
> |
info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 975 |
|
#else |
| 976 |
|
std::vector<int> numIntegrableObjectsPerMol = nIOPerMol; |
| 977 |
|
#endif |
