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#include "UseTheForce/fCutoffPolicy.h" |
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#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
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#include "UseTheForce/doForces_interface.h" |
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#include "UseTheForce/DarkSide/electrostatic_interface.h" |
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#include "UseTheForce/notifyCutoffs_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
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MoleculeStamp* molStamp; |
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int nMolWithSameStamp; |
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int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
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int nGroups = 0; //total cutoff groups defined in meta-data file |
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int nGroups = 0; //total cutoff groups defined in meta-data file |
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CutoffGroupStamp* cgStamp; |
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RigidBodyStamp* rbStamp; |
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int nRigidAtoms = 0; |
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} |
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|
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nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
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|
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nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
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|
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//calculate atoms in rigid bodies |
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|
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} |
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|
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//every free atom (atom does not belong to cutoff groups) is a cutoff group |
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//therefore the total number of cutoff groups in the system is equal to |
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//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
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//file plus the number of cutoff groups defined in meta-data file |
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//every free atom (atom does not belong to cutoff groups) is a cutoff |
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//group therefore the total number of cutoff groups in the system is |
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//equal to the total number of atoms minus number of atoms belong to |
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//cutoff group defined in meta-data file plus the number of cutoff |
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//groups defined in meta-data file |
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nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
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|
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//every free atom (atom does not belong to rigid bodies) is an integrable object |
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//therefore the total number of integrable objects in the system is equal to |
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//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
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//file plus the number of rigid bodies defined in meta-data file |
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nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
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|
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//every free atom (atom does not belong to rigid bodies) is an |
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//integrable object therefore the total number of integrable objects |
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//in the system is equal to the total number of atoms minus number of |
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//atoms belong to rigid body defined in meta-data file plus the number |
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//of rigid bodies defined in meta-data file |
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nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms |
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+ nGlobalRigidBodies_; |
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|
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nGlobalMols_ = molStampIds_.size(); |
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|
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#ifdef IS_MPI |
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int useDirectionalAtom = 0; |
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int useElectrostatics = 0; |
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//usePBC and useRF are from simParams |
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int usePBC = simParams_->getPBC(); |
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int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
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int useRF; |
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int useDW; |
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std::string myMethod; |
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|
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// set the useRF logical |
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useRF = 0; |
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useDW = 0; |
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|
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|
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if (simParams_->haveElectrostaticSummationMethod()) { |
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std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
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toUpper(myMethod); |
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if (myMethod == "REACTION_FIELD") { |
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useRF=1; |
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} else { |
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if (myMethod == "DAMPED_WOLF") { |
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useDW = 1; |
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} |
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} |
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} |
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|
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//loop over all of the atom types |
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for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
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useLennardJones |= (*i)->isLennardJones(); |
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temp = useFLARB; |
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MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
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|
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temp = useRF; |
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MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
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|
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temp = useDW; |
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MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
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|
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#endif |
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|
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fInfo_.SIM_uses_PBC = usePBC; |
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fInfo_.SIM_uses_EAM = useEAM; |
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fInfo_.SIM_uses_Shapes = useShape; |
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fInfo_.SIM_uses_FLARB = useFLARB; |
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fInfo_.SIM_uses_RF = useRF; |
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fInfo_.SIM_uses_DampedWolf = useDW; |
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|
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if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
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|
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if( myMethod == "REACTION_FIELD") { |
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|
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if (simParams_->haveDielectric()) { |
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fInfo_.dielect = simParams_->getDielectric(); |
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} else { |
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"\tsetting a dielectric constant!\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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} else { |
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fInfo_.dielect = 0.0; |
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} |
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} |
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|
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} |
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|
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totalMass = cg->getMass(); |
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for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
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mfact.push_back(atom->getMass()/totalMass); |
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// Check for massless groups - set mfact to 1 if true |
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if (totalMass != 0) |
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mfact.push_back(atom->getMass()/totalMass); |
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else |
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mfact.push_back( 1.0 ); |
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} |
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|
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} |
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|
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if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
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|
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if (!simParams_->haveRcut()){ |
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if (!simParams_->haveCutoffRadius()){ |
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sprintf(painCave.errMsg, |
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"SimCreator Warning: No value was set for the cutoffRadius.\n" |
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"\tOOPSE will use a default value of 15.0 angstroms" |
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simError(); |
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rcut = 15.0; |
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} else{ |
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rcut = simParams_->getRcut(); |
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rcut = simParams_->getCutoffRadius(); |
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} |
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|
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if (!simParams_->haveRsw()){ |
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if (!simParams_->haveSwitchingRadius()){ |
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sprintf(painCave.errMsg, |
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"SimCreator Warning: No value was set for switchingRadius.\n" |
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"\tOOPSE will use a default value of\n" |
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"\t0.95 * cutoffRadius for the switchingRadius\n"); |
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"\t0.85 * cutoffRadius for the switchingRadius\n"); |
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painCave.isFatal = 0; |
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simError(); |
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rsw = 0.95 * rcut; |
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rsw = 0.85 * rcut; |
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} else{ |
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rsw = simParams_->getRsw(); |
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rsw = simParams_->getSwitchingRadius(); |
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} |
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|
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} else { |
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// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
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//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
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|
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if (simParams_->haveRcut()) { |
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rcut = simParams_->getRcut(); |
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if (simParams_->haveCutoffRadius()) { |
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rcut = simParams_->getCutoffRadius(); |
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} else { |
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//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
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rcut = calcMaxCutoffRadius(); |
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} |
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|
857 |
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if (simParams_->haveRsw()) { |
858 |
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rsw = simParams_->getRsw(); |
857 |
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if (simParams_->haveSwitchingRadius()) { |
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rsw = simParams_->getSwitchingRadius(); |
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} else { |
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rsw = rcut; |
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} |
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int cp = TRADITIONAL_CUTOFF_POLICY; |
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if (simParams_->haveCutoffPolicy()) { |
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std::string myPolicy = simParams_->getCutoffPolicy(); |
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toUpper(myPolicy); |
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if (myPolicy == "MIX") { |
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cp = MIX_CUTOFF_POLICY; |
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} else { |
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} |
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} |
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} |
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|
895 |
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|
896 |
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if (simParams_->haveSkinThickness()) { |
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double skinThickness = simParams_->getSkinThickness(); |
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} |
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|
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notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
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// also send cutoff notification to electrostatics |
902 |
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setElectrostaticCutoffRadius(&rcut_, &rsw_); |
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} |
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|
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void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
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int errorOut; |
908 |
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int esm = NONE; |
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double alphaVal; |
910 |
+ |
double dielectric; |
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|
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errorOut = isError; |
913 |
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alphaVal = simParams_->getDampingAlpha(); |
914 |
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dielectric = simParams_->getDielectric(); |
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|
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if (simParams_->haveElectrostaticSummationMethod()) { |
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std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
918 |
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toUpper(myMethod); |
919 |
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if (myMethod == "NONE") { |
920 |
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esm = NONE; |
921 |
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} else { |
927 |
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if (!simParams_->haveDampingAlpha()) { |
928 |
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//throw error |
929 |
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sprintf( painCave.errMsg, |
930 |
< |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", simParams_->getDampingAlpha()); |
930 |
> |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal); |
931 |
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painCave.isFatal = 0; |
932 |
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simError(); |
933 |
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} |
887 |
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alphaVal = simParams_->getDampingAlpha(); |
934 |
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} else { |
935 |
< |
if (myMethod == "REACTION_FIELD") { |
935 |
> |
if (myMethod == "REACTION_FIELD") { |
936 |
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esm = REACTION_FIELD; |
937 |
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} else { |
938 |
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// throw error |
945 |
|
} |
946 |
|
} |
947 |
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} |
948 |
< |
initFortranFF( &esm, &alphaVal, &errorOut ); |
948 |
> |
// let's pass some summation method variables to fortran |
949 |
> |
setElectrostaticSummationMethod( &esm ); |
950 |
> |
setDampedWolfAlpha( &alphaVal ); |
951 |
> |
setReactionFieldDielectric( &dielectric ); |
952 |
> |
initFortranFF( &esm, &errorOut ); |
953 |
|
} |
954 |
|
|
955 |
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void SimInfo::addProperty(GenericData* genData) { |