| 240 |
|
|
| 241 |
|
globalIndex = mpiSim->divideLabor(); |
| 242 |
|
|
| 243 |
– |
|
| 244 |
– |
|
| 243 |
|
// set up the local variables |
| 244 |
|
|
| 245 |
|
int localMol, allMol; |
| 333 |
|
|
| 334 |
|
|
| 335 |
|
if( simnfo->n_SRI ){ |
| 336 |
+ |
|
| 337 |
+ |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
| 338 |
+ |
|
| 339 |
|
Exclude::createArray(simnfo->n_SRI); |
| 340 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
| 341 |
+ |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
| 342 |
|
simnfo->globalExcludes = new int; |
| 343 |
|
simnfo->n_exclude = tot_SRI; |
| 344 |
|
} |
| 356 |
|
// set the arrays into the SimInfo object |
| 357 |
|
|
| 358 |
|
simnfo->atoms = the_atoms; |
| 359 |
+ |
simnfo->molecules = the_molecules; |
| 360 |
|
simnfo->nGlobalExcludes = 0; |
| 361 |
|
simnfo->excludes = the_excludes; |
| 362 |
|
|
| 658 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
| 659 |
|
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
| 660 |
|
|
| 661 |
< |
|
| 661 |
> |
#ifdef IS_MPI |
| 662 |
> |
mpiSim->mpiRefresh(); |
| 663 |
> |
#endif |
| 664 |
|
|
| 665 |
|
// initialize the Fortran |
| 666 |
< |
|
| 666 |
> |
|
| 667 |
> |
|
| 668 |
|
simnfo->refreshSim(); |
| 669 |
|
|
| 670 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
| 701 |
|
BondStamp* currentBond; |
| 702 |
|
BendStamp* currentBend; |
| 703 |
|
TorsionStamp* currentTorsion; |
| 704 |
+ |
|
| 705 |
+ |
bond_pair* theBonds; |
| 706 |
+ |
bend_set* theBends; |
| 707 |
+ |
torsion_set* theTorsions; |
| 708 |
+ |
|
| 709 |
|
|
| 710 |
|
//init the forceField paramters |
| 711 |
|
|
| 712 |
|
the_ff->readParams(); |
| 713 |
|
|
| 714 |
|
|
| 715 |
< |
// init the molecules |
| 715 |
> |
// init the atoms |
| 716 |
|
|
| 717 |
+ |
double ux, uy, uz, u, uSqr; |
| 718 |
+ |
|
| 719 |
|
atomOffset = 0; |
| 720 |
|
excludeOffset = 0; |
| 721 |
|
for(i=0; i<simnfo->n_mol; i++){ |
| 732 |
|
info.myExcludes = &the_excludes[excludeOffset]; |
| 733 |
|
info.myBonds = new Bond*[info.nBonds]; |
| 734 |
|
info.myBends = new Bend*[info.nBends]; |
| 735 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
| 735 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
| 736 |
|
|
| 737 |
|
theBonds = new bond_pair[info.nBonds]; |
| 738 |
|
theBends = new bend_set[info.nBends]; |
| 742 |
|
|
| 743 |
|
for(j=0; j<info.nAtoms; j++){ |
| 744 |
|
|
| 745 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
| 745 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
| 746 |
|
if( currentAtom->haveOrientation() ){ |
| 747 |
|
|
| 748 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
| 783 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
| 784 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
| 785 |
|
|
| 786 |
< |
exI = theBonds[i].a; |
| 787 |
< |
exJ = theBonds[i].b; |
| 786 |
> |
exI = theBonds[j].a; |
| 787 |
> |
exJ = theBonds[j].b; |
| 788 |
|
|
| 789 |
|
// exclude_I must always be the smaller of the pair |
| 790 |
|
if( exI > exJ ){ |
| 800 |
|
|
| 801 |
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 802 |
|
#else // isn't MPI |
| 803 |
+ |
|
| 804 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 805 |
|
#endif //is_mpi |
| 806 |
|
} |
| 816 |
|
|
| 817 |
|
if( currentBend->haveExtras() ){ |
| 818 |
|
|
| 819 |
< |
extras = current_bend->getExtras(); |
| 819 |
> |
extras = currentBend->getExtras(); |
| 820 |
|
current_extra = extras; |
| 821 |
|
|
| 822 |
|
while( current_extra != NULL ){ |
| 838 |
|
|
| 839 |
|
default: |
| 840 |
|
sprintf( painCave.errMsg, |
| 841 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
| 841 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
| 842 |
|
"double nor an int.\n" |
| 843 |
|
"-->Bend[%d] in %s\n", |
| 844 |
|
j, comp_stamps[stampID]->getID() ); |
| 933 |
|
|
| 934 |
|
the_molecules[i].initialize( info ); |
| 935 |
|
atomOffset += info.nAtoms; |
| 936 |
+ |
delete[] theBonds; |
| 937 |
+ |
delete[] theBends; |
| 938 |
+ |
delete[] theTorsions; |
| 939 |
|
} |
| 940 |
|
|
| 941 |
+ |
#ifdef IS_MPI |
| 942 |
+ |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
| 943 |
+ |
MPIcheckPoint(); |
| 944 |
+ |
#endif // is_mpi |
| 945 |
+ |
|
| 946 |
|
// clean up the forcefield |
| 947 |
|
the_ff->calcRcut(); |
| 948 |
|
the_ff->cleanMe(); |
| 949 |
+ |
|
| 950 |
|
} |
| 951 |
|
|
| 952 |
|
void SimSetup::initFromBass( void ){ |
