| 54 |
|
// char* in_name; |
| 55 |
|
char* id; |
| 56 |
|
|
| 57 |
< |
int* hasErrors; |
| 57 |
> |
int hasErrors; |
| 58 |
|
|
| 59 |
|
|
| 60 |
|
MakeStamps* the_stamps = NULL; |
| 109 |
|
// Handle command line arguments. |
| 110 |
|
sysType = grabCmdArgs(); |
| 111 |
|
|
| 112 |
< |
// Keep me |
| 113 |
< |
if(in_name == NULL){ |
| 112 |
> |
// Keep me |
| 113 |
> |
if(in_name == NULL){ |
| 114 |
|
sprintf( painCave.errMsg, |
| 115 |
|
"No input bass file was specified.\n"); |
| 116 |
|
painCave.isFatal = 0; |
| 117 |
|
simError(); |
| 118 |
< |
usage(); |
| 118 |
> |
cmdline_parser_print_help(); |
| 119 |
|
} |
| 120 |
|
|
| 121 |
|
if( sysType < 0 ){ |
| 123 |
|
"No system type was specified.\n"); |
| 124 |
|
painCave.isFatal = 0; |
| 125 |
|
simError(); |
| 126 |
< |
usage(); |
| 126 |
> |
cmdline_parser_print_help(); |
| 127 |
|
} |
| 128 |
|
|
| 129 |
|
|
| 149 |
|
bsInfo.dt = the_globals->getDt(); |
| 150 |
|
bsInfo.runTime = the_globals->getRunTime(); |
| 151 |
|
|
| 152 |
+ |
std::cerr << "dt = " << bsInfo.dt << "\n"; |
| 153 |
+ |
|
| 154 |
|
// get the ones we know are there, yet still may need some work. |
| 155 |
|
bsInfo.nComponents = the_globals->getNComponents(); |
| 156 |
|
strcpy( bsInfo.forceField, the_globals->getForceField() ); |
| 290 |
|
} |
| 291 |
|
|
| 292 |
|
// get and set the boxSize |
| 293 |
+ |
|
| 294 |
+ |
bsInfo.haveBox = false; |
| 295 |
|
|
| 296 |
+ |
std::cerr << "Box setting..."; |
| 297 |
+ |
|
| 298 |
+ |
std::cerr <<" haveBox= " << the_globals->haveBox() << "\n"; |
| 299 |
+ |
|
| 300 |
|
if( the_globals->haveBox() ){ |
| 301 |
|
bsInfo.boxX = the_globals->getBox(); |
| 302 |
|
bsInfo.boxY = the_globals->getBox(); |
| 303 |
|
bsInfo.boxZ = the_globals->getBox(); |
| 304 |
+ |
bsInfo.haveBox = true; |
| 305 |
+ |
std::cerr<< "box=>yes\n"; |
| 306 |
|
} |
| 307 |
|
else if( the_globals->haveDensity() ){ |
| 308 |
|
|
| 311 |
|
bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) ); |
| 312 |
|
bsInfo.boxY = bsInfo.boxX; |
| 313 |
|
bsInfo.boxZ = bsInfo.boxY; |
| 314 |
+ |
bsInfo.haveBox = true; |
| 315 |
+ |
|
| 316 |
+ |
std::cerr<< "dens=>yes\n"; |
| 317 |
|
} |
| 318 |
|
else{ |
| 319 |
< |
if( !the_globals->haveBoxX() ){ |
| 307 |
< |
sprintf( painCave.errMsg, |
| 308 |
< |
"sysBuild error, no periodic BoxX size given.\n" ); |
| 309 |
< |
painCave.isFatal = 1; |
| 310 |
< |
simError(); |
| 311 |
< |
} |
| 312 |
< |
bsInfo.boxX = the_globals->getBoxX(); |
| 313 |
< |
|
| 314 |
< |
if( !the_globals->haveBoxY() ){ |
| 315 |
< |
sprintf( painCave.errMsg, |
| 316 |
< |
"sysBuild error, no periodic BoxY size given.\n" ); |
| 317 |
< |
painCave.isFatal = 1; |
| 318 |
< |
simError(); |
| 319 |
< |
} |
| 320 |
< |
bsInfo.boxY = the_globals->getBoxY(); |
| 321 |
< |
|
| 322 |
< |
if( !the_globals->haveBoxZ() ){ |
| 323 |
< |
sprintf( painCave.errMsg, |
| 324 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
| 325 |
< |
painCave.isFatal = 1; |
| 326 |
< |
simError(); |
| 327 |
< |
} |
| 328 |
< |
bsInfo.boxZ = the_globals->getBoxZ(); |
| 319 |
> |
std::cerr<< "none.\n"; |
| 320 |
|
} |
| 321 |
|
|
| 322 |
|
|
| 323 |
< |
//************************************************************ |
| 323 |
> |
// ************************************************************ |
| 324 |
|
// that should be all we need from bass. now to switch to the |
| 325 |
|
// appropriate system builder. |
| 326 |
|
// *********************************************************** |
| 327 |
< |
|
| 328 |
< |
|
| 327 |
> |
|
| 328 |
> |
nanoBuilder* buildNano; |
| 329 |
> |
|
| 330 |
|
switch( sysType ){ |
| 331 |
|
|
| 332 |
|
case BILAYER: |
| 335 |
|
|
| 336 |
|
case NANOPARTICLE: |
| 337 |
|
|
| 338 |
< |
// nanoBuilder buildNano(hasErrors); |
| 339 |
< |
|
| 340 |
< |
// buildNano.buildNanoParticle(); |
| 341 |
< |
|
| 338 |
> |
buildNano = new nanoBuilder(hasErrors); |
| 339 |
> |
|
| 340 |
> |
buildNano->buildNanoParticle(); |
| 341 |
> |
|
| 342 |
|
break; |
| 343 |
|
|
| 344 |
|
default: |
| 356 |
|
if( headStamp!= NULL ) delete headStamp; |
| 357 |
|
if( the_stamps != NULL ) delete the_stamps; |
| 358 |
|
if( the_globals != NULL ) delete the_globals; |
| 359 |
< |
if( the_components != NULL ) delete[] the_components; |
| 359 |
> |
// if( the_components != NULL ) delete[] the_components; |
| 360 |
|
|
| 361 |
|
if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol; |
| 362 |
|
if( bsInfo.compStamps != NULL ) delete[] bsInfo.compStamps; |
| 481 |
|
} |
| 482 |
|
|
| 483 |
|
if (args_info.inputs_num) { //Get input file name |
| 484 |
< |
in_name = args_info.inputs[1]; |
| 484 |
> |
in_name = args_info.inputs[0]; |
| 485 |
> |
cerr << in_name << "\n"; |
| 486 |
|
} |
| 487 |
|
else { |
| 488 |
|
sprintf( painCave.errMsg, |
