OOPSE/libmdtools/DumpWriter.cpp

#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 ){
    
    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();
    }
  }
#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 ){

    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();
    }

  }
#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\n",
                              i, worldRank );
                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\n",
                              i, worldRank );
                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:	947
Committed:	Thu Jan 15 14:22:16 2004 UTC (20 years, 5 months ago) by gezelter
File size:	15023 byte(s)
Log Message:	Documented the Spud Toss
#	User	Rev	Content
1	mmeineke	723	#define _FILE_OFFSET_BITS 64
2
3	gezelter	829	#include <string.h>
4	mmeineke	377	#include <iostream>
5			#include <fstream>
6	tim	929	#include <algorithm>
7			#include <utility>
8	mmeineke	377
9			#ifdef IS_MPI
10			#include <mpi.h>
11			#include "mpiSimulation.hpp"
12	mmeineke	440
13			namespace dWrite{
14	gezelter	907	void DieDieDie( void );
15	mmeineke	440	}
16
17			using namespace dWrite;
18	mmeineke	377	#endif //is_mpi
19
20			#include "ReadWrite.hpp"
21			#include "simError.h"
22
23			DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
24
25			entry_plug = the_entry_plug;
26
27			#ifdef IS_MPI
28			if(worldRank == 0 ){
29			#endif // is_mpi
30	tim	837
31
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			for(int i = 0; i < mpiSim->getMyNlocal();i++)
96			indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex()));
97
98			sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
99			}
100			#endif
101
102			void DumpWriter::writeDump(double currentTime){
103
104	tim	936	ofstream finalOut;
105	tim	934	vector<ofstream*> fileStreams;
106
107			#ifdef IS_MPI
108			if(worldRank == 0 ){
109	tim	936
110			finalOut.open( entry_plug->finalName, ios::out \| ios::trunc );
111			if( !finalOut ){
112			sprintf( painCave.errMsg,
113			"Could not open \"%s\" for final dump output.\n",
114			entry_plug->finalName );
115			painCave.isFatal = 1;
116			simError();
117			}
118	tim	934	}
119			#endif // is_mpi
120
121			fileStreams.push_back(&finalOut);
122			fileStreams.push_back(&dumpFile);
123
124			writeFrame(fileStreams, currentTime);
125	tim	936
126			#ifdef IS_MPI
127			finalOut.close();
128			#endif
129	tim	929
130			}
131
132			void DumpWriter::writeFinal(double currentTime){
133
134	tim	936	ofstream finalOut;
135	tim	934	vector<ofstream*> fileStreams;
136
137	tim	929	#ifdef IS_MPI
138			if(worldRank == 0 ){
139	tim	936
140			finalOut.open( entry_plug->finalName, ios::out \| ios::trunc );
141
142			if( !finalOut ){
143			sprintf( painCave.errMsg,
144			"Could not open \"%s\" for final dump output.\n",
145			entry_plug->finalName );
146			painCave.isFatal = 1;
147			simError();
148			}
149
150	tim	934	}
151	tim	929	#endif // is_mpi
152
153	tim	934	fileStreams.push_back(&finalOut);
154			writeFrame(fileStreams, currentTime);
155	tim	936
156			#ifdef IS_MPI
157			finalOut.close();
158			#endif
159	tim	929
160			}
161
162	tim	934	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
163	tim	929
164	mmeineke	377	const int BUFFERSIZE = 2000;
165	gezelter	912	const int MINIBUFFERSIZE = 100;
166	gezelter	907
167	tim	936	char tempBuffer[BUFFERSIZE];
168	mmeineke	377	char writeLine[BUFFERSIZE];
169
170	tim	934	int i, k;
171	gezelter	916
172	mmeineke	787	#ifdef IS_MPI
173	gezelter	916
174	gezelter	947	/*********************************************************************
175			* Documentation? You want DOCUMENTATION?
176			*
177			* Why all the potatoes below?
178			*
179			* To make a long story short, the original version of DumpWriter
180			* worked in the most inefficient way possible. Node 0 would
181			* poke each of the node for an individual atom's formatted data
182			* as node 0 worked its way down the global index. This was particularly
183			* inefficient since the method blocked all processors at every atom
184			* (and did it twice!).
185			*
186			* An intermediate version of DumpWriter could be described from Node
187			* zero's perspective as follows:
188			*
189			* 1) Have 100 of your friends stand in a circle.
190			* 2) When you say go, have all of them start tossing potatoes at
191			* you (one at a time).
192			* 3) Catch the potatoes.
193			*
194			* It was an improvement, but MPI has buffers and caches that could
195			* best be described in this analogy as "potato nets", so there's no
196			* need to block the processors atom-by-atom.
197			*
198			* This new and improved DumpWriter works in an even more efficient
199			* way:
200			*
201			* 1) Have 100 of your friend stand in a circle.
202			* 2) When you say go, have them start tossing 5-pound bags of
203			* potatoes at you.
204			* 3) Once you've caught a friend's bag of potatoes,
205			* toss them a spud to let them know they can toss another bag.
206			*
207			* How's THAT for documentation?
208			*
209			*********************************************************************/
210
211	gezelter	916	int *potatoes;
212			int myPotato;
213
214			int nProc;
215	tim	929	int j, which_node, done, which_atom, local_index, currentIndex;
216	gezelter	916	double atomData6[6];
217			double atomData13[13];
218	gezelter	907	int isDirectional;
219			char* atomTypeString;
220	gezelter	910	char MPIatomTypeString[MINIBUFFERSIZE];
221	gezelter	916
222	mmeineke	787	#else //is_mpi
223			int nAtoms = entry_plug->n_atoms;
224			#endif //is_mpi
225
226	mmeineke	377	double q[4];
227			DirectionalAtom* dAtom;
228			Atom** atoms = entry_plug->atoms;
229	mmeineke	670	double pos[3], vel[3];
230	tim	837
231	mmeineke	377	#ifndef IS_MPI
232	tim	934
233			for(k = 0; k < outFile.size(); k++){
234			*outFile[k] << nAtoms << "\n";
235	tim	837
236	tim	934	*outFile[k] << currentTime << ";\t"
237			<< entry_plug->Hmat[0][0] << "\t"
238			<< entry_plug->Hmat[1][0] << "\t"
239			<< entry_plug->Hmat[2][0] << ";\t"
240
241			<< entry_plug->Hmat[0][1] << "\t"
242			<< entry_plug->Hmat[1][1] << "\t"
243			<< entry_plug->Hmat[2][1] << ";\t"
244	tim	837
245	tim	934	<< entry_plug->Hmat[0][2] << "\t"
246			<< entry_plug->Hmat[1][2] << "\t"
247			<< entry_plug->Hmat[2][2] << ";";
248	mmeineke	572
249	tim	934	//write out additional parameters, such as chi and eta
250			*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
251			}
252
253	mmeineke	377	for( i=0; i<nAtoms; i++ ){
254	tim	837
255	mmeineke	670	atoms[i]->getPos(pos);
256			atoms[i]->getVel(vel);
257	mmeineke	377
258			sprintf( tempBuffer,
259			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
260			atoms[i]->getType(),
261	mmeineke	670	pos[0],
262			pos[1],
263			pos[2],
264			vel[0],
265			vel[1],
266			vel[2]);
267	mmeineke	377	strcpy( writeLine, tempBuffer );
268
269			if( atoms[i]->isDirectional() ){
270	tim	837
271	mmeineke	377	dAtom = (DirectionalAtom *)atoms[i];
272			dAtom->getQ( q );
273	tim	837
274	mmeineke	377	sprintf( tempBuffer,
275			"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
276			q[0],
277			q[1],
278			q[2],
279			q[3],
280			dAtom->getJx(),
281			dAtom->getJy(),
282			dAtom->getJz());
283			strcat( writeLine, tempBuffer );
284			}
285			else
286			strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
287	tim	837
288	tim	934	for(k = 0; k < outFile.size(); k++)
289			*outFile[k] << writeLine;
290	mmeineke	377	}
291
292			#else // is_mpi
293	gezelter	416
294	chuckv	913	/* code to find maximum tag value */
295	tim	919
296	tim	920	int *tagub, flag, MAXTAG;
297	chuckv	913	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
298			if (flag) {
299	tim	920	MAXTAG = *tagub;
300	chuckv	913	} else {
301			MAXTAG = 32767;
302	gezelter	916	}
303	mmeineke	440
304			int haveError;
305
306	mmeineke	447	MPI_Status istatus;
307	gezelter	416	int *AtomToProcMap = mpiSim->getAtomToProcMap();
308	tim	837
309	mmeineke	377	// write out header and node 0's coordinates
310	tim	837
311	mmeineke	377	if( worldRank == 0 ){
312	gezelter	916
313			// Node 0 needs a list of the magic potatoes for each processor;
314
315			nProc = mpiSim->getNumberProcessors();
316			potatoes = new int[nProc];
317
318	tim	934	//write out the comment lines
319	gezelter	916	for (i = 0; i < nProc; i++)
320			potatoes[i] = 0;
321
322	tim	934	for(k = 0; k < outFile.size(); k++){
323			*outFile[k] << mpiSim->getTotAtoms() << "\n";
324	tim	837
325	tim	934	*outFile[k] << currentTime << ";\t"
326			<< entry_plug->Hmat[0][0] << "\t"
327			<< entry_plug->Hmat[1][0] << "\t"
328			<< entry_plug->Hmat[2][0] << ";\t"
329	tim	837
330	tim	934	<< entry_plug->Hmat[0][1] << "\t"
331			<< entry_plug->Hmat[1][1] << "\t"
332			<< entry_plug->Hmat[2][1] << ";\t"
333	tim	837
334	tim	934	<< entry_plug->Hmat[0][2] << "\t"
335			<< entry_plug->Hmat[1][2] << "\t"
336			<< entry_plug->Hmat[2][2] << ";";
337
338			*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
339			}
340	tim	837
341	tim	929	currentIndex = 0;
342	tim	934
343	gezelter	416	for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
344	chuckv	913
345	gezelter	417	// Get the Node number which has this atom;
346	chuckv	913
347	tim	837	which_node = AtomToProcMap[i];
348	chuckv	913
349	gezelter	907	if (which_node != 0) {
350	gezelter	916
351			if (potatoes[which_node] + 3 >= MAXTAG) {
352			// The potato was going to exceed the maximum value,
353			// so wrap this processor potato back to 0:
354
355			potatoes[which_node] = 0;
356			MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
357
358			}
359
360			myPotato = potatoes[which_node];
361	gezelter	907
362	gezelter	910	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
363	gezelter	916	myPotato, MPI_COMM_WORLD, &istatus);
364	gezelter	907
365	tim	920	atomTypeString = MPIatomTypeString;
366
367	gezelter	916	myPotato++;
368
369	gezelter	907	MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
370	gezelter	916	myPotato, MPI_COMM_WORLD, &istatus);
371
372			myPotato++;
373	gezelter	907
374	gezelter	916	if (isDirectional) {
375			MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node,
376			myPotato, MPI_COMM_WORLD, &istatus);
377			} else {
378			MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node,
379			myPotato, MPI_COMM_WORLD, &istatus);
380	gezelter	907	}
381	gezelter	916
382			myPotato++;
383			potatoes[which_node] = myPotato;
384	gezelter	907
385			} else {
386
387	tim	934	haveError = 0;
388			which_atom = i;
389	gezelter	916
390	tim	929	local_index = indexArray[currentIndex].first;
391
392			if (which_atom == indexArray[currentIndex].second) {
393	gezelter	916
394	gezelter	907	atomTypeString = atoms[local_index]->getType();
395
396	tim	934	atoms[local_index]->getPos(pos);
397			atoms[local_index]->getVel(vel);
398	mmeineke	670
399	gezelter	916	atomData6[0] = pos[0];
400			atomData6[1] = pos[1];
401			atomData6[2] = pos[2];
402	tim	837
403	gezelter	916	atomData6[3] = vel[0];
404			atomData6[4] = vel[1];
405			atomData6[5] = vel[2];
406	gezelter	907
407			isDirectional = 0;
408
409	chuckv	436	if( atoms[local_index]->isDirectional() ){
410	tim	837
411	gezelter	907	isDirectional = 1;
412
413	chuckv	436	dAtom = (DirectionalAtom *)atoms[local_index];
414			dAtom->getQ( q );
415	gezelter	916
416			for (int j = 0; j < 6 ; j++)
417			atomData13[j] = atomData6[j];
418	gezelter	907
419	gezelter	916	atomData13[6] = q[0];
420			atomData13[7] = q[1];
421			atomData13[8] = q[2];
422			atomData13[9] = q[3];
423
424			atomData13[10] = dAtom->getJx();
425			atomData13[11] = dAtom->getJy();
426			atomData13[12] = dAtom->getJz();
427	gezelter	907	}
428	gezelter	916
429	gezelter	907	} else {
430	tim	934	sprintf(painCave.errMsg,
431			"Atom %d not found on processor %d\n",
432			i, worldRank );
433			haveError= 1;
434			simError();
435			}
436	gezelter	916
437	tim	934	if(haveError) DieDieDie();
438	gezelter	916
439	tim	929	currentIndex ++;
440	tim	926	}
441			// If we've survived to here, format the line:
442
443			if (!isDirectional) {
444
445	tim	934	sprintf( writeLine,
446			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
447			atomTypeString,
448			atomData6[0],
449			atomData6[1],
450			atomData6[2],
451			atomData6[3],
452			atomData6[4],
453			atomData6[5]);
454	tim	929
455	tim	934	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
456	tim	926
457			} else {
458
459	tim	934	sprintf( writeLine,
460			"%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",
461			atomTypeString,
462			atomData13[0],
463			atomData13[1],
464			atomData13[2],
465			atomData13[3],
466			atomData13[4],
467			atomData13[5],
468			atomData13[6],
469			atomData13[7],
470			atomData13[8],
471			atomData13[9],
472			atomData13[10],
473			atomData13[11],
474			atomData13[12]);
475	gezelter	907
476			}
477	tim	926
478	tim	934	for(k = 0; k < outFile.size(); k++)
479			*outFile[k] << writeLine;
480	mmeineke	377	}
481	tim	926
482	tim	934	for(k = 0; k < outFile.size(); k++)
483			outFile[k]->flush();
484
485	gezelter	907	sprintf( checkPointMsg,
486			"Sucessfully took a dump.\n");
487	tim	934
488	gezelter	907	MPIcheckPoint();
489	tim	934
490	tim	919	delete[] potatoes;
491	tim	934
492	gezelter	415	} else {
493	tim	837
494	gezelter	907	// worldRank != 0, so I'm a remote node.
495	gezelter	916
496			// Set my magic potato to 0:
497
498			myPotato = 0;
499	tim	929	currentIndex = 0;
500	gezelter	907
501			for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
502
503			// Am I the node which has this atom?
504
505			if (AtomToProcMap[i] == worldRank) {
506	tim	837
507	gezelter	916	if (myPotato + 3 >= MAXTAG) {
508
509			// The potato was going to exceed the maximum value,
510			// so wrap this processor potato back to 0 (and block until
511			// node 0 says we can go:
512
513			MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
514
515			}
516	tim	919	which_atom = i;
517	tim	929	local_index = indexArray[currentIndex].first;
518	tim	920
519	tim	929	if (which_atom == indexArray[currentIndex].second) {
520	gezelter	907
521			atomTypeString = atoms[local_index]->getType();
522	tim	837
523	tim	934	atoms[local_index]->getPos(pos);
524			atoms[local_index]->getVel(vel);
525	tim	837
526	gezelter	916	atomData6[0] = pos[0];
527			atomData6[1] = pos[1];
528			atomData6[2] = pos[2];
529	tim	837
530	gezelter	916	atomData6[3] = vel[0];
531			atomData6[4] = vel[1];
532			atomData6[5] = vel[2];
533	gezelter	907
534			isDirectional = 0;
535	tim	837
536	gezelter	907	if( atoms[local_index]->isDirectional() ){
537	mmeineke	377
538	gezelter	907	isDirectional = 1;
539
540			dAtom = (DirectionalAtom *)atoms[local_index];
541			dAtom->getQ( q );
542
543	gezelter	916	for (int j = 0; j < 6 ; j++)
544			atomData13[j] = atomData6[j];
545
546			atomData13[6] = q[0];
547			atomData13[7] = q[1];
548			atomData13[8] = q[2];
549			atomData13[9] = q[3];
550	tim	934
551	gezelter	916	atomData13[10] = dAtom->getJx();
552			atomData13[11] = dAtom->getJy();
553			atomData13[12] = dAtom->getJz();
554	gezelter	907	}
555	tim	837
556	gezelter	907	} else {
557	tim	934	sprintf(painCave.errMsg,
558			"Atom %d not found on processor %d\n",
559			i, worldRank );
560			haveError= 1;
561			simError();
562			}
563	tim	837
564	gezelter	916	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
565	tim	837
566	gezelter	916	// null terminate the string before sending (just in case):
567			MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
568	tim	837
569	gezelter	910	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
570	tim	934	myPotato, MPI_COMM_WORLD);
571	gezelter	907
572	gezelter	916	myPotato++;
573
574	gezelter	907	MPI_Send(&isDirectional, 1, MPI_INT, 0,
575	tim	934	myPotato, MPI_COMM_WORLD);
576	gezelter	907
577	gezelter	916	myPotato++;
578
579	gezelter	907	if (isDirectional) {
580
581	gezelter	916	MPI_Send(atomData13, 13, MPI_DOUBLE, 0,
582			myPotato, MPI_COMM_WORLD);
583	gezelter	907
584	gezelter	916	} else {
585
586			MPI_Send(atomData6, 6, MPI_DOUBLE, 0,
587			myPotato, MPI_COMM_WORLD);
588	gezelter	907	}
589	gezelter	916
590	tim	929	myPotato++;
591			currentIndex++;
592	mmeineke	377	}
593	gezelter	907	}
594	mmeineke	440
595	gezelter	907	sprintf( checkPointMsg,
596	gezelter	916	"Sucessfully took a dump.\n");
597	gezelter	907	MPIcheckPoint();
598
599	gezelter	916	}
600	gezelter	907
601	mmeineke	377	#endif // is_mpi
602			}
603	mmeineke	440
604			#ifdef IS_MPI
605
606			// a couple of functions to let us escape the write loop
607
608	gezelter	907	void dWrite::DieDieDie( void ){
609	tim	837
610	mmeineke	440	MPI_Finalize();
611			exit (0);
612			}
613
614			#endif //is_mpi