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"
#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", in_name);
            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:	1739
Committed:	Mon Nov 15 18:02:15 2004 UTC (20 years, 11 months ago) by tim
File size:	16409 byte(s)
Log Message:	finish DumpReader, DumpWriter.Next Step is LJFF and integrators
#	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	1492	#include "utils/simError.h"
16	tim	1739	#include "utils/MemoryUtils"
17			#ifdef IS_MPI
18	gezelter	1490
19			#include <mpi.h>
20			#define TAKE_THIS_TAG_CHAR 0
21			#define TAKE_THIS_TAG_INT 1
22	tim	1739
23	gezelter	1490	#endif // is_mpi
24
25
26	tim	1739	namespace oopse {
27	gezelter	1490
28	tim	1739	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
29			: info_(info), filename_(filename), isScanned_(false){
30	gezelter	1490
31			#ifdef IS_MPI
32	tim	1739
33			if (worldRank == 0) {
34	gezelter	1490	#endif
35
36	tim	1739	inFile_ = fopen(filename_.c_str(), "r");
37
38			if (inFile_ == NULL) {
39			sprintf(painCave.errMsg, "Cannot open file: %s\n", in_name);
40			painCave.isFatal = 1;
41			simError();
42			}
43
44	gezelter	1490	#ifdef IS_MPI
45	tim	1739
46			}
47
48			strcpy(checkPointMsg, "Dump file opened for reading successfully.");
49			MPIcheckPoint();
50
51	gezelter	1490	#endif
52	tim	1739
53			return;
54	gezelter	1490	}
55
56	tim	1739	DumpReader::~DumpReader() {
57
58	gezelter	1490	#ifdef IS_MPI
59	tim	1739
60			if (worldRank == 0) {
61	gezelter	1490	#endif
62
63	tim	1739	int error;
64			error = fclose(inFile_);
65	gezelter	1490
66	tim	1739	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	gezelter	1490	#ifdef IS_MPI
75	tim	1739
76			}
77
78			strcpy(checkPointMsg, "Dump file closed successfully.");
79			MPIcheckPoint();
80
81	gezelter	1490	#endif
82
83	tim	1739	return;
84	gezelter	1490	}
85
86	tim	1739	int DumpReader::getNFrames(void) {
87			if (!isScanned_)
88			scanFile();
89	gezelter	1490
90	tim	1739	return framePos_.size();
91	gezelter	1490	}
92
93	tim	1739	void DumpReader::scanFile(void) {
94	gezelter	1490	int i, j;
95			int lineNum = 0;
96	tim	1739	char readBuffer[maxBufferSize];
97			fpos_t * currPos;
98	gezelter	1490
99			#ifdef IS_MPI
100
101	tim	1739	if (worldRank == 0) {
102	gezelter	1490	#endif // is_mpi
103
104	tim	1739	rewind(inFile_);
105	gezelter	1490
106	tim	1739	currPos = new fpos_t;
107			fgetpos(inFile_, currPos);
108			fgets(readBuffer, sizeof(readBuffer), inFile_);
109			lineNum++;
110	gezelter	1490
111	tim	1739	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	gezelter	1490
120	tim	1739	while (!feof(inFile_)) {
121			framePos_.push_back(currPos);
122	gezelter	1490
123	tim	1739	i = atoi(readBuffer);
124	gezelter	1490
125	tim	1739	fgets(readBuffer, sizeof(readBuffer), inFile_);
126			lineNum++;
127	gezelter	1490
128	tim	1739	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	gezelter	1490
137	tim	1739	for(j = 0; j < i; j++) {
138			fgets(readBuffer, sizeof(readBuffer), inFile_);
139			lineNum++;
140	gezelter	1490
141	tim	1739	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	gezelter	1490
148	tim	1739	painCave.isFatal = 1;
149			simError();
150			}
151			}
152	gezelter	1490
153	tim	1739	currPos = new fpos_t;
154			fgetpos(inFile_, currPos);
155			fgets(readBuffer, sizeof(readBuffer), inFile_);
156			lineNum++;
157			}
158	gezelter	1490
159	tim	1739	delete currPos;
160			rewind(inFile_);
161	gezelter	1490
162	tim	1739	isScanned = true;
163	gezelter	1490
164	tim	1739	#ifdef IS_MPI
165	gezelter	1490
166	tim	1739	}
167	gezelter	1490
168	tim	1739	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
169			MPIcheckPoint();
170	gezelter	1490
171	tim	1739	#endif // is_mpi
172	gezelter	1490
173	tim	1739	}
174	gezelter	1490
175	tim	1739	void DumpReader::readFrame(int whichFrame) {
176			readSet(whichFrame);
177			}
178	gezelter	1490
179	tim	1739	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	gezelter	1490
185	tim	1739	Molecule* mol;
186			StuntDouble* integrableObject;
187			typename SimInfo::MoleculeIterator mi;
188			typename Molecule::IntegrableObjectIterator ii;
189	gezelter	1490
190	tim	1739	#ifndef IS_MPI
191	gezelter	1490
192	tim	1739	fsetpos(inFile_, framePos_[whichFrame]);
193			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
194	gezelter	1490
195	tim	1739	if (eof_test == NULL) {
196	gezelter	1490	sprintf(painCave.errMsg,
197	tim	1739	"DumpReader error: error reading 1st line of \"%s\"\n",
198			filename_.c_str());
199	gezelter	1490	painCave.isFatal = 1;
200			simError();
201			}
202
203	tim	1739	nTotObjs = atoi(read_buffer);
204	gezelter	1490
205	tim	1739	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	gezelter	1490
213	tim	1739	painCave.isFatal = 1;
214			simError();
215			}
216	gezelter	1490
217	tim	1739	//read the box mat from the comment line
218	gezelter	1490
219	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
220	gezelter	1490
221	tim	1739	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	gezelter	1490	}
227
228	tim	1739	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot(), info_->useInitState());
229	gezelter	1490
230	tim	1739	//parse dump lines
231	gezelter	1490
232	tim	1739	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
233	gezelter	1490
234	tim	1739	for (integrableObject = mol->beginIntegrableObject(i); integrableObject != NULL;
235			integrableObject = mol->nextIntegrableObject(i)) {
236	gezelter	1490
237	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
238	gezelter	1490
239	tim	1739	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	gezelter	1490
248	tim	1739	painCave.isFatal = 1;
249			simError();
250			}
251	gezelter	1490
252	tim	1739	parseDumpLine(read_buffer, integrableObjects[j]);
253
254			}
255	gezelter	1490	}
256
257	tim	1739	// MPI Section of code..........
258	gezelter	1490
259	tim	1739	#else //IS_MPI
260	gezelter	1490
261	tim	1739	// first thing first, suspend fatalities.
262			int masterNode = 0;
263			int nCurObj;
264			painCave.isEventLoop = 1;
265	gezelter	1490
266	tim	1739	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
267			int haveError;
268	gezelter	1490
269	tim	1739	MPI_Status istatus;
270			int nitems;
271	gezelter	1490
272	tim	1739	nTotObjs = info_->getNGlobalIntegrableObjects();
273			haveError = 0;
274	gezelter	1490
275	tim	1739	if (worldRank == masterNode) {
276			fsetpos(inFile_, framePos_[whichFrame]);
277	gezelter	1490
278	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
279	gezelter	1490
280	tim	1739	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	gezelter	1490
287	tim	1739	nitems = atoi(read_buffer);
288	gezelter	1490
289	tim	1739	// 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	gezelter	1490
293	tim	1739	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	gezelter	1490
301	tim	1739	painCave.isFatal = 1;
302			simError();
303	gezelter	1490	}
304
305	tim	1739	//read the boxMat from the comment line
306	gezelter	1490
307	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
308	gezelter	1490
309	tim	1739	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	gezelter	1490	}
315
316	tim	1739	//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	gezelter	1490
321	tim	1739	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
322			parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot(), info_->useInitState());
323	gezelter	1490
324	tim	1739	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
325			which_node = info_->getMolToProc(i);
326	gezelter	1490
327	tim	1739	if (which_node == masterNode) {
328			//molecules belong to master node
329	gezelter	1490
330	tim	1739	mol = info_->getMoleculeByGlobalIndex(i);
331	gezelter	1490
332	tim	1739	if (mol == NULL) {
333			strcpy(painCave.errMsg, "Molecule not found on node %d!", worldRank);
334			painCave.isFatal = 1;
335			simError();
336			}
337	gezelter	1490
338	tim	1739	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
339			integrableObject = mol->nextIntegrableObject(ii)){
340
341			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
342	gezelter	1490
343	tim	1739	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	gezelter	1490
352	tim	1739	painCave.isFatal = 1;
353			simError();
354			}
355	gezelter	1490
356	tim	1739	parseDumpLine(read_buffer, integrableObject);
357			}
358			} else {
359			//molecule belongs to slave nodes
360	gezelter	1490
361	tim	1739	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
362			MPI_COMM_WORLD, &istatus);
363	gezelter	1490
364	tim	1739	for(int j = 0; j < nCurObj; j++) {
365			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
366	gezelter	1490
367	tim	1739	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	gezelter	1490
376	tim	1739	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	gezelter	1490
389	tim	1739	/*@todo/
390			parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot(), info_->useInitState());
391	gezelter	1490
392	tim	1739	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
393			which_node = info_->getMolToProc(i);
394	gezelter	1490
395	tim	1739	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	gezelter	1490
407	tim	1739	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
408			MPI_COMM_WORLD);
409	gezelter	1490
410	tim	1739	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	gezelter	1490
416	tim	1739	parseDumpLine(read_buffer, integrableObject);
417			}
418
419			}
420
421			}
422
423			}
424	gezelter	1490
425	tim	1739	#endif
426	gezelter	1490
427	tim	1739	}
428	gezelter	1490
429	tim	1739	void DumpReader::parseDumpLine(char line, StuntDouble integrableObject) {
430	gezelter	1490
431	tim	1739	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	gezelter	1490
440	tim	1739	if (nTokens < ) {
441	gezelter	1490
442
443			}
444
445	tim	1739	std::string name = tokenizer.nextToken();
446	gezelter	1490
447	tim	1739	if (name != integrableObject->getType()) {
448
449	gezelter	1490	}
450
451	tim	1739	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	gezelter	1490
461	tim	1739	if (integrableObject->isDirectional()) {
462			q[0] = tokenizer.nextTokenAsFloat();
463			q[1] = tokenizer.nextTokenAsFloat();
464			q[2] = tokenizer.nextTokenAsFloat();
465			q[3] = tokenizer.nextTokenAsFloat();
466	gezelter	1490
467	tim	1739	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	gezelter	1490	}
490
491			}
492
493
494	tim	1739	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	gezelter	1490
501	tim	1739	StringTokenizer tokenizer(line);
502			int nTokens;
503	gezelter	1490
504	tim	1739	nTokens = tokenizer.countTokens();
505	gezelter	1490
506	tim	1739	//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	gezelter	1490	}
513
514	tim	1739	//read current time
515			currTime = tokenizer.nextTokenAsFloat();
516			if (useInitXSstate) {
517			s->setTime(currTime);
518	gezelter	1490	}
519
520	tim	1739	//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	gezelter	1490
532	tim	1739	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	gezelter	1490
538	tim	1739	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	gezelter	1490
554	tim	1739	s->setEta(eta);
555			}
556			}
557	gezelter	1490
558	tim	1739
559	gezelter	1490	}
560
561	tim	1739	}//end namespace oopse