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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 117 by mmeineke, Tue Sep 24 22:10:55 2002 UTC vs.
Revision 176 by mmeineke, Thu Nov 14 22:00:44 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"
14 + #endif
15 +
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 19 | Line 30 | void SimSetup::parseFile( char* fileName ){
30  
31   void SimSetup::parseFile( char* fileName ){
32  
33 <  inFileName = fileName;
34 <  set_interface_stamps( stamps, globals );
35 <  yacc_BASS( fileName );
33 > #ifdef IS_MPI
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 >
44 >    yacc_BASS( fileName );
45 >
46 > #ifdef IS_MPI
47 >    throwMPIEvent(NULL);
48 >  }
49 >  else receiveParse();
50 > #endif
51 >
52   }
53  
54 + #ifdef IS_MPI
55 + void SimSetup::receiveParse(void){
56 +
57 +    set_interface_stamps( stamps, globals );
58 +    mpiEventInit();
59 +    MPIcheckPoint();
60 +    mpiEventLoop();
61 +
62 + }
63 +
64 +
65 + void SimSetup::testMe(void){
66 +  bassDiag* dumpMe = new bassDiag(globals,stamps);
67 +  dumpMe->dumpStamps();
68 +  delete dumpMe;
69 + }
70 + #endif
71 +
72   void SimSetup::createSim( void ){
73  
74    MakeStamps *the_stamps;
# Line 43 | Line 88 | void SimSetup::createSim( void ){
88    n_components = the_globals->getNComponents();
89    strcpy( force_field, the_globals->getForceField() );
90    strcpy( ensemble, the_globals->getEnsemble() );
91 <  
91 >
92    if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
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];
111    comp_stamps = new MoleculeStamp*[n_components];
112 <  
112 >
113    if( !the_globals->haveNMol() ){
114 <    // we don't have the total number of molecules, so we assume it is
114 >    // we don't have the total number of molecules, so we assume it is
115      // given in each component
116  
117      tot_nmol = 0;
118      for( i=0; i<n_components; i++ ){
119 <      
119 >
120        if( !the_components[i]->haveNMol() ){
121          // we have a problem
122          std::cerr << "SimSetup Error. No global NMol or component NMol"
# Line 78 | Line 130 | void SimSetup::createSim( void ){
130    }
131    else{
132      std::cerr << "NOT A SUPPORTED FEATURE\n";
133 <    
133 >
134   //     tot_nmol = the_globals->getNMol();
135 <    
135 >
136   //     //we have the total number of molecules, now we check for molfractions
137   //     for( i=0; i<n_components; i++ ){
138 <      
138 >
139   //       if( !the_components[i]->haveMolFraction() ){
140 <        
140 >
141   //      if( !the_components[i]->haveNMol() ){
142   //        //we have a problem
143   //        std::cerr << "SimSetup error. Neither molFraction nor "
# Line 97 | Line 149 | void SimSetup::createSim( void ){
149  
150    for( i=0; i<n_components; i++ ){
151  
152 <    comp_stamps[i] =
152 >    comp_stamps[i] =
153        the_stamps->getMolecule( the_components[i]->getType() );
154    }
155  
104 –  
156  
157 +
158    // caclulate the number of atoms, bonds, bends and torsions
159  
160    tot_atoms = 0;
# Line 110 | Line 162 | void SimSetup::createSim( void ){
162    tot_bends = 0;
163    tot_torsions = 0;
164    for( i=0; i<n_components; i++ ){
165 <    
165 >
166      tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
167      tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
168      tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
169      tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
170    }
171 <  
171 >
172    tot_SRI = tot_bonds + tot_bends + tot_torsions;
173 <  
173 >
174    simnfo->n_atoms = tot_atoms;
175    simnfo->n_bonds = tot_bonds;
176    simnfo->n_bends = tot_bends;
# Line 126 | Line 178 | void SimSetup::createSim( void ){
178    simnfo->n_SRI = tot_SRI;
179  
180    // create the atom and short range interaction arrays
181 <  
181 >
182    the_atoms = new Atom*[tot_atoms];
183 +  Atom::createArrays(tot_atoms);
184    the_molecules = new Molecule[tot_nmol];
185 <  
186 <  
185 >
186 >
187    if( tot_SRI ){
188      the_sris = new SRI*[tot_SRI];
189      the_excludes = new ex_pair[tot_SRI];
# Line 142 | Line 195 | void SimSetup::createSim( void ){
195    simnfo->sr_interactions = the_sris;
196    simnfo->n_exclude = tot_SRI;
197    simnfo->excludes = the_excludes;
145 –  
198  
199 +
200    // initialize the arrays
201 <  
201 >
202    the_ff->setSimInfo( simnfo );
203 <    
203 >
204    makeAtoms();
205  
206    if( tot_bonds ){
# Line 188 | Line 241 | void SimSetup::createSim( void ){
241      simnfo->box_z = the_globals->getBox();
242    }
243    else if( the_globals->haveDensity() ){
244 <    
244 >
245      double vol;
246      vol = (double)tot_nmol / the_globals->getDensity();
247      simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
# Line 214 | Line 267 | void SimSetup::createSim( void ){
267      }
268      simnfo->box_z = the_globals->getBoxZ();
269    }
270 <    
218 <  if( the_globals->haveInitialConfig() ){
219 <    InitializeFromFile* fileInit;
220 <    fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
221 <    
222 <    fileInit->read_xyz( simnfo ); // default velocities on
270 >
271  
272 <    delete fileInit;    
273 <  }
274 <  else{
272 > //   if( the_globals->haveInitialConfig() ){
273 > //        InitializeFromFile* fileInit;
274 > //     fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
275 >
276 > //     fileInit->read_xyz( simnfo ); // default velocities on
277 >
278 > //     delete fileInit;
279 > //   }
280 > //   else{
281 >
282      initFromBass();
228 –  }
283  
230 –  if( the_globals->haveFinalConfig() ){
231 –    strcpy( simnfo->finalName, the_globals->getFinalConfig() );
232 –  }
233 –  else{
234 –    strcpy( simnfo->finalName, inFileName );
235 –    char* endTest;
236 –    int nameLength = strlen( simnfo->finalName );
237 –    endTest = &(simnfo->finalName[nameLength - 5]);
238 –    if( !strcmp( endTest, ".bass" ) ){
239 –      strcpy( endTest, ".eor" );
240 –    }
241 –    else if( !strcmp( endTest, ".BASS" ) ){
242 –      strcpy( endTest, ".eor" );
243 –    }
244 –    else{
245 –      endTest = &(simnfo->finalName[nameLength - 4]);
246 –      if( !strcmp( endTest, ".bss" ) ){
247 –        strcpy( endTest, ".eor" );
248 –      }
249 –      else if( !strcmp( endTest, ".mdl" ) ){
250 –        strcpy( endTest, ".eor" );
251 –      }
252 –      else{
253 –        strcat( simnfo->finalName, ".eor" );
254 –      }
255 –    }
256 –  }
257 –    
258 –  // make the sample and status out names
284  
285 <  strcpy( simnfo->sampleName, inFileName );
286 <  char* endTest;
287 <  int nameLength = strlen( simnfo->sampleName );
288 <  endTest = &(simnfo->sampleName[nameLength - 5]);
289 <  if( !strcmp( endTest, ".bass" ) ){
290 <    strcpy( endTest, ".dump" );
291 <  }
292 <  else if( !strcmp( endTest, ".BASS" ) ){
293 <    strcpy( endTest, ".dump" );
294 <  }
295 <  else{
296 <    endTest = &(simnfo->sampleName[nameLength - 4]);
297 <    if( !strcmp( endTest, ".bss" ) ){
298 <      strcpy( endTest, ".dump" );
299 <    }
300 <    else if( !strcmp( endTest, ".mdl" ) ){
301 <      strcpy( endTest, ".dump" );
302 <    }
303 <    else{
304 <      strcat( simnfo->sampleName, ".dump" );
305 <    }
306 <  }
307 <  
308 <  strcpy( simnfo->statusName, inFileName );
309 <  nameLength = strlen( simnfo->statusName );
310 <  endTest = &(simnfo->statusName[nameLength - 5]);
311 <  if( !strcmp( endTest, ".bass" ) ){
312 <    strcpy( endTest, ".stat" );
313 <  }
314 <  else if( !strcmp( endTest, ".BASS" ) ){
315 <    strcpy( endTest, ".stat" );
316 <  }
317 <  else{
318 <    endTest = &(simnfo->statusName[nameLength - 4]);
319 <    if( !strcmp( endTest, ".bss" ) ){
320 <      strcpy( endTest, ".stat" );
321 <    }
322 <    else if( !strcmp( endTest, ".mdl" ) ){
323 <      strcpy( endTest, ".stat" );
324 <    }
325 <    else{
326 <      strcat( simnfo->statusName, ".stat" );
327 <    }
328 <  }
329 <  
285 > //   }
286 >
287 > //   if( the_globals->haveFinalConfig() ){
288 > //     strcpy( simnfo->finalName, the_globals->getFinalConfig() );
289 > //   }
290 > //   else{
291 > //     strcpy( simnfo->finalName, inFileName );
292 > //     char* endTest;
293 > //     int nameLength = strlen( simnfo->finalName );
294 > //     endTest = &(simnfo->finalName[nameLength - 5]);
295 > //     if( !strcmp( endTest, ".bass" ) ){
296 > //       strcpy( endTest, ".eor" );
297 > //     }
298 > //     else if( !strcmp( endTest, ".BASS" ) ){
299 > //       strcpy( endTest, ".eor" );
300 > //     }
301 > //     else{
302 > //       endTest = &(simnfo->finalName[nameLength - 4]);
303 > //       if( !strcmp( endTest, ".bss" ) ){
304 > //      strcpy( endTest, ".eor" );
305 > //       }
306 > //       else if( !strcmp( endTest, ".mdl" ) ){
307 > //      strcpy( endTest, ".eor" );
308 > //       }
309 > //       else{
310 > //      strcat( simnfo->finalName, ".eor" );
311 > //       }
312 > //     }
313 > //   }
314 >
315 > //   // make the sample and status out names
316 >
317 > //   strcpy( simnfo->sampleName, inFileName );
318 > //   char* endTest;
319 > //   int nameLength = strlen( simnfo->sampleName );
320 > //   endTest = &(simnfo->sampleName[nameLength - 5]);
321 > //   if( !strcmp( endTest, ".bass" ) ){
322 > //     strcpy( endTest, ".dump" );
323 > //   }
324 > //   else if( !strcmp( endTest, ".BASS" ) ){
325 > //     strcpy( endTest, ".dump" );
326 > //   }
327 > //   else{
328 > //     endTest = &(simnfo->sampleName[nameLength - 4]);
329 > //     if( !strcmp( endTest, ".bss" ) ){
330 > //       strcpy( endTest, ".dump" );
331 > //     }
332 > //     else if( !strcmp( endTest, ".mdl" ) ){
333 > //       strcpy( endTest, ".dump" );
334 > //     }
335 > //     else{
336 > //       strcat( simnfo->sampleName, ".dump" );
337 > //     }
338 > //   }
339 >
340 > //   strcpy( simnfo->statusName, inFileName );
341 > //   nameLength = strlen( simnfo->statusName );
342 > //   endTest = &(simnfo->statusName[nameLength - 5]);
343 > //   if( !strcmp( endTest, ".bass" ) ){
344 > //     strcpy( endTest, ".stat" );
345 > //   }
346 > //   else if( !strcmp( endTest, ".BASS" ) ){
347 > //     strcpy( endTest, ".stat" );
348 > //   }
349 > //   else{
350 > //     endTest = &(simnfo->statusName[nameLength - 4]);
351 > //     if( !strcmp( endTest, ".bss" ) ){
352 > //       strcpy( endTest, ".stat" );
353 > //     }
354 > //     else if( !strcmp( endTest, ".mdl" ) ){
355 > //       strcpy( endTest, ".stat" );
356 > //     }
357 > //     else{
358 > //       strcat( simnfo->statusName, ".stat" );
359 > //     }
360 > //   }
361 >
362 >
363    // set the status, sample, and themal kick times
364  
365    if( the_globals->haveSampleTime() ){
366 <    simnfo->sampleTime = the_globals->getSampleTime();
366 >    simnfo->sampleTime = the_globals->getSampleTime();
367      simnfo->statusTime = simnfo->sampleTime;
368      simnfo->thermalTime = simnfo->sampleTime;
369    }
370    else{
371 <    simnfo->sampleTime = the_globals->getRunTime();
371 >    simnfo->sampleTime = the_globals->getRunTime();
372      simnfo->statusTime = simnfo->sampleTime;
373      simnfo->thermalTime = simnfo->sampleTime;
374    }
# Line 326 | Line 384 | void SimSetup::createSim( void ){
384    // check for the temperature set flag
385  
386    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
387 <  
388 <    
387 >
388 >
389    // make the longe range forces and the integrator
390 <  
390 >
391    new AllLong( simnfo );
392 <      
392 >
393    if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo );
394    if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo );
395    if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo );
396   }
397  
398   void SimSetup::makeAtoms( void ){
399 <  
399 >
400    int i, j, k, index;
401    double ux, uy, uz, uSqr, u;
402    AtomStamp* current_atom;
403    DirectionalAtom* dAtom;
404    int molIndex, molStart, molEnd, nMemb;
347 –  
405  
406 +
407    molIndex = 0;
408    index = 0;
409    for( i=0; i<n_components; i++ ){
410 <    
410 >
411      for( j=0; j<components_nmol[i]; j++ ){
412 <      
412 >
413        molStart = index;
414        nMemb = comp_stamps[i]->getNAtoms();
415        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
416 <        
416 >
417          current_atom = comp_stamps[i]->getAtom( k );
418 <        if( current_atom->haveOrientation() ){
418 >        if( current_atom->haveOrientation() ){
419  
420 <          dAtom = new DirectionalAtom;
420 >          dAtom = new DirectionalAtom(index);
421            simnfo->n_oriented++;
422            the_atoms[index] = dAtom;
423 <      
423 >
424            ux = current_atom->getOrntX();
425            uy = current_atom->getOrntY();
426            uz = current_atom->getOrntZ();
427 <          
427 >
428            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
429 <          
429 >
430            u = sqrt( uSqr );
431            ux = ux / u;
432            uy = uy / u;
433            uz = uz / u;
434 <          
434 >
435            dAtom->setSUx( ux );
436            dAtom->setSUy( uy );
437            dAtom->setSUz( uz );
438          }
439          else{
440 <          the_atoms[index] = new GeneralAtom;
440 >          the_atoms[index] = new GeneralAtom(index);
441          }
442          the_atoms[index]->setType( current_atom->getType() );
443          the_atoms[index]->setIndex( index );
444 <        
444 >
445          // increment the index and repeat;
446          index++;
447        }
448 <      
448 >
449        molEnd = index -1;
450        the_molecules[molIndex].setNMembers( nMemb );
451        the_molecules[molIndex].setStartAtom( molStart );
# Line 396 | Line 454 | void SimSetup::makeAtoms( void ){
454  
455      }
456    }
457 <  
457 >
458    the_ff->initializeAtoms();
459   }
460  
# Line 410 | Line 468 | void SimSetup::makeBonds( void ){
468    index = 0;
469    offset = 0;
470    for( i=0; i<n_components; i++ ){
471 <    
471 >
472      for( j=0; j<components_nmol[i]; j++ ){
473 <      
473 >
474        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
475 <        
475 >
476          current_bond = comp_stamps[i]->getBond( k );
477          the_bonds[index].a = current_bond->getA() + offset;
478          the_bonds[index].b = current_bond->getB() + offset;
# Line 428 | Line 486 | void SimSetup::makeBonds( void ){
486        offset += comp_stamps[i]->getNAtoms();
487      }
488    }
489 <  
489 >
490    the_ff->initializeBonds( the_bonds );
491   }
492  
# Line 442 | Line 500 | void SimSetup::makeBends( void ){
500    index = 0;
501    offset = 0;
502    for( i=0; i<n_components; i++ ){
503 <    
503 >
504      for( j=0; j<components_nmol[i]; j++ ){
505 <      
505 >
506        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
507 <        
507 >
508          current_bend = comp_stamps[i]->getBend( k );
509          the_bends[index].a = current_bend->getA() + offset;
510          the_bends[index].b = current_bend->getB() + offset;
# Line 461 | Line 519 | void SimSetup::makeBends( void ){
519        offset += comp_stamps[i]->getNAtoms();
520      }
521    }
522 <  
522 >
523    the_ff->initializeBends( the_bends );
524   }
525  
# Line 475 | Line 533 | void SimSetup::makeTorsions( void ){
533    index = 0;
534    offset = 0;
535    for( i=0; i<n_components; i++ ){
536 <    
536 >
537      for( j=0; j<components_nmol[i]; j++ ){
538 <      
538 >
539        for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
540 <        
540 >
541          current_torsion = comp_stamps[i]->getTorsion( k );
542          the_torsions[index].a = current_torsion->getA() + offset;
543          the_torsions[index].b = current_torsion->getB() + offset;
# Line 495 | Line 553 | void SimSetup::makeTorsions( void ){
553        offset += comp_stamps[i]->getNAtoms();
554      }
555    }
556 <  
556 >
557    the_ff->initializeTorsions( the_torsions );
558   }
559  
# Line 536 | Line 594 | void SimSetup::initFromBass( void ){
594      celly = simnfo->box_y / temp3;
595      cellz = simnfo->box_z / temp3;
596    }
597 <  
597 >
598    current_mol = 0;
599    current_comp_mol = 0;
600    current_comp = 0;
601    current_atom_ndx = 0;
602 <  
602 >
603    for( i=0; i < n_cells ; i++ ){
604      for( j=0; j < n_cells; j++ ){
605        for( k=0; k < n_cells; k++ ){
606 <        
606 >
607          makeElement( i * cellx,
608                       j * celly,
609                       k * cellz );
610 <        
610 >
611          makeElement( i * cellx + 0.5 * cellx,
612                       j * celly + 0.5 * celly,
613                       k * cellz );
614 <        
614 >
615          makeElement( i * cellx,
616                       j * celly + 0.5 * celly,
617                       k * cellz + 0.5 * cellz );
618 <        
618 >
619          makeElement( i * cellx + 0.5 * cellx,
620                       j * celly,
621                       k * cellz + 0.5 * cellz );
# Line 567 | Line 625 | void SimSetup::initFromBass( void ){
625  
626    if( have_extra ){
627      done = 0;
628 <    
628 >
629      int start_ndx;
630      for( i=0; i < (n_cells+1) && !done; i++ ){
631        for( j=0; j < (n_cells+1) && !done; j++ ){
632 <        
632 >
633          if( i < n_cells ){
634 <          
634 >
635            if( j < n_cells ){
636              start_ndx = n_cells;
637            }
638            else start_ndx = 0;
639          }
640          else start_ndx = 0;
641 <        
641 >
642          for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
643 <          
643 >
644            makeElement( i * cellx,
645                         j * celly,
646                         k * cellz );
647            done = ( current_mol >= tot_nmol );
648 <          
648 >
649            if( !done && n_per_extra > 1 ){
650              makeElement( i * cellx + 0.5 * cellx,
651                           j * celly + 0.5 * celly,
652                           k * cellz );
653              done = ( current_mol >= tot_nmol );
654            }
655 <          
655 >
656            if( !done && n_per_extra > 2){
657              makeElement( i * cellx,
658                           j * celly + 0.5 * celly,
659                           k * cellz + 0.5 * cellz );
660              done = ( current_mol >= tot_nmol );
661            }
662 <          
662 >
663            if( !done && n_per_extra > 3){
664              makeElement( i * cellx + 0.5 * cellx,
665                           j * celly,
# Line 612 | Line 670 | void SimSetup::initFromBass( void ){
670        }
671      }
672    }
673 <  
674 <  
673 >
674 >
675    for( i=0; i<simnfo->n_atoms; i++ ){
676      simnfo->atoms[i]->set_vx( 0.0 );
677      simnfo->atoms[i]->set_vy( 0.0 );
# Line 629 | Line 687 | void SimSetup::makeElement( double x, double y, double
687    double rotMat[3][3];
688  
689    for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
690 <    
690 >
691      current_atom = comp_stamps[current_comp]->getAtom( k );
692      if( !current_atom->havePosition() ){
693        std::cerr << "Component " << comp_stamps[current_comp]->getID()
# Line 639 | Line 697 | void SimSetup::makeElement( double x, double y, double
697                  << " position.\n";
698        exit(8);
699      }
700 <    
700 >
701      the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
702      the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
703      the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
704 <    
704 >
705      if( the_atoms[current_atom_ndx]->isDirectional() ){
706 <      
706 >
707        dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
708 <      
708 >
709        rotMat[0][0] = 1.0;
710        rotMat[0][1] = 0.0;
711        rotMat[0][2] = 0.0;
# Line 665 | Line 723 | void SimSetup::makeElement( double x, double y, double
723  
724      current_atom_ndx++;
725    }
726 <  
726 >
727    current_mol++;
728    current_comp_mol++;
729  
730    if( current_comp_mol >= components_nmol[current_comp] ){
731 <    
731 >
732      current_comp_mol = 0;
733      current_comp++;
734    }

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