OOPSE/libmdtools/DumpWriter.cpp

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

#ifdef IS_MPI
#include <mpi.h>
#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;

#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();
    }
  
    //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, game_over, 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::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, 
                             TAKE_THIS_TAG_INT);
        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
                             TAKE_THIS_TAG_CHAR, istatus);
        MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, 
                             TAKE_THIS_TAG_INT, istatus);
        
        if(!myStatus) nodeZeroError();

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

  } else {
    
    done = 0;
    while (!done) {
      
      MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, 
                           TAKE_THIS_TAG_INT, istatus);

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

      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, 
                           TAKE_THIS_TAG_INT, 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::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, 
                           TAKE_THIS_TAG_CHAR);
      MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, 
                            TAKE_THIS_TAG_INT);
    }
  }  
  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::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, 
                             TAKE_THIS_TAG_INT);
        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
                             TAKE_THIS_TAG_CHAR, istatus);
        MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, 
                             TAKE_THIS_TAG_INT, istatus);
        
        if(!myStatus) nodeZeroError();
      }
      
      finalOut << writeLine;
    }
    
    // kill everyone off:
    myStatus = -1;
    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
      MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, j, 
                           TAKE_THIS_TAG_INT);
    }

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

      MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, 
                           TAKE_THIS_TAG_INT, istatus);
      
      if(!myStatus) anonymousNodeDie();
      
      if(myStatus < 0) break;
      
      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, 
                           TAKE_THIS_TAG_INT, 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::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, 
                           TAKE_THIS_TAG_CHAR);
      MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, 
                            TAKE_THIS_TAG_INT);
    }
  }
  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::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, 
                          TAKE_THIS_TAG_INT);
  }  
  

  MPI_Finalize();
  exit (0);
  
}

void dWrite::anonymousNodeDie( void ){

  MPI_Finalize();
  exit (0);
}

#endif //is_mpi
Revision:	440
Committed:	Tue Apr 1 16:49:17 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	14296 byte(s)
Log Message:	Fixed DumpWriter to be more robust to errors. also added a little namespace to InitFromFile to wrap it's helper functions in MPI
#	User	Rev	Content
1	mmeineke	377	#include <cstring>
2			#include <iostream>
3			#include <fstream>
4
5			#ifdef IS_MPI
6			#include <mpi.h>
7	gezelter	416	#include <mpi++.h>
8	mmeineke	377	#include "mpiSimulation.hpp"
9	chuckv	436	#define TAKE_THIS_TAG_CHAR 1
10			#define TAKE_THIS_TAG_INT 2
11	mmeineke	440
12			namespace dWrite{
13			void nodeZeroError( void );
14			void anonymousNodeDie( void );
15			}
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
31
32
33			strcpy( outName, entry_plug->sampleName );
34
35			outFile.open(outName, ios::out \| ios::trunc );
36
37			if( !outFile ){
38
39			sprintf( painCave.errMsg,
40			"Could not open \"%s\" for dump output.\n",
41			outName);
42			painCave.isFatal = 1;
43			simError();
44			}
45
46			//outFile.setf( ios::scientific );
47
48			#ifdef IS_MPI
49			}
50
51			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			outFile.close();
64
65			#ifdef IS_MPI
66			}
67			#endif // is_mpi
68			}
69
70			void DumpWriter::writeDump( double currentTime ){
71
72			const int BUFFERSIZE = 2000;
73			char tempBuffer[BUFFERSIZE];
74			char writeLine[BUFFERSIZE];
75
76	gezelter	419	int i, j, which_node, done, game_over, which_atom, local_index;
77	mmeineke	377	double q[4];
78			DirectionalAtom* dAtom;
79			int nAtoms = entry_plug->n_atoms;
80			Atom** atoms = entry_plug->atoms;
81
82
83			#ifndef IS_MPI
84
85			outFile << nAtoms << "\n";
86
87			outFile << currentTime << "\t"
88			<< entry_plug->box_x << "\t"
89			<< entry_plug->box_y << "\t"
90			<< entry_plug->box_z << "\n";
91
92			for( i=0; i<nAtoms; i++ ){
93
94
95			sprintf( tempBuffer,
96			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
97			atoms[i]->getType(),
98			atoms[i]->getX(),
99			atoms[i]->getY(),
100			atoms[i]->getZ(),
101			atoms[i]->get_vx(),
102			atoms[i]->get_vy(),
103			atoms[i]->get_vz());
104			strcpy( writeLine, tempBuffer );
105
106			if( atoms[i]->isDirectional() ){
107
108			dAtom = (DirectionalAtom *)atoms[i];
109			dAtom->getQ( q );
110
111			sprintf( tempBuffer,
112			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
113			q[0],
114			q[1],
115			q[2],
116			q[3],
117			dAtom->getJx(),
118			dAtom->getJy(),
119			dAtom->getJz());
120			strcat( writeLine, tempBuffer );
121			}
122			else
123			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
124
125			outFile << writeLine;
126			}
127			outFile.flush();
128
129			#else // is_mpi
130	gezelter	416
131	mmeineke	440	// first thing first, suspend fatalities.
132			painCave.isEventLoop = 1;
133
134			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
135			int haveError;
136
137	gezelter	416	MPI::Status istatus;
138			int *AtomToProcMap = mpiSim->getAtomToProcMap();
139	gezelter	415
140	mmeineke	377	// write out header and node 0's coordinates
141	gezelter	415
142	mmeineke	377	if( worldRank == 0 ){
143			outFile << mpiSim->getTotAtoms() << "\n";
144	gezelter	415
145	mmeineke	377	outFile << currentTime << "\t"
146			<< entry_plug->box_x << "\t"
147			<< entry_plug->box_y << "\t"
148			<< entry_plug->box_z << "\n";
149	chuckv	434	outFile.flush();
150	gezelter	416	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
151	gezelter	417	// Get the Node number which has this atom;
152	mmeineke	377
153	gezelter	415	which_node = AtomToProcMap[i];
154
155	chuckv	436	if (which_node == 0 ) {
156	mmeineke	377
157	mmeineke	440	haveError = 0;
158	chuckv	436	which_atom = i;
159			local_index=-1;
160			for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
161			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
162			}
163			if (local_index != -1) {
164			//format the line
165			sprintf( tempBuffer,
166			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
167			atoms[local_index]->getType(),
168			atoms[local_index]->getX(),
169			atoms[local_index]->getY(),
170			atoms[local_index]->getZ(),
171			atoms[local_index]->get_vx(),
172			atoms[local_index]->get_vy(),
173			atoms[local_index]->get_vz()); // check here.
174			strcpy( writeLine, tempBuffer );
175	mmeineke	377
176	chuckv	436	if( atoms[local_index]->isDirectional() ){
177
178			dAtom = (DirectionalAtom *)atoms[local_index];
179			dAtom->getQ( q );
180
181			sprintf( tempBuffer,
182			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
183			q[0],
184			q[1],
185			q[2],
186			q[3],
187			dAtom->getJx(),
188			dAtom->getJy(),
189			dAtom->getJz());
190			strcat( writeLine, tempBuffer );
191
192			}
193			else
194			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
195			}
196			else {
197	mmeineke	440	sprintf(painCave.errMsg,
198			"Atom %d not found on processor %d\n",
199			i, worldRank );
200			haveError= 1;
201			simError();
202	chuckv	436	}
203	mmeineke	440
204			if(haveError) nodeZeroError();
205
206			}
207	chuckv	436	else {
208	mmeineke	440	myStatus = 1;
209			MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node,
210			TAKE_THIS_TAG_INT);
211	chuckv	436	MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
212	gezelter	416	MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
213	chuckv	436	TAKE_THIS_TAG_CHAR, istatus);
214	mmeineke	440	MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node,
215			TAKE_THIS_TAG_INT, istatus);
216
217			if(!myStatus) nodeZeroError();
218
219	mmeineke	377	}
220	gezelter	415
221	mmeineke	377	outFile << writeLine;
222	chuckv	434	outFile.flush();
223	mmeineke	377	}
224
225	gezelter	415	// kill everyone off:
226	mmeineke	440	myStatus = -1;
227	gezelter	416	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
228	mmeineke	440	MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, j,
229			TAKE_THIS_TAG_INT);
230	mmeineke	377	}
231
232	gezelter	415	} else {
233
234			done = 0;
235			while (!done) {
236	mmeineke	440
237			MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0,
238			TAKE_THIS_TAG_INT, istatus);
239
240			if(!myStatus) anonymousNodeDie();
241
242			if(myStatus < 0) break;
243
244	gezelter	416	MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
245	chuckv	436	TAKE_THIS_TAG_INT, istatus);
246	mmeineke	440
247			myStatus = 1;
248			local_index=-1;
249			for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
250			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
251			}
252			if (local_index != -1) {
253			//format the line
254			sprintf( tempBuffer,
255			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
256			atoms[local_index]->getType(),
257			atoms[local_index]->getX(),
258			atoms[local_index]->getY(),
259			atoms[local_index]->getZ(),
260			atoms[local_index]->get_vx(),
261			atoms[local_index]->get_vy(),
262			atoms[local_index]->get_vz()); // check here.
263			strcpy( writeLine, tempBuffer );
264
265			if( atoms[local_index]->isDirectional() ){
266	mmeineke	377
267	mmeineke	440	dAtom = (DirectionalAtom *)atoms[local_index];
268			dAtom->getQ( q );
269
270			sprintf( tempBuffer,
271			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
272			q[0],
273			q[1],
274			q[2],
275			q[3],
276			dAtom->getJx(),
277			dAtom->getJy(),
278			dAtom->getJz());
279			strcat( writeLine, tempBuffer );
280			}
281			else{
282			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
283			}
284			}
285			else {
286			sprintf(painCave.errMsg,
287			"Atom %d not found on processor %d\n",
288			which_atom, worldRank );
289			myStatus = 0;
290			simError();
291
292			strcpy( writeLine, "Hello, I'm an error.\n");
293	mmeineke	377	}
294	mmeineke	440
295			MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
296			TAKE_THIS_TAG_CHAR);
297			MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0,
298			TAKE_THIS_TAG_INT);
299	mmeineke	377	}
300	gezelter	415	}
301			outFile.flush();
302			sprintf( checkPointMsg,
303			"Sucessfully took a dump.\n");
304			MPIcheckPoint();
305	mmeineke	440
306			// last thing last, enable fatalities.
307			painCave.isEventLoop = 0;
308
309	mmeineke	377	#endif // is_mpi
310			}
311
312			void DumpWriter::writeFinal(){
313	gezelter	416
314	mmeineke	377	char finalName[500];
315			ofstream finalOut;
316	gezelter	416
317			const int BUFFERSIZE = 2000;
318			char tempBuffer[BUFFERSIZE];
319			char writeLine[BUFFERSIZE];
320
321			double q[4];
322			DirectionalAtom* dAtom;
323			int nAtoms = entry_plug->n_atoms;
324			Atom** atoms = entry_plug->atoms;
325	gezelter	419	int i, j, which_node, done, game_over, which_atom, local_index;
326	mmeineke	377
327	gezelter	416
328	mmeineke	377	#ifdef IS_MPI
329			if(worldRank == 0 ){
330			#endif // is_mpi
331
332			strcpy( finalName, entry_plug->finalName );
333
334			finalOut.open( finalName, ios::out \| ios::trunc );
335			if( !finalOut ){
336			sprintf( painCave.errMsg,
337			"Could not open \"%s\" for final dump output.\n",
338			finalName );
339			painCave.isFatal = 1;
340			simError();
341			}
342
343			// finalOut.setf( ios::scientific );
344
345			#ifdef IS_MPI
346			}
347
348			sprintf(checkPointMsg,"Opened file for final configuration\n");
349			MPIcheckPoint();
350
351			#endif //is_mpi
352
353	gezelter	415
354	mmeineke	377	#ifndef IS_MPI
355
356			finalOut << nAtoms << "\n";
357
358			finalOut << entry_plug->box_x << "\t"
359			<< entry_plug->box_y << "\t"
360			<< entry_plug->box_z << "\n";
361	gezelter	416
362	mmeineke	377	for( i=0; i<nAtoms; i++ ){
363
364			sprintf( tempBuffer,
365			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
366			atoms[i]->getType(),
367			atoms[i]->getX(),
368			atoms[i]->getY(),
369			atoms[i]->getZ(),
370			atoms[i]->get_vx(),
371			atoms[i]->get_vy(),
372			atoms[i]->get_vz());
373			strcpy( writeLine, tempBuffer );
374
375			if( atoms[i]->isDirectional() ){
376
377			dAtom = (DirectionalAtom *)atoms[i];
378			dAtom->getQ( q );
379
380			sprintf( tempBuffer,
381			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
382			q[0],
383			q[1],
384			q[2],
385			q[3],
386			dAtom->getJx(),
387			dAtom->getJy(),
388			dAtom->getJz());
389			strcat( writeLine, tempBuffer );
390			}
391			else
392			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
393
394			finalOut << writeLine;
395			}
396			finalOut.flush();
397	gezelter	415	finalOut.close();
398	mmeineke	377
399			#else // is_mpi
400	gezelter	415
401	mmeineke	440	// first thing first, suspend fatalities.
402			painCave.isEventLoop = 1;
403
404			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
405			int haveError;
406
407	gezelter	416	MPI::Status istatus;
408			int *AtomToProcMap = mpiSim->getAtomToProcMap();
409
410	mmeineke	377	// write out header and node 0's coordinates
411	gezelter	415
412	mmeineke	440	haveError = 0;
413	mmeineke	377	if( worldRank == 0 ){
414			finalOut << mpiSim->getTotAtoms() << "\n";
415	gezelter	415
416	mmeineke	377	finalOut << entry_plug->box_x << "\t"
417	gezelter	415	<< entry_plug->box_y << "\t"
418			<< entry_plug->box_z << "\n";
419	mmeineke	377
420	gezelter	416	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
421	gezelter	415	// Get the Node number which has this molecule:
422	mmeineke	377
423	gezelter	415	which_node = AtomToProcMap[i];
424
425	gezelter	416	if (which_node == mpiSim->getMyNode()) {
426	chuckv	437
427			which_atom = i;
428			local_index=-1;
429			for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
430			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
431			}
432			if (local_index != -1) {
433			sprintf( tempBuffer,
434			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
435			atoms[local_index]->getType(),
436			atoms[local_index]->getX(),
437			atoms[local_index]->getY(),
438			atoms[local_index]->getZ(),
439			atoms[local_index]->get_vx(),
440			atoms[local_index]->get_vy(),
441			atoms[local_index]->get_vz());
442			strcpy( writeLine, tempBuffer );
443	mmeineke	377
444	chuckv	437	if( atoms[local_index]->isDirectional() ){
445
446			dAtom = (DirectionalAtom *)atoms[local_index];
447			dAtom->getQ( q );
448
449			sprintf( tempBuffer,
450			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
451			q[0],
452			q[1],
453			q[2],
454			q[3],
455			dAtom->getJx(),
456			dAtom->getJy(),
457			dAtom->getJz());
458			strcat( writeLine, tempBuffer );
459			}
460			else
461			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
462			}
463			else {
464	mmeineke	440	sprintf(painCave.errMsg,
465			"Atom %d not found on processor %d\n",
466			i, worldRank );
467			haveError= 1;
468			simError();
469	chuckv	437	}
470	mmeineke	440
471			if(haveError) nodeZeroError();
472	chuckv	437
473	mmeineke	440	}
474			else {
475	gezelter	415
476	mmeineke	440	myStatus = 1;
477			MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node,
478			TAKE_THIS_TAG_INT);
479	chuckv	436	MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
480	gezelter	416	MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
481	mmeineke	440	TAKE_THIS_TAG_CHAR, istatus);
482			MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node,
483			TAKE_THIS_TAG_INT, istatus);
484
485			if(!myStatus) nodeZeroError();
486	mmeineke	377	}
487	gezelter	415
488	mmeineke	377	finalOut << writeLine;
489			}
490
491	gezelter	415	// kill everyone off:
492	mmeineke	440	myStatus = -1;
493			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
494			MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, j,
495			TAKE_THIS_TAG_INT);
496	mmeineke	377	}
497
498	gezelter	415	} else {
499
500			done = 0;
501			while (!done) {
502	mmeineke	440
503			MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0,
504			TAKE_THIS_TAG_INT, istatus);
505
506			if(!myStatus) anonymousNodeDie();
507
508			if(myStatus < 0) break;
509
510	gezelter	416	MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
511	chuckv	436	TAKE_THIS_TAG_INT, istatus);
512	mmeineke	440
513			myStatus = 1;
514			local_index=-1;
515			for (j=0; j < mpiSim->getMyNlocal(); j++) {
516			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
517			}
518			if (local_index != -1) {
519	mmeineke	377
520	mmeineke	440	//format the line
521			sprintf( tempBuffer,
522			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
523			atoms[local_index]->getType(),
524			atoms[local_index]->getX(),
525			atoms[local_index]->getY(),
526			atoms[local_index]->getZ(),
527			atoms[local_index]->get_vx(),
528			atoms[local_index]->get_vy(),
529			atoms[local_index]->get_vz()); // check here.
530			strcpy( writeLine, tempBuffer );
531
532			if( atoms[local_index]->isDirectional() ){
533	mmeineke	377
534	mmeineke	440	dAtom = (DirectionalAtom *)atoms[local_index];
535			dAtom->getQ( q );
536
537			sprintf( tempBuffer,
538			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
539			q[0],
540			q[1],
541			q[2],
542			q[3],
543			dAtom->getJx(),
544			dAtom->getJy(),
545			dAtom->getJz());
546			strcat( writeLine, tempBuffer );
547			}
548			else{
549			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
550			}
551			}
552			else {
553			sprintf(painCave.errMsg,
554			"Atom %d not found on processor %d\n",
555			which_atom, worldRank );
556			myStatus = 0;
557			simError();
558
559			strcpy( writeLine, "Hello, I'm an error.\n");
560	mmeineke	377	}
561	mmeineke	440
562			MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
563			TAKE_THIS_TAG_CHAR);
564			MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0,
565			TAKE_THIS_TAG_INT);
566	mmeineke	377	}
567	gezelter	419	}
568	gezelter	415	finalOut.flush();
569			sprintf( checkPointMsg,
570			"Sucessfully took a dump.\n");
571			MPIcheckPoint();
572	mmeineke	440
573	gezelter	415	if( worldRank == 0 ) finalOut.close();
574	mmeineke	377	#endif // is_mpi
575			}
576	mmeineke	440
577
578
579			#ifdef IS_MPI
580
581			// a couple of functions to let us escape the write loop
582
583			void dWrite::nodeZeroError( void ){
584			int j, myStatus;
585
586			myStatus = 0;
587			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
588			MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j,
589			TAKE_THIS_TAG_INT);
590			}
591
592
593			MPI_Finalize();
594			exit (0);
595
596			}
597
598			void dWrite::anonymousNodeDie( void ){
599
600			MPI_Finalize();
601			exit (0);
602			}
603
604			#endif //is_mpi