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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 1108 by tim, Wed Apr 14 15:37:41 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 +  vector<StuntDouble*>::iterator iter;
96 +
97    simnfo = the_simnfo;
98  
99  
# Line 99 | Line 107 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
107      simError();
108    }
109  
110 <  n_atoms = atoi( read_buffer );
110 >  nTotObjs = atoi( read_buffer );
111  
112 <  Atom **atoms = simnfo->atoms;
105 <  DirectionalAtom* dAtom;
106 <
107 <  if( n_atoms != simnfo->n_atoms ){
112 >  if( nTotObjs != simnfo->getTotIntegrableObjects() ){
113      sprintf( painCave.errMsg,
114               "Initialize from File error. %s n_atoms, %d, "
115               "does not match the BASS file's n_atoms, %d.\n",
116 <             c_in_name, n_atoms, simnfo->n_atoms );
116 >             c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
117      painCave.isFatal = 1;
118      simError();
119    }
120 <  
121 <  //read the box mat from the comment line
122 <  
120 >
121 >  //read the box mat from the comment line
122 >
123    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
124    if(eof_test == NULL){
125      sprintf( painCave.errMsg,
# Line 123 | Line 128 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
128      simError();
129    }
130  
131 <  parseErr = parseBoxLine( read_buffer, boxMat );
131 >  parseErr = parseCommentLine( read_buffer, simnfo);
132    if( parseErr != NULL ){
133      strcpy( painCave.errMsg, parseErr );
134      painCave.isFatal = 1;
135      simError();
136    }
137  
138 <  simnfo->setBoxM( boxMat );
138 >  //parse dump lines
139  
140 +  for( i=0; i < simnfo->n_mol; i++){
141  
142 <  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 <    }
142 >    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
143  
144 <    
145 <    parseErr = parseDumpLine( read_buffer, i );
146 <    if( parseErr != NULL ){
147 <      strcpy( painCave.errMsg, parseErr );
148 <      painCave.isFatal = 1;
149 <      simError();
150 <    }
144 >    for(iter = integrableObjects.begin(); iter!= integrableObjects.end(); iter++)
145 >
146 >      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
147 >      if(eof_test == NULL){
148 >        sprintf(painCave.errMsg,
149 >              "error in reading file %s\n"
150 >              "natoms  = %d; index = %d\n"
151 >              "error reading the line from the file.\n",
152 >              c_in_name, nTotObjs, i );
153 >        painCave.isFatal = 1;
154 >        simError();
155 >      }
156 >      
157 >      parseErr = parseDumpLine( read_buffer, *iter);
158 >      if( parseErr != NULL ){
159 >        strcpy( painCave.errMsg, parseErr );
160 >        painCave.isFatal = 1;
161 >        simError();
162 >      }
163    }
164  
165  
# Line 164 | Line 171 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
171  
172    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
173    int haveError;
174 <  
174 >
175    MPI_Status istatus;
176 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
176 >  int *MolToProcMap = mpiSim->getMolToProcMap();
177 >  int localIndex;
178 >  int nCurObj;
179  
171 –  
180    haveError = 0;
181    if (worldRank == 0) {
182  
183      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
184      if( eof_test == NULL ){
185        sprintf( painCave.errMsg,
186 <               "Error reading 1st line of %d \n ",c_in_name);
186 >               "Error reading 1st line of %s \n ",c_in_name);
187        haveError = 1;
188        simError();
189      }
190 <    
191 <    n_atoms = atoi( read_buffer );
192 <    
193 <    Atom **atoms = simnfo->atoms;
186 <    DirectionalAtom* dAtom;
187 <
188 <    // Check to see that the number of atoms in the intial configuration file is the
190 >
191 >    nTotObjs = atoi( read_buffer );
192 >
193 >    // Check to see that the number of integrable objects  in the intial configuration file is the
194      // same as declared in simBass.
195 <    
196 <    if( n_atoms != mpiSim->getTotAtoms() ){
195 >
196 >    if( nTotObjs != simnfo->getTotIntegrableObjects()){
197        sprintf( painCave.errMsg,
198                 "Initialize from File error. %s n_atoms, %d, "
199                 "does not match the BASS file's n_atoms, %d.\n",
200 <               c_in_name, n_atoms, simnfo->n_atoms );
200 >               c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
201        haveError= 1;
202        simError();
203      }
204 <    
205 <    //read the boxMat from the comment line
206 <    
204 >
205 >    //read the boxMat from the comment line
206 >
207      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
208      if(eof_test == NULL){
209        sprintf( painCave.errMsg,
# Line 206 | Line 211 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
211        haveError = 1;
212        simError();
213      }
214 <    
215 <    parseErr = parseBoxLine( read_buffer, boxMat );
214 >
215 >    //Every single processor will parse the comment line by itself
216 >    //By using this way, we might lose some efficiency, but if we want to add
217 >    //more parameters into comment line, we only need to modify function
218 >    //parseCommentLine
219 >
220 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
221 >
222 >    parseErr = parseCommentLine( read_buffer, simnfo);
223 >
224      if( parseErr != NULL ){
225        strcpy( painCave.errMsg, parseErr );
226        haveError = 1;
227        simError();
228      }
229  
230 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
231 <  
232 <    if(haveError) nodeZeroError();
230 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
231 >      which_node = MolToProcMap[i];
232 >      if(which_node == 0){
233 >       //molecules belong to master node
234  
235 <    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
236 <      
237 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
238 <      if(eof_test == NULL){
239 <        sprintf(painCave.errMsg,
240 <                "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();
235 >      localIndex = mpiSim->getGlobalToLocalMol(i);
236 >
237 >      if(localIndex == -1) {
238 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
239 >        haveError = 1;
240 >        simError();
241        }
233 –    
234 –      if(haveError) nodeZeroError();
242  
243 <      // Get the Node number which wants this atom:
244 <      which_node = AtomToProcMap[i];    
245 <      if (which_node == 0) {
246 <        parseErr = parseDumpLine( read_buffer, i );
247 <        if( parseErr != NULL ){
248 <          strcpy( painCave.errMsg, parseErr );
249 <          haveError = 1;
250 <          simError();
251 <        }    
252 <        if(haveError) nodeZeroError();
253 <      }
243 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
244 >       for(j=0; j < integrableObjects.size(); j++){
245 >        
246 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
247 >          if(eof_test == NULL){
248 >                sprintf(painCave.errMsg,
249 >                    "error in reading file %s\n"
250 >                    "natoms  = %d; index = %d\n"
251 >                    "error reading the line from the file.\n",
252 >                    c_in_name, nTotObjs, i );
253 >                haveError= 1;
254 >                simError();
255 >          }
256 >          
257 >          if(haveError) nodeZeroError();
258 >
259 >          parseDumpLine(read_buffer, integrableObjects[i]);
260 >          
261 >       }
262 >
263 >
264 >      }
265 >      else{
266 >      //molecule belongs to slave nodes
267 >
268 >        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
269 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
270        
271 <      else {
272 <      
273 <        myStatus = 1;
274 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
275 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
276 <        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
277 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
278 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
279 <                 MPI_COMM_WORLD);
280 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
281 <                 MPI_COMM_WORLD, &istatus);
282 <        
283 <        if(!myStatus) nodeZeroError();
271 >       for(j=0; j < integrableObjects.size(); j++){
272 >        
273 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
274 >          if(eof_test == NULL){
275 >                sprintf(painCave.errMsg,
276 >                    "error in reading file %s\n"
277 >                    "natoms  = %d; index = %d\n"
278 >                    "error reading the line from the file.\n",
279 >                    c_in_name, nTotObjs, i );
280 >                haveError= 1;
281 >                simError();
282 >          }
283 >          
284 >          if(haveError) nodeZeroError();
285 >
286 >            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
287 >                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
288 >          
289 >       }
290 >
291        }
292 +      
293      }
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 –    }
294      
295 <  } else {
296 <    
297 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
298 <
299 <    done = 0;
274 <    while (!done) {
275 <
276 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
277 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
295 >  }
296 >  else{
297 >  //actions taken at slave nodes
298 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
299 >      which_node = MolToProcMap[i];
300        
301 <      if(!myStatus) anonymousNodeDie();
301 >      if(which_node == worldRank){
302 >      //molecule with global index i belongs to this processor
303        
304 <      if(myStatus < 0) break;
304 >        localIndex = mpiSim->getGlobalToLocalMol(i);
305  
306 <      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
307 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
308 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
309 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
310 <      
311 <      myStatus = 1;
312 <      parseErr = parseDumpLine( read_buffer, which_atom );
313 <      if( parseErr != NULL ){
314 <        strcpy( painCave.errMsg, parseErr );
315 <        myStatus = 0;;
316 <        simError();
306 >        if(localIndex == -1) {
307 >          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
308 >          haveError = 1;
309 >          simError();
310 >        }
311 >
312 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
313 >
314 >        nCurObj = integrableObjects.size();
315 >        
316 >        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
317 >                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
318 >
319 >        for(j = 0; j < integrableObjects.size(); j++){
320 >
321 >          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
322 >                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
323 >
324 >          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
325 >
326 >          if( parseErr != NULL ){
327 >                strcpy( painCave.errMsg, parseErr );
328 >                simError();
329 >          }
330 >
331 >        }
332 >          
333        }
334        
296 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
297 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
298 –      
335      }
300 –  }
301 –    
302 – // last  thing last, enable  fatalities.
303 –  painCave.isEventLoop = 0;
304 –  simnfo->setBoxM( boxMat );
336  
337 <  
337 >  }
338   #endif
339   }
340  
341 < char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
341 > char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
342  
343 <  char *foo; // the pointer to the current string token
344 <  
345 <  double rx, ry, rz; // position place holders
346 <  double vx, vy, vz; // velocity placeholders
343 >  char *foo; // the pointer to the current string token
344 >
345 >  double pos[3]; // position place holders
346 >  double vel[3]; // velocity placeholders
347    double q[4]; // the quaternions
348 <  double jx, jy, jz; // angular velocity placeholders;
348 >  double ji[3]; // angular velocity placeholders;
349    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;
350  
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
351  
352    // set the string tokenizer
353 <  
353 >
354    foo = strtok(readLine, " ,;\t");
355 <  
355 >
356    // check the atom name to the current atom
357 <  
358 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
357 >
358 >  if( strcmp( foo, sd->getType() ) ){
359      sprintf( painCave.errMsg,
360 <             "Initialize from file error. Atom %s at index %d "
352 <             "in file %s does not"
360 >             "Initialize from file error.  Does not"
361               " match the BASS atom %s.\n",
362 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
362 >             sd->getType() );
363      return strdup( painCave.errMsg );
364    }
365 <    
365 >
366    // get the positions
367  
368    foo = strtok(NULL, " ,;\t");
369    if(foo == NULL){
370      sprintf( painCave.errMsg,
371 <             "error in reading postition x from %s\n"
372 <             "natoms  = %d, index = %d\n",
365 <             c_in_name, n_atoms, atomIndex );
371 >             "error in reading postition x from %s\n",
372 >             c_in_name);
373      return strdup( painCave.errMsg );
374    }
375 <  rx = atof( foo );
376 <  
375 >  pos[0] = atof( foo );
376 >
377    foo = strtok(NULL, " ,;\t");
378    if(foo == NULL){
379      sprintf( painCave.errMsg,
380 <             "error in reading postition y from %s\n"
381 <             "natoms  = %d, index = %d\n",
375 <             c_in_name, n_atoms, atomIndex );
380 >             "error in reading postition y from %s\n",
381 >             c_in_name);
382      return strdup( painCave.errMsg );
383    }
384 <  ry = atof( foo );
385 <    
384 >  pos[1] = atof( foo );
385 >
386    foo = strtok(NULL, " ,;\t");
387    if(foo == NULL){
388      sprintf( painCave.errMsg,
389 <             "error in reading postition z from %s\n"
390 <             "natoms  = %d, index = %d\n",
385 <             c_in_name, n_atoms, atomIndex );
389 >             "error in reading postition z from %s\n",
390 >             c_in_name);
391      return strdup( painCave.errMsg );
392    }
393 <  rz = atof( foo );    
393 >  pos[2] = atof( foo );
394  
395  
396    // get the velocities
# Line 393 | Line 398 | char* InitializeFromFile::parseDumpLine(char* readLine
398    foo = strtok(NULL, " ,;\t");
399    if(foo == NULL){
400      sprintf( painCave.errMsg,
401 <             "error in reading velocity x from %s\n"
402 <             "natoms  = %d, index = %d\n",
398 <             c_in_name, n_atoms, atomIndex );
401 >             "error in reading velocity x from %s\n",
402 >             c_in_name );
403      return strdup( painCave.errMsg );
404    }
405 <  vx = atof( foo );
406 <    
405 >  vel[0] = atof( foo );
406 >
407    foo = strtok(NULL, " ,;\t");
408    if(foo == NULL){
409      sprintf( painCave.errMsg,
410 <             "error in reading velocity y from %s\n"
411 <             "natoms  = %d, index = %d\n",
408 <             c_in_name, n_atoms, atomIndex );
410 >             "error in reading velocity x from %s\n",
411 >             c_in_name );
412      return strdup( painCave.errMsg );
413    }
414 <  vy = atof( foo );
415 <    
414 >  vel[1] = atof( foo );
415 >
416    foo = strtok(NULL, " ,;\t");
417    if(foo == NULL){
418      sprintf( painCave.errMsg,
419 <             "error in reading velocity z from %s\n"
420 <             "natoms  = %d, index = %d\n",
418 <             c_in_name, n_atoms, atomIndex );
419 >             "error in reading velocity x from %s\n",
420 >             c_in_name );
421      return strdup( painCave.errMsg );
422    }
423 <  vz = atof( foo );
424 <    
425 <    
423 >  vel[2] = atof( foo );
424 >
425 >
426 >  // add the positions and velocities to the atom
427 >
428 >  sd->setPos( pos );
429 >  sd->setVel( vel );
430 >
431 >  if (!sd->isDirectional())
432 >    return NULL;
433 >
434    // get the quaternions
435 <    
436 <  if( atoms[atomIndex]->isDirectional() ){
437 <      
435 >
436 >  if( sd->isDirectional() ){
437 >
438      foo = strtok(NULL, " ,;\t");
439      if(foo == NULL){
440 <      sprintf(painCave.errMsg,
441 <              "error in reading quaternion 0 from %s\n"
442 <              "natoms  = %d, index = %d\n",
433 <              c_in_name, n_atoms, atomIndex );
440 >      sprintf( painCave.errMsg,
441 >                     "error in reading velocity x from %s\n",
442 >                      c_in_name );
443        return strdup( painCave.errMsg );
444      }
445      q[0] = atof( foo );
446 <      
446 >
447      foo = strtok(NULL, " ,;\t");
448      if(foo == NULL){
449        sprintf( painCave.errMsg,
450 <               "error in reading quaternion 1 from %s\n"
451 <               "natoms  = %d, index = %d\n",
443 <               c_in_name, n_atoms, atomIndex );
450 >                     "error in reading velocity x from %s\n",
451 >                      c_in_name );
452        return strdup( painCave.errMsg );
453      }
454      q[1] = atof( foo );
455 <      
455 >
456      foo = strtok(NULL, " ,;\t");
457      if(foo == NULL){
458        sprintf( painCave.errMsg,
459 <               "error in reading quaternion 2 from %s\n"
460 <               "natoms  = %d, index = %d\n",
453 <               c_in_name, n_atoms, atomIndex );
459 >                     "error in reading velocity x from %s\n",
460 >                      c_in_name );
461        return strdup( painCave.errMsg );
462      }
463      q[2] = atof( foo );
464 <      
464 >
465      foo = strtok(NULL, " ,;\t");
466      if(foo == NULL){
467        sprintf( painCave.errMsg,
468 <               "error in reading quaternion 3 from %s\n"
469 <               "natoms  = %d, index = %d\n",
463 <               c_in_name, n_atoms, atomIndex );
468 >                     "error in reading velocity x from %s\n",
469 >                      c_in_name );
470        return strdup( painCave.errMsg );
471      }
472      q[3] = atof( foo );
473 <      
473 >
474      // get the angular velocities
475 <      
475 >
476      foo = strtok(NULL, " ,;\t");
477      if(foo == NULL){
478        sprintf( painCave.errMsg,
479 <               "error in reading angular momentum jx from %s\n"
480 <               "natoms  = %d, index = %d\n",
475 <               c_in_name, n_atoms, atomIndex );
479 >                     "error in reading velocity x from %s\n",
480 >                      c_in_name );
481        return strdup( painCave.errMsg );
482      }
483 <    jx = atof( foo );
484 <      
483 >    ji[0] = atof( foo );
484 >
485      foo = strtok(NULL, " ,;\t");
486      if(foo == NULL){
487        sprintf( painCave.errMsg,
488 <               "error in reading angular momentum jy from %s\n"
489 <               "natoms  = %d, index = %d\n",
485 <               c_in_name, n_atoms, atomIndex );
488 >                     "error in reading velocity x from %s\n",
489 >                      c_in_name );
490        return strdup( painCave.errMsg );
491      }
492 <    jy = atof(foo );
493 <      
492 >    ji[1] = atof(foo );
493 >
494      foo = strtok(NULL, " ,;\t");
495      if(foo == NULL){
496        sprintf( painCave.errMsg,
497 <               "error in reading angular momentum jz from %s\n"
498 <               "natoms  = %d, index = %d\n",
495 <               c_in_name, n_atoms, atomIndex );
497 >                     "error in reading velocity x from %s\n",
498 >                      c_in_name );
499        return strdup( painCave.errMsg );
500      }
501 <    jz = atof( foo );
499 <      
500 <    dAtom = ( DirectionalAtom* )atoms[atomIndex];
501 >    ji[2] = atof( foo );
502  
503 +
504      // check that the quaternion vector is normalized
505  
506      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
507 <      
507 >
508      qLength = sqrt( qSqr );
509      q[0] = q[0] / qLength;
510      q[1] = q[1] / qLength;
511      q[2] = q[2] / qLength;
512      q[3] = q[3] / qLength;
511 –      
512 –    dAtom->setQ( q );
513 –      
514 –    // add the angular velocities
513  
514 <    dAtom->setJx( jx );
515 <    dAtom->setJy( jy );
516 <    dAtom->setJz( jz );
514 >    // add quaternion and angular velocities
515 >
516 >    sd->setQ( q );
517 >    sd->setJ( ji );
518    }
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 );
519  
520 +
521 +
522    return NULL;
523   }
524  
525  
526 < char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){
526 > char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
527  
528 <  char *foo; // the pointer to the current string token
529 <  int j;
528 >  double currTime;
529 >  double boxMat[9];
530 >  double theBoxMat3[3][3];
531 >  double chi;
532 >  double integralOfChidt;
533 >  double eta[9];
534  
535 +  char *foo; // the pointer to the current string token
536 +
537    // set the string tokenizer
541 –  
542 –  foo = strtok(readLine, " ,;\t");
543 –  // ignore the first token which is the time stamp.
538  
539 <
540 <  // get the Hx vector
541 <
548 <  foo = strtok(NULL, " ,;\t");
539 >  foo = strtok(readLine, " ,;\t");
540 >  // set the timeToken.
541 >
542    if(foo == NULL){
543      sprintf( painCave.errMsg,
544 <             "error in reading Hx[0] from %s\n",
544 >             "error in reading Time from %s\n",
545               c_in_name );
546      return strdup( painCave.errMsg );
547    }
555 –  boxMat[0] = atof( foo );
556 –  
557 –  foo = strtok(NULL, " ,;\t");
558 –  if(foo == NULL){
559 –    sprintf( painCave.errMsg,
560 –             "error in reading Hx[1] from %s\n",
561 –             c_in_name );
562 –    return strdup( painCave.errMsg );
563 –  }
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 );    
548  
549 <  // get the Hy vector
549 >  currTime = atof( foo );
550 >  entry_plug->setTime( currTime );
551  
552 <  foo = strtok(NULL, " ,;\t");
553 <  if(foo == NULL){
554 <    sprintf( painCave.errMsg,
555 <             "error in reading Hy[0] from %s\n",
556 <             c_in_name );
557 <    return strdup( painCave.errMsg );
552 >  //get H-Matrix
553 >
554 >  for(int i = 0 ; i < 9; i++){
555 >    foo = strtok(NULL, " ,;\t");
556 >    if(foo == NULL){
557 >      sprintf( painCave.errMsg,
558 >               "error in reading H[%d] from %s\n", i, c_in_name );
559 >      return strdup( painCave.errMsg );
560 >    }
561 >    boxMat[i] = atof( foo );
562    }
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 );    
563  
564 <  // get the Hz vector
564 >  for(int i=0;i<3;i++)
565 >    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
566  
567 <  foo = strtok(NULL, " ,;\t");
568 <  if(foo == NULL){
569 <    sprintf( painCave.errMsg,
570 <             "error in reading Hz[0] from %s\n",
571 <             c_in_name );
572 <    return strdup( painCave.errMsg );
567 >  //set H-Matrix
568 >  entry_plug->setBoxM( theBoxMat3 );
569 >
570 >  //get chi and integralOfChidt, they should appear by pair
571 >
572 >  if( entry_plug->useInitXSstate ){
573 >    foo = strtok(NULL, " ,;\t\n");
574 >    if(foo != NULL){
575 >      chi = atof(foo);
576 >      
577 >      foo = strtok(NULL, " ,;\t\n");
578 >      if(foo == NULL){
579 >        sprintf( painCave.errMsg,
580 >                 "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
581 >        return strdup( painCave.errMsg );
582 >      }
583 >      integralOfChidt = atof( foo );
584 >      
585 >      //push chi and integralOfChidt into SimInfo::properties which can be
586 >      //retrieved by integrator later
587 >      DoubleData* chiValue = new DoubleData();
588 >      chiValue->setID(CHIVALUE_ID);
589 >      chiValue->setData(chi);
590 >      entry_plug->addProperty(chiValue);
591 >      
592 >      DoubleData* integralOfChidtValue = new DoubleData();
593 >      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
594 >      integralOfChidtValue->setData(integralOfChidt);
595 >      entry_plug->addProperty(integralOfChidtValue);
596 >      
597 >    }
598 >    else
599 >      return NULL;
600 >    
601 >    //get eta
602 >    foo = strtok(NULL, " ,;\t\n");
603 >    if(foo != NULL ){
604 >  
605 >      for(int i = 0 ; i < 9; i++){
606 >        
607 >        if(foo == NULL){
608 >          sprintf( painCave.errMsg,
609 >                   "error in reading eta[%d] from %s\n", i, c_in_name );
610 >          return strdup( painCave.errMsg );
611 >        }
612 >        eta[i] = atof( foo );
613 >        foo = strtok(NULL, " ,;\t\n");
614 >      }
615 >    }
616 >    else
617 >      return NULL;
618 >    
619 >    //push eta into SimInfo::properties which can be
620 >    //retrieved by integrator later
621 >    //entry_plug->setBoxM( theBoxMat3 );
622 >    DoubleArrayData* etaValue = new DoubleArrayData();
623 >    etaValue->setID(ETAVALUE_ID);
624 >    etaValue->setData(eta, 9);
625 >    entry_plug->addProperty(etaValue);
626    }
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 );    
627  
628    return NULL;
629   }
630  
636 –
631   #ifdef IS_MPI
632  
633   // a couple of functions to let us escape the read loop
634  
635   void initFile::nodeZeroError( void ){
636    int j, myStatus;
637 <  
637 >
638    myStatus = 0;
639 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
640 <    MPI_Send( &myStatus, 1, MPI_INT, j,
639 >  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
640 >    MPI_Send( &myStatus, 1, MPI_INT, j,
641                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
642 <  }  
649 <  
642 >  }
643  
644 +
645    MPI_Finalize();
646    exit (0);
647 <  
647 >
648   }
649  
650   void initFile::anonymousNodeDie( void ){

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