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){

#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;
  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_->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());

        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());

        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 < 14) {
            sprintf(painCave.errMsg,
                    "Not enough Tokens.\n");
            painCave.isFatal = 1;
            simError();
    }

    std::string name = tokenizer.nextToken();

    if (name != integrableObject->getType()) {
        
    }

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

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

        double qlen = q.length();
        if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
            
            sprintf(painCave.errMsg,
                    "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
            painCave.isFatal = 1;
            simError();
            
        } 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);
    }

}


void DumpReader::parseCommentLine(char* line, Snapshot* s) {
    double currTime;
    Mat3x3d hmat;
    double chi;
    double integralOfChiDt;
    Mat3x3d eta;

    StringTokenizer tokenizer(line);
    int nTokens;

    nTokens = tokenizer.countTokens();

    //comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
    if (nTokens < 10) {
            sprintf(painCave.errMsg,
                    "Not enough tokens in comment line: %s", line);
            painCave.isFatal = 1;
            simError();   
    }

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

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

        s->setEta(eta);
    }

    
}

}//end namespace oopse
Revision:	1808
Committed:	Tue Nov 30 23:14:29 2004 UTC (19 years, 9 months ago) by tim
File size:	16387 byte(s)
Log Message:	io get built, next is integrator
#	User	Rev	Content
1	gezelter	1490	#define _LARGEFILE_SOURCE64
2			#define _FILE_OFFSET_BITS 64
3
4			#include <sys/types.h>
5			#include <sys/stat.h>
6
7			#include <iostream>
8			#include <math.h>
9
10			#include <stdio.h>
11			#include <stdlib.h>
12			#include <string.h>
13
14	tim	1739	#include "io/DumpReader.hpp"
15	tim	1808	#include "primitives/Molecule.hpp"
16	tim	1492	#include "utils/simError.h"
17	tim	1784	#include "utils/MemoryUtils.hpp"
18	tim	1808	#include "utils/StringTokenizer.hpp"
19
20	tim	1739	#ifdef IS_MPI
21	gezelter	1490
22			#include <mpi.h>
23			#define TAKE_THIS_TAG_CHAR 0
24			#define TAKE_THIS_TAG_INT 1
25	tim	1739
26	gezelter	1490	#endif // is_mpi
27
28
29	tim	1739	namespace oopse {
30	gezelter	1490
31	tim	1739	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
32			: info_(info), filename_(filename), isScanned_(false){
33	gezelter	1490
34			#ifdef IS_MPI
35	tim	1739
36			if (worldRank == 0) {
37	gezelter	1490	#endif
38
39	tim	1739	inFile_ = fopen(filename_.c_str(), "r");
40
41			if (inFile_ == NULL) {
42	tim	1784	sprintf(painCave.errMsg, "Cannot open file: %s\n", filename_.c_str());
43	tim	1739	painCave.isFatal = 1;
44			simError();
45			}
46
47	gezelter	1490	#ifdef IS_MPI
48	tim	1739
49			}
50
51			strcpy(checkPointMsg, "Dump file opened for reading successfully.");
52			MPIcheckPoint();
53
54	gezelter	1490	#endif
55	tim	1739
56			return;
57	gezelter	1490	}
58
59	tim	1739	DumpReader::~DumpReader() {
60
61	gezelter	1490	#ifdef IS_MPI
62	tim	1739
63			if (worldRank == 0) {
64	gezelter	1490	#endif
65
66	tim	1739	int error;
67			error = fclose(inFile_);
68	gezelter	1490
69	tim	1739	if (error) {
70			sprintf(painCave.errMsg, "Error closing %s\n", filename_.c_str());
71			painCave.isFatal = 1;
72			simError();
73			}
74
75			MemoryUtils::deleteVectorOfPointer(framePos_);
76
77	gezelter	1490	#ifdef IS_MPI
78	tim	1739
79			}
80
81			strcpy(checkPointMsg, "Dump file closed successfully.");
82			MPIcheckPoint();
83
84	gezelter	1490	#endif
85
86	tim	1739	return;
87	gezelter	1490	}
88
89	tim	1739	int DumpReader::getNFrames(void) {
90			if (!isScanned_)
91			scanFile();
92	gezelter	1490
93	tim	1739	return framePos_.size();
94	gezelter	1490	}
95
96	tim	1739	void DumpReader::scanFile(void) {
97	gezelter	1490	int i, j;
98			int lineNum = 0;
99	tim	1739	char readBuffer[maxBufferSize];
100			fpos_t * currPos;
101	gezelter	1490
102			#ifdef IS_MPI
103
104	tim	1739	if (worldRank == 0) {
105	gezelter	1490	#endif // is_mpi
106
107	tim	1739	rewind(inFile_);
108	gezelter	1490
109	tim	1739	currPos = new fpos_t;
110			fgetpos(inFile_, currPos);
111			fgets(readBuffer, sizeof(readBuffer), inFile_);
112			lineNum++;
113	gezelter	1490
114	tim	1739	if (feof(inFile_)) {
115			sprintf(painCave.errMsg,
116			"File \"%s\" ended unexpectedly at line %d\n",
117			filename_.c_str(),
118			lineNum);
119			painCave.isFatal = 1;
120			simError();
121			}
122	gezelter	1490
123	tim	1739	while (!feof(inFile_)) {
124			framePos_.push_back(currPos);
125	gezelter	1490
126	tim	1739	i = atoi(readBuffer);
127	gezelter	1490
128	tim	1739	fgets(readBuffer, sizeof(readBuffer), inFile_);
129			lineNum++;
130	gezelter	1490
131	tim	1739	if (feof(inFile_)) {
132			sprintf(painCave.errMsg,
133			"File \"%s\" ended unexpectedly at line %d\n",
134			filename_.c_str(),
135			lineNum);
136			painCave.isFatal = 1;
137			simError();
138			}
139	gezelter	1490
140	tim	1739	for(j = 0; j < i; j++) {
141			fgets(readBuffer, sizeof(readBuffer), inFile_);
142			lineNum++;
143	gezelter	1490
144	tim	1739	if (feof(inFile_)) {
145			sprintf(painCave.errMsg,
146			"File \"%s\" ended unexpectedly at line %d,"
147			" with atom %d\n", filename_.c_str(),
148			lineNum,
149			j);
150	gezelter	1490
151	tim	1739	painCave.isFatal = 1;
152			simError();
153			}
154			}
155	gezelter	1490
156	tim	1739	currPos = new fpos_t;
157			fgetpos(inFile_, currPos);
158			fgets(readBuffer, sizeof(readBuffer), inFile_);
159			lineNum++;
160			}
161	gezelter	1490
162	tim	1739	delete currPos;
163			rewind(inFile_);
164	gezelter	1490
165	tim	1784	isScanned_ = true;
166	gezelter	1490
167	tim	1739	#ifdef IS_MPI
168	gezelter	1490
169	tim	1739	}
170	gezelter	1490
171	tim	1739	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
172			MPIcheckPoint();
173	gezelter	1490
174	tim	1739	#endif // is_mpi
175	gezelter	1490
176	tim	1739	}
177	gezelter	1490
178	tim	1739	void DumpReader::readFrame(int whichFrame) {
179			readSet(whichFrame);
180			}
181	gezelter	1490
182	tim	1739	void DumpReader::readSet(int whichFrame) {
183			int i;
184			int nTotObjs; // the number of atoms
185			char read_buffer[maxBufferSize]; //the line buffer for reading
186			char * eof_test; // ptr to see when we reach the end of the file
187	gezelter	1490
188	tim	1739	Molecule* mol;
189			StuntDouble* integrableObject;
190	tim	1808	SimInfo::MoleculeIterator mi;
191			Molecule::IntegrableObjectIterator ii;
192	gezelter	1490
193	tim	1739	#ifndef IS_MPI
194	gezelter	1490
195	tim	1739	fsetpos(inFile_, framePos_[whichFrame]);
196			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
197	gezelter	1490
198	tim	1739	if (eof_test == NULL) {
199	gezelter	1490	sprintf(painCave.errMsg,
200	tim	1739	"DumpReader error: error reading 1st line of \"%s\"\n",
201			filename_.c_str());
202	gezelter	1490	painCave.isFatal = 1;
203			simError();
204			}
205
206	tim	1739	nTotObjs = atoi(read_buffer);
207	gezelter	1490
208	tim	1739	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
209			sprintf(painCave.errMsg,
210			"DumpReader error. %s nIntegrable, %d, "
211			"does not match the meta-data file's nIntegrable, %d.\n",
212			filename_.c_str(),
213			nTotObjs,
214			info_->getNIntegrableObjects());
215	gezelter	1490
216	tim	1739	painCave.isFatal = 1;
217			simError();
218			}
219	gezelter	1490
220	tim	1739	//read the box mat from the comment line
221	gezelter	1490
222	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
223	gezelter	1490
224	tim	1739	if (eof_test == NULL) {
225			sprintf(painCave.errMsg, "error in reading commment in %s\n",
226			filename_.c_str());
227			painCave.isFatal = 1;
228			simError();
229	gezelter	1490	}
230
231	tim	1808	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
232	gezelter	1490
233	tim	1739	//parse dump lines
234	gezelter	1490
235	tim	1739	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
236	gezelter	1490
237	tim	1808	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
238			integrableObject = mol->nextIntegrableObject(ii)) {
239	gezelter	1490
240	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
241	gezelter	1490
242	tim	1739	if (eof_test == NULL) {
243			sprintf(painCave.errMsg,
244			"error in reading file %s\n"
245			"natoms = %d; index = %d\n"
246			"error reading the line from the file.\n",
247			filename_.c_str(),
248			nTotObjs,
249			i);
250	gezelter	1490
251	tim	1739	painCave.isFatal = 1;
252			simError();
253			}
254	gezelter	1490
255	tim	1808	parseDumpLine(read_buffer, integrableObject);
256	tim	1739
257	tim	1808	}
258	gezelter	1490	}
259
260	tim	1739	// MPI Section of code..........
261	gezelter	1490
262	tim	1739	#else //IS_MPI
263	gezelter	1490
264	tim	1739	// first thing first, suspend fatalities.
265			int masterNode = 0;
266			int nCurObj;
267			painCave.isEventLoop = 1;
268	gezelter	1490
269	tim	1739	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
270			int haveError;
271	gezelter	1490
272	tim	1739	MPI_Status istatus;
273			int nitems;
274	gezelter	1490
275	tim	1739	nTotObjs = info_->getNGlobalIntegrableObjects();
276			haveError = 0;
277	gezelter	1490
278	tim	1739	if (worldRank == masterNode) {
279			fsetpos(inFile_, framePos_[whichFrame]);
280	gezelter	1490
281	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
282	gezelter	1490
283	tim	1739	if (eof_test == NULL) {
284			sprintf(painCave.errMsg, "Error reading 1st line of %s \n ",
285			filename_.c_str());
286			painCave.isFatal = 1;
287			simError();
288			}
289	gezelter	1490
290	tim	1739	nitems = atoi(read_buffer);
291	gezelter	1490
292	tim	1739	// Check to see that the number of integrable objects in the
293			// intial configuration file is the same as derived from the
294			// meta-data file.
295	gezelter	1490
296	tim	1739	if (nTotObjs != nitems) {
297			sprintf(painCave.errMsg,
298			"DumpReader Error. %s nIntegrable, %d, "
299			"does not match the meta-data file's nIntegrable, %d.\n",
300			filename_.c_str(),
301			nTotObjs,
302			info_->getTotIntegrableObjects());
303	gezelter	1490
304	tim	1739	painCave.isFatal = 1;
305			simError();
306	gezelter	1490	}
307
308	tim	1739	//read the boxMat from the comment line
309	gezelter	1490
310	tim	1739	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
311	gezelter	1490
312	tim	1739	if (eof_test == NULL) {
313			sprintf(painCave.errMsg, "error in reading commment in %s\n",
314			filename_.c_str());
315			painCave.isFatal = 1;
316			simError();
317	gezelter	1490	}
318
319	tim	1739	//Every single processor will parse the comment line by itself
320			//By using this way, we might lose some efficiency, but if we want to add
321			//more parameters into comment line, we only need to modify function
322			//parseCommentLine
323	gezelter	1490
324	tim	1739	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
325	tim	1808	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
326	gezelter	1490
327	tim	1739	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
328			which_node = info_->getMolToProc(i);
329	gezelter	1490
330	tim	1739	if (which_node == masterNode) {
331			//molecules belong to master node
332	gezelter	1490
333	tim	1739	mol = info_->getMoleculeByGlobalIndex(i);
334	gezelter	1490
335	tim	1739	if (mol == NULL) {
336			strcpy(painCave.errMsg, "Molecule not found on node %d!", worldRank);
337			painCave.isFatal = 1;
338			simError();
339			}
340	gezelter	1490
341	tim	1739	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
342			integrableObject = mol->nextIntegrableObject(ii)){
343
344			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
345	gezelter	1490
346	tim	1739	if (eof_test == NULL) {
347			sprintf(painCave.errMsg,
348			"error in reading file %s\n"
349			"natoms = %d; index = %d\n"
350			"error reading the line from the file.\n",
351			filename_.c_str(),
352			nTotObjs,
353			i);
354	gezelter	1490
355	tim	1739	painCave.isFatal = 1;
356			simError();
357			}
358	gezelter	1490
359	tim	1739	parseDumpLine(read_buffer, integrableObject);
360			}
361			} else {
362			//molecule belongs to slave nodes
363	gezelter	1490
364	tim	1739	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
365			MPI_COMM_WORLD, &istatus);
366	gezelter	1490
367	tim	1739	for(int j = 0; j < nCurObj; j++) {
368			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
369	gezelter	1490
370	tim	1739	if (eof_test == NULL) {
371			sprintf(painCave.errMsg,
372			"error in reading file %s\n"
373			"natoms = %d; index = %d\n"
374			"error reading the line from the file.\n",
375			filename_.c_str(),
376			nTotObjs,
377			i);
378	gezelter	1490
379	tim	1739	painCave.isFatal = 1;
380			simError();
381			}
382
383			MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
384			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
385			}
386			}
387			}
388			} else {
389			//actions taken at slave nodes
390			MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
391	gezelter	1490
392	tim	1739	/*@todo/
393	tim	1808	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
394	gezelter	1490
395	tim	1739	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
396			which_node = info_->getMolToProc(i);
397	gezelter	1490
398	tim	1739	if (which_node == worldRank) {
399			//molecule with global index i belongs to this processor
400
401			mol = info_->getMoleculeByGlobalIndex(i);
402			if (mol == NULL) {
403			strcpy(painCave.errMsg, "Molecule not found on node %d!", worldRank);
404			painCave.isFatal = 1;
405			simError();
406			}
407
408			nCurObj = mol->getNIntegrableObjects();
409	gezelter	1490
410	tim	1739	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
411			MPI_COMM_WORLD);
412	gezelter	1490
413	tim	1739	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
414			integrableObject = mol->nextIntegrableObject(ii)){
415
416			MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
417			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
418	gezelter	1490
419	tim	1739	parseDumpLine(read_buffer, integrableObject);
420			}
421
422			}
423
424			}
425
426			}
427	gezelter	1490
428	tim	1739	#endif
429	gezelter	1490
430	tim	1739	}
431	gezelter	1490
432	tim	1739	void DumpReader::parseDumpLine(char line, StuntDouble integrableObject) {
433	gezelter	1490
434	tim	1739	Vector3d pos; // position place holders
435			Vector3d vel; // velocity placeholders
436			Quat4d q; // the quaternions
437			Vector3d ji; // angular velocity placeholders;
438			StringTokenizer tokenizer(line);
439			int nTokens;
440
441			nTokens = tokenizer.countTokens();
442	gezelter	1490
443	tim	1808	if (nTokens < 14) {
444			sprintf(painCave.errMsg,
445			"Not enough Tokens.\n");
446			painCave.isFatal = 1;
447			simError();
448	gezelter	1490	}
449
450	tim	1739	std::string name = tokenizer.nextToken();
451	gezelter	1490
452	tim	1739	if (name != integrableObject->getType()) {
453
454	gezelter	1490	}
455
456	tim	1739	pos[0] = tokenizer.nextTokenAsFloat();
457			pos[1] = tokenizer.nextTokenAsFloat();
458			pos[2] = tokenizer.nextTokenAsFloat();
459			integrableObject->setPos(pos);
460
461			vel[0] = tokenizer.nextTokenAsFloat();
462			vel[1] = tokenizer.nextTokenAsFloat();
463			vel[2] = tokenizer.nextTokenAsFloat();
464			integrableObject->setVel(vel);
465	gezelter	1490
466	tim	1739	if (integrableObject->isDirectional()) {
467	tim	1808
468	tim	1739	q[0] = tokenizer.nextTokenAsFloat();
469			q[1] = tokenizer.nextTokenAsFloat();
470			q[2] = tokenizer.nextTokenAsFloat();
471			q[3] = tokenizer.nextTokenAsFloat();
472	gezelter	1490
473	tim	1739	double qlen = q.length();
474			if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
475
476			sprintf(painCave.errMsg,
477			"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
478			painCave.isFatal = 1;
479			simError();
480
481			} else if (fabs(qlen - 1.0) > oopse::epsilon) { // check that the quaternion vector is normalized
482			sprintf(painCave.errMsg,
483			"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 != 1.0).\n");
484			painCave.isFatal = 0;
485			simError();
486
487			q.normalize();
488			}
489			integrableObject->setQ(q);
490
491			ji[0] = tokenizer.nextTokenAsFloat();
492			ji[1] = tokenizer.nextTokenAsFloat();
493			ji[2] = tokenizer.nextTokenAsFloat();
494			integrableObject->setJ(ji);
495	gezelter	1490	}
496
497			}
498
499
500	tim	1808	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
501	tim	1739	double currTime;
502			Mat3x3d hmat;
503			double chi;
504			double integralOfChiDt;
505			Mat3x3d eta;
506	gezelter	1490
507	tim	1739	StringTokenizer tokenizer(line);
508			int nTokens;
509	gezelter	1490
510	tim	1739	nTokens = tokenizer.countTokens();
511	gezelter	1490
512	tim	1739	//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens)
513			if (nTokens < 10) {
514			sprintf(painCave.errMsg,
515			"Not enough tokens in comment line: %s", line);
516			painCave.isFatal = 1;
517			simError();
518	gezelter	1490	}
519
520	tim	1739	//read current time
521			currTime = tokenizer.nextTokenAsFloat();
522	tim	1808	s->setTime(currTime);
523	gezelter	1490
524	tim	1739	//read h-matrix
525			hmat(0, 0) = tokenizer.nextTokenAsFloat();
526			hmat(0, 1) = tokenizer.nextTokenAsFloat();
527			hmat(0, 2) = tokenizer.nextTokenAsFloat();
528			hmat(1, 0) = tokenizer.nextTokenAsFloat();
529			hmat(1, 1) = tokenizer.nextTokenAsFloat();
530			hmat(1, 2) = tokenizer.nextTokenAsFloat();
531			hmat(2, 0) = tokenizer.nextTokenAsFloat();
532			hmat(2, 1) = tokenizer.nextTokenAsFloat();
533			hmat(2, 2) = tokenizer.nextTokenAsFloat();
534			s->setHmat(hmat);
535	gezelter	1490
536	tim	1808	//read chi and integrablOfChidt, they should apprear in pair
537			if (tokenizer.countTokens() >= 2) {
538			chi = tokenizer.nextTokenAsFloat();
539			integralOfChiDt = tokenizer.nextTokenAsFloat();
540	gezelter	1490
541	tim	1808	s->setChi(chi);
542			s->setIntegralOfChiDt(integralOfChiDt);
543			}
544
545			//read eta (eta is 3x3 matrix)
546			if (tokenizer.countTokens() >= 9) {
547			eta(0, 0) = tokenizer.nextTokenAsFloat();
548			eta(0, 1) = tokenizer.nextTokenAsFloat();
549			eta(0, 2) = tokenizer.nextTokenAsFloat();
550			eta(1, 0) = tokenizer.nextTokenAsFloat();
551			eta(1, 1) = tokenizer.nextTokenAsFloat();
552			eta(1, 2) = tokenizer.nextTokenAsFloat();
553			eta(2, 0) = tokenizer.nextTokenAsFloat();
554			eta(2, 1) = tokenizer.nextTokenAsFloat();
555			eta(2, 2) = tokenizer.nextTokenAsFloat();
556	gezelter	1490
557	tim	1808	s->setEta(eta);
558	tim	1739	}
559	gezelter	1490
560	tim	1739
561	gezelter	1490	}
562
563	tim	1739	}//end namespace oopse