| 1450 |
|
} |
| 1451 |
|
|
| 1452 |
|
void SimSetup::calcSysValues(void){ |
| 1453 |
< |
int i; |
| 1453 |
> |
int i, j; |
| 1454 |
> |
int ncutgroups, atomsingroups, ngroupsinstamp; |
| 1455 |
|
|
| 1456 |
|
int* molMembershipArray; |
| 1457 |
+ |
CutoffGroupStamp* cg; |
| 1458 |
|
|
| 1459 |
|
tot_atoms = 0; |
| 1460 |
|
tot_bonds = 0; |
| 1461 |
|
tot_bends = 0; |
| 1462 |
|
tot_torsions = 0; |
| 1463 |
|
tot_rigid = 0; |
| 1464 |
+ |
tot_groups = 0; |
| 1465 |
|
for (i = 0; i < n_components; i++){ |
| 1466 |
|
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
| 1467 |
|
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
| 1468 |
|
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
| 1469 |
|
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
| 1470 |
|
tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies(); |
| 1471 |
+ |
|
| 1472 |
+ |
ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
| 1473 |
+ |
atomsingroups = 0; |
| 1474 |
+ |
for (j=0; j < ncutgroups; j++) { |
| 1475 |
+ |
cg = comp_stamps[i]->getCutoffGroup(j); |
| 1476 |
+ |
atomsingroups += cg->getNMembers(); |
| 1477 |
+ |
} |
| 1478 |
+ |
ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups; |
| 1479 |
+ |
tot_groups += components_nmol[i] * ngroupsinstamp; |
| 1480 |
|
} |
| 1481 |
|
|
| 1482 |
|
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
| 1489 |
|
info[i].n_torsions = tot_torsions; |
| 1490 |
|
info[i].n_SRI = tot_SRI; |
| 1491 |
|
info[i].n_mol = tot_nmol; |
| 1492 |
< |
|
| 1492 |
> |
info[i].ngroup = tot_groups; |
| 1493 |
|
info[i].molMembershipArray = molMembershipArray; |
| 1494 |
|
} |
| 1495 |
|
} |
| 1500 |
|
int i, j, k; |
| 1501 |
|
int localMol, allMol; |
| 1502 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 1503 |
< |
int local_rigid; |
| 1503 |
> |
int local_rigid, local_groups; |
| 1504 |
|
vector<int> globalMolIndex; |
| 1505 |
+ |
int ncutgroups, atomsingroups, ngroupsinstamp; |
| 1506 |
+ |
CutoffGroupStamp* cg; |
| 1507 |
|
|
| 1508 |
|
mpiSim = new mpiSimulation(info); |
| 1509 |
|
|
| 1523 |
|
local_bends = 0; |
| 1524 |
|
local_torsions = 0; |
| 1525 |
|
local_rigid = 0; |
| 1526 |
+ |
local_groups = 0; |
| 1527 |
|
globalAtomCounter = 0; |
| 1528 |
|
|
| 1529 |
|
for (i = 0; i < n_components; i++){ |
| 1534 |
|
local_bends += comp_stamps[i]->getNBends(); |
| 1535 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
| 1536 |
|
local_rigid += comp_stamps[i]->getNRigidBodies(); |
| 1537 |
+ |
|
| 1538 |
+ |
ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
| 1539 |
+ |
atomsingroups = 0; |
| 1540 |
+ |
for (k=0; k < ncutgroups; k++) { |
| 1541 |
+ |
cg = comp_stamps[i]->getCutoffGroup(k); |
| 1542 |
+ |
atomsingroups += cg->getNMembers(); |
| 1543 |
+ |
} |
| 1544 |
+ |
ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + |
| 1545 |
+ |
ncutgroups; |
| 1546 |
+ |
local_groups += ngroupsinstamp; |
| 1547 |
+ |
|
| 1548 |
|
localMol++; |
| 1549 |
|
} |
| 1550 |
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
| 1557 |
|
} |
| 1558 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
| 1559 |
|
|
| 1560 |
< |
info[0].n_atoms = mpiSim->getLocalNatoms(); |
| 1560 |
> |
info[0].n_atoms = mpiSim->getNAtomsLocal(); |
| 1561 |
|
|
| 1536 |
– |
|
| 1562 |
|
if (local_atoms != info[0].n_atoms){ |
| 1563 |
|
sprintf(painCave.errMsg, |
| 1564 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
| 1568 |
|
simError(); |
| 1569 |
|
} |
| 1570 |
|
|
| 1571 |
+ |
info[0].ngroup = mpiSim->getNGroupsLocal(); |
| 1572 |
+ |
if (local_groups != info[0].ngroup){ |
| 1573 |
+ |
sprintf(painCave.errMsg, |
| 1574 |
+ |
"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n" |
| 1575 |
+ |
"\tlocalGroups (%d) are not equal.\n", |
| 1576 |
+ |
info[0].ngroup, local_groups); |
| 1577 |
+ |
painCave.isFatal = 1; |
| 1578 |
+ |
simError(); |
| 1579 |
+ |
} |
| 1580 |
+ |
|
| 1581 |
|
info[0].n_bonds = local_bonds; |
| 1582 |
|
info[0].n_bends = local_bends; |
| 1583 |
|
info[0].n_torsions = local_torsions; |
| 1614 |
|
|
| 1615 |
|
|
| 1616 |
|
molIndex = 0; |
| 1617 |
< |
for (i = 0; i < mpiSim->getTotNmol(); i++){ |
| 1617 |
> |
for (i = 0; i < mpiSim->getNMolGlobal(); i++){ |
| 1618 |
|
if (mol2proc[i] == worldRank){ |
| 1619 |
|
the_molecules[molIndex].setStampID(molCompType[i]); |
| 1620 |
|
the_molecules[molIndex].setMyIndex(molIndex); |
