| 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 |
+ |
#include "ConstraintManager.hpp" |
| 17 |
|
|
| 18 |
|
#ifdef IS_MPI |
| 19 |
|
#include "mpiBASS.h" |
| 158 |
|
|
| 159 |
|
initFortran(); |
| 160 |
|
|
| 161 |
+ |
//creat constraint manager |
| 162 |
+ |
for(int i = 0; i < nInfo; i++) |
| 163 |
+ |
info[i].consMan = new ConstraintManager(&info[i]); |
| 164 |
+ |
|
| 165 |
|
if (globals->haveMinimizer()) |
| 166 |
|
// make minimizer |
| 167 |
|
makeMinimizer(); |
| 176 |
|
int i, j, k; |
| 177 |
|
int exI, exJ, exK, exL, slI, slJ; |
| 178 |
|
int tempI, tempJ, tempK, tempL; |
| 179 |
< |
int molI; |
| 180 |
< |
int stampID, atomOffset, rbOffset; |
| 179 |
> |
int molI, globalID; |
| 180 |
> |
int stampID, atomOffset, rbOffset, groupOffset; |
| 181 |
|
molInit molInfo; |
| 182 |
|
DirectionalAtom* dAtom; |
| 183 |
|
RigidBody* myRB; |
| 204 |
|
char* molName; |
| 205 |
|
char rbName[100]; |
| 206 |
|
|
| 207 |
+ |
ConstraintPair* consPair; //constraint pair |
| 208 |
+ |
ConstraintElement* consElement1; //first element of constraint pair |
| 209 |
+ |
ConstraintElement* consElement2; //second element of constraint pair |
| 210 |
+ |
int whichRigidBody; |
| 211 |
+ |
int consAtomIndex; //index of constraint atom in rigid body's atom array |
| 212 |
+ |
vector<pair<int, int> > jointAtoms; |
| 213 |
+ |
double bondLength2; |
| 214 |
|
//init the forceField paramters |
| 215 |
|
|
| 216 |
|
the_ff->readParams(); |
| 222 |
|
for (k = 0; k < nInfo; k++){ |
| 223 |
|
the_ff->setSimInfo(&(info[k])); |
| 224 |
|
|
| 225 |
+ |
#ifdef IS_MPI |
| 226 |
+ |
info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()]; |
| 227 |
+ |
for (i = 0; i < mpiSim->getNAtomsGlobal(); i++) |
| 228 |
+ |
info[k].globalGroupMembership[i] = 0; |
| 229 |
+ |
#else |
| 230 |
+ |
info[k].globalGroupMembership = new int[info[k].n_atoms]; |
| 231 |
+ |
for (i = 0; i < info[k].n_atoms; i++) |
| 232 |
+ |
info[k].globalGroupMembership[i] = 0; |
| 233 |
+ |
#endif |
| 234 |
+ |
|
| 235 |
|
atomOffset = 0; |
| 236 |
+ |
groupOffset = 0; |
| 237 |
|
|
| 238 |
|
for (i = 0; i < info[k].n_mol; i++){ |
| 239 |
|
stampID = info[k].molecules[i].getStampID(); |
| 298 |
|
|
| 299 |
|
molInfo.myAtoms[j]->setType(currentAtom->getType()); |
| 300 |
|
#ifdef IS_MPI |
| 277 |
– |
|
| 301 |
|
molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]); |
| 279 |
– |
|
| 302 |
|
#endif // is_mpi |
| 303 |
|
} |
| 304 |
|
|
| 521 |
|
|
| 522 |
|
myCutoffGroup = new CutoffGroup(); |
| 523 |
|
|
| 524 |
+ |
#ifdef IS_MPI |
| 525 |
+ |
myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]); |
| 526 |
+ |
#else |
| 527 |
+ |
myCutoffGroup->setGlobalIndex(groupOffset); |
| 528 |
+ |
#endif |
| 529 |
+ |
|
| 530 |
|
for (int cg = 0; cg < nMembers; cg++) { |
| 531 |
|
|
| 532 |
|
// molI is atom numbering inside this molecule |
| 534 |
|
|
| 535 |
|
// tempI is atom numbering on local processor |
| 536 |
|
tempI = molI + atomOffset; |
| 509 |
– |
|
| 510 |
– |
myCutoffGroup->addAtom(info[k].atoms[tempI]); |
| 537 |
|
|
| 538 |
+ |
#ifdef IS_MPI |
| 539 |
+ |
globalID = info[k].atoms[tempI]->getGlobalIndex(); |
| 540 |
+ |
info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset]; |
| 541 |
+ |
#else |
| 542 |
+ |
globalID = info[k].atoms[tempI]->getIndex(); |
| 543 |
+ |
info[k].globalGroupMembership[globalID] = groupOffset; |
| 544 |
+ |
#endif |
| 545 |
+ |
myCutoffGroup->addAtom(info[k].atoms[tempI]); |
| 546 |
|
cutoffAtomSet.insert(tempI); |
| 547 |
|
} |
| 548 |
< |
|
| 548 |
> |
|
| 549 |
|
molInfo.myCutoffGroups.push_back(myCutoffGroup); |
| 550 |
< |
}//end for (j = 0; j < molInfo.nCutoffGroups; j++) |
| 550 |
> |
groupOffset++; |
| 551 |
|
|
| 552 |
< |
//creat a cutoff group for every atom in current molecule which does not belong to cutoffgroup defined at mdl file |
| 553 |
< |
|
| 552 |
> |
}//end for (j = 0; j < molInfo.nCutoffGroups; j++) |
| 553 |
> |
|
| 554 |
> |
|
| 555 |
> |
// create a cutoff group for every atom in current molecule which |
| 556 |
> |
// does not belong to cutoffgroup defined at mdl file |
| 557 |
> |
|
| 558 |
|
for(j = 0; j < molInfo.nAtoms; j++){ |
| 559 |
< |
|
| 559 |
> |
|
| 560 |
|
if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){ |
| 561 |
|
myCutoffGroup = new CutoffGroup(); |
| 562 |
|
myCutoffGroup->addAtom(molInfo.myAtoms[j]); |
| 525 |
– |
molInfo.myCutoffGroups.push_back(myCutoffGroup); |
| 526 |
– |
} |
| 563 |
|
|
| 564 |
+ |
#ifdef IS_MPI |
| 565 |
+ |
myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]); |
| 566 |
+ |
globalID = info[k].atoms[atomOffset + j]->getGlobalIndex(); |
| 567 |
+ |
info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset]; |
| 568 |
+ |
#else |
| 569 |
+ |
myCutoffGroup->setGlobalIndex(groupOffset); |
| 570 |
+ |
globalID = info[k].atoms[atomOffset + j]->getIndex(); |
| 571 |
+ |
info[k].globalGroupMembership[globalID] = groupOffset; |
| 572 |
+ |
#endif |
| 573 |
+ |
molInfo.myCutoffGroups.push_back(myCutoffGroup); |
| 574 |
+ |
groupOffset++; |
| 575 |
+ |
} |
| 576 |
|
} |
| 577 |
|
|
| 530 |
– |
|
| 531 |
– |
|
| 532 |
– |
|
| 578 |
|
// After this is all set up, scan through the atoms to |
| 579 |
|
// see if they can be added to the integrableObjects: |
| 580 |
|
|
| 605 |
|
info[k].integrableObjects.push_back(mySD); |
| 606 |
|
molInfo.myIntegrableObjects.push_back(mySD); |
| 607 |
|
} |
| 608 |
< |
|
| 564 |
< |
|
| 608 |
> |
|
| 609 |
|
// send the arrays off to the forceField for init. |
| 610 |
|
|
| 611 |
|
the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
| 614 |
|
the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
| 615 |
|
theTorsions); |
| 616 |
|
|
| 617 |
< |
info[k].molecules[i].initialize(molInfo); |
| 617 |
> |
|
| 618 |
> |
//creat ConstraintPair. |
| 619 |
> |
molInfo.myConstraintPairs.clear(); |
| 620 |
> |
|
| 621 |
> |
for (j = 0; j < molInfo.nBonds; j++){ |
| 622 |
> |
|
| 623 |
> |
//if bond is constrained bond, add it into constraint pair |
| 624 |
> |
if(molInfo.myBonds[j]->is_constrained()){ |
| 625 |
> |
|
| 626 |
> |
//if both atoms are in the same rigid body, just skip it |
| 627 |
> |
currentBond = comp_stamps[stampID]->getBond(j); |
| 628 |
> |
|
| 629 |
> |
if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){ |
| 630 |
> |
|
| 631 |
> |
tempI = currentBond->getA() + atomOffset; |
| 632 |
> |
if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex)) |
| 633 |
> |
consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex); |
| 634 |
> |
else |
| 635 |
> |
consElement1 = new ConstraintAtom(info[k].atoms[tempI]); |
| 636 |
> |
|
| 637 |
> |
tempJ = currentBond->getB() + atomOffset; |
| 638 |
> |
if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex)) |
| 639 |
> |
consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex); |
| 640 |
> |
else |
| 641 |
> |
consElement2 = new ConstraintAtom(info[k].atoms[tempJ]); |
| 642 |
> |
|
| 643 |
> |
bondLength2 = molInfo.myBonds[j]->get_constraint()->get_dsqr(); |
| 644 |
> |
consPair = new DistanceConstraintPair(consElement1, consElement2, bondLength2); |
| 645 |
> |
|
| 646 |
> |
molInfo.myConstraintPairs.push_back(consPair); |
| 647 |
> |
} |
| 648 |
> |
}//end if(molInfo.myBonds[j]->is_constrained()) |
| 649 |
> |
} |
| 650 |
> |
|
| 651 |
> |
//loop over rigid bodies, if two rigid bodies share same joint, creat a JointConstraintPair |
| 652 |
> |
for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){ |
| 653 |
> |
for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){ |
| 654 |
> |
|
| 655 |
> |
jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2); |
| 656 |
|
|
| 657 |
+ |
for(size_t m = 0; m < jointAtoms.size(); m++){ |
| 658 |
+ |
consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first); |
| 659 |
+ |
consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second); |
| 660 |
|
|
| 661 |
+ |
consPair = new JointConstraintPair(consElement1, consElement2); |
| 662 |
+ |
molInfo.myConstraintPairs.push_back(consPair); |
| 663 |
+ |
} |
| 664 |
+ |
|
| 665 |
+ |
} |
| 666 |
+ |
} |
| 667 |
+ |
|
| 668 |
+ |
|
| 669 |
+ |
info[k].molecules[i].initialize(molInfo); |
| 670 |
+ |
|
| 671 |
+ |
|
| 672 |
|
atomOffset += molInfo.nAtoms; |
| 673 |
|
delete[] theBonds; |
| 674 |
|
delete[] theBends; |
| 675 |
|
delete[] theTorsions; |
| 676 |
< |
} |
| 676 |
> |
} |
| 677 |
> |
|
| 678 |
> |
|
| 679 |
> |
|
| 680 |
> |
#ifdef IS_MPI |
| 681 |
> |
// Since the globalGroupMembership has been zero filled and we've only |
| 682 |
> |
// poked values into the atoms we know, we can do an Allreduce |
| 683 |
> |
// to get the full globalGroupMembership array (We think). |
| 684 |
> |
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
| 685 |
> |
// docs said we could. |
| 686 |
> |
|
| 687 |
> |
int* ggMjunk = new int[mpiSim->getNAtomsGlobal()]; |
| 688 |
> |
|
| 689 |
> |
MPI_Allreduce(info[k].globalGroupMembership, |
| 690 |
> |
ggMjunk, |
| 691 |
> |
mpiSim->getNAtomsGlobal(), |
| 692 |
> |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 693 |
> |
|
| 694 |
> |
for (i = 0; i < mpiSim->getNAtomsGlobal(); i++) |
| 695 |
> |
info[k].globalGroupMembership[i] = ggMjunk[i]; |
| 696 |
> |
|
| 697 |
> |
delete[] ggMjunk; |
| 698 |
> |
|
| 699 |
> |
#endif |
| 700 |
> |
|
| 701 |
> |
|
| 702 |
> |
|
| 703 |
|
} |
| 704 |
|
|
| 705 |
|
#ifdef IS_MPI |
| 1072 |
|
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
| 1073 |
|
|
| 1074 |
|
// check for thermodynamic integration |
| 1075 |
< |
if (globals->getUseThermInt()) { |
| 1075 |
> |
if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) { |
| 1076 |
|
if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
| 1077 |
< |
info[i].useThermInt = globals->getUseThermInt(); |
| 1077 |
> |
info[i].useSolidThermInt = globals->getUseSolidThermInt(); |
| 1078 |
|
info[i].thermIntLambda = globals->getThermIntLambda(); |
| 1079 |
|
info[i].thermIntK = globals->getThermIntK(); |
| 1080 |
|
|
| 1084 |
|
else { |
| 1085 |
|
sprintf(painCave.errMsg, |
| 1086 |
|
"SimSetup Error:\n" |
| 1087 |
< |
"\tKeyword useThermInt was set to 'true' but\n" |
| 1087 |
> |
"\tKeyword useSolidThermInt was set to 'true' but\n" |
| 1088 |
> |
"\tthermodynamicIntegrationLambda (and/or\n" |
| 1089 |
> |
"\tthermodynamicIntegrationK) was not specified.\n" |
| 1090 |
> |
"\tPlease provide a lambda value and k value in your .bass file.\n"); |
| 1091 |
> |
painCave.isFatal = 1; |
| 1092 |
> |
simError(); |
| 1093 |
> |
} |
| 1094 |
> |
} |
| 1095 |
> |
else if(globals->getUseLiquidThermInt()) { |
| 1096 |
> |
if (globals->getUseSolidThermInt()) { |
| 1097 |
> |
sprintf( painCave.errMsg, |
| 1098 |
> |
"SimSetup Warning: It appears that you have both solid and\n" |
| 1099 |
> |
"\tliquid thermodynamic integration activated in your .bass\n" |
| 1100 |
> |
"\tfile. To avoid confusion, specify only one technique in\n" |
| 1101 |
> |
"\tyour .bass file. Liquid-state thermodynamic integration\n" |
| 1102 |
> |
"\twill be assumed for the current simulation. If this is not\n" |
| 1103 |
> |
"\twhat you desire, set useSolidThermInt to 'true' and\n" |
| 1104 |
> |
"\tuseLiquidThermInt to 'false' in your .bass file.\n"); |
| 1105 |
> |
painCave.isFatal = 0; |
| 1106 |
> |
simError(); |
| 1107 |
> |
} |
| 1108 |
> |
if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
| 1109 |
> |
info[i].useLiquidThermInt = globals->getUseLiquidThermInt(); |
| 1110 |
> |
info[i].thermIntLambda = globals->getThermIntLambda(); |
| 1111 |
> |
info[i].thermIntK = globals->getThermIntK(); |
| 1112 |
> |
} |
| 1113 |
> |
else { |
| 1114 |
> |
sprintf(painCave.errMsg, |
| 1115 |
> |
"SimSetup Error:\n" |
| 1116 |
> |
"\tKeyword useLiquidThermInt was set to 'true' but\n" |
| 1117 |
|
"\tthermodynamicIntegrationLambda (and/or\n" |
| 1118 |
|
"\tthermodynamicIntegrationK) was not specified.\n" |
| 1119 |
|
"\tPlease provide a lambda value and k value in your .bass file.\n"); |
| 1124 |
|
else if(globals->haveThermIntLambda() || globals->haveThermIntK()){ |
| 1125 |
|
sprintf(painCave.errMsg, |
| 1126 |
|
"SimSetup Warning: If you want to use Thermodynamic\n" |
| 1127 |
< |
"\tIntegration, set useThermInt to 'true' in your .bass file.\n" |
| 1128 |
< |
"\tThe useThermInt keyword is 'false' by default, so your\n" |
| 1129 |
< |
"\tlambda and/or k values are being ignored.\n"); |
| 1127 |
> |
"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n" |
| 1128 |
> |
"\t'true' in your .bass file. These keywords are set to\n" |
| 1129 |
> |
"\t'false' by default, so your lambda and/or k values are\n" |
| 1130 |
> |
"\tbeing ignored.\n"); |
| 1131 |
|
painCave.isFatal = 0; |
| 1132 |
|
simError(); |
| 1133 |
|
} |
| 1652 |
|
int i, j, k; |
| 1653 |
|
int localMol, allMol; |
| 1654 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 1655 |
< |
int local_rigid; |
| 1655 |
> |
int local_rigid, local_groups; |
| 1656 |
|
vector<int> globalMolIndex; |
| 1657 |
+ |
int ncutgroups, atomsingroups, ngroupsinstamp; |
| 1658 |
+ |
CutoffGroupStamp* cg; |
| 1659 |
|
|
| 1660 |
|
mpiSim = new mpiSimulation(info); |
| 1661 |
|
|
| 1662 |
|
mpiSim->divideLabor(); |
| 1663 |
|
globalAtomIndex = mpiSim->getGlobalAtomIndex(); |
| 1664 |
+ |
globalGroupIndex = mpiSim->getGlobalGroupIndex(); |
| 1665 |
|
//globalMolIndex = mpiSim->getGlobalMolIndex(); |
| 1666 |
|
|
| 1667 |
|
// set up the local variables |
| 1676 |
|
local_bends = 0; |
| 1677 |
|
local_torsions = 0; |
| 1678 |
|
local_rigid = 0; |
| 1679 |
+ |
local_groups = 0; |
| 1680 |
|
globalAtomCounter = 0; |
| 1681 |
|
|
| 1682 |
|
for (i = 0; i < n_components; i++){ |
| 1687 |
|
local_bends += comp_stamps[i]->getNBends(); |
| 1688 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
| 1689 |
|
local_rigid += comp_stamps[i]->getNRigidBodies(); |
| 1690 |
+ |
|
| 1691 |
+ |
ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
| 1692 |
+ |
atomsingroups = 0; |
| 1693 |
+ |
for (k=0; k < ncutgroups; k++) { |
| 1694 |
+ |
cg = comp_stamps[i]->getCutoffGroup(k); |
| 1695 |
+ |
atomsingroups += cg->getNMembers(); |
| 1696 |
+ |
} |
| 1697 |
+ |
ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + |
| 1698 |
+ |
ncutgroups; |
| 1699 |
+ |
local_groups += ngroupsinstamp; |
| 1700 |
+ |
|
| 1701 |
|
localMol++; |
| 1702 |
|
} |
| 1703 |
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
| 1712 |
|
|
| 1713 |
|
info[0].n_atoms = mpiSim->getNAtomsLocal(); |
| 1714 |
|
|
| 1548 |
– |
|
| 1715 |
|
if (local_atoms != info[0].n_atoms){ |
| 1716 |
|
sprintf(painCave.errMsg, |
| 1717 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
| 1721 |
|
simError(); |
| 1722 |
|
} |
| 1723 |
|
|
| 1724 |
+ |
info[0].ngroup = mpiSim->getNGroupsLocal(); |
| 1725 |
+ |
if (local_groups != info[0].ngroup){ |
| 1726 |
+ |
sprintf(painCave.errMsg, |
| 1727 |
+ |
"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n" |
| 1728 |
+ |
"\tlocalGroups (%d) are not equal.\n", |
| 1729 |
+ |
info[0].ngroup, local_groups); |
| 1730 |
+ |
painCave.isFatal = 1; |
| 1731 |
+ |
simError(); |
| 1732 |
+ |
} |
| 1733 |
+ |
|
| 1734 |
|
info[0].n_bonds = local_bonds; |
| 1735 |
|
info[0].n_bends = local_bends; |
| 1736 |
|
info[0].n_torsions = local_torsions; |
