--- trunk/src/brains/SimInfo.cpp 2005/04/15 22:04:00 507 +++ trunk/src/brains/SimInfo.cpp 2005/09/15 00:14:35 598 @@ -52,6 +52,8 @@ #include "brains/SimInfo.hpp" #include "math/Vector3.hpp" #include "primitives/Molecule.hpp" +#include "UseTheForce/fCutoffPolicy.h" +#include "UseTheForce/fCoulombicCorrection.h" #include "UseTheForce/doForces_interface.h" #include "UseTheForce/notifyCutoffs_interface.h" #include "utils/MemoryUtils.hpp" @@ -462,7 +464,9 @@ namespace oopse { //setup fortran force field /** @deprecate */ int isError = 0; - initFortranFF( &fInfo_.SIM_uses_RF , &isError ); + + setupCoulombicCorrection( isError ); + if(isError){ sprintf( painCave.errMsg, "ForceField error: There was an error initializing the forceField in fortran.\n" ); @@ -511,6 +515,7 @@ namespace oopse { int useDipole = 0; int useGayBerne = 0; int useSticky = 0; + int useStickyPower = 0; int useShape = 0; int useFLARB = 0; //it is not in AtomType yet int useDirectionalAtom = 0; @@ -529,10 +534,11 @@ namespace oopse { useDipole |= (*i)->isDipole(); useGayBerne |= (*i)->isGayBerne(); useSticky |= (*i)->isSticky(); + useStickyPower |= (*i)->isStickyPower(); useShape |= (*i)->isShape(); } - if (useSticky || useDipole || useGayBerne || useShape) { + if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) { useDirectionalAtom = 1; } @@ -564,6 +570,9 @@ namespace oopse { temp = useSticky; MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + temp = useStickyPower; + MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + temp = useGayBerne; MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); @@ -578,6 +587,12 @@ namespace oopse { temp = useRF; MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + + temp = useUW; + MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); + + temp = useDW; + MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); #endif @@ -588,6 +603,7 @@ namespace oopse { fInfo_.SIM_uses_Charges = useCharge; fInfo_.SIM_uses_Dipoles = useDipole; fInfo_.SIM_uses_Sticky = useSticky; + fInfo_.SIM_uses_StickyPower = useStickyPower; fInfo_.SIM_uses_GayBerne = useGayBerne; fInfo_.SIM_uses_EAM = useEAM; fInfo_.SIM_uses_Shapes = useShape; @@ -824,14 +840,79 @@ namespace oopse { } } - void SimInfo::setupCutoff() { + void SimInfo::setupCutoff() { getCutoff(rcut_, rsw_); double rnblist = rcut_ + 1; // skin of neighbor list //Pass these cutoff radius etc. to fortran. This function should be called once and only once - notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); + + int cp = TRADITIONAL_CUTOFF_POLICY; + if (simParams_->haveCutoffPolicy()) { + std::string myPolicy = simParams_->getCutoffPolicy(); + if (myPolicy == "MIX") { + cp = MIX_CUTOFF_POLICY; + } else { + if (myPolicy == "MAX") { + cp = MAX_CUTOFF_POLICY; + } else { + if (myPolicy == "TRADITIONAL") { + cp = TRADITIONAL_CUTOFF_POLICY; + } else { + // throw error + sprintf( painCave.errMsg, + "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); + painCave.isFatal = 1; + simError(); + } + } + } + } + notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); } + void SimInfo::setupCoulombicCorrection( int isError ) { + + int errorOut; + int cc = NONE; + double alphaVal; + + errorOut = isError; + + if (simParams_->haveCoulombicCorrection()) { + std::string myCorrection = simParams_->getCoulombicCorrection(); + if (myCorrection == "NONE") { + cc = NONE; + } else { + if (myCorrection == "UNDAMPED_WOLF") { + cc = UNDAMPED_WOLF; + } else { + if (myCorrection == "WOLF") { + cc = WOLF; + if (!simParams_->haveDampingAlpha()) { + //throw error + sprintf( painCave.errMsg, + "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Wolf Coulombic Correction.", simParams_->getDampingAlpha()); + painCave.isFatal = 0; + simError(); + } + alphaVal = simParams_->getDampingAlpha(); + } else { + if (myCorrection == "REACTION_FIELD") { + cc = REACTION_FIELD; + } else { + // throw error + sprintf( painCave.errMsg, + "SimInfo error: Unknown coulombicCorrection. (Input file specified %s .)\n\tcoulombicCorrection must be one of: \"none\", \"undamped_wolf\", \"wolf\", or \"reaction_field\".", myCorrection.c_str() ); + painCave.isFatal = 1; + simError(); + } + } + } + } + } + initFortranFF( &fInfo_.SIM_uses_RF, &cc, &alphaVal, &errorOut ); + } + void SimInfo::addProperty(GenericData* genData) { properties_.addProperty(genData); } @@ -939,6 +1020,148 @@ namespace oopse { return o; } + + + /* + Returns center of mass and center of mass velocity in one function call. + */ + + void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ + SimInfo::MoleculeIterator i; + Molecule* mol; + + + double totalMass = 0.0; + + for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { + double mass = mol->getMass(); + totalMass += mass; + com += mass * mol->getCom(); + comVel += mass * mol->getComVel(); + } + +#ifdef IS_MPI + double tmpMass = totalMass; + Vector3d tmpCom(com); + Vector3d tmpComVel(comVel); + MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); +#endif + + com /= totalMass; + comVel /= totalMass; + } + + /* + Return intertia tensor for entire system and angular momentum Vector. + + + [ Ixx -Ixy -Ixz ] + J =| -Iyx Iyy -Iyz | + [ -Izx -Iyz Izz ] + */ + + void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ + + + double xx = 0.0; + double yy = 0.0; + double zz = 0.0; + double xy = 0.0; + double xz = 0.0; + double yz = 0.0; + Vector3d com(0.0); + Vector3d comVel(0.0); + + getComAll(com, comVel); + + SimInfo::MoleculeIterator i; + Molecule* mol; + + Vector3d thisq(0.0); + Vector3d thisv(0.0); + + double thisMass = 0.0; + + + + + for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { + + thisq = mol->getCom()-com; + thisv = mol->getComVel()-comVel; + thisMass = mol->getMass(); + // Compute moment of intertia coefficients. + xx += thisq[0]*thisq[0]*thisMass; + yy += thisq[1]*thisq[1]*thisMass; + zz += thisq[2]*thisq[2]*thisMass; + + // compute products of intertia + xy += thisq[0]*thisq[1]*thisMass; + xz += thisq[0]*thisq[2]*thisMass; + yz += thisq[1]*thisq[2]*thisMass; + + angularMomentum += cross( thisq, thisv ) * thisMass; + + } + + + inertiaTensor(0,0) = yy + zz; + inertiaTensor(0,1) = -xy; + inertiaTensor(0,2) = -xz; + inertiaTensor(1,0) = -xy; + inertiaTensor(1,1) = xx + zz; + inertiaTensor(1,2) = -yz; + inertiaTensor(2,0) = -xz; + inertiaTensor(2,1) = -yz; + inertiaTensor(2,2) = xx + yy; + +#ifdef IS_MPI + Mat3x3d tmpI(inertiaTensor); + Vector3d tmpAngMom; + MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); + MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); +#endif + + return; + } + + //Returns the angular momentum of the system + Vector3d SimInfo::getAngularMomentum(){ + + Vector3d com(0.0); + Vector3d comVel(0.0); + Vector3d angularMomentum(0.0); + + getComAll(com,comVel); + + SimInfo::MoleculeIterator i; + Molecule* mol; + + Vector3d thisr(0.0); + Vector3d thisp(0.0); + + double thisMass; + + for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { + thisMass = mol->getMass(); + thisr = mol->getCom()-com; + thisp = (mol->getComVel()-comVel)*thisMass; + + angularMomentum += cross( thisr, thisp ); + + } + +#ifdef IS_MPI + Vector3d tmpAngMom; + MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); +#endif + + return angularMomentum; + } + + }//end namespace oopse