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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1217 by xsun, Wed Jan 23 21:23:02 2008 UTC

# Line 1 | Line 1
1 < #define _LARGEFILE_SOURCE64
2 < #define _FILE_OFFSET_BITS 64
1 > /*
2 > * Copyright (c) 2005 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
19 > *    notice, this list of conditions and the following disclaimer.
20 > *
21 > * 3. Redistributions in binary form must reproduce the above copyright
22 > *    notice, this list of conditions and the following disclaimer in the
23 > *    documentation and/or other materials provided with the
24 > *    distribution.
25 > *
26 > * This software is provided "AS IS," without a warranty of any
27 > * kind. All express or implied conditions, representations and
28 > * warranties, including any implied warranty of merchantability,
29 > * fitness for a particular purpose or non-infringement, are hereby
30 > * excluded.  The University of Notre Dame and its licensors shall not
31 > * be liable for any damages suffered by licensee as a result of
32 > * using, modifying or distributing the software or its
33 > * derivatives. In no event will the University of Notre Dame or its
34 > * licensors be liable for any lost revenue, profit or data, or for
35 > * direct, indirect, special, consequential, incidental or punitive
36 > * damages, however caused and regardless of the theory of liability,
37 > * arising out of the use of or inability to use software, even if the
38 > * University of Notre Dame has been advised of the possibility of
39 > * such damages.
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  
4 – #include <string.h>
5 – #include <iostream>
6 – #include <fstream>
7 – #include <algorithm>
8 – #include <utility>
9 –
49   #ifdef IS_MPI
50   #include <mpi.h>
12 – #include "brains/mpiSimulation.hpp"
13 –
14 – namespace dWrite{
15 –  void DieDieDie( void );
16 – }
17 –
18 – using namespace dWrite;
51   #endif //is_mpi
52  
53 < #include "io/ReadWrite.hpp"
22 < #include "utils/simError.h"
53 > namespace oopse {
54  
55 < DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
55 >  DumpWriter::DumpWriter(SimInfo* info)
56 >    : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
57  
58 <  entry_plug = the_entry_plug;
59 <
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 <  if(worldRank == 0 ){
70 >
71 >    if (worldRank == 0) {
72   #endif // is_mpi
73 +        
74 +      dumpFile_ = createOStream(filename_);
75  
76 <    dumpFile.open(entry_plug->sampleName.c_str(), ios::out | 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  
83 <    if( !dumpFile ){
83 > #ifdef IS_MPI
84  
36 –      sprintf( painCave.errMsg,
37 –               "Could not open \"%s\" for dump output.\n",
38 –               entry_plug->sampleName.c_str());
39 –      painCave.isFatal = 1;
40 –      simError();
85      }
86  
87 < #ifdef IS_MPI
87 > #endif // is_mpi
88 >
89    }
90  
46 –  //sort the local atoms by global index
47 –  sortByGlobalIndex();
48 –  
49 –  sprintf( checkPointMsg,
50 –           "Sucessfully opened output file for dumping.\n");
51 –  MPIcheckPoint();
52 – #endif // is_mpi
53 – }
91  
92 < DumpWriter::~DumpWriter( ){
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 <  if(worldRank == 0 ){
109 >
110 >    if (worldRank == 0) {
111   #endif // is_mpi
112  
113 <    dumpFile.close();
113 >      
114 >      dumpFile_ = createOStream(filename_);
115  
116 < #ifdef IS_MPI
117 <  }
118 < #endif // is_mpi
119 < }
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 < /**
71 < * A hook function to load balancing
72 < */
125 >    }
126  
127 < void DumpWriter::update(){
75 <  sortByGlobalIndex();          
76 < }
77 <  
78 < /**
79 < * Auxiliary sorting function
80 < */
81 <
82 < bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83 <  return p1.second < p2.second;
84 < }
127 > #endif // is_mpi
128  
129 < /**
87 < * Sorting the local index by global index
88 < */
89 <
90 < void DumpWriter::sortByGlobalIndex(){
91 <  Molecule* mols = entry_plug->molecules;  
92 <  indexArray.clear();
129 >  }
130    
131 <  for(int i = 0; i < entry_plug->n_mol;i++)
132 <    indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
133 <  
134 <  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
135 < }
136 <
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 <
102 < void DumpWriter::writeDump(double currentTime){
103 <
104 <  ofstream finalOut;
105 <  vector<ofstream*> fileStreams;
106 <
146 >    
147   #ifdef IS_MPI
148 <  if(worldRank == 0 ){
149 < #endif    
110 <    finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
111 <    if( !finalOut ){
112 <      sprintf( painCave.errMsg,
113 <               "Could not open \"%s\" for final dump output.\n",
114 <               entry_plug->finalName.c_str() );
115 <      painCave.isFatal = 1;
116 <      simError();
117 <    }
118 < #ifdef IS_MPI
119 <  }
148 >    
149 >    if (worldRank == 0) {
150   #endif // is_mpi
151 <
152 <  fileStreams.push_back(&finalOut);
153 <  fileStreams.push_back(&dumpFile);
154 <
155 <  writeFrame(fileStreams, currentTime);
156 <
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 <  finalOut.close();
165 < #endif
130 <        
131 < }
164 >      
165 >    }
166  
167 < void DumpWriter::writeFinal(double currentTime){
167 >    
168 > #endif // is_mpi
169 >    
170 >  }
171  
172 <  ofstream finalOut;
136 <  vector<ofstream*> fileStreams;
172 >  DumpWriter::~DumpWriter() {
173  
174   #ifdef IS_MPI
175 <  if(worldRank == 0 ){
175 >
176 >    if (worldRank == 0) {
177   #endif // is_mpi
178 +      if (createDumpFile_){
179 +        writeClosing(*dumpFile_);
180 +        delete dumpFile_;
181 +      }
182 + #ifdef IS_MPI
183  
142 –    finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
143 –
144 –    if( !finalOut ){
145 –      sprintf( painCave.errMsg,
146 –               "Could not open \"%s\" for final dump output.\n",
147 –               entry_plug->finalName.c_str() );
148 –      painCave.isFatal = 1;
149 –      simError();
184      }
185  
152 – #ifdef IS_MPI
153 –  }
186   #endif // is_mpi
155 –  
156 –  fileStreams.push_back(&finalOut);  
157 –  writeFrame(fileStreams, currentTime);
187  
188 < #ifdef IS_MPI
160 <  finalOut.close();
161 < #endif
162 <  
163 < }
188 >  }
189  
190 < void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
190 >  void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
191  
192 <  const int BUFFERSIZE = 2000;
168 <  const int MINIBUFFERSIZE = 100;
192 >    char buffer[1024];
193  
194 <  char tempBuffer[BUFFERSIZE];  
171 <  char writeLine[BUFFERSIZE];
194 >    os << "    <FrameData>\n";
195  
196 <  int i;
197 <  unsigned int k;
196 >    RealType currentTime = s->getTime();
197 >    sprintf(buffer, "        Time: %.10g\n", currentTime);
198 >    os << buffer;
199  
200 < #ifdef IS_MPI
201 <  
202 <  /*********************************************************************
203 <   * Documentation?  You want DOCUMENTATION?
204 <   *
205 <   * Why all the potatoes below?  
206 <   *
183 <   * To make a long story short, the original version of DumpWriter
184 <   * worked in the most inefficient way possible.  Node 0 would
185 <   * poke each of the node for an individual atom's formatted data
186 <   * as node 0 worked its way down the global index. This was particularly
187 <   * inefficient since the method blocked all processors at every atom
188 <   * (and did it twice!).
189 <   *
190 <   * An intermediate version of DumpWriter could be described from Node
191 <   * zero's perspective as follows:
192 <   *
193 <   *  1) Have 100 of your friends stand in a circle.
194 <   *  2) When you say go, have all of them start tossing potatoes at
195 <   *     you (one at a time).
196 <   *  3) Catch the potatoes.
197 <   *
198 <   * It was an improvement, but MPI has buffers and caches that could
199 <   * best be described in this analogy as "potato nets", so there's no
200 <   * need to block the processors atom-by-atom.
201 <   *
202 <   * This new and improved DumpWriter works in an even more efficient
203 <   * way:
204 <   *
205 <   *  1) Have 100 of your friend stand in a circle.
206 <   *  2) When you say go, have them start tossing 5-pound bags of
207 <   *     potatoes at you.
208 <   *  3) Once you've caught a friend's bag of potatoes,
209 <   *     toss them a spud to let them know they can toss another bag.
210 <   *
211 <   * How's THAT for documentation?
212 <   *
213 <   *********************************************************************/
200 >    Mat3x3d hmat;
201 >    hmat = s->getHmat();
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 <  int *potatoes;
209 <  int myPotato;
208 >    RealType chi = s->getChi();
209 >    RealType integralOfChiDt = s->getIntegralOfChiDt();
210 >    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
211 >    os << buffer;
212  
213 <  int nProc;
214 <  int j, which_node, done, which_atom, local_index, currentIndex;
215 <  double atomData[13];
216 <  int isDirectional;
217 <  char* atomTypeString;
218 <  char MPIatomTypeString[MINIBUFFERSIZE];
219 <  int nObjects;
225 <  int msgLen; // the length of message actually recieved at master nodes
226 < #endif //is_mpi
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 <  double q[4], ji[3];
229 <  DirectionalAtom* dAtom;
230 <  double pos[3], vel[3];
231 <  int nTotObjects;
232 <  StuntDouble* sd;
233 <  char* molName;
234 <  vector<StuntDouble*> integrableObjects;
235 <  vector<StuntDouble*>::iterator iter;
236 <  nTotObjects = entry_plug->getTotIntegrableObjects();
237 < #ifndef IS_MPI
238 <  
239 <  for(k = 0; k < outFile.size(); k++){
240 <    *outFile[k] << nTotObjects << "\n";
241 <
242 <    *outFile[k] << currentTime << ";\t"
243 <               << entry_plug->Hmat[0][0] << "\t"
244 <                     << entry_plug->Hmat[1][0] << "\t"
245 <                     << entry_plug->Hmat[2][0] << ";\t"
246 <              
247 <               << entry_plug->Hmat[0][1] << "\t"
248 <                     << entry_plug->Hmat[1][1] << "\t"
249 <                     << entry_plug->Hmat[2][1] << ";\t"
250 <
251 <                     << entry_plug->Hmat[0][2] << "\t"
252 <                     << entry_plug->Hmat[1][2] << "\t"
253 <                     << entry_plug->Hmat[2][2] << ";";
254 <
255 <    //write out additional parameters, such as chi and eta
256 <    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
221 >    os << "    </FrameData>\n";
222    }
258 –  
259 –  for( i=0; i< entry_plug->n_mol; i++ ){
223  
224 <    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
262 <    molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
263 <    
264 <    for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
265 <      sd = *iter;
266 <      sd->getPos(pos);
267 <      sd->getVel(vel);
224 >  void DumpWriter::writeFrame(std::ostream& os) {
225  
226 <      sprintf( tempBuffer,
227 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
228 <             sd->getType(),
272 <             pos[0],
273 <             pos[1],
274 <             pos[2],
275 <             vel[0],
276 <             vel[1],
277 <             vel[2]);
278 <      strcpy( writeLine, tempBuffer );
226 > #ifdef IS_MPI
227 >    MPI_Status istatus;
228 > #endif
229  
230 <      if( sd->isDirectional() ){
230 >    Molecule* mol;
231 >    StuntDouble* integrableObject;
232 >    SimInfo::MoleculeIterator mi;
233 >    Molecule::IntegrableObjectIterator ii;
234  
235 <        sd->getQ( q );
236 <        sd->getJ( ji );
235 > #ifndef IS_MPI
236 >    os << "  <Snapshot>\n";
237 >
238 >    writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
239  
240 <        sprintf( tempBuffer,
241 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
242 <               q[0],
243 <               q[1],
244 <               q[2],
245 <               q[3],
246 <                 ji[0],
247 <                 ji[1],
293 <                 ji[2]);
294 <        strcat( writeLine, tempBuffer );
240 >    os << "    <StuntDoubles>\n";
241 >    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
242 >
243 >      
244 >      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
245 >           integrableObject = mol->nextIntegrableObject(ii)) {  
246 >          os << prepareDumpLine(integrableObject);
247 >          
248        }
249 <      else
250 <        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
249 >    }    
250 >    os << "    </StuntDoubles>\n";
251      
252 <      for(k = 0; k < outFile.size(); k++)
300 <        *outFile[k] << writeLine;      
301 <    }
252 >    os << "  </Snapshot>\n";
253  
254 < }
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  
305 – #else // is_mpi
260  
261 <  /* code to find maximum tag value */
262 <  
263 <  int *tagub, flag, MAXTAG;
264 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
265 <  if (flag) {
266 <    MAXTAG = *tagub;
267 <  } else {
314 <    MAXTAG = 32767;
315 <  }  
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 <  int haveError;
269 >    if (worldRank == masterNode) {      
270 >      os << "  <Snapshot>\n";  
271 >      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
272 >      os << "    <StuntDoubles>\n";
273 >        
274 >      os << buffer;
275  
276 <  MPI_Status istatus;
277 <  int nCurObj;
278 <  int *MolToProcMap = mpiSim->getMolToProcMap();
276 >      int nProc;
277 >      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
278 >      for (int i = 1; i < nProc; ++i) {
279  
280 <  // write out header and node 0's coordinates
280 >        // receive the length of the string buffer that was
281 >        // prepared by processor i
282  
283 <  if( worldRank == 0 ){
284 <
285 <    // Node 0 needs a list of the magic potatoes for each processor;
286 <
287 <    nProc = mpiSim->getNProcessors();
288 <    potatoes = new int[nProc];
289 <
290 <    //write out the comment lines
291 <    for (i = 0; i < nProc; i++)
292 <      potatoes[i] = 0;
293 <    
294 <      for(k = 0; k < outFile.size(); k++){
295 <        *outFile[k] << nTotObjects << "\n";
296 <
297 <        *outFile[k] << currentTime << ";\t"
298 <                         << entry_plug->Hmat[0][0] << "\t"
299 <                         << entry_plug->Hmat[1][0] << "\t"
300 <                         << entry_plug->Hmat[2][0] << ";\t"
343 <
344 <                         << entry_plug->Hmat[0][1] << "\t"
345 <                         << entry_plug->Hmat[1][1] << "\t"
346 <                         << entry_plug->Hmat[2][1] << ";\t"
347 <
348 <                         << entry_plug->Hmat[0][2] << "\t"
349 <                         << entry_plug->Hmat[1][2] << "\t"
350 <                         << entry_plug->Hmat[2][2] << ";";
351 <  
352 <        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
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 <    currentIndex = 0;
303 > #endif // is_mpi
304  
305 <    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
358 <      
359 <      // Get the Node number which has this atom;
360 <      
361 <      which_node = MolToProcMap[i];
362 <      
363 <      if (which_node != 0) {
364 <        
365 <        if (potatoes[which_node] + 1 >= MAXTAG) {
366 <          // The potato was going to exceed the maximum value,
367 <          // so wrap this processor potato back to 0:        
305 >  }
306  
307 <          potatoes[which_node] = 0;          
308 <          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
309 <          
310 <        }
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 <        myPotato = potatoes[which_node];        
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 <        //recieve the number of integrableObject in current molecule
324 <        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
325 <                 myPotato, MPI_COMM_WORLD, &istatus);
326 <        myPotato++;
327 <        
328 <        for(int l = 0; l < nCurObj; l++){
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 (potatoes[which_node] + 2 >= MAXTAG) {
336 <            // The potato was going to exceed the maximum value,
337 <            // so wrap this processor potato back to 0:        
338 <
339 <            potatoes[which_node] = 0;          
340 <            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
389 <            
390 <          }
391 <
392 <          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
393 <          myPotato, MPI_COMM_WORLD, &istatus);
394 <
395 <          atomTypeString = MPIatomTypeString;
396 <
397 <          myPotato++;
398 <
399 <          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
400 <          myPotato++;
401 <
402 <          MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
403 <
404 <          if(msgLen  == 13)
405 <            isDirectional = 1;
406 <          else
407 <            isDirectional = 0;
408 <          
409 <          // If we've survived to here, format the line:
410 <            
411 <          if (!isDirectional) {
412 <        
413 <            sprintf( writeLine,
414 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
415 <                 atomTypeString,
416 <                 atomData[0],
417 <                 atomData[1],
418 <                 atomData[2],
419 <                 atomData[3],
420 <                 atomData[4],
421 <                 atomData[5]);
422 <        
423 <           strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
424 <        
425 <          }
426 <          else {
427 <        
428 <                sprintf( writeLine,
429 <                         "%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",
430 <                         atomTypeString,
431 <                         atomData[0],
432 <                         atomData[1],
433 <                         atomData[2],
434 <                         atomData[3],
435 <                         atomData[4],
436 <                         atomData[5],
437 <                         atomData[6],
438 <                         atomData[7],
439 <                         atomData[8],
440 <                         atomData[9],
441 <                         atomData[10],
442 <                         atomData[11],
443 <                         atomData[12]);
444 <            
445 <          }
446 <          
447 <          for(k = 0; k < outFile.size(); k++)
448 <            *outFile[k] << writeLine;            
449 <
450 <        }// end for(int l =0)
451 <        potatoes[which_node] = myPotato;
452 <
453 <      }
454 <      else {
455 <        
456 <        haveError = 0;
457 <        
458 <            local_index = indexArray[currentIndex].first;        
459 <
460 <        integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
461 <
462 <        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
463 <                sd = *iter;
464 <            atomTypeString = sd->getType();
465 <            
466 <            sd->getPos(pos);
467 <            sd->getVel(vel);          
468 <          
469 <            atomData[0] = pos[0];
470 <            atomData[1] = pos[1];
471 <            atomData[2] = pos[2];
472 <
473 <            atomData[3] = vel[0];
474 <            atomData[4] = vel[1];
475 <            atomData[5] = vel[2];
335 >    if (needForceVector_) {
336 >      type += "ft";
337 >      Vector3d frc;
338 >      Vector3d trq;
339 >      frc = integrableObject->getFrc();
340 >      trq = integrableObject->getTrq();
341                
342 <            isDirectional = 0;
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 <            if( sd->isDirectional() ){
352 >  void DumpWriter::writeDump() {
353 >    writeFrame(*dumpFile_);
354 >  }
355  
356 <              isDirectional = 1;
357 <                
483 <              sd->getQ( q );
484 <              sd->getJ( ji );
485 <
486 <              for (int j = 0; j < 6 ; j++)
487 <                atomData[j] = atomData[j];            
488 <              
489 <              atomData[6] = q[0];
490 <              atomData[7] = q[1];
491 <              atomData[8] = q[2];
492 <              atomData[9] = q[3];
493 <              
494 <              atomData[10] = ji[0];
495 <              atomData[11] = ji[1];
496 <              atomData[12] = ji[2];
497 <            }
498 <            
499 <            // If we've survived to here, format the line:
500 <            
501 <            if (!isDirectional) {
502 <        
503 <              sprintf( writeLine,
504 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
505 <                 atomTypeString,
506 <                 atomData[0],
507 <                 atomData[1],
508 <                 atomData[2],
509 <                 atomData[3],
510 <                 atomData[4],
511 <                 atomData[5]);
512 <        
513 <             strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
514 <        
515 <            }
516 <            else {
517 <        
518 <                sprintf( writeLine,
519 <                         "%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",
520 <                         atomTypeString,
521 <                         atomData[0],
522 <                         atomData[1],
523 <                         atomData[2],
524 <                         atomData[3],
525 <                         atomData[4],
526 <                         atomData[5],
527 <                         atomData[6],
528 <                         atomData[7],
529 <                         atomData[8],
530 <                         atomData[9],
531 <                         atomData[10],
532 <                         atomData[11],
533 <                         atomData[12]);
534 <              
535 <            }
536 <            
537 <            for(k = 0; k < outFile.size(); k++)
538 <              *outFile[k] << writeLine;
539 <            
540 <            
541 <        }//end for(iter = integrableObject.begin())
542 <        
543 <      currentIndex++;
544 <      }
545 <
546 <    }//end for(i = 0; i < mpiSim->getNmol())
356 >  void DumpWriter::writeEor() {
357 >    std::ostream* eorStream;
358      
359 <    for(k = 0; k < outFile.size(); k++)
360 <      outFile[k]->flush();
361 <    
551 <    sprintf( checkPointMsg,
552 <             "Sucessfully took a dump.\n");
553 <    
554 <    MPIcheckPoint();        
555 <    
556 <    delete[] potatoes;
557 <    
558 <  } else {
359 > #ifdef IS_MPI
360 >    if (worldRank == 0) {
361 > #endif // is_mpi
362  
363 <    // worldRank != 0, so I'm a remote node.  
363 >      eorStream = createOStream(eorFilename_);
364  
365 <    // Set my magic potato to 0:
365 > #ifdef IS_MPI
366 >    }
367 > #endif // is_mpi    
368  
369 <    myPotato = 0;
565 <    currentIndex = 0;
566 <    
567 <    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
568 <      
569 <      // Am I the node which has this integrableObject?
570 <      
571 <      if (MolToProcMap[i] == worldRank) {
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 <        if (myPotato + 1 >= MAXTAG) {
575 <          
576 <          // The potato was going to exceed the maximum value,
577 <          // so wrap this processor potato back to 0 (and block until
578 <          // node 0 says we can go:
579 <          
580 <          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
581 <          
582 <        }
380 >  }
381  
584 –          local_index = indexArray[currentIndex].first;        
585 –          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
586 –          
587 –          nCurObj = integrableObjects.size();
588 –                      
589 –          MPI_Send(&nCurObj, 1, MPI_INT, 0,
590 –                             myPotato, MPI_COMM_WORLD);
591 –          myPotato++;
382  
383 <          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
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 <            if (myPotato + 2 >= MAXTAG) {
596 <          
597 <              // The potato was going to exceed the maximum value,
598 <              // so wrap this processor potato back to 0 (and block until
599 <              // node 0 says we can go:
600 <          
601 <              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
602 <              
603 <            }
604 <            
605 <            sd = *iter;
606 <            
607 <            atomTypeString = sd->getType();
390 >      buffers.push_back(dumpFile_->rdbuf());
391  
392 <            sd->getPos(pos);
610 <            sd->getVel(vel);
392 >      eorStream = createOStream(eorFilename_);
393  
394 <            atomData[0] = pos[0];
395 <            atomData[1] = pos[1];
396 <            atomData[2] = pos[2];
615 <
616 <            atomData[3] = vel[0];
617 <            atomData[4] = vel[1];
618 <            atomData[5] = vel[2];
619 <              
620 <            isDirectional = 0;
621 <
622 <            if( sd->isDirectional() ){
623 <
624 <                isDirectional = 1;
625 <                
626 <                sd->getQ( q );
627 <                sd->getJ( ji );
628 <                
629 <                
630 <                atomData[6] = q[0];
631 <                atomData[7] = q[1];
632 <                atomData[8] = q[2];
633 <                atomData[9] = q[3];
634 <      
635 <                atomData[10] = ji[0];
636 <                atomData[11] = ji[1];
637 <                atomData[12] = ji[2];
638 <              }
639 <
640 <            
641 <            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
642 <
643 <            // null terminate the string before sending (just in case):
644 <            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
645 <
646 <            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
647 <                             myPotato, MPI_COMM_WORLD);
648 <            
649 <            myPotato++;
650 <            
651 <            if (isDirectional) {
652 <
653 <              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
654 <                       myPotato, MPI_COMM_WORLD);
655 <              
656 <            } else {
657 <
658 <              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
659 <                       myPotato, MPI_COMM_WORLD);
660 <            }
661 <
662 <            myPotato++;  
663 <
664 <          }
665 <
666 <          currentIndex++;    
667 <          
668 <        }
669 <      
670 <      }
671 <
672 <    sprintf( checkPointMsg,
673 <             "Sucessfully took a dump.\n");
674 <    MPIcheckPoint();                
675 <    
394 >      buffers.push_back(eorStream->rdbuf());
395 >        
396 > #ifdef IS_MPI
397      }
398 + #endif // is_mpi    
399  
400 +    TeeBuf tbuf(buffers.begin(), buffers.end());
401 +    std::ostream os(&tbuf);
402  
403 <  
680 < #endif // is_mpi
681 < }
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 +  }
415  
416 < // a couple of functions to let us escape the write loop
416 >  std::ostream* DumpWriter::createOStream(const std::string& filename) {
417  
418 < void dWrite::DieDieDie( void ){
418 >    std::ostream* newOStream;
419 > #ifdef HAVE_LIBZ
420 >    if (needCompression_) {
421 >      newOStream = new ogzstream(filename.c_str());
422 >    } else {
423 >      newOStream = new std::ofstream(filename.c_str());
424 >    }
425 > #else
426 >    newOStream = new std::ofstream(filename.c_str());
427 > #endif
428 >    //write out MetaData first
429 >    (*newOStream) << "<OOPSE version=4>" << std::endl;
430 >    (*newOStream) << "  <MetaData>" << std::endl;
431 >    (*newOStream) << info_->getRawMetaData();
432 >    (*newOStream) << "  </MetaData>" << std::endl;
433 >    return newOStream;
434 >  }
435  
436 <  MPI_Finalize();
690 <  exit (0);
691 < }
436 >  void DumpWriter::writeClosing(std::ostream& os) {
437  
438 < #endif //is_mpi
438 >    os << "</OOPSE>\n";
439 >    os.flush();
440 >  }
441 >
442 > }//end namespace oopse

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