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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 1130 by tim, Thu Apr 22 14:55:17 2004 UTC

# Line 1 | Line 1
1 + #define _FILE_OFFSET_BITS 64
2   #include <iostream>
3 < #include <cmath>
3 > #include <math.h>
4  
5   #include <stdio.h>
6   #include <stdlib.h>
# Line 10 | Line 11
11  
12   #include "ReadWrite.hpp"
13   #include "simError.h"
14 + #include "GenericData.hpp"
15  
16   #ifdef IS_MPI
17   #include <mpi.h>
18   #include "mpiSimulation.hpp"
19 < #define TAKE_THIS_TAG_CHAR 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 | 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 >    cerr << "node " << worldRank << " finished  MPI_Bcast" << endl;
224 >
225 >    parseErr = parseCommentLine( read_buffer, simnfo);
226 >
227      if( parseErr != NULL ){
228        strcpy( painCave.errMsg, parseErr );
229        haveError = 1;
230        simError();
231      }
232  
233 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
234 <  
235 <    if(haveError) nodeZeroError();
233 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
234 >      which_node = MolToProcMap[i];
235 >      if(which_node == 0){
236 >       //molecules belong to master node
237  
238 <    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
239 <      
240 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
241 <      if(eof_test == NULL){
242 <        sprintf(painCave.errMsg,
243 <                "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();
238 >      localIndex = mpiSim->getGlobalToLocalMol(i);
239 >
240 >      if(localIndex == -1) {
241 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
242 >        haveError = 1;
243 >        simError();
244        }
236 –    
237 –      if(haveError) nodeZeroError();
245  
246 <      // Get the Node number which wants this atom:
247 <      which_node = AtomToProcMap[i];    
248 <      if (which_node == 0) {
249 <        parseErr = parseDumpLine( read_buffer, i );
250 <        if( parseErr != NULL ){
251 <          strcpy( painCave.errMsg, parseErr );
252 <          haveError = 1;
253 <          simError();
254 <        }    
255 <        if(haveError) nodeZeroError();
256 <      }
257 <      
258 <      else {
259 <      
260 <        myStatus = 1;
261 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
262 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
263 <        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
264 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
265 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
266 <                 MPI_COMM_WORLD);
260 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
261 <                 MPI_COMM_WORLD, &istatus);
262 <        
263 <        if(!myStatus) nodeZeroError();
246 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
247 >       for(j=0; j < integrableObjects.size(); j++){
248 >        
249 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
250 >          if(eof_test == NULL){
251 >                sprintf(painCave.errMsg,
252 >                    "error in reading file %s\n"
253 >                    "natoms  = %d; index = %d\n"
254 >                    "error reading the line from the file.\n",
255 >                    c_in_name, nTotObjs, i );
256 >                haveError= 1;
257 >                simError();
258 >          }
259 >          
260 >          if(haveError) nodeZeroError();
261 >
262 >          parseDumpLine(read_buffer, integrableObjects[j]);
263 >          
264 >       }
265 >
266 >
267        }
268 +      else{
269 +      //molecule belongs to slave nodes
270 +
271 +        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
272 +               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
273 +         cerr << "node " << worldRank << " finished  MPI_Send" << endl;  
274 +       for(j=0; j < nCurObj; j++){
275 +        
276 +          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
277 +          if(eof_test == NULL){
278 +                sprintf(painCave.errMsg,
279 +                    "error in reading file %s\n"
280 +                    "natoms  = %d; index = %d\n"
281 +                    "error reading the line from the file.\n",
282 +                    c_in_name, nTotObjs, i );
283 +                haveError= 1;
284 +                simError();
285 +          }
286 +          
287 +          if(haveError) nodeZeroError();
288 +
289 +            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
290 +                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
291 +           cerr << "node " << worldRank << " finished  MPI_Send" << endl;
292 +       }
293 +
294 +      }
295 +      
296      }
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 –    }
297      
298 <  } else {
299 <    
300 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
298 >  }
299 >  else{
300 >  //actions taken at slave nodes
301  
302 <    done = 0;
277 <    while (!done) {
302 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
303  
304 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
305 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
304 >    cerr << "node " << worldRank << " finished  MPI_Bcast" << endl;
305 >    parseErr = parseCommentLine( read_buffer, simnfo);
306 >
307 >    if( parseErr != NULL ){
308 >      strcpy( painCave.errMsg, parseErr );
309 >      haveError = 1;
310 >      simError();
311 >    }
312 >  
313 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
314 >      which_node = MolToProcMap[i];
315        
316 <      if(!myStatus) anonymousNodeDie();
316 >      if(which_node == worldRank){
317 >      //molecule with global index i belongs to this processor
318        
319 <      if(myStatus < 0) break;
319 >        localIndex = mpiSim->getGlobalToLocalMol(i);
320  
321 <      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
322 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
323 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
324 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
325 <      
326 <      myStatus = 1;
327 <      parseErr = parseDumpLine( read_buffer, which_atom );
328 <      if( parseErr != NULL ){
329 <        strcpy( painCave.errMsg, parseErr );
330 <        myStatus = 0;;
331 <        simError();
321 >        if(localIndex == -1) {
322 >          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
323 >          haveError = 1;
324 >          simError();
325 >        }
326 >
327 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
328 >
329 >        nCurObj = integrableObjects.size();
330 >        
331 >        MPI_Send(&nCurObj, 1, MPI_INT, 0,
332 >                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
333 >
334 >        cerr << "node " << worldRank << " finished  MPI_Send" << endl;
335 >        for(j = 0; j < integrableObjects.size(); j++){
336 >
337 >          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
338 >                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
339 >
340 >        cerr << "node " << worldRank << " finished  MPI_Recv" << endl;
341 >          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
342 >
343 >          if( parseErr != NULL ){
344 >                strcpy( painCave.errMsg, parseErr );
345 >                simError();
346 >          }
347 >
348 >        }
349 >          
350        }
351        
299 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
300 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
301 –      
352      }
303 –  }
304 –    
305 – // last  thing last, enable  fatalities.
306 –  painCave.isEventLoop = 0;
353  
354 <  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 <  
354 >  }
355   #endif
356   }
357  
358 < char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
358 > char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
359  
360 <  char *foo; // the pointer to the current string token
361 <  
362 <  double rx, ry, rz; // position place holders
363 <  double vx, vy, vz; // velocity placeholders
360 >  char *foo; // the pointer to the current string token
361 >
362 >  double pos[3]; // position place holders
363 >  double vel[3]; // velocity placeholders
364    double q[4]; // the quaternions
365 <  double jx, jy, jz; // angular velocity placeholders;
365 >  double ji[3]; // angular velocity placeholders;
366    double qSqr, qLength; // needed to normalize the quaternion vector.
326 –  
327 –  Atom **atoms = simnfo->atoms;
328 –  DirectionalAtom* dAtom;
329 –  
330 –  int j, n_atoms, atomIndex;
367  
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
368  
369    // set the string tokenizer
370 <  
370 >
371    foo = strtok(readLine, " ,;\t");
372 <  
372 >
373    // check the atom name to the current atom
374 <  
375 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
374 >
375 >  if( strcmp( foo, sd->getType() ) ){
376      sprintf( painCave.errMsg,
377 <             "Initialize from file error. Atom %s at index %d "
359 <             "in file %s does not"
377 >             "Initialize from file error.  Does not"
378               " match the BASS atom %s.\n",
379 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
379 >             sd->getType() );
380      return strdup( painCave.errMsg );
381    }
382 <    
382 >
383    // get the positions
384  
385    foo = strtok(NULL, " ,;\t");
386    if(foo == NULL){
387      sprintf( painCave.errMsg,
388 <             "error in reading postition x from %s\n"
389 <             "natoms  = %d, index = %d\n",
372 <             c_in_name, n_atoms, atomIndex );
388 >             "error in reading postition x from %s\n",
389 >             c_in_name);
390      return strdup( painCave.errMsg );
391    }
392 <  rx = atof( foo );
393 <  
392 >  pos[0] = atof( foo );
393 >
394    foo = strtok(NULL, " ,;\t");
395    if(foo == NULL){
396      sprintf( painCave.errMsg,
397 <             "error in reading postition y from %s\n"
398 <             "natoms  = %d, index = %d\n",
382 <             c_in_name, n_atoms, atomIndex );
397 >             "error in reading postition y from %s\n",
398 >             c_in_name);
399      return strdup( painCave.errMsg );
400    }
401 <  ry = atof( foo );
402 <    
401 >  pos[1] = atof( foo );
402 >
403    foo = strtok(NULL, " ,;\t");
404    if(foo == NULL){
405      sprintf( painCave.errMsg,
406 <             "error in reading postition z from %s\n"
407 <             "natoms  = %d, index = %d\n",
392 <             c_in_name, n_atoms, atomIndex );
406 >             "error in reading postition z from %s\n",
407 >             c_in_name);
408      return strdup( painCave.errMsg );
409    }
410 <  rz = atof( foo );    
410 >  pos[2] = atof( foo );
411  
412  
413    // get the velocities
# Line 400 | Line 415 | char* InitializeFromFile::parseDumpLine(char* readLine
415    foo = strtok(NULL, " ,;\t");
416    if(foo == NULL){
417      sprintf( painCave.errMsg,
418 <             "error in reading velocity x from %s\n"
419 <             "natoms  = %d, index = %d\n",
405 <             c_in_name, n_atoms, atomIndex );
418 >             "error in reading velocity x from %s\n",
419 >             c_in_name );
420      return strdup( painCave.errMsg );
421    }
422 <  vx = atof( foo );
423 <    
422 >  vel[0] = atof( foo );
423 >
424    foo = strtok(NULL, " ,;\t");
425    if(foo == NULL){
426      sprintf( painCave.errMsg,
427 <             "error in reading velocity y from %s\n"
428 <             "natoms  = %d, index = %d\n",
415 <             c_in_name, n_atoms, atomIndex );
427 >             "error in reading velocity x from %s\n",
428 >             c_in_name );
429      return strdup( painCave.errMsg );
430    }
431 <  vy = atof( foo );
432 <    
431 >  vel[1] = atof( foo );
432 >
433    foo = strtok(NULL, " ,;\t");
434    if(foo == NULL){
435      sprintf( painCave.errMsg,
436 <             "error in reading velocity z from %s\n"
437 <             "natoms  = %d, index = %d\n",
425 <             c_in_name, n_atoms, atomIndex );
436 >             "error in reading velocity x from %s\n",
437 >             c_in_name );
438      return strdup( painCave.errMsg );
439    }
440 <  vz = atof( foo );
441 <    
442 <    
440 >  vel[2] = atof( foo );
441 >
442 >
443 >  // add the positions and velocities to the atom
444 >
445 >  sd->setPos( pos );
446 >  sd->setVel( vel );
447 >
448 >  if (!sd->isDirectional())
449 >    return NULL;
450 >
451    // get the quaternions
452 <    
453 <  if( atoms[atomIndex]->isDirectional() ){
454 <      
452 >
453 >  if( sd->isDirectional() ){
454 >
455      foo = strtok(NULL, " ,;\t");
456      if(foo == NULL){
457 <      sprintf(painCave.errMsg,
458 <              "error in reading quaternion 0 from %s\n"
459 <              "natoms  = %d, index = %d\n",
440 <              c_in_name, n_atoms, atomIndex );
457 >      sprintf( painCave.errMsg,
458 >                     "error in reading velocity x from %s\n",
459 >                      c_in_name );
460        return strdup( painCave.errMsg );
461      }
462      q[0] = atof( foo );
463 <      
463 >
464      foo = strtok(NULL, " ,;\t");
465      if(foo == NULL){
466        sprintf( painCave.errMsg,
467 <               "error in reading quaternion 1 from %s\n"
468 <               "natoms  = %d, index = %d\n",
450 <               c_in_name, n_atoms, atomIndex );
467 >                     "error in reading velocity x from %s\n",
468 >                      c_in_name );
469        return strdup( painCave.errMsg );
470      }
471      q[1] = atof( foo );
472 <      
472 >
473      foo = strtok(NULL, " ,;\t");
474      if(foo == NULL){
475        sprintf( painCave.errMsg,
476 <               "error in reading quaternion 2 from %s\n"
477 <               "natoms  = %d, index = %d\n",
460 <               c_in_name, n_atoms, atomIndex );
476 >                     "error in reading velocity x from %s\n",
477 >                      c_in_name );
478        return strdup( painCave.errMsg );
479      }
480      q[2] = atof( foo );
481 <      
481 >
482      foo = strtok(NULL, " ,;\t");
483      if(foo == NULL){
484        sprintf( painCave.errMsg,
485 <               "error in reading quaternion 3 from %s\n"
486 <               "natoms  = %d, index = %d\n",
470 <               c_in_name, n_atoms, atomIndex );
485 >                     "error in reading velocity x from %s\n",
486 >                      c_in_name );
487        return strdup( painCave.errMsg );
488      }
489      q[3] = atof( foo );
490 <      
490 >
491      // get the angular velocities
492 <      
492 >
493      foo = strtok(NULL, " ,;\t");
494      if(foo == NULL){
495        sprintf( painCave.errMsg,
496 <               "error in reading angular momentum jx from %s\n"
497 <               "natoms  = %d, index = %d\n",
482 <               c_in_name, n_atoms, atomIndex );
496 >                     "error in reading velocity x from %s\n",
497 >                      c_in_name );
498        return strdup( painCave.errMsg );
499      }
500 <    jx = atof( foo );
501 <      
500 >    ji[0] = atof( foo );
501 >
502      foo = strtok(NULL, " ,;\t");
503      if(foo == NULL){
504        sprintf( painCave.errMsg,
505 <               "error in reading angular momentum jy from %s\n"
506 <               "natoms  = %d, index = %d\n",
492 <               c_in_name, n_atoms, atomIndex );
505 >                     "error in reading velocity x from %s\n",
506 >                      c_in_name );
507        return strdup( painCave.errMsg );
508      }
509 <    jy = atof(foo );
510 <      
509 >    ji[1] = atof(foo );
510 >
511      foo = strtok(NULL, " ,;\t");
512      if(foo == NULL){
513        sprintf( painCave.errMsg,
514 <               "error in reading angular momentum jz from %s\n"
515 <               "natoms  = %d, index = %d\n",
502 <               c_in_name, n_atoms, atomIndex );
514 >                     "error in reading velocity x from %s\n",
515 >                      c_in_name );
516        return strdup( painCave.errMsg );
517      }
518 <    jz = atof( foo );
506 <      
507 <    dAtom = ( DirectionalAtom* )atoms[atomIndex];
518 >    ji[2] = atof( foo );
519  
520 +
521      // check that the quaternion vector is normalized
522  
523      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
524 <      
524 >
525      qLength = sqrt( qSqr );
526      q[0] = q[0] / qLength;
527      q[1] = q[1] / qLength;
528      q[2] = q[2] / qLength;
529      q[3] = q[3] / qLength;
518 –      
519 –    dAtom->setQ( q );
520 –      
521 –    // add the angular velocities
530  
531 <    dAtom->setJx( jx );
532 <    dAtom->setJy( jy );
533 <    dAtom->setJz( jz );
531 >    // add quaternion and angular velocities
532 >
533 >    sd->setQ( q );
534 >    sd->setJ( ji );
535    }
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 );
536  
537 +
538 +
539    return NULL;
540   }
541  
542  
543 < char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){
543 > char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
544  
545 <  char *foo; // the pointer to the current string token
546 <  int j;
545 >  double currTime;
546 >  double boxMat[9];
547 >  double theBoxMat3[3][3];
548 >  double chi;
549 >  double integralOfChidt;
550 >  double eta[9];
551  
552 +  char *foo; // the pointer to the current string token
553 +
554    // set the string tokenizer
555 <  
555 >
556    foo = strtok(readLine, " ,;\t");
557    // set the timeToken.
558  
# Line 555 | Line 562 | char* InitializeFromFile::parseBoxLine(char* readLine,
562               c_in_name );
563      return strdup( painCave.errMsg );
564    }
565 <  simnfo->setTime( atof( foo ) );
565 >
566 >  currTime = atof( foo );
567 >  entry_plug->setTime( currTime );
568  
569 <  // get the Hx vector
569 >  //get H-Matrix
570  
571 <  foo = strtok(NULL, " ,;\t");
572 <  if(foo == NULL){
573 <    sprintf( painCave.errMsg,
574 <             "error in reading Hx[0] from %s\n",
575 <             c_in_name );
576 <    return strdup( painCave.errMsg );
571 >  for(int i = 0 ; i < 9; i++){
572 >    foo = strtok(NULL, " ,;\t");
573 >    if(foo == NULL){
574 >      sprintf( painCave.errMsg,
575 >               "error in reading H[%d] from %s\n", i, c_in_name );
576 >      return strdup( painCave.errMsg );
577 >    }
578 >    boxMat[i] = atof( foo );
579    }
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 );    
580  
581 <  // get the Hy vector
581 >  for(int i=0;i<3;i++)
582 >    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
583  
584 <  foo = strtok(NULL, " ,;\t");
585 <  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 );    
584 >  //set H-Matrix
585 >  entry_plug->setBoxM( theBoxMat3 );
586  
587 <  // get the Hz vector
587 >  //get chi and integralOfChidt, they should appear by pair
588  
589 <  foo = strtok(NULL, " ,;\t");
590 <  if(foo == NULL){
591 <    sprintf( painCave.errMsg,
592 <             "error in reading Hz[0] from %s\n",
593 <             c_in_name );
594 <    return strdup( painCave.errMsg );
589 >  if( entry_plug->useInitXSstate ){
590 >    foo = strtok(NULL, " ,;\t\n");
591 >    if(foo != NULL){
592 >      chi = atof(foo);
593 >      
594 >      foo = strtok(NULL, " ,;\t\n");
595 >      if(foo == NULL){
596 >        sprintf( painCave.errMsg,
597 >                 "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
598 >        return strdup( painCave.errMsg );
599 >      }
600 >      integralOfChidt = atof( foo );
601 >      
602 >      //push chi and integralOfChidt into SimInfo::properties which can be
603 >      //retrieved by integrator later
604 >      DoubleData* chiValue = new DoubleData();
605 >      chiValue->setID(CHIVALUE_ID);
606 >      chiValue->setData(chi);
607 >      entry_plug->addProperty(chiValue);
608 >      
609 >      DoubleData* integralOfChidtValue = new DoubleData();
610 >      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
611 >      integralOfChidtValue->setData(integralOfChidt);
612 >      entry_plug->addProperty(integralOfChidtValue);
613 >      
614 >    }
615 >    else
616 >      return NULL;
617 >    
618 >    //get eta
619 >    foo = strtok(NULL, " ,;\t\n");
620 >    if(foo != NULL ){
621 >  
622 >      for(int i = 0 ; i < 9; i++){
623 >        
624 >        if(foo == NULL){
625 >          sprintf( painCave.errMsg,
626 >                   "error in reading eta[%d] from %s\n", i, c_in_name );
627 >          return strdup( painCave.errMsg );
628 >        }
629 >        eta[i] = atof( foo );
630 >        foo = strtok(NULL, " ,;\t\n");
631 >      }
632 >    }
633 >    else
634 >      return NULL;
635 >    
636 >    //push eta into SimInfo::properties which can be
637 >    //retrieved by integrator later
638 >    
639 >    DoubleArrayData* etaValue = new DoubleArrayData();
640 >    etaValue->setID(ETAVALUE_ID);
641 >    etaValue->setData(eta, 9);
642 >    entry_plug->addProperty(etaValue);
643    }
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 );    
644  
645    return NULL;
646   }
647  
650 –
648   #ifdef IS_MPI
649  
650   // a couple of functions to let us escape the read loop
651  
652   void initFile::nodeZeroError( void ){
653    int j, myStatus;
654 <  
654 >
655    myStatus = 0;
656 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
657 <    MPI_Send( &myStatus, 1, MPI_INT, j,
656 >  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
657 >    MPI_Send( &myStatus, 1, MPI_INT, j,
658                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
659 <  }  
663 <  
659 >  }
660  
661 +
662    MPI_Finalize();
663    exit (0);
664 <  
664 >
665   }
666  
667   void initFile::anonymousNodeDie( void ){

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