# | Line 66 | Line 66 | void SimSetup::createSim( void ){ | |
---|---|---|
66 | ||
67 | MakeStamps *the_stamps; | |
68 | Globals* the_globals; | |
69 | < | int i, j; |
69 | > | ExtendedSystem* the_extendedsystem; |
70 | > | int i, j, k, globalAtomIndex; |
71 | ||
72 | // get the stamps and globals; | |
73 | the_stamps = stamps; | |
# | Line 80 | Line 81 | void SimSetup::createSim( void ){ | |
81 | // get the ones we know are there, yet still may need some work. | |
82 | n_components = the_globals->getNComponents(); | |
83 | strcpy( force_field, the_globals->getForceField() ); | |
84 | + | |
85 | + | // get the ensemble and set up an extended system if we need it: |
86 | strcpy( ensemble, the_globals->getEnsemble() ); | |
87 | + | if( !strcasecmp( ensemble, "NPT" ) ) { |
88 | + | the_extendedsystem = new ExtendedSystem( simnfo ); |
89 | + | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
90 | + | if (the_globals->haveTargetPressure()) |
91 | + | the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
92 | + | else { |
93 | + | sprintf( painCave.errMsg, |
94 | + | "SimSetup error: If you use the constant pressure\n" |
95 | + | " ensemble, you must set targetPressure.\n" |
96 | + | " This was found in the BASS file.\n"); |
97 | + | painCave.isFatal = 1; |
98 | + | simError(); |
99 | + | } |
100 | + | |
101 | + | if (the_globals->haveTauThermostat()) |
102 | + | the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
103 | + | else if (the_globals->haveQmass()) |
104 | + | the_extendedsystem->setQmass(the_globals->getQmass()); |
105 | + | else { |
106 | + | sprintf( painCave.errMsg, |
107 | + | "SimSetup error: If you use one of the constant temperature\n" |
108 | + | " ensembles, you must set either tauThermostat or qMass.\n" |
109 | + | " Neither of these was found in the BASS file.\n"); |
110 | + | painCave.isFatal = 1; |
111 | + | simError(); |
112 | + | } |
113 | + | |
114 | + | if (the_globals->haveTauBarostat()) |
115 | + | the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
116 | + | else { |
117 | + | sprintf( painCave.errMsg, |
118 | + | "SimSetup error: If you use the constant pressure\n" |
119 | + | " ensemble, you must set tauBarostat.\n" |
120 | + | " This was found in the BASS file.\n"); |
121 | + | painCave.isFatal = 1; |
122 | + | simError(); |
123 | + | } |
124 | + | |
125 | + | } else if ( !strcasecmp( ensemble, "NVT") ) { |
126 | + | the_extendedsystem = new ExtendedSystem( simnfo ); |
127 | + | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
128 | + | |
129 | + | if (the_globals->haveTauThermostat()) |
130 | + | the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
131 | + | else if (the_globals->haveQmass()) |
132 | + | the_extendedsystem->setQmass(the_globals->getQmass()); |
133 | + | else { |
134 | + | sprintf( painCave.errMsg, |
135 | + | "SimSetup error: If you use one of the constant temperature\n" |
136 | + | " ensembles, you must set either tauThermostat or qMass.\n" |
137 | + | " Neither of these was found in the BASS file.\n"); |
138 | + | painCave.isFatal = 1; |
139 | + | simError(); |
140 | + | } |
141 | + | |
142 | + | } else if ( !strcasecmp( ensemble, "NVE") ) { |
143 | + | } else { |
144 | + | sprintf( painCave.errMsg, |
145 | + | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
146 | + | "reverting to NVE for this simulation.\n", |
147 | + | ensemble ); |
148 | + | painCave.isFatal = 0; |
149 | + | simError(); |
150 | + | strcpy( ensemble, "NVE" ); |
151 | + | } |
152 | strcpy( simnfo->ensemble, ensemble ); | |
153 | ||
154 | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); | |
155 | simnfo->usePBC = the_globals->getPBC(); | |
156 | ||
157 | < | |
158 | < | |
159 | < | if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
160 | < | else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
161 | < | else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
162 | < | else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
157 | > | int usesDipoles = 0; |
158 | > | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
159 | > | the_ff = new TraPPE_ExFF(); |
160 | > | usesDipoles = 1; |
161 | > | } |
162 | > | else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
163 | else{ | |
164 | sprintf( painCave.errMsg, | |
165 | "SimSetup Error. Unrecognized force field -> %s\n", | |
# | Line 230 | Line 298 | void SimSetup::createSim( void ){ | |
298 | simnfo->n_torsions = tot_torsions; | |
299 | simnfo->n_SRI = tot_SRI; | |
300 | simnfo->n_mol = tot_nmol; | |
233 | – | |
301 | ||
302 | + | simnfo->molMembershipArray = new int[tot_atoms]; |
303 | + | |
304 | #ifdef IS_MPI | |
305 | ||
306 | // divide the molecules among processors here. | |
307 | ||
308 | mpiSim = new mpiSimulation( simnfo ); | |
309 | ||
241 | – | |
242 | – | |
310 | globalIndex = mpiSim->divideLabor(); | |
311 | ||
245 | – | |
246 | – | |
312 | // set up the local variables | |
313 | ||
314 | int localMol, allMol; | |
315 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
316 | + | |
317 | + | int* mol2proc = mpiSim->getMolToProcMap(); |
318 | + | int* molCompType = mpiSim->getMolComponentType(); |
319 | ||
320 | allMol = 0; | |
321 | localMol = 0; | |
# | Line 255 | Line 323 | void SimSetup::createSim( void ){ | |
323 | local_bonds = 0; | |
324 | local_bends = 0; | |
325 | local_torsions = 0; | |
326 | + | globalAtomIndex = 0; |
327 | + | |
328 | + | |
329 | for( i=0; i<n_components; i++ ){ | |
330 | ||
331 | for( j=0; j<components_nmol[i]; j++ ){ | |
332 | ||
333 | < | if( mpiSim->getMyMolStart() <= allMol && |
263 | < | allMol <= mpiSim->getMyMolEnd() ){ |
333 | > | if( mol2proc[allMol] == worldRank ){ |
334 | ||
335 | local_atoms += comp_stamps[i]->getNAtoms(); | |
336 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 268 | Line 338 | void SimSetup::createSim( void ){ | |
338 | local_torsions += comp_stamps[i]->getNTorsions(); | |
339 | localMol++; | |
340 | } | |
341 | < | allMol++; |
341 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
342 | > | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
343 | > | globalAtomIndex++; |
344 | > | } |
345 | > | |
346 | > | allMol++; |
347 | } | |
348 | } | |
349 | local_SRI = local_bonds + local_bends + local_torsions; | |
350 | ||
276 | – | |
351 | simnfo->n_atoms = mpiSim->getMyNlocal(); | |
352 | ||
353 | if( local_atoms != simnfo->n_atoms ){ | |
354 | sprintf( painCave.errMsg, | |
355 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" | |
356 | < | " localAtom (%d) are note equal.\n", |
356 | > | " localAtom (%d) are not equal.\n", |
357 | simnfo->n_atoms, | |
358 | local_atoms ); | |
359 | painCave.isFatal = 1; | |
# | Line 304 | Line 378 | void SimSetup::createSim( void ){ | |
378 | Atom::createArrays(simnfo->n_atoms); | |
379 | the_atoms = new Atom*[simnfo->n_atoms]; | |
380 | the_molecules = new Molecule[simnfo->n_mol]; | |
381 | + | int molIndex; |
382 | ||
383 | + | // initialize the molecule's stampID's |
384 | ||
385 | < | if( simnfo->n_SRI ){ |
386 | < | the_sris = new SRI*[simnfo->n_SRI]; |
387 | < | the_excludes = new int[2 * simnfo->n_SRI]; |
385 | > | #ifdef IS_MPI |
386 | > | |
387 | > | |
388 | > | molIndex = 0; |
389 | > | for(i=0; i<mpiSim->getTotNmol(); i++){ |
390 | > | |
391 | > | if(mol2proc[i] == worldRank ){ |
392 | > | the_molecules[molIndex].setStampID( molCompType[i] ); |
393 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
394 | > | the_molecules[molIndex].setGlobalIndex( i ); |
395 | > | molIndex++; |
396 | > | } |
397 | > | } |
398 | > | |
399 | > | #else // is_mpi |
400 | > | |
401 | > | molIndex = 0; |
402 | > | globalAtomIndex = 0; |
403 | > | for(i=0; i<n_components; i++){ |
404 | > | for(j=0; j<components_nmol[i]; j++ ){ |
405 | > | the_molecules[molIndex].setStampID( i ); |
406 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
407 | > | the_molecules[molIndex].setGlobalIndex( molIndex ); |
408 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
409 | > | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
410 | > | globalAtomIndex++; |
411 | > | } |
412 | > | molIndex++; |
413 | > | } |
414 | > | } |
415 | > | |
416 | > | |
417 | > | #endif // is_mpi |
418 | > | |
419 | > | |
420 | > | if( simnfo->n_SRI ){ |
421 | > | |
422 | > | Exclude::createArray(simnfo->n_SRI); |
423 | > | the_excludes = new Exclude*[simnfo->n_SRI]; |
424 | > | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
425 | simnfo->globalExcludes = new int; | |
426 | < | simnfo->n_exclude = tot_SRI; |
426 | > | simnfo->n_exclude = simnfo->n_SRI; |
427 | } | |
428 | else{ | |
429 | ||
430 | < | the_excludes = new int[2]; |
431 | < | the_excludes[0] = 0; |
432 | < | the_excludes[1] = 0; |
430 | > | Exclude::createArray( 1 ); |
431 | > | the_excludes = new Exclude*; |
432 | > | the_excludes[0] = new Exclude(0); |
433 | > | the_excludes[0]->setPair( 0,0 ); |
434 | simnfo->globalExcludes = new int; | |
435 | simnfo->globalExcludes[0] = 0; | |
436 | < | |
323 | < | simnfo->n_exclude = 1; |
436 | > | simnfo->n_exclude = 0; |
437 | } | |
438 | ||
439 | // set the arrays into the SimInfo object | |
440 | ||
441 | simnfo->atoms = the_atoms; | |
442 | < | simnfo->sr_interactions = the_sris; |
442 | > | simnfo->molecules = the_molecules; |
443 | simnfo->nGlobalExcludes = 0; | |
444 | simnfo->excludes = the_excludes; | |
445 | ||
# | Line 383 | Line 496 | void SimSetup::createSim( void ){ | |
496 | ||
497 | the_ff->setSimInfo( simnfo ); | |
498 | ||
499 | < | makeAtoms(); |
499 | > | makeMolecules(); |
500 | simnfo->identArray = new int[simnfo->n_atoms]; | |
501 | for(i=0; i<simnfo->n_atoms; i++){ | |
502 | simnfo->identArray[i] = the_atoms[i]->getIdent(); | |
503 | } | |
504 | ||
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 | – | |
505 | if (the_globals->getUseRF() ) { | |
506 | simnfo->useReactionField = 1; | |
507 | ||
# | Line 443 | Line 543 | void SimSetup::createSim( void ){ | |
543 | } | |
544 | simnfo->dielectric = the_globals->getDielectric(); | |
545 | } else { | |
546 | < | if (simnfo->n_dipoles) { |
546 | > | if (usesDipoles) { |
547 | ||
548 | if( !the_globals->haveECR() ){ | |
549 | sprintf( painCave.errMsg, | |
550 | < | "SimSetup Warning: using default value of 1/2 the smallest" |
550 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
551 | "box length for the electrostaticCutoffRadius.\n" | |
552 | "I hope you have a very fast processor!\n"); | |
553 | painCave.isFatal = 0; | |
# | Line 463 | Line 563 | void SimSetup::createSim( void ){ | |
563 | ||
564 | if( !the_globals->haveEST() ){ | |
565 | sprintf( painCave.errMsg, | |
566 | < | "SimSetup Warning: using default value of 5% of the" |
566 | > | "SimSetup Warning: using default value of 5%% of the " |
567 | "electrostaticCutoffRadius for the " | |
568 | "electrostaticSkinThickness\n" | |
569 | ); | |
# | Line 638 | Line 738 | void SimSetup::createSim( void ){ | |
738 | ||
739 | // new AllLong( simnfo ); | |
740 | ||
741 | < | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
742 | < | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
743 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
744 | < | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
741 | > | |
742 | > | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
743 | > | new Symplectic(simnfo, the_ff, the_extendedsystem); |
744 | > | } |
745 | > | else if( !strcmp( force_field, "LJ" ) ){ |
746 | > | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
747 | > | } |
748 | ||
749 | + | #ifdef IS_MPI |
750 | + | mpiSim->mpiRefresh(); |
751 | + | #endif |
752 | ||
647 | – | |
753 | // initialize the Fortran | |
754 | < | |
754 | > | |
755 | > | |
756 | simnfo->refreshSim(); | |
757 | ||
758 | if( !strcmp( simnfo->mixingRule, "standard") ){ | |
# | Line 674 | Line 780 | void SimSetup::makeMolecules( void ){ | |
780 | ||
781 | void SimSetup::makeMolecules( void ){ | |
782 | ||
783 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset; |
783 | > | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
784 | molInit info; | |
785 | DirectionalAtom* dAtom; | |
786 | + | LinkedAssign* extras; |
787 | + | LinkedAssign* current_extra; |
788 | AtomStamp* currentAtom; | |
789 | BondStamp* currentBond; | |
790 | BendStamp* currentBend; | |
791 | TorsionStamp* currentTorsion; | |
792 | + | |
793 | + | bond_pair* theBonds; |
794 | + | bend_set* theBends; |
795 | + | torsion_set* theTorsions; |
796 | + | |
797 | ||
798 | //init the forceField paramters | |
799 | ||
800 | the_ff->readParams(); | |
801 | ||
802 | ||
803 | < | // init the molecules |
803 | > | // init the atoms |
804 | ||
805 | + | double ux, uy, uz, u, uSqr; |
806 | + | |
807 | atomOffset = 0; | |
808 | + | excludeOffset = 0; |
809 | for(i=0; i<simnfo->n_mol; i++){ | |
810 | ||
811 | stampID = the_molecules[i].getStampID(); | |
# | Line 698 | Line 814 | void SimSetup::makeMolecules( void ){ | |
814 | info.nBonds = comp_stamps[stampID]->getNBonds(); | |
815 | info.nBends = comp_stamps[stampID]->getNBends(); | |
816 | info.nTorsions = comp_stamps[stampID]->getNTorsions(); | |
817 | < | |
817 | > | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
818 | > | |
819 | info.myAtoms = &the_atoms[atomOffset]; | |
820 | + | info.myExcludes = &the_excludes[excludeOffset]; |
821 | info.myBonds = new Bond*[info.nBonds]; | |
822 | info.myBends = new Bend*[info.nBends]; | |
823 | < | info.myTorsions = new Torsions*[info.nTorsions]; |
823 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
824 | ||
825 | theBonds = new bond_pair[info.nBonds]; | |
826 | theBends = new bend_set[info.nBends]; | |
# | Line 712 | Line 830 | void SimSetup::makeMolecules( void ){ | |
830 | ||
831 | for(j=0; j<info.nAtoms; j++){ | |
832 | ||
833 | < | currentAtom = theComponents[stampID]->getAtom( j ); |
833 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
834 | if( currentAtom->haveOrientation() ){ | |
835 | ||
836 | dAtom = new DirectionalAtom(j + atomOffset); | |
# | Line 747 | Line 865 | void SimSetup::makeMolecules( void ){ | |
865 | } | |
866 | ||
867 | // make the bonds | |
868 | < | for(j=0; j<nBonds; j++){ |
868 | > | for(j=0; j<info.nBonds; j++){ |
869 | ||
870 | currentBond = comp_stamps[stampID]->getBond( j ); | |
871 | theBonds[j].a = currentBond->getA() + atomOffset; | |
872 | theBonds[j].b = currentBond->getB() + atomOffset; | |
873 | ||
874 | < | exI = theBonds[i].a; |
875 | < | exJ = theBonds[i].b; |
874 | > | exI = theBonds[j].a; |
875 | > | exJ = theBonds[j].b; |
876 | ||
877 | // exclude_I must always be the smaller of the pair | |
878 | if( exI > exJ ){ | |
# | Line 763 | Line 881 | void SimSetup::makeMolecules( void ){ | |
881 | exJ = tempEx; | |
882 | } | |
883 | #ifdef IS_MPI | |
884 | + | tempEx = exI; |
885 | + | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
886 | + | tempEx = exJ; |
887 | + | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
888 | ||
889 | < | the_excludes[index*2] = |
768 | < | the_atoms[exI]->getGlobalIndex() + 1; |
769 | < | the_excludes[index*2 + 1] = |
770 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
771 | < | |
889 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
890 | #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) |
891 | ||
892 | + | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
893 | #endif //is_mpi | |
894 | < | |
895 | < | } |
894 | > | } |
895 | > | excludeOffset += info.nBonds; |
896 | ||
897 | < | |
898 | < | |
899 | < | |
900 | < | |
901 | < | |
902 | < | |
903 | < | |
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++ ){ |
897 | > | //make the bends |
898 | > | for(j=0; j<info.nBends; j++){ |
899 | > | |
900 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
901 | > | theBends[j].a = currentBend->getA() + atomOffset; |
902 | > | theBends[j].b = currentBend->getB() + atomOffset; |
903 | > | theBends[j].c = currentBend->getC() + atomOffset; |
904 | ||
905 | < | current_atom = comp_stamps[i]->getAtom( k ); |
822 | < | if( current_atom->haveOrientation() ){ |
905 | > | if( currentBend->haveExtras() ){ |
906 | ||
907 | < | dAtom = new DirectionalAtom(index); |
908 | < | simnfo->n_oriented++; |
826 | < | the_atoms[index] = dAtom; |
907 | > | extras = currentBend->getExtras(); |
908 | > | current_extra = extras; |
909 | ||
910 | < | ux = current_atom->getOrntX(); |
911 | < | uy = current_atom->getOrntY(); |
912 | < | uz = current_atom->getOrntZ(); |
913 | < | |
914 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
915 | < | |
916 | < | u = sqrt( uSqr ); |
917 | < | ux = ux / u; |
918 | < | uy = uy / u; |
919 | < | uz = uz / u; |
920 | < | |
921 | < | dAtom->setSUx( ux ); |
922 | < | dAtom->setSUy( uy ); |
923 | < | dAtom->setSUz( uz ); |
924 | < | } |
925 | < | else{ |
926 | < | the_atoms[index] = new GeneralAtom(index); |
927 | < | } |
928 | < | the_atoms[index]->setType( current_atom->getType() ); |
929 | < | the_atoms[index]->setIndex( index ); |
930 | < | |
931 | < | // increment the index and repeat; |
932 | < | index++; |
933 | < | } |
934 | < | |
935 | < | molEnd = index -1; |
936 | < | 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 |
861 | < | } |
862 | < | #endif //is_mpi |
863 | < | |
864 | < | molIndex++; |
865 | < | } |
866 | < | } |
867 | < | |
868 | < | #ifdef IS_MPI |
869 | < | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
870 | < | |
871 | < | delete[] globalIndex; |
872 | < | |
873 | < | mpiSim->mpiRefresh(); |
874 | < | #endif //IS_MPI |
875 | < | |
876 | < | the_ff->initializeAtoms(); |
877 | < | } |
878 | < | |
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 | < | |
894 | < | #ifdef IS_MPI |
895 | < | if( mpiSim->getMyMolStart() <= molIndex && |
896 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
897 | < | #endif // is_mpi |
898 | < | |
899 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
910 | > | while( current_extra != NULL ){ |
911 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
912 | > | |
913 | > | switch( current_extra->getType() ){ |
914 | > | |
915 | > | case 0: |
916 | > | theBends[j].ghost = |
917 | > | current_extra->getInt() + atomOffset; |
918 | > | theBends[j].isGhost = 1; |
919 | > | break; |
920 | > | |
921 | > | case 1: |
922 | > | theBends[j].ghost = |
923 | > | (int)current_extra->getDouble() + atomOffset; |
924 | > | theBends[j].isGhost = 1; |
925 | > | break; |
926 | > | |
927 | > | default: |
928 | > | sprintf( painCave.errMsg, |
929 | > | "SimSetup Error: ghostVectorSource was neither a " |
930 | > | "double nor an int.\n" |
931 | > | "-->Bend[%d] in %s\n", |
932 | > | j, comp_stamps[stampID]->getID() ); |
933 | > | painCave.isFatal = 1; |
934 | > | simError(); |
935 | > | } |
936 | > | } |
937 | ||
938 | < | current_bond = comp_stamps[i]->getBond( k ); |
939 | < | the_bonds[index].a = current_bond->getA() + offset; |
940 | < | the_bonds[index].b = current_bond->getB() + offset; |
941 | < | |
942 | < | exI = the_bonds[index].a; |
943 | < | exJ = the_bonds[index].b; |
944 | < | |
945 | < | // exclude_I must always be the smaller of the pair |
946 | < | if( exI > exJ ){ |
910 | < | tempEx = exI; |
911 | < | exI = exJ; |
912 | < | exJ = tempEx; |
938 | > | else{ |
939 | > | |
940 | > | sprintf( painCave.errMsg, |
941 | > | "SimSetup Error: unhandled bend assignment:\n" |
942 | > | " -->%s in Bend[%d] in %s\n", |
943 | > | current_extra->getlhs(), |
944 | > | j, comp_stamps[stampID]->getID() ); |
945 | > | painCave.isFatal = 1; |
946 | > | simError(); |
947 | } | |
914 | – | |
948 | ||
949 | < | #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 | < | |
923 | < | #else // isn't MPI |
924 | < | |
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) |
928 | < | #endif //is_mpi |
929 | < | |
930 | < | // increment the index and repeat; |
931 | < | index++; |
949 | > | current_extra = current_extra->getNext(); |
950 | } | |
951 | < | offset += comp_stamps[i]->getNAtoms(); |
951 | > | } |
952 | > | |
953 | > | if( !theBends[j].isGhost ){ |
954 | > | |
955 | > | exI = theBends[j].a; |
956 | > | exJ = theBends[j].c; |
957 | > | } |
958 | > | else{ |
959 | ||
960 | < | #ifdef IS_MPI |
960 | > | exI = theBends[j].a; |
961 | > | exJ = theBends[j].b; |
962 | } | |
937 | – | #endif //is_mpi |
963 | ||
964 | < | molIndex++; |
965 | < | } |
966 | < | } |
964 | > | // exclude_I must always be the smaller of the pair |
965 | > | if( exI > exJ ){ |
966 | > | tempEx = exI; |
967 | > | exI = exJ; |
968 | > | exJ = tempEx; |
969 | > | } |
970 | > | #ifdef IS_MPI |
971 | > | tempEx = exI; |
972 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
973 | > | tempEx = exJ; |
974 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
975 | > | |
976 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
977 | > | #else // isn't MPI |
978 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
979 | > | #endif //is_mpi |
980 | > | } |
981 | > | excludeOffset += info.nBends; |
982 | ||
983 | < | the_ff->initializeBonds( the_bonds ); |
984 | < | } |
983 | > | for(j=0; j<info.nTorsions; j++){ |
984 | > | |
985 | > | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
986 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
987 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
988 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
989 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
990 | > | |
991 | > | exI = theTorsions[j].a; |
992 | > | exJ = theTorsions[j].d; |
993 | ||
994 | < | void SimSetup::makeBends( void ){ |
994 | > | // exclude_I must always be the smaller of the pair |
995 | > | if( exI > exJ ){ |
996 | > | tempEx = exI; |
997 | > | exI = exJ; |
998 | > | exJ = tempEx; |
999 | > | } |
1000 | > | #ifdef IS_MPI |
1001 | > | tempEx = exI; |
1002 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1003 | > | tempEx = exJ; |
1004 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1005 | > | |
1006 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1007 | > | #else // isn't MPI |
1008 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1009 | > | #endif //is_mpi |
1010 | > | } |
1011 | > | excludeOffset += info.nTorsions; |
1012 | ||
1013 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1014 | < | bend_set* the_bends; |
950 | < | BendStamp* current_bend; |
951 | < | LinkedAssign* extras; |
952 | < | LinkedAssign* current_extra; |
953 | < | |
1013 | > | |
1014 | > | // send the arrays off to the forceField for init. |
1015 | ||
1016 | < | the_bends = new bend_set[tot_bends]; |
1017 | < | index = 0; |
1018 | < | offset = 0; |
1019 | < | molIndex = 0; |
959 | < | for( i=0; i<n_components; i++ ){ |
1016 | > | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1017 | > | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1018 | > | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1019 | > | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1020 | ||
961 | – | for( j=0; j<components_nmol[i]; j++ ){ |
1021 | ||
1022 | < | #ifdef IS_MPI |
964 | < | if( mpiSim->getMyMolStart() <= molIndex && |
965 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
966 | < | #endif // is_mpi |
967 | < | |
968 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
969 | < | |
970 | < | current_bend = comp_stamps[i]->getBend( k ); |
971 | < | 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 | < | } |
1022 | > | the_molecules[i].initialize( info ); |
1023 | ||
1024 | ||
1025 | < | #ifdef IS_MPI |
1026 | < | |
1027 | < | the_excludes[(index + tot_bonds)*2] = |
1028 | < | 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 | < | } |
1025 | > | atomOffset += info.nAtoms; |
1026 | > | delete[] theBonds; |
1027 | > | delete[] theBends; |
1028 | > | delete[] theTorsions; |
1029 | } | |
1030 | ||
1031 | #ifdef IS_MPI | |
1032 | < | sprintf( checkPointMsg, |
1072 | < | "Successfully created the bends list.\n" ); |
1032 | > | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1033 | MPIcheckPoint(); | |
1034 | #endif // is_mpi | |
1075 | – | |
1035 | ||
1036 | < | the_ff->initializeBends( the_bends ); |
1037 | < | } |
1036 | > | // clean up the forcefield |
1037 | > | the_ff->calcRcut(); |
1038 | > | the_ff->cleanMe(); |
1039 | ||
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 ); |
1040 | } | |
1041 | ||
1042 | void SimSetup::initFromBass( void ){ |
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