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;

  double pos[3], vel[3];
    

#ifndef IS_MPI
    
  outFile << nAtoms << "\n";
    
  outFile << currentTime << ";\t" 
          << entry_plug->Hmat[0][0] << "\t"
          << entry_plug->Hmat[1][0] << "\t"
          << entry_plug->Hmat[2][0] << ";\t"

          << entry_plug->Hmat[0][1] << "\t"
          << entry_plug->Hmat[1][1] << "\t"
          << entry_plug->Hmat[2][1] << ";\t"

          << entry_plug->Hmat[0][2] << "\t"
          << entry_plug->Hmat[1][2] << "\t"
          << entry_plug->Hmat[2][2] << ";\n";
    
  for( i=0; i<nAtoms; i++ ){
      
    atoms[i]->getPos(pos);
    atoms[i]->getVel(vel);

    sprintf( tempBuffer,
             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
             atoms[i]->getType(),
             pos[0],
             pos[1],
             pos[2],
             vel[0],
             vel[1],
             vel[2]);
    strcpy( writeLine, tempBuffer );

    if( atoms[i]->isDirectional() ){
        
      dAtom = (DirectionalAtom *)atoms[i];
      dAtom->getQ( q );
        
      sprintf( tempBuffer,
               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
               q[0],
               q[1],
               q[2],
               q[3],
               dAtom->getJx(),
               dAtom->getJy(),
               dAtom->getJz());
      strcat( writeLine, tempBuffer );
    }
    else
      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
      
    outFile << writeLine;
  }
  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->Hmat[0][0] << "\t"
            << entry_plug->Hmat[1][0] << "\t"
            << entry_plug->Hmat[2][0] << ";\t"
      
            << entry_plug->Hmat[0][1] << "\t"
            << entry_plug->Hmat[1][1] << "\t"
            << entry_plug->Hmat[2][1] << ";\t"
      
            << entry_plug->Hmat[0][2] << "\t"
            << entry_plug->Hmat[1][2] << "\t"
            << entry_plug->Hmat[2][2] << ";\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
          
          atoms[local_index]->getPos(pos);
          atoms[local_index]->getVel(vel);

          sprintf( tempBuffer,
                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                   atoms[local_index]->getType(),
                   pos[0],
                   pos[1],
                   pos[2],
                   vel[0],
                   vel[1],
                   vel[2]); // 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

        atoms[local_index]->getPos(pos);
        atoms[local_index]->getVel(vel);

        sprintf( tempBuffer,
                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                 atoms[local_index]->getType(),
                 pos[0],
                 pos[1],
                 pos[2],
                 vel[0],
                 vel[1],
                 vel[2]); // 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(double finalTime){

  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;
  
  double pos[3], vel[3];
  
#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 << finalTime << ";\t"
           << entry_plug->Hmat[0][0] << "\t"
           << entry_plug->Hmat[1][0] << "\t"
           << entry_plug->Hmat[2][0] << ";\t"
    
           << entry_plug->Hmat[0][1] << "\t"
           << entry_plug->Hmat[1][1] << "\t"
           << entry_plug->Hmat[2][1] << ";\t"
    
           << entry_plug->Hmat[0][2] << "\t"
           << entry_plug->Hmat[1][2] << "\t"
           << entry_plug->Hmat[2][2] << ";\n";
  
  for( i=0; i<nAtoms; i++ ){
      
    atoms[i]->getPos(pos);
    atoms[i]->getVel(vel);
    
    sprintf( tempBuffer,
             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
             atoms[i]->getType(),
             pos[0],
             pos[1],
             pos[2],
             vel[0],
             vel[1],
             vel[2]);
    strcpy( writeLine, tempBuffer );

    if( atoms[i]->isDirectional() ){
        
      dAtom = (DirectionalAtom *)atoms[i];
      dAtom->getQ( q );
        
      sprintf( tempBuffer,
               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
               q[0],
               q[1],
               q[2],
               q[3],
               dAtom->getJx(),
               dAtom->getJy(),
               dAtom->getJz());
      strcat( writeLine, tempBuffer );
    }
    else
      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
      
    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 << finalTime << ";\t"
             << entry_plug->Hmat[0][0] << "\t"
             << entry_plug->Hmat[1][0] << "\t"
             << entry_plug->Hmat[2][0] << ";\t"
      
             << entry_plug->Hmat[0][1] << "\t"
             << entry_plug->Hmat[1][1] << "\t"
             << entry_plug->Hmat[2][1] << ";\t"
      
             << entry_plug->Hmat[0][2] << "\t"
             << entry_plug->Hmat[1][2] << "\t"
             << entry_plug->Hmat[2][2] << ";\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) {    

          atoms[local_index]->getPos(pos);
          atoms[local_index]->getVel(vel);
          
          sprintf( tempBuffer,
                   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                   atoms[local_index]->getType(),
                   pos[0],
                   pos[1],
                   pos[2],
                   vel[0],
                   vel[1],
                   vel[2]);
          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) {

        atoms[local_index]->getPos(pos);
        atoms[local_index]->getVel(vel);

        //format the line
        sprintf( tempBuffer,
                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                 atoms[local_index]->getType(),
                 pos[0],
                 pos[1],
                 pos[2],
                 vel[0],
                 vel[1],
                 vel[2]); // 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:	670
Committed:	Thu Aug 7 21:47:18 2003 UTC (20 years, 11 months ago) by mmeineke
File size:	15044 byte(s)
Log Message:	switched SimInfo to use a system configuration from SimState rather than arrays from Atom
#	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	mmeineke	670
79			double pos[3], vel[3];
80	mmeineke	377
81
82			#ifndef IS_MPI
83
84			outFile << nAtoms << "\n";
85
86	mmeineke	586	outFile << currentTime << ";\t"
87	mmeineke	590	<< entry_plug->Hmat[0][0] << "\t"
88			<< entry_plug->Hmat[1][0] << "\t"
89			<< entry_plug->Hmat[2][0] << ";\t"
90	mmeineke	572
91	mmeineke	590	<< entry_plug->Hmat[0][1] << "\t"
92			<< entry_plug->Hmat[1][1] << "\t"
93			<< entry_plug->Hmat[2][1] << ";\t"
94	mmeineke	572
95	mmeineke	590	<< entry_plug->Hmat[0][2] << "\t"
96			<< entry_plug->Hmat[1][2] << "\t"
97			<< entry_plug->Hmat[2][2] << ";\n";
98	mmeineke	377
99			for( i=0; i<nAtoms; i++ ){
100
101	mmeineke	670	atoms[i]->getPos(pos);
102			atoms[i]->getVel(vel);
103	mmeineke	377
104			sprintf( tempBuffer,
105			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
106			atoms[i]->getType(),
107	mmeineke	670	pos[0],
108			pos[1],
109			pos[2],
110			vel[0],
111			vel[1],
112			vel[2]);
113	mmeineke	377	strcpy( writeLine, tempBuffer );
114
115			if( atoms[i]->isDirectional() ){
116
117			dAtom = (DirectionalAtom *)atoms[i];
118			dAtom->getQ( q );
119
120			sprintf( tempBuffer,
121			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
122			q[0],
123			q[1],
124			q[2],
125			q[3],
126			dAtom->getJx(),
127			dAtom->getJy(),
128			dAtom->getJz());
129			strcat( writeLine, tempBuffer );
130			}
131			else
132			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
133
134			outFile << writeLine;
135			}
136			outFile.flush();
137
138			#else // is_mpi
139	gezelter	416
140	mmeineke	440	// first thing first, suspend fatalities.
141			painCave.isEventLoop = 1;
142
143			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
144			int haveError;
145
146	mmeineke	447	MPI_Status istatus;
147	gezelter	416	int *AtomToProcMap = mpiSim->getAtomToProcMap();
148	gezelter	415
149	mmeineke	377	// write out header and node 0's coordinates
150	gezelter	415
151	mmeineke	377	if( worldRank == 0 ){
152			outFile << mpiSim->getTotAtoms() << "\n";
153	mmeineke	572
154	gezelter	591	outFile << currentTime << ";\t"
155			<< entry_plug->Hmat[0][0] << "\t"
156			<< entry_plug->Hmat[1][0] << "\t"
157			<< entry_plug->Hmat[2][0] << ";\t"
158	mmeineke	572
159	gezelter	591	<< entry_plug->Hmat[0][1] << "\t"
160			<< entry_plug->Hmat[1][1] << "\t"
161			<< entry_plug->Hmat[2][1] << ";\t"
162	mmeineke	572
163	gezelter	591	<< entry_plug->Hmat[0][2] << "\t"
164			<< entry_plug->Hmat[1][2] << "\t"
165			<< entry_plug->Hmat[2][2] << ";\n";
166
167	chuckv	434	outFile.flush();
168	gezelter	416	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
169	gezelter	417	// Get the Node number which has this atom;
170	mmeineke	377
171	gezelter	415	which_node = AtomToProcMap[i];
172
173	chuckv	436	if (which_node == 0 ) {
174	mmeineke	377
175	mmeineke	440	haveError = 0;
176	chuckv	436	which_atom = i;
177			local_index=-1;
178			for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
179			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
180			}
181			if (local_index != -1) {
182			//format the line
183	mmeineke	670
184			atoms[local_index]->getPos(pos);
185			atoms[local_index]->getVel(vel);
186
187	chuckv	436	sprintf( tempBuffer,
188			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
189			atoms[local_index]->getType(),
190	mmeineke	670	pos[0],
191			pos[1],
192			pos[2],
193			vel[0],
194			vel[1],
195			vel[2]); // check here.
196	chuckv	436	strcpy( writeLine, tempBuffer );
197	mmeineke	377
198	chuckv	436	if( atoms[local_index]->isDirectional() ){
199
200			dAtom = (DirectionalAtom *)atoms[local_index];
201			dAtom->getQ( q );
202
203			sprintf( tempBuffer,
204			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
205			q[0],
206			q[1],
207			q[2],
208			q[3],
209			dAtom->getJx(),
210			dAtom->getJy(),
211			dAtom->getJz());
212			strcat( writeLine, tempBuffer );
213
214			}
215			else
216			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
217			}
218			else {
219	mmeineke	440	sprintf(painCave.errMsg,
220			"Atom %d not found on processor %d\n",
221			i, worldRank );
222			haveError= 1;
223			simError();
224	chuckv	436	}
225	mmeineke	440
226			if(haveError) nodeZeroError();
227
228			}
229	chuckv	436	else {
230	mmeineke	440	myStatus = 1;
231	mmeineke	447	MPI_Send(&myStatus, 1, MPI_INT, which_node,
232			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
233			MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
234			MPI_COMM_WORLD);
235			MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
236			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
237			MPI_Recv(&myStatus, 1, MPI_INT, which_node,
238			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
239	mmeineke	440
240			if(!myStatus) nodeZeroError();
241
242	mmeineke	377	}
243	gezelter	415
244	mmeineke	377	outFile << writeLine;
245	chuckv	434	outFile.flush();
246	mmeineke	377	}
247
248	gezelter	415	// kill everyone off:
249	mmeineke	440	myStatus = -1;
250	gezelter	416	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
251	mmeineke	447	MPI_Send(&myStatus, 1, MPI_INT, j,
252			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
253	mmeineke	377	}
254
255	gezelter	415	} else {
256
257			done = 0;
258			while (!done) {
259	mmeineke	440
260	mmeineke	447	MPI_Recv(&myStatus, 1, MPI_INT, 0,
261			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
262	mmeineke	440
263			if(!myStatus) anonymousNodeDie();
264
265			if(myStatus < 0) break;
266
267	mmeineke	447	MPI_Recv(&which_atom, 1, MPI_INT, 0,
268			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
269	mmeineke	440
270			myStatus = 1;
271			local_index=-1;
272			for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
273			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
274			}
275			if (local_index != -1) {
276			//format the line
277	mmeineke	670
278			atoms[local_index]->getPos(pos);
279			atoms[local_index]->getVel(vel);
280
281	mmeineke	440	sprintf( tempBuffer,
282			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
283			atoms[local_index]->getType(),
284	mmeineke	670	pos[0],
285			pos[1],
286			pos[2],
287			vel[0],
288			vel[1],
289			vel[2]); // check here.
290	mmeineke	440	strcpy( writeLine, tempBuffer );
291
292			if( atoms[local_index]->isDirectional() ){
293	mmeineke	377
294	mmeineke	440	dAtom = (DirectionalAtom *)atoms[local_index];
295			dAtom->getQ( q );
296
297			sprintf( tempBuffer,
298			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
299			q[0],
300			q[1],
301			q[2],
302			q[3],
303			dAtom->getJx(),
304			dAtom->getJy(),
305			dAtom->getJz());
306			strcat( writeLine, tempBuffer );
307			}
308			else{
309			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
310			}
311			}
312			else {
313			sprintf(painCave.errMsg,
314			"Atom %d not found on processor %d\n",
315			which_atom, worldRank );
316			myStatus = 0;
317			simError();
318
319			strcpy( writeLine, "Hello, I'm an error.\n");
320	mmeineke	377	}
321	mmeineke	440
322	mmeineke	447	MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
323			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
324			MPI_Send( &myStatus, 1, MPI_INT, 0,
325			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
326	mmeineke	377	}
327	gezelter	415	}
328			outFile.flush();
329			sprintf( checkPointMsg,
330			"Sucessfully took a dump.\n");
331			MPIcheckPoint();
332	mmeineke	440
333			// last thing last, enable fatalities.
334			painCave.isEventLoop = 0;
335
336	mmeineke	377	#endif // is_mpi
337			}
338
339	mmeineke	572	void DumpWriter::writeFinal(double finalTime){
340	gezelter	416
341	mmeineke	377	char finalName[500];
342			ofstream finalOut;
343	gezelter	416
344			const int BUFFERSIZE = 2000;
345			char tempBuffer[BUFFERSIZE];
346			char writeLine[BUFFERSIZE];
347
348			double q[4];
349			DirectionalAtom* dAtom;
350			int nAtoms = entry_plug->n_atoms;
351			Atom** atoms = entry_plug->atoms;
352	gezelter	419	int i, j, which_node, done, game_over, which_atom, local_index;
353	mmeineke	377
354	mmeineke	670	double pos[3], vel[3];
355	gezelter	416
356	mmeineke	377	#ifdef IS_MPI
357			if(worldRank == 0 ){
358			#endif // is_mpi
359
360			strcpy( finalName, entry_plug->finalName );
361
362			finalOut.open( finalName, ios::out \| ios::trunc );
363			if( !finalOut ){
364			sprintf( painCave.errMsg,
365			"Could not open \"%s\" for final dump output.\n",
366			finalName );
367			painCave.isFatal = 1;
368			simError();
369			}
370
371			// finalOut.setf( ios::scientific );
372
373			#ifdef IS_MPI
374			}
375
376			sprintf(checkPointMsg,"Opened file for final configuration\n");
377			MPIcheckPoint();
378
379			#endif //is_mpi
380
381	gezelter	415
382	mmeineke	377	#ifndef IS_MPI
383
384			finalOut << nAtoms << "\n";
385
386	gezelter	591	finalOut << finalTime << ";\t"
387	mmeineke	590	<< entry_plug->Hmat[0][0] << "\t"
388			<< entry_plug->Hmat[1][0] << "\t"
389	gezelter	591	<< entry_plug->Hmat[2][0] << ";\t"
390	mmeineke	572
391	mmeineke	590	<< entry_plug->Hmat[0][1] << "\t"
392			<< entry_plug->Hmat[1][1] << "\t"
393	gezelter	591	<< entry_plug->Hmat[2][1] << ";\t"
394	mmeineke	572
395	mmeineke	590	<< entry_plug->Hmat[0][2] << "\t"
396			<< entry_plug->Hmat[1][2] << "\t"
397	gezelter	591	<< entry_plug->Hmat[2][2] << ";\n";
398	gezelter	416
399	mmeineke	377	for( i=0; i<nAtoms; i++ ){
400
401	mmeineke	670	atoms[i]->getPos(pos);
402			atoms[i]->getVel(vel);
403
404	mmeineke	377	sprintf( tempBuffer,
405			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
406			atoms[i]->getType(),
407	mmeineke	670	pos[0],
408			pos[1],
409			pos[2],
410			vel[0],
411			vel[1],
412			vel[2]);
413	mmeineke	377	strcpy( writeLine, tempBuffer );
414
415			if( atoms[i]->isDirectional() ){
416
417			dAtom = (DirectionalAtom *)atoms[i];
418			dAtom->getQ( q );
419
420			sprintf( tempBuffer,
421			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
422			q[0],
423			q[1],
424			q[2],
425			q[3],
426			dAtom->getJx(),
427			dAtom->getJy(),
428			dAtom->getJz());
429			strcat( writeLine, tempBuffer );
430			}
431			else
432			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
433
434			finalOut << writeLine;
435			}
436			finalOut.flush();
437	gezelter	415	finalOut.close();
438	mmeineke	377
439			#else // is_mpi
440	gezelter	415
441	mmeineke	440	// first thing first, suspend fatalities.
442			painCave.isEventLoop = 1;
443
444			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
445			int haveError;
446
447	mmeineke	447	MPI_Status istatus;
448	gezelter	416	int *AtomToProcMap = mpiSim->getAtomToProcMap();
449
450	mmeineke	377	// write out header and node 0's coordinates
451	gezelter	415
452	mmeineke	440	haveError = 0;
453	mmeineke	377	if( worldRank == 0 ){
454			finalOut << mpiSim->getTotAtoms() << "\n";
455	gezelter	415
456	gezelter	591	finalOut << finalTime << ";\t"
457			<< entry_plug->Hmat[0][0] << "\t"
458			<< entry_plug->Hmat[1][0] << "\t"
459			<< entry_plug->Hmat[2][0] << ";\t"
460	mmeineke	572
461	gezelter	591	<< entry_plug->Hmat[0][1] << "\t"
462			<< entry_plug->Hmat[1][1] << "\t"
463			<< entry_plug->Hmat[2][1] << ";\t"
464	mmeineke	572
465	gezelter	591	<< entry_plug->Hmat[0][2] << "\t"
466			<< entry_plug->Hmat[1][2] << "\t"
467			<< entry_plug->Hmat[2][2] << ";\n";
468	mmeineke	377
469	gezelter	416	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
470	gezelter	415	// Get the Node number which has this molecule:
471	mmeineke	377
472	gezelter	415	which_node = AtomToProcMap[i];
473
474	gezelter	416	if (which_node == mpiSim->getMyNode()) {
475	chuckv	437
476			which_atom = i;
477			local_index=-1;
478			for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
479			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
480			}
481	mmeineke	670	if (local_index != -1) {
482
483			atoms[local_index]->getPos(pos);
484			atoms[local_index]->getVel(vel);
485
486	chuckv	437	sprintf( tempBuffer,
487			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
488			atoms[local_index]->getType(),
489	mmeineke	670	pos[0],
490			pos[1],
491			pos[2],
492			vel[0],
493			vel[1],
494			vel[2]);
495	chuckv	437	strcpy( writeLine, tempBuffer );
496	mmeineke	377
497	chuckv	437	if( atoms[local_index]->isDirectional() ){
498
499			dAtom = (DirectionalAtom *)atoms[local_index];
500			dAtom->getQ( q );
501
502			sprintf( tempBuffer,
503			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
504			q[0],
505			q[1],
506			q[2],
507			q[3],
508			dAtom->getJx(),
509			dAtom->getJy(),
510			dAtom->getJz());
511			strcat( writeLine, tempBuffer );
512			}
513			else
514			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
515			}
516			else {
517	mmeineke	440	sprintf(painCave.errMsg,
518			"Atom %d not found on processor %d\n",
519			i, worldRank );
520			haveError= 1;
521			simError();
522	chuckv	437	}
523	mmeineke	440
524			if(haveError) nodeZeroError();
525	chuckv	437
526	mmeineke	440	}
527			else {
528	gezelter	415
529	mmeineke	440	myStatus = 1;
530	mmeineke	447	MPI_Send(&myStatus, 1, MPI_INT, which_node,
531			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
532			MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
533			MPI_COMM_WORLD);
534			MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
535			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
536			MPI_Recv(&myStatus, 1, MPI_INT, which_node,
537			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
538	mmeineke	440
539			if(!myStatus) nodeZeroError();
540	mmeineke	377	}
541	gezelter	415
542	mmeineke	377	finalOut << writeLine;
543			}
544
545	gezelter	415	// kill everyone off:
546	mmeineke	440	myStatus = -1;
547			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
548	mmeineke	447	MPI_Send(&myStatus, 1, MPI_INT, j,
549			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
550	mmeineke	377	}
551
552	gezelter	415	} else {
553
554			done = 0;
555			while (!done) {
556	mmeineke	440
557	mmeineke	447	MPI_Recv(&myStatus, 1, MPI_INT, 0,
558			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
559	mmeineke	440
560			if(!myStatus) anonymousNodeDie();
561
562			if(myStatus < 0) break;
563
564	mmeineke	447	MPI_Recv(&which_atom, 1, MPI_INT, 0,
565			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
566	mmeineke	440
567			myStatus = 1;
568			local_index=-1;
569			for (j=0; j < mpiSim->getMyNlocal(); j++) {
570			if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
571			}
572			if (local_index != -1) {
573	mmeineke	377
574	mmeineke	670	atoms[local_index]->getPos(pos);
575			atoms[local_index]->getVel(vel);
576
577	mmeineke	440	//format the line
578			sprintf( tempBuffer,
579			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
580			atoms[local_index]->getType(),
581	mmeineke	670	pos[0],
582			pos[1],
583			pos[2],
584			vel[0],
585			vel[1],
586			vel[2]); // check here.
587	mmeineke	440	strcpy( writeLine, tempBuffer );
588
589			if( atoms[local_index]->isDirectional() ){
590	mmeineke	377
591	mmeineke	440	dAtom = (DirectionalAtom *)atoms[local_index];
592			dAtom->getQ( q );
593
594			sprintf( tempBuffer,
595			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
596			q[0],
597			q[1],
598			q[2],
599			q[3],
600			dAtom->getJx(),
601			dAtom->getJy(),
602			dAtom->getJz());
603			strcat( writeLine, tempBuffer );
604			}
605			else{
606			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
607			}
608			}
609			else {
610			sprintf(painCave.errMsg,
611			"Atom %d not found on processor %d\n",
612			which_atom, worldRank );
613			myStatus = 0;
614			simError();
615
616			strcpy( writeLine, "Hello, I'm an error.\n");
617	mmeineke	377	}
618	mmeineke	440
619	mmeineke	447	MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0,
620			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
621			MPI_Send( &myStatus, 1, MPI_INT, 0,
622			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
623	mmeineke	377	}
624	gezelter	419	}
625	gezelter	415	finalOut.flush();
626			sprintf( checkPointMsg,
627			"Sucessfully took a dump.\n");
628			MPIcheckPoint();
629	mmeineke	440
630	gezelter	415	if( worldRank == 0 ) finalOut.close();
631	mmeineke	377	#endif // is_mpi
632			}
633	mmeineke	440
634
635
636			#ifdef IS_MPI
637
638			// a couple of functions to let us escape the write loop
639
640			void dWrite::nodeZeroError( void ){
641			int j, myStatus;
642
643			myStatus = 0;
644			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
645	mmeineke	447	MPI_Send( &myStatus, 1, MPI_INT, j,
646			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
647	mmeineke	440	}
648
649
650			MPI_Finalize();
651			exit (0);
652
653			}
654
655			void dWrite::anonymousNodeDie( void ){
656
657			MPI_Finalize();
658			exit (0);
659			}
660
661			#endif //is_mpi