--- trunk/src/brains/SimInfo.cpp 2005/04/15 22:04:00 507 +++ trunk/src/brains/SimInfo.cpp 2005/08/30 18:23:50 580 @@ -462,7 +462,8 @@ namespace oopse { //setup fortran force field /** @deprecate */ int isError = 0; - initFortranFF( &fInfo_.SIM_uses_RF , &isError ); + initFortranFF( &fInfo_.SIM_uses_RF, &fInfo_.SIM_uses_UW, + &fInfo_.SIM_uses_DW, &isError ); if(isError){ sprintf( painCave.errMsg, "ForceField error: There was an error initializing the forceField in fortran.\n" ); @@ -511,6 +512,7 @@ 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; @@ -518,6 +520,8 @@ namespace oopse { //usePBC and useRF are from simParams int usePBC = simParams_->getPBC(); int useRF = simParams_->getUseRF(); + int useUW = simParams_->getUseUndampedWolf(); + int useDW = simParams_->getUseDampedWolf(); //loop over all of the atom types for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { @@ -529,10 +533,11 @@ 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 +569,9 @@ 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 +586,12 @@ 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 @@ -588,11 +602,14 @@ 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; fInfo_.SIM_uses_FLARB = useFLARB; fInfo_.SIM_uses_RF = useRF; + fInfo_.SIM_uses_UW = useUW; + fInfo_.SIM_uses_DW = useDW; if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { @@ -939,6 +956,148 @@ 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