OOPSE/libmdtools/DumpWriter.cpp

#define _FILE_OFFSET_BITS 64

#include <string.h>
#include <iostream>
#include <fstream>
#include <algorithm>
#include <utility>

#ifdef IS_MPI
#include <mpi.h>
#include "mpiSimulation.hpp"

namespace dWrite{
  void DieDieDie( void );
}

using namespace dWrite;
#endif //is_mpi

#include "ReadWrite.hpp"
#include "simError.h"

DumpWriter::DumpWriter( SimInfo* the_entry_plug ){

  entry_plug = the_entry_plug;

#ifdef IS_MPI
  if(worldRank == 0 ){
#endif // is_mpi


    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );

    if( !dumpFile ){

      sprintf( painCave.errMsg,
               "Could not open \"%s\" for dump output.\n",
               entry_plug->sampleName);
      painCave.isFatal = 1;
      simError();
    }

#ifdef IS_MPI
  }

  //sort the local atoms by global index
  sortByGlobalIndex();
  
  sprintf( checkPointMsg,
           "Sucessfully opened output file for dumping.\n");
  MPIcheckPoint();
#endif // is_mpi
}

DumpWriter::~DumpWriter( ){

#ifdef IS_MPI
  if(worldRank == 0 ){
#endif // is_mpi

    dumpFile.close();

#ifdef IS_MPI
  }
#endif // is_mpi
}

#ifdef IS_MPI

/**
 * A hook function to load balancing
 */

void DumpWriter::update(){
  sortByGlobalIndex();          
}
  
/**
 * Auxiliary sorting function
 */
 
bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
  return p1.second < p2.second;
}

/**
 * Sorting the local index by global index
 */
 
void DumpWriter::sortByGlobalIndex(){
  Atom** atoms = entry_plug->atoms;
  
  indexArray.clear();
  
  for(int i = 0; i < mpiSim->getMyNlocal();i++)
    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
  
  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
}
#endif

void DumpWriter::writeDump(double currentTime){

  ofstream finalOut;
  vector<ofstream*> fileStreams;

#ifdef IS_MPI
  if(worldRank == 0 ){
    
    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );
    if( !finalOut ){
      sprintf( painCave.errMsg,
               "Could not open \"%s\" for final dump output.\n",
               entry_plug->finalName );
      painCave.isFatal = 1;
      simError();
    }
  }
#endif // is_mpi

  fileStreams.push_back(&finalOut); 
  fileStreams.push_back(&dumpFile);

  writeFrame(fileStreams, currentTime);

#ifdef IS_MPI
  finalOut.close();
#endif
        
}

void DumpWriter::writeFinal(double currentTime){

  ofstream finalOut;
  vector<ofstream*> fileStreams;

#ifdef IS_MPI
  if(worldRank == 0 ){

    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );

    if( !finalOut ){
      sprintf( painCave.errMsg,
               "Could not open \"%s\" for final dump output.\n",
               entry_plug->finalName );
      painCave.isFatal = 1;
      simError();
    }

  }
#endif // is_mpi
  
  fileStreams.push_back(&finalOut);  
  writeFrame(fileStreams, currentTime);

#ifdef IS_MPI
  finalOut.close();
#endif
  
}

void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){

  const int BUFFERSIZE = 2000;
  const int MINIBUFFERSIZE = 100;

  char tempBuffer[BUFFERSIZE];  
  char writeLine[BUFFERSIZE];

  int i, k;

#ifdef IS_MPI
  
  int *potatoes;
  int myPotato;

  int nProc;
  int j, which_node, done, which_atom, local_index, currentIndex;
  double atomData6[6];
  double atomData13[13];
  int isDirectional;
  char* atomTypeString;
  char MPIatomTypeString[MINIBUFFERSIZE];

#else //is_mpi
  int nAtoms = entry_plug->n_atoms;
#endif //is_mpi

  double q[4];
  DirectionalAtom* dAtom;
  Atom** atoms = entry_plug->atoms;
  double pos[3], vel[3];

#ifndef IS_MPI
  
  for(k = 0; k < outFile.size(); k++){
    *outFile[k] << nAtoms << "\n";

    *outFile[k] << currentTime << ";\t"
               << entry_plug->Hmat[0][0] << "\t"
                     << entry_plug->Hmat[1][0] << "\t"
                     << entry_plug->Hmat[2][0] << ";\t"
               
               << entry_plug->Hmat[0][1] << "\t"
                     << entry_plug->Hmat[1][1] << "\t"
                     << entry_plug->Hmat[2][1] << ";\t"

                     << entry_plug->Hmat[0][2] << "\t"
                     << entry_plug->Hmat[1][2] << "\t"
                     << entry_plug->Hmat[2][2] << ";";

    //write out additional parameters, such as chi and eta
    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
  }
  
  for( i=0; i<nAtoms; i++ ){

    atoms[i]->getPos(pos);
    atoms[i]->getVel(vel);

    sprintf( tempBuffer,
             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
             atoms[i]->getType(),
             pos[0],
             pos[1],
             pos[2],
             vel[0],
             vel[1],
             vel[2]);
    strcpy( writeLine, tempBuffer );

    if( atoms[i]->isDirectional() ){

      dAtom = (DirectionalAtom *)atoms[i];
      dAtom->getQ( q );

      sprintf( tempBuffer,
               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
               q[0],
               q[1],
               q[2],
               q[3],
               dAtom->getJx(),
               dAtom->getJy(),
               dAtom->getJz());
      strcat( writeLine, tempBuffer );
    }
    else
      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );

    for(k = 0; k < outFile.size(); k++)
      *outFile[k] << writeLine;
  }

#else // is_mpi

  /* code to find maximum tag value */
  
  int *tagub, flag, MAXTAG;
  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
  if (flag) {
    MAXTAG = *tagub;
  } else {
    MAXTAG = 32767;
  }  

  int haveError;

  MPI_Status istatus;
  int *AtomToProcMap = mpiSim->getAtomToProcMap();

  // write out header and node 0's coordinates

  if( worldRank == 0 ){

    // Node 0 needs a list of the magic potatoes for each processor;

    nProc = mpiSim->getNumberProcessors();
    potatoes = new int[nProc];

    //write out the comment lines
    for (i = 0; i < nProc; i++) 
      potatoes[i] = 0;
    
      for(k = 0; k < outFile.size(); k++){
        *outFile[k] << mpiSim->getTotAtoms() << "\n";

        *outFile[k] << currentTime << ";\t"
                         << entry_plug->Hmat[0][0] << "\t"
                         << entry_plug->Hmat[1][0] << "\t"
                         << entry_plug->Hmat[2][0] << ";\t"

                         << entry_plug->Hmat[0][1] << "\t"
                         << entry_plug->Hmat[1][1] << "\t"
                         << entry_plug->Hmat[2][1] << ";\t"

                         << entry_plug->Hmat[0][2] << "\t"
                         << entry_plug->Hmat[1][2] << "\t"
                         << entry_plug->Hmat[2][2] << ";";
  
        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
    }

    currentIndex = 0;

    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
      
      // Get the Node number which has this atom;
      
      which_node = AtomToProcMap[i];
      
      if (which_node != 0) {

        if (potatoes[which_node] + 3 >= MAXTAG) {
          // The potato was going to exceed the maximum value, 
          // so wrap this processor potato back to 0:         

          potatoes[which_node] = 0;          
          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
          
        }

        myPotato = potatoes[which_node];        
        
        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
                 myPotato, MPI_COMM_WORLD, &istatus);
        
        atomTypeString = MPIatomTypeString;
        
        myPotato++;

        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
                 myPotato, MPI_COMM_WORLD, &istatus);
               
        myPotato++;

        if (isDirectional) {          
          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
                   myPotato, MPI_COMM_WORLD, &istatus);
        } else {
          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
                   myPotato, MPI_COMM_WORLD, &istatus);          
        }
        
        myPotato++;
        potatoes[which_node] = myPotato;

      } else {
        
        haveError = 0;
              which_atom = i;
        
        local_index = indexArray[currentIndex].first;        
                
        if (which_atom == indexArray[currentIndex].second) {
          
          atomTypeString = atoms[local_index]->getType();

                atoms[local_index]->getPos(pos);
                atoms[local_index]->getVel(vel);          

          atomData6[0] = pos[0];
          atomData6[1] = pos[1];
          atomData6[2] = pos[2];

          atomData6[3] = vel[0];
          atomData6[4] = vel[1];
          atomData6[5] = vel[2];
          
          isDirectional = 0;

          if( atoms[local_index]->isDirectional() ){

            isDirectional = 1;
            
            dAtom = (DirectionalAtom *)atoms[local_index];
            dAtom->getQ( q );

            for (int j = 0; j < 6 ; j++)
              atomData13[j] = atomData6[j];            
            
            atomData13[6] = q[0];
            atomData13[7] = q[1];
            atomData13[8] = q[2];
            atomData13[9] = q[3];
            
            atomData13[10] = dAtom->getJx();
            atomData13[11] = dAtom->getJy();
            atomData13[12] = dAtom->getJz();
          }
          
        } else {
          sprintf(painCave.errMsg,
                              "Atom %d not found on processor %d\n",
                              i, worldRank );
                haveError= 1;
                simError();
              }
        
        if(haveError) DieDieDie();
        
        currentIndex ++;
      }
      // If we've survived to here, format the line:
      
      if (!isDirectional) {
        
        sprintf( writeLine,
                             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                             atomTypeString,
                             atomData6[0],
                             atomData6[1],
                             atomData6[2],
                             atomData6[3],
                             atomData6[4],
                             atomData6[5]);

              strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
        
      } else {
        
              sprintf( writeLine,
                             "%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",
                             atomTypeString,
                             atomData13[0],
                             atomData13[1],
                             atomData13[2],
                             atomData13[3],
                             atomData13[4],
                             atomData13[5],
                             atomData13[6],
                             atomData13[7],
                             atomData13[8],
                             atomData13[9],
                             atomData13[10],
                             atomData13[11],
                             atomData13[12]);
        
      }
      
      for(k = 0; k < outFile.size(); k++)
        *outFile[k] << writeLine;
    }
    
    for(k = 0; k < outFile.size(); k++)
      outFile[k]->flush();
    
    sprintf( checkPointMsg,
             "Sucessfully took a dump.\n");

    MPIcheckPoint();        

    delete[] potatoes;

  } else {

    // worldRank != 0, so I'm a remote node.  

    // Set my magic potato to 0:

    myPotato = 0;
    currentIndex = 0;
    
    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
      
      // Am I the node which has this atom?
      
      if (AtomToProcMap[i] == worldRank) {

        if (myPotato + 3 >= MAXTAG) {

          // The potato was going to exceed the maximum value, 
          // so wrap this processor potato back to 0 (and block until
          // node 0 says we can go:

          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
          
        }
        which_atom = i; 
        local_index = indexArray[currentIndex].first;        
                
        if (which_atom == indexArray[currentIndex].second) {
         
          atomTypeString = atoms[local_index]->getType();

                atoms[local_index]->getPos(pos);
                atoms[local_index]->getVel(vel);

          atomData6[0] = pos[0];
          atomData6[1] = pos[1];
          atomData6[2] = pos[2];

          atomData6[3] = vel[0];
          atomData6[4] = vel[1];
          atomData6[5] = vel[2];
          
          isDirectional = 0;

          if( atoms[local_index]->isDirectional() ){

            isDirectional = 1;
            
            dAtom = (DirectionalAtom *)atoms[local_index];
            dAtom->getQ( q );
            
            for (int j = 0; j < 6 ; j++)
              atomData13[j] = atomData6[j];
            
            atomData13[6] = q[0];
            atomData13[7] = q[1];
            atomData13[8] = q[2];
            atomData13[9] = q[3];
  
            atomData13[10] = dAtom->getJx();
            atomData13[11] = dAtom->getJy();
            atomData13[12] = dAtom->getJz();
          }

        } else {
                sprintf(painCave.errMsg,
                              "Atom %d not found on processor %d\n",
                              i, worldRank );
                haveError= 1;
                simError();
              }

        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);

        // null terminate the string before sending (just in case):
        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';

        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
                             myPotato, MPI_COMM_WORLD);
        
        myPotato++;

        MPI_Send(&isDirectional, 1, MPI_INT, 0,
                             myPotato, MPI_COMM_WORLD);
        
        myPotato++;
        
        if (isDirectional) {

          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
                   myPotato, MPI_COMM_WORLD);
          
        } else {

          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
                   myPotato, MPI_COMM_WORLD);
        }

        myPotato++;  
        currentIndex++;    
      }
    }

    sprintf( checkPointMsg,
             "Sucessfully took a dump.\n");
    MPIcheckPoint();        
    
  } 
  
#endif // is_mpi
}

#ifdef IS_MPI

// a couple of functions to let us escape the write loop

void dWrite::DieDieDie( void ){

  MPI_Finalize();
  exit (0);
}

#endif //is_mpi
Revision:	936
Committed:	Tue Jan 13 20:35:25 2004 UTC (20 years, 5 months ago) by tim
File size:	13504 byte(s)
Log Message:	open and close the eor file whenever it is used instead of rewinding it
#	User	Rev	Content
1	mmeineke	723	#define _FILE_OFFSET_BITS 64
2
3	gezelter	829	#include <string.h>
4	mmeineke	377	#include <iostream>
5			#include <fstream>
6	tim	929	#include <algorithm>
7			#include <utility>
8	mmeineke	377
9			#ifdef IS_MPI
10			#include <mpi.h>
11			#include "mpiSimulation.hpp"
12	mmeineke	440
13			namespace dWrite{
14	gezelter	907	void DieDieDie( void );
15	mmeineke	440	}
16
17			using namespace dWrite;
18	mmeineke	377	#endif //is_mpi
19
20			#include "ReadWrite.hpp"
21			#include "simError.h"
22
23			DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
24
25			entry_plug = the_entry_plug;
26
27			#ifdef IS_MPI
28			if(worldRank == 0 ){
29			#endif // is_mpi
30	tim	837
31
32	tim	929	dumpFile.open(entry_plug->sampleName, ios::out \| ios::trunc );
33	tim	837
34	tim	929	if( !dumpFile ){
35	tim	837
36	mmeineke	377	sprintf( painCave.errMsg,
37			"Could not open \"%s\" for dump output.\n",
38	tim	929	entry_plug->sampleName);
39	mmeineke	377	painCave.isFatal = 1;
40			simError();
41			}
42	mmeineke	469
43	mmeineke	377	#ifdef IS_MPI
44			}
45
46	tim	929	//sort the local atoms by global index
47			sortByGlobalIndex();
48
49	mmeineke	377	sprintf( checkPointMsg,
50			"Sucessfully opened output file for dumping.\n");
51			MPIcheckPoint();
52			#endif // is_mpi
53			}
54
55			DumpWriter::~DumpWriter( ){
56
57			#ifdef IS_MPI
58			if(worldRank == 0 ){
59			#endif // is_mpi
60
61	tim	929	dumpFile.close();
62	mmeineke	377
63			#ifdef IS_MPI
64			}
65			#endif // is_mpi
66			}
67
68	tim	929	#ifdef IS_MPI
69	tim	837
70	tim	929	/**
71			* A hook function to load balancing
72			*/
73
74			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			}
85
86			/**
87			* Sorting the local index by global index
88			*/
89
90			void DumpWriter::sortByGlobalIndex(){
91			Atom** atoms = entry_plug->atoms;
92
93			indexArray.clear();
94
95			for(int i = 0; i < mpiSim->getMyNlocal();i++)
96			indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97
98			sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
99			}
100			#endif
101
102			void DumpWriter::writeDump(double currentTime){
103
104	tim	936	ofstream finalOut;
105	tim	934	vector<ofstream*> fileStreams;
106
107			#ifdef IS_MPI
108			if(worldRank == 0 ){
109	tim	936
110			finalOut.open( entry_plug->finalName, 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 );
115			painCave.isFatal = 1;
116			simError();
117			}
118	tim	934	}
119			#endif // is_mpi
120
121			fileStreams.push_back(&finalOut);
122			fileStreams.push_back(&dumpFile);
123
124			writeFrame(fileStreams, currentTime);
125	tim	936
126			#ifdef IS_MPI
127			finalOut.close();
128			#endif
129	tim	929
130			}
131
132			void DumpWriter::writeFinal(double currentTime){
133
134	tim	936	ofstream finalOut;
135	tim	934	vector<ofstream*> fileStreams;
136
137	tim	929	#ifdef IS_MPI
138			if(worldRank == 0 ){
139	tim	936
140			finalOut.open( entry_plug->finalName, ios::out \| ios::trunc );
141
142			if( !finalOut ){
143			sprintf( painCave.errMsg,
144			"Could not open \"%s\" for final dump output.\n",
145			entry_plug->finalName );
146			painCave.isFatal = 1;
147			simError();
148			}
149
150	tim	934	}
151	tim	929	#endif // is_mpi
152
153	tim	934	fileStreams.push_back(&finalOut);
154			writeFrame(fileStreams, currentTime);
155	tim	936
156			#ifdef IS_MPI
157			finalOut.close();
158			#endif
159	tim	929
160			}
161
162	tim	934	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
163	tim	929
164	mmeineke	377	const int BUFFERSIZE = 2000;
165	gezelter	912	const int MINIBUFFERSIZE = 100;
166	gezelter	907
167	tim	936	char tempBuffer[BUFFERSIZE];
168	mmeineke	377	char writeLine[BUFFERSIZE];
169
170	tim	934	int i, k;
171	gezelter	916
172	mmeineke	787	#ifdef IS_MPI
173	gezelter	916
174			int *potatoes;
175			int myPotato;
176
177			int nProc;
178	tim	929	int j, which_node, done, which_atom, local_index, currentIndex;
179	gezelter	916	double atomData6[6];
180			double atomData13[13];
181	gezelter	907	int isDirectional;
182			char* atomTypeString;
183	gezelter	910	char MPIatomTypeString[MINIBUFFERSIZE];
184	gezelter	916
185	mmeineke	787	#else //is_mpi
186			int nAtoms = entry_plug->n_atoms;
187			#endif //is_mpi
188
189	mmeineke	377	double q[4];
190			DirectionalAtom* dAtom;
191			Atom** atoms = entry_plug->atoms;
192	mmeineke	670	double pos[3], vel[3];
193	tim	837
194	mmeineke	377	#ifndef IS_MPI
195	tim	934
196			for(k = 0; k < outFile.size(); k++){
197			*outFile[k] << nAtoms << "\n";
198	tim	837
199	tim	934	*outFile[k] << currentTime << ";\t"
200			<< entry_plug->Hmat[0][0] << "\t"
201			<< entry_plug->Hmat[1][0] << "\t"
202			<< entry_plug->Hmat[2][0] << ";\t"
203
204			<< entry_plug->Hmat[0][1] << "\t"
205			<< entry_plug->Hmat[1][1] << "\t"
206			<< entry_plug->Hmat[2][1] << ";\t"
207	tim	837
208	tim	934	<< entry_plug->Hmat[0][2] << "\t"
209			<< entry_plug->Hmat[1][2] << "\t"
210			<< entry_plug->Hmat[2][2] << ";";
211	mmeineke	572
212	tim	934	//write out additional parameters, such as chi and eta
213			*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
214			}
215
216	mmeineke	377	for( i=0; i<nAtoms; i++ ){
217	tim	837
218	mmeineke	670	atoms[i]->getPos(pos);
219			atoms[i]->getVel(vel);
220	mmeineke	377
221			sprintf( tempBuffer,
222			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
223			atoms[i]->getType(),
224	mmeineke	670	pos[0],
225			pos[1],
226			pos[2],
227			vel[0],
228			vel[1],
229			vel[2]);
230	mmeineke	377	strcpy( writeLine, tempBuffer );
231
232			if( atoms[i]->isDirectional() ){
233	tim	837
234	mmeineke	377	dAtom = (DirectionalAtom *)atoms[i];
235			dAtom->getQ( q );
236	tim	837
237	mmeineke	377	sprintf( tempBuffer,
238			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
239			q[0],
240			q[1],
241			q[2],
242			q[3],
243			dAtom->getJx(),
244			dAtom->getJy(),
245			dAtom->getJz());
246			strcat( writeLine, tempBuffer );
247			}
248			else
249			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
250	tim	837
251	tim	934	for(k = 0; k < outFile.size(); k++)
252			*outFile[k] << writeLine;
253	mmeineke	377	}
254
255			#else // is_mpi
256	gezelter	416
257	chuckv	913	/* code to find maximum tag value */
258	tim	919
259	tim	920	int *tagub, flag, MAXTAG;
260	chuckv	913	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
261			if (flag) {
262	tim	920	MAXTAG = *tagub;
263	chuckv	913	} else {
264			MAXTAG = 32767;
265	gezelter	916	}
266	mmeineke	440
267			int haveError;
268
269	mmeineke	447	MPI_Status istatus;
270	gezelter	416	int *AtomToProcMap = mpiSim->getAtomToProcMap();
271	tim	837
272	mmeineke	377	// write out header and node 0's coordinates
273	tim	837
274	mmeineke	377	if( worldRank == 0 ){
275	gezelter	916
276			// Node 0 needs a list of the magic potatoes for each processor;
277
278			nProc = mpiSim->getNumberProcessors();
279			potatoes = new int[nProc];
280
281	tim	934	//write out the comment lines
282	gezelter	916	for (i = 0; i < nProc; i++)
283			potatoes[i] = 0;
284
285	tim	934	for(k = 0; k < outFile.size(); k++){
286			*outFile[k] << mpiSim->getTotAtoms() << "\n";
287	tim	837
288	tim	934	*outFile[k] << currentTime << ";\t"
289			<< entry_plug->Hmat[0][0] << "\t"
290			<< entry_plug->Hmat[1][0] << "\t"
291			<< entry_plug->Hmat[2][0] << ";\t"
292	tim	837
293	tim	934	<< entry_plug->Hmat[0][1] << "\t"
294			<< entry_plug->Hmat[1][1] << "\t"
295			<< entry_plug->Hmat[2][1] << ";\t"
296	tim	837
297	tim	934	<< entry_plug->Hmat[0][2] << "\t"
298			<< entry_plug->Hmat[1][2] << "\t"
299			<< entry_plug->Hmat[2][2] << ";";
300
301			*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
302			}
303	tim	837
304	tim	929	currentIndex = 0;
305	tim	934
306	gezelter	416	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
307	chuckv	913
308	gezelter	417	// Get the Node number which has this atom;
309	chuckv	913
310	tim	837	which_node = AtomToProcMap[i];
311	chuckv	913
312	gezelter	907	if (which_node != 0) {
313	gezelter	916
314			if (potatoes[which_node] + 3 >= MAXTAG) {
315			// The potato was going to exceed the maximum value,
316			// so wrap this processor potato back to 0:
317
318			potatoes[which_node] = 0;
319			MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
320
321			}
322
323			myPotato = potatoes[which_node];
324	gezelter	907
325	gezelter	910	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
326	gezelter	916	myPotato, MPI_COMM_WORLD, &istatus);
327	gezelter	907
328	tim	920	atomTypeString = MPIatomTypeString;
329
330	gezelter	916	myPotato++;
331
332	gezelter	907	MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
333	gezelter	916	myPotato, MPI_COMM_WORLD, &istatus);
334
335			myPotato++;
336	gezelter	907
337	gezelter	916	if (isDirectional) {
338			MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
339			myPotato, MPI_COMM_WORLD, &istatus);
340			} else {
341			MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
342			myPotato, MPI_COMM_WORLD, &istatus);
343	gezelter	907	}
344	gezelter	916
345			myPotato++;
346			potatoes[which_node] = myPotato;
347	gezelter	907
348			} else {
349
350	tim	934	haveError = 0;
351			which_atom = i;
352	gezelter	916
353	tim	929	local_index = indexArray[currentIndex].first;
354
355			if (which_atom == indexArray[currentIndex].second) {
356	gezelter	916
357	gezelter	907	atomTypeString = atoms[local_index]->getType();
358
359	tim	934	atoms[local_index]->getPos(pos);
360			atoms[local_index]->getVel(vel);
361	mmeineke	670
362	gezelter	916	atomData6[0] = pos[0];
363			atomData6[1] = pos[1];
364			atomData6[2] = pos[2];
365	tim	837
366	gezelter	916	atomData6[3] = vel[0];
367			atomData6[4] = vel[1];
368			atomData6[5] = vel[2];
369	gezelter	907
370			isDirectional = 0;
371
372	chuckv	436	if( atoms[local_index]->isDirectional() ){
373	tim	837
374	gezelter	907	isDirectional = 1;
375
376	chuckv	436	dAtom = (DirectionalAtom *)atoms[local_index];
377			dAtom->getQ( q );
378	gezelter	916
379			for (int j = 0; j < 6 ; j++)
380			atomData13[j] = atomData6[j];
381	gezelter	907
382	gezelter	916	atomData13[6] = q[0];
383			atomData13[7] = q[1];
384			atomData13[8] = q[2];
385			atomData13[9] = q[3];
386
387			atomData13[10] = dAtom->getJx();
388			atomData13[11] = dAtom->getJy();
389			atomData13[12] = dAtom->getJz();
390	gezelter	907	}
391	gezelter	916
392	gezelter	907	} else {
393	tim	934	sprintf(painCave.errMsg,
394			"Atom %d not found on processor %d\n",
395			i, worldRank );
396			haveError= 1;
397			simError();
398			}
399	gezelter	916
400	tim	934	if(haveError) DieDieDie();
401	gezelter	916
402	tim	929	currentIndex ++;
403	tim	926	}
404			// If we've survived to here, format the line:
405
406			if (!isDirectional) {
407
408	tim	934	sprintf( writeLine,
409			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
410			atomTypeString,
411			atomData6[0],
412			atomData6[1],
413			atomData6[2],
414			atomData6[3],
415			atomData6[4],
416			atomData6[5]);
417	tim	929
418	tim	934	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
419	tim	926
420			} else {
421
422	tim	934	sprintf( writeLine,
423			"%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",
424			atomTypeString,
425			atomData13[0],
426			atomData13[1],
427			atomData13[2],
428			atomData13[3],
429			atomData13[4],
430			atomData13[5],
431			atomData13[6],
432			atomData13[7],
433			atomData13[8],
434			atomData13[9],
435			atomData13[10],
436			atomData13[11],
437			atomData13[12]);
438	gezelter	907
439			}
440	tim	926
441	tim	934	for(k = 0; k < outFile.size(); k++)
442			*outFile[k] << writeLine;
443	mmeineke	377	}
444	tim	926
445	tim	934	for(k = 0; k < outFile.size(); k++)
446			outFile[k]->flush();
447
448	gezelter	907	sprintf( checkPointMsg,
449			"Sucessfully took a dump.\n");
450	tim	934
451	gezelter	907	MPIcheckPoint();
452	tim	934
453	tim	919	delete[] potatoes;
454	tim	934
455	gezelter	415	} else {
456	tim	837
457	gezelter	907	// worldRank != 0, so I'm a remote node.
458	gezelter	916
459			// Set my magic potato to 0:
460
461			myPotato = 0;
462	tim	929	currentIndex = 0;
463	gezelter	907
464			for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
465
466			// Am I the node which has this atom?
467
468			if (AtomToProcMap[i] == worldRank) {
469	tim	837
470	gezelter	916	if (myPotato + 3 >= MAXTAG) {
471
472			// The potato was going to exceed the maximum value,
473			// so wrap this processor potato back to 0 (and block until
474			// node 0 says we can go:
475
476			MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
477
478			}
479	tim	919	which_atom = i;
480	tim	929	local_index = indexArray[currentIndex].first;
481	tim	920
482	tim	929	if (which_atom == indexArray[currentIndex].second) {
483	gezelter	907
484			atomTypeString = atoms[local_index]->getType();
485	tim	837
486	tim	934	atoms[local_index]->getPos(pos);
487			atoms[local_index]->getVel(vel);
488	tim	837
489	gezelter	916	atomData6[0] = pos[0];
490			atomData6[1] = pos[1];
491			atomData6[2] = pos[2];
492	tim	837
493	gezelter	916	atomData6[3] = vel[0];
494			atomData6[4] = vel[1];
495			atomData6[5] = vel[2];
496	gezelter	907
497			isDirectional = 0;
498	tim	837
499	gezelter	907	if( atoms[local_index]->isDirectional() ){
500	mmeineke	377
501	gezelter	907	isDirectional = 1;
502
503			dAtom = (DirectionalAtom *)atoms[local_index];
504			dAtom->getQ( q );
505
506	gezelter	916	for (int j = 0; j < 6 ; j++)
507			atomData13[j] = atomData6[j];
508
509			atomData13[6] = q[0];
510			atomData13[7] = q[1];
511			atomData13[8] = q[2];
512			atomData13[9] = q[3];
513	tim	934
514	gezelter	916	atomData13[10] = dAtom->getJx();
515			atomData13[11] = dAtom->getJy();
516			atomData13[12] = dAtom->getJz();
517	gezelter	907	}
518	tim	837
519	gezelter	907	} else {
520	tim	934	sprintf(painCave.errMsg,
521			"Atom %d not found on processor %d\n",
522			i, worldRank );
523			haveError= 1;
524			simError();
525			}
526	tim	837
527	gezelter	916	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
528	tim	837
529	gezelter	916	// null terminate the string before sending (just in case):
530			MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
531	tim	837
532	gezelter	910	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
533	tim	934	myPotato, MPI_COMM_WORLD);
534	gezelter	907
535	gezelter	916	myPotato++;
536
537	gezelter	907	MPI_Send(&isDirectional, 1, MPI_INT, 0,
538	tim	934	myPotato, MPI_COMM_WORLD);
539	gezelter	907
540	gezelter	916	myPotato++;
541
542	gezelter	907	if (isDirectional) {
543
544	gezelter	916	MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
545			myPotato, MPI_COMM_WORLD);
546	gezelter	907
547	gezelter	916	} else {
548
549			MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
550			myPotato, MPI_COMM_WORLD);
551	gezelter	907	}
552	gezelter	916
553	tim	929	myPotato++;
554			currentIndex++;
555	mmeineke	377	}
556	gezelter	907	}
557	mmeineke	440
558	gezelter	907	sprintf( checkPointMsg,
559	gezelter	916	"Sucessfully took a dump.\n");
560	gezelter	907	MPIcheckPoint();
561
562	gezelter	916	}
563	gezelter	907
564	mmeineke	377	#endif // is_mpi
565			}
566	mmeineke	440
567			#ifdef IS_MPI
568
569			// a couple of functions to let us escape the write loop
570
571	gezelter	907	void dWrite::DieDieDie( void ){
572	tim	837
573	mmeineke	440	MPI_Finalize();
574			exit (0);
575			}
576
577			#endif //is_mpi