OOPSE/libmdtools/DumpWriter.cpp

#define _LARGEFILE_SOURCE64
#define _FILE_OFFSET_BITS 64

#include <string.h>
#include <iostream>
#include <fstream>
#include <algorithm>
#include <utility>

#ifdef IS_MPI
#include <mpi.h>
#include "mpiSimulation.hpp"

namespace dWrite{
  void DieDieDie( void );
}

using namespace dWrite;
#endif //is_mpi

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

DumpWriter::DumpWriter( SimInfo* the_entry_plug ){

  entry_plug = the_entry_plug;

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

    dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc );

    if( !dumpFile ){

      sprintf( painCave.errMsg,
               "Could not open \"%s\" for dump output.\n",
               entry_plug->sampleName);
      painCave.isFatal = 1;
      simError();
    }

#ifdef IS_MPI
  }

  //sort the local atoms by global index
  sortByGlobalIndex();
  
  sprintf( checkPointMsg,
           "Sucessfully opened output file for dumping.\n");
  MPIcheckPoint();
#endif // is_mpi
}

DumpWriter::~DumpWriter( ){

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

    dumpFile.close();

#ifdef IS_MPI
  }
#endif // is_mpi
}

#ifdef IS_MPI

/**
 * A hook function to load balancing
 */

void DumpWriter::update(){
  sortByGlobalIndex();          
}
  
/**
 * Auxiliary sorting function
 */
 
bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
  return p1.second < p2.second;
}

/**
 * Sorting the local index by global index
 */
 
void DumpWriter::sortByGlobalIndex(){
  Atom** atoms = entry_plug->atoms;
  
  indexArray.clear();
  
  for(int i = 0; i < mpiSim->getMyNlocal();i++) 
    indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
  
  sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);    
}

#endif

void DumpWriter::writeDump(double currentTime){

  ofstream finalOut;
  vector<ofstream*> fileStreams;

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

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

  writeFrame(fileStreams, currentTime);

#ifdef IS_MPI
  finalOut.close();
#endif
        
}

void DumpWriter::writeFinal(double currentTime){

  ofstream finalOut;
  vector<ofstream*> fileStreams;

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

    finalOut.open( entry_plug->finalName, ios::out | ios::trunc );

    if( !finalOut ){
      sprintf( painCave.errMsg,
               "Could not open \"%s\" for final dump output.\n",
               entry_plug->finalName );
      painCave.isFatal = 1;
      simError();
    }

#ifdef IS_MPI
  }
#endif // is_mpi
  
  fileStreams.push_back(&finalOut);  
  writeFrame(fileStreams, currentTime);

#ifdef IS_MPI
  finalOut.close();
#endif
  
}

void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){

  const int BUFFERSIZE = 2000;
  const int MINIBUFFERSIZE = 100;

  char tempBuffer[BUFFERSIZE];  
  char writeLine[BUFFERSIZE];

  int i, k;

#ifdef IS_MPI
  
  /*********************************************************************
   * Documentation?  You want DOCUMENTATION?
   * 
   * Why all the potatoes below?  
   *
   * To make a long story short, the original version of DumpWriter
   * worked in the most inefficient way possible.  Node 0 would 
   * poke each of the node for an individual atom's formatted data 
   * as node 0 worked its way down the global index. This was particularly 
   * inefficient since the method blocked all processors at every atom 
   * (and did it twice!).
   *
   * An intermediate version of DumpWriter could be described from Node
   * zero's perspective as follows:
   * 
   *  1) Have 100 of your friends stand in a circle.
   *  2) When you say go, have all of them start tossing potatoes at
   *     you (one at a time).
   *  3) Catch the potatoes.
   *
   * It was an improvement, but MPI has buffers and caches that could 
   * best be described in this analogy as "potato nets", so there's no 
   * need to block the processors atom-by-atom.
   * 
   * This new and improved DumpWriter works in an even more efficient 
   * way:
   * 
   *  1) Have 100 of your friend stand in a circle.
   *  2) When you say go, have them start tossing 5-pound bags of 
   *     potatoes at you.
   *  3) Once you've caught a friend's bag of potatoes,
   *     toss them a spud to let them know they can toss another bag.
   *
   * How's THAT for documentation?
   *
   *********************************************************************/

  int *potatoes;
  int myPotato;

  int nProc;
  int j, which_node, done, which_atom, local_index, currentIndex;
  double atomData6[6];
  double atomData13[13];
  int isDirectional;
  char* atomTypeString;
  char MPIatomTypeString[MINIBUFFERSIZE];

#else //is_mpi
  int nAtoms = entry_plug->n_atoms;
#endif //is_mpi

  double q[4];
  DirectionalAtom* dAtom;
  Atom** atoms = entry_plug->atoms;
  double pos[3], vel[3];

#ifndef IS_MPI
  
  for(k = 0; k < outFile.size(); k++){
    *outFile[k] << nAtoms << "\n";

    *outFile[k] << currentTime << ";\t"
               << entry_plug->Hmat[0][0] << "\t"
                     << entry_plug->Hmat[1][0] << "\t"
                     << entry_plug->Hmat[2][0] << ";\t"
               
               << entry_plug->Hmat[0][1] << "\t"
                     << entry_plug->Hmat[1][1] << "\t"
                     << entry_plug->Hmat[2][1] << ";\t"

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

    //write out additional parameters, such as chi and eta
    *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
  }
  
  for( i=0; i<nAtoms; i++ ){

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

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

    if( atoms[i]->isDirectional() ){

      dAtom = (DirectionalAtom *)atoms[i];
      dAtom->getQ( q );

      sprintf( tempBuffer,
               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
               q[0],
               q[1],
               q[2],
               q[3],
               dAtom->getJx(),
               dAtom->getJy(),
               dAtom->getJz());
      strcat( writeLine, tempBuffer );
    }
    else
      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );

    for(k = 0; k < outFile.size(); k++)
      *outFile[k] << writeLine;
  }

#else // is_mpi

  /* code to find maximum tag value */
  
  int *tagub, flag, MAXTAG;
  MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
  if (flag) {
    MAXTAG = *tagub;
  } else {
    MAXTAG = 32767;
  }  

  int haveError;

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

  // write out header and node 0's coordinates

  if( worldRank == 0 ){

    // Node 0 needs a list of the magic potatoes for each processor;

    nProc = mpiSim->getNumberProcessors();
    potatoes = new int[nProc];

    //write out the comment lines
    for (i = 0; i < nProc; i++) 
      potatoes[i] = 0;
    
      for(k = 0; k < outFile.size(); k++){
        *outFile[k] << mpiSim->getTotAtoms() << "\n";

        *outFile[k] << currentTime << ";\t"
                         << entry_plug->Hmat[0][0] << "\t"
                         << entry_plug->Hmat[1][0] << "\t"
                         << entry_plug->Hmat[2][0] << ";\t"

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

                         << entry_plug->Hmat[0][2] << "\t"
                         << entry_plug->Hmat[1][2] << "\t"
                         << entry_plug->Hmat[2][2] << ";";
  
        *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
    }

    currentIndex = 0;

    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
      
      // Get the Node number which has this atom;
      
      which_node = AtomToProcMap[i];
      
      if (which_node != 0) {

        if (potatoes[which_node] + 3 >= MAXTAG) {
          // The potato was going to exceed the maximum value, 
          // so wrap this processor potato back to 0:         

          potatoes[which_node] = 0;          
          MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
          
        }

        myPotato = potatoes[which_node];        
        
        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
                 myPotato, MPI_COMM_WORLD, &istatus);
        
        atomTypeString = MPIatomTypeString;
        
        myPotato++;

        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
                 myPotato, MPI_COMM_WORLD, &istatus);
               
        myPotato++;

        if (isDirectional) {          
          MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
                   myPotato, MPI_COMM_WORLD, &istatus);
        } else {
          MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
                   myPotato, MPI_COMM_WORLD, &istatus);          
        }
        
        myPotato++;
        potatoes[which_node] = myPotato;

      } else {
        
        haveError = 0;
        which_atom = i;
        
          local_index = indexArray[currentIndex].first;        
          
          if (which_atom == indexArray[currentIndex].second) {
            
            atomTypeString = atoms[local_index]->getType();
            
          atoms[local_index]->getPos(pos);
          atoms[local_index]->getVel(vel);          
          
          atomData6[0] = pos[0];
          atomData6[1] = pos[1];
          atomData6[2] = pos[2];

          atomData6[3] = vel[0];
          atomData6[4] = vel[1];
          atomData6[5] = vel[2];
          
          isDirectional = 0;

          if( atoms[local_index]->isDirectional() ){

            isDirectional = 1;
            
            dAtom = (DirectionalAtom *)atoms[local_index];
            dAtom->getQ( q );

            for (int j = 0; j < 6 ; j++)
              atomData13[j] = atomData6[j];            
            
            atomData13[6] = q[0];
            atomData13[7] = q[1];
            atomData13[8] = q[2];
            atomData13[9] = q[3];
            
            atomData13[10] = dAtom->getJx();
            atomData13[11] = dAtom->getJy();
            atomData13[12] = dAtom->getJz();
          }
          
        } else {
          sprintf(painCave.errMsg,
                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
                  which_atom, worldRank, currentIndex, local_index );
          haveError= 1;
          simError();
        }
        
        if(haveError) DieDieDie();
        
        currentIndex++;
      }
      // If we've survived to here, format the line:
      
      if (!isDirectional) {
        
        sprintf( writeLine,
                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                 atomTypeString,
                 atomData6[0],
                 atomData6[1],
                 atomData6[2],
                 atomData6[3],
                 atomData6[4],
                 atomData6[5]);
        
        strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
        
      } else {
        
        sprintf( writeLine,
                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
                 atomTypeString,
                 atomData13[0],
                 atomData13[1],
                 atomData13[2],
                 atomData13[3],
                 atomData13[4],
                 atomData13[5],
                 atomData13[6],
                 atomData13[7],
                 atomData13[8],
                 atomData13[9],
                 atomData13[10],
                 atomData13[11],
                 atomData13[12]);
        
      }
      
      for(k = 0; k < outFile.size(); k++)
        *outFile[k] << writeLine;
    }
    
    for(k = 0; k < outFile.size(); k++)
      outFile[k]->flush();
    
    sprintf( checkPointMsg,
             "Sucessfully took a dump.\n");
    
    MPIcheckPoint();        
    
    delete[] potatoes;
    
  } else {

    // worldRank != 0, so I'm a remote node.  

    // Set my magic potato to 0:

    myPotato = 0;
    currentIndex = 0;
    
    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
      
      // Am I the node which has this atom?
      
      if (AtomToProcMap[i] == worldRank) {

        if (myPotato + 3 >= MAXTAG) {
          
          // The potato was going to exceed the maximum value, 
          // so wrap this processor potato back to 0 (and block until
          // node 0 says we can go:
          
          MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
          
        }
        which_atom = i; 

        local_index = indexArray[currentIndex].first;        
                
        if (which_atom == indexArray[currentIndex].second) {
         
          atomTypeString = atoms[local_index]->getType();
          
          atoms[local_index]->getPos(pos);
          atoms[local_index]->getVel(vel);
          
          atomData6[0] = pos[0];
          atomData6[1] = pos[1];
          atomData6[2] = pos[2];

          atomData6[3] = vel[0];
          atomData6[4] = vel[1];
          atomData6[5] = vel[2];
          
          isDirectional = 0;

          if( atoms[local_index]->isDirectional() ){

            isDirectional = 1;
            
            dAtom = (DirectionalAtom *)atoms[local_index];
            dAtom->getQ( q );
            
            for (int j = 0; j < 6 ; j++)
              atomData13[j] = atomData6[j];
            
            atomData13[6] = q[0];
            atomData13[7] = q[1];
            atomData13[8] = q[2];
            atomData13[9] = q[3];
  
            atomData13[10] = dAtom->getJx();
            atomData13[11] = dAtom->getJy();
            atomData13[12] = dAtom->getJz();
          }

        } else {
          sprintf(painCave.errMsg,
                  "Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
                  which_atom, worldRank, currentIndex, local_index );
          haveError= 1;
          simError();
        }
        
        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);

        // null terminate the string before sending (just in case):
        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';

        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
                             myPotato, MPI_COMM_WORLD);
        
        myPotato++;

        MPI_Send(&isDirectional, 1, MPI_INT, 0,
                             myPotato, MPI_COMM_WORLD);
        
        myPotato++;
        
        if (isDirectional) {

          MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
                   myPotato, MPI_COMM_WORLD);
          
        } else {

          MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
                   myPotato, MPI_COMM_WORLD);
        }

        myPotato++;  
        currentIndex++;    
      }
    }

    sprintf( checkPointMsg,
             "Sucessfully took a dump.\n");
    MPIcheckPoint();        
    
  } 
  
#endif // is_mpi
}

#ifdef IS_MPI

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

void dWrite::DieDieDie( void ){

  MPI_Finalize();
  exit (0);
}

#endif //is_mpi
Revision:	1078
Committed:	Tue Mar 2 20:32:40 2004 UTC (20 years, 5 months ago) by tim
File size:	14827 byte(s)
Log Message:	add LARGEFILE_SOURCE64 macro to support large file
#	User	Rev	Content
1	tim	1078	#define _LARGEFILE_SOURCE64
2	mmeineke	723	#define _FILE_OFFSET_BITS 64
3
4	gezelter	829	#include <string.h>
5	mmeineke	377	#include <iostream>
6			#include <fstream>
7	tim	929	#include <algorithm>
8			#include <utility>
9	mmeineke	377
10			#ifdef IS_MPI
11			#include <mpi.h>
12			#include "mpiSimulation.hpp"
13	mmeineke	440
14			namespace dWrite{
15	gezelter	907	void DieDieDie( void );
16	mmeineke	440	}
17
18			using namespace dWrite;
19	mmeineke	377	#endif //is_mpi
20
21			#include "ReadWrite.hpp"
22			#include "simError.h"
23
24			DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
25
26			entry_plug = the_entry_plug;
27
28			#ifdef IS_MPI
29			if(worldRank == 0 ){
30			#endif // is_mpi
31	tim	837
32	tim	929	dumpFile.open(entry_plug->sampleName, ios::out \| ios::trunc );
33	tim	837
34	tim	929	if( !dumpFile ){
35	tim	837
36	mmeineke	377	sprintf( painCave.errMsg,
37			"Could not open \"%s\" for dump output.\n",
38	tim	929	entry_plug->sampleName);
39	mmeineke	377	painCave.isFatal = 1;
40			simError();
41			}
42	mmeineke	469
43	mmeineke	377	#ifdef IS_MPI
44			}
45
46	tim	929	//sort the local atoms by global index
47			sortByGlobalIndex();
48
49	mmeineke	377	sprintf( checkPointMsg,
50			"Sucessfully opened output file for dumping.\n");
51			MPIcheckPoint();
52			#endif // is_mpi
53			}
54
55			DumpWriter::~DumpWriter( ){
56
57			#ifdef IS_MPI
58			if(worldRank == 0 ){
59			#endif // is_mpi
60
61	tim	929	dumpFile.close();
62	mmeineke	377
63			#ifdef IS_MPI
64			}
65			#endif // is_mpi
66			}
67
68	tim	929	#ifdef IS_MPI
69	tim	837
70	tim	929	/**
71			* A hook function to load balancing
72			*/
73
74			void DumpWriter::update(){
75			sortByGlobalIndex();
76			}
77
78			/**
79			* Auxiliary sorting function
80			*/
81
82			bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83			return p1.second < p2.second;
84			}
85
86			/**
87			* Sorting the local index by global index
88			*/
89
90			void DumpWriter::sortByGlobalIndex(){
91			Atom** atoms = entry_plug->atoms;
92
93			indexArray.clear();
94
95	chuckv	949	for(int i = 0; i < mpiSim->getMyNlocal();i++)
96	tim	929	indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97
98			sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
99			}
100	chuckv	949
101	tim	929	#endif
102
103			void DumpWriter::writeDump(double currentTime){
104
105	tim	936	ofstream finalOut;
106	tim	934	vector<ofstream*> fileStreams;
107
108			#ifdef IS_MPI
109			if(worldRank == 0 ){
110	tim	952	#endif
111	tim	936	finalOut.open( entry_plug->finalName, ios::out \| ios::trunc );
112			if( !finalOut ){
113			sprintf( painCave.errMsg,
114			"Could not open \"%s\" for final dump output.\n",
115			entry_plug->finalName );
116			painCave.isFatal = 1;
117			simError();
118			}
119	tim	952	#ifdef IS_MPI
120	tim	934	}
121			#endif // is_mpi
122
123			fileStreams.push_back(&finalOut);
124			fileStreams.push_back(&dumpFile);
125
126			writeFrame(fileStreams, currentTime);
127	tim	936
128			#ifdef IS_MPI
129			finalOut.close();
130			#endif
131	tim	929
132			}
133
134			void DumpWriter::writeFinal(double currentTime){
135
136	tim	936	ofstream finalOut;
137	tim	934	vector<ofstream*> fileStreams;
138
139	tim	929	#ifdef IS_MPI
140			if(worldRank == 0 ){
141	mmeineke	951	#endif // is_mpi
142	tim	936
143			finalOut.open( entry_plug->finalName, ios::out \| ios::trunc );
144
145			if( !finalOut ){
146			sprintf( painCave.errMsg,
147			"Could not open \"%s\" for final dump output.\n",
148			entry_plug->finalName );
149			painCave.isFatal = 1;
150			simError();
151			}
152
153	mmeineke	951	#ifdef IS_MPI
154	tim	934	}
155	tim	929	#endif // is_mpi
156
157	tim	934	fileStreams.push_back(&finalOut);
158			writeFrame(fileStreams, currentTime);
159	tim	936
160			#ifdef IS_MPI
161			finalOut.close();
162			#endif
163	tim	929
164			}
165
166	tim	934	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
167	tim	929
168	mmeineke	377	const int BUFFERSIZE = 2000;
169	gezelter	912	const int MINIBUFFERSIZE = 100;
170	gezelter	907
171	tim	936	char tempBuffer[BUFFERSIZE];
172	mmeineke	377	char writeLine[BUFFERSIZE];
173
174	tim	934	int i, k;
175	gezelter	916
176	mmeineke	787	#ifdef IS_MPI
177	gezelter	916
178	gezelter	947	/*********************************************************************
179			* Documentation? You want DOCUMENTATION?
180			*
181			* Why all the potatoes below?
182			*
183			* To make a long story short, the original version of DumpWriter
184			* worked in the most inefficient way possible. Node 0 would
185			* poke each of the node for an individual atom's formatted data
186			* as node 0 worked its way down the global index. This was particularly
187			* inefficient since the method blocked all processors at every atom
188			* (and did it twice!).
189			*
190			* An intermediate version of DumpWriter could be described from Node
191			* zero's perspective as follows:
192			*
193			* 1) Have 100 of your friends stand in a circle.
194			* 2) When you say go, have all of them start tossing potatoes at
195			* you (one at a time).
196			* 3) Catch the potatoes.
197			*
198			* It was an improvement, but MPI has buffers and caches that could
199			* best be described in this analogy as "potato nets", so there's no
200			* need to block the processors atom-by-atom.
201			*
202			* This new and improved DumpWriter works in an even more efficient
203			* way:
204			*
205			* 1) Have 100 of your friend stand in a circle.
206			* 2) When you say go, have them start tossing 5-pound bags of
207			* potatoes at you.
208			* 3) Once you've caught a friend's bag of potatoes,
209			* toss them a spud to let them know they can toss another bag.
210			*
211			* How's THAT for documentation?
212			*
213			*********************************************************************/
214
215	gezelter	916	int *potatoes;
216			int myPotato;
217
218			int nProc;
219	tim	929	int j, which_node, done, which_atom, local_index, currentIndex;
220	gezelter	916	double atomData6[6];
221			double atomData13[13];
222	gezelter	907	int isDirectional;
223			char* atomTypeString;
224	gezelter	910	char MPIatomTypeString[MINIBUFFERSIZE];
225	gezelter	916
226	mmeineke	787	#else //is_mpi
227			int nAtoms = entry_plug->n_atoms;
228			#endif //is_mpi
229
230	mmeineke	377	double q[4];
231			DirectionalAtom* dAtom;
232			Atom** atoms = entry_plug->atoms;
233	mmeineke	670	double pos[3], vel[3];
234	tim	837
235	mmeineke	377	#ifndef IS_MPI
236	tim	934
237			for(k = 0; k < outFile.size(); k++){
238			*outFile[k] << nAtoms << "\n";
239	tim	837
240	tim	934	*outFile[k] << currentTime << ";\t"
241			<< entry_plug->Hmat[0][0] << "\t"
242			<< entry_plug->Hmat[1][0] << "\t"
243			<< entry_plug->Hmat[2][0] << ";\t"
244
245			<< entry_plug->Hmat[0][1] << "\t"
246			<< entry_plug->Hmat[1][1] << "\t"
247			<< entry_plug->Hmat[2][1] << ";\t"
248	tim	837
249	tim	934	<< entry_plug->Hmat[0][2] << "\t"
250			<< entry_plug->Hmat[1][2] << "\t"
251			<< entry_plug->Hmat[2][2] << ";";
252	mmeineke	572
253	tim	934	//write out additional parameters, such as chi and eta
254			*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
255			}
256
257	mmeineke	377	for( i=0; i<nAtoms; i++ ){
258	tim	837
259	mmeineke	670	atoms[i]->getPos(pos);
260			atoms[i]->getVel(vel);
261	mmeineke	377
262			sprintf( tempBuffer,
263			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
264			atoms[i]->getType(),
265	mmeineke	670	pos[0],
266			pos[1],
267			pos[2],
268			vel[0],
269			vel[1],
270			vel[2]);
271	mmeineke	377	strcpy( writeLine, tempBuffer );
272
273			if( atoms[i]->isDirectional() ){
274	tim	837
275	mmeineke	377	dAtom = (DirectionalAtom *)atoms[i];
276			dAtom->getQ( q );
277	tim	837
278	mmeineke	377	sprintf( tempBuffer,
279			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
280			q[0],
281			q[1],
282			q[2],
283			q[3],
284			dAtom->getJx(),
285			dAtom->getJy(),
286			dAtom->getJz());
287			strcat( writeLine, tempBuffer );
288			}
289			else
290			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
291	tim	837
292	tim	934	for(k = 0; k < outFile.size(); k++)
293			*outFile[k] << writeLine;
294	mmeineke	377	}
295
296			#else // is_mpi
297	gezelter	416
298	chuckv	913	/* code to find maximum tag value */
299	tim	919
300	tim	920	int *tagub, flag, MAXTAG;
301	chuckv	913	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
302			if (flag) {
303	tim	920	MAXTAG = *tagub;
304	chuckv	913	} else {
305			MAXTAG = 32767;
306	gezelter	916	}
307	mmeineke	440
308			int haveError;
309
310	mmeineke	447	MPI_Status istatus;
311	gezelter	416	int *AtomToProcMap = mpiSim->getAtomToProcMap();
312	tim	837
313	mmeineke	377	// write out header and node 0's coordinates
314	tim	837
315	mmeineke	377	if( worldRank == 0 ){
316	gezelter	916
317			// Node 0 needs a list of the magic potatoes for each processor;
318
319			nProc = mpiSim->getNumberProcessors();
320			potatoes = new int[nProc];
321
322	tim	934	//write out the comment lines
323	gezelter	916	for (i = 0; i < nProc; i++)
324			potatoes[i] = 0;
325
326	tim	934	for(k = 0; k < outFile.size(); k++){
327			*outFile[k] << mpiSim->getTotAtoms() << "\n";
328	tim	837
329	tim	934	*outFile[k] << currentTime << ";\t"
330			<< entry_plug->Hmat[0][0] << "\t"
331			<< entry_plug->Hmat[1][0] << "\t"
332			<< entry_plug->Hmat[2][0] << ";\t"
333	tim	837
334	tim	934	<< entry_plug->Hmat[0][1] << "\t"
335			<< entry_plug->Hmat[1][1] << "\t"
336			<< entry_plug->Hmat[2][1] << ";\t"
337	tim	837
338	tim	934	<< entry_plug->Hmat[0][2] << "\t"
339			<< entry_plug->Hmat[1][2] << "\t"
340			<< entry_plug->Hmat[2][2] << ";";
341
342			*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
343			}
344	tim	837
345	tim	929	currentIndex = 0;
346	tim	934
347	gezelter	416	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
348	chuckv	913
349	gezelter	417	// Get the Node number which has this atom;
350	chuckv	913
351	tim	837	which_node = AtomToProcMap[i];
352	chuckv	913
353	gezelter	907	if (which_node != 0) {
354	gezelter	916
355			if (potatoes[which_node] + 3 >= MAXTAG) {
356			// The potato was going to exceed the maximum value,
357			// so wrap this processor potato back to 0:
358
359			potatoes[which_node] = 0;
360			MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
361
362			}
363
364			myPotato = potatoes[which_node];
365	gezelter	907
366	gezelter	910	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
367	gezelter	916	myPotato, MPI_COMM_WORLD, &istatus);
368	gezelter	907
369	tim	920	atomTypeString = MPIatomTypeString;
370
371	gezelter	916	myPotato++;
372
373	gezelter	907	MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
374	gezelter	916	myPotato, MPI_COMM_WORLD, &istatus);
375
376			myPotato++;
377	gezelter	907
378	gezelter	916	if (isDirectional) {
379			MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
380			myPotato, MPI_COMM_WORLD, &istatus);
381			} else {
382			MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
383			myPotato, MPI_COMM_WORLD, &istatus);
384	gezelter	907	}
385	gezelter	916
386			myPotato++;
387			potatoes[which_node] = myPotato;
388	gezelter	907
389			} else {
390
391	tim	934	haveError = 0;
392	chuckv	949	which_atom = i;
393	gezelter	916
394	chuckv	949	local_index = indexArray[currentIndex].first;
395	gezelter	916
396	chuckv	949	if (which_atom == indexArray[currentIndex].second) {
397
398			atomTypeString = atoms[local_index]->getType();
399
400			atoms[local_index]->getPos(pos);
401			atoms[local_index]->getVel(vel);
402
403	gezelter	916	atomData6[0] = pos[0];
404			atomData6[1] = pos[1];
405			atomData6[2] = pos[2];
406	tim	837
407	gezelter	916	atomData6[3] = vel[0];
408			atomData6[4] = vel[1];
409			atomData6[5] = vel[2];
410	gezelter	907
411			isDirectional = 0;
412
413	chuckv	436	if( atoms[local_index]->isDirectional() ){
414	tim	837
415	gezelter	907	isDirectional = 1;
416
417	chuckv	436	dAtom = (DirectionalAtom *)atoms[local_index];
418			dAtom->getQ( q );
419	gezelter	916
420			for (int j = 0; j < 6 ; j++)
421			atomData13[j] = atomData6[j];
422	gezelter	907
423	gezelter	916	atomData13[6] = q[0];
424			atomData13[7] = q[1];
425			atomData13[8] = q[2];
426			atomData13[9] = q[3];
427
428			atomData13[10] = dAtom->getJx();
429			atomData13[11] = dAtom->getJy();
430			atomData13[12] = dAtom->getJz();
431	gezelter	907	}
432	gezelter	916
433	gezelter	907	} else {
434	chuckv	949	sprintf(painCave.errMsg,
435			"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
436			which_atom, worldRank, currentIndex, local_index );
437			haveError= 1;
438			simError();
439			}
440	gezelter	916
441	tim	934	if(haveError) DieDieDie();
442	gezelter	916
443	chuckv	949	currentIndex++;
444	tim	926	}
445			// If we've survived to here, format the line:
446
447			if (!isDirectional) {
448
449	tim	934	sprintf( writeLine,
450	chuckv	949	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
451			atomTypeString,
452			atomData6[0],
453			atomData6[1],
454			atomData6[2],
455			atomData6[3],
456			atomData6[4],
457			atomData6[5]);
458	tim	926
459	chuckv	949	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
460
461	tim	926	} else {
462
463	chuckv	949	sprintf( writeLine,
464			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
465			atomTypeString,
466			atomData13[0],
467			atomData13[1],
468			atomData13[2],
469			atomData13[3],
470			atomData13[4],
471			atomData13[5],
472			atomData13[6],
473			atomData13[7],
474			atomData13[8],
475			atomData13[9],
476			atomData13[10],
477			atomData13[11],
478			atomData13[12]);
479	gezelter	907
480			}
481	tim	926
482	tim	934	for(k = 0; k < outFile.size(); k++)
483			*outFile[k] << writeLine;
484	mmeineke	377	}
485	tim	926
486	tim	934	for(k = 0; k < outFile.size(); k++)
487			outFile[k]->flush();
488
489	gezelter	907	sprintf( checkPointMsg,
490			"Sucessfully took a dump.\n");
491	chuckv	949
492	gezelter	907	MPIcheckPoint();
493	chuckv	949
494	tim	919	delete[] potatoes;
495	chuckv	949
496	gezelter	415	} else {
497	tim	837
498	gezelter	907	// worldRank != 0, so I'm a remote node.
499	gezelter	916
500			// Set my magic potato to 0:
501
502			myPotato = 0;
503	tim	929	currentIndex = 0;
504	gezelter	907
505			for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
506
507			// Am I the node which has this atom?
508
509			if (AtomToProcMap[i] == worldRank) {
510	tim	837
511	gezelter	916	if (myPotato + 3 >= MAXTAG) {
512	chuckv	949
513	gezelter	916	// The potato was going to exceed the maximum value,
514			// so wrap this processor potato back to 0 (and block until
515			// node 0 says we can go:
516	chuckv	949
517	gezelter	916	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
518
519			}
520	tim	919	which_atom = i;
521	chuckv	949
522			local_index = indexArray[currentIndex].first;
523	tim	920
524	chuckv	949	if (which_atom == indexArray[currentIndex].second) {
525	gezelter	907
526			atomTypeString = atoms[local_index]->getType();
527	chuckv	949
528			atoms[local_index]->getPos(pos);
529			atoms[local_index]->getVel(vel);
530
531	gezelter	916	atomData6[0] = pos[0];
532			atomData6[1] = pos[1];
533			atomData6[2] = pos[2];
534	tim	837
535	gezelter	916	atomData6[3] = vel[0];
536			atomData6[4] = vel[1];
537			atomData6[5] = vel[2];
538	gezelter	907
539			isDirectional = 0;
540	tim	837
541	gezelter	907	if( atoms[local_index]->isDirectional() ){
542	mmeineke	377
543	gezelter	907	isDirectional = 1;
544
545			dAtom = (DirectionalAtom *)atoms[local_index];
546			dAtom->getQ( q );
547
548	gezelter	916	for (int j = 0; j < 6 ; j++)
549			atomData13[j] = atomData6[j];
550
551			atomData13[6] = q[0];
552			atomData13[7] = q[1];
553			atomData13[8] = q[2];
554			atomData13[9] = q[3];
555	tim	934
556	gezelter	916	atomData13[10] = dAtom->getJx();
557			atomData13[11] = dAtom->getJy();
558			atomData13[12] = dAtom->getJz();
559	gezelter	907	}
560	tim	837
561	gezelter	907	} else {
562	chuckv	949	sprintf(painCave.errMsg,
563			"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n",
564			which_atom, worldRank, currentIndex, local_index );
565			haveError= 1;
566			simError();
567			}
568
569	gezelter	916	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
570	tim	837
571	gezelter	916	// null terminate the string before sending (just in case):
572			MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
573	tim	837
574	gezelter	910	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
575	tim	934	myPotato, MPI_COMM_WORLD);
576	gezelter	907
577	gezelter	916	myPotato++;
578
579	gezelter	907	MPI_Send(&isDirectional, 1, MPI_INT, 0,
580	tim	934	myPotato, MPI_COMM_WORLD);
581	gezelter	907
582	gezelter	916	myPotato++;
583
584	gezelter	907	if (isDirectional) {
585
586	gezelter	916	MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
587			myPotato, MPI_COMM_WORLD);
588	gezelter	907
589	gezelter	916	} else {
590
591			MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
592			myPotato, MPI_COMM_WORLD);
593	gezelter	907	}
594	gezelter	916
595	tim	929	myPotato++;
596			currentIndex++;
597	mmeineke	377	}
598	gezelter	907	}
599	mmeineke	440
600	gezelter	907	sprintf( checkPointMsg,
601	gezelter	916	"Sucessfully took a dump.\n");
602	gezelter	907	MPIcheckPoint();
603
604	gezelter	916	}
605	gezelter	907
606	mmeineke	377	#endif // is_mpi
607			}
608	mmeineke	440
609			#ifdef IS_MPI
610
611			// a couple of functions to let us escape the write loop
612
613	gezelter	907	void dWrite::DieDieDie( void ){
614	tim	837
615	mmeineke	440	MPI_Finalize();
616			exit (0);
617			}
618
619			#endif //is_mpi