src/io/DumpReader.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#define _LARGEFILE_SOURCE64
#define _FILE_OFFSET_BITS 64

#include <sys/types.h>
#include <sys/stat.h>

#include <iostream>
#include <math.h>

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "utils/MemoryUtils.hpp"
#include "utils/StringTokenizer.hpp"

#ifdef IS_MPI

#include <mpi.h>
#define TAKE_THIS_TAG_CHAR 0
#define TAKE_THIS_TAG_INT 1

#endif // is_mpi


namespace oopse {
  
  DumpReader::DumpReader(SimInfo* info, const std::string& filename)
    : info_(info), filename_(filename), isScanned_(false), nframes_(0) {
    
#ifdef IS_MPI
    
      if (worldRank == 0) {
#endif
      
        inFile_ = fopen(filename_.c_str(), "r");
      
        if (inFile_ == NULL) {
          sprintf(painCave.errMsg, "DumpReader: 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, "DumpReader Error: Error closing %s\n", filename_.c_str());
        painCave.isFatal = 1;            
        simError();
      }
      
      MemoryUtils::deletePointers(framePos_);
      
#ifdef IS_MPI
      
    }
    
    strcpy(checkPointMsg, "Dump file closed successfully.");
    MPIcheckPoint();
    
#endif
    
    return;
  }
  
  int DumpReader::getNFrames(void) {
    
    if (!isScanned_)
      scanFile();
    
    return nframes_;
  }
  
  void DumpReader::scanFile(void) {
    int i, j;
    int lineNum = 0;
    char readBuffer[maxBufferSize];
    fpos_t * currPos;
    
#ifdef IS_MPI
    
    if (worldRank == 0) {
#endif // is_mpi
      
      rewind(inFile_);
      
      currPos = new fpos_t;
      fgetpos(inFile_, currPos);
      fgets(readBuffer, sizeof(readBuffer), inFile_);
      lineNum++;
      
      if (feof(inFile_)) {
        sprintf(painCave.errMsg,
                "DumpReader Error: 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,
                  "DumpReader Error: 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,
                    "DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
                    " with atom %d\n", filename_.c_str(),
                    lineNum,
                    j);
            
            painCave.isFatal = 1;
            simError();
          }
        }
        
        currPos = new fpos_t;
        fgetpos(inFile_, currPos);
        fgets(readBuffer, sizeof(readBuffer), inFile_);
        lineNum++;
      }
      
      delete currPos;
      rewind(inFile_);
      
      nframes_ = framePos_.size();
#ifdef IS_MPI
    }
    
    MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
    
    strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
    MPIcheckPoint();
    
#endif // is_mpi
    
    isScanned_ = true;
  }
  
  void DumpReader::readFrame(int whichFrame) {
    int storageLayout = info_->getSnapshotManager()->getStorageLayout();
    
    if (storageLayout & DataStorage::dslPosition) {
      needPos_ = true;
    } else {
      needPos_ = false;
    }
    
    if (storageLayout & DataStorage::dslVelocity) {
      needVel_ = true;
    } else {
      needVel_ = false;
    }
    
    if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
      needQuaternion_ = true;
    } else {
      needQuaternion_ = false;
    }
    
    if (storageLayout & DataStorage::dslAngularMomentum) {
      needAngMom_ = true;
    } else {
      needAngMom_ = false;    
    }
    
    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_->getNGlobalIntegrableObjects());
      
      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, "DumpReader Error: error in reading commment in %s\n",
              filename_.c_str());
      painCave.isFatal = 1;
      simError();
    }
    
    parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
    
    //parse dump lines
    
    i = 0;
    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,
                  "DumpReader Error: 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);
        i++;
      }
    }
    
    // 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, "DumpReader Error: Error reading 1st line of %s \n ",
                filename_.c_str());
        painCave.isFatal = 1;
        simError();
      }
      
      nitems = atoi(read_buffer);
      
      // Check to see that the number of integrable objects in the
      // intial configuration file is the same as derived from the
      // meta-data file.
      
      if (nTotObjs != nitems) {
        sprintf(painCave.errMsg,
                "DumpReader Error. %s nIntegrable, %d, "
                "does not match the meta-data file's nIntegrable, %d.\n",
                filename_.c_str(),
                nTotObjs,
                info_->getNGlobalIntegrableObjects());
        
        painCave.isFatal = 1;
        simError();
      }
      
      //read the boxMat from the comment line
      
      eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
      
      if (eof_test == NULL) {
        sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
                filename_.c_str());
        painCave.isFatal = 1;
        simError();
      }
      
      //Every single processor will parse the comment line by itself
      //By using this way, we might lose some efficiency, but if we want to add
      //more parameters into comment line, we only need to modify function
      //parseCommentLine
      
      MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
      parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
      
      for(i = 0; i < info_->getNGlobalMolecules(); i++) {
        int which_node = info_->getMolToProc(i);
        
        if (which_node == masterNode) {
          //molecules belong to master node
          
          mol = info_->getMoleculeByGlobalIndex(i);
          
          if (mol == NULL) {
            sprintf(painCave.errMsg, "DumpReader Error: 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,
                      "DumpReader Error: 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,
                      "DumpReader Error: error in reading file %s\n"
                      "natoms  = %d; index = %d\n"
                      "error reading the line from the file.\n",
                      filename_.c_str(),
                      nTotObjs,
                      i);
              
              painCave.isFatal = 1;
              simError();
            }
            
            MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
                     TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
          }
        }
      }
    } else {
      //actions taken at slave nodes
      MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
      
      /**@todo*/
      parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
      
      for(i = 0; i < info_->getNGlobalMolecules(); i++) {
        int which_node = info_->getMolToProc(i);
        
        if (which_node == worldRank) {
          //molecule with global index i belongs to this processor
          
          mol = info_->getMoleculeByGlobalIndex(i);
          if (mol == NULL) {
            sprintf(painCave.errMsg, "DumpReader Error: 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,
              "DumpReader Error: Not enough Tokens.\n%s\n", line);
      painCave.isFatal = 1;
      simError();
    }
    
    std::string name = tokenizer.nextToken();
    
    if (name != integrableObject->getType()) {
      
      sprintf(painCave.errMsg,
              "DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
              name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
      painCave.isFatal = 1;
      simError();        
    }
    
    pos[0] = tokenizer.nextTokenAsDouble();
    pos[1] = tokenizer.nextTokenAsDouble();
    pos[2] = tokenizer.nextTokenAsDouble();
    if (needPos_) {
      integrableObject->setPos(pos);
    }
    
    vel[0] = tokenizer.nextTokenAsDouble();
    vel[1] = tokenizer.nextTokenAsDouble();
    vel[2] = tokenizer.nextTokenAsDouble();
    if (needVel_) {
      integrableObject->setVel(vel);
    }
    
    if (integrableObject->isDirectional()) {
      
      q[0] = tokenizer.nextTokenAsDouble();
      q[1] = tokenizer.nextTokenAsDouble();
      q[2] = tokenizer.nextTokenAsDouble();
      q[3] = tokenizer.nextTokenAsDouble();
      
      double qlen = q.length();
      if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
        
        sprintf(painCave.errMsg,
                "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
        painCave.isFatal = 1;
        simError();
        
      } 
      
      q.normalize();
      if (needQuaternion_) {           
        integrableObject->setQ(q);
      }
      
      ji[0] = tokenizer.nextTokenAsDouble();
      ji[1] = tokenizer.nextTokenAsDouble();
      ji[2] = tokenizer.nextTokenAsDouble();
      if (needAngMom_) {
        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,
              "DumpReader Error: Not enough tokens in comment line: %s", line);
      painCave.isFatal = 1;
      simError();   
    }
    
    //read current time
    currTime = tokenizer.nextTokenAsDouble();
    s->setTime(currTime);
    
    //read h-matrix
    hmat(0, 0) = tokenizer.nextTokenAsDouble();
    hmat(0, 1) = tokenizer.nextTokenAsDouble();
    hmat(0, 2) = tokenizer.nextTokenAsDouble();
    hmat(1, 0) = tokenizer.nextTokenAsDouble();
    hmat(1, 1) = tokenizer.nextTokenAsDouble();
    hmat(1, 2) = tokenizer.nextTokenAsDouble();
    hmat(2, 0) = tokenizer.nextTokenAsDouble();
    hmat(2, 1) = tokenizer.nextTokenAsDouble();
    hmat(2, 2) = tokenizer.nextTokenAsDouble();
    s->setHmat(hmat);
    
    //read chi and integralOfChidt, they should apprear in pair
    if (tokenizer.countTokens() >= 2) {
      chi = tokenizer.nextTokenAsDouble();
      integralOfChiDt = tokenizer.nextTokenAsDouble();            
      
      s->setChi(chi);
      s->setIntegralOfChiDt(integralOfChiDt);
    }
    
    //read eta (eta is 3x3 matrix)
    if (tokenizer.countTokens() >= 9) {
      eta(0, 0) = tokenizer.nextTokenAsDouble();
      eta(0, 1) = tokenizer.nextTokenAsDouble();
      eta(0, 2) = tokenizer.nextTokenAsDouble();
      eta(1, 0) = tokenizer.nextTokenAsDouble();
      eta(1, 1) = tokenizer.nextTokenAsDouble();
      eta(1, 2) = tokenizer.nextTokenAsDouble();
      eta(2, 0) = tokenizer.nextTokenAsDouble();
      eta(2, 1) = tokenizer.nextTokenAsDouble();
      eta(2, 2) = tokenizer.nextTokenAsDouble();      
      
      s->setEta(eta);
    }
    
    
  }
  
}//end namespace oopse
Revision:	507
Committed:	Fri Apr 15 22:04:00 2005 UTC (20 years ago) by gezelter
File size:	19150 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42	gezelter	2	#define _LARGEFILE_SOURCE64
43			#define _FILE_OFFSET_BITS 64
44
45			#include <sys/types.h>
46			#include <sys/stat.h>
47
48			#include <iostream>
49			#include <math.h>
50
51			#include <stdio.h>
52			#include <stdlib.h>
53			#include <string.h>
54
55	gezelter	246	#include "io/DumpReader.hpp"
56			#include "primitives/Molecule.hpp"
57	tim	3	#include "utils/simError.h"
58	gezelter	246	#include "utils/MemoryUtils.hpp"
59			#include "utils/StringTokenizer.hpp"
60	gezelter	2
61			#ifdef IS_MPI
62	gezelter	246
63	gezelter	2	#include <mpi.h>
64			#define TAKE_THIS_TAG_CHAR 0
65			#define TAKE_THIS_TAG_INT 1
66	gezelter	246
67	gezelter	2	#endif // is_mpi
68
69
70	gezelter	246	namespace oopse {
71	chrisfen	417
72			DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73	gezelter	507	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
74	chrisfen	417
75	gezelter	2	#ifdef IS_MPI
76	chrisfen	417
77	gezelter	507	if (worldRank == 0) {
78	gezelter	2	#endif
79	chrisfen	417
80	gezelter	507	inFile_ = fopen(filename_.c_str(), "r");
81	chrisfen	417
82	gezelter	507	if (inFile_ == NULL) {
83			sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
84			painCave.isFatal = 1;
85			simError();
86			}
87	chrisfen	417
88	gezelter	2	#ifdef IS_MPI
89	chrisfen	417
90	gezelter	507	}
91	chrisfen	417
92	gezelter	507	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
93			MPIcheckPoint();
94	chrisfen	417
95	gezelter	2	#endif
96	chrisfen	417
97	gezelter	507	return;
98			}
99	chrisfen	417
100			DumpReader::~DumpReader() {
101
102	gezelter	246	#ifdef IS_MPI
103	chrisfen	417
104	gezelter	246	if (worldRank == 0) {
105			#endif
106	chrisfen	417
107			int error;
108			error = fclose(inFile_);
109
110			if (error) {
111			sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
112			painCave.isFatal = 1;
113			simError();
114			}
115
116			MemoryUtils::deletePointers(framePos_);
117
118	gezelter	2	#ifdef IS_MPI
119	chrisfen	417
120	gezelter	2	}
121	chrisfen	417
122	gezelter	246	strcpy(checkPointMsg, "Dump file closed successfully.");
123			MPIcheckPoint();
124	chrisfen	417
125	gezelter	246	#endif
126	chrisfen	417
127	gezelter	246	return;
128	chrisfen	417	}
129
130			int DumpReader::getNFrames(void) {
131
132	gezelter	246	if (!isScanned_)
133	chrisfen	417	scanFile();
134
135	gezelter	246	return nframes_;
136	chrisfen	417	}
137
138			void DumpReader::scanFile(void) {
139			int i, j;
140			int lineNum = 0;
141			char readBuffer[maxBufferSize];
142			fpos_t * currPos;
143
144	gezelter	2	#ifdef IS_MPI
145	chrisfen	417
146	gezelter	246	if (worldRank == 0) {
147			#endif // is_mpi
148	chrisfen	417
149			rewind(inFile_);
150
151			currPos = new fpos_t;
152			fgetpos(inFile_, currPos);
153			fgets(readBuffer, sizeof(readBuffer), inFile_);
154			lineNum++;
155
156			if (feof(inFile_)) {
157			sprintf(painCave.errMsg,
158			"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
159			filename_.c_str(),
160			lineNum);
161			painCave.isFatal = 1;
162			simError();
163			}
164
165			while (!feof(inFile_)) {
166			framePos_.push_back(currPos);
167
168			i = atoi(readBuffer);
169
170	gezelter	246	fgets(readBuffer, sizeof(readBuffer), inFile_);
171			lineNum++;
172	chrisfen	417
173	gezelter	246	if (feof(inFile_)) {
174	chrisfen	417	sprintf(painCave.errMsg,
175			"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
176			filename_.c_str(),
177			lineNum);
178			painCave.isFatal = 1;
179			simError();
180			}
181
182			for(j = 0; j < i; j++) {
183			fgets(readBuffer, sizeof(readBuffer), inFile_);
184			lineNum++;
185
186			if (feof(inFile_)) {
187	gezelter	246	sprintf(painCave.errMsg,
188	chrisfen	417	"DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
189			" with atom %d\n", filename_.c_str(),
190			lineNum,
191			j);
192
193	gezelter	246	painCave.isFatal = 1;
194			simError();
195	chrisfen	417	}
196	gezelter	246	}
197
198	chrisfen	417	currPos = new fpos_t;
199			fgetpos(inFile_, currPos);
200			fgets(readBuffer, sizeof(readBuffer), inFile_);
201			lineNum++;
202			}
203
204			delete currPos;
205			rewind(inFile_);
206
207			nframes_ = framePos_.size();
208	gezelter	246	#ifdef IS_MPI
209	gezelter	2	}
210	chrisfen	417
211	gezelter	246	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
212	chrisfen	417
213	gezelter	246	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
214			MPIcheckPoint();
215	chrisfen	417
216	gezelter	246	#endif // is_mpi
217	chrisfen	417
218	gezelter	246	isScanned_ = true;
219	chrisfen	417	}
220
221			void DumpReader::readFrame(int whichFrame) {
222	tim	318	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
223	chrisfen	417
224	tim	318	if (storageLayout & DataStorage::dslPosition) {
225	chrisfen	417	needPos_ = true;
226	tim	318	} else {
227	chrisfen	417	needPos_ = false;
228	tim	318	}
229	chrisfen	417
230	tim	318	if (storageLayout & DataStorage::dslVelocity) {
231	chrisfen	417	needVel_ = true;
232	tim	318	} else {
233	chrisfen	417	needVel_ = false;
234	tim	318	}
235	chrisfen	417
236	tim	318	if (storageLayout & DataStorage::dslAmat \|\| storageLayout & DataStorage::dslElectroFrame) {
237	chrisfen	417	needQuaternion_ = true;
238	tim	318	} else {
239	chrisfen	417	needQuaternion_ = false;
240	tim	318	}
241	chrisfen	417
242	tim	318	if (storageLayout & DataStorage::dslAngularMomentum) {
243	chrisfen	417	needAngMom_ = true;
244	tim	318	} else {
245	chrisfen	417	needAngMom_ = false;
246	tim	318	}
247	chrisfen	417
248	gezelter	246	readSet(whichFrame);
249	chrisfen	417	}
250
251			void DumpReader::readSet(int whichFrame) {
252			int i;
253			int nTotObjs; // the number of atoms
254			char read_buffer[maxBufferSize]; //the line buffer for reading
255			char * eof_test; // ptr to see when we reach the end of the file
256
257			Molecule* mol;
258			StuntDouble* integrableObject;
259			SimInfo::MoleculeIterator mi;
260			Molecule::IntegrableObjectIterator ii;
261
262	gezelter	246	#ifndef IS_MPI
263	chrisfen	417
264	gezelter	246	fsetpos(inFile_, framePos_[whichFrame]);
265			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
266	chrisfen	417
267	gezelter	246	if (eof_test == NULL) {
268	chrisfen	417	sprintf(painCave.errMsg,
269			"DumpReader error: error reading 1st line of \"%s\"\n",
270			filename_.c_str());
271			painCave.isFatal = 1;
272			simError();
273	gezelter	2	}
274	chrisfen	417
275	gezelter	246	nTotObjs = atoi(read_buffer);
276	chrisfen	417
277	gezelter	246	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
278	chrisfen	417	sprintf(painCave.errMsg,
279			"DumpReader error. %s nIntegrable, %d, "
280			"does not match the meta-data file's nIntegrable, %d.\n",
281			filename_.c_str(),
282			nTotObjs,
283			info_->getNGlobalIntegrableObjects());
284
285			painCave.isFatal = 1;
286			simError();
287	gezelter	2	}
288	chrisfen	417
289	gezelter	246	//read the box mat from the comment line
290	chrisfen	417
291	gezelter	246	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
292	chrisfen	417
293	gezelter	246	if (eof_test == NULL) {
294	chrisfen	417	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
295			filename_.c_str());
296			painCave.isFatal = 1;
297			simError();
298	gezelter	246	}
299	chrisfen	417
300	gezelter	246	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
301	chrisfen	417
302	gezelter	246	//parse dump lines
303	chrisfen	417
304			i = 0;
305	gezelter	246	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
306	chrisfen	417
307			for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
308			integrableObject = mol->nextIntegrableObject(ii)) {
309
310			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
311
312			if (eof_test == NULL) {
313			sprintf(painCave.errMsg,
314			"DumpReader Error: error in reading file %s\n"
315			"natoms = %d; index = %d\n"
316			"error reading the line from the file.\n",
317			filename_.c_str(),
318			nTotObjs,
319			i);
320
321			painCave.isFatal = 1;
322			simError();
323			}
324
325			parseDumpLine(read_buffer, integrableObject);
326			i++;
327			}
328	gezelter	2	}
329	chrisfen	417
330	gezelter	246	// MPI Section of code..........
331	chrisfen	417
332	gezelter	246	#else //IS_MPI
333	chrisfen	417
334	gezelter	246	// first thing first, suspend fatalities.
335			int masterNode = 0;
336			int nCurObj;
337			painCave.isEventLoop = 1;
338	chrisfen	417
339	gezelter	246	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
340			int haveError;
341	chrisfen	417
342	gezelter	246	MPI_Status istatus;
343			int nitems;
344	chrisfen	417
345	gezelter	246	nTotObjs = info_->getNGlobalIntegrableObjects();
346			haveError = 0;
347	chrisfen	417
348	gezelter	246	if (worldRank == masterNode) {
349	chrisfen	417	fsetpos(inFile_, framePos_[whichFrame]);
350
351			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
352
353			if (eof_test == NULL) {
354			sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
355			filename_.c_str());
356			painCave.isFatal = 1;
357			simError();
358			}
359
360			nitems = atoi(read_buffer);
361
362			// Check to see that the number of integrable objects in the
363			// intial configuration file is the same as derived from the
364			// meta-data file.
365
366			if (nTotObjs != nitems) {
367			sprintf(painCave.errMsg,
368			"DumpReader Error. %s nIntegrable, %d, "
369			"does not match the meta-data file's nIntegrable, %d.\n",
370			filename_.c_str(),
371			nTotObjs,
372			info_->getNGlobalIntegrableObjects());
373
374			painCave.isFatal = 1;
375			simError();
376			}
377
378			//read the boxMat from the comment line
379
380			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
381
382			if (eof_test == NULL) {
383			sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
384			filename_.c_str());
385			painCave.isFatal = 1;
386			simError();
387			}
388
389			//Every single processor will parse the comment line by itself
390			//By using this way, we might lose some efficiency, but if we want to add
391			//more parameters into comment line, we only need to modify function
392			//parseCommentLine
393
394			MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
395			parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
396
397			for(i = 0; i < info_->getNGlobalMolecules(); i++) {
398			int which_node = info_->getMolToProc(i);
399
400			if (which_node == masterNode) {
401			//molecules belong to master node
402
403			mol = info_->getMoleculeByGlobalIndex(i);
404
405			if (mol == NULL) {
406			sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
407	gezelter	246	painCave.isFatal = 1;
408			simError();
409	chrisfen	417	}
410
411			for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
412			integrableObject = mol->nextIntegrableObject(ii)){
413
414			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
415
416			if (eof_test == NULL) {
417			sprintf(painCave.errMsg,
418			"DumpReader Error: error in reading file %s\n"
419			"natoms = %d; index = %d\n"
420			"error reading the line from the file.\n",
421			filename_.c_str(),
422			nTotObjs,
423			i);
424
425			painCave.isFatal = 1;
426			simError();
427			}
428
429			parseDumpLine(read_buffer, integrableObject);
430			}
431			} else {
432			//molecule belongs to slave nodes
433
434			MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
435			MPI_COMM_WORLD, &istatus);
436
437			for(int j = 0; j < nCurObj; j++) {
438			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
439
440			if (eof_test == NULL) {
441			sprintf(painCave.errMsg,
442			"DumpReader Error: error in reading file %s\n"
443			"natoms = %d; index = %d\n"
444			"error reading the line from the file.\n",
445			filename_.c_str(),
446			nTotObjs,
447			i);
448
449			painCave.isFatal = 1;
450			simError();
451			}
452
453			MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
454			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
455			}
456	gezelter	2	}
457	chrisfen	417	}
458			} else {
459			//actions taken at slave nodes
460			MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
461
462			/*@todo/
463			parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
464
465			for(i = 0; i < info_->getNGlobalMolecules(); i++) {
466			int which_node = info_->getMolToProc(i);
467
468			if (which_node == worldRank) {
469			//molecule with global index i belongs to this processor
470
471			mol = info_->getMoleculeByGlobalIndex(i);
472			if (mol == NULL) {
473			sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
474	gezelter	246	painCave.isFatal = 1;
475			simError();
476	chrisfen	417	}
477
478			nCurObj = mol->getNIntegrableObjects();
479
480			MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
481			MPI_COMM_WORLD);
482
483			for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
484			integrableObject = mol->nextIntegrableObject(ii)){
485	gezelter	246
486	chrisfen	417	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
487			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
488
489			parseDumpLine(read_buffer, integrableObject);
490			}
491
492	gezelter	246	}
493
494	chrisfen	417	}
495
496	gezelter	2	}
497	chrisfen	417
498	gezelter	246	#endif
499	chrisfen	417
500			}
501
502			void DumpReader::parseDumpLine(char line, StuntDouble integrableObject) {
503
504	gezelter	246	Vector3d pos; // position place holders
505			Vector3d vel; // velocity placeholders
506			Quat4d q; // the quaternions
507			Vector3d ji; // angular velocity placeholders;
508			StringTokenizer tokenizer(line);
509			int nTokens;
510
511			nTokens = tokenizer.countTokens();
512	chrisfen	417
513	gezelter	246	if (nTokens < 14) {
514	chrisfen	417	sprintf(painCave.errMsg,
515			"DumpReader Error: Not enough Tokens.\n%s\n", line);
516			painCave.isFatal = 1;
517			simError();
518	gezelter	2	}
519	chrisfen	417
520	gezelter	246	std::string name = tokenizer.nextToken();
521	chrisfen	417
522	gezelter	246	if (name != integrableObject->getType()) {
523	chrisfen	417
524			sprintf(painCave.errMsg,
525			"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
526			name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
527			painCave.isFatal = 1;
528			simError();
529	gezelter	2	}
530	chrisfen	417
531	gezelter	246	pos[0] = tokenizer.nextTokenAsDouble();
532			pos[1] = tokenizer.nextTokenAsDouble();
533			pos[2] = tokenizer.nextTokenAsDouble();
534	tim	318	if (needPos_) {
535	chrisfen	417	integrableObject->setPos(pos);
536	tim	318	}
537	gezelter	246
538			vel[0] = tokenizer.nextTokenAsDouble();
539			vel[1] = tokenizer.nextTokenAsDouble();
540			vel[2] = tokenizer.nextTokenAsDouble();
541	tim	318	if (needVel_) {
542	chrisfen	417	integrableObject->setVel(vel);
543	tim	318	}
544
545	gezelter	246	if (integrableObject->isDirectional()) {
546	chrisfen	417
547			q[0] = tokenizer.nextTokenAsDouble();
548			q[1] = tokenizer.nextTokenAsDouble();
549			q[2] = tokenizer.nextTokenAsDouble();
550			q[3] = tokenizer.nextTokenAsDouble();
551
552			double qlen = q.length();
553			if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
554	gezelter	246
555	chrisfen	417	sprintf(painCave.errMsg,
556			"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
557			painCave.isFatal = 1;
558			simError();
559
560			}
561
562			q.normalize();
563			if (needQuaternion_) {
564			integrableObject->setQ(q);
565			}
566
567			ji[0] = tokenizer.nextTokenAsDouble();
568			ji[1] = tokenizer.nextTokenAsDouble();
569			ji[2] = tokenizer.nextTokenAsDouble();
570			if (needAngMom_) {
571			integrableObject->setJ(ji);
572			}
573	gezelter	2	}
574	chrisfen	417
575			}
576
577
578			void DumpReader::parseCommentLine(char* line, Snapshot* s) {
579	gezelter	246	double currTime;
580			Mat3x3d hmat;
581			double chi;
582			double integralOfChiDt;
583			Mat3x3d eta;
584	chrisfen	417
585	gezelter	246	StringTokenizer tokenizer(line);
586			int nTokens;
587	chrisfen	417
588	gezelter	246	nTokens = tokenizer.countTokens();
589	chrisfen	417
590	gezelter	246	//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens)
591			if (nTokens < 10) {
592	chrisfen	417	sprintf(painCave.errMsg,
593			"DumpReader Error: Not enough tokens in comment line: %s", line);
594			painCave.isFatal = 1;
595			simError();
596	gezelter	2	}
597	chrisfen	417
598	gezelter	246	//read current time
599			currTime = tokenizer.nextTokenAsDouble();
600			s->setTime(currTime);
601
602			//read h-matrix
603			hmat(0, 0) = tokenizer.nextTokenAsDouble();
604			hmat(0, 1) = tokenizer.nextTokenAsDouble();
605			hmat(0, 2) = tokenizer.nextTokenAsDouble();
606			hmat(1, 0) = tokenizer.nextTokenAsDouble();
607			hmat(1, 1) = tokenizer.nextTokenAsDouble();
608			hmat(1, 2) = tokenizer.nextTokenAsDouble();
609			hmat(2, 0) = tokenizer.nextTokenAsDouble();
610			hmat(2, 1) = tokenizer.nextTokenAsDouble();
611			hmat(2, 2) = tokenizer.nextTokenAsDouble();
612			s->setHmat(hmat);
613
614	tim	318	//read chi and integralOfChidt, they should apprear in pair
615	gezelter	246	if (tokenizer.countTokens() >= 2) {
616	chrisfen	417	chi = tokenizer.nextTokenAsDouble();
617			integralOfChiDt = tokenizer.nextTokenAsDouble();
618
619			s->setChi(chi);
620			s->setIntegralOfChiDt(integralOfChiDt);
621	gezelter	2	}
622
623	gezelter	246	//read eta (eta is 3x3 matrix)
624			if (tokenizer.countTokens() >= 9) {
625	chrisfen	417	eta(0, 0) = tokenizer.nextTokenAsDouble();
626			eta(0, 1) = tokenizer.nextTokenAsDouble();
627			eta(0, 2) = tokenizer.nextTokenAsDouble();
628			eta(1, 0) = tokenizer.nextTokenAsDouble();
629			eta(1, 1) = tokenizer.nextTokenAsDouble();
630			eta(1, 2) = tokenizer.nextTokenAsDouble();
631			eta(2, 0) = tokenizer.nextTokenAsDouble();
632			eta(2, 1) = tokenizer.nextTokenAsDouble();
633			eta(2, 2) = tokenizer.nextTokenAsDouble();
634
635			s->setEta(eta);
636	gezelter	2	}
637
638	chrisfen	417
639			}
640
641	gezelter	246	}//end namespace oopse