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;

#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, 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:	483
Committed:	Wed Apr 9 04:06:43 2003 UTC (21 years, 2 months ago) by gezelter
File size:	14198 byte(s)
Log Message:	fixes for NPT and NVT
#	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			#ifdef IS_MPI
27			if(worldRank == 0 ){
28			#endif // is_mpi
29
30			strcpy( outName, entry_plug->sampleName );
31
32			outFile.open(outName, ios::out \| ios::trunc );
33
34			if( !outFile ){
35
36			sprintf( painCave.errMsg,
37			"Could not open \"%s\" for dump output.\n",
38			outName);
39			painCave.isFatal = 1;
40			simError();
41			}
42	mmeineke	469
43	mmeineke	377	//outFile.setf( ios::scientific );
44
45			#ifdef IS_MPI
46			}
47
48			sprintf( checkPointMsg,
49			"Sucessfully opened output file for dumping.\n");
50			MPIcheckPoint();
51			#endif // is_mpi
52			}
53
54			DumpWriter::~DumpWriter( ){
55
56			#ifdef IS_MPI
57			if(worldRank == 0 ){
58			#endif // is_mpi
59
60			outFile.close();
61
62			#ifdef IS_MPI
63			}
64			#endif // is_mpi
65			}
66
67			void DumpWriter::writeDump( double currentTime ){
68
69			const int BUFFERSIZE = 2000;
70			char tempBuffer[BUFFERSIZE];
71			char writeLine[BUFFERSIZE];
72
73	mmeineke	450	int i, j, which_node, done, which_atom, local_index;
74	mmeineke	377	double q[4];
75			DirectionalAtom* dAtom;
76			int nAtoms = entry_plug->n_atoms;
77			Atom** atoms = entry_plug->atoms;
78
79
80			#ifndef IS_MPI
81
82			outFile << nAtoms << "\n";
83
84			outFile << currentTime << "\t"
85			<< entry_plug->box_x << "\t"
86			<< entry_plug->box_y << "\t"
87			<< entry_plug->box_z << "\n";
88
89			for( i=0; i<nAtoms; i++ ){
90
91
92			sprintf( tempBuffer,
93			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
94			atoms[i]->getType(),
95			atoms[i]->getX(),
96			atoms[i]->getY(),
97			atoms[i]->getZ(),
98			atoms[i]->get_vx(),
99			atoms[i]->get_vy(),
100			atoms[i]->get_vz());
101			strcpy( writeLine, tempBuffer );
102
103			if( atoms[i]->isDirectional() ){
104
105			dAtom = (DirectionalAtom *)atoms[i];
106			dAtom->getQ( q );
107
108			sprintf( tempBuffer,
109			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
110			q[0],
111			q[1],
112			q[2],
113			q[3],
114			dAtom->getJx(),
115			dAtom->getJy(),
116			dAtom->getJz());
117			strcat( writeLine, tempBuffer );
118			}
119			else
120			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
121
122			outFile << writeLine;
123			}
124			outFile.flush();
125
126			#else // is_mpi
127	gezelter	416
128	mmeineke	440	// first thing first, suspend fatalities.
129			painCave.isEventLoop = 1;
130
131			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
132			int haveError;
133
134	mmeineke	447	MPI_Status istatus;
135	gezelter	416	int *AtomToProcMap = mpiSim->getAtomToProcMap();
136	gezelter	415
137	mmeineke	377	// write out header and node 0's coordinates
138	gezelter	415
139	mmeineke	377	if( worldRank == 0 ){
140			outFile << mpiSim->getTotAtoms() << "\n";
141	gezelter	415
142	mmeineke	377	outFile << currentTime << "\t"
143			<< entry_plug->box_x << "\t"
144			<< entry_plug->box_y << "\t"
145			<< entry_plug->box_z << "\n";
146	chuckv	434	outFile.flush();
147	gezelter	416	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
148	gezelter	417	// Get the Node number which has this atom;
149	mmeineke	377
150	gezelter	415	which_node = AtomToProcMap[i];
151
152	chuckv	436	if (which_node == 0 ) {
153	mmeineke	377
154	mmeineke	440	haveError = 0;
155	chuckv	436	which_atom = i;
156			local_index=-1;
157			for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
158			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
159			}
160			if (local_index != -1) {
161			//format the line
162			sprintf( tempBuffer,
163			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
164			atoms[local_index]->getType(),
165			atoms[local_index]->getX(),
166			atoms[local_index]->getY(),
167			atoms[local_index]->getZ(),
168			atoms[local_index]->get_vx(),
169			atoms[local_index]->get_vy(),
170			atoms[local_index]->get_vz()); // check here.
171			strcpy( writeLine, tempBuffer );
172	mmeineke	377
173	chuckv	436	if( atoms[local_index]->isDirectional() ){
174
175			dAtom = (DirectionalAtom *)atoms[local_index];
176			dAtom->getQ( q );
177
178			sprintf( tempBuffer,
179			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
180			q[0],
181			q[1],
182			q[2],
183			q[3],
184			dAtom->getJx(),
185			dAtom->getJy(),
186			dAtom->getJz());
187			strcat( writeLine, tempBuffer );
188
189			}
190			else
191			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
192			}
193			else {
194	mmeineke	440	sprintf(painCave.errMsg,
195			"Atom %d not found on processor %d\n",
196			i, worldRank );
197			haveError= 1;
198			simError();
199	chuckv	436	}
200	mmeineke	440
201			if(haveError) nodeZeroError();
202
203			}
204	chuckv	436	else {
205	mmeineke	440	myStatus = 1;
206	mmeineke	447	MPI_Send(&myStatus, 1, MPI_INT, which_node,
207			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
208			MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
209			MPI_COMM_WORLD);
210			MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
211			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
212			MPI_Recv(&myStatus, 1, MPI_INT, which_node,
213			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
214	mmeineke	440
215			if(!myStatus) nodeZeroError();
216
217	mmeineke	377	}
218	gezelter	415
219	mmeineke	377	outFile << writeLine;
220	chuckv	434	outFile.flush();
221	mmeineke	377	}
222
223	gezelter	415	// kill everyone off:
224	mmeineke	440	myStatus = -1;
225	gezelter	416	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
226	mmeineke	447	MPI_Send(&myStatus, 1, MPI_INT, j,
227			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
228	mmeineke	377	}
229
230	gezelter	415	} else {
231
232			done = 0;
233			while (!done) {
234	mmeineke	440
235	mmeineke	447	MPI_Recv(&myStatus, 1, MPI_INT, 0,
236			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
237	mmeineke	440
238			if(!myStatus) anonymousNodeDie();
239
240			if(myStatus < 0) break;
241
242	mmeineke	447	MPI_Recv(&which_atom, 1, MPI_INT, 0,
243			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
244	mmeineke	440
245			myStatus = 1;
246			local_index=-1;
247			for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
248			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
249			}
250			if (local_index != -1) {
251			//format the line
252			sprintf( tempBuffer,
253			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
254			atoms[local_index]->getType(),
255			atoms[local_index]->getX(),
256			atoms[local_index]->getY(),
257			atoms[local_index]->getZ(),
258			atoms[local_index]->get_vx(),
259			atoms[local_index]->get_vy(),
260			atoms[local_index]->get_vz()); // check here.
261			strcpy( writeLine, tempBuffer );
262
263			if( atoms[local_index]->isDirectional() ){
264	mmeineke	377
265	mmeineke	440	dAtom = (DirectionalAtom *)atoms[local_index];
266			dAtom->getQ( q );
267
268			sprintf( tempBuffer,
269			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
270			q[0],
271			q[1],
272			q[2],
273			q[3],
274			dAtom->getJx(),
275			dAtom->getJy(),
276			dAtom->getJz());
277			strcat( writeLine, tempBuffer );
278			}
279			else{
280			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
281			}
282			}
283			else {
284			sprintf(painCave.errMsg,
285			"Atom %d not found on processor %d\n",
286			which_atom, worldRank );
287			myStatus = 0;
288			simError();
289
290			strcpy( writeLine, "Hello, I'm an error.\n");
291	mmeineke	377	}
292	mmeineke	440
293	mmeineke	447	MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
294			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
295			MPI_Send( &myStatus, 1, MPI_INT, 0,
296			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
297	mmeineke	377	}
298	gezelter	415	}
299			outFile.flush();
300			sprintf( checkPointMsg,
301			"Sucessfully took a dump.\n");
302			MPIcheckPoint();
303	mmeineke	440
304			// last thing last, enable fatalities.
305			painCave.isEventLoop = 0;
306
307	mmeineke	377	#endif // is_mpi
308			}
309
310			void DumpWriter::writeFinal(){
311	gezelter	416
312	mmeineke	377	char finalName[500];
313			ofstream finalOut;
314	gezelter	416
315			const int BUFFERSIZE = 2000;
316			char tempBuffer[BUFFERSIZE];
317			char writeLine[BUFFERSIZE];
318
319			double q[4];
320			DirectionalAtom* dAtom;
321			int nAtoms = entry_plug->n_atoms;
322			Atom** atoms = entry_plug->atoms;
323	gezelter	419	int i, j, which_node, done, game_over, which_atom, local_index;
324	mmeineke	377
325	gezelter	416
326	mmeineke	377	#ifdef IS_MPI
327			if(worldRank == 0 ){
328			#endif // is_mpi
329
330			strcpy( finalName, entry_plug->finalName );
331
332			finalOut.open( finalName, ios::out \| ios::trunc );
333			if( !finalOut ){
334			sprintf( painCave.errMsg,
335			"Could not open \"%s\" for final dump output.\n",
336			finalName );
337			painCave.isFatal = 1;
338			simError();
339			}
340
341			// finalOut.setf( ios::scientific );
342
343			#ifdef IS_MPI
344			}
345
346			sprintf(checkPointMsg,"Opened file for final configuration\n");
347			MPIcheckPoint();
348
349			#endif //is_mpi
350
351	gezelter	415
352	mmeineke	377	#ifndef IS_MPI
353
354			finalOut << nAtoms << "\n";
355
356			finalOut << entry_plug->box_x << "\t"
357			<< entry_plug->box_y << "\t"
358			<< entry_plug->box_z << "\n";
359	gezelter	416
360	mmeineke	377	for( i=0; i<nAtoms; i++ ){
361
362			sprintf( tempBuffer,
363			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
364			atoms[i]->getType(),
365			atoms[i]->getX(),
366			atoms[i]->getY(),
367			atoms[i]->getZ(),
368			atoms[i]->get_vx(),
369			atoms[i]->get_vy(),
370			atoms[i]->get_vz());
371			strcpy( writeLine, tempBuffer );
372
373			if( atoms[i]->isDirectional() ){
374
375			dAtom = (DirectionalAtom *)atoms[i];
376			dAtom->getQ( q );
377
378			sprintf( tempBuffer,
379			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
380			q[0],
381			q[1],
382			q[2],
383			q[3],
384			dAtom->getJx(),
385			dAtom->getJy(),
386			dAtom->getJz());
387			strcat( writeLine, tempBuffer );
388			}
389			else
390			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
391
392			finalOut << writeLine;
393			}
394			finalOut.flush();
395	gezelter	415	finalOut.close();
396	mmeineke	377
397			#else // is_mpi
398	gezelter	415
399	mmeineke	440	// first thing first, suspend fatalities.
400			painCave.isEventLoop = 1;
401
402			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
403			int haveError;
404
405	mmeineke	447	MPI_Status istatus;
406	gezelter	416	int *AtomToProcMap = mpiSim->getAtomToProcMap();
407
408	mmeineke	377	// write out header and node 0's coordinates
409	gezelter	415
410	mmeineke	440	haveError = 0;
411	mmeineke	377	if( worldRank == 0 ){
412			finalOut << mpiSim->getTotAtoms() << "\n";
413	gezelter	415
414	mmeineke	377	finalOut << entry_plug->box_x << "\t"
415	gezelter	415	<< entry_plug->box_y << "\t"
416			<< entry_plug->box_z << "\n";
417	mmeineke	377
418	gezelter	416	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
419	gezelter	415	// Get the Node number which has this molecule:
420	mmeineke	377
421	gezelter	415	which_node = AtomToProcMap[i];
422
423	gezelter	416	if (which_node == mpiSim->getMyNode()) {
424	chuckv	437
425			which_atom = i;
426			local_index=-1;
427			for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
428			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
429			}
430			if (local_index != -1) {
431			sprintf( tempBuffer,
432			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
433			atoms[local_index]->getType(),
434			atoms[local_index]->getX(),
435			atoms[local_index]->getY(),
436			atoms[local_index]->getZ(),
437			atoms[local_index]->get_vx(),
438			atoms[local_index]->get_vy(),
439			atoms[local_index]->get_vz());
440			strcpy( writeLine, tempBuffer );
441	mmeineke	377
442	chuckv	437	if( atoms[local_index]->isDirectional() ){
443
444			dAtom = (DirectionalAtom *)atoms[local_index];
445			dAtom->getQ( q );
446
447			sprintf( tempBuffer,
448			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
449			q[0],
450			q[1],
451			q[2],
452			q[3],
453			dAtom->getJx(),
454			dAtom->getJy(),
455			dAtom->getJz());
456			strcat( writeLine, tempBuffer );
457			}
458			else
459			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
460			}
461			else {
462	mmeineke	440	sprintf(painCave.errMsg,
463			"Atom %d not found on processor %d\n",
464			i, worldRank );
465			haveError= 1;
466			simError();
467	chuckv	437	}
468	mmeineke	440
469			if(haveError) nodeZeroError();
470	chuckv	437
471	mmeineke	440	}
472			else {
473	gezelter	415
474	mmeineke	440	myStatus = 1;
475	mmeineke	447	MPI_Send(&myStatus, 1, MPI_INT, which_node,
476			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
477			MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
478			MPI_COMM_WORLD);
479			MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
480			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
481			MPI_Recv(&myStatus, 1, MPI_INT, which_node,
482			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
483	mmeineke	440
484			if(!myStatus) nodeZeroError();
485	mmeineke	377	}
486	gezelter	415
487	mmeineke	377	finalOut << writeLine;
488			}
489
490	gezelter	415	// kill everyone off:
491	mmeineke	440	myStatus = -1;
492			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
493	mmeineke	447	MPI_Send(&myStatus, 1, MPI_INT, j,
494			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
495	mmeineke	377	}
496
497	gezelter	415	} else {
498
499			done = 0;
500			while (!done) {
501	mmeineke	440
502	mmeineke	447	MPI_Recv(&myStatus, 1, MPI_INT, 0,
503			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
504	mmeineke	440
505			if(!myStatus) anonymousNodeDie();
506
507			if(myStatus < 0) break;
508
509	mmeineke	447	MPI_Recv(&which_atom, 1, MPI_INT, 0,
510			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
511	mmeineke	440
512			myStatus = 1;
513			local_index=-1;
514			for (j=0; j < mpiSim->getMyNlocal(); j++) {
515			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
516			}
517			if (local_index != -1) {
518	mmeineke	377
519	mmeineke	440	//format the line
520			sprintf( tempBuffer,
521			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
522			atoms[local_index]->getType(),
523			atoms[local_index]->getX(),
524			atoms[local_index]->getY(),
525			atoms[local_index]->getZ(),
526			atoms[local_index]->get_vx(),
527			atoms[local_index]->get_vy(),
528			atoms[local_index]->get_vz()); // check here.
529			strcpy( writeLine, tempBuffer );
530
531			if( atoms[local_index]->isDirectional() ){
532	mmeineke	377
533	mmeineke	440	dAtom = (DirectionalAtom *)atoms[local_index];
534			dAtom->getQ( q );
535
536			sprintf( tempBuffer,
537			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
538			q[0],
539			q[1],
540			q[2],
541			q[3],
542			dAtom->getJx(),
543			dAtom->getJy(),
544			dAtom->getJz());
545			strcat( writeLine, tempBuffer );
546			}
547			else{
548			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
549			}
550			}
551			else {
552			sprintf(painCave.errMsg,
553			"Atom %d not found on processor %d\n",
554			which_atom, worldRank );
555			myStatus = 0;
556			simError();
557
558			strcpy( writeLine, "Hello, I'm an error.\n");
559	mmeineke	377	}
560	mmeineke	440
561	mmeineke	447	MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
562			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
563			MPI_Send( &myStatus, 1, MPI_INT, 0,
564			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
565	mmeineke	377	}
566	gezelter	419	}
567	gezelter	415	finalOut.flush();
568			sprintf( checkPointMsg,
569			"Sucessfully took a dump.\n");
570			MPIcheckPoint();
571	mmeineke	440
572	gezelter	415	if( worldRank == 0 ) finalOut.close();
573	mmeineke	377	#endif // is_mpi
574			}
575	mmeineke	440
576
577
578			#ifdef IS_MPI
579
580			// a couple of functions to let us escape the write loop
581
582			void dWrite::nodeZeroError( void ){
583			int j, myStatus;
584
585			myStatus = 0;
586			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
587	mmeineke	447	MPI_Send( &myStatus, 1, MPI_INT, j,
588			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
589	mmeineke	440	}
590
591
592			MPI_Finalize();
593			exit (0);
594
595			}
596
597			void dWrite::anonymousNodeDie( void ){
598
599			MPI_Finalize();
600			exit (0);
601			}
602
603			#endif //is_mpi