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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 586 by mmeineke, Wed Jul 9 22:14:06 2003 UTC vs.
Revision 1113 by tim, Thu Apr 15 16:18:26 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>
# Line 26 | Line 28 | InitializeFromFile :: InitializeFromFile( char *in_nam
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 38 | 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 69 | Line 76 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
76   }
77  
78  
79 < void InitializeFromFile :: read_xyz( SimInfo* the_simnfo ){
79 > void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
80  
81 <  int i, j, done, which_node, which_atom; // loop counter
81 >  int i, j;
82  
76 –  const int BUFFERSIZE = 2000; // size of the read buffer
77 –  int n_atoms; // the number of atoms
78 –  char read_buffer[BUFFERSIZE]; //the line buffer for reading
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;
85 –  int procIndex;
86 –  double boxMat[9];
87 –  
93  
94 +  vector<StuntDouble*> integrableObjects;
95 +
96    simnfo = the_simnfo;
97  
98  
# Line 99 | Line 106 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
106      simError();
107    }
108  
109 <  n_atoms = atoi( read_buffer );
109 >  nTotObjs = atoi( read_buffer );
110  
111 <  Atom **atoms = simnfo->atoms;
105 <  DirectionalAtom* dAtom;
106 <
107 <  if( n_atoms != simnfo->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, simnfo->n_atoms );
115 >             c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
116      painCave.isFatal = 1;
117      simError();
118    }
119 <  
120 <  //read the box mat from 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 123 | Line 127 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
127      simError();
128    }
129  
130 <  parseErr = parseBoxLine( read_buffer, boxMat );
130 >  parseErr = parseCommentLine( read_buffer, simnfo);
131    if( parseErr != NULL ){
132      strcpy( painCave.errMsg, parseErr );
133      painCave.isFatal = 1;
134      simError();
135    }
136  
137 <  simnfo->setBoxM( boxMat );
137 >  //parse dump lines
138  
139 +  for( i=0; i < simnfo->n_mol; i++){
140  
141 <  for( i=0; i < n_atoms; i++){
137 <    
138 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
139 <    if(eof_test == NULL){
140 <      sprintf(painCave.errMsg,
141 <              "error in reading file %s\n"
142 <              "natoms  = %d; index = %d\n"
143 <              "error reading the line from the file.\n",
144 <              c_in_name, n_atoms, i );
145 <      painCave.isFatal = 1;
146 <      simError();
147 <    }
141 >    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
142  
143 <    
144 <    parseErr = parseDumpLine( read_buffer, i );
145 <    if( parseErr != NULL ){
146 <      strcpy( painCave.errMsg, parseErr );
147 <      painCave.isFatal = 1;
148 <      simError();
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  
158 –
165    // MPI Section of code..........
166   #else //IS_MPI
167  
# Line 164 | Line 170 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
170  
171    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
172    int haveError;
173 <  
173 >
174    MPI_Status istatus;
175 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
175 >  int *MolToProcMap = mpiSim->getMolToProcMap();
176 >  int localIndex;
177 >  int nCurObj;
178  
171 –  
179    haveError = 0;
180    if (worldRank == 0) {
181  
182      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
183      if( eof_test == NULL ){
184        sprintf( painCave.errMsg,
185 <               "Error reading 1st line of %d \n ",c_in_name);
185 >               "Error reading 1st line of %s \n ",c_in_name);
186        haveError = 1;
187        simError();
188      }
189 <    
190 <    n_atoms = atoi( read_buffer );
191 <    
192 <    Atom **atoms = simnfo->atoms;
186 <    DirectionalAtom* dAtom;
187 <
188 <    // Check to see that the number of atoms in the intial configuration file is the
189 >
190 >    nTotObjs = atoi( read_buffer );
191 >
192 >    // Check to see that the number of integrable objects  in the intial configuration file is the
193      // same as declared in simBass.
194 <    
195 <    if( n_atoms != mpiSim->getTotAtoms() ){
194 >
195 >    if( nTotObjs != simnfo->getTotIntegrableObjects()){
196        sprintf( painCave.errMsg,
197                 "Initialize from File error. %s n_atoms, %d, "
198                 "does not match the BASS file's n_atoms, %d.\n",
199 <               c_in_name, n_atoms, simnfo->n_atoms );
199 >               c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
200        haveError= 1;
201        simError();
202      }
203 <    
204 <    //read the boxMat from the comment line
205 <    
203 >
204 >    //read the boxMat from the comment line
205 >
206      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
207      if(eof_test == NULL){
208        sprintf( painCave.errMsg,
# Line 206 | Line 210 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
210        haveError = 1;
211        simError();
212      }
213 <    
214 <    parseErr = parseBoxLine( read_buffer, boxMat );
213 >
214 >    //Every single processor will parse the comment line by itself
215 >    //By using this way, we might lose some efficiency, but if we want to add
216 >    //more parameters into comment line, we only need to modify function
217 >    //parseCommentLine
218 >
219 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
220 >
221 >    parseErr = parseCommentLine( read_buffer, simnfo);
222 >
223      if( parseErr != NULL ){
224        strcpy( painCave.errMsg, parseErr );
225        haveError = 1;
226        simError();
227      }
228  
229 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
230 <  
231 <    if(haveError) nodeZeroError();
229 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
230 >      which_node = MolToProcMap[i];
231 >      if(which_node == 0){
232 >       //molecules belong to master node
233  
234 <    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
235 <      
236 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
237 <      if(eof_test == NULL){
238 <        sprintf(painCave.errMsg,
239 <                "error in reading file %s\n"
227 <                "natoms  = %d; index = %d\n"
228 <                "error reading the line from the file.\n",
229 <                c_in_name, n_atoms, i );
230 <        haveError= 1;
231 <        simError();
234 >      localIndex = mpiSim->getGlobalToLocalMol(i);
235 >
236 >      if(localIndex == -1) {
237 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
238 >        haveError = 1;
239 >        simError();
240        }
233 –    
234 –      if(haveError) nodeZeroError();
241  
242 <      // Get the Node number which wants this atom:
243 <      which_node = AtomToProcMap[i];    
244 <      if (which_node == 0) {
245 <        parseErr = parseDumpLine( read_buffer, i );
246 <        if( parseErr != NULL ){
247 <          strcpy( painCave.errMsg, parseErr );
248 <          haveError = 1;
249 <          simError();
250 <        }    
251 <        if(haveError) nodeZeroError();
252 <      }
253 <      
254 <      else {
255 <      
256 <        myStatus = 1;
251 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
252 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
253 <        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
254 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
255 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
256 <                 MPI_COMM_WORLD);
257 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
258 <                 MPI_COMM_WORLD, &istatus);
259 <        
260 <        if(!myStatus) nodeZeroError();
261 <      }
262 <    }
263 <    myStatus = -1;
264 <    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
265 <      MPI_Send( &myStatus, 1, MPI_INT, j,
266 <                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
267 <    }
268 <    
269 <  } else {
270 <    
271 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
242 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
243 >       for(j=0; j < integrableObjects.size(); j++){
244 >        
245 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
246 >          if(eof_test == NULL){
247 >                sprintf(painCave.errMsg,
248 >                    "error in reading file %s\n"
249 >                    "natoms  = %d; index = %d\n"
250 >                    "error reading the line from the file.\n",
251 >                    c_in_name, nTotObjs, i );
252 >                haveError= 1;
253 >                simError();
254 >          }
255 >          
256 >          if(haveError) nodeZeroError();
257  
258 <    done = 0;
259 <    while (!done) {
258 >          parseDumpLine(read_buffer, integrableObjects[i]);
259 >          
260 >       }
261  
276 –      MPI_Recv(&myStatus, 1, MPI_INT, 0,
277 –               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
278 –      
279 –      if(!myStatus) anonymousNodeDie();
280 –      
281 –      if(myStatus < 0) break;
262  
263 <      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
264 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
265 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
263 >      }
264 >      else{
265 >      //molecule belongs to slave nodes
266 >
267 >        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
268                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
269        
270 <      myStatus = 1;
271 <      parseErr = parseDumpLine( read_buffer, which_atom );
272 <      if( parseErr != NULL ){
273 <        strcpy( painCave.errMsg, parseErr );
274 <        myStatus = 0;;
275 <        simError();
270 >       for(j=0; j < integrableObjects.size(); j++){
271 >        
272 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
273 >          if(eof_test == NULL){
274 >                sprintf(painCave.errMsg,
275 >                    "error in reading file %s\n"
276 >                    "natoms  = %d; index = %d\n"
277 >                    "error reading the line from the file.\n",
278 >                    c_in_name, nTotObjs, i );
279 >                haveError= 1;
280 >                simError();
281 >          }
282 >          
283 >          if(haveError) nodeZeroError();
284 >
285 >            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
286 >                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
287 >          
288 >       }
289 >
290        }
291        
296 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
297 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
298 –      
292      }
293 +    
294    }
295 <    
296 < // last  thing last, enable  fatalities.
297 <  painCave.isEventLoop = 0;
298 <  simnfo->setBoxM( boxMat );
295 >  else{
296 >  //actions taken at slave nodes
297 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
298 >      which_node = MolToProcMap[i];
299 >      
300 >      if(which_node == worldRank){
301 >      //molecule with global index i belongs to this processor
302 >      
303 >        localIndex = mpiSim->getGlobalToLocalMol(i);
304  
305 <  
305 >        if(localIndex == -1) {
306 >          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
307 >          haveError = 1;
308 >          simError();
309 >        }
310 >
311 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
312 >
313 >        nCurObj = integrableObjects.size();
314 >        
315 >        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
316 >                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
317 >
318 >        for(j = 0; j < integrableObjects.size(); j++){
319 >
320 >          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
321 >                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
322 >
323 >          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
324 >
325 >          if( parseErr != NULL ){
326 >                strcpy( painCave.errMsg, parseErr );
327 >                simError();
328 >          }
329 >
330 >        }
331 >          
332 >      }
333 >      
334 >    }
335 >
336 >  }
337   #endif
338   }
339  
340 < char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
340 > char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
341  
342 <  char *foo; // the pointer to the current string token
343 <  
344 <  double rx, ry, rz; // position place holders
345 <  double vx, vy, vz; // velocity placeholders
342 >  char *foo; // the pointer to the current string token
343 >
344 >  double pos[3]; // position place holders
345 >  double vel[3]; // velocity placeholders
346    double q[4]; // the quaternions
347 <  double jx, jy, jz; // angular velocity placeholders;
347 >  double ji[3]; // angular velocity placeholders;
348    double qSqr, qLength; // needed to normalize the quaternion vector.
319 –  
320 –  Atom **atoms = simnfo->atoms;
321 –  DirectionalAtom* dAtom;
322 –  
323 –  int j, n_atoms, atomIndex;
349  
325 – #ifdef IS_MPI
326 –  n_atoms = mpiSim->getTotAtoms();
327 –  atomIndex=-1;        
328 –  for (j=0; j < mpiSim->getMyNlocal(); j++) {
329 –    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
330 –  }
331 –  if (atomIndex == -1) {
332 –    sprintf( painCave.errMsg,
333 –             "Initialize from file error. Atom at index %d "
334 –             "in file %s does not exist on processor %d .\n",
335 –             globalIndex, c_in_name, mpiSim->getMyNode() );
336 –    return strdup( painCave.errMsg );
337 –  }  
338 – #else
339 –  n_atoms = simnfo->n_atoms;
340 –  atomIndex = globalIndex;
341 – #endif // is_mpi
350  
351    // set the string tokenizer
352 <  
352 >
353    foo = strtok(readLine, " ,;\t");
354 <  
354 >
355    // check the atom name to the current atom
356 <  
357 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
356 >
357 >  if( strcmp( foo, sd->getType() ) ){
358      sprintf( painCave.errMsg,
359 <             "Initialize from file error. Atom %s at index %d "
352 <             "in file %s does not"
359 >             "Initialize from file error.  Does not"
360               " match the BASS atom %s.\n",
361 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
361 >             sd->getType() );
362      return strdup( painCave.errMsg );
363    }
364 <    
364 >
365    // get the positions
366  
367    foo = strtok(NULL, " ,;\t");
368    if(foo == NULL){
369      sprintf( painCave.errMsg,
370 <             "error in reading postition x from %s\n"
371 <             "natoms  = %d, index = %d\n",
365 <             c_in_name, n_atoms, atomIndex );
370 >             "error in reading postition x from %s\n",
371 >             c_in_name);
372      return strdup( painCave.errMsg );
373    }
374 <  rx = atof( foo );
375 <  
374 >  pos[0] = atof( foo );
375 >
376    foo = strtok(NULL, " ,;\t");
377    if(foo == NULL){
378      sprintf( painCave.errMsg,
379 <             "error in reading postition y from %s\n"
380 <             "natoms  = %d, index = %d\n",
375 <             c_in_name, n_atoms, atomIndex );
379 >             "error in reading postition y from %s\n",
380 >             c_in_name);
381      return strdup( painCave.errMsg );
382    }
383 <  ry = atof( foo );
384 <    
383 >  pos[1] = atof( foo );
384 >
385    foo = strtok(NULL, " ,;\t");
386    if(foo == NULL){
387      sprintf( painCave.errMsg,
388 <             "error in reading postition z from %s\n"
389 <             "natoms  = %d, index = %d\n",
385 <             c_in_name, n_atoms, atomIndex );
388 >             "error in reading postition z from %s\n",
389 >             c_in_name);
390      return strdup( painCave.errMsg );
391    }
392 <  rz = atof( foo );    
392 >  pos[2] = atof( foo );
393  
394  
395    // get the velocities
# Line 393 | Line 397 | char* InitializeFromFile::parseDumpLine(char* readLine
397    foo = strtok(NULL, " ,;\t");
398    if(foo == NULL){
399      sprintf( painCave.errMsg,
400 <             "error in reading velocity x from %s\n"
401 <             "natoms  = %d, index = %d\n",
398 <             c_in_name, n_atoms, atomIndex );
400 >             "error in reading velocity x from %s\n",
401 >             c_in_name );
402      return strdup( painCave.errMsg );
403    }
404 <  vx = atof( foo );
405 <    
404 >  vel[0] = atof( foo );
405 >
406    foo = strtok(NULL, " ,;\t");
407    if(foo == NULL){
408      sprintf( painCave.errMsg,
409 <             "error in reading velocity y from %s\n"
410 <             "natoms  = %d, index = %d\n",
408 <             c_in_name, n_atoms, atomIndex );
409 >             "error in reading velocity x from %s\n",
410 >             c_in_name );
411      return strdup( painCave.errMsg );
412    }
413 <  vy = atof( foo );
414 <    
413 >  vel[1] = atof( foo );
414 >
415    foo = strtok(NULL, " ,;\t");
416    if(foo == NULL){
417      sprintf( painCave.errMsg,
418 <             "error in reading velocity z from %s\n"
419 <             "natoms  = %d, index = %d\n",
418 <             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 <  vz = atof( foo );
423 <    
424 <    
422 >  vel[2] = atof( foo );
423 >
424 >
425 >  // add the positions and velocities to the atom
426 >
427 >  sd->setPos( pos );
428 >  sd->setVel( vel );
429 >
430 >  if (!sd->isDirectional())
431 >    return NULL;
432 >
433    // get the quaternions
434 <    
435 <  if( atoms[atomIndex]->isDirectional() ){
436 <      
434 >
435 >  if( sd->isDirectional() ){
436 >
437      foo = strtok(NULL, " ,;\t");
438      if(foo == NULL){
439 <      sprintf(painCave.errMsg,
440 <              "error in reading quaternion 0 from %s\n"
441 <              "natoms  = %d, index = %d\n",
433 <              c_in_name, n_atoms, atomIndex );
439 >      sprintf( painCave.errMsg,
440 >                     "error in reading velocity x from %s\n",
441 >                      c_in_name );
442        return strdup( painCave.errMsg );
443      }
444      q[0] = atof( foo );
445 <      
445 >
446      foo = strtok(NULL, " ,;\t");
447      if(foo == NULL){
448        sprintf( painCave.errMsg,
449 <               "error in reading quaternion 1 from %s\n"
450 <               "natoms  = %d, index = %d\n",
443 <               c_in_name, n_atoms, atomIndex );
449 >                     "error in reading velocity x from %s\n",
450 >                      c_in_name );
451        return strdup( painCave.errMsg );
452      }
453      q[1] = atof( foo );
454 <      
454 >
455      foo = strtok(NULL, " ,;\t");
456      if(foo == NULL){
457        sprintf( painCave.errMsg,
458 <               "error in reading quaternion 2 from %s\n"
459 <               "natoms  = %d, index = %d\n",
453 <               c_in_name, n_atoms, atomIndex );
458 >                     "error in reading velocity x from %s\n",
459 >                      c_in_name );
460        return strdup( painCave.errMsg );
461      }
462      q[2] = atof( foo );
463 <      
463 >
464      foo = strtok(NULL, " ,;\t");
465      if(foo == NULL){
466        sprintf( painCave.errMsg,
467 <               "error in reading quaternion 3 from %s\n"
468 <               "natoms  = %d, index = %d\n",
463 <               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[3] = atof( foo );
472 <      
472 >
473      // get the angular velocities
474 <      
474 >
475      foo = strtok(NULL, " ,;\t");
476      if(foo == NULL){
477        sprintf( painCave.errMsg,
478 <               "error in reading angular momentum jx from %s\n"
479 <               "natoms  = %d, index = %d\n",
475 <               c_in_name, n_atoms, atomIndex );
478 >                     "error in reading velocity x from %s\n",
479 >                      c_in_name );
480        return strdup( painCave.errMsg );
481      }
482 <    jx = atof( foo );
483 <      
482 >    ji[0] = atof( foo );
483 >
484      foo = strtok(NULL, " ,;\t");
485      if(foo == NULL){
486        sprintf( painCave.errMsg,
487 <               "error in reading angular momentum jy from %s\n"
488 <               "natoms  = %d, index = %d\n",
485 <               c_in_name, n_atoms, atomIndex );
487 >                     "error in reading velocity x from %s\n",
488 >                      c_in_name );
489        return strdup( painCave.errMsg );
490      }
491 <    jy = atof(foo );
492 <      
491 >    ji[1] = atof(foo );
492 >
493      foo = strtok(NULL, " ,;\t");
494      if(foo == NULL){
495        sprintf( painCave.errMsg,
496 <               "error in reading angular momentum jz from %s\n"
497 <               "natoms  = %d, index = %d\n",
495 <               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 <    jz = atof( foo );
499 <      
500 <    dAtom = ( DirectionalAtom* )atoms[atomIndex];
500 >    ji[2] = atof( foo );
501  
502 +
503      // check that the quaternion vector is normalized
504  
505      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
506 <      
506 >
507      qLength = sqrt( qSqr );
508      q[0] = q[0] / qLength;
509      q[1] = q[1] / qLength;
510      q[2] = q[2] / qLength;
511      q[3] = q[3] / qLength;
511 –      
512 –    dAtom->setQ( q );
513 –      
514 –    // add the angular velocities
512  
513 <    dAtom->setJx( jx );
514 <    dAtom->setJy( jy );
515 <    dAtom->setJz( jz );
513 >    // add quaternion and angular velocities
514 >
515 >    sd->setQ( q );
516 >    sd->setJ( ji );
517    }
520 –    
521 –  // add the positions and velocities to the atom
522 –    
523 –  atoms[atomIndex]->setX( rx );
524 –  atoms[atomIndex]->setY( ry );
525 –  atoms[atomIndex]->setZ( rz );
526 –    
527 –  atoms[atomIndex]->set_vx( vx );
528 –  atoms[atomIndex]->set_vy( vy );
529 –  atoms[atomIndex]->set_vz( vz );
518  
519 +
520 +
521    return NULL;
522   }
523  
524  
525 < char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){
525 > char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
526  
527 <  char *foo; // the pointer to the current string token
528 <  int j;
527 >  double currTime;
528 >  double boxMat[9];
529 >  double theBoxMat3[3][3];
530 >  double chi;
531 >  double integralOfChidt;
532 >  double eta[9];
533  
534 +  char *foo; // the pointer to the current string token
535 +
536    // set the string tokenizer
541 –  
542 –  foo = strtok(readLine, " ,;\t");
543 –  // ignore the first token which is the time stamp.
537  
538 <
539 <  // get the Hx vector
540 <
548 <  foo = strtok(NULL, " ,;\t");
549 <  if(foo == NULL){
550 <    sprintf( painCave.errMsg,
551 <             "error in reading Hx[0] from %s\n",
552 <             c_in_name );
553 <    return strdup( painCave.errMsg );
554 <  }
555 <  boxMat[0] = atof( foo );
556 <  
557 <  foo = strtok(NULL, " ,;\t");
538 >  foo = strtok(readLine, " ,;\t");
539 >  // set the timeToken.
540 >
541    if(foo == NULL){
542      sprintf( painCave.errMsg,
543 <             "error in reading Hx[1] from %s\n",
543 >             "error in reading Time from %s\n",
544               c_in_name );
545      return strdup( painCave.errMsg );
546    }
564 –  boxMat[1] = atof( foo );
565 –    
566 –  foo = strtok(NULL, " ,;\t");
567 –  if(foo == NULL){
568 –    sprintf( painCave.errMsg,
569 –             "error in reading Hx[2] from %s\n",
570 –             c_in_name );
571 –    return strdup( painCave.errMsg );
572 –  }
573 –  boxMat[2] = atof( foo );    
547  
548 <  // get the Hy vector
548 >  currTime = atof( foo );
549 >  entry_plug->setTime( currTime );
550  
551 <  foo = strtok(NULL, " ,;\t");
552 <  if(foo == NULL){
553 <    sprintf( painCave.errMsg,
554 <             "error in reading Hy[0] from %s\n",
555 <             c_in_name );
556 <    return strdup( painCave.errMsg );
551 >  //get H-Matrix
552 >
553 >  for(int i = 0 ; i < 9; i++){
554 >    foo = strtok(NULL, " ,;\t");
555 >    if(foo == NULL){
556 >      sprintf( painCave.errMsg,
557 >               "error in reading H[%d] from %s\n", i, c_in_name );
558 >      return strdup( painCave.errMsg );
559 >    }
560 >    boxMat[i] = atof( foo );
561    }
584 –  boxMat[3] = atof( foo );
585 –  
586 –  foo = strtok(NULL, " ,;\t");
587 –  if(foo == NULL){
588 –    sprintf( painCave.errMsg,
589 –             "error in reading Hy[1] from %s\n",
590 –             c_in_name );
591 –    return strdup( painCave.errMsg );
592 –  }
593 –  boxMat[4] = atof( foo );
594 –    
595 –  foo = strtok(NULL, " ,;\t");
596 –  if(foo == NULL){
597 –    sprintf( painCave.errMsg,
598 –             "error in reading Hy[2] from %s\n",
599 –             c_in_name );
600 –    return strdup( painCave.errMsg );
601 –  }
602 –  boxMat[5] = atof( foo );    
562  
563 <  // get the Hz vector
563 >  for(int i=0;i<3;i++)
564 >    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
565  
566 <  foo = strtok(NULL, " ,;\t");
567 <  if(foo == NULL){
568 <    sprintf( painCave.errMsg,
569 <             "error in reading Hz[0] from %s\n",
570 <             c_in_name );
571 <    return strdup( painCave.errMsg );
566 >  //set H-Matrix
567 >  entry_plug->setBoxM( theBoxMat3 );
568 >
569 >  //get chi and integralOfChidt, they should appear by pair
570 >
571 >  if( entry_plug->useInitXSstate ){
572 >    foo = strtok(NULL, " ,;\t\n");
573 >    if(foo != NULL){
574 >      chi = atof(foo);
575 >      
576 >      foo = strtok(NULL, " ,;\t\n");
577 >      if(foo == NULL){
578 >        sprintf( painCave.errMsg,
579 >                 "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
580 >        return strdup( painCave.errMsg );
581 >      }
582 >      integralOfChidt = atof( foo );
583 >      
584 >      //push chi and integralOfChidt into SimInfo::properties which can be
585 >      //retrieved by integrator later
586 >      DoubleData* chiValue = new DoubleData();
587 >      chiValue->setID(CHIVALUE_ID);
588 >      chiValue->setData(chi);
589 >      entry_plug->addProperty(chiValue);
590 >      
591 >      DoubleData* integralOfChidtValue = new DoubleData();
592 >      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
593 >      integralOfChidtValue->setData(integralOfChidt);
594 >      entry_plug->addProperty(integralOfChidtValue);
595 >      
596 >    }
597 >    else
598 >      return NULL;
599 >    
600 >    //get eta
601 >    foo = strtok(NULL, " ,;\t\n");
602 >    if(foo != NULL ){
603 >  
604 >      for(int i = 0 ; i < 9; i++){
605 >        
606 >        if(foo == NULL){
607 >          sprintf( painCave.errMsg,
608 >                   "error in reading eta[%d] from %s\n", i, c_in_name );
609 >          return strdup( painCave.errMsg );
610 >        }
611 >        eta[i] = atof( foo );
612 >        foo = strtok(NULL, " ,;\t\n");
613 >      }
614 >    }
615 >    else
616 >      return NULL;
617 >    
618 >    //push eta into SimInfo::properties which can be
619 >    //retrieved by integrator later
620 >    //entry_plug->setBoxM( theBoxMat3 );
621 >    DoubleArrayData* etaValue = new DoubleArrayData();
622 >    etaValue->setID(ETAVALUE_ID);
623 >    etaValue->setData(eta, 9);
624 >    entry_plug->addProperty(etaValue);
625    }
613 –  boxMat[6] = atof( foo );
614 –  
615 –  foo = strtok(NULL, " ,;\t");
616 –  if(foo == NULL){
617 –    sprintf( painCave.errMsg,
618 –             "error in reading Hz[1] from %s\n",
619 –             c_in_name );
620 –    return strdup( painCave.errMsg );
621 –  }
622 –  boxMat[7] = atof( foo );
623 –    
624 –  foo = strtok(NULL, " ,;\t");
625 –  if(foo == NULL){
626 –    sprintf( painCave.errMsg,
627 –             "error in reading Hz[2] from %s\n",
628 –             c_in_name );
629 –    return strdup( painCave.errMsg );
630 –  }
631 –  boxMat[8] = atof( foo );    
626  
627    return NULL;
628   }
629  
636 –
630   #ifdef IS_MPI
631  
632   // a couple of functions to let us escape the read loop
633  
634   void initFile::nodeZeroError( void ){
635    int j, myStatus;
636 <  
636 >
637    myStatus = 0;
638 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
639 <    MPI_Send( &myStatus, 1, MPI_INT, j,
638 >  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
639 >    MPI_Send( &myStatus, 1, MPI_INT, j,
640                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
641 <  }  
649 <  
641 >  }
642  
643 +
644    MPI_Finalize();
645    exit (0);
646 <  
646 >
647   }
648  
649   void initFile::anonymousNodeDie( void ){

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