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

void nodeZeroError( void );
void anonymousNodeDie( void );

#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 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 anonymousNodeDie( void ){

  MPI_Finalize();
  exit (0);
}

#endif //is_mpi
Revision:	436
Committed:	Fri Mar 28 21:45:03 2003 UTC (21 years, 3 months ago) by chuckv
File size:	13245 byte(s)
Log Message:	Bug fixes in read-write routines.
#	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	void nodeZeroError( void );
22	void anonymousNodeDie( void );
23
24	#endif // is_mpi
25
26	InitializeFromFile :: InitializeFromFile( char *in_name ){
27	#ifdef IS_MPI
28	if (worldRank == 0) {
29	#endif
30
31	c_in_file = fopen(in_name, "r");
32	if(c_in_file == NULL){
33	sprintf(painCave.errMsg,
34	"Cannot open file: %s\n", in_name);
35	painCave.isFatal = 1;
36	simError();
37	}
38
39	strcpy( c_in_name, in_name);
40	#ifdef IS_MPI
41	}
42	strcpy( checkPointMsg, "Infile opened for reading successfully." );
43	MPIcheckPoint();
44	#endif
45	return;
46	}
47
48	InitializeFromFile :: ~InitializeFromFile( ){
49	#ifdef IS_MPI
50	if (worldRank == 0) {
51	#endif
52	int error;
53	error = fclose( c_in_file );
54	if( error ){
55	sprintf( painCave.errMsg,
56	"Error closing %s\n", c_in_name );
57	simError();
58	}
59	#ifdef IS_MPI
60	}
61	strcpy( checkPointMsg, "Infile closed successfully." );
62	MPIcheckPoint();
63	#endif
64
65	return;
66	}
67
68
69	void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
70
71	int i, j, done, which_node, which_atom; // loop counter
72
73	const int BUFFERSIZE = 2000; // size of the read buffer
74	int n_atoms; // the number of atoms
75	char read_buffer[BUFFERSIZE]; //the line buffer for reading
76	#ifdef IS_MPI
77	char send_buffer[BUFFERSIZE];
78	#endif
79
80	char *eof_test; // ptr to see when we reach the end of the file
81	char *parseErr;
82	int procIndex;
83
84	entry_plug = the_entry_plug;
85
86
87	#ifndef IS_MPI
88	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
89	if( eof_test == NULL ){
90	sprintf( painCave.errMsg,
91	"InitializeFromFile error: error reading 1st line of \"%s\"\n",
92	c_in_name );
93	painCave.isFatal = 1;
94	simError();
95	}
96
97	n_atoms = atoi( read_buffer );
98
99	Atom **atoms = entry_plug->atoms;
100	DirectionalAtom* dAtom;
101
102	if( n_atoms != entry_plug->n_atoms ){
103	sprintf( painCave.errMsg,
104	"Initialize from File error. %s n_atoms, %d, "
105	"does not match the BASS file's n_atoms, %d.\n",
106	c_in_name, n_atoms, entry_plug->n_atoms );
107	painCave.isFatal = 1;
108	simError();
109	}
110
111	//read and toss the comment line
112
113	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
114	if(eof_test == NULL){
115	sprintf( painCave.errMsg,
116	"error in reading commment in %s\n", c_in_name);
117	painCave.isFatal = 1;
118	simError();
119	}
120
121	for( i=0; i < n_atoms; i++){
122
123	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
124	if(eof_test == NULL){
125	sprintf(painCave.errMsg,
126	"error in reading file %s\n"
127	"natoms = %d; index = %d\n"
128	"error reading the line from the file.\n",
129	c_in_name, n_atoms, i );
130	painCave.isFatal = 1;
131	simError();
132	}
133
134
135	parseErr = parseDumpLine( read_buffer, i );
136	if( parseErr != NULL ){
137	strcpy( painCave.errMsg, parseErr );
138	painCave.isFatal = 1;
139	simError();
140	}
141	}
142
143
144	// MPI Section of code..........
145	#else //IS_MPI
146
147	// first thing first, suspend fatalities.
148	painCave.isEventLoop = 1;
149
150	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
151	int haveError;
152
153	MPI::Status istatus;
154	int *AtomToProcMap = mpiSim->getAtomToProcMap();
155
156
157	haveError = 0;
158	if (worldRank == 0) {
159
160	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
161	if( eof_test == NULL ){
162	sprintf( painCave.errMsg,
163	"Error reading 1st line of %d \n ",c_in_name);
164	haveError = 1;
165	simError();
166	}
167
168	n_atoms = atoi( read_buffer );
169
170	Atom **atoms = entry_plug->atoms;
171	DirectionalAtom* dAtom;
172
173	// Check to see that the number of atoms in the intial configuration file is the
174	// same as declared in simBass.
175
176	if( n_atoms != mpiSim->getTotAtoms() ){
177	sprintf( painCave.errMsg,
178	"Initialize from File error. %s n_atoms, %d, "
179	"does not match the BASS file's n_atoms, %d.\n",
180	c_in_name, n_atoms, entry_plug->n_atoms );
181	haveError= 1;
182	simError();
183	}
184
185	//read and toss the comment line
186
187	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
188	if(eof_test == NULL){
189	sprintf( painCave.errMsg,
190	"error in reading commment in %s\n", c_in_name);
191	haveError= 1;
192	simError();
193	}
194
195	if(haveError) nodeZeroError();
196
197	for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
198
199	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
200	if(eof_test == NULL){
201	sprintf(painCave.errMsg,
202	"error in reading file %s\n"
203	"natoms = %d; index = %d\n"
204	"error reading the line from the file.\n",
205	c_in_name, n_atoms, i );
206	haveError= 1;
207	simError();
208	}
209
210	if(haveError) nodeZeroError();
211
212	// Get the Node number which wants this atom:
213	which_node = AtomToProcMap[i];
214	if (which_node == 0) {
215	parseErr = parseDumpLine( read_buffer, i );
216	if( parseErr != NULL ){
217	strcpy( painCave.errMsg, parseErr );
218	haveError = 1;
219	simError();
220	}
221	if(haveError) nodeZeroError();
222	}
223
224	else {
225
226	myStatus = 1;
227	MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node,
228	TAKE_THIS_TAG_INT);
229	MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
230	TAKE_THIS_TAG_CHAR);
231	MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT);
232	MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus);
233
234	if(!myStatus) nodeZeroError();
235	}
236	}
237	myStatus = -1;
238	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
239	MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j,
240	TAKE_THIS_TAG_INT);
241	}
242
243	} else {
244
245	done = 0;
246	while (!done) {
247
248	MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0,
249	TAKE_THIS_TAG_INT, istatus);
250
251	if(!myStatus) anonymousNodeDie();
252
253	if(myStatus < 0) break;
254
255	MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
256	TAKE_THIS_TAG_CHAR, istatus);
257	MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0,
258	TAKE_THIS_TAG_INT, istatus);
259
260	myStatus = 1;
261	parseErr = parseDumpLine( read_buffer, which_atom );
262	if( parseErr != NULL ){
263	strcpy( painCave.errMsg, parseErr );
264	myStatus = 0;;
265	simError();
266	}
267
268	MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0,
269	TAKE_THIS_TAG_INT);
270
271	}
272	}
273
274	// last thing last, enable fatalities.
275	painCave.isEventLoop = 0;
276
277	#endif
278	}
279
280	char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
281
282	char *foo; // the pointer to the current string token
283
284	double rx, ry, rz; // position place holders
285	double vx, vy, vz; // velocity placeholders
286	double q[4]; // the quaternions
287	double jx, jy, jz; // angular velocity placeholders;
288	double qSqr, qLength; // needed to normalize the quaternion vector.
289
290	Atom **atoms = entry_plug->atoms;
291	DirectionalAtom* dAtom;
292
293	int j, n_atoms, atomIndex;
294
295	#ifdef IS_MPI
296	n_atoms = mpiSim->getTotAtoms();
297	atomIndex=-1;
298	for (j=0; j < mpiSim->getMyNlocal(); j++) {
299	if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
300	}
301	if (atomIndex == -1) {
302	sprintf( painCave.errMsg,
303	"Initialize from file error. Atom at index %d "
304	"in file %s does not exist on processor %d .\n",
305	globalIndex, c_in_name, mpiSim->getMyNode() );
306	return strdup( painCave.errMsg );
307	}
308	#else
309	n_atoms = entry_plug->n_atoms;
310	atomIndex = globalIndex;
311	#endif // is_mpi
312
313	// set the string tokenizer
314
315	foo = strtok(readLine, " ,;\t");
316
317	// check the atom name to the current atom
318
319	if( strcmp( foo, atoms[atomIndex]->getType() ) ){
320	sprintf( painCave.errMsg,
321	"Initialize from file error. Atom %s at index %d "
322	"in file %s does not"
323	" match the BASS atom %s.\n",
324	foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
325	return strdup( painCave.errMsg );
326	}
327
328	// get the positions
329
330	foo = strtok(NULL, " ,;\t");
331	if(foo == NULL){
332	sprintf( painCave.errMsg,
333	"error in reading postition x from %s\n"
334	"natoms = %d, index = %d\n",
335	c_in_name, n_atoms, atomIndex );
336	return strdup( painCave.errMsg );
337	}
338	rx = atof( foo );
339
340	foo = strtok(NULL, " ,;\t");
341	if(foo == NULL){
342	sprintf( painCave.errMsg,
343	"error in reading postition y from %s\n"
344	"natoms = %d, index = %d\n",
345	c_in_name, n_atoms, atomIndex );
346	return strdup( painCave.errMsg );
347	}
348	ry = atof( foo );
349
350	foo = strtok(NULL, " ,;\t");
351	if(foo == NULL){
352	sprintf( painCave.errMsg,
353	"error in reading postition z from %s\n"
354	"natoms = %d, index = %d\n",
355	c_in_name, n_atoms, atomIndex );
356	return strdup( painCave.errMsg );
357	}
358	rz = atof( foo );
359
360
361	// get the velocities
362
363	foo = strtok(NULL, " ,;\t");
364	if(foo == NULL){
365	sprintf( painCave.errMsg,
366	"error in reading velocity x from %s\n"
367	"natoms = %d, index = %d\n",
368	c_in_name, n_atoms, atomIndex );
369	return strdup( painCave.errMsg );
370	}
371	vx = atof( foo );
372
373	foo = strtok(NULL, " ,;\t");
374	if(foo == NULL){
375	sprintf( painCave.errMsg,
376	"error in reading velocity y from %s\n"
377	"natoms = %d, index = %d\n",
378	c_in_name, n_atoms, atomIndex );
379	return strdup( painCave.errMsg );
380	}
381	vy = atof( foo );
382
383	foo = strtok(NULL, " ,;\t");
384	if(foo == NULL){
385	sprintf( painCave.errMsg,
386	"error in reading velocity z from %s\n"
387	"natoms = %d, index = %d\n",
388	c_in_name, n_atoms, atomIndex );
389	return strdup( painCave.errMsg );
390	}
391	vz = atof( foo );
392
393
394	// get the quaternions
395
396	if( atoms[atomIndex]->isDirectional() ){
397
398	foo = strtok(NULL, " ,;\t");
399	if(foo == NULL){
400	sprintf(painCave.errMsg,
401	"error in reading quaternion 0 from %s\n"
402	"natoms = %d, index = %d\n",
403	c_in_name, n_atoms, atomIndex );
404	return strdup( painCave.errMsg );
405	}
406	q[0] = atof( foo );
407
408	foo = strtok(NULL, " ,;\t");
409	if(foo == NULL){
410	sprintf( painCave.errMsg,
411	"error in reading quaternion 1 from %s\n"
412	"natoms = %d, index = %d\n",
413	c_in_name, n_atoms, atomIndex );
414	return strdup( painCave.errMsg );
415	}
416	q[1] = atof( foo );
417
418	foo = strtok(NULL, " ,;\t");
419	if(foo == NULL){
420	sprintf( painCave.errMsg,
421	"error in reading quaternion 2 from %s\n"
422	"natoms = %d, index = %d\n",
423	c_in_name, n_atoms, atomIndex );
424	return strdup( painCave.errMsg );
425	}
426	q[2] = atof( foo );
427
428	foo = strtok(NULL, " ,;\t");
429	if(foo == NULL){
430	sprintf( painCave.errMsg,
431	"error in reading quaternion 3 from %s\n"
432	"natoms = %d, index = %d\n",
433	c_in_name, n_atoms, atomIndex );
434	return strdup( painCave.errMsg );
435	}
436	q[3] = atof( foo );
437
438	// get the angular velocities
439
440	foo = strtok(NULL, " ,;\t");
441	if(foo == NULL){
442	sprintf( painCave.errMsg,
443	"error in reading angular momentum jx from %s\n"
444	"natoms = %d, index = %d\n",
445	c_in_name, n_atoms, atomIndex );
446	return strdup( painCave.errMsg );
447	}
448	jx = atof( foo );
449
450	foo = strtok(NULL, " ,;\t");
451	if(foo == NULL){
452	sprintf( painCave.errMsg,
453	"error in reading angular momentum jy from %s\n"
454	"natoms = %d, index = %d\n",
455	c_in_name, n_atoms, atomIndex );
456	return strdup( painCave.errMsg );
457	}
458	jy = atof(foo );
459
460	foo = strtok(NULL, " ,;\t");
461	if(foo == NULL){
462	sprintf( painCave.errMsg,
463	"error in reading angular momentum jz from %s\n"
464	"natoms = %d, index = %d\n",
465	c_in_name, n_atoms, atomIndex );
466	return strdup( painCave.errMsg );
467	}
468	jz = atof( foo );
469
470	dAtom = ( DirectionalAtom* )atoms[atomIndex];
471
472	// check that the quaternion vector is normalized
473
474	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
475
476	qLength = sqrt( qSqr );
477	q[0] = q[0] / qLength;
478	q[1] = q[1] / qLength;
479	q[2] = q[2] / qLength;
480	q[3] = q[3] / qLength;
481
482	dAtom->setQ( q );
483
484	// add the angular velocities
485
486	dAtom->setJx( jx );
487	dAtom->setJy( jy );
488	dAtom->setJz( jz );
489	}
490
491	// add the positions and velocities to the atom
492
493	atoms[atomIndex]->setX( rx );
494	atoms[atomIndex]->setY( ry );
495	atoms[atomIndex]->setZ( rz );
496
497	atoms[atomIndex]->set_vx( vx );
498	atoms[atomIndex]->set_vy( vy );
499	atoms[atomIndex]->set_vz( vz );
500
501	return NULL;
502	}
503
504
505	#ifdef IS_MPI
506
507	// a couple of functions to let us escape the read loop
508
509	void nodeZeroError( void ){
510	int j, myStatus;
511
512	myStatus = 0;
513	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
514	MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j,
515	TAKE_THIS_TAG_INT);
516	}
517
518
519	MPI_Finalize();
520	exit (0);
521
522	}
523
524	void anonymousNodeDie( void ){
525
526	MPI_Finalize();
527	exit (0);
528	}
529
530	#endif //is_mpi