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) {
    if (!isScanned_)
      scanFile();
        
    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:	2300
Committed:	Thu Sep 15 19:17:04 2005 UTC (18 years, 10 months ago) by tim
File size:	19198 byte(s)
Log Message:	Fix a bug in DumpReader in case readFrame is called without calling getNFrames
#	Content
1	/*
2	* 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	#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	#include "io/DumpReader.hpp"
56	#include "primitives/Molecule.hpp"
57	#include "utils/simError.h"
58	#include "utils/MemoryUtils.hpp"
59	#include "utils/StringTokenizer.hpp"
60
61	#ifdef IS_MPI
62
63	#include <mpi.h>
64	#define TAKE_THIS_TAG_CHAR 0
65	#define TAKE_THIS_TAG_INT 1
66
67	#endif // is_mpi
68
69
70	namespace oopse {
71
72	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73	: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
74
75	#ifdef IS_MPI
76
77	if (worldRank == 0) {
78	#endif
79
80	inFile_ = fopen(filename_.c_str(), "r");
81
82	if (inFile_ == NULL) {
83	sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
84	painCave.isFatal = 1;
85	simError();
86	}
87
88	#ifdef IS_MPI
89
90	}
91
92	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
93	MPIcheckPoint();
94
95	#endif
96
97	return;
98	}
99
100	DumpReader::~DumpReader() {
101
102	#ifdef IS_MPI
103
104	if (worldRank == 0) {
105	#endif
106
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	#ifdef IS_MPI
119
120	}
121
122	strcpy(checkPointMsg, "Dump file closed successfully.");
123	MPIcheckPoint();
124
125	#endif
126
127	return;
128	}
129
130	int DumpReader::getNFrames(void) {
131
132	if (!isScanned_)
133	scanFile();
134
135	return nframes_;
136	}
137
138	void DumpReader::scanFile(void) {
139	int i, j;
140	int lineNum = 0;
141	char readBuffer[maxBufferSize];
142	fpos_t * currPos;
143
144	#ifdef IS_MPI
145
146	if (worldRank == 0) {
147	#endif // is_mpi
148
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	fgets(readBuffer, sizeof(readBuffer), inFile_);
171	lineNum++;
172
173	if (feof(inFile_)) {
174	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	sprintf(painCave.errMsg,
188	"DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
189	" with atom %d\n", filename_.c_str(),
190	lineNum,
191	j);
192
193	painCave.isFatal = 1;
194	simError();
195	}
196	}
197
198	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	#ifdef IS_MPI
209	}
210
211	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
212
213	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
214	MPIcheckPoint();
215
216	#endif // is_mpi
217
218	isScanned_ = true;
219	}
220
221	void DumpReader::readFrame(int whichFrame) {
222	if (!isScanned_)
223	scanFile();
224
225	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
226
227	if (storageLayout & DataStorage::dslPosition) {
228	needPos_ = true;
229	} else {
230	needPos_ = false;
231	}
232
233	if (storageLayout & DataStorage::dslVelocity) {
234	needVel_ = true;
235	} else {
236	needVel_ = false;
237	}
238
239	if (storageLayout & DataStorage::dslAmat \|\| storageLayout & DataStorage::dslElectroFrame) {
240	needQuaternion_ = true;
241	} else {
242	needQuaternion_ = false;
243	}
244
245	if (storageLayout & DataStorage::dslAngularMomentum) {
246	needAngMom_ = true;
247	} else {
248	needAngMom_ = false;
249	}
250
251	readSet(whichFrame);
252	}
253
254	void DumpReader::readSet(int whichFrame) {
255	int i;
256	int nTotObjs; // the number of atoms
257	char read_buffer[maxBufferSize]; //the line buffer for reading
258	char * eof_test; // ptr to see when we reach the end of the file
259
260	Molecule* mol;
261	StuntDouble* integrableObject;
262	SimInfo::MoleculeIterator mi;
263	Molecule::IntegrableObjectIterator ii;
264
265	#ifndef IS_MPI
266
267	fsetpos(inFile_, framePos_[whichFrame]);
268	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
269
270	if (eof_test == NULL) {
271	sprintf(painCave.errMsg,
272	"DumpReader error: error reading 1st line of \"%s\"\n",
273	filename_.c_str());
274	painCave.isFatal = 1;
275	simError();
276	}
277
278	nTotObjs = atoi(read_buffer);
279
280	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
281	sprintf(painCave.errMsg,
282	"DumpReader error. %s nIntegrable, %d, "
283	"does not match the meta-data file's nIntegrable, %d.\n",
284	filename_.c_str(),
285	nTotObjs,
286	info_->getNGlobalIntegrableObjects());
287
288	painCave.isFatal = 1;
289	simError();
290	}
291
292	//read the box mat from the comment line
293
294	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
295
296	if (eof_test == NULL) {
297	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
298	filename_.c_str());
299	painCave.isFatal = 1;
300	simError();
301	}
302
303	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
304
305	//parse dump lines
306
307	i = 0;
308	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
309
310	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
311	integrableObject = mol->nextIntegrableObject(ii)) {
312
313	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
314
315	if (eof_test == NULL) {
316	sprintf(painCave.errMsg,
317	"DumpReader Error: error in reading file %s\n"
318	"natoms = %d; index = %d\n"
319	"error reading the line from the file.\n",
320	filename_.c_str(),
321	nTotObjs,
322	i);
323
324	painCave.isFatal = 1;
325	simError();
326	}
327
328	parseDumpLine(read_buffer, integrableObject);
329	i++;
330	}
331	}
332
333	// MPI Section of code..........
334
335	#else //IS_MPI
336
337	// first thing first, suspend fatalities.
338	int masterNode = 0;
339	int nCurObj;
340	painCave.isEventLoop = 1;
341
342	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
343	int haveError;
344
345	MPI_Status istatus;
346	int nitems;
347
348	nTotObjs = info_->getNGlobalIntegrableObjects();
349	haveError = 0;
350
351	if (worldRank == masterNode) {
352	fsetpos(inFile_, framePos_[whichFrame]);
353
354	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
355
356	if (eof_test == NULL) {
357	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
358	filename_.c_str());
359	painCave.isFatal = 1;
360	simError();
361	}
362
363	nitems = atoi(read_buffer);
364
365	// Check to see that the number of integrable objects in the
366	// intial configuration file is the same as derived from the
367	// meta-data file.
368
369	if (nTotObjs != nitems) {
370	sprintf(painCave.errMsg,
371	"DumpReader Error. %s nIntegrable, %d, "
372	"does not match the meta-data file's nIntegrable, %d.\n",
373	filename_.c_str(),
374	nTotObjs,
375	info_->getNGlobalIntegrableObjects());
376
377	painCave.isFatal = 1;
378	simError();
379	}
380
381	//read the boxMat from the comment line
382
383	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
384
385	if (eof_test == NULL) {
386	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
387	filename_.c_str());
388	painCave.isFatal = 1;
389	simError();
390	}
391
392	//Every single processor will parse the comment line by itself
393	//By using this way, we might lose some efficiency, but if we want to add
394	//more parameters into comment line, we only need to modify function
395	//parseCommentLine
396
397	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
398	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
399
400	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
401	int which_node = info_->getMolToProc(i);
402
403	if (which_node == masterNode) {
404	//molecules belong to master node
405
406	mol = info_->getMoleculeByGlobalIndex(i);
407
408	if (mol == NULL) {
409	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
410	painCave.isFatal = 1;
411	simError();
412	}
413
414	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
415	integrableObject = mol->nextIntegrableObject(ii)){
416
417	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
418
419	if (eof_test == NULL) {
420	sprintf(painCave.errMsg,
421	"DumpReader Error: error in reading file %s\n"
422	"natoms = %d; index = %d\n"
423	"error reading the line from the file.\n",
424	filename_.c_str(),
425	nTotObjs,
426	i);
427
428	painCave.isFatal = 1;
429	simError();
430	}
431
432	parseDumpLine(read_buffer, integrableObject);
433	}
434	} else {
435	//molecule belongs to slave nodes
436
437	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
438	MPI_COMM_WORLD, &istatus);
439
440	for(int j = 0; j < nCurObj; j++) {
441	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
442
443	if (eof_test == NULL) {
444	sprintf(painCave.errMsg,
445	"DumpReader Error: error in reading file %s\n"
446	"natoms = %d; index = %d\n"
447	"error reading the line from the file.\n",
448	filename_.c_str(),
449	nTotObjs,
450	i);
451
452	painCave.isFatal = 1;
453	simError();
454	}
455
456	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
457	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
458	}
459	}
460	}
461	} else {
462	//actions taken at slave nodes
463	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
464
465	/*@todo/
466	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
467
468	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
469	int which_node = info_->getMolToProc(i);
470
471	if (which_node == worldRank) {
472	//molecule with global index i belongs to this processor
473
474	mol = info_->getMoleculeByGlobalIndex(i);
475	if (mol == NULL) {
476	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
477	painCave.isFatal = 1;
478	simError();
479	}
480
481	nCurObj = mol->getNIntegrableObjects();
482
483	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
484	MPI_COMM_WORLD);
485
486	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
487	integrableObject = mol->nextIntegrableObject(ii)){
488
489	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
490	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
491
492	parseDumpLine(read_buffer, integrableObject);
493	}
494
495	}
496
497	}
498
499	}
500
501	#endif
502
503	}
504
505	void DumpReader::parseDumpLine(char line, StuntDouble integrableObject) {
506
507	Vector3d pos; // position place holders
508	Vector3d vel; // velocity placeholders
509	Quat4d q; // the quaternions
510	Vector3d ji; // angular velocity placeholders;
511	StringTokenizer tokenizer(line);
512	int nTokens;
513
514	nTokens = tokenizer.countTokens();
515
516	if (nTokens < 14) {
517	sprintf(painCave.errMsg,
518	"DumpReader Error: Not enough Tokens.\n%s\n", line);
519	painCave.isFatal = 1;
520	simError();
521	}
522
523	std::string name = tokenizer.nextToken();
524
525	if (name != integrableObject->getType()) {
526
527	sprintf(painCave.errMsg,
528	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
529	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
530	painCave.isFatal = 1;
531	simError();
532	}
533
534	pos[0] = tokenizer.nextTokenAsDouble();
535	pos[1] = tokenizer.nextTokenAsDouble();
536	pos[2] = tokenizer.nextTokenAsDouble();
537	if (needPos_) {
538	integrableObject->setPos(pos);
539	}
540
541	vel[0] = tokenizer.nextTokenAsDouble();
542	vel[1] = tokenizer.nextTokenAsDouble();
543	vel[2] = tokenizer.nextTokenAsDouble();
544	if (needVel_) {
545	integrableObject->setVel(vel);
546	}
547
548	if (integrableObject->isDirectional()) {
549
550	q[0] = tokenizer.nextTokenAsDouble();
551	q[1] = tokenizer.nextTokenAsDouble();
552	q[2] = tokenizer.nextTokenAsDouble();
553	q[3] = tokenizer.nextTokenAsDouble();
554
555	double qlen = q.length();
556	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
557
558	sprintf(painCave.errMsg,
559	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
560	painCave.isFatal = 1;
561	simError();
562
563	}
564
565	q.normalize();
566	if (needQuaternion_) {
567	integrableObject->setQ(q);
568	}
569
570	ji[0] = tokenizer.nextTokenAsDouble();
571	ji[1] = tokenizer.nextTokenAsDouble();
572	ji[2] = tokenizer.nextTokenAsDouble();
573	if (needAngMom_) {
574	integrableObject->setJ(ji);
575	}
576	}
577
578	}
579
580
581	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
582	double currTime;
583	Mat3x3d hmat;
584	double chi;
585	double integralOfChiDt;
586	Mat3x3d eta;
587
588	StringTokenizer tokenizer(line);
589	int nTokens;
590
591	nTokens = tokenizer.countTokens();
592
593	//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens)
594	if (nTokens < 10) {
595	sprintf(painCave.errMsg,
596	"DumpReader Error: Not enough tokens in comment line: %s", line);
597	painCave.isFatal = 1;
598	simError();
599	}
600
601	//read current time
602	currTime = tokenizer.nextTokenAsDouble();
603	s->setTime(currTime);
604
605	//read h-matrix
606	hmat(0, 0) = tokenizer.nextTokenAsDouble();
607	hmat(0, 1) = tokenizer.nextTokenAsDouble();
608	hmat(0, 2) = tokenizer.nextTokenAsDouble();
609	hmat(1, 0) = tokenizer.nextTokenAsDouble();
610	hmat(1, 1) = tokenizer.nextTokenAsDouble();
611	hmat(1, 2) = tokenizer.nextTokenAsDouble();
612	hmat(2, 0) = tokenizer.nextTokenAsDouble();
613	hmat(2, 1) = tokenizer.nextTokenAsDouble();
614	hmat(2, 2) = tokenizer.nextTokenAsDouble();
615	s->setHmat(hmat);
616
617	//read chi and integralOfChidt, they should apprear in pair
618	if (tokenizer.countTokens() >= 2) {
619	chi = tokenizer.nextTokenAsDouble();
620	integralOfChiDt = tokenizer.nextTokenAsDouble();
621
622	s->setChi(chi);
623	s->setIntegralOfChiDt(integralOfChiDt);
624	}
625
626	//read eta (eta is 3x3 matrix)
627	if (tokenizer.countTokens() >= 9) {
628	eta(0, 0) = tokenizer.nextTokenAsDouble();
629	eta(0, 1) = tokenizer.nextTokenAsDouble();
630	eta(0, 2) = tokenizer.nextTokenAsDouble();
631	eta(1, 0) = tokenizer.nextTokenAsDouble();
632	eta(1, 1) = tokenizer.nextTokenAsDouble();
633	eta(1, 2) = tokenizer.nextTokenAsDouble();
634	eta(2, 0) = tokenizer.nextTokenAsDouble();
635	eta(2, 1) = tokenizer.nextTokenAsDouble();
636	eta(2, 2) = tokenizer.nextTokenAsDouble();
637
638	s->setEta(eta);
639	}
640
641
642	}
643
644	}//end namespace oopse