src/io/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 "io/ReadWrite.hpp"
#include "utils/simError.h"
#include "utils/GenericData.hpp"

#ifdef IS_MPI
#include <mpi.h>
#include "brains/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 nIntegrable, %d, "
             "does not match the meta-data file's nIntegrable, %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 derived from the
    // meta-data file.

    if( nTotObjs != nItems){
      sprintf( painCave.errMsg,
               "Initialize from File error. %s nIntegrable, %d, "
               "does not match the meta-data file's nIntegrable, %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 meta-data 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:	1492
Committed:	Fri Sep 24 16:27:58 2004 UTC (19 years, 9 months ago) by tim
File size:	16227 byte(s)
Log Message:	change the #include in source files
#	Content
1	#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 "io/ReadWrite.hpp"
13	#include "utils/simError.h"
14	#include "utils/GenericData.hpp"
15
16	#ifdef IS_MPI
17	#include <mpi.h>
18	#include "brains/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 nIntegrable, %d, "
114	"does not match the meta-data file's nIntegrable, %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
195	// intial configuration file is the same as derived from the
196	// meta-data file.
197
198	if( nTotObjs != nItems){
199	sprintf( painCave.errMsg,
200	"Initialize from File error. %s nIntegrable, %d, "
201	"does not match the meta-data file's nIntegrable, %d.\n",
202	c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
203	haveError= 1;
204	simError();
205	}
206
207	//read the boxMat from the comment line
208
209	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
210	if(eof_test == NULL){
211	sprintf( painCave.errMsg,
212	"error in reading commment in %s\n", c_in_name);
213	haveError = 1;
214	simError();
215	}
216
217	//Every single processor will parse the comment line by itself
218	//By using this way, we might lose some efficiency, but if we want to add
219	//more parameters into comment line, we only need to modify function
220	//parseCommentLine
221
222	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
223
224
225	parseErr = parseCommentLine( read_buffer, simnfo);
226
227	if( parseErr != NULL ){
228	strcpy( painCave.errMsg, parseErr );
229	haveError = 1;
230	simError();
231	}
232
233	for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
234	which_node = MolToProcMap[i];
235	if(which_node == 0){
236	//molecules belong to master node
237
238	localIndex = mpiSim->getGlobalToLocalMol(i);
239
240	if(localIndex == -1) {
241	strcpy(painCave.errMsg, "Molecule not found on node 0!");
242	haveError = 1;
243	simError();
244	}
245
246	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
247	for(j=0; j < integrableObjects.size(); j++){
248
249	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
250	if(eof_test == NULL){
251	sprintf(painCave.errMsg,
252	"error in reading file %s\n"
253	"natoms = %d; index = %d\n"
254	"error reading the line from the file.\n",
255	c_in_name, nTotObjs, i );
256	haveError= 1;
257	simError();
258	}
259
260	if(haveError) nodeZeroError();
261
262	parseDumpLine(read_buffer, integrableObjects[j]);
263
264	}
265
266
267	}
268	else{
269	//molecule belongs to slave nodes
270
271	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
272	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
273
274	for(j=0; j < nCurObj; j++){
275
276	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
277	if(eof_test == NULL){
278	sprintf(painCave.errMsg,
279	"error in reading file %s\n"
280	"natoms = %d; index = %d\n"
281	"error reading the line from the file.\n",
282	c_in_name, nTotObjs, i );
283	haveError= 1;
284	simError();
285	}
286
287	if(haveError) nodeZeroError();
288
289	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
290	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
291
292	}
293
294	}
295
296	}
297
298	}
299	else{
300	//actions taken at slave nodes
301
302	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
303
304	parseErr = parseCommentLine( read_buffer, simnfo);
305
306	if( parseErr != NULL ){
307	strcpy( painCave.errMsg, parseErr );
308	haveError = 1;
309	simError();
310	}
311
312	for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
313	which_node = MolToProcMap[i];
314
315	if(which_node == worldRank){
316	//molecule with global index i belongs to this processor
317
318	localIndex = mpiSim->getGlobalToLocalMol(i);
319
320	if(localIndex == -1) {
321	sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
322	haveError = 1;
323	simError();
324	}
325
326	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
327
328	nCurObj = integrableObjects.size();
329
330	MPI_Send(&nCurObj, 1, MPI_INT, 0,
331	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
332
333	for(j = 0; j < integrableObjects.size(); j++){
334
335	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
336	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
337
338	parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
339
340	if( parseErr != NULL ){
341	strcpy( painCave.errMsg, parseErr );
342	simError();
343	}
344
345	}
346
347	}
348
349	}
350
351	}
352	#endif
353	}
354
355	char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
356
357	char *foo; // the pointer to the current string token
358
359	double pos[3]; // position place holders
360	double vel[3]; // velocity placeholders
361	double q[4]; // the quaternions
362	double ji[3]; // angular velocity placeholders;
363	double qSqr, qLength; // needed to normalize the quaternion vector.
364
365
366	// set the string tokenizer
367
368	foo = strtok(readLine, " ,;\t");
369
370	// check the atom name to the current atom
371
372	if( strcmp( foo, sd->getType() ) ){
373	sprintf( painCave.errMsg,
374	"Initialize from file error. Does not"
375	" match the meta-data atom %s.\n",
376	sd->getType() );
377	return strdup( painCave.errMsg );
378	}
379
380	// get the positions
381
382	foo = strtok(NULL, " ,;\t");
383	if(foo == NULL){
384	sprintf( painCave.errMsg,
385	"error in reading postition x from %s\n",
386	c_in_name);
387	return strdup( painCave.errMsg );
388	}
389	pos[0] = atof( foo );
390
391	foo = strtok(NULL, " ,;\t");
392	if(foo == NULL){
393	sprintf( painCave.errMsg,
394	"error in reading postition y from %s\n",
395	c_in_name);
396	return strdup( painCave.errMsg );
397	}
398	pos[1] = atof( foo );
399
400	foo = strtok(NULL, " ,;\t");
401	if(foo == NULL){
402	sprintf( painCave.errMsg,
403	"error in reading postition z from %s\n",
404	c_in_name);
405	return strdup( painCave.errMsg );
406	}
407	pos[2] = atof( foo );
408
409
410	// get the velocities
411
412	foo = strtok(NULL, " ,;\t");
413	if(foo == NULL){
414	sprintf( painCave.errMsg,
415	"error in reading velocity x from %s\n",
416	c_in_name );
417	return strdup( painCave.errMsg );
418	}
419	vel[0] = atof( foo );
420
421	foo = strtok(NULL, " ,;\t");
422	if(foo == NULL){
423	sprintf( painCave.errMsg,
424	"error in reading velocity x from %s\n",
425	c_in_name );
426	return strdup( painCave.errMsg );
427	}
428	vel[1] = atof( foo );
429
430	foo = strtok(NULL, " ,;\t");
431	if(foo == NULL){
432	sprintf( painCave.errMsg,
433	"error in reading velocity x from %s\n",
434	c_in_name );
435	return strdup( painCave.errMsg );
436	}
437	vel[2] = atof( foo );
438
439
440	// add the positions and velocities to the atom
441
442	sd->setPos( pos );
443	sd->setVel( vel );
444
445	if (!sd->isDirectional())
446	return NULL;
447
448	// get the quaternions
449
450	if( sd->isDirectional() ){
451
452	foo = strtok(NULL, " ,;\t");
453	if(foo == NULL){
454	sprintf( painCave.errMsg,
455	"error in reading velocity x from %s\n",
456	c_in_name );
457	return strdup( painCave.errMsg );
458	}
459	q[0] = atof( foo );
460
461	foo = strtok(NULL, " ,;\t");
462	if(foo == NULL){
463	sprintf( painCave.errMsg,
464	"error in reading velocity x from %s\n",
465	c_in_name );
466	return strdup( painCave.errMsg );
467	}
468	q[1] = atof( foo );
469
470	foo = strtok(NULL, " ,;\t");
471	if(foo == NULL){
472	sprintf( painCave.errMsg,
473	"error in reading velocity x from %s\n",
474	c_in_name );
475	return strdup( painCave.errMsg );
476	}
477	q[2] = atof( foo );
478
479	foo = strtok(NULL, " ,;\t");
480	if(foo == NULL){
481	sprintf( painCave.errMsg,
482	"error in reading velocity x from %s\n",
483	c_in_name );
484	return strdup( painCave.errMsg );
485	}
486	q[3] = atof( foo );
487
488	// get the angular velocities
489
490	foo = strtok(NULL, " ,;\t");
491	if(foo == NULL){
492	sprintf( painCave.errMsg,
493	"error in reading velocity x from %s\n",
494	c_in_name );
495	return strdup( painCave.errMsg );
496	}
497	ji[0] = atof( foo );
498
499	foo = strtok(NULL, " ,;\t");
500	if(foo == NULL){
501	sprintf( painCave.errMsg,
502	"error in reading velocity x from %s\n",
503	c_in_name );
504	return strdup( painCave.errMsg );
505	}
506	ji[1] = atof(foo );
507
508	foo = strtok(NULL, " ,;\t");
509	if(foo == NULL){
510	sprintf( painCave.errMsg,
511	"error in reading velocity x from %s\n",
512	c_in_name );
513	return strdup( painCave.errMsg );
514	}
515	ji[2] = atof( foo );
516
517
518	// check that the quaternion vector is normalized
519
520	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
521
522	if (fabs(qSqr) < 1e-6) {
523	sprintf(painCave.errMsg,
524	"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
525	return strdup(painCave.errMsg);
526	}
527
528	qLength = sqrt( qSqr );
529	q[0] = q[0] / qLength;
530	q[1] = q[1] / qLength;
531	q[2] = q[2] / qLength;
532	q[3] = q[3] / qLength;
533
534	// add quaternion and angular velocities
535
536	sd->setQ( q );
537	sd->setJ( ji );
538	}
539
540
541
542	return NULL;
543	}
544
545
546	char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
547
548	double currTime;
549	double boxMat[9];
550	double theBoxMat3[3][3];
551	double chi;
552	double integralOfChidt;
553	double eta[9];
554
555	char *foo; // the pointer to the current string token
556
557	// set the string tokenizer
558
559	foo = strtok(readLine, " ,;\t");
560	// set the timeToken.
561
562	if(foo == NULL){
563	sprintf( painCave.errMsg,
564	"error in reading Time from %s\n",
565	c_in_name );
566	return strdup( painCave.errMsg );
567	}
568
569	currTime = atof( foo );
570	entry_plug->setTime( currTime );
571
572	//get H-Matrix
573
574	for(int i = 0 ; i < 9; i++){
575	foo = strtok(NULL, " ,;\t");
576	if(foo == NULL){
577	sprintf( painCave.errMsg,
578	"error in reading H[%d] from %s\n", i, c_in_name );
579	return strdup( painCave.errMsg );
580	}
581	boxMat[i] = atof( foo );
582	}
583
584	for(int i=0;i<3;i++)
585	for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
586
587	//set H-Matrix
588	entry_plug->setBoxM( theBoxMat3 );
589
590	//get chi and integralOfChidt, they should appear by pair
591
592	if( entry_plug->useInitXSstate ){
593	foo = strtok(NULL, " ,;\t\n");
594	if(foo != NULL){
595	chi = atof(foo);
596
597	foo = strtok(NULL, " ,;\t\n");
598	if(foo == NULL){
599	sprintf( painCave.errMsg,
600	"chi and integralOfChidt should appear by pair in %s\n", c_in_name );
601	return strdup( painCave.errMsg );
602	}
603	integralOfChidt = atof( foo );
604
605	//push chi and integralOfChidt into SimInfo::properties which can be
606	//retrieved by integrator later
607	DoubleData* chiValue = new DoubleData();
608	chiValue->setID(CHIVALUE_ID);
609	chiValue->setData(chi);
610	entry_plug->addProperty(chiValue);
611
612	DoubleData* integralOfChidtValue = new DoubleData();
613	integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
614	integralOfChidtValue->setData(integralOfChidt);
615	entry_plug->addProperty(integralOfChidtValue);
616
617	}
618	else
619	return NULL;
620
621	//get eta
622	foo = strtok(NULL, " ,;\t\n");
623	if(foo != NULL ){
624
625	for(int i = 0 ; i < 9; i++){
626
627	if(foo == NULL){
628	sprintf( painCave.errMsg,
629	"error in reading eta[%d] from %s\n", i, c_in_name );
630	return strdup( painCave.errMsg );
631	}
632	eta[i] = atof( foo );
633	foo = strtok(NULL, " ,;\t\n");
634	}
635	}
636	else
637	return NULL;
638
639	//push eta into SimInfo::properties which can be
640	//retrieved by integrator later
641
642	DoubleArrayData* etaValue = new DoubleArrayData();
643	etaValue->setID(ETAVALUE_ID);
644	etaValue->setData(eta, 9);
645	entry_plug->addProperty(etaValue);
646	}
647
648	return NULL;
649	}
650
651	#ifdef IS_MPI
652
653	// a couple of functions to let us escape the read loop
654
655	void initFile::nodeZeroError( void ){
656	int j, myStatus;
657
658	myStatus = 0;
659	for (j = 0; j < mpiSim->getNProcessors(); j++) {
660	MPI_Send( &myStatus, 1, MPI_INT, j,
661	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
662	}
663
664
665	MPI_Finalize();
666	exit (0);
667
668	}
669
670	void initFile::anonymousNodeDie( void ){
671
672	MPI_Finalize();
673	exit (0);
674	}
675
676	#endif //is_mpi