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 :: read_xyz( SimInfo* the_entry_plug ){

  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;

  entry_plug = the_entry_plug;


#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 = entry_plug->atoms;
  DirectionalAtom* dAtom;

  if( n_atoms != entry_plug->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, entry_plug->n_atoms );
    painCave.isFatal = 1;
    simError();
  }
  
  //read and toss 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();
  }

  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 = entry_plug->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, entry_plug->n_atoms );
      haveError= 1;
      simError();
    }
    
    //read and toss 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();
    }
  
    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 {
    
    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;
   
#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 = entry_plug->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 = entry_plug->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;
}


#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:	447
Committed:	Thu Apr 3 20:21:54 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	13274 byte(s)
Log Message:	fixed some small things with simError.h
#	Content
1	#include <iostream>
2	#include <cmath>
3
4	#include <stdio.h>
5	#include <stdlib.h>
6	#include <string.h>
7	#include <unistd.h>
8	#include <sys/types.h>
9	#include <sys/stat.h>
10
11	#include "ReadWrite.hpp"
12	#include "simError.h"
13
14	#ifdef IS_MPI
15	#include <mpi.h>
16	#include "mpiSimulation.hpp"
17	#define TAKE_THIS_TAG_CHAR 0
18	#define TAKE_THIS_TAG_INT 1
19
20	namespace initFile{
21	void nodeZeroError( void );
22	void anonymousNodeDie( void );
23	}
24
25	using namespace initFile;
26
27	#endif // is_mpi
28
29	InitializeFromFile :: InitializeFromFile( char *in_name ){
30	#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	void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
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
87	entry_plug = the_entry_plug;
88
89
90	#ifndef IS_MPI
91	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
92	if( eof_test == NULL ){
93	sprintf( painCave.errMsg,
94	"InitializeFromFile error: error reading 1st line of \"%s\"\n",
95	c_in_name );
96	painCave.isFatal = 1;
97	simError();
98	}
99
100	n_atoms = atoi( read_buffer );
101
102	Atom **atoms = entry_plug->atoms;
103	DirectionalAtom* dAtom;
104
105	if( n_atoms != entry_plug->n_atoms ){
106	sprintf( painCave.errMsg,
107	"Initialize from File error. %s n_atoms, %d, "
108	"does not match the BASS file's n_atoms, %d.\n",
109	c_in_name, n_atoms, entry_plug->n_atoms );
110	painCave.isFatal = 1;
111	simError();
112	}
113
114	//read and toss the comment line
115
116	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
117	if(eof_test == NULL){
118	sprintf( painCave.errMsg,
119	"error in reading commment in %s\n", c_in_name);
120	painCave.isFatal = 1;
121	simError();
122	}
123
124	for( i=0; i < n_atoms; i++){
125
126	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
127	if(eof_test == NULL){
128	sprintf(painCave.errMsg,
129	"error in reading file %s\n"
130	"natoms = %d; index = %d\n"
131	"error reading the line from the file.\n",
132	c_in_name, n_atoms, i );
133	painCave.isFatal = 1;
134	simError();
135	}
136
137
138	parseErr = parseDumpLine( read_buffer, i );
139	if( parseErr != NULL ){
140	strcpy( painCave.errMsg, parseErr );
141	painCave.isFatal = 1;
142	simError();
143	}
144	}
145
146
147	// MPI Section of code..........
148	#else //IS_MPI
149
150	// first thing first, suspend fatalities.
151	painCave.isEventLoop = 1;
152
153	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
154	int haveError;
155
156	MPI_Status istatus;
157	int *AtomToProcMap = mpiSim->getAtomToProcMap();
158
159
160	haveError = 0;
161	if (worldRank == 0) {
162
163	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
164	if( eof_test == NULL ){
165	sprintf( painCave.errMsg,
166	"Error reading 1st line of %d \n ",c_in_name);
167	haveError = 1;
168	simError();
169	}
170
171	n_atoms = atoi( read_buffer );
172
173	Atom **atoms = entry_plug->atoms;
174	DirectionalAtom* dAtom;
175
176	// Check to see that the number of atoms in the intial configuration file is the
177	// same as declared in simBass.
178
179	if( n_atoms != mpiSim->getTotAtoms() ){
180	sprintf( painCave.errMsg,
181	"Initialize from File error. %s n_atoms, %d, "
182	"does not match the BASS file's n_atoms, %d.\n",
183	c_in_name, n_atoms, entry_plug->n_atoms );
184	haveError= 1;
185	simError();
186	}
187
188	//read and toss the comment line
189
190	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
191	if(eof_test == NULL){
192	sprintf( painCave.errMsg,
193	"error in reading commment in %s\n", c_in_name);
194	haveError= 1;
195	simError();
196	}
197
198	if(haveError) nodeZeroError();
199
200	for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
201
202	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
203	if(eof_test == NULL){
204	sprintf(painCave.errMsg,
205	"error in reading file %s\n"
206	"natoms = %d; index = %d\n"
207	"error reading the line from the file.\n",
208	c_in_name, n_atoms, i );
209	haveError= 1;
210	simError();
211	}
212
213	if(haveError) nodeZeroError();
214
215	// Get the Node number which wants this atom:
216	which_node = AtomToProcMap[i];
217	if (which_node == 0) {
218	parseErr = parseDumpLine( read_buffer, i );
219	if( parseErr != NULL ){
220	strcpy( painCave.errMsg, parseErr );
221	haveError = 1;
222	simError();
223	}
224	if(haveError) nodeZeroError();
225	}
226
227	else {
228
229	myStatus = 1;
230	MPI_Send(&myStatus, 1, MPI_INT, which_node,
231	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
232	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
233	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
234	MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
235	MPI_COMM_WORLD);
236	MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
237	MPI_COMM_WORLD, &istatus);
238
239	if(!myStatus) nodeZeroError();
240	}
241	}
242	myStatus = -1;
243	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
244	MPI_Send( &myStatus, 1, MPI_INT, j,
245	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
246	}
247
248	} else {
249
250	done = 0;
251	while (!done) {
252
253	MPI_Recv(&myStatus, 1, MPI_INT, 0,
254	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
255
256	if(!myStatus) anonymousNodeDie();
257
258	if(myStatus < 0) break;
259
260	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
261	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
262	MPI_Recv(&which_atom, 1, MPI_INT, 0,
263	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
264
265	myStatus = 1;
266	parseErr = parseDumpLine( read_buffer, which_atom );
267	if( parseErr != NULL ){
268	strcpy( painCave.errMsg, parseErr );
269	myStatus = 0;;
270	simError();
271	}
272
273	MPI_Send( &myStatus, 1, MPI_INT, 0,
274	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
275
276	}
277	}
278
279	// last thing last, enable fatalities.
280	painCave.isEventLoop = 0;
281
282	#endif
283	}
284
285	char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
286
287	char *foo; // the pointer to the current string token
288
289	double rx, ry, rz; // position place holders
290	double vx, vy, vz; // velocity placeholders
291	double q[4]; // the quaternions
292	double jx, jy, jz; // angular velocity placeholders;
293	double qSqr, qLength; // needed to normalize the quaternion vector.
294
295	Atom **atoms = entry_plug->atoms;
296	DirectionalAtom* dAtom;
297
298	int j, n_atoms, atomIndex;
299
300	#ifdef IS_MPI
301	n_atoms = mpiSim->getTotAtoms();
302	atomIndex=-1;
303	for (j=0; j < mpiSim->getMyNlocal(); j++) {
304	if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
305	}
306	if (atomIndex == -1) {
307	sprintf( painCave.errMsg,
308	"Initialize from file error. Atom at index %d "
309	"in file %s does not exist on processor %d .\n",
310	globalIndex, c_in_name, mpiSim->getMyNode() );
311	return strdup( painCave.errMsg );
312	}
313	#else
314	n_atoms = entry_plug->n_atoms;
315	atomIndex = globalIndex;
316	#endif // is_mpi
317
318	// set the string tokenizer
319
320	foo = strtok(readLine, " ,;\t");
321
322	// check the atom name to the current atom
323
324	if( strcmp( foo, atoms[atomIndex]->getType() ) ){
325	sprintf( painCave.errMsg,
326	"Initialize from file error. Atom %s at index %d "
327	"in file %s does not"
328	" match the BASS atom %s.\n",
329	foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
330	return strdup( painCave.errMsg );
331	}
332
333	// get the positions
334
335	foo = strtok(NULL, " ,;\t");
336	if(foo == NULL){
337	sprintf( painCave.errMsg,
338	"error in reading postition x from %s\n"
339	"natoms = %d, index = %d\n",
340	c_in_name, n_atoms, atomIndex );
341	return strdup( painCave.errMsg );
342	}
343	rx = atof( foo );
344
345	foo = strtok(NULL, " ,;\t");
346	if(foo == NULL){
347	sprintf( painCave.errMsg,
348	"error in reading postition y from %s\n"
349	"natoms = %d, index = %d\n",
350	c_in_name, n_atoms, atomIndex );
351	return strdup( painCave.errMsg );
352	}
353	ry = atof( foo );
354
355	foo = strtok(NULL, " ,;\t");
356	if(foo == NULL){
357	sprintf( painCave.errMsg,
358	"error in reading postition z from %s\n"
359	"natoms = %d, index = %d\n",
360	c_in_name, n_atoms, atomIndex );
361	return strdup( painCave.errMsg );
362	}
363	rz = atof( foo );
364
365
366	// get the velocities
367
368	foo = strtok(NULL, " ,;\t");
369	if(foo == NULL){
370	sprintf( painCave.errMsg,
371	"error in reading velocity x from %s\n"
372	"natoms = %d, index = %d\n",
373	c_in_name, n_atoms, atomIndex );
374	return strdup( painCave.errMsg );
375	}
376	vx = atof( foo );
377
378	foo = strtok(NULL, " ,;\t");
379	if(foo == NULL){
380	sprintf( painCave.errMsg,
381	"error in reading velocity y from %s\n"
382	"natoms = %d, index = %d\n",
383	c_in_name, n_atoms, atomIndex );
384	return strdup( painCave.errMsg );
385	}
386	vy = atof( foo );
387
388	foo = strtok(NULL, " ,;\t");
389	if(foo == NULL){
390	sprintf( painCave.errMsg,
391	"error in reading velocity z from %s\n"
392	"natoms = %d, index = %d\n",
393	c_in_name, n_atoms, atomIndex );
394	return strdup( painCave.errMsg );
395	}
396	vz = atof( foo );
397
398
399	// get the quaternions
400
401	if( atoms[atomIndex]->isDirectional() ){
402
403	foo = strtok(NULL, " ,;\t");
404	if(foo == NULL){
405	sprintf(painCave.errMsg,
406	"error in reading quaternion 0 from %s\n"
407	"natoms = %d, index = %d\n",
408	c_in_name, n_atoms, atomIndex );
409	return strdup( painCave.errMsg );
410	}
411	q[0] = atof( foo );
412
413	foo = strtok(NULL, " ,;\t");
414	if(foo == NULL){
415	sprintf( painCave.errMsg,
416	"error in reading quaternion 1 from %s\n"
417	"natoms = %d, index = %d\n",
418	c_in_name, n_atoms, atomIndex );
419	return strdup( painCave.errMsg );
420	}
421	q[1] = atof( foo );
422
423	foo = strtok(NULL, " ,;\t");
424	if(foo == NULL){
425	sprintf( painCave.errMsg,
426	"error in reading quaternion 2 from %s\n"
427	"natoms = %d, index = %d\n",
428	c_in_name, n_atoms, atomIndex );
429	return strdup( painCave.errMsg );
430	}
431	q[2] = atof( foo );
432
433	foo = strtok(NULL, " ,;\t");
434	if(foo == NULL){
435	sprintf( painCave.errMsg,
436	"error in reading quaternion 3 from %s\n"
437	"natoms = %d, index = %d\n",
438	c_in_name, n_atoms, atomIndex );
439	return strdup( painCave.errMsg );
440	}
441	q[3] = atof( foo );
442
443	// get the angular velocities
444
445	foo = strtok(NULL, " ,;\t");
446	if(foo == NULL){
447	sprintf( painCave.errMsg,
448	"error in reading angular momentum jx from %s\n"
449	"natoms = %d, index = %d\n",
450	c_in_name, n_atoms, atomIndex );
451	return strdup( painCave.errMsg );
452	}
453	jx = atof( foo );
454
455	foo = strtok(NULL, " ,;\t");
456	if(foo == NULL){
457	sprintf( painCave.errMsg,
458	"error in reading angular momentum jy from %s\n"
459	"natoms = %d, index = %d\n",
460	c_in_name, n_atoms, atomIndex );
461	return strdup( painCave.errMsg );
462	}
463	jy = atof(foo );
464
465	foo = strtok(NULL, " ,;\t");
466	if(foo == NULL){
467	sprintf( painCave.errMsg,
468	"error in reading angular momentum jz from %s\n"
469	"natoms = %d, index = %d\n",
470	c_in_name, n_atoms, atomIndex );
471	return strdup( painCave.errMsg );
472	}
473	jz = atof( foo );
474
475	dAtom = ( DirectionalAtom* )atoms[atomIndex];
476
477	// check that the quaternion vector is normalized
478
479	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
480
481	qLength = sqrt( qSqr );
482	q[0] = q[0] / qLength;
483	q[1] = q[1] / qLength;
484	q[2] = q[2] / qLength;
485	q[3] = q[3] / qLength;
486
487	dAtom->setQ( q );
488
489	// add the angular velocities
490
491	dAtom->setJx( jx );
492	dAtom->setJy( jy );
493	dAtom->setJz( jz );
494	}
495
496	// add the positions and velocities to the atom
497
498	atoms[atomIndex]->setX( rx );
499	atoms[atomIndex]->setY( ry );
500	atoms[atomIndex]->setZ( rz );
501
502	atoms[atomIndex]->set_vx( vx );
503	atoms[atomIndex]->set_vy( vy );
504	atoms[atomIndex]->set_vz( vz );
505
506	return NULL;
507	}
508
509
510	#ifdef IS_MPI
511
512	// a couple of functions to let us escape the read loop
513
514	void initFile::nodeZeroError( void ){
515	int j, myStatus;
516
517	myStatus = 0;
518	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
519	MPI_Send( &myStatus, 1, MPI_INT, j,
520	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
521	}
522
523
524	MPI_Finalize();
525	exit (0);
526
527	}
528
529	void initFile::anonymousNodeDie( void ){
530
531	MPI_Finalize();
532	exit (0);
533	}
534
535	#endif //is_mpi