| 44 |
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* @file SimCreator.cpp |
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* @author tlin |
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* @date 11/03/2004 |
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– |
* @time 13:51am |
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* @version 1.0 |
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*/ |
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#include <exception> |
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std::string mdRawData; |
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int metaDataBlockStart = -1; |
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int metaDataBlockEnd = -1; |
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< |
int i; |
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> |
int i, j; |
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streamoff mdOffset; |
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int mdFileVersion; |
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|
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+ |
// Create a string for embedding the version information in the MetaData |
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std::string version; |
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version.assign("## Last run using OpenMD Version: "); |
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version.append(OPENMD_VERSION_MAJOR); |
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version.append("."); |
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version.append(OPENMD_VERSION_MINOR); |
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|
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std::string svnrev; |
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//convert a macro from compiler to a string in c++ |
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STR_DEFINE(svnrev, SVN_REV ); |
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version.append(" Revision: "); |
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// If there's no SVN revision, just call this the RELEASE revision. |
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if (!svnrev.empty()) { |
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version.append(svnrev); |
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} else { |
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version.append("RELEASE"); |
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} |
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|
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#ifdef IS_MPI |
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const int masterNode = 0; |
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if (worldRank == masterNode) { |
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|
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mdRawData.clear(); |
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|
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bool foundVersion = false; |
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|
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for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) { |
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mdFile_.getline(buffer, bufferSize); |
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< |
mdRawData += buffer; |
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> |
std::string line = trimLeftCopy(buffer); |
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> |
j = CaseInsensitiveFind(line, "## Last run using OpenMD Version"); |
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> |
if (static_cast<size_t>(j) != string::npos) { |
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> |
foundVersion = true; |
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> |
mdRawData += version; |
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> |
} else { |
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mdRawData += buffer; |
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> |
} |
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mdRawData += "\n"; |
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} |
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< |
|
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> |
|
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> |
if (!foundVersion) mdRawData += version + "\n"; |
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> |
|
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mdFile_.close(); |
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|
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#ifdef IS_MPI |
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int nTarget; |
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int done; |
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int i; |
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int j; |
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int loops; |
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int which_proc; |
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int nProcessors; |
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int nGlobalMols = info->getNGlobalMolecules(); |
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std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: |
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|
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MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); |
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nProcessors = MPI::COMM_WORLD.Get_size(); |
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|
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if (nProcessors > nGlobalMols) { |
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sprintf(painCave.errMsg, |
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nTarget = (int)(precast + 0.5); |
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|
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for(i = 0; i < nGlobalMols; i++) { |
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+ |
|
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done = 0; |
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loops = 0; |
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|
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// and be done with it. |
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|
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if (loops > 100) { |
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|
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sprintf(painCave.errMsg, |
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< |
"I've tried 100 times to assign molecule %d to a " |
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< |
" processor, but can't find a good spot.\n" |
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< |
"I'm assigning it at random to processor %d.\n", |
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> |
"There have been 100 attempts to assign molecule %d to an\n" |
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> |
"\tunderworked processor, but there's no good place to\n" |
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> |
"\tleave it. OpenMD is assigning it at random to processor %d.\n", |
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i, which_proc); |
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< |
|
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> |
|
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painCave.isFatal = 0; |
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painCave.severity = OPENMD_INFO; |
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simError(); |
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|
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molToProcMap[i] = which_proc; |
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} |
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|
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delete myRandom; |
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< |
|
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> |
|
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// Spray out this nonsense to all other processors: |
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< |
|
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< |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
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> |
MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); |
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} else { |
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|
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// Listen to your marching orders from processor 0: |
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< |
|
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< |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
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> |
MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); |
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> |
|
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} |
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|
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info->setMolToProcMap(molToProcMap); |
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int beginRigidBodyIndex; |
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int beginCutoffGroupIndex; |
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int nGlobalAtoms = info->getNGlobalAtoms(); |
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+ |
int nGlobalRigidBodies = info->getNGlobalRigidBodies(); |
| 826 |
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|
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beginAtomIndex = 0; |
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//rigidbody's index begins right after atom's |
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// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
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// docs said we could. |
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std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0); |
| 892 |
< |
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
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< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
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> |
MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0], |
| 893 |
> |
&tmpGroupMembership[0], nGlobalAtoms, |
| 894 |
> |
MPI::INT, MPI::SUM); |
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info->setGlobalGroupMembership(tmpGroupMembership); |
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#else |
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info->setGlobalGroupMembership(globalGroupMembership); |
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#endif |
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|
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//fill molMembership |
| 901 |
< |
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
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> |
std::vector<int> globalMolMembership(info->getNGlobalAtoms() + |
| 902 |
> |
info->getNGlobalRigidBodies(), 0); |
| 903 |
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|
| 904 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 904 |
> |
for(mol = info->beginMolecule(mi); mol != NULL; |
| 905 |
> |
mol = info->nextMolecule(mi)) { |
| 906 |
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 907 |
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globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
| 908 |
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} |
| 909 |
+ |
for (rb = mol->beginRigidBody(ri); rb != NULL; |
| 910 |
+ |
rb = mol->nextRigidBody(ri)) { |
| 911 |
+ |
globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex(); |
| 912 |
+ |
} |
| 913 |
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} |
| 914 |
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|
| 915 |
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#ifdef IS_MPI |
| 916 |
< |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0); |
| 916 |
> |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms() + |
| 917 |
> |
info->getNGlobalRigidBodies(), 0); |
| 918 |
> |
MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0], |
| 919 |
> |
nGlobalAtoms + nGlobalRigidBodies, |
| 920 |
> |
MPI::INT, MPI::SUM); |
| 921 |
|
|
| 882 |
– |
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, |
| 883 |
– |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 884 |
– |
|
| 922 |
|
info->setGlobalMolMembership(tmpMolMembership); |
| 923 |
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#else |
| 924 |
|
info->setGlobalMolMembership(globalMolMembership); |
| 928 |
|
// here the molecules are listed by their global indices. |
| 929 |
|
|
| 930 |
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std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0); |
| 931 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 931 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 932 |
> |
mol = info->nextMolecule(mi)) { |
| 933 |
|
nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects(); |
| 934 |
|
} |
| 935 |
|
|
| 936 |
|
#ifdef IS_MPI |
| 937 |
|
std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0); |
| 938 |
< |
MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
| 939 |
< |
info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 938 |
> |
MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
| 939 |
> |
info->getNGlobalMolecules(), MPI::INT, MPI::SUM); |
| 940 |
|
#else |
| 941 |
|
std::vector<int> numIntegrableObjectsPerMol = nIOPerMol; |
| 942 |
|
#endif |
| 950 |
|
} |
| 951 |
|
|
| 952 |
|
std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL); |
| 953 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 953 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 954 |
> |
mol = info->nextMolecule(mi)) { |
| 955 |
|
int myGlobalIndex = mol->getGlobalIndex(); |
| 956 |
|
int globalIO = startingIOIndexForMol[myGlobalIndex]; |
| 957 |
|
for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL; |
| 967 |
|
} |
| 968 |
|
|
| 969 |
|
void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) { |
| 931 |
– |
Globals* simParams; |
| 932 |
– |
|
| 933 |
– |
simParams = info->getSimParams(); |
| 970 |
|
|
| 971 |
|
DumpReader reader(info, mdFileName); |
| 972 |
|
int nframes = reader.getNFrames(); |
| 973 |
< |
|
| 973 |
> |
|
| 974 |
|
if (nframes > 0) { |
| 975 |
|
reader.readFrame(nframes - 1); |
| 976 |
|
} else { |
