# | 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 | 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 | ||
83 | + | #ifdef IS_MPI |
84 | + | int done, which_node, which_atom; // loop counter |
85 | + | #endif //is_mpi |
86 | + | |
87 | const int BUFFERSIZE = 2000; // size of the read buffer | |
88 | int n_atoms; // the number of atoms | |
89 | < | char read_buffer[BUFFERSIZE]; //the line buffer for reading |
70 | < | #ifdef IS_MPI |
71 | < | char send_buffer[BUFFERSIZE]; |
72 | < | #endif |
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 |
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 | > | simnfo = the_simnfo; |
95 | ||
96 | ||
97 | #ifndef IS_MPI | |
# | Line 90 | Line 106 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
106 | ||
107 | n_atoms = atoi( read_buffer ); | |
108 | ||
109 | < | Atom **atoms = entry_plug->atoms; |
94 | < | DirectionalAtom* dAtom; |
95 | < | |
96 | < | if( n_atoms != entry_plug->n_atoms ){ |
109 | > | if( n_atoms != simnfo->n_atoms ){ |
110 | sprintf( painCave.errMsg, | |
111 | "Initialize from File error. %s n_atoms, %d, " | |
112 | "does not match the BASS file's n_atoms, %d.\n", | |
113 | < | c_in_name, n_atoms, entry_plug->n_atoms ); |
113 | > | c_in_name, n_atoms, simnfo->n_atoms ); |
114 | painCave.isFatal = 1; | |
115 | simError(); | |
116 | } | |
117 | < | |
118 | < | //read and toss the comment line |
119 | < | |
117 | > | |
118 | > | //read the box mat from the comment line |
119 | > | |
120 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
121 | if(eof_test == NULL){ | |
122 | sprintf( painCave.errMsg, | |
# | Line 112 | Line 125 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
125 | simError(); | |
126 | } | |
127 | ||
128 | + | |
129 | + | |
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 < n_atoms; i++){ | |
140 | < | |
140 | > | |
141 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
142 | if(eof_test == NULL){ | |
143 | sprintf(painCave.errMsg, | |
# | Line 125 | Line 149 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
149 | simError(); | |
150 | } | |
151 | ||
152 | < | |
152 | > | |
153 | parseErr = parseDumpLine( read_buffer, i ); | |
154 | if( parseErr != NULL ){ | |
155 | strcpy( painCave.errMsg, parseErr ); | |
156 | painCave.isFatal = 1; | |
157 | simError(); | |
158 | < | } |
158 | > | } |
159 | } | |
160 | ||
161 | ||
162 | // MPI Section of code.......... | |
163 | #else //IS_MPI | |
164 | ||
165 | < | int masterIndex; |
166 | < | int nodeAtomsStart; |
143 | < | int nodeAtomsEnd; |
144 | < | int mpiErr; |
145 | < | int sendError; |
165 | > | // first thing first, suspend fatalities. |
166 | > | painCave.isEventLoop = 1; |
167 | ||
168 | < | MPI_Status istatus[MPI_STATUS_SIZE]; |
168 | > | int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
169 | > | int haveError; |
170 | ||
171 | + | MPI_Status istatus; |
172 | + | int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
173 | + | |
174 | + | |
175 | + | haveError = 0; |
176 | if (worldRank == 0) { | |
177 | + | |
178 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
179 | if( eof_test == NULL ){ | |
180 | sprintf( painCave.errMsg, | |
181 | < | "Error reading 1st line of %d \n ",c_in_name); |
182 | < | painCave.isFatal = 1; |
181 | > | "Error reading 1st line of %s \n ",c_in_name); |
182 | > | haveError = 1; |
183 | simError(); | |
184 | } | |
185 | < | |
185 | > | |
186 | n_atoms = atoi( read_buffer ); | |
187 | < | |
160 | < | Atom **atoms = entry_plug->atoms; |
161 | < | DirectionalAtom* dAtom; |
162 | < | |
187 | > | |
188 | // Check to see that the number of atoms in the intial configuration file is the | |
189 | // same as declared in simBass. | |
190 | < | |
190 | > | |
191 | if( n_atoms != mpiSim->getTotAtoms() ){ | |
192 | sprintf( painCave.errMsg, | |
193 | "Initialize from File error. %s n_atoms, %d, " | |
194 | "does not match the BASS file's n_atoms, %d.\n", | |
195 | < | c_in_name, n_atoms, entry_plug->n_atoms ); |
196 | < | painCave.isFatal = 1; |
195 | > | c_in_name, n_atoms, simnfo->n_atoms ); |
196 | > | haveError= 1; |
197 | simError(); | |
198 | } | |
199 | < | |
200 | < | //read and toss the comment line |
201 | < | |
199 | > | |
200 | > | //read the boxMat from the comment line |
201 | > | |
202 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
203 | if(eof_test == NULL){ | |
204 | sprintf( painCave.errMsg, | |
205 | "error in reading commment in %s\n", c_in_name); | |
206 | < | painCave.isFatal = 1; |
206 | > | haveError = 1; |
207 | simError(); | |
208 | } | |
209 | < | |
210 | < | // Read Proc 0 share of the xyz file... |
211 | < | masterIndex = 0; |
212 | < | for( i=0; i <= mpiSim->getMyAtomEnd(); i++){ |
213 | < | |
209 | > | |
210 | > | //Every single processor will parse the comment line by itself |
211 | > | //By using this way, we might lose some efficiency, but if we want to add |
212 | > | //more parameters into comment line, we only need to modify function |
213 | > | //parseCommentLine |
214 | > | |
215 | > | MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
216 | > | |
217 | > | parseErr = parseCommentLine( read_buffer, simnfo); |
218 | > | |
219 | > | if( parseErr != NULL ){ |
220 | > | strcpy( painCave.errMsg, parseErr ); |
221 | > | haveError = 1; |
222 | > | simError(); |
223 | > | } |
224 | > | |
225 | > | for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
226 | > | |
227 | eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); | |
228 | if(eof_test == NULL){ | |
229 | sprintf(painCave.errMsg, | |
# | Line 193 | Line 231 | void InitializeFromFile :: read_xyz( SimInfo* the_entr | |
231 | "natoms = %d; index = %d\n" | |
232 | "error reading the line from the file.\n", | |
233 | c_in_name, n_atoms, i ); | |
234 | < | painCave.isFatal = 1; |
234 | > | haveError= 1; |
235 | simError(); | |
236 | } | |
237 | < | |
238 | < | parseErr = parseDumpLine( read_buffer, i ); |
239 | < | if( parseErr != NULL ){ |
240 | < | strcpy( painCave.errMsg, parseErr ); |
241 | < | painCave.isFatal = 1; |
242 | < | simError(); |
243 | < | } |
244 | < | masterIndex++; |
245 | < | } |
246 | < | } |
237 | > | |
238 | > | if(haveError) nodeZeroError(); |
239 | > | |
240 | > | // Get the Node number which wants this atom: |
241 | > | which_node = AtomToProcMap[i]; |
242 | > | if (which_node == 0) { |
243 | > | parseErr = parseDumpLine( read_buffer, i ); |
244 | > | if( parseErr != NULL ){ |
245 | > | strcpy( painCave.errMsg, parseErr ); |
246 | > | haveError = 1; |
247 | > | simError(); |
248 | > | } |
249 | > | if(haveError) nodeZeroError(); |
250 | > | } |
251 | ||
252 | < | sprintf(checkPointMsg, |
211 | < | "Node 0 has successfully read positions from input file."); |
212 | < | MPIcheckPoint(); |
252 | > | else { |
253 | ||
254 | < | for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
255 | < | procIndex++){ |
256 | < | if (worldRank == 0) { |
254 | > | myStatus = 1; |
255 | > | MPI_Send(&myStatus, 1, MPI_INT, which_node, |
256 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
257 | > | MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
258 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
259 | > | MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
260 | > | MPI_COMM_WORLD); |
261 | > | MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
262 | > | MPI_COMM_WORLD, &istatus); |
263 | ||
264 | < | mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD, |
265 | < | istatus); |
264 | > | if(!myStatus) nodeZeroError(); |
265 | > | } |
266 | > | } |
267 | > | myStatus = -1; |
268 | > | for (j = 1; j < mpiSim->getNumberProcessors(); j++) { |
269 | > | MPI_Send( &myStatus, 1, MPI_INT, j, |
270 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
271 | > | } |
272 | ||
273 | < | mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD, |
222 | < | istatus); |
223 | < | // Make sure where node 0 is reading from, matches where the receiving node |
224 | < | // expects it to be. |
273 | > | } else { |
274 | ||
275 | < | if (masterIndex != nodeAtomsStart){ |
227 | < | sendError = 1; |
228 | < | mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD); |
229 | < | sprintf(painCave.errMsg, |
230 | < | "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(); |
234 | < | } |
235 | < | sendError = 0; |
236 | < | 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(); |
275 | > | MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
276 | ||
277 | < | masterIndex++; |
278 | < | } |
277 | > | parseErr = parseCommentLine( read_buffer, simnfo); |
278 | > | |
279 | > | if( parseErr != NULL ){ |
280 | > | strcpy( painCave.errMsg, parseErr ); |
281 | > | haveError = 1; |
282 | > | simError(); |
283 | } | |
284 | ||
285 | ||
286 | < | else if(worldRank == procIndex){ |
287 | < | 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(); |
286 | > | done = 0; |
287 | > | while (!done) { |
288 | ||
289 | < | for ( i = 0; i < entry_plug->n_atoms; i++){ |
289 | > | MPI_Recv(&myStatus, 1, MPI_INT, 0, |
290 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
291 | ||
292 | < | 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); |
292 | > | if(!myStatus) anonymousNodeDie(); |
293 | ||
294 | + | if(myStatus < 0) break; |
295 | ||
296 | < | strcpy( painCave.errMsg, parseErr ); |
297 | < | painCave.isFatal = 1; |
298 | < | simError(); |
299 | < | } |
300 | < | sendError = 0; |
301 | < | mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD); |
296 | > | MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
297 | > | TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
298 | > | MPI_Recv(&which_atom, 1, MPI_INT, 0, |
299 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
300 | > | |
301 | > | myStatus = 1; |
302 | > | parseErr = parseDumpLine( read_buffer, which_atom ); |
303 | > | if( parseErr != NULL ){ |
304 | > | strcpy( painCave.errMsg, parseErr ); |
305 | > | myStatus = 0;; |
306 | > | simError(); |
307 | } | |
308 | < | } |
309 | < | sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex); |
310 | < | MPIcheckPoint(); |
308 | > | |
309 | > | MPI_Send( &myStatus, 1, MPI_INT, 0, |
310 | > | TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
311 | > | |
312 | > | } |
313 | } | |
314 | ||
315 | + | // last thing last, enable fatalities. |
316 | + | painCave.isEventLoop = 0; |
317 | + | |
318 | + | |
319 | + | |
320 | #endif | |
321 | } | |
322 | ||
323 | + | char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
324 | ||
325 | < | char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){ |
325 | > | char *foo; // the pointer to the current string token |
326 | ||
327 | < | char *foo; // the pointer to the current string token |
328 | < | |
307 | < | double rx, ry, rz; // position place holders |
308 | < | double vx, vy, vz; // velocity placeholders |
327 | > | double pos[3]; // position place holders |
328 | > | double vel[3]; // velocity placeholders |
329 | double q[4]; // the quaternions | |
330 | < | double jx, jy, jz; // angular velocity placeholders; |
330 | > | double ji[3]; // angular velocity placeholders; |
331 | double qSqr, qLength; // needed to normalize the quaternion vector. | |
332 | < | |
333 | < | Atom **atoms = entry_plug->atoms; |
332 | > | |
333 | > | Atom **atoms = simnfo->atoms; |
334 | DirectionalAtom* dAtom; | |
315 | – | |
316 | – | int n_atoms; |
335 | ||
336 | + | int n_atoms, atomIndex; |
337 | + | |
338 | #ifdef IS_MPI | |
339 | + | int j; |
340 | + | |
341 | n_atoms = mpiSim->getTotAtoms(); | |
342 | + | atomIndex=-1; |
343 | + | for (j=0; j < mpiSim->getMyNlocal(); j++) { |
344 | + | if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
345 | + | } |
346 | + | if (atomIndex == -1) { |
347 | + | sprintf( painCave.errMsg, |
348 | + | "Initialize from file error. Atom at index %d " |
349 | + | "in file %s does not exist on processor %d .\n", |
350 | + | globalIndex, c_in_name, mpiSim->getMyNode() ); |
351 | + | return strdup( painCave.errMsg ); |
352 | + | } |
353 | #else | |
354 | < | n_atoms = entry_plug->n_atoms; |
354 | > | n_atoms = simnfo->n_atoms; |
355 | > | atomIndex = globalIndex; |
356 | #endif // is_mpi | |
357 | ||
324 | – | |
358 | // set the string tokenizer | |
359 | < | |
359 | > | |
360 | foo = strtok(readLine, " ,;\t"); | |
361 | < | |
361 | > | |
362 | // check the atom name to the current atom | |
363 | < | |
363 | > | |
364 | if( strcmp( foo, atoms[atomIndex]->getType() ) ){ | |
365 | sprintf( painCave.errMsg, | |
366 | "Initialize from file error. Atom %s at index %d " | |
# | Line 336 | Line 369 | char* InitializeFromFile::parseDumpLine(char* readLine | |
369 | foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); | |
370 | return strdup( painCave.errMsg ); | |
371 | } | |
372 | < | |
372 | > | |
373 | // get the positions | |
374 | ||
375 | foo = strtok(NULL, " ,;\t"); | |
# | Line 347 | Line 380 | char* InitializeFromFile::parseDumpLine(char* readLine | |
380 | c_in_name, n_atoms, atomIndex ); | |
381 | return strdup( painCave.errMsg ); | |
382 | } | |
383 | < | rx = atof( foo ); |
384 | < | |
383 | > | pos[0] = atof( foo ); |
384 | > | |
385 | foo = strtok(NULL, " ,;\t"); | |
386 | if(foo == NULL){ | |
387 | sprintf( painCave.errMsg, | |
# | Line 357 | Line 390 | char* InitializeFromFile::parseDumpLine(char* readLine | |
390 | c_in_name, n_atoms, atomIndex ); | |
391 | return strdup( painCave.errMsg ); | |
392 | } | |
393 | < | ry = atof( foo ); |
394 | < | |
393 | > | pos[1] = atof( foo ); |
394 | > | |
395 | foo = strtok(NULL, " ,;\t"); | |
396 | if(foo == NULL){ | |
397 | sprintf( painCave.errMsg, | |
# | Line 367 | Line 400 | char* InitializeFromFile::parseDumpLine(char* readLine | |
400 | c_in_name, n_atoms, atomIndex ); | |
401 | return strdup( painCave.errMsg ); | |
402 | } | |
403 | < | rz = atof( foo ); |
403 | > | pos[2] = atof( foo ); |
404 | ||
405 | ||
406 | // get the velocities | |
# | Line 380 | Line 413 | char* InitializeFromFile::parseDumpLine(char* readLine | |
413 | c_in_name, n_atoms, atomIndex ); | |
414 | return strdup( painCave.errMsg ); | |
415 | } | |
416 | < | vx = atof( foo ); |
417 | < | |
416 | > | vel[0] = atof( foo ); |
417 | > | |
418 | foo = strtok(NULL, " ,;\t"); | |
419 | if(foo == NULL){ | |
420 | sprintf( painCave.errMsg, | |
# | Line 390 | Line 423 | char* InitializeFromFile::parseDumpLine(char* readLine | |
423 | c_in_name, n_atoms, atomIndex ); | |
424 | return strdup( painCave.errMsg ); | |
425 | } | |
426 | < | vy = atof( foo ); |
427 | < | |
426 | > | vel[1] = atof( foo ); |
427 | > | |
428 | foo = strtok(NULL, " ,;\t"); | |
429 | if(foo == NULL){ | |
430 | sprintf( painCave.errMsg, | |
# | Line 400 | Line 433 | char* InitializeFromFile::parseDumpLine(char* readLine | |
433 | c_in_name, n_atoms, atomIndex ); | |
434 | return strdup( painCave.errMsg ); | |
435 | } | |
436 | < | vz = atof( foo ); |
437 | < | |
438 | < | |
436 | > | vel[2] = atof( foo ); |
437 | > | |
438 | > | |
439 | // get the quaternions | |
440 | < | |
440 | > | |
441 | if( atoms[atomIndex]->isDirectional() ){ | |
442 | < | |
442 | > | |
443 | foo = strtok(NULL, " ,;\t"); | |
444 | if(foo == NULL){ | |
445 | sprintf(painCave.errMsg, | |
# | Line 416 | Line 449 | char* InitializeFromFile::parseDumpLine(char* readLine | |
449 | return strdup( painCave.errMsg ); | |
450 | } | |
451 | q[0] = atof( foo ); | |
452 | < | |
452 | > | |
453 | foo = strtok(NULL, " ,;\t"); | |
454 | if(foo == NULL){ | |
455 | sprintf( painCave.errMsg, | |
# | Line 426 | Line 459 | char* InitializeFromFile::parseDumpLine(char* readLine | |
459 | return strdup( painCave.errMsg ); | |
460 | } | |
461 | q[1] = atof( foo ); | |
462 | < | |
462 | > | |
463 | foo = strtok(NULL, " ,;\t"); | |
464 | if(foo == NULL){ | |
465 | sprintf( painCave.errMsg, | |
# | Line 436 | Line 469 | char* InitializeFromFile::parseDumpLine(char* readLine | |
469 | return strdup( painCave.errMsg ); | |
470 | } | |
471 | q[2] = atof( foo ); | |
472 | < | |
472 | > | |
473 | foo = strtok(NULL, " ,;\t"); | |
474 | if(foo == NULL){ | |
475 | sprintf( painCave.errMsg, | |
# | Line 446 | Line 479 | char* InitializeFromFile::parseDumpLine(char* readLine | |
479 | return strdup( painCave.errMsg ); | |
480 | } | |
481 | q[3] = atof( foo ); | |
482 | < | |
482 | > | |
483 | // get the angular velocities | |
484 | < | |
484 | > | |
485 | foo = strtok(NULL, " ,;\t"); | |
486 | if(foo == NULL){ | |
487 | sprintf( painCave.errMsg, | |
# | Line 457 | Line 490 | char* InitializeFromFile::parseDumpLine(char* readLine | |
490 | c_in_name, n_atoms, atomIndex ); | |
491 | return strdup( painCave.errMsg ); | |
492 | } | |
493 | < | jx = atof( foo ); |
494 | < | |
493 | > | ji[0] = atof( foo ); |
494 | > | |
495 | foo = strtok(NULL, " ,;\t"); | |
496 | if(foo == NULL){ | |
497 | sprintf( painCave.errMsg, | |
# | Line 467 | Line 500 | char* InitializeFromFile::parseDumpLine(char* readLine | |
500 | c_in_name, n_atoms, atomIndex ); | |
501 | return strdup( painCave.errMsg ); | |
502 | } | |
503 | < | jy = atof(foo ); |
504 | < | |
503 | > | ji[1] = atof(foo ); |
504 | > | |
505 | foo = strtok(NULL, " ,;\t"); | |
506 | if(foo == NULL){ | |
507 | sprintf( painCave.errMsg, | |
# | Line 477 | Line 510 | char* InitializeFromFile::parseDumpLine(char* readLine | |
510 | c_in_name, n_atoms, atomIndex ); | |
511 | return strdup( painCave.errMsg ); | |
512 | } | |
513 | < | jz = atof( foo ); |
514 | < | |
513 | > | ji[2] = atof( foo ); |
514 | > | |
515 | dAtom = ( DirectionalAtom* )atoms[atomIndex]; | |
516 | ||
517 | // check that the quaternion vector is normalized | |
518 | ||
519 | qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); | |
520 | < | |
520 | > | |
521 | qLength = sqrt( qSqr ); | |
522 | q[0] = q[0] / qLength; | |
523 | q[1] = q[1] / qLength; | |
524 | q[2] = q[2] / qLength; | |
525 | q[3] = q[3] / qLength; | |
526 | < | |
526 | > | |
527 | dAtom->setQ( q ); | |
528 | < | |
528 | > | |
529 | // add the angular velocities | |
530 | ||
531 | < | dAtom->setJx( jx ); |
499 | < | dAtom->setJy( jy ); |
500 | < | dAtom->setJz( jz ); |
531 | > | dAtom->setJ( ji ); |
532 | } | |
533 | < | |
533 | > | |
534 | // add the positions and velocities to the atom | |
535 | < | |
536 | < | atoms[atomIndex]->setX( rx ); |
537 | < | atoms[atomIndex]->setY( ry ); |
538 | < | atoms[atomIndex]->setZ( rz ); |
535 | > | |
536 | > | atoms[atomIndex]->setPos( pos ); |
537 | > | atoms[atomIndex]->setVel( vel ); |
538 | > | |
539 | > | return NULL; |
540 | > | } |
541 | > | |
542 | > | |
543 | > | char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
544 | > | |
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 | > | |
556 | > | foo = strtok(readLine, " ,;\t"); |
557 | > | // set the timeToken. |
558 | > | |
559 | > | if(foo == NULL){ |
560 | > | sprintf( painCave.errMsg, |
561 | > | "error in reading Time from %s\n", |
562 | > | c_in_name ); |
563 | > | return strdup( painCave.errMsg ); |
564 | > | } |
565 | > | |
566 | > | currTime = atof( foo ); |
567 | > | entry_plug->setTime( currTime ); |
568 | > | |
569 | > | //get H-Matrix |
570 | > | |
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 | > | } |
580 | > | |
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 | > | //set H-Matrix |
585 | > | entry_plug->setBoxM( theBoxMat3 ); |
586 | > | |
587 | > | //get chi and integralOfChidt, they should appear by pair |
588 | > | |
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 | < | atoms[atomIndex]->set_vx( vx ); |
619 | < | atoms[atomIndex]->set_vy( vy ); |
620 | < | atoms[atomIndex]->set_vz( vz ); |
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 | > | //entry_plug->setBoxM( theBoxMat3 ); |
639 | > | DoubleArrayData* etaValue = new DoubleArrayData(); |
640 | > | etaValue->setID(ETAVALUE_ID); |
641 | > | etaValue->setData(eta, 9); |
642 | > | entry_plug->addProperty(etaValue); |
643 | > | } |
644 | ||
645 | return NULL; | |
646 | } | |
647 | + | |
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 | + | |
655 | + | myStatus = 0; |
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 | + | } |
660 | + | |
661 | + | |
662 | + | MPI_Finalize(); |
663 | + | exit (0); |
664 | + | |
665 | + | } |
666 | + | |
667 | + | void initFile::anonymousNodeDie( void ){ |
668 | + | |
669 | + | MPI_Finalize(); |
670 | + | exit (0); |
671 | + | } |
672 | + | |
673 | + | #endif //is_mpi |
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