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:	2101
Committed:	Thu Mar 10 15:10:24 2005 UTC (19 years, 3 months ago) by chrisfen
File size:	19167 byte(s)
Log Message:	First commit of the new restraints code
#	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	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
223
224	if (storageLayout & DataStorage::dslPosition) {
225	needPos_ = true;
226	} else {
227	needPos_ = false;
228	}
229
230	if (storageLayout & DataStorage::dslVelocity) {
231	needVel_ = true;
232	} else {
233	needVel_ = false;
234	}
235
236	if (storageLayout & DataStorage::dslAmat \|\| storageLayout & DataStorage::dslElectroFrame) {
237	needQuaternion_ = true;
238	} else {
239	needQuaternion_ = false;
240	}
241
242	if (storageLayout & DataStorage::dslAngularMomentum) {
243	needAngMom_ = true;
244	} else {
245	needAngMom_ = false;
246	}
247
248	readSet(whichFrame);
249	}
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	#ifndef IS_MPI
263
264	fsetpos(inFile_, framePos_[whichFrame]);
265	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
266
267	if (eof_test == NULL) {
268	sprintf(painCave.errMsg,
269	"DumpReader error: error reading 1st line of \"%s\"\n",
270	filename_.c_str());
271	painCave.isFatal = 1;
272	simError();
273	}
274
275	nTotObjs = atoi(read_buffer);
276
277	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
278	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	}
288
289	//read the box mat from the comment line
290
291	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
292
293	if (eof_test == NULL) {
294	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
295	filename_.c_str());
296	painCave.isFatal = 1;
297	simError();
298	}
299
300	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
301
302	//parse dump lines
303
304	i = 0;
305	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
306
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	}
329
330	// MPI Section of code..........
331
332	#else //IS_MPI
333
334	// first thing first, suspend fatalities.
335	int masterNode = 0;
336	int nCurObj;
337	painCave.isEventLoop = 1;
338
339	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
340	int haveError;
341
342	MPI_Status istatus;
343	int nitems;
344
345	nTotObjs = info_->getNGlobalIntegrableObjects();
346	haveError = 0;
347
348	if (worldRank == masterNode) {
349	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	painCave.isFatal = 1;
408	simError();
409	}
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	}
457	}
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	painCave.isFatal = 1;
475	simError();
476	}
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
486	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	}
493
494	}
495
496	}
497
498	#endif
499
500	}
501
502	void DumpReader::parseDumpLine(char line, StuntDouble integrableObject) {
503
504	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
513	if (nTokens < 14) {
514	sprintf(painCave.errMsg,
515	"DumpReader Error: Not enough Tokens.\n%s\n", line);
516	painCave.isFatal = 1;
517	simError();
518	}
519
520	std::string name = tokenizer.nextToken();
521
522	if (name != integrableObject->getType()) {
523
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	}
530
531	pos[0] = tokenizer.nextTokenAsDouble();
532	pos[1] = tokenizer.nextTokenAsDouble();
533	pos[2] = tokenizer.nextTokenAsDouble();
534	if (needPos_) {
535	integrableObject->setPos(pos);
536	}
537
538	vel[0] = tokenizer.nextTokenAsDouble();
539	vel[1] = tokenizer.nextTokenAsDouble();
540	vel[2] = tokenizer.nextTokenAsDouble();
541	if (needVel_) {
542	integrableObject->setVel(vel);
543	}
544
545	if (integrableObject->isDirectional()) {
546
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
555	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	}
574
575	}
576
577
578	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
579	double currTime;
580	Mat3x3d hmat;
581	double chi;
582	double integralOfChiDt;
583	Mat3x3d eta;
584
585	StringTokenizer tokenizer(line);
586	int nTokens;
587
588	nTokens = tokenizer.countTokens();
589
590	//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens)
591	if (nTokens < 10) {
592	sprintf(painCave.errMsg,
593	"DumpReader Error: Not enough tokens in comment line: %s", line);
594	painCave.isFatal = 1;
595	simError();
596	}
597
598	//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	//read chi and integralOfChidt, they should apprear in pair
615	if (tokenizer.countTokens() >= 2) {
616	chi = tokenizer.nextTokenAsDouble();
617	integralOfChiDt = tokenizer.nextTokenAsDouble();
618
619	s->setChi(chi);
620	s->setIntegralOfChiDt(integralOfChiDt);
621	}
622
623	//read eta (eta is 3x3 matrix)
624	if (tokenizer.countTokens() >= 9) {
625	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	}
637
638
639	}
640
641	}//end namespace oopse