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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 251 by tim, Wed Jan 12 23:24:55 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
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   #ifdef IS_MPI
50   #include <mpi.h>
51   #endif //is_mpi
52  
53 < namespace oopse {
53 > namespace OpenMD {
54  
55 < DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
56 <                   : info_(info), filename_(filename){
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  
87 <    sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73 <    MPIcheckPoint();
87 > #endif // is_mpi
88  
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) {
111   #endif // is_mpi
112  
113 < }
113 >      
114 >      dumpFile_ = createOStream(filename_);
115  
116 < DumpWriter::~DumpWriter() {
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 + #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 <        dumpFile_.close();
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 +      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;
100 –    double chi;
101 –    double integralOfChiDt;
102 –    Mat3x3d eta;
103 –    
104 –    currentTime = s->getTime();
201      hmat = s->getHmat();
202 <    chi = s->getChi();
203 <    integralOfChiDt = s->getIntegralOfChiDt();
204 <    eta = s->getEta();
205 <    
206 <    os << currentTime << ";\t"
111 <         << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
112 <         << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
113 <         << 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"
121 <         << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
122 <        
123 <    os << std::endl;
124 < }
221 >    os << "    </FrameData>\n";
222 >  }
223  
224 < void DumpWriter::writeFrame(std::ostream& os) {
127 <    const int BUFFERSIZE = 2000;
128 <    const int MINIBUFFERSIZE = 100;
129 <
130 <    char tempBuffer[BUFFERSIZE];
131 <    char writeLine[BUFFERSIZE];
224 >  void DumpWriter::writeFrame(std::ostream& os) {
225  
226 <    Quat4d q;
227 <    Vector3d ji;
228 <    Vector3d pos;
136 <    Vector3d vel;
226 > #ifdef IS_MPI
227 >    MPI_Status istatus;
228 > #endif
229  
230      Molecule* mol;
231      StuntDouble* integrableObject;
232      SimInfo::MoleculeIterator mi;
233      Molecule::IntegrableObjectIterator ii;
142 –  
143 –    int nTotObjects;    
144 –    nTotObjects = info_->getNGlobalIntegrableObjects();
234  
235   #ifndef IS_MPI
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 <    os << nTotObjects << "\n";
244 <        
245 <    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
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 +    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  
155 –        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
156 –            integrableObject = mol->nextIntegrableObject(ii)) {
157 –                
260  
261 <            pos = integrableObject->getPos();
262 <            vel = integrableObject->getVel();
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 <            sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
270 <                    integrableObject->getType().c_str(),
271 <                    pos[0], pos[1], pos[2],
272 <                    vel[0], vel[1], vel[2]);
269 >    if (worldRank == masterNode) {      
270 >      os << "  <Snapshot>\n";  
271 >      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
272 >      os << "    <StuntDoubles>\n";
273 >        
274 >      os << buffer;
275  
276 <            strcpy(writeLine, tempBuffer);
276 >      int nProc;
277 >      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
278 >      for (int i = 1; i < nProc; ++i) {
279  
280 <            if (integrableObject->isDirectional()) {
281 <                q = integrableObject->getQ();
171 <                ji = integrableObject->getJ();
280 >        // receive the length of the string buffer that was
281 >        // prepared by processor i
282  
283 <                sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
284 <                        q[0], q[1], q[2], q[3],
285 <                        ji[0], ji[1], ji[2]);
286 <                strcat(writeLine, tempBuffer);
287 <            } else {
288 <                strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
289 <            }
290 <
181 <            os << writeLine;
182 <
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 < #else // is_mpi
295 <    /*********************************************************************
296 <     * Documentation?  You want DOCUMENTATION?
189 <     *
190 <     * Why all the potatoes below?  
191 <     *
192 <     * To make a long story short, the original version of DumpWriter
193 <     * worked in the most inefficient way possible.  Node 0 would
194 <     * poke each of the node for an individual atom's formatted data
195 <     * as node 0 worked its way down the global index. This was particularly
196 <     * inefficient since the method blocked all processors at every atom
197 <     * (and did it twice!).
198 <     *
199 <     * An intermediate version of DumpWriter could be described from Node
200 <     * zero's perspective as follows:
201 <     *
202 <     *  1) Have 100 of your friends stand in a circle.
203 <     *  2) When you say go, have all of them start tossing potatoes at
204 <     *     you (one at a time).
205 <     *  3) Catch the potatoes.
206 <     *
207 <     * It was an improvement, but MPI has buffers and caches that could
208 <     * best be described in this analogy as "potato nets", so there's no
209 <     * need to block the processors atom-by-atom.
210 <     *
211 <     * This new and improved DumpWriter works in an even more efficient
212 <     * way:
213 <     *
214 <     *  1) Have 100 of your friend stand in a circle.
215 <     *  2) When you say go, have them start tossing 5-pound bags of
216 <     *     potatoes at you.
217 <     *  3) Once you've caught a friend's bag of potatoes,
218 <     *     toss them a spud to let them know they can toss another bag.
219 <     *
220 <     * How's THAT for documentation?
221 <     *
222 <     *********************************************************************/
223 <    const int masterNode = 0;
224 <
225 <    int * potatoes;
226 <    int myPotato;
227 <    int nProc;
228 <    int which_node;
229 <    double atomData[13];
230 <    int isDirectional;
231 <    const char * atomTypeString;
232 <    char MPIatomTypeString[MINIBUFFERSIZE];
233 <    int msgLen; // the length of message actually recieved at master nodes
234 <    int haveError;
235 <    MPI_Status istatus;
236 <    int nCurObj;
237 <    
238 <    // code to find maximum tag value
239 <    int * tagub;
240 <    int flag;
241 <    int MAXTAG;
242 <    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
243 <
244 <    if (flag) {
245 <        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 <
324 <        os << nTotObjects << "\n";
325 <        writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
326 <
327 <        for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
328 <
329 <            // Get the Node number which has this atom;
330 <
331 <            which_node = info_->getMolToProc(i);
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 <            if (which_node != masterNode) { //current molecule is in slave node
336 <                if (potatoes[which_node] + 1 >= MAXTAG) {
337 <                    // The potato was going to exceed the maximum value,
338 <                    // so wrap this processor potato back to 0:        
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 <                    potatoes[which_node] = 0;
353 <                    MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
354 <                             MPI_COMM_WORLD);
280 <                }
352 >  void DumpWriter::writeDump() {
353 >    writeFrame(*dumpFile_);
354 >  }
355  
356 <                myPotato = potatoes[which_node];
356 >  void DumpWriter::writeEor() {
357 >    std::ostream* eorStream;
358 >    
359 > #ifdef IS_MPI
360 >    if (worldRank == 0) {
361 > #endif // is_mpi
362  
363 <                //recieve the number of integrableObject in current molecule
285 <                MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
286 <                         MPI_COMM_WORLD, &istatus);
287 <                myPotato++;
363 >      eorStream = createOStream(eorFilename_);
364  
365 <                for(int l = 0; l < nCurObj; l++) {
366 <                    if (potatoes[which_node] + 2 >= MAXTAG) {
367 <                        // The potato was going to exceed the maximum value,
292 <                        // so wrap this processor potato back to 0:        
365 > #ifdef IS_MPI
366 >    }
367 > #endif // is_mpi    
368  
369 <                        potatoes[which_node] = 0;
295 <                        MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
296 <                                 0, MPI_COMM_WORLD);
297 <                    }
369 >    writeFrame(*eorStream);
370  
371 <                    MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
372 <                             which_node, myPotato, MPI_COMM_WORLD,
373 <                             &istatus);
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 <                    atomTypeString = MPIatomTypeString;
380 >  }
381  
305 –                    myPotato++;
382  
383 <                    MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
384 <                             MPI_COMM_WORLD, &istatus);
385 <                    myPotato++;
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 <                    MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
390 >      buffers.push_back(dumpFile_->rdbuf());
391  
392 <                    if (msgLen == 13)
314 <                        isDirectional = 1;
315 <                    else
316 <                        isDirectional = 0;
392 >      eorStream = createOStream(eorFilename_);
393  
394 <                    // If we've survived to here, format the line:
319 <
320 <                    if (!isDirectional) {
321 <                        sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
322 <                                atomTypeString, atomData[0],
323 <                                atomData[1], atomData[2],
324 <                                atomData[3], atomData[4],
325 <                                atomData[5]);
326 <
327 <                        strcat(writeLine,
328 <                               "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
329 <                    } else {
330 <                        sprintf(writeLine,
331 <                                "%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",
332 <                                atomTypeString,
333 <                                atomData[0],
334 <                                atomData[1],
335 <                                atomData[2],
336 <                                atomData[3],
337 <                                atomData[4],
338 <                                atomData[5],
339 <                                atomData[6],
340 <                                atomData[7],
341 <                                atomData[8],
342 <                                atomData[9],
343 <                                atomData[10],
344 <                                atomData[11],
345 <                                atomData[12]);
346 <                    }
347 <
348 <                    os << writeLine;
349 <
350 <                } // end for(int l =0)
351 <
352 <                potatoes[which_node] = myPotato;
353 <            } else { //master node has current molecule
354 <
355 <                mol = info_->getMoleculeByGlobalIndex(i);
356 <
357 <                if (mol == NULL) {
358 <                    sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
359 <                    painCave.isFatal = 1;
360 <                    simError();
361 <                }
362 <                
363 <                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
364 <                    integrableObject = mol->nextIntegrableObject(ii)) {
365 <                        
366 <                    atomTypeString = integrableObject->getType().c_str();
367 <
368 <                    pos = integrableObject->getPos();
369 <                    vel = integrableObject->getVel();
370 <
371 <                    atomData[0] = pos[0];
372 <                    atomData[1] = pos[1];
373 <                    atomData[2] = pos[2];
374 <
375 <                    atomData[3] = vel[0];
376 <                    atomData[4] = vel[1];
377 <                    atomData[5] = vel[2];
378 <
379 <                    isDirectional = 0;
380 <
381 <                    if (integrableObject->isDirectional()) {
382 <                        isDirectional = 1;
383 <
384 <                        q = integrableObject->getQ();
385 <                        ji = integrableObject->getJ();
386 <
387 <                        for(int j = 0; j < 6; j++) {
388 <                            atomData[j] = atomData[j];
389 <                        }
390 <
391 <                        atomData[6] = q[0];
392 <                        atomData[7] = q[1];
393 <                        atomData[8] = q[2];
394 <                        atomData[9] = q[3];
395 <
396 <                        atomData[10] = ji[0];
397 <                        atomData[11] = ji[1];
398 <                        atomData[12] = ji[2];
399 <                    }
400 <
401 <                    // If we've survived to here, format the line:
402 <
403 <                    if (!isDirectional) {
404 <                        sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
405 <                                atomTypeString, atomData[0],
406 <                                atomData[1], atomData[2],
407 <                                atomData[3], atomData[4],
408 <                                atomData[5]);
409 <
410 <                        strcat(writeLine,
411 <                               "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
412 <                    } else {
413 <                        sprintf(writeLine,
414 <                                "%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",
415 <                                atomTypeString,
416 <                                atomData[0],
417 <                                atomData[1],
418 <                                atomData[2],
419 <                                atomData[3],
420 <                                atomData[4],
421 <                                atomData[5],
422 <                                atomData[6],
423 <                                atomData[7],
424 <                                atomData[8],
425 <                                atomData[9],
426 <                                atomData[10],
427 <                                atomData[11],
428 <                                atomData[12]);
429 <                    }
430 <
431 <
432 <                    os << writeLine;
433 <
434 <                } //end for(iter = integrableObject.begin())
435 <            }
436 <        } //end for(i = 0; i < mpiSim->getNmol())
437 <
438 <        os.flush();
394 >      buffers.push_back(eorStream->rdbuf());
395          
396 <        sprintf(checkPointMsg, "Sucessfully took a dump.\n");
397 <        MPIcheckPoint();
396 > #ifdef IS_MPI
397 >    }
398 > #endif // is_mpi    
399  
400 <        delete [] potatoes;
401 <    } else {
400 >    TeeBuf tbuf(buffers.begin(), buffers.end());
401 >    std::ostream os(&tbuf);
402  
403 <        // worldRank != 0, so I'm a remote node.  
403 >    writeFrame(os);
404  
405 <        // Set my magic potato to 0:
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 >  }
415  
416 <        myPotato = 0;
416 >  std::ostream* DumpWriter::createOStream(const std::string& filename) {
417  
418 <        for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
419 <
420 <            // Am I the node which has this integrableObject?
421 <            int whichNode = info_->getMolToProc(i);
422 <            if (whichNode == worldRank) {
423 <                if (myPotato + 1 >= MAXTAG) {
458 <
459 <                    // The potato was going to exceed the maximum value,
460 <                    // so wrap this processor potato back to 0 (and block until
461 <                    // node 0 says we can go:
462 <
463 <                    MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
464 <                             &istatus);
465 <                }
466 <
467 <                mol = info_->getMoleculeByGlobalIndex(i);
468 <
469 <                
470 <                nCurObj = mol->getNIntegrableObjects();
471 <
472 <                MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
473 <                myPotato++;
474 <
475 <                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
476 <                    integrableObject = mol->nextIntegrableObject(ii)) {
477 <
478 <                    if (myPotato + 2 >= MAXTAG) {
479 <
480 <                        // The potato was going to exceed the maximum value,
481 <                        // so wrap this processor potato back to 0 (and block until
482 <                        // node 0 says we can go:
483 <
484 <                        MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
485 <                                 &istatus);
486 <                    }
487 <
488 <                    atomTypeString = integrableObject->getType().c_str();
489 <
490 <                    pos = integrableObject->getPos();
491 <                    vel = integrableObject->getVel();
492 <
493 <                    atomData[0] = pos[0];
494 <                    atomData[1] = pos[1];
495 <                    atomData[2] = pos[2];
496 <
497 <                    atomData[3] = vel[0];
498 <                    atomData[4] = vel[1];
499 <                    atomData[5] = vel[2];
500 <
501 <                    isDirectional = 0;
502 <
503 <                    if (integrableObject->isDirectional()) {
504 <                        isDirectional = 1;
505 <
506 <                        q = integrableObject->getQ();
507 <                        ji = integrableObject->getJ();
508 <
509 <                        atomData[6] = q[0];
510 <                        atomData[7] = q[1];
511 <                        atomData[8] = q[2];
512 <                        atomData[9] = q[3];
513 <
514 <                        atomData[10] = ji[0];
515 <                        atomData[11] = ji[1];
516 <                        atomData[12] = ji[2];
517 <                    }
518 <
519 <                    strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
520 <
521 <                    // null terminate the  std::string before sending (just in case):
522 <                    MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
523 <
524 <                    MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
525 <                             myPotato, MPI_COMM_WORLD);
526 <
527 <                    myPotato++;
528 <
529 <                    if (isDirectional) {
530 <                        MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
531 <                                 MPI_COMM_WORLD);
532 <                    } else {
533 <                        MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
534 <                                 MPI_COMM_WORLD);
535 <                    }
536 <
537 <                    myPotato++;
538 <                }
539 <                    
540 <            }
541 <            
542 <        }
543 <        sprintf(checkPointMsg, "Sucessfully took a dump.\n");
544 <        MPIcheckPoint();
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) << "<OpenMD version=1>" << std::endl;
430 +    (*newOStream) << "  <MetaData>" << std::endl;
431 +    (*newOStream) << info_->getRawMetaData();
432 +    (*newOStream) << "  </MetaData>" << std::endl;
433 +    return newOStream;
434 +  }
435  
436 < #endif // is_mpi
436 >  void DumpWriter::writeClosing(std::ostream& os) {
437  
438 < }
438 >    os << "</OpenMD>\n";
439 >    os.flush();
440 >  }
441  
442 < }//end namespace oopse
442 > }//end namespace OpenMD

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