66 |
|
|
67 |
|
MakeStamps *the_stamps; |
68 |
|
Globals* the_globals; |
69 |
+ |
ExtendedSystem* the_extendedsystem; |
70 |
|
int i, j; |
71 |
|
|
72 |
|
// get the stamps and globals; |
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", |
310 |
|
|
311 |
|
globalIndex = mpiSim->divideLabor(); |
312 |
|
|
245 |
– |
|
246 |
– |
|
313 |
|
// set up the local variables |
314 |
|
|
315 |
|
int localMol, allMol; |
316 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
317 |
+ |
|
318 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
319 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
320 |
|
|
321 |
|
allMol = 0; |
322 |
|
localMol = 0; |
328 |
|
|
329 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
330 |
|
|
331 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
331 |
> |
if( mol2proc[j] == worldRank ){ |
332 |
|
|
333 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
334 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
347 |
|
if( local_atoms != simnfo->n_atoms ){ |
348 |
|
sprintf( painCave.errMsg, |
349 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
350 |
< |
" localAtom (%d) are note equal.\n", |
350 |
> |
" localAtom (%d) are not equal.\n", |
351 |
|
simnfo->n_atoms, |
352 |
|
local_atoms ); |
353 |
|
painCave.isFatal = 1; |
372 |
|
Atom::createArrays(simnfo->n_atoms); |
373 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
374 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
375 |
+ |
int molIndex; |
376 |
|
|
377 |
+ |
// initialize the molecule's stampID's |
378 |
|
|
379 |
+ |
#ifdef IS_MPI |
380 |
+ |
|
381 |
+ |
|
382 |
+ |
molIndex = 0; |
383 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
384 |
+ |
|
385 |
+ |
if(mol2proc[i] == worldRank ){ |
386 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
387 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
388 |
+ |
molIndex++; |
389 |
+ |
} |
390 |
+ |
} |
391 |
+ |
|
392 |
+ |
#else // is_mpi |
393 |
+ |
|
394 |
+ |
molIndex = 0; |
395 |
+ |
for(i=0; i<n_components; i++){ |
396 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
397 |
+ |
the_molecules[molIndex].setStampID( i ); |
398 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
399 |
+ |
molIndex++; |
400 |
+ |
} |
401 |
+ |
} |
402 |
+ |
|
403 |
+ |
|
404 |
+ |
#endif // is_mpi |
405 |
+ |
|
406 |
+ |
|
407 |
|
if( simnfo->n_SRI ){ |
408 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
409 |
< |
the_excludes = new int[2 * simnfo->n_SRI]; |
408 |
> |
|
409 |
> |
Exclude::createArray(simnfo->n_SRI); |
410 |
> |
the_excludes = new Exclude*[simnfo->n_SRI]; |
411 |
> |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
412 |
|
simnfo->globalExcludes = new int; |
413 |
< |
simnfo->n_exclude = tot_SRI; |
413 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
414 |
|
} |
415 |
|
else{ |
416 |
|
|
417 |
< |
the_excludes = new int[2]; |
418 |
< |
the_excludes[0] = 0; |
419 |
< |
the_excludes[1] = 0; |
417 |
> |
Exclude::createArray( 1 ); |
418 |
> |
the_excludes = new Exclude*; |
419 |
> |
the_excludes[0] = new Exclude(0); |
420 |
> |
the_excludes[0]->setPair( 0,0 ); |
421 |
|
simnfo->globalExcludes = new int; |
422 |
|
simnfo->globalExcludes[0] = 0; |
423 |
< |
|
323 |
< |
simnfo->n_exclude = 1; |
423 |
> |
simnfo->n_exclude = 0; |
424 |
|
} |
425 |
|
|
426 |
|
// set the arrays into the SimInfo object |
427 |
|
|
428 |
|
simnfo->atoms = the_atoms; |
429 |
< |
simnfo->sr_interactions = the_sris; |
429 |
> |
simnfo->molecules = the_molecules; |
430 |
|
simnfo->nGlobalExcludes = 0; |
431 |
|
simnfo->excludes = the_excludes; |
432 |
|
|
483 |
|
|
484 |
|
the_ff->setSimInfo( simnfo ); |
485 |
|
|
486 |
< |
makeAtoms(); |
486 |
> |
makeMolecules(); |
487 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
488 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
489 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
490 |
|
} |
491 |
|
|
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 |
– |
|
492 |
|
if (the_globals->getUseRF() ) { |
493 |
|
simnfo->useReactionField = 1; |
494 |
|
|
530 |
|
} |
531 |
|
simnfo->dielectric = the_globals->getDielectric(); |
532 |
|
} else { |
533 |
< |
if (simnfo->n_dipoles) { |
533 |
> |
if (usesDipoles) { |
534 |
|
|
535 |
|
if( !the_globals->haveECR() ){ |
536 |
|
sprintf( painCave.errMsg, |
537 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
537 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
538 |
|
"box length for the electrostaticCutoffRadius.\n" |
539 |
|
"I hope you have a very fast processor!\n"); |
540 |
|
painCave.isFatal = 0; |
550 |
|
|
551 |
|
if( !the_globals->haveEST() ){ |
552 |
|
sprintf( painCave.errMsg, |
553 |
< |
"SimSetup Warning: using default value of 5% of the" |
553 |
> |
"SimSetup Warning: using default value of 5%% of the " |
554 |
|
"electrostaticCutoffRadius for the " |
555 |
|
"electrostaticSkinThickness\n" |
556 |
|
); |
725 |
|
|
726 |
|
// new AllLong( simnfo ); |
727 |
|
|
641 |
– |
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 ); |
728 |
|
|
729 |
< |
|
729 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
730 |
> |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
731 |
> |
std::cerr << "called new Symplecic\n"; |
732 |
> |
fprintf( stderr, "called new Symplectic. stderr\n" ); |
733 |
> |
} |
734 |
> |
else if( !strcmp( force_field, "LJ" ) ){ |
735 |
> |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
736 |
> |
std::cerr << "called new Verlet\n"; |
737 |
> |
fprintf( stderr, "called new Verlet. stderr\n" ); |
738 |
> |
} |
739 |
> |
else { |
740 |
> |
std::cerr << "I'm a bug.\n"; |
741 |
> |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
742 |
> |
} |
743 |
> |
#ifdef IS_MPI |
744 |
> |
mpiSim->mpiRefresh(); |
745 |
> |
#endif |
746 |
|
|
747 |
|
// initialize the Fortran |
748 |
< |
|
748 |
> |
|
749 |
> |
|
750 |
|
simnfo->refreshSim(); |
751 |
|
|
752 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
774 |
|
|
775 |
|
void SimSetup::makeMolecules( void ){ |
776 |
|
|
777 |
< |
int i, j, exI, exJ, tempEx, stampID, atomOffset; |
777 |
> |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
778 |
|
molInit info; |
779 |
|
DirectionalAtom* dAtom; |
780 |
+ |
LinkedAssign* extras; |
781 |
+ |
LinkedAssign* current_extra; |
782 |
|
AtomStamp* currentAtom; |
783 |
|
BondStamp* currentBond; |
784 |
|
BendStamp* currentBend; |
785 |
|
TorsionStamp* currentTorsion; |
786 |
+ |
|
787 |
+ |
bond_pair* theBonds; |
788 |
+ |
bend_set* theBends; |
789 |
+ |
torsion_set* theTorsions; |
790 |
+ |
|
791 |
|
|
792 |
|
//init the forceField paramters |
793 |
|
|
794 |
|
the_ff->readParams(); |
795 |
|
|
796 |
|
|
797 |
< |
// init the molecules |
797 |
> |
// init the atoms |
798 |
|
|
799 |
+ |
double ux, uy, uz, u, uSqr; |
800 |
+ |
|
801 |
|
atomOffset = 0; |
802 |
+ |
excludeOffset = 0; |
803 |
|
for(i=0; i<simnfo->n_mol; i++){ |
804 |
|
|
805 |
|
stampID = the_molecules[i].getStampID(); |
808 |
|
info.nBonds = comp_stamps[stampID]->getNBonds(); |
809 |
|
info.nBends = comp_stamps[stampID]->getNBends(); |
810 |
|
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
811 |
< |
|
811 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
812 |
> |
|
813 |
|
info.myAtoms = &the_atoms[atomOffset]; |
814 |
+ |
info.myExcludes = &the_excludes[excludeOffset]; |
815 |
|
info.myBonds = new Bond*[info.nBonds]; |
816 |
|
info.myBends = new Bend*[info.nBends]; |
817 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
817 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
818 |
|
|
819 |
|
theBonds = new bond_pair[info.nBonds]; |
820 |
|
theBends = new bend_set[info.nBends]; |
824 |
|
|
825 |
|
for(j=0; j<info.nAtoms; j++){ |
826 |
|
|
827 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
827 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
828 |
|
if( currentAtom->haveOrientation() ){ |
829 |
|
|
830 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
859 |
|
} |
860 |
|
|
861 |
|
// make the bonds |
862 |
< |
for(j=0; j<nBonds; j++){ |
862 |
> |
for(j=0; j<info.nBonds; j++){ |
863 |
|
|
864 |
|
currentBond = comp_stamps[stampID]->getBond( j ); |
865 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
866 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
867 |
|
|
868 |
< |
exI = theBonds[i].a; |
869 |
< |
exJ = theBonds[i].b; |
868 |
> |
exI = theBonds[j].a; |
869 |
> |
exJ = theBonds[j].b; |
870 |
|
|
871 |
|
// exclude_I must always be the smaller of the pair |
872 |
|
if( exI > exJ ){ |
875 |
|
exJ = tempEx; |
876 |
|
} |
877 |
|
#ifdef IS_MPI |
878 |
+ |
tempEx = exI; |
879 |
+ |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
880 |
+ |
tempEx = exJ; |
881 |
+ |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
882 |
|
|
883 |
< |
the_excludes[index*2] = |
768 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
769 |
< |
the_excludes[index*2 + 1] = |
770 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
771 |
< |
|
883 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
884 |
|
#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) |
885 |
|
|
886 |
+ |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
887 |
|
#endif //is_mpi |
888 |
< |
|
889 |
< |
} |
888 |
> |
} |
889 |
> |
excludeOffset += info.nBonds; |
890 |
|
|
891 |
< |
|
892 |
< |
|
893 |
< |
|
894 |
< |
|
895 |
< |
|
896 |
< |
|
897 |
< |
|
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++ ){ |
891 |
> |
//make the bends |
892 |
> |
for(j=0; j<info.nBends; j++){ |
893 |
> |
|
894 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
895 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
896 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
897 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
898 |
|
|
899 |
< |
current_atom = comp_stamps[i]->getAtom( k ); |
822 |
< |
if( current_atom->haveOrientation() ){ |
899 |
> |
if( currentBend->haveExtras() ){ |
900 |
|
|
901 |
< |
dAtom = new DirectionalAtom(index); |
902 |
< |
simnfo->n_oriented++; |
826 |
< |
the_atoms[index] = dAtom; |
901 |
> |
extras = currentBend->getExtras(); |
902 |
> |
current_extra = extras; |
903 |
|
|
904 |
< |
ux = current_atom->getOrntX(); |
905 |
< |
uy = current_atom->getOrntY(); |
906 |
< |
uz = current_atom->getOrntZ(); |
907 |
< |
|
908 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
909 |
< |
|
910 |
< |
u = sqrt( uSqr ); |
911 |
< |
ux = ux / u; |
912 |
< |
uy = uy / u; |
913 |
< |
uz = uz / u; |
914 |
< |
|
915 |
< |
dAtom->setSUx( ux ); |
916 |
< |
dAtom->setSUy( uy ); |
917 |
< |
dAtom->setSUz( uz ); |
918 |
< |
} |
919 |
< |
else{ |
920 |
< |
the_atoms[index] = new GeneralAtom(index); |
921 |
< |
} |
922 |
< |
the_atoms[index]->setType( current_atom->getType() ); |
923 |
< |
the_atoms[index]->setIndex( index ); |
924 |
< |
|
925 |
< |
// increment the index and repeat; |
926 |
< |
index++; |
927 |
< |
} |
928 |
< |
|
929 |
< |
molEnd = index -1; |
930 |
< |
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++ ){ |
904 |
> |
while( current_extra != NULL ){ |
905 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
906 |
> |
|
907 |
> |
switch( current_extra->getType() ){ |
908 |
> |
|
909 |
> |
case 0: |
910 |
> |
theBends[j].ghost = |
911 |
> |
current_extra->getInt() + atomOffset; |
912 |
> |
theBends[j].isGhost = 1; |
913 |
> |
break; |
914 |
> |
|
915 |
> |
case 1: |
916 |
> |
theBends[j].ghost = |
917 |
> |
(int)current_extra->getDouble() + atomOffset; |
918 |
> |
theBends[j].isGhost = 1; |
919 |
> |
break; |
920 |
> |
|
921 |
> |
default: |
922 |
> |
sprintf( painCave.errMsg, |
923 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
924 |
> |
"double nor an int.\n" |
925 |
> |
"-->Bend[%d] in %s\n", |
926 |
> |
j, comp_stamps[stampID]->getID() ); |
927 |
> |
painCave.isFatal = 1; |
928 |
> |
simError(); |
929 |
> |
} |
930 |
> |
} |
931 |
|
|
932 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
933 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
934 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
935 |
< |
|
936 |
< |
exI = the_bonds[index].a; |
937 |
< |
exJ = the_bonds[index].b; |
938 |
< |
|
939 |
< |
// exclude_I must always be the smaller of the pair |
940 |
< |
if( exI > exJ ){ |
910 |
< |
tempEx = exI; |
911 |
< |
exI = exJ; |
912 |
< |
exJ = tempEx; |
932 |
> |
else{ |
933 |
> |
|
934 |
> |
sprintf( painCave.errMsg, |
935 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
936 |
> |
" -->%s in Bend[%d] in %s\n", |
937 |
> |
current_extra->getlhs(), |
938 |
> |
j, comp_stamps[stampID]->getID() ); |
939 |
> |
painCave.isFatal = 1; |
940 |
> |
simError(); |
941 |
|
} |
914 |
– |
|
942 |
|
|
943 |
< |
#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++; |
943 |
> |
current_extra = current_extra->getNext(); |
944 |
|
} |
945 |
< |
offset += comp_stamps[i]->getNAtoms(); |
945 |
> |
} |
946 |
> |
|
947 |
> |
if( !theBends[j].isGhost ){ |
948 |
> |
|
949 |
> |
exI = theBends[j].a; |
950 |
> |
exJ = theBends[j].c; |
951 |
> |
} |
952 |
> |
else{ |
953 |
|
|
954 |
< |
#ifdef IS_MPI |
954 |
> |
exI = theBends[j].a; |
955 |
> |
exJ = theBends[j].b; |
956 |
|
} |
937 |
– |
#endif //is_mpi |
957 |
|
|
958 |
< |
molIndex++; |
959 |
< |
} |
960 |
< |
} |
958 |
> |
// exclude_I must always be the smaller of the pair |
959 |
> |
if( exI > exJ ){ |
960 |
> |
tempEx = exI; |
961 |
> |
exI = exJ; |
962 |
> |
exJ = tempEx; |
963 |
> |
} |
964 |
> |
#ifdef IS_MPI |
965 |
> |
tempEx = exI; |
966 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
967 |
> |
tempEx = exJ; |
968 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
969 |
> |
|
970 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
971 |
> |
#else // isn't MPI |
972 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
973 |
> |
#endif //is_mpi |
974 |
> |
} |
975 |
> |
excludeOffset += info.nBends; |
976 |
|
|
977 |
< |
the_ff->initializeBonds( the_bonds ); |
978 |
< |
} |
977 |
> |
for(j=0; j<info.nTorsions; j++){ |
978 |
> |
|
979 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
980 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
981 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
982 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
983 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
984 |
> |
|
985 |
> |
exI = theTorsions[j].a; |
986 |
> |
exJ = theTorsions[j].d; |
987 |
|
|
988 |
< |
void SimSetup::makeBends( void ){ |
988 |
> |
// exclude_I must always be the smaller of the pair |
989 |
> |
if( exI > exJ ){ |
990 |
> |
tempEx = exI; |
991 |
> |
exI = exJ; |
992 |
> |
exJ = tempEx; |
993 |
> |
} |
994 |
> |
#ifdef IS_MPI |
995 |
> |
tempEx = exI; |
996 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
997 |
> |
tempEx = exJ; |
998 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
999 |
> |
|
1000 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1001 |
> |
#else // isn't MPI |
1002 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1003 |
> |
#endif //is_mpi |
1004 |
> |
} |
1005 |
> |
excludeOffset += info.nTorsions; |
1006 |
|
|
1007 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1008 |
< |
bend_set* the_bends; |
950 |
< |
BendStamp* current_bend; |
951 |
< |
LinkedAssign* extras; |
952 |
< |
LinkedAssign* current_extra; |
953 |
< |
|
1007 |
> |
|
1008 |
> |
// send the arrays off to the forceField for init. |
1009 |
|
|
1010 |
< |
the_bends = new bend_set[tot_bends]; |
1011 |
< |
index = 0; |
1012 |
< |
offset = 0; |
1013 |
< |
molIndex = 0; |
959 |
< |
for( i=0; i<n_components; i++ ){ |
1010 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1011 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1012 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1013 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1014 |
|
|
961 |
– |
for( j=0; j<components_nmol[i]; j++ ){ |
1015 |
|
|
1016 |
< |
#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 |
< |
} |
1016 |
> |
the_molecules[i].initialize( info ); |
1017 |
|
|
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 |
1018 |
|
|
1019 |
< |
molIndex++; |
1020 |
< |
} |
1019 |
> |
atomOffset += info.nAtoms; |
1020 |
> |
delete[] theBonds; |
1021 |
> |
delete[] theBends; |
1022 |
> |
delete[] theTorsions; |
1023 |
|
} |
1024 |
|
|
1025 |
|
#ifdef IS_MPI |
1026 |
< |
sprintf( checkPointMsg, |
1072 |
< |
"Successfully created the bends list.\n" ); |
1026 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1027 |
|
MPIcheckPoint(); |
1028 |
|
#endif // is_mpi |
1075 |
– |
|
1029 |
|
|
1030 |
< |
the_ff->initializeBends( the_bends ); |
1031 |
< |
} |
1030 |
> |
// clean up the forcefield |
1031 |
> |
the_ff->calcRcut(); |
1032 |
> |
the_ff->cleanMe(); |
1033 |
|
|
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 ); |
1034 |
|
} |
1035 |
|
|
1036 |
|
void SimSetup::initFromBass( void ){ |