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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 536 by mmeineke, Fri May 16 14:28:27 2003 UTC

# Line 1 | Line 1
1   #include <cstdlib>
2   #include <cstdio>
3   #include <cstring>
4 + #include <cmath>
5  
6   #include "simError.h"
7 + #include "parse_me.h"
8 + #include "MakeStamps.hpp"
9 + #include "Globals.hpp"
10 + #include "SimInfo.hpp"
11  
12 + #include "sysBuild.hpp"
13   #include "bilayerSys.hpp"
14  
15 < // quick case asignments
15 > // this routine is defined in BASS_interface.cpp
16 > extern void set_interface_stamps( MakeStamps* ms, Globals* g );
17  
18 +
19 + // case asignments
20   #define BILAYER 1
21  
22  
23   char* program_name;
24 + bassInfo bsInfo;
25   void usage(void);
26  
27  
# Line 23 | Line 33 | int main( int argc, char* argv[]){
33    char current_flag;
34    char* out_prefix;
35    char* in_name;
36 +  char* id;
37    
38 <  sysBuildInfo info;
38 >  includeLinked* headInc;
39 >  includeLinked* prevInc;
40 >  includeLinked* currInc;
41  
42 <  // initialize simError
43 <  initSimError();
42 >  MakeStamps* the_stamps = NULL;
43 >  Globals* the_globals = NULL;
44 >  Component** the_components = NULL;
45 >  LinkedMolStamp* headStamp = NULL;
46 >  LinkedMolStamp* currStamp;
47  
48 +  // initialize all functions and variables
49  
50 <  program_name = argv[0]; /*save the program name in case we need it*/
50 >  initSimError();
51 >  program_name = argv[0];
52    sysType = -1;
53    have_prefix = 0;
54    isRandom = 0;
55    in_name = NULL;
56 +  headInc = NULL;
57 +
58 +  bsInfo.includes = NULL;
59 +  bsInfo.componentsNmol = NULL;
60 +  bsInfo.compStamps = NULL;
61 +  bsInfo.havePressure = 0;
62 +  bsInfo.haveTauBarostat = 0;
63 +  bsInfo.haveTauThermostat = 0;
64 +  bsInfo.haveQmass = 0;
65 +
66 +  headStamp = new LinkedMolStamp();
67 +  the_stamps = new MakeStamps();
68 +  the_globals = new Globals();
69 +  set_interface_stamps( the_stamps, the_globals );
70 +
71 +  // parse command line arguments
72 +
73    for( i = 1; i < argc; i++){
74      
75      if(argv[i][0] =='-'){
# Line 53 | Line 88 | int main( int argc, char* argv[]){
88              simError();
89              usage();
90            }
91 +
92            sysType = BILAYER;
93 +
94 +          i++;
95 +          if( i>=argc ){
96 +            sprintf( painCave.errMsg,
97 +                     "\n"
98 +                     "not enough arguments for bilayer\n");
99 +            painCave.isFatal = 0;
100 +            simError();
101 +            usage();
102 +          }      
103 +          strcpy( bsInfo.lipidName, argv[i] );
104 +          
105 +          i++;
106 +          if( i>=argc ){
107 +            sprintf( painCave.errMsg,
108 +                     "\n"
109 +                     "not enough arguments for bilayer\n");
110 +            painCave.isFatal = 0;
111 +            simError();
112 +            usage();
113 +          }      
114 +          strcpy( bsInfo.waterName, argv[i] );
115 +
116          }
117  
118          else{
# Line 85 | Line 144 | int main( int argc, char* argv[]){
144              done = 1;
145              break;
146  
147 +          case 'I':
148 +            // -I <include> => the include file.
149 +
150 +            i++;
151 +            if( headInc == NULL ){
152 +              headInc = new includeLinked;
153 +              headInc->next = NULL;
154 +              strcpy( headInc->name, argv[i] );
155 +            }
156 +            else{
157 +              prevInc = headInc;
158 +              currInc = headInc->next;
159 +              while( currInc != NULL ){
160 +                prevInc = currInc;
161 +                currInc = prevInc->next;
162 +              }
163 +              currInc = new includeLinked;
164 +              currInc->next = NULL;
165 +              strcpy( currInc->name, argv[i] );
166 +              prevInc->next = currInc;
167 +            }
168 +            
169 +            done = 1;
170 +            break;
171 +
172            case 'h':
173              // -h => give the usage
174              
# Line 149 | Line 233 | int main( int argc, char* argv[]){
233    if( !have_prefix ){
234      out_prefix = strdup( "donkey" );
235    }
152 –  
153 –  info.in_name = in_name;
154 –  info.out_prefix = out_prefix;
155 –  info.isRandom = isRandom;
236    
237 <  // switch the system type
237 >  // set command line info into the bassInfo struct
238 >  
239 >  bsInfo.outPrefix = out_prefix;
240 >  bsInfo.includes = headInc;
241 >  
242  
243 +  // open and parse the bass file.
244 +
245 +  set_interface_stamps( the_stamps, the_globals );
246 +  yacc_BASS( in_name );  
247 +
248 +  // set the easy ones first
249 +  bsInfo.targetTemp = the_globals->getTargetTemp();
250 +  bsInfo.dt = the_globals->getDt();
251 +  bsInfo.runTime = the_globals->getRunTime();
252 +
253 +  // get the ones we know are there, yet still may need some work.
254 +  bsInfo.nComponents = the_globals->getNComponents();
255 +  strcpy( bsInfo.forceField, the_globals->getForceField() );
256 +
257 +  // get the ensemble:
258 +  strcpy( bsInfo.ensemble, the_globals->getEnsemble() );
259 +  if( !strcasecmp( bsInfo.ensemble, "NPT" ) ) {
260 +    
261 +    if (the_globals->haveTargetPressure()){
262 +      bsInfo.targetPressure = the_globals->getTargetPressure();
263 +      bsInfo.havePressure = 1;
264 +    }
265 +    else {
266 +      sprintf( painCave.errMsg,
267 +               "sysBuild error: If you use the constant pressure\n"
268 +               "    ensemble, you must set targetPressure.\n"
269 +               "    This was found in the BASS file.\n");
270 +      painCave.isFatal = 1;
271 +      simError();
272 +    }
273 +
274 +    if (the_globals->haveTauThermostat()){
275 +      bsInfo.tauThermostat = the_globals->getTauThermostat();
276 +      bsInfo.haveTauThermostat = 1;;
277 +    }
278 +    else if (the_globals->haveQmass()){
279 +      bsInfo.Qmass = the_globals->getQmass();
280 +      bsInfo.haveQmass = 1;
281 +    }
282 +    else {
283 +      sprintf( painCave.errMsg,
284 +               "sysBuild error: If you use one of the constant temperature\n"
285 +               "    ensembles, you must set either tauThermostat or qMass.\n"
286 +               "    Neither of these was found in the BASS file.\n");
287 +      painCave.isFatal = 1;
288 +      simError();
289 +    }
290 +
291 +    if (the_globals->haveTauBarostat()){
292 +      bsInfo.tauBarostat = the_globals->getTauBarostat();
293 +      bsInfo.haveTauBarostat = 1;
294 +    }                                    
295 +    else {
296 +      sprintf( painCave.errMsg,
297 +               "sysBuild error: If you use the constant pressure\n"
298 +               "    ensemble, you must set tauBarostat.\n"
299 +               "    This was found in the BASS file.\n");
300 +      painCave.isFatal = 1;
301 +      simError();
302 +    }
303 +
304 +  }
305 +  else if ( !strcasecmp( bsInfo.ensemble, "NVT") ) {
306 +
307 +    if (the_globals->haveTauThermostat()){
308 +      bsInfo.tauThermostat = the_globals->getTauThermostat();
309 +      bsInfo.haveTauThermostat = 1;
310 +    }
311 +    else if (the_globals->haveQmass()){
312 +      bsInfo.Qmass = the_globals->getQmass();
313 +      bsInfo.haveQmass = 1;
314 +    }
315 +    else {
316 +      sprintf( painCave.errMsg,
317 +               "sysBuild error: If you use one of the constant temperature\n"
318 +               "    ensembles, you must set either tauThermostat or qMass.\n"
319 +               "    Neither of these was found in the BASS file.\n");
320 +      painCave.isFatal = 1;
321 +      simError();
322 +    }
323 +    
324 +  }
325 +  else if ( !strcasecmp( bsInfo.ensemble, "NVE") ) {
326 +    
327 +    // nothing special for now
328 +  }
329 +  else {
330 +    sprintf( painCave.errMsg,
331 +             "sysBuild Warning. Unrecognized Ensemble -> %s, "
332 +             "reverting to NVE for this simulation.\n",
333 +             bsInfo.ensemble );
334 +    painCave.isFatal = 0;
335 +    simError();
336 +    strcpy( bsInfo.ensemble, "NVE" );
337 +  }  
338 +
339 +
340 +  // get the components and calculate the tot_nMol and indvidual n_mol
341 +
342 +  the_components = the_globals->getComponents();
343 +  bsInfo.componentsNmol = new int[bsInfo.nComponents];
344 +  bsInfo.compStamps = new MoleculeStamp*[bsInfo.nComponents];  
345 +  bsInfo.totNmol = 0;
346 +  for( i=0; i<bsInfo.nComponents; i++ ){
347 +    
348 +    if( !the_components[i]->haveNMol() ){
349 +      // we have a problem
350 +      sprintf( painCave.errMsg,
351 +               "sysBuild Error. No component NMol"
352 +               " given. Cannot calculate the number of atoms.\n" );
353 +      painCave.isFatal = 1;
354 +      simError();
355 +    }
356 +    
357 +    bsInfo.totNmol += the_components[i]->getNMol();
358 +    bsInfo.componentsNmol[i] = the_components[i]->getNMol();
359 +  }
360 +
361 +  // make an array of molecule stamps that match the components used.
362 +  // also extract the used stamps out into a separate linked list
363 +  
364 +  for( i=0; i<bsInfo.nComponents; i++ ){
365 +
366 +    id = the_components[i]->getType();
367 +    bsInfo.compStamps[i] = NULL;
368 +    
369 +    // check to make sure the component isn't already in the list
370 +
371 +    bsInfo.compStamps[i] = headStamp->match( id );
372 +    if( bsInfo.compStamps[i] == NULL ){
373 +      
374 +      // extract the component from the list;
375 +      
376 +      currStamp = the_stamps->extractMolStamp( id );
377 +      if( currStamp == NULL ){
378 +        sprintf( painCave.errMsg,
379 +                 "sysBuild error: Component \"%s\" was not found in the "
380 +                 "list of declared molecules\n",
381 +                 id );
382 +        painCave.isFatal = 1;
383 +        simError();
384 +      }
385 +      
386 +      headStamp->add( currStamp );
387 +      bsInfo.compStamps[i] = headStamp->match( id );
388 +    }
389 +  }
390 +
391 +  // get and set the boxSize
392 +
393 +  if( the_globals->haveBox() ){
394 +    bsInfo.boxX = the_globals->getBox();
395 +    bsInfo.boxY = the_globals->getBox();
396 +    bsInfo.boxZ = the_globals->getBox();
397 +  }
398 +  else if( the_globals->haveDensity() ){
399 +
400 +    double vol;
401 +    vol = (double)bsInfo.totNmol / the_globals->getDensity();
402 +    bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) );
403 +    bsInfo.boxY = bsInfo.boxX;
404 +    bsInfo.boxZ = bsInfo.boxY;
405 +  }
406 +  else{
407 +    if( !the_globals->haveBoxX() ){
408 +      sprintf( painCave.errMsg,
409 +               "sysBuild error, no periodic BoxX size given.\n" );
410 +      painCave.isFatal = 1;
411 +      simError();
412 +    }
413 +    bsInfo.boxX = the_globals->getBoxX();
414 +
415 +    if( !the_globals->haveBoxY() ){
416 +      sprintf( painCave.errMsg,
417 +               "sysBuild error, no periodic BoxY size given.\n" );
418 +      painCave.isFatal = 1;
419 +      simError();
420 +    }
421 +    bsInfo.boxY = the_globals->getBoxY();
422 +
423 +    if( !the_globals->haveBoxZ() ){
424 +      sprintf( painCave.errMsg,
425 +               "SimSetup error, no periodic BoxZ size given.\n" );
426 +      painCave.isFatal = 1;
427 +      simError();
428 +    }
429 +    bsInfo.boxZ = the_globals->getBoxZ();
430 +  }
431 +  
432 +
433 +  //************************************************************
434 +  // that should be all we need from bass. now to switch to the
435 +  // appropriate system builder.
436 +  // ***********************************************************
437 +
438 +
439    switch( sysType ){
440      
441    case BILAYER:
442      
443 <    buildBilayer( info );
443 >    buildBilayer( isRandom );
444      break;
445  
446    default:
# Line 170 | Line 450 | int main( int argc, char* argv[]){
450      simError();
451    }
452    
453 +
454 +
455 +  // clean up memory;
456 +
457 +  if( headStamp!= NULL )       delete headStamp;
458 +  if( the_stamps != NULL )     delete the_stamps;
459 +  if( the_globals != NULL )    delete the_globals;
460 +  if( the_components != NULL ) delete[] the_components;
461 +  
462 +  if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol;
463 +  if( bsInfo.compStamps != NULL )     delete[] bsInfo.compStamps;
464 +  if( bsInfo.includes != NULL ){
465 +    prevInc = bsInfo.includes;
466 +    while( prevInc != NULL ){
467 +      currInc = prevInc->next;
468 +      delete prevInc;
469 +      prevInc = currInc;
470 +    }
471 +  }
472 +      
473    return 0;
474   }
475  
# Line 188 | Line 488 | void usage(){
488                  "  ------\n"
489                  "   -h              Display this message\n"
490                  "   -o <prefix>     The output prefix\n"
491 +                "   -I <include>    File name that should be included at the top of the\n"
492 +                "                     output bass file.\n"
493                  "   -r              toggle the random option\n"
494                  "\n"
495                  "  long:\n"
496                  "  -----\n"
497 <                "   --bilayer       Tries to build a basic bilayer with the specified number\n"
498 <                "                     of lipids in the input bass file. The bilayer will be\n"
499 <                "                     surrounded by the number of solvent molecules given\n"
500 <                "                     in the bass file.\n"
501 <                "                      -note: combined with \"-r\" the simulation will start in\n"
502 <                "                             an FCC lattice with randomly assigned latice\n"
201 <                "                             sites for all atoms involved.\n"
497 >                "   --bilayer <lipid> <water>  Tries to build a basic bilayer with the specified number\n"
498 >                "                              of lipids in the input bass file. The bilayer will be\n"
499 >                "                              surrounded by the number of solvent molecules given\n"
500 >                "                              in the bass file.\n"
501 >                "                                -note: combined with \"-r\" the simulation will start\n"
502 >                "                                 the lipids randomly oriented in a sea of waters.\n"
503                  "\n"
504                  "\n",
505                  program_name);

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