OOPSE-1.0/libmdtools/InitializeFromFile.cpp

#define _FILE_OFFSET_BITS 64
#include <iostream>
#include <math.h>

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>

#include "ReadWrite.hpp"
#include "simError.h"
#include "GenericData.hpp"

#ifdef IS_MPI
#include <mpi.h>
#include "mpiSimulation.hpp"
#define TAKE_THIS_TAG_CHAR 3134
#define TAKE_THIS_TAG_INT 3135

namespace initFile{
  void nodeZeroError( void );
  void anonymousNodeDie( void );
}

using namespace initFile;

#endif // is_mpi

InitializeFromFile::InitializeFromFile( char *in_name ){

#ifdef IS_MPI
  if (worldRank == 0) {
#endif

  c_in_file = fopen(in_name, "r");
  if(c_in_file == NULL){
    sprintf(painCave.errMsg,
            "Cannot open file: %s\n", in_name);
    painCave.isFatal = 1;
    simError();
  }

  strcpy( c_in_name, in_name);
#ifdef IS_MPI
  }
  else{
          sprintf( c_in_name, "mpiNodeParser_%d", worldRank );
  }
  
  strcpy( checkPointMsg, "Infile opened for reading successfully." );
  MPIcheckPoint();
#endif
  return;
}

InitializeFromFile::~InitializeFromFile( ){
#ifdef IS_MPI
  if (worldRank == 0) {
#endif
  int error;
  error = fclose( c_in_file );
  if( error ){
    sprintf( painCave.errMsg,
             "Error closing %s\n", c_in_name );
    simError();
  }
#ifdef IS_MPI
  }
  strcpy( checkPointMsg, "Infile closed successfully." );
  MPIcheckPoint();
#endif

  return;
}


void InitializeFromFile :: readInit( SimInfo* the_simnfo ){

  int i, j;

#ifdef IS_MPI
  int done, which_node, which_atom; // loop counter
#endif //is_mpi

  const int BUFFERSIZE = 2000; // size of the read buffer
  int nTotObjs; // the number of atoms
  char read_buffer[BUFFERSIZE]; //the line buffer for reading

  char *eof_test; // ptr to see when we reach the end of the file
  char *parseErr;

  vector<StuntDouble*> integrableObjects;

  simnfo = the_simnfo;


#ifndef IS_MPI
  eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
  if( eof_test == NULL ){
    sprintf( painCave.errMsg,
             "InitializeFromFile error: error reading 1st line of \"%s\"\n",
             c_in_name );
    painCave.isFatal = 1;
    simError();
  }

  nTotObjs = atoi( read_buffer );

  if( nTotObjs != simnfo->getTotIntegrableObjects() ){
    sprintf( painCave.errMsg,
             "Initialize from File error. %s n_atoms, %d, "
             "does not match the BASS file's n_atoms, %d.\n",
             c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
    painCave.isFatal = 1;
    simError();
  }

  //read the box mat from the comment line

  eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
  if(eof_test == NULL){
    sprintf( painCave.errMsg,
             "error in reading commment in %s\n", c_in_name);
    painCave.isFatal = 1;
    simError();
  }

  parseErr = parseCommentLine( read_buffer, simnfo);
  if( parseErr != NULL ){
    strcpy( painCave.errMsg, parseErr );
    painCave.isFatal = 1;
    simError();
  }

  //parse dump lines

  for( i=0; i < simnfo->n_mol; i++){

    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();

    for(j = 0; j < integrableObjects.size(); j++){

      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
      if(eof_test == NULL){
        sprintf(painCave.errMsg,
              "error in reading file %s\n"
              "natoms  = %d; index = %d\n"
              "error reading the line from the file.\n",
              c_in_name, nTotObjs, i );
        painCave.isFatal = 1;
        simError();
      }
      
      parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
      if( parseErr != NULL ){
        strcpy( painCave.errMsg, parseErr );
        painCave.isFatal = 1;
        simError();
      }
    }
  }

  // MPI Section of code..........
#else //IS_MPI

  // first thing first, suspend fatalities.
  painCave.isEventLoop = 1;

  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
  int haveError;

  MPI_Status istatus;
  int *MolToProcMap = mpiSim->getMolToProcMap();
  int localIndex;
  int nCurObj;
  int nItems;

  nTotObjs = simnfo->getTotIntegrableObjects();
  haveError = 0;
  if (worldRank == 0) {

    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
    if( eof_test == NULL ){
      sprintf( painCave.errMsg,
               "Error reading 1st line of %s \n ",c_in_name);
      haveError = 1;
      simError();
    }

    nItems = atoi( read_buffer );

    // Check to see that the number of integrable objects  in the intial configuration file is the
    // same as declared in simBass.

    if( nTotObjs != nItems){
      sprintf( painCave.errMsg,
               "Initialize from File error. %s n_atoms, %d, "
               "does not match the BASS file's n_atoms, %d.\n",
               c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
      haveError= 1;
      simError();
    }

    //read the boxMat from the comment line

    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
    if(eof_test == NULL){
      sprintf( painCave.errMsg,
               "error in reading commment in %s\n", c_in_name);
      haveError = 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, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);


    parseErr = parseCommentLine( read_buffer, simnfo);

    if( parseErr != NULL ){
      strcpy( painCave.errMsg, parseErr );
      haveError = 1;
      simError();
    }

    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
      which_node = MolToProcMap[i];
      if(which_node == 0){
       //molecules belong to master node

      localIndex = mpiSim->getGlobalToLocalMol(i);

      if(localIndex == -1) {
        strcpy(painCave.errMsg, "Molecule not found on node 0!");
        haveError = 1;
        simError();
      }

       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
       for(j=0; j < integrableObjects.size(); j++){
        
          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
          if(eof_test == NULL){
                sprintf(painCave.errMsg,
                    "error in reading file %s\n"
                    "natoms  = %d; index = %d\n"
                    "error reading the line from the file.\n",
                    c_in_name, nTotObjs, i );
                haveError= 1;
                simError();
          }
          
          if(haveError) nodeZeroError();

          parseDumpLine(read_buffer, integrableObjects[j]);
           
       }


      }
      else{
      //molecule belongs to slave nodes

        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);

       for(j=0; j < nCurObj; j++){
        
          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
          if(eof_test == NULL){
                sprintf(painCave.errMsg,
                    "error in reading file %s\n"
                    "natoms  = %d; index = %d\n"
                    "error reading the line from the file.\n",
                    c_in_name, nTotObjs, i );
                haveError= 1;
                simError();
          }
          
          if(haveError) nodeZeroError();

            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);

       }

      }
      
    }
    
  }
  else{
  //actions taken at slave nodes

    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);

    parseErr = parseCommentLine( read_buffer, simnfo);

    if( parseErr != NULL ){
      strcpy( painCave.errMsg, parseErr );
      haveError = 1;
      simError();
    }
  
    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
      which_node = MolToProcMap[i];
      
      if(which_node == worldRank){
      //molecule with global index i belongs to this processor
      
        localIndex = mpiSim->getGlobalToLocalMol(i);

        if(localIndex == -1) {
          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
          haveError = 1;
          simError();
        }

        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        

        nCurObj = integrableObjects.size();
        
        MPI_Send(&nCurObj, 1, MPI_INT, 0,
                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);

        for(j = 0; j < integrableObjects.size(); j++){

          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);

          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);

          if( parseErr != NULL ){
                strcpy( painCave.errMsg, parseErr );
                simError();
          }

        }
          
      }
      
    }

  }
#endif
}

char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){

  char *foo; // the pointer to the current string token

  double pos[3]; // position place holders
  double vel[3]; // velocity placeholders
  double q[4]; // the quaternions
  double ji[3]; // angular velocity placeholders;
  double qSqr, qLength; // needed to normalize the quaternion vector.


  // set the string tokenizer

  foo = strtok(readLine, " ,;\t");

  // check the atom name to the current atom

  if( strcmp( foo, sd->getType() ) ){
    sprintf( painCave.errMsg,
             "Initialize from file error.  Does not"
             " match the BASS atom %s.\n",
             sd->getType() );
    return strdup( painCave.errMsg );
  }

  // get the positions

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading postition x from %s\n",
             c_in_name);
    return strdup( painCave.errMsg );
  }
  pos[0] = atof( foo );

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading postition y from %s\n",
             c_in_name);
    return strdup( painCave.errMsg );
  }
  pos[1] = atof( foo );

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading postition z from %s\n",
             c_in_name);
    return strdup( painCave.errMsg );
  }
  pos[2] = atof( foo );


  // get the velocities

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity x from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  vel[0] = atof( foo );

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity x from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  vel[1] = atof( foo );

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity x from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  vel[2] = atof( foo );


  // add the positions and velocities to the atom

  sd->setPos( pos );
  sd->setVel( vel );

  if (!sd->isDirectional())
    return NULL;

  // get the quaternions

  if( sd->isDirectional() ){

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    q[0] = atof( foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    q[1] = atof( foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    q[2] = atof( foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    q[3] = atof( foo );

    // get the angular velocities

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    ji[0] = atof( foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    ji[1] = atof(foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    ji[2] = atof( foo );


    // check that the quaternion vector is normalized

    qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);

    if (fabs(qSqr) < 1e-6) {
      sprintf(painCave.errMsg,
          "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
       return strdup(painCave.errMsg);
    }
    
    qLength = sqrt( qSqr );
    q[0] = q[0] / qLength;
    q[1] = q[1] / qLength;
    q[2] = q[2] / qLength;
    q[3] = q[3] / qLength;

    // add quaternion and angular velocities

    sd->setQ( q );
    sd->setJ( ji );
  }


  return NULL;
}


char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){

  double currTime;
  double boxMat[9];
  double theBoxMat3[3][3];
  double chi;
  double integralOfChidt;
  double eta[9];

  char *foo; // the pointer to the current string token

  // set the string tokenizer

  foo = strtok(readLine, " ,;\t");
  // set the timeToken.

  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Time from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }

  currTime = atof( foo );
  entry_plug->setTime( currTime );

  //get H-Matrix

  for(int i = 0 ; i < 9; i++){
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading H[%d] from %s\n", i, c_in_name );
      return strdup( painCave.errMsg );
    }
    boxMat[i] = atof( foo );
  }

  for(int i=0;i<3;i++)
    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];

  //set H-Matrix
  entry_plug->setBoxM( theBoxMat3 );

  //get chi and integralOfChidt, they should appear by pair

  if( entry_plug->useInitXSstate ){
    foo = strtok(NULL, " ,;\t\n");
    if(foo != NULL){
      chi = atof(foo);
      
      foo = strtok(NULL, " ,;\t\n");
      if(foo == NULL){
        sprintf( painCave.errMsg,
                 "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
        return strdup( painCave.errMsg );
      }
      integralOfChidt = atof( foo );
      
      //push chi and integralOfChidt into SimInfo::properties which can be
      //retrieved by integrator later
      DoubleData* chiValue = new DoubleData();
      chiValue->setID(CHIVALUE_ID);
      chiValue->setData(chi);
      entry_plug->addProperty(chiValue);
      
      DoubleData* integralOfChidtValue = new DoubleData();
      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
      integralOfChidtValue->setData(integralOfChidt);
      entry_plug->addProperty(integralOfChidtValue);
      
    }
    else
      return NULL;
    
    //get eta
    foo = strtok(NULL, " ,;\t\n");
    if(foo != NULL ){
  
      for(int i = 0 ; i < 9; i++){
        
        if(foo == NULL){
          sprintf( painCave.errMsg,
                   "error in reading eta[%d] from %s\n", i, c_in_name );
          return strdup( painCave.errMsg );
        }
        eta[i] = atof( foo );
        foo = strtok(NULL, " ,;\t\n");
      }
    }
    else
      return NULL;
    
    //push eta into SimInfo::properties which can be
    //retrieved by integrator later
    
    DoubleArrayData* etaValue = new DoubleArrayData();
    etaValue->setID(ETAVALUE_ID);
    etaValue->setData(eta, 9);
    entry_plug->addProperty(etaValue);
  }

  return NULL;
}

#ifdef IS_MPI

// a couple of functions to let us escape the read loop

void initFile::nodeZeroError( void ){
  int j, myStatus;

  myStatus = 0;
  for (j = 0; j < mpiSim->getNProcessors(); j++) {
    MPI_Send( &myStatus, 1, MPI_INT, j,
              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
  }


  MPI_Finalize();
  exit (0);

}

void initFile::anonymousNodeDie( void ){

  MPI_Finalize();
  exit (0);
}

#endif //is_mpi
Revision:	1334
Committed:	Fri Jul 16 18:58:03 2004 UTC (19 years, 11 months ago) by gezelter
File size:	16156 byte(s)
Log Message:	Initial import of OOPSE-1.0 source tree
#	User	Rev	Content
1	gezelter	1334	#define _FILE_OFFSET_BITS 64
2			#include <iostream>
3			#include <math.h>
4
5			#include <stdio.h>
6			#include <stdlib.h>
7			#include <string.h>
8			#include <unistd.h>
9			#include <sys/types.h>
10			#include <sys/stat.h>
11
12			#include "ReadWrite.hpp"
13			#include "simError.h"
14			#include "GenericData.hpp"
15
16			#ifdef IS_MPI
17			#include <mpi.h>
18			#include "mpiSimulation.hpp"
19			#define TAKE_THIS_TAG_CHAR 3134
20			#define TAKE_THIS_TAG_INT 3135
21
22			namespace initFile{
23			void nodeZeroError( void );
24			void anonymousNodeDie( void );
25			}
26
27			using namespace initFile;
28
29			#endif // is_mpi
30
31			InitializeFromFile::InitializeFromFile( char *in_name ){
32
33			#ifdef IS_MPI
34			if (worldRank == 0) {
35			#endif
36
37			c_in_file = fopen(in_name, "r");
38			if(c_in_file == NULL){
39			sprintf(painCave.errMsg,
40			"Cannot open file: %s\n", in_name);
41			painCave.isFatal = 1;
42			simError();
43			}
44
45			strcpy( c_in_name, in_name);
46			#ifdef IS_MPI
47			}
48			else{
49			sprintf( c_in_name, "mpiNodeParser_%d", worldRank );
50			}
51
52			strcpy( checkPointMsg, "Infile opened for reading successfully." );
53			MPIcheckPoint();
54			#endif
55			return;
56			}
57
58			InitializeFromFile::~InitializeFromFile( ){
59			#ifdef IS_MPI
60			if (worldRank == 0) {
61			#endif
62			int error;
63			error = fclose( c_in_file );
64			if( error ){
65			sprintf( painCave.errMsg,
66			"Error closing %s\n", c_in_name );
67			simError();
68			}
69			#ifdef IS_MPI
70			}
71			strcpy( checkPointMsg, "Infile closed successfully." );
72			MPIcheckPoint();
73			#endif
74
75			return;
76			}
77
78
79			void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
80
81			int i, j;
82
83			#ifdef IS_MPI
84			int done, which_node, which_atom; // loop counter
85			#endif //is_mpi
86
87			const int BUFFERSIZE = 2000; // size of the read buffer
88			int nTotObjs; // the number of atoms
89			char read_buffer[BUFFERSIZE]; //the line buffer for reading
90
91			char *eof_test; // ptr to see when we reach the end of the file
92			char *parseErr;
93
94			vector<StuntDouble*> integrableObjects;
95
96			simnfo = the_simnfo;
97
98
99			#ifndef IS_MPI
100			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
101			if( eof_test == NULL ){
102			sprintf( painCave.errMsg,
103			"InitializeFromFile error: error reading 1st line of \"%s\"\n",
104			c_in_name );
105			painCave.isFatal = 1;
106			simError();
107			}
108
109			nTotObjs = atoi( read_buffer );
110
111			if( nTotObjs != simnfo->getTotIntegrableObjects() ){
112			sprintf( painCave.errMsg,
113			"Initialize from File error. %s n_atoms, %d, "
114			"does not match the BASS file's n_atoms, %d.\n",
115			c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
116			painCave.isFatal = 1;
117			simError();
118			}
119
120			//read the box mat from the comment line
121
122			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
123			if(eof_test == NULL){
124			sprintf( painCave.errMsg,
125			"error in reading commment in %s\n", c_in_name);
126			painCave.isFatal = 1;
127			simError();
128			}
129
130			parseErr = parseCommentLine( read_buffer, simnfo);
131			if( parseErr != NULL ){
132			strcpy( painCave.errMsg, parseErr );
133			painCave.isFatal = 1;
134			simError();
135			}
136
137			//parse dump lines
138
139			for( i=0; i < simnfo->n_mol; i++){
140
141			integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
142
143			for(j = 0; j < integrableObjects.size(); j++){
144
145			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
146			if(eof_test == NULL){
147			sprintf(painCave.errMsg,
148			"error in reading file %s\n"
149			"natoms = %d; index = %d\n"
150			"error reading the line from the file.\n",
151			c_in_name, nTotObjs, i );
152			painCave.isFatal = 1;
153			simError();
154			}
155
156			parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
157			if( parseErr != NULL ){
158			strcpy( painCave.errMsg, parseErr );
159			painCave.isFatal = 1;
160			simError();
161			}
162			}
163			}
164
165			// MPI Section of code..........
166			#else //IS_MPI
167
168			// first thing first, suspend fatalities.
169			painCave.isEventLoop = 1;
170
171			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
172			int haveError;
173
174			MPI_Status istatus;
175			int *MolToProcMap = mpiSim->getMolToProcMap();
176			int localIndex;
177			int nCurObj;
178			int nItems;
179
180			nTotObjs = simnfo->getTotIntegrableObjects();
181			haveError = 0;
182			if (worldRank == 0) {
183
184			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
185			if( eof_test == NULL ){
186			sprintf( painCave.errMsg,
187			"Error reading 1st line of %s \n ",c_in_name);
188			haveError = 1;
189			simError();
190			}
191
192			nItems = atoi( read_buffer );
193
194			// Check to see that the number of integrable objects in the intial configuration file is the
195			// same as declared in simBass.
196
197			if( nTotObjs != nItems){
198			sprintf( painCave.errMsg,
199			"Initialize from File error. %s n_atoms, %d, "
200			"does not match the BASS file's n_atoms, %d.\n",
201			c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
202			haveError= 1;
203			simError();
204			}
205
206			//read the boxMat from the comment line
207
208			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
209			if(eof_test == NULL){
210			sprintf( painCave.errMsg,
211			"error in reading commment in %s\n", c_in_name);
212			haveError = 1;
213			simError();
214			}
215
216			//Every single processor will parse the comment line by itself
217			//By using this way, we might lose some efficiency, but if we want to add
218			//more parameters into comment line, we only need to modify function
219			//parseCommentLine
220
221			MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
222
223
224			parseErr = parseCommentLine( read_buffer, simnfo);
225
226			if( parseErr != NULL ){
227			strcpy( painCave.errMsg, parseErr );
228			haveError = 1;
229			simError();
230			}
231
232			for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
233			which_node = MolToProcMap[i];
234			if(which_node == 0){
235			//molecules belong to master node
236
237			localIndex = mpiSim->getGlobalToLocalMol(i);
238
239			if(localIndex == -1) {
240			strcpy(painCave.errMsg, "Molecule not found on node 0!");
241			haveError = 1;
242			simError();
243			}
244
245			integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
246			for(j=0; j < integrableObjects.size(); j++){
247
248			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
249			if(eof_test == NULL){
250			sprintf(painCave.errMsg,
251			"error in reading file %s\n"
252			"natoms = %d; index = %d\n"
253			"error reading the line from the file.\n",
254			c_in_name, nTotObjs, i );
255			haveError= 1;
256			simError();
257			}
258
259			if(haveError) nodeZeroError();
260
261			parseDumpLine(read_buffer, integrableObjects[j]);
262
263			}
264
265
266			}
267			else{
268			//molecule belongs to slave nodes
269
270			MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
271			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
272
273			for(j=0; j < nCurObj; j++){
274
275			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
276			if(eof_test == NULL){
277			sprintf(painCave.errMsg,
278			"error in reading file %s\n"
279			"natoms = %d; index = %d\n"
280			"error reading the line from the file.\n",
281			c_in_name, nTotObjs, i );
282			haveError= 1;
283			simError();
284			}
285
286			if(haveError) nodeZeroError();
287
288			MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
289			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
290
291			}
292
293			}
294
295			}
296
297			}
298			else{
299			//actions taken at slave nodes
300
301			MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
302
303			parseErr = parseCommentLine( read_buffer, simnfo);
304
305			if( parseErr != NULL ){
306			strcpy( painCave.errMsg, parseErr );
307			haveError = 1;
308			simError();
309			}
310
311			for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
312			which_node = MolToProcMap[i];
313
314			if(which_node == worldRank){
315			//molecule with global index i belongs to this processor
316
317			localIndex = mpiSim->getGlobalToLocalMol(i);
318
319			if(localIndex == -1) {
320			sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
321			haveError = 1;
322			simError();
323			}
324
325			integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
326
327			nCurObj = integrableObjects.size();
328
329			MPI_Send(&nCurObj, 1, MPI_INT, 0,
330			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
331
332			for(j = 0; j < integrableObjects.size(); j++){
333
334			MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
335			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
336
337			parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
338
339			if( parseErr != NULL ){
340			strcpy( painCave.errMsg, parseErr );
341			simError();
342			}
343
344			}
345
346			}
347
348			}
349
350			}
351			#endif
352			}
353
354			char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
355
356			char *foo; // the pointer to the current string token
357
358			double pos[3]; // position place holders
359			double vel[3]; // velocity placeholders
360			double q[4]; // the quaternions
361			double ji[3]; // angular velocity placeholders;
362			double qSqr, qLength; // needed to normalize the quaternion vector.
363
364
365			// set the string tokenizer
366
367			foo = strtok(readLine, " ,;\t");
368
369			// check the atom name to the current atom
370
371			if( strcmp( foo, sd->getType() ) ){
372			sprintf( painCave.errMsg,
373			"Initialize from file error. Does not"
374			" match the BASS atom %s.\n",
375			sd->getType() );
376			return strdup( painCave.errMsg );
377			}
378
379			// get the positions
380
381			foo = strtok(NULL, " ,;\t");
382			if(foo == NULL){
383			sprintf( painCave.errMsg,
384			"error in reading postition x from %s\n",
385			c_in_name);
386			return strdup( painCave.errMsg );
387			}
388			pos[0] = atof( foo );
389
390			foo = strtok(NULL, " ,;\t");
391			if(foo == NULL){
392			sprintf( painCave.errMsg,
393			"error in reading postition y from %s\n",
394			c_in_name);
395			return strdup( painCave.errMsg );
396			}
397			pos[1] = atof( foo );
398
399			foo = strtok(NULL, " ,;\t");
400			if(foo == NULL){
401			sprintf( painCave.errMsg,
402			"error in reading postition z from %s\n",
403			c_in_name);
404			return strdup( painCave.errMsg );
405			}
406			pos[2] = atof( foo );
407
408
409			// get the velocities
410
411			foo = strtok(NULL, " ,;\t");
412			if(foo == NULL){
413			sprintf( painCave.errMsg,
414			"error in reading velocity x from %s\n",
415			c_in_name );
416			return strdup( painCave.errMsg );
417			}
418			vel[0] = atof( foo );
419
420			foo = strtok(NULL, " ,;\t");
421			if(foo == NULL){
422			sprintf( painCave.errMsg,
423			"error in reading velocity x from %s\n",
424			c_in_name );
425			return strdup( painCave.errMsg );
426			}
427			vel[1] = atof( foo );
428
429			foo = strtok(NULL, " ,;\t");
430			if(foo == NULL){
431			sprintf( painCave.errMsg,
432			"error in reading velocity x from %s\n",
433			c_in_name );
434			return strdup( painCave.errMsg );
435			}
436			vel[2] = atof( foo );
437
438
439			// add the positions and velocities to the atom
440
441			sd->setPos( pos );
442			sd->setVel( vel );
443
444			if (!sd->isDirectional())
445			return NULL;
446
447			// get the quaternions
448
449			if( sd->isDirectional() ){
450
451			foo = strtok(NULL, " ,;\t");
452			if(foo == NULL){
453			sprintf( painCave.errMsg,
454			"error in reading velocity x from %s\n",
455			c_in_name );
456			return strdup( painCave.errMsg );
457			}
458			q[0] = atof( foo );
459
460			foo = strtok(NULL, " ,;\t");
461			if(foo == NULL){
462			sprintf( painCave.errMsg,
463			"error in reading velocity x from %s\n",
464			c_in_name );
465			return strdup( painCave.errMsg );
466			}
467			q[1] = atof( foo );
468
469			foo = strtok(NULL, " ,;\t");
470			if(foo == NULL){
471			sprintf( painCave.errMsg,
472			"error in reading velocity x from %s\n",
473			c_in_name );
474			return strdup( painCave.errMsg );
475			}
476			q[2] = atof( foo );
477
478			foo = strtok(NULL, " ,;\t");
479			if(foo == NULL){
480			sprintf( painCave.errMsg,
481			"error in reading velocity x from %s\n",
482			c_in_name );
483			return strdup( painCave.errMsg );
484			}
485			q[3] = atof( foo );
486
487			// get the angular velocities
488
489			foo = strtok(NULL, " ,;\t");
490			if(foo == NULL){
491			sprintf( painCave.errMsg,
492			"error in reading velocity x from %s\n",
493			c_in_name );
494			return strdup( painCave.errMsg );
495			}
496			ji[0] = atof( foo );
497
498			foo = strtok(NULL, " ,;\t");
499			if(foo == NULL){
500			sprintf( painCave.errMsg,
501			"error in reading velocity x from %s\n",
502			c_in_name );
503			return strdup( painCave.errMsg );
504			}
505			ji[1] = atof(foo );
506
507			foo = strtok(NULL, " ,;\t");
508			if(foo == NULL){
509			sprintf( painCave.errMsg,
510			"error in reading velocity x from %s\n",
511			c_in_name );
512			return strdup( painCave.errMsg );
513			}
514			ji[2] = atof( foo );
515
516
517			// check that the quaternion vector is normalized
518
519			qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
520
521			if (fabs(qSqr) < 1e-6) {
522			sprintf(painCave.errMsg,
523			"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
524			return strdup(painCave.errMsg);
525			}
526
527			qLength = sqrt( qSqr );
528			q[0] = q[0] / qLength;
529			q[1] = q[1] / qLength;
530			q[2] = q[2] / qLength;
531			q[3] = q[3] / qLength;
532
533			// add quaternion and angular velocities
534
535			sd->setQ( q );
536			sd->setJ( ji );
537			}
538
539
540
541			return NULL;
542			}
543
544
545			char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
546
547			double currTime;
548			double boxMat[9];
549			double theBoxMat3[3][3];
550			double chi;
551			double integralOfChidt;
552			double eta[9];
553
554			char *foo; // the pointer to the current string token
555
556			// set the string tokenizer
557
558			foo = strtok(readLine, " ,;\t");
559			// set the timeToken.
560
561			if(foo == NULL){
562			sprintf( painCave.errMsg,
563			"error in reading Time from %s\n",
564			c_in_name );
565			return strdup( painCave.errMsg );
566			}
567
568			currTime = atof( foo );
569			entry_plug->setTime( currTime );
570
571			//get H-Matrix
572
573			for(int i = 0 ; i < 9; i++){
574			foo = strtok(NULL, " ,;\t");
575			if(foo == NULL){
576			sprintf( painCave.errMsg,
577			"error in reading H[%d] from %s\n", i, c_in_name );
578			return strdup( painCave.errMsg );
579			}
580			boxMat[i] = atof( foo );
581			}
582
583			for(int i=0;i<3;i++)
584			for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
585
586			//set H-Matrix
587			entry_plug->setBoxM( theBoxMat3 );
588
589			//get chi and integralOfChidt, they should appear by pair
590
591			if( entry_plug->useInitXSstate ){
592			foo = strtok(NULL, " ,;\t\n");
593			if(foo != NULL){
594			chi = atof(foo);
595
596			foo = strtok(NULL, " ,;\t\n");
597			if(foo == NULL){
598			sprintf( painCave.errMsg,
599			"chi and integralOfChidt should appear by pair in %s\n", c_in_name );
600			return strdup( painCave.errMsg );
601			}
602			integralOfChidt = atof( foo );
603
604			//push chi and integralOfChidt into SimInfo::properties which can be
605			//retrieved by integrator later
606			DoubleData* chiValue = new DoubleData();
607			chiValue->setID(CHIVALUE_ID);
608			chiValue->setData(chi);
609			entry_plug->addProperty(chiValue);
610
611			DoubleData* integralOfChidtValue = new DoubleData();
612			integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
613			integralOfChidtValue->setData(integralOfChidt);
614			entry_plug->addProperty(integralOfChidtValue);
615
616			}
617			else
618			return NULL;
619
620			//get eta
621			foo = strtok(NULL, " ,;\t\n");
622			if(foo != NULL ){
623
624			for(int i = 0 ; i < 9; i++){
625
626			if(foo == NULL){
627			sprintf( painCave.errMsg,
628			"error in reading eta[%d] from %s\n", i, c_in_name );
629			return strdup( painCave.errMsg );
630			}
631			eta[i] = atof( foo );
632			foo = strtok(NULL, " ,;\t\n");
633			}
634			}
635			else
636			return NULL;
637
638			//push eta into SimInfo::properties which can be
639			//retrieved by integrator later
640
641			DoubleArrayData* etaValue = new DoubleArrayData();
642			etaValue->setID(ETAVALUE_ID);
643			etaValue->setData(eta, 9);
644			entry_plug->addProperty(etaValue);
645			}
646
647			return NULL;
648			}
649
650			#ifdef IS_MPI
651
652			// a couple of functions to let us escape the read loop
653
654			void initFile::nodeZeroError( void ){
655			int j, myStatus;
656
657			myStatus = 0;
658			for (j = 0; j < mpiSim->getNProcessors(); j++) {
659			MPI_Send( &myStatus, 1, MPI_INT, j,
660			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
661			}
662
663
664			MPI_Finalize();
665			exit (0);
666
667			}
668
669			void initFile::anonymousNodeDie( void ){
670
671			MPI_Finalize();
672			exit (0);
673			}
674
675			#endif //is_mpi