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root/OpenMD/trunk/src/io/DumpWriter.cpp
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Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 221 by chrisfen, Tue Nov 23 22:48:31 2004 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

# Line 1 | Line 1
1 < #define _LARGEFILE_SOURCE64
2 < #define _FILE_OFFSET_BITS 64
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. Redistributions of source code must retain the above copyright
10 > *    notice, this list of conditions and the following disclaimer.
11 > *
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.
16 > *
17 > * This software is provided "AS IS," without a warranty of any
18 > * kind. All express or implied conditions, representations and
19 > * warranties, including any implied warranty of merchantability,
20 > * fitness for a particular purpose or non-infringement, are hereby
21 > * excluded.  The University of Notre Dame and its licensors shall not
22 > * be liable for any damages suffered by licensee as a result of
23 > * using, modifying or distributing the software or its
24 > * derivatives. In no event will the University of Notre Dame or its
25 > * licensors be liable for any lost revenue, profit or data, or for
26 > * direct, indirect, special, consequential, incidental or punitive
27 > * damages, however caused and regardless of the theory of liability,
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, 234107 (2008).          
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41 > */
42  
43 < #include <string.h>
5 < #include <iostream>
6 < #include <fstream>
7 < #include <algorithm>
8 < #include <utility>
43 > #include "config.h"
44  
45   #ifdef IS_MPI
46   #include <mpi.h>
47 < #include "brains/mpiSimulation.hpp"
47 > #endif
48 >
49 > #include "io/DumpWriter.hpp"
50 > #include "primitives/Molecule.hpp"
51 > #include "utils/simError.h"
52 > #include "io/basic_teebuf.hpp"
53 > #ifdef HAVE_ZLIB
54 > #include "io/gzstream.hpp"
55 > #endif
56 > #include "io/Globals.hpp"
57  
58 < namespace dWrite{
59 <  void DieDieDie( void );
60 < }
58 > #ifdef _MSC_VER
59 > #define isnan(x) _isnan((x))
60 > #define isinf(x) (!_finite(x) && !_isnan(x))
61 > #endif
62  
63 < using namespace dWrite;
64 < #endif //is_mpi
63 > using namespace std;
64 > namespace OpenMD {
65  
66 < #include "io/ReadWrite.hpp"
67 < #include "utils/simError.h"
66 >  DumpWriter::DumpWriter(SimInfo* info)
67 >    : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
68  
69 < DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
69 >    Globals* simParams = info->getSimParams();
70 >    needCompression_   = simParams->getCompressDumpFile();
71 >    needForceVector_   = simParams->getOutputForceVector();
72 >    needParticlePot_   = simParams->getOutputParticlePotential();
73 >    needFlucQ_         = simParams->getOutputFluctuatingCharges();
74 >    needElectricField_ = simParams->getOutputElectricField();
75  
76 <  entry_plug = the_entry_plug;
76 >    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
77 >      doSiteData_ = true;
78 >    } else {
79 >      doSiteData_ = false;
80 >    }
81  
82 +    createDumpFile_ = true;
83 + #ifdef HAVE_LIBZ
84 +    if (needCompression_) {
85 +      filename_ += ".gz";
86 +      eorFilename_ += ".gz";
87 +    }
88 + #endif
89 +    
90   #ifdef IS_MPI
91 <  if(worldRank == 0 ){
91 >
92 >    if (worldRank == 0) {
93   #endif // is_mpi
94 +        
95 +      dumpFile_ = createOStream(filename_);
96  
97 <    dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
97 >      if (!dumpFile_) {
98 >        sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
99 >                filename_.c_str());
100 >        painCave.isFatal = 1;
101 >        simError();
102 >      }
103  
104 <    if( !dumpFile ){
104 > #ifdef IS_MPI
105  
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();
106      }
107  
108 < #ifdef IS_MPI
108 > #endif // is_mpi
109 >
110    }
111  
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 }
112  
113 < DumpWriter::~DumpWriter( ){
113 >  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
114 >    : info_(info), filename_(filename){
115  
116 < #ifdef IS_MPI
117 <  if(worldRank == 0 ){
59 < #endif // is_mpi
116 >    Globals* simParams = info->getSimParams();
117 >    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
118  
119 <    dumpFile.close();
119 >    needCompression_   = simParams->getCompressDumpFile();
120 >    needForceVector_   = simParams->getOutputForceVector();
121 >    needParticlePot_   = simParams->getOutputParticlePotential();
122 >    needFlucQ_         = simParams->getOutputFluctuatingCharges();
123 >    needElectricField_ = simParams->getOutputElectricField();
124  
125 +    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
126 +      doSiteData_ = true;
127 +    } else {
128 +      doSiteData_ = false;
129 +    }
130 +
131 +    createDumpFile_ = true;
132 + #ifdef HAVE_LIBZ
133 +    if (needCompression_) {
134 +      filename_ += ".gz";
135 +      eorFilename_ += ".gz";
136 +    }
137 + #endif
138 +    
139   #ifdef IS_MPI
140 <  }
140 >
141 >    if (worldRank == 0) {
142   #endif // is_mpi
66 }
143  
144 +      
145 +      dumpFile_ = createOStream(filename_);
146 +
147 +      if (!dumpFile_) {
148 +        sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
149 +                filename_.c_str());
150 +        painCave.isFatal = 1;
151 +        simError();
152 +      }
153 +
154   #ifdef IS_MPI
155  
156 < /**
71 < * A hook function to load balancing
72 < */
156 >    }
157  
158 < 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 < }
158 > #endif // is_mpi
159  
160 < /**
87 < * Sorting the local index by global index
88 < */
89 <
90 < void DumpWriter::sortByGlobalIndex(){
91 <  Molecule* mols = entry_plug->molecules;  
92 <  indexArray.clear();
160 >  }
161    
162 <  for(int i = 0; i < entry_plug->n_mol;i++)
163 <    indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
164 <  
165 <  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
166 < }
162 >  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
163 >    : info_(info), filename_(filename){
164 >    
165 >    Globals* simParams = info->getSimParams();
166 >    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
167 >    
168 >    needCompression_   = simParams->getCompressDumpFile();
169 >    needForceVector_   = simParams->getOutputForceVector();
170 >    needParticlePot_   = simParams->getOutputParticlePotential();
171 >    needFlucQ_         = simParams->getOutputFluctuatingCharges();
172 >    needElectricField_ = simParams->getOutputElectricField();
173  
174 < #endif
174 >    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
175 >      doSiteData_ = true;
176 >    } else {
177 >      doSiteData_ = false;
178 >    }
179  
180 < void DumpWriter::writeDump(double currentTime){
181 <
182 <  ofstream finalOut;
183 <  vector<ofstream*> fileStreams;
106 <
107 < #ifdef IS_MPI
108 <  if(worldRank == 0 ){
109 < #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();
180 > #ifdef HAVE_LIBZ
181 >    if (needCompression_) {
182 >      filename_ += ".gz";
183 >      eorFilename_ += ".gz";
184      }
185 + #endif
186 +    
187   #ifdef IS_MPI
188 <  }
188 >    
189 >    if (worldRank == 0) {
190   #endif // is_mpi
191 +      
192 +      createDumpFile_ = writeDumpFile;
193 +      if (createDumpFile_) {
194 +        dumpFile_ = createOStream(filename_);
195 +      
196 +        if (!dumpFile_) {
197 +          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
198 +                  filename_.c_str());
199 +          painCave.isFatal = 1;
200 +          simError();
201 +        }
202 +      }
203 + #ifdef IS_MPI
204 +      
205 +    }
206  
207 <  fileStreams.push_back(&finalOut);
208 <  fileStreams.push_back(&dumpFile);
207 >    
208 > #endif // is_mpi
209 >    
210 >  }
211  
212 <  writeFrame(fileStreams, currentTime);
212 >  DumpWriter::~DumpWriter() {
213  
214   #ifdef IS_MPI
128  finalOut.close();
129 #endif
130        
131 }
215  
216 < void DumpWriter::writeFinal(double currentTime){
216 >    if (worldRank == 0) {
217 > #endif // is_mpi
218 >      if (createDumpFile_){
219 >        writeClosing(*dumpFile_);
220 >        delete dumpFile_;
221 >      }
222 > #ifdef IS_MPI
223  
224 <  ofstream finalOut;
136 <  vector<ofstream*> fileStreams;
224 >    }
225  
138 #ifdef IS_MPI
139  if(worldRank == 0 ){
226   #endif // is_mpi
227  
228 <    finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
228 >  }
229  
230 <    if( !finalOut ){
230 >  void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
231 >
232 >    char buffer[1024];
233 >
234 >    os << "    <FrameData>\n";
235 >
236 >    RealType currentTime = s->getTime();
237 >
238 >    if (isinf(currentTime) || isnan(currentTime)) {      
239        sprintf( painCave.errMsg,
240 <               "Could not open \"%s\" for final dump output.\n",
147 <               entry_plug->finalName.c_str() );
240 >               "DumpWriter detected a numerical error writing the time");      
241        painCave.isFatal = 1;
242        simError();
243      }
244 +    
245 +    sprintf(buffer, "        Time: %.10g\n", currentTime);
246 +    os << buffer;
247  
248 < #ifdef IS_MPI
249 <  }
154 < #endif // is_mpi
155 <  
156 <  fileStreams.push_back(&finalOut);  
157 <  writeFrame(fileStreams, currentTime);
248 >    Mat3x3d hmat;
249 >    hmat = s->getHmat();
250  
251 < #ifdef IS_MPI
252 <  finalOut.close();
253 < #endif
254 <  
255 < }
251 >    for (unsigned int i = 0; i < 3; i++) {
252 >      for (unsigned int j = 0; j < 3; j++) {
253 >        if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {      
254 >          sprintf( painCave.errMsg,
255 >                   "DumpWriter detected a numerical error writing the box");
256 >          painCave.isFatal = 1;
257 >          simError();
258 >        }        
259 >      }
260 >    }
261 >    
262 >    sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
263 >            hmat(0, 0), hmat(1, 0), hmat(2, 0),
264 >            hmat(0, 1), hmat(1, 1), hmat(2, 1),
265 >            hmat(0, 2), hmat(1, 2), hmat(2, 2));
266 >    os << buffer;
267  
268 < void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
268 >    pair<RealType, RealType> thermostat = s->getThermostat();
269  
270 <  const int BUFFERSIZE = 2000;
271 <  const int MINIBUFFERSIZE = 100;
270 >    if (isinf(thermostat.first)  || isnan(thermostat.first) ||
271 >        isinf(thermostat.second) || isnan(thermostat.second)) {      
272 >      sprintf( painCave.errMsg,
273 >               "DumpWriter detected a numerical error writing the thermostat");
274 >      painCave.isFatal = 1;
275 >      simError();
276 >    }
277 >    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first,
278 >            thermostat.second);
279 >    os << buffer;
280  
281 <  char tempBuffer[BUFFERSIZE];  
282 <  char writeLine[BUFFERSIZE];
281 >    Mat3x3d eta;
282 >    eta = s->getBarostat();
283  
284 <  int i;
285 <  unsigned int k;
284 >    for (unsigned int i = 0; i < 3; i++) {
285 >      for (unsigned int j = 0; j < 3; j++) {
286 >        if (isinf(eta(i,j)) || isnan(eta(i,j))) {      
287 >          sprintf( painCave.errMsg,
288 >                   "DumpWriter detected a numerical error writing the barostat");
289 >          painCave.isFatal = 1;
290 >          simError();
291 >        }        
292 >      }
293 >    }
294  
295 < #ifdef IS_MPI
296 <  
297 <  /*********************************************************************
298 <   * Documentation?  You want DOCUMENTATION?
299 <   *
181 <   * Why all the potatoes below?  
182 <   *
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 <   *********************************************************************/
295 >    sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
296 >            eta(0, 0), eta(1, 0), eta(2, 0),
297 >            eta(0, 1), eta(1, 1), eta(2, 1),
298 >            eta(0, 2), eta(1, 2), eta(2, 2));
299 >    os << buffer;
300  
301 <  int *potatoes;
216 <  int myPotato;
217 <
218 <  int nProc;
219 <  int j, which_node, done, which_atom, local_index, currentIndex;
220 <  double atomData[13];
221 <  int isDirectional;
222 <  char* atomTypeString;
223 <  char MPIatomTypeString[MINIBUFFERSIZE];
224 <  int nObjects;
225 <  int msgLen; // the length of message actually recieved at master nodes
226 < #endif //is_mpi
227 <
228 <  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;
301 >    os << "    </FrameData>\n";
302    }
258  
259  for( i=0; i< entry_plug->n_mol; i++ ){
303  
304 <    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);
304 >  void DumpWriter::writeFrame(std::ostream& os) {
305  
306 <      sprintf( tempBuffer,
307 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
308 <             sd->getType(),
272 <             pos[0],
273 <             pos[1],
274 <             pos[2],
275 <             vel[0],
276 <             vel[1],
277 <             vel[2]);
278 <      strcpy( writeLine, tempBuffer );
306 > #ifdef IS_MPI
307 >    MPI::Status istatus;
308 > #endif
309  
310 <      if( sd->isDirectional() ){
310 >    Molecule* mol;
311 >    StuntDouble* sd;
312 >    SimInfo::MoleculeIterator mi;
313 >    Molecule::IntegrableObjectIterator ii;
314 >    RigidBody::AtomIterator ai;
315  
316 <        sd->getQ( q );
317 <        sd->getJ( ji );
316 > #ifndef IS_MPI
317 >    os << "  <Snapshot>\n";
318 >
319 >    writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
320  
321 <        sprintf( tempBuffer,
322 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
323 <               q[0],
324 <               q[1],
325 <               q[2],
326 <               q[3],
327 <                 ji[0],
328 <                 ji[1],
293 <                 ji[2]);
294 <        strcat( writeLine, tempBuffer );
321 >    os << "    <StuntDoubles>\n";
322 >    for (mol = info_->beginMolecule(mi); mol != NULL;
323 >         mol = info_->nextMolecule(mi)) {
324 >      
325 >      for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
326 >           sd = mol->nextIntegrableObject(ii)) {        
327 >          os << prepareDumpLine(sd);
328 >          
329        }
330 <      else
331 <        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298 <    
299 <      for(k = 0; k < outFile.size(); k++)
300 <        *outFile[k] << writeLine;      
301 <    }
302 <    
303 <  }
330 >    }    
331 >    os << "    </StuntDoubles>\n";
332  
333 < #else // is_mpi
333 >    if (doSiteData_) {
334 >      os << "    <SiteData>\n";
335 >      for (mol = info_->beginMolecule(mi); mol != NULL;
336 >           mol = info_->nextMolecule(mi)) {
337 >              
338 >        for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
339 >           sd = mol->nextIntegrableObject(ii)) {        
340  
341 <  /* code to find maximum tag value */
342 <  
343 <  int *tagub, flag, MAXTAG;
310 <  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
311 <  if (flag) {
312 <    MAXTAG = *tagub;
313 <  } else {
314 <    MAXTAG = 32767;
315 <  }  
341 >          int ioIndex = sd->getGlobalIntegrableObjectIndex();
342 >          // do one for the IO itself
343 >          os << prepareSiteLine(sd, ioIndex, 0);
344  
345 <  int haveError;
345 >          if (sd->isRigidBody()) {
346 >            
347 >            RigidBody* rb = static_cast<RigidBody*>(sd);
348 >            int siteIndex = 0;
349 >            for (Atom* atom = rb->beginAtom(ai); atom != NULL;  
350 >                 atom = rb->nextAtom(ai)) {                                            
351 >              os << prepareSiteLine(atom, ioIndex, siteIndex);
352 >              siteIndex++;
353 >            }
354 >          }
355 >        }
356 >      }    
357 >      os << "    </SiteData>\n";
358 >    }
359 >    os << "  </Snapshot>\n";
360  
361 <  MPI_Status istatus;
362 <  int nCurObj;
321 <  int *MolToProcMap = mpiSim->getMolToProcMap();
361 >    os.flush();
362 > #else
363  
364 <  // write out header and node 0's coordinates
364 >    const int masterNode = 0;
365 >    int worldRank = MPI::COMM_WORLD.Get_rank();
366 >    int nProc = MPI::COMM_WORLD.Get_size();
367  
368 <  if( worldRank == 0 ){
368 >    if (worldRank == masterNode) {      
369 >      os << "  <Snapshot>\n";  
370 >      writeFrameProperties(os,
371 >                           info_->getSnapshotManager()->getCurrentSnapshot());
372 >      os << "    <StuntDoubles>\n";
373 >    }
374  
375 <    // Node 0 needs a list of the magic potatoes for each processor;
376 <
377 <    nProc = mpiSim->getNProcessors();
378 <    potatoes = new int[nProc];
379 <
380 <    //write out the comment lines
381 <    for (i = 0; i < nProc; i++)
382 <      potatoes[i] = 0;
335 <    
336 <    for(k = 0; k < outFile.size(); k++){
337 <      *outFile[k] << nTotObjects << "\n";
338 <      
339 <      *outFile[k] << currentTime << ";\t"
340 <                  << entry_plug->Hmat[0][0] << "\t"
341 <                  << entry_plug->Hmat[1][0] << "\t"
342 <                  << 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()
353 <                  << endl;
375 >    //every node prepares the dump lines for integrable objects belong to itself
376 >    std::string buffer;
377 >    for (mol = info_->beginMolecule(mi); mol != NULL;
378 >         mol = info_->nextMolecule(mi)) {
379 >      for (sd = mol->beginIntegrableObject(ii); sd != NULL;
380 >           sd = mol->nextIntegrableObject(ii)) {        
381 >        buffer += prepareDumpLine(sd);
382 >      }
383      }
384      
385 <    currentIndex = 0;
386 <    
358 <    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
385 >    if (worldRank == masterNode) {      
386 >      os << buffer;
387        
388 <      // Get the Node number which has this atom;
389 <      
390 <      which_node = MolToProcMap[i];
363 <      
364 <      if (which_node != 0) {
365 <        
366 <        if (potatoes[which_node] + 1 >= MAXTAG) {
367 <          // The potato was going to exceed the maximum value,
368 <          // so wrap this processor potato back to 0:        
388 >      for (int i = 1; i < nProc; ++i) {
389 >        // tell processor i to start sending us data:
390 >        MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
391  
392 <          potatoes[which_node] = 0;          
393 <          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
394 <                   MPI_COMM_WORLD);
395 <          
392 >        // receive the length of the string buffer that was
393 >        // prepared by processor i:        
394 >        int recvLength;
395 >        MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
396 >                             istatus);
397 >
398 >        // create a buffer to receive the data
399 >        char* recvBuffer = new char[recvLength];
400 >        if (recvBuffer == NULL) {
401 >        } else {
402 >          // receive the data:
403 >          MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
404 >                               MPI::ANY_TAG, istatus);
405 >          // send it to the file:
406 >          os << recvBuffer;
407 >          // get rid of the receive buffer:
408 >          delete [] recvBuffer;
409          }
410 +      }
411 +    } else {
412 +      int sendBufferLength = buffer.size() + 1;
413 +      int myturn = 0;
414 +      for (int i = 1; i < nProc; ++i){
415 +        // wait for the master node to call our number:
416 +        MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
417 +        if (myturn == worldRank){
418 +          // send the length of our buffer:
419 +          MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
420  
421 <        myPotato = potatoes[which_node];        
421 >          // send our buffer:
422 >          MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
423 >                               MPI::CHAR, masterNode, 0);
424  
425 <        //recieve the number of integrableObject in current molecule
426 <        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
427 <                 myPotato, MPI_COMM_WORLD, &istatus);
428 <        myPotato++;
429 <        
430 <        for(int l = 0; l < nCurObj; l++){
431 <
385 <          if (potatoes[which_node] + 2 >= MAXTAG) {
386 <            // The potato was going to exceed the maximum value,
387 <            // so wrap this processor potato back to 0:        
388 <
389 <            potatoes[which_node] = 0;          
390 <            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
391 <            
392 <          }
393 <
394 <          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
395 <          myPotato, MPI_COMM_WORLD, &istatus);
396 <
397 <          atomTypeString = MPIatomTypeString;
398 <
399 <          myPotato++;
400 <
401 <          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
402 <          myPotato++;
403 <
404 <          MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
405 <
406 <          if(msgLen  == 13)
407 <            isDirectional = 1;
408 <          else
409 <            isDirectional = 0;
410 <          
411 <          // If we've survived to here, format the line:
412 <            
413 <          if (!isDirectional) {
414 <        
415 <            sprintf( writeLine,
416 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
417 <                 atomTypeString,
418 <                 atomData[0],
419 <                 atomData[1],
420 <                 atomData[2],
421 <                 atomData[3],
422 <                 atomData[4],
423 <                 atomData[5]);
424 <        
425 <           strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
426 <        
427 <          }
428 <          else {
429 <        
430 <                sprintf( writeLine,
431 <                         "%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",
432 <                         atomTypeString,
433 <                         atomData[0],
434 <                         atomData[1],
435 <                         atomData[2],
436 <                         atomData[3],
437 <                         atomData[4],
438 <                         atomData[5],
439 <                         atomData[6],
440 <                         atomData[7],
441 <                         atomData[8],
442 <                         atomData[9],
443 <                         atomData[10],
444 <                         atomData[11],
445 <                         atomData[12]);
446 <            
447 <          }
448 <          
449 <          for(k = 0; k < outFile.size(); k++)
450 <            *outFile[k] << writeLine;            
425 >        }
426 >      }
427 >    }
428 >    
429 >    if (worldRank == masterNode) {      
430 >      os << "    </StuntDoubles>\n";
431 >    }
432  
433 <        }// end for(int l =0)
434 <        potatoes[which_node] = myPotato;
435 <        
433 >    if (doSiteData_) {
434 >      if (worldRank == masterNode) {
435 >        os << "    <SiteData>\n";
436        }
437 <      else {
438 <        
439 <        haveError = 0;
440 <        
441 <            local_index = indexArray[currentIndex].first;        
442 <            
443 <            integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
437 >      buffer.clear();
438 >      for (mol = info_->beginMolecule(mi); mol != NULL;
439 >           mol = info_->nextMolecule(mi)) {
440 >              
441 >        for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
442 >             sd = mol->nextIntegrableObject(ii)) {      
443 >          
444 >          int ioIndex = sd->getGlobalIntegrableObjectIndex();
445 >          // do one for the IO itself
446 >          buffer += prepareSiteLine(sd, ioIndex, 0);
447  
448 <        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
465 <                sd = *iter;
466 <            atomTypeString = sd->getType();
467 <            
468 <            sd->getPos(pos);
469 <            sd->getVel(vel);          
470 <          
471 <            atomData[0] = pos[0];
472 <            atomData[1] = pos[1];
473 <            atomData[2] = pos[2];
474 <
475 <            atomData[3] = vel[0];
476 <            atomData[4] = vel[1];
477 <            atomData[5] = vel[2];
478 <              
479 <            isDirectional = 0;
480 <
481 <            if( sd->isDirectional() ){
482 <
483 <              isDirectional = 1;
484 <                
485 <              sd->getQ( q );
486 <              sd->getJ( ji );
487 <
488 <              for (int j = 0; j < 6 ; j++)
489 <                atomData[j] = atomData[j];            
490 <              
491 <              atomData[6] = q[0];
492 <              atomData[7] = q[1];
493 <              atomData[8] = q[2];
494 <              atomData[9] = q[3];
495 <              
496 <              atomData[10] = ji[0];
497 <              atomData[11] = ji[1];
498 <              atomData[12] = ji[2];
499 <            }
448 >          if (sd->isRigidBody()) {
449              
450 <            // If we've survived to here, format the line:
451 <            
452 <            if (!isDirectional) {
453 <        
454 <              sprintf( writeLine,
455 <                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
507 <                 atomTypeString,
508 <                 atomData[0],
509 <                 atomData[1],
510 <                 atomData[2],
511 <                 atomData[3],
512 <                 atomData[4],
513 <                 atomData[5]);
514 <        
515 <             strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
516 <        
517 <            }
518 <            else {
519 <        
520 <                sprintf( writeLine,
521 <                         "%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",
522 <                         atomTypeString,
523 <                         atomData[0],
524 <                         atomData[1],
525 <                         atomData[2],
526 <                         atomData[3],
527 <                         atomData[4],
528 <                         atomData[5],
529 <                         atomData[6],
530 <                         atomData[7],
531 <                         atomData[8],
532 <                         atomData[9],
533 <                         atomData[10],
534 <                         atomData[11],
535 <                         atomData[12]);
536 <              
450 >            RigidBody* rb = static_cast<RigidBody*>(sd);
451 >            int siteIndex = 0;
452 >            for (Atom* atom = rb->beginAtom(ai); atom != NULL;  
453 >                 atom = rb->nextAtom(ai)) {                                            
454 >              buffer += prepareSiteLine(atom, ioIndex, siteIndex);
455 >              siteIndex++;
456              }
457 <            
458 <            for(k = 0; k < outFile.size(); k++)
540 <              *outFile[k] << writeLine;
541 <            
542 <            
543 <        }//end for(iter = integrableObject.begin())
544 <        
545 <      currentIndex++;
457 >          }
458 >        }
459        }
460  
461 <    }//end for(i = 0; i < mpiSim->getNmol())
461 >      if (worldRank == masterNode) {    
462 >        os << buffer;
463 >        
464 >        for (int i = 1; i < nProc; ++i) {
465 >          
466 >          // tell processor i to start sending us data:
467 >          MPI::COMM_WORLD.Bcast(&i, 1, MPI::INT, masterNode);
468 >          
469 >          // receive the length of the string buffer that was
470 >          // prepared by processor i:        
471 >          int recvLength;
472 >          MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, MPI::ANY_TAG,
473 >                               istatus);
474 >          
475 >          // create a buffer to receive the data
476 >          char* recvBuffer = new char[recvLength];
477 >          if (recvBuffer == NULL) {
478 >          } else {
479 >            // receive the data:
480 >            MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i,
481 >                                 MPI::ANY_TAG, istatus);
482 >            // send it to the file:
483 >            os << recvBuffer;
484 >            // get rid of the receive buffer:
485 >            delete [] recvBuffer;
486 >          }
487 >        }      
488 >      } else {
489 >        int sendBufferLength = buffer.size() + 1;
490 >        int myturn = 0;
491 >        for (int i = 1; i < nProc; ++i){
492 >          // wait for the master node to call our number:
493 >          MPI::COMM_WORLD.Bcast(&myturn, 1, MPI::INT, masterNode);
494 >          if (myturn == worldRank){
495 >            // send the length of our buffer:
496 >            MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
497 >            // send our buffer:
498 >            MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
499 >                                 MPI::CHAR, masterNode, 0);
500 >          }
501 >        }
502 >      }
503 >      
504 >      if (worldRank == masterNode) {    
505 >        os << "    </SiteData>\n";
506 >      }
507 >    }
508      
509 <    for(k = 0; k < outFile.size(); k++)
510 <      outFile[k]->flush();
509 >    if (worldRank == masterNode) {
510 >      os << "  </Snapshot>\n";
511 >      os.flush();
512 >    }
513      
514 <    sprintf( checkPointMsg,
554 <             "Sucessfully took a dump.\n");
514 > #endif // is_mpi
515      
516 <    MPIcheckPoint();        
557 <    
558 <    delete[] potatoes;
559 <    
560 <  } else {
516 >  }
517  
518 <    // worldRank != 0, so I'm a remote node.  
518 >  std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
519 >        
520 >    int index = sd->getGlobalIntegrableObjectIndex();
521 >    std::string type("pv");
522 >    std::string line;
523 >    char tempBuffer[4096];
524  
525 <    // Set my magic potato to 0:
525 >    Vector3d pos;
526 >    Vector3d vel;
527 >    pos = sd->getPos();
528  
529 <    myPotato = 0;
530 <    currentIndex = 0;
531 <    
532 <    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
533 <      
534 <      // Am I the node which has this integrableObject?
535 <      
536 <      if (MolToProcMap[i] == worldRank) {
529 >    if (isinf(pos[0]) || isnan(pos[0]) ||
530 >        isinf(pos[1]) || isnan(pos[1]) ||
531 >        isinf(pos[2]) || isnan(pos[2]) ) {      
532 >      sprintf( painCave.errMsg,
533 >               "DumpWriter detected a numerical error writing the position"
534 >               " for object %d", index);      
535 >      painCave.isFatal = 1;
536 >      simError();
537 >    }
538  
539 +    vel = sd->getVel();        
540  
541 <        if (myPotato + 1 >= MAXTAG) {
542 <          
543 <          // The potato was going to exceed the maximum value,
544 <          // so wrap this processor potato back to 0 (and block until
545 <          // node 0 says we can go:
546 <          
547 <          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
548 <          
549 <        }
541 >    if (isinf(vel[0]) || isnan(vel[0]) ||
542 >        isinf(vel[1]) || isnan(vel[1]) ||
543 >        isinf(vel[2]) || isnan(vel[2]) ) {      
544 >      sprintf( painCave.errMsg,
545 >               "DumpWriter detected a numerical error writing the velocity"
546 >               " for object %d", index);      
547 >      painCave.isFatal = 1;
548 >      simError();
549 >    }
550  
551 <          local_index = indexArray[currentIndex].first;        
552 <          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
553 <          
554 <          nCurObj = integrableObjects.size();
590 <                      
591 <          MPI_Send(&nCurObj, 1, MPI_INT, 0,
592 <                   myPotato, MPI_COMM_WORLD);
593 <          myPotato++;
551 >    sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
552 >            pos[0], pos[1], pos[2],
553 >            vel[0], vel[1], vel[2]);                    
554 >    line += tempBuffer;
555  
556 <          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
556 >    if (sd->isDirectional()) {
557 >      type += "qj";
558 >      Quat4d q;
559 >      Vector3d ji;
560 >      q = sd->getQ();
561  
562 <            if (myPotato + 2 >= MAXTAG) {
563 <          
564 <              // The potato was going to exceed the maximum value,
565 <              // so wrap this processor potato back to 0 (and block until
566 <              // node 0 says we can go:
567 <          
568 <              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
569 <              
570 <            }
571 <            
607 <            sd = *iter;
608 <            
609 <            atomTypeString = sd->getType();
562 >      if (isinf(q[0]) || isnan(q[0]) ||
563 >          isinf(q[1]) || isnan(q[1]) ||
564 >          isinf(q[2]) || isnan(q[2]) ||
565 >          isinf(q[3]) || isnan(q[3]) ) {      
566 >        sprintf( painCave.errMsg,
567 >                 "DumpWriter detected a numerical error writing the quaternion"
568 >                 " for object %d", index);      
569 >        painCave.isFatal = 1;
570 >        simError();
571 >      }
572  
573 <            sd->getPos(pos);
612 <            sd->getVel(vel);
573 >      ji = sd->getJ();
574  
575 <            atomData[0] = pos[0];
576 <            atomData[1] = pos[1];
577 <            atomData[2] = pos[2];
575 >      if (isinf(ji[0]) || isnan(ji[0]) ||
576 >          isinf(ji[1]) || isnan(ji[1]) ||
577 >          isinf(ji[2]) || isnan(ji[2]) ) {      
578 >        sprintf( painCave.errMsg,
579 >                 "DumpWriter detected a numerical error writing the angular"
580 >                 " momentum for object %d", index);      
581 >        painCave.isFatal = 1;
582 >        simError();
583 >      }
584  
585 <            atomData[3] = vel[0];
586 <            atomData[4] = vel[1];
587 <            atomData[5] = vel[2];
588 <              
589 <            isDirectional = 0;
585 >      sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
586 >              q[0], q[1], q[2], q[3],
587 >              ji[0], ji[1], ji[2]);
588 >      line += tempBuffer;
589 >    }
590  
591 <            if( sd->isDirectional() ){
592 <
593 <                isDirectional = 1;
594 <                
595 <                sd->getQ( q );
596 <                sd->getJ( ji );
597 <                
598 <                
599 <                atomData[6] = q[0];
600 <                atomData[7] = q[1];
601 <                atomData[8] = q[2];
602 <                atomData[9] = q[3];
591 >    if (needForceVector_) {
592 >      type += "f";
593 >      Vector3d frc = sd->getFrc();
594 >      if (isinf(frc[0]) || isnan(frc[0]) ||
595 >          isinf(frc[1]) || isnan(frc[1]) ||
596 >          isinf(frc[2]) || isnan(frc[2]) ) {      
597 >        sprintf( painCave.errMsg,
598 >                 "DumpWriter detected a numerical error writing the force"
599 >                 " for object %d", index);      
600 >        painCave.isFatal = 1;
601 >        simError();
602 >      }
603 >      sprintf(tempBuffer, " %13e %13e %13e",
604 >              frc[0], frc[1], frc[2]);
605 >      line += tempBuffer;
606        
607 <                atomData[10] = ji[0];
608 <                atomData[11] = ji[1];
609 <                atomData[12] = ji[2];
610 <              }
607 >      if (sd->isDirectional()) {
608 >        type += "t";
609 >        Vector3d trq = sd->getTrq();        
610 >        if (isinf(trq[0]) || isnan(trq[0]) ||
611 >            isinf(trq[1]) || isnan(trq[1]) ||
612 >            isinf(trq[2]) || isnan(trq[2]) ) {      
613 >          sprintf( painCave.errMsg,
614 >                   "DumpWriter detected a numerical error writing the torque"
615 >                   " for object %d", index);      
616 >          painCave.isFatal = 1;
617 >          simError();
618 >        }        
619 >        sprintf(tempBuffer, " %13e %13e %13e",
620 >                trq[0], trq[1], trq[2]);
621 >        line += tempBuffer;
622 >      }      
623 >    }
624  
625 <            
626 <            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
625 >    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
626 >    return std::string(tempBuffer);
627 >  }
628  
629 <            // null terminate the string before sending (just in case):
630 <            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
629 >  std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
630 >    int storageLayout = info_->getSnapshotManager()->getStorageLayout();
631  
632 <            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
633 <                             myPotato, MPI_COMM_WORLD);
634 <            
635 <            myPotato++;
652 <            
653 <            if (isDirectional) {
632 >    std::string id;
633 >    std::string type;
634 >    std::string line;
635 >    char tempBuffer[4096];
636  
637 <              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
638 <                       myPotato, MPI_COMM_WORLD);
637 >    if (sd->isRigidBody()) {
638 >      sprintf(tempBuffer, "%10d           ", ioIndex);
639 >      id = std::string(tempBuffer);
640 >    } else {
641 >      sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
642 >      id = std::string(tempBuffer);
643 >    }
644                
645 <            } else {
645 >    if (needFlucQ_) {
646 >      if (storageLayout & DataStorage::dslFlucQPosition) {
647 >        type += "c";
648 >        RealType fqPos = sd->getFlucQPos();
649 >        if (isinf(fqPos) || isnan(fqPos) ) {      
650 >          sprintf( painCave.errMsg,
651 >                   "DumpWriter detected a numerical error writing the"
652 >                   " fluctuating charge for object %s", id.c_str());      
653 >          painCave.isFatal = 1;
654 >          simError();
655 >        }
656 >        sprintf(tempBuffer, " %13e ", fqPos);
657 >        line += tempBuffer;
658 >      }
659  
660 <              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
661 <                       myPotato, MPI_COMM_WORLD);
662 <            }
660 >      if (storageLayout & DataStorage::dslFlucQVelocity) {
661 >        type += "w";    
662 >        RealType fqVel = sd->getFlucQVel();
663 >        if (isinf(fqVel) || isnan(fqVel) ) {      
664 >          sprintf( painCave.errMsg,
665 >                   "DumpWriter detected a numerical error writing the"
666 >                   " fluctuating charge velocity for object %s", id.c_str());      
667 >          painCave.isFatal = 1;
668 >          simError();
669 >        }
670 >        sprintf(tempBuffer, " %13e ", fqVel);
671 >        line += tempBuffer;
672 >      }
673  
674 <            myPotato++;  
675 <
674 >      if (needForceVector_) {
675 >        if (storageLayout & DataStorage::dslFlucQForce) {          
676 >          type += "g";
677 >          RealType fqFrc = sd->getFlucQFrc();        
678 >          if (isinf(fqFrc) || isnan(fqFrc) ) {      
679 >            sprintf( painCave.errMsg,
680 >                     "DumpWriter detected a numerical error writing the"
681 >                     " fluctuating charge force for object %s", id.c_str());      
682 >            painCave.isFatal = 1;
683 >            simError();
684            }
685 +          sprintf(tempBuffer, " %13e ", fqFrc);        
686 +          line += tempBuffer;
687 +        }
688 +      }
689 +    }
690 +    
691 +    if (needElectricField_) {
692 +      if (storageLayout & DataStorage::dslElectricField) {
693 +        type += "e";
694 +        Vector3d eField= sd->getElectricField();
695 +        if (isinf(eField[0]) || isnan(eField[0]) ||
696 +            isinf(eField[1]) || isnan(eField[1]) ||
697 +            isinf(eField[2]) || isnan(eField[2]) ) {      
698 +          sprintf( painCave.errMsg,
699 +                   "DumpWriter detected a numerical error writing the electric"
700 +                   " field for object %s", id.c_str());      
701 +          painCave.isFatal = 1;
702 +          simError();
703 +        }
704 +        sprintf(tempBuffer, " %13e %13e %13e",
705 +                eField[0], eField[1], eField[2]);
706 +        line += tempBuffer;
707 +      }
708 +    }
709  
710 <          currentIndex++;    
711 <          
710 >
711 >    if (needParticlePot_) {
712 >      if (storageLayout & DataStorage::dslParticlePot) {
713 >        type += "u";
714 >        RealType particlePot = sd->getParticlePot();
715 >        if (isinf(particlePot) || isnan(particlePot)) {      
716 >          sprintf( painCave.errMsg,
717 >                   "DumpWriter detected a numerical error writing the particle "
718 >                   " potential for object %s", id.c_str());      
719 >          painCave.isFatal = 1;
720 >          simError();
721          }
722 <      
722 >        sprintf(tempBuffer, " %13e", particlePot);
723 >        line += tempBuffer;
724        }
725 +    }
726 +  
727 +    sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
728 +    return std::string(tempBuffer);
729 +  }
730  
731 <    sprintf( checkPointMsg,
732 <             "Successfully took a dump.\n");
733 <    MPIcheckPoint();                
731 >  void DumpWriter::writeDump() {
732 >    writeFrame(*dumpFile_);
733 >  }
734 >
735 >  void DumpWriter::writeEor() {
736 >    std::ostream* eorStream;
737      
738 + #ifdef IS_MPI
739 +    if (worldRank == 0) {
740 + #endif // is_mpi
741 +      
742 +      eorStream = createOStream(eorFilename_);
743 +
744 + #ifdef IS_MPI
745 +    }
746 + #endif
747 +    
748 +    writeFrame(*eorStream);
749 +      
750 + #ifdef IS_MPI
751 +    if (worldRank == 0) {
752 + #endif
753 +      
754 +      writeClosing(*eorStream);
755 +      delete eorStream;
756 +      
757 + #ifdef IS_MPI
758 +    }
759 + #endif // is_mpi  
760 +
761    }
762 <  
762 >
763 >
764 >  void DumpWriter::writeDumpAndEor() {
765 >    std::vector<std::streambuf*> buffers;
766 >    std::ostream* eorStream;
767 > #ifdef IS_MPI
768 >    if (worldRank == 0) {
769   #endif // is_mpi
681 }
770  
771 +      buffers.push_back(dumpFile_->rdbuf());
772 +
773 +      eorStream = createOStream(eorFilename_);
774 +
775 +      buffers.push_back(eorStream->rdbuf());
776 +        
777   #ifdef IS_MPI
778 +    }
779 + #endif // is_mpi    
780  
781 < // a couple of functions to let us escape the write loop
781 >    TeeBuf tbuf(buffers.begin(), buffers.end());
782 >    std::ostream os(&tbuf);
783  
784 < void dWrite::DieDieDie( void ){
784 >    writeFrame(os);
785  
786 <  MPI_Finalize();
787 <  exit (0);
788 < }
786 > #ifdef IS_MPI
787 >    if (worldRank == 0) {
788 > #endif // is_mpi
789 >      writeClosing(*eorStream);
790 >      delete eorStream;
791 > #ifdef IS_MPI
792 >    }
793 > #endif // is_mpi  
794 >    
795 >  }
796  
797 < #endif //is_mpi
797 >  std::ostream* DumpWriter::createOStream(const std::string& filename) {
798 >
799 >    std::ostream* newOStream;
800 > #ifdef HAVE_ZLIB
801 >    if (needCompression_) {
802 >      newOStream = new ogzstream(filename.c_str());
803 >    } else {
804 >      newOStream = new std::ofstream(filename.c_str());
805 >    }
806 > #else
807 >    newOStream = new std::ofstream(filename.c_str());
808 > #endif
809 >    //write out MetaData first
810 >    (*newOStream) << "<OpenMD version=2>" << std::endl;
811 >    (*newOStream) << "  <MetaData>" << std::endl;
812 >    (*newOStream) << info_->getRawMetaData();
813 >    (*newOStream) << "  </MetaData>" << std::endl;
814 >    return newOStream;
815 >  }
816 >
817 >  void DumpWriter::writeClosing(std::ostream& os) {
818 >
819 >    os << "</OpenMD>\n";
820 >    os.flush();
821 >  }
822 >
823 > }//end namespace OpenMD

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 221 by chrisfen, Tue Nov 23 22:48:31 2004 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

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