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root/OpenMD/trunk/src/io/DumpWriter.cpp
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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 395 by tim, Thu Mar 3 14:40:20 2005 UTC vs.
Revision 1217 by xsun, Wed Jan 23 21:23:02 2008 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# 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
52  
53   namespace oopse {
54  
55 < DumpWriter::DumpWriter(SimInfo* info)
56 <                   : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
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) {
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      }
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){
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) {
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      }
126  
127 <    sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
102 <    MPIcheckPoint();
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 < }
167 >    
168 > #endif // is_mpi
169 >    
170 >  }
171  
172 < DumpWriter::~DumpWriter() {
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      }
185  
186   #endif // is_mpi
187  
188 < }
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"
222 <         << 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";
153 < }
221 >    os << "    </FrameData>\n";
222 >  }
223  
224 < void DumpWriter::writeFrame(std::ostream& os) {
156 <    const int BUFFERSIZE = 2000;
157 <    const int MINIBUFFERSIZE = 100;
224 >  void DumpWriter::writeFrame(std::ostream& os) {
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 <
237 <
238 <    os << nTotObjects << "\n";
179 <        
180 <    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
236 >    os << "  <Snapshot>\n";
237 >
238 >    writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
239  
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 <                
243 >      
244 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
245 >           integrableObject = mol->nextIntegrableObject(ii)) {  
246 >          os << prepareDumpLine(integrableObject);
247 >          
248 >      }
249 >    }    
250 >    os << "    </StuntDoubles>\n";
251 >    
252 >    os << "  </Snapshot>\n";
253  
254 <            pos = integrableObject->getPos();
255 <            vel = integrableObject->getVel();
254 >    os.flush();
255 > #else
256 >    //every node prepares the dump lines for integrable objects belong to itself
257 >    std::string buffer;
258 >    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
259  
191 –            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]);
260  
261 <            strcpy(writeLine, tempBuffer);
261 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
262 >           integrableObject = mol->nextIntegrableObject(ii)) {  
263 >          buffer += prepareDumpLine(integrableObject);
264 >      }
265 >    }
266 >    
267 >    const int masterNode = 0;
268  
269 <            if (integrableObject->isDirectional()) {
270 <                q = integrableObject->getQ();
271 <                ji = integrableObject->getJ();
269 >    if (worldRank == masterNode) {      
270 >      os << "  <Snapshot>\n";  
271 >      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
272 >      os << "    <StuntDoubles>\n";
273 >        
274 >      os << buffer;
275  
276 <                sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
277 <                        q[0], q[1], q[2], q[3],
278 <                        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 <            }
276 >      int nProc;
277 >      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
278 >      for (int i = 1; i < nProc; ++i) {
279  
280 <            os << writeLine;
280 >        // receive the length of the string buffer that was
281 >        // prepared by processor i
282  
283 +        int recvLength;
284 +        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
285 +        char* recvBuffer = new char[recvLength];
286 +        if (recvBuffer == NULL) {
287 +        } else {
288 +          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
289 +          os << recvBuffer;
290 +          delete recvBuffer;
291          }
292 <    }
293 <
294 <    os.flush();
295 < #else // is_mpi
296 <    /*********************************************************************
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;
292 >      }
293 >      os << "    </StuntDoubles>\n";
294 >      
295 >      os << "  </Snapshot>\n";
296 >      os.flush();
297      } else {
298 <        MAXTAG = 32767;
298 >      int sendBufferLength = buffer.size() + 1;
299 >      MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
300 >      MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
301      }
302  
303 <    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
303 > #endif // is_mpi
304  
305 <        // Node 0 needs a list of the magic potatoes for each processor;
305 >  }
306  
307 <        MPI_Comm_size(MPI_COMM_WORLD, &nProc);
308 <        potatoes = new int[nProc];
307 >  std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
308 >        
309 >    int index = integrableObject->getGlobalIntegrableObjectIndex();
310 >    std::string type("pv");
311 >    std::string line;
312 >    char tempBuffer[4096];
313  
314 <        //write out the comment lines
315 <        for(int i = 0; i < nProc; i++) {
316 <            potatoes[i] = 0;
317 <        }
314 >    Vector3d pos;
315 >    Vector3d vel;
316 >    pos = integrableObject->getPos();
317 >    vel = integrableObject->getVel();          
318 >    sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
319 >            pos[0], pos[1], pos[2],
320 >            vel[0], vel[1], vel[2]);                    
321 >    line += tempBuffer;
322  
323 +    if (integrableObject->isDirectional()) {
324 +      type += "qj";
325 +      Quat4d q;
326 +      Vector3d ji;
327 +      q = integrableObject->getQ();
328 +      ji = integrableObject->getJ();
329 +      sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
330 +              q[0], q[1], q[2], q[3],
331 +              ji[0], ji[1], ji[2]);
332 +      line += tempBuffer;
333 +    }
334  
335 <        os << nTotObjects << "\n";
336 <        writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
337 <
338 <        for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
339 <
340 <            // Get the Node number which has this atom;
341 <
342 <            which_node = info_->getMolToProc(i);
343 <
344 <            if (which_node != masterNode) { //current molecule is in slave node
345 <                if (potatoes[which_node] + 1 >= MAXTAG) {
303 <                    // The potato was going to exceed the maximum value,
304 <                    // so wrap this processor potato back to 0:        
305 <
306 <                    potatoes[which_node] = 0;
307 <                    MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
308 <                             MPI_COMM_WORLD);
309 <                }
310 <
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();
335 >    if (needForceVector_) {
336 >      type += "ft";
337 >      Vector3d frc;
338 >      Vector3d trq;
339 >      frc = integrableObject->getFrc();
340 >      trq = integrableObject->getTrq();
341 >              
342 >      sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e",
343 >              frc[0], frc[1], frc[2],
344 >              trq[0], trq[1], trq[2]);
345 >      line += tempBuffer;
346      }
347 +        
348 +    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
349 +    return std::string(tempBuffer);
350 +  }
351  
352 < #endif // is_mpi
352 >  void DumpWriter::writeDump() {
353 >    writeFrame(*dumpFile_);
354 >  }
355  
356 < }
357 <
574 < void DumpWriter::writeDump() {
575 <    writeFrame(dumpFile_);
576 <
577 < }
578 <
579 < void DumpWriter::writeEor() {
580 <    std::ofstream eorStream;
356 >  void DumpWriter::writeEor() {
357 >    std::ostream* eorStream;
358      
359   #ifdef IS_MPI
360      if (worldRank == 0) {
361   #endif // is_mpi
362  
363 <        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 <        }
363 >      eorStream = createOStream(eorFilename_);
364  
365   #ifdef IS_MPI
366      }
367   #endif // is_mpi    
368  
369 <    writeFrame(eorStream);
599 < }
369 >    writeFrame(*eorStream);
370  
371 + #ifdef IS_MPI
372 +    if (worldRank == 0) {
373 + #endif // is_mpi
374 +      writeClosing(*eorStream);
375 +      delete eorStream;
376 + #ifdef IS_MPI
377 +    }
378 + #endif // is_mpi  
379  
380 < void DumpWriter::writeDumpAndEor() {
381 <    std::ofstream eorStream;
380 >  }
381 >
382 >
383 >  void DumpWriter::writeDumpAndEor() {
384      std::vector<std::streambuf*> buffers;
385 +    std::ostream* eorStream;
386   #ifdef IS_MPI
387      if (worldRank == 0) {
388   #endif // is_mpi
389  
390 <        buffers.push_back(dumpFile_.rdbuf());
390 >      buffers.push_back(dumpFile_->rdbuf());
391  
392 <        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 <        }
392 >      eorStream = createOStream(eorFilename_);
393  
394 <        buffers.push_back(eorStream.rdbuf());
394 >      buffers.push_back(eorStream->rdbuf());
395          
396   #ifdef IS_MPI
397      }
# Line 626 | Line 401 | void DumpWriter::writeDumpAndEor() {
401      std::ostream os(&tbuf);
402  
403      writeFrame(os);
404 +
405 + #ifdef IS_MPI
406 +    if (worldRank == 0) {
407 + #endif // is_mpi
408 +      writeClosing(*eorStream);
409 +      delete eorStream;
410 + #ifdef IS_MPI
411 +    }
412 + #endif // is_mpi  
413      
414 < }
414 >  }
415  
416 +  std::ostream* DumpWriter::createOStream(const std::string& filename) {
417  
418 +    std::ostream* newOStream;
419 + #ifdef HAVE_LIBZ
420 +    if (needCompression_) {
421 +      newOStream = new ogzstream(filename.c_str());
422 +    } else {
423 +      newOStream = new std::ofstream(filename.c_str());
424 +    }
425 + #else
426 +    newOStream = new std::ofstream(filename.c_str());
427 + #endif
428 +    //write out MetaData first
429 +    (*newOStream) << "<OOPSE version=4>" << std::endl;
430 +    (*newOStream) << "  <MetaData>" << std::endl;
431 +    (*newOStream) << info_->getRawMetaData();
432 +    (*newOStream) << "  </MetaData>" << std::endl;
433 +    return newOStream;
434 +  }
435  
436 +  void DumpWriter::writeClosing(std::ostream& os) {
437 +
438 +    os << "</OOPSE>\n";
439 +    os.flush();
440 +  }
441 +
442   }//end namespace oopse

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