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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 643 by mmeineke, Mon Jul 21 21:27:40 2003 UTC vs.
Revision 1129 by tim, Thu Apr 22 03:29:30 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 71 | Line 78 | void InitializeFromFile :: readInit( SimInfo* the_simn
78  
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 –  double theBoxMat3[3][3];
93  
94 +  vector<StuntDouble*> integrableObjects;
95 +
96    simnfo = the_simnfo;
97  
98  
# Line 99 | Line 106 | void InitializeFromFile :: readInit( 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 :: readInit( 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 <  for(i=0;i<3;i++)
134 <    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
137 >  //parse dump lines
138  
139 <  simnfo->setBoxM( theBoxMat3 );
139 >  for( i=0; i < simnfo->n_mol; i++){
140  
141 +    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
142  
143 <  for( i=0; i < n_atoms; i++){
140 <    
141 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
142 <    if(eof_test == NULL){
143 <      sprintf(painCave.errMsg,
144 <              "error in reading file %s\n"
145 <              "natoms  = %d; index = %d\n"
146 <              "error reading the line from the file.\n",
147 <              c_in_name, n_atoms, i );
148 <      painCave.isFatal = 1;
149 <      simError();
150 <    }
143 >    for(j = 0; j < integrableObjects.size(); j++){
144  
145 <    
146 <    parseErr = parseDumpLine( read_buffer, i );
147 <    if( parseErr != NULL ){
148 <      strcpy( painCave.errMsg, parseErr );
149 <      painCave.isFatal = 1;
150 <      simError();
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  
161 –
165    // MPI Section of code..........
166   #else //IS_MPI
167  
# Line 167 | Line 170 | void InitializeFromFile :: readInit( 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;
189 <    DirectionalAtom* dAtom;
190 <
191 <    // 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 209 | Line 212 | void InitializeFromFile :: readInit( 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 >    parseErr = parseCommentLine( read_buffer, simnfo);
224 >
225      if( parseErr != NULL ){
226        strcpy( painCave.errMsg, parseErr );
227        haveError = 1;
228        simError();
229      }
230  
231 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
232 <  
233 <    if(haveError) nodeZeroError();
231 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
232 >      which_node = MolToProcMap[i];
233 >      if(which_node == 0){
234 >       //molecules belong to master node
235  
236 <    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
237 <      
238 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
239 <      if(eof_test == NULL){
240 <        sprintf(painCave.errMsg,
241 <                "error in reading file %s\n"
230 <                "natoms  = %d; index = %d\n"
231 <                "error reading the line from the file.\n",
232 <                c_in_name, n_atoms, i );
233 <        haveError= 1;
234 <        simError();
236 >      localIndex = mpiSim->getGlobalToLocalMol(i);
237 >
238 >      if(localIndex == -1) {
239 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
240 >        haveError = 1;
241 >        simError();
242        }
236 –    
237 –      if(haveError) nodeZeroError();
243  
244 <      // Get the Node number which wants this atom:
245 <      which_node = AtomToProcMap[i];    
246 <      if (which_node == 0) {
247 <        parseErr = parseDumpLine( read_buffer, i );
248 <        if( parseErr != NULL ){
249 <          strcpy( painCave.errMsg, parseErr );
250 <          haveError = 1;
251 <          simError();
252 <        }    
253 <        if(haveError) nodeZeroError();
254 <      }
244 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
245 >       for(j=0; j < integrableObjects.size(); j++){
246 >        
247 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
248 >          if(eof_test == NULL){
249 >                sprintf(painCave.errMsg,
250 >                    "error in reading file %s\n"
251 >                    "natoms  = %d; index = %d\n"
252 >                    "error reading the line from the file.\n",
253 >                    c_in_name, nTotObjs, i );
254 >                haveError= 1;
255 >                simError();
256 >          }
257 >          
258 >          if(haveError) nodeZeroError();
259 >
260 >          parseDumpLine(read_buffer, integrableObjects[j]);
261 >          
262 >       }
263 >
264 >
265 >      }
266 >      else{
267 >      //molecule belongs to slave nodes
268 >
269 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
270 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
271        
272 <      else {
273 <      
274 <        myStatus = 1;
275 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
276 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
277 <        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
278 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
279 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
280 <                 MPI_COMM_WORLD);
281 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
282 <                 MPI_COMM_WORLD, &istatus);
283 <        
284 <        if(!myStatus) nodeZeroError();
272 >       for(j=0; j < integrableObjects.size(); j++){
273 >        
274 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
275 >          if(eof_test == NULL){
276 >                sprintf(painCave.errMsg,
277 >                    "error in reading file %s\n"
278 >                    "natoms  = %d; index = %d\n"
279 >                    "error reading the line from the file.\n",
280 >                    c_in_name, nTotObjs, i );
281 >                haveError= 1;
282 >                simError();
283 >          }
284 >          
285 >          if(haveError) nodeZeroError();
286 >
287 >            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
288 >                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
289 >          
290 >       }
291 >
292        }
293 +      
294      }
266 –    myStatus = -1;
267 –    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
268 –      MPI_Send( &myStatus, 1, MPI_INT, j,
269 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
270 –    }
295      
296 <  } else {
297 <    
298 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
296 >  }
297 >  else{
298 >  //actions taken at slave nodes
299  
300 <    done = 0;
277 <    while (!done) {
300 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
301  
302 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
303 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
302 >    parseErr = parseCommentLine( read_buffer, simnfo);
303 >
304 >    if( parseErr != NULL ){
305 >      strcpy( painCave.errMsg, parseErr );
306 >      haveError = 1;
307 >      simError();
308 >    }
309 >  
310 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
311 >      which_node = MolToProcMap[i];
312        
313 <      if(!myStatus) anonymousNodeDie();
313 >      if(which_node == worldRank){
314 >      //molecule with global index i belongs to this processor
315        
316 <      if(myStatus < 0) break;
316 >        localIndex = mpiSim->getGlobalToLocalMol(i);
317  
318 <      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
319 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
320 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
321 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
322 <      
323 <      myStatus = 1;
324 <      parseErr = parseDumpLine( read_buffer, which_atom );
325 <      if( parseErr != NULL ){
326 <        strcpy( painCave.errMsg, parseErr );
327 <        myStatus = 0;;
328 <        simError();
318 >        if(localIndex == -1) {
319 >          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
320 >          haveError = 1;
321 >          simError();
322 >        }
323 >
324 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
325 >
326 >        nCurObj = integrableObjects.size();
327 >        
328 >        MPI_Send(&nCurObj, 1, MPI_INT, 0,
329 >                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
330 >
331 >        for(j = 0; j < integrableObjects.size(); j++){
332 >
333 >          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
334 >                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
335 >
336 >          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
337 >
338 >          if( parseErr != NULL ){
339 >                strcpy( painCave.errMsg, parseErr );
340 >                simError();
341 >          }
342 >
343 >        }
344 >          
345        }
346        
299 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
300 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
301 –      
347      }
303 –  }
304 –    
305 – // last  thing last, enable  fatalities.
306 –  painCave.isEventLoop = 0;
348  
349 <  for(i=0;i<3;i++)
309 <    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
310 <
311 <  simnfo->setBoxM( theBoxMat3 );
312 <
313 <  
349 >  }
350   #endif
351   }
352  
353 < char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
353 > char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
354  
355 <  char *foo; // the pointer to the current string token
356 <  
357 <  double rx, ry, rz; // position place holders
358 <  double vx, vy, vz; // velocity placeholders
355 >  char *foo; // the pointer to the current string token
356 >
357 >  double pos[3]; // position place holders
358 >  double vel[3]; // velocity placeholders
359    double q[4]; // the quaternions
360 <  double jx, jy, jz; // angular velocity placeholders;
360 >  double ji[3]; // angular velocity placeholders;
361    double qSqr, qLength; // needed to normalize the quaternion vector.
326 –  
327 –  Atom **atoms = simnfo->atoms;
328 –  DirectionalAtom* dAtom;
329 –  
330 –  int j, n_atoms, atomIndex;
362  
332 – #ifdef IS_MPI
333 –  n_atoms = mpiSim->getTotAtoms();
334 –  atomIndex=-1;        
335 –  for (j=0; j < mpiSim->getMyNlocal(); j++) {
336 –    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
337 –  }
338 –  if (atomIndex == -1) {
339 –    sprintf( painCave.errMsg,
340 –             "Initialize from file error. Atom at index %d "
341 –             "in file %s does not exist on processor %d .\n",
342 –             globalIndex, c_in_name, mpiSim->getMyNode() );
343 –    return strdup( painCave.errMsg );
344 –  }  
345 – #else
346 –  n_atoms = simnfo->n_atoms;
347 –  atomIndex = globalIndex;
348 – #endif // is_mpi
363  
364    // set the string tokenizer
365 <  
365 >
366    foo = strtok(readLine, " ,;\t");
367 <  
367 >
368    // check the atom name to the current atom
369 <  
370 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
369 >
370 >  if( strcmp( foo, sd->getType() ) ){
371      sprintf( painCave.errMsg,
372 <             "Initialize from file error. Atom %s at index %d "
359 <             "in file %s does not"
372 >             "Initialize from file error.  Does not"
373               " match the BASS atom %s.\n",
374 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
374 >             sd->getType() );
375      return strdup( painCave.errMsg );
376    }
377 <    
377 >
378    // get the positions
379  
380    foo = strtok(NULL, " ,;\t");
381    if(foo == NULL){
382      sprintf( painCave.errMsg,
383 <             "error in reading postition x from %s\n"
384 <             "natoms  = %d, index = %d\n",
372 <             c_in_name, n_atoms, atomIndex );
383 >             "error in reading postition x from %s\n",
384 >             c_in_name);
385      return strdup( painCave.errMsg );
386    }
387 <  rx = atof( foo );
388 <  
387 >  pos[0] = atof( foo );
388 >
389    foo = strtok(NULL, " ,;\t");
390    if(foo == NULL){
391      sprintf( painCave.errMsg,
392 <             "error in reading postition y from %s\n"
393 <             "natoms  = %d, index = %d\n",
382 <             c_in_name, n_atoms, atomIndex );
392 >             "error in reading postition y from %s\n",
393 >             c_in_name);
394      return strdup( painCave.errMsg );
395    }
396 <  ry = atof( foo );
397 <    
396 >  pos[1] = atof( foo );
397 >
398    foo = strtok(NULL, " ,;\t");
399    if(foo == NULL){
400      sprintf( painCave.errMsg,
401 <             "error in reading postition z from %s\n"
402 <             "natoms  = %d, index = %d\n",
392 <             c_in_name, n_atoms, atomIndex );
401 >             "error in reading postition z from %s\n",
402 >             c_in_name);
403      return strdup( painCave.errMsg );
404    }
405 <  rz = atof( foo );    
405 >  pos[2] = atof( foo );
406  
407  
408    // get the velocities
# Line 400 | Line 410 | char* InitializeFromFile::parseDumpLine(char* readLine
410    foo = strtok(NULL, " ,;\t");
411    if(foo == NULL){
412      sprintf( painCave.errMsg,
413 <             "error in reading velocity x from %s\n"
414 <             "natoms  = %d, index = %d\n",
405 <             c_in_name, n_atoms, atomIndex );
413 >             "error in reading velocity x from %s\n",
414 >             c_in_name );
415      return strdup( painCave.errMsg );
416    }
417 <  vx = atof( foo );
418 <    
417 >  vel[0] = atof( foo );
418 >
419    foo = strtok(NULL, " ,;\t");
420    if(foo == NULL){
421      sprintf( painCave.errMsg,
422 <             "error in reading velocity y from %s\n"
423 <             "natoms  = %d, index = %d\n",
415 <             c_in_name, n_atoms, atomIndex );
422 >             "error in reading velocity x from %s\n",
423 >             c_in_name );
424      return strdup( painCave.errMsg );
425    }
426 <  vy = atof( foo );
427 <    
426 >  vel[1] = atof( foo );
427 >
428    foo = strtok(NULL, " ,;\t");
429    if(foo == NULL){
430      sprintf( painCave.errMsg,
431 <             "error in reading velocity z from %s\n"
432 <             "natoms  = %d, index = %d\n",
425 <             c_in_name, n_atoms, atomIndex );
431 >             "error in reading velocity x from %s\n",
432 >             c_in_name );
433      return strdup( painCave.errMsg );
434    }
435 <  vz = atof( foo );
436 <    
437 <    
435 >  vel[2] = atof( foo );
436 >
437 >
438 >  // add the positions and velocities to the atom
439 >
440 >  sd->setPos( pos );
441 >  sd->setVel( vel );
442 >
443 >  if (!sd->isDirectional())
444 >    return NULL;
445 >
446    // get the quaternions
447 <    
448 <  if( atoms[atomIndex]->isDirectional() ){
449 <      
447 >
448 >  if( sd->isDirectional() ){
449 >
450      foo = strtok(NULL, " ,;\t");
451      if(foo == NULL){
452 <      sprintf(painCave.errMsg,
453 <              "error in reading quaternion 0 from %s\n"
454 <              "natoms  = %d, index = %d\n",
440 <              c_in_name, n_atoms, atomIndex );
452 >      sprintf( painCave.errMsg,
453 >                     "error in reading velocity x from %s\n",
454 >                      c_in_name );
455        return strdup( painCave.errMsg );
456      }
457      q[0] = atof( foo );
458 <      
458 >
459      foo = strtok(NULL, " ,;\t");
460      if(foo == NULL){
461        sprintf( painCave.errMsg,
462 <               "error in reading quaternion 1 from %s\n"
463 <               "natoms  = %d, index = %d\n",
450 <               c_in_name, n_atoms, atomIndex );
462 >                     "error in reading velocity x from %s\n",
463 >                      c_in_name );
464        return strdup( painCave.errMsg );
465      }
466      q[1] = atof( foo );
467 <      
467 >
468      foo = strtok(NULL, " ,;\t");
469      if(foo == NULL){
470        sprintf( painCave.errMsg,
471 <               "error in reading quaternion 2 from %s\n"
472 <               "natoms  = %d, index = %d\n",
460 <               c_in_name, n_atoms, atomIndex );
471 >                     "error in reading velocity x from %s\n",
472 >                      c_in_name );
473        return strdup( painCave.errMsg );
474      }
475      q[2] = atof( foo );
476 <      
476 >
477      foo = strtok(NULL, " ,;\t");
478      if(foo == NULL){
479        sprintf( painCave.errMsg,
480 <               "error in reading quaternion 3 from %s\n"
481 <               "natoms  = %d, index = %d\n",
470 <               c_in_name, n_atoms, atomIndex );
480 >                     "error in reading velocity x from %s\n",
481 >                      c_in_name );
482        return strdup( painCave.errMsg );
483      }
484      q[3] = atof( foo );
485 <      
485 >
486      // get the angular velocities
487 <      
487 >
488      foo = strtok(NULL, " ,;\t");
489      if(foo == NULL){
490        sprintf( painCave.errMsg,
491 <               "error in reading angular momentum jx from %s\n"
492 <               "natoms  = %d, index = %d\n",
482 <               c_in_name, n_atoms, atomIndex );
491 >                     "error in reading velocity x from %s\n",
492 >                      c_in_name );
493        return strdup( painCave.errMsg );
494      }
495 <    jx = atof( foo );
496 <      
495 >    ji[0] = atof( foo );
496 >
497      foo = strtok(NULL, " ,;\t");
498      if(foo == NULL){
499        sprintf( painCave.errMsg,
500 <               "error in reading angular momentum jy from %s\n"
501 <               "natoms  = %d, index = %d\n",
492 <               c_in_name, n_atoms, atomIndex );
500 >                     "error in reading velocity x from %s\n",
501 >                      c_in_name );
502        return strdup( painCave.errMsg );
503      }
504 <    jy = atof(foo );
505 <      
504 >    ji[1] = atof(foo );
505 >
506      foo = strtok(NULL, " ,;\t");
507      if(foo == NULL){
508        sprintf( painCave.errMsg,
509 <               "error in reading angular momentum jz from %s\n"
510 <               "natoms  = %d, index = %d\n",
502 <               c_in_name, n_atoms, atomIndex );
509 >                     "error in reading velocity x from %s\n",
510 >                      c_in_name );
511        return strdup( painCave.errMsg );
512      }
513 <    jz = atof( foo );
506 <      
507 <    dAtom = ( DirectionalAtom* )atoms[atomIndex];
513 >    ji[2] = atof( foo );
514  
515 +
516      // check that the quaternion vector is normalized
517  
518      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
519 <      
519 >
520      qLength = sqrt( qSqr );
521      q[0] = q[0] / qLength;
522      q[1] = q[1] / qLength;
523      q[2] = q[2] / qLength;
524      q[3] = q[3] / qLength;
518 –      
519 –    dAtom->setQ( q );
520 –      
521 –    // add the angular velocities
525  
526 <    dAtom->setJx( jx );
527 <    dAtom->setJy( jy );
528 <    dAtom->setJz( jz );
526 >    // add quaternion and angular velocities
527 >
528 >    sd->setQ( q );
529 >    sd->setJ( ji );
530    }
527 –    
528 –  // add the positions and velocities to the atom
529 –    
530 –  atoms[atomIndex]->setX( rx );
531 –  atoms[atomIndex]->setY( ry );
532 –  atoms[atomIndex]->setZ( rz );
533 –    
534 –  atoms[atomIndex]->set_vx( vx );
535 –  atoms[atomIndex]->set_vy( vy );
536 –  atoms[atomIndex]->set_vz( vz );
531  
532 +
533 +
534    return NULL;
535   }
536  
537  
538 < char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){
538 > char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
539  
540 <  char *foo; // the pointer to the current string token
541 <  int j;
540 >  double currTime;
541 >  double boxMat[9];
542 >  double theBoxMat3[3][3];
543 >  double chi;
544 >  double integralOfChidt;
545 >  double eta[9];
546  
547 +  char *foo; // the pointer to the current string token
548 +
549    // set the string tokenizer
550 <  
550 >
551    foo = strtok(readLine, " ,;\t");
552    // set the timeToken.
553  
# Line 555 | Line 557 | char* InitializeFromFile::parseBoxLine(char* readLine,
557               c_in_name );
558      return strdup( painCave.errMsg );
559    }
558 –  simnfo->setTime( atof( foo ) );
560  
561 <  // get the Hx vector
561 >  currTime = atof( foo );
562 >  entry_plug->setTime( currTime );
563  
564 <  foo = strtok(NULL, " ,;\t");
565 <  if(foo == NULL){
566 <    sprintf( painCave.errMsg,
567 <             "error in reading Hx[0] from %s\n",
568 <             c_in_name );
569 <    return strdup( painCave.errMsg );
564 >  //get H-Matrix
565 >
566 >  for(int i = 0 ; i < 9; i++){
567 >    foo = strtok(NULL, " ,;\t");
568 >    if(foo == NULL){
569 >      sprintf( painCave.errMsg,
570 >               "error in reading H[%d] from %s\n", i, c_in_name );
571 >      return strdup( painCave.errMsg );
572 >    }
573 >    boxMat[i] = atof( foo );
574    }
569 –  boxMat[0] = atof( foo );
570 –  
571 –  foo = strtok(NULL, " ,;\t");
572 –  if(foo == NULL){
573 –    sprintf( painCave.errMsg,
574 –             "error in reading Hx[1] from %s\n",
575 –             c_in_name );
576 –    return strdup( painCave.errMsg );
577 –  }
578 –  boxMat[1] = atof( foo );
579 –    
580 –  foo = strtok(NULL, " ,;\t");
581 –  if(foo == NULL){
582 –    sprintf( painCave.errMsg,
583 –             "error in reading Hx[2] from %s\n",
584 –             c_in_name );
585 –    return strdup( painCave.errMsg );
586 –  }
587 –  boxMat[2] = atof( foo );    
575  
576 <  // get the Hy vector
576 >  for(int i=0;i<3;i++)
577 >    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
578  
579 <  foo = strtok(NULL, " ,;\t");
580 <  if(foo == NULL){
593 <    sprintf( painCave.errMsg,
594 <             "error in reading Hy[0] from %s\n",
595 <             c_in_name );
596 <    return strdup( painCave.errMsg );
597 <  }
598 <  boxMat[3] = atof( foo );
599 <  
600 <  foo = strtok(NULL, " ,;\t");
601 <  if(foo == NULL){
602 <    sprintf( painCave.errMsg,
603 <             "error in reading Hy[1] from %s\n",
604 <             c_in_name );
605 <    return strdup( painCave.errMsg );
606 <  }
607 <  boxMat[4] = atof( foo );
608 <    
609 <  foo = strtok(NULL, " ,;\t");
610 <  if(foo == NULL){
611 <    sprintf( painCave.errMsg,
612 <             "error in reading Hy[2] from %s\n",
613 <             c_in_name );
614 <    return strdup( painCave.errMsg );
615 <  }
616 <  boxMat[5] = atof( foo );    
579 >  //set H-Matrix
580 >  entry_plug->setBoxM( theBoxMat3 );
581  
582 <  // get the Hz vector
582 >  //get chi and integralOfChidt, they should appear by pair
583  
584 <  foo = strtok(NULL, " ,;\t");
585 <  if(foo == NULL){
586 <    sprintf( painCave.errMsg,
587 <             "error in reading Hz[0] from %s\n",
588 <             c_in_name );
589 <    return strdup( painCave.errMsg );
584 >  if( entry_plug->useInitXSstate ){
585 >    foo = strtok(NULL, " ,;\t\n");
586 >    if(foo != NULL){
587 >      chi = atof(foo);
588 >      
589 >      foo = strtok(NULL, " ,;\t\n");
590 >      if(foo == NULL){
591 >        sprintf( painCave.errMsg,
592 >                 "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
593 >        return strdup( painCave.errMsg );
594 >      }
595 >      integralOfChidt = atof( foo );
596 >      
597 >      //push chi and integralOfChidt into SimInfo::properties which can be
598 >      //retrieved by integrator later
599 >      DoubleData* chiValue = new DoubleData();
600 >      chiValue->setID(CHIVALUE_ID);
601 >      chiValue->setData(chi);
602 >      entry_plug->addProperty(chiValue);
603 >      
604 >      DoubleData* integralOfChidtValue = new DoubleData();
605 >      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
606 >      integralOfChidtValue->setData(integralOfChidt);
607 >      entry_plug->addProperty(integralOfChidtValue);
608 >      
609 >    }
610 >    else
611 >      return NULL;
612 >    
613 >    //get eta
614 >    foo = strtok(NULL, " ,;\t\n");
615 >    if(foo != NULL ){
616 >  
617 >      for(int i = 0 ; i < 9; i++){
618 >        
619 >        if(foo == NULL){
620 >          sprintf( painCave.errMsg,
621 >                   "error in reading eta[%d] from %s\n", i, c_in_name );
622 >          return strdup( painCave.errMsg );
623 >        }
624 >        eta[i] = atof( foo );
625 >        foo = strtok(NULL, " ,;\t\n");
626 >      }
627 >    }
628 >    else
629 >      return NULL;
630 >    
631 >    //push eta into SimInfo::properties which can be
632 >    //retrieved by integrator later
633 >    
634 >    DoubleArrayData* etaValue = new DoubleArrayData();
635 >    etaValue->setID(ETAVALUE_ID);
636 >    etaValue->setData(eta, 9);
637 >    entry_plug->addProperty(etaValue);
638    }
627 –  boxMat[6] = atof( foo );
628 –  
629 –  foo = strtok(NULL, " ,;\t");
630 –  if(foo == NULL){
631 –    sprintf( painCave.errMsg,
632 –             "error in reading Hz[1] from %s\n",
633 –             c_in_name );
634 –    return strdup( painCave.errMsg );
635 –  }
636 –  boxMat[7] = atof( foo );
637 –    
638 –  foo = strtok(NULL, " ,;\t");
639 –  if(foo == NULL){
640 –    sprintf( painCave.errMsg,
641 –             "error in reading Hz[2] from %s\n",
642 –             c_in_name );
643 –    return strdup( painCave.errMsg );
644 –  }
645 –  boxMat[8] = atof( foo );    
639  
640    return NULL;
641   }
642  
650 –
643   #ifdef IS_MPI
644  
645   // a couple of functions to let us escape the read loop
646  
647   void initFile::nodeZeroError( void ){
648    int j, myStatus;
649 <  
649 >
650    myStatus = 0;
651 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
652 <    MPI_Send( &myStatus, 1, MPI_INT, j,
651 >  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
652 >    MPI_Send( &myStatus, 1, MPI_INT, j,
653                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
654 <  }  
663 <  
654 >  }
655  
656 +
657    MPI_Finalize();
658    exit (0);
659 <  
659 >
660   }
661  
662   void initFile::anonymousNodeDie( void ){

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