OOPSE/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 0
#define TAKE_THIS_TAG_INT 1

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;

  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();
    }

    nTotObjs = 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 != 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());
      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->getTotNmol(); 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[i]);
           
       }


      }
      else{
      //molecule belongs to slave nodes

        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
      
       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();

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

      }
      
    }
    
  }
  else{
  //actions taken at slave nodes
    for (i=0 ; i < mpiSim->getTotNmol(); 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_Recv(&nCurObj, 1, MPI_INT, 0,
                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);

        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]);

    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
    //entry_plug->setBoxM( theBoxMat3 );
    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->getNumberProcessors(); 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:	1113
Committed:	Thu Apr 15 16:18:26 2004 UTC (20 years, 2 months ago) by tim
File size:	15756 byte(s)
Log Message:	fix whole bunch of bugs :-)
#	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 "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 0
20	#define TAKE_THIS_TAG_INT 1
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
179	haveError = 0;
180	if (worldRank == 0) {
181
182	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
183	if( eof_test == NULL ){
184	sprintf( painCave.errMsg,
185	"Error reading 1st line of %s \n ",c_in_name);
186	haveError = 1;
187	simError();
188	}
189
190	nTotObjs = atoi( read_buffer );
191
192	// Check to see that the number of integrable objects in the intial configuration file is the
193	// same as declared in simBass.
194
195	if( nTotObjs != simnfo->getTotIntegrableObjects()){
196	sprintf( painCave.errMsg,
197	"Initialize from File error. %s n_atoms, %d, "
198	"does not match the BASS file's n_atoms, %d.\n",
199	c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
200	haveError= 1;
201	simError();
202	}
203
204	//read the boxMat from the comment line
205
206	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
207	if(eof_test == NULL){
208	sprintf( painCave.errMsg,
209	"error in reading commment in %s\n", c_in_name);
210	haveError = 1;
211	simError();
212	}
213
214	//Every single processor will parse the comment line by itself
215	//By using this way, we might lose some efficiency, but if we want to add
216	//more parameters into comment line, we only need to modify function
217	//parseCommentLine
218
219	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
220
221	parseErr = parseCommentLine( read_buffer, simnfo);
222
223	if( parseErr != NULL ){
224	strcpy( painCave.errMsg, parseErr );
225	haveError = 1;
226	simError();
227	}
228
229	for (i=0 ; i < mpiSim->getTotNmol(); i++) {
230	which_node = MolToProcMap[i];
231	if(which_node == 0){
232	//molecules belong to master node
233
234	localIndex = mpiSim->getGlobalToLocalMol(i);
235
236	if(localIndex == -1) {
237	strcpy(painCave.errMsg, "Molecule not found on node 0!");
238	haveError = 1;
239	simError();
240	}
241
242	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
243	for(j=0; j < integrableObjects.size(); j++){
244
245	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
246	if(eof_test == NULL){
247	sprintf(painCave.errMsg,
248	"error in reading file %s\n"
249	"natoms = %d; index = %d\n"
250	"error reading the line from the file.\n",
251	c_in_name, nTotObjs, i );
252	haveError= 1;
253	simError();
254	}
255
256	if(haveError) nodeZeroError();
257
258	parseDumpLine(read_buffer, integrableObjects[i]);
259
260	}
261
262
263	}
264	else{
265	//molecule belongs to slave nodes
266
267	MPI_Recv(&nCurObj, 1, MPI_INT, 0,
268	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
269
270	for(j=0; j < integrableObjects.size(); j++){
271
272	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
273	if(eof_test == NULL){
274	sprintf(painCave.errMsg,
275	"error in reading file %s\n"
276	"natoms = %d; index = %d\n"
277	"error reading the line from the file.\n",
278	c_in_name, nTotObjs, i );
279	haveError= 1;
280	simError();
281	}
282
283	if(haveError) nodeZeroError();
284
285	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
286	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
287
288	}
289
290	}
291
292	}
293
294	}
295	else{
296	//actions taken at slave nodes
297	for (i=0 ; i < mpiSim->getTotNmol(); i++) {
298	which_node = MolToProcMap[i];
299
300	if(which_node == worldRank){
301	//molecule with global index i belongs to this processor
302
303	localIndex = mpiSim->getGlobalToLocalMol(i);
304
305	if(localIndex == -1) {
306	sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
307	haveError = 1;
308	simError();
309	}
310
311	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
312
313	nCurObj = integrableObjects.size();
314
315	MPI_Recv(&nCurObj, 1, MPI_INT, 0,
316	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
317
318	for(j = 0; j < integrableObjects.size(); j++){
319
320	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
321	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
322
323	parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
324
325	if( parseErr != NULL ){
326	strcpy( painCave.errMsg, parseErr );
327	simError();
328	}
329
330	}
331
332	}
333
334	}
335
336	}
337	#endif
338	}
339
340	char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
341
342	char *foo; // the pointer to the current string token
343
344	double pos[3]; // position place holders
345	double vel[3]; // velocity placeholders
346	double q[4]; // the quaternions
347	double ji[3]; // angular velocity placeholders;
348	double qSqr, qLength; // needed to normalize the quaternion vector.
349
350
351	// set the string tokenizer
352
353	foo = strtok(readLine, " ,;\t");
354
355	// check the atom name to the current atom
356
357	if( strcmp( foo, sd->getType() ) ){
358	sprintf( painCave.errMsg,
359	"Initialize from file error. Does not"
360	" match the BASS atom %s.\n",
361	sd->getType() );
362	return strdup( painCave.errMsg );
363	}
364
365	// get the positions
366
367	foo = strtok(NULL, " ,;\t");
368	if(foo == NULL){
369	sprintf( painCave.errMsg,
370	"error in reading postition x from %s\n",
371	c_in_name);
372	return strdup( painCave.errMsg );
373	}
374	pos[0] = atof( foo );
375
376	foo = strtok(NULL, " ,;\t");
377	if(foo == NULL){
378	sprintf( painCave.errMsg,
379	"error in reading postition y from %s\n",
380	c_in_name);
381	return strdup( painCave.errMsg );
382	}
383	pos[1] = atof( foo );
384
385	foo = strtok(NULL, " ,;\t");
386	if(foo == NULL){
387	sprintf( painCave.errMsg,
388	"error in reading postition z from %s\n",
389	c_in_name);
390	return strdup( painCave.errMsg );
391	}
392	pos[2] = atof( foo );
393
394
395	// get the velocities
396
397	foo = strtok(NULL, " ,;\t");
398	if(foo == NULL){
399	sprintf( painCave.errMsg,
400	"error in reading velocity x from %s\n",
401	c_in_name );
402	return strdup( painCave.errMsg );
403	}
404	vel[0] = atof( foo );
405
406	foo = strtok(NULL, " ,;\t");
407	if(foo == NULL){
408	sprintf( painCave.errMsg,
409	"error in reading velocity x from %s\n",
410	c_in_name );
411	return strdup( painCave.errMsg );
412	}
413	vel[1] = atof( foo );
414
415	foo = strtok(NULL, " ,;\t");
416	if(foo == NULL){
417	sprintf( painCave.errMsg,
418	"error in reading velocity x from %s\n",
419	c_in_name );
420	return strdup( painCave.errMsg );
421	}
422	vel[2] = atof( foo );
423
424
425	// add the positions and velocities to the atom
426
427	sd->setPos( pos );
428	sd->setVel( vel );
429
430	if (!sd->isDirectional())
431	return NULL;
432
433	// get the quaternions
434
435	if( sd->isDirectional() ){
436
437	foo = strtok(NULL, " ,;\t");
438	if(foo == NULL){
439	sprintf( painCave.errMsg,
440	"error in reading velocity x from %s\n",
441	c_in_name );
442	return strdup( painCave.errMsg );
443	}
444	q[0] = atof( foo );
445
446	foo = strtok(NULL, " ,;\t");
447	if(foo == NULL){
448	sprintf( painCave.errMsg,
449	"error in reading velocity x from %s\n",
450	c_in_name );
451	return strdup( painCave.errMsg );
452	}
453	q[1] = atof( foo );
454
455	foo = strtok(NULL, " ,;\t");
456	if(foo == NULL){
457	sprintf( painCave.errMsg,
458	"error in reading velocity x from %s\n",
459	c_in_name );
460	return strdup( painCave.errMsg );
461	}
462	q[2] = atof( foo );
463
464	foo = strtok(NULL, " ,;\t");
465	if(foo == NULL){
466	sprintf( painCave.errMsg,
467	"error in reading velocity x from %s\n",
468	c_in_name );
469	return strdup( painCave.errMsg );
470	}
471	q[3] = atof( foo );
472
473	// get the angular velocities
474
475	foo = strtok(NULL, " ,;\t");
476	if(foo == NULL){
477	sprintf( painCave.errMsg,
478	"error in reading velocity x from %s\n",
479	c_in_name );
480	return strdup( painCave.errMsg );
481	}
482	ji[0] = atof( foo );
483
484	foo = strtok(NULL, " ,;\t");
485	if(foo == NULL){
486	sprintf( painCave.errMsg,
487	"error in reading velocity x from %s\n",
488	c_in_name );
489	return strdup( painCave.errMsg );
490	}
491	ji[1] = atof(foo );
492
493	foo = strtok(NULL, " ,;\t");
494	if(foo == NULL){
495	sprintf( painCave.errMsg,
496	"error in reading velocity x from %s\n",
497	c_in_name );
498	return strdup( painCave.errMsg );
499	}
500	ji[2] = atof( foo );
501
502
503	// check that the quaternion vector is normalized
504
505	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
506
507	qLength = sqrt( qSqr );
508	q[0] = q[0] / qLength;
509	q[1] = q[1] / qLength;
510	q[2] = q[2] / qLength;
511	q[3] = q[3] / qLength;
512
513	// add quaternion and angular velocities
514
515	sd->setQ( q );
516	sd->setJ( ji );
517	}
518
519
520
521	return NULL;
522	}
523
524
525	char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
526
527	double currTime;
528	double boxMat[9];
529	double theBoxMat3[3][3];
530	double chi;
531	double integralOfChidt;
532	double eta[9];
533
534	char *foo; // the pointer to the current string token
535
536	// set the string tokenizer
537
538	foo = strtok(readLine, " ,;\t");
539	// set the timeToken.
540
541	if(foo == NULL){
542	sprintf( painCave.errMsg,
543	"error in reading Time from %s\n",
544	c_in_name );
545	return strdup( painCave.errMsg );
546	}
547
548	currTime = atof( foo );
549	entry_plug->setTime( currTime );
550
551	//get H-Matrix
552
553	for(int i = 0 ; i < 9; i++){
554	foo = strtok(NULL, " ,;\t");
555	if(foo == NULL){
556	sprintf( painCave.errMsg,
557	"error in reading H[%d] from %s\n", i, c_in_name );
558	return strdup( painCave.errMsg );
559	}
560	boxMat[i] = atof( foo );
561	}
562
563	for(int i=0;i<3;i++)
564	for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
565
566	//set H-Matrix
567	entry_plug->setBoxM( theBoxMat3 );
568
569	//get chi and integralOfChidt, they should appear by pair
570
571	if( entry_plug->useInitXSstate ){
572	foo = strtok(NULL, " ,;\t\n");
573	if(foo != NULL){
574	chi = atof(foo);
575
576	foo = strtok(NULL, " ,;\t\n");
577	if(foo == NULL){
578	sprintf( painCave.errMsg,
579	"chi and integralOfChidt should appear by pair in %s\n", c_in_name );
580	return strdup( painCave.errMsg );
581	}
582	integralOfChidt = atof( foo );
583
584	//push chi and integralOfChidt into SimInfo::properties which can be
585	//retrieved by integrator later
586	DoubleData* chiValue = new DoubleData();
587	chiValue->setID(CHIVALUE_ID);
588	chiValue->setData(chi);
589	entry_plug->addProperty(chiValue);
590
591	DoubleData* integralOfChidtValue = new DoubleData();
592	integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
593	integralOfChidtValue->setData(integralOfChidt);
594	entry_plug->addProperty(integralOfChidtValue);
595
596	}
597	else
598	return NULL;
599
600	//get eta
601	foo = strtok(NULL, " ,;\t\n");
602	if(foo != NULL ){
603
604	for(int i = 0 ; i < 9; i++){
605
606	if(foo == NULL){
607	sprintf( painCave.errMsg,
608	"error in reading eta[%d] from %s\n", i, c_in_name );
609	return strdup( painCave.errMsg );
610	}
611	eta[i] = atof( foo );
612	foo = strtok(NULL, " ,;\t\n");
613	}
614	}
615	else
616	return NULL;
617
618	//push eta into SimInfo::properties which can be
619	//retrieved by integrator later
620	//entry_plug->setBoxM( theBoxMat3 );
621	DoubleArrayData* etaValue = new DoubleArrayData();
622	etaValue->setID(ETAVALUE_ID);
623	etaValue->setData(eta, 9);
624	entry_plug->addProperty(etaValue);
625	}
626
627	return NULL;
628	}
629
630	#ifdef IS_MPI
631
632	// a couple of functions to let us escape the read loop
633
634	void initFile::nodeZeroError( void ){
635	int j, myStatus;
636
637	myStatus = 0;
638	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
639	MPI_Send( &myStatus, 1, MPI_INT, j,
640	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
641	}
642
643
644	MPI_Finalize();
645	exit (0);
646
647	}
648
649	void initFile::anonymousNodeDie( void ){
650
651	MPI_Finalize();
652	exit (0);
653	}
654
655	#endif //is_mpi