| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
|
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
– |
|
| 42 |
|
|
| 43 |
+ |
#ifdef IS_MPI |
| 44 |
+ |
#include <mpi.h> |
| 45 |
+ |
#endif |
| 46 |
+ |
|
| 47 |
|
#include <sys/types.h> |
| 48 |
|
#include <sys/stat.h> |
| 49 |
|
|
| 62 |
|
#include "utils/StringTokenizer.hpp" |
| 63 |
|
#include "restraints/ObjectRestraint.hpp" |
| 64 |
|
#include "restraints/MolecularRestraint.hpp" |
| 62 |
– |
|
| 63 |
– |
#ifdef IS_MPI |
| 64 |
– |
|
| 65 |
– |
#include <mpi.h> |
| 66 |
– |
#endif |
| 65 |
|
|
| 66 |
|
namespace OpenMD { |
| 67 |
|
|
| 68 |
|
void RestReader::scanFile(){ |
| 69 |
< |
int lineNo = 0; |
| 69 |
> |
|
| 70 |
|
std::streampos prevPos; |
| 71 |
< |
std::streampos currPos; |
| 71 |
> |
std::streampos currPos; |
| 72 |
|
|
| 73 |
|
#ifdef IS_MPI |
| 74 |
|
|
| 80 |
|
prevPos = currPos; |
| 81 |
|
|
| 82 |
|
bool foundOpenSnapshotTag = false; |
| 83 |
< |
|
| 83 |
> |
int lineNo = 0; |
| 84 |
|
while(!foundOpenSnapshotTag && inFile_->getline(buffer, bufferSize)) { |
| 85 |
|
++lineNo; |
| 86 |
|
|
| 88 |
|
currPos = inFile_->tellg(); |
| 89 |
|
if (line.find("<Snapshot>")!= std::string::npos) { |
| 90 |
|
foundOpenSnapshotTag = true; |
| 91 |
< |
framePos_ = prevPos; |
| 91 |
> |
framePos_ = (long long) prevPos; |
| 92 |
|
} |
| 93 |
|
prevPos = currPos; |
| 94 |
|
} |
| 95 |
|
|
| 96 |
|
#ifdef IS_MPI |
| 97 |
|
} |
| 98 |
< |
MPI::COMM_WORLD.Bcast(&framePos_, 1, MPI::INT, 0); |
| 98 |
> |
MPI_Bcast(&framePos_, 1, MPI_LONG_LONG, 0, MPI_COMM_WORLD); |
| 99 |
|
#endif // is_mpi |
| 100 |
|
} |
| 101 |
|
|
| 130 |
|
} |
| 131 |
|
|
| 132 |
|
int sendBufferSize = sendBuffer.size(); |
| 133 |
< |
MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode); |
| 134 |
< |
MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize, |
| 135 |
< |
MPI::CHAR, masterNode); |
| 133 |
> |
MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 134 |
> |
MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, |
| 135 |
> |
MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 136 |
|
|
| 137 |
|
sstream.str(sendBuffer); |
| 138 |
|
} else { |
| 139 |
|
int sendBufferSize; |
| 140 |
< |
MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode); |
| 140 |
> |
MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 141 |
|
char * recvBuffer = new char[sendBufferSize+1]; |
| 142 |
|
assert(recvBuffer); |
| 143 |
|
recvBuffer[sendBufferSize] = '\0'; |
| 144 |
< |
MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode); |
| 144 |
> |
MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, |
| 145 |
> |
MPI_COMM_WORLD); |
| 146 |
|
sstream.str(recvBuffer); |
| 147 |
|
delete [] recvBuffer; |
| 148 |
|
} |
| 367 |
|
|
| 368 |
|
// is this io restrained? |
| 369 |
|
GenericData* data = sd->getPropertyByName("Restraint"); |
| 371 |
– |
ObjectRestraint* oRest; |
| 370 |
|
|
| 371 |
|
if (data != NULL) { |
| 372 |
|
// make sure we can reinterpret the generic data as restraint data: |
| 374 |
|
if (restData != NULL) { |
| 375 |
|
// make sure we can reinterpet the restraint data as a pointer to |
| 376 |
|
// an ObjectRestraint: |
| 377 |
< |
oRest = dynamic_cast<ObjectRestraint*>(restData->getData()); |
| 377 |
> |
ObjectRestraint* oRest = dynamic_cast<ObjectRestraint*>(restData->getData()); |
| 378 |
|
if (oRest != NULL) { |
| 379 |
|
if (sd->isDirectional()) { |
| 380 |
|
oRest->setReferenceStructure(pos, q.toRotationMatrix3()); |
