| 10 |
|
#include "Integrator.hpp" |
| 11 |
|
#include "simError.h" |
| 12 |
|
#include "RigidBody.hpp" |
| 13 |
– |
//#include "ConjugateMinimizer.hpp" |
| 13 |
|
#include "OOPSEMinimizer.hpp" |
| 14 |
+ |
//#include "ConstraintElement.hpp" |
| 15 |
+ |
//#include "ConstraintPair.hpp" |
| 16 |
|
|
| 17 |
|
#ifdef IS_MPI |
| 18 |
|
#include "mpiBASS.h" |
| 199 |
|
char* molName; |
| 200 |
|
char rbName[100]; |
| 201 |
|
|
| 202 |
+ |
//ConstraintPair* consPair; //constraint pair |
| 203 |
+ |
//ConstraintElement* consElement1; //first element of constraint pair |
| 204 |
+ |
//ConstraintElement* consElement2; //second element of constraint pair |
| 205 |
+ |
//int whichRigidBody; |
| 206 |
+ |
//int consAtomIndex; //index of constraint atom in rigid body's atom array |
| 207 |
+ |
//vector<pair<int, int> > jointAtoms; |
| 208 |
|
//init the forceField paramters |
| 209 |
|
|
| 210 |
|
the_ff->readParams(); |
| 217 |
|
the_ff->setSimInfo(&(info[k])); |
| 218 |
|
|
| 219 |
|
atomOffset = 0; |
| 220 |
+ |
groupOffset = 0; |
| 221 |
|
|
| 222 |
|
for (i = 0; i < info[k].n_mol; i++){ |
| 223 |
|
stampID = info[k].molecules[i].getStampID(); |
| 506 |
|
nMembers = currentCutoffGroup->getNMembers(); |
| 507 |
|
|
| 508 |
|
myCutoffGroup = new CutoffGroup(); |
| 509 |
+ |
myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]); |
| 510 |
|
|
| 511 |
|
for (int cg = 0; cg < nMembers; cg++) { |
| 512 |
|
|
| 515 |
|
|
| 516 |
|
// tempI is atom numbering on local processor |
| 517 |
|
tempI = molI + atomOffset; |
| 518 |
< |
|
| 518 |
> |
|
| 519 |
> |
#ifdef IS_MPI |
| 520 |
> |
globalID = info[k].atoms[tempI]->getGlobalIndex() |
| 521 |
> |
#else |
| 522 |
> |
globalID = info[k].atoms[tempI]->getIndex(); |
| 523 |
> |
#endif |
| 524 |
> |
|
| 525 |
> |
globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset]; |
| 526 |
> |
|
| 527 |
|
myCutoffGroup->addAtom(info[k].atoms[tempI]); |
| 528 |
|
|
| 529 |
|
cutoffAtomSet.insert(tempI); |
| 530 |
|
} |
| 531 |
< |
|
| 531 |
> |
|
| 532 |
|
molInfo.myCutoffGroups.push_back(myCutoffGroup); |
| 533 |
+ |
groupOffset++; |
| 534 |
+ |
|
| 535 |
|
}//end for (j = 0; j < molInfo.nCutoffGroups; j++) |
| 536 |
|
|
| 537 |
|
//creat a cutoff group for every atom in current molecule which does not belong to cutoffgroup defined at mdl file |
| 541 |
|
if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){ |
| 542 |
|
myCutoffGroup = new CutoffGroup(); |
| 543 |
|
myCutoffGroup->addAtom(molInfo.myAtoms[j]); |
| 544 |
+ |
myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]); |
| 545 |
+ |
#ifdef IS_MPI |
| 546 |
+ |
globalID = info[k].atoms[atomOffset + j]->getGlobalIndex() |
| 547 |
+ |
#else |
| 548 |
+ |
globalID = info[k].atoms[atomOffset + j]->getIndex(); |
| 549 |
+ |
#endif |
| 550 |
+ |
globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset]; |
| 551 |
|
molInfo.myCutoffGroups.push_back(myCutoffGroup); |
| 552 |
+ |
groupOffset++; |
| 553 |
|
} |
| 554 |
|
|
| 555 |
|
} |
| 556 |
|
|
| 530 |
– |
|
| 531 |
– |
|
| 532 |
– |
|
| 557 |
|
// After this is all set up, scan through the atoms to |
| 558 |
|
// see if they can be added to the integrableObjects: |
| 559 |
|
|
| 584 |
|
info[k].integrableObjects.push_back(mySD); |
| 585 |
|
molInfo.myIntegrableObjects.push_back(mySD); |
| 586 |
|
} |
| 587 |
< |
|
| 587 |
> |
|
| 588 |
> |
|
| 589 |
> |
/* |
| 590 |
> |
|
| 591 |
> |
//creat ConstraintPair. |
| 592 |
> |
molInfo.myConstraintPair.clear(); |
| 593 |
|
|
| 594 |
+ |
for (j = 0; j < molInfo.nBonds; j++){ |
| 595 |
+ |
|
| 596 |
+ |
//if both atoms are in the same rigid body, just skip it |
| 597 |
+ |
currentBond = comp_stamps[stampID]->getBond(j); |
| 598 |
+ |
if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){ |
| 599 |
+ |
|
| 600 |
+ |
tempI = currentBond->getA() + atomOffset; |
| 601 |
+ |
if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex)) |
| 602 |
+ |
consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex); |
| 603 |
+ |
else |
| 604 |
+ |
consElement1 = new ConstraintAtom(info[k].atoms[tempI]); |
| 605 |
+ |
|
| 606 |
+ |
tempJ = currentBond->getB() + atomOffset; |
| 607 |
+ |
if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex)) |
| 608 |
+ |
consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex); |
| 609 |
+ |
else |
| 610 |
+ |
consElement2 = new ConstraintAtom(info[k].atoms[tempJ]); |
| 611 |
+ |
|
| 612 |
+ |
consPair = new DistanceConstraintPair(consElement1, consElement2); |
| 613 |
+ |
molInfo.myConstraintPairs.push_back(consPair); |
| 614 |
+ |
} |
| 615 |
+ |
} |
| 616 |
+ |
|
| 617 |
+ |
//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair |
| 618 |
+ |
for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){ |
| 619 |
+ |
for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){ |
| 620 |
+ |
|
| 621 |
+ |
jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2); |
| 622 |
+ |
|
| 623 |
+ |
for(size_t m = 0; m < jointAtoms.size(); m++){ |
| 624 |
+ |
consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first); |
| 625 |
+ |
consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second); |
| 626 |
+ |
|
| 627 |
+ |
consPair = new JointConstraintPair(consElement1, consElement2); |
| 628 |
+ |
molInfo.myConstraintPairs.push_back(consPair); |
| 629 |
+ |
} |
| 630 |
+ |
|
| 631 |
+ |
} |
| 632 |
+ |
} |
| 633 |
+ |
|
| 634 |
+ |
*/ |
| 635 |
|
// send the arrays off to the forceField for init. |
| 636 |
|
|
| 637 |
|
the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
| 1020 |
|
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
| 1021 |
|
|
| 1022 |
|
// check for thermodynamic integration |
| 1023 |
< |
if (globals->getUseThermInt()) { |
| 1023 |
> |
if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) { |
| 1024 |
|
if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
| 1025 |
< |
info[i].useThermInt = globals->getUseThermInt(); |
| 1025 |
> |
info[i].useSolidThermInt = globals->getUseSolidThermInt(); |
| 1026 |
|
info[i].thermIntLambda = globals->getThermIntLambda(); |
| 1027 |
|
info[i].thermIntK = globals->getThermIntK(); |
| 1028 |
|
|
| 1032 |
|
else { |
| 1033 |
|
sprintf(painCave.errMsg, |
| 1034 |
|
"SimSetup Error:\n" |
| 1035 |
< |
"\tKeyword useThermInt was set to 'true' but\n" |
| 1035 |
> |
"\tKeyword useSolidThermInt was set to 'true' but\n" |
| 1036 |
> |
"\tthermodynamicIntegrationLambda (and/or\n" |
| 1037 |
> |
"\tthermodynamicIntegrationK) was not specified.\n" |
| 1038 |
> |
"\tPlease provide a lambda value and k value in your .bass file.\n"); |
| 1039 |
> |
painCave.isFatal = 1; |
| 1040 |
> |
simError(); |
| 1041 |
> |
} |
| 1042 |
> |
} |
| 1043 |
> |
else if(globals->getUseLiquidThermInt()) { |
| 1044 |
> |
if (globals->getUseSolidThermInt()) { |
| 1045 |
> |
sprintf( painCave.errMsg, |
| 1046 |
> |
"SimSetup Warning: It appears that you have both solid and\n" |
| 1047 |
> |
"\tliquid thermodynamic integration activated in your .bass\n" |
| 1048 |
> |
"\tfile. To avoid confusion, specify only one technique in\n" |
| 1049 |
> |
"\tyour .bass file. Liquid-state thermodynamic integration\n" |
| 1050 |
> |
"\twill be assumed for the current simulation. If this is not\n" |
| 1051 |
> |
"\twhat you desire, set useSolidThermInt to 'true' and\n" |
| 1052 |
> |
"\tuseLiquidThermInt to 'false' in your .bass file.\n"); |
| 1053 |
> |
painCave.isFatal = 0; |
| 1054 |
> |
simError(); |
| 1055 |
> |
} |
| 1056 |
> |
if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
| 1057 |
> |
info[i].useLiquidThermInt = globals->getUseLiquidThermInt(); |
| 1058 |
> |
info[i].thermIntLambda = globals->getThermIntLambda(); |
| 1059 |
> |
info[i].thermIntK = globals->getThermIntK(); |
| 1060 |
> |
} |
| 1061 |
> |
else { |
| 1062 |
> |
sprintf(painCave.errMsg, |
| 1063 |
> |
"SimSetup Error:\n" |
| 1064 |
> |
"\tKeyword useLiquidThermInt was set to 'true' but\n" |
| 1065 |
|
"\tthermodynamicIntegrationLambda (and/or\n" |
| 1066 |
|
"\tthermodynamicIntegrationK) was not specified.\n" |
| 1067 |
|
"\tPlease provide a lambda value and k value in your .bass file.\n"); |
| 1072 |
|
else if(globals->haveThermIntLambda() || globals->haveThermIntK()){ |
| 1073 |
|
sprintf(painCave.errMsg, |
| 1074 |
|
"SimSetup Warning: If you want to use Thermodynamic\n" |
| 1075 |
< |
"\tIntegration, set useThermInt to 'true' in your .bass file.\n" |
| 1076 |
< |
"\tThe useThermInt keyword is 'false' by default, so your\n" |
| 1077 |
< |
"\tlambda and/or k values are being ignored.\n"); |
| 1075 |
> |
"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n" |
| 1076 |
> |
"\t'true' in your .bass file. These keywords are set to\n" |
| 1077 |
> |
"\t'false' by default, so your lambda and/or k values are\n" |
| 1078 |
> |
"\tbeing ignored.\n"); |
| 1079 |
|
painCave.isFatal = 0; |
| 1080 |
|
simError(); |
| 1081 |
|
} |
| 1600 |
|
int i, j, k; |
| 1601 |
|
int localMol, allMol; |
| 1602 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 1603 |
< |
int local_rigid; |
| 1603 |
> |
int local_rigid, local_groups; |
| 1604 |
|
vector<int> globalMolIndex; |
| 1605 |
+ |
int ncutgroups, atomsingroups, ngroupsinstamp; |
| 1606 |
+ |
CutoffGroupStamp* cg; |
| 1607 |
|
|
| 1608 |
|
mpiSim = new mpiSimulation(info); |
| 1609 |
|
|
| 1623 |
|
local_bends = 0; |
| 1624 |
|
local_torsions = 0; |
| 1625 |
|
local_rigid = 0; |
| 1626 |
+ |
local_groups = 0; |
| 1627 |
|
globalAtomCounter = 0; |
| 1628 |
|
|
| 1629 |
|
for (i = 0; i < n_components; i++){ |
| 1634 |
|
local_bends += comp_stamps[i]->getNBends(); |
| 1635 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
| 1636 |
|
local_rigid += comp_stamps[i]->getNRigidBodies(); |
| 1637 |
+ |
|
| 1638 |
+ |
ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
| 1639 |
+ |
atomsingroups = 0; |
| 1640 |
+ |
for (k=0; k < ncutgroups; k++) { |
| 1641 |
+ |
cg = comp_stamps[i]->getCutoffGroup(k); |
| 1642 |
+ |
atomsingroups += cg->getNMembers(); |
| 1643 |
+ |
} |
| 1644 |
+ |
ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + |
| 1645 |
+ |
ncutgroups; |
| 1646 |
+ |
local_groups += ngroupsinstamp; |
| 1647 |
+ |
|
| 1648 |
|
localMol++; |
| 1649 |
|
} |
| 1650 |
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
| 1659 |
|
|
| 1660 |
|
info[0].n_atoms = mpiSim->getNAtomsLocal(); |
| 1661 |
|
|
| 1548 |
– |
|
| 1662 |
|
if (local_atoms != info[0].n_atoms){ |
| 1663 |
|
sprintf(painCave.errMsg, |
| 1664 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
| 1668 |
|
simError(); |
| 1669 |
|
} |
| 1670 |
|
|
| 1671 |
+ |
info[0].ngroup = mpiSim->getNGroupsLocal(); |
| 1672 |
+ |
if (local_groups != info[0].ngroup){ |
| 1673 |
+ |
sprintf(painCave.errMsg, |
| 1674 |
+ |
"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n" |
| 1675 |
+ |
"\tlocalGroups (%d) are not equal.\n", |
| 1676 |
+ |
info[0].ngroup, local_groups); |
| 1677 |
+ |
painCave.isFatal = 1; |
| 1678 |
+ |
simError(); |
| 1679 |
+ |
} |
| 1680 |
+ |
|
| 1681 |
|
info[0].n_bonds = local_bonds; |
| 1682 |
|
info[0].n_bends = local_bends; |
| 1683 |
|
info[0].n_torsions = local_torsions; |
