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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 502 by mmeineke, Tue Apr 15 21:47:54 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 85 | Line 120 | int main( int argc, char* argv[]){
120              done = 1;
121              break;
122  
123 +          case 'I':
124 +            // -I <include> => the include file.
125 +
126 +            i++;
127 +            if( headInc == NULL ){
128 +              headInc = new includeLinked;
129 +              headInc->next = NULL;
130 +              strcpy( headInc->name, argv[i] );
131 +            }
132 +            else{
133 +              prevInc = headInc;
134 +              currInc = headInc->next;
135 +              while( currInc != NULL ){
136 +                prevInc = currInc;
137 +                currInc = prevInc->next;
138 +              }
139 +              currInc = new includeLinked;
140 +              currInc->next = NULL;
141 +              strcpy( currInc->name, argv[i] );
142 +              prevInc->next = currInc;
143 +            }
144 +            
145 +            done = 1;
146 +            break;
147 +
148            case 'h':
149              // -h => give the usage
150              
# Line 149 | Line 209 | int main( int argc, char* argv[]){
209    if( !have_prefix ){
210      out_prefix = strdup( "donkey" );
211    }
152 –  
153 –  info.in_name = in_name;
154 –  info.out_prefix = out_prefix;
155 –  info.isRandom = isRandom;
212    
213 <  // switch the system type
213 >  // set command line info into the bassInfo struct
214 >  
215 >  bsInfo.outPrefix = out_prefix;
216 >  bsInfo.includes = headInc;
217 >  
218 >
219 >  // open and parse the bass file.
220 >
221 >  set_interface_stamps( the_stamps, the_globals );
222 >  yacc_BASS( in_name );  
223 >
224 >  // set the easy ones first
225 >  bsInfo.targetTemp = the_globals->getTargetTemp();
226 >  bsInfo.dt = the_globals->getDt();
227 >  bsInfo.runTime = the_globals->getRunTime();
228 >
229 >  // get the ones we know are there, yet still may need some work.
230 >  bsInfo.nComponents = the_globals->getNComponents();
231 >  strcpy( bsInfo.forceField, the_globals->getForceField() );
232 >
233 >  // get the ensemble:
234 >  strcpy( bsInfo.ensemble, the_globals->getEnsemble() );
235 >  if( !strcasecmp( bsInfo.ensemble, "NPT" ) ) {
236 >    
237 >    if (the_globals->haveTargetPressure()){
238 >      bsInfo.targetPressure = the_globals->getTargetPressure();
239 >      bsInfo.havePressure = 1;
240 >    }
241 >    else {
242 >      sprintf( painCave.errMsg,
243 >               "sysBuild error: If you use the constant pressure\n"
244 >               "    ensemble, you must set targetPressure.\n"
245 >               "    This was found in the BASS file.\n");
246 >      painCave.isFatal = 1;
247 >      simError();
248 >    }
249 >
250 >    if (the_globals->haveTauThermostat()){
251 >      bsInfo.tauThermostat = the_globals->getTauThermostat();
252 >      bsInfo.haveTauThermostat = 1;;
253 >    }
254 >    else if (the_globals->haveQmass()){
255 >      bsInfo.Qmass = the_globals->getQmass();
256 >      bsInfo.haveQmass = 1;
257 >    }
258 >    else {
259 >      sprintf( painCave.errMsg,
260 >               "sysBuild error: If you use one of the constant temperature\n"
261 >               "    ensembles, you must set either tauThermostat or qMass.\n"
262 >               "    Neither of these was found in the BASS file.\n");
263 >      painCave.isFatal = 1;
264 >      simError();
265 >    }
266 >
267 >    if (the_globals->haveTauBarostat()){
268 >      bsInfo.tauBarostat = the_globals->getTauBarostat();
269 >      bsInfo.haveTauBarostat = 1;
270 >    }                                    
271 >    else {
272 >      sprintf( painCave.errMsg,
273 >               "sysBuild error: If you use the constant pressure\n"
274 >               "    ensemble, you must set tauBarostat.\n"
275 >               "    This was found in the BASS file.\n");
276 >      painCave.isFatal = 1;
277 >      simError();
278 >    }
279 >
280 >  }
281 >  else if ( !strcasecmp( bsInfo.ensemble, "NVT") ) {
282 >
283 >    if (the_globals->haveTauThermostat()){
284 >      bsInfo.tauThermostat = the_globals->getTauThermostat();
285 >      bsInfo.haveTauThermostat = 1;
286 >    }
287 >    else if (the_globals->haveQmass()){
288 >      bsInfo.Qmass = the_globals->getQmass();
289 >      bsInfo.haveQmass = 1;
290 >    }
291 >    else {
292 >      sprintf( painCave.errMsg,
293 >               "sysBuild error: If you use one of the constant temperature\n"
294 >               "    ensembles, you must set either tauThermostat or qMass.\n"
295 >               "    Neither of these was found in the BASS file.\n");
296 >      painCave.isFatal = 1;
297 >      simError();
298 >    }
299 >    
300 >  }
301 >  else if ( !strcasecmp( bsInfo.ensemble, "NVE") ) {
302 >    
303 >    // nothing special for now
304 >  }
305 >  else {
306 >    sprintf( painCave.errMsg,
307 >             "sysBuild Warning. Unrecognized Ensemble -> %s, "
308 >             "reverting to NVE for this simulation.\n",
309 >             bsInfo.ensemble );
310 >    painCave.isFatal = 0;
311 >    simError();
312 >    strcpy( bsInfo.ensemble, "NVE" );
313 >  }  
314  
315 +
316 +  // get the components and calculate the tot_nMol and indvidual n_mol
317 +
318 +  the_components = the_globals->getComponents();
319 +  bsInfo.componentsNmol = new int[bsInfo.nComponents];
320 +  bsInfo.compStamps = new MoleculeStamp*[bsInfo.nComponents];  
321 +  bsInfo.totNmol = 0;
322 +  for( i=0; i<bsInfo.nComponents; i++ ){
323 +    
324 +    if( !the_components[i]->haveNMol() ){
325 +      // we have a problem
326 +      sprintf( painCave.errMsg,
327 +               "sysBuild Error. No component NMol"
328 +               " given. Cannot calculate the number of atoms.\n" );
329 +      painCave.isFatal = 1;
330 +      simError();
331 +    }
332 +    
333 +    bsInfo.totNmol += the_components[i]->getNMol();
334 +    bsInfo.componentsNmol[i] = the_components[i]->getNMol();
335 +  }
336 +
337 +  // make an array of molecule stamps that match the components used.
338 +  // also extract the used stamps out into a separate linked list
339 +  
340 +  for( i=0; i<bsInfo.nComponents; i++ ){
341 +
342 +    id = the_components[i]->getType();
343 +    bsInfo.compStamps[i] = NULL;
344 +    
345 +    // check to make sure the component isn't already in the list
346 +
347 +    bsInfo.compStamps[i] = headStamp->match( id );
348 +    if( bsInfo.compStamps[i] == NULL ){
349 +      
350 +      // extract the component from the list;
351 +      
352 +      currStamp = the_stamps->extractMolStamp( id );
353 +      if( currStamp == NULL ){
354 +        sprintf( painCave.errMsg,
355 +                 "sysBuild error: Component \"%s\" was not found in the "
356 +                 "list of declared molecules\n",
357 +                 id );
358 +        painCave.isFatal = 1;
359 +        simError();
360 +      }
361 +      
362 +      headStamp->add( currStamp );
363 +      bsInfo.compStamps[i] = headStamp->match( id );
364 +    }
365 +  }
366 +
367 +  // get and set the boxSize
368 +
369 +  if( the_globals->haveBox() ){
370 +    bsInfo.boxX = the_globals->getBox();
371 +    bsInfo.boxY = the_globals->getBox();
372 +    bsInfo.boxZ = the_globals->getBox();
373 +  }
374 +  else if( the_globals->haveDensity() ){
375 +
376 +    double vol;
377 +    vol = (double)bsInfo.totNmol / the_globals->getDensity();
378 +    bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) );
379 +    bsInfo.boxY = bsInfo.boxX;
380 +    bsInfo.boxZ = bsInfo.boxY;
381 +  }
382 +  else{
383 +    if( !the_globals->haveBoxX() ){
384 +      sprintf( painCave.errMsg,
385 +               "sysBuild error, no periodic BoxX size given.\n" );
386 +      painCave.isFatal = 1;
387 +      simError();
388 +    }
389 +    bsInfo.boxX = the_globals->getBoxX();
390 +
391 +    if( !the_globals->haveBoxY() ){
392 +      sprintf( painCave.errMsg,
393 +               "sysBuild error, no periodic BoxY size given.\n" );
394 +      painCave.isFatal = 1;
395 +      simError();
396 +    }
397 +    bsInfo.boxY = the_globals->getBoxY();
398 +
399 +    if( !the_globals->haveBoxZ() ){
400 +      sprintf( painCave.errMsg,
401 +               "SimSetup error, no periodic BoxZ size given.\n" );
402 +      painCave.isFatal = 1;
403 +      simError();
404 +    }
405 +    bsInfo.boxZ = the_globals->getBoxZ();
406 +  }
407 +  
408 +
409 +  //************************************************************
410 +  // that should be all we need from bass. now to switch to the
411 +  // appropriate system builder.
412 +  // ***********************************************************
413 +
414 +
415    switch( sysType ){
416      
417    case BILAYER:
418      
419 <    buildBilayer( info );
419 >    buildBilayer( isRandom );
420      break;
421  
422    default:
# Line 170 | Line 426 | int main( int argc, char* argv[]){
426      simError();
427    }
428    
429 +
430 +
431 +  // clean up memory;
432 +
433 +  if( headStamp!= NULL )       delete headStamp;
434 +  if( the_stamps != NULL )     delete the_stamps;
435 +  if( the_globals != NULL )    delete the_globals;
436 +  if( the_components != NULL ) delete[] the_components;
437 +  
438 +  if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol;
439 +  if( bsInfo.compStamps != NULL )     delete[] bsInfo.compStamps;
440 +  if( bsInfo.includes != NULL ){
441 +    prevInc = bsInfo.includes;
442 +    while( prevInc != NULL ){
443 +      currInc = prevInc->next;
444 +      delete prevInc;
445 +      prevInc = currInc;
446 +    }
447 +  }
448 +      
449    return 0;
450   }
451  
# Line 188 | Line 464 | void usage(){
464                  "  ------\n"
465                  "   -h              Display this message\n"
466                  "   -o <prefix>     The output prefix\n"
467 +                "   -I <include>    File name that should be included at the top of the\n"
468 +                "                     output bass file.\n"
469                  "   -r              toggle the random option\n"
470                  "\n"
471                  "  long:\n"

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