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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 1131 by tim, Thu Apr 22 21:33:55 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 0
20 < #define TAKE_THIS_TAG_INT 1
19 > #define TAKE_THIS_TAG_CHAR 3134
20 > #define TAKE_THIS_TAG_INT 3135
21  
22   namespace initFile{
23    void nodeZeroError( void );
# Line 26 | Line 28 | 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 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 | InitializeFromFile :: ~InitializeFromFile( ){
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 >  int nItems;
179  
180 <  
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);
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 = simnfo->atoms;
186 <    DirectionalAtom* dAtom;
187 <
188 <    // 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, simnfo->n_atoms );
201 >               c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
202        haveError= 1;
203        simError();
204      }
205 <    
206 <    //read the boxMat from 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,
# Line 206 | Line 212 | void InitializeFromFile :: read_xyz( SimInfo* the_simn
212        haveError = 1;
213        simError();
214      }
215 <    
216 <    parseErr = parseBoxLine( read_buffer, boxMat );
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 >
224 >    parseErr = parseCommentLine( read_buffer, simnfo);
225 >
226      if( parseErr != NULL ){
227        strcpy( painCave.errMsg, parseErr );
228        haveError = 1;
229        simError();
230      }
231  
232 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
233 <  
234 <    if(haveError) nodeZeroError();
232 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
233 >      which_node = MolToProcMap[i];
234 >      if(which_node == 0){
235 >       //molecules belong to master node
236  
237 <    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
238 <      
239 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
240 <      if(eof_test == NULL){
241 <        sprintf(painCave.errMsg,
242 <                "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();
237 >      localIndex = mpiSim->getGlobalToLocalMol(i);
238 >
239 >      if(localIndex == -1) {
240 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
241 >        haveError = 1;
242 >        simError();
243        }
233 –    
234 –      if(haveError) nodeZeroError();
244  
245 <      // Get the Node number which wants this atom:
246 <      which_node = AtomToProcMap[i];    
247 <      if (which_node == 0) {
248 <        parseErr = parseDumpLine( read_buffer, i );
249 <        if( parseErr != NULL ){
250 <          strcpy( painCave.errMsg, parseErr );
251 <          haveError = 1;
252 <          simError();
253 <        }    
254 <        if(haveError) nodeZeroError();
255 <      }
256 <      
257 <      else {
258 <      
259 <        myStatus = 1;
260 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
261 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
262 <        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
263 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
264 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
265 <                 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();
245 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
246 >       for(j=0; j < integrableObjects.size(); j++){
247 >        
248 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
249 >          if(eof_test == NULL){
250 >                sprintf(painCave.errMsg,
251 >                    "error in reading file %s\n"
252 >                    "natoms  = %d; index = %d\n"
253 >                    "error reading the line from the file.\n",
254 >                    c_in_name, nTotObjs, i );
255 >                haveError= 1;
256 >                simError();
257 >          }
258 >          
259 >          if(haveError) nodeZeroError();
260 >
261 >          parseDumpLine(read_buffer, integrableObjects[j]);
262 >          
263 >       }
264 >
265 >
266        }
267 +      else{
268 +      //molecule belongs to slave nodes
269 +
270 +        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
271 +               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
272 +
273 +       for(j=0; j < nCurObj; j++){
274 +        
275 +          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
276 +          if(eof_test == NULL){
277 +                sprintf(painCave.errMsg,
278 +                    "error in reading file %s\n"
279 +                    "natoms  = %d; index = %d\n"
280 +                    "error reading the line from the file.\n",
281 +                    c_in_name, nTotObjs, i );
282 +                haveError= 1;
283 +                simError();
284 +          }
285 +          
286 +          if(haveError) nodeZeroError();
287 +
288 +            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
289 +                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
290 +
291 +       }
292 +
293 +      }
294 +      
295      }
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 –    }
296      
297 <  } else {
298 <    
299 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
297 >  }
298 >  else{
299 >  //actions taken at slave nodes
300  
301 <    done = 0;
274 <    while (!done) {
301 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
302  
303 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
304 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
303 >    parseErr = parseCommentLine( read_buffer, simnfo);
304 >
305 >    if( parseErr != NULL ){
306 >      strcpy( painCave.errMsg, parseErr );
307 >      haveError = 1;
308 >      simError();
309 >    }
310 >  
311 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
312 >      which_node = MolToProcMap[i];
313        
314 <      if(!myStatus) anonymousNodeDie();
314 >      if(which_node == worldRank){
315 >      //molecule with global index i belongs to this processor
316        
317 <      if(myStatus < 0) break;
317 >        localIndex = mpiSim->getGlobalToLocalMol(i);
318  
319 <      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
320 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
321 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
322 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
323 <      
324 <      myStatus = 1;
325 <      parseErr = parseDumpLine( read_buffer, which_atom );
326 <      if( parseErr != NULL ){
327 <        strcpy( painCave.errMsg, parseErr );
328 <        myStatus = 0;;
329 <        simError();
319 >        if(localIndex == -1) {
320 >          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
321 >          haveError = 1;
322 >          simError();
323 >        }
324 >
325 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
326 >
327 >        nCurObj = integrableObjects.size();
328 >        
329 >        MPI_Send(&nCurObj, 1, MPI_INT, 0,
330 >                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
331 >
332 >        for(j = 0; j < integrableObjects.size(); j++){
333 >
334 >          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
335 >                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
336 >
337 >          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
338 >
339 >          if( parseErr != NULL ){
340 >                strcpy( painCave.errMsg, parseErr );
341 >                simError();
342 >          }
343 >
344 >        }
345 >          
346        }
347        
296 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
297 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
298 –      
348      }
300 –  }
301 –    
302 – // last  thing last, enable  fatalities.
303 –  painCave.isEventLoop = 0;
304 –  simnfo->setBoxM( boxMat );
349  
350 <  
350 >  }
351   #endif
352   }
353  
354 < char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
354 > char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
355  
356 <  char *foo; // the pointer to the current string token
357 <  
358 <  double rx, ry, rz; // position place holders
359 <  double vx, vy, vz; // velocity placeholders
356 >  char *foo; // the pointer to the current string token
357 >
358 >  double pos[3]; // position place holders
359 >  double vel[3]; // velocity placeholders
360    double q[4]; // the quaternions
361 <  double jx, jy, jz; // angular velocity placeholders;
361 >  double ji[3]; // angular velocity placeholders;
362    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;
363  
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
364  
365    // set the string tokenizer
366 <  
366 >
367    foo = strtok(readLine, " ,;\t");
368 <  
368 >
369    // check the atom name to the current atom
370 <  
371 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
370 >
371 >  if( strcmp( foo, sd->getType() ) ){
372      sprintf( painCave.errMsg,
373 <             "Initialize from file error. Atom %s at index %d "
352 <             "in file %s does not"
373 >             "Initialize from file error.  Does not"
374               " match the BASS atom %s.\n",
375 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
375 >             sd->getType() );
376      return strdup( painCave.errMsg );
377    }
378 <    
378 >
379    // get the positions
380  
381    foo = strtok(NULL, " ,;\t");
382    if(foo == NULL){
383      sprintf( painCave.errMsg,
384 <             "error in reading postition x from %s\n"
385 <             "natoms  = %d, index = %d\n",
365 <             c_in_name, n_atoms, atomIndex );
384 >             "error in reading postition x from %s\n",
385 >             c_in_name);
386      return strdup( painCave.errMsg );
387    }
388 <  rx = atof( foo );
389 <  
388 >  pos[0] = atof( foo );
389 >
390    foo = strtok(NULL, " ,;\t");
391    if(foo == NULL){
392      sprintf( painCave.errMsg,
393 <             "error in reading postition y from %s\n"
394 <             "natoms  = %d, index = %d\n",
375 <             c_in_name, n_atoms, atomIndex );
393 >             "error in reading postition y from %s\n",
394 >             c_in_name);
395      return strdup( painCave.errMsg );
396    }
397 <  ry = atof( foo );
398 <    
397 >  pos[1] = atof( foo );
398 >
399    foo = strtok(NULL, " ,;\t");
400    if(foo == NULL){
401      sprintf( painCave.errMsg,
402 <             "error in reading postition z from %s\n"
403 <             "natoms  = %d, index = %d\n",
385 <             c_in_name, n_atoms, atomIndex );
402 >             "error in reading postition z from %s\n",
403 >             c_in_name);
404      return strdup( painCave.errMsg );
405    }
406 <  rz = atof( foo );    
406 >  pos[2] = atof( foo );
407  
408  
409    // get the velocities
# Line 393 | Line 411 | char* InitializeFromFile::parseDumpLine(char* readLine
411    foo = strtok(NULL, " ,;\t");
412    if(foo == NULL){
413      sprintf( painCave.errMsg,
414 <             "error in reading velocity x from %s\n"
415 <             "natoms  = %d, index = %d\n",
398 <             c_in_name, n_atoms, atomIndex );
414 >             "error in reading velocity x from %s\n",
415 >             c_in_name );
416      return strdup( painCave.errMsg );
417    }
418 <  vx = atof( foo );
419 <    
418 >  vel[0] = atof( foo );
419 >
420    foo = strtok(NULL, " ,;\t");
421    if(foo == NULL){
422      sprintf( painCave.errMsg,
423 <             "error in reading velocity y from %s\n"
424 <             "natoms  = %d, index = %d\n",
408 <             c_in_name, n_atoms, atomIndex );
423 >             "error in reading velocity x from %s\n",
424 >             c_in_name );
425      return strdup( painCave.errMsg );
426    }
427 <  vy = atof( foo );
428 <    
427 >  vel[1] = atof( foo );
428 >
429    foo = strtok(NULL, " ,;\t");
430    if(foo == NULL){
431      sprintf( painCave.errMsg,
432 <             "error in reading velocity z from %s\n"
433 <             "natoms  = %d, index = %d\n",
418 <             c_in_name, n_atoms, atomIndex );
432 >             "error in reading velocity x from %s\n",
433 >             c_in_name );
434      return strdup( painCave.errMsg );
435    }
436 <  vz = atof( foo );
437 <    
438 <    
436 >  vel[2] = atof( foo );
437 >
438 >
439 >  // add the positions and velocities to the atom
440 >
441 >  sd->setPos( pos );
442 >  sd->setVel( vel );
443 >
444 >  if (!sd->isDirectional())
445 >    return NULL;
446 >
447    // get the quaternions
448 <    
449 <  if( atoms[atomIndex]->isDirectional() ){
450 <      
448 >
449 >  if( sd->isDirectional() ){
450 >
451      foo = strtok(NULL, " ,;\t");
452      if(foo == NULL){
453 <      sprintf(painCave.errMsg,
454 <              "error in reading quaternion 0 from %s\n"
455 <              "natoms  = %d, index = %d\n",
433 <              c_in_name, n_atoms, atomIndex );
453 >      sprintf( painCave.errMsg,
454 >                     "error in reading velocity x from %s\n",
455 >                      c_in_name );
456        return strdup( painCave.errMsg );
457      }
458      q[0] = atof( foo );
459 <      
459 >
460      foo = strtok(NULL, " ,;\t");
461      if(foo == NULL){
462        sprintf( painCave.errMsg,
463 <               "error in reading quaternion 1 from %s\n"
464 <               "natoms  = %d, index = %d\n",
443 <               c_in_name, n_atoms, atomIndex );
463 >                     "error in reading velocity x from %s\n",
464 >                      c_in_name );
465        return strdup( painCave.errMsg );
466      }
467      q[1] = atof( foo );
468 <      
468 >
469      foo = strtok(NULL, " ,;\t");
470      if(foo == NULL){
471        sprintf( painCave.errMsg,
472 <               "error in reading quaternion 2 from %s\n"
473 <               "natoms  = %d, index = %d\n",
453 <               c_in_name, n_atoms, atomIndex );
472 >                     "error in reading velocity x from %s\n",
473 >                      c_in_name );
474        return strdup( painCave.errMsg );
475      }
476      q[2] = atof( foo );
477 <      
477 >
478      foo = strtok(NULL, " ,;\t");
479      if(foo == NULL){
480        sprintf( painCave.errMsg,
481 <               "error in reading quaternion 3 from %s\n"
482 <               "natoms  = %d, index = %d\n",
463 <               c_in_name, n_atoms, atomIndex );
481 >                     "error in reading velocity x from %s\n",
482 >                      c_in_name );
483        return strdup( painCave.errMsg );
484      }
485      q[3] = atof( foo );
486 <      
486 >
487      // get the angular velocities
488 <      
488 >
489      foo = strtok(NULL, " ,;\t");
490      if(foo == NULL){
491        sprintf( painCave.errMsg,
492 <               "error in reading angular momentum jx from %s\n"
493 <               "natoms  = %d, index = %d\n",
475 <               c_in_name, n_atoms, atomIndex );
492 >                     "error in reading velocity x from %s\n",
493 >                      c_in_name );
494        return strdup( painCave.errMsg );
495      }
496 <    jx = atof( foo );
497 <      
496 >    ji[0] = atof( foo );
497 >
498      foo = strtok(NULL, " ,;\t");
499      if(foo == NULL){
500        sprintf( painCave.errMsg,
501 <               "error in reading angular momentum jy from %s\n"
502 <               "natoms  = %d, index = %d\n",
485 <               c_in_name, n_atoms, atomIndex );
501 >                     "error in reading velocity x from %s\n",
502 >                      c_in_name );
503        return strdup( painCave.errMsg );
504      }
505 <    jy = atof(foo );
506 <      
505 >    ji[1] = atof(foo );
506 >
507      foo = strtok(NULL, " ,;\t");
508      if(foo == NULL){
509        sprintf( painCave.errMsg,
510 <               "error in reading angular momentum jz from %s\n"
511 <               "natoms  = %d, index = %d\n",
495 <               c_in_name, n_atoms, atomIndex );
510 >                     "error in reading velocity x from %s\n",
511 >                      c_in_name );
512        return strdup( painCave.errMsg );
513      }
514 <    jz = atof( foo );
499 <      
500 <    dAtom = ( DirectionalAtom* )atoms[atomIndex];
514 >    ji[2] = atof( foo );
515  
516 +
517      // check that the quaternion vector is normalized
518  
519      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
520 <      
520 >
521      qLength = sqrt( qSqr );
522      q[0] = q[0] / qLength;
523      q[1] = q[1] / qLength;
524      q[2] = q[2] / qLength;
525      q[3] = q[3] / qLength;
511 –      
512 –    dAtom->setQ( q );
513 –      
514 –    // add the angular velocities
526  
527 <    dAtom->setJx( jx );
528 <    dAtom->setJy( jy );
529 <    dAtom->setJz( jz );
527 >    // add quaternion and angular velocities
528 >
529 >    sd->setQ( q );
530 >    sd->setJ( ji );
531    }
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 );
532  
533 +
534 +
535    return NULL;
536   }
537  
538  
539 < char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){
539 > char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
540  
541 <  char *foo; // the pointer to the current string token
542 <  int j;
541 >  double currTime;
542 >  double boxMat[9];
543 >  double theBoxMat3[3][3];
544 >  double chi;
545 >  double integralOfChidt;
546 >  double eta[9];
547  
548 <  // set the string tokenizer
541 <  
542 <  foo = strtok(readLine, " ,;\t");
543 <  // ignore the first token which is the time stamp.
548 >  char *foo; // the pointer to the current string token
549  
550 +  // set the string tokenizer
551  
552 <  // get the Hx vector
552 >  foo = strtok(readLine, " ,;\t");
553 >  // set the timeToken.
554  
548 –  foo = strtok(NULL, " ,;\t");
555    if(foo == NULL){
556      sprintf( painCave.errMsg,
557 <             "error in reading Hx[0] from %s\n",
557 >             "error in reading Time from %s\n",
558               c_in_name );
559      return strdup( painCave.errMsg );
560    }
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 );    
561  
562 <  // get the Hy vector
562 >  currTime = atof( foo );
563 >  entry_plug->setTime( currTime );
564  
565 <  foo = strtok(NULL, " ,;\t");
566 <  if(foo == NULL){
567 <    sprintf( painCave.errMsg,
568 <             "error in reading Hy[0] from %s\n",
569 <             c_in_name );
570 <    return strdup( painCave.errMsg );
565 >  //get H-Matrix
566 >
567 >  for(int i = 0 ; i < 9; i++){
568 >    foo = strtok(NULL, " ,;\t");
569 >    if(foo == NULL){
570 >      sprintf( painCave.errMsg,
571 >               "error in reading H[%d] from %s\n", i, c_in_name );
572 >      return strdup( painCave.errMsg );
573 >    }
574 >    boxMat[i] = atof( foo );
575    }
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 );    
576  
577 <  // get the Hz vector
577 >  for(int i=0;i<3;i++)
578 >    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
579  
580 <  foo = strtok(NULL, " ,;\t");
581 <  if(foo == NULL){
582 <    sprintf( painCave.errMsg,
583 <             "error in reading Hz[0] from %s\n",
584 <             c_in_name );
585 <    return strdup( painCave.errMsg );
580 >  //set H-Matrix
581 >  entry_plug->setBoxM( theBoxMat3 );
582 >
583 >  //get chi and integralOfChidt, they should appear by pair
584 >
585 >  if( entry_plug->useInitXSstate ){
586 >    foo = strtok(NULL, " ,;\t\n");
587 >    if(foo != NULL){
588 >      chi = atof(foo);
589 >      
590 >      foo = strtok(NULL, " ,;\t\n");
591 >      if(foo == NULL){
592 >        sprintf( painCave.errMsg,
593 >                 "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
594 >        return strdup( painCave.errMsg );
595 >      }
596 >      integralOfChidt = atof( foo );
597 >      
598 >      //push chi and integralOfChidt into SimInfo::properties which can be
599 >      //retrieved by integrator later
600 >      DoubleData* chiValue = new DoubleData();
601 >      chiValue->setID(CHIVALUE_ID);
602 >      chiValue->setData(chi);
603 >      entry_plug->addProperty(chiValue);
604 >      
605 >      DoubleData* integralOfChidtValue = new DoubleData();
606 >      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
607 >      integralOfChidtValue->setData(integralOfChidt);
608 >      entry_plug->addProperty(integralOfChidtValue);
609 >      
610 >    }
611 >    else
612 >      return NULL;
613 >    
614 >    //get eta
615 >    foo = strtok(NULL, " ,;\t\n");
616 >    if(foo != NULL ){
617 >  
618 >      for(int i = 0 ; i < 9; i++){
619 >        
620 >        if(foo == NULL){
621 >          sprintf( painCave.errMsg,
622 >                   "error in reading eta[%d] from %s\n", i, c_in_name );
623 >          return strdup( painCave.errMsg );
624 >        }
625 >        eta[i] = atof( foo );
626 >        foo = strtok(NULL, " ,;\t\n");
627 >      }
628 >    }
629 >    else
630 >      return NULL;
631 >    
632 >    //push eta into SimInfo::properties which can be
633 >    //retrieved by integrator later
634 >    
635 >    DoubleArrayData* etaValue = new DoubleArrayData();
636 >    etaValue->setID(ETAVALUE_ID);
637 >    etaValue->setData(eta, 9);
638 >    entry_plug->addProperty(etaValue);
639    }
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 );    
640  
641    return NULL;
642   }
643  
636 –
644   #ifdef IS_MPI
645  
646   // a couple of functions to let us escape the read loop
647  
648   void initFile::nodeZeroError( void ){
649    int j, myStatus;
650 <  
650 >
651    myStatus = 0;
652 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
653 <    MPI_Send( &myStatus, 1, MPI_INT, j,
652 >  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
653 >    MPI_Send( &myStatus, 1, MPI_INT, j,
654                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
655 <  }  
649 <  
655 >  }
656  
657 +
658    MPI_Finalize();
659    exit (0);
660 <  
660 >
661   }
662  
663   void initFile::anonymousNodeDie( void ){

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