src/io/DumpWriter.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include "io/DumpWriter.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "io/basic_teebuf.hpp"
#ifdef IS_MPI
#include <mpi.h>
#endif //is_mpi

namespace oopse {

DumpWriter::DumpWriter(SimInfo* info) 
                   : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
#ifdef IS_MPI

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

        dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);

        if (!dumpFile_) {
            sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
                    filename_.c_str());
            painCave.isFatal = 1;
            simError();
        }

#ifdef IS_MPI

    }

    sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
    MPIcheckPoint();

#endif // is_mpi

}


DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) 
                   : info_(info), filename_(filename){
#ifdef IS_MPI

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

        eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
        dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);

        if (!dumpFile_) {
            sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
                    filename_.c_str());
            painCave.isFatal = 1;
            simError();
        }

#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

        dumpFile_.close();

#ifdef IS_MPI

    }

#endif // is_mpi

}

void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {

    double currentTime;
    Mat3x3d hmat;
    double chi;
    double integralOfChiDt;
    Mat3x3d eta;
    
    currentTime = s->getTime();
    hmat = s->getHmat();
    chi = s->getChi();
    integralOfChiDt = s->getIntegralOfChiDt();
    eta = s->getEta();
    
    os << currentTime << ";\t" 
         << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t" 
         << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
         << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";

    //write out additional parameters, such as chi and eta

    os << chi << "\t" << integralOfChiDt << "\t;";

    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t" 
         << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
         << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
        
    os << "\n";
}

void DumpWriter::writeFrame(std::ostream& os) {
    const int BUFFERSIZE = 2000;
    const int MINIBUFFERSIZE = 100;

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

    Quat4d q;
    Vector3d ji;
    Vector3d pos;
    Vector3d vel;

    Molecule* mol;
    StuntDouble* integrableObject;
    SimInfo::MoleculeIterator mi;
    Molecule::IntegrableObjectIterator ii;
  
    int nTotObjects;    
    nTotObjects = info_->getNGlobalIntegrableObjects();

#ifndef IS_MPI


    os << nTotObjects << "\n";
        
    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());

    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {

        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
            integrableObject = mol->nextIntegrableObject(ii)) { 
                

            pos = integrableObject->getPos();
            vel = integrableObject->getVel();

            sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                    integrableObject->getType().c_str(), 
                    pos[0], pos[1], pos[2],
                    vel[0], vel[1], vel[2]);

            strcpy(writeLine, tempBuffer);

            if (integrableObject->isDirectional()) {
                q = integrableObject->getQ();
                ji = integrableObject->getJ();

                sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", 
                        q[0], q[1], q[2], q[3],
                        ji[0], ji[1], ji[2]);
                strcat(writeLine, tempBuffer);
            } else {
                strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
            }

            os << writeLine;

        }
    }

    os.flush();
#else // 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?
     *
     *********************************************************************/
    const int masterNode = 0;

    int * potatoes;
    int myPotato;
    int nProc;
    int which_node;
    double atomData[13];
    int isDirectional;
    char MPIatomTypeString[MINIBUFFERSIZE];
    int msgLen; // the length of message actually recieved at master nodes
    int haveError;
    MPI_Status istatus;
    int nCurObj;
    
    // code to find maximum tag value
    int * tagub;
    int flag;
    int MAXTAG;
    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);

    if (flag) {
        MAXTAG = *tagub;
    } else {
        MAXTAG = 32767;
    }

    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file

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

        MPI_Comm_size(MPI_COMM_WORLD, &nProc);
        potatoes = new int[nProc];

        //write out the comment lines
        for(int i = 0; i < nProc; i++) {
            potatoes[i] = 0;
        }


        os << nTotObjects << "\n";
        writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());

        for(int i = 0; i < info_->getNGlobalMolecules(); i++) {

            // Get the Node number which has this atom;

            which_node = info_->getMolToProc(i);

            if (which_node != masterNode) { //current molecule is in slave node
                if (potatoes[which_node] + 1 >= MAXTAG) {
                    // The potato was going to exceed the maximum value, 
                    // so wrap this processor potato back to 0:         

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

                myPotato = potatoes[which_node];

                //recieve the number of integrableObject in current molecule
                MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
                         MPI_COMM_WORLD, &istatus);
                myPotato++;

                for(int l = 0; l < nCurObj; l++) {
                    if (potatoes[which_node] + 2 >= MAXTAG) {
                        // The potato was going to exceed the maximum value, 
                        // so wrap this processor potato back to 0:         

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

                    MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
                             which_node, myPotato, MPI_COMM_WORLD,
                             &istatus);

                    myPotato++;

                    MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
                             MPI_COMM_WORLD, &istatus);
                    myPotato++;

                    MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);

                    if (msgLen == 13)
                        isDirectional = 1;
                    else
                        isDirectional = 0;

                    // 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",
                                MPIatomTypeString, atomData[0],
                                atomData[1], atomData[2],
                                atomData[3], atomData[4],
                                atomData[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",
                                MPIatomTypeString,
                                atomData[0],
                                atomData[1],
                                atomData[2],
                                atomData[3],
                                atomData[4],
                                atomData[5],
                                atomData[6],
                                atomData[7],
                                atomData[8],
                                atomData[9],
                                atomData[10],
                                atomData[11],
                                atomData[12]);
                    }

                    os << writeLine;

                } // end for(int l =0)

                potatoes[which_node] = myPotato;
            } else { //master node has current molecule

                mol = info_->getMoleculeByGlobalIndex(i);

                if (mol == NULL) {
                    sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
                    painCave.isFatal = 1;
                    simError();
                }
                
                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
                    integrableObject = mol->nextIntegrableObject(ii)) {      

                    pos = integrableObject->getPos();
                    vel = integrableObject->getVel();

                    atomData[0] = pos[0];
                    atomData[1] = pos[1];
                    atomData[2] = pos[2];

                    atomData[3] = vel[0];
                    atomData[4] = vel[1];
                    atomData[5] = vel[2];

                    isDirectional = 0;

                    if (integrableObject->isDirectional()) {
                        isDirectional = 1;

                        q = integrableObject->getQ();
                        ji = integrableObject->getJ();

                        for(int j = 0; j < 6; j++) {
                            atomData[j] = atomData[j];
                        }

                        atomData[6] = q[0];
                        atomData[7] = q[1];
                        atomData[8] = q[2];
                        atomData[9] = q[3];

                        atomData[10] = ji[0];
                        atomData[11] = ji[1];
                        atomData[12] = ji[2];
                    }

                    // 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",
                                integrableObject->getType().c_str(), atomData[0],
                                atomData[1], atomData[2],
                                atomData[3], atomData[4],
                                atomData[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",
                                integrableObject->getType().c_str(),
                                atomData[0],
                                atomData[1],
                                atomData[2],
                                atomData[3],
                                atomData[4],
                                atomData[5],
                                atomData[6],
                                atomData[7],
                                atomData[8],
                                atomData[9],
                                atomData[10],
                                atomData[11],
                                atomData[12]);
                    }


                    os << writeLine;

                } //end for(iter = integrableObject.begin())
            }
        } //end for(i = 0; i < mpiSim->getNmol())

        os.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;

        for(int i = 0; i < info_->getNGlobalMolecules(); i++) {

            // Am I the node which has this integrableObject?
            int whichNode = info_->getMolToProc(i);
            if (whichNode == worldRank) {
                if (myPotato + 1 >= 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);
                }

                mol = info_->getMoleculeByGlobalIndex(i);

                
                nCurObj = mol->getNIntegrableObjects();

                MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
                myPotato++;

                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
                    integrableObject = mol->nextIntegrableObject(ii)) {

                    if (myPotato + 2 >= 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);
                    }

                    pos = integrableObject->getPos();
                    vel = integrableObject->getVel();

                    atomData[0] = pos[0];
                    atomData[1] = pos[1];
                    atomData[2] = pos[2];

                    atomData[3] = vel[0];
                    atomData[4] = vel[1];
                    atomData[5] = vel[2];

                    isDirectional = 0;

                    if (integrableObject->isDirectional()) {
                        isDirectional = 1;

                        q = integrableObject->getQ();
                        ji = integrableObject->getJ();

                        atomData[6] = q[0];
                        atomData[7] = q[1];
                        atomData[8] = q[2];
                        atomData[9] = q[3];

                        atomData[10] = ji[0];
                        atomData[11] = ji[1];
                        atomData[12] = ji[2];
                    }

                    strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);

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

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

                    myPotato++;

                    if (isDirectional) {
                        MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
                                 MPI_COMM_WORLD);
                    } else {
                        MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
                                 MPI_COMM_WORLD);
                    }

                    myPotato++;
                }
                    
            }
            
        }
        sprintf(checkPointMsg, "Sucessfully took a dump.\n");
        MPIcheckPoint();
    }

#endif // is_mpi

}

void DumpWriter::writeDump() {
    writeFrame(dumpFile_);

}

void DumpWriter::writeEor() {
    std::ofstream eorStream;
    
#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi

        eorStream.open(eorFilename_.c_str());
        if (!eorStream.is_open()) {
            sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
                    eorFilename_.c_str());
            painCave.isFatal = 1;
            simError();
        }

#ifdef IS_MPI
    }
#endif // is_mpi    

    writeFrame(eorStream);
}


void DumpWriter::writeDumpAndEor() {
    std::ofstream eorStream;
    std::vector<std::streambuf*> buffers;
#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi

        buffers.push_back(dumpFile_.rdbuf());

        eorStream.open(eorFilename_.c_str());
        if (!eorStream.is_open()) {
            sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
                    eorFilename_.c_str());
            painCave.isFatal = 1;
            simError();
        }

        buffers.push_back(eorStream.rdbuf());
        
#ifdef IS_MPI
    }
#endif // is_mpi    

    TeeBuf tbuf(buffers.begin(), buffers.end());
    std::ostream os(&tbuf);

    writeFrame(os);
    
}


}//end namespace oopse
Revision:	2079
Committed:	Thu Mar 3 14:40:20 2005 UTC (19 years, 4 months ago) by tim
File size:	20729 byte(s)
Log Message:	avoid using const char*(hope can fixed the missing atom type problem)
#	User	Rev	Content
1	gezelter	1930	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "io/DumpWriter.hpp"
43			#include "primitives/Molecule.hpp"
44			#include "utils/simError.h"
45	tim	2060	#include "io/basic_teebuf.hpp"
46	gezelter	1490	#ifdef IS_MPI
47			#include <mpi.h>
48	gezelter	1930	#endif //is_mpi
49	gezelter	1490
50	gezelter	1930	namespace oopse {
51	gezelter	1490
52	tim	2060	DumpWriter::DumpWriter(SimInfo* info)
53			: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
54			#ifdef IS_MPI
55
56			if (worldRank == 0) {
57			#endif // is_mpi
58
59			dumpFile_.open(filename_.c_str(), std::ios::out \| std::ios::trunc);
60
61			if (!dumpFile_) {
62			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
63			filename_.c_str());
64			painCave.isFatal = 1;
65			simError();
66			}
67
68			#ifdef IS_MPI
69
70			}
71
72			sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73			MPIcheckPoint();
74
75			#endif // is_mpi
76
77			}
78
79
80	gezelter	1930	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
81			: info_(info), filename_(filename){
82			#ifdef IS_MPI
83	gezelter	1490
84	gezelter	1930	if (worldRank == 0) {
85			#endif // is_mpi
86	gezelter	1490
87	tim	2060	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
88	gezelter	1930	dumpFile_.open(filename_.c_str(), std::ios::out \| std::ios::trunc);
89	gezelter	1490
90	gezelter	1930	if (!dumpFile_) {
91			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
92			filename_.c_str());
93			painCave.isFatal = 1;
94			simError();
95			}
96	gezelter	1490
97			#ifdef IS_MPI
98
99			}
100
101	gezelter	1930	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
102			MPIcheckPoint();
103	gezelter	1490
104			#endif // is_mpi
105	gezelter	1930
106	gezelter	1490	}
107
108	gezelter	1930	DumpWriter::~DumpWriter() {
109	gezelter	1490
110			#ifdef IS_MPI
111	gezelter	1930
112			if (worldRank == 0) {
113	gezelter	1490	#endif // is_mpi
114
115	gezelter	1930	dumpFile_.close();
116	gezelter	1490
117			#ifdef IS_MPI
118	gezelter	1930
119			}
120
121	gezelter	1490	#endif // is_mpi
122	gezelter	1930
123	gezelter	1490	}
124
125	gezelter	1930	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
126	gezelter	1490
127	gezelter	1930	double currentTime;
128			Mat3x3d hmat;
129			double chi;
130			double integralOfChiDt;
131			Mat3x3d eta;
132
133			currentTime = s->getTime();
134			hmat = s->getHmat();
135			chi = s->getChi();
136			integralOfChiDt = s->getIntegralOfChiDt();
137			eta = s->getEta();
138
139			os << currentTime << ";\t"
140			<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
141			<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
142			<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
143	gezelter	1490
144	gezelter	1930	//write out additional parameters, such as chi and eta
145
146			os << chi << "\t" << integralOfChiDt << "\t;";
147
148			os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
149			<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
150			<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
151
152	tim	2060	os << "\n";
153	gezelter	1490	}
154
155	gezelter	1930	void DumpWriter::writeFrame(std::ostream& os) {
156			const int BUFFERSIZE = 2000;
157			const int MINIBUFFERSIZE = 100;
158
159			char tempBuffer[BUFFERSIZE];
160			char writeLine[BUFFERSIZE];
161
162			Quat4d q;
163			Vector3d ji;
164			Vector3d pos;
165			Vector3d vel;
166
167			Molecule* mol;
168			StuntDouble* integrableObject;
169			SimInfo::MoleculeIterator mi;
170			Molecule::IntegrableObjectIterator ii;
171	gezelter	1490
172	gezelter	1930	int nTotObjects;
173			nTotObjects = info_->getNGlobalIntegrableObjects();
174	gezelter	1490
175	gezelter	1930	#ifndef IS_MPI
176	gezelter	1490
177
178	gezelter	1930	os << nTotObjects << "\n";
179
180			writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
181	gezelter	1490
182	gezelter	1930	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
183	gezelter	1490
184	gezelter	1930	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
185			integrableObject = mol->nextIntegrableObject(ii)) {
186
187	gezelter	1490
188	gezelter	1930	pos = integrableObject->getPos();
189			vel = integrableObject->getVel();
190	gezelter	1490
191	gezelter	1930	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
192			integrableObject->getType().c_str(),
193			pos[0], pos[1], pos[2],
194			vel[0], vel[1], vel[2]);
195	gezelter	1490
196	gezelter	1930	strcpy(writeLine, tempBuffer);
197	gezelter	1490
198	gezelter	1930	if (integrableObject->isDirectional()) {
199			q = integrableObject->getQ();
200			ji = integrableObject->getJ();
201	gezelter	1490
202	gezelter	1930	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
203			q[0], q[1], q[2], q[3],
204			ji[0], ji[1], ji[2]);
205			strcat(writeLine, tempBuffer);
206			} else {
207			strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
208			}
209	gezelter	1490
210	gezelter	1930	os << writeLine;
211	gezelter	1490
212	gezelter	1930	}
213	gezelter	1490	}
214
215	tim	2008	os.flush();
216	gezelter	1930	#else // is_mpi
217			/*********************************************************************
218			* Documentation? You want DOCUMENTATION?
219			*
220			* Why all the potatoes below?
221			*
222			* To make a long story short, the original version of DumpWriter
223			* worked in the most inefficient way possible. Node 0 would
224			* poke each of the node for an individual atom's formatted data
225			* as node 0 worked its way down the global index. This was particularly
226			* inefficient since the method blocked all processors at every atom
227			* (and did it twice!).
228			*
229			* An intermediate version of DumpWriter could be described from Node
230			* zero's perspective as follows:
231			*
232			* 1) Have 100 of your friends stand in a circle.
233			* 2) When you say go, have all of them start tossing potatoes at
234			* you (one at a time).
235			* 3) Catch the potatoes.
236			*
237			* It was an improvement, but MPI has buffers and caches that could
238			* best be described in this analogy as "potato nets", so there's no
239			* need to block the processors atom-by-atom.
240			*
241			* This new and improved DumpWriter works in an even more efficient
242			* way:
243			*
244			* 1) Have 100 of your friend stand in a circle.
245			* 2) When you say go, have them start tossing 5-pound bags of
246			* potatoes at you.
247			* 3) Once you've caught a friend's bag of potatoes,
248			* toss them a spud to let them know they can toss another bag.
249			*
250			* How's THAT for documentation?
251			*
252			*********************************************************************/
253			const int masterNode = 0;
254	gezelter	1490
255	gezelter	1930	int * potatoes;
256			int myPotato;
257			int nProc;
258			int which_node;
259			double atomData[13];
260			int isDirectional;
261			char MPIatomTypeString[MINIBUFFERSIZE];
262			int msgLen; // the length of message actually recieved at master nodes
263			int haveError;
264			MPI_Status istatus;
265			int nCurObj;
266
267			// code to find maximum tag value
268			int * tagub;
269			int flag;
270			int MAXTAG;
271			MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
272	gezelter	1490
273	gezelter	1930	if (flag) {
274			MAXTAG = *tagub;
275			} else {
276			MAXTAG = 32767;
277			}
278	gezelter	1490
279	gezelter	1930	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
280	gezelter	1490
281	gezelter	1930	// Node 0 needs a list of the magic potatoes for each processor;
282	gezelter	1490
283	gezelter	1930	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
284			potatoes = new int[nProc];
285	gezelter	1490
286	gezelter	1930	//write out the comment lines
287			for(int i = 0; i < nProc; i++) {
288			potatoes[i] = 0;
289			}
290	gezelter	1490
291
292	gezelter	1930	os << nTotObjects << "\n";
293			writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
294	gezelter	1490
295	gezelter	1930	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
296	gezelter	1490
297	gezelter	1930	// Get the Node number which has this atom;
298	gezelter	1490
299	gezelter	1930	which_node = info_->getMolToProc(i);
300	gezelter	1490
301	gezelter	1930	if (which_node != masterNode) { //current molecule is in slave node
302			if (potatoes[which_node] + 1 >= MAXTAG) {
303			// The potato was going to exceed the maximum value,
304			// so wrap this processor potato back to 0:
305	gezelter	1490
306	gezelter	1930	potatoes[which_node] = 0;
307			MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
308			MPI_COMM_WORLD);
309			}
310	gezelter	1490
311	gezelter	1930	myPotato = potatoes[which_node];
312	gezelter	1490
313	gezelter	1930	//recieve the number of integrableObject in current molecule
314			MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
315			MPI_COMM_WORLD, &istatus);
316			myPotato++;
317	gezelter	1490
318	gezelter	1930	for(int l = 0; l < nCurObj; l++) {
319			if (potatoes[which_node] + 2 >= MAXTAG) {
320			// The potato was going to exceed the maximum value,
321			// so wrap this processor potato back to 0:
322	gezelter	1490
323	gezelter	1930	potatoes[which_node] = 0;
324			MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
325			0, MPI_COMM_WORLD);
326			}
327	gezelter	1490
328	gezelter	1930	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
329			which_node, myPotato, MPI_COMM_WORLD,
330			&istatus);
331	gezelter	1490
332	gezelter	1930	myPotato++;
333	gezelter	1490
334	gezelter	1930	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
335			MPI_COMM_WORLD, &istatus);
336			myPotato++;
337	gezelter	1490
338	gezelter	1930	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
339	gezelter	1490
340	gezelter	1930	if (msgLen == 13)
341			isDirectional = 1;
342			else
343			isDirectional = 0;
344	gezelter	1490
345	gezelter	1930	// If we've survived to here, format the line:
346	gezelter	1490
347	gezelter	1930	if (!isDirectional) {
348			sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
349	tim	2079	MPIatomTypeString, atomData[0],
350	gezelter	1930	atomData[1], atomData[2],
351			atomData[3], atomData[4],
352			atomData[5]);
353	gezelter	1490
354	gezelter	1930	strcat(writeLine,
355			"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
356			} else {
357			sprintf(writeLine,
358			"%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",
359	tim	2079	MPIatomTypeString,
360	gezelter	1930	atomData[0],
361			atomData[1],
362			atomData[2],
363			atomData[3],
364			atomData[4],
365			atomData[5],
366			atomData[6],
367			atomData[7],
368			atomData[8],
369			atomData[9],
370			atomData[10],
371			atomData[11],
372			atomData[12]);
373			}
374	gezelter	1490
375	gezelter	1930	os << writeLine;
376	gezelter	1490
377	gezelter	1930	} // end for(int l =0)
378	gezelter	1490
379	gezelter	1930	potatoes[which_node] = myPotato;
380			} else { //master node has current molecule
381	gezelter	1490
382	gezelter	1930	mol = info_->getMoleculeByGlobalIndex(i);
383	gezelter	1490
384	gezelter	1930	if (mol == NULL) {
385			sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
386			painCave.isFatal = 1;
387			simError();
388			}
389
390			for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
391	tim	2079	integrableObject = mol->nextIntegrableObject(ii)) {
392	gezelter	1490
393	gezelter	1930	pos = integrableObject->getPos();
394			vel = integrableObject->getVel();
395	gezelter	1490
396	gezelter	1930	atomData[0] = pos[0];
397			atomData[1] = pos[1];
398			atomData[2] = pos[2];
399	gezelter	1490
400	gezelter	1930	atomData[3] = vel[0];
401			atomData[4] = vel[1];
402			atomData[5] = vel[2];
403	gezelter	1490
404	gezelter	1930	isDirectional = 0;
405	gezelter	1490
406	gezelter	1930	if (integrableObject->isDirectional()) {
407			isDirectional = 1;
408	gezelter	1490
409	gezelter	1930	q = integrableObject->getQ();
410			ji = integrableObject->getJ();
411	gezelter	1490
412	gezelter	1930	for(int j = 0; j < 6; j++) {
413			atomData[j] = atomData[j];
414			}
415	gezelter	1490
416	gezelter	1930	atomData[6] = q[0];
417			atomData[7] = q[1];
418			atomData[8] = q[2];
419			atomData[9] = q[3];
420	gezelter	1490
421	gezelter	1930	atomData[10] = ji[0];
422			atomData[11] = ji[1];
423			atomData[12] = ji[2];
424			}
425	gezelter	1490
426	gezelter	1930	// If we've survived to here, format the line:
427	gezelter	1490
428	gezelter	1930	if (!isDirectional) {
429			sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
430	tim	2079	integrableObject->getType().c_str(), atomData[0],
431	gezelter	1930	atomData[1], atomData[2],
432			atomData[3], atomData[4],
433			atomData[5]);
434	gezelter	1490
435	gezelter	1930	strcat(writeLine,
436			"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
437			} else {
438			sprintf(writeLine,
439			"%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",
440	tim	2079	integrableObject->getType().c_str(),
441	gezelter	1930	atomData[0],
442			atomData[1],
443			atomData[2],
444			atomData[3],
445			atomData[4],
446			atomData[5],
447			atomData[6],
448			atomData[7],
449			atomData[8],
450			atomData[9],
451			atomData[10],
452			atomData[11],
453			atomData[12]);
454			}
455	gezelter	1490
456
457	gezelter	1930	os << writeLine;
458	gezelter	1490
459	gezelter	1930	} //end for(iter = integrableObject.begin())
460			}
461			} //end for(i = 0; i < mpiSim->getNmol())
462	gezelter	1490
463	gezelter	1930	os.flush();
464	tim	1935
465	gezelter	1930	sprintf(checkPointMsg, "Sucessfully took a dump.\n");
466			MPIcheckPoint();
467	gezelter	1490
468	gezelter	1930	delete [] potatoes;
469			} else {
470	gezelter	1490
471	gezelter	1930	// worldRank != 0, so I'm a remote node.
472	gezelter	1490
473	gezelter	1930	// Set my magic potato to 0:
474	gezelter	1490
475	gezelter	1930	myPotato = 0;
476	gezelter	1490
477	gezelter	1930	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
478	gezelter	1490
479	gezelter	1930	// Am I the node which has this integrableObject?
480			int whichNode = info_->getMolToProc(i);
481			if (whichNode == worldRank) {
482			if (myPotato + 1 >= MAXTAG) {
483	gezelter	1490
484	gezelter	1930	// The potato was going to exceed the maximum value,
485			// so wrap this processor potato back to 0 (and block until
486			// node 0 says we can go:
487	gezelter	1490
488	gezelter	1930	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
489			&istatus);
490			}
491	gezelter	1490
492	gezelter	1930	mol = info_->getMoleculeByGlobalIndex(i);
493
494	gezelter	1490
495	gezelter	1930	nCurObj = mol->getNIntegrableObjects();
496	gezelter	1490
497	gezelter	1930	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
498			myPotato++;
499	gezelter	1490
500	gezelter	1930	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
501			integrableObject = mol->nextIntegrableObject(ii)) {
502	gezelter	1490
503	gezelter	1930	if (myPotato + 2 >= MAXTAG) {
504	gezelter	1490
505	gezelter	1930	// The potato was going to exceed the maximum value,
506			// so wrap this processor potato back to 0 (and block until
507			// node 0 says we can go:
508	gezelter	1490
509	gezelter	1930	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
510			&istatus);
511			}
512	gezelter	1490
513	gezelter	1930	pos = integrableObject->getPos();
514			vel = integrableObject->getVel();
515	gezelter	1490
516	gezelter	1930	atomData[0] = pos[0];
517			atomData[1] = pos[1];
518			atomData[2] = pos[2];
519	gezelter	1490
520	gezelter	1930	atomData[3] = vel[0];
521			atomData[4] = vel[1];
522			atomData[5] = vel[2];
523	gezelter	1490
524	gezelter	1930	isDirectional = 0;
525	gezelter	1490
526	gezelter	1930	if (integrableObject->isDirectional()) {
527			isDirectional = 1;
528	gezelter	1490
529	gezelter	1930	q = integrableObject->getQ();
530			ji = integrableObject->getJ();
531	gezelter	1490
532	gezelter	1930	atomData[6] = q[0];
533			atomData[7] = q[1];
534			atomData[8] = q[2];
535			atomData[9] = q[3];
536
537			atomData[10] = ji[0];
538			atomData[11] = ji[1];
539			atomData[12] = ji[2];
540			}
541
542	tim	2079	strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE);
543	gezelter	1930
544			// null terminate the std::string before sending (just in case):
545			MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
546
547			MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
548			myPotato, MPI_COMM_WORLD);
549
550			myPotato++;
551
552			if (isDirectional) {
553			MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
554			MPI_COMM_WORLD);
555			} else {
556			MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
557			MPI_COMM_WORLD);
558			}
559
560			myPotato++;
561			}
562
563			}
564
565			}
566			sprintf(checkPointMsg, "Sucessfully took a dump.\n");
567			MPIcheckPoint();
568			}
569
570			#endif // is_mpi
571
572	gezelter	1490	}
573
574	tim	2060	void DumpWriter::writeDump() {
575			writeFrame(dumpFile_);
576
577			}
578
579			void DumpWriter::writeEor() {
580			std::ofstream eorStream;
581
582			#ifdef IS_MPI
583			if (worldRank == 0) {
584			#endif // is_mpi
585
586			eorStream.open(eorFilename_.c_str());
587			if (!eorStream.is_open()) {
588			sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
589			eorFilename_.c_str());
590			painCave.isFatal = 1;
591			simError();
592			}
593
594			#ifdef IS_MPI
595			}
596			#endif // is_mpi
597
598			writeFrame(eorStream);
599			}
600
601
602			void DumpWriter::writeDumpAndEor() {
603			std::ofstream eorStream;
604			std::vector<std::streambuf*> buffers;
605			#ifdef IS_MPI
606			if (worldRank == 0) {
607			#endif // is_mpi
608
609			buffers.push_back(dumpFile_.rdbuf());
610
611			eorStream.open(eorFilename_.c_str());
612			if (!eorStream.is_open()) {
613			sprintf(painCave.errMsg, "DumpWriter : Could not open \"%s\" for writing.\n",
614			eorFilename_.c_str());
615			painCave.isFatal = 1;
616			simError();
617			}
618
619			buffers.push_back(eorStream.rdbuf());
620
621			#ifdef IS_MPI
622			}
623			#endif // is_mpi
624
625			TeeBuf tbuf(buffers.begin(), buffers.end());
626			std::ostream os(&tbuf);
627
628			writeFrame(os);
629
630			}
631
632
633
634	gezelter	1930	}//end namespace oopse