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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 1437 by gezelter, Wed Apr 21 14:59:18 2010 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 +
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, const std::string& filename)
58 <                   : info_(info), filename_(filename){
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  
79 – DumpWriter::~DumpWriter() {
93  
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 <        dumpFile_.close();
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 +      }
124 +
125   #ifdef IS_MPI
126  
127      }
128  
129   #endif // is_mpi
130  
131 < }
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  
96 – void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
97 –
98 –    double currentTime;
99 –    Mat3x3d hmat;
100 –    double chi;
101 –    double integralOfChiDt;
102 –    Mat3x3d eta;
169      
170 <    currentTime = s->getTime();
105 <    hmat = s->getHmat();
106 <    chi = s->getChi();
107 <    integralOfChiDt = s->getIntegralOfChiDt();
108 <    eta = s->getEta();
170 > #endif // is_mpi
171      
172 <    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";
172 >  }
173  
174 <    //write out additional parameters, such as chi and eta
174 >  DumpWriter::~DumpWriter() {
175  
176 <    os << chi << "\t" << integralOfChiDt << "\t;";
176 > #ifdef IS_MPI
177  
178 <    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
179 <         << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
180 <         << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
181 <        
182 <    os << std::endl;
183 < }
178 >    if (worldRank == 0) {
179 > #endif // is_mpi
180 >      if (createDumpFile_){
181 >        writeClosing(*dumpFile_);
182 >        delete dumpFile_;
183 >      }
184 > #ifdef IS_MPI
185  
186 < void DumpWriter::writeFrame(std::ostream& os) {
127 <    const int BUFFERSIZE = 2000;
128 <    const int MINIBUFFERSIZE = 100;
186 >    }
187  
188 <    char tempBuffer[BUFFERSIZE];
131 <    char writeLine[BUFFERSIZE];
188 > #endif // is_mpi
189  
190 <    Quat4d q;
134 <    Vector3d ji;
135 <    Vector3d pos;
136 <    Vector3d vel;
190 >  }
191  
192 <    Molecule* mol;
139 <    StuntDouble* integrableObject;
140 <    SimInfo::MoleculeIterator mi;
141 <    Molecule::IntegrableObjectIterator ii;
142 <  
143 <    int nTotObjects;    
144 <    nTotObjects = info_->getNGlobalIntegrableObjects();
192 >  void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
193  
194 < #ifndef IS_MPI
194 >    char buffer[1024];
195  
196 +    os << "    <FrameData>\n";
197  
198 <    os << nTotObjects << "\n";
150 <        
151 <    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
198 >    RealType currentTime = s->getTime();
199  
200 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
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 >    sprintf(buffer, "        Time: %.10g\n", currentTime);
208 >    os << buffer;
209  
210 <        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
211 <            integrableObject = mol->nextIntegrableObject(ii)) {
157 <                
210 >    Mat3x3d hmat;
211 >    hmat = s->getHmat();
212  
213 <            pos = integrableObject->getPos();
214 <            vel = integrableObject->getVel();
215 <
216 <            sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
217 <                    integrableObject->getType().c_str(),
218 <                    pos[0], pos[1], pos[2],
219 <                    vel[0], vel[1], vel[2]);
220 <
221 <            strcpy(writeLine, tempBuffer);
222 <
223 <            if (integrableObject->isDirectional()) {
224 <                q = integrableObject->getQ();
225 <                ji = integrableObject->getJ();
226 <
227 <                sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
228 <                        q[0], q[1], q[2], q[3],
175 <                        ji[0], ji[1], ji[2]);
176 <                strcat(writeLine, tempBuffer);
177 <            } else {
178 <                strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
179 <            }
180 <
181 <            os << writeLine;
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 >    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 <        }
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 < #else // is_mpi
243 <    /*********************************************************************
188 <     * 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;
242 >    Mat3x3d eta;
243 >    eta = s->getEta();
244  
245 <    int * potatoes;
246 <    int myPotato;
247 <    int nProc;
248 <    int which_node;
249 <    double atomData[13];
250 <    int isDirectional;
251 <    const char * atomTypeString;
252 <    char MPIatomTypeString[MINIBUFFERSIZE];
253 <    int msgLen; // the length of message actually recieved at master nodes
254 <    int haveError;
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 >    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 >    os << "    </FrameData>\n";
263 >  }
264 >
265 >  void DumpWriter::writeFrame(std::ostream& os) {
266 >
267 > #ifdef IS_MPI
268      MPI_Status istatus;
269 <    int nCurObj;
269 > #endif
270 >
271 >    Molecule* mol;
272 >    StuntDouble* integrableObject;
273 >    SimInfo::MoleculeIterator mi;
274 >    Molecule::IntegrableObjectIterator ii;
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 >      
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 <    // 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);
293 >    os << "  </Snapshot>\n";
294  
295 <    if (flag) {
296 <        MAXTAG = *tagub;
297 <    } else {
298 <        MAXTAG = 32767;
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 >
301 >
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 <    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
310 >    if (worldRank == masterNode) {      
311 >      os << "  <Snapshot>\n";  
312 >      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
313 >      os << "    <StuntDoubles>\n";
314 >        
315 >      os << buffer;
316  
317 <        // Node 0 needs a list of the magic potatoes for each processor;
317 >      int nProc;
318 >      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
319 >      for (int i = 1; i < nProc; ++i) {
320  
321 <        MPI_Comm_size(MPI_COMM_WORLD, &nProc);
322 <        potatoes = new int[nProc];
321 >        // receive the length of the string buffer that was
322 >        // prepared by processor i
323  
324 <        //write out the comment lines
325 <        for(int i = 0; i < nProc; i++) {
326 <            potatoes[i] = 0;
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 +      os << "    </StuntDoubles>\n";
335 +      
336 +      os << "  </Snapshot>\n";
337 +      os.flush();
338 +    } else {
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 + #endif // is_mpi
345  
346 <        os << nTotObjects << "\n";
264 <        writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
346 >  }
347  
348 <        for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
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 <            // Get the Node number which has this atom;
355 >    Vector3d pos;
356 >    Vector3d vel;
357 >    pos = integrableObject->getPos();
358  
359 <            which_node = info_->getMolToProc(i);
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 >    vel = integrableObject->getVel();          
370 >
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 >    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 >    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;
278 <                    MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
279 <                             MPI_COMM_WORLD);
280 <                }
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,
292 <                        // so wrap this processor potato back to 0:        
421 >    if (needForceVector_) {
422 >      type += "f";
423 >      Vector3d frc;
424  
425 <                        potatoes[which_node] = 0;
295 <                        MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
296 <                                 0, MPI_COMM_WORLD);
297 <                    }
425 >      frc = integrableObject->getFrc();
426  
427 <                    MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
428 <                             which_node, myPotato, MPI_COMM_WORLD,
429 <                             &istatus);
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 >        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 >        
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 <                    atomTypeString = MPIatomTypeString;
466 >  void DumpWriter::writeDump() {
467 >    writeFrame(*dumpFile_);
468 >  }
469  
470 <                    myPotato++;
470 >  void DumpWriter::writeEor() {
471 >    std::ostream* eorStream;
472 >    
473 > #ifdef IS_MPI
474 >    if (worldRank == 0) {
475 > #endif // is_mpi
476  
477 <                    MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
308 <                             MPI_COMM_WORLD, &istatus);
309 <                    myPotato++;
477 >      eorStream = createOStream(eorFilename_);
478  
479 <                    MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
479 > #ifdef IS_MPI
480 >    }
481 > #endif // is_mpi    
482  
483 <                    if (msgLen == 13)
314 <                        isDirectional = 1;
315 <                    else
316 <                        isDirectional = 0;
483 >    writeFrame(*eorStream);
484  
485 <                    // If we've survived to here, format the line:
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 <                    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]);
494 >  }
495  
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 –                    }
496  
497 <                    os << writeLine;
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 <                } // end for(int l =0)
504 >      buffers.push_back(dumpFile_->rdbuf());
505  
506 <                potatoes[which_node] = myPotato;
353 <            } else { //master node has current molecule
506 >      eorStream = createOStream(eorFilename_);
507  
508 <                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();
508 >      buffers.push_back(eorStream->rdbuf());
509          
510 <        sprintf(checkPointMsg, "Sucessfully took a dump.\n");
511 <        MPIcheckPoint();
510 > #ifdef IS_MPI
511 >    }
512 > #endif // is_mpi    
513  
514 <        delete [] potatoes;
515 <    } else {
514 >    TeeBuf tbuf(buffers.begin(), buffers.end());
515 >    std::ostream os(&tbuf);
516  
517 <        // worldRank != 0, so I'm a remote node.  
517 >    writeFrame(os);
518  
519 <        // Set my magic potato to 0:
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 >  }
529  
530 <        myPotato = 0;
530 >  std::ostream* DumpWriter::createOStream(const std::string& filename) {
531  
532 <        for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
533 <
534 <            // Am I the node which has this integrableObject?
535 <            int whichNode = info_->getMolToProc(i);
536 <            if (whichNode == worldRank) {
537 <                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();
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 < #endif // is_mpi
550 >  void DumpWriter::writeClosing(std::ostream& os) {
551  
552 < }
552 >    os << "</OpenMD>\n";
553 >    os.flush();
554 >  }
555  
556 < }//end namespace oopse
556 > }//end namespace OpenMD

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