42 |
|
#include "io/DumpWriter.hpp" |
43 |
|
#include "primitives/Molecule.hpp" |
44 |
|
#include "utils/simError.h" |
45 |
< |
|
45 |
> |
#include "io/basic_teebuf.hpp" |
46 |
|
#ifdef IS_MPI |
47 |
|
#include <mpi.h> |
48 |
|
#endif //is_mpi |
49 |
|
|
50 |
|
namespace oopse { |
51 |
+ |
|
52 |
+ |
DumpWriter::DumpWriter(SimInfo* info) |
53 |
+ |
: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){ |
54 |
+ |
#ifdef IS_MPI |
55 |
+ |
|
56 |
+ |
if (worldRank == 0) { |
57 |
+ |
#endif // is_mpi |
58 |
+ |
|
59 |
+ |
dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc); |
60 |
+ |
|
61 |
+ |
if (!dumpFile_) { |
62 |
+ |
sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
63 |
+ |
filename_.c_str()); |
64 |
+ |
painCave.isFatal = 1; |
65 |
+ |
simError(); |
66 |
+ |
} |
67 |
+ |
|
68 |
+ |
#ifdef IS_MPI |
69 |
+ |
|
70 |
+ |
} |
71 |
+ |
|
72 |
+ |
sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
73 |
+ |
MPIcheckPoint(); |
74 |
+ |
|
75 |
+ |
#endif // is_mpi |
76 |
+ |
|
77 |
+ |
} |
78 |
+ |
|
79 |
|
|
80 |
|
DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) |
81 |
|
: info_(info), filename_(filename){ |
84 |
|
if (worldRank == 0) { |
85 |
|
#endif // is_mpi |
86 |
|
|
87 |
+ |
eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
88 |
|
dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc); |
89 |
|
|
90 |
|
if (!dumpFile_) { |
149 |
|
<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t" |
150 |
|
<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";"; |
151 |
|
|
152 |
< |
os << std::endl; |
152 |
> |
os << "\n"; |
153 |
|
} |
154 |
|
|
155 |
|
void DumpWriter::writeFrame(std::ostream& os) { |
212 |
|
} |
213 |
|
} |
214 |
|
|
215 |
+ |
os.flush(); |
216 |
|
#else // is_mpi |
217 |
|
/********************************************************************* |
218 |
|
* Documentation? You want DOCUMENTATION? |
258 |
|
int which_node; |
259 |
|
double atomData[13]; |
260 |
|
int isDirectional; |
231 |
– |
const char * atomTypeString; |
261 |
|
char MPIatomTypeString[MINIBUFFERSIZE]; |
262 |
|
int msgLen; // the length of message actually recieved at master nodes |
263 |
|
int haveError; |
328 |
|
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, |
329 |
|
which_node, myPotato, MPI_COMM_WORLD, |
330 |
|
&istatus); |
302 |
– |
|
303 |
– |
atomTypeString = MPIatomTypeString; |
331 |
|
|
332 |
|
myPotato++; |
333 |
|
|
346 |
|
|
347 |
|
if (!isDirectional) { |
348 |
|
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
349 |
< |
atomTypeString, atomData[0], |
349 |
> |
MPIatomTypeString, atomData[0], |
350 |
|
atomData[1], atomData[2], |
351 |
|
atomData[3], atomData[4], |
352 |
|
atomData[5]); |
356 |
|
} else { |
357 |
|
sprintf(writeLine, |
358 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
359 |
< |
atomTypeString, |
359 |
> |
MPIatomTypeString, |
360 |
|
atomData[0], |
361 |
|
atomData[1], |
362 |
|
atomData[2], |
388 |
|
} |
389 |
|
|
390 |
|
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
391 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
365 |
< |
|
366 |
< |
atomTypeString = integrableObject->getType().c_str(); |
391 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
392 |
|
|
393 |
|
pos = integrableObject->getPos(); |
394 |
|
vel = integrableObject->getVel(); |
427 |
|
|
428 |
|
if (!isDirectional) { |
429 |
|
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
430 |
< |
atomTypeString, atomData[0], |
430 |
> |
integrableObject->getType().c_str(), atomData[0], |
431 |
|
atomData[1], atomData[2], |
432 |
|
atomData[3], atomData[4], |
433 |
|
atomData[5]); |
437 |
|
} else { |
438 |
|
sprintf(writeLine, |
439 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
440 |
< |
atomTypeString, |
440 |
> |
integrableObject->getType().c_str(), |
441 |
|
atomData[0], |
442 |
|
atomData[1], |
443 |
|
atomData[2], |
461 |
|
} //end for(i = 0; i < mpiSim->getNmol()) |
462 |
|
|
463 |
|
os.flush(); |
464 |
< |
std::cout << "master" << std::endl; |
464 |
> |
|
465 |
|
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
441 |
– |
|
466 |
|
MPIcheckPoint(); |
467 |
|
|
468 |
|
delete [] potatoes; |
510 |
|
&istatus); |
511 |
|
} |
512 |
|
|
489 |
– |
atomTypeString = integrableObject->getType().c_str(); |
490 |
– |
|
513 |
|
pos = integrableObject->getPos(); |
514 |
|
vel = integrableObject->getVel(); |
515 |
|
|
539 |
|
atomData[12] = ji[2]; |
540 |
|
} |
541 |
|
|
542 |
< |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
542 |
> |
strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE); |
543 |
|
|
544 |
|
// null terminate the std::string before sending (just in case): |
545 |
|
MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0'; |
563 |
|
} |
564 |
|
|
565 |
|
} |
544 |
– |
std::cout << "slave" << std::endl; |
566 |
|
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
567 |
|
MPIcheckPoint(); |
568 |
|
} |
571 |
|
|
572 |
|
} |
573 |
|
|
574 |
+ |
void DumpWriter::writeDump() { |
575 |
+ |
writeFrame(dumpFile_); |
576 |
+ |
|
577 |
+ |
} |
578 |
+ |
|
579 |
+ |
void DumpWriter::writeEor() { |
580 |
+ |
std::ofstream eorStream; |
581 |
+ |
|
582 |
+ |
#ifdef IS_MPI |
583 |
+ |
if (worldRank == 0) { |
584 |
+ |
#endif // is_mpi |
585 |
+ |
|
586 |
+ |
eorStream.open(eorFilename_.c_str()); |
587 |
+ |
if (!eorStream.is_open()) { |
588 |
+ |
sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n", |
589 |
+ |
eorFilename_.c_str()); |
590 |
+ |
painCave.isFatal = 1; |
591 |
+ |
simError(); |
592 |
+ |
} |
593 |
+ |
|
594 |
+ |
#ifdef IS_MPI |
595 |
+ |
} |
596 |
+ |
#endif // is_mpi |
597 |
+ |
|
598 |
+ |
writeFrame(eorStream); |
599 |
+ |
} |
600 |
+ |
|
601 |
+ |
|
602 |
+ |
void DumpWriter::writeDumpAndEor() { |
603 |
+ |
std::ofstream eorStream; |
604 |
+ |
std::vector<std::streambuf*> buffers; |
605 |
+ |
#ifdef IS_MPI |
606 |
+ |
if (worldRank == 0) { |
607 |
+ |
#endif // is_mpi |
608 |
+ |
|
609 |
+ |
buffers.push_back(dumpFile_.rdbuf()); |
610 |
+ |
|
611 |
+ |
eorStream.open(eorFilename_.c_str()); |
612 |
+ |
if (!eorStream.is_open()) { |
613 |
+ |
sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n", |
614 |
+ |
eorFilename_.c_str()); |
615 |
+ |
painCave.isFatal = 1; |
616 |
+ |
simError(); |
617 |
+ |
} |
618 |
+ |
|
619 |
+ |
buffers.push_back(eorStream.rdbuf()); |
620 |
+ |
|
621 |
+ |
#ifdef IS_MPI |
622 |
+ |
} |
623 |
+ |
#endif // is_mpi |
624 |
+ |
|
625 |
+ |
TeeBuf tbuf(buffers.begin(), buffers.end()); |
626 |
+ |
std::ostream os(&tbuf); |
627 |
+ |
|
628 |
+ |
writeFrame(os); |
629 |
+ |
|
630 |
+ |
} |
631 |
+ |
|
632 |
+ |
|
633 |
+ |
|
634 |
|
}//end namespace oopse |