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#include "brains/SimInfo.hpp" |
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#include "math/Vector3.hpp" |
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#include "primitives/Molecule.hpp" |
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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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//setup fortran force field |
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/** @deprecate */ |
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int isError = 0; |
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initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
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|
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setupElectrostaticSummationMethod( isError ); |
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|
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if(isError){ |
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sprintf( painCave.errMsg, |
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"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
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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 useRF = simParams_->getUseRF(); |
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int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
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int useRF; |
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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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if (simParams_->haveElectrostaticSummationMethod()) { |
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myMethod = simParams_->getElectrostaticSummationMethod(); |
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if (myMethod == "REACTION_FIELD") |
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useRF = 1; |
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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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|
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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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|
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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_FLARB = useFLARB; |
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fInfo_.SIM_uses_RF = useRF; |
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|
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if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
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if( fInfo_.SIM_uses_Dipoles && 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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|
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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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simError(); |
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rsw = 0.95 * 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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|
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if (simParams_->haveRsw()) { |
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rsw = simParams_->getRsw(); |
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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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} |
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} |
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|
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void SimInfo::setupCutoff() { |
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void SimInfo::setupCutoff() { |
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getCutoff(rcut_, rsw_); |
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double rnblist = rcut_ + 1; // skin of neighbor list |
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|
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//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
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notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
860 |
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|
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int cp = TRADITIONAL_CUTOFF_POLICY; |
862 |
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if (simParams_->haveCutoffPolicy()) { |
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std::string myPolicy = simParams_->getCutoffPolicy(); |
864 |
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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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if (myPolicy == "MAX") { |
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cp = MAX_CUTOFF_POLICY; |
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} else { |
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if (myPolicy == "TRADITIONAL") { |
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cp = TRADITIONAL_CUTOFF_POLICY; |
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} else { |
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// throw error |
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sprintf( painCave.errMsg, |
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"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
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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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|
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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 |
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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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|
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int errorOut; |
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int esm = NONE; |
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> |
double alphaVal; |
899 |
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double dielectric; |
900 |
> |
|
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errorOut = isError; |
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alphaVal = simParams_->getDampingAlpha(); |
903 |
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dielectric = simParams_->getDielectric(); |
904 |
> |
|
905 |
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if (simParams_->haveElectrostaticSummationMethod()) { |
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> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
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> |
toUpper(myMethod); |
908 |
> |
if (myMethod == "NONE") { |
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> |
esm = NONE; |
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> |
} else { |
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> |
if (myMethod == "UNDAMPED_WOLF") { |
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> |
esm = UNDAMPED_WOLF; |
913 |
> |
} else { |
914 |
> |
if (myMethod == "DAMPED_WOLF") { |
915 |
> |
esm = DAMPED_WOLF; |
916 |
> |
if (!simParams_->haveDampingAlpha()) { |
917 |
> |
//throw error |
918 |
> |
sprintf( painCave.errMsg, |
919 |
> |
"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); |
920 |
> |
painCave.isFatal = 0; |
921 |
> |
simError(); |
922 |
> |
} |
923 |
> |
} else { |
924 |
> |
if (myMethod == "REACTION_FIELD") { |
925 |
> |
esm = REACTION_FIELD; |
926 |
> |
} else { |
927 |
> |
// throw error |
928 |
> |
sprintf( painCave.errMsg, |
929 |
> |
"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() ); |
930 |
> |
painCave.isFatal = 1; |
931 |
> |
simError(); |
932 |
> |
} |
933 |
> |
} |
934 |
> |
} |
935 |
> |
} |
936 |
> |
} |
937 |
> |
// let's pass some summation method variables to fortran |
938 |
> |
setElectrostaticSummationMethod( &esm ); |
939 |
> |
setDampedWolfAlpha( &alphaVal ); |
940 |
> |
setReactionFieldDielectric( &dielectric ); |
941 |
> |
initFortranFF( &esm, &errorOut ); |
942 |
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} |
943 |
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|
944 |
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void SimInfo::addProperty(GenericData* genData) { |
1084 |
|
|
1085 |
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/* |
1086 |
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Return intertia tensor for entire system and angular momentum Vector. |
1087 |
+ |
|
1088 |
+ |
|
1089 |
+ |
[ Ixx -Ixy -Ixz ] |
1090 |
+ |
J =| -Iyx Iyy -Iyz | |
1091 |
+ |
[ -Izx -Iyz Izz ] |
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*/ |
1093 |
|
|
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void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1140 |
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inertiaTensor(0,1) = -xy; |
1141 |
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inertiaTensor(0,2) = -xz; |
1142 |
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inertiaTensor(1,0) = -xy; |
1143 |
< |
inertiaTensor(2,0) = xx + zz; |
1143 |
> |
inertiaTensor(1,1) = xx + zz; |
1144 |
|
inertiaTensor(1,2) = -yz; |
1145 |
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inertiaTensor(2,0) = -xz; |
1146 |
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inertiaTensor(2,1) = -yz; |
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SimInfo::MoleculeIterator i; |
1169 |
|
Molecule* mol; |
1170 |
|
|
1171 |
< |
Vector3d thisq(0.0); |
1172 |
< |
Vector3d thisv(0.0); |
1171 |
> |
Vector3d thisr(0.0); |
1172 |
> |
Vector3d thisp(0.0); |
1173 |
|
|
1174 |
< |
double thisMass = 0.0; |
1174 |
> |
double thisMass; |
1175 |
|
|
1176 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1177 |
< |
thisq = mol->getCom()-com; |
1178 |
< |
thisv = mol->getComVel()-comVel; |
1179 |
< |
thisMass = mol->getMass(); |
1072 |
< |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1177 |
> |
thisMass = mol->getMass(); |
1178 |
> |
thisr = mol->getCom()-com; |
1179 |
> |
thisp = (mol->getComVel()-comVel)*thisMass; |
1180 |
|
|
1181 |
+ |
angularMomentum += cross( thisr, thisp ); |
1182 |
+ |
|
1183 |
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} |
1184 |
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|
1185 |
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#ifdef IS_MPI |