| 950 |
|
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
| 951 |
|
|
| 952 |
|
// check for thermodynamic integration |
| 953 |
< |
if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
| 954 |
< |
info[i].thermIntLambda = globals->getThermIntLambda(); |
| 955 |
< |
info[i].thermIntK = globals->getThermIntK(); |
| 956 |
< |
info[i].useThermInt = 1; |
| 957 |
< |
|
| 958 |
< |
Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK); |
| 959 |
< |
info[i].restraint = myRestraint; |
| 953 |
> |
if (globals->getUseThermInt()) { |
| 954 |
> |
if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
| 955 |
> |
info[i].useThermInt = globals->getUseThermInt(); |
| 956 |
> |
info[i].thermIntLambda = globals->getThermIntLambda(); |
| 957 |
> |
info[i].thermIntK = globals->getThermIntK(); |
| 958 |
> |
|
| 959 |
> |
Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK); |
| 960 |
> |
info[i].restraint = myRestraint; |
| 961 |
> |
} |
| 962 |
> |
else { |
| 963 |
> |
sprintf(painCave.errMsg, |
| 964 |
> |
"SimSetup Error:\n" |
| 965 |
> |
"\tKeyword useThermInt was set to 'true' but\n" |
| 966 |
> |
"\tthermodynamicIntegrationLambda (and/or\n" |
| 967 |
> |
"\tthermodynamicIntegrationK) was not specified.\n" |
| 968 |
> |
"\tPlease provide a lambda value and k value in your .bass file.\n"); |
| 969 |
> |
painCave.isFatal = 1; |
| 970 |
> |
simError(); |
| 971 |
> |
} |
| 972 |
|
} |
| 973 |
+ |
else if(globals->haveThermIntLambda() || globals->haveThermIntK()){ |
| 974 |
+ |
sprintf(painCave.errMsg, |
| 975 |
+ |
"SimSetup Warning: If you want to use Thermodynamic\n" |
| 976 |
+ |
"\tIntegration, set useThermInt to 'true' in your .bass file.\n" |
| 977 |
+ |
"\tThe useThermInt keyword is 'false' by default, so your\n" |
| 978 |
+ |
"\tlambda and/or k values are being ignored.\n"); |
| 979 |
+ |
painCave.isFatal = 0; |
| 980 |
+ |
simError(); |
| 981 |
+ |
} |
| 982 |
|
} |
| 983 |
|
|
| 984 |
|
//setup seed for random number generator |
| 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 |
|
} |
| 1543 |
|
} |
| 1544 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
| 1545 |
|
|
| 1546 |
< |
info[0].n_atoms = mpiSim->getMyNlocal(); |
| 1546 |
> |
info[0].n_atoms = mpiSim->getNAtomsLocal(); |
| 1547 |
|
|
| 1548 |
|
|
| 1549 |
|
if (local_atoms != info[0].n_atoms){ |
| 1591 |
|
|
| 1592 |
|
|
| 1593 |
|
molIndex = 0; |
| 1594 |
< |
for (i = 0; i < mpiSim->getTotNmol(); i++){ |
| 1594 |
> |
for (i = 0; i < mpiSim->getNMolGlobal(); i++){ |
| 1595 |
|
if (mol2proc[i] == worldRank){ |
| 1596 |
|
the_molecules[molIndex].setStampID(molCompType[i]); |
| 1597 |
|
the_molecules[molIndex].setMyIndex(molIndex); |
