src/io/DumpReader.cpp

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

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

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

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

        s->setEta(eta);
    }

    
}

}//end namespace oopse
Revision:	1886
Committed:	Wed Dec 15 16:13:35 2004 UTC (19 years, 9 months ago) by tim
File size:	16201 byte(s)
Log Message:	MPI in NVE is working
#	User	Rev	Content
1	gezelter	1490	#define _LARGEFILE_SOURCE64
2			#define _FILE_OFFSET_BITS 64
3
4			#include <sys/types.h>
5			#include <sys/stat.h>
6
7			#include <iostream>
8			#include <math.h>
9
10			#include <stdio.h>
11			#include <stdlib.h>
12			#include <string.h>
13
14	tim	1739	#include "io/DumpReader.hpp"
15	tim	1808	#include "primitives/Molecule.hpp"
16	tim	1492	#include "utils/simError.h"
17	tim	1784	#include "utils/MemoryUtils.hpp"
18	tim	1808	#include "utils/StringTokenizer.hpp"
19
20	tim	1739	#ifdef IS_MPI
21	gezelter	1490
22			#include <mpi.h>
23			#define TAKE_THIS_TAG_CHAR 0
24			#define TAKE_THIS_TAG_INT 1
25	tim	1739
26	gezelter	1490	#endif // is_mpi
27
28
29	tim	1739	namespace oopse {
30	gezelter	1490
31	tim	1739	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
32	tim	1885	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
33	gezelter	1490
34			#ifdef IS_MPI
35	tim	1739
36			if (worldRank == 0) {
37	gezelter	1490	#endif
38
39	tim	1739	inFile_ = fopen(filename_.c_str(), "r");
40
41			if (inFile_ == NULL) {
42	tim	1784	sprintf(painCave.errMsg, "Cannot open file: %s\n", filename_.c_str());
43	tim	1739	painCave.isFatal = 1;
44			simError();
45			}
46
47	gezelter	1490	#ifdef IS_MPI
48	tim	1739
49			}
50
51			strcpy(checkPointMsg, "Dump file opened for reading successfully.");
52			MPIcheckPoint();
53
54	gezelter	1490	#endif
55	tim	1739
56			return;
57	gezelter	1490	}
58
59	tim	1739	DumpReader::~DumpReader() {
60
61	gezelter	1490	#ifdef IS_MPI
62	tim	1739
63			if (worldRank == 0) {
64	gezelter	1490	#endif
65
66	tim	1739	int error;
67			error = fclose(inFile_);
68	gezelter	1490
69	tim	1739	if (error) {
70			sprintf(painCave.errMsg, "Error closing %s\n", filename_.c_str());
71			painCave.isFatal = 1;
72			simError();
73			}
74
75			MemoryUtils::deleteVectorOfPointer(framePos_);
76
77	gezelter	1490	#ifdef IS_MPI
78	tim	1739
79			}
80
81			strcpy(checkPointMsg, "Dump file closed successfully.");
82			MPIcheckPoint();
83
84	gezelter	1490	#endif
85
86	tim	1739	return;
87	gezelter	1490	}
88
89	tim	1739	int DumpReader::getNFrames(void) {
90	gezelter	1490
91	tim	1886	if (!isScanned_)
92			scanFile();
93	tim	1885
94	tim	1886	return nframes_;
95	gezelter	1490	}
96
97	tim	1739	void DumpReader::scanFile(void) {
98	gezelter	1490	int i, j;
99			int lineNum = 0;
100	tim	1739	char readBuffer[maxBufferSize];
101			fpos_t * currPos;
102	gezelter	1490
103			#ifdef IS_MPI
104
105	tim	1739	if (worldRank == 0) {
106	gezelter	1490	#endif // is_mpi
107
108	tim	1739	rewind(inFile_);
109	gezelter	1490
110	tim	1739	currPos = new fpos_t;
111			fgetpos(inFile_, currPos);
112			fgets(readBuffer, sizeof(readBuffer), inFile_);
113			lineNum++;
114	gezelter	1490
115	tim	1739	if (feof(inFile_)) {
116			sprintf(painCave.errMsg,
117			"File \"%s\" ended unexpectedly at line %d\n",
118			filename_.c_str(),
119			lineNum);
120			painCave.isFatal = 1;
121			simError();
122			}
123	gezelter	1490
124	tim	1739	while (!feof(inFile_)) {
125			framePos_.push_back(currPos);
126	gezelter	1490
127	tim	1739	i = atoi(readBuffer);
128	gezelter	1490
129	tim	1739	fgets(readBuffer, sizeof(readBuffer), inFile_);
130			lineNum++;
131	gezelter	1490
132	tim	1739	if (feof(inFile_)) {
133			sprintf(painCave.errMsg,
134			"File \"%s\" ended unexpectedly at line %d\n",
135			filename_.c_str(),
136			lineNum);
137			painCave.isFatal = 1;
138			simError();
139			}
140	gezelter	1490
141	tim	1739	for(j = 0; j < i; j++) {
142			fgets(readBuffer, sizeof(readBuffer), inFile_);
143			lineNum++;
144	gezelter	1490
145	tim	1739	if (feof(inFile_)) {
146			sprintf(painCave.errMsg,
147			"File \"%s\" ended unexpectedly at line %d,"
148			" with atom %d\n", filename_.c_str(),
149			lineNum,
150			j);
151	gezelter	1490
152	tim	1739	painCave.isFatal = 1;
153			simError();
154			}
155			}
156	gezelter	1490
157	tim	1739	currPos = new fpos_t;
158			fgetpos(inFile_, currPos);
159			fgets(readBuffer, sizeof(readBuffer), inFile_);
160			lineNum++;
161			}
162	gezelter	1490
163	tim	1739	delete currPos;
164			rewind(inFile_);
165	tim	1886
166	tim	1885	nframes_ = framePos_.size();
167	tim	1739	#ifdef IS_MPI
168			}
169	gezelter	1490
170	tim	1886	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
171
172	tim	1739	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
173			MPIcheckPoint();
174	gezelter	1490
175	tim	1739	#endif // is_mpi
176	gezelter	1490
177	tim	1886	isScanned_ = true;
178	tim	1739	}
179	gezelter	1490
180	tim	1739	void DumpReader::readFrame(int whichFrame) {
181			readSet(whichFrame);
182			}
183	gezelter	1490
184	tim	1739	void DumpReader::readSet(int whichFrame) {
185			int i;
186			int nTotObjs; // the number of atoms
187			char read_buffer[maxBufferSize]; //the line buffer for reading
188			char * eof_test; // ptr to see when we reach the end of the file
189	gezelter	1490
190	tim	1739	Molecule* mol;
191			StuntDouble* integrableObject;
192	tim	1808	SimInfo::MoleculeIterator mi;
193			Molecule::IntegrableObjectIterator ii;
194	gezelter	1490
195	tim	1739	#ifndef IS_MPI
196	gezelter	1490
197	tim	1739	fsetpos(inFile_, framePos_[whichFrame]);
198			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
199	gezelter	1490
200	tim	1739	if (eof_test == NULL) {
201	gezelter	1490	sprintf(painCave.errMsg,
202	tim	1739	"DumpReader error: error reading 1st line of \"%s\"\n",
203			filename_.c_str());
204	gezelter	1490	painCave.isFatal = 1;
205			simError();
206			}
207
208	tim	1739	nTotObjs = atoi(read_buffer);
209	gezelter	1490
210	tim	1739	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
211			sprintf(painCave.errMsg,
212			"DumpReader error. %s nIntegrable, %d, "
213			"does not match the meta-data file's nIntegrable, %d.\n",
214			filename_.c_str(),
215			nTotObjs,
216			info_->getNIntegrableObjects());
217	gezelter	1490
218	tim	1739	painCave.isFatal = 1;
219			simError();
220			}
221	gezelter	1490
222	tim	1739	//read the box mat from the comment line
223	gezelter	1490
224	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
225	gezelter	1490
226	tim	1739	if (eof_test == NULL) {
227			sprintf(painCave.errMsg, "error in reading commment in %s\n",
228			filename_.c_str());
229			painCave.isFatal = 1;
230			simError();
231	gezelter	1490	}
232
233	tim	1808	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
234	gezelter	1490
235	tim	1739	//parse dump lines
236	gezelter	1490
237	tim	1739	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
238	gezelter	1490
239	tim	1808	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
240			integrableObject = mol->nextIntegrableObject(ii)) {
241	gezelter	1490
242	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
243	gezelter	1490
244	tim	1739	if (eof_test == NULL) {
245			sprintf(painCave.errMsg,
246			"error in reading file %s\n"
247			"natoms = %d; index = %d\n"
248			"error reading the line from the file.\n",
249			filename_.c_str(),
250			nTotObjs,
251			i);
252	gezelter	1490
253	tim	1739	painCave.isFatal = 1;
254			simError();
255			}
256	gezelter	1490
257	tim	1808	parseDumpLine(read_buffer, integrableObject);
258	tim	1739
259	tim	1808	}
260	gezelter	1490	}
261
262	tim	1739	// MPI Section of code..........
263	gezelter	1490
264	tim	1739	#else //IS_MPI
265	gezelter	1490
266	tim	1739	// first thing first, suspend fatalities.
267			int masterNode = 0;
268			int nCurObj;
269			painCave.isEventLoop = 1;
270	gezelter	1490
271	tim	1739	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
272			int haveError;
273	gezelter	1490
274	tim	1739	MPI_Status istatus;
275			int nitems;
276	gezelter	1490
277	tim	1739	nTotObjs = info_->getNGlobalIntegrableObjects();
278			haveError = 0;
279	gezelter	1490
280	tim	1739	if (worldRank == masterNode) {
281			fsetpos(inFile_, framePos_[whichFrame]);
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, "Error reading 1st line of %s \n ",
287			filename_.c_str());
288			painCave.isFatal = 1;
289			simError();
290			}
291	gezelter	1490
292	tim	1739	nitems = atoi(read_buffer);
293	gezelter	1490
294	tim	1739	// Check to see that the number of integrable objects in the
295			// intial configuration file is the same as derived from the
296			// meta-data file.
297	gezelter	1490
298	tim	1739	if (nTotObjs != nitems) {
299			sprintf(painCave.errMsg,
300			"DumpReader Error. %s nIntegrable, %d, "
301			"does not match the meta-data file's nIntegrable, %d.\n",
302			filename_.c_str(),
303			nTotObjs,
304	tim	1883	info_->getNGlobalIntegrableObjects());
305	gezelter	1490
306	tim	1739	painCave.isFatal = 1;
307			simError();
308	gezelter	1490	}
309
310	tim	1739	//read the boxMat from the comment line
311	gezelter	1490
312	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
313	gezelter	1490
314	tim	1739	if (eof_test == NULL) {
315			sprintf(painCave.errMsg, "error in reading commment in %s\n",
316			filename_.c_str());
317			painCave.isFatal = 1;
318			simError();
319	gezelter	1490	}
320
321	tim	1739	//Every single processor will parse the comment line by itself
322			//By using this way, we might lose some efficiency, but if we want to add
323			//more parameters into comment line, we only need to modify function
324			//parseCommentLine
325	gezelter	1490
326	tim	1739	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
327	tim	1808	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
328	gezelter	1490
329	tim	1739	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
330	tim	1883	int which_node = info_->getMolToProc(i);
331	gezelter	1490
332	tim	1739	if (which_node == masterNode) {
333			//molecules belong to master node
334	gezelter	1490
335	tim	1739	mol = info_->getMoleculeByGlobalIndex(i);
336	gezelter	1490
337	tim	1739	if (mol == NULL) {
338	tim	1884	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
339	tim	1739	painCave.isFatal = 1;
340			simError();
341			}
342	gezelter	1490
343	tim	1739	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
344			integrableObject = mol->nextIntegrableObject(ii)){
345
346			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
347	gezelter	1490
348	tim	1739	if (eof_test == NULL) {
349			sprintf(painCave.errMsg,
350			"error in reading file %s\n"
351			"natoms = %d; index = %d\n"
352			"error reading the line from the file.\n",
353			filename_.c_str(),
354			nTotObjs,
355			i);
356	gezelter	1490
357	tim	1739	painCave.isFatal = 1;
358			simError();
359			}
360	gezelter	1490
361	tim	1739	parseDumpLine(read_buffer, integrableObject);
362			}
363			} else {
364			//molecule belongs to slave nodes
365	gezelter	1490
366	tim	1739	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
367			MPI_COMM_WORLD, &istatus);
368	gezelter	1490
369	tim	1739	for(int j = 0; j < nCurObj; j++) {
370			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
371	gezelter	1490
372	tim	1739	if (eof_test == NULL) {
373			sprintf(painCave.errMsg,
374			"error in reading file %s\n"
375			"natoms = %d; index = %d\n"
376			"error reading the line from the file.\n",
377			filename_.c_str(),
378			nTotObjs,
379			i);
380	gezelter	1490
381	tim	1739	painCave.isFatal = 1;
382			simError();
383			}
384
385			MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
386			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
387			}
388			}
389			}
390			} else {
391			//actions taken at slave nodes
392			MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
393	gezelter	1490
394	tim	1739	/*@todo/
395	tim	1808	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
396	gezelter	1490
397	tim	1739	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
398	tim	1883	int which_node = info_->getMolToProc(i);
399	gezelter	1490
400	tim	1739	if (which_node == worldRank) {
401			//molecule with global index i belongs to this processor
402
403			mol = info_->getMoleculeByGlobalIndex(i);
404			if (mol == NULL) {
405	tim	1884	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
406	tim	1739	painCave.isFatal = 1;
407			simError();
408			}
409
410			nCurObj = mol->getNIntegrableObjects();
411	gezelter	1490
412	tim	1739	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
413			MPI_COMM_WORLD);
414	gezelter	1490
415	tim	1739	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
416			integrableObject = mol->nextIntegrableObject(ii)){
417
418			MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
419			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
420	gezelter	1490
421	tim	1739	parseDumpLine(read_buffer, integrableObject);
422			}
423
424			}
425
426			}
427
428			}
429	gezelter	1490
430	tim	1739	#endif
431	gezelter	1490
432	tim	1739	}
433	gezelter	1490
434	tim	1739	void DumpReader::parseDumpLine(char line, StuntDouble integrableObject) {
435	gezelter	1490
436	tim	1739	Vector3d pos; // position place holders
437			Vector3d vel; // velocity placeholders
438			Quat4d q; // the quaternions
439			Vector3d ji; // angular velocity placeholders;
440			StringTokenizer tokenizer(line);
441			int nTokens;
442
443			nTokens = tokenizer.countTokens();
444	gezelter	1490
445	tim	1808	if (nTokens < 14) {
446			sprintf(painCave.errMsg,
447			"Not enough Tokens.\n");
448			painCave.isFatal = 1;
449			simError();
450	gezelter	1490	}
451
452	tim	1739	std::string name = tokenizer.nextToken();
453	gezelter	1490
454	tim	1739	if (name != integrableObject->getType()) {
455
456	gezelter	1490	}
457
458	tim	1739	pos[0] = tokenizer.nextTokenAsFloat();
459			pos[1] = tokenizer.nextTokenAsFloat();
460			pos[2] = tokenizer.nextTokenAsFloat();
461			integrableObject->setPos(pos);
462
463			vel[0] = tokenizer.nextTokenAsFloat();
464			vel[1] = tokenizer.nextTokenAsFloat();
465			vel[2] = tokenizer.nextTokenAsFloat();
466			integrableObject->setVel(vel);
467	gezelter	1490
468	tim	1739	if (integrableObject->isDirectional()) {
469	tim	1808
470	tim	1739	q[0] = tokenizer.nextTokenAsFloat();
471			q[1] = tokenizer.nextTokenAsFloat();
472			q[2] = tokenizer.nextTokenAsFloat();
473			q[3] = tokenizer.nextTokenAsFloat();
474	gezelter	1490
475	tim	1739	double qlen = q.length();
476			if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
477
478			sprintf(painCave.errMsg,
479			"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
480			painCave.isFatal = 1;
481			simError();
482
483	tim	1864	}
484
485			q.normalize();
486
487	tim	1739	integrableObject->setQ(q);
488
489			ji[0] = tokenizer.nextTokenAsFloat();
490			ji[1] = tokenizer.nextTokenAsFloat();
491			ji[2] = tokenizer.nextTokenAsFloat();
492			integrableObject->setJ(ji);
493	gezelter	1490	}
494
495			}
496
497
498	tim	1808	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
499	tim	1739	double currTime;
500			Mat3x3d hmat;
501			double chi;
502			double integralOfChiDt;
503			Mat3x3d eta;
504	gezelter	1490
505	tim	1739	StringTokenizer tokenizer(line);
506			int nTokens;
507	gezelter	1490
508	tim	1739	nTokens = tokenizer.countTokens();
509	gezelter	1490
510	tim	1739	//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens)
511			if (nTokens < 10) {
512			sprintf(painCave.errMsg,
513			"Not enough tokens in comment line: %s", line);
514			painCave.isFatal = 1;
515			simError();
516	gezelter	1490	}
517
518	tim	1739	//read current time
519			currTime = tokenizer.nextTokenAsFloat();
520	tim	1808	s->setTime(currTime);
521	gezelter	1490
522	tim	1739	//read h-matrix
523			hmat(0, 0) = tokenizer.nextTokenAsFloat();
524			hmat(0, 1) = tokenizer.nextTokenAsFloat();
525			hmat(0, 2) = tokenizer.nextTokenAsFloat();
526			hmat(1, 0) = tokenizer.nextTokenAsFloat();
527			hmat(1, 1) = tokenizer.nextTokenAsFloat();
528			hmat(1, 2) = tokenizer.nextTokenAsFloat();
529			hmat(2, 0) = tokenizer.nextTokenAsFloat();
530			hmat(2, 1) = tokenizer.nextTokenAsFloat();
531			hmat(2, 2) = tokenizer.nextTokenAsFloat();
532			s->setHmat(hmat);
533	gezelter	1490
534	tim	1808	//read chi and integrablOfChidt, they should apprear in pair
535			if (tokenizer.countTokens() >= 2) {
536			chi = tokenizer.nextTokenAsFloat();
537			integralOfChiDt = tokenizer.nextTokenAsFloat();
538	gezelter	1490
539	tim	1808	s->setChi(chi);
540			s->setIntegralOfChiDt(integralOfChiDt);
541			}
542
543			//read eta (eta is 3x3 matrix)
544			if (tokenizer.countTokens() >= 9) {
545			eta(0, 0) = tokenizer.nextTokenAsFloat();
546			eta(0, 1) = tokenizer.nextTokenAsFloat();
547			eta(0, 2) = tokenizer.nextTokenAsFloat();
548			eta(1, 0) = tokenizer.nextTokenAsFloat();
549			eta(1, 1) = tokenizer.nextTokenAsFloat();
550			eta(1, 2) = tokenizer.nextTokenAsFloat();
551			eta(2, 0) = tokenizer.nextTokenAsFloat();
552			eta(2, 1) = tokenizer.nextTokenAsFloat();
553			eta(2, 2) = tokenizer.nextTokenAsFloat();
554	gezelter	1490
555	tim	1808	s->setEta(eta);
556	tim	1739	}
557	gezelter	1490
558	tim	1739
559	gezelter	1490	}
560
561	tim	1739	}//end namespace oopse