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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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//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 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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|
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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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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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#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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|
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if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
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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); |
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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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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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notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
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// also send cutoff notification to electrostatics |
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setElectrostaticCutoffRadius(&rcut_); |
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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; |
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double dielectric; |
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|
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errorOut = isError; |
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alphaVal = simParams_->getDampingAlpha(); |
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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 == "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; |
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} else { |
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if (myMethod == "DAMPED_WOLF") { |
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esm = DAMPED_WOLF; |
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if (!simParams_->haveDampingAlpha()) { |
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//throw error |
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sprintf( painCave.errMsg, |
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"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); |
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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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if (myMethod == "REACTION_FIELD") { |
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esm = REACTION_FIELD; |
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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 electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.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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// let's pass some summation method variables to fortran |
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setElectrostaticSummationMethod( &esm ); |
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setDampedWolfAlpha( &alphaVal ); |
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setReactionFieldDielectric( &dielectric ); |
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initFortranFF( &esm, &errorOut ); |
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} |
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|
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void SimInfo::addProperty(GenericData* genData) { |
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properties_.addProperty(genData); |
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} |
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|
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/* |
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Return intertia tensor for entire system and angular momentum Vector. |
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|
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|
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[ Ixx -Ixy -Ixz ] |
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J =| -Iyx Iyy -Iyz | |
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[ -Izx -Iyz Izz ] |
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*/ |
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|
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void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
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inertiaTensor(0,1) = -xy; |
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inertiaTensor(0,2) = -xz; |
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inertiaTensor(1,0) = -xy; |
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inertiaTensor(2,0) = xx + zz; |
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inertiaTensor(1,1) = xx + zz; |
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inertiaTensor(1,2) = -yz; |
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inertiaTensor(2,0) = -xz; |
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inertiaTensor(2,1) = -yz; |
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SimInfo::MoleculeIterator i; |
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Molecule* mol; |
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|
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Vector3d thisq(0.0); |
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< |
Vector3d thisv(0.0); |
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> |
Vector3d thisr(0.0); |
1142 |
> |
Vector3d thisp(0.0); |
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|
|
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< |
double thisMass = 0.0; |
1144 |
> |
double thisMass; |
1145 |
|
|
1146 |
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for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1147 |
< |
thisq = mol->getCom()-com; |
1148 |
< |
thisv = mol->getComVel()-comVel; |
1149 |
< |
thisMass = mol->getMass(); |
1072 |
< |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1147 |
> |
thisMass = mol->getMass(); |
1148 |
> |
thisr = mol->getCom()-com; |
1149 |
> |
thisp = (mol->getComVel()-comVel)*thisMass; |
1150 |
|
|
1151 |
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angularMomentum += cross( thisr, thisp ); |
1152 |
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|
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} |
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|
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#ifdef IS_MPI |