mdtools/md_code/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"


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; // 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;


  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


  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);
      painCave.isFatal = 1;
      simError();
    }
    
    n_atoms = atoi( read_buffer );
    
    Atom **atoms = entry_plug->atoms;
    DirectionalAtom* dAtom;
    
    if( n_atoms != entry_plug->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 );
      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();
    }    
  }
#endif
}


char* IntitializeFromFile::parseDumpLine(char* readLine, int atomIndex){

  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 n_atoms;

#ifdef IS_MPI
  n_atoms = entry_plug->mpiSim->getTotAtoms();
#else
  n_atoms = entry_plug->n_atoms;
#endi // 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;
}
Revision:	209
Committed:	Fri Dec 13 17:59:52 2002 UTC (21 years, 7 months ago) by mmeineke
File size:	10086 byte(s)
Log Message:	* empty log message *
#	User	Rev	Content
1	mmeineke	10	#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	mmeineke	162	#include "simError.h"
13	mmeineke	10
14
15			InitializeFromFile :: InitializeFromFile( char *in_name ){
16	chuckv	206	#ifdef IS_MPI
17			if (worldRank == 0) {
18			#endif
19	mmeineke	10
20			c_in_file = fopen(in_name, "r");
21			if(c_in_file == NULL){
22	mmeineke	162	sprintf(painCave.errMsg,
23			"Cannot open file: %s\n", in_name);
24			painCave.isFatal = 1;
25			simError();
26	mmeineke	10	}
27
28			strcpy( c_in_name, in_name);
29	chuckv	206	#ifdef IS_MPI
30			}
31			strcpy( checkPointMsg, "Infile opened for reading successfully." );
32			MPIcheckPoint();
33			#endif
34	mmeineke	10	return;
35			}
36
37			InitializeFromFile :: ~InitializeFromFile( ){
38	chuckv	206	#ifdef IS_MPI
39			if (worldRank == 0) {
40			#endif
41	mmeineke	10	int error;
42			error = fclose( c_in_file );
43			if( error ){
44	mmeineke	162	sprintf( painCave.errMsg,
45			"Error closing %s\n", c_in_name );
46			simError();
47	mmeineke	10	}
48	chuckv	206	#ifdef IS_MPI
49			}
50			strcpy( checkPointMsg, "Infile closed successfully." );
51			MPIcheckPoint();
52			#endif
53
54	mmeineke	10	return;
55			}
56
57
58	chuckv	206	void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
59	mmeineke	10
60			int i; // loop counter
61
62	mmeineke	209	const int BUFFERSIZE = 2000; // size of the read buffer
63	mmeineke	10	int n_atoms; // the number of atoms
64	mmeineke	209	char read_buffer[BUFFERSIZE]; //the line buffer for reading
65	chuckv	206	#ifdef IS_MPI
66	mmeineke	209	char send_buffer[BUFFERSIZE];
67	chuckv	206	#endif
68
69	mmeineke	10	char *eof_test; // ptr to see when we reach the end of the file
70	mmeineke	209	char *parseErr;
71	mmeineke	10
72
73	chuckv	206	entry_plug = the_entry_plug
74
75
76			#ifndef IS_MPI
77	mmeineke	10	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
78			if( eof_test == NULL ){
79	mmeineke	209	sprintf( painCave.errMsg,
80			"InitializeFromFile error: error reading 1st line of \"%s\"\n",
81			c_in_name );
82			painCave.isFatal = 1;
83			simError();
84	mmeineke	10	}
85
86	mmeineke	209	n_atoms = atoi( read_buffer );
87	mmeineke	10
88			Atom **atoms = entry_plug->atoms;
89			DirectionalAtom* dAtom;
90
91			if( n_atoms != entry_plug->n_atoms ){
92	mmeineke	162	sprintf( painCave.errMsg,
93	mmeineke	10	"Initialize from File error. %s n_atoms, %d, "
94			"does not match the BASS file's n_atoms, %d.\n",
95			c_in_name, n_atoms, entry_plug->n_atoms );
96	mmeineke	162	painCave.isFatal = 1;
97			simError();
98	mmeineke	10	}
99
100			//read and toss the comment line
101
102			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
103			if(eof_test == NULL){
104	mmeineke	162	sprintf( painCave.errMsg,
105			"error in reading commment in %s\n", c_in_name);
106			painCave.isFatal = 1;
107			simError();
108	mmeineke	10	}
109
110			for( i=0; i < n_atoms; i++){
111
112			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
113			if(eof_test == NULL){
114	mmeineke	162	sprintf(painCave.errMsg,
115			"error in reading file %s\n"
116			"natoms = %d; index = %d\n"
117			"error reading the line from the file.\n",
118			c_in_name, n_atoms, i );
119			painCave.isFatal = 1;
120			simError();
121	mmeineke	10	}
122
123
124	mmeineke	209	parseErr = parseDumpLine( read_buffer, i );
125			if( parseErr != NULL ){
126			strcpy( painCave.errMsg, parseErr );
127	mmeineke	162	painCave.isFatal = 1;
128			simError();
129	mmeineke	209	}
130	mmeineke	10	}
131	chuckv	206
132
133			// MPI Section of code..........
134			#else //IS_MPI
135
136
137
138
139			if (worldRank == 0) {
140			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
141			if( eof_test == NULL ){
142			sprintf( painCave.errMsg,
143			"Error reading 1st line of %d \n ",c_in_name);
144			painCave.isFatal = 1;
145			simError();
146			}
147
148	mmeineke	209	n_atoms = atoi( read_buffer );
149	chuckv	206
150			Atom **atoms = entry_plug->atoms;
151			DirectionalAtom* dAtom;
152
153	mmeineke	209	if( n_atoms != entry_plug->mpiSim->getTotAtoms() ){
154	chuckv	206	sprintf( painCave.errMsg,
155			"Initialize from File error. %s n_atoms, %d, "
156			"does not match the BASS file's n_atoms, %d.\n",
157			c_in_name, n_atoms, entry_plug->n_atoms );
158			painCave.isFatal = 1;
159			simError();
160			}
161
162			//read and toss the comment line
163
164			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
165			if(eof_test == NULL){
166			sprintf( painCave.errMsg,
167			"error in reading commment in %s\n", c_in_name);
168			painCave.isFatal = 1;
169			simError();
170			}
171			}
172	mmeineke	209
173	chuckv	206	for( i=0; i < n_atoms; i++){
174
175			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
176			if(eof_test == NULL){
177			sprintf(painCave.errMsg,
178			"error in reading file %s\n"
179			"natoms = %d; index = %d\n"
180			"error reading the line from the file.\n",
181			c_in_name, n_atoms, i );
182			painCave.isFatal = 1;
183			simError();
184			}
185
186	mmeineke	209	parseErr = parseDumpLine( read_buffer, i );
187			if( parseErr != NULL ){
188			strcpy( painCave.errMsg, parseErr );
189	chuckv	206	painCave.isFatal = 1;
190			simError();
191	mmeineke	209	}
192			}
193			#endif
194			}
195
196
197			char* IntitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
198
199			char *foo; // the pointer to the current string token
200
201			double rx, ry, rz; // position place holders
202			double vx, vy, vz; // velocity placeholders
203			double q[4]; // the quaternions
204			double jx, jy, jz; // angular velocity placeholders;
205			double qSqr, qLength; // needed to normalize the quaternion vector.
206
207			Atom **atoms = entry_plug->atoms;
208			DirectionalAtom* dAtom;
209
210			int n_atoms;
211
212			#ifdef IS_MPI
213			n_atoms = entry_plug->mpiSim->getTotAtoms();
214			#else
215			n_atoms = entry_plug->n_atoms;
216			#endi // is_mpi
217
218
219			// set the string tokenizer
220
221			foo = strtok(readLine, " ,;\t");
222
223			// check the atom name to the current atom
224
225			if( strcmp( foo, atoms[atomIndex]->getType() ) ){
226			sprintf( painCave.errMsg,
227			"Initialize from file error. Atom %s at index %d "
228			"in file %s does not"
229			" match the BASS atom %s.\n",
230			foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
231			return strdup( painCave.errMsg );
232			}
233	chuckv	206
234	mmeineke	209	// get the positions
235	chuckv	206
236	mmeineke	209	foo = strtok(NULL, " ,;\t");
237			if(foo == NULL){
238			sprintf( painCave.errMsg,
239			"error in reading postition x from %s\n"
240			"natoms = %d, index = %d\n",
241			c_in_name, n_atoms, atomIndex );
242			return strdup( painCave.errMsg );
243			}
244			rx = atof( foo );
245
246			foo = strtok(NULL, " ,;\t");
247			if(foo == NULL){
248			sprintf( painCave.errMsg,
249			"error in reading postition y from %s\n"
250			"natoms = %d, index = %d\n",
251			c_in_name, n_atoms, atomIndex );
252			return strdup( painCave.errMsg );
253			}
254			ry = atof( foo );
255
256			foo = strtok(NULL, " ,;\t");
257			if(foo == NULL){
258			sprintf( painCave.errMsg,
259			"error in reading postition z from %s\n"
260			"natoms = %d, index = %d\n",
261			c_in_name, n_atoms, atomIndex );
262			return strdup( painCave.errMsg );
263			}
264			rz = atof( foo );
265
266
267			// get the velocities
268
269			foo = strtok(NULL, " ,;\t");
270			if(foo == NULL){
271			sprintf( painCave.errMsg,
272			"error in reading velocity x from %s\n"
273			"natoms = %d, index = %d\n",
274			c_in_name, n_atoms, atomIndex );
275			return strdup( painCave.errMsg );
276			}
277			vx = atof( foo );
278
279			foo = strtok(NULL, " ,;\t");
280			if(foo == NULL){
281			sprintf( painCave.errMsg,
282			"error in reading velocity y from %s\n"
283			"natoms = %d, index = %d\n",
284			c_in_name, n_atoms, atomIndex );
285			return strdup( painCave.errMsg );
286			}
287			vy = atof( foo );
288
289			foo = strtok(NULL, " ,;\t");
290			if(foo == NULL){
291			sprintf( painCave.errMsg,
292			"error in reading velocity z from %s\n"
293			"natoms = %d, index = %d\n",
294			c_in_name, n_atoms, atomIndex );
295			return strdup( painCave.errMsg );
296			}
297			vz = atof( foo );
298
299
300			// get the quaternions
301
302			if( atoms[atomIndex]->isDirectional() ){
303
304	chuckv	206	foo = strtok(NULL, " ,;\t");
305			if(foo == NULL){
306	mmeineke	209	sprintf(painCave.errMsg,
307			"error in reading quaternion 0 from %s\n"
308			"natoms = %d, index = %d\n",
309			c_in_name, n_atoms, atomIndex );
310			return strdup( painCave.errMsg );
311			}
312			q[0] = atof( foo );
313
314			foo = strtok(NULL, " ,;\t");
315			if(foo == NULL){
316	chuckv	206	sprintf( painCave.errMsg,
317	mmeineke	209	"error in reading quaternion 1 from %s\n"
318	chuckv	206	"natoms = %d, index = %d\n",
319	mmeineke	209	c_in_name, n_atoms, atomIndex );
320			return strdup( painCave.errMsg );
321	chuckv	206	}
322	mmeineke	209	q[1] = atof( foo );
323
324	chuckv	206	foo = strtok(NULL, " ,;\t");
325			if(foo == NULL){
326			sprintf( painCave.errMsg,
327	mmeineke	209	"error in reading quaternion 2 from %s\n"
328	chuckv	206	"natoms = %d, index = %d\n",
329	mmeineke	209	c_in_name, n_atoms, atomIndex );
330			return strdup( painCave.errMsg );
331	chuckv	206	}
332	mmeineke	209	q[2] = atof( foo );
333
334	chuckv	206	foo = strtok(NULL, " ,;\t");
335			if(foo == NULL){
336			sprintf( painCave.errMsg,
337	mmeineke	209	"error in reading quaternion 3 from %s\n"
338	chuckv	206	"natoms = %d, index = %d\n",
339	mmeineke	209	c_in_name, n_atoms, atomIndex );
340			return strdup( painCave.errMsg );
341	chuckv	206	}
342	mmeineke	209	q[3] = atof( foo );
343
344			// get the angular velocities
345
346	chuckv	206	foo = strtok(NULL, " ,;\t");
347			if(foo == NULL){
348			sprintf( painCave.errMsg,
349	mmeineke	209	"error in reading angular momentum jx from %s\n"
350	chuckv	206	"natoms = %d, index = %d\n",
351	mmeineke	209	c_in_name, n_atoms, atomIndex );
352			return strdup( painCave.errMsg );
353	chuckv	206	}
354	mmeineke	209	jx = atof( foo );
355
356	chuckv	206	foo = strtok(NULL, " ,;\t");
357			if(foo == NULL){
358			sprintf( painCave.errMsg,
359	mmeineke	209	"error in reading angular momentum jy from %s\n"
360	chuckv	206	"natoms = %d, index = %d\n",
361	mmeineke	209	c_in_name, n_atoms, atomIndex );
362			return strdup( painCave.errMsg );
363	chuckv	206	}
364	mmeineke	209	jy = atof(foo );
365
366	chuckv	206	foo = strtok(NULL, " ,;\t");
367			if(foo == NULL){
368			sprintf( painCave.errMsg,
369	mmeineke	209	"error in reading angular momentum jz from %s\n"
370	chuckv	206	"natoms = %d, index = %d\n",
371	mmeineke	209	c_in_name, n_atoms, atomIndex );
372			return strdup( painCave.errMsg );
373	chuckv	206	}
374	mmeineke	209	jz = atof( foo );
375	chuckv	206
376	mmeineke	209	dAtom = ( DirectionalAtom* )atoms[atomIndex];
377	chuckv	206
378	mmeineke	209	// check that the quaternion vector is normalized
379	chuckv	206
380	mmeineke	209	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
381	chuckv	206
382	mmeineke	209	qLength = sqrt( qSqr );
383			q[0] = q[0] / qLength;
384			q[1] = q[1] / qLength;
385			q[2] = q[2] / qLength;
386			q[3] = q[3] / qLength;
387	chuckv	206
388	mmeineke	209	dAtom->setQ( q );
389	chuckv	206
390	mmeineke	209	// add the angular velocities
391	chuckv	206
392	mmeineke	209	dAtom->setJx( jx );
393			dAtom->setJy( jy );
394			dAtom->setJz( jz );
395			}
396	chuckv	206
397	mmeineke	209	// add the positions and velocities to the atom
398	chuckv	206
399	mmeineke	209	atoms[atomIndex]->setX( rx );
400			atoms[atomIndex]->setY( ry );
401			atoms[atomIndex]->setZ( rz );
402	chuckv	206
403	mmeineke	209	atoms[atomIndex]->set_vx( vx );
404			atoms[atomIndex]->set_vy( vy );
405			atoms[atomIndex]->set_vz( vz );
406
407			return NULL;
408	mmeineke	10	}