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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 1268 by tim, Fri Jun 11 17:16:21 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 3134
20 + #define TAKE_THIS_TAG_INT 3135
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 | InitializeFromFile :: ~InitializeFromFile( ){
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  
96 +  simnfo = the_simnfo;
97  
98 +
99   #ifndef IS_MPI
100    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
101    if( eof_test == NULL ){
# Line 88 | Line 106 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
106      simError();
107    }
108  
109 <  n_atoms = atoi( read_buffer );
109 >  nTotObjs = atoi( read_buffer );
110  
111 <  Atom **atoms = entry_plug->atoms;
94 <  DirectionalAtom* dAtom;
95 <
96 <  if( n_atoms != entry_plug->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, entry_plug->n_atoms );
115 >             c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
116      painCave.isFatal = 1;
117      simError();
118    }
119 <  
120 <  //read and toss 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 112 | Line 127 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
127      simError();
128    }
129  
130 <  for( i=0; i < n_atoms; i++){
131 <    
132 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
133 <    if(eof_test == NULL){
134 <      sprintf(painCave.errMsg,
120 <              "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 <    }
127 <
128 <    
129 <    parseErr = parseDumpLine( read_buffer, i );
130 <    if( parseErr != NULL ){
131 <      strcpy( painCave.errMsg, parseErr );
132 <      painCave.isFatal = 1;
133 <      simError();
134 <    }    
130 >  parseErr = parseCommentLine( read_buffer, simnfo);
131 >  if( parseErr != NULL ){
132 >    strcpy( painCave.errMsg, parseErr );
133 >    painCave.isFatal = 1;
134 >    simError();
135    }
136  
137 +  //parse dump lines
138  
139 +  for( i=0; i < simnfo->n_mol; i++){
140 +
141 +    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
142 +
143 +    for(j = 0; j < integrableObjects.size(); j++){
144 +
145 +      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
146 +      if(eof_test == NULL){
147 +        sprintf(painCave.errMsg,
148 +              "error in reading file %s\n"
149 +              "natoms  = %d; index = %d\n"
150 +              "error reading the line from the file.\n",
151 +              c_in_name, nTotObjs, i );
152 +        painCave.isFatal = 1;
153 +        simError();
154 +      }
155 +      
156 +      parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
157 +      if( parseErr != NULL ){
158 +        strcpy( painCave.errMsg, parseErr );
159 +        painCave.isFatal = 1;
160 +        simError();
161 +      }
162 +    }
163 +  }
164 +
165    // MPI Section of code..........
166   #else //IS_MPI
167  
168 <  int masterIndex;
169 <  int nodeAtomsStart;
143 <  int nodeAtomsEnd;
144 <  int mpiErr;
145 <  int sendError;
168 >  // first thing first, suspend fatalities.
169 >  painCave.isEventLoop = 1;
170  
171 <  MPI_Status istatus[MPI_STATUS_SIZE];
171 >  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
172 >  int haveError;
173  
174 +  MPI_Status istatus;
175 +  int *MolToProcMap = mpiSim->getMolToProcMap();
176 +  int localIndex;
177 +  int nCurObj;
178 +  int nItems;
179 +
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);
188 <      painCave.isFatal = 1;
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 = entry_plug->atoms;
161 <    DirectionalAtom* dAtom;
162 <
163 <    // 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, entry_plug->n_atoms );
202 <      painCave.isFatal = 1;
201 >               c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
202 >      haveError= 1;
203        simError();
204      }
205 <    
206 <    //read and toss 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,
211                 "error in reading commment in %s\n", c_in_name);
212 <      painCave.isFatal = 1;
212 >      haveError = 1;
213        simError();
214      }
215 <  
216 <    // Read Proc 0 share of the xyz file...
217 <    masterIndex = 0;
218 <    for( i=0; i <= mpiSim->getMyAtomEnd(); i++){
219 <    
220 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
221 <      if(eof_test == NULL){
222 <        sprintf(painCave.errMsg,
223 <                "error in reading file %s\n"
224 <                "natoms  = %d; index = %d\n"
225 <                "error reading the line from the file.\n",
226 <                c_in_name, n_atoms, i );
227 <        painCave.isFatal = 1;
228 <        simError();
229 <      }
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++;
215 >
216 >    //Every single processor will parse the comment line by itself
217 >    //By using this way, we might lose some efficiency, but if we want to add
218 >    //more parameters into comment line, we only need to modify function
219 >    //parseCommentLine
220 >
221 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
222 >
223 >
224 >    parseErr = parseCommentLine( read_buffer, simnfo);
225 >
226 >    if( parseErr != NULL ){
227 >      strcpy( painCave.errMsg, parseErr );
228 >      haveError = 1;
229 >      simError();
230      }
208 –  }
231  
232 <  sprintf(checkPointMsg,
233 <          "Node 0 has successfully read positions from input file.");
234 <  MPIcheckPoint();
232 >    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
233 >      which_node = MolToProcMap[i];
234 >      if(which_node == 0){
235 >       //molecules belong to master node
236  
237 <  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
215 <         procIndex++){
216 <    if (worldRank == 0) {
237 >      localIndex = mpiSim->getGlobalToLocalMol(i);
238  
239 <      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
240 <               istatus);
239 >      if(localIndex == -1) {
240 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
241 >        haveError = 1;
242 >        simError();
243 >      }
244  
245 <      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
246 <               istatus);
247 <      // Make sure where node 0 is reading from, matches where the receiving node
248 <      // expects it to be.
245 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
246 >       for(j=0; j < integrableObjects.size(); j++){
247 >        
248 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
249 >          if(eof_test == NULL){
250 >                sprintf(painCave.errMsg,
251 >                    "error in reading file %s\n"
252 >                    "natoms  = %d; index = %d\n"
253 >                    "error reading the line from the file.\n",
254 >                    c_in_name, nTotObjs, i );
255 >                haveError= 1;
256 >                simError();
257 >          }
258 >          
259 >          if(haveError) nodeZeroError();
260  
261 <      if (masterIndex != nodeAtomsStart){
262 <        sendError = 1;
263 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
264 <        sprintf(painCave.errMsg,
265 <                "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();
261 >          parseDumpLine(read_buffer, integrableObjects[j]);
262 >          
263 >       }
264 >
265 >
266        }
267 <      sendError = 0;
268 <      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
237 <      
238 <      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
239 <        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
240 <        if(eof_test == NULL){
241 <          
242 <          sprintf(read_buffer,"ERROR");
243 <          mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
244 <          
245 <          sprintf(painCave.errMsg,
246 <                  "error in reading file %s\n"
247 <                  "natoms  = %d; index = %d\n"
248 <                  "error reading the line from the file.\n",
249 <                  c_in_name, n_atoms, i );
250 <          painCave.isFatal = 1;
251 <          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();
267 >      else{
268 >      //molecule belongs to slave nodes
269  
270 <        masterIndex++;
270 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
271 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
272 >
273 >       for(j=0; j < nCurObj; j++){
274 >        
275 >          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
276 >          if(eof_test == NULL){
277 >                sprintf(painCave.errMsg,
278 >                    "error in reading file %s\n"
279 >                    "natoms  = %d; index = %d\n"
280 >                    "error reading the line from the file.\n",
281 >                    c_in_name, nTotObjs, i );
282 >                haveError= 1;
283 >                simError();
284 >          }
285 >          
286 >          if(haveError) nodeZeroError();
287 >
288 >            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
289 >                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
290 >
291 >       }
292 >
293        }
294 +      
295      }
296 +    
297 +  }
298 +  else{
299 +  //actions taken at slave nodes
300  
301 +    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
302  
303 <    else if(worldRank == procIndex){
304 <      nodeAtomsStart = mpiSim->getMyAtomStart();
305 <      nodeAtomsEnd = mpiSim->getMyAtomEnd();
306 <      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
307 <      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
303 >    parseErr = parseCommentLine( read_buffer, simnfo);
304 >
305 >    if( parseErr != NULL ){
306 >      strcpy( painCave.errMsg, parseErr );
307 >      haveError = 1;
308 >      simError();
309 >    }
310 >  
311 >    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
312 >      which_node = MolToProcMap[i];
313        
314 <      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
315 <               istatus);
316 <      if (sendError) MPIcheckPoint();
314 >      if(which_node == worldRank){
315 >      //molecule with global index i belongs to this processor
316 >      
317 >        localIndex = mpiSim->getGlobalToLocalMol(i);
318  
319 <      for ( i = 0; i < entry_plug->n_atoms; i++){
319 >        if(localIndex == -1) {
320 >          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
321 >          haveError = 1;
322 >          simError();
323 >        }
324  
325 <        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);
325 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
326  
327 +        nCurObj = integrableObjects.size();
328 +        
329 +        MPI_Send(&nCurObj, 1, MPI_INT, 0,
330 +                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
331  
332 <          strcpy( painCave.errMsg, parseErr );
333 <          painCave.isFatal = 1;
334 <          simError();
335 <        }
336 <        sendError = 0;
337 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
332 >        for(j = 0; j < integrableObjects.size(); j++){
333 >
334 >          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
335 >                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
336 >
337 >          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
338 >
339 >          if( parseErr != NULL ){
340 >                strcpy( painCave.errMsg, parseErr );
341 >                simError();
342 >          }
343 >
344 >        }
345 >          
346        }
347 +      
348      }
295 –    sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
296 –    MPIcheckPoint();
297 –  }
349  
350 +  }
351   #endif
352   }
353  
354 + char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
355  
356 < char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
356 >  char *foo; // the pointer to the current string token
357  
358 <  char *foo; // the pointer to the current string token
359 <  
307 <  double rx, ry, rz; // position place holders
308 <  double vx, vy, vz; // velocity placeholders
358 >  double pos[3]; // position place holders
359 >  double vel[3]; // velocity placeholders
360    double q[4]; // the quaternions
361 <  double jx, jy, jz; // angular velocity placeholders;
361 >  double ji[3]; // angular velocity placeholders;
362    double qSqr, qLength; // needed to normalize the quaternion vector.
312 –  
313 –  Atom **atoms = entry_plug->atoms;
314 –  DirectionalAtom* dAtom;
315 –  
316 –  int n_atoms;
363  
318 – #ifdef IS_MPI
319 –  n_atoms = mpiSim->getTotAtoms();
320 – #else
321 –  n_atoms = entry_plug->n_atoms;
322 – #endif // is_mpi
364  
324 –
365    // set the string tokenizer
366 <  
366 >
367    foo = strtok(readLine, " ,;\t");
368 <  
368 >
369    // check the atom name to the current atom
370 <  
371 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
370 >
371 >  if( strcmp( foo, sd->getType() ) ){
372      sprintf( painCave.errMsg,
373 <             "Initialize from file error. Atom %s at index %d "
334 <             "in file %s does not"
373 >             "Initialize from file error.  Does not"
374               " match the BASS atom %s.\n",
375 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
375 >             sd->getType() );
376      return strdup( painCave.errMsg );
377    }
378 <    
378 >
379    // get the positions
380  
381    foo = strtok(NULL, " ,;\t");
382    if(foo == NULL){
383      sprintf( painCave.errMsg,
384 <             "error in reading postition x from %s\n"
385 <             "natoms  = %d, index = %d\n",
347 <             c_in_name, n_atoms, atomIndex );
384 >             "error in reading postition x from %s\n",
385 >             c_in_name);
386      return strdup( painCave.errMsg );
387    }
388 <  rx = atof( foo );
389 <  
388 >  pos[0] = atof( foo );
389 >
390    foo = strtok(NULL, " ,;\t");
391    if(foo == NULL){
392      sprintf( painCave.errMsg,
393 <             "error in reading postition y from %s\n"
394 <             "natoms  = %d, index = %d\n",
357 <             c_in_name, n_atoms, atomIndex );
393 >             "error in reading postition y from %s\n",
394 >             c_in_name);
395      return strdup( painCave.errMsg );
396    }
397 <  ry = atof( foo );
398 <    
397 >  pos[1] = atof( foo );
398 >
399    foo = strtok(NULL, " ,;\t");
400    if(foo == NULL){
401      sprintf( painCave.errMsg,
402 <             "error in reading postition z from %s\n"
403 <             "natoms  = %d, index = %d\n",
367 <             c_in_name, n_atoms, atomIndex );
402 >             "error in reading postition z from %s\n",
403 >             c_in_name);
404      return strdup( painCave.errMsg );
405    }
406 <  rz = atof( foo );    
406 >  pos[2] = atof( foo );
407  
408  
409    // get the velocities
# Line 375 | Line 411 | char* InitializeFromFile::parseDumpLine(char* readLine
411    foo = strtok(NULL, " ,;\t");
412    if(foo == NULL){
413      sprintf( painCave.errMsg,
414 <             "error in reading velocity x from %s\n"
415 <             "natoms  = %d, index = %d\n",
380 <             c_in_name, n_atoms, atomIndex );
414 >             "error in reading velocity x from %s\n",
415 >             c_in_name );
416      return strdup( painCave.errMsg );
417    }
418 <  vx = atof( foo );
419 <    
418 >  vel[0] = atof( foo );
419 >
420    foo = strtok(NULL, " ,;\t");
421    if(foo == NULL){
422      sprintf( painCave.errMsg,
423 <             "error in reading velocity y from %s\n"
424 <             "natoms  = %d, index = %d\n",
390 <             c_in_name, n_atoms, atomIndex );
423 >             "error in reading velocity x from %s\n",
424 >             c_in_name );
425      return strdup( painCave.errMsg );
426    }
427 <  vy = atof( foo );
428 <    
427 >  vel[1] = atof( foo );
428 >
429    foo = strtok(NULL, " ,;\t");
430    if(foo == NULL){
431      sprintf( painCave.errMsg,
432 <             "error in reading velocity z from %s\n"
433 <             "natoms  = %d, index = %d\n",
400 <             c_in_name, n_atoms, atomIndex );
432 >             "error in reading velocity x from %s\n",
433 >             c_in_name );
434      return strdup( painCave.errMsg );
435    }
436 <  vz = atof( foo );
437 <    
438 <    
436 >  vel[2] = atof( foo );
437 >
438 >
439 >  // add the positions and velocities to the atom
440 >
441 >  sd->setPos( pos );
442 >  sd->setVel( vel );
443 >
444 >  if (!sd->isDirectional())
445 >    return NULL;
446 >
447    // get the quaternions
448 <    
449 <  if( atoms[atomIndex]->isDirectional() ){
450 <      
448 >
449 >  if( sd->isDirectional() ){
450 >
451      foo = strtok(NULL, " ,;\t");
452      if(foo == NULL){
453 <      sprintf(painCave.errMsg,
454 <              "error in reading quaternion 0 from %s\n"
455 <              "natoms  = %d, index = %d\n",
415 <              c_in_name, n_atoms, atomIndex );
453 >      sprintf( painCave.errMsg,
454 >                     "error in reading velocity x from %s\n",
455 >                      c_in_name );
456        return strdup( painCave.errMsg );
457      }
458      q[0] = atof( foo );
459 <      
459 >
460      foo = strtok(NULL, " ,;\t");
461      if(foo == NULL){
462        sprintf( painCave.errMsg,
463 <               "error in reading quaternion 1 from %s\n"
464 <               "natoms  = %d, index = %d\n",
425 <               c_in_name, n_atoms, atomIndex );
463 >                     "error in reading velocity x from %s\n",
464 >                      c_in_name );
465        return strdup( painCave.errMsg );
466      }
467      q[1] = atof( foo );
468 <      
468 >
469      foo = strtok(NULL, " ,;\t");
470      if(foo == NULL){
471        sprintf( painCave.errMsg,
472 <               "error in reading quaternion 2 from %s\n"
473 <               "natoms  = %d, index = %d\n",
435 <               c_in_name, n_atoms, atomIndex );
472 >                     "error in reading velocity x from %s\n",
473 >                      c_in_name );
474        return strdup( painCave.errMsg );
475      }
476      q[2] = atof( foo );
477 <      
477 >
478      foo = strtok(NULL, " ,;\t");
479      if(foo == NULL){
480        sprintf( painCave.errMsg,
481 <               "error in reading quaternion 3 from %s\n"
482 <               "natoms  = %d, index = %d\n",
445 <               c_in_name, n_atoms, atomIndex );
481 >                     "error in reading velocity x from %s\n",
482 >                      c_in_name );
483        return strdup( painCave.errMsg );
484      }
485      q[3] = atof( foo );
486 <      
486 >
487      // get the angular velocities
488 <      
488 >
489      foo = strtok(NULL, " ,;\t");
490      if(foo == NULL){
491        sprintf( painCave.errMsg,
492 <               "error in reading angular momentum jx from %s\n"
493 <               "natoms  = %d, index = %d\n",
457 <               c_in_name, n_atoms, atomIndex );
492 >                     "error in reading velocity x from %s\n",
493 >                      c_in_name );
494        return strdup( painCave.errMsg );
495      }
496 <    jx = atof( foo );
497 <      
496 >    ji[0] = atof( foo );
497 >
498      foo = strtok(NULL, " ,;\t");
499      if(foo == NULL){
500        sprintf( painCave.errMsg,
501 <               "error in reading angular momentum jy from %s\n"
502 <               "natoms  = %d, index = %d\n",
467 <               c_in_name, n_atoms, atomIndex );
501 >                     "error in reading velocity x from %s\n",
502 >                      c_in_name );
503        return strdup( painCave.errMsg );
504      }
505 <    jy = atof(foo );
506 <      
505 >    ji[1] = atof(foo );
506 >
507      foo = strtok(NULL, " ,;\t");
508      if(foo == NULL){
509        sprintf( painCave.errMsg,
510 <               "error in reading angular momentum jz from %s\n"
511 <               "natoms  = %d, index = %d\n",
477 <               c_in_name, n_atoms, atomIndex );
510 >                     "error in reading velocity x from %s\n",
511 >                      c_in_name );
512        return strdup( painCave.errMsg );
513      }
514 <    jz = atof( foo );
481 <      
482 <    dAtom = ( DirectionalAtom* )atoms[atomIndex];
514 >    ji[2] = atof( foo );
515  
516 +
517      // check that the quaternion vector is normalized
518  
519      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
520 <      
520 >
521 >    if (fabs(qSqr) < 1e-6) {
522 >      sprintf(painCave.errMsg,
523 >          "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
524 >       return strdup(painCave.errMsg);
525 >    }
526 >    
527      qLength = sqrt( qSqr );
528      q[0] = q[0] / qLength;
529      q[1] = q[1] / qLength;
530      q[2] = q[2] / qLength;
531      q[3] = q[3] / qLength;
493 –      
494 –    dAtom->setQ( q );
495 –      
496 –    // add the angular velocities
532  
533 <    dAtom->setJx( jx );
534 <    dAtom->setJy( jy );
535 <    dAtom->setJz( jz );
533 >    // add quaternion and angular velocities
534 >
535 >    sd->setQ( q );
536 >    sd->setJ( ji );
537    }
538 +
539 +
540 +
541 +  return NULL;
542 + }
543 +
544 +
545 + char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
546 +
547 +  double currTime;
548 +  double boxMat[9];
549 +  double theBoxMat3[3][3];
550 +  double chi;
551 +  double integralOfChidt;
552 +  double eta[9];
553 +
554 +  char *foo; // the pointer to the current string token
555 +
556 +  // set the string tokenizer
557 +
558 +  foo = strtok(readLine, " ,;\t");
559 +  // set the timeToken.
560 +
561 +  if(foo == NULL){
562 +    sprintf( painCave.errMsg,
563 +             "error in reading Time from %s\n",
564 +             c_in_name );
565 +    return strdup( painCave.errMsg );
566 +  }
567 +
568 +  currTime = atof( foo );
569 +  entry_plug->setTime( currTime );
570 +
571 +  //get H-Matrix
572 +
573 +  for(int i = 0 ; i < 9; i++){
574 +    foo = strtok(NULL, " ,;\t");
575 +    if(foo == NULL){
576 +      sprintf( painCave.errMsg,
577 +               "error in reading H[%d] from %s\n", i, c_in_name );
578 +      return strdup( painCave.errMsg );
579 +    }
580 +    boxMat[i] = atof( foo );
581 +  }
582 +
583 +  for(int i=0;i<3;i++)
584 +    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
585 +
586 +  //set H-Matrix
587 +  entry_plug->setBoxM( theBoxMat3 );
588 +
589 +  //get chi and integralOfChidt, they should appear by pair
590 +
591 +  if( entry_plug->useInitXSstate ){
592 +    foo = strtok(NULL, " ,;\t\n");
593 +    if(foo != NULL){
594 +      chi = atof(foo);
595 +      
596 +      foo = strtok(NULL, " ,;\t\n");
597 +      if(foo == NULL){
598 +        sprintf( painCave.errMsg,
599 +                 "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
600 +        return strdup( painCave.errMsg );
601 +      }
602 +      integralOfChidt = atof( foo );
603 +      
604 +      //push chi and integralOfChidt into SimInfo::properties which can be
605 +      //retrieved by integrator later
606 +      DoubleData* chiValue = new DoubleData();
607 +      chiValue->setID(CHIVALUE_ID);
608 +      chiValue->setData(chi);
609 +      entry_plug->addProperty(chiValue);
610 +      
611 +      DoubleData* integralOfChidtValue = new DoubleData();
612 +      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
613 +      integralOfChidtValue->setData(integralOfChidt);
614 +      entry_plug->addProperty(integralOfChidtValue);
615 +      
616 +    }
617 +    else
618 +      return NULL;
619      
620 <  // add the positions and velocities to the atom
620 >    //get eta
621 >    foo = strtok(NULL, " ,;\t\n");
622 >    if(foo != NULL ){
623 >  
624 >      for(int i = 0 ; i < 9; i++){
625 >        
626 >        if(foo == NULL){
627 >          sprintf( painCave.errMsg,
628 >                   "error in reading eta[%d] from %s\n", i, c_in_name );
629 >          return strdup( painCave.errMsg );
630 >        }
631 >        eta[i] = atof( foo );
632 >        foo = strtok(NULL, " ,;\t\n");
633 >      }
634 >    }
635 >    else
636 >      return NULL;
637      
638 <  atoms[atomIndex]->setX( rx );
639 <  atoms[atomIndex]->setY( ry );
507 <  atoms[atomIndex]->setZ( rz );
638 >    //push eta into SimInfo::properties which can be
639 >    //retrieved by integrator later
640      
641 <  atoms[atomIndex]->set_vx( vx );
642 <  atoms[atomIndex]->set_vy( vy );
643 <  atoms[atomIndex]->set_vz( vz );
641 >    DoubleArrayData* etaValue = new DoubleArrayData();
642 >    etaValue->setID(ETAVALUE_ID);
643 >    etaValue->setData(eta, 9);
644 >    entry_plug->addProperty(etaValue);
645 >  }
646  
647    return NULL;
648   }
649 +
650 + #ifdef IS_MPI
651 +
652 + // a couple of functions to let us escape the read loop
653 +
654 + void initFile::nodeZeroError( void ){
655 +  int j, myStatus;
656 +
657 +  myStatus = 0;
658 +  for (j = 0; j < mpiSim->getNProcessors(); j++) {
659 +    MPI_Send( &myStatus, 1, MPI_INT, j,
660 +              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
661 +  }
662 +
663 +
664 +  MPI_Finalize();
665 +  exit (0);
666 +
667 + }
668 +
669 + void initFile::anonymousNodeDie( void ){
670 +
671 +  MPI_Finalize();
672 +  exit (0);
673 + }
674 +
675 + #endif //is_mpi

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