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root/group/trunk/OOPSE/utils/sysBuild.cpp
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Comparing trunk/OOPSE/utils/sysBuild.cpp (file contents):
Revision 498 by mmeineke, Mon Apr 14 21:22:54 2003 UTC vs.
Revision 598 by chuckv, Mon Jul 14 21:35:45 2003 UTC

# Line 1 | Line 1
1 +
2   #include <cstdlib>
3   #include <cstdio>
4   #include <cstring>
5 + #include <cmath>
6  
7   #include "simError.h"
8 + #include "parse_me.h"
9 + #include "MakeStamps.hpp"
10 + #include "Globals.hpp"
11 + #include "SimInfo.hpp"
12  
13 + #include "sysBuild.hpp"
14   #include "bilayerSys.hpp"
15 + #include "nanoBuilder.hpp"
16  
17 < // quick case asignments
17 > // this routine is defined in BASS_interface.cpp
18 > extern void set_interface_stamps( MakeStamps* ms, Globals* g );
19  
20 +
21 + // case asignments
22   #define BILAYER 1
23 + #define NANOPARTICLE 2
24  
13 –
25   char* program_name;
26 + bassInfo bsInfo;
27   void usage(void);
28  
29  
# Line 23 | Line 35 | int main( int argc, char* argv[]){
35    char current_flag;
36    char* out_prefix;
37    char* in_name;
38 +  char* id;
39    
40 <  sysBuildInfo info;
40 >  includeLinked* headInc;
41 >  includeLinked* prevInc;
42 >  includeLinked* currInc;
43  
44 <  // initialize simError
45 <  initSimError();
44 >  MakeStamps* the_stamps = NULL;
45 >  Globals* the_globals = NULL;
46 >  Component** the_components = NULL;
47 >  LinkedMolStamp* headStamp = NULL;
48 >  LinkedMolStamp* currStamp;
49  
50 +  // initialize all functions and variables
51  
52 <  program_name = argv[0]; /*save the program name in case we need it*/
52 >  initSimError();
53 >  program_name = argv[0];
54    sysType = -1;
55    have_prefix = 0;
56    isRandom = 0;
57    in_name = NULL;
58 +  headInc = NULL;
59 +
60 +  bsInfo.includes = NULL;
61 +  bsInfo.componentsNmol = NULL;
62 +  bsInfo.compStamps = NULL;
63 +  bsInfo.havePressure = 0;
64 +  bsInfo.haveTauBarostat = 0;
65 +  bsInfo.haveTauThermostat = 0;
66 +  bsInfo.haveQmass = 0;
67 +
68 +  headStamp = new LinkedMolStamp();
69 +  the_stamps = new MakeStamps();
70 +  the_globals = new Globals();
71 +  set_interface_stamps( the_stamps, the_globals );
72 +
73 +  // parse command line arguments
74 +
75    for( i = 1; i < argc; i++){
76      
77      if(argv[i][0] =='-'){
# Line 53 | Line 90 | int main( int argc, char* argv[]){
90              simError();
91              usage();
92            }
93 +
94            sysType = BILAYER;
95 +
96 +          i++;
97 +          if( i>=argc ){
98 +            sprintf( painCave.errMsg,
99 +                     "\n"
100 +                     "not enough arguments for bilayer\n");
101 +            painCave.isFatal = 0;
102 +            simError();
103 +            usage();
104 +          }      
105 +          strcpy( bsInfo.lipidName, argv[i] );
106 +          
107 +          i++;
108 +          if( i>=argc ){
109 +            sprintf( painCave.errMsg,
110 +                     "\n"
111 +                     "not enough arguments for bilayer\n");
112 +            painCave.isFatal = 0;
113 +            simError();
114 +            usage();
115 +          }      
116 +          strcpy( bsInfo.waterName, argv[i] );
117 +
118          }
119  
120          else{
# Line 64 | Line 125 | int main( int argc, char* argv[]){
125            usage();
126          }
127        }
128 +      else if( !strcmp( argv[i], "--nanoparticle" ) ){
129 +        if( sysType > 0 ){
130 +            sprintf( painCave.errMsg,
131 +                     "You cannot specify more than one system to build.\n" );
132 +            painCave.isFatal = 0;
133 +            simError();
134 +            usage();
135 +          }
136 +
137 +          sysType = NANOPARTICLE;
138 +
139 +          i++;
140 +          if( i>=argc ){
141 +            sprintf( painCave.errMsg,
142 +                     "\n"
143 +                     "not enough arguments for nanoparticle\n");
144 +            painCave.isFatal = 0;
145 +            simError();
146 +            usage();
147 +          }      
148 +          strcpy( bsInfo.coreName, argv[i] );
149 +          
150 +          i++;
151 +          if( i>=argc ){
152 +            sprintf( painCave.errMsg,
153 +                     "\n"
154 +                     "not enough arguments for nanoparticle\n");
155 +            painCave.isFatal = 0;
156 +            simError();
157 +            usage();
158 +          }      
159 +          strcpy( bsInfo.shellName, argv[i] );
160 +
161 +        }
162 +
163 +        else{
164 +          sprintf( painCave.errMsg,
165 +                   "Invalid option \"%s\"\n", argv[i] );
166 +          painCave.isFatal = 0;
167 +          simError();
168 +          usage();
169 +        }
170 +      }
171        
172        else{
173          
# Line 85 | Line 189 | int main( int argc, char* argv[]){
189              done = 1;
190              break;
191  
192 +          case 'I':
193 +            // -I <include> => the include file.
194 +
195 +            i++;
196 +            if( headInc == NULL ){
197 +              headInc = new includeLinked;
198 +              headInc->next = NULL;
199 +              strcpy( headInc->name, argv[i] );
200 +            }
201 +            else{
202 +              prevInc = headInc;
203 +              currInc = headInc->next;
204 +              while( currInc != NULL ){
205 +                prevInc = currInc;
206 +                currInc = prevInc->next;
207 +              }
208 +              currInc = new includeLinked;
209 +              currInc->next = NULL;
210 +              strcpy( currInc->name, argv[i] );
211 +              prevInc->next = currInc;
212 +            }
213 +            
214 +            done = 1;
215 +            break;
216 +
217            case 'h':
218              // -h => give the usage
219              
# Line 149 | Line 278 | int main( int argc, char* argv[]){
278    if( !have_prefix ){
279      out_prefix = strdup( "donkey" );
280    }
152 –  
153 –  info.in_name = in_name;
154 –  info.out_prefix = out_prefix;
155 –  info.isRandom = isRandom;
281    
282 <  // switch the system type
282 >  // set command line info into the bassInfo struct
283 >  
284 >  bsInfo.outPrefix = out_prefix;
285 >  bsInfo.includes = headInc;
286 >  
287 >
288 >  // open and parse the bass file.
289 >
290 >  set_interface_stamps( the_stamps, the_globals );
291 >  yacc_BASS( in_name );  
292 >
293 >  // set the easy ones first
294 >  bsInfo.targetTemp = the_globals->getTargetTemp();
295 >  bsInfo.dt = the_globals->getDt();
296 >  bsInfo.runTime = the_globals->getRunTime();
297 >
298 >  // get the ones we know are there, yet still may need some work.
299 >  bsInfo.nComponents = the_globals->getNComponents();
300 >  strcpy( bsInfo.forceField, the_globals->getForceField() );
301 >
302 >  // get the ensemble:
303 >  strcpy( bsInfo.ensemble, the_globals->getEnsemble() );
304 >  if( !strcasecmp( bsInfo.ensemble, "NPT" ) ) {
305 >    
306 >    if (the_globals->haveTargetPressure()){
307 >      bsInfo.targetPressure = the_globals->getTargetPressure();
308 >      bsInfo.havePressure = 1;
309 >    }
310 >    else {
311 >      sprintf( painCave.errMsg,
312 >               "sysBuild error: If you use the constant pressure\n"
313 >               "    ensemble, you must set targetPressure.\n"
314 >               "    This was found in the BASS file.\n");
315 >      painCave.isFatal = 1;
316 >      simError();
317 >    }
318 >
319 >    if (the_globals->haveTauThermostat()){
320 >      bsInfo.tauThermostat = the_globals->getTauThermostat();
321 >      bsInfo.haveTauThermostat = 1;;
322 >    }
323 >    else if (the_globals->haveQmass()){
324 >      bsInfo.Qmass = the_globals->getQmass();
325 >      bsInfo.haveQmass = 1;
326 >    }
327 >    else {
328 >      sprintf( painCave.errMsg,
329 >               "sysBuild error: If you use one of the constant temperature\n"
330 >               "    ensembles, you must set either tauThermostat or qMass.\n"
331 >               "    Neither of these was found in the BASS file.\n");
332 >      painCave.isFatal = 1;
333 >      simError();
334 >    }
335  
336 +    if (the_globals->haveTauBarostat()){
337 +      bsInfo.tauBarostat = the_globals->getTauBarostat();
338 +      bsInfo.haveTauBarostat = 1;
339 +    }                                    
340 +    else {
341 +      sprintf( painCave.errMsg,
342 +               "sysBuild error: If you use the constant pressure\n"
343 +               "    ensemble, you must set tauBarostat.\n"
344 +               "    This was found in the BASS file.\n");
345 +      painCave.isFatal = 1;
346 +      simError();
347 +    }
348 +
349 +  }
350 +  else if ( !strcasecmp( bsInfo.ensemble, "NVT") ) {
351 +
352 +    if (the_globals->haveTauThermostat()){
353 +      bsInfo.tauThermostat = the_globals->getTauThermostat();
354 +      bsInfo.haveTauThermostat = 1;
355 +    }
356 +    else if (the_globals->haveQmass()){
357 +      bsInfo.Qmass = the_globals->getQmass();
358 +      bsInfo.haveQmass = 1;
359 +    }
360 +    else {
361 +      sprintf( painCave.errMsg,
362 +               "sysBuild error: If you use one of the constant temperature\n"
363 +               "    ensembles, you must set either tauThermostat or qMass.\n"
364 +               "    Neither of these was found in the BASS file.\n");
365 +      painCave.isFatal = 1;
366 +      simError();
367 +    }
368 +    
369 +  }
370 +  else if ( !strcasecmp( bsInfo.ensemble, "NVE") ) {
371 +    
372 +    // nothing special for now
373 +  }
374 +  else {
375 +    sprintf( painCave.errMsg,
376 +             "sysBuild Warning. Unrecognized Ensemble -> %s, "
377 +             "reverting to NVE for this simulation.\n",
378 +             bsInfo.ensemble );
379 +    painCave.isFatal = 0;
380 +    simError();
381 +    strcpy( bsInfo.ensemble, "NVE" );
382 +  }  
383 +
384 +
385 +  // get the components and calculate the tot_nMol and indvidual n_mol
386 +
387 +  the_components = the_globals->getComponents();
388 +  bsInfo.componentsNmol = new int[bsInfo.nComponents];
389 +  bsInfo.compStamps = new MoleculeStamp*[bsInfo.nComponents];  
390 +  bsInfo.totNmol = 0;
391 +  for( i=0; i<bsInfo.nComponents; i++ ){
392 +    
393 +    if( !the_components[i]->haveNMol() ){
394 +      // we have a problem
395 +      sprintf( painCave.errMsg,
396 +               "sysBuild Error. No component NMol"
397 +               " given. Cannot calculate the number of atoms.\n" );
398 +      painCave.isFatal = 1;
399 +      simError();
400 +    }
401 +    
402 +    bsInfo.totNmol += the_components[i]->getNMol();
403 +    bsInfo.componentsNmol[i] = the_components[i]->getNMol();
404 +  }
405 +
406 +  // make an array of molecule stamps that match the components used.
407 +  // also extract the used stamps out into a separate linked list
408 +  
409 +  for( i=0; i<bsInfo.nComponents; i++ ){
410 +
411 +    id = the_components[i]->getType();
412 +    bsInfo.compStamps[i] = NULL;
413 +    
414 +    // check to make sure the component isn't already in the list
415 +
416 +    bsInfo.compStamps[i] = headStamp->match( id );
417 +    if( bsInfo.compStamps[i] == NULL ){
418 +      
419 +      // extract the component from the list;
420 +      
421 +      currStamp = the_stamps->extractMolStamp( id );
422 +      if( currStamp == NULL ){
423 +        sprintf( painCave.errMsg,
424 +                 "sysBuild error: Component \"%s\" was not found in the "
425 +                 "list of declared molecules\n",
426 +                 id );
427 +        painCave.isFatal = 1;
428 +        simError();
429 +      }
430 +      
431 +      headStamp->add( currStamp );
432 +      bsInfo.compStamps[i] = headStamp->match( id );
433 +    }
434 +  }
435 +
436 +  // get and set the boxSize
437 +
438 +  if( the_globals->haveBox() ){
439 +    bsInfo.boxX = the_globals->getBox();
440 +    bsInfo.boxY = the_globals->getBox();
441 +    bsInfo.boxZ = the_globals->getBox();
442 +  }
443 +  else if( the_globals->haveDensity() ){
444 +
445 +    double vol;
446 +    vol = (double)bsInfo.totNmol / the_globals->getDensity();
447 +    bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) );
448 +    bsInfo.boxY = bsInfo.boxX;
449 +    bsInfo.boxZ = bsInfo.boxY;
450 +  }
451 +  else{
452 +    if( !the_globals->haveBoxX() ){
453 +      sprintf( painCave.errMsg,
454 +               "sysBuild error, no periodic BoxX size given.\n" );
455 +      painCave.isFatal = 1;
456 +      simError();
457 +    }
458 +    bsInfo.boxX = the_globals->getBoxX();
459 +
460 +    if( !the_globals->haveBoxY() ){
461 +      sprintf( painCave.errMsg,
462 +               "sysBuild error, no periodic BoxY size given.\n" );
463 +      painCave.isFatal = 1;
464 +      simError();
465 +    }
466 +    bsInfo.boxY = the_globals->getBoxY();
467 +
468 +    if( !the_globals->haveBoxZ() ){
469 +      sprintf( painCave.errMsg,
470 +               "SimSetup error, no periodic BoxZ size given.\n" );
471 +      painCave.isFatal = 1;
472 +      simError();
473 +    }
474 +    bsInfo.boxZ = the_globals->getBoxZ();
475 +  }
476 +  
477 +
478 +  //************************************************************
479 +  // that should be all we need from bass. now to switch to the
480 +  // appropriate system builder.
481 +  // ***********************************************************
482 +
483 +
484    switch( sysType ){
485      
486    case BILAYER:
487      
488 <    buildBilayer( info );
488 >    buildBilayer( isRandom );
489      break;
490  
491 +  case NANO:
492 +
493 +
494 +    break;
495 +
496    default:
497      sprintf( painCave.errMsg,
498               "Unknown system type: %d\n", sysType );
499      painCave.isFatal = 1;
500      simError();
501 +
502    }
503    
504 +
505 +
506 +  // clean up memory;
507 +
508 +  if( headStamp!= NULL )       delete headStamp;
509 +  if( the_stamps != NULL )     delete the_stamps;
510 +  if( the_globals != NULL )    delete the_globals;
511 +  if( the_components != NULL ) delete[] the_components;
512 +  
513 +  if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol;
514 +  if( bsInfo.compStamps != NULL )     delete[] bsInfo.compStamps;
515 +  if( bsInfo.includes != NULL ){
516 +    prevInc = bsInfo.includes;
517 +    while( prevInc != NULL ){
518 +      currInc = prevInc->next;
519 +      delete prevInc;
520 +      prevInc = currInc;
521 +    }
522 +  }
523 +      
524    return 0;
525   }
526  
# Line 188 | Line 539 | void usage(){
539                  "  ------\n"
540                  "   -h              Display this message\n"
541                  "   -o <prefix>     The output prefix\n"
542 +                "   -I <include>    File name that should be included at the top of the\n"
543 +                "                     output bass file.\n"
544                  "   -r              toggle the random option\n"
545                  "\n"
546                  "  long:\n"
547                  "  -----\n"
548 <                "   --bilayer       Tries to build a basic bilayer with the specified number\n"
549 <                "                     of lipids in the input bass file. The bilayer will be\n"
550 <                "                     surrounded by the number of solvent molecules given\n"
551 <                "                     in the bass file.\n"
552 <                "                      -note: combined with \"-r\" the simulation will start in\n"
553 <                "                             an FCC lattice with randomly assigned latice\n"
201 <                "                             sites for all atoms involved.\n"
548 >                "   --bilayer <lipid> <water>  Tries to build a basic bilayer with the specified number\n"
549 >                "                              of lipids in the input bass file. The bilayer will be\n"
550 >                "                              surrounded by the number of solvent molecules given\n"
551 >                "                              in the bass file.\n"
552 >                "                                -note: combined with \"-r\" the simulation will start\n"
553 >                "                                 the lipids randomly oriented in a sea of waters.\n"
554                  "\n"
555                  "\n",
556                  program_name);

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