| 1 |
#include <stdio.h> |
| 2 |
#include <stdlib.h> |
| 3 |
#include <string.h> |
| 4 |
#include <math.h> |
| 5 |
#include <unistd.h> |
| 6 |
#include <sys/types.h> |
| 7 |
#include <sys/stat.h> |
| 8 |
|
| 9 |
struct coords{ |
| 10 |
double x,y,z; // cartesian coords |
| 11 |
double q[4]; // the quanternions |
| 12 |
char name[30]; |
| 13 |
}; |
| 14 |
|
| 15 |
struct linked_xyz{ |
| 16 |
struct coords *r; |
| 17 |
double time; |
| 18 |
double boxX, boxY, boxZ; |
| 19 |
struct linked_xyz *next; |
| 20 |
}; |
| 21 |
|
| 22 |
char *program_name; /*the name of the program */ |
| 23 |
int printWater = 0; |
| 24 |
int printDipole = 0; |
| 25 |
|
| 26 |
void usage(void); |
| 27 |
|
| 28 |
void rotWrite( FILE* out_file, struct coords* theSSD ); |
| 29 |
|
| 30 |
void setRot( double A[3][3], double q[4] ); |
| 31 |
|
| 32 |
void rotMe( double A[3][3], double r[3] ); |
| 33 |
|
| 34 |
void map( double *x, double *y, double *z, double centerX, double centerY, |
| 35 |
double centerZ, double boxX, double boxY, double boxZ ); |
| 36 |
|
| 37 |
int main(argc, argv) |
| 38 |
int argc; |
| 39 |
char *argv[]; |
| 40 |
{ |
| 41 |
|
| 42 |
|
| 43 |
struct coords *out_coords; |
| 44 |
|
| 45 |
int i, j, k, l; /* loop counters */ |
| 46 |
mode_t dir_mode = S_IRWXU; |
| 47 |
|
| 48 |
int lineCount = 0; //the line number |
| 49 |
int newN; // the new number of atoms |
| 50 |
int nSSD=0; // the number of SSD per frame |
| 51 |
|
| 52 |
unsigned int nAtoms; /*the number of atoms in each time step */ |
| 53 |
char read_buffer[1000]; /*the line buffer for reading */ |
| 54 |
char *eof_test; /*ptr to see when we reach the end of the file */ |
| 55 |
char *foo; /*the pointer to the current string token */ |
| 56 |
FILE *in_file; /* the input file */ |
| 57 |
FILE *out_file; /*the output file */ |
| 58 |
char *out_prefix = NULL; /*the prefix of the output file */ |
| 59 |
char out_name[500]; /*the output name */ |
| 60 |
int have_outName =0; |
| 61 |
char in_name[500]; // the input file name |
| 62 |
char temp_name[500]; |
| 63 |
char *root_name = NULL; /*the root name of the input file */ |
| 64 |
unsigned int n_out = 0; /*keeps track of which output file is being written*/ |
| 65 |
|
| 66 |
|
| 67 |
int skipFrames = 1; |
| 68 |
|
| 69 |
struct linked_xyz *current_frame; |
| 70 |
struct linked_xyz *temp_frame; |
| 71 |
|
| 72 |
int nframes =0; |
| 73 |
|
| 74 |
int wrap = 0; |
| 75 |
|
| 76 |
double cX = 0.0; |
| 77 |
double cY = 0.0; |
| 78 |
double cZ = 0.0; |
| 79 |
|
| 80 |
double mcX, mcY, mcZ; |
| 81 |
double newCX, newCY, newCZ; |
| 82 |
double dx, dy, dz; |
| 83 |
int mcount; |
| 84 |
|
| 85 |
int repeatX = 0; |
| 86 |
int repeatY = 0; |
| 87 |
int repeatZ = 0; |
| 88 |
|
| 89 |
int nRepeatX = 0; |
| 90 |
int nRepeatY = 0; |
| 91 |
int nRepeatZ = 0; |
| 92 |
|
| 93 |
struct coords* rCopy; |
| 94 |
|
| 95 |
int done; |
| 96 |
char current_flag; |
| 97 |
|
| 98 |
program_name = argv[0]; /*save the program name in case we need it*/ |
| 99 |
|
| 100 |
for( i = 1; i < argc; i++){ |
| 101 |
|
| 102 |
if(argv[i][0] =='-'){ |
| 103 |
|
| 104 |
if(argv[i][1] == '-' ){ |
| 105 |
|
| 106 |
// parse long word options |
| 107 |
|
| 108 |
if( !strcmp( argv[i], "--repeatX" ) ){ |
| 109 |
repeatX = 1; |
| 110 |
i++; |
| 111 |
nRepeatX = atoi( argv[i] ); |
| 112 |
} |
| 113 |
|
| 114 |
else if( !strcmp( argv[i], "--repeatY" ) ){ |
| 115 |
repeatY = 1; |
| 116 |
i++; |
| 117 |
nRepeatY = atoi( argv[i] ); |
| 118 |
} |
| 119 |
|
| 120 |
else if( !strcmp( argv[i], "--repeatZ" ) ){ |
| 121 |
repeatZ = 1; |
| 122 |
i++; |
| 123 |
nRepeatZ = atoi( argv[i] ); |
| 124 |
} |
| 125 |
|
| 126 |
else{ |
| 127 |
fprintf( stderr, |
| 128 |
"Invalid option \"%s\"\n", argv[i] ); |
| 129 |
usage(); |
| 130 |
} |
| 131 |
} |
| 132 |
|
| 133 |
else{ |
| 134 |
|
| 135 |
// parse single character options |
| 136 |
|
| 137 |
done =0; |
| 138 |
j = 1; |
| 139 |
current_flag = argv[i][j]; |
| 140 |
while( (current_flag != '\0') && (!done) ){ |
| 141 |
|
| 142 |
switch(current_flag){ |
| 143 |
|
| 144 |
case 'o': |
| 145 |
// -o <prefix> => the output |
| 146 |
|
| 147 |
i++; |
| 148 |
strcpy( out_name, argv[i] ); |
| 149 |
have_outName = 1; |
| 150 |
done = 1; |
| 151 |
break; |
| 152 |
|
| 153 |
case 'n': |
| 154 |
// -n <#> => print every <#> frames |
| 155 |
|
| 156 |
i++; |
| 157 |
skipFrames = atoi(argv[i]); |
| 158 |
done = 1; |
| 159 |
break; |
| 160 |
|
| 161 |
case 'h': |
| 162 |
// -h => give the usage |
| 163 |
|
| 164 |
usage(); |
| 165 |
break; |
| 166 |
|
| 167 |
case 'd': |
| 168 |
// print the dipoles |
| 169 |
|
| 170 |
printDipole = 1; |
| 171 |
break; |
| 172 |
|
| 173 |
case 'w': |
| 174 |
// print the waters |
| 175 |
|
| 176 |
printWater = 1; |
| 177 |
break; |
| 178 |
|
| 179 |
case 'm': |
| 180 |
// map to a periodic box |
| 181 |
|
| 182 |
wrap = 1; |
| 183 |
break; |
| 184 |
|
| 185 |
default: |
| 186 |
|
| 187 |
(void)fprintf(stderr, "Bad option \"-%s\"\n", current_flag); |
| 188 |
usage(); |
| 189 |
} |
| 190 |
j++; |
| 191 |
current_flag = argv[i][j]; |
| 192 |
} |
| 193 |
} |
| 194 |
} |
| 195 |
|
| 196 |
else{ |
| 197 |
|
| 198 |
if( root_name != NULL ){ |
| 199 |
fprintf( stderr, |
| 200 |
"Error at \"%s\", program does not currently support\n" |
| 201 |
"more than one input file.\n" |
| 202 |
"\n", |
| 203 |
argv[i]); |
| 204 |
usage(); |
| 205 |
} |
| 206 |
|
| 207 |
root_name = argv[i]; |
| 208 |
} |
| 209 |
} |
| 210 |
|
| 211 |
if(root_name == NULL){ |
| 212 |
usage(); |
| 213 |
} |
| 214 |
|
| 215 |
sprintf( in_name, "%s", root_name ); |
| 216 |
if( !have_outName ) sprintf( out_name, "%s.xyz", root_name ); |
| 217 |
|
| 218 |
in_file = fopen(in_name, "r"); |
| 219 |
if(in_file == NULL){ |
| 220 |
printf("Cannot open file \"%s\" for reading.\n", in_name); |
| 221 |
exit(8); |
| 222 |
} |
| 223 |
|
| 224 |
out_file = fopen( out_name, "w" ); |
| 225 |
if( out_file == NULL ){ |
| 226 |
printf("Cannot open file \"%s\" for writing.\n", out_name); |
| 227 |
exit(8); |
| 228 |
} |
| 229 |
|
| 230 |
// start reading the first frame |
| 231 |
|
| 232 |
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
| 233 |
lineCount++; |
| 234 |
|
| 235 |
current_frame = (struct linked_xyz *)malloc(sizeof(struct linked_xyz)); |
| 236 |
current_frame->next = NULL; |
| 237 |
|
| 238 |
|
| 239 |
while(eof_test != NULL){ |
| 240 |
|
| 241 |
(void)sscanf(read_buffer, "%d", &nAtoms); |
| 242 |
current_frame->r = |
| 243 |
(struct coords *)calloc(nAtoms, sizeof(struct coords)); |
| 244 |
|
| 245 |
// read and the comment line and grab the time and box dimensions |
| 246 |
|
| 247 |
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
| 248 |
lineCount++; |
| 249 |
if(eof_test == NULL){ |
| 250 |
printf("error in reading file at line: %d\n", lineCount); |
| 251 |
exit(8); |
| 252 |
} |
| 253 |
|
| 254 |
foo = strtok( read_buffer, " ,;\t" ); |
| 255 |
sscanf( read_buffer, "%lf", ¤t_frame->time ); |
| 256 |
|
| 257 |
foo = strtok(NULL, " ,;\t"); |
| 258 |
if(foo == NULL){ |
| 259 |
printf("error in reading file at line: %d\n", lineCount); |
| 260 |
exit(8); |
| 261 |
} |
| 262 |
(void)sscanf(foo, "%lf",¤t_frame->boxX); |
| 263 |
|
| 264 |
foo = strtok(NULL, " ,;\t"); |
| 265 |
if(foo == NULL){ |
| 266 |
printf("error in reading file at line: %d\n", lineCount); |
| 267 |
exit(8); |
| 268 |
} |
| 269 |
(void)sscanf(foo, "%lf",¤t_frame->boxY); |
| 270 |
|
| 271 |
foo = strtok(NULL, " ,;\t"); |
| 272 |
if(foo == NULL){ |
| 273 |
printf("error in reading file at line: %d\n", lineCount); |
| 274 |
exit(8); |
| 275 |
} |
| 276 |
(void)sscanf(foo, "%lf",¤t_frame->boxZ); |
| 277 |
|
| 278 |
for( i=0; i < nAtoms; i++){ |
| 279 |
|
| 280 |
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
| 281 |
lineCount++; |
| 282 |
if(eof_test == NULL){ |
| 283 |
printf("error in reading file at line: %d\n", lineCount); |
| 284 |
exit(8); |
| 285 |
} |
| 286 |
|
| 287 |
foo = strtok(read_buffer, " ,;\t"); |
| 288 |
if ( !strcmp( "SSD", foo ) ) nSSD++; |
| 289 |
(void)strcpy(current_frame->r[i].name, foo); //copy the atom name |
| 290 |
|
| 291 |
// next we grab the positions |
| 292 |
|
| 293 |
foo = strtok(NULL, " ,;\t"); |
| 294 |
if(foo == NULL){ |
| 295 |
printf("error in reading postition x from %s\n" |
| 296 |
"natoms = %d, line = %d\n", |
| 297 |
in_name, nAtoms, lineCount ); |
| 298 |
exit(8); |
| 299 |
} |
| 300 |
(void)sscanf( foo, "%lf", ¤t_frame->r[i].x ); |
| 301 |
|
| 302 |
foo = strtok(NULL, " ,;\t"); |
| 303 |
if(foo == NULL){ |
| 304 |
printf("error in reading postition y from %s\n" |
| 305 |
"natoms = %d, line = %d\n", |
| 306 |
in_name, nAtoms, lineCount ); |
| 307 |
exit(8); |
| 308 |
} |
| 309 |
(void)sscanf( foo, "%lf", ¤t_frame->r[i].y ); |
| 310 |
|
| 311 |
foo = strtok(NULL, " ,;\t"); |
| 312 |
if(foo == NULL){ |
| 313 |
printf("error in reading postition z from %s\n" |
| 314 |
"natoms = %d, line = %d\n", |
| 315 |
in_name, nAtoms, lineCount ); |
| 316 |
exit(8); |
| 317 |
} |
| 318 |
(void)sscanf( foo, "%lf", ¤t_frame->r[i].z ); |
| 319 |
|
| 320 |
// get the velocities |
| 321 |
|
| 322 |
foo = strtok(NULL, " ,;\t"); |
| 323 |
if(foo == NULL){ |
| 324 |
printf("error in reading velocity x from %s\n" |
| 325 |
"natoms = %d, line = %d\n", |
| 326 |
in_name, nAtoms, lineCount ); |
| 327 |
exit(8); |
| 328 |
} |
| 329 |
|
| 330 |
|
| 331 |
foo = strtok(NULL, " ,;\t"); |
| 332 |
if(foo == NULL){ |
| 333 |
printf("error in reading velocity y from %s\n" |
| 334 |
"natoms = %d, line = %d\n", |
| 335 |
in_name, nAtoms, lineCount ); |
| 336 |
exit(8); |
| 337 |
} |
| 338 |
|
| 339 |
|
| 340 |
foo = strtok(NULL, " ,;\t"); |
| 341 |
if(foo == NULL){ |
| 342 |
printf("error in reading velocity z from %s\n" |
| 343 |
"natoms = %d, line = %d\n", |
| 344 |
in_name, nAtoms, lineCount ); |
| 345 |
exit(8); |
| 346 |
} |
| 347 |
|
| 348 |
// get the quaternions |
| 349 |
|
| 350 |
foo = strtok(NULL, " ,;\t"); |
| 351 |
if(foo == NULL){ |
| 352 |
printf("error in reading quaternion 0 from %s\n" |
| 353 |
"natoms = %d, line = %d\n", |
| 354 |
in_name, nAtoms, lineCount ); |
| 355 |
exit(8); |
| 356 |
} |
| 357 |
(void)sscanf( foo, "%lf", ¤t_frame->r[i].q[0] ); |
| 358 |
|
| 359 |
foo = strtok(NULL, " ,;\t"); |
| 360 |
if(foo == NULL){ |
| 361 |
printf("error in reading quaternion 1 from %s\n" |
| 362 |
"natoms = %d, line = %d\n", |
| 363 |
in_name, nAtoms, lineCount ); |
| 364 |
exit(8); |
| 365 |
} |
| 366 |
(void)sscanf( foo, "%lf", ¤t_frame->r[i].q[1] ); |
| 367 |
|
| 368 |
foo = strtok(NULL, " ,;\t"); |
| 369 |
if(foo == NULL){ |
| 370 |
printf("error in reading quaternion 2 from %s\n" |
| 371 |
"natoms = %d, line = %d\n", |
| 372 |
in_name, nAtoms, lineCount ); |
| 373 |
exit(8); |
| 374 |
} |
| 375 |
(void)sscanf( foo, "%lf", ¤t_frame->r[i].q[2] ); |
| 376 |
|
| 377 |
foo = strtok(NULL, " ,;\t"); |
| 378 |
if(foo == NULL){ |
| 379 |
printf("error in reading quaternion 3 from %s\n" |
| 380 |
"natoms = %d, line = %d\n", |
| 381 |
in_name, nAtoms, lineCount ); |
| 382 |
exit(8); |
| 383 |
} |
| 384 |
(void)sscanf( foo, "%lf", ¤t_frame->r[i].q[3] ); |
| 385 |
|
| 386 |
// get the angular velocities |
| 387 |
|
| 388 |
foo = strtok(NULL, " ,;\t"); |
| 389 |
if(foo == NULL){ |
| 390 |
printf("error in reading angular momentum jx from %s\n" |
| 391 |
"natoms = %d, line = %d\n", |
| 392 |
in_name, nAtoms, lineCount ); |
| 393 |
exit(8); |
| 394 |
} |
| 395 |
|
| 396 |
foo = strtok(NULL, " ,;\t"); |
| 397 |
if(foo == NULL){ |
| 398 |
printf("error in reading angular momentum jy from %s\n" |
| 399 |
"natoms = %d, line = %d\n", |
| 400 |
in_name, nAtoms, lineCount ); |
| 401 |
exit(8); |
| 402 |
} |
| 403 |
|
| 404 |
foo = strtok(NULL, " ,;\t"); |
| 405 |
if(foo == NULL){ |
| 406 |
printf("error in reading angular momentum jz from %s\n" |
| 407 |
"natoms = %d, line = %d\n", |
| 408 |
in_name, nAtoms, lineCount ); |
| 409 |
exit(8); |
| 410 |
} |
| 411 |
} |
| 412 |
|
| 413 |
// if necassary, wrap into the periodic image |
| 414 |
|
| 415 |
if(wrap){ |
| 416 |
|
| 417 |
for( i=0; i<nAtoms; i++ ){ |
| 418 |
|
| 419 |
/* |
| 420 |
if( !strcmp( current_frame->r[i].name, "HEAD" ) ){ |
| 421 |
|
| 422 |
// find the center of the lipid |
| 423 |
|
| 424 |
mcX = 0.0; |
| 425 |
mcY = 0.0; |
| 426 |
mcZ = 0.0; |
| 427 |
mcount = 0; |
| 428 |
|
| 429 |
mcX += current_frame->r[i].x; |
| 430 |
mcY += current_frame->r[i].y; |
| 431 |
mcZ += current_frame->r[i].z; |
| 432 |
mcount++; |
| 433 |
i++; |
| 434 |
|
| 435 |
while( strcmp( current_frame->r[i].name, "HEAD" ) && |
| 436 |
strcmp( current_frame->r[i].name, "SSD" ) ){ |
| 437 |
|
| 438 |
mcX += current_frame->r[i].x; |
| 439 |
mcY += current_frame->r[i].y; |
| 440 |
mcZ += current_frame->r[i].z; |
| 441 |
mcount++; |
| 442 |
i++; |
| 443 |
} |
| 444 |
|
| 445 |
mcX /= mcount; |
| 446 |
mcY /= mcount; |
| 447 |
mcZ /= mcount; |
| 448 |
|
| 449 |
newCX = mcX; |
| 450 |
newCY = mcY; |
| 451 |
newCZ = mcZ; |
| 452 |
|
| 453 |
map( &newCX, &newCY, &newCZ, |
| 454 |
cX, cY, cZ, |
| 455 |
current_frame->boxX, |
| 456 |
current_frame->boxY, |
| 457 |
current_frame->boxZ ); |
| 458 |
|
| 459 |
dx = mcX - newCX; |
| 460 |
dy = mcY - newCY; |
| 461 |
dz = mcZ - newCZ; |
| 462 |
|
| 463 |
for(j=(i-mcount); j<mcount; j++ ){ |
| 464 |
|
| 465 |
current_frame->r[j].x -= dx; |
| 466 |
current_frame->r[j].y -= dy; |
| 467 |
current_frame->r[j].z -= dz; |
| 468 |
} |
| 469 |
|
| 470 |
i--; // so we don't skip the next atom |
| 471 |
} |
| 472 |
*/ |
| 473 |
// else |
| 474 |
map( ¤t_frame->r[i].x, |
| 475 |
¤t_frame->r[i].y, |
| 476 |
¤t_frame->r[i].z, |
| 477 |
cX, cY, cZ, |
| 478 |
current_frame->boxX, |
| 479 |
current_frame->boxY, |
| 480 |
current_frame->boxZ ); |
| 481 |
|
| 482 |
} |
| 483 |
} |
| 484 |
|
| 485 |
|
| 486 |
|
| 487 |
|
| 488 |
nframes++; |
| 489 |
|
| 490 |
// write out here |
| 491 |
|
| 492 |
if(printWater) newN = nAtoms + ( nSSD * 3 ); |
| 493 |
else newN = nAtoms - nSSD; |
| 494 |
|
| 495 |
newN *= (nRepeatX+1); |
| 496 |
newN *= (nRepeatY+1); |
| 497 |
newN *= (nRepeatZ+1); |
| 498 |
|
| 499 |
if( !(nframes%skipFrames) ){ |
| 500 |
fprintf( out_file, |
| 501 |
"%d\n" |
| 502 |
"%lf\t%lf\t%lf\t%lf\n", |
| 503 |
newN, current_frame->time, |
| 504 |
current_frame->boxX, current_frame->boxY, |
| 505 |
current_frame->boxZ ); |
| 506 |
|
| 507 |
rCopy = (struct coords*) |
| 508 |
calloc( nAtoms, sizeof( struct coords )); |
| 509 |
|
| 510 |
for(i=0; i<nAtoms; i++){ |
| 511 |
rCopy[i].q[0] = current_frame->r[i].q[0]; |
| 512 |
rCopy[i].q[1] = current_frame->r[i].q[1]; |
| 513 |
rCopy[i].q[2] = current_frame->r[i].q[2]; |
| 514 |
rCopy[i].q[3] = current_frame->r[i].q[3]; |
| 515 |
|
| 516 |
strcpy(rCopy[i].name, current_frame->r[i].name); |
| 517 |
} |
| 518 |
|
| 519 |
for(j=0; j<(nRepeatX+1); j++){ |
| 520 |
for(k=0; k<(nRepeatY+1); k++){ |
| 521 |
for(l=0; l<(nRepeatZ+1); l++){ |
| 522 |
|
| 523 |
for(i=0; i<nAtoms; i++){ |
| 524 |
rCopy[i].x = current_frame->r[i].x + (j * current_frame->boxX); |
| 525 |
rCopy[i].y = current_frame->r[i].y + (k * current_frame->boxY); |
| 526 |
rCopy[i].z = current_frame->r[i].z + (l * current_frame->boxZ); |
| 527 |
|
| 528 |
if( !strcmp( "SSD", rCopy[i].name ) ){ |
| 529 |
|
| 530 |
rotWrite( out_file, &rCopy[i] ); |
| 531 |
} |
| 532 |
|
| 533 |
else if( !strcmp( "HEAD", rCopy[i].name ) ){ |
| 534 |
|
| 535 |
rotWrite( out_file, &rCopy[i] ); |
| 536 |
} |
| 537 |
else{ |
| 538 |
|
| 539 |
fprintf( out_file, |
| 540 |
"%s\t%lf\t%lf\t%lf\n", |
| 541 |
rCopy[i].name, |
| 542 |
rCopy[i].x, |
| 543 |
rCopy[i].y, |
| 544 |
rCopy[i].z ); |
| 545 |
} |
| 546 |
} |
| 547 |
} |
| 548 |
} |
| 549 |
} |
| 550 |
|
| 551 |
free( rCopy ); |
| 552 |
} |
| 553 |
|
| 554 |
/*free up memory */ |
| 555 |
|
| 556 |
temp_frame = current_frame->next; |
| 557 |
current_frame->next = NULL; |
| 558 |
|
| 559 |
if(temp_frame != NULL){ |
| 560 |
|
| 561 |
free(temp_frame->r); |
| 562 |
free(temp_frame); |
| 563 |
} |
| 564 |
|
| 565 |
/* make a new frame */ |
| 566 |
|
| 567 |
temp_frame = (struct linked_xyz *)malloc(sizeof(struct linked_xyz)); |
| 568 |
temp_frame->next = current_frame; |
| 569 |
current_frame = temp_frame; |
| 570 |
|
| 571 |
nSSD = 0; |
| 572 |
|
| 573 |
eof_test = fgets(read_buffer, sizeof(read_buffer), in_file); |
| 574 |
lineCount++; |
| 575 |
} |
| 576 |
|
| 577 |
(void)fclose(in_file); |
| 578 |
|
| 579 |
return 0; |
| 580 |
|
| 581 |
} |
| 582 |
|
| 583 |
|
| 584 |
|
| 585 |
void rotWrite( FILE* out_file, struct coords* theDipole ){ |
| 586 |
|
| 587 |
double u[3]; |
| 588 |
double h1[3]; |
| 589 |
double h2[3]; |
| 590 |
double ox[3]; |
| 591 |
|
| 592 |
double A[3][3]; |
| 593 |
|
| 594 |
|
| 595 |
|
| 596 |
u[0] = 0.0; u[1] = 0.0; u[2] = 1.0; |
| 597 |
|
| 598 |
h1[0] = 0.0; h1[1] = -0.75695; h1[2] = 0.5206; |
| 599 |
|
| 600 |
h2[0] = 0.0; h2[1] = 0.75695; h2[2] = 0.5206; |
| 601 |
|
| 602 |
ox[0] = 0.0; ox[1] = 0.0; ox[2] = -0.0654; |
| 603 |
|
| 604 |
|
| 605 |
setRot( A, theDipole->q ); |
| 606 |
rotMe( A, u ); |
| 607 |
|
| 608 |
if( !strcmp( "SSD", theDipole->name )){ |
| 609 |
|
| 610 |
rotMe( A, h1 ); |
| 611 |
rotMe( A, h2 ); |
| 612 |
rotMe( A, ox ); |
| 613 |
|
| 614 |
if( printWater ){ |
| 615 |
|
| 616 |
if(printDipole) { |
| 617 |
|
| 618 |
fprintf( out_file, |
| 619 |
"X\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 620 |
theDipole->x, |
| 621 |
theDipole->y, |
| 622 |
theDipole->z, |
| 623 |
u[0], u[1], u[2] ); |
| 624 |
} |
| 625 |
else{ |
| 626 |
|
| 627 |
fprintf( out_file, |
| 628 |
"X\t%lf\t%lf\t%lf\n", |
| 629 |
theDipole->x, |
| 630 |
theDipole->y, |
| 631 |
theDipole->z ); |
| 632 |
} |
| 633 |
|
| 634 |
fprintf( out_file, |
| 635 |
"O\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n", |
| 636 |
theDipole->x + ox[0], |
| 637 |
theDipole->y + ox[1], |
| 638 |
theDipole->z + ox[2] ); |
| 639 |
|
| 640 |
fprintf( out_file, |
| 641 |
"H\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n", |
| 642 |
theDipole->x + h1[0], |
| 643 |
theDipole->y + h1[1], |
| 644 |
theDipole->z + h1[2] ); |
| 645 |
|
| 646 |
fprintf( out_file, |
| 647 |
"H\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n", |
| 648 |
theDipole->x + h2[0], |
| 649 |
theDipole->y + h2[1], |
| 650 |
theDipole->z + h2[2] ); |
| 651 |
} |
| 652 |
} |
| 653 |
|
| 654 |
else if( !strcmp( "HEAD", theDipole->name )) { |
| 655 |
|
| 656 |
if( printDipole ){ |
| 657 |
|
| 658 |
fprintf( out_file, |
| 659 |
"HEAD\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 660 |
theDipole->x, |
| 661 |
theDipole->y, |
| 662 |
theDipole->z, |
| 663 |
u[0], u[1], u[2] ); |
| 664 |
} |
| 665 |
else{ |
| 666 |
|
| 667 |
fprintf( out_file, |
| 668 |
"HEAD\t%lf\t%lf\t%lf\n", |
| 669 |
theDipole->x, |
| 670 |
theDipole->y, |
| 671 |
theDipole->z ); |
| 672 |
} |
| 673 |
} |
| 674 |
} |
| 675 |
|
| 676 |
|
| 677 |
void setRot( double A[3][3], double the_q[4] ){ |
| 678 |
|
| 679 |
double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
| 680 |
|
| 681 |
q0Sqr = the_q[0] * the_q[0]; |
| 682 |
q1Sqr = the_q[1] * the_q[1]; |
| 683 |
q2Sqr = the_q[2] * the_q[2]; |
| 684 |
q3Sqr = the_q[3] * the_q[3]; |
| 685 |
|
| 686 |
A[0][0] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
| 687 |
A[0][1] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
| 688 |
A[0][2] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
| 689 |
|
| 690 |
A[1][0] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
| 691 |
A[1][1] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
| 692 |
A[1][2] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
| 693 |
|
| 694 |
A[2][0] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
| 695 |
A[2][1] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
| 696 |
A[2][2] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
| 697 |
} |
| 698 |
|
| 699 |
|
| 700 |
|
| 701 |
void rotMe( double A[3][3], double r[3] ){ |
| 702 |
|
| 703 |
int i,j; |
| 704 |
double rb[3]; // the body frame vector |
| 705 |
|
| 706 |
for(i=0; i<3; i++ ){ |
| 707 |
rb[i] = r[i]; |
| 708 |
} |
| 709 |
|
| 710 |
for( i=0; i<3; i++ ){ |
| 711 |
r[i] = 0.0; |
| 712 |
|
| 713 |
for( j=0; j<3; j++ ){ |
| 714 |
r[i] += A[j][i] * rb[j]; |
| 715 |
} |
| 716 |
} |
| 717 |
} |
| 718 |
|
| 719 |
|
| 720 |
|
| 721 |
/*************************************************************************** |
| 722 |
* prints out the usage for the command line arguments, then exits. |
| 723 |
***************************************************************************/ |
| 724 |
|
| 725 |
void usage(){ |
| 726 |
(void)fprintf(stderr, |
| 727 |
"The proper usage is: %s [options] <dumpfile>\n" |
| 728 |
"\n" |
| 729 |
"Options:\n" |
| 730 |
"\n" |
| 731 |
" -h Display this message\n" |
| 732 |
" -o <out_name> The output file (Defaults to <dumpfile>.xyz)\n" |
| 733 |
" -d print the dipole moments\n" |
| 734 |
" -w print the waters\n" |
| 735 |
" -m map to the periodic box\n" |
| 736 |
" -n <#> print every <#> frames\n" |
| 737 |
"\n" |
| 738 |
" --repeatX <#> The number of images to repeat in the x direction\n" |
| 739 |
" --repeatY <#> The number of images to repeat in the y direction\n" |
| 740 |
" --repeatZ <#> The number of images to repeat in the z direction\n" |
| 741 |
|
| 742 |
"\n", |
| 743 |
|
| 744 |
program_name); |
| 745 |
exit(8); |
| 746 |
} |
| 747 |
|
| 748 |
void map( x, y, z, centerX, centerY, centerZ, boxX, boxY, boxZ ) |
| 749 |
double *x, *y, *z; |
| 750 |
double centerX, centerY, centerZ; |
| 751 |
double boxX, boxY, boxZ; |
| 752 |
{ |
| 753 |
|
| 754 |
*x -= centerX; |
| 755 |
*y -= centerY; |
| 756 |
*z -= centerZ; |
| 757 |
|
| 758 |
if(*x < 0) *x -= boxX * (double)( (int)( (*x / boxX) - 0.5 ) ); |
| 759 |
else *x -= boxX * (double)( (int)( (*x / boxX ) + 0.5)); |
| 760 |
|
| 761 |
if(*y < 0) *y -= boxY * (double)( (int)( (*y / boxY) - 0.5 ) ); |
| 762 |
else *y -= boxY * (double)( (int)( (*y / boxY ) + 0.5)); |
| 763 |
|
| 764 |
if(*z < 0) *z -= boxZ * (double)( (int)( (*z / boxZ) - 0.5 ) ); |
| 765 |
else *z -= boxZ * (double)( (int)( (*z / boxZ ) + 0.5)); |
| 766 |
} |
