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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 324 by tim, Sun Feb 13 19:10:25 2005 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  
4 – #include <string.h>
5 – #include <iostream>
6 – #include <fstream>
7 – #include <algorithm>
8 – #include <utility>
9 –
46   #ifdef IS_MPI
47   #include <mpi.h>
12 – #include "brains/mpiSimulation.hpp"
13 –
14 – namespace dWrite{
15 –  void DieDieDie( void );
16 – }
17 –
18 – using namespace dWrite;
48   #endif //is_mpi
49  
50 < #include "io/ReadWrite.hpp"
22 < #include "utils/simError.h"
50 > namespace oopse {
51  
52 < DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
53 <
26 <  entry_plug = the_entry_plug;
27 <
52 > DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
53 >                   : info_(info), filename_(filename){
54   #ifdef IS_MPI
55 <  if(worldRank == 0 ){
55 >
56 >    if (worldRank == 0) {
57   #endif // is_mpi
58  
59 <    dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
59 >        dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);
60  
61 <    if( !dumpFile ){
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  
68 <      sprintf( painCave.errMsg,
69 <               "Could not open \"%s\" for dump output.\n",
38 <               entry_plug->sampleName.c_str());
39 <      painCave.isFatal = 1;
40 <      simError();
68 > #ifdef IS_MPI
69 >
70      }
71  
72 < #ifdef IS_MPI
73 <  }
72 >    sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73 >    MPIcheckPoint();
74  
46 –  //sort the local atoms by global index
47 –  sortByGlobalIndex();
48 –  
49 –  sprintf( checkPointMsg,
50 –           "Sucessfully opened output file for dumping.\n");
51 –  MPIcheckPoint();
75   #endif // is_mpi
76 +
77   }
78  
79 < DumpWriter::~DumpWriter( ){
79 > DumpWriter::~DumpWriter() {
80  
81   #ifdef IS_MPI
82 <  if(worldRank == 0 ){
82 >
83 >    if (worldRank == 0) {
84   #endif // is_mpi
85  
86 <    dumpFile.close();
86 >        dumpFile_.close();
87  
88   #ifdef IS_MPI
89 <  }
89 >
90 >    }
91 >
92   #endif // is_mpi
93 +
94   }
95  
96 < #ifdef IS_MPI
96 > void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
97  
98 < /**
99 < * A hook function to load balancing
100 < */
98 >    double currentTime;
99 >    Mat3x3d hmat;
100 >    double chi;
101 >    double integralOfChiDt;
102 >    Mat3x3d eta;
103 >    
104 >    currentTime = s->getTime();
105 >    hmat = s->getHmat();
106 >    chi = s->getChi();
107 >    integralOfChiDt = s->getIntegralOfChiDt();
108 >    eta = s->getEta();
109 >    
110 >    os << currentTime << ";\t"
111 >         << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
112 >         << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
113 >         << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
114  
115 < 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 < }
115 >    //write out additional parameters, such as chi and eta
116  
117 < /**
118 < * Sorting the local index by global index
119 < */
120 <
121 < void DumpWriter::sortByGlobalIndex(){
122 <  Molecule* mols = entry_plug->molecules;  
123 <  indexArray.clear();
93 <  
94 <  for(int i = 0; i < entry_plug->n_mol;i++)
95 <    indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
96 <  
97 <  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
117 >    os << chi << "\t" << integralOfChiDt << "\t;";
118 >
119 >    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
120 >         << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
121 >         << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
122 >        
123 >    os << std::endl;
124   }
125  
126 < #endif
126 > void DumpWriter::writeFrame(std::ostream& os) {
127 >    const int BUFFERSIZE = 2000;
128 >    const int MINIBUFFERSIZE = 100;
129  
130 < void DumpWriter::writeDump(double currentTime){
130 >    char tempBuffer[BUFFERSIZE];
131 >    char writeLine[BUFFERSIZE];
132  
133 <  ofstream finalOut;
134 <  vector<ofstream*> fileStreams;
133 >    Quat4d q;
134 >    Vector3d ji;
135 >    Vector3d pos;
136 >    Vector3d vel;
137  
138 < #ifdef IS_MPI
139 <  if(worldRank == 0 ){
140 < #endif    
141 <    finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
142 <    if( !finalOut ){
143 <      sprintf( painCave.errMsg,
144 <               "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 <  }
120 < #endif // is_mpi
138 >    Molecule* mol;
139 >    StuntDouble* integrableObject;
140 >    SimInfo::MoleculeIterator mi;
141 >    Molecule::IntegrableObjectIterator ii;
142 >  
143 >    int nTotObjects;    
144 >    nTotObjects = info_->getNGlobalIntegrableObjects();
145  
146 <  fileStreams.push_back(&finalOut);
123 <  fileStreams.push_back(&dumpFile);
146 > #ifndef IS_MPI
147  
125 –  writeFrame(fileStreams, currentTime);
148  
149 < #ifdef IS_MPI
150 <  finalOut.close();
151 < #endif
130 <        
131 < }
149 >    os << nTotObjects << "\n";
150 >        
151 >    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
152  
153 < void DumpWriter::writeFinal(double currentTime){
153 >    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
154  
155 <  ofstream finalOut;
156 <  vector<ofstream*> fileStreams;
155 >        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
156 >            integrableObject = mol->nextIntegrableObject(ii)) {
157 >                
158  
159 < #ifdef IS_MPI
160 <  if(worldRank == 0 ){
140 < #endif // is_mpi
159 >            pos = integrableObject->getPos();
160 >            vel = integrableObject->getVel();
161  
162 <    finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
162 >            sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
163 >                    integrableObject->getType().c_str(),
164 >                    pos[0], pos[1], pos[2],
165 >                    vel[0], vel[1], vel[2]);
166  
167 <    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();
150 <    }
167 >            strcpy(writeLine, tempBuffer);
168  
169 < #ifdef IS_MPI
170 <  }
171 < #endif // is_mpi
155 <  
156 <  fileStreams.push_back(&finalOut);  
157 <  writeFrame(fileStreams, currentTime);
169 >            if (integrableObject->isDirectional()) {
170 >                q = integrableObject->getQ();
171 >                ji = integrableObject->getJ();
172  
173 < #ifdef IS_MPI
174 <  finalOut.close();
175 < #endif
176 <  
177 < }
173 >                sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
174 >                        q[0], q[1], q[2], q[3],
175 >                        ji[0], ji[1], ji[2]);
176 >                strcat(writeLine, tempBuffer);
177 >            } else {
178 >                strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
179 >            }
180  
181 < void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
181 >            os << writeLine;
182  
183 <  const int BUFFERSIZE = 2000;
184 <  const int MINIBUFFERSIZE = 100;
183 >        }
184 >    }
185  
186 <  char tempBuffer[BUFFERSIZE];  
187 <  char writeLine[BUFFERSIZE];
188 <
189 <  int i;
190 <  unsigned int k;
186 >    os.flush();
187 > #else // is_mpi
188 >    /*********************************************************************
189 >     * Documentation?  You want DOCUMENTATION?
190 >     *
191 >     * Why all the potatoes below?  
192 >     *
193 >     * To make a long story short, the original version of DumpWriter
194 >     * worked in the most inefficient way possible.  Node 0 would
195 >     * poke each of the node for an individual atom's formatted data
196 >     * as node 0 worked its way down the global index. This was particularly
197 >     * inefficient since the method blocked all processors at every atom
198 >     * (and did it twice!).
199 >     *
200 >     * An intermediate version of DumpWriter could be described from Node
201 >     * zero's perspective as follows:
202 >     *
203 >     *  1) Have 100 of your friends stand in a circle.
204 >     *  2) When you say go, have all of them start tossing potatoes at
205 >     *     you (one at a time).
206 >     *  3) Catch the potatoes.
207 >     *
208 >     * It was an improvement, but MPI has buffers and caches that could
209 >     * best be described in this analogy as "potato nets", so there's no
210 >     * need to block the processors atom-by-atom.
211 >     *
212 >     * This new and improved DumpWriter works in an even more efficient
213 >     * way:
214 >     *
215 >     *  1) Have 100 of your friend stand in a circle.
216 >     *  2) When you say go, have them start tossing 5-pound bags of
217 >     *     potatoes at you.
218 >     *  3) Once you've caught a friend's bag of potatoes,
219 >     *     toss them a spud to let them know they can toss another bag.
220 >     *
221 >     * How's THAT for documentation?
222 >     *
223 >     *********************************************************************/
224 >    const int masterNode = 0;
225  
226 < #ifdef IS_MPI
227 <  
228 <  /*********************************************************************
229 <   * Documentation?  You want DOCUMENTATION?
230 <   *
231 <   * Why all the potatoes below?  
232 <   *
233 <   * To make a long story short, the original version of DumpWriter
234 <   * worked in the most inefficient way possible.  Node 0 would
235 <   * poke each of the node for an individual atom's formatted data
236 <   * as node 0 worked its way down the global index. This was particularly
237 <   * inefficient since the method blocked all processors at every atom
238 <   * (and did it twice!).
239 <   *
240 <   * An intermediate version of DumpWriter could be described from Node
241 <   * zero's perspective as follows:
242 <   *
243 <   *  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 <   *********************************************************************/
226 >    int * potatoes;
227 >    int myPotato;
228 >    int nProc;
229 >    int which_node;
230 >    double atomData[13];
231 >    int isDirectional;
232 >    const char * atomTypeString;
233 >    char MPIatomTypeString[MINIBUFFERSIZE];
234 >    int msgLen; // the length of message actually recieved at master nodes
235 >    int haveError;
236 >    MPI_Status istatus;
237 >    int nCurObj;
238 >    
239 >    // code to find maximum tag value
240 >    int * tagub;
241 >    int flag;
242 >    int MAXTAG;
243 >    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
244  
245 <  int *potatoes;
246 <  int myPotato;
245 >    if (flag) {
246 >        MAXTAG = *tagub;
247 >    } else {
248 >        MAXTAG = 32767;
249 >    }
250  
251 <  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
251 >    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
252  
253 <  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";
253 >        // Node 0 needs a list of the magic potatoes for each processor;
254  
255 <    *outFile[k] << currentTime << ";\t"
256 <               << 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"
255 >        MPI_Comm_size(MPI_COMM_WORLD, &nProc);
256 >        potatoes = new int[nProc];
257  
258 <                     << entry_plug->Hmat[0][2] << "\t"
259 <                     << entry_plug->Hmat[1][2] << "\t"
260 <                     << entry_plug->Hmat[2][2] << ";";
258 >        //write out the comment lines
259 >        for(int i = 0; i < nProc; i++) {
260 >            potatoes[i] = 0;
261 >        }
262  
255 –    //write out additional parameters, such as chi and eta
256 –    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
257 –  }
258 –  
259 –  for( i=0; i< entry_plug->n_mol; i++ ){
263  
264 <    integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
265 <    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);
264 >        os << nTotObjects << "\n";
265 >        writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
266  
267 <      sprintf( tempBuffer,
270 <             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
271 <             sd->getType(),
272 <             pos[0],
273 <             pos[1],
274 <             pos[2],
275 <             vel[0],
276 <             vel[1],
277 <             vel[2]);
278 <      strcpy( writeLine, tempBuffer );
267 >        for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
268  
269 <      if( sd->isDirectional() ){
269 >            // Get the Node number which has this atom;
270  
271 <        sd->getQ( q );
283 <        sd->getJ( ji );
271 >            which_node = info_->getMolToProc(i);
272  
273 <        sprintf( tempBuffer,
274 <               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
275 <               q[0],
276 <               q[1],
289 <               q[2],
290 <               q[3],
291 <                 ji[0],
292 <                 ji[1],
293 <                 ji[2]);
294 <        strcat( writeLine, tempBuffer );
295 <      }
296 <      else
297 <        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 <  }
273 >            if (which_node != masterNode) { //current molecule is in slave node
274 >                if (potatoes[which_node] + 1 >= MAXTAG) {
275 >                    // The potato was going to exceed the maximum value,
276 >                    // so wrap this processor potato back to 0:        
277  
278 < #else // is_mpi
278 >                    potatoes[which_node] = 0;
279 >                    MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
280 >                             MPI_COMM_WORLD);
281 >                }
282  
283 <  /* code to find maximum tag value */
308 <  
309 <  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 <  }  
283 >                myPotato = potatoes[which_node];
284  
285 <  int haveError;
285 >                //recieve the number of integrableObject in current molecule
286 >                MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
287 >                         MPI_COMM_WORLD, &istatus);
288 >                myPotato++;
289  
290 <  MPI_Status istatus;
291 <  int nCurObj;
292 <  int *MolToProcMap = mpiSim->getMolToProcMap();
290 >                for(int l = 0; l < nCurObj; l++) {
291 >                    if (potatoes[which_node] + 2 >= MAXTAG) {
292 >                        // The potato was going to exceed the maximum value,
293 >                        // so wrap this processor potato back to 0:        
294  
295 <  // write out header and node 0's coordinates
295 >                        potatoes[which_node] = 0;
296 >                        MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
297 >                                 0, MPI_COMM_WORLD);
298 >                    }
299  
300 <  if( worldRank == 0 ){
300 >                    MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
301 >                             which_node, myPotato, MPI_COMM_WORLD,
302 >                             &istatus);
303  
304 <    // Node 0 needs a list of the magic potatoes for each processor;
304 >                    atomTypeString = MPIatomTypeString;
305  
306 <    nProc = mpiSim->getNProcessors();
330 <    potatoes = new int[nProc];
306 >                    myPotato++;
307  
308 <    //write out the comment lines
309 <    for (i = 0; i < nProc; i++)
310 <      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;
354 <    }
355 <    
356 <    currentIndex = 0;
357 <    
358 <    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
359 <      
360 <      // Get the Node number which has this atom;
361 <      
362 <      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:        
369 <
370 <          potatoes[which_node] = 0;          
371 <          MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
372 <                   MPI_COMM_WORLD);
373 <          
374 <        }
375 <
376 <        myPotato = potatoes[which_node];        
377 <
378 <        //recieve the number of integrableObject in current molecule
379 <        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
380 <                 myPotato, MPI_COMM_WORLD, &istatus);
381 <        myPotato++;
382 <        
383 <        for(int l = 0; l < nCurObj; l++){
308 >                    MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
309 >                             MPI_COMM_WORLD, &istatus);
310 >                    myPotato++;
311  
312 <          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:        
312 >                    MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
313  
314 <            potatoes[which_node] = 0;          
315 <            MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
316 <            
317 <          }
314 >                    if (msgLen == 13)
315 >                        isDirectional = 1;
316 >                    else
317 >                        isDirectional = 0;
318  
319 <          MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
395 <          myPotato, MPI_COMM_WORLD, &istatus);
319 >                    // If we've survived to here, format the line:
320  
321 <          atomTypeString = MPIatomTypeString;
321 >                    if (!isDirectional) {
322 >                        sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
323 >                                atomTypeString, atomData[0],
324 >                                atomData[1], atomData[2],
325 >                                atomData[3], atomData[4],
326 >                                atomData[5]);
327  
328 <          myPotato++;
328 >                        strcat(writeLine,
329 >                               "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
330 >                    } else {
331 >                        sprintf(writeLine,
332 >                                "%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",
333 >                                atomTypeString,
334 >                                atomData[0],
335 >                                atomData[1],
336 >                                atomData[2],
337 >                                atomData[3],
338 >                                atomData[4],
339 >                                atomData[5],
340 >                                atomData[6],
341 >                                atomData[7],
342 >                                atomData[8],
343 >                                atomData[9],
344 >                                atomData[10],
345 >                                atomData[11],
346 >                                atomData[12]);
347 >                    }
348  
349 <          MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
402 <          myPotato++;
349 >                    os << writeLine;
350  
351 <          MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
351 >                } // end for(int l =0)
352  
353 <          if(msgLen  == 13)
354 <            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;            
353 >                potatoes[which_node] = myPotato;
354 >            } else { //master node has current molecule
355  
356 <        }// end for(int l =0)
453 <        potatoes[which_node] = myPotato;
454 <        
455 <      }
456 <      else {
457 <        
458 <        haveError = 0;
459 <        
460 <            local_index = indexArray[currentIndex].first;        
461 <            
462 <            integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
356 >                mol = info_->getMoleculeByGlobalIndex(i);
357  
358 <        for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){    
359 <                sd = *iter;
360 <            atomTypeString = sd->getType();
361 <            
362 <            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;
358 >                if (mol == NULL) {
359 >                    sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
360 >                    painCave.isFatal = 1;
361 >                    simError();
362 >                }
363                  
364 <              sd->getQ( q );
365 <              sd->getJ( ji );
364 >                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
365 >                    integrableObject = mol->nextIntegrableObject(ii)) {
366 >                        
367 >                    atomTypeString = integrableObject->getType().c_str();
368  
369 <              for (int j = 0; j < 6 ; j++)
370 <                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 <            }
500 <            
501 <            // If we've survived to here, format the line:
502 <            
503 <            if (!isDirectional) {
504 <        
505 <              sprintf( writeLine,
506 <                 "%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 <              
537 <            }
538 <            
539 <            for(k = 0; k < outFile.size(); k++)
540 <              *outFile[k] << writeLine;
541 <            
542 <            
543 <        }//end for(iter = integrableObject.begin())
544 <        
545 <      currentIndex++;
546 <      }
369 >                    pos = integrableObject->getPos();
370 >                    vel = integrableObject->getVel();
371  
372 <    }//end for(i = 0; i < mpiSim->getNmol())
373 <    
374 <    for(k = 0; k < outFile.size(); k++)
551 <      outFile[k]->flush();
552 <    
553 <    sprintf( checkPointMsg,
554 <             "Sucessfully took a dump.\n");
555 <    
556 <    MPIcheckPoint();        
557 <    
558 <    delete[] potatoes;
559 <    
560 <  } else {
372 >                    atomData[0] = pos[0];
373 >                    atomData[1] = pos[1];
374 >                    atomData[2] = pos[2];
375  
376 <    // worldRank != 0, so I'm a remote node.  
376 >                    atomData[3] = vel[0];
377 >                    atomData[4] = vel[1];
378 >                    atomData[5] = vel[2];
379  
380 <    // Set my magic potato to 0:
380 >                    isDirectional = 0;
381  
382 <    myPotato = 0;
383 <    currentIndex = 0;
568 <    
569 <    for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
570 <      
571 <      // Am I the node which has this integrableObject?
572 <      
573 <      if (MolToProcMap[i] == worldRank) {
382 >                    if (integrableObject->isDirectional()) {
383 >                        isDirectional = 1;
384  
385 +                        q = integrableObject->getQ();
386 +                        ji = integrableObject->getJ();
387  
388 <        if (myPotato + 1 >= MAXTAG) {
389 <          
390 <          // The potato was going to exceed the maximum value,
579 <          // so wrap this processor potato back to 0 (and block until
580 <          // node 0 says we can go:
581 <          
582 <          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
583 <          
584 <        }
388 >                        for(int j = 0; j < 6; j++) {
389 >                            atomData[j] = atomData[j];
390 >                        }
391  
392 <          local_index = indexArray[currentIndex].first;        
393 <          integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
394 <          
395 <          nCurObj = integrableObjects.size();
590 <                      
591 <          MPI_Send(&nCurObj, 1, MPI_INT, 0,
592 <                   myPotato, MPI_COMM_WORLD);
593 <          myPotato++;
392 >                        atomData[6] = q[0];
393 >                        atomData[7] = q[1];
394 >                        atomData[8] = q[2];
395 >                        atomData[9] = q[3];
396  
397 <          for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
397 >                        atomData[10] = ji[0];
398 >                        atomData[11] = ji[1];
399 >                        atomData[12] = ji[2];
400 >                    }
401  
402 <            if (myPotato + 2 >= MAXTAG) {
403 <          
404 <              // The potato was going to exceed the maximum value,
405 <              // so wrap this processor potato back to 0 (and block until
406 <              // node 0 says we can go:
407 <          
408 <              MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
409 <              
402 >                    // If we've survived to here, format the line:
403 >
404 >                    if (!isDirectional) {
405 >                        sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
406 >                                atomTypeString, atomData[0],
407 >                                atomData[1], atomData[2],
408 >                                atomData[3], atomData[4],
409 >                                atomData[5]);
410 >
411 >                        strcat(writeLine,
412 >                               "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
413 >                    } else {
414 >                        sprintf(writeLine,
415 >                                "%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",
416 >                                atomTypeString,
417 >                                atomData[0],
418 >                                atomData[1],
419 >                                atomData[2],
420 >                                atomData[3],
421 >                                atomData[4],
422 >                                atomData[5],
423 >                                atomData[6],
424 >                                atomData[7],
425 >                                atomData[8],
426 >                                atomData[9],
427 >                                atomData[10],
428 >                                atomData[11],
429 >                                atomData[12]);
430 >                    }
431 >
432 >
433 >                    os << writeLine;
434 >
435 >                } //end for(iter = integrableObject.begin())
436              }
437 <            
607 <            sd = *iter;
608 <            
609 <            atomTypeString = sd->getType();
437 >        } //end for(i = 0; i < mpiSim->getNmol())
438  
439 <            sd->getPos(pos);
440 <            sd->getVel(vel);
439 >        os.flush();
440 >        
441 >        sprintf(checkPointMsg, "Sucessfully took a dump.\n");
442 >        MPIcheckPoint();
443  
444 <            atomData[0] = pos[0];
445 <            atomData[1] = pos[1];
616 <            atomData[2] = pos[2];
444 >        delete [] potatoes;
445 >    } else {
446  
447 <            atomData[3] = vel[0];
619 <            atomData[4] = vel[1];
620 <            atomData[5] = vel[2];
621 <              
622 <            isDirectional = 0;
447 >        // worldRank != 0, so I'm a remote node.  
448  
449 <            if( sd->isDirectional() ){
449 >        // Set my magic potato to 0:
450  
451 <                isDirectional = 1;
451 >        myPotato = 0;
452 >
453 >        for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
454 >
455 >            // Am I the node which has this integrableObject?
456 >            int whichNode = info_->getMolToProc(i);
457 >            if (whichNode == worldRank) {
458 >                if (myPotato + 1 >= MAXTAG) {
459 >
460 >                    // The potato was going to exceed the maximum value,
461 >                    // so wrap this processor potato back to 0 (and block until
462 >                    // node 0 says we can go:
463 >
464 >                    MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
465 >                             &istatus);
466 >                }
467 >
468 >                mol = info_->getMoleculeByGlobalIndex(i);
469 >
470                  
471 <                sd->getQ( q );
629 <                sd->getJ( ji );
630 <                
631 <                
632 <                atomData[6] = q[0];
633 <                atomData[7] = q[1];
634 <                atomData[8] = q[2];
635 <                atomData[9] = q[3];
636 <      
637 <                atomData[10] = ji[0];
638 <                atomData[11] = ji[1];
639 <                atomData[12] = ji[2];
640 <              }
471 >                nCurObj = mol->getNIntegrableObjects();
472  
473 <            
474 <            strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
473 >                MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
474 >                myPotato++;
475  
476 <            // null terminate the string before sending (just in case):
477 <            MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
476 >                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
477 >                    integrableObject = mol->nextIntegrableObject(ii)) {
478  
479 <            MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
649 <                             myPotato, MPI_COMM_WORLD);
650 <            
651 <            myPotato++;
652 <            
653 <            if (isDirectional) {
479 >                    if (myPotato + 2 >= MAXTAG) {
480  
481 <              MPI_Send(atomData, 13, MPI_DOUBLE, 0,
482 <                       myPotato, MPI_COMM_WORLD);
483 <              
658 <            } else {
481 >                        // The potato was going to exceed the maximum value,
482 >                        // so wrap this processor potato back to 0 (and block until
483 >                        // node 0 says we can go:
484  
485 <              MPI_Send(atomData, 6, MPI_DOUBLE, 0,
486 <                       myPotato, MPI_COMM_WORLD);
487 <            }
485 >                        MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
486 >                                 &istatus);
487 >                    }
488  
489 <            myPotato++;  
489 >                    atomTypeString = integrableObject->getType().c_str();
490  
491 <          }
491 >                    pos = integrableObject->getPos();
492 >                    vel = integrableObject->getVel();
493  
494 <          currentIndex++;    
495 <          
496 <        }
671 <      
672 <      }
494 >                    atomData[0] = pos[0];
495 >                    atomData[1] = pos[1];
496 >                    atomData[2] = pos[2];
497  
498 <    sprintf( checkPointMsg,
499 <             "Successfully took a dump.\n");
500 <    MPIcheckPoint();                
677 <    
678 <  }
679 <  
680 < #endif // is_mpi
681 < }
498 >                    atomData[3] = vel[0];
499 >                    atomData[4] = vel[1];
500 >                    atomData[5] = vel[2];
501  
502 < #ifdef IS_MPI
502 >                    isDirectional = 0;
503  
504 < // a couple of functions to let us escape the write loop
504 >                    if (integrableObject->isDirectional()) {
505 >                        isDirectional = 1;
506  
507 < void dWrite::DieDieDie( void ){
507 >                        q = integrableObject->getQ();
508 >                        ji = integrableObject->getJ();
509  
510 <  MPI_Finalize();
511 <  exit (0);
510 >                        atomData[6] = q[0];
511 >                        atomData[7] = q[1];
512 >                        atomData[8] = q[2];
513 >                        atomData[9] = q[3];
514 >
515 >                        atomData[10] = ji[0];
516 >                        atomData[11] = ji[1];
517 >                        atomData[12] = ji[2];
518 >                    }
519 >
520 >                    strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
521 >
522 >                    // null terminate the  std::string before sending (just in case):
523 >                    MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
524 >
525 >                    MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
526 >                             myPotato, MPI_COMM_WORLD);
527 >
528 >                    myPotato++;
529 >
530 >                    if (isDirectional) {
531 >                        MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
532 >                                 MPI_COMM_WORLD);
533 >                    } else {
534 >                        MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
535 >                                 MPI_COMM_WORLD);
536 >                    }
537 >
538 >                    myPotato++;
539 >                }
540 >                    
541 >            }
542 >            
543 >        }
544 >        sprintf(checkPointMsg, "Sucessfully took a dump.\n");
545 >        MPIcheckPoint();
546 >    }
547 >
548 > #endif // is_mpi
549 >
550   }
551  
552 < #endif //is_mpi
552 > }//end namespace oopse

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