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#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h" |
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#include "UseTheForce/DarkSide/fSwitchingFunctionType.h" |
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#include "UseTheForce/doForces_interface.h" |
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#include "UseTheForce/DarkSide/neighborLists_interface.h" |
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#include "UseTheForce/DarkSide/electrostatic_interface.h" |
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#include "UseTheForce/DarkSide/switcheroo_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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#include "io/ForceFieldOptions.hpp" |
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#include "UseTheForce/ForceField.hpp" |
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|
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|
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#ifdef IS_MPI |
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#include "UseTheForce/mpiComponentPlan.h" |
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#include "UseTheForce/DarkSide/simParallel_interface.h" |
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// set the useRF logical |
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useRF = 0; |
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useSF = 0; |
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useSP = 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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useRF = 1; |
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} else if (myMethod == "SHIFTED_FORCE"){ |
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useSF = 1; |
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} else if (myMethod == "SHIFTED_POTENTIAL"){ |
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fInfo_.SIM_uses_SF = useSF; |
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fInfo_.SIM_uses_SP = useSP; |
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fInfo_.SIM_uses_BoxDipole = useBoxDipole; |
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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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sprintf(painCave.errMsg, |
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"SimSetup Error: No Dielectric constant was set.\n" |
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"\tYou are trying to use Reaction Field without" |
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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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|
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} |
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|
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void SimInfo::setupFortranSim() { |
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"succesfully sent the simulation information to fortran.\n"); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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|
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// Setup number of neighbors in neighbor list if present |
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if (simParams_->haveNeighborListNeighbors()) { |
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int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
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setNeighbors(&nlistNeighbors); |
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} |
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|
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|
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} |
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|
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|
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RealType dielectric; |
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|
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errorOut = isError; |
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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(); |
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if (myMethod == "SHIFTED_FORCE") { |
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esm = SHIFTED_FORCE; |
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} else { |
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if (myMethod == "REACTION_FIELD") { |
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if (myMethod == "REACTION_FIELD") { |
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esm = REACTION_FIELD; |
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dielectric = simParams_->getDielectric(); |
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if (!simParams_->haveDielectric()) { |
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// throw warning |
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sprintf( painCave.errMsg, |
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"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n" |
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"\tA default value of %f will be used for the dielectric.\n", dielectric); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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} else { |
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// throw error |
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sprintf( painCave.errMsg, |
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"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_); |
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painCave.isFatal = 0; |
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simError(); |
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} else { |
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alphaVal = simParams_->getDampingAlpha(); |
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} |
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|
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} else { |
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// throw error |
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sprintf( painCave.errMsg, |
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|
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void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) { |
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IOIndexToIntegrableObject= v; |
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} |
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|
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/* Returns the Volume of the simulation based on a ellipsoid with semi-axes |
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based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3 |
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where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to |
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V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536. |
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*/ |
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void SimInfo::getGyrationalVolume(RealType &volume){ |
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Mat3x3d intTensor; |
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RealType det; |
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Vector3d dummyAngMom; |
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RealType sysconstants; |
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RealType geomCnst; |
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|
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geomCnst = 3.0/2.0; |
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/* Get the inertial tensor and angular momentum for free*/ |
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getInertiaTensor(intTensor,dummyAngMom); |
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|
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det = intTensor.determinant(); |
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sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
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volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det); |
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return; |
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} |
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|
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void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){ |
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Mat3x3d intTensor; |
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Vector3d dummyAngMom; |
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RealType sysconstants; |
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RealType geomCnst; |
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|
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geomCnst = 3.0/2.0; |
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/* Get the inertial tensor and angular momentum for free*/ |
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getInertiaTensor(intTensor,dummyAngMom); |
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|
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detI = intTensor.determinant(); |
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sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
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volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI); |
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return; |
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} |
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/* |
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void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) { |
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assert( v.size() == nAtoms_ + nRigidBodies_); |
