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, "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, "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,
                    "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,
                        "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,
                            "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_->getNIntegrableObjects());

        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, "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,
                        "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, "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, "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, "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,
                                "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,
                                "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, "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,
                    "Not enough Tokens.\n");
            painCave.isFatal = 1;
            simError();
    }

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

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

    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,
                    "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,
                    "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:	1927
Committed:	Wed Jan 12 17:14:35 2005 UTC (20 years, 6 months ago) by tim
File size:	18312 byte(s)
Log Message:	change license
#	User	Rev	Content
1	tim	1927	/*
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	1490	#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	tim	1739	#include "io/DumpReader.hpp"
56	tim	1808	#include "primitives/Molecule.hpp"
57	tim	1492	#include "utils/simError.h"
58	tim	1784	#include "utils/MemoryUtils.hpp"
59	tim	1808	#include "utils/StringTokenizer.hpp"
60
61	tim	1739	#ifdef IS_MPI
62	gezelter	1490
63			#include <mpi.h>
64			#define TAKE_THIS_TAG_CHAR 0
65			#define TAKE_THIS_TAG_INT 1
66	tim	1739
67	gezelter	1490	#endif // is_mpi
68
69
70	tim	1739	namespace oopse {
71	gezelter	1490
72	tim	1739	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73	tim	1885	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
74	gezelter	1490
75			#ifdef IS_MPI
76	tim	1739
77			if (worldRank == 0) {
78	gezelter	1490	#endif
79
80	tim	1739	inFile_ = fopen(filename_.c_str(), "r");
81
82			if (inFile_ == NULL) {
83	tim	1784	sprintf(painCave.errMsg, "Cannot open file: %s\n", filename_.c_str());
84	tim	1739	painCave.isFatal = 1;
85			simError();
86			}
87
88	gezelter	1490	#ifdef IS_MPI
89	tim	1739
90			}
91
92			strcpy(checkPointMsg, "Dump file opened for reading successfully.");
93			MPIcheckPoint();
94
95	gezelter	1490	#endif
96	tim	1739
97			return;
98	gezelter	1490	}
99
100	tim	1739	DumpReader::~DumpReader() {
101
102	gezelter	1490	#ifdef IS_MPI
103	tim	1739
104			if (worldRank == 0) {
105	gezelter	1490	#endif
106
107	tim	1739	int error;
108			error = fclose(inFile_);
109	gezelter	1490
110	tim	1739	if (error) {
111			sprintf(painCave.errMsg, "Error closing %s\n", filename_.c_str());
112			painCave.isFatal = 1;
113			simError();
114			}
115
116			MemoryUtils::deleteVectorOfPointer(framePos_);
117
118	gezelter	1490	#ifdef IS_MPI
119	tim	1739
120			}
121
122			strcpy(checkPointMsg, "Dump file closed successfully.");
123			MPIcheckPoint();
124
125	gezelter	1490	#endif
126
127	tim	1739	return;
128	gezelter	1490	}
129
130	tim	1739	int DumpReader::getNFrames(void) {
131	gezelter	1490
132	tim	1886	if (!isScanned_)
133			scanFile();
134	tim	1885
135	tim	1886	return nframes_;
136	gezelter	1490	}
137
138	tim	1739	void DumpReader::scanFile(void) {
139	gezelter	1490	int i, j;
140			int lineNum = 0;
141	tim	1739	char readBuffer[maxBufferSize];
142			fpos_t * currPos;
143	gezelter	1490
144			#ifdef IS_MPI
145
146	tim	1739	if (worldRank == 0) {
147	gezelter	1490	#endif // is_mpi
148
149	tim	1739	rewind(inFile_);
150	gezelter	1490
151	tim	1739	currPos = new fpos_t;
152			fgetpos(inFile_, currPos);
153			fgets(readBuffer, sizeof(readBuffer), inFile_);
154			lineNum++;
155	gezelter	1490
156	tim	1739	if (feof(inFile_)) {
157			sprintf(painCave.errMsg,
158			"File \"%s\" ended unexpectedly at line %d\n",
159			filename_.c_str(),
160			lineNum);
161			painCave.isFatal = 1;
162			simError();
163			}
164	gezelter	1490
165	tim	1739	while (!feof(inFile_)) {
166			framePos_.push_back(currPos);
167	gezelter	1490
168	tim	1739	i = atoi(readBuffer);
169	gezelter	1490
170	tim	1739	fgets(readBuffer, sizeof(readBuffer), inFile_);
171			lineNum++;
172	gezelter	1490
173	tim	1739	if (feof(inFile_)) {
174			sprintf(painCave.errMsg,
175			"File \"%s\" ended unexpectedly at line %d\n",
176			filename_.c_str(),
177			lineNum);
178			painCave.isFatal = 1;
179			simError();
180			}
181	gezelter	1490
182	tim	1739	for(j = 0; j < i; j++) {
183			fgets(readBuffer, sizeof(readBuffer), inFile_);
184			lineNum++;
185	gezelter	1490
186	tim	1739	if (feof(inFile_)) {
187			sprintf(painCave.errMsg,
188			"File \"%s\" ended unexpectedly at line %d,"
189			" with atom %d\n", filename_.c_str(),
190			lineNum,
191			j);
192	gezelter	1490
193	tim	1739	painCave.isFatal = 1;
194			simError();
195			}
196			}
197	gezelter	1490
198	tim	1739	currPos = new fpos_t;
199			fgetpos(inFile_, currPos);
200			fgets(readBuffer, sizeof(readBuffer), inFile_);
201			lineNum++;
202			}
203	gezelter	1490
204	tim	1739	delete currPos;
205			rewind(inFile_);
206	tim	1886
207	tim	1885	nframes_ = framePos_.size();
208	tim	1739	#ifdef IS_MPI
209			}
210	gezelter	1490
211	tim	1886	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
212
213	tim	1739	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
214			MPIcheckPoint();
215	gezelter	1490
216	tim	1739	#endif // is_mpi
217	gezelter	1490
218	tim	1886	isScanned_ = true;
219	tim	1739	}
220	gezelter	1490
221	tim	1739	void DumpReader::readFrame(int whichFrame) {
222			readSet(whichFrame);
223			}
224	gezelter	1490
225	tim	1739	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	1490
231	tim	1739	Molecule* mol;
232			StuntDouble* integrableObject;
233	tim	1808	SimInfo::MoleculeIterator mi;
234			Molecule::IntegrableObjectIterator ii;
235	gezelter	1490
236	tim	1739	#ifndef IS_MPI
237	gezelter	1490
238	tim	1739	fsetpos(inFile_, framePos_[whichFrame]);
239			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
240	gezelter	1490
241	tim	1739	if (eof_test == NULL) {
242	gezelter	1490	sprintf(painCave.errMsg,
243	tim	1739	"DumpReader error: error reading 1st line of \"%s\"\n",
244			filename_.c_str());
245	gezelter	1490	painCave.isFatal = 1;
246			simError();
247			}
248
249	tim	1739	nTotObjs = atoi(read_buffer);
250	gezelter	1490
251	tim	1739	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			info_->getNIntegrableObjects());
258	gezelter	1490
259	tim	1739	painCave.isFatal = 1;
260			simError();
261			}
262	gezelter	1490
263	tim	1739	//read the box mat from the comment line
264	gezelter	1490
265	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
266	gezelter	1490
267	tim	1739	if (eof_test == NULL) {
268			sprintf(painCave.errMsg, "error in reading commment in %s\n",
269			filename_.c_str());
270			painCave.isFatal = 1;
271			simError();
272	gezelter	1490	}
273
274	tim	1808	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
275	gezelter	1490
276	tim	1739	//parse dump lines
277	gezelter	1490
278	tim	1739	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
279	gezelter	1490
280	tim	1808	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
281			integrableObject = mol->nextIntegrableObject(ii)) {
282	gezelter	1490
283	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
284	gezelter	1490
285	tim	1739	if (eof_test == NULL) {
286			sprintf(painCave.errMsg,
287			"error in reading file %s\n"
288			"natoms = %d; index = %d\n"
289			"error reading the line from the file.\n",
290			filename_.c_str(),
291			nTotObjs,
292			i);
293	gezelter	1490
294	tim	1739	painCave.isFatal = 1;
295			simError();
296			}
297	gezelter	1490
298	tim	1808	parseDumpLine(read_buffer, integrableObject);
299	tim	1739
300	tim	1808	}
301	gezelter	1490	}
302
303	tim	1739	// MPI Section of code..........
304	gezelter	1490
305	tim	1739	#else //IS_MPI
306	gezelter	1490
307	tim	1739	// first thing first, suspend fatalities.
308			int masterNode = 0;
309			int nCurObj;
310			painCave.isEventLoop = 1;
311	gezelter	1490
312	tim	1739	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
313			int haveError;
314	gezelter	1490
315	tim	1739	MPI_Status istatus;
316			int nitems;
317	gezelter	1490
318	tim	1739	nTotObjs = info_->getNGlobalIntegrableObjects();
319			haveError = 0;
320	gezelter	1490
321	tim	1739	if (worldRank == masterNode) {
322			fsetpos(inFile_, framePos_[whichFrame]);
323	gezelter	1490
324	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
325	gezelter	1490
326	tim	1739	if (eof_test == NULL) {
327			sprintf(painCave.errMsg, "Error reading 1st line of %s \n ",
328			filename_.c_str());
329			painCave.isFatal = 1;
330			simError();
331			}
332	gezelter	1490
333	tim	1739	nitems = atoi(read_buffer);
334	gezelter	1490
335	tim	1739	// 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	1490
339	tim	1739	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	tim	1883	info_->getNGlobalIntegrableObjects());
346	gezelter	1490
347	tim	1739	painCave.isFatal = 1;
348			simError();
349	gezelter	1490	}
350
351	tim	1739	//read the boxMat from the comment line
352	gezelter	1490
353	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
354	gezelter	1490
355	tim	1739	if (eof_test == NULL) {
356			sprintf(painCave.errMsg, "error in reading commment in %s\n",
357			filename_.c_str());
358			painCave.isFatal = 1;
359			simError();
360	gezelter	1490	}
361
362	tim	1739	//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	1490
367	tim	1739	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
368	tim	1808	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
369	gezelter	1490
370	tim	1739	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
371	tim	1883	int which_node = info_->getMolToProc(i);
372	gezelter	1490
373	tim	1739	if (which_node == masterNode) {
374			//molecules belong to master node
375	gezelter	1490
376	tim	1739	mol = info_->getMoleculeByGlobalIndex(i);
377	gezelter	1490
378	tim	1739	if (mol == NULL) {
379	tim	1884	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
380	tim	1739	painCave.isFatal = 1;
381			simError();
382			}
383	gezelter	1490
384	tim	1739	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	1490
389	tim	1739	if (eof_test == NULL) {
390			sprintf(painCave.errMsg,
391			"error in reading file %s\n"
392			"natoms = %d; index = %d\n"
393			"error reading the line from the file.\n",
394			filename_.c_str(),
395			nTotObjs,
396			i);
397	gezelter	1490
398	tim	1739	painCave.isFatal = 1;
399			simError();
400			}
401	gezelter	1490
402	tim	1739	parseDumpLine(read_buffer, integrableObject);
403			}
404			} else {
405			//molecule belongs to slave nodes
406	gezelter	1490
407	tim	1739	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
408			MPI_COMM_WORLD, &istatus);
409	gezelter	1490
410	tim	1739	for(int j = 0; j < nCurObj; j++) {
411			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
412	gezelter	1490
413	tim	1739	if (eof_test == NULL) {
414			sprintf(painCave.errMsg,
415			"error in reading file %s\n"
416			"natoms = %d; index = %d\n"
417			"error reading the line from the file.\n",
418			filename_.c_str(),
419			nTotObjs,
420			i);
421	gezelter	1490
422	tim	1739	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	1490
435	tim	1739	/*@todo/
436	tim	1808	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
437	gezelter	1490
438	tim	1739	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
439	tim	1883	int which_node = info_->getMolToProc(i);
440	gezelter	1490
441	tim	1739	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	1884	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
447	tim	1739	painCave.isFatal = 1;
448			simError();
449			}
450
451			nCurObj = mol->getNIntegrableObjects();
452	gezelter	1490
453	tim	1739	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
454			MPI_COMM_WORLD);
455	gezelter	1490
456	tim	1739	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	1490
462	tim	1739	parseDumpLine(read_buffer, integrableObject);
463			}
464
465			}
466
467			}
468
469			}
470	gezelter	1490
471	tim	1739	#endif
472	gezelter	1490
473	tim	1739	}
474	gezelter	1490
475	tim	1739	void DumpReader::parseDumpLine(char line, StuntDouble integrableObject) {
476	gezelter	1490
477	tim	1739	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	1490
486	tim	1808	if (nTokens < 14) {
487			sprintf(painCave.errMsg,
488			"Not enough Tokens.\n");
489			painCave.isFatal = 1;
490			simError();
491	gezelter	1490	}
492
493	tim	1739	std::string name = tokenizer.nextToken();
494	gezelter	1490
495	tim	1739	if (name != integrableObject->getType()) {
496
497	gezelter	1490	}
498
499	tim	1901	pos[0] = tokenizer.nextTokenAsDouble();
500			pos[1] = tokenizer.nextTokenAsDouble();
501			pos[2] = tokenizer.nextTokenAsDouble();
502	tim	1739	integrableObject->setPos(pos);
503
504	tim	1901	vel[0] = tokenizer.nextTokenAsDouble();
505			vel[1] = tokenizer.nextTokenAsDouble();
506			vel[2] = tokenizer.nextTokenAsDouble();
507	tim	1739	integrableObject->setVel(vel);
508	gezelter	1490
509	tim	1739	if (integrableObject->isDirectional()) {
510	tim	1808
511	tim	1901	q[0] = tokenizer.nextTokenAsDouble();
512			q[1] = tokenizer.nextTokenAsDouble();
513			q[2] = tokenizer.nextTokenAsDouble();
514			q[3] = tokenizer.nextTokenAsDouble();
515	gezelter	1490
516	tim	1739	double qlen = q.length();
517			if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
518
519			sprintf(painCave.errMsg,
520			"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
521			painCave.isFatal = 1;
522			simError();
523
524	tim	1864	}
525
526			q.normalize();
527
528	tim	1739	integrableObject->setQ(q);
529
530	tim	1901	ji[0] = tokenizer.nextTokenAsDouble();
531			ji[1] = tokenizer.nextTokenAsDouble();
532			ji[2] = tokenizer.nextTokenAsDouble();
533	tim	1739	integrableObject->setJ(ji);
534	gezelter	1490	}
535
536			}
537
538
539	tim	1808	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
540	tim	1739	double currTime;
541			Mat3x3d hmat;
542			double chi;
543			double integralOfChiDt;
544			Mat3x3d eta;
545	gezelter	1490
546	tim	1739	StringTokenizer tokenizer(line);
547			int nTokens;
548	gezelter	1490
549	tim	1739	nTokens = tokenizer.countTokens();
550	gezelter	1490
551	tim	1739	//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens)
552			if (nTokens < 10) {
553			sprintf(painCave.errMsg,
554			"Not enough tokens in comment line: %s", line);
555			painCave.isFatal = 1;
556			simError();
557	gezelter	1490	}
558
559	tim	1739	//read current time
560	tim	1901	currTime = tokenizer.nextTokenAsDouble();
561	tim	1808	s->setTime(currTime);
562	gezelter	1490
563	tim	1739	//read h-matrix
564	tim	1901	hmat(0, 0) = tokenizer.nextTokenAsDouble();
565			hmat(0, 1) = tokenizer.nextTokenAsDouble();
566			hmat(0, 2) = tokenizer.nextTokenAsDouble();
567			hmat(1, 0) = tokenizer.nextTokenAsDouble();
568			hmat(1, 1) = tokenizer.nextTokenAsDouble();
569			hmat(1, 2) = tokenizer.nextTokenAsDouble();
570			hmat(2, 0) = tokenizer.nextTokenAsDouble();
571			hmat(2, 1) = tokenizer.nextTokenAsDouble();
572			hmat(2, 2) = tokenizer.nextTokenAsDouble();
573	tim	1739	s->setHmat(hmat);
574	gezelter	1490
575	tim	1808	//read chi and integrablOfChidt, they should apprear in pair
576			if (tokenizer.countTokens() >= 2) {
577	tim	1901	chi = tokenizer.nextTokenAsDouble();
578			integralOfChiDt = tokenizer.nextTokenAsDouble();
579	gezelter	1490
580	tim	1808	s->setChi(chi);
581			s->setIntegralOfChiDt(integralOfChiDt);
582			}
583
584			//read eta (eta is 3x3 matrix)
585			if (tokenizer.countTokens() >= 9) {
586	tim	1901	eta(0, 0) = tokenizer.nextTokenAsDouble();
587			eta(0, 1) = tokenizer.nextTokenAsDouble();
588			eta(0, 2) = tokenizer.nextTokenAsDouble();
589			eta(1, 0) = tokenizer.nextTokenAsDouble();
590			eta(1, 1) = tokenizer.nextTokenAsDouble();
591			eta(1, 2) = tokenizer.nextTokenAsDouble();
592			eta(2, 0) = tokenizer.nextTokenAsDouble();
593			eta(2, 1) = tokenizer.nextTokenAsDouble();
594			eta(2, 2) = tokenizer.nextTokenAsDouble();
595	gezelter	1490
596	tim	1808	s->setEta(eta);
597	tim	1739	}
598	gezelter	1490
599	tim	1739
600	gezelter	1490	}
601
602	tim	1739	}//end namespace oopse