OOPSE/libmdtools/InitializeFromFile.cpp

#include <iostream>
#include <cmath>

#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"

#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 ){

  std::cerr << "Hello from Initialize from file.\n";

#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
  }
 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, done, which_node, which_atom; // loop counter

  const int BUFFERSIZE = 2000; // size of the read buffer
  int n_atoms; // the number of atoms
  char read_buffer[BUFFERSIZE]; //the line buffer for reading 
#ifdef IS_MPI
  char send_buffer[BUFFERSIZE];
#endif

  char *eof_test; // ptr to see when we reach the end of the file 
  char *parseErr;
  int procIndex;
  double currTime;
  double boxMat[9];
  double theBoxMat3[3][3];

  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();
  }

  n_atoms = atoi( read_buffer );

  Atom **atoms = simnfo->atoms;
  DirectionalAtom* dAtom;

  if( n_atoms != simnfo->n_atoms ){
    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, n_atoms, simnfo->n_atoms );
    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 = parseBoxLine( read_buffer, boxMat, currTime );
  if( parseErr != NULL ){
    strcpy( painCave.errMsg, parseErr );
    painCave.isFatal = 1;
    simError();
  }

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

  simnfo->setBoxM( theBoxMat3 );
  simnfo->setTime( currTime );


  for( i=0; i < n_atoms; i++){
    
    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, n_atoms, i );
      painCave.isFatal = 1;
      simError();
    }

    
    parseErr = parseDumpLine( read_buffer, i );
    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 *AtomToProcMap = mpiSim->getAtomToProcMap();

  
  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 %d \n ",c_in_name);
      haveError = 1;
      simError();
    }
    
    n_atoms = atoi( read_buffer );
    
    Atom **atoms = simnfo->atoms;
    DirectionalAtom* dAtom;
 
    // Check to see that the number of atoms in the intial configuration file is the
    // same as declared in simBass.
    
    if( n_atoms != mpiSim->getTotAtoms() ){
      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, n_atoms, simnfo->n_atoms );
      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();
    }
    
    parseErr = parseBoxLine( read_buffer, boxMat, currTime );
    if( parseErr != NULL ){
      strcpy( painCave.errMsg, parseErr );
      haveError = 1;
      simError();
    }

    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
  
    if(haveError) nodeZeroError();

    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
      
      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, n_atoms, i );
        haveError= 1;
        simError();
      }
    
      if(haveError) nodeZeroError();

      // Get the Node number which wants this atom:
      which_node = AtomToProcMap[i];     
      if (which_node == 0) {
        parseErr = parseDumpLine( read_buffer, i );
        if( parseErr != NULL ){
          strcpy( painCave.errMsg, parseErr );
          haveError = 1;
          simError();
        }    
        if(haveError) nodeZeroError();
      } 
      
      else {
       
        myStatus = 1;
        MPI_Send(&myStatus, 1, MPI_INT, which_node, 
                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, 
                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
                 MPI_COMM_WORLD);
        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, 
                 MPI_COMM_WORLD, &istatus);
        
        if(!myStatus) nodeZeroError();
      }
    }
    myStatus = -1;
    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
      MPI_Send( &myStatus, 1, MPI_INT, j, 
                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
    }
    
  } else {
    
    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);

    done = 0;
    while (!done) {

      MPI_Recv(&myStatus, 1, MPI_INT, 0, 
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
      
      if(!myStatus) anonymousNodeDie();
      
      if(myStatus < 0) break;

      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, 
               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
      MPI_Recv(&which_atom, 1, MPI_INT, 0, 
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
      
      myStatus = 1;
      parseErr = parseDumpLine( read_buffer, which_atom );
      if( parseErr != NULL ){
        strcpy( painCave.errMsg, parseErr );
        myStatus = 0;;
        simError();
      }
      
      MPI_Send( &myStatus, 1, MPI_INT, 0, 
                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
      
    }
  }
     
 // last  thing last, enable  fatalities.
  painCave.isEventLoop = 0;

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

  simnfo->setBoxM( theBoxMat3 );
  simnfo->setTime( currTime );

   
#endif
}

char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){

  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 jx, jy, jz; // angular velocity placeholders;
  double qSqr, qLength; // needed to normalize the quaternion vector.
  
  Atom **atoms = simnfo->atoms;
  DirectionalAtom* dAtom;
  
  int j, n_atoms, atomIndex;

#ifdef IS_MPI
  n_atoms = mpiSim->getTotAtoms();
  atomIndex=-1;        
  for (j=0; j < mpiSim->getMyNlocal(); j++) {
    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
  }
  if (atomIndex == -1) {
    sprintf( painCave.errMsg,
             "Initialize from file error. Atom at index %d "
             "in file %s does not exist on processor %d .\n",
             globalIndex, c_in_name, mpiSim->getMyNode() );
    return strdup( painCave.errMsg );
  }  
#else
  n_atoms = simnfo->n_atoms;
  atomIndex = globalIndex;
#endif // is_mpi

  // set the string tokenizer
  
  foo = strtok(readLine, " ,;\t");
  
  // check the atom name to the current atom
  
  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
    sprintf( painCave.errMsg,
             "Initialize from file error. Atom %s at index %d "
             "in file %s does not"
             " match the BASS atom %s.\n",
             foo, atomIndex, c_in_name, atoms[atomIndex]->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"
             "natoms  = %d, index = %d\n",
             c_in_name, n_atoms, atomIndex );
    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"
             "natoms  = %d, index = %d\n",
             c_in_name, n_atoms, atomIndex );
    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"
             "natoms  = %d, index = %d\n",
             c_in_name, n_atoms, atomIndex );
    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"
             "natoms  = %d, index = %d\n",
             c_in_name, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  vel[0] = atof( foo );
    
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity y from %s\n"
             "natoms  = %d, index = %d\n",
             c_in_name, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  vel[1] = atof( foo );
    
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity z from %s\n"
             "natoms  = %d, index = %d\n",
             c_in_name, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  vel[2] = atof( foo );
    
    
  // get the quaternions
    
  if( atoms[atomIndex]->isDirectional() ){
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf(painCave.errMsg,
              "error in reading quaternion 0 from %s\n"
              "natoms  = %d, index = %d\n",
              c_in_name, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    q[0] = atof( foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading quaternion 1 from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    q[1] = atof( foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading quaternion 2 from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    q[2] = atof( foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading quaternion 3 from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, atomIndex );
      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 angular momentum jx from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    jx = atof( foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading angular momentum jy from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    jy = atof(foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading angular momentum jz from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    jz = atof( foo );
      
    dAtom = ( DirectionalAtom* )atoms[atomIndex];

    // 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;
      
    dAtom->setQ( q );
      
    // add the angular velocities

    dAtom->setJx( jx );
    dAtom->setJy( jy );
    dAtom->setJz( jz );
  }
    
  // add the positions and velocities to the atom
    
  atoms[atomIndex]->setPos( pos );
  atoms[atomIndex]->setVel( vel );

  return NULL;
}


char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9],
                                       double &time ){

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

  // 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 );
  }
  time = atof( foo );

  // get the Hx vector

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hx[0] from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  boxMat[0] = atof( foo );
   
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hx[1] from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  boxMat[1] = atof( foo );
     
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hx[2] from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  boxMat[2] = atof( foo );    

  // get the Hy vector

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hy[0] from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  boxMat[3] = atof( foo );
   
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hy[1] from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  boxMat[4] = atof( foo );
     
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hy[2] from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  boxMat[5] = atof( foo );    

  // get the Hz vector

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hz[0] from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  boxMat[6] = atof( foo );
   
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hz[1] from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  boxMat[7] = atof( foo );
     
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hz[2] from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  boxMat[8] = atof( foo );    

  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:	689
Committed:	Tue Aug 12 19:56:49 2003 UTC (22 years, 2 months ago) by tim
File size:	16584 byte(s)
Log Message:	debugging globals
#	Content
1	#include <iostream>
2	#include <cmath>
3
4	#include <stdio.h>
5	#include <stdlib.h>
6	#include <string.h>
7	#include <unistd.h>
8	#include <sys/types.h>
9	#include <sys/stat.h>
10
11	#include "ReadWrite.hpp"
12	#include "simError.h"
13
14	#ifdef IS_MPI
15	#include <mpi.h>
16	#include "mpiSimulation.hpp"
17	#define TAKE_THIS_TAG_CHAR 0
18	#define TAKE_THIS_TAG_INT 1
19
20	namespace initFile{
21	void nodeZeroError( void );
22	void anonymousNodeDie( void );
23	}
24
25	using namespace initFile;
26
27	#endif // is_mpi
28
29	InitializeFromFile::InitializeFromFile( char *in_name ){
30
31	std::cerr << "Hello from Initialize from file.\n";
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	strcpy( checkPointMsg, "Infile opened for reading successfully." );
49	MPIcheckPoint();
50	#endif
51	return;
52	}
53
54	InitializeFromFile::~InitializeFromFile( ){
55	#ifdef IS_MPI
56	if (worldRank == 0) {
57	#endif
58	int error;
59	error = fclose( c_in_file );
60	if( error ){
61	sprintf( painCave.errMsg,
62	"Error closing %s\n", c_in_name );
63	simError();
64	}
65	#ifdef IS_MPI
66	}
67	strcpy( checkPointMsg, "Infile closed successfully." );
68	MPIcheckPoint();
69	#endif
70
71	return;
72	}
73
74
75	void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
76
77	int i, j, done, which_node, which_atom; // loop counter
78
79	const int BUFFERSIZE = 2000; // size of the read buffer
80	int n_atoms; // the number of atoms
81	char read_buffer[BUFFERSIZE]; //the line buffer for reading
82	#ifdef IS_MPI
83	char send_buffer[BUFFERSIZE];
84	#endif
85
86	char *eof_test; // ptr to see when we reach the end of the file
87	char *parseErr;
88	int procIndex;
89	double currTime;
90	double boxMat[9];
91	double theBoxMat3[3][3];
92
93	simnfo = the_simnfo;
94
95
96	#ifndef IS_MPI
97	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
98	if( eof_test == NULL ){
99	sprintf( painCave.errMsg,
100	"InitializeFromFile error: error reading 1st line of \"%s\"\n",
101	c_in_name );
102	painCave.isFatal = 1;
103	simError();
104	}
105
106	n_atoms = atoi( read_buffer );
107
108	Atom **atoms = simnfo->atoms;
109	DirectionalAtom* dAtom;
110
111	if( n_atoms != simnfo->n_atoms ){
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, n_atoms, simnfo->n_atoms );
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 = parseBoxLine( read_buffer, boxMat, currTime );
131	if( parseErr != NULL ){
132	strcpy( painCave.errMsg, parseErr );
133	painCave.isFatal = 1;
134	simError();
135	}
136
137	for(i=0;i<3;i++)
138	for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
139
140	simnfo->setBoxM( theBoxMat3 );
141	simnfo->setTime( currTime );
142
143
144	for( i=0; i < n_atoms; i++){
145
146	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
147	if(eof_test == NULL){
148	sprintf(painCave.errMsg,
149	"error in reading file %s\n"
150	"natoms = %d; index = %d\n"
151	"error reading the line from the file.\n",
152	c_in_name, n_atoms, i );
153	painCave.isFatal = 1;
154	simError();
155	}
156
157
158	parseErr = parseDumpLine( read_buffer, i );
159	if( parseErr != NULL ){
160	strcpy( painCave.errMsg, parseErr );
161	painCave.isFatal = 1;
162	simError();
163	}
164	}
165
166
167	// MPI Section of code..........
168	#else //IS_MPI
169
170	// first thing first, suspend fatalities.
171	painCave.isEventLoop = 1;
172
173	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
174	int haveError;
175
176	MPI_Status istatus;
177	int *AtomToProcMap = mpiSim->getAtomToProcMap();
178
179
180	haveError = 0;
181	if (worldRank == 0) {
182
183	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
184	if( eof_test == NULL ){
185	sprintf( painCave.errMsg,
186	"Error reading 1st line of %d \n ",c_in_name);
187	haveError = 1;
188	simError();
189	}
190
191	n_atoms = atoi( read_buffer );
192
193	Atom **atoms = simnfo->atoms;
194	DirectionalAtom* dAtom;
195
196	// Check to see that the number of atoms in the intial configuration file is the
197	// same as declared in simBass.
198
199	if( n_atoms != mpiSim->getTotAtoms() ){
200	sprintf( painCave.errMsg,
201	"Initialize from File error. %s n_atoms, %d, "
202	"does not match the BASS file's n_atoms, %d.\n",
203	c_in_name, n_atoms, simnfo->n_atoms );
204	haveError= 1;
205	simError();
206	}
207
208	//read the boxMat from the comment line
209
210	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
211	if(eof_test == NULL){
212	sprintf( painCave.errMsg,
213	"error in reading commment in %s\n", c_in_name);
214	haveError = 1;
215	simError();
216	}
217
218	parseErr = parseBoxLine( read_buffer, boxMat, currTime );
219	if( parseErr != NULL ){
220	strcpy( painCave.errMsg, parseErr );
221	haveError = 1;
222	simError();
223	}
224
225	MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
226	MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
227
228	if(haveError) nodeZeroError();
229
230	for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
231
232	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
233	if(eof_test == NULL){
234	sprintf(painCave.errMsg,
235	"error in reading file %s\n"
236	"natoms = %d; index = %d\n"
237	"error reading the line from the file.\n",
238	c_in_name, n_atoms, i );
239	haveError= 1;
240	simError();
241	}
242
243	if(haveError) nodeZeroError();
244
245	// Get the Node number which wants this atom:
246	which_node = AtomToProcMap[i];
247	if (which_node == 0) {
248	parseErr = parseDumpLine( read_buffer, i );
249	if( parseErr != NULL ){
250	strcpy( painCave.errMsg, parseErr );
251	haveError = 1;
252	simError();
253	}
254	if(haveError) nodeZeroError();
255	}
256
257	else {
258
259	myStatus = 1;
260	MPI_Send(&myStatus, 1, MPI_INT, which_node,
261	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
262	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
263	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
264	MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
265	MPI_COMM_WORLD);
266	MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
267	MPI_COMM_WORLD, &istatus);
268
269	if(!myStatus) nodeZeroError();
270	}
271	}
272	myStatus = -1;
273	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
274	MPI_Send( &myStatus, 1, MPI_INT, j,
275	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
276	}
277
278	} else {
279
280	MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
281	MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
282
283	done = 0;
284	while (!done) {
285
286	MPI_Recv(&myStatus, 1, MPI_INT, 0,
287	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
288
289	if(!myStatus) anonymousNodeDie();
290
291	if(myStatus < 0) break;
292
293	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
294	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
295	MPI_Recv(&which_atom, 1, MPI_INT, 0,
296	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
297
298	myStatus = 1;
299	parseErr = parseDumpLine( read_buffer, which_atom );
300	if( parseErr != NULL ){
301	strcpy( painCave.errMsg, parseErr );
302	myStatus = 0;;
303	simError();
304	}
305
306	MPI_Send( &myStatus, 1, MPI_INT, 0,
307	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
308
309	}
310	}
311
312	// last thing last, enable fatalities.
313	painCave.isEventLoop = 0;
314
315	for(i=0;i<3;i++)
316	for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
317
318	simnfo->setBoxM( theBoxMat3 );
319	simnfo->setTime( currTime );
320
321
322	#endif
323	}
324
325	char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
326
327	char *foo; // the pointer to the current string token
328
329	double pos[3]; // position place holders
330	double vel[3]; // velocity placeholders
331	double q[4]; // the quaternions
332	double jx, jy, jz; // angular velocity placeholders;
333	double qSqr, qLength; // needed to normalize the quaternion vector.
334
335	Atom **atoms = simnfo->atoms;
336	DirectionalAtom* dAtom;
337
338	int j, n_atoms, atomIndex;
339
340	#ifdef IS_MPI
341	n_atoms = mpiSim->getTotAtoms();
342	atomIndex=-1;
343	for (j=0; j < mpiSim->getMyNlocal(); j++) {
344	if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
345	}
346	if (atomIndex == -1) {
347	sprintf( painCave.errMsg,
348	"Initialize from file error. Atom at index %d "
349	"in file %s does not exist on processor %d .\n",
350	globalIndex, c_in_name, mpiSim->getMyNode() );
351	return strdup( painCave.errMsg );
352	}
353	#else
354	n_atoms = simnfo->n_atoms;
355	atomIndex = globalIndex;
356	#endif // is_mpi
357
358	// set the string tokenizer
359
360	foo = strtok(readLine, " ,;\t");
361
362	// check the atom name to the current atom
363
364	if( strcmp( foo, atoms[atomIndex]->getType() ) ){
365	sprintf( painCave.errMsg,
366	"Initialize from file error. Atom %s at index %d "
367	"in file %s does not"
368	" match the BASS atom %s.\n",
369	foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
370	return strdup( painCave.errMsg );
371	}
372
373	// get the positions
374
375	foo = strtok(NULL, " ,;\t");
376	if(foo == NULL){
377	sprintf( painCave.errMsg,
378	"error in reading postition x from %s\n"
379	"natoms = %d, index = %d\n",
380	c_in_name, n_atoms, atomIndex );
381	return strdup( painCave.errMsg );
382	}
383	pos[0] = atof( foo );
384
385	foo = strtok(NULL, " ,;\t");
386	if(foo == NULL){
387	sprintf( painCave.errMsg,
388	"error in reading postition y from %s\n"
389	"natoms = %d, index = %d\n",
390	c_in_name, n_atoms, atomIndex );
391	return strdup( painCave.errMsg );
392	}
393	pos[1] = atof( foo );
394
395	foo = strtok(NULL, " ,;\t");
396	if(foo == NULL){
397	sprintf( painCave.errMsg,
398	"error in reading postition z from %s\n"
399	"natoms = %d, index = %d\n",
400	c_in_name, n_atoms, atomIndex );
401	return strdup( painCave.errMsg );
402	}
403	pos[2] = atof( foo );
404
405
406	// get the velocities
407
408	foo = strtok(NULL, " ,;\t");
409	if(foo == NULL){
410	sprintf( painCave.errMsg,
411	"error in reading velocity x from %s\n"
412	"natoms = %d, index = %d\n",
413	c_in_name, n_atoms, atomIndex );
414	return strdup( painCave.errMsg );
415	}
416	vel[0] = atof( foo );
417
418	foo = strtok(NULL, " ,;\t");
419	if(foo == NULL){
420	sprintf( painCave.errMsg,
421	"error in reading velocity y from %s\n"
422	"natoms = %d, index = %d\n",
423	c_in_name, n_atoms, atomIndex );
424	return strdup( painCave.errMsg );
425	}
426	vel[1] = atof( foo );
427
428	foo = strtok(NULL, " ,;\t");
429	if(foo == NULL){
430	sprintf( painCave.errMsg,
431	"error in reading velocity z from %s\n"
432	"natoms = %d, index = %d\n",
433	c_in_name, n_atoms, atomIndex );
434	return strdup( painCave.errMsg );
435	}
436	vel[2] = atof( foo );
437
438
439	// get the quaternions
440
441	if( atoms[atomIndex]->isDirectional() ){
442
443	foo = strtok(NULL, " ,;\t");
444	if(foo == NULL){
445	sprintf(painCave.errMsg,
446	"error in reading quaternion 0 from %s\n"
447	"natoms = %d, index = %d\n",
448	c_in_name, n_atoms, atomIndex );
449	return strdup( painCave.errMsg );
450	}
451	q[0] = atof( foo );
452
453	foo = strtok(NULL, " ,;\t");
454	if(foo == NULL){
455	sprintf( painCave.errMsg,
456	"error in reading quaternion 1 from %s\n"
457	"natoms = %d, index = %d\n",
458	c_in_name, n_atoms, atomIndex );
459	return strdup( painCave.errMsg );
460	}
461	q[1] = atof( foo );
462
463	foo = strtok(NULL, " ,;\t");
464	if(foo == NULL){
465	sprintf( painCave.errMsg,
466	"error in reading quaternion 2 from %s\n"
467	"natoms = %d, index = %d\n",
468	c_in_name, n_atoms, atomIndex );
469	return strdup( painCave.errMsg );
470	}
471	q[2] = atof( foo );
472
473	foo = strtok(NULL, " ,;\t");
474	if(foo == NULL){
475	sprintf( painCave.errMsg,
476	"error in reading quaternion 3 from %s\n"
477	"natoms = %d, index = %d\n",
478	c_in_name, n_atoms, atomIndex );
479	return strdup( painCave.errMsg );
480	}
481	q[3] = atof( foo );
482
483	// get the angular velocities
484
485	foo = strtok(NULL, " ,;\t");
486	if(foo == NULL){
487	sprintf( painCave.errMsg,
488	"error in reading angular momentum jx from %s\n"
489	"natoms = %d, index = %d\n",
490	c_in_name, n_atoms, atomIndex );
491	return strdup( painCave.errMsg );
492	}
493	jx = atof( foo );
494
495	foo = strtok(NULL, " ,;\t");
496	if(foo == NULL){
497	sprintf( painCave.errMsg,
498	"error in reading angular momentum jy from %s\n"
499	"natoms = %d, index = %d\n",
500	c_in_name, n_atoms, atomIndex );
501	return strdup( painCave.errMsg );
502	}
503	jy = atof(foo );
504
505	foo = strtok(NULL, " ,;\t");
506	if(foo == NULL){
507	sprintf( painCave.errMsg,
508	"error in reading angular momentum jz from %s\n"
509	"natoms = %d, index = %d\n",
510	c_in_name, n_atoms, atomIndex );
511	return strdup( painCave.errMsg );
512	}
513	jz = atof( foo );
514
515	dAtom = ( DirectionalAtom* )atoms[atomIndex];
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	qLength = sqrt( qSqr );
522	q[0] = q[0] / qLength;
523	q[1] = q[1] / qLength;
524	q[2] = q[2] / qLength;
525	q[3] = q[3] / qLength;
526
527	dAtom->setQ( q );
528
529	// add the angular velocities
530
531	dAtom->setJx( jx );
532	dAtom->setJy( jy );
533	dAtom->setJz( jz );
534	}
535
536	// add the positions and velocities to the atom
537
538	atoms[atomIndex]->setPos( pos );
539	atoms[atomIndex]->setVel( vel );
540
541	return NULL;
542	}
543
544
545	char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9],
546	double &time ){
547
548	char *foo; // the pointer to the current string token
549	int j;
550
551	// set the string tokenizer
552
553	foo = strtok(readLine, " ,;\t");
554	// set the timeToken.
555
556	if(foo == NULL){
557	sprintf( painCave.errMsg,
558	"error in reading Time from %s\n",
559	c_in_name );
560	return strdup( painCave.errMsg );
561	}
562	time = atof( foo );
563
564	// get the Hx vector
565
566	foo = strtok(NULL, " ,;\t");
567	if(foo == NULL){
568	sprintf( painCave.errMsg,
569	"error in reading Hx[0] from %s\n",
570	c_in_name );
571	return strdup( painCave.errMsg );
572	}
573	boxMat[0] = atof( foo );
574
575	foo = strtok(NULL, " ,;\t");
576	if(foo == NULL){
577	sprintf( painCave.errMsg,
578	"error in reading Hx[1] from %s\n",
579	c_in_name );
580	return strdup( painCave.errMsg );
581	}
582	boxMat[1] = atof( foo );
583
584	foo = strtok(NULL, " ,;\t");
585	if(foo == NULL){
586	sprintf( painCave.errMsg,
587	"error in reading Hx[2] from %s\n",
588	c_in_name );
589	return strdup( painCave.errMsg );
590	}
591	boxMat[2] = atof( foo );
592
593	// get the Hy vector
594
595	foo = strtok(NULL, " ,;\t");
596	if(foo == NULL){
597	sprintf( painCave.errMsg,
598	"error in reading Hy[0] from %s\n",
599	c_in_name );
600	return strdup( painCave.errMsg );
601	}
602	boxMat[3] = atof( foo );
603
604	foo = strtok(NULL, " ,;\t");
605	if(foo == NULL){
606	sprintf( painCave.errMsg,
607	"error in reading Hy[1] from %s\n",
608	c_in_name );
609	return strdup( painCave.errMsg );
610	}
611	boxMat[4] = atof( foo );
612
613	foo = strtok(NULL, " ,;\t");
614	if(foo == NULL){
615	sprintf( painCave.errMsg,
616	"error in reading Hy[2] from %s\n",
617	c_in_name );
618	return strdup( painCave.errMsg );
619	}
620	boxMat[5] = atof( foo );
621
622	// get the Hz vector
623
624	foo = strtok(NULL, " ,;\t");
625	if(foo == NULL){
626	sprintf( painCave.errMsg,
627	"error in reading Hz[0] from %s\n",
628	c_in_name );
629	return strdup( painCave.errMsg );
630	}
631	boxMat[6] = atof( foo );
632
633	foo = strtok(NULL, " ,;\t");
634	if(foo == NULL){
635	sprintf( painCave.errMsg,
636	"error in reading Hz[1] from %s\n",
637	c_in_name );
638	return strdup( painCave.errMsg );
639	}
640	boxMat[7] = atof( foo );
641
642	foo = strtok(NULL, " ,;\t");
643	if(foo == NULL){
644	sprintf( painCave.errMsg,
645	"error in reading Hz[2] from %s\n",
646	c_in_name );
647	return strdup( painCave.errMsg );
648	}
649	boxMat[8] = atof( foo );
650
651	return NULL;
652	}
653
654
655	#ifdef IS_MPI
656
657	// a couple of functions to let us escape the read loop
658
659	void initFile::nodeZeroError( void ){
660	int j, myStatus;
661
662	myStatus = 0;
663	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
664	MPI_Send( &myStatus, 1, MPI_INT, j,
665	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
666	}
667
668
669	MPI_Finalize();
670	exit (0);
671
672	}
673
674	void initFile::anonymousNodeDie( void ){
675
676	MPI_Finalize();
677	exit (0);
678	}
679
680	#endif //is_mpi