| 1 |
#define _FILE_OFFSET_BITS 64 |
| 2 |
#include <iostream> |
| 3 |
#include <math.h> |
| 4 |
|
| 5 |
#include <stdio.h> |
| 6 |
#include <stdlib.h> |
| 7 |
#include <string.h> |
| 8 |
#include <unistd.h> |
| 9 |
#include <sys/types.h> |
| 10 |
#include <sys/stat.h> |
| 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 |
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 ){ |
| 32 |
|
| 33 |
#ifdef IS_MPI |
| 34 |
if (worldRank == 0) { |
| 35 |
#endif |
| 36 |
|
| 37 |
c_in_file = fopen(in_name, "r"); |
| 38 |
if(c_in_file == NULL){ |
| 39 |
sprintf(painCave.errMsg, |
| 40 |
"Cannot open file: %s\n", in_name); |
| 41 |
painCave.isFatal = 1; |
| 42 |
simError(); |
| 43 |
} |
| 44 |
|
| 45 |
strcpy( c_in_name, in_name); |
| 46 |
#ifdef IS_MPI |
| 47 |
} |
| 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; |
| 56 |
} |
| 57 |
|
| 58 |
InitializeFromFile::~InitializeFromFile( ){ |
| 59 |
#ifdef IS_MPI |
| 60 |
if (worldRank == 0) { |
| 61 |
#endif |
| 62 |
int error; |
| 63 |
error = fclose( c_in_file ); |
| 64 |
if( error ){ |
| 65 |
sprintf( painCave.errMsg, |
| 66 |
"Error closing %s\n", c_in_name ); |
| 67 |
simError(); |
| 68 |
} |
| 69 |
#ifdef IS_MPI |
| 70 |
} |
| 71 |
strcpy( checkPointMsg, "Infile closed successfully." ); |
| 72 |
MPIcheckPoint(); |
| 73 |
#endif |
| 74 |
|
| 75 |
return; |
| 76 |
} |
| 77 |
|
| 78 |
|
| 79 |
void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
| 80 |
|
| 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 nTotObjs; // the number of atoms |
| 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 |
| 92 |
char *parseErr; |
| 93 |
|
| 94 |
vector<StuntDouble*> integrableObjects; |
| 95 |
|
| 96 |
simnfo = the_simnfo; |
| 97 |
|
| 98 |
|
| 99 |
#ifndef IS_MPI |
| 100 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 101 |
if( eof_test == NULL ){ |
| 102 |
sprintf( painCave.errMsg, |
| 103 |
"InitializeFromFile error: error reading 1st line of \"%s\"\n", |
| 104 |
c_in_name ); |
| 105 |
painCave.isFatal = 1; |
| 106 |
simError(); |
| 107 |
} |
| 108 |
|
| 109 |
nTotObjs = atoi( read_buffer ); |
| 110 |
|
| 111 |
if( nTotObjs != simnfo->getTotIntegrableObjects() ){ |
| 112 |
sprintf( painCave.errMsg, |
| 113 |
"Initialize from File error. %s n_atoms, %d, " |
| 114 |
"does not match the BASS file's n_atoms, %d.\n", |
| 115 |
c_in_name, nTotObjs, simnfo->getTotIntegrableObjects()); |
| 116 |
painCave.isFatal = 1; |
| 117 |
simError(); |
| 118 |
} |
| 119 |
|
| 120 |
//read the box mat from the comment line |
| 121 |
|
| 122 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 123 |
if(eof_test == NULL){ |
| 124 |
sprintf( painCave.errMsg, |
| 125 |
"error in reading commment in %s\n", c_in_name); |
| 126 |
painCave.isFatal = 1; |
| 127 |
simError(); |
| 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 < simnfo->n_mol; i++){ |
| 140 |
|
| 141 |
integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
| 142 |
|
| 143 |
for(j = 0; j < integrableObjects.size(); j++){ |
| 144 |
|
| 145 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 146 |
if(eof_test == NULL){ |
| 147 |
sprintf(painCave.errMsg, |
| 148 |
"error in reading file %s\n" |
| 149 |
"natoms = %d; index = %d\n" |
| 150 |
"error reading the line from the file.\n", |
| 151 |
c_in_name, nTotObjs, i ); |
| 152 |
painCave.isFatal = 1; |
| 153 |
simError(); |
| 154 |
} |
| 155 |
|
| 156 |
parseErr = parseDumpLine( read_buffer, integrableObjects[j]); |
| 157 |
if( parseErr != NULL ){ |
| 158 |
strcpy( painCave.errMsg, parseErr ); |
| 159 |
painCave.isFatal = 1; |
| 160 |
simError(); |
| 161 |
} |
| 162 |
} |
| 163 |
} |
| 164 |
|
| 165 |
// MPI Section of code.......... |
| 166 |
#else //IS_MPI |
| 167 |
|
| 168 |
// first thing first, suspend fatalities. |
| 169 |
painCave.isEventLoop = 1; |
| 170 |
|
| 171 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
| 172 |
int haveError; |
| 173 |
|
| 174 |
MPI_Status istatus; |
| 175 |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
| 176 |
int localIndex; |
| 177 |
int nCurObj; |
| 178 |
int nItems; |
| 179 |
|
| 180 |
nTotObjs = simnfo->getTotIntegrableObjects(); |
| 181 |
haveError = 0; |
| 182 |
if (worldRank == 0) { |
| 183 |
|
| 184 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 185 |
if( eof_test == NULL ){ |
| 186 |
sprintf( painCave.errMsg, |
| 187 |
"Error reading 1st line of %s \n ",c_in_name); |
| 188 |
haveError = 1; |
| 189 |
simError(); |
| 190 |
} |
| 191 |
|
| 192 |
nItems = atoi( read_buffer ); |
| 193 |
|
| 194 |
// Check to see that the number of integrable objects in the intial configuration file is the |
| 195 |
// same as declared in simBass. |
| 196 |
|
| 197 |
if( nTotObjs != nItems){ |
| 198 |
sprintf( painCave.errMsg, |
| 199 |
"Initialize from File error. %s n_atoms, %d, " |
| 200 |
"does not match the BASS file's n_atoms, %d.\n", |
| 201 |
c_in_name, nTotObjs, simnfo->getTotIntegrableObjects()); |
| 202 |
haveError= 1; |
| 203 |
simError(); |
| 204 |
} |
| 205 |
|
| 206 |
//read the boxMat from the comment line |
| 207 |
|
| 208 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 209 |
if(eof_test == NULL){ |
| 210 |
sprintf( painCave.errMsg, |
| 211 |
"error in reading commment in %s\n", c_in_name); |
| 212 |
haveError = 1; |
| 213 |
simError(); |
| 214 |
} |
| 215 |
|
| 216 |
//Every single processor will parse the comment line by itself |
| 217 |
//By using this way, we might lose some efficiency, but if we want to add |
| 218 |
//more parameters into comment line, we only need to modify function |
| 219 |
//parseCommentLine |
| 220 |
|
| 221 |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
| 222 |
|
| 223 |
parseErr = parseCommentLine( read_buffer, simnfo); |
| 224 |
|
| 225 |
if( parseErr != NULL ){ |
| 226 |
strcpy( painCave.errMsg, parseErr ); |
| 227 |
haveError = 1; |
| 228 |
simError(); |
| 229 |
} |
| 230 |
|
| 231 |
for (i=0 ; i < mpiSim->getTotNmol(); i++) { |
| 232 |
which_node = MolToProcMap[i]; |
| 233 |
if(which_node == 0){ |
| 234 |
//molecules belong to master node |
| 235 |
|
| 236 |
localIndex = mpiSim->getGlobalToLocalMol(i); |
| 237 |
|
| 238 |
if(localIndex == -1) { |
| 239 |
strcpy(painCave.errMsg, "Molecule not found on node 0!"); |
| 240 |
haveError = 1; |
| 241 |
simError(); |
| 242 |
} |
| 243 |
|
| 244 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
| 245 |
for(j=0; j < integrableObjects.size(); j++){ |
| 246 |
|
| 247 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 248 |
if(eof_test == NULL){ |
| 249 |
sprintf(painCave.errMsg, |
| 250 |
"error in reading file %s\n" |
| 251 |
"natoms = %d; index = %d\n" |
| 252 |
"error reading the line from the file.\n", |
| 253 |
c_in_name, nTotObjs, i ); |
| 254 |
haveError= 1; |
| 255 |
simError(); |
| 256 |
} |
| 257 |
|
| 258 |
if(haveError) nodeZeroError(); |
| 259 |
|
| 260 |
parseDumpLine(read_buffer, integrableObjects[j]); |
| 261 |
|
| 262 |
} |
| 263 |
|
| 264 |
|
| 265 |
} |
| 266 |
else{ |
| 267 |
//molecule belongs to slave nodes |
| 268 |
|
| 269 |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
| 270 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
| 271 |
|
| 272 |
for(j=0; j < integrableObjects.size(); j++){ |
| 273 |
|
| 274 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 275 |
if(eof_test == NULL){ |
| 276 |
sprintf(painCave.errMsg, |
| 277 |
"error in reading file %s\n" |
| 278 |
"natoms = %d; index = %d\n" |
| 279 |
"error reading the line from the file.\n", |
| 280 |
c_in_name, nTotObjs, i ); |
| 281 |
haveError= 1; |
| 282 |
simError(); |
| 283 |
} |
| 284 |
|
| 285 |
if(haveError) nodeZeroError(); |
| 286 |
|
| 287 |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
| 288 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
| 289 |
|
| 290 |
} |
| 291 |
|
| 292 |
} |
| 293 |
|
| 294 |
} |
| 295 |
|
| 296 |
} |
| 297 |
else{ |
| 298 |
//actions taken at slave nodes |
| 299 |
|
| 300 |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
| 301 |
|
| 302 |
parseErr = parseCommentLine( read_buffer, simnfo); |
| 303 |
|
| 304 |
if( parseErr != NULL ){ |
| 305 |
strcpy( painCave.errMsg, parseErr ); |
| 306 |
haveError = 1; |
| 307 |
simError(); |
| 308 |
} |
| 309 |
|
| 310 |
for (i=0 ; i < mpiSim->getTotNmol(); i++) { |
| 311 |
which_node = MolToProcMap[i]; |
| 312 |
|
| 313 |
if(which_node == worldRank){ |
| 314 |
//molecule with global index i belongs to this processor |
| 315 |
|
| 316 |
localIndex = mpiSim->getGlobalToLocalMol(i); |
| 317 |
|
| 318 |
if(localIndex == -1) { |
| 319 |
sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
| 320 |
haveError = 1; |
| 321 |
simError(); |
| 322 |
} |
| 323 |
|
| 324 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
| 325 |
|
| 326 |
nCurObj = integrableObjects.size(); |
| 327 |
|
| 328 |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
| 329 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 330 |
|
| 331 |
for(j = 0; j < integrableObjects.size(); j++){ |
| 332 |
|
| 333 |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
| 334 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
| 335 |
|
| 336 |
parseErr = parseDumpLine(read_buffer, integrableObjects[j]); |
| 337 |
|
| 338 |
if( parseErr != NULL ){ |
| 339 |
strcpy( painCave.errMsg, parseErr ); |
| 340 |
simError(); |
| 341 |
} |
| 342 |
|
| 343 |
} |
| 344 |
|
| 345 |
} |
| 346 |
|
| 347 |
} |
| 348 |
|
| 349 |
} |
| 350 |
#endif |
| 351 |
} |
| 352 |
|
| 353 |
char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){ |
| 354 |
|
| 355 |
char *foo; // the pointer to the current string token |
| 356 |
|
| 357 |
double pos[3]; // position place holders |
| 358 |
double vel[3]; // velocity placeholders |
| 359 |
double q[4]; // the quaternions |
| 360 |
double ji[3]; // angular velocity placeholders; |
| 361 |
double qSqr, qLength; // needed to normalize the quaternion vector. |
| 362 |
|
| 363 |
|
| 364 |
// set the string tokenizer |
| 365 |
|
| 366 |
foo = strtok(readLine, " ,;\t"); |
| 367 |
|
| 368 |
// check the atom name to the current atom |
| 369 |
|
| 370 |
if( strcmp( foo, sd->getType() ) ){ |
| 371 |
sprintf( painCave.errMsg, |
| 372 |
"Initialize from file error. Does not" |
| 373 |
" match the BASS atom %s.\n", |
| 374 |
sd->getType() ); |
| 375 |
return strdup( painCave.errMsg ); |
| 376 |
} |
| 377 |
|
| 378 |
// get the positions |
| 379 |
|
| 380 |
foo = strtok(NULL, " ,;\t"); |
| 381 |
if(foo == NULL){ |
| 382 |
sprintf( painCave.errMsg, |
| 383 |
"error in reading postition x from %s\n", |
| 384 |
c_in_name); |
| 385 |
return strdup( painCave.errMsg ); |
| 386 |
} |
| 387 |
pos[0] = atof( foo ); |
| 388 |
|
| 389 |
foo = strtok(NULL, " ,;\t"); |
| 390 |
if(foo == NULL){ |
| 391 |
sprintf( painCave.errMsg, |
| 392 |
"error in reading postition y from %s\n", |
| 393 |
c_in_name); |
| 394 |
return strdup( painCave.errMsg ); |
| 395 |
} |
| 396 |
pos[1] = atof( foo ); |
| 397 |
|
| 398 |
foo = strtok(NULL, " ,;\t"); |
| 399 |
if(foo == NULL){ |
| 400 |
sprintf( painCave.errMsg, |
| 401 |
"error in reading postition z from %s\n", |
| 402 |
c_in_name); |
| 403 |
return strdup( painCave.errMsg ); |
| 404 |
} |
| 405 |
pos[2] = atof( foo ); |
| 406 |
|
| 407 |
|
| 408 |
// get the velocities |
| 409 |
|
| 410 |
foo = strtok(NULL, " ,;\t"); |
| 411 |
if(foo == NULL){ |
| 412 |
sprintf( painCave.errMsg, |
| 413 |
"error in reading velocity x from %s\n", |
| 414 |
c_in_name ); |
| 415 |
return strdup( painCave.errMsg ); |
| 416 |
} |
| 417 |
vel[0] = atof( foo ); |
| 418 |
|
| 419 |
foo = strtok(NULL, " ,;\t"); |
| 420 |
if(foo == NULL){ |
| 421 |
sprintf( painCave.errMsg, |
| 422 |
"error in reading velocity x from %s\n", |
| 423 |
c_in_name ); |
| 424 |
return strdup( painCave.errMsg ); |
| 425 |
} |
| 426 |
vel[1] = atof( foo ); |
| 427 |
|
| 428 |
foo = strtok(NULL, " ,;\t"); |
| 429 |
if(foo == NULL){ |
| 430 |
sprintf( painCave.errMsg, |
| 431 |
"error in reading velocity x from %s\n", |
| 432 |
c_in_name ); |
| 433 |
return strdup( painCave.errMsg ); |
| 434 |
} |
| 435 |
vel[2] = atof( foo ); |
| 436 |
|
| 437 |
|
| 438 |
// add the positions and velocities to the atom |
| 439 |
|
| 440 |
sd->setPos( pos ); |
| 441 |
sd->setVel( vel ); |
| 442 |
|
| 443 |
if (!sd->isDirectional()) |
| 444 |
return NULL; |
| 445 |
|
| 446 |
// get the quaternions |
| 447 |
|
| 448 |
if( sd->isDirectional() ){ |
| 449 |
|
| 450 |
foo = strtok(NULL, " ,;\t"); |
| 451 |
if(foo == NULL){ |
| 452 |
sprintf( painCave.errMsg, |
| 453 |
"error in reading velocity x from %s\n", |
| 454 |
c_in_name ); |
| 455 |
return strdup( painCave.errMsg ); |
| 456 |
} |
| 457 |
q[0] = atof( foo ); |
| 458 |
|
| 459 |
foo = strtok(NULL, " ,;\t"); |
| 460 |
if(foo == NULL){ |
| 461 |
sprintf( painCave.errMsg, |
| 462 |
"error in reading velocity x from %s\n", |
| 463 |
c_in_name ); |
| 464 |
return strdup( painCave.errMsg ); |
| 465 |
} |
| 466 |
q[1] = atof( foo ); |
| 467 |
|
| 468 |
foo = strtok(NULL, " ,;\t"); |
| 469 |
if(foo == NULL){ |
| 470 |
sprintf( painCave.errMsg, |
| 471 |
"error in reading velocity x from %s\n", |
| 472 |
c_in_name ); |
| 473 |
return strdup( painCave.errMsg ); |
| 474 |
} |
| 475 |
q[2] = atof( foo ); |
| 476 |
|
| 477 |
foo = strtok(NULL, " ,;\t"); |
| 478 |
if(foo == NULL){ |
| 479 |
sprintf( painCave.errMsg, |
| 480 |
"error in reading velocity x from %s\n", |
| 481 |
c_in_name ); |
| 482 |
return strdup( painCave.errMsg ); |
| 483 |
} |
| 484 |
q[3] = atof( foo ); |
| 485 |
|
| 486 |
// get the angular velocities |
| 487 |
|
| 488 |
foo = strtok(NULL, " ,;\t"); |
| 489 |
if(foo == NULL){ |
| 490 |
sprintf( painCave.errMsg, |
| 491 |
"error in reading velocity x from %s\n", |
| 492 |
c_in_name ); |
| 493 |
return strdup( painCave.errMsg ); |
| 494 |
} |
| 495 |
ji[0] = atof( foo ); |
| 496 |
|
| 497 |
foo = strtok(NULL, " ,;\t"); |
| 498 |
if(foo == NULL){ |
| 499 |
sprintf( painCave.errMsg, |
| 500 |
"error in reading velocity x from %s\n", |
| 501 |
c_in_name ); |
| 502 |
return strdup( painCave.errMsg ); |
| 503 |
} |
| 504 |
ji[1] = atof(foo ); |
| 505 |
|
| 506 |
foo = strtok(NULL, " ,;\t"); |
| 507 |
if(foo == NULL){ |
| 508 |
sprintf( painCave.errMsg, |
| 509 |
"error in reading velocity x from %s\n", |
| 510 |
c_in_name ); |
| 511 |
return strdup( painCave.errMsg ); |
| 512 |
} |
| 513 |
ji[2] = atof( foo ); |
| 514 |
|
| 515 |
|
| 516 |
// check that the quaternion vector is normalized |
| 517 |
|
| 518 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
| 519 |
|
| 520 |
qLength = sqrt( qSqr ); |
| 521 |
q[0] = q[0] / qLength; |
| 522 |
q[1] = q[1] / qLength; |
| 523 |
q[2] = q[2] / qLength; |
| 524 |
q[3] = q[3] / qLength; |
| 525 |
|
| 526 |
// add quaternion and angular velocities |
| 527 |
|
| 528 |
sd->setQ( q ); |
| 529 |
sd->setJ( ji ); |
| 530 |
} |
| 531 |
|
| 532 |
|
| 533 |
|
| 534 |
return NULL; |
| 535 |
} |
| 536 |
|
| 537 |
|
| 538 |
char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
| 539 |
|
| 540 |
double currTime; |
| 541 |
double boxMat[9]; |
| 542 |
double theBoxMat3[3][3]; |
| 543 |
double chi; |
| 544 |
double integralOfChidt; |
| 545 |
double eta[9]; |
| 546 |
|
| 547 |
char *foo; // the pointer to the current string token |
| 548 |
|
| 549 |
// set the string tokenizer |
| 550 |
|
| 551 |
foo = strtok(readLine, " ,;\t"); |
| 552 |
// set the timeToken. |
| 553 |
|
| 554 |
if(foo == NULL){ |
| 555 |
sprintf( painCave.errMsg, |
| 556 |
"error in reading Time from %s\n", |
| 557 |
c_in_name ); |
| 558 |
return strdup( painCave.errMsg ); |
| 559 |
} |
| 560 |
|
| 561 |
currTime = atof( foo ); |
| 562 |
entry_plug->setTime( currTime ); |
| 563 |
|
| 564 |
//get H-Matrix |
| 565 |
|
| 566 |
for(int i = 0 ; i < 9; i++){ |
| 567 |
foo = strtok(NULL, " ,;\t"); |
| 568 |
if(foo == NULL){ |
| 569 |
sprintf( painCave.errMsg, |
| 570 |
"error in reading H[%d] from %s\n", i, c_in_name ); |
| 571 |
return strdup( painCave.errMsg ); |
| 572 |
} |
| 573 |
boxMat[i] = atof( foo ); |
| 574 |
} |
| 575 |
|
| 576 |
for(int i=0;i<3;i++) |
| 577 |
for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
| 578 |
|
| 579 |
//set H-Matrix |
| 580 |
entry_plug->setBoxM( theBoxMat3 ); |
| 581 |
|
| 582 |
//get chi and integralOfChidt, they should appear by pair |
| 583 |
|
| 584 |
if( entry_plug->useInitXSstate ){ |
| 585 |
foo = strtok(NULL, " ,;\t\n"); |
| 586 |
if(foo != NULL){ |
| 587 |
chi = atof(foo); |
| 588 |
|
| 589 |
foo = strtok(NULL, " ,;\t\n"); |
| 590 |
if(foo == NULL){ |
| 591 |
sprintf( painCave.errMsg, |
| 592 |
"chi and integralOfChidt should appear by pair in %s\n", c_in_name ); |
| 593 |
return strdup( painCave.errMsg ); |
| 594 |
} |
| 595 |
integralOfChidt = atof( foo ); |
| 596 |
|
| 597 |
//push chi and integralOfChidt into SimInfo::properties which can be |
| 598 |
//retrieved by integrator later |
| 599 |
DoubleData* chiValue = new DoubleData(); |
| 600 |
chiValue->setID(CHIVALUE_ID); |
| 601 |
chiValue->setData(chi); |
| 602 |
entry_plug->addProperty(chiValue); |
| 603 |
|
| 604 |
DoubleData* integralOfChidtValue = new DoubleData(); |
| 605 |
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
| 606 |
integralOfChidtValue->setData(integralOfChidt); |
| 607 |
entry_plug->addProperty(integralOfChidtValue); |
| 608 |
|
| 609 |
} |
| 610 |
else |
| 611 |
return NULL; |
| 612 |
|
| 613 |
//get eta |
| 614 |
foo = strtok(NULL, " ,;\t\n"); |
| 615 |
if(foo != NULL ){ |
| 616 |
|
| 617 |
for(int i = 0 ; i < 9; i++){ |
| 618 |
|
| 619 |
if(foo == NULL){ |
| 620 |
sprintf( painCave.errMsg, |
| 621 |
"error in reading eta[%d] from %s\n", i, c_in_name ); |
| 622 |
return strdup( painCave.errMsg ); |
| 623 |
} |
| 624 |
eta[i] = atof( foo ); |
| 625 |
foo = strtok(NULL, " ,;\t\n"); |
| 626 |
} |
| 627 |
} |
| 628 |
else |
| 629 |
return NULL; |
| 630 |
|
| 631 |
//push eta into SimInfo::properties which can be |
| 632 |
//retrieved by integrator later |
| 633 |
|
| 634 |
DoubleArrayData* etaValue = new DoubleArrayData(); |
| 635 |
etaValue->setID(ETAVALUE_ID); |
| 636 |
etaValue->setData(eta, 9); |
| 637 |
entry_plug->addProperty(etaValue); |
| 638 |
} |
| 639 |
|
| 640 |
return NULL; |
| 641 |
} |
| 642 |
|
| 643 |
#ifdef IS_MPI |
| 644 |
|
| 645 |
// a couple of functions to let us escape the read loop |
| 646 |
|
| 647 |
void initFile::nodeZeroError( void ){ |
| 648 |
int j, myStatus; |
| 649 |
|
| 650 |
myStatus = 0; |
| 651 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
| 652 |
MPI_Send( &myStatus, 1, MPI_INT, j, |
| 653 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 654 |
} |
| 655 |
|
| 656 |
|
| 657 |
MPI_Finalize(); |
| 658 |
exit (0); |
| 659 |
|
| 660 |
} |
| 661 |
|
| 662 |
void initFile::anonymousNodeDie( void ){ |
| 663 |
|
| 664 |
MPI_Finalize(); |
| 665 |
exit (0); |
| 666 |
} |
| 667 |
|
| 668 |
#endif //is_mpi |
