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 <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::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, 
                             TAKE_THIS_TAG_INT);
        MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, 
                             TAKE_THIS_TAG_CHAR);
        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
        MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus);
        
        if(!myStatus) nodeZeroError();
      }
    }
    myStatus = -1;
    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
      MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, 
                            TAKE_THIS_TAG_INT);
    }
    
  } else {
    
    done = 0;
    while (!done) {

      MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, 
                           TAKE_THIS_TAG_INT, istatus);
      
      if(!myStatus) anonymousNodeDie();
      
      if(myStatus < 0) break;

      MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, 
                           TAKE_THIS_TAG_CHAR, istatus);
      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, 
                           TAKE_THIS_TAG_INT, istatus);
      
      myStatus = 1;
      parseErr = parseDumpLine( read_buffer, which_atom );
      if( parseErr != NULL ){
        strcpy( painCave.errMsg, parseErr );
        myStatus = 0;;
        simError();
      }
      
      MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, 
                            TAKE_THIS_TAG_INT);
      
    }
  }
     
 // 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::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, 
                          TAKE_THIS_TAG_INT);
  }  
  

  MPI_Finalize();
  exit (0);
  
}

void initFile::anonymousNodeDie( void ){

  MPI_Finalize();
  exit (0);
}

#endif //is_mpi
Revision:	440
Committed:	Tue Apr 1 16:49:17 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	13318 byte(s)
Log Message:	Fixed DumpWriter to be more robust to errors. also added a little namespace to InitFromFile to wrap it's helper functions in MPI
#	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 <mpi++.h>
17	#include "mpiSimulation.hpp"
18	#define TAKE_THIS_TAG_CHAR 0
19	#define TAKE_THIS_TAG_INT 1
20
21	namespace initFile{
22	void nodeZeroError( void );
23	void anonymousNodeDie( void );
24	}
25
26	using namespace initFile;
27
28	#endif // is_mpi
29
30	InitializeFromFile :: InitializeFromFile( char *in_name ){
31	#ifdef IS_MPI
32	if (worldRank == 0) {
33	#endif
34
35	c_in_file = fopen(in_name, "r");
36	if(c_in_file == NULL){
37	sprintf(painCave.errMsg,
38	"Cannot open file: %s\n", in_name);
39	painCave.isFatal = 1;
40	simError();
41	}
42
43	strcpy( c_in_name, in_name);
44	#ifdef IS_MPI
45	}
46	strcpy( checkPointMsg, "Infile opened for reading successfully." );
47	MPIcheckPoint();
48	#endif
49	return;
50	}
51
52	InitializeFromFile :: ~InitializeFromFile( ){
53	#ifdef IS_MPI
54	if (worldRank == 0) {
55	#endif
56	int error;
57	error = fclose( c_in_file );
58	if( error ){
59	sprintf( painCave.errMsg,
60	"Error closing %s\n", c_in_name );
61	simError();
62	}
63	#ifdef IS_MPI
64	}
65	strcpy( checkPointMsg, "Infile closed successfully." );
66	MPIcheckPoint();
67	#endif
68
69	return;
70	}
71
72
73	void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
74
75	int i, j, done, which_node, which_atom; // loop counter
76
77	const int BUFFERSIZE = 2000; // size of the read buffer
78	int n_atoms; // the number of atoms
79	char read_buffer[BUFFERSIZE]; //the line buffer for reading
80	#ifdef IS_MPI
81	char send_buffer[BUFFERSIZE];
82	#endif
83
84	char *eof_test; // ptr to see when we reach the end of the file
85	char *parseErr;
86	int procIndex;
87
88	entry_plug = the_entry_plug;
89
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	"InitializeFromFile 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 = entry_plug->atoms;
104	DirectionalAtom* dAtom;
105
106	if( n_atoms != entry_plug->n_atoms ){
107	sprintf( painCave.errMsg,
108	"Initialize from File error. %s n_atoms, %d, "
109	"does not match the BASS file's n_atoms, %d.\n",
110	c_in_name, n_atoms, entry_plug->n_atoms );
111	painCave.isFatal = 1;
112	simError();
113	}
114
115	//read and toss 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	for( i=0; i < n_atoms; i++){
126
127	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
128	if(eof_test == NULL){
129	sprintf(painCave.errMsg,
130	"error in reading file %s\n"
131	"natoms = %d; index = %d\n"
132	"error reading the line from the file.\n",
133	c_in_name, n_atoms, i );
134	painCave.isFatal = 1;
135	simError();
136	}
137
138
139	parseErr = parseDumpLine( read_buffer, i );
140	if( parseErr != NULL ){
141	strcpy( painCave.errMsg, parseErr );
142	painCave.isFatal = 1;
143	simError();
144	}
145	}
146
147
148	// MPI Section of code..........
149	#else //IS_MPI
150
151	// first thing first, suspend fatalities.
152	painCave.isEventLoop = 1;
153
154	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
155	int haveError;
156
157	MPI::Status istatus;
158	int *AtomToProcMap = mpiSim->getAtomToProcMap();
159
160
161	haveError = 0;
162	if (worldRank == 0) {
163
164	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
165	if( eof_test == NULL ){
166	sprintf( painCave.errMsg,
167	"Error reading 1st line of %d \n ",c_in_name);
168	haveError = 1;
169	simError();
170	}
171
172	n_atoms = atoi( read_buffer );
173
174	Atom **atoms = entry_plug->atoms;
175	DirectionalAtom* dAtom;
176
177	// Check to see that the number of atoms in the intial configuration file is the
178	// same as declared in simBass.
179
180	if( n_atoms != mpiSim->getTotAtoms() ){
181	sprintf( painCave.errMsg,
182	"Initialize from File error. %s n_atoms, %d, "
183	"does not match the BASS file's n_atoms, %d.\n",
184	c_in_name, n_atoms, entry_plug->n_atoms );
185	haveError= 1;
186	simError();
187	}
188
189	//read and toss the comment line
190
191	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
192	if(eof_test == NULL){
193	sprintf( painCave.errMsg,
194	"error in reading commment in %s\n", c_in_name);
195	haveError= 1;
196	simError();
197	}
198
199	if(haveError) nodeZeroError();
200
201	for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
202
203	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
204	if(eof_test == NULL){
205	sprintf(painCave.errMsg,
206	"error in reading file %s\n"
207	"natoms = %d; index = %d\n"
208	"error reading the line from the file.\n",
209	c_in_name, n_atoms, i );
210	haveError= 1;
211	simError();
212	}
213
214	if(haveError) nodeZeroError();
215
216	// Get the Node number which wants this atom:
217	which_node = AtomToProcMap[i];
218	if (which_node == 0) {
219	parseErr = parseDumpLine( read_buffer, i );
220	if( parseErr != NULL ){
221	strcpy( painCave.errMsg, parseErr );
222	haveError = 1;
223	simError();
224	}
225	if(haveError) nodeZeroError();
226	}
227
228	else {
229
230	myStatus = 1;
231	MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node,
232	TAKE_THIS_TAG_INT);
233	MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
234	TAKE_THIS_TAG_CHAR);
235	MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
236	MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus);
237
238	if(!myStatus) nodeZeroError();
239	}
240	}
241	myStatus = -1;
242	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
243	MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j,
244	TAKE_THIS_TAG_INT);
245	}
246
247	} else {
248
249	done = 0;
250	while (!done) {
251
252	MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0,
253	TAKE_THIS_TAG_INT, istatus);
254
255	if(!myStatus) anonymousNodeDie();
256
257	if(myStatus < 0) break;
258
259	MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
260	TAKE_THIS_TAG_CHAR, istatus);
261	MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
262	TAKE_THIS_TAG_INT, istatus);
263
264	myStatus = 1;
265	parseErr = parseDumpLine( read_buffer, which_atom );
266	if( parseErr != NULL ){
267	strcpy( painCave.errMsg, parseErr );
268	myStatus = 0;;
269	simError();
270	}
271
272	MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0,
273	TAKE_THIS_TAG_INT);
274
275	}
276	}
277
278	// last thing last, enable fatalities.
279	painCave.isEventLoop = 0;
280
281	#endif
282	}
283
284	char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
285
286	char *foo; // the pointer to the current string token
287
288	double rx, ry, rz; // position place holders
289	double vx, vy, vz; // velocity placeholders
290	double q[4]; // the quaternions
291	double jx, jy, jz; // angular velocity placeholders;
292	double qSqr, qLength; // needed to normalize the quaternion vector.
293
294	Atom **atoms = entry_plug->atoms;
295	DirectionalAtom* dAtom;
296
297	int j, n_atoms, atomIndex;
298
299	#ifdef IS_MPI
300	n_atoms = mpiSim->getTotAtoms();
301	atomIndex=-1;
302	for (j=0; j < mpiSim->getMyNlocal(); j++) {
303	if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
304	}
305	if (atomIndex == -1) {
306	sprintf( painCave.errMsg,
307	"Initialize from file error. Atom at index %d "
308	"in file %s does not exist on processor %d .\n",
309	globalIndex, c_in_name, mpiSim->getMyNode() );
310	return strdup( painCave.errMsg );
311	}
312	#else
313	n_atoms = entry_plug->n_atoms;
314	atomIndex = globalIndex;
315	#endif // is_mpi
316
317	// set the string tokenizer
318
319	foo = strtok(readLine, " ,;\t");
320
321	// check the atom name to the current atom
322
323	if( strcmp( foo, atoms[atomIndex]->getType() ) ){
324	sprintf( painCave.errMsg,
325	"Initialize from file error. Atom %s at index %d "
326	"in file %s does not"
327	" match the BASS atom %s.\n",
328	foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
329	return strdup( painCave.errMsg );
330	}
331
332	// get the positions
333
334	foo = strtok(NULL, " ,;\t");
335	if(foo == NULL){
336	sprintf( painCave.errMsg,
337	"error in reading postition x from %s\n"
338	"natoms = %d, index = %d\n",
339	c_in_name, n_atoms, atomIndex );
340	return strdup( painCave.errMsg );
341	}
342	rx = atof( foo );
343
344	foo = strtok(NULL, " ,;\t");
345	if(foo == NULL){
346	sprintf( painCave.errMsg,
347	"error in reading postition y from %s\n"
348	"natoms = %d, index = %d\n",
349	c_in_name, n_atoms, atomIndex );
350	return strdup( painCave.errMsg );
351	}
352	ry = atof( foo );
353
354	foo = strtok(NULL, " ,;\t");
355	if(foo == NULL){
356	sprintf( painCave.errMsg,
357	"error in reading postition z from %s\n"
358	"natoms = %d, index = %d\n",
359	c_in_name, n_atoms, atomIndex );
360	return strdup( painCave.errMsg );
361	}
362	rz = atof( foo );
363
364
365	// get the velocities
366
367	foo = strtok(NULL, " ,;\t");
368	if(foo == NULL){
369	sprintf( painCave.errMsg,
370	"error in reading velocity x from %s\n"
371	"natoms = %d, index = %d\n",
372	c_in_name, n_atoms, atomIndex );
373	return strdup( painCave.errMsg );
374	}
375	vx = atof( foo );
376
377	foo = strtok(NULL, " ,;\t");
378	if(foo == NULL){
379	sprintf( painCave.errMsg,
380	"error in reading velocity y from %s\n"
381	"natoms = %d, index = %d\n",
382	c_in_name, n_atoms, atomIndex );
383	return strdup( painCave.errMsg );
384	}
385	vy = atof( foo );
386
387	foo = strtok(NULL, " ,;\t");
388	if(foo == NULL){
389	sprintf( painCave.errMsg,
390	"error in reading velocity z from %s\n"
391	"natoms = %d, index = %d\n",
392	c_in_name, n_atoms, atomIndex );
393	return strdup( painCave.errMsg );
394	}
395	vz = atof( foo );
396
397
398	// get the quaternions
399
400	if( atoms[atomIndex]->isDirectional() ){
401
402	foo = strtok(NULL, " ,;\t");
403	if(foo == NULL){
404	sprintf(painCave.errMsg,
405	"error in reading quaternion 0 from %s\n"
406	"natoms = %d, index = %d\n",
407	c_in_name, n_atoms, atomIndex );
408	return strdup( painCave.errMsg );
409	}
410	q[0] = atof( foo );
411
412	foo = strtok(NULL, " ,;\t");
413	if(foo == NULL){
414	sprintf( painCave.errMsg,
415	"error in reading quaternion 1 from %s\n"
416	"natoms = %d, index = %d\n",
417	c_in_name, n_atoms, atomIndex );
418	return strdup( painCave.errMsg );
419	}
420	q[1] = atof( foo );
421
422	foo = strtok(NULL, " ,;\t");
423	if(foo == NULL){
424	sprintf( painCave.errMsg,
425	"error in reading quaternion 2 from %s\n"
426	"natoms = %d, index = %d\n",
427	c_in_name, n_atoms, atomIndex );
428	return strdup( painCave.errMsg );
429	}
430	q[2] = atof( foo );
431
432	foo = strtok(NULL, " ,;\t");
433	if(foo == NULL){
434	sprintf( painCave.errMsg,
435	"error in reading quaternion 3 from %s\n"
436	"natoms = %d, index = %d\n",
437	c_in_name, n_atoms, atomIndex );
438	return strdup( painCave.errMsg );
439	}
440	q[3] = atof( foo );
441
442	// get the angular velocities
443
444	foo = strtok(NULL, " ,;\t");
445	if(foo == NULL){
446	sprintf( painCave.errMsg,
447	"error in reading angular momentum jx from %s\n"
448	"natoms = %d, index = %d\n",
449	c_in_name, n_atoms, atomIndex );
450	return strdup( painCave.errMsg );
451	}
452	jx = atof( foo );
453
454	foo = strtok(NULL, " ,;\t");
455	if(foo == NULL){
456	sprintf( painCave.errMsg,
457	"error in reading angular momentum jy from %s\n"
458	"natoms = %d, index = %d\n",
459	c_in_name, n_atoms, atomIndex );
460	return strdup( painCave.errMsg );
461	}
462	jy = atof(foo );
463
464	foo = strtok(NULL, " ,;\t");
465	if(foo == NULL){
466	sprintf( painCave.errMsg,
467	"error in reading angular momentum jz from %s\n"
468	"natoms = %d, index = %d\n",
469	c_in_name, n_atoms, atomIndex );
470	return strdup( painCave.errMsg );
471	}
472	jz = atof( foo );
473
474	dAtom = ( DirectionalAtom* )atoms[atomIndex];
475
476	// check that the quaternion vector is normalized
477
478	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
479
480	qLength = sqrt( qSqr );
481	q[0] = q[0] / qLength;
482	q[1] = q[1] / qLength;
483	q[2] = q[2] / qLength;
484	q[3] = q[3] / qLength;
485
486	dAtom->setQ( q );
487
488	// add the angular velocities
489
490	dAtom->setJx( jx );
491	dAtom->setJy( jy );
492	dAtom->setJz( jz );
493	}
494
495	// add the positions and velocities to the atom
496
497	atoms[atomIndex]->setX( rx );
498	atoms[atomIndex]->setY( ry );
499	atoms[atomIndex]->setZ( rz );
500
501	atoms[atomIndex]->set_vx( vx );
502	atoms[atomIndex]->set_vy( vy );
503	atoms[atomIndex]->set_vz( vz );
504
505	return NULL;
506	}
507
508
509	#ifdef IS_MPI
510
511	// a couple of functions to let us escape the read loop
512
513	void initFile::nodeZeroError( void ){
514	int j, myStatus;
515
516	myStatus = 0;
517	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
518	MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j,
519	TAKE_THIS_TAG_INT);
520	}
521
522
523	MPI_Finalize();
524	exit (0);
525
526	}
527
528	void initFile::anonymousNodeDie( void ){
529
530	MPI_Finalize();
531	exit (0);
532	}
533
534	#endif //is_mpi