# | Line 12 | Line 12 | |
---|---|---|
12 | #include "mpiSimulation.hpp" | |
13 | #endif | |
14 | ||
15 | + | // some defines for ensemble and Forcefield cases |
16 | + | |
17 | + | #define NVE_ENS 0 |
18 | + | #define NVT_ENS 1 |
19 | + | #define NPTi_ENS 2 |
20 | + | #define NPTf_ENS 3 |
21 | + | |
22 | + | |
23 | + | #define FF_DUFF 0 |
24 | + | #define FF_LJ 1 |
25 | + | |
26 | + | |
27 | SimSetup::SimSetup(){ | |
28 | stamps = new MakeStamps(); | |
29 | globals = new Globals(); | |
# | Line 66 | Line 78 | void SimSetup::createSim( void ){ | |
78 | ||
79 | MakeStamps *the_stamps; | |
80 | Globals* the_globals; | |
81 | < | int i, j; |
81 | > | int i, j, k, globalAtomIndex; |
82 | > | |
83 | > | int ensembleCase; |
84 | > | int ffCase; |
85 | > | |
86 | > | ensembleCase = -1; |
87 | > | ffCase = -1; |
88 | ||
89 | // get the stamps and globals; | |
90 | the_stamps = stamps; | |
# | Line 80 | Line 98 | void SimSetup::createSim( void ){ | |
98 | // get the ones we know are there, yet still may need some work. | |
99 | n_components = the_globals->getNComponents(); | |
100 | strcpy( force_field, the_globals->getForceField() ); | |
101 | + | |
102 | + | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
103 | + | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
104 | + | else{ |
105 | + | sprintf( painCave.errMsg, |
106 | + | "SimSetup Error. Unrecognized force field -> %s\n", |
107 | + | force_field ); |
108 | + | painCave.isFatal = 1; |
109 | + | simError(); |
110 | + | } |
111 | + | |
112 | + | // get the ensemble: |
113 | strcpy( ensemble, the_globals->getEnsemble() ); | |
114 | + | |
115 | + | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
116 | + | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
117 | + | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
118 | + | ensembleCase = NPTi_ENS; |
119 | + | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
120 | + | else{ |
121 | + | sprintf( painCave.errMsg, |
122 | + | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
123 | + | "reverting to NVE for this simulation.\n", |
124 | + | ensemble ); |
125 | + | painCave.isFatal = 0; |
126 | + | simError(); |
127 | + | strcpy( ensemble, "NVE" ); |
128 | + | ensembleCase = NVE_ENS; |
129 | + | } |
130 | strcpy( simnfo->ensemble, ensemble ); | |
131 | ||
132 | + | |
133 | + | // if( !strcasecmp( ensemble, "NPT" ) ) { |
134 | + | // the_extendedsystem = new ExtendedSystem( simnfo ); |
135 | + | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
136 | + | // if (the_globals->haveTargetPressure()) |
137 | + | // the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
138 | + | // else { |
139 | + | // sprintf( painCave.errMsg, |
140 | + | // "SimSetup error: If you use the constant pressure\n" |
141 | + | // " ensemble, you must set targetPressure.\n" |
142 | + | // " This was found in the BASS file.\n"); |
143 | + | // painCave.isFatal = 1; |
144 | + | // simError(); |
145 | + | // } |
146 | + | |
147 | + | // if (the_globals->haveTauThermostat()) |
148 | + | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
149 | + | // else if (the_globals->haveQmass()) |
150 | + | // the_extendedsystem->setQmass(the_globals->getQmass()); |
151 | + | // else { |
152 | + | // sprintf( painCave.errMsg, |
153 | + | // "SimSetup error: If you use one of the constant temperature\n" |
154 | + | // " ensembles, you must set either tauThermostat or qMass.\n" |
155 | + | // " Neither of these was found in the BASS file.\n"); |
156 | + | // painCave.isFatal = 1; |
157 | + | // simError(); |
158 | + | // } |
159 | + | |
160 | + | // if (the_globals->haveTauBarostat()) |
161 | + | // the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
162 | + | // else { |
163 | + | // sprintf( painCave.errMsg, |
164 | + | // "SimSetup error: If you use the constant pressure\n" |
165 | + | // " ensemble, you must set tauBarostat.\n" |
166 | + | // " This was found in the BASS file.\n"); |
167 | + | // painCave.isFatal = 1; |
168 | + | // simError(); |
169 | + | // } |
170 | + | |
171 | + | // } else if ( !strcasecmp( ensemble, "NVT") ) { |
172 | + | // the_extendedsystem = new ExtendedSystem( simnfo ); |
173 | + | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
174 | + | |
175 | + | // if (the_globals->haveTauThermostat()) |
176 | + | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
177 | + | // else if (the_globals->haveQmass()) |
178 | + | // the_extendedsystem->setQmass(the_globals->getQmass()); |
179 | + | // else { |
180 | + | // sprintf( painCave.errMsg, |
181 | + | // "SimSetup error: If you use one of the constant temperature\n" |
182 | + | // " ensembles, you must set either tauThermostat or qMass.\n" |
183 | + | // " Neither of these was found in the BASS file.\n"); |
184 | + | // painCave.isFatal = 1; |
185 | + | // simError(); |
186 | + | // } |
187 | + | |
188 | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); | |
189 | simnfo->usePBC = the_globals->getPBC(); | |
190 | ||
191 | + | int usesDipoles = 0; |
192 | + | switch( ffCase ){ |
193 | ||
194 | < | |
195 | < | if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
196 | < | else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
197 | < | else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
198 | < | else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
199 | < | else{ |
194 | > | case FF_DUFF: |
195 | > | the_ff = new DUFF(); |
196 | > | usesDipoles = 1; |
197 | > | break; |
198 | > | |
199 | > | case FF_LJ: |
200 | > | the_ff = new LJFF(); |
201 | > | break; |
202 | > | |
203 | > | default: |
204 | sprintf( painCave.errMsg, | |
205 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
98 | < | force_field ); |
205 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
206 | painCave.isFatal = 1; | |
207 | simError(); | |
208 | } | |
# | Line 105 | Line 212 | void SimSetup::createSim( void ){ | |
212 | MPIcheckPoint(); | |
213 | #endif // is_mpi | |
214 | ||
108 | – | |
109 | – | |
215 | // get the components and calculate the tot_nMol and indvidual n_mol | |
216 | the_components = the_globals->getComponents(); | |
217 | components_nmol = new int[n_components]; | |
# | Line 230 | Line 335 | void SimSetup::createSim( void ){ | |
335 | simnfo->n_torsions = tot_torsions; | |
336 | simnfo->n_SRI = tot_SRI; | |
337 | simnfo->n_mol = tot_nmol; | |
233 | – | |
338 | ||
339 | + | simnfo->molMembershipArray = new int[tot_atoms]; |
340 | + | |
341 | #ifdef IS_MPI | |
342 | ||
343 | // divide the molecules among processors here. | |
344 | ||
345 | mpiSim = new mpiSimulation( simnfo ); | |
346 | ||
241 | – | |
242 | – | |
347 | globalIndex = mpiSim->divideLabor(); | |
348 | ||
245 | – | |
246 | – | |
349 | // set up the local variables | |
350 | ||
351 | int localMol, allMol; | |
352 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
353 | + | |
354 | + | int* mol2proc = mpiSim->getMolToProcMap(); |
355 | + | int* molCompType = mpiSim->getMolComponentType(); |
356 | ||
357 | allMol = 0; | |
358 | localMol = 0; | |
# | Line 255 | Line 360 | void SimSetup::createSim( void ){ | |
360 | local_bonds = 0; | |
361 | local_bends = 0; | |
362 | local_torsions = 0; | |
363 | + | globalAtomIndex = 0; |
364 | + | |
365 | + | |
366 | for( i=0; i<n_components; i++ ){ | |
367 | ||
368 | for( j=0; j<components_nmol[i]; j++ ){ | |
369 | ||
370 | < | if( mpiSim->getMyMolStart() <= allMol && |
263 | < | allMol <= mpiSim->getMyMolEnd() ){ |
370 | > | if( mol2proc[allMol] == worldRank ){ |
371 | ||
372 | local_atoms += comp_stamps[i]->getNAtoms(); | |
373 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 268 | Line 375 | void SimSetup::createSim( void ){ | |
375 | local_torsions += comp_stamps[i]->getNTorsions(); | |
376 | localMol++; | |
377 | } | |
378 | < | allMol++; |
378 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
379 | > | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
380 | > | globalAtomIndex++; |
381 | > | } |
382 | > | |
383 | > | allMol++; |
384 | } | |
385 | } | |
386 | local_SRI = local_bonds + local_bends + local_torsions; | |
387 | ||
276 | – | |
388 | simnfo->n_atoms = mpiSim->getMyNlocal(); | |
389 | ||
390 | if( local_atoms != simnfo->n_atoms ){ | |
391 | sprintf( painCave.errMsg, | |
392 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" | |
393 | < | " localAtom (%d) are note equal.\n", |
393 | > | " localAtom (%d) are not equal.\n", |
394 | simnfo->n_atoms, | |
395 | local_atoms ); | |
396 | painCave.isFatal = 1; | |
# | Line 304 | Line 415 | void SimSetup::createSim( void ){ | |
415 | Atom::createArrays(simnfo->n_atoms); | |
416 | the_atoms = new Atom*[simnfo->n_atoms]; | |
417 | the_molecules = new Molecule[simnfo->n_mol]; | |
418 | + | int molIndex; |
419 | ||
420 | + | // initialize the molecule's stampID's |
421 | ||
422 | < | if( simnfo->n_SRI ){ |
423 | < | the_sris = new SRI*[simnfo->n_SRI]; |
424 | < | the_excludes = new int[2 * simnfo->n_SRI]; |
422 | > | #ifdef IS_MPI |
423 | > | |
424 | > | |
425 | > | molIndex = 0; |
426 | > | for(i=0; i<mpiSim->getTotNmol(); i++){ |
427 | > | |
428 | > | if(mol2proc[i] == worldRank ){ |
429 | > | the_molecules[molIndex].setStampID( molCompType[i] ); |
430 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
431 | > | the_molecules[molIndex].setGlobalIndex( i ); |
432 | > | molIndex++; |
433 | > | } |
434 | > | } |
435 | > | |
436 | > | #else // is_mpi |
437 | > | |
438 | > | molIndex = 0; |
439 | > | globalAtomIndex = 0; |
440 | > | for(i=0; i<n_components; i++){ |
441 | > | for(j=0; j<components_nmol[i]; j++ ){ |
442 | > | the_molecules[molIndex].setStampID( i ); |
443 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
444 | > | the_molecules[molIndex].setGlobalIndex( molIndex ); |
445 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
446 | > | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
447 | > | globalAtomIndex++; |
448 | > | } |
449 | > | molIndex++; |
450 | > | } |
451 | > | } |
452 | > | |
453 | > | |
454 | > | #endif // is_mpi |
455 | > | |
456 | > | |
457 | > | if( simnfo->n_SRI ){ |
458 | > | |
459 | > | Exclude::createArray(simnfo->n_SRI); |
460 | > | the_excludes = new Exclude*[simnfo->n_SRI]; |
461 | > | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
462 | simnfo->globalExcludes = new int; | |
463 | < | simnfo->n_exclude = tot_SRI; |
463 | > | simnfo->n_exclude = simnfo->n_SRI; |
464 | } | |
465 | else{ | |
466 | ||
467 | < | the_excludes = new int[2]; |
468 | < | the_excludes[0] = 0; |
469 | < | the_excludes[1] = 0; |
467 | > | Exclude::createArray( 1 ); |
468 | > | the_excludes = new Exclude*; |
469 | > | the_excludes[0] = new Exclude(0); |
470 | > | the_excludes[0]->setPair( 0,0 ); |
471 | simnfo->globalExcludes = new int; | |
472 | simnfo->globalExcludes[0] = 0; | |
473 | < | |
323 | < | simnfo->n_exclude = 1; |
473 | > | simnfo->n_exclude = 0; |
474 | } | |
475 | ||
476 | // set the arrays into the SimInfo object | |
477 | ||
478 | simnfo->atoms = the_atoms; | |
479 | < | simnfo->sr_interactions = the_sris; |
479 | > | simnfo->molecules = the_molecules; |
480 | simnfo->nGlobalExcludes = 0; | |
481 | simnfo->excludes = the_excludes; | |
482 | ||
483 | ||
484 | // get some of the tricky things that may still be in the globals | |
485 | ||
486 | < | |
486 | > | double boxVector[3]; |
487 | if( the_globals->haveBox() ){ | |
488 | < | simnfo->box_x = the_globals->getBox(); |
489 | < | simnfo->box_y = the_globals->getBox(); |
490 | < | simnfo->box_z = the_globals->getBox(); |
488 | > | boxVector[0] = the_globals->getBox(); |
489 | > | boxVector[1] = the_globals->getBox(); |
490 | > | boxVector[2] = the_globals->getBox(); |
491 | > | |
492 | > | simnfo->setBox( boxVector ); |
493 | } | |
494 | else if( the_globals->haveDensity() ){ | |
495 | ||
496 | double vol; | |
497 | vol = (double)tot_nmol / the_globals->getDensity(); | |
498 | < | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
499 | < | simnfo->box_y = simnfo->box_x; |
500 | < | simnfo->box_z = simnfo->box_x; |
498 | > | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
499 | > | boxVector[1] = boxVector[0]; |
500 | > | boxVector[2] = boxVector[0]; |
501 | > | |
502 | > | simnfo->setBox( boxVector ); |
503 | } | |
504 | else{ | |
505 | if( !the_globals->haveBoxX() ){ | |
# | Line 354 | Line 508 | void SimSetup::createSim( void ){ | |
508 | painCave.isFatal = 1; | |
509 | simError(); | |
510 | } | |
511 | < | simnfo->box_x = the_globals->getBoxX(); |
511 | > | boxVector[0] = the_globals->getBoxX(); |
512 | ||
513 | if( !the_globals->haveBoxY() ){ | |
514 | sprintf( painCave.errMsg, | |
# | Line 362 | Line 516 | void SimSetup::createSim( void ){ | |
516 | painCave.isFatal = 1; | |
517 | simError(); | |
518 | } | |
519 | < | simnfo->box_y = the_globals->getBoxY(); |
519 | > | boxVector[1] = the_globals->getBoxY(); |
520 | ||
521 | if( !the_globals->haveBoxZ() ){ | |
522 | sprintf( painCave.errMsg, | |
# | Line 370 | Line 524 | void SimSetup::createSim( void ){ | |
524 | painCave.isFatal = 1; | |
525 | simError(); | |
526 | } | |
527 | < | simnfo->box_z = the_globals->getBoxZ(); |
527 | > | boxVector[2] = the_globals->getBoxZ(); |
528 | > | |
529 | > | simnfo->setBox( boxVector ); |
530 | } | |
531 | ||
532 | #ifdef IS_MPI | |
# | Line 383 | Line 539 | void SimSetup::createSim( void ){ | |
539 | ||
540 | the_ff->setSimInfo( simnfo ); | |
541 | ||
542 | < | makeAtoms(); |
542 | > | makeMolecules(); |
543 | simnfo->identArray = new int[simnfo->n_atoms]; | |
544 | for(i=0; i<simnfo->n_atoms; i++){ | |
545 | simnfo->identArray[i] = the_atoms[i]->getIdent(); | |
546 | } | |
547 | ||
392 | – | if( tot_bonds ){ |
393 | – | makeBonds(); |
394 | – | } |
395 | – | |
396 | – | if( tot_bends ){ |
397 | – | makeBends(); |
398 | – | } |
399 | – | |
400 | – | if( tot_torsions ){ |
401 | – | makeTorsions(); |
402 | – | } |
403 | – | |
404 | – | |
548 | if (the_globals->getUseRF() ) { | |
549 | simnfo->useReactionField = 1; | |
550 | ||
# | Line 413 | Line 556 | void SimSetup::createSim( void ){ | |
556 | painCave.isFatal = 0; | |
557 | simError(); | |
558 | double smallest; | |
559 | < | smallest = simnfo->box_x; |
560 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
561 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
559 | > | smallest = simnfo->boxLx; |
560 | > | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
561 | > | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
562 | simnfo->ecr = 0.5 * smallest; | |
563 | } else { | |
564 | simnfo->ecr = the_globals->getECR(); | |
# | Line 443 | Line 586 | void SimSetup::createSim( void ){ | |
586 | } | |
587 | simnfo->dielectric = the_globals->getDielectric(); | |
588 | } else { | |
589 | < | if (simnfo->n_dipoles) { |
589 | > | if (usesDipoles) { |
590 | ||
591 | if( !the_globals->haveECR() ){ | |
592 | sprintf( painCave.errMsg, | |
593 | < | "SimSetup Warning: using default value of 1/2 the smallest" |
593 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
594 | "box length for the electrostaticCutoffRadius.\n" | |
595 | "I hope you have a very fast processor!\n"); | |
596 | painCave.isFatal = 0; | |
597 | simError(); | |
598 | double smallest; | |
599 | < | smallest = simnfo->box_x; |
600 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
601 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
599 | > | smallest = simnfo->boxLx; |
600 | > | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
601 | > | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
602 | simnfo->ecr = 0.5 * smallest; | |
603 | } else { | |
604 | simnfo->ecr = the_globals->getECR(); | |
# | Line 463 | Line 606 | void SimSetup::createSim( void ){ | |
606 | ||
607 | if( !the_globals->haveEST() ){ | |
608 | sprintf( painCave.errMsg, | |
609 | < | "SimSetup Warning: using default value of 5% of the" |
609 | > | "SimSetup Warning: using default value of 5%% of the " |
610 | "electrostaticCutoffRadius for the " | |
611 | "electrostaticSkinThickness\n" | |
612 | ); | |
# | Line 634 | Line 777 | void SimSetup::createSim( void ){ | |
777 | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); | |
778 | ||
779 | ||
780 | < | // // make the longe range forces and the integrator |
781 | < | |
782 | < | // new AllLong( simnfo ); |
783 | < | |
784 | < | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 | < | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
643 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
644 | < | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
780 | > | // make the integrator |
781 | > | |
782 | > | |
783 | > | NVT* myNVT = NULL; |
784 | > | switch( ensembleCase ){ |
785 | ||
786 | + | case NVE_ENS: |
787 | + | new NVE( simnfo, the_ff ); |
788 | + | break; |
789 | ||
790 | + | case NVT_ENS: |
791 | + | myNVT = new NVT( simnfo, the_ff ); |
792 | + | myNVT->setTargetTemp(the_globals->getTargetTemp()); |
793 | ||
794 | + | if (the_globals->haveTauThermostat()) |
795 | + | myNVT->setTauThermostat(the_globals->getTauThermostat()); |
796 | + | // else if (the_globals->haveQmass()) |
797 | + | // myNVT->setQmass(the_globals->getQmass()); |
798 | + | else { |
799 | + | sprintf( painCave.errMsg, |
800 | + | "SimSetup error: If you use the NVT\n" |
801 | + | " ensemble, you must set either tauThermostat or qMass.\n" |
802 | + | " Neither of these was found in the BASS file.\n"); |
803 | + | painCave.isFatal = 1; |
804 | + | simError(); |
805 | + | } |
806 | + | break; |
807 | + | |
808 | + | default: |
809 | + | sprintf( painCave.errMsg, |
810 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
811 | + | painCave.isFatal = 1; |
812 | + | simError(); |
813 | + | } |
814 | + | |
815 | + | |
816 | + | #ifdef IS_MPI |
817 | + | mpiSim->mpiRefresh(); |
818 | + | #endif |
819 | + | |
820 | // initialize the Fortran | |
821 | < | |
821 | > | |
822 | > | |
823 | simnfo->refreshSim(); | |
824 | ||
825 | if( !strcmp( simnfo->mixingRule, "standard") ){ | |
# | Line 674 | Line 847 | void SimSetup::makeMolecules( void ){ | |
847 | ||
848 | void SimSetup::makeMolecules( void ){ | |
849 | ||
850 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset; |
850 | > | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
851 | molInit info; | |
852 | DirectionalAtom* dAtom; | |
853 | + | LinkedAssign* extras; |
854 | + | LinkedAssign* current_extra; |
855 | AtomStamp* currentAtom; | |
856 | BondStamp* currentBond; | |
857 | BendStamp* currentBend; | |
858 | TorsionStamp* currentTorsion; | |
859 | + | |
860 | + | bond_pair* theBonds; |
861 | + | bend_set* theBends; |
862 | + | torsion_set* theTorsions; |
863 | + | |
864 | ||
865 | //init the forceField paramters | |
866 | ||
867 | the_ff->readParams(); | |
868 | ||
869 | ||
870 | < | // init the molecules |
870 | > | // init the atoms |
871 | ||
872 | + | double ux, uy, uz, u, uSqr; |
873 | + | |
874 | atomOffset = 0; | |
875 | + | excludeOffset = 0; |
876 | for(i=0; i<simnfo->n_mol; i++){ | |
877 | ||
878 | stampID = the_molecules[i].getStampID(); | |
# | Line 698 | Line 881 | void SimSetup::makeMolecules( void ){ | |
881 | info.nBonds = comp_stamps[stampID]->getNBonds(); | |
882 | info.nBends = comp_stamps[stampID]->getNBends(); | |
883 | info.nTorsions = comp_stamps[stampID]->getNTorsions(); | |
884 | < | |
884 | > | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
885 | > | |
886 | info.myAtoms = &the_atoms[atomOffset]; | |
887 | + | info.myExcludes = &the_excludes[excludeOffset]; |
888 | info.myBonds = new Bond*[info.nBonds]; | |
889 | info.myBends = new Bend*[info.nBends]; | |
890 | < | info.myTorsions = new Torsions*[info.nTorsions]; |
890 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
891 | ||
892 | theBonds = new bond_pair[info.nBonds]; | |
893 | theBends = new bend_set[info.nBends]; | |
# | Line 712 | Line 897 | void SimSetup::makeMolecules( void ){ | |
897 | ||
898 | for(j=0; j<info.nAtoms; j++){ | |
899 | ||
900 | < | currentAtom = theComponents[stampID]->getAtom( j ); |
900 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
901 | if( currentAtom->haveOrientation() ){ | |
902 | ||
903 | dAtom = new DirectionalAtom(j + atomOffset); | |
# | Line 747 | Line 932 | void SimSetup::makeMolecules( void ){ | |
932 | } | |
933 | ||
934 | // make the bonds | |
935 | < | for(j=0; j<nBonds; j++){ |
935 | > | for(j=0; j<info.nBonds; j++){ |
936 | ||
937 | currentBond = comp_stamps[stampID]->getBond( j ); | |
938 | theBonds[j].a = currentBond->getA() + atomOffset; | |
939 | theBonds[j].b = currentBond->getB() + atomOffset; | |
940 | ||
941 | < | exI = theBonds[i].a; |
942 | < | exJ = theBonds[i].b; |
941 | > | exI = theBonds[j].a; |
942 | > | exJ = theBonds[j].b; |
943 | ||
944 | // exclude_I must always be the smaller of the pair | |
945 | if( exI > exJ ){ | |
# | Line 763 | Line 948 | void SimSetup::makeMolecules( void ){ | |
948 | exJ = tempEx; | |
949 | } | |
950 | #ifdef IS_MPI | |
951 | + | tempEx = exI; |
952 | + | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
953 | + | tempEx = exJ; |
954 | + | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
955 | ||
956 | < | the_excludes[index*2] = |
768 | < | the_atoms[exI]->getGlobalIndex() + 1; |
769 | < | the_excludes[index*2 + 1] = |
770 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
771 | < | |
956 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
957 | #else // isn't MPI | |
773 | – | |
774 | – | the_excludes[index*2] = exI + 1; |
775 | – | the_excludes[index*2 + 1] = exJ + 1; |
776 | – | // fortran index from 1 (hence the +1 in the indexing) |
958 | ||
959 | + | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
960 | #endif //is_mpi | |
961 | < | |
962 | < | } |
961 | > | } |
962 | > | excludeOffset += info.nBonds; |
963 | ||
964 | < | |
965 | < | |
966 | < | |
967 | < | |
968 | < | |
969 | < | |
970 | < | |
789 | < | |
790 | < | |
791 | < | |
792 | < | |
793 | < | |
794 | < | |
795 | < | |
796 | < | void SimSetup::makeAtoms( void ){ |
797 | < | |
798 | < | int i, j, k, index; |
799 | < | double ux, uy, uz, uSqr, u; |
800 | < | AtomStamp* current_atom; |
801 | < | |
802 | < | DirectionalAtom* dAtom; |
803 | < | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
804 | < | |
805 | < | lMolIndex = 0; |
806 | < | molIndex = 0; |
807 | < | index = 0; |
808 | < | for( i=0; i<n_components; i++ ){ |
809 | < | |
810 | < | for( j=0; j<components_nmol[i]; j++ ){ |
811 | < | |
812 | < | #ifdef IS_MPI |
813 | < | if( mpiSim->getMyMolStart() <= molIndex && |
814 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
815 | < | #endif // is_mpi |
816 | < | |
817 | < | molStart = index; |
818 | < | nMemb = comp_stamps[i]->getNAtoms(); |
819 | < | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
964 | > | //make the bends |
965 | > | for(j=0; j<info.nBends; j++){ |
966 | > | |
967 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
968 | > | theBends[j].a = currentBend->getA() + atomOffset; |
969 | > | theBends[j].b = currentBend->getB() + atomOffset; |
970 | > | theBends[j].c = currentBend->getC() + atomOffset; |
971 | ||
972 | < | current_atom = comp_stamps[i]->getAtom( k ); |
822 | < | if( current_atom->haveOrientation() ){ |
972 | > | if( currentBend->haveExtras() ){ |
973 | ||
974 | < | dAtom = new DirectionalAtom(index); |
975 | < | simnfo->n_oriented++; |
826 | < | the_atoms[index] = dAtom; |
827 | < | |
828 | < | ux = current_atom->getOrntX(); |
829 | < | uy = current_atom->getOrntY(); |
830 | < | uz = current_atom->getOrntZ(); |
831 | < | |
832 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
833 | < | |
834 | < | u = sqrt( uSqr ); |
835 | < | ux = ux / u; |
836 | < | uy = uy / u; |
837 | < | uz = uz / u; |
974 | > | extras = currentBend->getExtras(); |
975 | > | current_extra = extras; |
976 | ||
977 | < | dAtom->setSUx( ux ); |
978 | < | dAtom->setSUy( uy ); |
979 | < | dAtom->setSUz( uz ); |
977 | > | while( current_extra != NULL ){ |
978 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
979 | > | |
980 | > | switch( current_extra->getType() ){ |
981 | > | |
982 | > | case 0: |
983 | > | theBends[j].ghost = |
984 | > | current_extra->getInt() + atomOffset; |
985 | > | theBends[j].isGhost = 1; |
986 | > | break; |
987 | > | |
988 | > | case 1: |
989 | > | theBends[j].ghost = |
990 | > | (int)current_extra->getDouble() + atomOffset; |
991 | > | theBends[j].isGhost = 1; |
992 | > | break; |
993 | > | |
994 | > | default: |
995 | > | sprintf( painCave.errMsg, |
996 | > | "SimSetup Error: ghostVectorSource was neither a " |
997 | > | "double nor an int.\n" |
998 | > | "-->Bend[%d] in %s\n", |
999 | > | j, comp_stamps[stampID]->getID() ); |
1000 | > | painCave.isFatal = 1; |
1001 | > | simError(); |
1002 | > | } |
1003 | } | |
1004 | + | |
1005 | else{ | |
1006 | < | the_atoms[index] = new GeneralAtom(index); |
1006 | > | |
1007 | > | sprintf( painCave.errMsg, |
1008 | > | "SimSetup Error: unhandled bend assignment:\n" |
1009 | > | " -->%s in Bend[%d] in %s\n", |
1010 | > | current_extra->getlhs(), |
1011 | > | j, comp_stamps[stampID]->getID() ); |
1012 | > | painCave.isFatal = 1; |
1013 | > | simError(); |
1014 | } | |
846 | – | the_atoms[index]->setType( current_atom->getType() ); |
847 | – | the_atoms[index]->setIndex( index ); |
1015 | ||
1016 | < | // increment the index and repeat; |
850 | < | index++; |
1016 | > | current_extra = current_extra->getNext(); |
1017 | } | |
1018 | + | } |
1019 | + | |
1020 | + | if( !theBends[j].isGhost ){ |
1021 | + | |
1022 | + | exI = theBends[j].a; |
1023 | + | exJ = theBends[j].c; |
1024 | + | } |
1025 | + | else{ |
1026 | ||
1027 | < | molEnd = index -1; |
1028 | < | the_molecules[lMolIndex].setNMembers( nMemb ); |
855 | < | the_molecules[lMolIndex].setStartAtom( molStart ); |
856 | < | the_molecules[lMolIndex].setEndAtom( molEnd ); |
857 | < | the_molecules[lMolIndex].setStampID( i ); |
858 | < | lMolIndex++; |
859 | < | |
860 | < | #ifdef IS_MPI |
1027 | > | exI = theBends[j].a; |
1028 | > | exJ = theBends[j].b; |
1029 | } | |
862 | – | #endif //is_mpi |
1030 | ||
1031 | < | molIndex++; |
1031 | > | // exclude_I must always be the smaller of the pair |
1032 | > | if( exI > exJ ){ |
1033 | > | tempEx = exI; |
1034 | > | exI = exJ; |
1035 | > | exJ = tempEx; |
1036 | > | } |
1037 | > | #ifdef IS_MPI |
1038 | > | tempEx = exI; |
1039 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1040 | > | tempEx = exJ; |
1041 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1042 | > | |
1043 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1044 | > | #else // isn't MPI |
1045 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1046 | > | #endif //is_mpi |
1047 | } | |
1048 | < | } |
1048 | > | excludeOffset += info.nBends; |
1049 | ||
1050 | < | #ifdef IS_MPI |
1051 | < | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
1052 | < | |
1053 | < | delete[] globalIndex; |
1050 | > | for(j=0; j<info.nTorsions; j++){ |
1051 | > | |
1052 | > | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1053 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1054 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1055 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1056 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1057 | > | |
1058 | > | exI = theTorsions[j].a; |
1059 | > | exJ = theTorsions[j].d; |
1060 | ||
1061 | < | mpiSim->mpiRefresh(); |
1062 | < | #endif //IS_MPI |
1063 | < | |
1064 | < | the_ff->initializeAtoms(); |
1065 | < | } |
1066 | < | |
879 | < | void SimSetup::makeBonds( void ){ |
880 | < | |
881 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
882 | < | bond_pair* the_bonds; |
883 | < | BondStamp* current_bond; |
884 | < | |
885 | < | the_bonds = new bond_pair[tot_bonds]; |
886 | < | index = 0; |
887 | < | offset = 0; |
888 | < | molIndex = 0; |
889 | < | |
890 | < | for( i=0; i<n_components; i++ ){ |
891 | < | |
892 | < | for( j=0; j<components_nmol[i]; j++ ){ |
893 | < | |
1061 | > | // exclude_I must always be the smaller of the pair |
1062 | > | if( exI > exJ ){ |
1063 | > | tempEx = exI; |
1064 | > | exI = exJ; |
1065 | > | exJ = tempEx; |
1066 | > | } |
1067 | #ifdef IS_MPI | |
1068 | < | if( mpiSim->getMyMolStart() <= molIndex && |
1069 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1070 | < | #endif // is_mpi |
1071 | < | |
1072 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
1073 | < | |
901 | < | current_bond = comp_stamps[i]->getBond( k ); |
902 | < | the_bonds[index].a = current_bond->getA() + offset; |
903 | < | the_bonds[index].b = current_bond->getB() + offset; |
904 | < | |
905 | < | exI = the_bonds[index].a; |
906 | < | exJ = the_bonds[index].b; |
907 | < | |
908 | < | // exclude_I must always be the smaller of the pair |
909 | < | if( exI > exJ ){ |
910 | < | tempEx = exI; |
911 | < | exI = exJ; |
912 | < | exJ = tempEx; |
913 | < | } |
914 | < | |
915 | < | |
916 | < | #ifdef IS_MPI |
917 | < | |
918 | < | the_excludes[index*2] = |
919 | < | the_atoms[exI]->getGlobalIndex() + 1; |
920 | < | the_excludes[index*2 + 1] = |
921 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
922 | < | |
1068 | > | tempEx = exI; |
1069 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1070 | > | tempEx = exJ; |
1071 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1072 | > | |
1073 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1074 | #else // isn't MPI | |
1075 | < | |
925 | < | the_excludes[index*2] = exI + 1; |
926 | < | the_excludes[index*2 + 1] = exJ + 1; |
927 | < | // fortran index from 1 (hence the +1 in the indexing) |
1075 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1076 | #endif //is_mpi | |
1077 | < | |
1078 | < | // increment the index and repeat; |
931 | < | index++; |
932 | < | } |
933 | < | offset += comp_stamps[i]->getNAtoms(); |
934 | < | |
935 | < | #ifdef IS_MPI |
936 | < | } |
937 | < | #endif //is_mpi |
938 | < | |
939 | < | molIndex++; |
940 | < | } |
941 | < | } |
1077 | > | } |
1078 | > | excludeOffset += info.nTorsions; |
1079 | ||
1080 | < | the_ff->initializeBonds( the_bonds ); |
1081 | < | } |
1080 | > | |
1081 | > | // send the arrays off to the forceField for init. |
1082 | ||
1083 | < | void SimSetup::makeBends( void ){ |
1083 | > | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1084 | > | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1085 | > | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1086 | > | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1087 | ||
948 | – | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
949 | – | bend_set* the_bends; |
950 | – | BendStamp* current_bend; |
951 | – | LinkedAssign* extras; |
952 | – | LinkedAssign* current_extra; |
953 | – | |
1088 | ||
1089 | < | the_bends = new bend_set[tot_bends]; |
956 | < | index = 0; |
957 | < | offset = 0; |
958 | < | molIndex = 0; |
959 | < | for( i=0; i<n_components; i++ ){ |
960 | < | |
961 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1089 | > | the_molecules[i].initialize( info ); |
1090 | ||
963 | – | #ifdef IS_MPI |
964 | – | if( mpiSim->getMyMolStart() <= molIndex && |
965 | – | molIndex <= mpiSim->getMyMolEnd() ){ |
966 | – | #endif // is_mpi |
1091 | ||
1092 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
1093 | < | |
1094 | < | current_bend = comp_stamps[i]->getBend( k ); |
1095 | < | the_bends[index].a = current_bend->getA() + offset; |
972 | < | the_bends[index].b = current_bend->getB() + offset; |
973 | < | the_bends[index].c = current_bend->getC() + offset; |
974 | < | |
975 | < | if( current_bend->haveExtras() ){ |
976 | < | |
977 | < | extras = current_bend->getExtras(); |
978 | < | current_extra = extras; |
979 | < | |
980 | < | while( current_extra != NULL ){ |
981 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
982 | < | |
983 | < | switch( current_extra->getType() ){ |
984 | < | |
985 | < | case 0: |
986 | < | the_bends[index].ghost = |
987 | < | current_extra->getInt() + offset; |
988 | < | the_bends[index].isGhost = 1; |
989 | < | break; |
990 | < | |
991 | < | case 1: |
992 | < | the_bends[index].ghost = |
993 | < | (int)current_extra->getDouble() + offset; |
994 | < | the_bends[index].isGhost = 1; |
995 | < | break; |
996 | < | |
997 | < | default: |
998 | < | sprintf( painCave.errMsg, |
999 | < | "SimSetup Error: ghostVectorSource was neiter a " |
1000 | < | "double nor an int.\n" |
1001 | < | "-->Bend[%d] in %s\n", |
1002 | < | k, comp_stamps[i]->getID() ); |
1003 | < | painCave.isFatal = 1; |
1004 | < | simError(); |
1005 | < | } |
1006 | < | } |
1007 | < | |
1008 | < | else{ |
1009 | < | |
1010 | < | sprintf( painCave.errMsg, |
1011 | < | "SimSetup Error: unhandled bend assignment:\n" |
1012 | < | " -->%s in Bend[%d] in %s\n", |
1013 | < | current_extra->getlhs(), |
1014 | < | k, comp_stamps[i]->getID() ); |
1015 | < | painCave.isFatal = 1; |
1016 | < | simError(); |
1017 | < | } |
1018 | < | |
1019 | < | current_extra = current_extra->getNext(); |
1020 | < | } |
1021 | < | } |
1022 | < | |
1023 | < | if( !the_bends[index].isGhost ){ |
1024 | < | |
1025 | < | exI = the_bends[index].a; |
1026 | < | exJ = the_bends[index].c; |
1027 | < | } |
1028 | < | else{ |
1029 | < | |
1030 | < | exI = the_bends[index].a; |
1031 | < | exJ = the_bends[index].b; |
1032 | < | } |
1033 | < | |
1034 | < | // exclude_I must always be the smaller of the pair |
1035 | < | if( exI > exJ ){ |
1036 | < | tempEx = exI; |
1037 | < | exI = exJ; |
1038 | < | exJ = tempEx; |
1039 | < | } |
1040 | < | |
1041 | < | |
1042 | < | #ifdef IS_MPI |
1043 | < | |
1044 | < | the_excludes[(index + tot_bonds)*2] = |
1045 | < | the_atoms[exI]->getGlobalIndex() + 1; |
1046 | < | the_excludes[(index + tot_bonds)*2 + 1] = |
1047 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
1048 | < | |
1049 | < | #else // isn't MPI |
1050 | < | |
1051 | < | the_excludes[(index + tot_bonds)*2] = exI + 1; |
1052 | < | the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
1053 | < | // fortran index from 1 (hence the +1 in the indexing) |
1054 | < | #endif //is_mpi |
1055 | < | |
1056 | < | |
1057 | < | // increment the index and repeat; |
1058 | < | index++; |
1059 | < | } |
1060 | < | offset += comp_stamps[i]->getNAtoms(); |
1061 | < | |
1062 | < | #ifdef IS_MPI |
1063 | < | } |
1064 | < | #endif //is_mpi |
1065 | < | |
1066 | < | molIndex++; |
1067 | < | } |
1092 | > | atomOffset += info.nAtoms; |
1093 | > | delete[] theBonds; |
1094 | > | delete[] theBends; |
1095 | > | delete[] theTorsions; |
1096 | } | |
1097 | ||
1098 | #ifdef IS_MPI | |
1099 | < | sprintf( checkPointMsg, |
1072 | < | "Successfully created the bends list.\n" ); |
1099 | > | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1100 | MPIcheckPoint(); | |
1101 | #endif // is_mpi | |
1075 | – | |
1102 | ||
1103 | < | the_ff->initializeBends( the_bends ); |
1104 | < | } |
1103 | > | // clean up the forcefield |
1104 | > | the_ff->calcRcut(); |
1105 | > | the_ff->cleanMe(); |
1106 | ||
1080 | – | void SimSetup::makeTorsions( void ){ |
1081 | – | |
1082 | – | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1083 | – | torsion_set* the_torsions; |
1084 | – | TorsionStamp* current_torsion; |
1085 | – | |
1086 | – | the_torsions = new torsion_set[tot_torsions]; |
1087 | – | index = 0; |
1088 | – | offset = 0; |
1089 | – | molIndex = 0; |
1090 | – | for( i=0; i<n_components; i++ ){ |
1091 | – | |
1092 | – | for( j=0; j<components_nmol[i]; j++ ){ |
1093 | – | |
1094 | – | #ifdef IS_MPI |
1095 | – | if( mpiSim->getMyMolStart() <= molIndex && |
1096 | – | molIndex <= mpiSim->getMyMolEnd() ){ |
1097 | – | #endif // is_mpi |
1098 | – | |
1099 | – | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1100 | – | |
1101 | – | current_torsion = comp_stamps[i]->getTorsion( k ); |
1102 | – | the_torsions[index].a = current_torsion->getA() + offset; |
1103 | – | the_torsions[index].b = current_torsion->getB() + offset; |
1104 | – | the_torsions[index].c = current_torsion->getC() + offset; |
1105 | – | the_torsions[index].d = current_torsion->getD() + offset; |
1106 | – | |
1107 | – | exI = the_torsions[index].a; |
1108 | – | exJ = the_torsions[index].d; |
1109 | – | |
1110 | – | |
1111 | – | // exclude_I must always be the smaller of the pair |
1112 | – | if( exI > exJ ){ |
1113 | – | tempEx = exI; |
1114 | – | exI = exJ; |
1115 | – | exJ = tempEx; |
1116 | – | } |
1117 | – | |
1118 | – | |
1119 | – | #ifdef IS_MPI |
1120 | – | |
1121 | – | the_excludes[(index + tot_bonds + tot_bends)*2] = |
1122 | – | the_atoms[exI]->getGlobalIndex() + 1; |
1123 | – | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1124 | – | the_atoms[exJ]->getGlobalIndex() + 1; |
1125 | – | |
1126 | – | #else // isn't MPI |
1127 | – | |
1128 | – | the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
1129 | – | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
1130 | – | // fortran indexes from 1 (hence the +1 in the indexing) |
1131 | – | #endif //is_mpi |
1132 | – | |
1133 | – | |
1134 | – | // increment the index and repeat; |
1135 | – | index++; |
1136 | – | } |
1137 | – | offset += comp_stamps[i]->getNAtoms(); |
1138 | – | |
1139 | – | #ifdef IS_MPI |
1140 | – | } |
1141 | – | #endif //is_mpi |
1142 | – | |
1143 | – | molIndex++; |
1144 | – | } |
1145 | – | } |
1146 | – | |
1147 | – | the_ff->initializeTorsions( the_torsions ); |
1107 | } | |
1108 | ||
1109 | void SimSetup::initFromBass( void ){ | |
# | Line 1166 | Line 1125 | void SimSetup::initFromBass( void ){ | |
1125 | have_extra =1; | |
1126 | ||
1127 | n_cells = (int)temp3 - 1; | |
1128 | < | cellx = simnfo->box_x / temp3; |
1129 | < | celly = simnfo->box_y / temp3; |
1130 | < | cellz = simnfo->box_z / temp3; |
1128 | > | cellx = simnfo->boxLx / temp3; |
1129 | > | celly = simnfo->boxLy / temp3; |
1130 | > | cellz = simnfo->boxLz / temp3; |
1131 | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); | |
1132 | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); | |
1133 | n_per_extra = (int)ceil( temp1 ); | |
# | Line 1183 | Line 1142 | void SimSetup::initFromBass( void ){ | |
1142 | } | |
1143 | else{ | |
1144 | n_cells = (int)temp3; | |
1145 | < | cellx = simnfo->box_x / temp3; |
1146 | < | celly = simnfo->box_y / temp3; |
1147 | < | cellz = simnfo->box_z / temp3; |
1145 | > | cellx = simnfo->boxLx / temp3; |
1146 | > | celly = simnfo->boxLy / temp3; |
1147 | > | cellz = simnfo->boxLz / temp3; |
1148 | } | |
1149 | ||
1150 | current_mol = 0; |
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