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"

#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
  }
 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 n_atoms; // 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;

  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 );

  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 %s \n ",c_in_name);
      haveError = 1;
      simError();
    }
    
    n_atoms = atoi( read_buffer );
    
    // 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 n_atoms, atomIndex;

#ifdef IS_MPI
  int j;

  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 

  // 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:	830
Committed:	Tue Oct 28 16:20:28 2003 UTC (20 years, 8 months ago) by gezelter
File size:	16405 byte(s)
Log Message:	fixes for compatibility
#	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
15	#ifdef IS_MPI
16	#include <mpi.h>
17	#include "mpiSimulation.hpp"
18	#define TAKE_THIS_TAG_CHAR 0
19	#define TAKE_THIS_TAG_INT 1
20
21	namespace initFile{
22	void nodeZeroError( void );
23	void anonymousNodeDie( void );
24	}
25
26	using namespace initFile;
27
28	#endif // is_mpi
29
30	InitializeFromFile::InitializeFromFile( char *in_name ){
31
32	#ifdef IS_MPI
33	if (worldRank == 0) {
34	#endif
35
36	c_in_file = fopen(in_name, "r");
37	if(c_in_file == NULL){
38	sprintf(painCave.errMsg,
39	"Cannot open file: %s\n", in_name);
40	painCave.isFatal = 1;
41	simError();
42	}
43
44	strcpy( c_in_name, in_name);
45	#ifdef IS_MPI
46	}
47	strcpy( checkPointMsg, "Infile opened for reading successfully." );
48	MPIcheckPoint();
49	#endif
50	return;
51	}
52
53	InitializeFromFile::~InitializeFromFile( ){
54	#ifdef IS_MPI
55	if (worldRank == 0) {
56	#endif
57	int error;
58	error = fclose( c_in_file );
59	if( error ){
60	sprintf( painCave.errMsg,
61	"Error closing %s\n", c_in_name );
62	simError();
63	}
64	#ifdef IS_MPI
65	}
66	strcpy( checkPointMsg, "Infile closed successfully." );
67	MPIcheckPoint();
68	#endif
69
70	return;
71	}
72
73
74	void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
75
76	int i, j;
77
78	#ifdef IS_MPI
79	int done, which_node, which_atom; // loop counter
80	#endif //is_mpi
81
82	const int BUFFERSIZE = 2000; // size of the read buffer
83	int n_atoms; // the number of atoms
84	char read_buffer[BUFFERSIZE]; //the line buffer for reading
85
86	char *eof_test; // ptr to see when we reach the end of the file
87	char *parseErr;
88
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	if( n_atoms != simnfo->n_atoms ){
109	sprintf( painCave.errMsg,
110	"Initialize from File error. %s n_atoms, %d, "
111	"does not match the BASS file's n_atoms, %d.\n",
112	c_in_name, n_atoms, simnfo->n_atoms );
113	painCave.isFatal = 1;
114	simError();
115	}
116
117	//read the box mat from the comment line
118
119	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
120	if(eof_test == NULL){
121	sprintf( painCave.errMsg,
122	"error in reading commment in %s\n", c_in_name);
123	painCave.isFatal = 1;
124	simError();
125	}
126
127	parseErr = parseBoxLine( read_buffer, boxMat, currTime );
128	if( parseErr != NULL ){
129	strcpy( painCave.errMsg, parseErr );
130	painCave.isFatal = 1;
131	simError();
132	}
133
134	for(i=0;i<3;i++)
135	for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
136
137	simnfo->setBoxM( theBoxMat3 );
138	simnfo->setTime( currTime );
139
140
141	for( i=0; i < n_atoms; i++){
142
143	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
144	if(eof_test == NULL){
145	sprintf(painCave.errMsg,
146	"error in reading file %s\n"
147	"natoms = %d; index = %d\n"
148	"error reading the line from the file.\n",
149	c_in_name, n_atoms, i );
150	painCave.isFatal = 1;
151	simError();
152	}
153
154
155	parseErr = parseDumpLine( read_buffer, i );
156	if( parseErr != NULL ){
157	strcpy( painCave.errMsg, parseErr );
158	painCave.isFatal = 1;
159	simError();
160	}
161	}
162
163
164	// MPI Section of code..........
165	#else //IS_MPI
166
167	// first thing first, suspend fatalities.
168	painCave.isEventLoop = 1;
169
170	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
171	int haveError;
172
173	MPI_Status istatus;
174	int *AtomToProcMap = mpiSim->getAtomToProcMap();
175
176
177	haveError = 0;
178	if (worldRank == 0) {
179
180	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
181	if( eof_test == NULL ){
182	sprintf( painCave.errMsg,
183	"Error reading 1st line of %s \n ",c_in_name);
184	haveError = 1;
185	simError();
186	}
187
188	n_atoms = atoi( read_buffer );
189
190	// Check to see that the number of atoms in the intial configuration file is the
191	// same as declared in simBass.
192
193	if( n_atoms != mpiSim->getTotAtoms() ){
194	sprintf( painCave.errMsg,
195	"Initialize from File error. %s n_atoms, %d, "
196	"does not match the BASS file's n_atoms, %d.\n",
197	c_in_name, n_atoms, simnfo->n_atoms );
198	haveError= 1;
199	simError();
200	}
201
202	//read the boxMat from the comment line
203
204	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
205	if(eof_test == NULL){
206	sprintf( painCave.errMsg,
207	"error in reading commment in %s\n", c_in_name);
208	haveError = 1;
209	simError();
210	}
211
212	parseErr = parseBoxLine( read_buffer, boxMat, currTime );
213	if( parseErr != NULL ){
214	strcpy( painCave.errMsg, parseErr );
215	haveError = 1;
216	simError();
217	}
218
219	MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
220	MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
221
222	if(haveError) nodeZeroError();
223
224	for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
225
226	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
227	if(eof_test == NULL){
228	sprintf(painCave.errMsg,
229	"error in reading file %s\n"
230	"natoms = %d; index = %d\n"
231	"error reading the line from the file.\n",
232	c_in_name, n_atoms, i );
233	haveError= 1;
234	simError();
235	}
236
237	if(haveError) nodeZeroError();
238
239	// Get the Node number which wants this atom:
240	which_node = AtomToProcMap[i];
241	if (which_node == 0) {
242	parseErr = parseDumpLine( read_buffer, i );
243	if( parseErr != NULL ){
244	strcpy( painCave.errMsg, parseErr );
245	haveError = 1;
246	simError();
247	}
248	if(haveError) nodeZeroError();
249	}
250
251	else {
252
253	myStatus = 1;
254	MPI_Send(&myStatus, 1, MPI_INT, which_node,
255	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
256	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
257	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
258	MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
259	MPI_COMM_WORLD);
260	MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
261	MPI_COMM_WORLD, &istatus);
262
263	if(!myStatus) nodeZeroError();
264	}
265	}
266	myStatus = -1;
267	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
268	MPI_Send( &myStatus, 1, MPI_INT, j,
269	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
270	}
271
272	} else {
273
274	MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
275	MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
276
277	done = 0;
278	while (!done) {
279
280	MPI_Recv(&myStatus, 1, MPI_INT, 0,
281	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
282
283	if(!myStatus) anonymousNodeDie();
284
285	if(myStatus < 0) break;
286
287	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
288	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
289	MPI_Recv(&which_atom, 1, MPI_INT, 0,
290	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
291
292	myStatus = 1;
293	parseErr = parseDumpLine( read_buffer, which_atom );
294	if( parseErr != NULL ){
295	strcpy( painCave.errMsg, parseErr );
296	myStatus = 0;;
297	simError();
298	}
299
300	MPI_Send( &myStatus, 1, MPI_INT, 0,
301	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
302
303	}
304	}
305
306	// last thing last, enable fatalities.
307	painCave.isEventLoop = 0;
308
309	for(i=0;i<3;i++)
310	for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
311
312	simnfo->setBoxM( theBoxMat3 );
313	simnfo->setTime( currTime );
314
315
316	#endif
317	}
318
319	char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
320
321	char *foo; // the pointer to the current string token
322
323	double pos[3]; // position place holders
324	double vel[3]; // velocity placeholders
325	double q[4]; // the quaternions
326	double jx, jy, jz; // angular velocity placeholders;
327	double qSqr, qLength; // needed to normalize the quaternion vector.
328
329	Atom **atoms = simnfo->atoms;
330	DirectionalAtom* dAtom;
331
332	int n_atoms, atomIndex;
333
334	#ifdef IS_MPI
335	int j;
336
337	n_atoms = mpiSim->getTotAtoms();
338	atomIndex=-1;
339	for (j=0; j < mpiSim->getMyNlocal(); j++) {
340	if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
341	}
342	if (atomIndex == -1) {
343	sprintf( painCave.errMsg,
344	"Initialize from file error. Atom at index %d "
345	"in file %s does not exist on processor %d .\n",
346	globalIndex, c_in_name, mpiSim->getMyNode() );
347	return strdup( painCave.errMsg );
348	}
349	#else
350	n_atoms = simnfo->n_atoms;
351	atomIndex = globalIndex;
352	#endif // is_mpi
353
354	// set the string tokenizer
355
356	foo = strtok(readLine, " ,;\t");
357
358	// check the atom name to the current atom
359
360	if( strcmp( foo, atoms[atomIndex]->getType() ) ){
361	sprintf( painCave.errMsg,
362	"Initialize from file error. Atom %s at index %d "
363	"in file %s does not"
364	" match the BASS atom %s.\n",
365	foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
366	return strdup( painCave.errMsg );
367	}
368
369	// get the positions
370
371	foo = strtok(NULL, " ,;\t");
372	if(foo == NULL){
373	sprintf( painCave.errMsg,
374	"error in reading postition x from %s\n"
375	"natoms = %d, index = %d\n",
376	c_in_name, n_atoms, atomIndex );
377	return strdup( painCave.errMsg );
378	}
379	pos[0] = atof( foo );
380
381	foo = strtok(NULL, " ,;\t");
382	if(foo == NULL){
383	sprintf( painCave.errMsg,
384	"error in reading postition y from %s\n"
385	"natoms = %d, index = %d\n",
386	c_in_name, n_atoms, atomIndex );
387	return strdup( painCave.errMsg );
388	}
389	pos[1] = atof( foo );
390
391	foo = strtok(NULL, " ,;\t");
392	if(foo == NULL){
393	sprintf( painCave.errMsg,
394	"error in reading postition z from %s\n"
395	"natoms = %d, index = %d\n",
396	c_in_name, n_atoms, atomIndex );
397	return strdup( painCave.errMsg );
398	}
399	pos[2] = atof( foo );
400
401
402	// get the velocities
403
404	foo = strtok(NULL, " ,;\t");
405	if(foo == NULL){
406	sprintf( painCave.errMsg,
407	"error in reading velocity x from %s\n"
408	"natoms = %d, index = %d\n",
409	c_in_name, n_atoms, atomIndex );
410	return strdup( painCave.errMsg );
411	}
412	vel[0] = atof( foo );
413
414	foo = strtok(NULL, " ,;\t");
415	if(foo == NULL){
416	sprintf( painCave.errMsg,
417	"error in reading velocity y from %s\n"
418	"natoms = %d, index = %d\n",
419	c_in_name, n_atoms, atomIndex );
420	return strdup( painCave.errMsg );
421	}
422	vel[1] = atof( foo );
423
424	foo = strtok(NULL, " ,;\t");
425	if(foo == NULL){
426	sprintf( painCave.errMsg,
427	"error in reading velocity z from %s\n"
428	"natoms = %d, index = %d\n",
429	c_in_name, n_atoms, atomIndex );
430	return strdup( painCave.errMsg );
431	}
432	vel[2] = atof( foo );
433
434
435	// get the quaternions
436
437	if( atoms[atomIndex]->isDirectional() ){
438
439	foo = strtok(NULL, " ,;\t");
440	if(foo == NULL){
441	sprintf(painCave.errMsg,
442	"error in reading quaternion 0 from %s\n"
443	"natoms = %d, index = %d\n",
444	c_in_name, n_atoms, atomIndex );
445	return strdup( painCave.errMsg );
446	}
447	q[0] = atof( foo );
448
449	foo = strtok(NULL, " ,;\t");
450	if(foo == NULL){
451	sprintf( painCave.errMsg,
452	"error in reading quaternion 1 from %s\n"
453	"natoms = %d, index = %d\n",
454	c_in_name, n_atoms, atomIndex );
455	return strdup( painCave.errMsg );
456	}
457	q[1] = atof( foo );
458
459	foo = strtok(NULL, " ,;\t");
460	if(foo == NULL){
461	sprintf( painCave.errMsg,
462	"error in reading quaternion 2 from %s\n"
463	"natoms = %d, index = %d\n",
464	c_in_name, n_atoms, atomIndex );
465	return strdup( painCave.errMsg );
466	}
467	q[2] = atof( foo );
468
469	foo = strtok(NULL, " ,;\t");
470	if(foo == NULL){
471	sprintf( painCave.errMsg,
472	"error in reading quaternion 3 from %s\n"
473	"natoms = %d, index = %d\n",
474	c_in_name, n_atoms, atomIndex );
475	return strdup( painCave.errMsg );
476	}
477	q[3] = atof( foo );
478
479	// get the angular velocities
480
481	foo = strtok(NULL, " ,;\t");
482	if(foo == NULL){
483	sprintf( painCave.errMsg,
484	"error in reading angular momentum jx from %s\n"
485	"natoms = %d, index = %d\n",
486	c_in_name, n_atoms, atomIndex );
487	return strdup( painCave.errMsg );
488	}
489	jx = atof( foo );
490
491	foo = strtok(NULL, " ,;\t");
492	if(foo == NULL){
493	sprintf( painCave.errMsg,
494	"error in reading angular momentum jy from %s\n"
495	"natoms = %d, index = %d\n",
496	c_in_name, n_atoms, atomIndex );
497	return strdup( painCave.errMsg );
498	}
499	jy = atof(foo );
500
501	foo = strtok(NULL, " ,;\t");
502	if(foo == NULL){
503	sprintf( painCave.errMsg,
504	"error in reading angular momentum jz from %s\n"
505	"natoms = %d, index = %d\n",
506	c_in_name, n_atoms, atomIndex );
507	return strdup( painCave.errMsg );
508	}
509	jz = atof( foo );
510
511	dAtom = ( DirectionalAtom* )atoms[atomIndex];
512
513	// check that the quaternion vector is normalized
514
515	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
516
517	qLength = sqrt( qSqr );
518	q[0] = q[0] / qLength;
519	q[1] = q[1] / qLength;
520	q[2] = q[2] / qLength;
521	q[3] = q[3] / qLength;
522
523	dAtom->setQ( q );
524
525	// add the angular velocities
526
527	dAtom->setJx( jx );
528	dAtom->setJy( jy );
529	dAtom->setJz( jz );
530	}
531
532	// add the positions and velocities to the atom
533
534	atoms[atomIndex]->setPos( pos );
535	atoms[atomIndex]->setVel( vel );
536
537	return NULL;
538	}
539
540
541	char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9],
542	double &time ){
543
544	char *foo; // the pointer to the current string token
545
546	// set the string tokenizer
547
548	foo = strtok(readLine, " ,;\t");
549	// set the timeToken.
550
551	if(foo == NULL){
552	sprintf( painCave.errMsg,
553	"error in reading Time from %s\n",
554	c_in_name );
555	return strdup( painCave.errMsg );
556	}
557	time = atof( foo );
558
559	// get the Hx vector
560
561	foo = strtok(NULL, " ,;\t");
562	if(foo == NULL){
563	sprintf( painCave.errMsg,
564	"error in reading Hx[0] from %s\n",
565	c_in_name );
566	return strdup( painCave.errMsg );
567	}
568	boxMat[0] = atof( foo );
569
570	foo = strtok(NULL, " ,;\t");
571	if(foo == NULL){
572	sprintf( painCave.errMsg,
573	"error in reading Hx[1] from %s\n",
574	c_in_name );
575	return strdup( painCave.errMsg );
576	}
577	boxMat[1] = atof( foo );
578
579	foo = strtok(NULL, " ,;\t");
580	if(foo == NULL){
581	sprintf( painCave.errMsg,
582	"error in reading Hx[2] from %s\n",
583	c_in_name );
584	return strdup( painCave.errMsg );
585	}
586	boxMat[2] = atof( foo );
587
588	// get the Hy vector
589
590	foo = strtok(NULL, " ,;\t");
591	if(foo == NULL){
592	sprintf( painCave.errMsg,
593	"error in reading Hy[0] from %s\n",
594	c_in_name );
595	return strdup( painCave.errMsg );
596	}
597	boxMat[3] = atof( foo );
598
599	foo = strtok(NULL, " ,;\t");
600	if(foo == NULL){
601	sprintf( painCave.errMsg,
602	"error in reading Hy[1] from %s\n",
603	c_in_name );
604	return strdup( painCave.errMsg );
605	}
606	boxMat[4] = atof( foo );
607
608	foo = strtok(NULL, " ,;\t");
609	if(foo == NULL){
610	sprintf( painCave.errMsg,
611	"error in reading Hy[2] from %s\n",
612	c_in_name );
613	return strdup( painCave.errMsg );
614	}
615	boxMat[5] = atof( foo );
616
617	// get the Hz vector
618
619	foo = strtok(NULL, " ,;\t");
620	if(foo == NULL){
621	sprintf( painCave.errMsg,
622	"error in reading Hz[0] from %s\n",
623	c_in_name );
624	return strdup( painCave.errMsg );
625	}
626	boxMat[6] = atof( foo );
627
628	foo = strtok(NULL, " ,;\t");
629	if(foo == NULL){
630	sprintf( painCave.errMsg,
631	"error in reading Hz[1] from %s\n",
632	c_in_name );
633	return strdup( painCave.errMsg );
634	}
635	boxMat[7] = atof( foo );
636
637	foo = strtok(NULL, " ,;\t");
638	if(foo == NULL){
639	sprintf( painCave.errMsg,
640	"error in reading Hz[2] from %s\n",
641	c_in_name );
642	return strdup( painCave.errMsg );
643	}
644	boxMat[8] = atof( foo );
645
646	return NULL;
647	}
648
649
650	#ifdef IS_MPI
651
652	// a couple of functions to let us escape the read loop
653
654	void initFile::nodeZeroError( void ){
655	int j, myStatus;
656
657	myStatus = 0;
658	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
659	MPI_Send( &myStatus, 1, MPI_INT, j,
660	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
661	}
662
663
664	MPI_Finalize();
665	exit (0);
666
667	}
668
669	void initFile::anonymousNodeDie( void ){
670
671	MPI_Finalize();
672	exit (0);
673	}
674
675	#endif //is_mpi