1 |
tim |
1078 |
#define _LARGEFILE_SOURCE64 |
2 |
mmeineke |
643 |
#define _FILE_OFFSET_BITS 64 |
3 |
|
|
|
4 |
mmeineke |
804 |
#include <sys/types.h> |
5 |
|
|
#include <sys/stat.h> |
6 |
|
|
|
7 |
gezelter |
637 |
#include <iostream> |
8 |
gezelter |
829 |
#include <math.h> |
9 |
gezelter |
637 |
|
10 |
|
|
#include <stdio.h> |
11 |
|
|
#include <stdlib.h> |
12 |
|
|
#include <string.h> |
13 |
|
|
|
14 |
mmeineke |
804 |
|
15 |
gezelter |
637 |
#include "ReadWrite.hpp" |
16 |
|
|
#include "simError.h" |
17 |
|
|
|
18 |
|
|
#ifdef IS_MPI |
19 |
|
|
#include <mpi.h> |
20 |
|
|
#include "mpiSimulation.hpp" |
21 |
|
|
#define TAKE_THIS_TAG_CHAR 0 |
22 |
|
|
#define TAKE_THIS_TAG_INT 1 |
23 |
mmeineke |
647 |
#endif // is_mpi |
24 |
gezelter |
637 |
|
25 |
|
|
namespace dumpRead{ |
26 |
mmeineke |
647 |
|
27 |
|
|
#ifdef IS_MPI |
28 |
gezelter |
637 |
void nodeZeroError( void ); |
29 |
|
|
void anonymousNodeDie( void ); |
30 |
mmeineke |
647 |
#endif // is_mpi |
31 |
mmeineke |
646 |
|
32 |
gezelter |
637 |
} |
33 |
|
|
|
34 |
|
|
using namespace dumpRead; |
35 |
|
|
|
36 |
|
|
|
37 |
tim |
1074 |
DumpReader :: DumpReader(const char *in_name ){ |
38 |
mmeineke |
647 |
|
39 |
|
|
isScanned = false; |
40 |
mmeineke |
804 |
headFP = new FilePos; |
41 |
mmeineke |
647 |
|
42 |
gezelter |
637 |
#ifdef IS_MPI |
43 |
|
|
if (worldRank == 0) { |
44 |
|
|
#endif |
45 |
|
|
|
46 |
mmeineke |
647 |
inFile = fopen(in_name, "r"); |
47 |
|
|
if(inFile == NULL){ |
48 |
gezelter |
637 |
sprintf(painCave.errMsg, |
49 |
|
|
"Cannot open file: %s\n", in_name); |
50 |
|
|
painCave.isFatal = 1; |
51 |
|
|
simError(); |
52 |
|
|
} |
53 |
|
|
|
54 |
mmeineke |
647 |
strcpy( inName, in_name); |
55 |
gezelter |
637 |
#ifdef IS_MPI |
56 |
|
|
} |
57 |
|
|
strcpy( checkPointMsg, "Dump file opened for reading successfully." ); |
58 |
|
|
MPIcheckPoint(); |
59 |
|
|
#endif |
60 |
|
|
return; |
61 |
|
|
} |
62 |
|
|
|
63 |
|
|
DumpReader :: ~DumpReader( ){ |
64 |
|
|
#ifdef IS_MPI |
65 |
|
|
if (worldRank == 0) { |
66 |
|
|
#endif |
67 |
|
|
int error; |
68 |
mmeineke |
647 |
error = fclose( inFile ); |
69 |
gezelter |
637 |
if( error ){ |
70 |
|
|
sprintf( painCave.errMsg, |
71 |
mmeineke |
647 |
"Error closing %s\n", inName ); |
72 |
gezelter |
637 |
simError(); |
73 |
|
|
} |
74 |
|
|
#ifdef IS_MPI |
75 |
|
|
} |
76 |
|
|
strcpy( checkPointMsg, "Dump file closed successfully." ); |
77 |
|
|
MPIcheckPoint(); |
78 |
|
|
#endif |
79 |
|
|
|
80 |
|
|
return; |
81 |
|
|
} |
82 |
|
|
|
83 |
mmeineke |
647 |
int DumpReader::getNframes( void ){ |
84 |
gezelter |
637 |
|
85 |
mmeineke |
647 |
if( !isScanned ) scanFile(); |
86 |
|
|
return nFrames; |
87 |
|
|
} |
88 |
mmeineke |
643 |
|
89 |
mmeineke |
647 |
void DumpReader::scanFile( void ){ |
90 |
|
|
|
91 |
|
|
int vectorSize; |
92 |
|
|
int i, j, k; |
93 |
|
|
int lineNum = 0; |
94 |
|
|
char readBuffer[2000]; |
95 |
|
|
char* foo; |
96 |
|
|
fpos_t *currPos; |
97 |
mmeineke |
804 |
double time; |
98 |
mmeineke |
647 |
|
99 |
mmeineke |
804 |
FilePos *currFP; |
100 |
|
|
|
101 |
|
|
|
102 |
mmeineke |
647 |
#ifdef IS_MPI |
103 |
|
|
if( worldRank == 0 ){ |
104 |
|
|
#endif // is_mpi |
105 |
|
|
|
106 |
|
|
rewind( inFile ); |
107 |
|
|
|
108 |
|
|
currPos = new fpos_t; |
109 |
|
|
fgetpos( inFile, currPos ); |
110 |
mmeineke |
804 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
111 |
mmeineke |
647 |
lineNum++; |
112 |
mmeineke |
804 |
if( feof( inFile ) ){ |
113 |
mmeineke |
647 |
sprintf( painCave.errMsg, |
114 |
|
|
"File \"%s\" ended unexpectedly at line %d\n", |
115 |
|
|
inName, |
116 |
|
|
lineNum ); |
117 |
|
|
painCave.isFatal = 1; |
118 |
|
|
simError(); |
119 |
|
|
} |
120 |
|
|
|
121 |
mmeineke |
804 |
nFrames = 0; |
122 |
|
|
while( !feof( inFile ) ){ |
123 |
|
|
|
124 |
|
|
headFP->add( currPos ); |
125 |
|
|
nFrames++; |
126 |
|
|
|
127 |
mmeineke |
647 |
i = atoi(readBuffer); |
128 |
|
|
|
129 |
mmeineke |
804 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
130 |
mmeineke |
647 |
lineNum++; |
131 |
mmeineke |
804 |
if( feof( inFile ) ){ |
132 |
mmeineke |
647 |
sprintf( painCave.errMsg, |
133 |
|
|
"File \"%s\" ended unexpectedly at line %d\n", |
134 |
|
|
inName, |
135 |
|
|
lineNum ); |
136 |
|
|
painCave.isFatal = 1; |
137 |
|
|
simError(); |
138 |
|
|
} |
139 |
|
|
|
140 |
mmeineke |
804 |
// if(outTime){ |
141 |
|
|
// foo = strtok( readBuffer, " ,;\t" ); |
142 |
|
|
// time = atof( foo ); |
143 |
|
|
// } |
144 |
mmeineke |
647 |
|
145 |
|
|
for(j=0; j<i; j++){ |
146 |
|
|
|
147 |
mmeineke |
804 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
148 |
mmeineke |
647 |
lineNum++; |
149 |
mmeineke |
804 |
if( feof( inFile ) ){ |
150 |
mmeineke |
647 |
sprintf( painCave.errMsg, |
151 |
|
|
"File \"%s\" ended unexpectedly at line %d," |
152 |
|
|
" with atom %d\n", |
153 |
|
|
inName, |
154 |
|
|
lineNum, |
155 |
|
|
j ); |
156 |
|
|
painCave.isFatal = 1; |
157 |
|
|
simError(); |
158 |
|
|
} |
159 |
|
|
|
160 |
|
|
} |
161 |
|
|
|
162 |
|
|
currPos = new fpos_t; |
163 |
|
|
fgetpos( inFile, currPos ); |
164 |
mmeineke |
804 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
165 |
mmeineke |
647 |
lineNum++; |
166 |
|
|
} |
167 |
|
|
|
168 |
|
|
delete currPos; |
169 |
|
|
rewind( inFile ); |
170 |
|
|
|
171 |
mmeineke |
804 |
frameStart = new FilePos*[nFrames]; |
172 |
|
|
currFP = headFP; |
173 |
|
|
for(i=0; i<nFrames; i++){ |
174 |
|
|
|
175 |
|
|
currFP = currFP->getNext(); |
176 |
|
|
if( currFP == NULL ){ |
177 |
|
|
sprintf( painCave.errMsg, |
178 |
|
|
"DumpReader error: scanFile FilePos mismatch at " |
179 |
|
|
"nFrames = %d\n", |
180 |
|
|
i ); |
181 |
|
|
painCave.isFatal = 1; |
182 |
|
|
simError(); |
183 |
|
|
} |
184 |
|
|
|
185 |
|
|
frameStart[i] = currFP; |
186 |
|
|
} |
187 |
|
|
|
188 |
|
|
isScanned = true; |
189 |
|
|
|
190 |
mmeineke |
647 |
#ifdef IS_MPI |
191 |
|
|
} |
192 |
|
|
strcpy( checkPointMsg, "Successfully scanned DumpFile\n" ); |
193 |
|
|
MPIcheckPoint(); |
194 |
|
|
#endif // is_mpi |
195 |
|
|
} |
196 |
|
|
|
197 |
mmeineke |
656 |
void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){ |
198 |
mmeineke |
647 |
|
199 |
mmeineke |
656 |
simnfo = the_simnfo; |
200 |
mmeineke |
647 |
|
201 |
mmeineke |
656 |
this->readSet( whichFrame ); |
202 |
|
|
} |
203 |
gezelter |
637 |
|
204 |
mmeineke |
656 |
|
205 |
|
|
|
206 |
|
|
void DumpReader :: readSet( int whichFrame ){ |
207 |
|
|
|
208 |
gezelter |
637 |
int i, j, done, which_node, which_atom; // loop counter |
209 |
|
|
|
210 |
|
|
const int BUFFERSIZE = 2000; // size of the read buffer |
211 |
|
|
int n_atoms; // the number of atoms |
212 |
|
|
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
213 |
|
|
#ifdef IS_MPI |
214 |
|
|
char send_buffer[BUFFERSIZE]; |
215 |
|
|
#endif |
216 |
|
|
|
217 |
|
|
char *eof_test; // ptr to see when we reach the end of the file |
218 |
|
|
char *parseErr; |
219 |
|
|
int procIndex; |
220 |
|
|
double boxMat[9]; |
221 |
|
|
double theBoxMat3[3][3]; |
222 |
mmeineke |
804 |
double time; |
223 |
|
|
|
224 |
mmeineke |
656 |
fpos_t *framePos; |
225 |
|
|
|
226 |
|
|
#ifndef IS_MPI |
227 |
|
|
|
228 |
mmeineke |
804 |
framePos = frameStart[whichFrame]->getPos(); |
229 |
gezelter |
637 |
|
230 |
tim |
1074 |
fsetpos(inFile, framePos); |
231 |
mmeineke |
656 |
|
232 |
gezelter |
637 |
|
233 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
234 |
gezelter |
637 |
if( eof_test == NULL ){ |
235 |
|
|
sprintf( painCave.errMsg, |
236 |
|
|
"DumpReader error: error reading 1st line of \"%s\"\n", |
237 |
mmeineke |
647 |
inName ); |
238 |
gezelter |
637 |
painCave.isFatal = 1; |
239 |
|
|
simError(); |
240 |
|
|
} |
241 |
|
|
|
242 |
|
|
n_atoms = atoi( read_buffer ); |
243 |
|
|
|
244 |
|
|
Atom **atoms = simnfo->atoms; |
245 |
|
|
DirectionalAtom* dAtom; |
246 |
|
|
|
247 |
|
|
if( n_atoms != simnfo->n_atoms ){ |
248 |
|
|
sprintf( painCave.errMsg, |
249 |
|
|
"DumpReader error. %s n_atoms, %d, " |
250 |
|
|
"does not match the BASS file's n_atoms, %d.\n", |
251 |
mmeineke |
647 |
inName, n_atoms, simnfo->n_atoms ); |
252 |
gezelter |
637 |
painCave.isFatal = 1; |
253 |
|
|
simError(); |
254 |
|
|
} |
255 |
|
|
|
256 |
|
|
//read the box mat from the comment line |
257 |
|
|
|
258 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
259 |
gezelter |
637 |
if(eof_test == NULL){ |
260 |
|
|
sprintf( painCave.errMsg, |
261 |
mmeineke |
647 |
"error in reading commment in %s\n", inName); |
262 |
gezelter |
637 |
painCave.isFatal = 1; |
263 |
|
|
simError(); |
264 |
|
|
} |
265 |
|
|
|
266 |
|
|
parseErr = parseCommentLine( read_buffer, time, boxMat ); |
267 |
|
|
if( parseErr != NULL ){ |
268 |
|
|
strcpy( painCave.errMsg, parseErr ); |
269 |
|
|
painCave.isFatal = 1; |
270 |
|
|
simError(); |
271 |
|
|
} |
272 |
|
|
|
273 |
|
|
simnfo->setTime( time ); |
274 |
|
|
|
275 |
|
|
for(i=0;i<3;i++) |
276 |
|
|
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
277 |
|
|
|
278 |
|
|
|
279 |
|
|
simnfo->setBoxM( theBoxMat3 ); |
280 |
|
|
|
281 |
|
|
|
282 |
|
|
for( i=0; i < n_atoms; i++){ |
283 |
|
|
|
284 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
285 |
gezelter |
637 |
if(eof_test == NULL){ |
286 |
|
|
sprintf(painCave.errMsg, |
287 |
|
|
"error in reading file %s\n" |
288 |
|
|
"natoms = %d; index = %d\n" |
289 |
|
|
"error reading the line from the file.\n", |
290 |
mmeineke |
647 |
inName, n_atoms, i ); |
291 |
gezelter |
637 |
painCave.isFatal = 1; |
292 |
|
|
simError(); |
293 |
|
|
} |
294 |
|
|
|
295 |
|
|
|
296 |
|
|
parseErr = parseDumpLine( read_buffer, i ); |
297 |
|
|
if( parseErr != NULL ){ |
298 |
|
|
strcpy( painCave.errMsg, parseErr ); |
299 |
|
|
painCave.isFatal = 1; |
300 |
|
|
simError(); |
301 |
|
|
} |
302 |
|
|
} |
303 |
|
|
|
304 |
|
|
|
305 |
|
|
// MPI Section of code.......... |
306 |
|
|
#else //IS_MPI |
307 |
|
|
|
308 |
|
|
// first thing first, suspend fatalities. |
309 |
|
|
painCave.isEventLoop = 1; |
310 |
|
|
|
311 |
|
|
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
312 |
|
|
int haveError; |
313 |
|
|
|
314 |
|
|
MPI_Status istatus; |
315 |
|
|
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
316 |
|
|
|
317 |
|
|
|
318 |
|
|
haveError = 0; |
319 |
|
|
if (worldRank == 0) { |
320 |
tim |
1074 |
fsetpos(inFile, framePos); |
321 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
322 |
gezelter |
637 |
if( eof_test == NULL ){ |
323 |
|
|
sprintf( painCave.errMsg, |
324 |
mmeineke |
647 |
"Error reading 1st line of %d \n ",inName); |
325 |
gezelter |
637 |
haveError = 1; |
326 |
|
|
simError(); |
327 |
|
|
} |
328 |
|
|
|
329 |
|
|
n_atoms = atoi( read_buffer ); |
330 |
|
|
|
331 |
|
|
Atom **atoms = simnfo->atoms; |
332 |
|
|
DirectionalAtom* dAtom; |
333 |
|
|
|
334 |
|
|
// Check to see that the number of atoms in the intial configuration file is the |
335 |
|
|
// same as declared in simBass. |
336 |
|
|
|
337 |
|
|
if( n_atoms != mpiSim->getTotAtoms() ){ |
338 |
|
|
sprintf( painCave.errMsg, |
339 |
|
|
"Initialize from File error. %s n_atoms, %d, " |
340 |
|
|
"does not match the BASS file's n_atoms, %d.\n", |
341 |
mmeineke |
647 |
inName, n_atoms, simnfo->n_atoms ); |
342 |
gezelter |
637 |
haveError= 1; |
343 |
|
|
simError(); |
344 |
|
|
} |
345 |
|
|
|
346 |
|
|
//read the time and boxMat from the comment line |
347 |
|
|
|
348 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
349 |
gezelter |
637 |
if(eof_test == NULL){ |
350 |
|
|
sprintf( painCave.errMsg, |
351 |
mmeineke |
647 |
"error in reading commment in %s\n", inName); |
352 |
gezelter |
637 |
haveError = 1; |
353 |
|
|
simError(); |
354 |
|
|
} |
355 |
|
|
|
356 |
|
|
parseErr = parseCommentLine( read_buffer, time, boxMat ); |
357 |
|
|
if( parseErr != NULL ){ |
358 |
|
|
strcpy( painCave.errMsg, parseErr ); |
359 |
|
|
haveError = 1; |
360 |
|
|
simError(); |
361 |
|
|
} |
362 |
|
|
|
363 |
mmeineke |
804 |
MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
364 |
gezelter |
637 |
|
365 |
|
|
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
366 |
|
|
|
367 |
|
|
if(haveError) nodeZeroError(); |
368 |
|
|
|
369 |
|
|
for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
370 |
|
|
|
371 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
372 |
gezelter |
637 |
if(eof_test == NULL){ |
373 |
|
|
sprintf(painCave.errMsg, |
374 |
|
|
"error in reading file %s\n" |
375 |
|
|
"natoms = %d; index = %d\n" |
376 |
|
|
"error reading the line from the file.\n", |
377 |
mmeineke |
647 |
inName, n_atoms, i ); |
378 |
gezelter |
637 |
haveError= 1; |
379 |
|
|
simError(); |
380 |
|
|
} |
381 |
|
|
|
382 |
|
|
if(haveError) nodeZeroError(); |
383 |
|
|
|
384 |
|
|
// Get the Node number which wants this atom: |
385 |
|
|
which_node = AtomToProcMap[i]; |
386 |
|
|
if (which_node == 0) { |
387 |
|
|
parseErr = parseDumpLine( read_buffer, i ); |
388 |
|
|
if( parseErr != NULL ){ |
389 |
|
|
strcpy( painCave.errMsg, parseErr ); |
390 |
|
|
haveError = 1; |
391 |
|
|
simError(); |
392 |
|
|
} |
393 |
|
|
if(haveError) nodeZeroError(); |
394 |
|
|
} |
395 |
|
|
|
396 |
|
|
else { |
397 |
|
|
|
398 |
|
|
myStatus = 1; |
399 |
|
|
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
400 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
401 |
|
|
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
402 |
|
|
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
403 |
|
|
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
404 |
|
|
MPI_COMM_WORLD); |
405 |
|
|
MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
406 |
|
|
MPI_COMM_WORLD, &istatus); |
407 |
|
|
|
408 |
|
|
if(!myStatus) nodeZeroError(); |
409 |
|
|
} |
410 |
|
|
} |
411 |
|
|
myStatus = -1; |
412 |
|
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
413 |
|
|
MPI_Send( &myStatus, 1, MPI_INT, j, |
414 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
415 |
|
|
} |
416 |
|
|
|
417 |
|
|
} else { |
418 |
|
|
|
419 |
mmeineke |
804 |
MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
420 |
gezelter |
637 |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
421 |
|
|
|
422 |
|
|
done = 0; |
423 |
|
|
while (!done) { |
424 |
|
|
|
425 |
|
|
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
426 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
427 |
|
|
|
428 |
|
|
if(!myStatus) anonymousNodeDie(); |
429 |
|
|
|
430 |
|
|
if(myStatus < 0) break; |
431 |
|
|
|
432 |
|
|
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
433 |
|
|
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
434 |
|
|
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
435 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
436 |
|
|
|
437 |
|
|
myStatus = 1; |
438 |
|
|
parseErr = parseDumpLine( read_buffer, which_atom ); |
439 |
|
|
if( parseErr != NULL ){ |
440 |
|
|
strcpy( painCave.errMsg, parseErr ); |
441 |
|
|
myStatus = 0;; |
442 |
|
|
simError(); |
443 |
|
|
} |
444 |
|
|
|
445 |
|
|
MPI_Send( &myStatus, 1, MPI_INT, 0, |
446 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
447 |
|
|
|
448 |
|
|
} |
449 |
|
|
} |
450 |
|
|
|
451 |
|
|
// last thing last, enable fatalities. |
452 |
|
|
painCave.isEventLoop = 0; |
453 |
|
|
|
454 |
|
|
simnfo->setTime( time ); |
455 |
|
|
|
456 |
|
|
for(i=0;i<3;i++) |
457 |
|
|
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
458 |
|
|
|
459 |
|
|
simnfo->setBoxM( theBoxMat3 ); |
460 |
|
|
|
461 |
|
|
|
462 |
|
|
#endif |
463 |
|
|
} |
464 |
|
|
|
465 |
|
|
char* DumpReader::parseDumpLine(char* readLine, int globalIndex){ |
466 |
|
|
|
467 |
|
|
char *foo; // the pointer to the current string token |
468 |
|
|
|
469 |
mmeineke |
804 |
double pos[3]; // position place holders |
470 |
|
|
double vel[3]; // velocity placeholders |
471 |
gezelter |
637 |
double q[4]; // the quaternions |
472 |
|
|
double jx, jy, jz; // angular velocity placeholders; |
473 |
|
|
double qSqr, qLength; // needed to normalize the quaternion vector. |
474 |
|
|
|
475 |
|
|
Atom **atoms = simnfo->atoms; |
476 |
|
|
DirectionalAtom* dAtom; |
477 |
|
|
|
478 |
|
|
int j, n_atoms, atomIndex; |
479 |
|
|
|
480 |
|
|
#ifdef IS_MPI |
481 |
|
|
n_atoms = mpiSim->getTotAtoms(); |
482 |
|
|
atomIndex=-1; |
483 |
|
|
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
484 |
|
|
if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
485 |
|
|
} |
486 |
|
|
if (atomIndex == -1) { |
487 |
|
|
sprintf( painCave.errMsg, |
488 |
|
|
"Initialize from file error. Atom at index %d " |
489 |
|
|
"in file %s does not exist on processor %d .\n", |
490 |
mmeineke |
647 |
globalIndex, inName, mpiSim->getMyNode() ); |
491 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
492 |
|
|
} |
493 |
|
|
#else |
494 |
|
|
n_atoms = simnfo->n_atoms; |
495 |
|
|
atomIndex = globalIndex; |
496 |
|
|
#endif // is_mpi |
497 |
|
|
|
498 |
|
|
// set the string tokenizer |
499 |
|
|
|
500 |
|
|
foo = strtok(readLine, " ,;\t"); |
501 |
tim |
1074 |
atoms[atomIndex]->setType(foo); |
502 |
gezelter |
637 |
// check the atom name to the current atom |
503 |
|
|
|
504 |
tim |
1074 |
//if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
505 |
|
|
// sprintf( painCave.errMsg, |
506 |
|
|
// "Initialize from file error. Atom %s at index %d " |
507 |
|
|
// "in file %s does not" |
508 |
|
|
// " match the BASS atom %s.\n", |
509 |
|
|
// foo, atomIndex, inName, atoms[atomIndex]->getType() ); |
510 |
|
|
// return strdup( painCave.errMsg ); |
511 |
|
|
//} |
512 |
gezelter |
637 |
|
513 |
|
|
// get the positions |
514 |
|
|
|
515 |
|
|
foo = strtok(NULL, " ,;\t"); |
516 |
|
|
if(foo == NULL){ |
517 |
|
|
sprintf( painCave.errMsg, |
518 |
|
|
"error in reading postition x from %s\n" |
519 |
|
|
"natoms = %d, index = %d\n", |
520 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
521 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
522 |
|
|
} |
523 |
mmeineke |
804 |
pos[0] = atof( foo ); |
524 |
gezelter |
637 |
|
525 |
|
|
foo = strtok(NULL, " ,;\t"); |
526 |
|
|
if(foo == NULL){ |
527 |
|
|
sprintf( painCave.errMsg, |
528 |
|
|
"error in reading postition y from %s\n" |
529 |
|
|
"natoms = %d, index = %d\n", |
530 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
531 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
532 |
|
|
} |
533 |
mmeineke |
804 |
pos[1] = atof( foo ); |
534 |
gezelter |
637 |
|
535 |
|
|
foo = strtok(NULL, " ,;\t"); |
536 |
|
|
if(foo == NULL){ |
537 |
|
|
sprintf( painCave.errMsg, |
538 |
|
|
"error in reading postition z from %s\n" |
539 |
|
|
"natoms = %d, index = %d\n", |
540 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
541 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
542 |
|
|
} |
543 |
mmeineke |
804 |
pos[2] = atof( foo ); |
544 |
gezelter |
637 |
|
545 |
|
|
|
546 |
|
|
// get the velocities |
547 |
|
|
|
548 |
|
|
foo = strtok(NULL, " ,;\t"); |
549 |
|
|
if(foo == NULL){ |
550 |
|
|
sprintf( painCave.errMsg, |
551 |
|
|
"error in reading velocity x from %s\n" |
552 |
|
|
"natoms = %d, index = %d\n", |
553 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
554 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
555 |
|
|
} |
556 |
mmeineke |
804 |
vel[0] = atof( foo ); |
557 |
gezelter |
637 |
|
558 |
|
|
foo = strtok(NULL, " ,;\t"); |
559 |
|
|
if(foo == NULL){ |
560 |
|
|
sprintf( painCave.errMsg, |
561 |
|
|
"error in reading velocity y from %s\n" |
562 |
|
|
"natoms = %d, index = %d\n", |
563 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
564 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
565 |
|
|
} |
566 |
mmeineke |
804 |
vel[1] = atof( foo ); |
567 |
gezelter |
637 |
|
568 |
|
|
foo = strtok(NULL, " ,;\t"); |
569 |
|
|
if(foo == NULL){ |
570 |
|
|
sprintf( painCave.errMsg, |
571 |
|
|
"error in reading velocity z from %s\n" |
572 |
|
|
"natoms = %d, index = %d\n", |
573 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
574 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
575 |
|
|
} |
576 |
mmeineke |
804 |
vel[2] = atof( foo ); |
577 |
gezelter |
637 |
|
578 |
|
|
|
579 |
|
|
// get the quaternions |
580 |
|
|
|
581 |
|
|
if( atoms[atomIndex]->isDirectional() ){ |
582 |
|
|
|
583 |
|
|
foo = strtok(NULL, " ,;\t"); |
584 |
|
|
if(foo == NULL){ |
585 |
|
|
sprintf(painCave.errMsg, |
586 |
|
|
"error in reading quaternion 0 from %s\n" |
587 |
|
|
"natoms = %d, index = %d\n", |
588 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
589 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
590 |
|
|
} |
591 |
|
|
q[0] = atof( foo ); |
592 |
|
|
|
593 |
|
|
foo = strtok(NULL, " ,;\t"); |
594 |
|
|
if(foo == NULL){ |
595 |
|
|
sprintf( painCave.errMsg, |
596 |
|
|
"error in reading quaternion 1 from %s\n" |
597 |
|
|
"natoms = %d, index = %d\n", |
598 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
599 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
600 |
|
|
} |
601 |
|
|
q[1] = atof( foo ); |
602 |
|
|
|
603 |
|
|
foo = strtok(NULL, " ,;\t"); |
604 |
|
|
if(foo == NULL){ |
605 |
|
|
sprintf( painCave.errMsg, |
606 |
|
|
"error in reading quaternion 2 from %s\n" |
607 |
|
|
"natoms = %d, index = %d\n", |
608 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
609 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
610 |
|
|
} |
611 |
|
|
q[2] = atof( foo ); |
612 |
|
|
|
613 |
|
|
foo = strtok(NULL, " ,;\t"); |
614 |
|
|
if(foo == NULL){ |
615 |
|
|
sprintf( painCave.errMsg, |
616 |
|
|
"error in reading quaternion 3 from %s\n" |
617 |
|
|
"natoms = %d, index = %d\n", |
618 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
619 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
620 |
|
|
} |
621 |
|
|
q[3] = atof( foo ); |
622 |
|
|
|
623 |
|
|
// get the angular velocities |
624 |
|
|
|
625 |
|
|
foo = strtok(NULL, " ,;\t"); |
626 |
|
|
if(foo == NULL){ |
627 |
|
|
sprintf( painCave.errMsg, |
628 |
|
|
"error in reading angular momentum jx from %s\n" |
629 |
|
|
"natoms = %d, index = %d\n", |
630 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
631 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
632 |
|
|
} |
633 |
|
|
jx = atof( foo ); |
634 |
|
|
|
635 |
|
|
foo = strtok(NULL, " ,;\t"); |
636 |
|
|
if(foo == NULL){ |
637 |
|
|
sprintf( painCave.errMsg, |
638 |
|
|
"error in reading angular momentum jy from %s\n" |
639 |
|
|
"natoms = %d, index = %d\n", |
640 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
641 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
642 |
|
|
} |
643 |
|
|
jy = atof(foo ); |
644 |
|
|
|
645 |
|
|
foo = strtok(NULL, " ,;\t"); |
646 |
|
|
if(foo == NULL){ |
647 |
|
|
sprintf( painCave.errMsg, |
648 |
|
|
"error in reading angular momentum jz from %s\n" |
649 |
|
|
"natoms = %d, index = %d\n", |
650 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
651 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
652 |
|
|
} |
653 |
|
|
jz = atof( foo ); |
654 |
|
|
|
655 |
|
|
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
656 |
|
|
|
657 |
|
|
// check that the quaternion vector is normalized |
658 |
|
|
|
659 |
|
|
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
660 |
|
|
|
661 |
|
|
qLength = sqrt( qSqr ); |
662 |
|
|
q[0] = q[0] / qLength; |
663 |
|
|
q[1] = q[1] / qLength; |
664 |
|
|
q[2] = q[2] / qLength; |
665 |
|
|
q[3] = q[3] / qLength; |
666 |
|
|
|
667 |
|
|
dAtom->setQ( q ); |
668 |
|
|
|
669 |
|
|
// add the angular velocities |
670 |
|
|
|
671 |
|
|
dAtom->setJx( jx ); |
672 |
|
|
dAtom->setJy( jy ); |
673 |
|
|
dAtom->setJz( jz ); |
674 |
|
|
} |
675 |
|
|
|
676 |
|
|
// add the positions and velocities to the atom |
677 |
|
|
|
678 |
mmeineke |
804 |
atoms[atomIndex]->setPos( pos ); |
679 |
|
|
atoms[atomIndex]->setVel( vel ); |
680 |
|
|
|
681 |
gezelter |
637 |
return NULL; |
682 |
|
|
} |
683 |
|
|
|
684 |
|
|
|
685 |
mmeineke |
804 |
char* DumpReader::parseCommentLine(char* readLine, double &time, |
686 |
gezelter |
637 |
double boxMat[9]){ |
687 |
|
|
|
688 |
|
|
char *foo; // the pointer to the current string token |
689 |
|
|
int j; |
690 |
mmeineke |
847 |
double chi, integralOfChidt; |
691 |
|
|
double eta[9]; |
692 |
gezelter |
637 |
|
693 |
|
|
// set the string tokenizer |
694 |
|
|
|
695 |
|
|
foo = strtok(readLine, " ,;\t"); |
696 |
|
|
if(foo == NULL){ |
697 |
|
|
sprintf( painCave.errMsg, |
698 |
|
|
"error in reading time from %s\n", |
699 |
mmeineke |
647 |
inName ); |
700 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
701 |
|
|
} |
702 |
|
|
time = atof( foo ); |
703 |
|
|
|
704 |
|
|
// get the Hx vector |
705 |
|
|
|
706 |
|
|
foo = strtok(NULL, " ,;\t"); |
707 |
|
|
if(foo == NULL){ |
708 |
|
|
sprintf( painCave.errMsg, |
709 |
|
|
"error in reading Hx[0] from %s\n", |
710 |
mmeineke |
647 |
inName ); |
711 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
712 |
|
|
} |
713 |
|
|
boxMat[0] = atof( foo ); |
714 |
|
|
|
715 |
|
|
foo = strtok(NULL, " ,;\t"); |
716 |
|
|
if(foo == NULL){ |
717 |
|
|
sprintf( painCave.errMsg, |
718 |
|
|
"error in reading Hx[1] from %s\n", |
719 |
mmeineke |
647 |
inName ); |
720 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
721 |
|
|
} |
722 |
|
|
boxMat[1] = atof( foo ); |
723 |
|
|
|
724 |
|
|
foo = strtok(NULL, " ,;\t"); |
725 |
|
|
if(foo == NULL){ |
726 |
|
|
sprintf( painCave.errMsg, |
727 |
|
|
"error in reading Hx[2] from %s\n", |
728 |
mmeineke |
647 |
inName ); |
729 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
730 |
|
|
} |
731 |
|
|
boxMat[2] = atof( foo ); |
732 |
|
|
|
733 |
|
|
// get the Hy vector |
734 |
|
|
|
735 |
|
|
foo = strtok(NULL, " ,;\t"); |
736 |
|
|
if(foo == NULL){ |
737 |
|
|
sprintf( painCave.errMsg, |
738 |
|
|
"error in reading Hy[0] from %s\n", |
739 |
mmeineke |
647 |
inName ); |
740 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
741 |
|
|
} |
742 |
|
|
boxMat[3] = atof( foo ); |
743 |
|
|
|
744 |
|
|
foo = strtok(NULL, " ,;\t"); |
745 |
|
|
if(foo == NULL){ |
746 |
|
|
sprintf( painCave.errMsg, |
747 |
|
|
"error in reading Hy[1] from %s\n", |
748 |
mmeineke |
647 |
inName ); |
749 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
750 |
|
|
} |
751 |
|
|
boxMat[4] = atof( foo ); |
752 |
|
|
|
753 |
|
|
foo = strtok(NULL, " ,;\t"); |
754 |
|
|
if(foo == NULL){ |
755 |
|
|
sprintf( painCave.errMsg, |
756 |
|
|
"error in reading Hy[2] from %s\n", |
757 |
mmeineke |
647 |
inName ); |
758 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
759 |
|
|
} |
760 |
|
|
boxMat[5] = atof( foo ); |
761 |
|
|
|
762 |
|
|
// get the Hz vector |
763 |
|
|
|
764 |
|
|
foo = strtok(NULL, " ,;\t"); |
765 |
|
|
if(foo == NULL){ |
766 |
|
|
sprintf( painCave.errMsg, |
767 |
|
|
"error in reading Hz[0] from %s\n", |
768 |
mmeineke |
647 |
inName ); |
769 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
770 |
|
|
} |
771 |
|
|
boxMat[6] = atof( foo ); |
772 |
|
|
|
773 |
|
|
foo = strtok(NULL, " ,;\t"); |
774 |
|
|
if(foo == NULL){ |
775 |
|
|
sprintf( painCave.errMsg, |
776 |
|
|
"error in reading Hz[1] from %s\n", |
777 |
mmeineke |
647 |
inName ); |
778 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
779 |
|
|
} |
780 |
|
|
boxMat[7] = atof( foo ); |
781 |
|
|
|
782 |
|
|
foo = strtok(NULL, " ,;\t"); |
783 |
|
|
if(foo == NULL){ |
784 |
|
|
sprintf( painCave.errMsg, |
785 |
|
|
"error in reading Hz[2] from %s\n", |
786 |
mmeineke |
647 |
inName ); |
787 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
788 |
|
|
} |
789 |
|
|
boxMat[8] = atof( foo ); |
790 |
|
|
|
791 |
|
|
return NULL; |
792 |
mmeineke |
847 |
|
793 |
|
|
//get chi and integralOfChidt, they should appear by pair |
794 |
|
|
foo = strtok(NULL, " ,;\t\n"); |
795 |
|
|
if(foo != NULL){ |
796 |
|
|
chi = atof(foo); |
797 |
|
|
|
798 |
|
|
foo = strtok(NULL, " ,;\t\n"); |
799 |
|
|
if(foo == NULL){ |
800 |
|
|
sprintf( painCave.errMsg, |
801 |
|
|
"chi and integralOfChidt should appear by pair in %s\n", inName ); |
802 |
|
|
return strdup( painCave.errMsg ); |
803 |
|
|
} |
804 |
|
|
integralOfChidt = atof( foo ); |
805 |
|
|
|
806 |
|
|
//push chi and integralOfChidt into SimInfo::properties which can be |
807 |
|
|
//retrieved by integrator later |
808 |
|
|
DoubleData* chiValue = new DoubleData(); |
809 |
|
|
chiValue->setID(CHIVALUE_ID); |
810 |
|
|
chiValue->setData(chi); |
811 |
|
|
simnfo->addProperty(chiValue); |
812 |
|
|
|
813 |
|
|
DoubleData* integralOfChidtValue = new DoubleData(); |
814 |
|
|
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
815 |
|
|
integralOfChidtValue->setData(integralOfChidt); |
816 |
|
|
simnfo->addProperty(integralOfChidtValue); |
817 |
|
|
|
818 |
|
|
} |
819 |
|
|
else |
820 |
|
|
return NULL; |
821 |
|
|
|
822 |
|
|
//get eta |
823 |
|
|
for(int i = 0 ; i < 9; i++){ |
824 |
|
|
foo = strtok(NULL, " ,;\t"); |
825 |
|
|
if(foo == NULL){ |
826 |
|
|
sprintf( painCave.errMsg, |
827 |
|
|
"error in reading eta[%d] from %s\n", i, inName ); |
828 |
|
|
return strdup( painCave.errMsg ); |
829 |
|
|
} |
830 |
|
|
eta[i] = atof( foo ); |
831 |
|
|
} |
832 |
|
|
|
833 |
|
|
//push eta into SimInfo::properties which can be |
834 |
|
|
//retrieved by integrator later |
835 |
|
|
//simnfo->setBoxM( theBoxMat3 ); |
836 |
|
|
DoubleArrayData* etaValue = new DoubleArrayData(); |
837 |
|
|
etaValue->setID(ETAVALUE_ID); |
838 |
|
|
etaValue->setData(eta, 9); |
839 |
|
|
simnfo->addProperty(etaValue); |
840 |
|
|
|
841 |
|
|
|
842 |
|
|
return NULL; |
843 |
|
|
|
844 |
|
|
|
845 |
|
|
|
846 |
gezelter |
637 |
} |
847 |
|
|
|
848 |
|
|
|
849 |
|
|
#ifdef IS_MPI |
850 |
|
|
|
851 |
|
|
// a couple of functions to let us escape the read loop |
852 |
|
|
|
853 |
mmeineke |
804 |
void dumpRead::nodeZeroError( void ){ |
854 |
gezelter |
637 |
int j, myStatus; |
855 |
|
|
|
856 |
|
|
myStatus = 0; |
857 |
|
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
858 |
|
|
MPI_Send( &myStatus, 1, MPI_INT, j, |
859 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
860 |
|
|
} |
861 |
|
|
|
862 |
|
|
|
863 |
|
|
MPI_Finalize(); |
864 |
|
|
exit (0); |
865 |
|
|
|
866 |
|
|
} |
867 |
|
|
|
868 |
mmeineke |
804 |
void dumpRead::anonymousNodeDie( void ){ |
869 |
gezelter |
637 |
|
870 |
|
|
MPI_Finalize(); |
871 |
|
|
exit (0); |
872 |
|
|
} |
873 |
|
|
|
874 |
|
|
#endif //is_mpi |