1 |
#define _FILE_OFFSET_BITS 64 |
2 |
|
3 |
#include <stdio.h> |
4 |
#include <stdlib.h> |
5 |
#include <sys/types.h> |
6 |
#include <sys/stat.h> |
7 |
#include <string.h> |
8 |
|
9 |
#include "params.h" |
10 |
#include "tcProps.h" |
11 |
#include "readWrite.h" |
12 |
|
13 |
|
14 |
#define BUFFER_SIZE 2000 |
15 |
int isScanned; |
16 |
int fileOpen; |
17 |
int nFrames; |
18 |
double *frameTimes; |
19 |
FILE* inFile; |
20 |
char* inName; |
21 |
|
22 |
struct linkedPos{ |
23 |
|
24 |
fpos_t *myPos; |
25 |
double timeStamp; |
26 |
double Hmat[3][3]; |
27 |
struct linkedPos* next; |
28 |
}; |
29 |
|
30 |
struct staticPos{ |
31 |
|
32 |
fpos_t *myPos; |
33 |
double Hmat[3][3]; |
34 |
}; |
35 |
struct staticPos* posArray; |
36 |
|
37 |
void parseDumpLine( char readBuffer[BUFFER_SIZE], int index, |
38 |
struct atomCoord* atoms ); |
39 |
void setU( double q[4], double u[3] ); |
40 |
void normalizeQ( double q[4] ); |
41 |
|
42 |
void openFile( void ){ |
43 |
|
44 |
inFile = fopen(inName, "r"); |
45 |
if(inFile ==NULL){ |
46 |
fprintf(stderr, |
47 |
"Error opening file \"%s\"\n", |
48 |
inName); |
49 |
exit(0); |
50 |
} |
51 |
|
52 |
fileOpen = 1; |
53 |
} |
54 |
|
55 |
void closeFile( void ){ |
56 |
|
57 |
fclose( inFile ); |
58 |
|
59 |
fileOpen = 0; |
60 |
} |
61 |
|
62 |
void setFrames( void ){ |
63 |
|
64 |
int i,j,k; |
65 |
struct linkedPos* headPos; |
66 |
struct linkedPos* currPos; |
67 |
fpos_t *currPT; |
68 |
char readBuffer[BUFFER_SIZE]; |
69 |
char trash[BUFFER_SIZE]; |
70 |
char* foo; |
71 |
int lineNum = 0; |
72 |
|
73 |
|
74 |
if( !fileOpen ){ |
75 |
fprintf(stderr, |
76 |
"Attempt to scan the file without first opening the file.\n" ); |
77 |
exit(0); |
78 |
} |
79 |
|
80 |
|
81 |
nFrames = 0; |
82 |
headPos = (struct linkedPos*)malloc(sizeof(struct linkedPos)); |
83 |
currPos = headPos; |
84 |
|
85 |
currPT = (fpos_t *)malloc(sizeof(fpos_t)); |
86 |
fgetpos(inFile, currPT); |
87 |
|
88 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
89 |
lineNum++; |
90 |
if( feof( inFile ) ){ |
91 |
fprintf( stderr, |
92 |
"File \"%s\" ended unexpectedly at line %d\n", |
93 |
inName, |
94 |
lineNum ); |
95 |
exit(0); |
96 |
} |
97 |
|
98 |
while( !feof( inFile ) ){ |
99 |
|
100 |
currPos->next = (struct linkedPos*)malloc(sizeof(struct linkedPos)); |
101 |
currPos = currPos->next; |
102 |
currPos->myPos = currPT; |
103 |
nFrames++; |
104 |
|
105 |
i = atoi(readBuffer); |
106 |
|
107 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
108 |
lineNum++; |
109 |
if( feof( inFile ) ){ |
110 |
fprintf( stderr, |
111 |
"File \"%s\" ended unexpectedly at line %d\n", |
112 |
inName, |
113 |
lineNum ); |
114 |
exit(0); |
115 |
} |
116 |
|
117 |
|
118 |
// parse the comment line |
119 |
|
120 |
foo = strtok(readBuffer, " ,;\t"); |
121 |
|
122 |
if(foo == NULL){ |
123 |
fprintf(stderr, |
124 |
"error in reading time from %s at line %d\n", |
125 |
inName, lineNum ); |
126 |
exit(0); |
127 |
} |
128 |
currPos->timeStamp = atof( foo ); |
129 |
|
130 |
// get the Hx vector |
131 |
|
132 |
foo = strtok(NULL, " ,;\t"); |
133 |
if(foo == NULL){ |
134 |
fprintf(stderr, |
135 |
"error in reading Hx[0] from %s at line %d\n", |
136 |
inName, lineNum ); |
137 |
exit(0); |
138 |
} |
139 |
currPos->Hmat[0][0] = atof( foo ); |
140 |
|
141 |
foo = strtok(NULL, " ,;\t"); |
142 |
if(foo == NULL){ |
143 |
fprintf(stderr, |
144 |
"error in reading Hx[1] from %s at line %d\n", |
145 |
inName, lineNum ); |
146 |
exit(0); |
147 |
} |
148 |
currPos->Hmat[1][0] = atof( foo ); |
149 |
|
150 |
foo = strtok(NULL, " ,;\t"); |
151 |
if(foo == NULL){ |
152 |
fprintf(stderr, |
153 |
"error in reading Hx[2] from %s at line %d\n", |
154 |
inName, lineNum ); |
155 |
exit(0); |
156 |
} |
157 |
currPos->Hmat[2][0] = atof( foo ); |
158 |
|
159 |
// get the Hy vector |
160 |
|
161 |
foo = strtok(NULL, " ,;\t"); |
162 |
if(foo == NULL){ |
163 |
fprintf(stderr, |
164 |
"error in reading Hy[0] from %s at line %d\n", |
165 |
inName, lineNum ); |
166 |
exit(0); |
167 |
} |
168 |
currPos->Hmat[0][1] = atof( foo ); |
169 |
|
170 |
foo = strtok(NULL, " ,;\t"); |
171 |
if(foo == NULL){ |
172 |
fprintf(stderr, |
173 |
"error in reading Hy[1] from %s at line %d\n", |
174 |
inName, lineNum ); |
175 |
exit(0); |
176 |
} |
177 |
currPos->Hmat[1][1] = atof( foo ); |
178 |
|
179 |
foo = strtok(NULL, " ,;\t"); |
180 |
if(foo == NULL){ |
181 |
fprintf(stderr, |
182 |
"error in reading Hy[2] from %s at line %d\n", |
183 |
inName, lineNum ); |
184 |
exit(0); |
185 |
} |
186 |
currPos->Hmat[2][1] = atof( foo ); |
187 |
|
188 |
// get the Hz vector |
189 |
|
190 |
foo = strtok(NULL, " ,;\t"); |
191 |
if(foo == NULL){ |
192 |
fprintf(stderr, |
193 |
"error in reading Hz[0] from %s at line %d\n", |
194 |
inName, lineNum ); |
195 |
exit(0); |
196 |
} |
197 |
currPos->Hmat[0][2] = atof( foo ); |
198 |
|
199 |
foo = strtok(NULL, " ,;\t"); |
200 |
if(foo == NULL){ |
201 |
fprintf(stderr, |
202 |
"error in reading Hz[1] from %s at line %d\n", |
203 |
inName, lineNum ); |
204 |
exit(0); |
205 |
} |
206 |
currPos->Hmat[1][2] = atof( foo ); |
207 |
|
208 |
foo = strtok(NULL, " ,;\t"); |
209 |
if(foo == NULL){ |
210 |
fprintf(stderr, |
211 |
"error in reading Hz[2] from %s at line %d\n", |
212 |
inName, lineNum ); |
213 |
exit(0); |
214 |
} |
215 |
currPos->Hmat[2][2] = atof( foo ); |
216 |
|
217 |
// skip the atoms |
218 |
|
219 |
for(j=0; j<i; j++){ |
220 |
|
221 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
222 |
lineNum++; |
223 |
if( feof( inFile ) ){ |
224 |
fprintf( stderr, |
225 |
"File \"%s\" ended unexpectedly at line %d," |
226 |
" with atom %d\n", |
227 |
inName, |
228 |
lineNum, |
229 |
j ); |
230 |
exit(0); |
231 |
} |
232 |
} |
233 |
|
234 |
currPT = (fpos_t *)malloc(sizeof(fpos_t)); |
235 |
fgetpos(inFile, currPT); |
236 |
|
237 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
238 |
lineNum++; |
239 |
} |
240 |
|
241 |
// allocate the static position array |
242 |
|
243 |
posArray = (struct staticPos*)calloc(nFrames, sizeof(struct staticPos)); |
244 |
frameTimes = (double *)calloc(nFrames, sizeof(double) ); |
245 |
|
246 |
i=0; |
247 |
currPos = headPos->next; |
248 |
while( currPos != NULL ){ |
249 |
|
250 |
if(i>=nFrames){ |
251 |
|
252 |
fprintf( stderr, |
253 |
"The number of frame pointers exceeded the number of frames.\n" |
254 |
" OOPS!\n" ); |
255 |
exit(0); |
256 |
} |
257 |
|
258 |
frameTimes[i] = currPos->timeStamp; |
259 |
posArray[i].myPos = currPos->myPos; |
260 |
for(j=0;j<3;j++){ |
261 |
for(k=0;k<3;k++){ |
262 |
posArray[i].Hmat[j][k] = currPos->Hmat[j][k]; |
263 |
} |
264 |
} |
265 |
|
266 |
i++; |
267 |
currPos = currPos->next; |
268 |
} |
269 |
|
270 |
// clean up the linked list |
271 |
|
272 |
currPos = headPos; |
273 |
while( currPos != NULL ){ |
274 |
headPos = currPos; |
275 |
currPos = headPos->next; |
276 |
free(headPos); |
277 |
} |
278 |
|
279 |
|
280 |
isScanned = 1; |
281 |
} |
282 |
|
283 |
|
284 |
void readFrame(int theFrame, struct atomCoord* atoms, double Hmat[3][3] ){ |
285 |
|
286 |
// list of 'a priori' constants |
287 |
|
288 |
const int nLipAtoms = NL_ATOMS; |
289 |
const int nBonds = NBONDS; |
290 |
const int nLipids = NLIPIDS; |
291 |
const int nSSD = NSSD; |
292 |
const int nAtoms = nLipAtoms * nLipids + nSSD; |
293 |
|
294 |
fpos_t *framePos; |
295 |
char readBuffer[BUFFER_SIZE]; |
296 |
|
297 |
int i, j, k; |
298 |
|
299 |
|
300 |
// quick checks |
301 |
|
302 |
if (theFrame >= nFrames){ |
303 |
|
304 |
fprintf(stderr, |
305 |
"frame %d, is out of range\n", |
306 |
theFrame ); |
307 |
exit(0); |
308 |
} |
309 |
|
310 |
if( !fileOpen ){ |
311 |
|
312 |
fprintf( stderr, |
313 |
"File is closed, cannot read frame %d.\n", |
314 |
theFrame ); |
315 |
exit(0); |
316 |
} |
317 |
|
318 |
// access the frame |
319 |
|
320 |
framePos = posArray[theFrame].myPos; |
321 |
fsetpos( inFile, framePos ); |
322 |
|
323 |
for(j=0;j<3;j++){ |
324 |
for(k=0;k<3;k++){ |
325 |
Hmat[j][k] = posArray[theFrame].Hmat[j][k]; |
326 |
} |
327 |
} |
328 |
|
329 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
330 |
if( feof( inFile ) ){ |
331 |
fprintf( stderr, |
332 |
"File \"%s\" ended unexpectedly in Frame %d\n", |
333 |
inName, |
334 |
theFrame ); |
335 |
exit(0); |
336 |
} |
337 |
|
338 |
i = atoi( readBuffer ); |
339 |
if( i != nAtoms ){ |
340 |
fprintf( stderr, |
341 |
"Error in frame %d: frame atoms, %d, does not params atoms, %d\n", |
342 |
theFrame, |
343 |
i, |
344 |
nAtoms ); |
345 |
exit(0); |
346 |
} |
347 |
|
348 |
// read and toss the comment line |
349 |
|
350 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
351 |
if( feof( inFile ) ){ |
352 |
fprintf( stderr, |
353 |
"File \"%s\" ended unexpectedly in Frame %d\n", |
354 |
inName, |
355 |
theFrame ); |
356 |
exit(0); |
357 |
} |
358 |
|
359 |
// read the atoms |
360 |
|
361 |
for( i=0; i < nAtoms; i++){ |
362 |
|
363 |
fgets( readBuffer, sizeof( readBuffer ), inFile ); |
364 |
if( feof( inFile ) ){ |
365 |
fprintf( stderr, |
366 |
"File \"%s\" ended unexpectedly in Frame %d at atom %d\n", |
367 |
inName, |
368 |
theFrame, |
369 |
i ); |
370 |
exit(0); |
371 |
} |
372 |
|
373 |
|
374 |
parseDumpLine( readBuffer, i, atoms ); |
375 |
} |
376 |
} |
377 |
|
378 |
void parseDumpLine( char readLine[BUFFER_SIZE], int i, |
379 |
struct atomCoord* atoms ){ |
380 |
|
381 |
const int nLipAtoms = NL_ATOMS; |
382 |
const int nBonds = NBONDS; |
383 |
const int nLipids = NLIPIDS; |
384 |
const int nSSD = NSSD; |
385 |
const int nAtoms = nLipAtoms * nLipids + nSSD; |
386 |
|
387 |
char* foo; |
388 |
double q[4]; |
389 |
|
390 |
// set the string tokenizer |
391 |
|
392 |
foo = strtok(readLine, " ,;\t"); |
393 |
|
394 |
// check the atom ID |
395 |
|
396 |
switch( atoms[i].type ){ |
397 |
|
398 |
case HEAD: |
399 |
if( strcmp(foo, "HEAD") ){ |
400 |
fprintf( stderr, |
401 |
"Atom %s does not match master array type \"HEAD\".\n", |
402 |
foo ); |
403 |
exit(0); |
404 |
} |
405 |
break; |
406 |
|
407 |
case CH: |
408 |
if( strcmp(foo, "CH") ){ |
409 |
fprintf( stderr, |
410 |
"Atom %s does not match master array type \"CH\".\n", |
411 |
foo ); |
412 |
exit(0); |
413 |
} |
414 |
break; |
415 |
|
416 |
case CH2: |
417 |
if( strcmp(foo, "CH2") ){ |
418 |
fprintf( stderr, |
419 |
"Atom %s does not match master array type \"CH2\".\n", |
420 |
foo ); |
421 |
exit(0); |
422 |
} |
423 |
break; |
424 |
|
425 |
case CH3: |
426 |
if( strcmp(foo, "CH3") ){ |
427 |
fprintf( stderr, |
428 |
"Atom %s does not match master array type \"CH3\".\n", |
429 |
foo ); |
430 |
exit(0); |
431 |
} |
432 |
break; |
433 |
|
434 |
case SSD: |
435 |
if( strcmp(foo, "SSD") ){ |
436 |
fprintf( stderr, |
437 |
"Atom %s does not match master array type \"SSD\".\n", |
438 |
foo ); |
439 |
exit(0); |
440 |
} |
441 |
break; |
442 |
|
443 |
default: |
444 |
fprintf(stderr, |
445 |
"Atom %d is an unrecognized enumeration\n", |
446 |
i ); |
447 |
exit(0); |
448 |
} |
449 |
|
450 |
// get the positions |
451 |
|
452 |
foo = strtok(NULL, " ,;\t"); |
453 |
if(foo == NULL){ |
454 |
fprintf( stderr, |
455 |
"error in reading postition x from %s\n" |
456 |
"natoms = %d, i = %d\n", |
457 |
inName, nAtoms, i ); |
458 |
exit(0); |
459 |
} |
460 |
atoms[i].pos[0] = atof( foo ); |
461 |
|
462 |
foo = strtok(NULL, " ,;\t"); |
463 |
if(foo == NULL){ |
464 |
fprintf( stderr, |
465 |
"error in reading postition y from %s\n" |
466 |
"natoms = %d, i = %d\n", |
467 |
inName, nAtoms, i ); |
468 |
exit(0); |
469 |
} |
470 |
atoms[i].pos[1] = atof( foo ); |
471 |
|
472 |
foo = strtok(NULL, " ,;\t"); |
473 |
if(foo == NULL){ |
474 |
fprintf( stderr, |
475 |
"error in reading postition z from %s\n" |
476 |
"natoms = %d, i = %d\n", |
477 |
inName, nAtoms, i ); |
478 |
exit(0); |
479 |
} |
480 |
atoms[i].pos[2] = atof( foo ); |
481 |
|
482 |
|
483 |
// get the velocities |
484 |
|
485 |
foo = strtok(NULL, " ,;\t"); |
486 |
if(foo == NULL){ |
487 |
fprintf( stderr, |
488 |
"error in reading velocity x from %s\n" |
489 |
"natoms = %d, i = %d\n", |
490 |
inName, nAtoms, i ); |
491 |
exit(0); |
492 |
} |
493 |
atoms[i].vel[0] = atof( foo ); |
494 |
|
495 |
foo = strtok(NULL, " ,;\t"); |
496 |
if(foo == NULL){ |
497 |
fprintf( stderr, |
498 |
"error in reading velocity y from %s\n" |
499 |
"natoms = %d, i = %d\n", |
500 |
inName, nAtoms, i ); |
501 |
exit(0); |
502 |
} |
503 |
atoms[i].vel[1] = atof( foo ); |
504 |
|
505 |
foo = strtok(NULL, " ,;\t"); |
506 |
if(foo == NULL){ |
507 |
fprintf( stderr, |
508 |
"error in reading velocity z from %s\n" |
509 |
"natoms = %d, i = %d\n", |
510 |
inName, nAtoms, i ); |
511 |
exit(0); |
512 |
} |
513 |
atoms[i].vel[2] = atof( foo ); |
514 |
|
515 |
|
516 |
// get the quaternions |
517 |
|
518 |
if( (atoms[i].type == HEAD) || (atoms[i].type == SSD) ){ |
519 |
|
520 |
foo = strtok(NULL, " ,;\t"); |
521 |
if(foo == NULL){ |
522 |
fprintf( stderr, |
523 |
"error in reading quaternion 0 from %s\n" |
524 |
"natoms = %d, i = %d\n", |
525 |
inName, nAtoms, i ); |
526 |
exit(0); |
527 |
} |
528 |
q[0] = atof( foo ); |
529 |
|
530 |
foo = strtok(NULL, " ,;\t"); |
531 |
if(foo == NULL){ |
532 |
fprintf( stderr, |
533 |
"error in reading quaternion 1 from %s\n" |
534 |
"natoms = %d, i = %d\n", |
535 |
inName, nAtoms, i ); |
536 |
exit(0); |
537 |
} |
538 |
q[1] = atof( foo ); |
539 |
|
540 |
foo = strtok(NULL, " ,;\t"); |
541 |
if(foo == NULL){ |
542 |
fprintf( stderr, |
543 |
"error in reading quaternion 2 from %s\n" |
544 |
"natoms = %d, i = %d\n", |
545 |
inName, nAtoms, i ); |
546 |
exit(0); |
547 |
} |
548 |
q[2] = atof( foo ); |
549 |
|
550 |
foo = strtok(NULL, " ,;\t"); |
551 |
if(foo == NULL){ |
552 |
fprintf( stderr, |
553 |
"error in reading quaternion 3 from %s\n" |
554 |
"natoms = %d, i = %d\n", |
555 |
inName, nAtoms, i ); |
556 |
exit(0); |
557 |
} |
558 |
q[3] = atof( foo ); |
559 |
|
560 |
normalizeQ( q ); |
561 |
|
562 |
setU( q, atoms[i].u ); |
563 |
} |
564 |
} |
565 |
|
566 |
|
567 |
void setU( double the_q[4], double u[3] ){ |
568 |
|
569 |
double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
570 |
double A[3][3]; |
571 |
double rb[3]; |
572 |
int i,j,k; |
573 |
|
574 |
// initialize the axis |
575 |
|
576 |
rb[0] = 0.0; |
577 |
rb[1] = 0.0; |
578 |
rb[2] = 1.0; |
579 |
|
580 |
// set the rotation matrix |
581 |
|
582 |
q0Sqr = the_q[0] * the_q[0]; |
583 |
q1Sqr = the_q[1] * the_q[1]; |
584 |
q2Sqr = the_q[2] * the_q[2]; |
585 |
q3Sqr = the_q[3] * the_q[3]; |
586 |
|
587 |
A[0][0] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
588 |
A[0][1] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
589 |
A[0][2] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
590 |
|
591 |
A[1][0] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
592 |
A[1][1] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
593 |
A[1][2] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
594 |
|
595 |
A[2][0] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
596 |
A[2][1] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
597 |
A[2][2] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
598 |
|
599 |
// perform the rotation |
600 |
|
601 |
for( i=0; i<3; i++ ){ |
602 |
u[i] = 0.0; |
603 |
|
604 |
for( j=0; j<3; j++ ){ |
605 |
u[i] += A[j][i] * rb[j]; |
606 |
} |
607 |
} |
608 |
} |
609 |
|
610 |
void normalizeQ( double q[4] ){ |
611 |
|
612 |
double qSqr, qL; |
613 |
int i; |
614 |
|
615 |
qSqr = 0.0; |
616 |
for(i=0;i<4;i++) |
617 |
qSqr += q[i] * q[i]; |
618 |
|
619 |
for(i=0;i<4;i++) |
620 |
q[i] /= qSqr; |
621 |
} |
622 |
|
623 |
double scanSmallestZ(int startFrame){ |
624 |
double smallest; |
625 |
int i; |
626 |
|
627 |
smallest = posArray[startFrame].Hmat[2][2]; |
628 |
for(i=startFrame;i<nFrames;i++) |
629 |
smallest = |
630 |
(smallest<posArray[i].Hmat[2][2])? smallest : posArray[i].Hmat[2][2]; |
631 |
|
632 |
return smallest; |
633 |
} |
634 |
|
635 |
double calcAverageXY( double startTime ){ |
636 |
|
637 |
int i, count, startFrame, startFound; |
638 |
double avg; |
639 |
|
640 |
startFound = 0; |
641 |
startFrame = -1; |
642 |
while( !startFound ){ |
643 |
|
644 |
startFrame++; |
645 |
|
646 |
if(startFrame >= nFrames){ |
647 |
|
648 |
fprintf( stderr, |
649 |
"Start Time, %G, was not found in the dump file.\n", |
650 |
startTime ); |
651 |
exit(0); |
652 |
} |
653 |
|
654 |
if(startTime <= frameTimes[startFrame]) |
655 |
startFound = 1; |
656 |
|
657 |
|
658 |
} |
659 |
|
660 |
avg = 0.0; |
661 |
count = 0; |
662 |
for(i=startFrame;i<nFrames;i++){ |
663 |
avg += posArray[i].Hmat[0][0] * posArray[i].Hmat[1][1]; |
664 |
count++; |
665 |
} |
666 |
avg /= (double)count; |
667 |
|
668 |
return avg; |
669 |
} |