src/io/DumpReader.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.
 */
 
#define _LARGEFILE_SOURCE64
#define _FILE_OFFSET_BITS 64

#include <sys/types.h>
#include <sys/stat.h>

#include <iostream>
#include <math.h>

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "utils/MemoryUtils.hpp"
#include "utils/StringTokenizer.hpp"

#ifdef IS_MPI

#include <mpi.h>
#define TAKE_THIS_TAG_CHAR 0
#define TAKE_THIS_TAG_INT 1

#endif // is_mpi


namespace oopse {

DumpReader::DumpReader(SimInfo* info, const std::string& filename)
                     : info_(info), filename_(filename), isScanned_(false), nframes_(0) {

#ifdef IS_MPI

    if (worldRank == 0) {
#endif

        inFile_ = fopen(filename_.c_str(), "r");

        if (inFile_ == NULL) {
            sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
            painCave.isFatal = 1;
            simError();
        }

#ifdef IS_MPI

    }

    strcpy(checkPointMsg, "Dump file opened for reading successfully.");
    MPIcheckPoint();

#endif

    return;
}

DumpReader::~DumpReader() {

#ifdef IS_MPI

    if (worldRank == 0) {
#endif

        int error;
        error = fclose(inFile_);

        if (error) {
            sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
            painCave.isFatal = 1;            
            simError();
        }

        MemoryUtils::deleteVectorOfPointer(framePos_);

#ifdef IS_MPI

    }

    strcpy(checkPointMsg, "Dump file closed successfully.");
    MPIcheckPoint();

#endif

    return;
}

int DumpReader::getNFrames(void) {

    if (!isScanned_)
        scanFile();

    return nframes_;
}

void DumpReader::scanFile(void) {
  int i, j;
  int lineNum = 0;
  char readBuffer[maxBufferSize];
  fpos_t * currPos;

#ifdef IS_MPI

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

        rewind(inFile_);

        currPos = new fpos_t;
        fgetpos(inFile_, currPos);
        fgets(readBuffer, sizeof(readBuffer), inFile_);
        lineNum++;

        if (feof(inFile_)) {
            sprintf(painCave.errMsg,
                    "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
                    filename_.c_str(),
                    lineNum);
            painCave.isFatal = 1;
            simError();
        }

        while (!feof(inFile_)) {
            framePos_.push_back(currPos);

            i = atoi(readBuffer);

            fgets(readBuffer, sizeof(readBuffer), inFile_);
            lineNum++;

            if (feof(inFile_)) {
                sprintf(painCave.errMsg,
                        "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
                        filename_.c_str(),
                        lineNum);
                painCave.isFatal = 1;
                simError();
            }

            for(j = 0; j < i; j++) {
                fgets(readBuffer, sizeof(readBuffer), inFile_);
                lineNum++;

                if (feof(inFile_)) {
                    sprintf(painCave.errMsg,
                            "DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
                                " with atom %d\n", filename_.c_str(),
                            lineNum,
                            j);

                    painCave.isFatal = 1;
                    simError();
                }
            }

            currPos = new fpos_t;
            fgetpos(inFile_, currPos);
            fgets(readBuffer, sizeof(readBuffer), inFile_);
            lineNum++;
        }

        delete currPos;
        rewind(inFile_);
        
        nframes_ = framePos_.size();
#ifdef IS_MPI
    }

    MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);

    strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
    MPIcheckPoint();

#endif // is_mpi

    isScanned_ = true;
}

void DumpReader::readFrame(int whichFrame) {
    readSet(whichFrame);
}

void DumpReader::readSet(int whichFrame) {
  int i;
  int nTotObjs;                  // the number of atoms
  char read_buffer[maxBufferSize];  //the line buffer for reading
  char * eof_test;               // ptr to see when we reach the end of the file

  Molecule* mol;
  StuntDouble* integrableObject;
  SimInfo::MoleculeIterator mi;
  Molecule::IntegrableObjectIterator ii;

#ifndef IS_MPI

    fsetpos(inFile_, framePos_[whichFrame]);
    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);

    if (eof_test == NULL) {
        sprintf(painCave.errMsg,
                "DumpReader error: error reading 1st line of \"%s\"\n",
                filename_.c_str());
        painCave.isFatal = 1;
        simError();
    }

    nTotObjs = atoi(read_buffer);

    if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
        sprintf(painCave.errMsg,
                "DumpReader error. %s nIntegrable, %d, "
                    "does not match the meta-data file's nIntegrable, %d.\n",
                filename_.c_str(),
                nTotObjs,
                info_->getNGlobalIntegrableObjects());

        painCave.isFatal = 1;
        simError();
    }

    //read the box mat from the comment line

    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);

    if (eof_test == NULL) {
        sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
                filename_.c_str());
        painCave.isFatal = 1;
        simError();
    }

    parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());

    //parse dump lines

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

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

            eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);

            if (eof_test == NULL) {
                sprintf(painCave.errMsg,
                        "DumpReader Error: error in reading file %s\n"
                            "natoms  = %d; index = %d\n"
                            "error reading the line from the file.\n",
                        filename_.c_str(),
                        nTotObjs,
                        i);

                painCave.isFatal = 1;
                simError();
            }

            parseDumpLine(read_buffer, integrableObject);
            
            }
    }

    // MPI Section of code..........

#else //IS_MPI

    // first thing first, suspend fatalities.
    int masterNode = 0;
    int nCurObj;
    painCave.isEventLoop = 1;

    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
    int haveError;

    MPI_Status istatus;
    int nitems;

    nTotObjs = info_->getNGlobalIntegrableObjects();
    haveError = 0;

    if (worldRank == masterNode) {
        fsetpos(inFile_, framePos_[whichFrame]);

        eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);

        if (eof_test == NULL) {
            sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
                    filename_.c_str());
            painCave.isFatal = 1;
            simError();
        }

        nitems = atoi(read_buffer);

        // Check to see that the number of integrable objects in the
        // intial configuration file is the same as derived from the
        // meta-data file.

        if (nTotObjs != nitems) {
            sprintf(painCave.errMsg,
                    "DumpReader Error. %s nIntegrable, %d, "
                        "does not match the meta-data file's nIntegrable, %d.\n",
                    filename_.c_str(),
                    nTotObjs,
                    info_->getNGlobalIntegrableObjects());

            painCave.isFatal = 1;
            simError();
        }

        //read the boxMat from the comment line

        eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);

        if (eof_test == NULL) {
            sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
                    filename_.c_str());
            painCave.isFatal = 1;
            simError();
        }

        //Every single processor will parse the comment line by itself
        //By using this way, we might lose some efficiency, but if we want to add
        //more parameters into comment line, we only need to modify function
        //parseCommentLine

        MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
        parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());

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

            if (which_node == masterNode) {
                //molecules belong to master node

                mol = info_->getMoleculeByGlobalIndex(i);

                if (mol == NULL) {
                    sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
                        painCave.isFatal = 1;
                    simError();
                }

                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
                       integrableObject = mol->nextIntegrableObject(ii)){
                        
                    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);

                    if (eof_test == NULL) {
                        sprintf(painCave.errMsg,
                                "DumpReader Error: error in reading file %s\n"
                                    "natoms  = %d; index = %d\n"
                                    "error reading the line from the file.\n",
                                filename_.c_str(),
                                nTotObjs,
                                i);

                        painCave.isFatal = 1;
                        simError();
                    }

                    parseDumpLine(read_buffer, integrableObject);
                }
            } else {
                //molecule belongs to slave nodes

                MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
                         MPI_COMM_WORLD, &istatus);

                for(int j = 0; j < nCurObj; j++) {
                    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);

                    if (eof_test == NULL) {
                        sprintf(painCave.errMsg,
                                "DumpReader Error: error in reading file %s\n"
                                    "natoms  = %d; index = %d\n"
                                    "error reading the line from the file.\n",
                                filename_.c_str(),
                                nTotObjs,
                                i);

                        painCave.isFatal = 1;
                        simError();
                    }
                    
                    MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
                             TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
                }
            }
        }
    } else {
        //actions taken at slave nodes
        MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);

        /**@todo*/
        parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());

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

            if (which_node == worldRank) {
                //molecule with global index i belongs to this processor
                
                mol = info_->getMoleculeByGlobalIndex(i);
                if (mol == NULL) {
                    sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
                    painCave.isFatal = 1;
                    simError();
                }
                
                nCurObj = mol->getNIntegrableObjects();

                MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
                         MPI_COMM_WORLD);

                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
                       integrableObject = mol->nextIntegrableObject(ii)){
                        
                    MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
                             TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);

                    parseDumpLine(read_buffer, integrableObject);
                }
                       
            }
            
        }
        
    }

#endif

}

void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {

    Vector3d pos;  // position place holders
    Vector3d vel;  // velocity placeholders
    Quat4d q;    // the quaternions
    Vector3d ji;   // angular velocity placeholders;
    StringTokenizer tokenizer(line);
    int nTokens;
    
    nTokens = tokenizer.countTokens();

    if (nTokens < 14) {
            sprintf(painCave.errMsg,
                    "DumpReader Error: Not enough Tokens.\n");
            painCave.isFatal = 1;
            simError();
    }

    std::string name = tokenizer.nextToken();

    if (name != integrableObject->getType()) {

            sprintf(painCave.errMsg,
                    "DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
                    name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
            painCave.isFatal = 1;
            simError();        
    }

    pos[0] = tokenizer.nextTokenAsDouble();
    pos[1] = tokenizer.nextTokenAsDouble();
    pos[2] = tokenizer.nextTokenAsDouble();
    integrableObject->setPos(pos);
    
    vel[0] = tokenizer.nextTokenAsDouble();
    vel[1] = tokenizer.nextTokenAsDouble();
    vel[2] = tokenizer.nextTokenAsDouble();
    integrableObject->setVel(vel);

    if (integrableObject->isDirectional()) {
        
        q[0] = tokenizer.nextTokenAsDouble();
        q[1] = tokenizer.nextTokenAsDouble();
        q[2] = tokenizer.nextTokenAsDouble();
        q[3] = tokenizer.nextTokenAsDouble();

        double qlen = q.length();
        if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
            
            sprintf(painCave.errMsg,
                    "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
            painCave.isFatal = 1;
            simError();
            
        } 

        q.normalize();
               
        integrableObject->setQ(q);
        
        ji[0] = tokenizer.nextTokenAsDouble();
        ji[1] = tokenizer.nextTokenAsDouble();
        ji[2] = tokenizer.nextTokenAsDouble();
        integrableObject->setJ(ji);
    }

}


void DumpReader::parseCommentLine(char* line, Snapshot* s) {
    double currTime;
    Mat3x3d hmat;
    double chi;
    double integralOfChiDt;
    Mat3x3d eta;

    StringTokenizer tokenizer(line);
    int nTokens;

    nTokens = tokenizer.countTokens();

    //comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
    if (nTokens < 10) {
            sprintf(painCave.errMsg,
                    "DumpReader Error: Not enough tokens in comment line: %s", line);
            painCave.isFatal = 1;
            simError();   
    }

    //read current time
    currTime = tokenizer.nextTokenAsDouble();
    s->setTime(currTime);
    
    //read h-matrix
    hmat(0, 0) = tokenizer.nextTokenAsDouble();
    hmat(0, 1) = tokenizer.nextTokenAsDouble();
    hmat(0, 2) = tokenizer.nextTokenAsDouble();
    hmat(1, 0) = tokenizer.nextTokenAsDouble();
    hmat(1, 1) = tokenizer.nextTokenAsDouble();
    hmat(1, 2) = tokenizer.nextTokenAsDouble();
    hmat(2, 0) = tokenizer.nextTokenAsDouble();
    hmat(2, 1) = tokenizer.nextTokenAsDouble();
    hmat(2, 2) = tokenizer.nextTokenAsDouble();
    s->setHmat(hmat);
    
    //read chi and integrablOfChidt, they should apprear in pair
    if (tokenizer.countTokens() >= 2) {
        chi = tokenizer.nextTokenAsDouble();
        integralOfChiDt = tokenizer.nextTokenAsDouble();            

        s->setChi(chi);
        s->setIntegralOfChiDt(integralOfChiDt);
    }
    
    //read eta (eta is 3x3 matrix)
    if (tokenizer.countTokens() >= 9) {
        eta(0, 0) = tokenizer.nextTokenAsDouble();
        eta(0, 1) = tokenizer.nextTokenAsDouble();
        eta(0, 2) = tokenizer.nextTokenAsDouble();
        eta(1, 0) = tokenizer.nextTokenAsDouble();
        eta(1, 1) = tokenizer.nextTokenAsDouble();
        eta(1, 2) = tokenizer.nextTokenAsDouble();
        eta(2, 0) = tokenizer.nextTokenAsDouble();
        eta(2, 1) = tokenizer.nextTokenAsDouble();
        eta(2, 2) = tokenizer.nextTokenAsDouble();      

        s->setEta(eta);
    }

    
}

}//end namespace oopse
Revision:	274
Committed:	Tue Jan 25 21:59:18 2005 UTC (20 years, 3 months ago) by tim
File size:	18893 byte(s)
Log Message:	fix a bug in SimInfo, use number of cutoff stamp as counter to loop over rigidbody stamp
#	User	Rev	Content
1	gezelter	246	/*
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	gezelter	2	#define _LARGEFILE_SOURCE64
43			#define _FILE_OFFSET_BITS 64
44
45			#include <sys/types.h>
46			#include <sys/stat.h>
47
48			#include <iostream>
49			#include <math.h>
50
51			#include <stdio.h>
52			#include <stdlib.h>
53			#include <string.h>
54
55	gezelter	246	#include "io/DumpReader.hpp"
56			#include "primitives/Molecule.hpp"
57	tim	3	#include "utils/simError.h"
58	gezelter	246	#include "utils/MemoryUtils.hpp"
59			#include "utils/StringTokenizer.hpp"
60	gezelter	2
61			#ifdef IS_MPI
62	gezelter	246
63	gezelter	2	#include <mpi.h>
64			#define TAKE_THIS_TAG_CHAR 0
65			#define TAKE_THIS_TAG_INT 1
66	gezelter	246
67	gezelter	2	#endif // is_mpi
68
69
70	gezelter	246	namespace oopse {
71	gezelter	2
72	gezelter	246	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73			: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
74	gezelter	2
75			#ifdef IS_MPI
76
77	gezelter	246	if (worldRank == 0) {
78	gezelter	2	#endif
79
80	gezelter	246	inFile_ = fopen(filename_.c_str(), "r");
81
82			if (inFile_ == NULL) {
83	tim	273	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
84	gezelter	246	painCave.isFatal = 1;
85			simError();
86			}
87
88	gezelter	2	#ifdef IS_MPI
89
90	gezelter	246	}
91	gezelter	2
92	gezelter	246	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
93			MPIcheckPoint();
94
95	gezelter	2	#endif
96
97	gezelter	246	return;
98	gezelter	2	}
99
100	gezelter	246	DumpReader::~DumpReader() {
101	gezelter	2
102	gezelter	246	#ifdef IS_MPI
103	gezelter	2
104	gezelter	246	if (worldRank == 0) {
105			#endif
106	gezelter	2
107	gezelter	246	int error;
108			error = fclose(inFile_);
109	gezelter	2
110	gezelter	246	if (error) {
111	tim	274	sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
112	gezelter	246	painCave.isFatal = 1;
113			simError();
114			}
115
116			MemoryUtils::deleteVectorOfPointer(framePos_);
117
118	gezelter	2	#ifdef IS_MPI
119	gezelter	246
120	gezelter	2	}
121
122	gezelter	246	strcpy(checkPointMsg, "Dump file closed successfully.");
123			MPIcheckPoint();
124	gezelter	2
125	gezelter	246	#endif
126	gezelter	2
127	gezelter	246	return;
128	gezelter	2	}
129
130	gezelter	246	int DumpReader::getNFrames(void) {
131	gezelter	2
132	gezelter	246	if (!isScanned_)
133			scanFile();
134	gezelter	2
135	gezelter	246	return nframes_;
136	gezelter	2	}
137
138	gezelter	246	void DumpReader::scanFile(void) {
139			int i, j;
140			int lineNum = 0;
141			char readBuffer[maxBufferSize];
142			fpos_t * currPos;
143	gezelter	2
144			#ifdef IS_MPI
145
146	gezelter	246	if (worldRank == 0) {
147			#endif // is_mpi
148	gezelter	2
149	gezelter	246	rewind(inFile_);
150	gezelter	2
151	gezelter	246	currPos = new fpos_t;
152			fgetpos(inFile_, currPos);
153			fgets(readBuffer, sizeof(readBuffer), inFile_);
154			lineNum++;
155	gezelter	2
156	gezelter	246	if (feof(inFile_)) {
157			sprintf(painCave.errMsg,
158	tim	274	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
159	gezelter	246	filename_.c_str(),
160			lineNum);
161			painCave.isFatal = 1;
162			simError();
163			}
164	gezelter	2
165	gezelter	246	while (!feof(inFile_)) {
166			framePos_.push_back(currPos);
167	gezelter	2
168	gezelter	246	i = atoi(readBuffer);
169	gezelter	2
170	gezelter	246	fgets(readBuffer, sizeof(readBuffer), inFile_);
171			lineNum++;
172	gezelter	2
173	gezelter	246	if (feof(inFile_)) {
174			sprintf(painCave.errMsg,
175	tim	274	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
176	gezelter	246	filename_.c_str(),
177			lineNum);
178			painCave.isFatal = 1;
179			simError();
180			}
181	gezelter	2
182	gezelter	246	for(j = 0; j < i; j++) {
183			fgets(readBuffer, sizeof(readBuffer), inFile_);
184			lineNum++;
185	gezelter	2
186	gezelter	246	if (feof(inFile_)) {
187			sprintf(painCave.errMsg,
188	tim	274	"DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
189	gezelter	246	" with atom %d\n", filename_.c_str(),
190			lineNum,
191			j);
192	gezelter	2
193	gezelter	246	painCave.isFatal = 1;
194			simError();
195			}
196			}
197	gezelter	2
198	gezelter	246	currPos = new fpos_t;
199			fgetpos(inFile_, currPos);
200			fgets(readBuffer, sizeof(readBuffer), inFile_);
201			lineNum++;
202			}
203	gezelter	2
204	gezelter	246	delete currPos;
205			rewind(inFile_);
206
207			nframes_ = framePos_.size();
208			#ifdef IS_MPI
209	gezelter	2	}
210
211	gezelter	246	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
212	gezelter	2
213	gezelter	246	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
214			MPIcheckPoint();
215	gezelter	2
216	gezelter	246	#endif // is_mpi
217	gezelter	2
218	gezelter	246	isScanned_ = true;
219			}
220	gezelter	2
221	gezelter	246	void DumpReader::readFrame(int whichFrame) {
222			readSet(whichFrame);
223			}
224	gezelter	2
225	gezelter	246	void DumpReader::readSet(int whichFrame) {
226			int i;
227			int nTotObjs; // the number of atoms
228			char read_buffer[maxBufferSize]; //the line buffer for reading
229			char * eof_test; // ptr to see when we reach the end of the file
230	gezelter	2
231	gezelter	246	Molecule* mol;
232			StuntDouble* integrableObject;
233			SimInfo::MoleculeIterator mi;
234			Molecule::IntegrableObjectIterator ii;
235	gezelter	2
236	gezelter	246	#ifndef IS_MPI
237	gezelter	2
238	gezelter	246	fsetpos(inFile_, framePos_[whichFrame]);
239			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
240	gezelter	2
241	gezelter	246	if (eof_test == NULL) {
242			sprintf(painCave.errMsg,
243			"DumpReader error: error reading 1st line of \"%s\"\n",
244			filename_.c_str());
245			painCave.isFatal = 1;
246			simError();
247	gezelter	2	}
248
249	gezelter	246	nTotObjs = atoi(read_buffer);
250	gezelter	2
251	gezelter	246	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
252			sprintf(painCave.errMsg,
253			"DumpReader error. %s nIntegrable, %d, "
254			"does not match the meta-data file's nIntegrable, %d.\n",
255			filename_.c_str(),
256			nTotObjs,
257	tim	273	info_->getNGlobalIntegrableObjects());
258	gezelter	2
259	gezelter	246	painCave.isFatal = 1;
260			simError();
261	gezelter	2	}
262
263	gezelter	246	//read the box mat from the comment line
264	gezelter	2
265	gezelter	246	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
266	gezelter	2
267	gezelter	246	if (eof_test == NULL) {
268	tim	274	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
269	gezelter	246	filename_.c_str());
270			painCave.isFatal = 1;
271	gezelter	2	simError();
272	gezelter	246	}
273	gezelter	2
274	gezelter	246	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
275	gezelter	2
276	gezelter	246	//parse dump lines
277	gezelter	2
278	gezelter	246	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
279	gezelter	2
280	gezelter	246	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
281			integrableObject = mol->nextIntegrableObject(ii)) {
282	gezelter	2
283	gezelter	246	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
284	gezelter	2
285	gezelter	246	if (eof_test == NULL) {
286			sprintf(painCave.errMsg,
287	tim	274	"DumpReader Error: error in reading file %s\n"
288	gezelter	246	"natoms = %d; index = %d\n"
289			"error reading the line from the file.\n",
290			filename_.c_str(),
291			nTotObjs,
292			i);
293	gezelter	2
294	gezelter	246	painCave.isFatal = 1;
295			simError();
296			}
297
298			parseDumpLine(read_buffer, integrableObject);
299
300			}
301	gezelter	2	}
302
303	gezelter	246	// MPI Section of code..........
304	gezelter	2
305	gezelter	246	#else //IS_MPI
306	gezelter	2
307	gezelter	246	// first thing first, suspend fatalities.
308			int masterNode = 0;
309			int nCurObj;
310			painCave.isEventLoop = 1;
311	gezelter	2
312	gezelter	246	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
313			int haveError;
314	gezelter	2
315	gezelter	246	MPI_Status istatus;
316			int nitems;
317	gezelter	2
318	gezelter	246	nTotObjs = info_->getNGlobalIntegrableObjects();
319			haveError = 0;
320	gezelter	2
321	gezelter	246	if (worldRank == masterNode) {
322			fsetpos(inFile_, framePos_[whichFrame]);
323	gezelter	2
324	gezelter	246	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
325	gezelter	2
326	gezelter	246	if (eof_test == NULL) {
327	tim	274	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
328	gezelter	246	filename_.c_str());
329			painCave.isFatal = 1;
330			simError();
331	gezelter	2	}
332
333	gezelter	246	nitems = atoi(read_buffer);
334	gezelter	2
335	gezelter	246	// Check to see that the number of integrable objects in the
336			// intial configuration file is the same as derived from the
337			// meta-data file.
338	gezelter	2
339	gezelter	246	if (nTotObjs != nitems) {
340			sprintf(painCave.errMsg,
341			"DumpReader Error. %s nIntegrable, %d, "
342			"does not match the meta-data file's nIntegrable, %d.\n",
343			filename_.c_str(),
344			nTotObjs,
345			info_->getNGlobalIntegrableObjects());
346	gezelter	2
347	gezelter	246	painCave.isFatal = 1;
348			simError();
349			}
350	gezelter	2
351	gezelter	246	//read the boxMat from the comment line
352	gezelter	2
353	gezelter	246	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
354	gezelter	2
355	gezelter	246	if (eof_test == NULL) {
356	tim	274	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
357	gezelter	246	filename_.c_str());
358			painCave.isFatal = 1;
359			simError();
360			}
361	gezelter	2
362	gezelter	246	//Every single processor will parse the comment line by itself
363			//By using this way, we might lose some efficiency, but if we want to add
364			//more parameters into comment line, we only need to modify function
365			//parseCommentLine
366	gezelter	2
367	gezelter	246	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
368			parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
369	gezelter	2
370	gezelter	246	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
371			int which_node = info_->getMolToProc(i);
372	gezelter	2
373	gezelter	246	if (which_node == masterNode) {
374			//molecules belong to master node
375	gezelter	2
376	gezelter	246	mol = info_->getMoleculeByGlobalIndex(i);
377	gezelter	2
378	gezelter	246	if (mol == NULL) {
379	tim	274	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
380	gezelter	246	painCave.isFatal = 1;
381			simError();
382			}
383	gezelter	2
384	gezelter	246	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
385			integrableObject = mol->nextIntegrableObject(ii)){
386
387			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
388	gezelter	2
389	gezelter	246	if (eof_test == NULL) {
390			sprintf(painCave.errMsg,
391	tim	274	"DumpReader Error: error in reading file %s\n"
392	gezelter	246	"natoms = %d; index = %d\n"
393			"error reading the line from the file.\n",
394			filename_.c_str(),
395			nTotObjs,
396			i);
397	gezelter	2
398	gezelter	246	painCave.isFatal = 1;
399			simError();
400			}
401	gezelter	2
402	gezelter	246	parseDumpLine(read_buffer, integrableObject);
403			}
404			} else {
405			//molecule belongs to slave nodes
406	gezelter	2
407	gezelter	246	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
408			MPI_COMM_WORLD, &istatus);
409	gezelter	2
410	gezelter	246	for(int j = 0; j < nCurObj; j++) {
411			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
412	gezelter	2
413	gezelter	246	if (eof_test == NULL) {
414			sprintf(painCave.errMsg,
415	tim	274	"DumpReader Error: error in reading file %s\n"
416	gezelter	246	"natoms = %d; index = %d\n"
417			"error reading the line from the file.\n",
418			filename_.c_str(),
419			nTotObjs,
420			i);
421	gezelter	2
422	gezelter	246	painCave.isFatal = 1;
423			simError();
424			}
425
426			MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
427			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
428			}
429			}
430			}
431			} else {
432			//actions taken at slave nodes
433			MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
434	gezelter	2
435	gezelter	246	/*@todo/
436			parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
437	gezelter	2
438	gezelter	246	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
439			int which_node = info_->getMolToProc(i);
440	gezelter	2
441	gezelter	246	if (which_node == worldRank) {
442			//molecule with global index i belongs to this processor
443
444			mol = info_->getMoleculeByGlobalIndex(i);
445			if (mol == NULL) {
446	tim	274	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
447	gezelter	246	painCave.isFatal = 1;
448			simError();
449			}
450
451			nCurObj = mol->getNIntegrableObjects();
452	gezelter	2
453	gezelter	246	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
454			MPI_COMM_WORLD);
455	gezelter	2
456	gezelter	246	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
457			integrableObject = mol->nextIntegrableObject(ii)){
458
459			MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
460			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
461	gezelter	2
462	gezelter	246	parseDumpLine(read_buffer, integrableObject);
463			}
464
465			}
466
467			}
468
469	gezelter	2	}
470
471	gezelter	246	#endif
472	gezelter	2
473	gezelter	246	}
474	gezelter	2
475	gezelter	246	void DumpReader::parseDumpLine(char line, StuntDouble integrableObject) {
476	gezelter	2
477	gezelter	246	Vector3d pos; // position place holders
478			Vector3d vel; // velocity placeholders
479			Quat4d q; // the quaternions
480			Vector3d ji; // angular velocity placeholders;
481			StringTokenizer tokenizer(line);
482			int nTokens;
483
484			nTokens = tokenizer.countTokens();
485	gezelter	2
486	gezelter	246	if (nTokens < 14) {
487			sprintf(painCave.errMsg,
488	tim	274	"DumpReader Error: Not enough Tokens.\n");
489	gezelter	246	painCave.isFatal = 1;
490			simError();
491	gezelter	2	}
492
493	gezelter	246	std::string name = tokenizer.nextToken();
494
495			if (name != integrableObject->getType()) {
496	tim	274
497			sprintf(painCave.errMsg,
498			"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
499			name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
500			painCave.isFatal = 1;
501			simError();
502	gezelter	2	}
503
504	gezelter	246	pos[0] = tokenizer.nextTokenAsDouble();
505			pos[1] = tokenizer.nextTokenAsDouble();
506			pos[2] = tokenizer.nextTokenAsDouble();
507			integrableObject->setPos(pos);
508
509			vel[0] = tokenizer.nextTokenAsDouble();
510			vel[1] = tokenizer.nextTokenAsDouble();
511			vel[2] = tokenizer.nextTokenAsDouble();
512			integrableObject->setVel(vel);
513	gezelter	2
514	gezelter	246	if (integrableObject->isDirectional()) {
515
516			q[0] = tokenizer.nextTokenAsDouble();
517			q[1] = tokenizer.nextTokenAsDouble();
518			q[2] = tokenizer.nextTokenAsDouble();
519			q[3] = tokenizer.nextTokenAsDouble();
520	gezelter	2
521	gezelter	246	double qlen = q.length();
522			if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
523
524			sprintf(painCave.errMsg,
525	tim	274	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
526	gezelter	246	painCave.isFatal = 1;
527			simError();
528
529			}
530	gezelter	2
531	gezelter	246	q.normalize();
532
533			integrableObject->setQ(q);
534
535			ji[0] = tokenizer.nextTokenAsDouble();
536			ji[1] = tokenizer.nextTokenAsDouble();
537			ji[2] = tokenizer.nextTokenAsDouble();
538			integrableObject->setJ(ji);
539	gezelter	2	}
540
541			}
542
543
544	gezelter	246	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
545			double currTime;
546			Mat3x3d hmat;
547			double chi;
548			double integralOfChiDt;
549			Mat3x3d eta;
550	gezelter	2
551	gezelter	246	StringTokenizer tokenizer(line);
552			int nTokens;
553	gezelter	2
554	gezelter	246	nTokens = tokenizer.countTokens();
555	gezelter	2
556	gezelter	246	//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens)
557			if (nTokens < 10) {
558			sprintf(painCave.errMsg,
559	tim	274	"DumpReader Error: Not enough tokens in comment line: %s", line);
560	gezelter	246	painCave.isFatal = 1;
561			simError();
562	gezelter	2	}
563
564	gezelter	246	//read current time
565			currTime = tokenizer.nextTokenAsDouble();
566			s->setTime(currTime);
567
568			//read h-matrix
569			hmat(0, 0) = tokenizer.nextTokenAsDouble();
570			hmat(0, 1) = tokenizer.nextTokenAsDouble();
571			hmat(0, 2) = tokenizer.nextTokenAsDouble();
572			hmat(1, 0) = tokenizer.nextTokenAsDouble();
573			hmat(1, 1) = tokenizer.nextTokenAsDouble();
574			hmat(1, 2) = tokenizer.nextTokenAsDouble();
575			hmat(2, 0) = tokenizer.nextTokenAsDouble();
576			hmat(2, 1) = tokenizer.nextTokenAsDouble();
577			hmat(2, 2) = tokenizer.nextTokenAsDouble();
578			s->setHmat(hmat);
579
580			//read chi and integrablOfChidt, they should apprear in pair
581			if (tokenizer.countTokens() >= 2) {
582			chi = tokenizer.nextTokenAsDouble();
583			integralOfChiDt = tokenizer.nextTokenAsDouble();
584	gezelter	2
585	gezelter	246	s->setChi(chi);
586			s->setIntegralOfChiDt(integralOfChiDt);
587	gezelter	2	}
588
589	gezelter	246	//read eta (eta is 3x3 matrix)
590			if (tokenizer.countTokens() >= 9) {
591			eta(0, 0) = tokenizer.nextTokenAsDouble();
592			eta(0, 1) = tokenizer.nextTokenAsDouble();
593			eta(0, 2) = tokenizer.nextTokenAsDouble();
594			eta(1, 0) = tokenizer.nextTokenAsDouble();
595			eta(1, 1) = tokenizer.nextTokenAsDouble();
596			eta(1, 2) = tokenizer.nextTokenAsDouble();
597			eta(2, 0) = tokenizer.nextTokenAsDouble();
598			eta(2, 1) = tokenizer.nextTokenAsDouble();
599			eta(2, 2) = tokenizer.nextTokenAsDouble();
600
601			s->setEta(eta);
602	gezelter	2	}
603	gezelter	246
604	gezelter	2
605			}
606
607	gezelter	246	}//end namespace oopse