| 1 |
#include <iostream> |
| 2 |
#include <cmath> |
| 3 |
|
| 4 |
#include <stdio.h> |
| 5 |
#include <stdlib.h> |
| 6 |
#include <string.h> |
| 7 |
#include <unistd.h> |
| 8 |
#include <sys/types.h> |
| 9 |
#include <sys/stat.h> |
| 10 |
|
| 11 |
#include "ReadWrite.hpp" |
| 12 |
#include "simError.h" |
| 13 |
|
| 14 |
#ifdef IS_MPI |
| 15 |
#include <mpi.h> |
| 16 |
#include <mpi++.h> |
| 17 |
#include "mpiSimulation.hpp" |
| 18 |
#define TAKE_THIS_TAG 0 |
| 19 |
#endif // is_mpi |
| 20 |
|
| 21 |
InitializeFromFile :: InitializeFromFile( char *in_name ){ |
| 22 |
#ifdef IS_MPI |
| 23 |
if (worldRank == 0) { |
| 24 |
#endif |
| 25 |
|
| 26 |
c_in_file = fopen(in_name, "r"); |
| 27 |
if(c_in_file == NULL){ |
| 28 |
sprintf(painCave.errMsg, |
| 29 |
"Cannot open file: %s\n", in_name); |
| 30 |
painCave.isFatal = 1; |
| 31 |
simError(); |
| 32 |
} |
| 33 |
|
| 34 |
strcpy( c_in_name, in_name); |
| 35 |
#ifdef IS_MPI |
| 36 |
} |
| 37 |
strcpy( checkPointMsg, "Infile opened for reading successfully." ); |
| 38 |
MPIcheckPoint(); |
| 39 |
#endif |
| 40 |
return; |
| 41 |
} |
| 42 |
|
| 43 |
InitializeFromFile :: ~InitializeFromFile( ){ |
| 44 |
#ifdef IS_MPI |
| 45 |
if (worldRank == 0) { |
| 46 |
#endif |
| 47 |
int error; |
| 48 |
error = fclose( c_in_file ); |
| 49 |
if( error ){ |
| 50 |
sprintf( painCave.errMsg, |
| 51 |
"Error closing %s\n", c_in_name ); |
| 52 |
simError(); |
| 53 |
} |
| 54 |
#ifdef IS_MPI |
| 55 |
} |
| 56 |
strcpy( checkPointMsg, "Infile closed successfully." ); |
| 57 |
MPIcheckPoint(); |
| 58 |
#endif |
| 59 |
|
| 60 |
return; |
| 61 |
} |
| 62 |
|
| 63 |
|
| 64 |
void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
| 65 |
|
| 66 |
int i, j, done, which_node, which_atom; // loop counter |
| 67 |
|
| 68 |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 69 |
int n_atoms; // the number of atoms |
| 70 |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
| 71 |
#ifdef IS_MPI |
| 72 |
char send_buffer[BUFFERSIZE]; |
| 73 |
#endif |
| 74 |
|
| 75 |
char *eof_test; // ptr to see when we reach the end of the file |
| 76 |
char *parseErr; |
| 77 |
int procIndex; |
| 78 |
|
| 79 |
entry_plug = the_entry_plug; |
| 80 |
|
| 81 |
|
| 82 |
#ifndef IS_MPI |
| 83 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 84 |
if( eof_test == NULL ){ |
| 85 |
sprintf( painCave.errMsg, |
| 86 |
"InitializeFromFile error: error reading 1st line of \"%s\"\n", |
| 87 |
c_in_name ); |
| 88 |
painCave.isFatal = 1; |
| 89 |
simError(); |
| 90 |
} |
| 91 |
|
| 92 |
n_atoms = atoi( read_buffer ); |
| 93 |
|
| 94 |
Atom **atoms = entry_plug->atoms; |
| 95 |
DirectionalAtom* dAtom; |
| 96 |
|
| 97 |
if( n_atoms != entry_plug->n_atoms ){ |
| 98 |
sprintf( painCave.errMsg, |
| 99 |
"Initialize from File error. %s n_atoms, %d, " |
| 100 |
"does not match the BASS file's n_atoms, %d.\n", |
| 101 |
c_in_name, n_atoms, entry_plug->n_atoms ); |
| 102 |
painCave.isFatal = 1; |
| 103 |
simError(); |
| 104 |
} |
| 105 |
|
| 106 |
//read and toss the comment line |
| 107 |
|
| 108 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 109 |
if(eof_test == NULL){ |
| 110 |
sprintf( painCave.errMsg, |
| 111 |
"error in reading commment in %s\n", c_in_name); |
| 112 |
painCave.isFatal = 1; |
| 113 |
simError(); |
| 114 |
} |
| 115 |
|
| 116 |
for( i=0; i < n_atoms; i++){ |
| 117 |
|
| 118 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 119 |
if(eof_test == NULL){ |
| 120 |
sprintf(painCave.errMsg, |
| 121 |
"error in reading file %s\n" |
| 122 |
"natoms = %d; index = %d\n" |
| 123 |
"error reading the line from the file.\n", |
| 124 |
c_in_name, n_atoms, i ); |
| 125 |
painCave.isFatal = 1; |
| 126 |
simError(); |
| 127 |
} |
| 128 |
|
| 129 |
|
| 130 |
parseErr = parseDumpLine( read_buffer, i ); |
| 131 |
if( parseErr != NULL ){ |
| 132 |
strcpy( painCave.errMsg, parseErr ); |
| 133 |
painCave.isFatal = 1; |
| 134 |
simError(); |
| 135 |
} |
| 136 |
} |
| 137 |
|
| 138 |
|
| 139 |
// MPI Section of code.......... |
| 140 |
#else //IS_MPI |
| 141 |
|
| 142 |
MPI::Status istatus; |
| 143 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
| 144 |
|
| 145 |
if (worldRank == 0) { |
| 146 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 147 |
if( eof_test == NULL ){ |
| 148 |
sprintf( painCave.errMsg, |
| 149 |
"Error reading 1st line of %d \n ",c_in_name); |
| 150 |
painCave.isFatal = 1; |
| 151 |
simError(); |
| 152 |
} |
| 153 |
|
| 154 |
n_atoms = atoi( read_buffer ); |
| 155 |
|
| 156 |
Atom **atoms = entry_plug->atoms; |
| 157 |
DirectionalAtom* dAtom; |
| 158 |
|
| 159 |
// Check to see that the number of atoms in the intial configuration file is the |
| 160 |
// same as declared in simBass. |
| 161 |
|
| 162 |
if( n_atoms != mpiSim->getTotAtoms() ){ |
| 163 |
sprintf( painCave.errMsg, |
| 164 |
"Initialize from File error. %s n_atoms, %d, " |
| 165 |
"does not match the BASS file's n_atoms, %d.\n", |
| 166 |
c_in_name, n_atoms, entry_plug->n_atoms ); |
| 167 |
painCave.isFatal = 1; |
| 168 |
simError(); |
| 169 |
} |
| 170 |
|
| 171 |
//read and toss the comment line |
| 172 |
|
| 173 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 174 |
if(eof_test == NULL){ |
| 175 |
sprintf( painCave.errMsg, |
| 176 |
"error in reading commment in %s\n", c_in_name); |
| 177 |
painCave.isFatal = 1; |
| 178 |
simError(); |
| 179 |
} |
| 180 |
|
| 181 |
|
| 182 |
for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
| 183 |
|
| 184 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 185 |
if(eof_test == NULL){ |
| 186 |
sprintf(painCave.errMsg, |
| 187 |
"error in reading file %s\n" |
| 188 |
"natoms = %d; index = %d\n" |
| 189 |
"error reading the line from the file.\n", |
| 190 |
c_in_name, n_atoms, i ); |
| 191 |
painCave.isFatal = 1; |
| 192 |
simError(); |
| 193 |
} |
| 194 |
|
| 195 |
// Get the Node number which wants this atom: |
| 196 |
which_node = AtomToProcMap[i]; |
| 197 |
if (which_node == mpiSim->getMyNode()) { |
| 198 |
parseErr = parseDumpLine( read_buffer, i ); |
| 199 |
if( parseErr != NULL ){ |
| 200 |
strcpy( painCave.errMsg, parseErr ); |
| 201 |
painCave.isFatal = 1; |
| 202 |
simError(); |
| 203 |
} |
| 204 |
} else { |
| 205 |
MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
| 206 |
TAKE_THIS_TAG); |
| 207 |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
| 208 |
} |
| 209 |
} |
| 210 |
sprintf(read_buffer, "GAMEOVER"); |
| 211 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
| 212 |
MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, j, |
| 213 |
TAKE_THIS_TAG); |
| 214 |
} |
| 215 |
|
| 216 |
} else { |
| 217 |
|
| 218 |
done = 0; |
| 219 |
while (!done) { |
| 220 |
MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
| 221 |
TAKE_THIS_TAG, istatus); |
| 222 |
if (strcmp(read_buffer, "GAMEOVER")) { |
| 223 |
done = 1; |
| 224 |
continue; |
| 225 |
} else { |
| 226 |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
| 227 |
TAKE_THIS_TAG, istatus); |
| 228 |
|
| 229 |
parseErr = parseDumpLine( read_buffer, which_atom ); |
| 230 |
if( parseErr != NULL ){ |
| 231 |
strcpy( painCave.errMsg, parseErr ); |
| 232 |
painCave.isFatal = 1; |
| 233 |
simError(); |
| 234 |
} |
| 235 |
} |
| 236 |
} |
| 237 |
} |
| 238 |
|
| 239 |
#endif |
| 240 |
} |
| 241 |
|
| 242 |
char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
| 243 |
|
| 244 |
char *foo; // the pointer to the current string token |
| 245 |
|
| 246 |
double rx, ry, rz; // position place holders |
| 247 |
double vx, vy, vz; // velocity placeholders |
| 248 |
double q[4]; // the quaternions |
| 249 |
double jx, jy, jz; // angular velocity placeholders; |
| 250 |
double qSqr, qLength; // needed to normalize the quaternion vector. |
| 251 |
|
| 252 |
Atom **atoms = entry_plug->atoms; |
| 253 |
DirectionalAtom* dAtom; |
| 254 |
|
| 255 |
int j, n_atoms, atomIndex; |
| 256 |
|
| 257 |
#ifdef IS_MPI |
| 258 |
n_atoms = mpiSim->getTotAtoms(); |
| 259 |
atomIndex=-1; |
| 260 |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
| 261 |
if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
| 262 |
} |
| 263 |
if (atomIndex == -1) { |
| 264 |
sprintf( painCave.errMsg, |
| 265 |
"Initialize from file error. Atom at index %d " |
| 266 |
"in file %s does not exist on processor %d .\n", |
| 267 |
globalIndex, c_in_name, mpiSim->getMyNode() ); |
| 268 |
return strdup( painCave.errMsg ); |
| 269 |
} |
| 270 |
#else |
| 271 |
n_atoms = entry_plug->n_atoms; |
| 272 |
atomIndex = globalIndex; |
| 273 |
#endif // is_mpi |
| 274 |
|
| 275 |
// set the string tokenizer |
| 276 |
|
| 277 |
foo = strtok(readLine, " ,;\t"); |
| 278 |
|
| 279 |
// check the atom name to the current atom |
| 280 |
|
| 281 |
if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
| 282 |
sprintf( painCave.errMsg, |
| 283 |
"Initialize from file error. Atom %s at index %d " |
| 284 |
"in file %s does not" |
| 285 |
" match the BASS atom %s.\n", |
| 286 |
foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
| 287 |
return strdup( painCave.errMsg ); |
| 288 |
} |
| 289 |
|
| 290 |
// get the positions |
| 291 |
|
| 292 |
foo = strtok(NULL, " ,;\t"); |
| 293 |
if(foo == NULL){ |
| 294 |
sprintf( painCave.errMsg, |
| 295 |
"error in reading postition x from %s\n" |
| 296 |
"natoms = %d, index = %d\n", |
| 297 |
c_in_name, n_atoms, atomIndex ); |
| 298 |
return strdup( painCave.errMsg ); |
| 299 |
} |
| 300 |
rx = atof( foo ); |
| 301 |
|
| 302 |
foo = strtok(NULL, " ,;\t"); |
| 303 |
if(foo == NULL){ |
| 304 |
sprintf( painCave.errMsg, |
| 305 |
"error in reading postition y from %s\n" |
| 306 |
"natoms = %d, index = %d\n", |
| 307 |
c_in_name, n_atoms, atomIndex ); |
| 308 |
return strdup( painCave.errMsg ); |
| 309 |
} |
| 310 |
ry = atof( foo ); |
| 311 |
|
| 312 |
foo = strtok(NULL, " ,;\t"); |
| 313 |
if(foo == NULL){ |
| 314 |
sprintf( painCave.errMsg, |
| 315 |
"error in reading postition z from %s\n" |
| 316 |
"natoms = %d, index = %d\n", |
| 317 |
c_in_name, n_atoms, atomIndex ); |
| 318 |
return strdup( painCave.errMsg ); |
| 319 |
} |
| 320 |
rz = atof( foo ); |
| 321 |
|
| 322 |
|
| 323 |
// get the velocities |
| 324 |
|
| 325 |
foo = strtok(NULL, " ,;\t"); |
| 326 |
if(foo == NULL){ |
| 327 |
sprintf( painCave.errMsg, |
| 328 |
"error in reading velocity x from %s\n" |
| 329 |
"natoms = %d, index = %d\n", |
| 330 |
c_in_name, n_atoms, atomIndex ); |
| 331 |
return strdup( painCave.errMsg ); |
| 332 |
} |
| 333 |
vx = atof( foo ); |
| 334 |
|
| 335 |
foo = strtok(NULL, " ,;\t"); |
| 336 |
if(foo == NULL){ |
| 337 |
sprintf( painCave.errMsg, |
| 338 |
"error in reading velocity y from %s\n" |
| 339 |
"natoms = %d, index = %d\n", |
| 340 |
c_in_name, n_atoms, atomIndex ); |
| 341 |
return strdup( painCave.errMsg ); |
| 342 |
} |
| 343 |
vy = atof( foo ); |
| 344 |
|
| 345 |
foo = strtok(NULL, " ,;\t"); |
| 346 |
if(foo == NULL){ |
| 347 |
sprintf( painCave.errMsg, |
| 348 |
"error in reading velocity z from %s\n" |
| 349 |
"natoms = %d, index = %d\n", |
| 350 |
c_in_name, n_atoms, atomIndex ); |
| 351 |
return strdup( painCave.errMsg ); |
| 352 |
} |
| 353 |
vz = atof( foo ); |
| 354 |
|
| 355 |
|
| 356 |
// get the quaternions |
| 357 |
|
| 358 |
if( atoms[atomIndex]->isDirectional() ){ |
| 359 |
|
| 360 |
foo = strtok(NULL, " ,;\t"); |
| 361 |
if(foo == NULL){ |
| 362 |
sprintf(painCave.errMsg, |
| 363 |
"error in reading quaternion 0 from %s\n" |
| 364 |
"natoms = %d, index = %d\n", |
| 365 |
c_in_name, n_atoms, atomIndex ); |
| 366 |
return strdup( painCave.errMsg ); |
| 367 |
} |
| 368 |
q[0] = atof( foo ); |
| 369 |
|
| 370 |
foo = strtok(NULL, " ,;\t"); |
| 371 |
if(foo == NULL){ |
| 372 |
sprintf( painCave.errMsg, |
| 373 |
"error in reading quaternion 1 from %s\n" |
| 374 |
"natoms = %d, index = %d\n", |
| 375 |
c_in_name, n_atoms, atomIndex ); |
| 376 |
return strdup( painCave.errMsg ); |
| 377 |
} |
| 378 |
q[1] = atof( foo ); |
| 379 |
|
| 380 |
foo = strtok(NULL, " ,;\t"); |
| 381 |
if(foo == NULL){ |
| 382 |
sprintf( painCave.errMsg, |
| 383 |
"error in reading quaternion 2 from %s\n" |
| 384 |
"natoms = %d, index = %d\n", |
| 385 |
c_in_name, n_atoms, atomIndex ); |
| 386 |
return strdup( painCave.errMsg ); |
| 387 |
} |
| 388 |
q[2] = atof( foo ); |
| 389 |
|
| 390 |
foo = strtok(NULL, " ,;\t"); |
| 391 |
if(foo == NULL){ |
| 392 |
sprintf( painCave.errMsg, |
| 393 |
"error in reading quaternion 3 from %s\n" |
| 394 |
"natoms = %d, index = %d\n", |
| 395 |
c_in_name, n_atoms, atomIndex ); |
| 396 |
return strdup( painCave.errMsg ); |
| 397 |
} |
| 398 |
q[3] = atof( foo ); |
| 399 |
|
| 400 |
// get the angular velocities |
| 401 |
|
| 402 |
foo = strtok(NULL, " ,;\t"); |
| 403 |
if(foo == NULL){ |
| 404 |
sprintf( painCave.errMsg, |
| 405 |
"error in reading angular momentum jx from %s\n" |
| 406 |
"natoms = %d, index = %d\n", |
| 407 |
c_in_name, n_atoms, atomIndex ); |
| 408 |
return strdup( painCave.errMsg ); |
| 409 |
} |
| 410 |
jx = atof( foo ); |
| 411 |
|
| 412 |
foo = strtok(NULL, " ,;\t"); |
| 413 |
if(foo == NULL){ |
| 414 |
sprintf( painCave.errMsg, |
| 415 |
"error in reading angular momentum jy from %s\n" |
| 416 |
"natoms = %d, index = %d\n", |
| 417 |
c_in_name, n_atoms, atomIndex ); |
| 418 |
return strdup( painCave.errMsg ); |
| 419 |
} |
| 420 |
jy = atof(foo ); |
| 421 |
|
| 422 |
foo = strtok(NULL, " ,;\t"); |
| 423 |
if(foo == NULL){ |
| 424 |
sprintf( painCave.errMsg, |
| 425 |
"error in reading angular momentum jz from %s\n" |
| 426 |
"natoms = %d, index = %d\n", |
| 427 |
c_in_name, n_atoms, atomIndex ); |
| 428 |
return strdup( painCave.errMsg ); |
| 429 |
} |
| 430 |
jz = atof( foo ); |
| 431 |
|
| 432 |
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
| 433 |
|
| 434 |
// check that the quaternion vector is normalized |
| 435 |
|
| 436 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
| 437 |
|
| 438 |
qLength = sqrt( qSqr ); |
| 439 |
q[0] = q[0] / qLength; |
| 440 |
q[1] = q[1] / qLength; |
| 441 |
q[2] = q[2] / qLength; |
| 442 |
q[3] = q[3] / qLength; |
| 443 |
|
| 444 |
dAtom->setQ( q ); |
| 445 |
|
| 446 |
// add the angular velocities |
| 447 |
|
| 448 |
dAtom->setJx( jx ); |
| 449 |
dAtom->setJy( jy ); |
| 450 |
dAtom->setJz( jz ); |
| 451 |
} |
| 452 |
|
| 453 |
// add the positions and velocities to the atom |
| 454 |
|
| 455 |
atoms[atomIndex]->setX( rx ); |
| 456 |
atoms[atomIndex]->setY( ry ); |
| 457 |
atoms[atomIndex]->setZ( rz ); |
| 458 |
|
| 459 |
atoms[atomIndex]->set_vx( vx ); |
| 460 |
atoms[atomIndex]->set_vy( vy ); |
| 461 |
atoms[atomIndex]->set_vz( vz ); |
| 462 |
|
| 463 |
return NULL; |
| 464 |
} |
