# | Line 43 | Line 43 | |
---|---|---|
43 | #include "primitives/Molecule.hpp" | |
44 | #include "utils/simError.h" | |
45 | #include "io/basic_teebuf.hpp" | |
46 | + | #include "io/gzstream.hpp" |
47 | + | #include "io/Globals.hpp" |
48 | + | |
49 | #ifdef IS_MPI | |
50 | #include <mpi.h> | |
51 | #endif //is_mpi | |
# | Line 51 | Line 54 | namespace oopse { | |
54 | ||
55 | DumpWriter::DumpWriter(SimInfo* info) | |
56 | : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){ | |
57 | + | |
58 | + | Globals* simParams = info->getSimParams(); |
59 | + | needCompression_ = simParams->getCompressDumpFile(); |
60 | + | needForceVector_ = simParams->getOutputForceVector(); |
61 | + | createDumpFile_ = true; |
62 | + | #ifdef HAVE_LIBZ |
63 | + | if (needCompression_) { |
64 | + | filename_ += ".gz"; |
65 | + | eorFilename_ += ".gz"; |
66 | + | } |
67 | + | #endif |
68 | + | |
69 | #ifdef IS_MPI | |
70 | ||
71 | < | if (worldRank == 0) { |
71 | > | if (worldRank == 0) { |
72 | #endif // is_mpi | |
73 | + | |
74 | + | dumpFile_ = createOStream(filename_); |
75 | ||
76 | < | dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc); |
76 | > | if (!dumpFile_) { |
77 | > | sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
78 | > | filename_.c_str()); |
79 | > | painCave.isFatal = 1; |
80 | > | simError(); |
81 | > | } |
82 | ||
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 | – | |
83 | #ifdef IS_MPI | |
84 | ||
85 | < | } |
85 | > | } |
86 | ||
72 | – | sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
73 | – | MPIcheckPoint(); |
74 | – | |
87 | #endif // is_mpi | |
88 | ||
89 | < | } |
89 | > | } |
90 | ||
91 | ||
92 | DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) | |
93 | : info_(info), filename_(filename){ | |
94 | + | |
95 | + | Globals* simParams = info->getSimParams(); |
96 | + | eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
97 | + | |
98 | + | needCompression_ = simParams->getCompressDumpFile(); |
99 | + | needForceVector_ = simParams->getOutputForceVector(); |
100 | + | createDumpFile_ = true; |
101 | + | #ifdef HAVE_LIBZ |
102 | + | if (needCompression_) { |
103 | + | filename_ += ".gz"; |
104 | + | eorFilename_ += ".gz"; |
105 | + | } |
106 | + | #endif |
107 | + | |
108 | #ifdef IS_MPI | |
109 | ||
110 | < | if (worldRank == 0) { |
110 | > | if (worldRank == 0) { |
111 | #endif // is_mpi | |
112 | ||
113 | < | eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
114 | < | dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc); |
113 | > | |
114 | > | dumpFile_ = createOStream(filename_); |
115 | ||
116 | < | if (!dumpFile_) { |
117 | < | sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
118 | < | filename_.c_str()); |
119 | < | painCave.isFatal = 1; |
120 | < | simError(); |
121 | < | } |
116 | > | if (!dumpFile_) { |
117 | > | sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
118 | > | filename_.c_str()); |
119 | > | painCave.isFatal = 1; |
120 | > | simError(); |
121 | > | } |
122 | ||
123 | #ifdef IS_MPI | |
124 | ||
125 | < | } |
125 | > | } |
126 | ||
101 | – | sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
102 | – | MPIcheckPoint(); |
103 | – | |
127 | #endif // is_mpi | |
128 | ||
129 | + | } |
130 | + | |
131 | + | DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile) |
132 | + | : info_(info), filename_(filename){ |
133 | + | |
134 | + | Globals* simParams = info->getSimParams(); |
135 | + | eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
136 | + | |
137 | + | needCompression_ = simParams->getCompressDumpFile(); |
138 | + | needForceVector_ = simParams->getOutputForceVector(); |
139 | + | |
140 | + | #ifdef HAVE_LIBZ |
141 | + | if (needCompression_) { |
142 | + | filename_ += ".gz"; |
143 | + | eorFilename_ += ".gz"; |
144 | } | |
145 | + | #endif |
146 | + | |
147 | + | #ifdef IS_MPI |
148 | + | |
149 | + | if (worldRank == 0) { |
150 | + | #endif // is_mpi |
151 | + | |
152 | + | createDumpFile_ = writeDumpFile; |
153 | + | if (createDumpFile_) { |
154 | + | dumpFile_ = createOStream(filename_); |
155 | + | |
156 | + | if (!dumpFile_) { |
157 | + | sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
158 | + | filename_.c_str()); |
159 | + | painCave.isFatal = 1; |
160 | + | simError(); |
161 | + | } |
162 | + | } |
163 | + | #ifdef IS_MPI |
164 | + | |
165 | + | } |
166 | ||
167 | + | |
168 | + | #endif // is_mpi |
169 | + | |
170 | + | } |
171 | + | |
172 | DumpWriter::~DumpWriter() { | |
173 | ||
174 | #ifdef IS_MPI | |
175 | ||
176 | if (worldRank == 0) { | |
177 | #endif // is_mpi | |
178 | < | |
179 | < | dumpFile_.close(); |
180 | < | |
178 | > | if (createDumpFile_){ |
179 | > | writeClosing(*dumpFile_); |
180 | > | delete dumpFile_; |
181 | > | } |
182 | #ifdef IS_MPI | |
183 | ||
184 | } | |
# | Line 122 | Line 187 | namespace oopse { | |
187 | ||
188 | } | |
189 | ||
190 | < | void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) { |
190 | > | void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) { |
191 | ||
192 | < | double currentTime; |
192 | > | char buffer[1024]; |
193 | > | |
194 | > | os << " <FrameData>\n"; |
195 | > | |
196 | > | RealType currentTime = s->getTime(); |
197 | > | sprintf(buffer, " Time: %.10g\n", currentTime); |
198 | > | os << buffer; |
199 | > | |
200 | Mat3x3d hmat; | |
129 | – | double chi; |
130 | – | double integralOfChiDt; |
131 | – | Mat3x3d eta; |
132 | – | |
133 | – | currentTime = s->getTime(); |
201 | hmat = s->getHmat(); | |
202 | < | chi = s->getChi(); |
203 | < | integralOfChiDt = s->getIntegralOfChiDt(); |
204 | < | eta = s->getEta(); |
205 | < | |
206 | < | os << currentTime << ";\t" |
140 | < | << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t" |
141 | < | << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t" |
142 | < | << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t"; |
202 | > | sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", |
203 | > | hmat(0, 0), hmat(1, 0), hmat(2, 0), |
204 | > | hmat(0, 1), hmat(1, 1), hmat(2, 1), |
205 | > | hmat(0, 2), hmat(1, 2), hmat(2, 2)); |
206 | > | os << buffer; |
207 | ||
208 | < | //write out additional parameters, such as chi and eta |
208 | > | RealType chi = s->getChi(); |
209 | > | RealType integralOfChiDt = s->getIntegralOfChiDt(); |
210 | > | sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt); |
211 | > | os << buffer; |
212 | ||
213 | < | os << chi << "\t" << integralOfChiDt << "\t;"; |
213 | > | Mat3x3d eta; |
214 | > | eta = s->getEta(); |
215 | > | sprintf(buffer, " Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", |
216 | > | eta(0, 0), eta(1, 0), eta(2, 0), |
217 | > | eta(0, 1), eta(1, 1), eta(2, 1), |
218 | > | eta(0, 2), eta(1, 2), eta(2, 2)); |
219 | > | os << buffer; |
220 | ||
221 | < | os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t" |
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 << "\n"; |
221 | > | os << " </FrameData>\n"; |
222 | } | |
223 | ||
224 | void DumpWriter::writeFrame(std::ostream& os) { | |
156 | – | const int BUFFERSIZE = 2000; |
157 | – | const int MINIBUFFERSIZE = 100; |
225 | ||
226 | < | char tempBuffer[BUFFERSIZE]; |
227 | < | char writeLine[BUFFERSIZE]; |
226 | > | #ifdef IS_MPI |
227 | > | MPI_Status istatus; |
228 | > | #endif |
229 | ||
162 | – | Quat4d q; |
163 | – | Vector3d ji; |
164 | – | Vector3d pos; |
165 | – | Vector3d vel; |
166 | – | |
230 | Molecule* mol; | |
231 | StuntDouble* integrableObject; | |
232 | SimInfo::MoleculeIterator mi; | |
233 | Molecule::IntegrableObjectIterator ii; | |
171 | – | |
172 | – | int nTotObjects; |
173 | – | nTotObjects = info_->getNGlobalIntegrableObjects(); |
234 | ||
235 | #ifndef IS_MPI | |
236 | + | os << " <Snapshot>\n"; |
237 | + | |
238 | + | writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
239 | ||
240 | < | |
178 | < | os << nTotObjects << "\n"; |
179 | < | |
180 | < | writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
181 | < | |
240 | > | os << " <StuntDoubles>\n"; |
241 | for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { | |
242 | ||
243 | for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; | |
244 | < | integrableObject = mol->nextIntegrableObject(ii)) { |
245 | < | |
244 | > | integrableObject = mol->nextIntegrableObject(ii)) { |
245 | > | os << prepareDumpLine(integrableObject); |
246 | ||
247 | < | pos = integrableObject->getPos(); |
248 | < | vel = integrableObject->getVel(); |
247 | > | } |
248 | > | } |
249 | > | os << " </StuntDoubles>\n"; |
250 | ||
251 | < | sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
192 | < | integrableObject->getType().c_str(), |
193 | < | pos[0], pos[1], pos[2], |
194 | < | vel[0], vel[1], vel[2]); |
251 | > | os << " </Snapshot>\n"; |
252 | ||
253 | < | strcpy(writeLine, tempBuffer); |
254 | < | |
255 | < | if (integrableObject->isDirectional()) { |
256 | < | q = integrableObject->getQ(); |
257 | < | ji = integrableObject->getJ(); |
258 | < | |
259 | < | sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
260 | < | q[0], q[1], q[2], q[3], |
261 | < | ji[0], ji[1], ji[2]); |
205 | < | strcat(writeLine, tempBuffer); |
206 | < | } else { |
207 | < | strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
208 | < | } |
209 | < | |
210 | < | os << writeLine; |
211 | < | |
253 | > | os.flush(); |
254 | > | #else |
255 | > | //every node prepares the dump lines for integrable objects belong to itself |
256 | > | std::string buffer; |
257 | > | for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
258 | > | |
259 | > | for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
260 | > | integrableObject = mol->nextIntegrableObject(ii)) { |
261 | > | buffer += prepareDumpLine(integrableObject); |
262 | } | |
263 | } | |
264 | < | |
215 | < | os.flush(); |
216 | < | #else // is_mpi |
217 | < | /********************************************************************* |
218 | < | * Documentation? You want DOCUMENTATION? |
219 | < | * |
220 | < | * Why all the potatoes below? |
221 | < | * |
222 | < | * To make a long story short, the original version of DumpWriter |
223 | < | * worked in the most inefficient way possible. Node 0 would |
224 | < | * poke each of the node for an individual atom's formatted data |
225 | < | * as node 0 worked its way down the global index. This was particularly |
226 | < | * inefficient since the method blocked all processors at every atom |
227 | < | * (and did it twice!). |
228 | < | * |
229 | < | * An intermediate version of DumpWriter could be described from Node |
230 | < | * zero's perspective as follows: |
231 | < | * |
232 | < | * 1) Have 100 of your friends stand in a circle. |
233 | < | * 2) When you say go, have all of them start tossing potatoes at |
234 | < | * you (one at a time). |
235 | < | * 3) Catch the potatoes. |
236 | < | * |
237 | < | * It was an improvement, but MPI has buffers and caches that could |
238 | < | * best be described in this analogy as "potato nets", so there's no |
239 | < | * need to block the processors atom-by-atom. |
240 | < | * |
241 | < | * This new and improved DumpWriter works in an even more efficient |
242 | < | * way: |
243 | < | * |
244 | < | * 1) Have 100 of your friend stand in a circle. |
245 | < | * 2) When you say go, have them start tossing 5-pound bags of |
246 | < | * potatoes at you. |
247 | < | * 3) Once you've caught a friend's bag of potatoes, |
248 | < | * toss them a spud to let them know they can toss another bag. |
249 | < | * |
250 | < | * How's THAT for documentation? |
251 | < | * |
252 | < | *********************************************************************/ |
264 | > | |
265 | const int masterNode = 0; | |
266 | ||
267 | < | int * potatoes; |
268 | < | int myPotato; |
269 | < | int nProc; |
270 | < | int which_node; |
271 | < | double atomData[13]; |
272 | < | int isDirectional; |
261 | < | char MPIatomTypeString[MINIBUFFERSIZE]; |
262 | < | int msgLen; // the length of message actually recieved at master nodes |
263 | < | int haveError; |
264 | < | MPI_Status istatus; |
265 | < | int nCurObj; |
266 | < | |
267 | < | // code to find maximum tag value |
268 | < | int * tagub; |
269 | < | int flag; |
270 | < | int MAXTAG; |
271 | < | MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
267 | > | if (worldRank == masterNode) { |
268 | > | os << " <Snapshot>\n"; |
269 | > | writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
270 | > | os << " <StuntDoubles>\n"; |
271 | > | |
272 | > | os << buffer; |
273 | ||
274 | < | if (flag) { |
274 | < | MAXTAG = *tagub; |
275 | < | } else { |
276 | < | MAXTAG = 32767; |
277 | < | } |
278 | < | |
279 | < | if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file |
280 | < | |
281 | < | // Node 0 needs a list of the magic potatoes for each processor; |
282 | < | |
274 | > | int nProc; |
275 | MPI_Comm_size(MPI_COMM_WORLD, &nProc); | |
276 | < | potatoes = new int[nProc]; |
276 | > | for (int i = 1; i < nProc; ++i) { |
277 | ||
278 | < | //write out the comment lines |
279 | < | for(int i = 0; i < nProc; i++) { |
288 | < | potatoes[i] = 0; |
289 | < | } |
278 | > | // receive the length of the string buffer that was |
279 | > | // prepared by processor i |
280 | ||
281 | + | int recvLength; |
282 | + | MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus); |
283 | + | char* recvBuffer = new char[recvLength]; |
284 | + | if (recvBuffer == NULL) { |
285 | + | } else { |
286 | + | MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus); |
287 | + | os << recvBuffer; |
288 | + | delete recvBuffer; |
289 | + | } |
290 | + | } |
291 | + | os << " </StuntDoubles>\n"; |
292 | + | |
293 | + | os << " </Snapshot>\n"; |
294 | + | os.flush(); |
295 | + | } else { |
296 | + | int sendBufferLength = buffer.size() + 1; |
297 | + | MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
298 | + | MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
299 | + | } |
300 | ||
301 | < | os << nTotObjects << "\n"; |
293 | < | writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
301 | > | #endif // is_mpi |
302 | ||
303 | < | for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
303 | > | } |
304 | ||
305 | < | // Get the Node number which has this atom; |
305 | > | std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) { |
306 | > | |
307 | > | int index = integrableObject->getGlobalIntegrableObjectIndex(); |
308 | > | std::string type("pv"); |
309 | > | std::string line; |
310 | > | char tempBuffer[4096]; |
311 | ||
312 | < | which_node = info_->getMolToProc(i); |
312 | > | Vector3d pos; |
313 | > | Vector3d vel; |
314 | > | pos = integrableObject->getPos(); |
315 | > | vel = integrableObject->getVel(); |
316 | > | sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e", |
317 | > | pos[0], pos[1], pos[2], |
318 | > | vel[0], vel[1], vel[2]); |
319 | > | line += tempBuffer; |
320 | ||
321 | < | if (which_node != masterNode) { //current molecule is in slave node |
322 | < | if (potatoes[which_node] + 1 >= MAXTAG) { |
323 | < | // The potato was going to exceed the maximum value, |
324 | < | // so wrap this processor potato back to 0: |
325 | < | |
326 | < | potatoes[which_node] = 0; |
327 | < | MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, |
328 | < | MPI_COMM_WORLD); |
329 | < | } |
330 | < | |
311 | < | myPotato = potatoes[which_node]; |
312 | < | |
313 | < | //recieve the number of integrableObject in current molecule |
314 | < | MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, |
315 | < | MPI_COMM_WORLD, &istatus); |
316 | < | myPotato++; |
317 | < | |
318 | < | for(int l = 0; l < nCurObj; l++) { |
319 | < | if (potatoes[which_node] + 2 >= MAXTAG) { |
320 | < | // The potato was going to exceed the maximum value, |
321 | < | // so wrap this processor potato back to 0: |
322 | < | |
323 | < | potatoes[which_node] = 0; |
324 | < | MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, |
325 | < | 0, MPI_COMM_WORLD); |
326 | < | } |
327 | < | |
328 | < | MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, |
329 | < | which_node, myPotato, MPI_COMM_WORLD, |
330 | < | &istatus); |
331 | < | |
332 | < | myPotato++; |
333 | < | |
334 | < | MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, |
335 | < | MPI_COMM_WORLD, &istatus); |
336 | < | myPotato++; |
337 | < | |
338 | < | MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
339 | < | |
340 | < | if (msgLen == 13) |
341 | < | isDirectional = 1; |
342 | < | else |
343 | < | isDirectional = 0; |
344 | < | |
345 | < | // If we've survived to here, format the line: |
346 | < | |
347 | < | if (!isDirectional) { |
348 | < | sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
349 | < | MPIatomTypeString, atomData[0], |
350 | < | atomData[1], atomData[2], |
351 | < | atomData[3], atomData[4], |
352 | < | atomData[5]); |
353 | < | |
354 | < | strcat(writeLine, |
355 | < | "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
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 | < | MPIatomTypeString, |
360 | < | atomData[0], |
361 | < | atomData[1], |
362 | < | atomData[2], |
363 | < | atomData[3], |
364 | < | atomData[4], |
365 | < | atomData[5], |
366 | < | atomData[6], |
367 | < | atomData[7], |
368 | < | atomData[8], |
369 | < | atomData[9], |
370 | < | atomData[10], |
371 | < | atomData[11], |
372 | < | atomData[12]); |
373 | < | } |
374 | < | |
375 | < | os << writeLine; |
376 | < | |
377 | < | } // end for(int l =0) |
378 | < | |
379 | < | potatoes[which_node] = myPotato; |
380 | < | } else { //master node has current molecule |
381 | < | |
382 | < | mol = info_->getMoleculeByGlobalIndex(i); |
383 | < | |
384 | < | if (mol == NULL) { |
385 | < | sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank); |
386 | < | painCave.isFatal = 1; |
387 | < | simError(); |
388 | < | } |
389 | < | |
390 | < | for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
391 | < | integrableObject = mol->nextIntegrableObject(ii)) { |
392 | < | |
393 | < | pos = integrableObject->getPos(); |
394 | < | vel = integrableObject->getVel(); |
395 | < | |
396 | < | atomData[0] = pos[0]; |
397 | < | atomData[1] = pos[1]; |
398 | < | atomData[2] = pos[2]; |
399 | < | |
400 | < | atomData[3] = vel[0]; |
401 | < | atomData[4] = vel[1]; |
402 | < | atomData[5] = vel[2]; |
403 | < | |
404 | < | isDirectional = 0; |
405 | < | |
406 | < | if (integrableObject->isDirectional()) { |
407 | < | isDirectional = 1; |
408 | < | |
409 | < | q = integrableObject->getQ(); |
410 | < | ji = integrableObject->getJ(); |
411 | < | |
412 | < | for(int j = 0; j < 6; j++) { |
413 | < | atomData[j] = atomData[j]; |
414 | < | } |
415 | < | |
416 | < | atomData[6] = q[0]; |
417 | < | atomData[7] = q[1]; |
418 | < | atomData[8] = q[2]; |
419 | < | atomData[9] = q[3]; |
420 | < | |
421 | < | atomData[10] = ji[0]; |
422 | < | atomData[11] = ji[1]; |
423 | < | atomData[12] = ji[2]; |
424 | < | } |
425 | < | |
426 | < | // If we've survived to here, format the line: |
427 | < | |
428 | < | if (!isDirectional) { |
429 | < | sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
430 | < | integrableObject->getType().c_str(), atomData[0], |
431 | < | atomData[1], atomData[2], |
432 | < | atomData[3], atomData[4], |
433 | < | atomData[5]); |
434 | < | |
435 | < | strcat(writeLine, |
436 | < | "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
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 | < | integrableObject->getType().c_str(), |
441 | < | atomData[0], |
442 | < | atomData[1], |
443 | < | atomData[2], |
444 | < | atomData[3], |
445 | < | atomData[4], |
446 | < | atomData[5], |
447 | < | atomData[6], |
448 | < | atomData[7], |
449 | < | atomData[8], |
450 | < | atomData[9], |
451 | < | atomData[10], |
452 | < | atomData[11], |
453 | < | atomData[12]); |
454 | < | } |
455 | < | |
456 | < | |
457 | < | os << writeLine; |
458 | < | |
459 | < | } //end for(iter = integrableObject.begin()) |
460 | < | } |
461 | < | } //end for(i = 0; i < mpiSim->getNmol()) |
462 | < | |
463 | < | os.flush(); |
464 | < | |
465 | < | sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
466 | < | MPIcheckPoint(); |
467 | < | |
468 | < | delete [] potatoes; |
469 | < | } else { |
470 | < | |
471 | < | // worldRank != 0, so I'm a remote node. |
472 | < | |
473 | < | // Set my magic potato to 0: |
474 | < | |
475 | < | myPotato = 0; |
476 | < | |
477 | < | for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
478 | < | |
479 | < | // Am I the node which has this integrableObject? |
480 | < | int whichNode = info_->getMolToProc(i); |
481 | < | if (whichNode == worldRank) { |
482 | < | if (myPotato + 1 >= MAXTAG) { |
483 | < | |
484 | < | // The potato was going to exceed the maximum value, |
485 | < | // so wrap this processor potato back to 0 (and block until |
486 | < | // node 0 says we can go: |
487 | < | |
488 | < | MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
489 | < | &istatus); |
490 | < | } |
491 | < | |
492 | < | mol = info_->getMoleculeByGlobalIndex(i); |
493 | < | |
494 | < | |
495 | < | nCurObj = mol->getNIntegrableObjects(); |
496 | < | |
497 | < | MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); |
498 | < | myPotato++; |
499 | < | |
500 | < | for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
501 | < | integrableObject = mol->nextIntegrableObject(ii)) { |
502 | < | |
503 | < | if (myPotato + 2 >= MAXTAG) { |
504 | < | |
505 | < | // The potato was going to exceed the maximum value, |
506 | < | // so wrap this processor potato back to 0 (and block until |
507 | < | // node 0 says we can go: |
508 | < | |
509 | < | MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
510 | < | &istatus); |
511 | < | } |
512 | < | |
513 | < | pos = integrableObject->getPos(); |
514 | < | vel = integrableObject->getVel(); |
515 | < | |
516 | < | atomData[0] = pos[0]; |
517 | < | atomData[1] = pos[1]; |
518 | < | atomData[2] = pos[2]; |
519 | < | |
520 | < | atomData[3] = vel[0]; |
521 | < | atomData[4] = vel[1]; |
522 | < | atomData[5] = vel[2]; |
523 | < | |
524 | < | isDirectional = 0; |
525 | < | |
526 | < | if (integrableObject->isDirectional()) { |
527 | < | isDirectional = 1; |
528 | < | |
529 | < | q = integrableObject->getQ(); |
530 | < | ji = integrableObject->getJ(); |
531 | < | |
532 | < | atomData[6] = q[0]; |
533 | < | atomData[7] = q[1]; |
534 | < | atomData[8] = q[2]; |
535 | < | atomData[9] = q[3]; |
536 | < | |
537 | < | atomData[10] = ji[0]; |
538 | < | atomData[11] = ji[1]; |
539 | < | atomData[12] = ji[2]; |
540 | < | } |
541 | < | |
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'; |
546 | < | |
547 | < | MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
548 | < | myPotato, MPI_COMM_WORLD); |
549 | < | |
550 | < | myPotato++; |
551 | < | |
552 | < | if (isDirectional) { |
553 | < | MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato, |
554 | < | MPI_COMM_WORLD); |
555 | < | } else { |
556 | < | MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato, |
557 | < | MPI_COMM_WORLD); |
558 | < | } |
559 | < | |
560 | < | myPotato++; |
561 | < | } |
562 | < | |
563 | < | } |
564 | < | |
565 | < | } |
566 | < | sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
567 | < | MPIcheckPoint(); |
321 | > | if (integrableObject->isDirectional()) { |
322 | > | type += "qj"; |
323 | > | Quat4d q; |
324 | > | Vector3d ji; |
325 | > | q = integrableObject->getQ(); |
326 | > | ji = integrableObject->getJ(); |
327 | > | sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e", |
328 | > | q[0], q[1], q[2], q[3], |
329 | > | ji[0], ji[1], ji[2]); |
330 | > | line += tempBuffer; |
331 | } | |
332 | ||
333 | < | #endif // is_mpi |
334 | < | |
333 | > | if (needForceVector_) { |
334 | > | type += "ft"; |
335 | > | Vector3d frc; |
336 | > | Vector3d trq; |
337 | > | frc = integrableObject->getFrc(); |
338 | > | trq = integrableObject->getTrq(); |
339 | > | |
340 | > | sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e", |
341 | > | frc[0], frc[1], frc[2], |
342 | > | trq[0], trq[1], trq[2]); |
343 | > | line += tempBuffer; |
344 | > | } |
345 | > | |
346 | > | sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str()); |
347 | > | return std::string(tempBuffer); |
348 | } | |
349 | ||
350 | void DumpWriter::writeDump() { | |
351 | < | writeFrame(dumpFile_); |
576 | < | |
351 | > | writeFrame(*dumpFile_); |
352 | } | |
353 | ||
354 | void DumpWriter::writeEor() { | |
355 | < | std::ofstream eorStream; |
355 | > | std::ostream* eorStream; |
356 | ||
357 | #ifdef IS_MPI | |
358 | if (worldRank == 0) { | |
359 | #endif // is_mpi | |
360 | ||
361 | < | 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 | < | } |
361 | > | eorStream = createOStream(eorFilename_); |
362 | ||
363 | #ifdef IS_MPI | |
364 | } | |
365 | #endif // is_mpi | |
366 | ||
367 | < | writeFrame(eorStream); |
367 | > | writeFrame(*eorStream); |
368 | > | |
369 | > | #ifdef IS_MPI |
370 | > | if (worldRank == 0) { |
371 | > | #endif // is_mpi |
372 | > | writeClosing(*eorStream); |
373 | > | delete eorStream; |
374 | > | #ifdef IS_MPI |
375 | > | } |
376 | > | #endif // is_mpi |
377 | > | |
378 | } | |
379 | ||
380 | ||
381 | void DumpWriter::writeDumpAndEor() { | |
603 | – | std::ofstream eorStream; |
382 | std::vector<std::streambuf*> buffers; | |
383 | + | std::ostream* eorStream; |
384 | #ifdef IS_MPI | |
385 | if (worldRank == 0) { | |
386 | #endif // is_mpi | |
387 | ||
388 | < | buffers.push_back(dumpFile_.rdbuf()); |
388 | > | buffers.push_back(dumpFile_->rdbuf()); |
389 | ||
390 | < | 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 | < | } |
390 | > | eorStream = createOStream(eorFilename_); |
391 | ||
392 | < | buffers.push_back(eorStream.rdbuf()); |
392 | > | buffers.push_back(eorStream->rdbuf()); |
393 | ||
394 | #ifdef IS_MPI | |
395 | } | |
# | Line 626 | Line 399 | namespace oopse { | |
399 | std::ostream os(&tbuf); | |
400 | ||
401 | writeFrame(os); | |
402 | + | |
403 | + | #ifdef IS_MPI |
404 | + | if (worldRank == 0) { |
405 | + | #endif // is_mpi |
406 | + | writeClosing(*eorStream); |
407 | + | delete eorStream; |
408 | + | #ifdef IS_MPI |
409 | + | } |
410 | + | #endif // is_mpi |
411 | ||
412 | } | |
413 | ||
414 | + | std::ostream* DumpWriter::createOStream(const std::string& filename) { |
415 | ||
416 | + | std::ostream* newOStream; |
417 | + | #ifdef HAVE_LIBZ |
418 | + | if (needCompression_) { |
419 | + | newOStream = new ogzstream(filename.c_str()); |
420 | + | } else { |
421 | + | newOStream = new std::ofstream(filename.c_str()); |
422 | + | } |
423 | + | #else |
424 | + | newOStream = new std::ofstream(filename.c_str()); |
425 | + | #endif |
426 | + | //write out MetaData first |
427 | + | (*newOStream) << "<OOPSE version=4>" << std::endl; |
428 | + | (*newOStream) << " <MetaData>" << std::endl; |
429 | + | (*newOStream) << info_->getRawMetaData(); |
430 | + | (*newOStream) << " </MetaData>" << std::endl; |
431 | + | return newOStream; |
432 | + | } |
433 | ||
434 | + | void DumpWriter::writeClosing(std::ostream& os) { |
435 | + | |
436 | + | os << "</OOPSE>\n"; |
437 | + | os.flush(); |
438 | + | } |
439 | + | |
440 | }//end namespace oopse |
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