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();
    }

    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
  }

  //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();
    finalOut.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){

  vector<ofstream*> fileStreams;

#ifdef IS_MPI
  if(worldRank == 0 ){
    finalOut.seekp(0);
  }
#endif // is_mpi

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

  writeFrame(fileStreams, currentTime);
        
}

void DumpWriter::writeFinal(double currentTime){

  vector<ofstream*> fileStreams;

#ifdef IS_MPI
  if(worldRank == 0 ){
    finalOut.seekp(0);
  }
#endif // is_mpi
  
  fileStreams.push_back(&finalOut);  
  writeFrame(fileStreams, currentTime);
  
}

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:	934
Committed:	Tue Jan 13 20:04:28 2004 UTC (20 years, 5 months ago) by tim
File size:	13174 byte(s)
Log Message:	change the interface of writeFrame
#	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	tim	934	finalOut.open( entry_plug->finalName, ios::out \| ios::trunc );
44			if( !finalOut ){
45			sprintf( painCave.errMsg,
46			"Could not open \"%s\" for final dump output.\n",
47			entry_plug->finalName );
48			painCave.isFatal = 1;
49			simError();
50			}
51	mmeineke	377
52			#ifdef IS_MPI
53			}
54
55	tim	929	//sort the local atoms by global index
56			sortByGlobalIndex();
57
58	mmeineke	377	sprintf( checkPointMsg,
59			"Sucessfully opened output file for dumping.\n");
60			MPIcheckPoint();
61			#endif // is_mpi
62			}
63
64			DumpWriter::~DumpWriter( ){
65
66			#ifdef IS_MPI
67			if(worldRank == 0 ){
68			#endif // is_mpi
69
70	tim	929	dumpFile.close();
71	tim	934	finalOut.close();
72	mmeineke	377
73			#ifdef IS_MPI
74			}
75			#endif // is_mpi
76			}
77
78	tim	929	#ifdef IS_MPI
79	tim	837
80	tim	929	/**
81			* A hook function to load balancing
82			*/
83
84			void DumpWriter::update(){
85			sortByGlobalIndex();
86			}
87
88			/**
89			* Auxiliary sorting function
90			*/
91
92			bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
93			return p1.second < p2.second;
94			}
95
96			/**
97			* Sorting the local index by global index
98			*/
99
100			void DumpWriter::sortByGlobalIndex(){
101			Atom** atoms = entry_plug->atoms;
102
103			indexArray.clear();
104
105			for(int i = 0; i < mpiSim->getMyNlocal();i++)
106			indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
107
108			sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
109			}
110			#endif
111
112			void DumpWriter::writeDump(double currentTime){
113
114	tim	934	vector<ofstream*> fileStreams;
115
116			#ifdef IS_MPI
117			if(worldRank == 0 ){
118			finalOut.seekp(0);
119			}
120			#endif // is_mpi
121
122			fileStreams.push_back(&finalOut);
123			fileStreams.push_back(&dumpFile);
124
125			writeFrame(fileStreams, currentTime);
126	tim	929
127			}
128
129			void DumpWriter::writeFinal(double currentTime){
130
131	tim	934	vector<ofstream*> fileStreams;
132
133	tim	929	#ifdef IS_MPI
134			if(worldRank == 0 ){
135	tim	934	finalOut.seekp(0);
136			}
137	tim	929	#endif // is_mpi
138
139	tim	934	fileStreams.push_back(&finalOut);
140			writeFrame(fileStreams, currentTime);
141	tim	929
142			}
143
144	tim	934	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
145	tim	929
146	mmeineke	377	const int BUFFERSIZE = 2000;
147	gezelter	912	const int MINIBUFFERSIZE = 100;
148	gezelter	907
149	mmeineke	377	char tempBuffer[BUFFERSIZE];
150			char writeLine[BUFFERSIZE];
151
152	tim	934	int i, k;
153	gezelter	916
154	mmeineke	787	#ifdef IS_MPI
155	gezelter	916
156			int *potatoes;
157			int myPotato;
158
159			int nProc;
160	tim	929	int j, which_node, done, which_atom, local_index, currentIndex;
161	gezelter	916	double atomData6[6];
162			double atomData13[13];
163	gezelter	907	int isDirectional;
164			char* atomTypeString;
165	gezelter	910	char MPIatomTypeString[MINIBUFFERSIZE];
166	gezelter	916
167	mmeineke	787	#else //is_mpi
168			int nAtoms = entry_plug->n_atoms;
169			#endif //is_mpi
170
171	mmeineke	377	double q[4];
172			DirectionalAtom* dAtom;
173			Atom** atoms = entry_plug->atoms;
174	mmeineke	670	double pos[3], vel[3];
175	tim	837
176	mmeineke	377	#ifndef IS_MPI
177	tim	934
178			for(k = 0; k < outFile.size(); k++){
179			*outFile[k] << nAtoms << "\n";
180	tim	837
181	tim	934	*outFile[k] << currentTime << ";\t"
182			<< entry_plug->Hmat[0][0] << "\t"
183			<< entry_plug->Hmat[1][0] << "\t"
184			<< entry_plug->Hmat[2][0] << ";\t"
185
186			<< entry_plug->Hmat[0][1] << "\t"
187			<< entry_plug->Hmat[1][1] << "\t"
188			<< entry_plug->Hmat[2][1] << ";\t"
189	tim	837
190	tim	934	<< entry_plug->Hmat[0][2] << "\t"
191			<< entry_plug->Hmat[1][2] << "\t"
192			<< entry_plug->Hmat[2][2] << ";";
193	mmeineke	572
194	tim	934	//write out additional parameters, such as chi and eta
195			*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
196			}
197
198	mmeineke	377	for( i=0; i<nAtoms; i++ ){
199	tim	837
200	mmeineke	670	atoms[i]->getPos(pos);
201			atoms[i]->getVel(vel);
202	mmeineke	377
203			sprintf( tempBuffer,
204			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
205			atoms[i]->getType(),
206	mmeineke	670	pos[0],
207			pos[1],
208			pos[2],
209			vel[0],
210			vel[1],
211			vel[2]);
212	mmeineke	377	strcpy( writeLine, tempBuffer );
213
214			if( atoms[i]->isDirectional() ){
215	tim	837
216	mmeineke	377	dAtom = (DirectionalAtom *)atoms[i];
217			dAtom->getQ( q );
218	tim	837
219	mmeineke	377	sprintf( tempBuffer,
220			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
221			q[0],
222			q[1],
223			q[2],
224			q[3],
225			dAtom->getJx(),
226			dAtom->getJy(),
227			dAtom->getJz());
228			strcat( writeLine, tempBuffer );
229			}
230			else
231			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
232	tim	837
233	tim	934	for(k = 0; k < outFile.size(); k++)
234			*outFile[k] << writeLine;
235	mmeineke	377	}
236
237			#else // is_mpi
238	gezelter	416
239	chuckv	913	/* code to find maximum tag value */
240	tim	919
241	tim	920	int *tagub, flag, MAXTAG;
242	chuckv	913	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
243			if (flag) {
244	tim	920	MAXTAG = *tagub;
245	chuckv	913	} else {
246			MAXTAG = 32767;
247	gezelter	916	}
248	mmeineke	440
249			int haveError;
250
251	mmeineke	447	MPI_Status istatus;
252	gezelter	416	int *AtomToProcMap = mpiSim->getAtomToProcMap();
253	tim	837
254	mmeineke	377	// write out header and node 0's coordinates
255	tim	837
256	mmeineke	377	if( worldRank == 0 ){
257	gezelter	916
258			// Node 0 needs a list of the magic potatoes for each processor;
259
260			nProc = mpiSim->getNumberProcessors();
261			potatoes = new int[nProc];
262
263	tim	934	//write out the comment lines
264	gezelter	916	for (i = 0; i < nProc; i++)
265			potatoes[i] = 0;
266
267	tim	934	for(k = 0; k < outFile.size(); k++){
268			*outFile[k] << mpiSim->getTotAtoms() << "\n";
269	tim	837
270	tim	934	*outFile[k] << currentTime << ";\t"
271			<< entry_plug->Hmat[0][0] << "\t"
272			<< entry_plug->Hmat[1][0] << "\t"
273			<< entry_plug->Hmat[2][0] << ";\t"
274	tim	837
275	tim	934	<< entry_plug->Hmat[0][1] << "\t"
276			<< entry_plug->Hmat[1][1] << "\t"
277			<< entry_plug->Hmat[2][1] << ";\t"
278	tim	837
279	tim	934	<< entry_plug->Hmat[0][2] << "\t"
280			<< entry_plug->Hmat[1][2] << "\t"
281			<< entry_plug->Hmat[2][2] << ";";
282
283			*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
284			}
285	tim	837
286	tim	929	currentIndex = 0;
287	tim	934
288	gezelter	416	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
289	chuckv	913
290	gezelter	417	// Get the Node number which has this atom;
291	chuckv	913
292	tim	837	which_node = AtomToProcMap[i];
293	chuckv	913
294	gezelter	907	if (which_node != 0) {
295	gezelter	916
296			if (potatoes[which_node] + 3 >= MAXTAG) {
297			// The potato was going to exceed the maximum value,
298			// so wrap this processor potato back to 0:
299
300			potatoes[which_node] = 0;
301			MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
302
303			}
304
305			myPotato = potatoes[which_node];
306	gezelter	907
307	gezelter	910	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
308	gezelter	916	myPotato, MPI_COMM_WORLD, &istatus);
309	gezelter	907
310	tim	920	atomTypeString = MPIatomTypeString;
311
312	gezelter	916	myPotato++;
313
314	gezelter	907	MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
315	gezelter	916	myPotato, MPI_COMM_WORLD, &istatus);
316
317			myPotato++;
318	gezelter	907
319	gezelter	916	if (isDirectional) {
320			MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
321			myPotato, MPI_COMM_WORLD, &istatus);
322			} else {
323			MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
324			myPotato, MPI_COMM_WORLD, &istatus);
325	gezelter	907	}
326	gezelter	916
327			myPotato++;
328			potatoes[which_node] = myPotato;
329	gezelter	907
330			} else {
331
332	tim	934	haveError = 0;
333			which_atom = i;
334	gezelter	916
335	tim	929	local_index = indexArray[currentIndex].first;
336
337			if (which_atom == indexArray[currentIndex].second) {
338	gezelter	916
339	gezelter	907	atomTypeString = atoms[local_index]->getType();
340
341	tim	934	atoms[local_index]->getPos(pos);
342			atoms[local_index]->getVel(vel);
343	mmeineke	670
344	gezelter	916	atomData6[0] = pos[0];
345			atomData6[1] = pos[1];
346			atomData6[2] = pos[2];
347	tim	837
348	gezelter	916	atomData6[3] = vel[0];
349			atomData6[4] = vel[1];
350			atomData6[5] = vel[2];
351	gezelter	907
352			isDirectional = 0;
353
354	chuckv	436	if( atoms[local_index]->isDirectional() ){
355	tim	837
356	gezelter	907	isDirectional = 1;
357
358	chuckv	436	dAtom = (DirectionalAtom *)atoms[local_index];
359			dAtom->getQ( q );
360	gezelter	916
361			for (int j = 0; j < 6 ; j++)
362			atomData13[j] = atomData6[j];
363	gezelter	907
364	gezelter	916	atomData13[6] = q[0];
365			atomData13[7] = q[1];
366			atomData13[8] = q[2];
367			atomData13[9] = q[3];
368
369			atomData13[10] = dAtom->getJx();
370			atomData13[11] = dAtom->getJy();
371			atomData13[12] = dAtom->getJz();
372	gezelter	907	}
373	gezelter	916
374	gezelter	907	} else {
375	tim	934	sprintf(painCave.errMsg,
376			"Atom %d not found on processor %d\n",
377			i, worldRank );
378			haveError= 1;
379			simError();
380			}
381	gezelter	916
382	tim	934	if(haveError) DieDieDie();
383	gezelter	916
384	tim	929	currentIndex ++;
385	tim	926	}
386			// If we've survived to here, format the line:
387
388			if (!isDirectional) {
389
390	tim	934	sprintf( writeLine,
391			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
392			atomTypeString,
393			atomData6[0],
394			atomData6[1],
395			atomData6[2],
396			atomData6[3],
397			atomData6[4],
398			atomData6[5]);
399	tim	929
400	tim	934	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
401	tim	926
402			} else {
403
404	tim	934	sprintf( writeLine,
405			"%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",
406			atomTypeString,
407			atomData13[0],
408			atomData13[1],
409			atomData13[2],
410			atomData13[3],
411			atomData13[4],
412			atomData13[5],
413			atomData13[6],
414			atomData13[7],
415			atomData13[8],
416			atomData13[9],
417			atomData13[10],
418			atomData13[11],
419			atomData13[12]);
420	gezelter	907
421			}
422	tim	926
423	tim	934	for(k = 0; k < outFile.size(); k++)
424			*outFile[k] << writeLine;
425	mmeineke	377	}
426	tim	926
427	tim	934	for(k = 0; k < outFile.size(); k++)
428			outFile[k]->flush();
429
430	gezelter	907	sprintf( checkPointMsg,
431			"Sucessfully took a dump.\n");
432	tim	934
433	gezelter	907	MPIcheckPoint();
434	tim	934
435	tim	919	delete[] potatoes;
436	tim	934
437	gezelter	415	} else {
438	tim	837
439	gezelter	907	// worldRank != 0, so I'm a remote node.
440	gezelter	916
441			// Set my magic potato to 0:
442
443			myPotato = 0;
444	tim	929	currentIndex = 0;
445	gezelter	907
446			for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
447
448			// Am I the node which has this atom?
449
450			if (AtomToProcMap[i] == worldRank) {
451	tim	837
452	gezelter	916	if (myPotato + 3 >= MAXTAG) {
453
454			// The potato was going to exceed the maximum value,
455			// so wrap this processor potato back to 0 (and block until
456			// node 0 says we can go:
457
458			MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
459
460			}
461	tim	919	which_atom = i;
462	tim	929	local_index = indexArray[currentIndex].first;
463	tim	920
464	tim	929	if (which_atom == indexArray[currentIndex].second) {
465	gezelter	907
466			atomTypeString = atoms[local_index]->getType();
467	tim	837
468	tim	934	atoms[local_index]->getPos(pos);
469			atoms[local_index]->getVel(vel);
470	tim	837
471	gezelter	916	atomData6[0] = pos[0];
472			atomData6[1] = pos[1];
473			atomData6[2] = pos[2];
474	tim	837
475	gezelter	916	atomData6[3] = vel[0];
476			atomData6[4] = vel[1];
477			atomData6[5] = vel[2];
478	gezelter	907
479			isDirectional = 0;
480	tim	837
481	gezelter	907	if( atoms[local_index]->isDirectional() ){
482	mmeineke	377
483	gezelter	907	isDirectional = 1;
484
485			dAtom = (DirectionalAtom *)atoms[local_index];
486			dAtom->getQ( q );
487
488	gezelter	916	for (int j = 0; j < 6 ; j++)
489			atomData13[j] = atomData6[j];
490
491			atomData13[6] = q[0];
492			atomData13[7] = q[1];
493			atomData13[8] = q[2];
494			atomData13[9] = q[3];
495	tim	934
496	gezelter	916	atomData13[10] = dAtom->getJx();
497			atomData13[11] = dAtom->getJy();
498			atomData13[12] = dAtom->getJz();
499	gezelter	907	}
500	tim	837
501	gezelter	907	} else {
502	tim	934	sprintf(painCave.errMsg,
503			"Atom %d not found on processor %d\n",
504			i, worldRank );
505			haveError= 1;
506			simError();
507			}
508	tim	837
509	gezelter	916	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
510	tim	837
511	gezelter	916	// null terminate the string before sending (just in case):
512			MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
513	tim	837
514	gezelter	910	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
515	tim	934	myPotato, MPI_COMM_WORLD);
516	gezelter	907
517	gezelter	916	myPotato++;
518
519	gezelter	907	MPI_Send(&isDirectional, 1, MPI_INT, 0,
520	tim	934	myPotato, MPI_COMM_WORLD);
521	gezelter	907
522	gezelter	916	myPotato++;
523
524	gezelter	907	if (isDirectional) {
525
526	gezelter	916	MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
527			myPotato, MPI_COMM_WORLD);
528	gezelter	907
529	gezelter	916	} else {
530
531			MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
532			myPotato, MPI_COMM_WORLD);
533	gezelter	907	}
534	gezelter	916
535	tim	929	myPotato++;
536			currentIndex++;
537	mmeineke	377	}
538	gezelter	907	}
539	mmeineke	440
540	gezelter	907	sprintf( checkPointMsg,
541	gezelter	916	"Sucessfully took a dump.\n");
542	gezelter	907	MPIcheckPoint();
543
544	gezelter	916	}
545	gezelter	907
546	mmeineke	377	#endif // is_mpi
547			}
548	mmeineke	440
549			#ifdef IS_MPI
550
551			// a couple of functions to let us escape the write loop
552
553	gezelter	907	void dWrite::DieDieDie( void ){
554	tim	837
555	mmeineke	440	MPI_Finalize();
556			exit (0);
557			}
558
559			#endif //is_mpi