OOPSE/libmdtools/DumpWriter.cpp

#include <cstring>
#include <iostream>
#include <fstream>

#ifdef IS_MPI
#include <mpi.h>
#include "mpiSimulation.hpp"
#define TAKE_THIS_TAG_CHAR 1
#define TAKE_THIS_TAG_INT 2

namespace dWrite{
  void nodeZeroError( void );
  void anonymousNodeDie( void );
}

using namespace dWrite;
#endif //is_mpi

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

DumpWriter::DumpWriter( SimInfo* the_entry_plug ){

  entry_plug = the_entry_plug;

  std::cerr << "Look at me I'm a freebird!\n";

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

    std::cerr << "me TOO!\n";

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

#ifdef IS_MPI
  }

  sprintf( checkPointMsg,
           "Sucessfully opened output file for dumping.\n");
  MPIcheckPoint();
#endif // is_mpi
}

DumpWriter::~DumpWriter( ){

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

    outFile.close();

#ifdef IS_MPI
  }
#endif // is_mpi
}

void DumpWriter::writeDump( double currentTime ){
  
  const int BUFFERSIZE = 2000;
  char tempBuffer[BUFFERSIZE];
  char writeLine[BUFFERSIZE];

  int i, j, which_node, done, which_atom, local_index;
  double q[4];
  DirectionalAtom* dAtom;
  int nAtoms = entry_plug->n_atoms;
  Atom** atoms = entry_plug->atoms;
    

#ifndef IS_MPI
    
  outFile << nAtoms << "\n";
    
  outFile << currentTime << "\t" 
          << entry_plug->box_x << "\t"
          << entry_plug->box_y << "\t"
          << entry_plug->box_z << "\n";
    
  for( i=0; i<nAtoms; i++ ){
      

    sprintf( tempBuffer,
             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
             atoms[i]->getType(),
             atoms[i]->getX(),
             atoms[i]->getY(),
             atoms[i]->getZ(),
             atoms[i]->get_vx(),
             atoms[i]->get_vy(),
             atoms[i]->get_vz());
    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;
  }
  outFile.flush();

#else // is_mpi

  // first thing first, suspend fatalities.
  painCave.isEventLoop = 1;

  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
  int haveError;

  MPI_Status istatus;
  int *AtomToProcMap = mpiSim->getAtomToProcMap();
  
  // write out header and node 0's coordinates
  
  if( worldRank == 0 ){
    outFile << mpiSim->getTotAtoms() << "\n";
    
    outFile << currentTime << "\t" 
            << entry_plug->box_x << "\t"
            << entry_plug->box_y << "\t"
            << entry_plug->box_z << "\n";
    outFile.flush();
    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
      // Get the Node number which has this atom;
      
      which_node = AtomToProcMap[i];     
      
      if (which_node == 0 ) {
        
        haveError = 0;
        which_atom = i;
        local_index=-1;        
        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
        }
        if (local_index != -1) {
          //format the line
          sprintf( tempBuffer,
                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                   atoms[local_index]->getType(),
                   atoms[local_index]->getX(),
                   atoms[local_index]->getY(),
                   atoms[local_index]->getZ(),
                   atoms[local_index]->get_vx(),
                   atoms[local_index]->get_vy(),
                   atoms[local_index]->get_vz()); // check here.
          strcpy( writeLine, tempBuffer );
          
          if( atoms[local_index]->isDirectional() ){
            
            dAtom = (DirectionalAtom *)atoms[local_index];
            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" );       
        }
        else {
          sprintf(painCave.errMsg,
                  "Atom %d not found on processor %d\n",
                  i, worldRank );
          haveError= 1;
          simError();
        } 
        
        if(haveError) nodeZeroError();

      }
      else {
        myStatus = 1;
        MPI_Send(&myStatus, 1, MPI_INT, which_node, 
                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, 
                 MPI_COMM_WORLD);
        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
        MPI_Recv(&myStatus, 1, MPI_INT, which_node, 
                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
        
        if(!myStatus) nodeZeroError();

      }
      
      outFile << writeLine;
      outFile.flush();
    }
    
    // kill everyone off:
    myStatus = -1;
    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
      MPI_Send(&myStatus, 1, MPI_INT, j, 
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
    }

  } else {
    
    done = 0;
    while (!done) {
      
      MPI_Recv(&myStatus, 1, MPI_INT, 0, 
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);

      if(!myStatus) anonymousNodeDie();
      
      if(myStatus < 0) break;

      MPI_Recv(&which_atom, 1, MPI_INT, 0, 
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
      
      myStatus = 1;
      local_index=-1;        
      for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
      }
      if (local_index != -1) {
        //format the line
        sprintf( tempBuffer,
                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                 atoms[local_index]->getType(),
                 atoms[local_index]->getX(),
                 atoms[local_index]->getY(),
                 atoms[local_index]->getZ(),
                 atoms[local_index]->get_vx(),
                 atoms[local_index]->get_vy(),
                 atoms[local_index]->get_vz()); // check here.
        strcpy( writeLine, tempBuffer );
        
        if( atoms[local_index]->isDirectional() ){
          
          dAtom = (DirectionalAtom *)atoms[local_index];
          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" );
        }
      } 
      else {
        sprintf(painCave.errMsg,
                "Atom %d not found on processor %d\n",
                which_atom, worldRank );
        myStatus = 0;
        simError();

        strcpy( writeLine, "Hello, I'm an error.\n");
      }

      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, 
               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
      MPI_Send( &myStatus, 1, MPI_INT, 0, 
                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
    }
  }  
  outFile.flush();
  sprintf( checkPointMsg,
           "Sucessfully took a dump.\n");
  MPIcheckPoint();

 // last  thing last, enable  fatalities.
  painCave.isEventLoop = 0;

#endif // is_mpi
}

void DumpWriter::writeFinal(){

  char finalName[500];
  ofstream finalOut;

  const int BUFFERSIZE = 2000;
  char tempBuffer[BUFFERSIZE];
  char writeLine[BUFFERSIZE];  

  double q[4];
  DirectionalAtom* dAtom;
  int nAtoms = entry_plug->n_atoms;
  Atom** atoms = entry_plug->atoms;
  int i, j, which_node, done, game_over, which_atom, local_index;
  
  
#ifdef IS_MPI
  if(worldRank == 0 ){
#endif // is_mpi
    
    strcpy( finalName, entry_plug->finalName );
    
    finalOut.open( finalName, ios::out | ios::trunc );
    if( !finalOut ){
      sprintf( painCave.errMsg,
               "Could not open \"%s\" for final dump output.\n",
               finalName );
      painCave.isFatal = 1;
      simError();
    }
    
    // finalOut.setf( ios::scientific );
    
#ifdef IS_MPI
  }
  
  sprintf(checkPointMsg,"Opened file for final configuration\n");
  MPIcheckPoint();  
  
#endif //is_mpi

  
#ifndef IS_MPI
    
  finalOut << nAtoms << "\n";
    
  finalOut << entry_plug->box_x << "\t"
           << entry_plug->box_y << "\t"
           << entry_plug->box_z << "\n";
  
  for( i=0; i<nAtoms; i++ ){
      
    sprintf( tempBuffer,
             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
             atoms[i]->getType(),
             atoms[i]->getX(),
             atoms[i]->getY(),
             atoms[i]->getZ(),
             atoms[i]->get_vx(),
             atoms[i]->get_vy(),
             atoms[i]->get_vz());
    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" );
      
    finalOut << writeLine;
  }
  finalOut.flush();
  finalOut.close();

#else // is_mpi
  
  // first thing first, suspend fatalities.
  painCave.isEventLoop = 1;

  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
  int haveError;

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

  // write out header and node 0's coordinates
  
  haveError = 0;
  if( worldRank == 0 ){
    finalOut << mpiSim->getTotAtoms() << "\n";
    
    finalOut << entry_plug->box_x << "\t"
            << entry_plug->box_y << "\t"
            << entry_plug->box_z << "\n";
    
    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
      // Get the Node number which has this molecule:
      
      which_node = AtomToProcMap[i];     
      
      if (which_node == mpiSim->getMyNode()) {

        which_atom = i;
        local_index=-1;        
        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
        }
        if (local_index != -1) {        
          sprintf( tempBuffer,
                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                   atoms[local_index]->getType(),
                   atoms[local_index]->getX(),
                   atoms[local_index]->getY(),
                   atoms[local_index]->getZ(),
                   atoms[local_index]->get_vx(),
                   atoms[local_index]->get_vy(),
                   atoms[local_index]->get_vz());
          strcpy( writeLine, tempBuffer );
          
          if( atoms[local_index]->isDirectional() ){
            
            dAtom = (DirectionalAtom *)atoms[local_index];
            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" );       
        }
        else {
          sprintf(painCave.errMsg,
                  "Atom %d not found on processor %d\n",
                  i, worldRank );
          haveError= 1;
          simError();
        } 

        if(haveError) nodeZeroError();
     
      } 
      else {
        
        myStatus = 1;
        MPI_Send(&myStatus, 1, MPI_INT, which_node, 
                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
                 MPI_COMM_WORLD);
        MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
        MPI_Recv(&myStatus, 1, MPI_INT, which_node, 
                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
        
        if(!myStatus) nodeZeroError();
      }
      
      finalOut << writeLine;
    }
    
    // kill everyone off:
    myStatus = -1;
    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
      MPI_Send(&myStatus, 1, MPI_INT, j, 
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
    }

  } else {
    
    done = 0;
    while (!done) {

      MPI_Recv(&myStatus, 1, MPI_INT, 0, 
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
      
      if(!myStatus) anonymousNodeDie();
      
      if(myStatus < 0) break;
      
      MPI_Recv(&which_atom, 1, MPI_INT, 0, 
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
      
      myStatus = 1;
      local_index=-1;        
      for (j=0; j < mpiSim->getMyNlocal(); j++) {
        if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
      }
      if (local_index != -1) {

        //format the line
        sprintf( tempBuffer,
                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                 atoms[local_index]->getType(),
                 atoms[local_index]->getX(),
                 atoms[local_index]->getY(),
                 atoms[local_index]->getZ(),
                 atoms[local_index]->get_vx(),
                 atoms[local_index]->get_vy(),
                 atoms[local_index]->get_vz()); // check here.
        strcpy( writeLine, tempBuffer );
        
        if( atoms[local_index]->isDirectional() ){
          
          dAtom = (DirectionalAtom *)atoms[local_index];
          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" );
        }
      } 
      else {
        sprintf(painCave.errMsg,
                "Atom %d not found on processor %d\n",
                which_atom, worldRank );
        myStatus = 0;
        simError();
        
        strcpy( writeLine, "Hello, I'm an error.\n");
      }

      MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, 
               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
      MPI_Send( &myStatus, 1, MPI_INT, 0, 
                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
    }
  }
  finalOut.flush();
  sprintf( checkPointMsg,
           "Sucessfully took a dump.\n");
  MPIcheckPoint();
  
  if( worldRank == 0 ) finalOut.close();    
#endif // is_mpi
}


#ifdef IS_MPI

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

void dWrite::nodeZeroError( void ){
  int j, myStatus;
  
  myStatus = 0;
  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
    MPI_Send( &myStatus, 1, MPI_INT, j, 
              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
  }  
  

  MPI_Finalize();
  exit (0);
  
}

void dWrite::anonymousNodeDie( void ){

  MPI_Finalize();
  exit (0);
}

#endif //is_mpi
Revision:	469
Committed:	Mon Apr 7 20:06:31 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	14284 byte(s)
Log Message:	bug fixes
#	User	Rev	Content
1	mmeineke	377	#include <cstring>
2			#include <iostream>
3			#include <fstream>
4
5			#ifdef IS_MPI
6			#include <mpi.h>
7			#include "mpiSimulation.hpp"
8	chuckv	436	#define TAKE_THIS_TAG_CHAR 1
9			#define TAKE_THIS_TAG_INT 2
10	mmeineke	440
11			namespace dWrite{
12			void nodeZeroError( void );
13			void anonymousNodeDie( void );
14			}
15
16			using namespace dWrite;
17	mmeineke	377	#endif //is_mpi
18
19			#include "ReadWrite.hpp"
20			#include "simError.h"
21
22			DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
23
24			entry_plug = the_entry_plug;
25
26	mmeineke	469	std::cerr << "Look at me I'm a freebird!\n";
27
28	mmeineke	377	#ifdef IS_MPI
29			if(worldRank == 0 ){
30			#endif // is_mpi
31
32
33
34			strcpy( outName, entry_plug->sampleName );
35
36			outFile.open(outName, ios::out \| ios::trunc );
37
38			if( !outFile ){
39
40			sprintf( painCave.errMsg,
41			"Could not open \"%s\" for dump output.\n",
42			outName);
43			painCave.isFatal = 1;
44			simError();
45			}
46	mmeineke	469
47			std::cerr << "me TOO!\n";
48
49	mmeineke	377	//outFile.setf( ios::scientific );
50
51			#ifdef IS_MPI
52			}
53
54			sprintf( checkPointMsg,
55			"Sucessfully opened output file for dumping.\n");
56			MPIcheckPoint();
57			#endif // is_mpi
58			}
59
60			DumpWriter::~DumpWriter( ){
61
62			#ifdef IS_MPI
63			if(worldRank == 0 ){
64			#endif // is_mpi
65
66			outFile.close();
67
68			#ifdef IS_MPI
69			}
70			#endif // is_mpi
71			}
72
73			void DumpWriter::writeDump( double currentTime ){
74
75			const int BUFFERSIZE = 2000;
76			char tempBuffer[BUFFERSIZE];
77			char writeLine[BUFFERSIZE];
78
79	mmeineke	450	int i, j, which_node, done, which_atom, local_index;
80	mmeineke	377	double q[4];
81			DirectionalAtom* dAtom;
82			int nAtoms = entry_plug->n_atoms;
83			Atom** atoms = entry_plug->atoms;
84
85
86			#ifndef IS_MPI
87
88			outFile << nAtoms << "\n";
89
90			outFile << currentTime << "\t"
91			<< entry_plug->box_x << "\t"
92			<< entry_plug->box_y << "\t"
93			<< entry_plug->box_z << "\n";
94
95			for( i=0; i<nAtoms; i++ ){
96
97
98			sprintf( tempBuffer,
99			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
100			atoms[i]->getType(),
101			atoms[i]->getX(),
102			atoms[i]->getY(),
103			atoms[i]->getZ(),
104			atoms[i]->get_vx(),
105			atoms[i]->get_vy(),
106			atoms[i]->get_vz());
107			strcpy( writeLine, tempBuffer );
108
109			if( atoms[i]->isDirectional() ){
110
111			dAtom = (DirectionalAtom *)atoms[i];
112			dAtom->getQ( q );
113
114			sprintf( tempBuffer,
115			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
116			q[0],
117			q[1],
118			q[2],
119			q[3],
120			dAtom->getJx(),
121			dAtom->getJy(),
122			dAtom->getJz());
123			strcat( writeLine, tempBuffer );
124			}
125			else
126			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
127
128			outFile << writeLine;
129			}
130			outFile.flush();
131
132			#else // is_mpi
133	gezelter	416
134	mmeineke	440	// first thing first, suspend fatalities.
135			painCave.isEventLoop = 1;
136
137			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
138			int haveError;
139
140	mmeineke	447	MPI_Status istatus;
141	gezelter	416	int *AtomToProcMap = mpiSim->getAtomToProcMap();
142	gezelter	415
143	mmeineke	377	// write out header and node 0's coordinates
144	gezelter	415
145	mmeineke	377	if( worldRank == 0 ){
146			outFile << mpiSim->getTotAtoms() << "\n";
147	gezelter	415
148	mmeineke	377	outFile << currentTime << "\t"
149			<< entry_plug->box_x << "\t"
150			<< entry_plug->box_y << "\t"
151			<< entry_plug->box_z << "\n";
152	chuckv	434	outFile.flush();
153	gezelter	416	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
154	gezelter	417	// Get the Node number which has this atom;
155	mmeineke	377
156	gezelter	415	which_node = AtomToProcMap[i];
157
158	chuckv	436	if (which_node == 0 ) {
159	mmeineke	377
160	mmeineke	440	haveError = 0;
161	chuckv	436	which_atom = i;
162			local_index=-1;
163			for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
164			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
165			}
166			if (local_index != -1) {
167			//format the line
168			sprintf( tempBuffer,
169			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
170			atoms[local_index]->getType(),
171			atoms[local_index]->getX(),
172			atoms[local_index]->getY(),
173			atoms[local_index]->getZ(),
174			atoms[local_index]->get_vx(),
175			atoms[local_index]->get_vy(),
176			atoms[local_index]->get_vz()); // check here.
177			strcpy( writeLine, tempBuffer );
178	mmeineke	377
179	chuckv	436	if( atoms[local_index]->isDirectional() ){
180
181			dAtom = (DirectionalAtom *)atoms[local_index];
182			dAtom->getQ( q );
183
184			sprintf( tempBuffer,
185			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
186			q[0],
187			q[1],
188			q[2],
189			q[3],
190			dAtom->getJx(),
191			dAtom->getJy(),
192			dAtom->getJz());
193			strcat( writeLine, tempBuffer );
194
195			}
196			else
197			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
198			}
199			else {
200	mmeineke	440	sprintf(painCave.errMsg,
201			"Atom %d not found on processor %d\n",
202			i, worldRank );
203			haveError= 1;
204			simError();
205	chuckv	436	}
206	mmeineke	440
207			if(haveError) nodeZeroError();
208
209			}
210	chuckv	436	else {
211	mmeineke	440	myStatus = 1;
212	mmeineke	447	MPI_Send(&myStatus, 1, MPI_INT, which_node,
213			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
214			MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
215			MPI_COMM_WORLD);
216			MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
217			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
218			MPI_Recv(&myStatus, 1, MPI_INT, which_node,
219			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
220	mmeineke	440
221			if(!myStatus) nodeZeroError();
222
223	mmeineke	377	}
224	gezelter	415
225	mmeineke	377	outFile << writeLine;
226	chuckv	434	outFile.flush();
227	mmeineke	377	}
228
229	gezelter	415	// kill everyone off:
230	mmeineke	440	myStatus = -1;
231	gezelter	416	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
232	mmeineke	447	MPI_Send(&myStatus, 1, MPI_INT, j,
233			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
234	mmeineke	377	}
235
236	gezelter	415	} else {
237
238			done = 0;
239			while (!done) {
240	mmeineke	440
241	mmeineke	447	MPI_Recv(&myStatus, 1, MPI_INT, 0,
242			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
243	mmeineke	440
244			if(!myStatus) anonymousNodeDie();
245
246			if(myStatus < 0) break;
247
248	mmeineke	447	MPI_Recv(&which_atom, 1, MPI_INT, 0,
249			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
250	mmeineke	440
251			myStatus = 1;
252			local_index=-1;
253			for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
254			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
255			}
256			if (local_index != -1) {
257			//format the line
258			sprintf( tempBuffer,
259			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
260			atoms[local_index]->getType(),
261			atoms[local_index]->getX(),
262			atoms[local_index]->getY(),
263			atoms[local_index]->getZ(),
264			atoms[local_index]->get_vx(),
265			atoms[local_index]->get_vy(),
266			atoms[local_index]->get_vz()); // check here.
267			strcpy( writeLine, tempBuffer );
268
269			if( atoms[local_index]->isDirectional() ){
270	mmeineke	377
271	mmeineke	440	dAtom = (DirectionalAtom *)atoms[local_index];
272			dAtom->getQ( q );
273
274			sprintf( tempBuffer,
275			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
276			q[0],
277			q[1],
278			q[2],
279			q[3],
280			dAtom->getJx(),
281			dAtom->getJy(),
282			dAtom->getJz());
283			strcat( writeLine, tempBuffer );
284			}
285			else{
286			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
287			}
288			}
289			else {
290			sprintf(painCave.errMsg,
291			"Atom %d not found on processor %d\n",
292			which_atom, worldRank );
293			myStatus = 0;
294			simError();
295
296			strcpy( writeLine, "Hello, I'm an error.\n");
297	mmeineke	377	}
298	mmeineke	440
299	mmeineke	447	MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
300			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
301			MPI_Send( &myStatus, 1, MPI_INT, 0,
302			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
303	mmeineke	377	}
304	gezelter	415	}
305			outFile.flush();
306			sprintf( checkPointMsg,
307			"Sucessfully took a dump.\n");
308			MPIcheckPoint();
309	mmeineke	440
310			// last thing last, enable fatalities.
311			painCave.isEventLoop = 0;
312
313	mmeineke	377	#endif // is_mpi
314			}
315
316			void DumpWriter::writeFinal(){
317	gezelter	416
318	mmeineke	377	char finalName[500];
319			ofstream finalOut;
320	gezelter	416
321			const int BUFFERSIZE = 2000;
322			char tempBuffer[BUFFERSIZE];
323			char writeLine[BUFFERSIZE];
324
325			double q[4];
326			DirectionalAtom* dAtom;
327			int nAtoms = entry_plug->n_atoms;
328			Atom** atoms = entry_plug->atoms;
329	gezelter	419	int i, j, which_node, done, game_over, which_atom, local_index;
330	mmeineke	377
331	gezelter	416
332	mmeineke	377	#ifdef IS_MPI
333			if(worldRank == 0 ){
334			#endif // is_mpi
335
336			strcpy( finalName, entry_plug->finalName );
337
338			finalOut.open( finalName, ios::out \| ios::trunc );
339			if( !finalOut ){
340			sprintf( painCave.errMsg,
341			"Could not open \"%s\" for final dump output.\n",
342			finalName );
343			painCave.isFatal = 1;
344			simError();
345			}
346
347			// finalOut.setf( ios::scientific );
348
349			#ifdef IS_MPI
350			}
351
352			sprintf(checkPointMsg,"Opened file for final configuration\n");
353			MPIcheckPoint();
354
355			#endif //is_mpi
356
357	gezelter	415
358	mmeineke	377	#ifndef IS_MPI
359
360			finalOut << nAtoms << "\n";
361
362			finalOut << entry_plug->box_x << "\t"
363			<< entry_plug->box_y << "\t"
364			<< entry_plug->box_z << "\n";
365	gezelter	416
366	mmeineke	377	for( i=0; i<nAtoms; i++ ){
367
368			sprintf( tempBuffer,
369			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
370			atoms[i]->getType(),
371			atoms[i]->getX(),
372			atoms[i]->getY(),
373			atoms[i]->getZ(),
374			atoms[i]->get_vx(),
375			atoms[i]->get_vy(),
376			atoms[i]->get_vz());
377			strcpy( writeLine, tempBuffer );
378
379			if( atoms[i]->isDirectional() ){
380
381			dAtom = (DirectionalAtom *)atoms[i];
382			dAtom->getQ( q );
383
384			sprintf( tempBuffer,
385			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
386			q[0],
387			q[1],
388			q[2],
389			q[3],
390			dAtom->getJx(),
391			dAtom->getJy(),
392			dAtom->getJz());
393			strcat( writeLine, tempBuffer );
394			}
395			else
396			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
397
398			finalOut << writeLine;
399			}
400			finalOut.flush();
401	gezelter	415	finalOut.close();
402	mmeineke	377
403			#else // is_mpi
404	gezelter	415
405	mmeineke	440	// first thing first, suspend fatalities.
406			painCave.isEventLoop = 1;
407
408			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
409			int haveError;
410
411	mmeineke	447	MPI_Status istatus;
412	gezelter	416	int *AtomToProcMap = mpiSim->getAtomToProcMap();
413
414	mmeineke	377	// write out header and node 0's coordinates
415	gezelter	415
416	mmeineke	440	haveError = 0;
417	mmeineke	377	if( worldRank == 0 ){
418			finalOut << mpiSim->getTotAtoms() << "\n";
419	gezelter	415
420	mmeineke	377	finalOut << entry_plug->box_x << "\t"
421	gezelter	415	<< entry_plug->box_y << "\t"
422			<< entry_plug->box_z << "\n";
423	mmeineke	377
424	gezelter	416	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
425	gezelter	415	// Get the Node number which has this molecule:
426	mmeineke	377
427	gezelter	415	which_node = AtomToProcMap[i];
428
429	gezelter	416	if (which_node == mpiSim->getMyNode()) {
430	chuckv	437
431			which_atom = i;
432			local_index=-1;
433			for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
434			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
435			}
436			if (local_index != -1) {
437			sprintf( tempBuffer,
438			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
439			atoms[local_index]->getType(),
440			atoms[local_index]->getX(),
441			atoms[local_index]->getY(),
442			atoms[local_index]->getZ(),
443			atoms[local_index]->get_vx(),
444			atoms[local_index]->get_vy(),
445			atoms[local_index]->get_vz());
446			strcpy( writeLine, tempBuffer );
447	mmeineke	377
448	chuckv	437	if( atoms[local_index]->isDirectional() ){
449
450			dAtom = (DirectionalAtom *)atoms[local_index];
451			dAtom->getQ( q );
452
453			sprintf( tempBuffer,
454			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
455			q[0],
456			q[1],
457			q[2],
458			q[3],
459			dAtom->getJx(),
460			dAtom->getJy(),
461			dAtom->getJz());
462			strcat( writeLine, tempBuffer );
463			}
464			else
465			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
466			}
467			else {
468	mmeineke	440	sprintf(painCave.errMsg,
469			"Atom %d not found on processor %d\n",
470			i, worldRank );
471			haveError= 1;
472			simError();
473	chuckv	437	}
474	mmeineke	440
475			if(haveError) nodeZeroError();
476	chuckv	437
477	mmeineke	440	}
478			else {
479	gezelter	415
480	mmeineke	440	myStatus = 1;
481	mmeineke	447	MPI_Send(&myStatus, 1, MPI_INT, which_node,
482			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
483			MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
484			MPI_COMM_WORLD);
485			MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
486			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
487			MPI_Recv(&myStatus, 1, MPI_INT, which_node,
488			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
489	mmeineke	440
490			if(!myStatus) nodeZeroError();
491	mmeineke	377	}
492	gezelter	415
493	mmeineke	377	finalOut << writeLine;
494			}
495
496	gezelter	415	// kill everyone off:
497	mmeineke	440	myStatus = -1;
498			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
499	mmeineke	447	MPI_Send(&myStatus, 1, MPI_INT, j,
500			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
501	mmeineke	377	}
502
503	gezelter	415	} else {
504
505			done = 0;
506			while (!done) {
507	mmeineke	440
508	mmeineke	447	MPI_Recv(&myStatus, 1, MPI_INT, 0,
509			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
510	mmeineke	440
511			if(!myStatus) anonymousNodeDie();
512
513			if(myStatus < 0) break;
514
515	mmeineke	447	MPI_Recv(&which_atom, 1, MPI_INT, 0,
516			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
517	mmeineke	440
518			myStatus = 1;
519			local_index=-1;
520			for (j=0; j < mpiSim->getMyNlocal(); j++) {
521			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
522			}
523			if (local_index != -1) {
524	mmeineke	377
525	mmeineke	440	//format the line
526			sprintf( tempBuffer,
527			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
528			atoms[local_index]->getType(),
529			atoms[local_index]->getX(),
530			atoms[local_index]->getY(),
531			atoms[local_index]->getZ(),
532			atoms[local_index]->get_vx(),
533			atoms[local_index]->get_vy(),
534			atoms[local_index]->get_vz()); // check here.
535			strcpy( writeLine, tempBuffer );
536
537			if( atoms[local_index]->isDirectional() ){
538	mmeineke	377
539	mmeineke	440	dAtom = (DirectionalAtom *)atoms[local_index];
540			dAtom->getQ( q );
541
542			sprintf( tempBuffer,
543			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
544			q[0],
545			q[1],
546			q[2],
547			q[3],
548			dAtom->getJx(),
549			dAtom->getJy(),
550			dAtom->getJz());
551			strcat( writeLine, tempBuffer );
552			}
553			else{
554			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
555			}
556			}
557			else {
558			sprintf(painCave.errMsg,
559			"Atom %d not found on processor %d\n",
560			which_atom, worldRank );
561			myStatus = 0;
562			simError();
563
564			strcpy( writeLine, "Hello, I'm an error.\n");
565	mmeineke	377	}
566	mmeineke	440
567	mmeineke	447	MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
568			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
569			MPI_Send( &myStatus, 1, MPI_INT, 0,
570			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
571	mmeineke	377	}
572	gezelter	419	}
573	gezelter	415	finalOut.flush();
574			sprintf( checkPointMsg,
575			"Sucessfully took a dump.\n");
576			MPIcheckPoint();
577	mmeineke	440
578	gezelter	415	if( worldRank == 0 ) finalOut.close();
579	mmeineke	377	#endif // is_mpi
580			}
581	mmeineke	440
582
583
584			#ifdef IS_MPI
585
586			// a couple of functions to let us escape the write loop
587
588			void dWrite::nodeZeroError( void ){
589			int j, myStatus;
590
591			myStatus = 0;
592			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
593	mmeineke	447	MPI_Send( &myStatus, 1, MPI_INT, j,
594			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
595	mmeineke	440	}
596
597
598			MPI_Finalize();
599			exit (0);
600
601			}
602
603			void dWrite::anonymousNodeDie( void ){
604
605			MPI_Finalize();
606			exit (0);
607			}
608
609			#endif //is_mpi