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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 376 by tim, Thu Feb 24 20:55:07 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)
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 +    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  
184 –        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
185 –            integrableObject = mol->nextIntegrableObject(ii)) {
186 –                
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();
200 <                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 <
210 <            os << writeLine;
211 <
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 +      os << "    </StuntDoubles>\n";
294 +      
295 +      os << "  </Snapshot>\n";
296 +      os.flush();
297 +    } else {
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 <    os.flush();
216 < #else // is_mpi
217 <    /*********************************************************************
218 <     * Documentation?  You want DOCUMENTATION?
219 <     *
220 <     * Why all the potatoes below?  
221 <     *
222 <     * To make a long story short, the original version of DumpWriter
223 <     * worked in the most inefficient way possible.  Node 0 would
224 <     * poke each of the node for an individual atom's formatted data
225 <     * as node 0 worked its way down the global index. This was particularly
226 <     * inefficient since the method blocked all processors at every atom
227 <     * (and did it twice!).
228 <     *
229 <     * An intermediate version of DumpWriter could be described from Node
230 <     * zero's perspective as follows:
231 <     *
232 <     *  1) Have 100 of your friends stand in a circle.
233 <     *  2) When you say go, have all of them start tossing potatoes at
234 <     *     you (one at a time).
235 <     *  3) Catch the potatoes.
236 <     *
237 <     * It was an improvement, but MPI has buffers and caches that could
238 <     * best be described in this analogy as "potato nets", so there's no
239 <     * need to block the processors atom-by-atom.
240 <     *
241 <     * This new and improved DumpWriter works in an even more efficient
242 <     * way:
243 <     *
244 <     *  1) Have 100 of your friend stand in a circle.
245 <     *  2) When you say go, have them start tossing 5-pound bags of
246 <     *     potatoes at you.
247 <     *  3) Once you've caught a friend's bag of potatoes,
248 <     *     toss them a spud to let them know they can toss another bag.
249 <     *
250 <     * How's THAT for documentation?
251 <     *
252 <     *********************************************************************/
253 <    const int masterNode = 0;
303 > #endif // is_mpi
304  
305 <    int * potatoes;
256 <    int myPotato;
257 <    int nProc;
258 <    int which_node;
259 <    double atomData[13];
260 <    int isDirectional;
261 <    const char * atomTypeString;
262 <    char MPIatomTypeString[MINIBUFFERSIZE];
263 <    int msgLen; // the length of message actually recieved at master nodes
264 <    int haveError;
265 <    MPI_Status istatus;
266 <    int nCurObj;
267 <    
268 <    // code to find maximum tag value
269 <    int * tagub;
270 <    int flag;
271 <    int MAXTAG;
272 <    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
305 >  }
306  
307 <    if (flag) {
308 <        MAXTAG = *tagub;
309 <    } else {
310 <        MAXTAG = 32767;
311 <    }
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 <    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
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 <        // Node 0 needs a list of the magic potatoes for each processor;
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 <        MPI_Comm_size(MPI_COMM_WORLD, &nProc);
336 <        potatoes = new int[nProc];
337 <
338 <        //write out the comment lines
339 <        for(int i = 0; i < nProc; i++) {
340 <            potatoes[i] = 0;
341 <        }
342 <
343 <
344 <        os << nTotObjects << "\n";
345 <        writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
295 <
296 <        for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
297 <
298 <            // Get the Node number which has this atom;
299 <
300 <            which_node = info_->getMolToProc(i);
301 <
302 <            if (which_node != masterNode) { //current molecule is in slave node
303 <                if (potatoes[which_node] + 1 >= MAXTAG) {
304 <                    // The potato was going to exceed the maximum value,
305 <                    // so wrap this processor potato back to 0:        
306 <
307 <                    potatoes[which_node] = 0;
308 <                    MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
309 <                             MPI_COMM_WORLD);
310 <                }
311 <
312 <                myPotato = potatoes[which_node];
313 <
314 <                //recieve the number of integrableObject in current molecule
315 <                MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
316 <                         MPI_COMM_WORLD, &istatus);
317 <                myPotato++;
318 <
319 <                for(int l = 0; l < nCurObj; l++) {
320 <                    if (potatoes[which_node] + 2 >= MAXTAG) {
321 <                        // The potato was going to exceed the maximum value,
322 <                        // so wrap this processor potato back to 0:        
323 <
324 <                        potatoes[which_node] = 0;
325 <                        MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
326 <                                 0, MPI_COMM_WORLD);
327 <                    }
328 <
329 <                    MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
330 <                             which_node, myPotato, MPI_COMM_WORLD,
331 <                             &istatus);
332 <
333 <                    atomTypeString = MPIatomTypeString;
334 <
335 <                    myPotato++;
336 <
337 <                    MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
338 <                             MPI_COMM_WORLD, &istatus);
339 <                    myPotato++;
340 <
341 <                    MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
342 <
343 <                    if (msgLen == 13)
344 <                        isDirectional = 1;
345 <                    else
346 <                        isDirectional = 0;
347 <
348 <                    // If we've survived to here, format the line:
349 <
350 <                    if (!isDirectional) {
351 <                        sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
352 <                                atomTypeString, atomData[0],
353 <                                atomData[1], atomData[2],
354 <                                atomData[3], atomData[4],
355 <                                atomData[5]);
356 <
357 <                        strcat(writeLine,
358 <                               "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
359 <                    } else {
360 <                        sprintf(writeLine,
361 <                                "%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",
362 <                                atomTypeString,
363 <                                atomData[0],
364 <                                atomData[1],
365 <                                atomData[2],
366 <                                atomData[3],
367 <                                atomData[4],
368 <                                atomData[5],
369 <                                atomData[6],
370 <                                atomData[7],
371 <                                atomData[8],
372 <                                atomData[9],
373 <                                atomData[10],
374 <                                atomData[11],
375 <                                atomData[12]);
376 <                    }
377 <
378 <                    os << writeLine;
379 <
380 <                } // end for(int l =0)
381 <
382 <                potatoes[which_node] = myPotato;
383 <            } else { //master node has current molecule
384 <
385 <                mol = info_->getMoleculeByGlobalIndex(i);
386 <
387 <                if (mol == NULL) {
388 <                    sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
389 <                    painCave.isFatal = 1;
390 <                    simError();
391 <                }
392 <                
393 <                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
394 <                    integrableObject = mol->nextIntegrableObject(ii)) {
395 <                        
396 <                    atomTypeString = integrableObject->getType().c_str();
397 <
398 <                    pos = integrableObject->getPos();
399 <                    vel = integrableObject->getVel();
400 <
401 <                    atomData[0] = pos[0];
402 <                    atomData[1] = pos[1];
403 <                    atomData[2] = pos[2];
404 <
405 <                    atomData[3] = vel[0];
406 <                    atomData[4] = vel[1];
407 <                    atomData[5] = vel[2];
408 <
409 <                    isDirectional = 0;
410 <
411 <                    if (integrableObject->isDirectional()) {
412 <                        isDirectional = 1;
413 <
414 <                        q = integrableObject->getQ();
415 <                        ji = integrableObject->getJ();
416 <
417 <                        for(int j = 0; j < 6; j++) {
418 <                            atomData[j] = atomData[j];
419 <                        }
420 <
421 <                        atomData[6] = q[0];
422 <                        atomData[7] = q[1];
423 <                        atomData[8] = q[2];
424 <                        atomData[9] = q[3];
425 <
426 <                        atomData[10] = ji[0];
427 <                        atomData[11] = ji[1];
428 <                        atomData[12] = ji[2];
429 <                    }
430 <
431 <                    // If we've survived to here, format the line:
432 <
433 <                    if (!isDirectional) {
434 <                        sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
435 <                                atomTypeString, atomData[0],
436 <                                atomData[1], atomData[2],
437 <                                atomData[3], atomData[4],
438 <                                atomData[5]);
439 <
440 <                        strcat(writeLine,
441 <                               "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
442 <                    } else {
443 <                        sprintf(writeLine,
444 <                                "%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",
445 <                                atomTypeString,
446 <                                atomData[0],
447 <                                atomData[1],
448 <                                atomData[2],
449 <                                atomData[3],
450 <                                atomData[4],
451 <                                atomData[5],
452 <                                atomData[6],
453 <                                atomData[7],
454 <                                atomData[8],
455 <                                atomData[9],
456 <                                atomData[10],
457 <                                atomData[11],
458 <                                atomData[12]);
459 <                    }
460 <
461 <
462 <                    os << writeLine;
463 <
464 <                } //end for(iter = integrableObject.begin())
465 <            }
466 <        } //end for(i = 0; i < mpiSim->getNmol())
467 <
468 <        os.flush();
469 <        
470 <        sprintf(checkPointMsg, "Sucessfully took a dump.\n");
471 <        MPIcheckPoint();
472 <
473 <        delete [] potatoes;
474 <    } else {
475 <
476 <        // worldRank != 0, so I'm a remote node.  
477 <
478 <        // Set my magic potato to 0:
479 <
480 <        myPotato = 0;
481 <
482 <        for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
483 <
484 <            // Am I the node which has this integrableObject?
485 <            int whichNode = info_->getMolToProc(i);
486 <            if (whichNode == worldRank) {
487 <                if (myPotato + 1 >= MAXTAG) {
488 <
489 <                    // The potato was going to exceed the maximum value,
490 <                    // so wrap this processor potato back to 0 (and block until
491 <                    // node 0 says we can go:
492 <
493 <                    MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
494 <                             &istatus);
495 <                }
496 <
497 <                mol = info_->getMoleculeByGlobalIndex(i);
498 <
499 <                
500 <                nCurObj = mol->getNIntegrableObjects();
501 <
502 <                MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
503 <                myPotato++;
504 <
505 <                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
506 <                    integrableObject = mol->nextIntegrableObject(ii)) {
507 <
508 <                    if (myPotato + 2 >= MAXTAG) {
509 <
510 <                        // The potato was going to exceed the maximum value,
511 <                        // so wrap this processor potato back to 0 (and block until
512 <                        // node 0 says we can go:
513 <
514 <                        MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
515 <                                 &istatus);
516 <                    }
517 <
518 <                    atomTypeString = integrableObject->getType().c_str();
519 <
520 <                    pos = integrableObject->getPos();
521 <                    vel = integrableObject->getVel();
522 <
523 <                    atomData[0] = pos[0];
524 <                    atomData[1] = pos[1];
525 <                    atomData[2] = pos[2];
526 <
527 <                    atomData[3] = vel[0];
528 <                    atomData[4] = vel[1];
529 <                    atomData[5] = vel[2];
530 <
531 <                    isDirectional = 0;
532 <
533 <                    if (integrableObject->isDirectional()) {
534 <                        isDirectional = 1;
535 <
536 <                        q = integrableObject->getQ();
537 <                        ji = integrableObject->getJ();
538 <
539 <                        atomData[6] = q[0];
540 <                        atomData[7] = q[1];
541 <                        atomData[8] = q[2];
542 <                        atomData[9] = q[3];
543 <
544 <                        atomData[10] = ji[0];
545 <                        atomData[11] = ji[1];
546 <                        atomData[12] = ji[2];
547 <                    }
548 <
549 <                    strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
550 <
551 <                    // null terminate the  std::string before sending (just in case):
552 <                    MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
553 <
554 <                    MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
555 <                             myPotato, MPI_COMM_WORLD);
556 <
557 <                    myPotato++;
558 <
559 <                    if (isDirectional) {
560 <                        MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
561 <                                 MPI_COMM_WORLD);
562 <                    } else {
563 <                        MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
564 <                                 MPI_COMM_WORLD);
565 <                    }
566 <
567 <                    myPotato++;
568 <                }
569 <                    
570 <            }
571 <            
572 <        }
573 <        sprintf(checkPointMsg, "Sucessfully took a dump.\n");
574 <        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 <
581 < void DumpWriter::writeDump() {
582 <    writeFrame(dumpFile_);
583 <
584 < }
585 <
586 < void DumpWriter::writeEor() {
587 <    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());
594 <        if (!eorStream.is_open()) {
595 <            sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
596 <                    eorFilename_.c_str());
597 <            painCave.isFatal = 1;
598 <            simError();
599 <        }
363 >      eorStream = createOStream(eorFilename_);
364  
365   #ifdef IS_MPI
366      }
367   #endif // is_mpi    
368  
369 <    writeFrame(eorStream);
606 < }
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());
619 <        if (!eorStream.is_open()) {
620 <            sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
621 <                    eorFilename_.c_str());
622 <            painCave.isFatal = 1;
623 <            simError();
624 <        }
392 >      eorStream = createOStream(eorFilename_);
393  
394 <        buffers.push_back(eorStream.rdbuf());
394 >      buffers.push_back(eorStream->rdbuf());
395          
396   #ifdef IS_MPI
397      }
# Line 633 | 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) << "<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 < }//end namespace oopse
436 >  void DumpWriter::writeClosing(std::ostream& os) {
437 >
438 >    os << "</OpenMD>\n";
439 >    os.flush();
440 >  }
441 >
442 > }//end namespace OpenMD

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