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 "utils/simError.h"
#include "utils/MemoryUtils.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){

#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 framePos_.size();
}

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;

#ifdef IS_MPI

    }

    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;
  typename SimInfo::MoleculeIterator mi;
  typename 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(), info_->useInitState());

    //parse dump lines

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

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

            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, integrableObjects[j]);
            
        }
    }

    // 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_->getTotIntegrableObjects());

            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(), info_->useInitState());

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

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

                mol = info_->getMoleculeByGlobalIndex(i);

                if (mol == NULL) {
                    strcpy(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(), info_->useInitState());

        for(i = 0; i < info_->getNGlobalMolecules(); i++) {
            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) {
                    strcpy(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 < ) {


    }

    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();
            
        } else if (fabs(qlen - 1.0) > oopse::epsilon) { // check that the quaternion vector is normalized
            sprintf(painCave.errMsg,
                    "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2  != 1.0).\n");
            painCave.isFatal = 0;
            simError();        
            
            q.normalize();
        }        
        integrableObject->setQ(q);
        
        ji[0] = tokenizer.nextTokenAsFloat();
        ji[1] = tokenizer.nextTokenAsFloat();
        ji[2] = tokenizer.nextTokenAsFloat();
        integrableObject->setJ(ji);
    }

}


char *DumpReader::parseCommentLine(char* line, Snapshot* s, bool useInitXSstate) {
    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();
    if (useInitXSstate) {
        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);
    
    if (useInitXSstate) {
        //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:	1784
Committed:	Wed Nov 24 22:12:12 2004 UTC (19 years, 7 months ago) by tim
File size:	16424 byte(s)
Log Message:	more get built
#	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 "utils/simError.h"
16	#include "utils/MemoryUtils.hpp"
17	#ifdef IS_MPI
18
19	#include <mpi.h>
20	#define TAKE_THIS_TAG_CHAR 0
21	#define TAKE_THIS_TAG_INT 1
22
23	#endif // is_mpi
24
25
26	namespace oopse {
27
28	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
29	: info_(info), filename_(filename), isScanned_(false){
30
31	#ifdef IS_MPI
32
33	if (worldRank == 0) {
34	#endif
35
36	inFile_ = fopen(filename_.c_str(), "r");
37
38	if (inFile_ == NULL) {
39	sprintf(painCave.errMsg, "Cannot open file: %s\n", filename_.c_str());
40	painCave.isFatal = 1;
41	simError();
42	}
43
44	#ifdef IS_MPI
45
46	}
47
48	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
49	MPIcheckPoint();
50
51	#endif
52
53	return;
54	}
55
56	DumpReader::~DumpReader() {
57
58	#ifdef IS_MPI
59
60	if (worldRank == 0) {
61	#endif
62
63	int error;
64	error = fclose(inFile_);
65
66	if (error) {
67	sprintf(painCave.errMsg, "Error closing %s\n", filename_.c_str());
68	painCave.isFatal = 1;
69	simError();
70	}
71
72	MemoryUtils::deleteVectorOfPointer(framePos_);
73
74	#ifdef IS_MPI
75
76	}
77
78	strcpy(checkPointMsg, "Dump file closed successfully.");
79	MPIcheckPoint();
80
81	#endif
82
83	return;
84	}
85
86	int DumpReader::getNFrames(void) {
87	if (!isScanned_)
88	scanFile();
89
90	return framePos_.size();
91	}
92
93	void DumpReader::scanFile(void) {
94	int i, j;
95	int lineNum = 0;
96	char readBuffer[maxBufferSize];
97	fpos_t * currPos;
98
99	#ifdef IS_MPI
100
101	if (worldRank == 0) {
102	#endif // is_mpi
103
104	rewind(inFile_);
105
106	currPos = new fpos_t;
107	fgetpos(inFile_, currPos);
108	fgets(readBuffer, sizeof(readBuffer), inFile_);
109	lineNum++;
110
111	if (feof(inFile_)) {
112	sprintf(painCave.errMsg,
113	"File \"%s\" ended unexpectedly at line %d\n",
114	filename_.c_str(),
115	lineNum);
116	painCave.isFatal = 1;
117	simError();
118	}
119
120	while (!feof(inFile_)) {
121	framePos_.push_back(currPos);
122
123	i = atoi(readBuffer);
124
125	fgets(readBuffer, sizeof(readBuffer), inFile_);
126	lineNum++;
127
128	if (feof(inFile_)) {
129	sprintf(painCave.errMsg,
130	"File \"%s\" ended unexpectedly at line %d\n",
131	filename_.c_str(),
132	lineNum);
133	painCave.isFatal = 1;
134	simError();
135	}
136
137	for(j = 0; j < i; j++) {
138	fgets(readBuffer, sizeof(readBuffer), inFile_);
139	lineNum++;
140
141	if (feof(inFile_)) {
142	sprintf(painCave.errMsg,
143	"File \"%s\" ended unexpectedly at line %d,"
144	" with atom %d\n", filename_.c_str(),
145	lineNum,
146	j);
147
148	painCave.isFatal = 1;
149	simError();
150	}
151	}
152
153	currPos = new fpos_t;
154	fgetpos(inFile_, currPos);
155	fgets(readBuffer, sizeof(readBuffer), inFile_);
156	lineNum++;
157	}
158
159	delete currPos;
160	rewind(inFile_);
161
162	isScanned_ = true;
163
164	#ifdef IS_MPI
165
166	}
167
168	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
169	MPIcheckPoint();
170
171	#endif // is_mpi
172
173	}
174
175	void DumpReader::readFrame(int whichFrame) {
176	readSet(whichFrame);
177	}
178
179	void DumpReader::readSet(int whichFrame) {
180	int i;
181	int nTotObjs; // the number of atoms
182	char read_buffer[maxBufferSize]; //the line buffer for reading
183	char * eof_test; // ptr to see when we reach the end of the file
184
185	Molecule* mol;
186	StuntDouble* integrableObject;
187	typename SimInfo::MoleculeIterator mi;
188	typename Molecule::IntegrableObjectIterator ii;
189
190	#ifndef IS_MPI
191
192	fsetpos(inFile_, framePos_[whichFrame]);
193	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
194
195	if (eof_test == NULL) {
196	sprintf(painCave.errMsg,
197	"DumpReader error: error reading 1st line of \"%s\"\n",
198	filename_.c_str());
199	painCave.isFatal = 1;
200	simError();
201	}
202
203	nTotObjs = atoi(read_buffer);
204
205	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
206	sprintf(painCave.errMsg,
207	"DumpReader error. %s nIntegrable, %d, "
208	"does not match the meta-data file's nIntegrable, %d.\n",
209	filename_.c_str(),
210	nTotObjs,
211	info_->getNIntegrableObjects());
212
213	painCave.isFatal = 1;
214	simError();
215	}
216
217	//read the box mat from the comment line
218
219	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
220
221	if (eof_test == NULL) {
222	sprintf(painCave.errMsg, "error in reading commment in %s\n",
223	filename_.c_str());
224	painCave.isFatal = 1;
225	simError();
226	}
227
228	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot(), info_->useInitState());
229
230	//parse dump lines
231
232	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
233
234	for (integrableObject = mol->beginIntegrableObject(i); integrableObject != NULL;
235	integrableObject = mol->nextIntegrableObject(i)) {
236
237	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
238
239	if (eof_test == NULL) {
240	sprintf(painCave.errMsg,
241	"error in reading file %s\n"
242	"natoms = %d; index = %d\n"
243	"error reading the line from the file.\n",
244	filename_.c_str(),
245	nTotObjs,
246	i);
247
248	painCave.isFatal = 1;
249	simError();
250	}
251
252	parseDumpLine(read_buffer, integrableObjects[j]);
253
254	}
255	}
256
257	// MPI Section of code..........
258
259	#else //IS_MPI
260
261	// first thing first, suspend fatalities.
262	int masterNode = 0;
263	int nCurObj;
264	painCave.isEventLoop = 1;
265
266	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
267	int haveError;
268
269	MPI_Status istatus;
270	int nitems;
271
272	nTotObjs = info_->getNGlobalIntegrableObjects();
273	haveError = 0;
274
275	if (worldRank == masterNode) {
276	fsetpos(inFile_, framePos_[whichFrame]);
277
278	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
279
280	if (eof_test == NULL) {
281	sprintf(painCave.errMsg, "Error reading 1st line of %s \n ",
282	filename_.c_str());
283	painCave.isFatal = 1;
284	simError();
285	}
286
287	nitems = atoi(read_buffer);
288
289	// Check to see that the number of integrable objects in the
290	// intial configuration file is the same as derived from the
291	// meta-data file.
292
293	if (nTotObjs != nitems) {
294	sprintf(painCave.errMsg,
295	"DumpReader Error. %s nIntegrable, %d, "
296	"does not match the meta-data file's nIntegrable, %d.\n",
297	filename_.c_str(),
298	nTotObjs,
299	info_->getTotIntegrableObjects());
300
301	painCave.isFatal = 1;
302	simError();
303	}
304
305	//read the boxMat from the comment line
306
307	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
308
309	if (eof_test == NULL) {
310	sprintf(painCave.errMsg, "error in reading commment in %s\n",
311	filename_.c_str());
312	painCave.isFatal = 1;
313	simError();
314	}
315
316	//Every single processor will parse the comment line by itself
317	//By using this way, we might lose some efficiency, but if we want to add
318	//more parameters into comment line, we only need to modify function
319	//parseCommentLine
320
321	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
322	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot(), info_->useInitState());
323
324	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
325	which_node = info_->getMolToProc(i);
326
327	if (which_node == masterNode) {
328	//molecules belong to master node
329
330	mol = info_->getMoleculeByGlobalIndex(i);
331
332	if (mol == NULL) {
333	strcpy(painCave.errMsg, "Molecule not found on node %d!", worldRank);
334	painCave.isFatal = 1;
335	simError();
336	}
337
338	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
339	integrableObject = mol->nextIntegrableObject(ii)){
340
341	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
342
343	if (eof_test == NULL) {
344	sprintf(painCave.errMsg,
345	"error in reading file %s\n"
346	"natoms = %d; index = %d\n"
347	"error reading the line from the file.\n",
348	filename_.c_str(),
349	nTotObjs,
350	i);
351
352	painCave.isFatal = 1;
353	simError();
354	}
355
356	parseDumpLine(read_buffer, integrableObject);
357	}
358	} else {
359	//molecule belongs to slave nodes
360
361	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
362	MPI_COMM_WORLD, &istatus);
363
364	for(int j = 0; j < nCurObj; j++) {
365	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
366
367	if (eof_test == NULL) {
368	sprintf(painCave.errMsg,
369	"error in reading file %s\n"
370	"natoms = %d; index = %d\n"
371	"error reading the line from the file.\n",
372	filename_.c_str(),
373	nTotObjs,
374	i);
375
376	painCave.isFatal = 1;
377	simError();
378	}
379
380	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
381	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
382	}
383	}
384	}
385	} else {
386	//actions taken at slave nodes
387	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
388
389	/*@todo/
390	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot(), info_->useInitState());
391
392	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
393	which_node = info_->getMolToProc(i);
394
395	if (which_node == worldRank) {
396	//molecule with global index i belongs to this processor
397
398	mol = info_->getMoleculeByGlobalIndex(i);
399	if (mol == NULL) {
400	strcpy(painCave.errMsg, "Molecule not found on node %d!", worldRank);
401	painCave.isFatal = 1;
402	simError();
403	}
404
405	nCurObj = mol->getNIntegrableObjects();
406
407	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
408	MPI_COMM_WORLD);
409
410	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
411	integrableObject = mol->nextIntegrableObject(ii)){
412
413	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
414	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
415
416	parseDumpLine(read_buffer, integrableObject);
417	}
418
419	}
420
421	}
422
423	}
424
425	#endif
426
427	}
428
429	void DumpReader::parseDumpLine(char line, StuntDouble integrableObject) {
430
431	Vector3d pos; // position place holders
432	Vector3d vel; // velocity placeholders
433	Quat4d q; // the quaternions
434	Vector3d ji; // angular velocity placeholders;
435	StringTokenizer tokenizer(line);
436	int nTokens;
437
438	nTokens = tokenizer.countTokens();
439
440	if (nTokens < ) {
441
442
443	}
444
445	std::string name = tokenizer.nextToken();
446
447	if (name != integrableObject->getType()) {
448
449	}
450
451	pos[0] = tokenizer.nextTokenAsFloat();
452	pos[1] = tokenizer.nextTokenAsFloat();
453	pos[2] = tokenizer.nextTokenAsFloat();
454	integrableObject->setPos(pos);
455
456	vel[0] = tokenizer.nextTokenAsFloat();
457	vel[1] = tokenizer.nextTokenAsFloat();
458	vel[2] = tokenizer.nextTokenAsFloat();
459	integrableObject->setVel(vel);
460
461	if (integrableObject->isDirectional()) {
462	q[0] = tokenizer.nextTokenAsFloat();
463	q[1] = tokenizer.nextTokenAsFloat();
464	q[2] = tokenizer.nextTokenAsFloat();
465	q[3] = tokenizer.nextTokenAsFloat();
466
467	double qlen = q.length();
468	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
469
470	sprintf(painCave.errMsg,
471	"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
472	painCave.isFatal = 1;
473	simError();
474
475	} else if (fabs(qlen - 1.0) > oopse::epsilon) { // check that the quaternion vector is normalized
476	sprintf(painCave.errMsg,
477	"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 != 1.0).\n");
478	painCave.isFatal = 0;
479	simError();
480
481	q.normalize();
482	}
483	integrableObject->setQ(q);
484
485	ji[0] = tokenizer.nextTokenAsFloat();
486	ji[1] = tokenizer.nextTokenAsFloat();
487	ji[2] = tokenizer.nextTokenAsFloat();
488	integrableObject->setJ(ji);
489	}
490
491	}
492
493
494	char DumpReader::parseCommentLine(char line, Snapshot* s, bool useInitXSstate) {
495	double currTime;
496	Mat3x3d hmat;
497	double chi;
498	double integralOfChiDt;
499	Mat3x3d eta;
500
501	StringTokenizer tokenizer(line);
502	int nTokens;
503
504	nTokens = tokenizer.countTokens();
505
506	//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens)
507	if (nTokens < 10) {
508	sprintf(painCave.errMsg,
509	"Not enough tokens in comment line: %s", line);
510	painCave.isFatal = 1;
511	simError();
512	}
513
514	//read current time
515	currTime = tokenizer.nextTokenAsFloat();
516	if (useInitXSstate) {
517	s->setTime(currTime);
518	}
519
520	//read h-matrix
521	hmat(0, 0) = tokenizer.nextTokenAsFloat();
522	hmat(0, 1) = tokenizer.nextTokenAsFloat();
523	hmat(0, 2) = tokenizer.nextTokenAsFloat();
524	hmat(1, 0) = tokenizer.nextTokenAsFloat();
525	hmat(1, 1) = tokenizer.nextTokenAsFloat();
526	hmat(1, 2) = tokenizer.nextTokenAsFloat();
527	hmat(2, 0) = tokenizer.nextTokenAsFloat();
528	hmat(2, 1) = tokenizer.nextTokenAsFloat();
529	hmat(2, 2) = tokenizer.nextTokenAsFloat();
530	s->setHmat(hmat);
531
532	if (useInitXSstate) {
533	//read chi and integrablOfChidt, they should apprear in pair
534	if (tokenizer.countTokens() >= 2) {
535	chi = tokenizer.nextTokenAsFloat();
536	integralOfChiDt = tokenizer.nextTokenAsFloat();
537
538	s->setChi(chi);
539	s->setIntegralOfChiDt(integralOfChiDt);
540	}
541
542	//read eta (eta is 3x3 matrix)
543	if (tokenizer.countTokens() >= 9) {
544	eta(0, 0) = tokenizer.nextTokenAsFloat();
545	eta(0, 1) = tokenizer.nextTokenAsFloat();
546	eta(0, 2) = tokenizer.nextTokenAsFloat();
547	eta(1, 0) = tokenizer.nextTokenAsFloat();
548	eta(1, 1) = tokenizer.nextTokenAsFloat();
549	eta(1, 2) = tokenizer.nextTokenAsFloat();
550	eta(2, 0) = tokenizer.nextTokenAsFloat();
551	eta(2, 1) = tokenizer.nextTokenAsFloat();
552	eta(2, 2) = tokenizer.nextTokenAsFloat();
553
554	s->setEta(eta);
555	}
556	}
557
558
559	}
560
561	}//end namespace oopse