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.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:	1901
Committed:	Tue Jan 4 22:18:36 2005 UTC (19 years, 6 months ago) by tim
File size:	16235 byte(s)
Log Message:	constraints in progress
#	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
91	if (!isScanned_)
92	scanFile();
93
94	return nframes_;
95	}
96
97	void DumpReader::scanFile(void) {
98	int i, j;
99	int lineNum = 0;
100	char readBuffer[maxBufferSize];
101	fpos_t * currPos;
102
103	#ifdef IS_MPI
104
105	if (worldRank == 0) {
106	#endif // is_mpi
107
108	rewind(inFile_);
109
110	currPos = new fpos_t;
111	fgetpos(inFile_, currPos);
112	fgets(readBuffer, sizeof(readBuffer), inFile_);
113	lineNum++;
114
115	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
124	while (!feof(inFile_)) {
125	framePos_.push_back(currPos);
126
127	i = atoi(readBuffer);
128
129	fgets(readBuffer, sizeof(readBuffer), inFile_);
130	lineNum++;
131
132	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
141	for(j = 0; j < i; j++) {
142	fgets(readBuffer, sizeof(readBuffer), inFile_);
143	lineNum++;
144
145	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
152	painCave.isFatal = 1;
153	simError();
154	}
155	}
156
157	currPos = new fpos_t;
158	fgetpos(inFile_, currPos);
159	fgets(readBuffer, sizeof(readBuffer), inFile_);
160	lineNum++;
161	}
162
163	delete currPos;
164	rewind(inFile_);
165
166	nframes_ = framePos_.size();
167	#ifdef IS_MPI
168	}
169
170	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
171
172	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
173	MPIcheckPoint();
174
175	#endif // is_mpi
176
177	isScanned_ = true;
178	}
179
180	void DumpReader::readFrame(int whichFrame) {
181	readSet(whichFrame);
182	}
183
184	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
190	Molecule* mol;
191	StuntDouble* integrableObject;
192	SimInfo::MoleculeIterator mi;
193	Molecule::IntegrableObjectIterator ii;
194
195	#ifndef IS_MPI
196
197	fsetpos(inFile_, framePos_[whichFrame]);
198	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
199
200	if (eof_test == NULL) {
201	sprintf(painCave.errMsg,
202	"DumpReader error: error reading 1st line of \"%s\"\n",
203	filename_.c_str());
204	painCave.isFatal = 1;
205	simError();
206	}
207
208	nTotObjs = atoi(read_buffer);
209
210	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
218	painCave.isFatal = 1;
219	simError();
220	}
221
222	//read the box mat from the comment line
223
224	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
225
226	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	}
232
233	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
234
235	//parse dump lines
236
237	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
238
239	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
240	integrableObject = mol->nextIntegrableObject(ii)) {
241
242	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
243
244	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
253	painCave.isFatal = 1;
254	simError();
255	}
256
257	parseDumpLine(read_buffer, integrableObject);
258
259	}
260	}
261
262	// MPI Section of code..........
263
264	#else //IS_MPI
265
266	// first thing first, suspend fatalities.
267	int masterNode = 0;
268	int nCurObj;
269	painCave.isEventLoop = 1;
270
271	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
272	int haveError;
273
274	MPI_Status istatus;
275	int nitems;
276
277	nTotObjs = info_->getNGlobalIntegrableObjects();
278	haveError = 0;
279
280	if (worldRank == masterNode) {
281	fsetpos(inFile_, framePos_[whichFrame]);
282
283	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
284
285	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
292	nitems = atoi(read_buffer);
293
294	// 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
298	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	info_->getNGlobalIntegrableObjects());
305
306	painCave.isFatal = 1;
307	simError();
308	}
309
310	//read the boxMat from the comment line
311
312	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
313
314	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	}
320
321	//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
326	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
327	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
328
329	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
330	int which_node = info_->getMolToProc(i);
331
332	if (which_node == masterNode) {
333	//molecules belong to master node
334
335	mol = info_->getMoleculeByGlobalIndex(i);
336
337	if (mol == NULL) {
338	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
339	painCave.isFatal = 1;
340	simError();
341	}
342
343	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
344	integrableObject = mol->nextIntegrableObject(ii)){
345
346	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
347
348	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
357	painCave.isFatal = 1;
358	simError();
359	}
360
361	parseDumpLine(read_buffer, integrableObject);
362	}
363	} else {
364	//molecule belongs to slave nodes
365
366	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
367	MPI_COMM_WORLD, &istatus);
368
369	for(int j = 0; j < nCurObj; j++) {
370	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
371
372	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
381	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
394	/*@todo/
395	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
396
397	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
398	int which_node = info_->getMolToProc(i);
399
400	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	sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
406	painCave.isFatal = 1;
407	simError();
408	}
409
410	nCurObj = mol->getNIntegrableObjects();
411
412	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
413	MPI_COMM_WORLD);
414
415	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
421	parseDumpLine(read_buffer, integrableObject);
422	}
423
424	}
425
426	}
427
428	}
429
430	#endif
431
432	}
433
434	void DumpReader::parseDumpLine(char line, StuntDouble integrableObject) {
435
436	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
445	if (nTokens < 14) {
446	sprintf(painCave.errMsg,
447	"Not enough Tokens.\n");
448	painCave.isFatal = 1;
449	simError();
450	}
451
452	std::string name = tokenizer.nextToken();
453
454	if (name != integrableObject->getType()) {
455
456	}
457
458	pos[0] = tokenizer.nextTokenAsDouble();
459	pos[1] = tokenizer.nextTokenAsDouble();
460	pos[2] = tokenizer.nextTokenAsDouble();
461	integrableObject->setPos(pos);
462
463	vel[0] = tokenizer.nextTokenAsDouble();
464	vel[1] = tokenizer.nextTokenAsDouble();
465	vel[2] = tokenizer.nextTokenAsDouble();
466	integrableObject->setVel(vel);
467
468	if (integrableObject->isDirectional()) {
469
470	q[0] = tokenizer.nextTokenAsDouble();
471	q[1] = tokenizer.nextTokenAsDouble();
472	q[2] = tokenizer.nextTokenAsDouble();
473	q[3] = tokenizer.nextTokenAsDouble();
474
475	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	}
484
485	q.normalize();
486
487	integrableObject->setQ(q);
488
489	ji[0] = tokenizer.nextTokenAsDouble();
490	ji[1] = tokenizer.nextTokenAsDouble();
491	ji[2] = tokenizer.nextTokenAsDouble();
492	integrableObject->setJ(ji);
493	}
494
495	}
496
497
498	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
499	double currTime;
500	Mat3x3d hmat;
501	double chi;
502	double integralOfChiDt;
503	Mat3x3d eta;
504
505	StringTokenizer tokenizer(line);
506	int nTokens;
507
508	nTokens = tokenizer.countTokens();
509
510	//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	}
517
518	//read current time
519	currTime = tokenizer.nextTokenAsDouble();
520	s->setTime(currTime);
521
522	//read h-matrix
523	hmat(0, 0) = tokenizer.nextTokenAsDouble();
524	hmat(0, 1) = tokenizer.nextTokenAsDouble();
525	hmat(0, 2) = tokenizer.nextTokenAsDouble();
526	hmat(1, 0) = tokenizer.nextTokenAsDouble();
527	hmat(1, 1) = tokenizer.nextTokenAsDouble();
528	hmat(1, 2) = tokenizer.nextTokenAsDouble();
529	hmat(2, 0) = tokenizer.nextTokenAsDouble();
530	hmat(2, 1) = tokenizer.nextTokenAsDouble();
531	hmat(2, 2) = tokenizer.nextTokenAsDouble();
532	s->setHmat(hmat);
533
534	//read chi and integrablOfChidt, they should apprear in pair
535	if (tokenizer.countTokens() >= 2) {
536	chi = tokenizer.nextTokenAsDouble();
537	integralOfChiDt = tokenizer.nextTokenAsDouble();
538
539	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.nextTokenAsDouble();
546	eta(0, 1) = tokenizer.nextTokenAsDouble();
547	eta(0, 2) = tokenizer.nextTokenAsDouble();
548	eta(1, 0) = tokenizer.nextTokenAsDouble();
549	eta(1, 1) = tokenizer.nextTokenAsDouble();
550	eta(1, 2) = tokenizer.nextTokenAsDouble();
551	eta(2, 0) = tokenizer.nextTokenAsDouble();
552	eta(2, 1) = tokenizer.nextTokenAsDouble();
553	eta(2, 2) = tokenizer.nextTokenAsDouble();
554
555	s->setEta(eta);
556	}
557
558
559	}
560
561	}//end namespace oopse