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_ = new std::ifstream(filename_.c_str()); 
      
      if (inFile_->fail()) { 
        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 
      
      delete inFile_; 
      
#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]; 
    std::streampos  currPos; 
     
#ifdef IS_MPI 
     
    if (worldRank == 0) { 
#endif // is_mpi 
       
      inFile_->seekg (0, std::ios::beg); 
       
 
      currPos = inFile_->tellg(); 
      inFile_->getline(readBuffer, sizeof(readBuffer)); 
      lineNum++; 
       
      if (inFile_->eof()) { 
        sprintf(painCave.errMsg, 
                "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n", 
                filename_.c_str(), 
                lineNum); 
        painCave.isFatal = 1; 
        simError(); 
      } 
       
      while (!inFile_->eof()) { 
        framePos_.push_back(currPos); 
         
        i = atoi(readBuffer); 
         
        inFile_->getline(readBuffer, sizeof(readBuffer)); 
        lineNum++; 
         
        if (inFile_->eof()) { 
          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++) { 
          inFile_->getline(readBuffer, sizeof(readBuffer)); 
          lineNum++; 
           
          if (inFile_->eof()) { 
            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 = inFile_->tellg(); 
        inFile_->getline(readBuffer, sizeof(readBuffer)); 
        lineNum++; 
      } 
 
      inFile_->seekg (0, std::ios::beg); 
       
      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 
    inFile_->clear();  
    inFile_->seekg(framePos_[whichFrame]); 
         
    if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { 
      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 
     
     
    if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { 
      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)) {            
         
         
         
        if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { 
          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) { 
      inFile_->clear();             
      inFile_->seekg(framePos_[whichFrame]); 
       
      if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { 
        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 
       
       
       
      if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { 
        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)){ 
             
             
             
            if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { 
              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++) { 
             
             
            if (!inFile_->getline(read_buffer, sizeof(read_buffer))) { 
              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(); 
       
      RealType 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) { 
    RealType currTime; 
    Mat3x3d hmat; 
    RealType chi; 
    RealType 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:	2903
Committed:	Wed Jun 28 14:35:14 2006 UTC (18 years ago) by chrisfen
File size:	19385 byte(s)
Log Message:	more efficient file reading for thermodynamic integration, and fixed some formatting
#	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_ = new std::ifstream(filename_.c_str());
81
82	if (inFile_->fail()) {
83	sprintf(painCave.errMsg,
84	"DumpReader: Cannot open file: %s\n",
85	filename_.c_str());
86	painCave.isFatal = 1;
87	simError();
88	}
89
90	#ifdef IS_MPI
91
92	}
93
94	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95	MPIcheckPoint();
96
97	#endif
98
99	return;
100	}
101
102	DumpReader::~DumpReader() {
103
104	#ifdef IS_MPI
105
106	if (worldRank == 0) {
107	#endif
108
109	delete inFile_;
110
111	#ifdef IS_MPI
112
113	}
114
115	strcpy(checkPointMsg, "Dump file closed successfully.");
116	MPIcheckPoint();
117
118	#endif
119
120	return;
121	}
122
123	int DumpReader::getNFrames(void) {
124
125	if (!isScanned_)
126	scanFile();
127
128	return nframes_;
129	}
130
131	void DumpReader::scanFile(void) {
132	int i, j;
133	int lineNum = 0;
134	char readBuffer[maxBufferSize];
135	std::streampos currPos;
136
137	#ifdef IS_MPI
138
139	if (worldRank == 0) {
140	#endif // is_mpi
141
142	inFile_->seekg (0, std::ios::beg);
143
144
145	currPos = inFile_->tellg();
146	inFile_->getline(readBuffer, sizeof(readBuffer));
147	lineNum++;
148
149	if (inFile_->eof()) {
150	sprintf(painCave.errMsg,
151	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
152	filename_.c_str(),
153	lineNum);
154	painCave.isFatal = 1;
155	simError();
156	}
157
158	while (!inFile_->eof()) {
159	framePos_.push_back(currPos);
160
161	i = atoi(readBuffer);
162
163	inFile_->getline(readBuffer, sizeof(readBuffer));
164	lineNum++;
165
166	if (inFile_->eof()) {
167	sprintf(painCave.errMsg,
168	"DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
169	filename_.c_str(),
170	lineNum);
171	painCave.isFatal = 1;
172	simError();
173	}
174
175	for(j = 0; j < i; j++) {
176	inFile_->getline(readBuffer, sizeof(readBuffer));
177	lineNum++;
178
179	if (inFile_->eof()) {
180	sprintf(painCave.errMsg,
181	"DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
182	" with atom %d\n", filename_.c_str(),
183	lineNum,
184	j);
185
186	painCave.isFatal = 1;
187	simError();
188	}
189	}
190
191	currPos = inFile_->tellg();
192	inFile_->getline(readBuffer, sizeof(readBuffer));
193	lineNum++;
194	}
195
196	inFile_->seekg (0, std::ios::beg);
197
198	nframes_ = framePos_.size();
199	#ifdef IS_MPI
200	}
201
202	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
203
204	strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
205	MPIcheckPoint();
206
207	#endif // is_mpi
208
209	isScanned_ = true;
210	}
211
212	void DumpReader::readFrame(int whichFrame) {
213	if (!isScanned_)
214	scanFile();
215
216	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
217
218	if (storageLayout & DataStorage::dslPosition) {
219	needPos_ = true;
220	} else {
221	needPos_ = false;
222	}
223
224	if (storageLayout & DataStorage::dslVelocity) {
225	needVel_ = true;
226	} else {
227	needVel_ = false;
228	}
229
230	if (storageLayout & DataStorage::dslAmat \|\| storageLayout & DataStorage::dslElectroFrame) {
231	needQuaternion_ = true;
232	} else {
233	needQuaternion_ = false;
234	}
235
236	if (storageLayout & DataStorage::dslAngularMomentum) {
237	needAngMom_ = true;
238	} else {
239	needAngMom_ = false;
240	}
241
242	readSet(whichFrame);
243	}
244
245	void DumpReader::readSet(int whichFrame) {
246	int i;
247	int nTotObjs; // the number of atoms
248	char read_buffer[maxBufferSize]; //the line buffer for reading
249	char * eof_test; // ptr to see when we reach the end of the file
250
251	Molecule* mol;
252	StuntDouble* integrableObject;
253	SimInfo::MoleculeIterator mi;
254	Molecule::IntegrableObjectIterator ii;
255
256	#ifndef IS_MPI
257	inFile_->clear();
258	inFile_->seekg(framePos_[whichFrame]);
259
260	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
261	sprintf(painCave.errMsg,
262	"DumpReader error: error reading 1st line of \"%s\"\n",
263	filename_.c_str());
264	painCave.isFatal = 1;
265	simError();
266	}
267
268	nTotObjs = atoi(read_buffer);
269
270	if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
271	sprintf(painCave.errMsg,
272	"DumpReader error. %s nIntegrable, %d, "
273	"does not match the meta-data file's nIntegrable, %d.\n",
274	filename_.c_str(),
275	nTotObjs,
276	info_->getNGlobalIntegrableObjects());
277
278	painCave.isFatal = 1;
279	simError();
280	}
281
282	//read the box mat from the comment line
283
284
285	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
286	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
287	filename_.c_str());
288	painCave.isFatal = 1;
289	simError();
290	}
291
292	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
293
294	//parse dump lines
295
296	i = 0;
297	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
298
299	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
300	integrableObject = mol->nextIntegrableObject(ii)) {
301
302
303
304	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
305	sprintf(painCave.errMsg,
306	"DumpReader Error: error in reading file %s\n"
307	"natoms = %d; index = %d\n"
308	"error reading the line from the file.\n",
309	filename_.c_str(),
310	nTotObjs,
311	i);
312
313	painCave.isFatal = 1;
314	simError();
315	}
316
317	parseDumpLine(read_buffer, integrableObject);
318	i++;
319	}
320	}
321
322	// MPI Section of code..........
323
324	#else //IS_MPI
325
326	// first thing first, suspend fatalities.
327	int masterNode = 0;
328	int nCurObj;
329	painCave.isEventLoop = 1;
330
331	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
332	int haveError;
333
334	MPI_Status istatus;
335	int nitems;
336
337	nTotObjs = info_->getNGlobalIntegrableObjects();
338	haveError = 0;
339
340	if (worldRank == masterNode) {
341	inFile_->clear();
342	inFile_->seekg(framePos_[whichFrame]);
343
344	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
345	sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
346	filename_.c_str());
347	painCave.isFatal = 1;
348	simError();
349	}
350
351	nitems = atoi(read_buffer);
352
353	// Check to see that the number of integrable objects in the
354	// intial configuration file is the same as derived from the
355	// meta-data file.
356
357	if (nTotObjs != nitems) {
358	sprintf(painCave.errMsg,
359	"DumpReader Error. %s nIntegrable, %d, "
360	"does not match the meta-data file's nIntegrable, %d.\n",
361	filename_.c_str(),
362	nTotObjs,
363	info_->getNGlobalIntegrableObjects());
364
365	painCave.isFatal = 1;
366	simError();
367	}
368
369	//read the boxMat from the comment line
370
371
372
373	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
374	sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
375	filename_.c_str());
376	painCave.isFatal = 1;
377	simError();
378	}
379
380	//Every single processor will parse the comment line by itself
381	//By using this way, we might lose some efficiency, but if we want to add
382	//more parameters into comment line, we only need to modify function
383	//parseCommentLine
384
385	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
386	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
387
388	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
389	int which_node = info_->getMolToProc(i);
390
391	if (which_node == masterNode) {
392	//molecules belong to master node
393
394	mol = info_->getMoleculeByGlobalIndex(i);
395
396	if (mol == NULL) {
397	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
398	painCave.isFatal = 1;
399	simError();
400	}
401
402	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
403	integrableObject = mol->nextIntegrableObject(ii)){
404
405
406
407	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
408	sprintf(painCave.errMsg,
409	"DumpReader Error: error in reading file %s\n"
410	"natoms = %d; index = %d\n"
411	"error reading the line from the file.\n",
412	filename_.c_str(),
413	nTotObjs,
414	i);
415
416	painCave.isFatal = 1;
417	simError();
418	}
419
420	parseDumpLine(read_buffer, integrableObject);
421	}
422	} else {
423	//molecule belongs to slave nodes
424
425	MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
426	MPI_COMM_WORLD, &istatus);
427
428	for(int j = 0; j < nCurObj; j++) {
429
430
431	if (!inFile_->getline(read_buffer, sizeof(read_buffer))) {
432	sprintf(painCave.errMsg,
433	"DumpReader Error: error in reading file %s\n"
434	"natoms = %d; index = %d\n"
435	"error reading the line from the file.\n",
436	filename_.c_str(),
437	nTotObjs,
438	i);
439
440	painCave.isFatal = 1;
441	simError();
442	}
443
444	MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
445	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
446	}
447	}
448	}
449	} else {
450	//actions taken at slave nodes
451	MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
452
453	/*@todo/
454	parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
455
456	for(i = 0; i < info_->getNGlobalMolecules(); i++) {
457	int which_node = info_->getMolToProc(i);
458
459	if (which_node == worldRank) {
460	//molecule with global index i belongs to this processor
461
462	mol = info_->getMoleculeByGlobalIndex(i);
463	if (mol == NULL) {
464	sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
465	painCave.isFatal = 1;
466	simError();
467	}
468
469	nCurObj = mol->getNIntegrableObjects();
470
471	MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
472	MPI_COMM_WORLD);
473
474	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
475	integrableObject = mol->nextIntegrableObject(ii)){
476
477	MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
478	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
479
480	parseDumpLine(read_buffer, integrableObject);
481	}
482
483	}
484
485	}
486
487	}
488
489	#endif
490
491	}
492
493	void DumpReader::parseDumpLine(char line, StuntDouble integrableObject) {
494
495	Vector3d pos; // position place holders
496	Vector3d vel; // velocity placeholders
497	Quat4d q; // the quaternions
498	Vector3d ji; // angular velocity placeholders;
499	StringTokenizer tokenizer(line);
500	int nTokens;
501
502	nTokens = tokenizer.countTokens();
503
504	if (nTokens < 14) {
505	sprintf(painCave.errMsg,
506	"DumpReader Error: Not enough Tokens.\n%s\n", line);
507	painCave.isFatal = 1;
508	simError();
509	}
510
511	std::string name = tokenizer.nextToken();
512
513	if (name != integrableObject->getType()) {
514
515	sprintf(painCave.errMsg,
516	"DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
517	name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
518	painCave.isFatal = 1;
519	simError();
520	}
521
522	pos[0] = tokenizer.nextTokenAsDouble();
523	pos[1] = tokenizer.nextTokenAsDouble();
524	pos[2] = tokenizer.nextTokenAsDouble();
525	if (needPos_) {
526	integrableObject->setPos(pos);
527	}
528
529	vel[0] = tokenizer.nextTokenAsDouble();
530	vel[1] = tokenizer.nextTokenAsDouble();
531	vel[2] = tokenizer.nextTokenAsDouble();
532	if (needVel_) {
533	integrableObject->setVel(vel);
534	}
535
536	if (integrableObject->isDirectional()) {
537
538	q[0] = tokenizer.nextTokenAsDouble();
539	q[1] = tokenizer.nextTokenAsDouble();
540	q[2] = tokenizer.nextTokenAsDouble();
541	q[3] = tokenizer.nextTokenAsDouble();
542
543	RealType qlen = q.length();
544	if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
545
546	sprintf(painCave.errMsg,
547	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
548	painCave.isFatal = 1;
549	simError();
550
551	}
552
553	q.normalize();
554	if (needQuaternion_) {
555	integrableObject->setQ(q);
556	}
557
558	ji[0] = tokenizer.nextTokenAsDouble();
559	ji[1] = tokenizer.nextTokenAsDouble();
560	ji[2] = tokenizer.nextTokenAsDouble();
561	if (needAngMom_) {
562	integrableObject->setJ(ji);
563	}
564	}
565
566	}
567
568
569	void DumpReader::parseCommentLine(char* line, Snapshot* s) {
570	RealType currTime;
571	Mat3x3d hmat;
572	RealType chi;
573	RealType integralOfChiDt;
574	Mat3x3d eta;
575
576	StringTokenizer tokenizer(line);
577	int nTokens;
578
579	nTokens = tokenizer.countTokens();
580
581	//comment line should at least contain 10 tokens: current time(1 token) and h-matrix(9 tokens)
582	if (nTokens < 10) {
583	sprintf(painCave.errMsg,
584	"DumpReader Error: Not enough tokens in comment line: %s", line);
585	painCave.isFatal = 1;
586	simError();
587	}
588
589	//read current time
590	currTime = tokenizer.nextTokenAsDouble();
591	s->setTime(currTime);
592
593	//read h-matrix
594	hmat(0, 0) = tokenizer.nextTokenAsDouble();
595	hmat(0, 1) = tokenizer.nextTokenAsDouble();
596	hmat(0, 2) = tokenizer.nextTokenAsDouble();
597	hmat(1, 0) = tokenizer.nextTokenAsDouble();
598	hmat(1, 1) = tokenizer.nextTokenAsDouble();
599	hmat(1, 2) = tokenizer.nextTokenAsDouble();
600	hmat(2, 0) = tokenizer.nextTokenAsDouble();
601	hmat(2, 1) = tokenizer.nextTokenAsDouble();
602	hmat(2, 2) = tokenizer.nextTokenAsDouble();
603	s->setHmat(hmat);
604
605	//read chi and integralOfChidt, they should apprear in pair
606	if (tokenizer.countTokens() >= 2) {
607	chi = tokenizer.nextTokenAsDouble();
608	integralOfChiDt = tokenizer.nextTokenAsDouble();
609
610	s->setChi(chi);
611	s->setIntegralOfChiDt(integralOfChiDt);
612	}
613
614	//read eta (eta is 3x3 matrix)
615	if (tokenizer.countTokens() >= 9) {
616	eta(0, 0) = tokenizer.nextTokenAsDouble();
617	eta(0, 1) = tokenizer.nextTokenAsDouble();
618	eta(0, 2) = tokenizer.nextTokenAsDouble();
619	eta(1, 0) = tokenizer.nextTokenAsDouble();
620	eta(1, 1) = tokenizer.nextTokenAsDouble();
621	eta(1, 2) = tokenizer.nextTokenAsDouble();
622	eta(2, 0) = tokenizer.nextTokenAsDouble();
623	eta(2, 1) = tokenizer.nextTokenAsDouble();
624	eta(2, 2) = tokenizer.nextTokenAsDouble();
625
626	s->setEta(eta);
627	}
628
629
630	}
631
632	}//end namespace oopse