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1 | < | /* |
2 | < | * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
1 | > | /* |
2 | > | * Copyright (c) 2009 The University of Notre Dame. All Rights Reserved. |
3 | * | |
4 | * The University of Notre Dame grants you ("Licensee") a | |
5 | * non-exclusive, royalty free, license to use, modify and | |
6 | * redistribute this software in source and binary code form, provided | |
7 | * that the following conditions are met: | |
8 | * | |
9 | < | * 1. Acknowledgement of the program authors must be made in any |
10 | < | * publication of scientific results based in part on use of the |
11 | < | * program. An acceptable form of acknowledgement is citation of |
12 | < | * the article in which the program was described (Matthew |
13 | < | * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
14 | < | * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
15 | < | * Parallel Simulation Engine for Molecular Dynamics," |
16 | < | * J. Comput. Chem. 26, pp. 252-271 (2005)) |
17 | < | * |
18 | < | * 2. Redistributions of source code must retain the above copyright |
9 | > | * 1. Redistributions of source code must retain the above copyright |
10 | * notice, this list of conditions and the following disclaimer. | |
11 | * | |
12 | < | * 3. Redistributions in binary form must reproduce the above copyright |
12 | > | * 2. Redistributions in binary form must reproduce the above copyright |
13 | * notice, this list of conditions and the following disclaimer in the | |
14 | * documentation and/or other materials provided with the | |
15 | * distribution. | |
# | Line 37 | Line 28 | |
28 | * arising out of the use of or inability to use software, even if the | |
29 | * University of Notre Dame has been advised of the possibility of | |
30 | * such damages. | |
31 | + | * |
32 | + | * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
33 | + | * research, please cite the appropriate papers when you publish your |
34 | + | * work. Good starting points are: |
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). |
39 | + | * [4] Vardeman & Gezelter, in progress (2009). |
40 | */ | |
41 | ||
42 | #include "io/DumpWriter.hpp" | |
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 | + | |
50 | #ifdef IS_MPI | |
51 | #include <mpi.h> | |
52 | #endif //is_mpi | |
53 | ||
54 | < | namespace oopse { |
54 | > | using namespace std; |
55 | > | namespace OpenMD { |
56 | ||
57 | < | DumpWriter::DumpWriter(SimInfo* info) |
58 | < | : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){ |
57 | > | DumpWriter::DumpWriter(SimInfo* info) |
58 | > | : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){ |
59 | > | |
60 | > | Globals* simParams = info->getSimParams(); |
61 | > | needCompression_ = simParams->getCompressDumpFile(); |
62 | > | needForceVector_ = simParams->getOutputForceVector(); |
63 | > | createDumpFile_ = true; |
64 | > | #ifdef HAVE_LIBZ |
65 | > | if (needCompression_) { |
66 | > | filename_ += ".gz"; |
67 | > | eorFilename_ += ".gz"; |
68 | > | } |
69 | > | #endif |
70 | > | |
71 | #ifdef IS_MPI | |
72 | ||
73 | if (worldRank == 0) { | |
74 | #endif // is_mpi | |
75 | + | |
76 | + | dumpFile_ = createOStream(filename_); |
77 | ||
78 | < | dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc); |
78 | > | if (!dumpFile_) { |
79 | > | sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
80 | > | filename_.c_str()); |
81 | > | painCave.isFatal = 1; |
82 | > | simError(); |
83 | > | } |
84 | ||
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 | – | |
85 | #ifdef IS_MPI | |
86 | ||
87 | } | |
88 | ||
72 | – | sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
73 | – | MPIcheckPoint(); |
74 | – | |
89 | #endif // is_mpi | |
90 | ||
91 | < | } |
91 | > | } |
92 | ||
93 | ||
94 | < | DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) |
95 | < | : info_(info), filename_(filename){ |
94 | > | DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) |
95 | > | : info_(info), filename_(filename){ |
96 | > | |
97 | > | Globals* simParams = info->getSimParams(); |
98 | > | eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
99 | > | |
100 | > | needCompression_ = simParams->getCompressDumpFile(); |
101 | > | needForceVector_ = simParams->getOutputForceVector(); |
102 | > | createDumpFile_ = true; |
103 | > | #ifdef HAVE_LIBZ |
104 | > | if (needCompression_) { |
105 | > | filename_ += ".gz"; |
106 | > | eorFilename_ += ".gz"; |
107 | > | } |
108 | > | #endif |
109 | > | |
110 | #ifdef IS_MPI | |
111 | ||
112 | if (worldRank == 0) { | |
113 | #endif // is_mpi | |
114 | ||
115 | < | eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
116 | < | dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc); |
115 | > | |
116 | > | dumpFile_ = createOStream(filename_); |
117 | ||
118 | < | if (!dumpFile_) { |
119 | < | sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
120 | < | filename_.c_str()); |
121 | < | painCave.isFatal = 1; |
122 | < | simError(); |
123 | < | } |
118 | > | if (!dumpFile_) { |
119 | > | sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
120 | > | filename_.c_str()); |
121 | > | painCave.isFatal = 1; |
122 | > | simError(); |
123 | > | } |
124 | ||
125 | #ifdef IS_MPI | |
126 | ||
127 | } | |
128 | ||
129 | < | sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
102 | < | MPIcheckPoint(); |
129 | > | #endif // is_mpi |
130 | ||
131 | + | } |
132 | + | |
133 | + | DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile) |
134 | + | : info_(info), filename_(filename){ |
135 | + | |
136 | + | Globals* simParams = info->getSimParams(); |
137 | + | eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
138 | + | |
139 | + | needCompression_ = simParams->getCompressDumpFile(); |
140 | + | needForceVector_ = simParams->getOutputForceVector(); |
141 | + | |
142 | + | #ifdef HAVE_LIBZ |
143 | + | if (needCompression_) { |
144 | + | filename_ += ".gz"; |
145 | + | eorFilename_ += ".gz"; |
146 | + | } |
147 | + | #endif |
148 | + | |
149 | + | #ifdef IS_MPI |
150 | + | |
151 | + | if (worldRank == 0) { |
152 | #endif // is_mpi | |
153 | + | |
154 | + | createDumpFile_ = writeDumpFile; |
155 | + | if (createDumpFile_) { |
156 | + | dumpFile_ = createOStream(filename_); |
157 | + | |
158 | + | if (!dumpFile_) { |
159 | + | sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
160 | + | filename_.c_str()); |
161 | + | painCave.isFatal = 1; |
162 | + | simError(); |
163 | + | } |
164 | + | } |
165 | + | #ifdef IS_MPI |
166 | + | |
167 | + | } |
168 | ||
169 | < | } |
169 | > | |
170 | > | #endif // is_mpi |
171 | > | |
172 | > | } |
173 | ||
174 | < | DumpWriter::~DumpWriter() { |
174 | > | DumpWriter::~DumpWriter() { |
175 | ||
176 | #ifdef IS_MPI | |
177 | ||
178 | if (worldRank == 0) { | |
179 | #endif // is_mpi | |
180 | < | |
181 | < | dumpFile_.close(); |
182 | < | |
180 | > | if (createDumpFile_){ |
181 | > | writeClosing(*dumpFile_); |
182 | > | delete dumpFile_; |
183 | > | } |
184 | #ifdef IS_MPI | |
185 | ||
186 | } | |
187 | ||
188 | #endif // is_mpi | |
189 | ||
190 | < | } |
190 | > | } |
191 | ||
192 | < | void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) { |
192 | > | void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) { |
193 | ||
194 | < | double currentTime; |
195 | < | Mat3x3d hmat; |
196 | < | double chi; |
197 | < | double integralOfChiDt; |
198 | < | Mat3x3d eta; |
194 | > | char buffer[1024]; |
195 | > | |
196 | > | os << " <FrameData>\n"; |
197 | > | |
198 | > | RealType currentTime = s->getTime(); |
199 | > | |
200 | > | if (isinf(currentTime) || isnan(currentTime)) { |
201 | > | sprintf( painCave.errMsg, |
202 | > | "DumpWriter detected a numerical error writing the time"); |
203 | > | painCave.isFatal = 1; |
204 | > | simError(); |
205 | > | } |
206 | ||
207 | < | currentTime = s->getTime(); |
207 | > | sprintf(buffer, " Time: %.10g\n", currentTime); |
208 | > | os << buffer; |
209 | > | |
210 | > | Mat3x3d hmat; |
211 | hmat = s->getHmat(); | |
212 | < | chi = s->getChi(); |
213 | < | integralOfChiDt = s->getIntegralOfChiDt(); |
214 | < | eta = s->getEta(); |
212 | > | |
213 | > | for (unsigned int i = 0; i < 3; i++) { |
214 | > | for (unsigned int j = 0; j < 3; j++) { |
215 | > | if (isinf(hmat(i,j)) || isnan(hmat(i,j))) { |
216 | > | sprintf( painCave.errMsg, |
217 | > | "DumpWriter detected a numerical error writing the box"); |
218 | > | painCave.isFatal = 1; |
219 | > | simError(); |
220 | > | } |
221 | > | } |
222 | > | } |
223 | ||
224 | < | os << currentTime << ";\t" |
225 | < | << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t" |
226 | < | << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t" |
227 | < | << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t"; |
224 | > | sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", |
225 | > | hmat(0, 0), hmat(1, 0), hmat(2, 0), |
226 | > | hmat(0, 1), hmat(1, 1), hmat(2, 1), |
227 | > | hmat(0, 2), hmat(1, 2), hmat(2, 2)); |
228 | > | os << buffer; |
229 | ||
230 | < | //write out additional parameters, such as chi and eta |
230 | > | RealType chi = s->getChi(); |
231 | > | RealType integralOfChiDt = s->getIntegralOfChiDt(); |
232 | > | if (isinf(chi) || isnan(chi) || |
233 | > | isinf(integralOfChiDt) || isnan(integralOfChiDt)) { |
234 | > | sprintf( painCave.errMsg, |
235 | > | "DumpWriter detected a numerical error writing the thermostat"); |
236 | > | painCave.isFatal = 1; |
237 | > | simError(); |
238 | > | } |
239 | > | sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt); |
240 | > | os << buffer; |
241 | ||
242 | < | os << chi << "\t" << integralOfChiDt << "\t;"; |
242 | > | Mat3x3d eta; |
243 | > | eta = s->getEta(); |
244 | ||
245 | < | os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t" |
246 | < | << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t" |
247 | < | << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";"; |
248 | < | |
249 | < | os << "\n"; |
250 | < | } |
245 | > | for (unsigned int i = 0; i < 3; i++) { |
246 | > | for (unsigned int j = 0; j < 3; j++) { |
247 | > | if (isinf(eta(i,j)) || isnan(eta(i,j))) { |
248 | > | sprintf( painCave.errMsg, |
249 | > | "DumpWriter detected a numerical error writing the barostat"); |
250 | > | painCave.isFatal = 1; |
251 | > | simError(); |
252 | > | } |
253 | > | } |
254 | > | } |
255 | ||
256 | < | void DumpWriter::writeFrame(std::ostream& os) { |
257 | < | const int BUFFERSIZE = 2000; |
258 | < | const int MINIBUFFERSIZE = 100; |
259 | < | |
260 | < | char tempBuffer[BUFFERSIZE]; |
160 | < | char writeLine[BUFFERSIZE]; |
256 | > | sprintf(buffer, " Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", |
257 | > | eta(0, 0), eta(1, 0), eta(2, 0), |
258 | > | eta(0, 1), eta(1, 1), eta(2, 1), |
259 | > | eta(0, 2), eta(1, 2), eta(2, 2)); |
260 | > | os << buffer; |
261 | ||
262 | < | Quat4d q; |
263 | < | Vector3d ji; |
164 | < | Vector3d pos; |
165 | < | Vector3d vel; |
262 | > | os << " </FrameData>\n"; |
263 | > | } |
264 | ||
265 | + | void DumpWriter::writeFrame(std::ostream& os) { |
266 | + | |
267 | + | #ifdef IS_MPI |
268 | + | MPI_Status istatus; |
269 | + | #endif |
270 | + | |
271 | Molecule* mol; | |
272 | StuntDouble* integrableObject; | |
273 | SimInfo::MoleculeIterator mi; | |
274 | Molecule::IntegrableObjectIterator ii; | |
171 | – | |
172 | – | int nTotObjects; |
173 | – | nTotObjects = info_->getNGlobalIntegrableObjects(); |
275 | ||
276 | #ifndef IS_MPI | |
277 | + | os << " <Snapshot>\n"; |
278 | + | |
279 | + | writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
280 | ||
281 | + | os << " <StuntDoubles>\n"; |
282 | + | for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
283 | ||
284 | < | os << nTotObjects << "\n"; |
285 | < | |
286 | < | writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
284 | > | |
285 | > | for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
286 | > | integrableObject = mol->nextIntegrableObject(ii)) { |
287 | > | os << prepareDumpLine(integrableObject); |
288 | > | |
289 | > | } |
290 | > | } |
291 | > | os << " </StuntDoubles>\n"; |
292 | > | |
293 | > | os << " </Snapshot>\n"; |
294 | ||
295 | + | os.flush(); |
296 | + | #else |
297 | + | //every node prepares the dump lines for integrable objects belong to itself |
298 | + | std::string buffer; |
299 | for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { | |
300 | ||
184 | – | for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
185 | – | integrableObject = mol->nextIntegrableObject(ii)) { |
186 | – | |
301 | ||
302 | < | pos = integrableObject->getPos(); |
303 | < | vel = integrableObject->getVel(); |
302 | > | for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
303 | > | integrableObject = mol->nextIntegrableObject(ii)) { |
304 | > | buffer += prepareDumpLine(integrableObject); |
305 | > | } |
306 | > | } |
307 | > | |
308 | > | const int masterNode = 0; |
309 | ||
310 | < | sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
311 | < | integrableObject->getType().c_str(), |
312 | < | pos[0], pos[1], pos[2], |
313 | < | vel[0], vel[1], vel[2]); |
310 | > | if (worldRank == masterNode) { |
311 | > | os << " <Snapshot>\n"; |
312 | > | writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
313 | > | os << " <StuntDoubles>\n"; |
314 | > | |
315 | > | os << buffer; |
316 | ||
317 | < | strcpy(writeLine, tempBuffer); |
317 | > | int nProc; |
318 | > | MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
319 | > | for (int i = 1; i < nProc; ++i) { |
320 | ||
321 | < | if (integrableObject->isDirectional()) { |
322 | < | q = integrableObject->getQ(); |
200 | < | ji = integrableObject->getJ(); |
321 | > | // receive the length of the string buffer that was |
322 | > | // prepared by processor i |
323 | ||
324 | < | sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
325 | < | q[0], q[1], q[2], q[3], |
326 | < | ji[0], ji[1], ji[2]); |
327 | < | strcat(writeLine, tempBuffer); |
328 | < | } else { |
329 | < | strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
330 | < | } |
331 | < | |
210 | < | os << writeLine; |
211 | < | |
324 | > | int recvLength; |
325 | > | MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus); |
326 | > | char* recvBuffer = new char[recvLength]; |
327 | > | if (recvBuffer == NULL) { |
328 | > | } else { |
329 | > | MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus); |
330 | > | os << recvBuffer; |
331 | > | delete [] recvBuffer; |
332 | } | |
333 | < | } |
334 | < | |
335 | < | os.flush(); |
336 | < | #else // is_mpi |
337 | < | /********************************************************************* |
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 | < | *********************************************************************/ |
253 | < | const int masterNode = 0; |
254 | < | |
255 | < | int * potatoes; |
256 | < | int myPotato; |
257 | < | int nProc; |
258 | < | int which_node; |
259 | < | double atomData[13]; |
260 | < | 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); |
272 | < | |
273 | < | if (flag) { |
274 | < | MAXTAG = *tagub; |
333 | > | } |
334 | > | os << " </StuntDoubles>\n"; |
335 | > | |
336 | > | os << " </Snapshot>\n"; |
337 | > | os.flush(); |
338 | } else { | |
339 | < | MAXTAG = 32767; |
339 | > | int sendBufferLength = buffer.size() + 1; |
340 | > | MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
341 | > | MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); |
342 | } | |
343 | ||
344 | < | if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file |
344 | > | #endif // is_mpi |
345 | ||
346 | < | // Node 0 needs a list of the magic potatoes for each processor; |
346 | > | } |
347 | ||
348 | < | MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
349 | < | potatoes = new int[nProc]; |
348 | > | std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) { |
349 | > | |
350 | > | int index = integrableObject->getGlobalIntegrableObjectIndex(); |
351 | > | std::string type("pv"); |
352 | > | std::string line; |
353 | > | char tempBuffer[4096]; |
354 | ||
355 | < | //write out the comment lines |
356 | < | for(int i = 0; i < nProc; i++) { |
357 | < | potatoes[i] = 0; |
289 | < | } |
355 | > | Vector3d pos; |
356 | > | Vector3d vel; |
357 | > | pos = integrableObject->getPos(); |
358 | ||
359 | + | if (isinf(pos[0]) || isnan(pos[0]) || |
360 | + | isinf(pos[1]) || isnan(pos[1]) || |
361 | + | isinf(pos[2]) || isnan(pos[2]) ) { |
362 | + | sprintf( painCave.errMsg, |
363 | + | "DumpWriter detected a numerical error writing the position" |
364 | + | " for object %d", index); |
365 | + | painCave.isFatal = 1; |
366 | + | simError(); |
367 | + | } |
368 | ||
369 | < | os << nTotObjects << "\n"; |
293 | < | writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
369 | > | vel = integrableObject->getVel(); |
370 | ||
371 | < | for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
371 | > | if (isinf(vel[0]) || isnan(vel[0]) || |
372 | > | isinf(vel[1]) || isnan(vel[1]) || |
373 | > | isinf(vel[2]) || isnan(vel[2]) ) { |
374 | > | sprintf( painCave.errMsg, |
375 | > | "DumpWriter detected a numerical error writing the velocity" |
376 | > | " for object %d", index); |
377 | > | painCave.isFatal = 1; |
378 | > | simError(); |
379 | > | } |
380 | ||
381 | < | // Get the Node number which has this atom; |
381 | > | sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e", |
382 | > | pos[0], pos[1], pos[2], |
383 | > | vel[0], vel[1], vel[2]); |
384 | > | line += tempBuffer; |
385 | ||
386 | < | which_node = info_->getMolToProc(i); |
386 | > | if (integrableObject->isDirectional()) { |
387 | > | type += "qj"; |
388 | > | Quat4d q; |
389 | > | Vector3d ji; |
390 | > | q = integrableObject->getQ(); |
391 | ||
392 | < | if (which_node != masterNode) { //current molecule is in slave node |
393 | < | if (potatoes[which_node] + 1 >= MAXTAG) { |
394 | < | // The potato was going to exceed the maximum value, |
395 | < | // so wrap this processor potato back to 0: |
392 | > | if (isinf(q[0]) || isnan(q[0]) || |
393 | > | isinf(q[1]) || isnan(q[1]) || |
394 | > | isinf(q[2]) || isnan(q[2]) || |
395 | > | isinf(q[3]) || isnan(q[3]) ) { |
396 | > | sprintf( painCave.errMsg, |
397 | > | "DumpWriter detected a numerical error writing the quaternion" |
398 | > | " for object %d", index); |
399 | > | painCave.isFatal = 1; |
400 | > | simError(); |
401 | > | } |
402 | ||
403 | < | potatoes[which_node] = 0; |
307 | < | MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, |
308 | < | MPI_COMM_WORLD); |
309 | < | } |
403 | > | ji = integrableObject->getJ(); |
404 | ||
405 | < | myPotato = potatoes[which_node]; |
405 | > | if (isinf(ji[0]) || isnan(ji[0]) || |
406 | > | isinf(ji[1]) || isnan(ji[1]) || |
407 | > | isinf(ji[2]) || isnan(ji[2]) ) { |
408 | > | sprintf( painCave.errMsg, |
409 | > | "DumpWriter detected a numerical error writing the angular" |
410 | > | " momentum for object %d", index); |
411 | > | painCave.isFatal = 1; |
412 | > | simError(); |
413 | > | } |
414 | ||
415 | < | //recieve the number of integrableObject in current molecule |
416 | < | MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, |
417 | < | MPI_COMM_WORLD, &istatus); |
418 | < | myPotato++; |
415 | > | sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e", |
416 | > | q[0], q[1], q[2], q[3], |
417 | > | ji[0], ji[1], ji[2]); |
418 | > | line += tempBuffer; |
419 | > | } |
420 | ||
421 | < | for(int l = 0; l < nCurObj; l++) { |
422 | < | if (potatoes[which_node] + 2 >= MAXTAG) { |
423 | < | // The potato was going to exceed the maximum value, |
321 | < | // so wrap this processor potato back to 0: |
421 | > | if (needForceVector_) { |
422 | > | type += "f"; |
423 | > | Vector3d frc; |
424 | ||
425 | < | potatoes[which_node] = 0; |
324 | < | MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, |
325 | < | 0, MPI_COMM_WORLD); |
326 | < | } |
425 | > | frc = integrableObject->getFrc(); |
426 | ||
427 | < | MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, |
428 | < | which_node, myPotato, MPI_COMM_WORLD, |
429 | < | &istatus); |
430 | < | |
431 | < | myPotato++; |
432 | < | |
433 | < | MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, |
434 | < | MPI_COMM_WORLD, &istatus); |
435 | < | myPotato++; |
436 | < | |
437 | < | MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
438 | < | |
439 | < | if (msgLen == 13) |
440 | < | isDirectional = 1; |
441 | < | else |
442 | < | 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(); |
427 | > | if (isinf(frc[0]) || isnan(frc[0]) || |
428 | > | isinf(frc[1]) || isnan(frc[1]) || |
429 | > | isinf(frc[2]) || isnan(frc[2]) ) { |
430 | > | sprintf( painCave.errMsg, |
431 | > | "DumpWriter detected a numerical error writing the force" |
432 | > | " for object %d", index); |
433 | > | painCave.isFatal = 1; |
434 | > | simError(); |
435 | > | } |
436 | > | sprintf(tempBuffer, " %13e %13e %13e", |
437 | > | frc[0], frc[1], frc[2]); |
438 | > | line += tempBuffer; |
439 | > | |
440 | > | if (integrableObject->isDirectional()) { |
441 | > | type += "t"; |
442 | > | Vector3d trq; |
443 | ||
444 | < | sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
445 | < | MPIcheckPoint(); |
446 | < | |
447 | < | delete [] potatoes; |
448 | < | } else { |
449 | < | |
450 | < | // worldRank != 0, so I'm a remote node. |
451 | < | |
452 | < | // Set my magic potato to 0: |
453 | < | |
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 | < | |
444 | > | trq = integrableObject->getTrq(); |
445 | > | |
446 | > | if (isinf(trq[0]) || isnan(trq[0]) || |
447 | > | isinf(trq[1]) || isnan(trq[1]) || |
448 | > | isinf(trq[2]) || isnan(trq[2]) ) { |
449 | > | sprintf( painCave.errMsg, |
450 | > | "DumpWriter detected a numerical error writing the torque" |
451 | > | " for object %d", index); |
452 | > | painCave.isFatal = 1; |
453 | > | simError(); |
454 | } | |
455 | < | sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
456 | < | MPIcheckPoint(); |
455 | > | |
456 | > | sprintf(tempBuffer, " %13e %13e %13e", |
457 | > | trq[0], trq[1], trq[2]); |
458 | > | line += tempBuffer; |
459 | > | } |
460 | } | |
461 | + | |
462 | + | sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str()); |
463 | + | return std::string(tempBuffer); |
464 | + | } |
465 | ||
466 | < | #endif // is_mpi |
466 | > | void DumpWriter::writeDump() { |
467 | > | writeFrame(*dumpFile_); |
468 | > | } |
469 | ||
470 | < | } |
471 | < | |
574 | < | void DumpWriter::writeDump() { |
575 | < | writeFrame(dumpFile_); |
576 | < | |
577 | < | } |
578 | < | |
579 | < | void DumpWriter::writeEor() { |
580 | < | std::ofstream eorStream; |
470 | > | void DumpWriter::writeEor() { |
471 | > | std::ostream* eorStream; |
472 | ||
473 | #ifdef IS_MPI | |
474 | if (worldRank == 0) { | |
475 | #endif // is_mpi | |
476 | ||
477 | < | 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 | < | } |
477 | > | eorStream = createOStream(eorFilename_); |
478 | ||
479 | #ifdef IS_MPI | |
480 | } | |
481 | #endif // is_mpi | |
482 | ||
483 | < | writeFrame(eorStream); |
599 | < | } |
483 | > | writeFrame(*eorStream); |
484 | ||
485 | + | #ifdef IS_MPI |
486 | + | if (worldRank == 0) { |
487 | + | #endif // is_mpi |
488 | + | writeClosing(*eorStream); |
489 | + | delete eorStream; |
490 | + | #ifdef IS_MPI |
491 | + | } |
492 | + | #endif // is_mpi |
493 | ||
494 | < | void DumpWriter::writeDumpAndEor() { |
495 | < | std::ofstream eorStream; |
494 | > | } |
495 | > | |
496 | > | |
497 | > | void DumpWriter::writeDumpAndEor() { |
498 | std::vector<std::streambuf*> buffers; | |
499 | + | std::ostream* eorStream; |
500 | #ifdef IS_MPI | |
501 | if (worldRank == 0) { | |
502 | #endif // is_mpi | |
503 | ||
504 | < | buffers.push_back(dumpFile_.rdbuf()); |
504 | > | buffers.push_back(dumpFile_->rdbuf()); |
505 | ||
506 | < | 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 | < | } |
506 | > | eorStream = createOStream(eorFilename_); |
507 | ||
508 | < | buffers.push_back(eorStream.rdbuf()); |
508 | > | buffers.push_back(eorStream->rdbuf()); |
509 | ||
510 | #ifdef IS_MPI | |
511 | } | |
# | Line 626 | Line 515 | void DumpWriter::writeDumpAndEor() { | |
515 | std::ostream os(&tbuf); | |
516 | ||
517 | writeFrame(os); | |
518 | + | |
519 | + | #ifdef IS_MPI |
520 | + | if (worldRank == 0) { |
521 | + | #endif // is_mpi |
522 | + | writeClosing(*eorStream); |
523 | + | delete eorStream; |
524 | + | #ifdef IS_MPI |
525 | + | } |
526 | + | #endif // is_mpi |
527 | ||
528 | < | } |
528 | > | } |
529 | ||
530 | + | std::ostream* DumpWriter::createOStream(const std::string& filename) { |
531 | ||
532 | + | std::ostream* newOStream; |
533 | + | #ifdef HAVE_LIBZ |
534 | + | if (needCompression_) { |
535 | + | newOStream = new ogzstream(filename.c_str()); |
536 | + | } else { |
537 | + | newOStream = new std::ofstream(filename.c_str()); |
538 | + | } |
539 | + | #else |
540 | + | newOStream = new std::ofstream(filename.c_str()); |
541 | + | #endif |
542 | + | //write out MetaData first |
543 | + | (*newOStream) << "<OpenMD version=1>" << std::endl; |
544 | + | (*newOStream) << " <MetaData>" << std::endl; |
545 | + | (*newOStream) << info_->getRawMetaData(); |
546 | + | (*newOStream) << " </MetaData>" << std::endl; |
547 | + | return newOStream; |
548 | + | } |
549 | ||
550 | < | }//end namespace oopse |
550 | > | void DumpWriter::writeClosing(std::ostream& os) { |
551 | > | |
552 | > | os << "</OpenMD>\n"; |
553 | > | os.flush(); |
554 | > | } |
555 | > | |
556 | > | }//end namespace OpenMD |
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