| 1 |
#include <cstdlib> |
| 2 |
#include <cstdio> |
| 3 |
#include <cstring> |
| 4 |
#include <cmath> |
| 5 |
#include <iostream> |
| 6 |
|
| 7 |
#include "cmdline.h" |
| 8 |
#include "simError.h" |
| 9 |
#include "parse_me.h" |
| 10 |
#include "MakeStamps.hpp" |
| 11 |
#include "Globals.hpp" |
| 12 |
#include "SimInfo.hpp" |
| 13 |
|
| 14 |
#include "sysBuild.hpp" |
| 15 |
#include "latticeBuilder.hpp" |
| 16 |
#include "bilayerSys.hpp" |
| 17 |
#include "nanoBuilder.hpp" |
| 18 |
|
| 19 |
// this routine is defined in BASS_interface.cpp |
| 20 |
extern void set_interface_stamps( MakeStamps* ms, Globals* g ); |
| 21 |
|
| 22 |
|
| 23 |
// case asignments |
| 24 |
#define BILAYER 1 |
| 25 |
#define NANOPARTICLE 2 |
| 26 |
|
| 27 |
char* program_name; |
| 28 |
bassInfo bsInfo; |
| 29 |
void usage(void); |
| 30 |
int grabCmdArgs(void); |
| 31 |
|
| 32 |
|
| 33 |
|
| 34 |
|
| 35 |
int have_prefix; |
| 36 |
char* out_prefix; |
| 37 |
char* in_name; |
| 38 |
int isRandom; |
| 39 |
includeLinked* headInc; |
| 40 |
includeLinked* prevInc; |
| 41 |
includeLinked* currInc; |
| 42 |
gengetopt_args_info args_info; |
| 43 |
|
| 44 |
|
| 45 |
int main( int argc, char* argv[]){ |
| 46 |
|
| 47 |
int i,j,k; |
| 48 |
int sysType; |
| 49 |
int done; |
| 50 |
char current_flag; |
| 51 |
// int have_prefix; |
| 52 |
// char* out_prefix; |
| 53 |
// char* in_name; |
| 54 |
char* id; |
| 55 |
|
| 56 |
int hasErrors; |
| 57 |
|
| 58 |
// initialize all functions and variables |
| 59 |
|
| 60 |
initSimError(); |
| 61 |
program_name = argv[0]; |
| 62 |
sysType = -1; |
| 63 |
have_prefix = 0; |
| 64 |
isRandom = 0; |
| 65 |
in_name = NULL; |
| 66 |
headInc = NULL; |
| 67 |
|
| 68 |
bsInfo.includes = NULL; |
| 69 |
|
| 70 |
|
| 71 |
// parse command line arguments |
| 72 |
|
| 73 |
if (cmdline_parser (argc, argv, &args_info) != 0) |
| 74 |
exit(1) ; |
| 75 |
|
| 76 |
// Handle command line arguments. |
| 77 |
sysType = grabCmdArgs(); |
| 78 |
|
| 79 |
// Keep me |
| 80 |
if(in_name == NULL){ |
| 81 |
sprintf( painCave.errMsg, |
| 82 |
"No input bass file was specified.\n"); |
| 83 |
painCave.isFatal = 0; |
| 84 |
simError(); |
| 85 |
cmdline_parser_print_help(); |
| 86 |
} |
| 87 |
|
| 88 |
if( sysType < 0 ){ |
| 89 |
sprintf( painCave.errMsg, |
| 90 |
"No system type was specified.\n"); |
| 91 |
painCave.isFatal = 0; |
| 92 |
simError(); |
| 93 |
cmdline_parser_print_help(); |
| 94 |
} |
| 95 |
|
| 96 |
|
| 97 |
// if no output prefix is given default to "donkey". |
| 98 |
|
| 99 |
if( !have_prefix ){ |
| 100 |
out_prefix = strdup( "donkey" ); |
| 101 |
} |
| 102 |
|
| 103 |
// set command line info into the bassInfo struct |
| 104 |
|
| 105 |
bsInfo.outPrefix = out_prefix; |
| 106 |
bsInfo.includes = headInc; |
| 107 |
|
| 108 |
// open and parse the bass file. |
| 109 |
|
| 110 |
set_interface_stamps( the_stamps, the_globals ); |
| 111 |
yacc_BASS( in_name ); |
| 112 |
|
| 113 |
// set the easy ones first |
| 114 |
bsInfo.targetTemp = the_globals->getTargetTemp(); |
| 115 |
bsInfo.dt = the_globals->getDt(); |
| 116 |
bsInfo.runTime = the_globals->getRunTime(); |
| 117 |
|
| 118 |
// get the ones we know are there, yet still may need some work. |
| 119 |
bsInfo.nComponents = the_globals->getNComponents(); |
| 120 |
strcpy( bsInfo.forceField, the_globals->getForceField() ); |
| 121 |
|
| 122 |
// get the ensemble: |
| 123 |
strcpy( bsInfo.ensemble, the_globals->getEnsemble() ); |
| 124 |
if( !strcasecmp( bsInfo.ensemble, "NPT" ) ) { |
| 125 |
|
| 126 |
if (the_globals->haveTargetPressure()){ |
| 127 |
bsInfo.targetPressure = the_globals->getTargetPressure(); |
| 128 |
bsInfo.havePressure = 1; |
| 129 |
} |
| 130 |
else { |
| 131 |
sprintf( painCave.errMsg, |
| 132 |
"sysBuild error: If you use the constant pressure\n" |
| 133 |
" ensemble, you must set targetPressure.\n" |
| 134 |
" This was found in the BASS file.\n"); |
| 135 |
painCave.isFatal = 1; |
| 136 |
simError(); |
| 137 |
} |
| 138 |
|
| 139 |
if (the_globals->haveTauThermostat()){ |
| 140 |
bsInfo.tauThermostat = the_globals->getTauThermostat(); |
| 141 |
bsInfo.haveTauThermostat = 1;; |
| 142 |
} |
| 143 |
else if (the_globals->haveQmass()){ |
| 144 |
bsInfo.Qmass = the_globals->getQmass(); |
| 145 |
bsInfo.haveQmass = 1; |
| 146 |
} |
| 147 |
else { |
| 148 |
sprintf( painCave.errMsg, |
| 149 |
"sysBuild error: If you use one of the constant temperature\n" |
| 150 |
" ensembles, you must set either tauThermostat or qMass.\n" |
| 151 |
" Neither of these was found in the BASS file.\n"); |
| 152 |
painCave.isFatal = 1; |
| 153 |
simError(); |
| 154 |
} |
| 155 |
|
| 156 |
if (the_globals->haveTauBarostat()){ |
| 157 |
bsInfo.tauBarostat = the_globals->getTauBarostat(); |
| 158 |
bsInfo.haveTauBarostat = 1; |
| 159 |
} |
| 160 |
else { |
| 161 |
sprintf( painCave.errMsg, |
| 162 |
"sysBuild error: If you use the constant pressure\n" |
| 163 |
" ensemble, you must set tauBarostat.\n" |
| 164 |
" This was found in the BASS file.\n"); |
| 165 |
painCave.isFatal = 1; |
| 166 |
simError(); |
| 167 |
} |
| 168 |
|
| 169 |
} |
| 170 |
else if ( !strcasecmp( bsInfo.ensemble, "NVT") ) { |
| 171 |
|
| 172 |
if (the_globals->haveTauThermostat()){ |
| 173 |
bsInfo.tauThermostat = the_globals->getTauThermostat(); |
| 174 |
bsInfo.haveTauThermostat = 1; |
| 175 |
} |
| 176 |
else if (the_globals->haveQmass()){ |
| 177 |
bsInfo.Qmass = the_globals->getQmass(); |
| 178 |
bsInfo.haveQmass = 1; |
| 179 |
} |
| 180 |
else { |
| 181 |
sprintf( painCave.errMsg, |
| 182 |
"sysBuild error: If you use one of the constant temperature\n" |
| 183 |
" ensembles, you must set either tauThermostat or qMass.\n" |
| 184 |
" Neither of these was found in the BASS file.\n"); |
| 185 |
painCave.isFatal = 1; |
| 186 |
simError(); |
| 187 |
} |
| 188 |
|
| 189 |
} |
| 190 |
else if ( !strcasecmp( bsInfo.ensemble, "NVE") ) { |
| 191 |
|
| 192 |
// nothing special for now |
| 193 |
} |
| 194 |
else { |
| 195 |
sprintf( painCave.errMsg, |
| 196 |
"sysBuild Warning. Unrecognized Ensemble -> %s, " |
| 197 |
"reverting to NVE for this simulation.\n", |
| 198 |
bsInfo.ensemble ); |
| 199 |
painCave.isFatal = 0; |
| 200 |
simError(); |
| 201 |
strcpy( bsInfo.ensemble, "NVE" ); |
| 202 |
} |
| 203 |
|
| 204 |
|
| 205 |
// get the components and calculate the tot_nMol and indvidual n_mol |
| 206 |
|
| 207 |
the_components = the_globals->getComponents(); |
| 208 |
bsInfo.componentsNmol = new int[bsInfo.nComponents]; |
| 209 |
bsInfo.compStamps = new MoleculeStamp*[bsInfo.nComponents]; |
| 210 |
bsInfo.totNmol = 0; |
| 211 |
for( i=0; i<bsInfo.nComponents; i++ ){ |
| 212 |
|
| 213 |
if( !the_components[i]->haveNMol() ){ |
| 214 |
// we have a problem |
| 215 |
sprintf( painCave.errMsg, |
| 216 |
"sysBuild Error. No component NMol" |
| 217 |
" given. Cannot calculate the number of atoms.\n" ); |
| 218 |
painCave.isFatal = 1; |
| 219 |
simError(); |
| 220 |
} |
| 221 |
|
| 222 |
bsInfo.totNmol += the_components[i]->getNMol(); |
| 223 |
bsInfo.componentsNmol[i] = the_components[i]->getNMol(); |
| 224 |
} |
| 225 |
|
| 226 |
// make an array of molecule stamps that match the components used. |
| 227 |
// also extract the used stamps out into a separate linked list |
| 228 |
|
| 229 |
for( i=0; i<bsInfo.nComponents; i++ ){ |
| 230 |
|
| 231 |
id = the_components[i]->getType(); |
| 232 |
bsInfo.compStamps[i] = NULL; |
| 233 |
|
| 234 |
// check to make sure the component isn't already in the list |
| 235 |
|
| 236 |
bsInfo.compStamps[i] = headStamp->match( id ); |
| 237 |
if( bsInfo.compStamps[i] == NULL ){ |
| 238 |
|
| 239 |
// extract the component from the list; |
| 240 |
|
| 241 |
currStamp = the_stamps->extractMolStamp( id ); |
| 242 |
if( currStamp == NULL ){ |
| 243 |
sprintf( painCave.errMsg, |
| 244 |
"sysBuild error: Component \"%s\" was not found in the " |
| 245 |
"list of declared molecules\n", |
| 246 |
id ); |
| 247 |
painCave.isFatal = 1; |
| 248 |
simError(); |
| 249 |
} |
| 250 |
|
| 251 |
headStamp->add( currStamp ); |
| 252 |
bsInfo.compStamps[i] = headStamp->match( id ); |
| 253 |
} |
| 254 |
} |
| 255 |
|
| 256 |
// get and set the boxSize |
| 257 |
|
| 258 |
bsInfo.haveBox = false; |
| 259 |
|
| 260 |
std::cerr << "Box setting..."; |
| 261 |
|
| 262 |
std::cerr <<" haveBox= " << the_globals->haveBox() << "\n"; |
| 263 |
|
| 264 |
if( the_globals->haveBox() ){ |
| 265 |
bsInfo.boxX = the_globals->getBox(); |
| 266 |
bsInfo.boxY = the_globals->getBox(); |
| 267 |
bsInfo.boxZ = the_globals->getBox(); |
| 268 |
bsInfo.haveBox = true; |
| 269 |
std::cerr<< "box=>yes\n"; |
| 270 |
} |
| 271 |
else if( the_globals->haveDensity() ){ |
| 272 |
|
| 273 |
double vol; |
| 274 |
vol = (double)bsInfo.totNmol / the_globals->getDensity(); |
| 275 |
bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) ); |
| 276 |
bsInfo.boxY = bsInfo.boxX; |
| 277 |
bsInfo.boxZ = bsInfo.boxY; |
| 278 |
bsInfo.haveBox = true; |
| 279 |
|
| 280 |
std::cerr<< "dens=>yes\n"; |
| 281 |
} |
| 282 |
else{ |
| 283 |
std::cerr<< "none.\n"; |
| 284 |
} |
| 285 |
|
| 286 |
|
| 287 |
// ************************************************************ |
| 288 |
// that should be all we need from bass. now to switch to the |
| 289 |
// appropriate system builder. |
| 290 |
// *********************************************************** |
| 291 |
|
| 292 |
nanoBuilder* buildNano; |
| 293 |
|
| 294 |
switch( sysType ){ |
| 295 |
|
| 296 |
case BILAYER: |
| 297 |
buildBilayer( isRandom ); |
| 298 |
break; |
| 299 |
|
| 300 |
case NANOPARTICLE: |
| 301 |
|
| 302 |
buildNano = new nanoBuilder(hasErrors); |
| 303 |
|
| 304 |
buildNano->buildNanoParticle(); |
| 305 |
|
| 306 |
break; |
| 307 |
|
| 308 |
default: |
| 309 |
sprintf( painCave.errMsg, |
| 310 |
"Unknown system type: %d\n", sysType ); |
| 311 |
painCave.isFatal = 1; |
| 312 |
simError(); |
| 313 |
|
| 314 |
} |
| 315 |
|
| 316 |
|
| 317 |
|
| 318 |
// clean up memory; |
| 319 |
|
| 320 |
if( headStamp!= NULL ) delete headStamp; |
| 321 |
if( the_stamps != NULL ) delete the_stamps; |
| 322 |
if( the_globals != NULL ) delete the_globals; |
| 323 |
// if( the_components != NULL ) delete[] the_components; |
| 324 |
|
| 325 |
if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol; |
| 326 |
if( bsInfo.compStamps != NULL ) delete[] bsInfo.compStamps; |
| 327 |
if( bsInfo.includes != NULL ){ |
| 328 |
prevInc = bsInfo.includes; |
| 329 |
while( prevInc != NULL ){ |
| 330 |
currInc = prevInc->next; |
| 331 |
delete prevInc; |
| 332 |
prevInc = currInc; |
| 333 |
} |
| 334 |
} |
| 335 |
|
| 336 |
return 0; |
| 337 |
} |
| 338 |
|
| 339 |
|
| 340 |
|
| 341 |
/* Parses command line arguments. Returns systype. If systype is -1, |
| 342 |
sysType was undefined. |
| 343 |
*/ |
| 344 |
int grabCmdArgs(){ |
| 345 |
int sysType; |
| 346 |
int i; |
| 347 |
|
| 348 |
sysType = -1; |
| 349 |
|
| 350 |
/* Handle model arguments first....*/ |
| 351 |
|
| 352 |
if (args_info.bilayer_given){ //Test for bilayer system. |
| 353 |
sysType = BILAYER; |
| 354 |
if ((args_info.water_given) && (args_info.lipid_given)){ |
| 355 |
strcpy( bsInfo.lipidName, args_info.lipid_arg ); |
| 356 |
strcpy( bsInfo.waterName, args_info.water_arg ); |
| 357 |
} |
| 358 |
else { |
| 359 |
sprintf( painCave.errMsg, |
| 360 |
"You must specify a lipid and water model for bilayer.\n" ); |
| 361 |
painCave.isFatal = 0; |
| 362 |
simError(); |
| 363 |
cmdline_parser_print_help(); |
| 364 |
} |
| 365 |
} |
| 366 |
|
| 367 |
// Test for nanoparticle system. |
| 368 |
if (args_info.nanoparticle_given){ |
| 369 |
sysType = NANOPARTICLE; |
| 370 |
if (!args_info.core_given){ |
| 371 |
sprintf( painCave.errMsg, |
| 372 |
"You must specify core model for nanoparticle.\n" ); |
| 373 |
painCave.isFatal = 0; |
| 374 |
simError(); |
| 375 |
cmdline_parser_print_help(); |
| 376 |
} |
| 377 |
|
| 378 |
// set core model |
| 379 |
strcpy( bsInfo.coreName, args_info.core_arg ); |
| 380 |
if (args_info.shell_given){ |
| 381 |
bsInfo.buildCoreShell = 1; |
| 382 |
strcpy( bsInfo.shellName, args_info.shell_arg ); |
| 383 |
|
| 384 |
|
| 385 |
} |
| 386 |
|
| 387 |
// Check for vacancies. |
| 388 |
if (args_info.vacancies_given){ |
| 389 |
|
| 390 |
if (!args_info.vacancyradius_given){ // Make sure that a vacancy radius was given. |
| 391 |
sprintf( painCave.errMsg, |
| 392 |
"You must specify a vacancy radius for building vacancies.\n" ); |
| 393 |
painCave.isFatal = 0; |
| 394 |
simError(); |
| 395 |
cmdline_parser_print_help(); |
| 396 |
} |
| 397 |
bsInfo.hasVacancies = 1; |
| 398 |
bsInfo.vacancyRadius = args_info.vacancyradius_arg; |
| 399 |
} |
| 400 |
else if (args_info.vacancyradius_given){ |
| 401 |
sprintf( painCave.errMsg, |
| 402 |
"You must specify vacancies=percent for vacancy radius.\n" ); |
| 403 |
painCave.isFatal = 0; |
| 404 |
simError(); |
| 405 |
cmdline_parser_print_help(); |
| 406 |
} |
| 407 |
|
| 408 |
if (args_info.randomparticle_given){ |
| 409 |
bsInfo.isRandomParticle = 1; |
| 410 |
bsInfo.soluteX = args_info.randomparticle_arg; |
| 411 |
} |
| 412 |
|
| 413 |
} |
| 414 |
/* ---------------Now do general arguments-----------------------*/ |
| 415 |
|
| 416 |
if (args_info.output_given){ //Output File (defaults to donkey if not specified. |
| 417 |
out_prefix = args_info.output_arg; |
| 418 |
have_prefix = 1; |
| 419 |
} |
| 420 |
|
| 421 |
if (args_info.include_given){ // Deal with multiple include files. |
| 422 |
for( i = 0; i < args_info.include_given;++i){ |
| 423 |
if( headInc == NULL ){ |
| 424 |
headInc = new includeLinked; |
| 425 |
headInc->next = NULL; |
| 426 |
strcpy( headInc->name, args_info.include_arg[i] ); |
| 427 |
} |
| 428 |
else{ |
| 429 |
prevInc = headInc; |
| 430 |
currInc = headInc->next; |
| 431 |
while( currInc != NULL ){ |
| 432 |
prevInc = currInc; |
| 433 |
currInc = prevInc->next; |
| 434 |
} |
| 435 |
currInc = new includeLinked; |
| 436 |
currInc->next = NULL; |
| 437 |
strcpy( currInc->name, args_info.include_arg[i] ); |
| 438 |
prevInc->next = currInc; |
| 439 |
} |
| 440 |
} |
| 441 |
} |
| 442 |
|
| 443 |
if (args_info.random_given){ // Random Particle |
| 444 |
isRandom = 1;; |
| 445 |
} |
| 446 |
|
| 447 |
if (args_info.inputs_num) { //Get input file name |
| 448 |
in_name = args_info.inputs[0]; |
| 449 |
cerr << in_name << "\n"; |
| 450 |
} |
| 451 |
else { |
| 452 |
sprintf( painCave.errMsg, |
| 453 |
"You must specify a input file name.\n" ); |
| 454 |
painCave.isFatal = 0; |
| 455 |
simError(); |
| 456 |
cmdline_parser_print_help(); |
| 457 |
|
| 458 |
} |
| 459 |
|
| 460 |
return sysType; |
| 461 |
} |
| 462 |
|
| 463 |
|
| 464 |
|
| 465 |
|
| 466 |
|
| 467 |
|
| 468 |
|
| 469 |
|
| 470 |
|
| 471 |
|
| 472 |
/*************************************************************************** |
| 473 |
* prints out the usage for the command line arguments, then exits. |
| 474 |
***************************************************************************/ |
| 475 |
|
| 476 |
void usage(){ |
| 477 |
(void)fprintf(stdout, |
| 478 |
"The proper usage is: %s [options] <input bass>\n" |
| 479 |
"\n" |
| 480 |
"Options:\n" |
| 481 |
"\n" |
| 482 |
" short:\n" |
| 483 |
" ------\n" |
| 484 |
" -h Display this message\n" |
| 485 |
" -o <prefix> The output prefix\n" |
| 486 |
" -I <include> File name that should be included at the top of the\n" |
| 487 |
" output bass file.\n" |
| 488 |
" -r toggle the random option\n" |
| 489 |
"\n" |
| 490 |
" long:\n" |
| 491 |
" -----\n" |
| 492 |
" --bilayer <lipid> <water> Tries to build a basic bilayer with the specified number\n" |
| 493 |
" of lipids in the input bass file. The bilayer will be\n" |
| 494 |
" surrounded by the number of solvent molecules given\n" |
| 495 |
" in the bass file.\n" |
| 496 |
" -note: combined with \"-r\" the simulation will start\n" |
| 497 |
" the lipids randomly oriented in a sea of waters.\n" |
| 498 |
"\n" |
| 499 |
"\n", |
| 500 |
program_name); |
| 501 |
exit(8); |
| 502 |
} |
