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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 2004 UTC

# Line 1 | Line 1
1 + #define _FILE_OFFSET_BITS 64
2   #include <iostream>
3 < #include <cmath>
3 > #include <math.h>
4  
5   #include <stdio.h>
6   #include <stdlib.h>
# Line 10 | Line 11
11  
12   #include "ReadWrite.hpp"
13   #include "simError.h"
14 + #include "GenericData.hpp"
15  
16   #ifdef IS_MPI
17 + #include <mpi.h>
18   #include "mpiSimulation.hpp"
19 + #define TAKE_THIS_TAG_CHAR 0
20 + #define TAKE_THIS_TAG_INT 1
21  
22 < #define TAKE_THIS_TAG 0
22 > namespace initFile{
23 >  void nodeZeroError( void );
24 >  void anonymousNodeDie( void );
25 > }
26 >
27 > 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 29 | 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 60 | Line 76 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
76   }
77  
78  
79 < void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
79 > void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
80  
81 <  int i; // loop counter
81 >  int i, j;
82  
67 –  const int BUFFERSIZE = 2000; // size of the read buffer
68 –  int n_atoms; // the number of atoms
69 –  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;
76 –  int procIndex;
93  
94 <  entry_plug = the_entry_plug;
94 >  vector<StuntDouble*> integrableObjects;
95 >  vector<StuntDouble*>::iterator iter;
96  
97 +  simnfo = the_simnfo;
98  
99 +
100   #ifndef IS_MPI
101    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
102    if( eof_test == NULL ){
# Line 88 | Line 107 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
107      simError();
108    }
109  
110 <  n_atoms = atoi( read_buffer );
110 >  nTotObjs = atoi( read_buffer );
111  
112 <  Atom **atoms = entry_plug->atoms;
94 <  DirectionalAtom* dAtom;
95 <
96 <  if( n_atoms != entry_plug->n_atoms ){
112 >  if( nTotObjs != simnfo->getTotIntegrableObjects() ){
113      sprintf( painCave.errMsg,
114               "Initialize from File error. %s n_atoms, %d, "
115               "does not match the BASS file's n_atoms, %d.\n",
116 <             c_in_name, n_atoms, entry_plug->n_atoms );
116 >             c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
117      painCave.isFatal = 1;
118      simError();
119    }
120 <  
121 <  //read and toss the comment line
122 <  
120 >
121 >  //read the box mat from the comment line
122 >
123    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
124    if(eof_test == NULL){
125      sprintf( painCave.errMsg,
# Line 112 | Line 128 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
128      simError();
129    }
130  
131 <  for( i=0; i < n_atoms; i++){
132 <    
133 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
134 <    if(eof_test == NULL){
135 <      sprintf(painCave.errMsg,
136 <              "error in reading file %s\n"
121 <              "natoms  = %d; index = %d\n"
122 <              "error reading the line from the file.\n",
123 <              c_in_name, n_atoms, i );
124 <      painCave.isFatal = 1;
125 <      simError();
126 <    }
131 >  parseErr = parseCommentLine( read_buffer, simnfo);
132 >  if( parseErr != NULL ){
133 >    strcpy( painCave.errMsg, parseErr );
134 >    painCave.isFatal = 1;
135 >    simError();
136 >  }
137  
138 <    
139 <    parseErr = parseDumpLine( read_buffer, i );
140 <    if( parseErr != NULL ){
141 <      strcpy( painCave.errMsg, parseErr );
142 <      painCave.isFatal = 1;
143 <      simError();
144 <    }    
138 >  //parse dump lines
139 >
140 >  for( i=0; i < simnfo->n_mol; i++){
141 >
142 >    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
143 >
144 >    for(iter = integrableObjects.begin(); iter!= integrableObjects.end(); iter++)
145 >
146 >      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
147 >      if(eof_test == NULL){
148 >        sprintf(painCave.errMsg,
149 >              "error in reading file %s\n"
150 >              "natoms  = %d; index = %d\n"
151 >              "error reading the line from the file.\n",
152 >              c_in_name, nTotObjs, i );
153 >        painCave.isFatal = 1;
154 >        simError();
155 >      }
156 >      
157 >      parseErr = parseDumpLine( read_buffer, *iter);
158 >      if( parseErr != NULL ){
159 >        strcpy( painCave.errMsg, parseErr );
160 >        painCave.isFatal = 1;
161 >        simError();
162 >      }
163    }
164  
165  
166    // MPI Section of code..........
167   #else //IS_MPI
168  
169 <  int masterIndex;
170 <  int nodeAtomsStart;
143 <  int nodeAtomsEnd;
144 <  int mpiErr;
145 <  int sendError;
169 >  // first thing first, suspend fatalities.
170 >  painCave.isEventLoop = 1;
171  
172 <  MPI_Status istatus[MPI_STATUS_SIZE];
172 >  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
173 >  int haveError;
174  
175 +  MPI_Status istatus;
176 +  int *MolToProcMap = mpiSim->getMolToProcMap();
177 +  int localIndex;
178 +  int nCurObj;
179 +
180 +  haveError = 0;
181    if (worldRank == 0) {
182 +
183      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
184      if( eof_test == NULL ){
185        sprintf( painCave.errMsg,
186 <               "Error reading 1st line of %d \n ",c_in_name);
187 <      painCave.isFatal = 1;
186 >               "Error reading 1st line of %s \n ",c_in_name);
187 >      haveError = 1;
188        simError();
189      }
190 <    
191 <    n_atoms = atoi( read_buffer );
192 <    
193 <    Atom **atoms = entry_plug->atoms;
161 <    DirectionalAtom* dAtom;
162 <
163 <    // Check to see that the number of atoms in the intial configuration file is the
190 >
191 >    nTotObjs = atoi( read_buffer );
192 >
193 >    // Check to see that the number of integrable objects  in the intial configuration file is the
194      // same as declared in simBass.
195 <    
196 <    if( n_atoms != mpiSim->getTotAtoms() ){
195 >
196 >    if( nTotObjs != simnfo->getTotIntegrableObjects()){
197        sprintf( painCave.errMsg,
198                 "Initialize from File error. %s n_atoms, %d, "
199                 "does not match the BASS file's n_atoms, %d.\n",
200 <               c_in_name, n_atoms, entry_plug->n_atoms );
201 <      painCave.isFatal = 1;
200 >               c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
201 >      haveError= 1;
202        simError();
203      }
204 <    
205 <    //read and toss the comment line
206 <    
204 >
205 >    //read the boxMat from the comment line
206 >
207      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
208      if(eof_test == NULL){
209        sprintf( painCave.errMsg,
210                 "error in reading commment in %s\n", c_in_name);
211 <      painCave.isFatal = 1;
211 >      haveError = 1;
212        simError();
213      }
214 <  
215 <    // Read Proc 0 share of the xyz file...
216 <    masterIndex = 0;
217 <    for( i=0; i <= mpiSim->getMyAtomEnd(); i++){
218 <    
219 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
220 <      if(eof_test == NULL){
221 <        sprintf(painCave.errMsg,
222 <                "error in reading file %s\n"
223 <                "natoms  = %d; index = %d\n"
224 <                "error reading the line from the file.\n",
225 <                c_in_name, n_atoms, i );
226 <        painCave.isFatal = 1;
227 <        simError();
198 <      }
199 <    
200 <      parseErr = parseDumpLine( read_buffer, i );
201 <      if( parseErr != NULL ){
202 <        strcpy( painCave.errMsg, parseErr );
203 <        painCave.isFatal = 1;
204 <        simError();
205 <      }    
206 <      masterIndex++;
214 >
215 >    //Every single processor will parse the comment line by itself
216 >    //By using this way, we might lose some efficiency, but if we want to add
217 >    //more parameters into comment line, we only need to modify function
218 >    //parseCommentLine
219 >
220 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
221 >
222 >    parseErr = parseCommentLine( read_buffer, simnfo);
223 >
224 >    if( parseErr != NULL ){
225 >      strcpy( painCave.errMsg, parseErr );
226 >      haveError = 1;
227 >      simError();
228      }
208 –  }
229  
230 <  sprintf(checkPointMsg,
231 <          "Node 0 has successfully read positions from input file.");
232 <  MPIcheckPoint();
230 >    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
231 >      which_node = MolToProcMap[i];
232 >      if(which_node == 0){
233 >       //molecules belong to master node
234  
235 <  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
215 <         procIndex++){
216 <    if (worldRank == 0) {
235 >      localIndex = mpiSim->getGlobalToLocalMol(i);
236  
237 <      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
238 <               istatus);
237 >      if(localIndex == -1) {
238 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
239 >        haveError = 1;
240 >        simError();
241 >      }
242  
243 <      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
244 <               istatus);
245 <      // Make sure where node 0 is reading from, matches where the receiving node
246 <      // expects it to be.
243 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
244 >       for(j=0; j < integrableObjects.size(); j++){
245 >        
246 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
247 >          if(eof_test == NULL){
248 >                sprintf(painCave.errMsg,
249 >                    "error in reading file %s\n"
250 >                    "natoms  = %d; index = %d\n"
251 >                    "error reading the line from the file.\n",
252 >                    c_in_name, nTotObjs, i );
253 >                haveError= 1;
254 >                simError();
255 >          }
256 >          
257 >          if(haveError) nodeZeroError();
258  
259 <      if (masterIndex != nodeAtomsStart){
260 <        sendError = 1;
261 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
262 <        sprintf(painCave.errMsg,
263 <                "Initialize from file error: atoms start index (%d) for "
231 <                "node %d not equal to master index (%d)",nodeAtomsStart,procIndex,masterIndex );
232 <        painCave.isFatal = 1;
233 <        simError();
259 >          parseDumpLine(read_buffer, integrableObjects[i]);
260 >          
261 >       }
262 >
263 >
264        }
265 <      sendError = 0;
266 <      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
265 >      else{
266 >      //molecule belongs to slave nodes
267 >
268 >        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
269 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
270        
271 <      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
272 <        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
273 <        if(eof_test == NULL){
274 <          
275 <          sprintf(read_buffer,"ERROR");
276 <          mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
277 <          
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, n_atoms, i );
283 <          painCave.isFatal = 1;
284 <          simError();
252 <        }
253 <        
254 <        mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
255 <        mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
256 <                          istatus);
257 <        if (sendError) MPIcheckPoint();
271 >       for(j=0; j < integrableObjects.size(); j++){
272 >        
273 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
274 >          if(eof_test == NULL){
275 >                sprintf(painCave.errMsg,
276 >                    "error in reading file %s\n"
277 >                    "natoms  = %d; index = %d\n"
278 >                    "error reading the line from the file.\n",
279 >                    c_in_name, nTotObjs, i );
280 >                haveError= 1;
281 >                simError();
282 >          }
283 >          
284 >          if(haveError) nodeZeroError();
285  
286 <        masterIndex++;
286 >            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
287 >                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
288 >          
289 >       }
290 >
291        }
292 +      
293      }
294 +    
295 +  }
296 +  else{
297 +  //actions taken at slave nodes
298 +    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
299 +      which_node = MolToProcMap[i];
300 +      
301 +      if(which_node == worldRank){
302 +      //molecule with global index i belongs to this processor
303 +      
304 +        localIndex = mpiSim->getGlobalToLocalMol(i);
305  
306 +        if(localIndex == -1) {
307 +          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
308 +          haveError = 1;
309 +          simError();
310 +        }
311  
312 <    else if(worldRank == procIndex){
265 <      nodeAtomsStart = mpiSim->getMyAtomStart();
266 <      nodeAtomsEnd = mpiSim->getMyAtomEnd();
267 <      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
268 <      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
269 <      
270 <      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
271 <               istatus);
272 <      if (sendError) MPIcheckPoint();
312 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
313  
314 <      for ( i = 0; i < entry_plug->n_atoms; i++){
314 >        nCurObj = integrableObjects.size();
315 >        
316 >        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
317 >                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
318  
319 <        mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
277 <                          istatus);
278 <        
279 <        if(!strcmp(read_buffer, "ERROR")) MPIcheckPoint();
280 <        
281 <        parseErr = parseDumpLine( read_buffer, i );
282 <        if( parseErr != NULL ){
283 <          sendError = 1;
284 <          mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
319 >        for(j = 0; j < integrableObjects.size(); j++){
320  
321 +          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
322 +                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
323  
324 <          strcpy( painCave.errMsg, parseErr );
325 <          painCave.isFatal = 1;
326 <          simError();
327 <        }
328 <        sendError = 0;
329 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
324 >          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
325 >
326 >          if( parseErr != NULL ){
327 >                strcpy( painCave.errMsg, parseErr );
328 >                simError();
329 >          }
330 >
331 >        }
332 >          
333        }
334 +      
335      }
295 –    sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
296 –    MPIcheckPoint();
297 –  }
336  
337 +  }
338   #endif
339   }
340  
341 + char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
342  
343 < char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
343 >  char *foo; // the pointer to the current string token
344  
345 <  char *foo; // the pointer to the current string token
346 <  
307 <  double rx, ry, rz; // position place holders
308 <  double vx, vy, vz; // velocity placeholders
345 >  double pos[3]; // position place holders
346 >  double vel[3]; // velocity placeholders
347    double q[4]; // the quaternions
348 <  double jx, jy, jz; // angular velocity placeholders;
348 >  double ji[3]; // angular velocity placeholders;
349    double qSqr, qLength; // needed to normalize the quaternion vector.
312 –  
313 –  Atom **atoms = entry_plug->atoms;
314 –  DirectionalAtom* dAtom;
315 –  
316 –  int n_atoms;
350  
318 – #ifdef IS_MPI
319 –  n_atoms = mpiSim->getTotAtoms();
320 – #else
321 –  n_atoms = entry_plug->n_atoms;
322 – #endif // is_mpi
351  
324 –
352    // set the string tokenizer
353 <  
353 >
354    foo = strtok(readLine, " ,;\t");
355 <  
355 >
356    // check the atom name to the current atom
357 <  
358 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
357 >
358 >  if( strcmp( foo, sd->getType() ) ){
359      sprintf( painCave.errMsg,
360 <             "Initialize from file error. Atom %s at index %d "
334 <             "in file %s does not"
360 >             "Initialize from file error.  Does not"
361               " match the BASS atom %s.\n",
362 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
362 >             sd->getType() );
363      return strdup( painCave.errMsg );
364    }
365 <    
365 >
366    // get the positions
367  
368    foo = strtok(NULL, " ,;\t");
369    if(foo == NULL){
370      sprintf( painCave.errMsg,
371 <             "error in reading postition x from %s\n"
372 <             "natoms  = %d, index = %d\n",
347 <             c_in_name, n_atoms, atomIndex );
371 >             "error in reading postition x from %s\n",
372 >             c_in_name);
373      return strdup( painCave.errMsg );
374    }
375 <  rx = atof( foo );
376 <  
375 >  pos[0] = atof( foo );
376 >
377    foo = strtok(NULL, " ,;\t");
378    if(foo == NULL){
379      sprintf( painCave.errMsg,
380 <             "error in reading postition y from %s\n"
381 <             "natoms  = %d, index = %d\n",
357 <             c_in_name, n_atoms, atomIndex );
380 >             "error in reading postition y from %s\n",
381 >             c_in_name);
382      return strdup( painCave.errMsg );
383    }
384 <  ry = atof( foo );
385 <    
384 >  pos[1] = atof( foo );
385 >
386    foo = strtok(NULL, " ,;\t");
387    if(foo == NULL){
388      sprintf( painCave.errMsg,
389 <             "error in reading postition z from %s\n"
390 <             "natoms  = %d, index = %d\n",
367 <             c_in_name, n_atoms, atomIndex );
389 >             "error in reading postition z from %s\n",
390 >             c_in_name);
391      return strdup( painCave.errMsg );
392    }
393 <  rz = atof( foo );    
393 >  pos[2] = atof( foo );
394  
395  
396    // get the velocities
# Line 375 | Line 398 | char* InitializeFromFile::parseDumpLine(char* readLine
398    foo = strtok(NULL, " ,;\t");
399    if(foo == NULL){
400      sprintf( painCave.errMsg,
401 <             "error in reading velocity x from %s\n"
402 <             "natoms  = %d, index = %d\n",
380 <             c_in_name, n_atoms, atomIndex );
401 >             "error in reading velocity x from %s\n",
402 >             c_in_name );
403      return strdup( painCave.errMsg );
404    }
405 <  vx = atof( foo );
406 <    
405 >  vel[0] = atof( foo );
406 >
407    foo = strtok(NULL, " ,;\t");
408    if(foo == NULL){
409      sprintf( painCave.errMsg,
410 <             "error in reading velocity y from %s\n"
411 <             "natoms  = %d, index = %d\n",
390 <             c_in_name, n_atoms, atomIndex );
410 >             "error in reading velocity x from %s\n",
411 >             c_in_name );
412      return strdup( painCave.errMsg );
413    }
414 <  vy = atof( foo );
415 <    
414 >  vel[1] = atof( foo );
415 >
416    foo = strtok(NULL, " ,;\t");
417    if(foo == NULL){
418      sprintf( painCave.errMsg,
419 <             "error in reading velocity z from %s\n"
420 <             "natoms  = %d, index = %d\n",
400 <             c_in_name, n_atoms, atomIndex );
419 >             "error in reading velocity x from %s\n",
420 >             c_in_name );
421      return strdup( painCave.errMsg );
422    }
423 <  vz = atof( foo );
424 <    
425 <    
423 >  vel[2] = atof( foo );
424 >
425 >
426 >  // add the positions and velocities to the atom
427 >
428 >  sd->setPos( pos );
429 >  sd->setVel( vel );
430 >
431 >  if (!sd->isDirectional())
432 >    return NULL;
433 >
434    // get the quaternions
435 <    
436 <  if( atoms[atomIndex]->isDirectional() ){
437 <      
435 >
436 >  if( sd->isDirectional() ){
437 >
438      foo = strtok(NULL, " ,;\t");
439      if(foo == NULL){
440 <      sprintf(painCave.errMsg,
441 <              "error in reading quaternion 0 from %s\n"
442 <              "natoms  = %d, index = %d\n",
415 <              c_in_name, n_atoms, atomIndex );
440 >      sprintf( painCave.errMsg,
441 >                     "error in reading velocity x from %s\n",
442 >                      c_in_name );
443        return strdup( painCave.errMsg );
444      }
445      q[0] = atof( foo );
446 <      
446 >
447      foo = strtok(NULL, " ,;\t");
448      if(foo == NULL){
449        sprintf( painCave.errMsg,
450 <               "error in reading quaternion 1 from %s\n"
451 <               "natoms  = %d, index = %d\n",
425 <               c_in_name, n_atoms, atomIndex );
450 >                     "error in reading velocity x from %s\n",
451 >                      c_in_name );
452        return strdup( painCave.errMsg );
453      }
454      q[1] = atof( foo );
455 <      
455 >
456      foo = strtok(NULL, " ,;\t");
457      if(foo == NULL){
458        sprintf( painCave.errMsg,
459 <               "error in reading quaternion 2 from %s\n"
460 <               "natoms  = %d, index = %d\n",
435 <               c_in_name, n_atoms, atomIndex );
459 >                     "error in reading velocity x from %s\n",
460 >                      c_in_name );
461        return strdup( painCave.errMsg );
462      }
463      q[2] = atof( foo );
464 <      
464 >
465      foo = strtok(NULL, " ,;\t");
466      if(foo == NULL){
467        sprintf( painCave.errMsg,
468 <               "error in reading quaternion 3 from %s\n"
469 <               "natoms  = %d, index = %d\n",
445 <               c_in_name, n_atoms, atomIndex );
468 >                     "error in reading velocity x from %s\n",
469 >                      c_in_name );
470        return strdup( painCave.errMsg );
471      }
472      q[3] = atof( foo );
473 <      
473 >
474      // get the angular velocities
475 <      
475 >
476      foo = strtok(NULL, " ,;\t");
477      if(foo == NULL){
478        sprintf( painCave.errMsg,
479 <               "error in reading angular momentum jx from %s\n"
480 <               "natoms  = %d, index = %d\n",
457 <               c_in_name, n_atoms, atomIndex );
479 >                     "error in reading velocity x from %s\n",
480 >                      c_in_name );
481        return strdup( painCave.errMsg );
482      }
483 <    jx = atof( foo );
484 <      
483 >    ji[0] = atof( foo );
484 >
485      foo = strtok(NULL, " ,;\t");
486      if(foo == NULL){
487        sprintf( painCave.errMsg,
488 <               "error in reading angular momentum jy from %s\n"
489 <               "natoms  = %d, index = %d\n",
467 <               c_in_name, n_atoms, atomIndex );
488 >                     "error in reading velocity x from %s\n",
489 >                      c_in_name );
490        return strdup( painCave.errMsg );
491      }
492 <    jy = atof(foo );
493 <      
492 >    ji[1] = atof(foo );
493 >
494      foo = strtok(NULL, " ,;\t");
495      if(foo == NULL){
496        sprintf( painCave.errMsg,
497 <               "error in reading angular momentum jz from %s\n"
498 <               "natoms  = %d, index = %d\n",
477 <               c_in_name, n_atoms, atomIndex );
497 >                     "error in reading velocity x from %s\n",
498 >                      c_in_name );
499        return strdup( painCave.errMsg );
500      }
501 <    jz = atof( foo );
481 <      
482 <    dAtom = ( DirectionalAtom* )atoms[atomIndex];
501 >    ji[2] = atof( foo );
502  
503 +
504      // check that the quaternion vector is normalized
505  
506      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
507 <      
507 >
508      qLength = sqrt( qSqr );
509      q[0] = q[0] / qLength;
510      q[1] = q[1] / qLength;
511      q[2] = q[2] / qLength;
512      q[3] = q[3] / qLength;
493 –      
494 –    dAtom->setQ( q );
495 –      
496 –    // add the angular velocities
513  
514 <    dAtom->setJx( jx );
515 <    dAtom->setJy( jy );
516 <    dAtom->setJz( jz );
514 >    // add quaternion and angular velocities
515 >
516 >    sd->setQ( q );
517 >    sd->setJ( ji );
518    }
519 +
520 +
521 +
522 +  return NULL;
523 + }
524 +
525 +
526 + char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
527 +
528 +  double currTime;
529 +  double boxMat[9];
530 +  double theBoxMat3[3][3];
531 +  double chi;
532 +  double integralOfChidt;
533 +  double eta[9];
534 +
535 +  char *foo; // the pointer to the current string token
536 +
537 +  // set the string tokenizer
538 +
539 +  foo = strtok(readLine, " ,;\t");
540 +  // set the timeToken.
541 +
542 +  if(foo == NULL){
543 +    sprintf( painCave.errMsg,
544 +             "error in reading Time from %s\n",
545 +             c_in_name );
546 +    return strdup( painCave.errMsg );
547 +  }
548 +
549 +  currTime = atof( foo );
550 +  entry_plug->setTime( currTime );
551 +
552 +  //get H-Matrix
553 +
554 +  for(int i = 0 ; i < 9; i++){
555 +    foo = strtok(NULL, " ,;\t");
556 +    if(foo == NULL){
557 +      sprintf( painCave.errMsg,
558 +               "error in reading H[%d] from %s\n", i, c_in_name );
559 +      return strdup( painCave.errMsg );
560 +    }
561 +    boxMat[i] = atof( foo );
562 +  }
563 +
564 +  for(int i=0;i<3;i++)
565 +    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
566 +
567 +  //set H-Matrix
568 +  entry_plug->setBoxM( theBoxMat3 );
569 +
570 +  //get chi and integralOfChidt, they should appear by pair
571 +
572 +  if( entry_plug->useInitXSstate ){
573 +    foo = strtok(NULL, " ,;\t\n");
574 +    if(foo != NULL){
575 +      chi = atof(foo);
576 +      
577 +      foo = strtok(NULL, " ,;\t\n");
578 +      if(foo == NULL){
579 +        sprintf( painCave.errMsg,
580 +                 "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
581 +        return strdup( painCave.errMsg );
582 +      }
583 +      integralOfChidt = atof( foo );
584 +      
585 +      //push chi and integralOfChidt into SimInfo::properties which can be
586 +      //retrieved by integrator later
587 +      DoubleData* chiValue = new DoubleData();
588 +      chiValue->setID(CHIVALUE_ID);
589 +      chiValue->setData(chi);
590 +      entry_plug->addProperty(chiValue);
591 +      
592 +      DoubleData* integralOfChidtValue = new DoubleData();
593 +      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
594 +      integralOfChidtValue->setData(integralOfChidt);
595 +      entry_plug->addProperty(integralOfChidtValue);
596 +      
597 +    }
598 +    else
599 +      return NULL;
600      
601 <  // add the positions and velocities to the atom
601 >    //get eta
602 >    foo = strtok(NULL, " ,;\t\n");
603 >    if(foo != NULL ){
604 >  
605 >      for(int i = 0 ; i < 9; i++){
606 >        
607 >        if(foo == NULL){
608 >          sprintf( painCave.errMsg,
609 >                   "error in reading eta[%d] from %s\n", i, c_in_name );
610 >          return strdup( painCave.errMsg );
611 >        }
612 >        eta[i] = atof( foo );
613 >        foo = strtok(NULL, " ,;\t\n");
614 >      }
615 >    }
616 >    else
617 >      return NULL;
618      
619 <  atoms[atomIndex]->setX( rx );
620 <  atoms[atomIndex]->setY( ry );
621 <  atoms[atomIndex]->setZ( rz );
622 <    
623 <  atoms[atomIndex]->set_vx( vx );
624 <  atoms[atomIndex]->set_vy( vy );
625 <  atoms[atomIndex]->set_vz( vz );
619 >    //push eta into SimInfo::properties which can be
620 >    //retrieved by integrator later
621 >    //entry_plug->setBoxM( theBoxMat3 );
622 >    DoubleArrayData* etaValue = new DoubleArrayData();
623 >    etaValue->setID(ETAVALUE_ID);
624 >    etaValue->setData(eta, 9);
625 >    entry_plug->addProperty(etaValue);
626 >  }
627  
628    return NULL;
629   }
630 +
631 + #ifdef IS_MPI
632 +
633 + // a couple of functions to let us escape the read loop
634 +
635 + void initFile::nodeZeroError( void ){
636 +  int j, myStatus;
637 +
638 +  myStatus = 0;
639 +  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
640 +    MPI_Send( &myStatus, 1, MPI_INT, j,
641 +              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
642 +  }
643 +
644 +
645 +  MPI_Finalize();
646 +  exit (0);
647 +
648 + }
649 +
650 + void initFile::anonymousNodeDie( void ){
651 +
652 +  MPI_Finalize();
653 +  exit (0);
654 + }
655 +
656 + #endif //is_mpi

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