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) {
#ifdef IS_MPI

    if (worldRank == 0) {
#endif

        if (!isScanned_)
            scanFile();

        return nframes_;
#ifdef IS_MPI
    }
#endif    
}

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_);

        isScanned_ = true;

        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

}

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:	1885
Committed:	Tue Dec 14 21:57:47 2004 UTC (19 years, 9 months ago) by tim
File size:	16293 byte(s)
Log Message:	fix a bug in DumpReader. Master nodes does not brocast the total number of frames
#	Content
1	#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	#include "io/DumpReader.hpp"
15	#include "primitives/Molecule.hpp"
16	#include "utils/simError.h"
17	#include "utils/MemoryUtils.hpp"
18	#include "utils/StringTokenizer.hpp"
19
20	#ifdef IS_MPI
21
22	#include <mpi.h>
23	#define TAKE_THIS_TAG_CHAR 0
24	#define TAKE_THIS_TAG_INT 1
25
26	#endif // is_mpi
27
28
29	namespace oopse {
30
31	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
32	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
33
34	#ifdef IS_MPI
35
36	if (worldRank == 0) {
37	#endif
38
39	inFile_ = fopen(filename_.c_str(), "r");
40
41	if (inFile_ == NULL) {
42	sprintf(painCave.errMsg, "Cannot open file: %s\n", filename_.c_str());
43	painCave.isFatal = 1;
44	simError();
45	}
46
47	#ifdef IS_MPI
48
49	}
50
51	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
52	MPIcheckPoint();
53
54	#endif
55
56	return;
57	}
58
59	DumpReader::~DumpReader() {
60
61	#ifdef IS_MPI
62
63	if (worldRank == 0) {
64	#endif
65
66	int error;
67	error = fclose(inFile_);
68
69	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	#ifdef IS_MPI
78
79	}
80
81	strcpy(checkPointMsg, "Dump file closed successfully.");
82	MPIcheckPoint();
83
84	#endif
85
86	return;
87	}
88
89	int DumpReader::getNFrames(void) {
90	#ifdef IS_MPI
91
92	if (worldRank == 0) {
93	#endif
94
95	if (!isScanned_)
96	scanFile();
97
98	return nframes_;
99	#ifdef IS_MPI
100	}
101	#endif
102	}
103
104	void DumpReader::scanFile(void) {
105	int i, j;
106	int lineNum = 0;
107	char readBuffer[maxBufferSize];
108	fpos_t * currPos;
109
110	#ifdef IS_MPI
111
112	if (worldRank == 0) {
113	#endif // is_mpi
114
115	rewind(inFile_);
116
117	currPos = new fpos_t;
118	fgetpos(inFile_, currPos);
119	fgets(readBuffer, sizeof(readBuffer), inFile_);
120	lineNum++;
121
122	if (feof(inFile_)) {
123	sprintf(painCave.errMsg,
124	"File \"%s\" ended unexpectedly at line %d\n",
125	filename_.c_str(),
126	lineNum);
127	painCave.isFatal = 1;
128	simError();
129	}
130
131	while (!feof(inFile_)) {
132	framePos_.push_back(currPos);
133
134	i = atoi(readBuffer);
135
136	fgets(readBuffer, sizeof(readBuffer), inFile_);
137	lineNum++;
138
139	if (feof(inFile_)) {
140	sprintf(painCave.errMsg,
141	"File \"%s\" ended unexpectedly at line %d\n",
142	filename_.c_str(),
143	lineNum);
144	painCave.isFatal = 1;
145	simError();
146	}
147
148	for(j = 0; j < i; j++) {
149	fgets(readBuffer, sizeof(readBuffer), inFile_);
150	lineNum++;
151
152	if (feof(inFile_)) {
153	sprintf(painCave.errMsg,
154	"File \"%s\" ended unexpectedly at line %d,"
155	" with atom %d\n", filename_.c_str(),
156	lineNum,
157	j);
158
159	painCave.isFatal = 1;
160	simError();
161	}
162	}
163
164	currPos = new fpos_t;
165	fgetpos(inFile_, currPos);
166	fgets(readBuffer, sizeof(readBuffer), inFile_);
167	lineNum++;
168	}
169
170	delete currPos;
171	rewind(inFile_);
172
173	isScanned_ = true;
174
175	nframes_ = framePos_.size();
176	#ifdef IS_MPI
177	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
178
179	}
180
181	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
182	MPIcheckPoint();
183
184	#endif // is_mpi
185
186	}
187
188	void DumpReader::readFrame(int whichFrame) {
189	readSet(whichFrame);
190	}
191
192	void DumpReader::readSet(int whichFrame) {
193	int i;
194	int nTotObjs; // the number of atoms
195	char read_buffer[maxBufferSize]; //the line buffer for reading
196	char * eof_test; // ptr to see when we reach the end of the file
197
198	Molecule* mol;
199	StuntDouble* integrableObject;
200	SimInfo::MoleculeIterator mi;
201	Molecule::IntegrableObjectIterator ii;
202
203	#ifndef IS_MPI
204
205	fsetpos(inFile_, framePos_[whichFrame]);
206	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
207
208	if (eof_test == NULL) {
209	sprintf(painCave.errMsg,
210	"DumpReader error: error reading 1st line of \"%s\"\n",
211	filename_.c_str());
212	painCave.isFatal = 1;
213	simError();
214	}
215
216	nTotObjs = atoi(read_buffer);
217
218	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
219	sprintf(painCave.errMsg,
220	"DumpReader error. %s nIntegrable, %d, "
221	"does not match the meta-data file's nIntegrable, %d.\n",
222	filename_.c_str(),
223	nTotObjs,
224	info_->getNIntegrableObjects());
225
226	painCave.isFatal = 1;
227	simError();
228	}
229
230	//read the box mat from the comment line
231
232	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
233
234	if (eof_test == NULL) {
235	sprintf(painCave.errMsg, "error in reading commment in %s\n",
236	filename_.c_str());
237	painCave.isFatal = 1;
238	simError();
239	}
240
241	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
242
243	//parse dump lines
244
245	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
246
247	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
248	integrableObject = mol->nextIntegrableObject(ii)) {
249
250	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
251
252	if (eof_test == NULL) {
253	sprintf(painCave.errMsg,
254	"error in reading file %s\n"
255	"natoms = %d; index = %d\n"
256	"error reading the line from the file.\n",
257	filename_.c_str(),
258	nTotObjs,
259	i);
260
261	painCave.isFatal = 1;
262	simError();
263	}
264
265	parseDumpLine(read_buffer, integrableObject);
266
267	}
268	}
269
270	// MPI Section of code..........
271
272	#else //IS_MPI
273
274	// first thing first, suspend fatalities.
275	int masterNode = 0;
276	int nCurObj;
277	painCave.isEventLoop = 1;
278
279	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
280	int haveError;
281
282	MPI_Status istatus;
283	int nitems;
284
285	nTotObjs = info_->getNGlobalIntegrableObjects();
286	haveError = 0;
287
288	if (worldRank == masterNode) {
289	fsetpos(inFile_, framePos_[whichFrame]);
290
291	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
292
293	if (eof_test == NULL) {
294	sprintf(painCave.errMsg, "Error reading 1st line of %s \n ",
295	filename_.c_str());
296	painCave.isFatal = 1;
297	simError();
298	}
299
300	nitems = atoi(read_buffer);
301
302	// Check to see that the number of integrable objects in the
303	// intial configuration file is the same as derived from the
304	// meta-data file.
305
306	if (nTotObjs != nitems) {
307	sprintf(painCave.errMsg,
308	"DumpReader Error. %s nIntegrable, %d, "
309	"does not match the meta-data file's nIntegrable, %d.\n",
310	filename_.c_str(),
311	nTotObjs,
312	info_->getNGlobalIntegrableObjects());
313
314	painCave.isFatal = 1;
315	simError();
316	}
317
318	//read the boxMat from the comment line
319
320	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
321
322	if (eof_test == NULL) {
323	sprintf(painCave.errMsg, "error in reading commment in %s\n",
324	filename_.c_str());
325	painCave.isFatal = 1;
326	simError();
327	}
328
329	//Every single processor will parse the comment line by itself
330	//By using this way, we might lose some efficiency, but if we want to add
331	//more parameters into comment line, we only need to modify function
332	//parseCommentLine
333
334	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
335	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
336
337	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
338	int which_node = info_->getMolToProc(i);
339
340	if (which_node == masterNode) {
341	//molecules belong to master node
342
343	mol = info_->getMoleculeByGlobalIndex(i);
344
345	if (mol == NULL) {
346	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
347	painCave.isFatal = 1;
348	simError();
349	}
350
351	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
352	integrableObject = mol->nextIntegrableObject(ii)){
353
354	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
355
356	if (eof_test == NULL) {
357	sprintf(painCave.errMsg,
358	"error in reading file %s\n"
359	"natoms = %d; index = %d\n"
360	"error reading the line from the file.\n",
361	filename_.c_str(),
362	nTotObjs,
363	i);
364
365	painCave.isFatal = 1;
366	simError();
367	}
368
369	parseDumpLine(read_buffer, integrableObject);
370	}
371	} else {
372	//molecule belongs to slave nodes
373
374	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
375	MPI_COMM_WORLD, &istatus);
376
377	for(int j = 0; j < nCurObj; j++) {
378	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
379
380	if (eof_test == NULL) {
381	sprintf(painCave.errMsg,
382	"error in reading file %s\n"
383	"natoms = %d; index = %d\n"
384	"error reading the line from the file.\n",
385	filename_.c_str(),
386	nTotObjs,
387	i);
388
389	painCave.isFatal = 1;
390	simError();
391	}
392
393	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
394	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
395	}
396	}
397	}
398	} else {
399	//actions taken at slave nodes
400	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
401
402	/*@todo/
403	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
404
405	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
406	int which_node = info_->getMolToProc(i);
407
408	if (which_node == worldRank) {
409	//molecule with global index i belongs to this processor
410
411	mol = info_->getMoleculeByGlobalIndex(i);
412	if (mol == NULL) {
413	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
414	painCave.isFatal = 1;
415	simError();
416	}
417
418	nCurObj = mol->getNIntegrableObjects();
419
420	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
421	MPI_COMM_WORLD);
422
423	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
424	integrableObject = mol->nextIntegrableObject(ii)){
425
426	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
427	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
428
429	parseDumpLine(read_buffer, integrableObject);
430	}
431
432	}
433
434	}
435
436	}
437
438	#endif
439
440	}
441
442	void DumpReader::parseDumpLine(char line, StuntDouble integrableObject) {
443
444	Vector3d pos; // position place holders
445	Vector3d vel; // velocity placeholders
446	Quat4d q; // the quaternions
447	Vector3d ji; // angular velocity placeholders;
448	StringTokenizer tokenizer(line);
449	int nTokens;
450
451	nTokens = tokenizer.countTokens();
452
453	if (nTokens < 14) {
454	sprintf(painCave.errMsg,
455	"Not enough Tokens.\n");
456	painCave.isFatal = 1;
457	simError();
458	}
459
460	std::string name = tokenizer.nextToken();
461
462	if (name != integrableObject->getType()) {
463
464	}
465
466	pos[0] = tokenizer.nextTokenAsFloat();
467	pos[1] = tokenizer.nextTokenAsFloat();
468	pos[2] = tokenizer.nextTokenAsFloat();
469	integrableObject->setPos(pos);
470
471	vel[0] = tokenizer.nextTokenAsFloat();
472	vel[1] = tokenizer.nextTokenAsFloat();
473	vel[2] = tokenizer.nextTokenAsFloat();
474	integrableObject->setVel(vel);
475
476	if (integrableObject->isDirectional()) {
477
478	q[0] = tokenizer.nextTokenAsFloat();
479	q[1] = tokenizer.nextTokenAsFloat();
480	q[2] = tokenizer.nextTokenAsFloat();
481	q[3] = tokenizer.nextTokenAsFloat();
482
483	double qlen = q.length();
484	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
485
486	sprintf(painCave.errMsg,
487	"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
488	painCave.isFatal = 1;
489	simError();
490
491	}
492
493	q.normalize();
494
495	integrableObject->setQ(q);
496
497	ji[0] = tokenizer.nextTokenAsFloat();
498	ji[1] = tokenizer.nextTokenAsFloat();
499	ji[2] = tokenizer.nextTokenAsFloat();
500	integrableObject->setJ(ji);
501	}
502
503	}
504
505
506	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
507	double currTime;
508	Mat3x3d hmat;
509	double chi;
510	double integralOfChiDt;
511	Mat3x3d eta;
512
513	StringTokenizer tokenizer(line);
514	int nTokens;
515
516	nTokens = tokenizer.countTokens();
517
518	//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens)
519	if (nTokens < 10) {
520	sprintf(painCave.errMsg,
521	"Not enough tokens in comment line: %s", line);
522	painCave.isFatal = 1;
523	simError();
524	}
525
526	//read current time
527	currTime = tokenizer.nextTokenAsFloat();
528	s->setTime(currTime);
529
530	//read h-matrix
531	hmat(0, 0) = tokenizer.nextTokenAsFloat();
532	hmat(0, 1) = tokenizer.nextTokenAsFloat();
533	hmat(0, 2) = tokenizer.nextTokenAsFloat();
534	hmat(1, 0) = tokenizer.nextTokenAsFloat();
535	hmat(1, 1) = tokenizer.nextTokenAsFloat();
536	hmat(1, 2) = tokenizer.nextTokenAsFloat();
537	hmat(2, 0) = tokenizer.nextTokenAsFloat();
538	hmat(2, 1) = tokenizer.nextTokenAsFloat();
539	hmat(2, 2) = tokenizer.nextTokenAsFloat();
540	s->setHmat(hmat);
541
542	//read chi and integrablOfChidt, they should apprear in pair
543	if (tokenizer.countTokens() >= 2) {
544	chi = tokenizer.nextTokenAsFloat();
545	integralOfChiDt = tokenizer.nextTokenAsFloat();
546
547	s->setChi(chi);
548	s->setIntegralOfChiDt(integralOfChiDt);
549	}
550
551	//read eta (eta is 3x3 matrix)
552	if (tokenizer.countTokens() >= 9) {
553	eta(0, 0) = tokenizer.nextTokenAsFloat();
554	eta(0, 1) = tokenizer.nextTokenAsFloat();
555	eta(0, 2) = tokenizer.nextTokenAsFloat();
556	eta(1, 0) = tokenizer.nextTokenAsFloat();
557	eta(1, 1) = tokenizer.nextTokenAsFloat();
558	eta(1, 2) = tokenizer.nextTokenAsFloat();
559	eta(2, 0) = tokenizer.nextTokenAsFloat();
560	eta(2, 1) = tokenizer.nextTokenAsFloat();
561	eta(2, 2) = tokenizer.nextTokenAsFloat();
562
563	s->setEta(eta);
564	}
565
566
567	}
568
569	}//end namespace oopse