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root/group/trunk/mdtools/interface_implementation/SimSetup.cpp
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Comparing trunk/mdtools/interface_implementation/SimSetup.cpp (file contents):
Revision 139 by chuckv, Wed Oct 16 21:07:16 2002 UTC vs.
Revision 184 by mmeineke, Thu Nov 21 20:33:06 2002 UTC

# Line 6 | Line 6
6   #include "parse_me.h"
7   #include "LRI.hpp"
8   #include "Integrator.hpp"
9 + #include "simError.h"
10 +
11   #ifdef IS_MPI
12   #include "mpiBASS.h"
13   #include "bassDiag.hpp"
# Line 14 | Line 16 | SimSetup::SimSetup(){
16   SimSetup::SimSetup(){
17    stamps = new MakeStamps();
18    globals = new Globals();
19 +  
20 + #ifdef IS_MPI
21 +  strcpy( checkPointMsg, "SimSetup creation successful" );
22 +  MPIcheckPoint();
23 + #endif // IS_MPI
24   }
25  
26   SimSetup::~SimSetup(){
# Line 23 | Line 30 | void SimSetup::parseFile( char* fileName ){
30  
31   void SimSetup::parseFile( char* fileName ){
32  
26 –  inFileName = fileName;
27 –  set_interface_stamps( stamps, globals );
33   #ifdef IS_MPI
34 <  mpiEventInit();
34 >  if( worldRank == 0 ){
35 > #endif // is_mpi
36 >    
37 >    inFileName = fileName;
38 >    set_interface_stamps( stamps, globals );
39 >    
40 > #ifdef IS_MPI
41 >    mpiEventInit();
42   #endif
43 <  yacc_BASS( fileName );
43 >
44 >    yacc_BASS( fileName );
45 >
46   #ifdef IS_MPI
47 <  throwMPIEvent(NULL);
47 >    throwMPIEvent(NULL);
48 >  }
49 >  else receiveParse();
50   #endif
51  
52   }
# Line 40 | Line 56 | void SimSetup::receiveParse(void){
56  
57      set_interface_stamps( stamps, globals );
58      mpiEventInit();
59 +    MPIcheckPoint();
60      mpiEventLoop();
61  
62   }
# Line 51 | Line 68 | void SimSetup::testMe(void){
68    delete dumpMe;
69   }
70   #endif
71 +
72   void SimSetup::createSim( void ){
73  
74    MakeStamps *the_stamps;
# Line 75 | Line 93 | void SimSetup::createSim( void ){
93    else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
94    else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
95    else{
96 <    std::cerr<< "SimSetup Error. Unrecognized force field -> "
97 <             << force_field << "\n";
98 <    exit(8);
96 >    sprintf( painCave.errMsg,
97 >             "SimSetup Error. Unrecognized force field -> %s\n",
98 >             force_field );
99 >    painCave.isFatal = 1;
100 >    simError();
101    }
102  
103 + #ifdef IS_MPI
104 +  strcpy( checkPointMsg, "ForceField creation successful" );
105 +  MPIcheckPoint();
106 + #endif // is_mpi
107 +
108    // get the components and calculate the tot_nMol and indvidual n_mol
109    the_components = the_globals->getComponents();
110    components_nmol = new int[n_components];
# Line 154 | Line 179 | void SimSetup::createSim( void ){
179  
180    // create the atom and short range interaction arrays
181  
182 +  Atom::createArrays(tot_atoms);
183    the_atoms = new Atom*[tot_atoms];
184    the_molecules = new Molecule[tot_nmol];
185  
# Line 254 | Line 280 | void SimSetup::createSim( void ){
280   //   else{
281  
282      initFromBass();
257 –
258 –
259 – //   }
260 –
261 – //   if( the_globals->haveFinalConfig() ){
262 – //     strcpy( simnfo->finalName, the_globals->getFinalConfig() );
263 – //   }
264 – //   else{
265 – //     strcpy( simnfo->finalName, inFileName );
266 – //     char* endTest;
267 – //     int nameLength = strlen( simnfo->finalName );
268 – //     endTest = &(simnfo->finalName[nameLength - 5]);
269 – //     if( !strcmp( endTest, ".bass" ) ){
270 – //       strcpy( endTest, ".eor" );
271 – //     }
272 – //     else if( !strcmp( endTest, ".BASS" ) ){
273 – //       strcpy( endTest, ".eor" );
274 – //     }
275 – //     else{
276 – //       endTest = &(simnfo->finalName[nameLength - 4]);
277 – //       if( !strcmp( endTest, ".bss" ) ){
278 – //      strcpy( endTest, ".eor" );
279 – //       }
280 – //       else if( !strcmp( endTest, ".mdl" ) ){
281 – //      strcpy( endTest, ".eor" );
282 – //       }
283 – //       else{
284 – //      strcat( simnfo->finalName, ".eor" );
285 – //       }
286 – //     }
287 – //   }
283  
289 – //   // make the sample and status out names
284  
291 – //   strcpy( simnfo->sampleName, inFileName );
292 – //   char* endTest;
293 – //   int nameLength = strlen( simnfo->sampleName );
294 – //   endTest = &(simnfo->sampleName[nameLength - 5]);
295 – //   if( !strcmp( endTest, ".bass" ) ){
296 – //     strcpy( endTest, ".dump" );
285   //   }
298 – //   else if( !strcmp( endTest, ".BASS" ) ){
299 – //     strcpy( endTest, ".dump" );
300 – //   }
301 – //   else{
302 – //     endTest = &(simnfo->sampleName[nameLength - 4]);
303 – //     if( !strcmp( endTest, ".bss" ) ){
304 – //       strcpy( endTest, ".dump" );
305 – //     }
306 – //     else if( !strcmp( endTest, ".mdl" ) ){
307 – //       strcpy( endTest, ".dump" );
308 – //     }
309 – //     else{
310 – //       strcat( simnfo->sampleName, ".dump" );
311 – //     }
312 – //   }
286  
287 < //   strcpy( simnfo->statusName, inFileName );
288 < //   nameLength = strlen( simnfo->statusName );
289 < //   endTest = &(simnfo->statusName[nameLength - 5]);
290 < //   if( !strcmp( endTest, ".bass" ) ){
291 < //     strcpy( endTest, ".stat" );
292 < //   }
293 < //   else if( !strcmp( endTest, ".BASS" ) ){
294 < //     strcpy( endTest, ".stat" );
295 < //   }
296 < //   else{
297 < //     endTest = &(simnfo->statusName[nameLength - 4]);
298 < //     if( !strcmp( endTest, ".bss" ) ){
299 < //       strcpy( endTest, ".stat" );
300 < //     }
301 < //     else if( !strcmp( endTest, ".mdl" ) ){
302 < //       strcpy( endTest, ".stat" );
303 < //     }
304 < //     else{
305 < //       strcat( simnfo->statusName, ".stat" );
306 < //     }
307 < //   }
308 <
287 > #ifdef IS_MPI
288 >    if( worldRank == TESTWRITE ){
289 > #endif // is_mpi
290 >      
291 >      fprintf( stderr,
292 >               "infile name is \"%s\"\n",
293 >               inFileName );
294 >      
295 >      inFileName = "./butane.bass";
296 >        
297 >      if( the_globals->haveFinalConfig() ){
298 >        strcpy( simnfo->finalName, the_globals->getFinalConfig() );
299 >      }
300 >      else{
301 >        strcpy( simnfo->finalName, inFileName );
302 >        char* endTest;
303 >        int nameLength = strlen( simnfo->finalName );
304 >        endTest = &(simnfo->finalName[nameLength - 5]);
305 >        if( !strcmp( endTest, ".bass" ) ){
306 >          strcpy( endTest, ".eor" );
307 >        }
308 >        else if( !strcmp( endTest, ".BASS" ) ){
309 >          strcpy( endTest, ".eor" );
310 >        }
311 >        else{
312 >          endTest = &(simnfo->finalName[nameLength - 4]);
313 >          if( !strcmp( endTest, ".bss" ) ){
314 >            strcpy( endTest, ".eor" );
315 >          }
316 >          else if( !strcmp( endTest, ".mdl" ) ){
317 >            strcpy( endTest, ".eor" );
318 >          }
319 >          else{
320 >            strcat( simnfo->finalName, ".eor" );
321 >          }
322 >        }
323 >      }
324 >      
325 >      // make the sample and status out names
326 >      
327 >      strcpy( simnfo->sampleName, inFileName );
328 >      char* endTest;
329 >      int nameLength = strlen( simnfo->sampleName );
330 >      endTest = &(simnfo->sampleName[nameLength - 5]);
331 >      if( !strcmp( endTest, ".bass" ) ){
332 >        strcpy( endTest, ".dump" );
333 >      }
334 >      else if( !strcmp( endTest, ".BASS" ) ){
335 >        strcpy( endTest, ".dump" );
336 >      }
337 >      else{
338 >        endTest = &(simnfo->sampleName[nameLength - 4]);
339 >        if( !strcmp( endTest, ".bss" ) ){
340 >          strcpy( endTest, ".dump" );
341 >        }
342 >        else if( !strcmp( endTest, ".mdl" ) ){
343 >          strcpy( endTest, ".dump" );
344 >        }
345 >        else{
346 >          strcat( simnfo->sampleName, ".dump" );
347 >        }
348 >      }
349 >      
350 >      strcpy( simnfo->statusName, inFileName );
351 >      nameLength = strlen( simnfo->statusName );
352 >      endTest = &(simnfo->statusName[nameLength - 5]);
353 >      if( !strcmp( endTest, ".bass" ) ){
354 >        strcpy( endTest, ".stat" );
355 >      }
356 >      else if( !strcmp( endTest, ".BASS" ) ){
357 >        strcpy( endTest, ".stat" );
358 >      }
359 >      else{
360 >        endTest = &(simnfo->statusName[nameLength - 4]);
361 >        if( !strcmp( endTest, ".bss" ) ){
362 >          strcpy( endTest, ".stat" );
363 >        }
364 >        else if( !strcmp( endTest, ".mdl" ) ){
365 >          strcpy( endTest, ".stat" );
366 >        }
367 >        else{
368 >          strcat( simnfo->statusName, ".stat" );
369 >        }
370 >      }
371 >      
372 > #ifdef IS_MPI
373 >    }
374 > #endif // is_mpi
375  
376    // set the status, sample, and themal kick times
377  
# Line 391 | Line 430 | void SimSetup::makeAtoms( void ){
430          current_atom = comp_stamps[i]->getAtom( k );
431          if( current_atom->haveOrientation() ){
432  
433 <          dAtom = new DirectionalAtom;
433 >          dAtom = new DirectionalAtom(index);
434            simnfo->n_oriented++;
435            the_atoms[index] = dAtom;
436  
# Line 411 | Line 450 | void SimSetup::makeAtoms( void ){
450            dAtom->setSUz( uz );
451          }
452          else{
453 <          the_atoms[index] = new GeneralAtom;
453 >          the_atoms[index] = new GeneralAtom(index);
454          }
455          the_atoms[index]->setType( current_atom->getType() );
456          the_atoms[index]->setIndex( index );

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