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();
    }

    //outFile.setf( ios::scientific );

#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){
  
// write to eor file
  writeFinal(currentTime);

//write to dump file
  writeFrame(dumpFile, currentTime);
        
}

void DumpWriter::writeFinal(double currentTime){

  ofstream finalOut;    
  
  //Open eor file
#ifdef IS_MPI
  if(worldRank == 0 ){
#endif // is_mpi

    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();
    }
    
#ifdef IS_MPI
  }
#endif
  
  //write to eor file  
  writeFrame(finalOut, currentTime); 
  
  //close eor file      
#ifdef IS_MPI
  if(worldRank == 0 ){
    finalOut.close();
  }
#endif // is_mpi

}

void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){

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

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

  int i;

#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

  outFile << nAtoms << "\n";

  outFile << 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 << entry_plug->the_integrator->getAdditionalParameters();
  outFile << 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" );

    outFile << 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];

    for (i = 0; i < nProc; i++) 
      potatoes[i] = 0;
    
    outFile << mpiSim->getTotAtoms() << "\n";

    outFile << 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 << entry_plug->the_integrator->getAdditionalParameters();
    outFile << endl;
    outFile.flush();
    
    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]);
        
      }
      
      outFile << writeLine;
    }
    

    outFile.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:	929
Committed:	Tue Jan 13 15:46:49 2004 UTC (20 years, 5 months ago) by tim
File size:	12186 byte(s)
Log Message:	Merge the code of writeFinal and writeDump; Adding sortingIndex into DumpWriter; Fix a bug of writing last frame twice in integrator
#	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	//outFile.setf( ios::scientific );
44
45			#ifdef IS_MPI
46			}
47
48	tim	929	//sort the local atoms by global index
49			sortByGlobalIndex();
50
51	mmeineke	377	sprintf( checkPointMsg,
52			"Sucessfully opened output file for dumping.\n");
53			MPIcheckPoint();
54			#endif // is_mpi
55			}
56
57			DumpWriter::~DumpWriter( ){
58
59			#ifdef IS_MPI
60			if(worldRank == 0 ){
61			#endif // is_mpi
62
63	tim	929	dumpFile.close();
64	mmeineke	377
65			#ifdef IS_MPI
66			}
67			#endif // is_mpi
68			}
69
70	tim	929	#ifdef IS_MPI
71	tim	837
72	tim	929	/**
73			* A hook function to load balancing
74			*/
75
76			void DumpWriter::update(){
77			sortByGlobalIndex();
78			}
79
80			/**
81			* Auxiliary sorting function
82			*/
83
84			bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
85			return p1.second < p2.second;
86			}
87
88			/**
89			* Sorting the local index by global index
90			*/
91
92			void DumpWriter::sortByGlobalIndex(){
93			Atom** atoms = entry_plug->atoms;
94
95			indexArray.clear();
96
97			for(int i = 0; i < mpiSim->getMyNlocal();i++)
98			indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
99
100			sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
101			}
102			#endif
103
104			void DumpWriter::writeDump(double currentTime){
105
106			// write to eor file
107			writeFinal(currentTime);
108
109			//write to dump file
110			writeFrame(dumpFile, currentTime);
111
112			}
113
114			void DumpWriter::writeFinal(double currentTime){
115
116			ofstream finalOut;
117
118			//Open eor file
119			#ifdef IS_MPI
120			if(worldRank == 0 ){
121			#endif // is_mpi
122
123			finalOut.open( entry_plug->finalName, ios::out \| ios::trunc );
124			if( !finalOut ){
125			sprintf( painCave.errMsg,
126			"Could not open \"%s\" for final dump output.\n",
127			entry_plug->finalName );
128			painCave.isFatal = 1;
129			simError();
130			}
131
132			#ifdef IS_MPI
133			}
134			#endif
135
136			//write to eor file
137			writeFrame(finalOut, currentTime);
138
139			//close eor file
140			#ifdef IS_MPI
141			if(worldRank == 0 ){
142			finalOut.close();
143			}
144			#endif // is_mpi
145
146			}
147
148			void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){
149
150	mmeineke	377	const int BUFFERSIZE = 2000;
151	gezelter	912	const int MINIBUFFERSIZE = 100;
152	gezelter	907
153	mmeineke	377	char tempBuffer[BUFFERSIZE];
154			char writeLine[BUFFERSIZE];
155
156	mmeineke	787	int i;
157	gezelter	916
158	mmeineke	787	#ifdef IS_MPI
159	gezelter	916
160			int *potatoes;
161			int myPotato;
162
163			int nProc;
164	tim	929	int j, which_node, done, which_atom, local_index, currentIndex;
165	gezelter	916	double atomData6[6];
166			double atomData13[13];
167	gezelter	907	int isDirectional;
168			char* atomTypeString;
169	gezelter	910	char MPIatomTypeString[MINIBUFFERSIZE];
170	gezelter	916
171	mmeineke	787	#else //is_mpi
172			int nAtoms = entry_plug->n_atoms;
173			#endif //is_mpi
174
175	mmeineke	377	double q[4];
176			DirectionalAtom* dAtom;
177			Atom** atoms = entry_plug->atoms;
178	mmeineke	670	double pos[3], vel[3];
179	tim	837
180	mmeineke	377	#ifndef IS_MPI
181	tim	837
182	mmeineke	377	outFile << nAtoms << "\n";
183	tim	837
184			outFile << currentTime << ";\t"
185	mmeineke	590	<< entry_plug->Hmat[0][0] << "\t"
186			<< entry_plug->Hmat[1][0] << "\t"
187			<< entry_plug->Hmat[2][0] << ";\t"
188	mmeineke	572
189	mmeineke	590	<< entry_plug->Hmat[0][1] << "\t"
190			<< entry_plug->Hmat[1][1] << "\t"
191			<< entry_plug->Hmat[2][1] << ";\t"
192	mmeineke	572
193	mmeineke	590	<< entry_plug->Hmat[0][2] << "\t"
194			<< entry_plug->Hmat[1][2] << "\t"
195	tim	837	<< entry_plug->Hmat[2][2] << ";";
196			//write out additional parameters, such as chi and eta
197			outFile << entry_plug->the_integrator->getAdditionalParameters();
198			outFile << endl;
199
200	mmeineke	377	for( i=0; i<nAtoms; i++ ){
201	tim	837
202	mmeineke	670	atoms[i]->getPos(pos);
203			atoms[i]->getVel(vel);
204	mmeineke	377
205			sprintf( tempBuffer,
206			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
207			atoms[i]->getType(),
208	mmeineke	670	pos[0],
209			pos[1],
210			pos[2],
211			vel[0],
212			vel[1],
213			vel[2]);
214	mmeineke	377	strcpy( writeLine, tempBuffer );
215
216			if( atoms[i]->isDirectional() ){
217	tim	837
218	mmeineke	377	dAtom = (DirectionalAtom *)atoms[i];
219			dAtom->getQ( q );
220	tim	837
221	mmeineke	377	sprintf( tempBuffer,
222			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
223			q[0],
224			q[1],
225			q[2],
226			q[3],
227			dAtom->getJx(),
228			dAtom->getJy(),
229			dAtom->getJz());
230			strcat( writeLine, tempBuffer );
231			}
232			else
233			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
234	tim	837
235	mmeineke	377	outFile << writeLine;
236			}
237
238			#else // is_mpi
239	gezelter	416
240	chuckv	913	/* code to find maximum tag value */
241	tim	919
242	tim	920	int *tagub, flag, MAXTAG;
243	chuckv	913	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
244			if (flag) {
245	tim	920	MAXTAG = *tagub;
246	chuckv	913	} else {
247			MAXTAG = 32767;
248	gezelter	916	}
249	mmeineke	440
250			int haveError;
251
252	mmeineke	447	MPI_Status istatus;
253	gezelter	416	int *AtomToProcMap = mpiSim->getAtomToProcMap();
254	tim	837
255	mmeineke	377	// write out header and node 0's coordinates
256	tim	837
257	mmeineke	377	if( worldRank == 0 ){
258	gezelter	916
259			// Node 0 needs a list of the magic potatoes for each processor;
260
261			nProc = mpiSim->getNumberProcessors();
262			potatoes = new int[nProc];
263
264			for (i = 0; i < nProc; i++)
265			potatoes[i] = 0;
266
267	mmeineke	377	outFile << mpiSim->getTotAtoms() << "\n";
268	tim	837
269			outFile << currentTime << ";\t"
270	gezelter	591	<< entry_plug->Hmat[0][0] << "\t"
271			<< entry_plug->Hmat[1][0] << "\t"
272			<< entry_plug->Hmat[2][0] << ";\t"
273	tim	837
274	gezelter	591	<< entry_plug->Hmat[0][1] << "\t"
275			<< entry_plug->Hmat[1][1] << "\t"
276			<< entry_plug->Hmat[2][1] << ";\t"
277	tim	837
278	gezelter	591	<< entry_plug->Hmat[0][2] << "\t"
279			<< entry_plug->Hmat[1][2] << "\t"
280	tim	837	<< entry_plug->Hmat[2][2] << ";";
281
282			outFile << entry_plug->the_integrator->getAdditionalParameters();
283			outFile << endl;
284	chuckv	434	outFile.flush();
285	tim	929
286			currentIndex = 0;
287	gezelter	416	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
288	chuckv	913
289	gezelter	417	// Get the Node number which has this atom;
290	chuckv	913
291	tim	837	which_node = AtomToProcMap[i];
292	chuckv	913
293	gezelter	907	if (which_node != 0) {
294	gezelter	916
295			if (potatoes[which_node] + 3 >= MAXTAG) {
296			// The potato was going to exceed the maximum value,
297			// so wrap this processor potato back to 0:
298
299			potatoes[which_node] = 0;
300			MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
301
302			}
303
304			myPotato = potatoes[which_node];
305	gezelter	907
306	gezelter	910	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
307	gezelter	916	myPotato, MPI_COMM_WORLD, &istatus);
308	gezelter	907
309	tim	920	atomTypeString = MPIatomTypeString;
310
311	gezelter	916	myPotato++;
312
313	gezelter	907	MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
314	gezelter	916	myPotato, MPI_COMM_WORLD, &istatus);
315
316			myPotato++;
317	gezelter	907
318	gezelter	916	if (isDirectional) {
319			MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
320			myPotato, MPI_COMM_WORLD, &istatus);
321			} else {
322			MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
323			myPotato, MPI_COMM_WORLD, &istatus);
324	gezelter	907	}
325	gezelter	916
326			myPotato++;
327			potatoes[which_node] = myPotato;
328	gezelter	907
329			} else {
330
331	mmeineke	440	haveError = 0;
332	chuckv	436	which_atom = i;
333	gezelter	916
334	tim	929	local_index = indexArray[currentIndex].first;
335
336			if (which_atom == indexArray[currentIndex].second) {
337	gezelter	916
338	gezelter	907	atomTypeString = atoms[local_index]->getType();
339
340	mmeineke	670	atoms[local_index]->getPos(pos);
341	gezelter	916	atoms[local_index]->getVel(vel);
342	mmeineke	670
343	gezelter	916	atomData6[0] = pos[0];
344			atomData6[1] = pos[1];
345			atomData6[2] = pos[2];
346	tim	837
347	gezelter	916	atomData6[3] = vel[0];
348			atomData6[4] = vel[1];
349			atomData6[5] = vel[2];
350	gezelter	907
351			isDirectional = 0;
352
353	chuckv	436	if( atoms[local_index]->isDirectional() ){
354	tim	837
355	gezelter	907	isDirectional = 1;
356
357	chuckv	436	dAtom = (DirectionalAtom *)atoms[local_index];
358			dAtom->getQ( q );
359	gezelter	916
360			for (int j = 0; j < 6 ; j++)
361			atomData13[j] = atomData6[j];
362	gezelter	907
363	gezelter	916	atomData13[6] = q[0];
364			atomData13[7] = q[1];
365			atomData13[8] = q[2];
366			atomData13[9] = q[3];
367
368			atomData13[10] = dAtom->getJx();
369			atomData13[11] = dAtom->getJy();
370			atomData13[12] = dAtom->getJz();
371	gezelter	907	}
372	gezelter	916
373	gezelter	907	} else {
374	mmeineke	440	sprintf(painCave.errMsg,
375			"Atom %d not found on processor %d\n",
376			i, worldRank );
377			haveError= 1;
378			simError();
379	tim	837	}
380	gezelter	916
381	gezelter	907	if(haveError) DieDieDie();
382	gezelter	916
383	tim	929	currentIndex ++;
384	tim	926	}
385			// If we've survived to here, format the line:
386
387			if (!isDirectional) {
388
389	tim	929	sprintf( writeLine,
390	tim	926	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
391			atomTypeString,
392			atomData6[0],
393			atomData6[1],
394			atomData6[2],
395			atomData6[3],
396			atomData6[4],
397			atomData6[5]);
398	tim	929
399	tim	926	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
400
401			} else {
402
403	tim	929	sprintf( writeLine,
404	tim	926	"%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",
405			atomTypeString,
406			atomData13[0],
407			atomData13[1],
408			atomData13[2],
409			atomData13[3],
410			atomData13[4],
411			atomData13[5],
412			atomData13[6],
413			atomData13[7],
414			atomData13[8],
415			atomData13[9],
416			atomData13[10],
417			atomData13[11],
418			atomData13[12]);
419	gezelter	907
420			}
421	tim	926
422			outFile << writeLine;
423	mmeineke	377	}
424	tim	926
425	mmeineke	377
426	gezelter	907	outFile.flush();
427			sprintf( checkPointMsg,
428			"Sucessfully took a dump.\n");
429			MPIcheckPoint();
430	tim	919	delete[] potatoes;
431	gezelter	415	} else {
432	tim	837
433	gezelter	907	// worldRank != 0, so I'm a remote node.
434	gezelter	916
435			// Set my magic potato to 0:
436
437			myPotato = 0;
438	tim	929	currentIndex = 0;
439	gezelter	907
440			for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
441
442			// Am I the node which has this atom?
443
444			if (AtomToProcMap[i] == worldRank) {
445	tim	837
446	gezelter	916	if (myPotato + 3 >= MAXTAG) {
447
448			// The potato was going to exceed the maximum value,
449			// so wrap this processor potato back to 0 (and block until
450			// node 0 says we can go:
451
452			MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
453
454			}
455	tim	919	which_atom = i;
456	tim	929	local_index = indexArray[currentIndex].first;
457	tim	920
458	tim	929	if (which_atom == indexArray[currentIndex].second) {
459	gezelter	907
460			atomTypeString = atoms[local_index]->getType();
461	tim	837
462	gezelter	907	atoms[local_index]->getPos(pos);
463			atoms[local_index]->getVel(vel);
464	tim	837
465	gezelter	916	atomData6[0] = pos[0];
466			atomData6[1] = pos[1];
467			atomData6[2] = pos[2];
468	tim	837
469	gezelter	916	atomData6[3] = vel[0];
470			atomData6[4] = vel[1];
471			atomData6[5] = vel[2];
472	gezelter	907
473			isDirectional = 0;
474	tim	837
475	gezelter	907	if( atoms[local_index]->isDirectional() ){
476	mmeineke	377
477	gezelter	907	isDirectional = 1;
478
479			dAtom = (DirectionalAtom *)atoms[local_index];
480			dAtom->getQ( q );
481
482	gezelter	916	for (int j = 0; j < 6 ; j++)
483			atomData13[j] = atomData6[j];
484
485			atomData13[6] = q[0];
486			atomData13[7] = q[1];
487			atomData13[8] = q[2];
488			atomData13[9] = q[3];
489	mmeineke	670
490	gezelter	916	atomData13[10] = dAtom->getJx();
491			atomData13[11] = dAtom->getJy();
492			atomData13[12] = dAtom->getJz();
493	gezelter	907	}
494	tim	837
495	gezelter	907	} else {
496			sprintf(painCave.errMsg,
497			"Atom %d not found on processor %d\n",
498			i, worldRank );
499			haveError= 1;
500			simError();
501			}
502	tim	837
503	gezelter	916	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
504	tim	837
505	gezelter	916	// null terminate the string before sending (just in case):
506			MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
507	tim	837
508	gezelter	910	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
509	gezelter	916	myPotato, MPI_COMM_WORLD);
510	gezelter	907
511	gezelter	916	myPotato++;
512
513	gezelter	907	MPI_Send(&isDirectional, 1, MPI_INT, 0,
514	gezelter	916	myPotato, MPI_COMM_WORLD);
515	gezelter	907
516	gezelter	916	myPotato++;
517
518	gezelter	907	if (isDirectional) {
519
520	gezelter	916	MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
521			myPotato, MPI_COMM_WORLD);
522	gezelter	907
523	gezelter	916	} else {
524
525			MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
526			myPotato, MPI_COMM_WORLD);
527	gezelter	907	}
528	gezelter	916
529	tim	929	myPotato++;
530			currentIndex++;
531	mmeineke	377	}
532	gezelter	907	}
533	mmeineke	440
534	gezelter	907	sprintf( checkPointMsg,
535	gezelter	916	"Sucessfully took a dump.\n");
536	gezelter	907	MPIcheckPoint();
537
538	gezelter	916	}
539	gezelter	907
540	mmeineke	377	#endif // is_mpi
541			}
542	mmeineke	440
543			#ifdef IS_MPI
544
545			// a couple of functions to let us escape the write loop
546
547	gezelter	907	void dWrite::DieDieDie( void ){
548	tim	837
549	mmeineke	440	MPI_Finalize();
550			exit (0);
551			}
552
553			#endif //is_mpi