| 255 |
|
std::string mdRawData; |
| 256 |
|
int metaDataBlockStart = -1; |
| 257 |
|
int metaDataBlockEnd = -1; |
| 258 |
< |
int i; |
| 258 |
> |
int i, j; |
| 259 |
|
streamoff mdOffset(0); |
| 260 |
|
int mdFileVersion; |
| 261 |
|
|
| 262 |
+ |
// Create a string for embedding the version information in the MetaData |
| 263 |
+ |
std::string version; |
| 264 |
+ |
version.assign("## Last run using OpenMD Version: "); |
| 265 |
+ |
version.append(OPENMD_VERSION_MAJOR); |
| 266 |
+ |
version.append("."); |
| 267 |
+ |
version.append(OPENMD_VERSION_MINOR); |
| 268 |
|
|
| 269 |
+ |
std::string svnrev; |
| 270 |
+ |
//convert a macro from compiler to a string in c++ |
| 271 |
+ |
STR_DEFINE(svnrev, SVN_REV ); |
| 272 |
+ |
version.append(" Revision: "); |
| 273 |
+ |
// If there's no SVN revision, just call this the RELEASE revision. |
| 274 |
+ |
if (!svnrev.empty()) { |
| 275 |
+ |
version.append(svnrev); |
| 276 |
+ |
} else { |
| 277 |
+ |
version.append("RELEASE"); |
| 278 |
+ |
} |
| 279 |
+ |
|
| 280 |
|
#ifdef IS_MPI |
| 281 |
|
const int masterNode = 0; |
| 282 |
|
if (worldRank == masterNode) { |
| 371 |
|
|
| 372 |
|
mdRawData.clear(); |
| 373 |
|
|
| 374 |
+ |
bool foundVersion = false; |
| 375 |
+ |
|
| 376 |
|
for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) { |
| 377 |
|
mdFile_.getline(buffer, bufferSize); |
| 378 |
< |
mdRawData += buffer; |
| 378 |
> |
std::string line = trimLeftCopy(buffer); |
| 379 |
> |
j = CaseInsensitiveFind(line, "## Last run using OpenMD Version"); |
| 380 |
> |
if (static_cast<size_t>(j) != string::npos) { |
| 381 |
> |
foundVersion = true; |
| 382 |
> |
mdRawData += version; |
| 383 |
> |
} else { |
| 384 |
> |
mdRawData += buffer; |
| 385 |
> |
} |
| 386 |
|
mdRawData += "\n"; |
| 387 |
|
} |
| 388 |
< |
|
| 388 |
> |
|
| 389 |
> |
if (!foundVersion) mdRawData += version + "\n"; |
| 390 |
> |
|
| 391 |
|
mdFile_.close(); |
| 392 |
|
|
| 393 |
|
#ifdef IS_MPI |
| 815 |
|
int beginRigidBodyIndex; |
| 816 |
|
int beginCutoffGroupIndex; |
| 817 |
|
int nGlobalAtoms = info->getNGlobalAtoms(); |
| 818 |
+ |
int nGlobalRigidBodies = info->getNGlobalRigidBodies(); |
| 819 |
|
|
| 820 |
|
beginAtomIndex = 0; |
| 821 |
|
//rigidbody's index begins right after atom's |
| 891 |
|
#endif |
| 892 |
|
|
| 893 |
|
//fill molMembership |
| 894 |
< |
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
| 894 |
> |
std::vector<int> globalMolMembership(info->getNGlobalAtoms() + |
| 895 |
> |
info->getNGlobalRigidBodies(), 0); |
| 896 |
|
|
| 897 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 897 |
> |
for(mol = info->beginMolecule(mi); mol != NULL; |
| 898 |
> |
mol = info->nextMolecule(mi)) { |
| 899 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 900 |
|
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
| 901 |
+ |
} |
| 902 |
+ |
for (rb = mol->beginRigidBody(ri); rb != NULL; |
| 903 |
+ |
rb = mol->nextRigidBody(ri)) { |
| 904 |
+ |
globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex(); |
| 905 |
|
} |
| 906 |
|
} |
| 907 |
|
|
| 908 |
|
#ifdef IS_MPI |
| 909 |
< |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0); |
| 909 |
> |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms() + |
| 910 |
> |
info->getNGlobalRigidBodies(), 0); |
| 911 |
|
MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0], |
| 912 |
< |
nGlobalAtoms, |
| 912 |
> |
nGlobalAtoms + nGlobalRigidBodies, |
| 913 |
|
MPI::INT, MPI::SUM); |
| 914 |
|
|
| 915 |
|
info->setGlobalMolMembership(tmpMolMembership); |
| 921 |
|
// here the molecules are listed by their global indices. |
| 922 |
|
|
| 923 |
|
std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0); |
| 924 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 924 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 925 |
> |
mol = info->nextMolecule(mi)) { |
| 926 |
|
nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects(); |
| 927 |
|
} |
| 928 |
|
|
| 943 |
|
} |
| 944 |
|
|
| 945 |
|
std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL); |
| 946 |
< |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 946 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; |
| 947 |
> |
mol = info->nextMolecule(mi)) { |
| 948 |
|
int myGlobalIndex = mol->getGlobalIndex(); |
| 949 |
|
int globalIO = startingIOIndexForMol[myGlobalIndex]; |
| 950 |
|
for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL; |
