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#include "Integrator.hpp" |
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#include "simError.h" |
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#include "RigidBody.hpp" |
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//#include "ConjugateMinimizer.hpp" |
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#include "OOPSEMinimizer.hpp" |
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//#include "ConstraintElement.hpp" |
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//#include "ConstraintPair.hpp" |
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|
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#ifdef IS_MPI |
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#include "mpiBASS.h" |
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char* molName; |
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char rbName[100]; |
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|
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//ConstraintPair* consPair; //constraint pair |
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//ConstraintElement* consElement1; //first element of constraint pair |
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//ConstraintElement* consElement2; //second element of constraint pair |
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//int whichRigidBody; |
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//int consAtomIndex; //index of constraint atom in rigid body's atom array |
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//vector<pair<int, int> > jointAtoms; |
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//init the forceField paramters |
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|
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the_ff->readParams(); |
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the_ff->setSimInfo(&(info[k])); |
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|
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atomOffset = 0; |
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groupOffset = 0; |
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|
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for (i = 0; i < info[k].n_mol; i++){ |
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stampID = info[k].molecules[i].getStampID(); |
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nMembers = currentCutoffGroup->getNMembers(); |
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|
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myCutoffGroup = new CutoffGroup(); |
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myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]); |
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|
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for (int cg = 0; cg < nMembers; cg++) { |
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// tempI is atom numbering on local processor |
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tempI = molI + atomOffset; |
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| 518 |
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|
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#ifdef IS_MPI |
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globalID = info[k].atoms[tempI]->getGlobalIndex() |
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#else |
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globalID = info[k].atoms[tempI]->getIndex(); |
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#endif |
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|
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globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset]; |
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|
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myCutoffGroup->addAtom(info[k].atoms[tempI]); |
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|
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cutoffAtomSet.insert(tempI); |
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} |
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| 531 |
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|
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molInfo.myCutoffGroups.push_back(myCutoffGroup); |
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groupOffset++; |
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|
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}//end for (j = 0; j < molInfo.nCutoffGroups; j++) |
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|
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//creat a cutoff group for every atom in current molecule which does not belong to cutoffgroup defined at mdl file |
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if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){ |
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myCutoffGroup = new CutoffGroup(); |
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myCutoffGroup->addAtom(molInfo.myAtoms[j]); |
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myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]); |
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#ifdef IS_MPI |
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globalID = info[k].atoms[atomOffset + j]->getGlobalIndex() |
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#else |
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globalID = info[k].atoms[atomOffset + j]->getIndex(); |
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#endif |
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globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset]; |
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molInfo.myCutoffGroups.push_back(myCutoffGroup); |
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groupOffset++; |
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} |
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|
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} |
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// After this is all set up, scan through the atoms to |
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// see if they can be added to the integrableObjects: |
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|
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info[k].integrableObjects.push_back(mySD); |
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molInfo.myIntegrableObjects.push_back(mySD); |
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} |
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|
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|
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/* |
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|
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//creat ConstraintPair. |
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molInfo.myConstraintPair.clear(); |
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|
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for (j = 0; j < molInfo.nBonds; j++){ |
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|
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//if both atoms are in the same rigid body, just skip it |
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currentBond = comp_stamps[stampID]->getBond(j); |
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if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){ |
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|
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tempI = currentBond->getA() + atomOffset; |
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if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex)) |
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consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex); |
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else |
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consElement1 = new ConstraintAtom(info[k].atoms[tempI]); |
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> |
|
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tempJ = currentBond->getB() + atomOffset; |
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if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex)) |
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consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex); |
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else |
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consElement2 = new ConstraintAtom(info[k].atoms[tempJ]); |
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> |
|
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consPair = new DistanceConstraintPair(consElement1, consElement2); |
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molInfo.myConstraintPairs.push_back(consPair); |
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} |
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} |
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|
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> |
//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair |
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> |
for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){ |
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for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){ |
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|
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jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2); |
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> |
|
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for(size_t m = 0; m < jointAtoms.size(); m++){ |
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consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first); |
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consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second); |
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> |
|
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> |
consPair = new JointConstraintPair(consElement1, consElement2); |
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> |
molInfo.myConstraintPairs.push_back(consPair); |
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} |
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> |
|
| 631 |
> |
} |
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> |
} |
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|
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+ |
*/ |
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// send the arrays off to the forceField for init. |
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|
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the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
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info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
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|
| 1022 |
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// check for thermodynamic integration |
| 1023 |
< |
if (globals->getUseThermInt()) { |
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> |
if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) { |
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|
if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
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< |
info[i].useThermInt = globals->getUseThermInt(); |
| 1025 |
> |
info[i].useSolidThermInt = globals->getUseSolidThermInt(); |
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|
info[i].thermIntLambda = globals->getThermIntLambda(); |
| 1027 |
|
info[i].thermIntK = globals->getThermIntK(); |
| 1028 |
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|
| 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"); |
| 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"); |
| 1068 |
+ |
painCave.isFatal = 1; |
| 1069 |
+ |
simError(); |
| 1070 |
+ |
} |
| 1071 |
+ |
} |
| 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 |
|
} |
