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 |
+ |
the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
91 |
+ |
} else if ( !strcasecmp( ensemble, "NVT") ) { |
92 |
+ |
the_extendedsystem = new ExtendedSystem( simnfo ); |
93 |
+ |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
94 |
+ |
} else if ( !strcasecmp( ensemble, "NVE") ) { |
95 |
+ |
} else { |
96 |
+ |
sprintf( painCave.errMsg, |
97 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
98 |
+ |
"reverting to NVE for this simulation.\n", |
99 |
+ |
ensemble ); |
100 |
+ |
painCave.isFatal = 0; |
101 |
+ |
simError(); |
102 |
+ |
strcpy( ensemble, "NVE" ); |
103 |
+ |
} |
104 |
|
strcpy( simnfo->ensemble, ensemble ); |
105 |
|
|
106 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
107 |
|
simnfo->usePBC = the_globals->getPBC(); |
108 |
|
|
109 |
< |
|
110 |
< |
|
91 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
92 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
93 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
94 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
109 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
110 |
> |
else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
111 |
|
else{ |
112 |
|
sprintf( painCave.errMsg, |
113 |
|
"SimSetup Error. Unrecognized force field -> %s\n", |
258 |
|
|
259 |
|
globalIndex = mpiSim->divideLabor(); |
260 |
|
|
245 |
– |
|
246 |
– |
|
261 |
|
// set up the local variables |
262 |
|
|
263 |
|
int localMol, allMol; |
264 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
265 |
+ |
|
266 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
267 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
268 |
|
|
269 |
|
allMol = 0; |
270 |
|
localMol = 0; |
276 |
|
|
277 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
278 |
|
|
279 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
279 |
> |
if( mol2proc[j] == worldRank ){ |
280 |
|
|
281 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
282 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
295 |
|
if( local_atoms != simnfo->n_atoms ){ |
296 |
|
sprintf( painCave.errMsg, |
297 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
298 |
< |
" localAtom (%d) are note equal.\n", |
298 |
> |
" localAtom (%d) are not equal.\n", |
299 |
|
simnfo->n_atoms, |
300 |
|
local_atoms ); |
301 |
|
painCave.isFatal = 1; |
320 |
|
Atom::createArrays(simnfo->n_atoms); |
321 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
322 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
323 |
+ |
int molIndex; |
324 |
|
|
325 |
+ |
// initialize the molecule's stampID's |
326 |
|
|
327 |
+ |
#ifdef IS_MPI |
328 |
+ |
|
329 |
+ |
|
330 |
+ |
molIndex = 0; |
331 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
332 |
+ |
|
333 |
+ |
if(mol2proc[i] == worldRank ){ |
334 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
335 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
336 |
+ |
molIndex++; |
337 |
+ |
} |
338 |
+ |
} |
339 |
+ |
|
340 |
+ |
#else // is_mpi |
341 |
+ |
|
342 |
+ |
molIndex = 0; |
343 |
+ |
for(i=0; i<n_components; i++){ |
344 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
345 |
+ |
the_molecules[molIndex].setStampID( i ); |
346 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
347 |
+ |
molIndex++; |
348 |
+ |
} |
349 |
+ |
} |
350 |
+ |
|
351 |
+ |
|
352 |
+ |
#endif // is_mpi |
353 |
+ |
|
354 |
+ |
|
355 |
|
if( simnfo->n_SRI ){ |
356 |
+ |
|
357 |
|
Exclude::createArray(simnfo->n_SRI); |
358 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
359 |
+ |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
360 |
|
simnfo->globalExcludes = new int; |
361 |
< |
simnfo->n_exclude = tot_SRI; |
361 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
362 |
|
} |
363 |
|
else{ |
364 |
|
|
374 |
|
// set the arrays into the SimInfo object |
375 |
|
|
376 |
|
simnfo->atoms = the_atoms; |
377 |
< |
simnfo->sr_interactions = the_sris; |
377 |
> |
simnfo->molecules = the_molecules; |
378 |
|
simnfo->nGlobalExcludes = 0; |
379 |
|
simnfo->excludes = the_excludes; |
380 |
|
|
431 |
|
|
432 |
|
the_ff->setSimInfo( simnfo ); |
433 |
|
|
434 |
< |
makeAtoms(); |
434 |
> |
makeMolecules(); |
435 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
436 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
437 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
438 |
|
} |
439 |
|
|
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 |
– |
|
440 |
|
if (the_globals->getUseRF() ) { |
441 |
|
simnfo->useReactionField = 1; |
442 |
|
|
673 |
|
|
674 |
|
// new AllLong( simnfo ); |
675 |
|
|
676 |
< |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
677 |
< |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
678 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
679 |
< |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
680 |
< |
|
676 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo, |
677 |
> |
the_ff, |
678 |
> |
the_extendedsystem); |
679 |
> |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, |
680 |
> |
the_ff, |
681 |
> |
the_extendedsystem ); |
682 |
|
|
683 |
+ |
#ifdef IS_MPI |
684 |
+ |
mpiSim->mpiRefresh(); |
685 |
+ |
#endif |
686 |
|
|
687 |
|
// initialize the Fortran |
688 |
< |
|
688 |
> |
|
689 |
> |
|
690 |
|
simnfo->refreshSim(); |
691 |
|
|
692 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
723 |
|
BondStamp* currentBond; |
724 |
|
BendStamp* currentBend; |
725 |
|
TorsionStamp* currentTorsion; |
726 |
+ |
|
727 |
+ |
bond_pair* theBonds; |
728 |
+ |
bend_set* theBends; |
729 |
+ |
torsion_set* theTorsions; |
730 |
+ |
|
731 |
|
|
732 |
|
//init the forceField paramters |
733 |
|
|
734 |
|
the_ff->readParams(); |
735 |
|
|
736 |
|
|
737 |
< |
// init the molecules |
737 |
> |
// init the atoms |
738 |
|
|
739 |
+ |
double ux, uy, uz, u, uSqr; |
740 |
+ |
|
741 |
|
atomOffset = 0; |
742 |
|
excludeOffset = 0; |
743 |
|
for(i=0; i<simnfo->n_mol; i++){ |
754 |
|
info.myExcludes = &the_excludes[excludeOffset]; |
755 |
|
info.myBonds = new Bond*[info.nBonds]; |
756 |
|
info.myBends = new Bend*[info.nBends]; |
757 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
757 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
758 |
|
|
759 |
|
theBonds = new bond_pair[info.nBonds]; |
760 |
|
theBends = new bend_set[info.nBends]; |
764 |
|
|
765 |
|
for(j=0; j<info.nAtoms; j++){ |
766 |
|
|
767 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
767 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
768 |
|
if( currentAtom->haveOrientation() ){ |
769 |
|
|
770 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
805 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
806 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
807 |
|
|
808 |
< |
exI = theBonds[i].a; |
809 |
< |
exJ = theBonds[i].b; |
808 |
> |
exI = theBonds[j].a; |
809 |
> |
exJ = theBonds[j].b; |
810 |
|
|
811 |
|
// exclude_I must always be the smaller of the pair |
812 |
|
if( exI > exJ ){ |
822 |
|
|
823 |
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
824 |
|
#else // isn't MPI |
825 |
+ |
|
826 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
827 |
|
#endif //is_mpi |
828 |
|
} |
838 |
|
|
839 |
|
if( currentBend->haveExtras() ){ |
840 |
|
|
841 |
< |
extras = current_bend->getExtras(); |
841 |
> |
extras = currentBend->getExtras(); |
842 |
|
current_extra = extras; |
843 |
|
|
844 |
|
while( current_extra != NULL ){ |
860 |
|
|
861 |
|
default: |
862 |
|
sprintf( painCave.errMsg, |
863 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
863 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
864 |
|
"double nor an int.\n" |
865 |
|
"-->Bend[%d] in %s\n", |
866 |
|
j, comp_stamps[stampID]->getID() ); |
945 |
|
excludeOffset += info.nTorsions; |
946 |
|
|
947 |
|
|
948 |
+ |
// send the arrays off to the forceField for init. |
949 |
|
|
950 |
+ |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
951 |
+ |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
952 |
+ |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
953 |
+ |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
954 |
|
|
902 |
– |
|
903 |
– |
|
904 |
– |
|
905 |
– |
|
906 |
– |
void SimSetup::makeAtoms( void ){ |
907 |
– |
|
908 |
– |
int i, j, k, index; |
909 |
– |
double ux, uy, uz, uSqr, u; |
910 |
– |
AtomStamp* current_atom; |
911 |
– |
|
912 |
– |
DirectionalAtom* dAtom; |
913 |
– |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
914 |
– |
|
915 |
– |
lMolIndex = 0; |
916 |
– |
molIndex = 0; |
917 |
– |
index = 0; |
918 |
– |
for( i=0; i<n_components; i++ ){ |
919 |
– |
|
920 |
– |
for( j=0; j<components_nmol[i]; j++ ){ |
921 |
– |
|
922 |
– |
#ifdef IS_MPI |
923 |
– |
if( mpiSim->getMyMolStart() <= molIndex && |
924 |
– |
molIndex <= mpiSim->getMyMolEnd() ){ |
925 |
– |
#endif // is_mpi |
926 |
– |
|
927 |
– |
molStart = index; |
928 |
– |
nMemb = comp_stamps[i]->getNAtoms(); |
929 |
– |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
930 |
– |
|
931 |
– |
current_atom = comp_stamps[i]->getAtom( k ); |
932 |
– |
if( current_atom->haveOrientation() ){ |
933 |
– |
|
934 |
– |
dAtom = new DirectionalAtom(index); |
935 |
– |
simnfo->n_oriented++; |
936 |
– |
the_atoms[index] = dAtom; |
937 |
– |
|
938 |
– |
ux = current_atom->getOrntX(); |
939 |
– |
uy = current_atom->getOrntY(); |
940 |
– |
uz = current_atom->getOrntZ(); |
941 |
– |
|
942 |
– |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
943 |
– |
|
944 |
– |
u = sqrt( uSqr ); |
945 |
– |
ux = ux / u; |
946 |
– |
uy = uy / u; |
947 |
– |
uz = uz / u; |
948 |
– |
|
949 |
– |
dAtom->setSUx( ux ); |
950 |
– |
dAtom->setSUy( uy ); |
951 |
– |
dAtom->setSUz( uz ); |
952 |
– |
} |
953 |
– |
else{ |
954 |
– |
the_atoms[index] = new GeneralAtom(index); |
955 |
– |
} |
956 |
– |
the_atoms[index]->setType( current_atom->getType() ); |
957 |
– |
the_atoms[index]->setIndex( index ); |
958 |
– |
|
959 |
– |
// increment the index and repeat; |
960 |
– |
index++; |
961 |
– |
} |
962 |
– |
|
963 |
– |
molEnd = index -1; |
964 |
– |
the_molecules[lMolIndex].setNMembers( nMemb ); |
965 |
– |
the_molecules[lMolIndex].setStartAtom( molStart ); |
966 |
– |
the_molecules[lMolIndex].setEndAtom( molEnd ); |
967 |
– |
the_molecules[lMolIndex].setStampID( i ); |
968 |
– |
lMolIndex++; |
969 |
– |
|
970 |
– |
#ifdef IS_MPI |
971 |
– |
} |
972 |
– |
#endif //is_mpi |
973 |
– |
|
974 |
– |
molIndex++; |
975 |
– |
} |
976 |
– |
} |
977 |
– |
|
978 |
– |
#ifdef IS_MPI |
979 |
– |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
980 |
– |
|
981 |
– |
delete[] globalIndex; |
982 |
– |
|
983 |
– |
mpiSim->mpiRefresh(); |
984 |
– |
#endif //IS_MPI |
985 |
– |
|
986 |
– |
the_ff->initializeAtoms(); |
987 |
– |
} |
988 |
– |
|
989 |
– |
void SimSetup::makeBonds( void ){ |
990 |
– |
|
991 |
– |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
992 |
– |
bond_pair* the_bonds; |
993 |
– |
BondStamp* current_bond; |
994 |
– |
|
995 |
– |
the_bonds = new bond_pair[tot_bonds]; |
996 |
– |
index = 0; |
997 |
– |
offset = 0; |
998 |
– |
molIndex = 0; |
999 |
– |
|
1000 |
– |
for( i=0; i<n_components; i++ ){ |
1001 |
– |
|
1002 |
– |
for( j=0; j<components_nmol[i]; j++ ){ |
1003 |
– |
|
1004 |
– |
#ifdef IS_MPI |
1005 |
– |
if( mpiSim->getMyMolStart() <= molIndex && |
1006 |
– |
molIndex <= mpiSim->getMyMolEnd() ){ |
1007 |
– |
#endif // is_mpi |
1008 |
– |
|
1009 |
– |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
1010 |
– |
|
1011 |
– |
current_bond = comp_stamps[i]->getBond( k ); |
1012 |
– |
the_bonds[index].a = current_bond->getA() + offset; |
1013 |
– |
the_bonds[index].b = current_bond->getB() + offset; |
955 |
|
|
956 |
< |
exI = the_bonds[index].a; |
1016 |
< |
exJ = the_bonds[index].b; |
1017 |
< |
|
1018 |
< |
// exclude_I must always be the smaller of the pair |
1019 |
< |
if( exI > exJ ){ |
1020 |
< |
tempEx = exI; |
1021 |
< |
exI = exJ; |
1022 |
< |
exJ = tempEx; |
1023 |
< |
} |
1024 |
< |
|
1025 |
< |
|
1026 |
< |
#ifdef IS_MPI |
1027 |
< |
|
1028 |
< |
the_excludes[index*2] = |
1029 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
1030 |
< |
the_excludes[index*2 + 1] = |
1031 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
1032 |
< |
|
1033 |
< |
#else // isn't MPI |
1034 |
< |
|
1035 |
< |
the_excludes[index*2] = exI + 1; |
1036 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
1037 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
1038 |
< |
#endif //is_mpi |
1039 |
< |
|
1040 |
< |
// increment the index and repeat; |
1041 |
< |
index++; |
1042 |
< |
} |
1043 |
< |
offset += comp_stamps[i]->getNAtoms(); |
1044 |
< |
|
1045 |
< |
#ifdef IS_MPI |
1046 |
< |
} |
1047 |
< |
#endif //is_mpi |
1048 |
< |
|
1049 |
< |
molIndex++; |
1050 |
< |
} |
1051 |
< |
} |
1052 |
< |
|
1053 |
< |
the_ff->initializeBonds( the_bonds ); |
1054 |
< |
} |
1055 |
< |
|
1056 |
< |
void SimSetup::makeBends( void ){ |
1057 |
< |
|
1058 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1059 |
< |
bend_set* the_bends; |
1060 |
< |
BendStamp* current_bend; |
1061 |
< |
LinkedAssign* extras; |
1062 |
< |
LinkedAssign* current_extra; |
1063 |
< |
|
1064 |
< |
|
1065 |
< |
the_bends = new bend_set[tot_bends]; |
1066 |
< |
index = 0; |
1067 |
< |
offset = 0; |
1068 |
< |
molIndex = 0; |
1069 |
< |
for( i=0; i<n_components; i++ ){ |
1070 |
< |
|
1071 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
1072 |
< |
|
1073 |
< |
#ifdef IS_MPI |
1074 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
1075 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
1076 |
< |
#endif // is_mpi |
1077 |
< |
|
1078 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
1079 |
< |
|
1080 |
< |
current_bend = comp_stamps[i]->getBend( k ); |
1081 |
< |
the_bends[index].a = current_bend->getA() + offset; |
1082 |
< |
the_bends[index].b = current_bend->getB() + offset; |
1083 |
< |
the_bends[index].c = current_bend->getC() + offset; |
1084 |
< |
|
1085 |
< |
if( current_bend->haveExtras() ){ |
1086 |
< |
|
1087 |
< |
extras = current_bend->getExtras(); |
1088 |
< |
current_extra = extras; |
1089 |
< |
|
1090 |
< |
while( current_extra != NULL ){ |
1091 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
1092 |
< |
|
1093 |
< |
switch( current_extra->getType() ){ |
1094 |
< |
|
1095 |
< |
case 0: |
1096 |
< |
the_bends[index].ghost = |
1097 |
< |
current_extra->getInt() + offset; |
1098 |
< |
the_bends[index].isGhost = 1; |
1099 |
< |
break; |
1100 |
< |
|
1101 |
< |
case 1: |
1102 |
< |
the_bends[index].ghost = |
1103 |
< |
(int)current_extra->getDouble() + offset; |
1104 |
< |
the_bends[index].isGhost = 1; |
1105 |
< |
break; |
1106 |
< |
|
1107 |
< |
default: |
1108 |
< |
sprintf( painCave.errMsg, |
1109 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
1110 |
< |
"double nor an int.\n" |
1111 |
< |
"-->Bend[%d] in %s\n", |
1112 |
< |
k, comp_stamps[i]->getID() ); |
1113 |
< |
painCave.isFatal = 1; |
1114 |
< |
simError(); |
1115 |
< |
} |
1116 |
< |
} |
1117 |
< |
|
1118 |
< |
else{ |
1119 |
< |
|
1120 |
< |
sprintf( painCave.errMsg, |
1121 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
1122 |
< |
" -->%s in Bend[%d] in %s\n", |
1123 |
< |
current_extra->getlhs(), |
1124 |
< |
k, comp_stamps[i]->getID() ); |
1125 |
< |
painCave.isFatal = 1; |
1126 |
< |
simError(); |
1127 |
< |
} |
1128 |
< |
|
1129 |
< |
current_extra = current_extra->getNext(); |
1130 |
< |
} |
1131 |
< |
} |
1132 |
< |
|
1133 |
< |
if( !the_bends[index].isGhost ){ |
1134 |
< |
|
1135 |
< |
exI = the_bends[index].a; |
1136 |
< |
exJ = the_bends[index].c; |
1137 |
< |
} |
1138 |
< |
else{ |
1139 |
< |
|
1140 |
< |
exI = the_bends[index].a; |
1141 |
< |
exJ = the_bends[index].b; |
1142 |
< |
} |
1143 |
< |
|
1144 |
< |
// exclude_I must always be the smaller of the pair |
1145 |
< |
if( exI > exJ ){ |
1146 |
< |
tempEx = exI; |
1147 |
< |
exI = exJ; |
1148 |
< |
exJ = tempEx; |
1149 |
< |
} |
956 |
> |
the_molecules[i].initialize( info ); |
957 |
|
|
958 |
|
|
959 |
< |
#ifdef IS_MPI |
960 |
< |
|
961 |
< |
the_excludes[(index + tot_bonds)*2] = |
962 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
1156 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
1157 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
1158 |
< |
|
1159 |
< |
#else // isn't MPI |
1160 |
< |
|
1161 |
< |
the_excludes[(index + tot_bonds)*2] = exI + 1; |
1162 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
1163 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
1164 |
< |
#endif //is_mpi |
1165 |
< |
|
1166 |
< |
|
1167 |
< |
// increment the index and repeat; |
1168 |
< |
index++; |
1169 |
< |
} |
1170 |
< |
offset += comp_stamps[i]->getNAtoms(); |
1171 |
< |
|
1172 |
< |
#ifdef IS_MPI |
1173 |
< |
} |
1174 |
< |
#endif //is_mpi |
1175 |
< |
|
1176 |
< |
molIndex++; |
1177 |
< |
} |
959 |
> |
atomOffset += info.nAtoms; |
960 |
> |
delete[] theBonds; |
961 |
> |
delete[] theBends; |
962 |
> |
delete[] theTorsions; |
963 |
|
} |
964 |
|
|
965 |
|
#ifdef IS_MPI |
966 |
< |
sprintf( checkPointMsg, |
1182 |
< |
"Successfully created the bends list.\n" ); |
966 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
967 |
|
MPIcheckPoint(); |
968 |
|
#endif // is_mpi |
1185 |
– |
|
969 |
|
|
970 |
< |
the_ff->initializeBends( the_bends ); |
971 |
< |
} |
970 |
> |
// clean up the forcefield |
971 |
> |
the_ff->calcRcut(); |
972 |
> |
the_ff->cleanMe(); |
973 |
|
|
1190 |
– |
void SimSetup::makeTorsions( void ){ |
1191 |
– |
|
1192 |
– |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1193 |
– |
torsion_set* the_torsions; |
1194 |
– |
TorsionStamp* current_torsion; |
1195 |
– |
|
1196 |
– |
the_torsions = new torsion_set[tot_torsions]; |
1197 |
– |
index = 0; |
1198 |
– |
offset = 0; |
1199 |
– |
molIndex = 0; |
1200 |
– |
for( i=0; i<n_components; i++ ){ |
1201 |
– |
|
1202 |
– |
for( j=0; j<components_nmol[i]; j++ ){ |
1203 |
– |
|
1204 |
– |
#ifdef IS_MPI |
1205 |
– |
if( mpiSim->getMyMolStart() <= molIndex && |
1206 |
– |
molIndex <= mpiSim->getMyMolEnd() ){ |
1207 |
– |
#endif // is_mpi |
1208 |
– |
|
1209 |
– |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1210 |
– |
|
1211 |
– |
current_torsion = comp_stamps[i]->getTorsion( k ); |
1212 |
– |
the_torsions[index].a = current_torsion->getA() + offset; |
1213 |
– |
the_torsions[index].b = current_torsion->getB() + offset; |
1214 |
– |
the_torsions[index].c = current_torsion->getC() + offset; |
1215 |
– |
the_torsions[index].d = current_torsion->getD() + offset; |
1216 |
– |
|
1217 |
– |
exI = the_torsions[index].a; |
1218 |
– |
exJ = the_torsions[index].d; |
1219 |
– |
|
1220 |
– |
|
1221 |
– |
// exclude_I must always be the smaller of the pair |
1222 |
– |
if( exI > exJ ){ |
1223 |
– |
tempEx = exI; |
1224 |
– |
exI = exJ; |
1225 |
– |
exJ = tempEx; |
1226 |
– |
} |
1227 |
– |
|
1228 |
– |
|
1229 |
– |
#ifdef IS_MPI |
1230 |
– |
|
1231 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = |
1232 |
– |
the_atoms[exI]->getGlobalIndex() + 1; |
1233 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1234 |
– |
the_atoms[exJ]->getGlobalIndex() + 1; |
1235 |
– |
|
1236 |
– |
#else // isn't MPI |
1237 |
– |
|
1238 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
1239 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
1240 |
– |
// fortran indexes from 1 (hence the +1 in the indexing) |
1241 |
– |
#endif //is_mpi |
1242 |
– |
|
1243 |
– |
|
1244 |
– |
// increment the index and repeat; |
1245 |
– |
index++; |
1246 |
– |
} |
1247 |
– |
offset += comp_stamps[i]->getNAtoms(); |
1248 |
– |
|
1249 |
– |
#ifdef IS_MPI |
1250 |
– |
} |
1251 |
– |
#endif //is_mpi |
1252 |
– |
|
1253 |
– |
molIndex++; |
1254 |
– |
} |
1255 |
– |
} |
1256 |
– |
|
1257 |
– |
the_ff->initializeTorsions( the_torsions ); |
974 |
|
} |
975 |
|
|
976 |
|
void SimSetup::initFromBass( void ){ |