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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 1130 by tim, Thu Apr 22 14:55:17 2004 UTC

# Line 1 | Line 1
1 + #define _FILE_OFFSET_BITS 64
2   #include <iostream>
3 < #include <cmath>
3 > #include <math.h>
4  
5   #include <stdio.h>
6   #include <stdlib.h>
# Line 10 | Line 11
11  
12   #include "ReadWrite.hpp"
13   #include "simError.h"
14 + #include "GenericData.hpp"
15  
16   #ifdef IS_MPI
17 + #include <mpi.h>
18   #include "mpiSimulation.hpp"
19 + #define TAKE_THIS_TAG_CHAR 3134
20 + #define TAKE_THIS_TAG_INT 3135
21  
22 < #define TAKE_THIS_TAG 0
22 > namespace initFile{
23 >  void nodeZeroError( void );
24 >  void anonymousNodeDie( void );
25 > }
26 >
27 > using namespace initFile;
28 >
29   #endif // is_mpi
30  
31 < InitializeFromFile :: InitializeFromFile( char *in_name ){
31 > InitializeFromFile::InitializeFromFile( char *in_name ){
32 >
33   #ifdef IS_MPI
34    if (worldRank == 0) {
35   #endif
# Line 29 | Line 41 | InitializeFromFile :: InitializeFromFile( char *in_nam
41      painCave.isFatal = 1;
42      simError();
43    }
44 <  
44 >
45    strcpy( c_in_name, in_name);
46   #ifdef IS_MPI
47    }
48 < strcpy( checkPointMsg, "Infile opened for reading successfully." );
48 >  else{
49 >          sprintf( c_in_name, "mpiNodeParser_%d", worldRank );
50 >  }
51 >  
52 >  strcpy( checkPointMsg, "Infile opened for reading successfully." );
53    MPIcheckPoint();
54   #endif
55 <  return;  
55 >  return;
56   }
57  
58 < InitializeFromFile :: ~InitializeFromFile( ){
58 > InitializeFromFile::~InitializeFromFile( ){
59   #ifdef IS_MPI
60    if (worldRank == 0) {
61   #endif
# Line 60 | Line 76 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
76   }
77  
78  
79 < void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
79 > void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
80  
81 <  int i; // loop counter
81 >  int i, j;
82  
67 –  const int BUFFERSIZE = 2000; // size of the read buffer
68 –  int n_atoms; // the number of atoms
69 –  char read_buffer[BUFFERSIZE]; //the line buffer for reading
83   #ifdef IS_MPI
84 <  char send_buffer[BUFFERSIZE];
85 < #endif
84 >  int done, which_node, which_atom; // loop counter
85 > #endif //is_mpi
86  
87 <  char *eof_test; // ptr to see when we reach the end of the file
87 >  const int BUFFERSIZE = 2000; // size of the read buffer
88 >  int nTotObjs; // the number of atoms
89 >  char read_buffer[BUFFERSIZE]; //the line buffer for reading
90 >
91 >  char *eof_test; // ptr to see when we reach the end of the file
92    char *parseErr;
76 –  int procIndex;
93  
94 <  entry_plug = the_entry_plug;
94 >  vector<StuntDouble*> integrableObjects;
95  
96 +  simnfo = the_simnfo;
97  
98 +
99   #ifndef IS_MPI
100    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
101    if( eof_test == NULL ){
# Line 88 | Line 106 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
106      simError();
107    }
108  
109 <  n_atoms = atoi( read_buffer );
109 >  nTotObjs = atoi( read_buffer );
110  
111 <  Atom **atoms = entry_plug->atoms;
94 <  DirectionalAtom* dAtom;
95 <
96 <  if( n_atoms != entry_plug->n_atoms ){
111 >  if( nTotObjs != simnfo->getTotIntegrableObjects() ){
112      sprintf( painCave.errMsg,
113               "Initialize from File error. %s n_atoms, %d, "
114               "does not match the BASS file's n_atoms, %d.\n",
115 <             c_in_name, n_atoms, entry_plug->n_atoms );
115 >             c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
116      painCave.isFatal = 1;
117      simError();
118    }
119 <  
120 <  //read and toss the comment line
121 <  
119 >
120 >  //read the box mat from the comment line
121 >
122    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
123    if(eof_test == NULL){
124      sprintf( painCave.errMsg,
# Line 112 | Line 127 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
127      simError();
128    }
129  
130 <  for( i=0; i < n_atoms; i++){
131 <    
132 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
133 <    if(eof_test == NULL){
134 <      sprintf(painCave.errMsg,
120 <              "error in reading file %s\n"
121 <              "natoms  = %d; index = %d\n"
122 <              "error reading the line from the file.\n",
123 <              c_in_name, n_atoms, i );
124 <      painCave.isFatal = 1;
125 <      simError();
126 <    }
127 <
128 <    
129 <    parseErr = parseDumpLine( read_buffer, i );
130 <    if( parseErr != NULL ){
131 <      strcpy( painCave.errMsg, parseErr );
132 <      painCave.isFatal = 1;
133 <      simError();
134 <    }    
130 >  parseErr = parseCommentLine( read_buffer, simnfo);
131 >  if( parseErr != NULL ){
132 >    strcpy( painCave.errMsg, parseErr );
133 >    painCave.isFatal = 1;
134 >    simError();
135    }
136  
137 +  //parse dump lines
138  
139 +  for( i=0; i < simnfo->n_mol; i++){
140 +
141 +    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
142 +
143 +    for(j = 0; j < integrableObjects.size(); j++){
144 +
145 +      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
146 +      if(eof_test == NULL){
147 +        sprintf(painCave.errMsg,
148 +              "error in reading file %s\n"
149 +              "natoms  = %d; index = %d\n"
150 +              "error reading the line from the file.\n",
151 +              c_in_name, nTotObjs, i );
152 +        painCave.isFatal = 1;
153 +        simError();
154 +      }
155 +      
156 +      parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
157 +      if( parseErr != NULL ){
158 +        strcpy( painCave.errMsg, parseErr );
159 +        painCave.isFatal = 1;
160 +        simError();
161 +      }
162 +    }
163 +  }
164 +
165    // MPI Section of code..........
166   #else //IS_MPI
167  
168 <  int masterIndex;
169 <  int nodeAtomsStart;
143 <  int nodeAtomsEnd;
144 <  int mpiErr;
145 <  int sendError;
168 >  // first thing first, suspend fatalities.
169 >  painCave.isEventLoop = 1;
170  
171 <  MPI_Status istatus[MPI_STATUS_SIZE];
171 >  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
172 >  int haveError;
173  
174 +  MPI_Status istatus;
175 +  int *MolToProcMap = mpiSim->getMolToProcMap();
176 +  int localIndex;
177 +  int nCurObj;
178 +  int nItems;
179 +
180 +  nTotObjs = simnfo->getTotIntegrableObjects();
181 +  haveError = 0;
182    if (worldRank == 0) {
183 +
184      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
185      if( eof_test == NULL ){
186        sprintf( painCave.errMsg,
187 <               "Error reading 1st line of %d \n ",c_in_name);
188 <      painCave.isFatal = 1;
187 >               "Error reading 1st line of %s \n ",c_in_name);
188 >      haveError = 1;
189        simError();
190      }
191 <    
192 <    n_atoms = atoi( read_buffer );
193 <    
194 <    Atom **atoms = entry_plug->atoms;
161 <    DirectionalAtom* dAtom;
162 <
163 <    // Check to see that the number of atoms in the intial configuration file is the
191 >
192 >    nItems = atoi( read_buffer );
193 >
194 >    // Check to see that the number of integrable objects  in the intial configuration file is the
195      // same as declared in simBass.
196 <    
197 <    if( n_atoms != mpiSim->getTotAtoms() ){
196 >
197 >    if( nTotObjs != nItems){
198        sprintf( painCave.errMsg,
199                 "Initialize from File error. %s n_atoms, %d, "
200                 "does not match the BASS file's n_atoms, %d.\n",
201 <               c_in_name, n_atoms, entry_plug->n_atoms );
202 <      painCave.isFatal = 1;
201 >               c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
202 >      haveError= 1;
203        simError();
204      }
205 <    
206 <    //read and toss the comment line
207 <    
205 >
206 >    //read the boxMat from the comment line
207 >
208      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
209      if(eof_test == NULL){
210        sprintf( painCave.errMsg,
211                 "error in reading commment in %s\n", c_in_name);
212 <      painCave.isFatal = 1;
212 >      haveError = 1;
213        simError();
214      }
215 <  
216 <    // Read Proc 0 share of the xyz file...
217 <    masterIndex = 0;
218 <    for( i=0; i <= mpiSim->getMyAtomEnd(); i++){
219 <    
220 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
221 <      if(eof_test == NULL){
222 <        sprintf(painCave.errMsg,
223 <                "error in reading file %s\n"
224 <                "natoms  = %d; index = %d\n"
225 <                "error reading the line from the file.\n",
226 <                c_in_name, n_atoms, i );
227 <        painCave.isFatal = 1;
228 <        simError();
229 <      }
230 <    
200 <      parseErr = parseDumpLine( read_buffer, i );
201 <      if( parseErr != NULL ){
202 <        strcpy( painCave.errMsg, parseErr );
203 <        painCave.isFatal = 1;
204 <        simError();
205 <      }    
206 <      masterIndex++;
215 >
216 >    //Every single processor will parse the comment line by itself
217 >    //By using this way, we might lose some efficiency, but if we want to add
218 >    //more parameters into comment line, we only need to modify function
219 >    //parseCommentLine
220 >
221 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
222 >
223 >    cerr << "node " << worldRank << " finished  MPI_Bcast" << endl;
224 >
225 >    parseErr = parseCommentLine( read_buffer, simnfo);
226 >
227 >    if( parseErr != NULL ){
228 >      strcpy( painCave.errMsg, parseErr );
229 >      haveError = 1;
230 >      simError();
231      }
208 –  }
232  
233 <  sprintf(checkPointMsg,
234 <          "Node 0 has successfully read positions from input file.");
235 <  MPIcheckPoint();
233 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
234 >      which_node = MolToProcMap[i];
235 >      if(which_node == 0){
236 >       //molecules belong to master node
237  
238 <  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
215 <         procIndex++){
216 <    if (worldRank == 0) {
238 >      localIndex = mpiSim->getGlobalToLocalMol(i);
239  
240 <      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
241 <               istatus);
240 >      if(localIndex == -1) {
241 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
242 >        haveError = 1;
243 >        simError();
244 >      }
245  
246 <      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
247 <               istatus);
248 <      // Make sure where node 0 is reading from, matches where the receiving node
249 <      // expects it to be.
246 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
247 >       for(j=0; j < integrableObjects.size(); j++){
248 >        
249 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
250 >          if(eof_test == NULL){
251 >                sprintf(painCave.errMsg,
252 >                    "error in reading file %s\n"
253 >                    "natoms  = %d; index = %d\n"
254 >                    "error reading the line from the file.\n",
255 >                    c_in_name, nTotObjs, i );
256 >                haveError= 1;
257 >                simError();
258 >          }
259 >          
260 >          if(haveError) nodeZeroError();
261  
262 <      if (masterIndex != nodeAtomsStart){
263 <        sendError = 1;
264 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
265 <        sprintf(painCave.errMsg,
266 <                "Initialize from file error: atoms start index (%d) for "
231 <                "node %d not equal to master index (%d)",nodeAtomsStart,procIndex,masterIndex );
232 <        painCave.isFatal = 1;
233 <        simError();
262 >          parseDumpLine(read_buffer, integrableObjects[j]);
263 >          
264 >       }
265 >
266 >
267        }
268 <      sendError = 0;
269 <      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
237 <      
238 <      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
239 <        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
240 <        if(eof_test == NULL){
241 <          
242 <          sprintf(read_buffer,"ERROR");
243 <          mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
244 <          
245 <          sprintf(painCave.errMsg,
246 <                  "error in reading file %s\n"
247 <                  "natoms  = %d; index = %d\n"
248 <                  "error reading the line from the file.\n",
249 <                  c_in_name, n_atoms, i );
250 <          painCave.isFatal = 1;
251 <          simError();
252 <        }
253 <        
254 <        mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
255 <        mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
256 <                          istatus);
257 <        if (sendError) MPIcheckPoint();
268 >      else{
269 >      //molecule belongs to slave nodes
270  
271 <        masterIndex++;
271 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
272 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
273 >         cerr << "node " << worldRank << " finished  MPI_Send" << endl;  
274 >       for(j=0; j < nCurObj; j++){
275 >        
276 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
277 >          if(eof_test == NULL){
278 >                sprintf(painCave.errMsg,
279 >                    "error in reading file %s\n"
280 >                    "natoms  = %d; index = %d\n"
281 >                    "error reading the line from the file.\n",
282 >                    c_in_name, nTotObjs, i );
283 >                haveError= 1;
284 >                simError();
285 >          }
286 >          
287 >          if(haveError) nodeZeroError();
288 >
289 >            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
290 >                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
291 >           cerr << "node " << worldRank << " finished  MPI_Send" << endl;
292 >       }
293 >
294        }
295 +      
296      }
297 +    
298 +  }
299 +  else{
300 +  //actions taken at slave nodes
301  
302 +    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
303  
304 <    else if(worldRank == procIndex){
305 <      nodeAtomsStart = mpiSim->getMyAtomStart();
306 <      nodeAtomsEnd = mpiSim->getMyAtomEnd();
307 <      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
308 <      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
304 >    cerr << "node " << worldRank << " finished  MPI_Bcast" << endl;
305 >    parseErr = parseCommentLine( read_buffer, simnfo);
306 >
307 >    if( parseErr != NULL ){
308 >      strcpy( painCave.errMsg, parseErr );
309 >      haveError = 1;
310 >      simError();
311 >    }
312 >  
313 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
314 >      which_node = MolToProcMap[i];
315        
316 <      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
317 <               istatus);
318 <      if (sendError) MPIcheckPoint();
316 >      if(which_node == worldRank){
317 >      //molecule with global index i belongs to this processor
318 >      
319 >        localIndex = mpiSim->getGlobalToLocalMol(i);
320  
321 <      for ( i = 0; i < entry_plug->n_atoms; i++){
321 >        if(localIndex == -1) {
322 >          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
323 >          haveError = 1;
324 >          simError();
325 >        }
326  
327 <        mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
277 <                          istatus);
278 <        
279 <        if(!strcmp(read_buffer, "ERROR")) MPIcheckPoint();
280 <        
281 <        parseErr = parseDumpLine( read_buffer, i );
282 <        if( parseErr != NULL ){
283 <          sendError = 1;
284 <          mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
327 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
328  
329 +        nCurObj = integrableObjects.size();
330 +        
331 +        MPI_Send(&nCurObj, 1, MPI_INT, 0,
332 +                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
333  
334 <          strcpy( painCave.errMsg, parseErr );
335 <          painCave.isFatal = 1;
336 <          simError();
337 <        }
338 <        sendError = 0;
339 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
334 >        cerr << "node " << worldRank << " finished  MPI_Send" << endl;
335 >        for(j = 0; j < integrableObjects.size(); j++){
336 >
337 >          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
338 >                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
339 >
340 >        cerr << "node " << worldRank << " finished  MPI_Recv" << endl;
341 >          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
342 >
343 >          if( parseErr != NULL ){
344 >                strcpy( painCave.errMsg, parseErr );
345 >                simError();
346 >          }
347 >
348 >        }
349 >          
350        }
351 +      
352      }
295 –    sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
296 –    MPIcheckPoint();
297 –  }
353  
354 +  }
355   #endif
356   }
357  
358 + char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
359  
360 < char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
360 >  char *foo; // the pointer to the current string token
361  
362 <  char *foo; // the pointer to the current string token
363 <  
307 <  double rx, ry, rz; // position place holders
308 <  double vx, vy, vz; // velocity placeholders
362 >  double pos[3]; // position place holders
363 >  double vel[3]; // velocity placeholders
364    double q[4]; // the quaternions
365 <  double jx, jy, jz; // angular velocity placeholders;
365 >  double ji[3]; // angular velocity placeholders;
366    double qSqr, qLength; // needed to normalize the quaternion vector.
312 –  
313 –  Atom **atoms = entry_plug->atoms;
314 –  DirectionalAtom* dAtom;
315 –  
316 –  int n_atoms;
367  
318 – #ifdef IS_MPI
319 –  n_atoms = mpiSim->getTotAtoms();
320 – #else
321 –  n_atoms = entry_plug->n_atoms;
322 – #endif // is_mpi
368  
324 –
369    // set the string tokenizer
370 <  
370 >
371    foo = strtok(readLine, " ,;\t");
372 <  
372 >
373    // check the atom name to the current atom
374 <  
375 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
374 >
375 >  if( strcmp( foo, sd->getType() ) ){
376      sprintf( painCave.errMsg,
377 <             "Initialize from file error. Atom %s at index %d "
334 <             "in file %s does not"
377 >             "Initialize from file error.  Does not"
378               " match the BASS atom %s.\n",
379 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
379 >             sd->getType() );
380      return strdup( painCave.errMsg );
381    }
382 <    
382 >
383    // get the positions
384  
385    foo = strtok(NULL, " ,;\t");
386    if(foo == NULL){
387      sprintf( painCave.errMsg,
388 <             "error in reading postition x from %s\n"
389 <             "natoms  = %d, index = %d\n",
347 <             c_in_name, n_atoms, atomIndex );
388 >             "error in reading postition x from %s\n",
389 >             c_in_name);
390      return strdup( painCave.errMsg );
391    }
392 <  rx = atof( foo );
393 <  
392 >  pos[0] = atof( foo );
393 >
394    foo = strtok(NULL, " ,;\t");
395    if(foo == NULL){
396      sprintf( painCave.errMsg,
397 <             "error in reading postition y from %s\n"
398 <             "natoms  = %d, index = %d\n",
357 <             c_in_name, n_atoms, atomIndex );
397 >             "error in reading postition y from %s\n",
398 >             c_in_name);
399      return strdup( painCave.errMsg );
400    }
401 <  ry = atof( foo );
402 <    
401 >  pos[1] = atof( foo );
402 >
403    foo = strtok(NULL, " ,;\t");
404    if(foo == NULL){
405      sprintf( painCave.errMsg,
406 <             "error in reading postition z from %s\n"
407 <             "natoms  = %d, index = %d\n",
367 <             c_in_name, n_atoms, atomIndex );
406 >             "error in reading postition z from %s\n",
407 >             c_in_name);
408      return strdup( painCave.errMsg );
409    }
410 <  rz = atof( foo );    
410 >  pos[2] = atof( foo );
411  
412  
413    // get the velocities
# Line 375 | Line 415 | char* InitializeFromFile::parseDumpLine(char* readLine
415    foo = strtok(NULL, " ,;\t");
416    if(foo == NULL){
417      sprintf( painCave.errMsg,
418 <             "error in reading velocity x from %s\n"
419 <             "natoms  = %d, index = %d\n",
380 <             c_in_name, n_atoms, atomIndex );
418 >             "error in reading velocity x from %s\n",
419 >             c_in_name );
420      return strdup( painCave.errMsg );
421    }
422 <  vx = atof( foo );
423 <    
422 >  vel[0] = atof( foo );
423 >
424    foo = strtok(NULL, " ,;\t");
425    if(foo == NULL){
426      sprintf( painCave.errMsg,
427 <             "error in reading velocity y from %s\n"
428 <             "natoms  = %d, index = %d\n",
390 <             c_in_name, n_atoms, atomIndex );
427 >             "error in reading velocity x from %s\n",
428 >             c_in_name );
429      return strdup( painCave.errMsg );
430    }
431 <  vy = atof( foo );
432 <    
431 >  vel[1] = atof( foo );
432 >
433    foo = strtok(NULL, " ,;\t");
434    if(foo == NULL){
435      sprintf( painCave.errMsg,
436 <             "error in reading velocity z from %s\n"
437 <             "natoms  = %d, index = %d\n",
400 <             c_in_name, n_atoms, atomIndex );
436 >             "error in reading velocity x from %s\n",
437 >             c_in_name );
438      return strdup( painCave.errMsg );
439    }
440 <  vz = atof( foo );
441 <    
442 <    
440 >  vel[2] = atof( foo );
441 >
442 >
443 >  // add the positions and velocities to the atom
444 >
445 >  sd->setPos( pos );
446 >  sd->setVel( vel );
447 >
448 >  if (!sd->isDirectional())
449 >    return NULL;
450 >
451    // get the quaternions
452 <    
453 <  if( atoms[atomIndex]->isDirectional() ){
454 <      
452 >
453 >  if( sd->isDirectional() ){
454 >
455      foo = strtok(NULL, " ,;\t");
456      if(foo == NULL){
457 <      sprintf(painCave.errMsg,
458 <              "error in reading quaternion 0 from %s\n"
459 <              "natoms  = %d, index = %d\n",
415 <              c_in_name, n_atoms, atomIndex );
457 >      sprintf( painCave.errMsg,
458 >                     "error in reading velocity x from %s\n",
459 >                      c_in_name );
460        return strdup( painCave.errMsg );
461      }
462      q[0] = atof( foo );
463 <      
463 >
464      foo = strtok(NULL, " ,;\t");
465      if(foo == NULL){
466        sprintf( painCave.errMsg,
467 <               "error in reading quaternion 1 from %s\n"
468 <               "natoms  = %d, index = %d\n",
425 <               c_in_name, n_atoms, atomIndex );
467 >                     "error in reading velocity x from %s\n",
468 >                      c_in_name );
469        return strdup( painCave.errMsg );
470      }
471      q[1] = atof( foo );
472 <      
472 >
473      foo = strtok(NULL, " ,;\t");
474      if(foo == NULL){
475        sprintf( painCave.errMsg,
476 <               "error in reading quaternion 2 from %s\n"
477 <               "natoms  = %d, index = %d\n",
435 <               c_in_name, n_atoms, atomIndex );
476 >                     "error in reading velocity x from %s\n",
477 >                      c_in_name );
478        return strdup( painCave.errMsg );
479      }
480      q[2] = atof( foo );
481 <      
481 >
482      foo = strtok(NULL, " ,;\t");
483      if(foo == NULL){
484        sprintf( painCave.errMsg,
485 <               "error in reading quaternion 3 from %s\n"
486 <               "natoms  = %d, index = %d\n",
445 <               c_in_name, n_atoms, atomIndex );
485 >                     "error in reading velocity x from %s\n",
486 >                      c_in_name );
487        return strdup( painCave.errMsg );
488      }
489      q[3] = atof( foo );
490 <      
490 >
491      // get the angular velocities
492 <      
492 >
493      foo = strtok(NULL, " ,;\t");
494      if(foo == NULL){
495        sprintf( painCave.errMsg,
496 <               "error in reading angular momentum jx from %s\n"
497 <               "natoms  = %d, index = %d\n",
457 <               c_in_name, n_atoms, atomIndex );
496 >                     "error in reading velocity x from %s\n",
497 >                      c_in_name );
498        return strdup( painCave.errMsg );
499      }
500 <    jx = atof( foo );
501 <      
500 >    ji[0] = atof( foo );
501 >
502      foo = strtok(NULL, " ,;\t");
503      if(foo == NULL){
504        sprintf( painCave.errMsg,
505 <               "error in reading angular momentum jy from %s\n"
506 <               "natoms  = %d, index = %d\n",
467 <               c_in_name, n_atoms, atomIndex );
505 >                     "error in reading velocity x from %s\n",
506 >                      c_in_name );
507        return strdup( painCave.errMsg );
508      }
509 <    jy = atof(foo );
510 <      
509 >    ji[1] = atof(foo );
510 >
511      foo = strtok(NULL, " ,;\t");
512      if(foo == NULL){
513        sprintf( painCave.errMsg,
514 <               "error in reading angular momentum jz from %s\n"
515 <               "natoms  = %d, index = %d\n",
477 <               c_in_name, n_atoms, atomIndex );
514 >                     "error in reading velocity x from %s\n",
515 >                      c_in_name );
516        return strdup( painCave.errMsg );
517      }
518 <    jz = atof( foo );
481 <      
482 <    dAtom = ( DirectionalAtom* )atoms[atomIndex];
518 >    ji[2] = atof( foo );
519  
520 +
521      // check that the quaternion vector is normalized
522  
523      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
524 <      
524 >
525      qLength = sqrt( qSqr );
526      q[0] = q[0] / qLength;
527      q[1] = q[1] / qLength;
528      q[2] = q[2] / qLength;
529      q[3] = q[3] / qLength;
493 –      
494 –    dAtom->setQ( q );
495 –      
496 –    // add the angular velocities
530  
531 <    dAtom->setJx( jx );
532 <    dAtom->setJy( jy );
533 <    dAtom->setJz( jz );
531 >    // add quaternion and angular velocities
532 >
533 >    sd->setQ( q );
534 >    sd->setJ( ji );
535    }
536 +
537 +
538 +
539 +  return NULL;
540 + }
541 +
542 +
543 + char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
544 +
545 +  double currTime;
546 +  double boxMat[9];
547 +  double theBoxMat3[3][3];
548 +  double chi;
549 +  double integralOfChidt;
550 +  double eta[9];
551 +
552 +  char *foo; // the pointer to the current string token
553 +
554 +  // set the string tokenizer
555 +
556 +  foo = strtok(readLine, " ,;\t");
557 +  // set the timeToken.
558 +
559 +  if(foo == NULL){
560 +    sprintf( painCave.errMsg,
561 +             "error in reading Time from %s\n",
562 +             c_in_name );
563 +    return strdup( painCave.errMsg );
564 +  }
565 +
566 +  currTime = atof( foo );
567 +  entry_plug->setTime( currTime );
568 +
569 +  //get H-Matrix
570 +
571 +  for(int i = 0 ; i < 9; i++){
572 +    foo = strtok(NULL, " ,;\t");
573 +    if(foo == NULL){
574 +      sprintf( painCave.errMsg,
575 +               "error in reading H[%d] from %s\n", i, c_in_name );
576 +      return strdup( painCave.errMsg );
577 +    }
578 +    boxMat[i] = atof( foo );
579 +  }
580 +
581 +  for(int i=0;i<3;i++)
582 +    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
583 +
584 +  //set H-Matrix
585 +  entry_plug->setBoxM( theBoxMat3 );
586 +
587 +  //get chi and integralOfChidt, they should appear by pair
588 +
589 +  if( entry_plug->useInitXSstate ){
590 +    foo = strtok(NULL, " ,;\t\n");
591 +    if(foo != NULL){
592 +      chi = atof(foo);
593 +      
594 +      foo = strtok(NULL, " ,;\t\n");
595 +      if(foo == NULL){
596 +        sprintf( painCave.errMsg,
597 +                 "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
598 +        return strdup( painCave.errMsg );
599 +      }
600 +      integralOfChidt = atof( foo );
601 +      
602 +      //push chi and integralOfChidt into SimInfo::properties which can be
603 +      //retrieved by integrator later
604 +      DoubleData* chiValue = new DoubleData();
605 +      chiValue->setID(CHIVALUE_ID);
606 +      chiValue->setData(chi);
607 +      entry_plug->addProperty(chiValue);
608 +      
609 +      DoubleData* integralOfChidtValue = new DoubleData();
610 +      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
611 +      integralOfChidtValue->setData(integralOfChidt);
612 +      entry_plug->addProperty(integralOfChidtValue);
613 +      
614 +    }
615 +    else
616 +      return NULL;
617      
618 <  // add the positions and velocities to the atom
618 >    //get eta
619 >    foo = strtok(NULL, " ,;\t\n");
620 >    if(foo != NULL ){
621 >  
622 >      for(int i = 0 ; i < 9; i++){
623 >        
624 >        if(foo == NULL){
625 >          sprintf( painCave.errMsg,
626 >                   "error in reading eta[%d] from %s\n", i, c_in_name );
627 >          return strdup( painCave.errMsg );
628 >        }
629 >        eta[i] = atof( foo );
630 >        foo = strtok(NULL, " ,;\t\n");
631 >      }
632 >    }
633 >    else
634 >      return NULL;
635      
636 <  atoms[atomIndex]->setX( rx );
637 <  atoms[atomIndex]->setY( ry );
507 <  atoms[atomIndex]->setZ( rz );
636 >    //push eta into SimInfo::properties which can be
637 >    //retrieved by integrator later
638      
639 <  atoms[atomIndex]->set_vx( vx );
640 <  atoms[atomIndex]->set_vy( vy );
641 <  atoms[atomIndex]->set_vz( vz );
639 >    DoubleArrayData* etaValue = new DoubleArrayData();
640 >    etaValue->setID(ETAVALUE_ID);
641 >    etaValue->setData(eta, 9);
642 >    entry_plug->addProperty(etaValue);
643 >  }
644  
645    return NULL;
646   }
647 +
648 + #ifdef IS_MPI
649 +
650 + // a couple of functions to let us escape the read loop
651 +
652 + void initFile::nodeZeroError( void ){
653 +  int j, myStatus;
654 +
655 +  myStatus = 0;
656 +  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
657 +    MPI_Send( &myStatus, 1, MPI_INT, j,
658 +              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
659 +  }
660 +
661 +
662 +  MPI_Finalize();
663 +  exit (0);
664 +
665 + }
666 +
667 + void initFile::anonymousNodeDie( void ){
668 +
669 +  MPI_Finalize();
670 +  exit (0);
671 + }
672 +
673 + #endif //is_mpi

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