OOPSE/libmdtools/DumpReader.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 dumpRead{
  void nodeZeroError( void );
  void anonymousNodeDie( void );
}

using namespace dumpRead;

#endif // is_mpi

DumpReader :: DumpReader( 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, "Dump file opened for reading successfully." );
  MPIcheckPoint();
#endif
  return;  
}

DumpReader :: ~DumpReader( ){
#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, "Dump file closed successfully." );
  MPIcheckPoint();
#endif

  return;
}


void DumpReader :: getFrame( SimInfo* the_simnfo, int whichFrame){

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

  simnfo->setTime( time );
  
  for(i=0;i<3;i++)
    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
  

  simnfo->setBoxM( theBoxMat3 );
  

  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 time and 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 = parseCommentLine( read_buffer, time, boxMat );
    if( parseErr != NULL ){
      strcpy( painCave.errMsg, parseErr );
      haveError = 1;
      simError();
    }

    MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
    
    MPI_Bcast(boxMat, 9, 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(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
    MPI_Bcast(boxMat, 9, 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;

  simnfo->setTime( time );

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

  simnfo->setBoxM( theBoxMat3 );

   
#endif
}

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

  char *foo; // the pointer to the current string token 
  
  double rx, ry, rz; // position place holders
  double vx, vy, vz; // 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 );
  }
  rx = 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 );
  }
  ry = 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 );
  }
  rz = 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 );
  }
  vx = 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 );
  }
  vy = 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 );
  }
  vz = 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]->setX( rx );
  atoms[atomIndex]->setY( ry );
  atoms[atomIndex]->setZ( rz );
    
  atoms[atomIndex]->set_vx( vx );
  atoms[atomIndex]->set_vy( vy );
  atoms[atomIndex]->set_vz( vz );

  return NULL;
}


char* DumpReader::parseCommentLine(char* readLine, double time, 
                                   double boxMat[9]){

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

  // set the string tokenizer
  
  foo = strtok(readLine, " ,;\t");
  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:	637
Committed:	Thu Jul 17 21:50:01 2003 UTC (20 years, 11 months ago) by gezelter
File size:	16593 byte(s)
Log Message:	Started work on a DumpReader
#	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 dumpRead{
21	void nodeZeroError( void );
22	void anonymousNodeDie( void );
23	}
24
25	using namespace dumpRead;
26
27	#endif // is_mpi
28
29	DumpReader :: DumpReader( char *in_name ){
30	#ifdef IS_MPI
31	if (worldRank == 0) {
32	#endif
33
34	c_in_file = fopen(in_name, "r");
35	if(c_in_file == NULL){
36	sprintf(painCave.errMsg,
37	"Cannot open file: %s\n", in_name);
38	painCave.isFatal = 1;
39	simError();
40	}
41
42	strcpy( c_in_name, in_name);
43	#ifdef IS_MPI
44	}
45	strcpy( checkPointMsg, "Dump file opened for reading successfully." );
46	MPIcheckPoint();
47	#endif
48	return;
49	}
50
51	DumpReader :: ~DumpReader( ){
52	#ifdef IS_MPI
53	if (worldRank == 0) {
54	#endif
55	int error;
56	error = fclose( c_in_file );
57	if( error ){
58	sprintf( painCave.errMsg,
59	"Error closing %s\n", c_in_name );
60	simError();
61	}
62	#ifdef IS_MPI
63	}
64	strcpy( checkPointMsg, "Dump file closed successfully." );
65	MPIcheckPoint();
66	#endif
67
68	return;
69	}
70
71
72	void DumpReader :: getFrame( SimInfo* the_simnfo, int whichFrame){
73
74	int i, j, done, which_node, which_atom; // loop counter
75
76	const int BUFFERSIZE = 2000; // size of the read buffer
77	int n_atoms; // the number of atoms
78	char read_buffer[BUFFERSIZE]; //the line buffer for reading
79	#ifdef IS_MPI
80	char send_buffer[BUFFERSIZE];
81	#endif
82
83	char *eof_test; // ptr to see when we reach the end of the file
84	char *parseErr;
85	int procIndex;
86	double boxMat[9];
87	double theBoxMat3[3][3];
88
89	simnfo = the_simnfo;
90
91	#ifndef IS_MPI
92	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
93	if( eof_test == NULL ){
94	sprintf( painCave.errMsg,
95	"DumpReader error: error reading 1st line of \"%s\"\n",
96	c_in_name );
97	painCave.isFatal = 1;
98	simError();
99	}
100
101	n_atoms = atoi( read_buffer );
102
103	Atom **atoms = simnfo->atoms;
104	DirectionalAtom* dAtom;
105
106	if( n_atoms != simnfo->n_atoms ){
107	sprintf( painCave.errMsg,
108	"DumpReader error. %s n_atoms, %d, "
109	"does not match the BASS file's n_atoms, %d.\n",
110	c_in_name, n_atoms, simnfo->n_atoms );
111	painCave.isFatal = 1;
112	simError();
113	}
114
115	//read the box mat from the comment line
116
117	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
118	if(eof_test == NULL){
119	sprintf( painCave.errMsg,
120	"error in reading commment in %s\n", c_in_name);
121	painCave.isFatal = 1;
122	simError();
123	}
124
125	parseErr = parseCommentLine( read_buffer, time, boxMat );
126	if( parseErr != NULL ){
127	strcpy( painCave.errMsg, parseErr );
128	painCave.isFatal = 1;
129	simError();
130	}
131
132	simnfo->setTime( time );
133
134	for(i=0;i<3;i++)
135	for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
136
137
138	simnfo->setBoxM( theBoxMat3 );
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 %d \n ",c_in_name);
184	haveError = 1;
185	simError();
186	}
187
188	n_atoms = atoi( read_buffer );
189
190	Atom **atoms = simnfo->atoms;
191	DirectionalAtom* dAtom;
192
193	// Check to see that the number of atoms in the intial configuration file is the
194	// same as declared in simBass.
195
196	if( n_atoms != mpiSim->getTotAtoms() ){
197	sprintf( painCave.errMsg,
198	"Initialize from File error. %s n_atoms, %d, "
199	"does not match the BASS file's n_atoms, %d.\n",
200	c_in_name, n_atoms, simnfo->n_atoms );
201	haveError= 1;
202	simError();
203	}
204
205	//read the time and boxMat from the comment line
206
207	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
208	if(eof_test == NULL){
209	sprintf( painCave.errMsg,
210	"error in reading commment in %s\n", c_in_name);
211	haveError = 1;
212	simError();
213	}
214
215	parseErr = parseCommentLine( read_buffer, time, boxMat );
216	if( parseErr != NULL ){
217	strcpy( painCave.errMsg, parseErr );
218	haveError = 1;
219	simError();
220	}
221
222	MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
223
224	MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
225
226	if(haveError) nodeZeroError();
227
228	for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
229
230	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
231	if(eof_test == NULL){
232	sprintf(painCave.errMsg,
233	"error in reading file %s\n"
234	"natoms = %d; index = %d\n"
235	"error reading the line from the file.\n",
236	c_in_name, n_atoms, i );
237	haveError= 1;
238	simError();
239	}
240
241	if(haveError) nodeZeroError();
242
243	// Get the Node number which wants this atom:
244	which_node = AtomToProcMap[i];
245	if (which_node == 0) {
246	parseErr = parseDumpLine( read_buffer, i );
247	if( parseErr != NULL ){
248	strcpy( painCave.errMsg, parseErr );
249	haveError = 1;
250	simError();
251	}
252	if(haveError) nodeZeroError();
253	}
254
255	else {
256
257	myStatus = 1;
258	MPI_Send(&myStatus, 1, MPI_INT, which_node,
259	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
260	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
261	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
262	MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
263	MPI_COMM_WORLD);
264	MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
265	MPI_COMM_WORLD, &istatus);
266
267	if(!myStatus) nodeZeroError();
268	}
269	}
270	myStatus = -1;
271	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
272	MPI_Send( &myStatus, 1, MPI_INT, j,
273	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
274	}
275
276	} else {
277
278	MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
279	MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
280
281	done = 0;
282	while (!done) {
283
284	MPI_Recv(&myStatus, 1, MPI_INT, 0,
285	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
286
287	if(!myStatus) anonymousNodeDie();
288
289	if(myStatus < 0) break;
290
291	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
292	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
293	MPI_Recv(&which_atom, 1, MPI_INT, 0,
294	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
295
296	myStatus = 1;
297	parseErr = parseDumpLine( read_buffer, which_atom );
298	if( parseErr != NULL ){
299	strcpy( painCave.errMsg, parseErr );
300	myStatus = 0;;
301	simError();
302	}
303
304	MPI_Send( &myStatus, 1, MPI_INT, 0,
305	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
306
307	}
308	}
309
310	// last thing last, enable fatalities.
311	painCave.isEventLoop = 0;
312
313	simnfo->setTime( time );
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
320
321	#endif
322	}
323
324	char* DumpReader::parseDumpLine(char* readLine, int globalIndex){
325
326	char *foo; // the pointer to the current string token
327
328	double rx, ry, rz; // position place holders
329	double vx, vy, vz; // velocity placeholders
330	double q[4]; // the quaternions
331	double jx, jy, jz; // angular velocity placeholders;
332	double qSqr, qLength; // needed to normalize the quaternion vector.
333
334	Atom **atoms = simnfo->atoms;
335	DirectionalAtom* dAtom;
336
337	int j, n_atoms, atomIndex;
338
339	#ifdef IS_MPI
340	n_atoms = mpiSim->getTotAtoms();
341	atomIndex=-1;
342	for (j=0; j < mpiSim->getMyNlocal(); j++) {
343	if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
344	}
345	if (atomIndex == -1) {
346	sprintf( painCave.errMsg,
347	"Initialize from file error. Atom at index %d "
348	"in file %s does not exist on processor %d .\n",
349	globalIndex, c_in_name, mpiSim->getMyNode() );
350	return strdup( painCave.errMsg );
351	}
352	#else
353	n_atoms = simnfo->n_atoms;
354	atomIndex = globalIndex;
355	#endif // is_mpi
356
357	// set the string tokenizer
358
359	foo = strtok(readLine, " ,;\t");
360
361	// check the atom name to the current atom
362
363	if( strcmp( foo, atoms[atomIndex]->getType() ) ){
364	sprintf( painCave.errMsg,
365	"Initialize from file error. Atom %s at index %d "
366	"in file %s does not"
367	" match the BASS atom %s.\n",
368	foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
369	return strdup( painCave.errMsg );
370	}
371
372	// get the positions
373
374	foo = strtok(NULL, " ,;\t");
375	if(foo == NULL){
376	sprintf( painCave.errMsg,
377	"error in reading postition x from %s\n"
378	"natoms = %d, index = %d\n",
379	c_in_name, n_atoms, atomIndex );
380	return strdup( painCave.errMsg );
381	}
382	rx = atof( foo );
383
384	foo = strtok(NULL, " ,;\t");
385	if(foo == NULL){
386	sprintf( painCave.errMsg,
387	"error in reading postition y from %s\n"
388	"natoms = %d, index = %d\n",
389	c_in_name, n_atoms, atomIndex );
390	return strdup( painCave.errMsg );
391	}
392	ry = atof( foo );
393
394	foo = strtok(NULL, " ,;\t");
395	if(foo == NULL){
396	sprintf( painCave.errMsg,
397	"error in reading postition z from %s\n"
398	"natoms = %d, index = %d\n",
399	c_in_name, n_atoms, atomIndex );
400	return strdup( painCave.errMsg );
401	}
402	rz = atof( foo );
403
404
405	// get the velocities
406
407	foo = strtok(NULL, " ,;\t");
408	if(foo == NULL){
409	sprintf( painCave.errMsg,
410	"error in reading velocity x from %s\n"
411	"natoms = %d, index = %d\n",
412	c_in_name, n_atoms, atomIndex );
413	return strdup( painCave.errMsg );
414	}
415	vx = atof( foo );
416
417	foo = strtok(NULL, " ,;\t");
418	if(foo == NULL){
419	sprintf( painCave.errMsg,
420	"error in reading velocity y from %s\n"
421	"natoms = %d, index = %d\n",
422	c_in_name, n_atoms, atomIndex );
423	return strdup( painCave.errMsg );
424	}
425	vy = atof( foo );
426
427	foo = strtok(NULL, " ,;\t");
428	if(foo == NULL){
429	sprintf( painCave.errMsg,
430	"error in reading velocity z from %s\n"
431	"natoms = %d, index = %d\n",
432	c_in_name, n_atoms, atomIndex );
433	return strdup( painCave.errMsg );
434	}
435	vz = atof( foo );
436
437
438	// get the quaternions
439
440	if( atoms[atomIndex]->isDirectional() ){
441
442	foo = strtok(NULL, " ,;\t");
443	if(foo == NULL){
444	sprintf(painCave.errMsg,
445	"error in reading quaternion 0 from %s\n"
446	"natoms = %d, index = %d\n",
447	c_in_name, n_atoms, atomIndex );
448	return strdup( painCave.errMsg );
449	}
450	q[0] = atof( foo );
451
452	foo = strtok(NULL, " ,;\t");
453	if(foo == NULL){
454	sprintf( painCave.errMsg,
455	"error in reading quaternion 1 from %s\n"
456	"natoms = %d, index = %d\n",
457	c_in_name, n_atoms, atomIndex );
458	return strdup( painCave.errMsg );
459	}
460	q[1] = atof( foo );
461
462	foo = strtok(NULL, " ,;\t");
463	if(foo == NULL){
464	sprintf( painCave.errMsg,
465	"error in reading quaternion 2 from %s\n"
466	"natoms = %d, index = %d\n",
467	c_in_name, n_atoms, atomIndex );
468	return strdup( painCave.errMsg );
469	}
470	q[2] = atof( foo );
471
472	foo = strtok(NULL, " ,;\t");
473	if(foo == NULL){
474	sprintf( painCave.errMsg,
475	"error in reading quaternion 3 from %s\n"
476	"natoms = %d, index = %d\n",
477	c_in_name, n_atoms, atomIndex );
478	return strdup( painCave.errMsg );
479	}
480	q[3] = atof( foo );
481
482	// get the angular velocities
483
484	foo = strtok(NULL, " ,;\t");
485	if(foo == NULL){
486	sprintf( painCave.errMsg,
487	"error in reading angular momentum jx from %s\n"
488	"natoms = %d, index = %d\n",
489	c_in_name, n_atoms, atomIndex );
490	return strdup( painCave.errMsg );
491	}
492	jx = atof( foo );
493
494	foo = strtok(NULL, " ,;\t");
495	if(foo == NULL){
496	sprintf( painCave.errMsg,
497	"error in reading angular momentum jy from %s\n"
498	"natoms = %d, index = %d\n",
499	c_in_name, n_atoms, atomIndex );
500	return strdup( painCave.errMsg );
501	}
502	jy = atof(foo );
503
504	foo = strtok(NULL, " ,;\t");
505	if(foo == NULL){
506	sprintf( painCave.errMsg,
507	"error in reading angular momentum jz from %s\n"
508	"natoms = %d, index = %d\n",
509	c_in_name, n_atoms, atomIndex );
510	return strdup( painCave.errMsg );
511	}
512	jz = atof( foo );
513
514	dAtom = ( DirectionalAtom* )atoms[atomIndex];
515
516	// check that the quaternion vector is normalized
517
518	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
519
520	qLength = sqrt( qSqr );
521	q[0] = q[0] / qLength;
522	q[1] = q[1] / qLength;
523	q[2] = q[2] / qLength;
524	q[3] = q[3] / qLength;
525
526	dAtom->setQ( q );
527
528	// add the angular velocities
529
530	dAtom->setJx( jx );
531	dAtom->setJy( jy );
532	dAtom->setJz( jz );
533	}
534
535	// add the positions and velocities to the atom
536
537	atoms[atomIndex]->setX( rx );
538	atoms[atomIndex]->setY( ry );
539	atoms[atomIndex]->setZ( rz );
540
541	atoms[atomIndex]->set_vx( vx );
542	atoms[atomIndex]->set_vy( vy );
543	atoms[atomIndex]->set_vz( vz );
544
545	return NULL;
546	}
547
548
549	char* DumpReader::parseCommentLine(char* readLine, double time,
550	double boxMat[9]){
551
552	char *foo; // the pointer to the current string token
553	int j;
554
555	// set the string tokenizer
556
557	foo = strtok(readLine, " ,;\t");
558	if(foo == NULL){
559	sprintf( painCave.errMsg,
560	"error in reading time from %s\n",
561	c_in_name );
562	return strdup( painCave.errMsg );
563	}
564	time = atof( foo );
565
566	// get the Hx vector
567
568	foo = strtok(NULL, " ,;\t");
569	if(foo == NULL){
570	sprintf( painCave.errMsg,
571	"error in reading Hx[0] from %s\n",
572	c_in_name );
573	return strdup( painCave.errMsg );
574	}
575	boxMat[0] = atof( foo );
576
577	foo = strtok(NULL, " ,;\t");
578	if(foo == NULL){
579	sprintf( painCave.errMsg,
580	"error in reading Hx[1] from %s\n",
581	c_in_name );
582	return strdup( painCave.errMsg );
583	}
584	boxMat[1] = atof( foo );
585
586	foo = strtok(NULL, " ,;\t");
587	if(foo == NULL){
588	sprintf( painCave.errMsg,
589	"error in reading Hx[2] from %s\n",
590	c_in_name );
591	return strdup( painCave.errMsg );
592	}
593	boxMat[2] = atof( foo );
594
595	// get the Hy vector
596
597	foo = strtok(NULL, " ,;\t");
598	if(foo == NULL){
599	sprintf( painCave.errMsg,
600	"error in reading Hy[0] from %s\n",
601	c_in_name );
602	return strdup( painCave.errMsg );
603	}
604	boxMat[3] = atof( foo );
605
606	foo = strtok(NULL, " ,;\t");
607	if(foo == NULL){
608	sprintf( painCave.errMsg,
609	"error in reading Hy[1] from %s\n",
610	c_in_name );
611	return strdup( painCave.errMsg );
612	}
613	boxMat[4] = atof( foo );
614
615	foo = strtok(NULL, " ,;\t");
616	if(foo == NULL){
617	sprintf( painCave.errMsg,
618	"error in reading Hy[2] from %s\n",
619	c_in_name );
620	return strdup( painCave.errMsg );
621	}
622	boxMat[5] = atof( foo );
623
624	// get the Hz vector
625
626	foo = strtok(NULL, " ,;\t");
627	if(foo == NULL){
628	sprintf( painCave.errMsg,
629	"error in reading Hz[0] from %s\n",
630	c_in_name );
631	return strdup( painCave.errMsg );
632	}
633	boxMat[6] = atof( foo );
634
635	foo = strtok(NULL, " ,;\t");
636	if(foo == NULL){
637	sprintf( painCave.errMsg,
638	"error in reading Hz[1] from %s\n",
639	c_in_name );
640	return strdup( painCave.errMsg );
641	}
642	boxMat[7] = atof( foo );
643
644	foo = strtok(NULL, " ,;\t");
645	if(foo == NULL){
646	sprintf( painCave.errMsg,
647	"error in reading Hz[2] from %s\n",
648	c_in_name );
649	return strdup( painCave.errMsg );
650	}
651	boxMat[8] = atof( foo );
652
653	return NULL;
654	}
655
656
657	#ifdef IS_MPI
658
659	// a couple of functions to let us escape the read loop
660
661	void initFile::nodeZeroError( void ){
662	int j, myStatus;
663
664	myStatus = 0;
665	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
666	MPI_Send( &myStatus, 1, MPI_INT, j,
667	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
668	}
669
670
671	MPI_Finalize();
672	exit (0);
673
674	}
675
676	void initFile::anonymousNodeDie( void ){
677
678	MPI_Finalize();
679	exit (0);
680	}
681
682	#endif //is_mpi