| 1 |
#include <cstdlib> |
| 2 |
#include <cstdio> |
| 3 |
#include <cstring> |
| 4 |
|
| 5 |
#include <iostream> |
| 6 |
using namespace std; |
| 7 |
|
| 8 |
#ifdef IS_MPI |
| 9 |
#include <mpi.h> |
| 10 |
#include <mpi++.h> |
| 11 |
#endif //is_mpi |
| 12 |
|
| 13 |
#include "ForceFields.hpp" |
| 14 |
#include "SRI.hpp" |
| 15 |
#include "simError.h" |
| 16 |
|
| 17 |
#include <fortranWrappers.hpp> |
| 18 |
|
| 19 |
#ifdef IS_MPI |
| 20 |
#include "mpiForceField.h" |
| 21 |
#endif // is_mpi |
| 22 |
|
| 23 |
|
| 24 |
|
| 25 |
namespace { |
| 26 |
|
| 27 |
// Declare the structures that will be passed by the parser and MPI |
| 28 |
|
| 29 |
typedef struct{ |
| 30 |
char name[15]; |
| 31 |
double mass; |
| 32 |
double epslon; |
| 33 |
double sigma; |
| 34 |
int ident; |
| 35 |
int last; // 0 -> default |
| 36 |
// 1 -> in MPI: tells nodes to stop listening |
| 37 |
} atomStruct; |
| 38 |
|
| 39 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ); |
| 40 |
|
| 41 |
#ifdef IS_MPI |
| 42 |
|
| 43 |
MPI_Datatype mpiAtomStructType; |
| 44 |
|
| 45 |
#endif |
| 46 |
} |
| 47 |
|
| 48 |
|
| 49 |
//**************************************************************** |
| 50 |
// begins the actual forcefield stuff. |
| 51 |
//**************************************************************** |
| 52 |
|
| 53 |
|
| 54 |
LJ_FF::LJ_FF(){ |
| 55 |
|
| 56 |
char fileName[200]; |
| 57 |
char* ffPath_env = "FORCE_PARAM_PATH"; |
| 58 |
char* ffPath; |
| 59 |
char temp[200]; |
| 60 |
char errMsg[1000]; |
| 61 |
|
| 62 |
// do the funtion wrapping |
| 63 |
wrapMeFF( this ); |
| 64 |
|
| 65 |
#ifdef IS_MPI |
| 66 |
int i; |
| 67 |
|
| 68 |
// ********************************************************************** |
| 69 |
// Init the atomStruct mpi type |
| 70 |
|
| 71 |
atomStruct atomProto; // mpiPrototype |
| 72 |
int atomBC[3] = {15,3,2}; // block counts |
| 73 |
MPI_Aint atomDspls[3]; // displacements |
| 74 |
MPI_Datatype atomMbrTypes[3]; // member mpi types |
| 75 |
|
| 76 |
MPI_Address(&atomProto.name, &atomDspls[0]); |
| 77 |
MPI_Address(&atomProto.mass, &atomDspls[1]); |
| 78 |
MPI_Address(&atomProto.ident, &atomDspls[2]); |
| 79 |
|
| 80 |
atomMbrTypes[0] = MPI_CHAR; |
| 81 |
atomMbrTypes[1] = MPI_DOUBLE; |
| 82 |
atomMbrTypes[2] = MPI_INT; |
| 83 |
|
| 84 |
for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0]; |
| 85 |
|
| 86 |
MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType); |
| 87 |
MPI_Type_commit(&mpiAtomStructType); |
| 88 |
|
| 89 |
// *********************************************************************** |
| 90 |
|
| 91 |
if( worldRank == 0 ){ |
| 92 |
#endif |
| 93 |
|
| 94 |
// generate the force file name |
| 95 |
|
| 96 |
strcpy( fileName, "LJ_FF.frc" ); |
| 97 |
// fprintf( stderr,"Trying to open %s\n", fileName ); |
| 98 |
|
| 99 |
// attempt to open the file in the current directory first. |
| 100 |
|
| 101 |
frcFile = fopen( fileName, "r" ); |
| 102 |
|
| 103 |
if( frcFile == NULL ){ |
| 104 |
|
| 105 |
// next see if the force path enviorment variable is set |
| 106 |
|
| 107 |
ffPath = getenv( ffPath_env ); |
| 108 |
if( ffPath == NULL ) { |
| 109 |
sprintf( painCave.errMsg, |
| 110 |
"Error opening the force field parameter file: %s\n" |
| 111 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
| 112 |
"vairable?\n", |
| 113 |
fileName ); |
| 114 |
painCave.isFatal = 1; |
| 115 |
simError(); |
| 116 |
} |
| 117 |
|
| 118 |
|
| 119 |
strcpy( temp, ffPath ); |
| 120 |
strcat( temp, "/" ); |
| 121 |
strcat( temp, fileName ); |
| 122 |
strcpy( fileName, temp ); |
| 123 |
|
| 124 |
frcFile = fopen( fileName, "r" ); |
| 125 |
|
| 126 |
if( frcFile == NULL ){ |
| 127 |
|
| 128 |
sprintf( painCave.errMsg, |
| 129 |
"Error opening the force field parameter file: %s\n" |
| 130 |
"Have you tried setting the FORCE_PARAM_PATH environment " |
| 131 |
"vairable?\n", |
| 132 |
fileName ); |
| 133 |
painCave.isFatal = 1; |
| 134 |
simError(); |
| 135 |
} |
| 136 |
} |
| 137 |
|
| 138 |
#ifdef IS_MPI |
| 139 |
} |
| 140 |
|
| 141 |
sprintf( checkPointMsg, "LJ_FF file opened sucessfully." ); |
| 142 |
MPIcheckPoint(); |
| 143 |
|
| 144 |
#endif // is_mpi |
| 145 |
} |
| 146 |
|
| 147 |
|
| 148 |
LJ_FF::~LJ_FF(){ |
| 149 |
|
| 150 |
#ifdef IS_MPI |
| 151 |
if( worldRank == 0 ){ |
| 152 |
#endif // is_mpi |
| 153 |
|
| 154 |
fclose( frcFile ); |
| 155 |
|
| 156 |
#ifdef IS_MPI |
| 157 |
} |
| 158 |
#endif // is_mpi |
| 159 |
} |
| 160 |
|
| 161 |
|
| 162 |
|
| 163 |
void LJ_FF::initializeAtoms( void ){ |
| 164 |
|
| 165 |
class LinkedType { |
| 166 |
public: |
| 167 |
LinkedType(){ |
| 168 |
next = NULL; |
| 169 |
name[0] = '\0'; |
| 170 |
} |
| 171 |
~LinkedType(){ if( next != NULL ) delete next; } |
| 172 |
|
| 173 |
LinkedType* find(char* key){ |
| 174 |
if( !strcmp(name, key) ) return this; |
| 175 |
if( next != NULL ) return next->find(key); |
| 176 |
return NULL; |
| 177 |
} |
| 178 |
|
| 179 |
|
| 180 |
void add( atomStruct &info ){ |
| 181 |
|
| 182 |
// check for duplicates |
| 183 |
|
| 184 |
if( !strcmp( info.name, name ) ){ |
| 185 |
sprintf( painCave.errMsg, |
| 186 |
"Duplicate LJ atom type \"%s\" found in " |
| 187 |
"the LJ_FF param file./n", |
| 188 |
name ); |
| 189 |
painCave.isFatal = 1; |
| 190 |
simError(); |
| 191 |
} |
| 192 |
|
| 193 |
if( next != NULL ) next->add(info); |
| 194 |
else{ |
| 195 |
next = new LinkedType(); |
| 196 |
strcpy(next->name, info.name); |
| 197 |
next->mass = info.mass; |
| 198 |
next->epslon = info.epslon; |
| 199 |
next->sigma = info.sigma; |
| 200 |
next->ident = info.ident; |
| 201 |
} |
| 202 |
} |
| 203 |
|
| 204 |
|
| 205 |
#ifdef IS_MPI |
| 206 |
|
| 207 |
void duplicate( atomStruct &info ){ |
| 208 |
strcpy(info.name, name); |
| 209 |
info.mass = mass; |
| 210 |
info.epslon = epslon; |
| 211 |
info.sigma = sigma; |
| 212 |
info.ident = ident; |
| 213 |
info.last = 0; |
| 214 |
} |
| 215 |
|
| 216 |
|
| 217 |
#endif |
| 218 |
|
| 219 |
char name[15]; |
| 220 |
double mass; |
| 221 |
double epslon; |
| 222 |
double sigma; |
| 223 |
int ident; |
| 224 |
LinkedType* next; |
| 225 |
}; |
| 226 |
|
| 227 |
LinkedType* headAtomType; |
| 228 |
LinkedType* currentAtomType; |
| 229 |
atomStruct info; |
| 230 |
info.last = 1; // initialize last to have the last set. |
| 231 |
// if things go well, last will be set to 0 |
| 232 |
|
| 233 |
int i; |
| 234 |
int identNum; |
| 235 |
|
| 236 |
Atom** the_atoms; |
| 237 |
int nAtoms; |
| 238 |
the_atoms = entry_plug->atoms; |
| 239 |
nAtoms = entry_plug->n_atoms; |
| 240 |
|
| 241 |
|
| 242 |
#ifdef IS_MPI |
| 243 |
if( worldRank == 0 ){ |
| 244 |
#endif |
| 245 |
|
| 246 |
// read in the atom types. |
| 247 |
|
| 248 |
headAtomType = new LinkedType; |
| 249 |
|
| 250 |
fastForward( "AtomTypes", "initializeAtoms" ); |
| 251 |
|
| 252 |
// we are now at the AtomTypes section. |
| 253 |
|
| 254 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 255 |
lineNum++; |
| 256 |
|
| 257 |
|
| 258 |
// read a line, and start parseing out the atom types |
| 259 |
|
| 260 |
if( eof_test == NULL ){ |
| 261 |
sprintf( painCave.errMsg, |
| 262 |
"Error in reading Atoms from force file at line %d.\n", |
| 263 |
lineNum ); |
| 264 |
painCave.isFatal = 1; |
| 265 |
simError(); |
| 266 |
} |
| 267 |
|
| 268 |
identNum = 1; |
| 269 |
// stop reading at end of file, or at next section |
| 270 |
while( readLine[0] != '#' && eof_test != NULL ){ |
| 271 |
|
| 272 |
// toss comment lines |
| 273 |
if( readLine[0] != '!' ){ |
| 274 |
|
| 275 |
// the parser returns 0 if the line was blank |
| 276 |
if( parseAtomLJ( readLine, lineNum, info ) ){ |
| 277 |
info.ident = identNum; |
| 278 |
headAtomType->add( info );; |
| 279 |
identNum++; |
| 280 |
} |
| 281 |
} |
| 282 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 283 |
lineNum++; |
| 284 |
} |
| 285 |
|
| 286 |
#ifdef IS_MPI |
| 287 |
|
| 288 |
// send out the linked list to all the other processes |
| 289 |
|
| 290 |
sprintf( checkPointMsg, |
| 291 |
"LJ_FF atom structures read successfully." ); |
| 292 |
MPIcheckPoint(); |
| 293 |
|
| 294 |
currentAtomType = headAtomType->next; //skip the first element who is a place holder. |
| 295 |
while( currentAtomType != NULL ){ |
| 296 |
currentAtomType->duplicate( info ); |
| 297 |
|
| 298 |
|
| 299 |
|
| 300 |
sendFrcStruct( &info, mpiAtomStructType ); |
| 301 |
|
| 302 |
sprintf( checkPointMsg, |
| 303 |
"successfully sent lJ force type: \"%s\"\n", |
| 304 |
info.name ); |
| 305 |
MPIcheckPoint(); |
| 306 |
|
| 307 |
currentAtomType = currentAtomType->next; |
| 308 |
} |
| 309 |
info.last = 1; |
| 310 |
sendFrcStruct( &info, mpiAtomStructType ); |
| 311 |
|
| 312 |
} |
| 313 |
|
| 314 |
else{ |
| 315 |
|
| 316 |
// listen for node 0 to send out the force params |
| 317 |
|
| 318 |
MPIcheckPoint(); |
| 319 |
|
| 320 |
headAtomType = new LinkedType; |
| 321 |
recieveFrcStruct( &info, mpiAtomStructType ); |
| 322 |
|
| 323 |
while( !info.last ){ |
| 324 |
|
| 325 |
|
| 326 |
|
| 327 |
headAtomType->add( info ); |
| 328 |
|
| 329 |
MPIcheckPoint(); |
| 330 |
|
| 331 |
recieveFrcStruct( &info, mpiAtomStructType ); |
| 332 |
} |
| 333 |
} |
| 334 |
#endif // is_mpi |
| 335 |
|
| 336 |
// call new A_types in fortran |
| 337 |
|
| 338 |
int isError; |
| 339 |
|
| 340 |
// dummy variables |
| 341 |
int isLJ = 1; |
| 342 |
int isDipole = 0; |
| 343 |
int isSSD = 0; |
| 344 |
int isGB = 0; |
| 345 |
double w0 = 0.0; |
| 346 |
double v0 = 0.0; |
| 347 |
double dipole = 0.0; |
| 348 |
|
| 349 |
|
| 350 |
currentAtomType = headAtomType; |
| 351 |
while( currentAtomType != NULL ){ |
| 352 |
|
| 353 |
if( currentAtomType->name[0] != '\0' ){ |
| 354 |
isError = 0; |
| 355 |
newAtype( &(currentAtomType->ident), |
| 356 |
&(currentAtomType->mass), |
| 357 |
&(currentAtomType->epslon), |
| 358 |
&(currentAtomType->sigma), |
| 359 |
&isLJ, &isSSD, &isDipole, &isGB, &w0, &v0, &dipole, |
| 360 |
&isError ); |
| 361 |
if( isError ){ |
| 362 |
sprintf( painCave.errMsg, |
| 363 |
"Error initializing the \"%s\" atom type in fortran\n", |
| 364 |
currentAtomType->name ); |
| 365 |
painCave.isFatal = 1; |
| 366 |
simError(); |
| 367 |
} |
| 368 |
} |
| 369 |
currentAtomType = currentAtomType->next; |
| 370 |
} |
| 371 |
|
| 372 |
#ifdef IS_MPI |
| 373 |
sprintf( checkPointMsg, |
| 374 |
"LJ_FF atom structures successfully sent to fortran\n" ); |
| 375 |
MPIcheckPoint(); |
| 376 |
#endif // is_mpi |
| 377 |
|
| 378 |
|
| 379 |
|
| 380 |
// initialize the atoms |
| 381 |
|
| 382 |
double bigSigma = 0.0; |
| 383 |
Atom* thisAtom; |
| 384 |
|
| 385 |
for( i=0; i<nAtoms; i++ ){ |
| 386 |
|
| 387 |
currentAtomType = headAtomType->find( the_atoms[i]->getType() ); |
| 388 |
if( currentAtomType == NULL ){ |
| 389 |
sprintf( painCave.errMsg, |
| 390 |
"AtomType error, %s not found in force file.\n", |
| 391 |
the_atoms[i]->getType() ); |
| 392 |
painCave.isFatal = 1; |
| 393 |
simError(); |
| 394 |
} |
| 395 |
|
| 396 |
the_atoms[i]->setMass( currentAtomType->mass ); |
| 397 |
the_atoms[i]->setEpslon( currentAtomType->epslon ); |
| 398 |
the_atoms[i]->setSigma( currentAtomType->sigma ); |
| 399 |
the_atoms[i]->setIdent( currentAtomType->ident ); |
| 400 |
the_atoms[i]->setLJ(); |
| 401 |
|
| 402 |
if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma; |
| 403 |
} |
| 404 |
|
| 405 |
|
| 406 |
#ifdef IS_MPI |
| 407 |
double tempBig = bigSigma; |
| 408 |
MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX ); |
| 409 |
#endif //is_mpi |
| 410 |
|
| 411 |
//calc rCut and rList |
| 412 |
|
| 413 |
entry_plug->rCut = 2.5 * bigSigma; |
| 414 |
if(entry_plug->rCut > (entry_plug->box_x / 2.0)) entry_plug->rCut = entry_plug->box_x / 2.0; |
| 415 |
if(entry_plug->rCut > (entry_plug->box_y / 2.0)) entry_plug->rCut = entry_plug->box_y / 2.0; |
| 416 |
if(entry_plug->rCut > (entry_plug->box_z / 2.0)) entry_plug->rCut = entry_plug->box_z / 2.0; |
| 417 |
|
| 418 |
entry_plug->rList = entry_plug->rCut + 1.0; |
| 419 |
|
| 420 |
// clean up the memory |
| 421 |
|
| 422 |
delete headAtomType; |
| 423 |
|
| 424 |
#ifdef IS_MPI |
| 425 |
sprintf( checkPointMsg, "LJ_FF atoms initialized succesfully" ); |
| 426 |
MPIcheckPoint(); |
| 427 |
#endif // is_mpi |
| 428 |
|
| 429 |
this->initFortran(); |
| 430 |
entry_plug->refreshSim(); |
| 431 |
|
| 432 |
} |
| 433 |
|
| 434 |
void LJ_FF::initializeBonds( bond_pair* the_bonds ){ |
| 435 |
|
| 436 |
if( entry_plug->n_bonds ){ |
| 437 |
sprintf( painCave.errMsg, |
| 438 |
"LJ_FF does not support bonds.\n" ); |
| 439 |
painCave.isFatal = 1; |
| 440 |
simError(); |
| 441 |
} |
| 442 |
#ifdef IS_MPI |
| 443 |
MPIcheckPoint(); |
| 444 |
#endif // is_mpi |
| 445 |
|
| 446 |
} |
| 447 |
|
| 448 |
void LJ_FF::initializeBends( bend_set* the_bends ){ |
| 449 |
|
| 450 |
if( entry_plug->n_bends ){ |
| 451 |
sprintf( painCave.errMsg, |
| 452 |
"LJ_FF does not support bends.\n" ); |
| 453 |
painCave.isFatal = 1; |
| 454 |
simError(); |
| 455 |
} |
| 456 |
#ifdef IS_MPI |
| 457 |
MPIcheckPoint(); |
| 458 |
#endif // is_mpi |
| 459 |
|
| 460 |
} |
| 461 |
|
| 462 |
void LJ_FF::initializeTorsions( torsion_set* the_torsions ){ |
| 463 |
|
| 464 |
if( entry_plug->n_torsions ){ |
| 465 |
sprintf( painCave.errMsg, |
| 466 |
"LJ_FF does not support torsions.\n" ); |
| 467 |
painCave.isFatal = 1; |
| 468 |
simError(); |
| 469 |
} |
| 470 |
#ifdef IS_MPI |
| 471 |
MPIcheckPoint(); |
| 472 |
#endif // is_mpi |
| 473 |
|
| 474 |
} |
| 475 |
|
| 476 |
void LJ_FF::fastForward( char* stopText, char* searchOwner ){ |
| 477 |
|
| 478 |
int foundText = 0; |
| 479 |
char* the_token; |
| 480 |
|
| 481 |
rewind( frcFile ); |
| 482 |
lineNum = 0; |
| 483 |
|
| 484 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 485 |
lineNum++; |
| 486 |
if( eof_test == NULL ){ |
| 487 |
sprintf( painCave.errMsg, "Error fast forwarding force file for %s: " |
| 488 |
" file is empty.\n", |
| 489 |
searchOwner ); |
| 490 |
painCave.isFatal = 1; |
| 491 |
simError(); |
| 492 |
} |
| 493 |
|
| 494 |
|
| 495 |
while( !foundText ){ |
| 496 |
while( eof_test != NULL && readLine[0] != '#' ){ |
| 497 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 498 |
lineNum++; |
| 499 |
} |
| 500 |
if( eof_test == NULL ){ |
| 501 |
sprintf( painCave.errMsg, |
| 502 |
"Error fast forwarding force file for %s at " |
| 503 |
"line %d: file ended unexpectedly.\n", |
| 504 |
searchOwner, |
| 505 |
lineNum ); |
| 506 |
painCave.isFatal = 1; |
| 507 |
simError(); |
| 508 |
} |
| 509 |
|
| 510 |
the_token = strtok( readLine, " ,;\t#\n" ); |
| 511 |
foundText = !strcmp( stopText, the_token ); |
| 512 |
|
| 513 |
if( !foundText ){ |
| 514 |
eof_test = fgets( readLine, sizeof(readLine), frcFile ); |
| 515 |
lineNum++; |
| 516 |
|
| 517 |
if( eof_test == NULL ){ |
| 518 |
sprintf( painCave.errMsg, |
| 519 |
"Error fast forwarding force file for %s at " |
| 520 |
"line %d: file ended unexpectedly.\n", |
| 521 |
searchOwner, |
| 522 |
lineNum ); |
| 523 |
painCave.isFatal = 1; |
| 524 |
simError(); |
| 525 |
} |
| 526 |
} |
| 527 |
} |
| 528 |
} |
| 529 |
|
| 530 |
|
| 531 |
|
| 532 |
int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){ |
| 533 |
|
| 534 |
char* the_token; |
| 535 |
|
| 536 |
the_token = strtok( lineBuffer, " \n\t,;" ); |
| 537 |
if( the_token != NULL ){ |
| 538 |
|
| 539 |
strcpy( info.name, the_token ); |
| 540 |
|
| 541 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 542 |
sprintf( painCave.errMsg, |
| 543 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 544 |
painCave.isFatal = 1; |
| 545 |
simError(); |
| 546 |
} |
| 547 |
|
| 548 |
info.mass = atof( the_token ); |
| 549 |
|
| 550 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 551 |
sprintf( painCave.errMsg, |
| 552 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 553 |
painCave.isFatal = 1; |
| 554 |
simError(); |
| 555 |
} |
| 556 |
|
| 557 |
info.epslon = atof( the_token ); |
| 558 |
|
| 559 |
if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){ |
| 560 |
sprintf( painCave.errMsg, |
| 561 |
"Error parseing AtomTypes: line %d\n", lineNum ); |
| 562 |
painCave.isFatal = 1; |
| 563 |
simError(); |
| 564 |
} |
| 565 |
|
| 566 |
info.sigma = atof( the_token ); |
| 567 |
|
| 568 |
return 1; |
| 569 |
} |
| 570 |
else return 0; |
| 571 |
} |
