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 ){
#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 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 );
  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 );


  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 );
    if( parseErr != NULL ){
      strcpy( painCave.errMsg, parseErr );
      haveError = 1;
      simError();
    }

    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(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;

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

  simnfo->setBoxM( theBoxMat3 );

   
#endif
}

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

  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 );
  }
  simnfo->setTime( 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:	643
Committed:	Mon Jul 21 21:27:40 2003 UTC (20 years, 11 months ago) by mmeineke
File size:	16414 byte(s)
Log Message:	some initial changes to Dumpwriter and friends to accomadate random file access
#	User	Rev	Content
1	mmeineke	377	#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	gezelter	417	#include <mpi.h>
16	mmeineke	377	#include "mpiSimulation.hpp"
17	chuckv	436	#define TAKE_THIS_TAG_CHAR 0
18			#define TAKE_THIS_TAG_INT 1
19
20	mmeineke	440	namespace initFile{
21			void nodeZeroError( void );
22			void anonymousNodeDie( void );
23			}
24	chuckv	436
25	mmeineke	440	using namespace initFile;
26
27	mmeineke	377	#endif // is_mpi
28
29			InitializeFromFile :: InitializeFromFile( 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, "Infile opened for reading successfully." );
46			MPIcheckPoint();
47			#endif
48			return;
49			}
50
51			InitializeFromFile :: ~InitializeFromFile( ){
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, "Infile closed successfully." );
65			MPIcheckPoint();
66			#endif
67
68			return;
69			}
70
71
72	mmeineke	641	void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
73	mmeineke	377
74	gezelter	417	int i, j, done, which_node, which_atom; // loop counter
75	mmeineke	377
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	mmeineke	586	double boxMat[9];
87	mmeineke	590	double theBoxMat3[3][3];
88	mmeineke	377
89	mmeineke	586	simnfo = the_simnfo;
90	mmeineke	377
91
92			#ifndef IS_MPI
93			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
94			if( eof_test == NULL ){
95			sprintf( painCave.errMsg,
96			"InitializeFromFile error: error reading 1st line of \"%s\"\n",
97			c_in_name );
98			painCave.isFatal = 1;
99			simError();
100			}
101
102			n_atoms = atoi( read_buffer );
103
104	mmeineke	586	Atom **atoms = simnfo->atoms;
105	mmeineke	377	DirectionalAtom* dAtom;
106
107	mmeineke	586	if( n_atoms != simnfo->n_atoms ){
108	mmeineke	377	sprintf( painCave.errMsg,
109			"Initialize from File error. %s n_atoms, %d, "
110			"does not match the BASS file's n_atoms, %d.\n",
111	mmeineke	586	c_in_name, n_atoms, simnfo->n_atoms );
112	mmeineke	377	painCave.isFatal = 1;
113			simError();
114			}
115
116	mmeineke	586	//read the box mat from the comment line
117	mmeineke	377
118			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
119			if(eof_test == NULL){
120			sprintf( painCave.errMsg,
121			"error in reading commment in %s\n", c_in_name);
122			painCave.isFatal = 1;
123			simError();
124			}
125
126	mmeineke	586	parseErr = parseBoxLine( read_buffer, boxMat );
127			if( parseErr != NULL ){
128			strcpy( painCave.errMsg, parseErr );
129			painCave.isFatal = 1;
130			simError();
131			}
132
133	mmeineke	590	for(i=0;i<3;i++)
134			for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
135	mmeineke	586
136	mmeineke	590	simnfo->setBoxM( theBoxMat3 );
137	mmeineke	586
138	mmeineke	590
139	mmeineke	377	for( i=0; i < n_atoms; i++){
140
141			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
142			if(eof_test == NULL){
143			sprintf(painCave.errMsg,
144			"error in reading file %s\n"
145			"natoms = %d; index = %d\n"
146			"error reading the line from the file.\n",
147			c_in_name, n_atoms, i );
148			painCave.isFatal = 1;
149			simError();
150			}
151
152
153			parseErr = parseDumpLine( read_buffer, i );
154			if( parseErr != NULL ){
155			strcpy( painCave.errMsg, parseErr );
156			painCave.isFatal = 1;
157			simError();
158	mmeineke	586	}
159	mmeineke	377	}
160
161
162			// MPI Section of code..........
163			#else //IS_MPI
164
165	chuckv	436	// first thing first, suspend fatalities.
166			painCave.isEventLoop = 1;
167
168			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
169			int haveError;
170
171	mmeineke	447	MPI_Status istatus;
172	gezelter	417	int *AtomToProcMap = mpiSim->getAtomToProcMap();
173	mmeineke	377
174	chuckv	436
175			haveError = 0;
176	mmeineke	377	if (worldRank == 0) {
177	chuckv	436
178	mmeineke	377	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
179			if( eof_test == NULL ){
180			sprintf( painCave.errMsg,
181			"Error reading 1st line of %d \n ",c_in_name);
182	chuckv	436	haveError = 1;
183	mmeineke	377	simError();
184			}
185
186			n_atoms = atoi( read_buffer );
187
188	mmeineke	586	Atom **atoms = simnfo->atoms;
189	mmeineke	377	DirectionalAtom* dAtom;
190
191			// Check to see that the number of atoms in the intial configuration file is the
192			// same as declared in simBass.
193
194			if( n_atoms != mpiSim->getTotAtoms() ){
195			sprintf( painCave.errMsg,
196			"Initialize from File error. %s n_atoms, %d, "
197			"does not match the BASS file's n_atoms, %d.\n",
198	mmeineke	586	c_in_name, n_atoms, simnfo->n_atoms );
199	chuckv	436	haveError= 1;
200	mmeineke	377	simError();
201			}
202
203	mmeineke	586	//read the boxMat from the comment line
204	mmeineke	377
205			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
206			if(eof_test == NULL){
207			sprintf( painCave.errMsg,
208			"error in reading commment in %s\n", c_in_name);
209	mmeineke	586	haveError = 1;
210	mmeineke	377	simError();
211			}
212	mmeineke	586
213			parseErr = parseBoxLine( read_buffer, boxMat );
214			if( parseErr != NULL ){
215			strcpy( painCave.errMsg, parseErr );
216			haveError = 1;
217			simError();
218			}
219
220			MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
221	mmeineke	377
222	chuckv	436	if(haveError) nodeZeroError();
223	gezelter	417
224			for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
225
226	mmeineke	377	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	chuckv	436	haveError= 1;
234	mmeineke	377	simError();
235			}
236
237	chuckv	436	if(haveError) nodeZeroError();
238
239	gezelter	417	// Get the Node number which wants this atom:
240			which_node = AtomToProcMap[i];
241	chuckv	436	if (which_node == 0) {
242	gezelter	417	parseErr = parseDumpLine( read_buffer, i );
243			if( parseErr != NULL ){
244			strcpy( painCave.errMsg, parseErr );
245	chuckv	436	haveError = 1;
246	gezelter	417	simError();
247			}
248	chuckv	436	if(haveError) nodeZeroError();
249			}
250
251			else {
252
253			myStatus = 1;
254	mmeineke	447	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	chuckv	436
263			if(!myStatus) nodeZeroError();
264	mmeineke	377	}
265			}
266	chuckv	436	myStatus = -1;
267	gezelter	417	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
268	mmeineke	447	MPI_Send( &myStatus, 1, MPI_INT, j,
269			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
270	gezelter	417	}
271	gezelter	419
272	gezelter	417	} else {
273	gezelter	419
274	mmeineke	586	MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
275
276	gezelter	417	done = 0;
277			while (!done) {
278	chuckv	436
279	mmeineke	447	MPI_Recv(&myStatus, 1, MPI_INT, 0,
280			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
281	chuckv	436
282			if(!myStatus) anonymousNodeDie();
283
284			if(myStatus < 0) break;
285
286	mmeineke	447	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
287			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
288			MPI_Recv(&which_atom, 1, MPI_INT, 0,
289			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
290	chuckv	436
291			myStatus = 1;
292			parseErr = parseDumpLine( read_buffer, which_atom );
293			if( parseErr != NULL ){
294			strcpy( painCave.errMsg, parseErr );
295			myStatus = 0;;
296			simError();
297	mmeineke	377	}
298	chuckv	436
299	mmeineke	447	MPI_Send( &myStatus, 1, MPI_INT, 0,
300			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
301	chuckv	436
302	mmeineke	377	}
303			}
304	chuckv	436
305			// last thing last, enable fatalities.
306			painCave.isEventLoop = 0;
307	mmeineke	586
308	mmeineke	590	for(i=0;i<3;i++)
309			for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
310
311			simnfo->setBoxM( theBoxMat3 );
312
313	chuckv	436
314	mmeineke	377	#endif
315			}
316
317	gezelter	419	char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
318	mmeineke	377
319			char *foo; // the pointer to the current string token
320
321			double rx, ry, rz; // position place holders
322			double vx, vy, vz; // velocity placeholders
323			double q[4]; // the quaternions
324			double jx, jy, jz; // angular velocity placeholders;
325			double qSqr, qLength; // needed to normalize the quaternion vector.
326
327	mmeineke	586	Atom **atoms = simnfo->atoms;
328	mmeineke	377	DirectionalAtom* dAtom;
329
330	gezelter	419	int j, n_atoms, atomIndex;
331	mmeineke	377
332			#ifdef IS_MPI
333			n_atoms = mpiSim->getTotAtoms();
334	gezelter	419	atomIndex=-1;
335			for (j=0; j < mpiSim->getMyNlocal(); j++) {
336			if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
337			}
338			if (atomIndex == -1) {
339			sprintf( painCave.errMsg,
340			"Initialize from file error. Atom at index %d "
341			"in file %s does not exist on processor %d .\n",
342			globalIndex, c_in_name, mpiSim->getMyNode() );
343			return strdup( painCave.errMsg );
344			}
345	mmeineke	377	#else
346	mmeineke	586	n_atoms = simnfo->n_atoms;
347	gezelter	419	atomIndex = globalIndex;
348	mmeineke	377	#endif // is_mpi
349
350			// set the string tokenizer
351
352			foo = strtok(readLine, " ,;\t");
353
354			// check the atom name to the current atom
355
356			if( strcmp( foo, atoms[atomIndex]->getType() ) ){
357			sprintf( painCave.errMsg,
358			"Initialize from file error. Atom %s at index %d "
359			"in file %s does not"
360			" match the BASS atom %s.\n",
361			foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
362			return strdup( painCave.errMsg );
363			}
364
365			// get the positions
366
367			foo = strtok(NULL, " ,;\t");
368			if(foo == NULL){
369			sprintf( painCave.errMsg,
370			"error in reading postition x from %s\n"
371			"natoms = %d, index = %d\n",
372			c_in_name, n_atoms, atomIndex );
373			return strdup( painCave.errMsg );
374			}
375			rx = atof( foo );
376
377			foo = strtok(NULL, " ,;\t");
378			if(foo == NULL){
379			sprintf( painCave.errMsg,
380			"error in reading postition y from %s\n"
381			"natoms = %d, index = %d\n",
382			c_in_name, n_atoms, atomIndex );
383			return strdup( painCave.errMsg );
384			}
385			ry = atof( foo );
386
387			foo = strtok(NULL, " ,;\t");
388			if(foo == NULL){
389			sprintf( painCave.errMsg,
390			"error in reading postition z from %s\n"
391			"natoms = %d, index = %d\n",
392			c_in_name, n_atoms, atomIndex );
393			return strdup( painCave.errMsg );
394			}
395			rz = atof( foo );
396
397
398			// get the velocities
399
400			foo = strtok(NULL, " ,;\t");
401			if(foo == NULL){
402			sprintf( painCave.errMsg,
403			"error in reading velocity x from %s\n"
404			"natoms = %d, index = %d\n",
405			c_in_name, n_atoms, atomIndex );
406			return strdup( painCave.errMsg );
407			}
408			vx = atof( foo );
409
410			foo = strtok(NULL, " ,;\t");
411			if(foo == NULL){
412			sprintf( painCave.errMsg,
413			"error in reading velocity y from %s\n"
414			"natoms = %d, index = %d\n",
415			c_in_name, n_atoms, atomIndex );
416			return strdup( painCave.errMsg );
417			}
418			vy = atof( foo );
419
420			foo = strtok(NULL, " ,;\t");
421			if(foo == NULL){
422			sprintf( painCave.errMsg,
423			"error in reading velocity z from %s\n"
424			"natoms = %d, index = %d\n",
425			c_in_name, n_atoms, atomIndex );
426			return strdup( painCave.errMsg );
427			}
428			vz = atof( foo );
429
430
431			// get the quaternions
432
433			if( atoms[atomIndex]->isDirectional() ){
434
435			foo = strtok(NULL, " ,;\t");
436			if(foo == NULL){
437			sprintf(painCave.errMsg,
438			"error in reading quaternion 0 from %s\n"
439			"natoms = %d, index = %d\n",
440			c_in_name, n_atoms, atomIndex );
441			return strdup( painCave.errMsg );
442			}
443			q[0] = atof( foo );
444
445			foo = strtok(NULL, " ,;\t");
446			if(foo == NULL){
447			sprintf( painCave.errMsg,
448			"error in reading quaternion 1 from %s\n"
449			"natoms = %d, index = %d\n",
450			c_in_name, n_atoms, atomIndex );
451			return strdup( painCave.errMsg );
452			}
453			q[1] = atof( foo );
454
455			foo = strtok(NULL, " ,;\t");
456			if(foo == NULL){
457			sprintf( painCave.errMsg,
458			"error in reading quaternion 2 from %s\n"
459			"natoms = %d, index = %d\n",
460			c_in_name, n_atoms, atomIndex );
461			return strdup( painCave.errMsg );
462			}
463			q[2] = atof( foo );
464
465			foo = strtok(NULL, " ,;\t");
466			if(foo == NULL){
467			sprintf( painCave.errMsg,
468			"error in reading quaternion 3 from %s\n"
469			"natoms = %d, index = %d\n",
470			c_in_name, n_atoms, atomIndex );
471			return strdup( painCave.errMsg );
472			}
473			q[3] = atof( foo );
474
475			// get the angular velocities
476
477			foo = strtok(NULL, " ,;\t");
478			if(foo == NULL){
479			sprintf( painCave.errMsg,
480			"error in reading angular momentum jx from %s\n"
481			"natoms = %d, index = %d\n",
482			c_in_name, n_atoms, atomIndex );
483			return strdup( painCave.errMsg );
484			}
485			jx = atof( foo );
486
487			foo = strtok(NULL, " ,;\t");
488			if(foo == NULL){
489			sprintf( painCave.errMsg,
490			"error in reading angular momentum jy from %s\n"
491			"natoms = %d, index = %d\n",
492			c_in_name, n_atoms, atomIndex );
493			return strdup( painCave.errMsg );
494			}
495			jy = atof(foo );
496
497			foo = strtok(NULL, " ,;\t");
498			if(foo == NULL){
499			sprintf( painCave.errMsg,
500			"error in reading angular momentum jz from %s\n"
501			"natoms = %d, index = %d\n",
502			c_in_name, n_atoms, atomIndex );
503			return strdup( painCave.errMsg );
504			}
505			jz = atof( foo );
506
507			dAtom = ( DirectionalAtom* )atoms[atomIndex];
508
509			// check that the quaternion vector is normalized
510
511			qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
512
513			qLength = sqrt( qSqr );
514			q[0] = q[0] / qLength;
515			q[1] = q[1] / qLength;
516			q[2] = q[2] / qLength;
517			q[3] = q[3] / qLength;
518
519			dAtom->setQ( q );
520
521			// add the angular velocities
522
523			dAtom->setJx( jx );
524			dAtom->setJy( jy );
525			dAtom->setJz( jz );
526			}
527
528			// add the positions and velocities to the atom
529
530			atoms[atomIndex]->setX( rx );
531			atoms[atomIndex]->setY( ry );
532			atoms[atomIndex]->setZ( rz );
533
534			atoms[atomIndex]->set_vx( vx );
535			atoms[atomIndex]->set_vy( vy );
536			atoms[atomIndex]->set_vz( vz );
537
538			return NULL;
539			}
540	chuckv	436
541
542	mmeineke	586	char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){
543
544			char *foo; // the pointer to the current string token
545			int j;
546
547			// set the string tokenizer
548
549			foo = strtok(readLine, " ,;\t");
550	mmeineke	641	// set the timeToken.
551	mmeineke	586
552	mmeineke	641	if(foo == NULL){
553			sprintf( painCave.errMsg,
554			"error in reading Time from %s\n",
555			c_in_name );
556			return strdup( painCave.errMsg );
557			}
558	mmeineke	643	simnfo->setTime( atof( foo ) );
559	mmeineke	586
560			// get the Hx vector
561
562			foo = strtok(NULL, " ,;\t");
563			if(foo == NULL){
564			sprintf( painCave.errMsg,
565			"error in reading Hx[0] from %s\n",
566			c_in_name );
567			return strdup( painCave.errMsg );
568			}
569			boxMat[0] = atof( foo );
570
571			foo = strtok(NULL, " ,;\t");
572			if(foo == NULL){
573			sprintf( painCave.errMsg,
574			"error in reading Hx[1] from %s\n",
575			c_in_name );
576			return strdup( painCave.errMsg );
577			}
578			boxMat[1] = atof( foo );
579
580			foo = strtok(NULL, " ,;\t");
581			if(foo == NULL){
582			sprintf( painCave.errMsg,
583			"error in reading Hx[2] from %s\n",
584			c_in_name );
585			return strdup( painCave.errMsg );
586			}
587			boxMat[2] = atof( foo );
588
589			// get the Hy vector
590
591			foo = strtok(NULL, " ,;\t");
592			if(foo == NULL){
593			sprintf( painCave.errMsg,
594			"error in reading Hy[0] from %s\n",
595			c_in_name );
596			return strdup( painCave.errMsg );
597			}
598			boxMat[3] = atof( foo );
599
600			foo = strtok(NULL, " ,;\t");
601			if(foo == NULL){
602			sprintf( painCave.errMsg,
603			"error in reading Hy[1] from %s\n",
604			c_in_name );
605			return strdup( painCave.errMsg );
606			}
607			boxMat[4] = atof( foo );
608
609			foo = strtok(NULL, " ,;\t");
610			if(foo == NULL){
611			sprintf( painCave.errMsg,
612			"error in reading Hy[2] from %s\n",
613			c_in_name );
614			return strdup( painCave.errMsg );
615			}
616			boxMat[5] = atof( foo );
617
618			// get the Hz vector
619
620			foo = strtok(NULL, " ,;\t");
621			if(foo == NULL){
622			sprintf( painCave.errMsg,
623			"error in reading Hz[0] from %s\n",
624			c_in_name );
625			return strdup( painCave.errMsg );
626			}
627			boxMat[6] = atof( foo );
628
629			foo = strtok(NULL, " ,;\t");
630			if(foo == NULL){
631			sprintf( painCave.errMsg,
632			"error in reading Hz[1] from %s\n",
633			c_in_name );
634			return strdup( painCave.errMsg );
635			}
636			boxMat[7] = atof( foo );
637
638			foo = strtok(NULL, " ,;\t");
639			if(foo == NULL){
640			sprintf( painCave.errMsg,
641			"error in reading Hz[2] from %s\n",
642			c_in_name );
643			return strdup( painCave.errMsg );
644			}
645			boxMat[8] = atof( foo );
646
647			return NULL;
648			}
649
650
651	chuckv	436	#ifdef IS_MPI
652
653			// a couple of functions to let us escape the read loop
654
655	mmeineke	440	void initFile::nodeZeroError( void ){
656	chuckv	436	int j, myStatus;
657
658			myStatus = 0;
659			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
660	mmeineke	447	MPI_Send( &myStatus, 1, MPI_INT, j,
661			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
662	chuckv	436	}
663
664
665			MPI_Finalize();
666			exit (0);
667
668			}
669
670	mmeineke	440	void initFile::anonymousNodeDie( void ){
671	chuckv	436
672			MPI_Finalize();
673			exit (0);
674			}
675
676			#endif //is_mpi