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#include <iostream> |
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using namespace std; |
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#include <stdlib.h> |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif // is_mpi |
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#ifdef PROFILE |
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#include "mdProfile.hpp" |
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#endif |
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|
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#include "simError.h" |
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#include "ForceFields.hpp" |
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#include "Atom.hpp" |
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#include "fortranWrappers.hpp" |
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void ForceFields::calcRcut( void ){ |
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#ifdef IS_MPI |
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double tempBig = bigSigma; |
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MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX, |
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MPI_COMM_WORLD); |
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#endif //is_mpi |
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|
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//calc rCut and rList |
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|
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entry_plug->setDefaultRcut( 2.5 * bigSigma ); |
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} |
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void ForceFields::setRcut( double LJrcut ) { |
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#ifdef IS_MPI |
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double tempBig = bigSigma; |
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MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX, |
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MPI_COMM_WORLD); |
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#endif //is_mpi |
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|
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if (LJrcut < 2.5 * bigSigma) { |
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sprintf( painCave.errMsg, |
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"Setting Lennard-Jones cutoff radius to %lf.\n" |
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"\tThis value is smaller than %lf, which is\n" |
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"\t2.5 * bigSigma, where bigSigma is the largest\n" |
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"\tvalue of sigma present in the simulation.\n" |
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"\tThis is potentially a problem since the LJ potential may\n" |
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"\tbe appreciable at this distance. If you don't want the\n" |
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"\tsmaller cutoff, change the LJrcut variable.\n", |
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LJrcut, 2.5*bigSigma); |
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painCave.isFatal = 0; |
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simError(); |
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} else { |
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sprintf( painCave.errMsg, |
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"Setting Lennard-Jones cutoff radius to %lf.\n" |
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"\tThis value is larger than %lf, which is\n" |
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"\t2.5 * bigSigma, where bigSigma is the largest\n" |
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"\tvalue of sigma present in the simulation. This should\n" |
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"\tnot be a problem, but could adversely effect performance.\n", |
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LJrcut, 2.5*bigSigma); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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//calc rCut and rList |
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|
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entry_plug->setDefaultRcut( LJrcut ); |
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} |
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void ForceFields::doForces( int calcPot, int calcStress ){ |
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int i, j, isError; |
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double* frc; |
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double* pos; |
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double* trq; |
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double* A; |
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double* u_l; |
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double* rc; |
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double* massRatio; |
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double factor; |
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SimState* config; |
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|
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Molecule* myMols; |
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Atom** myAtoms; |
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int numAtom; |
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int curIndex; |
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double mtot; |
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int numMol; |
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int numCutoffGroups; |
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CutoffGroup* myCutoffGroup; |
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vector<CutoffGroup*>::iterator iterCutoff; |
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double com[3]; |
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vector<double> rcGroup; |
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short int passedCalcPot = (short int)calcPot; |
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short int passedCalcStress = (short int)calcStress; |
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|
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// forces are zeroed here, before any are accumulated. |
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// NOTE: do not rezero the forces in Fortran. |
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|
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for(i=0; i<entry_plug->n_atoms; i++){ |
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entry_plug->atoms[i]->zeroForces(); |
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} |
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#ifdef PROFILE |
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startProfile(pro7); |
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#endif |
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|
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for(i=0; i<entry_plug->n_mol; i++ ){ |
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// CalcForces in molecules takes care of mapping rigid body coordinates |
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// into atomic coordinates |
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entry_plug->molecules[i].calcForces(); |
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} |
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#ifdef PROFILE |
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endProfile( pro7 ); |
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#endif |
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config = entry_plug->getConfiguration(); |
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frc = config->getFrcArray(); |
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pos = config->getPosArray(); |
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trq = config->getTrqArray(); |
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A = config->getAmatArray(); |
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u_l = config->getUlArray(); |
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|
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if(entry_plug->haveCutoffGroups){ |
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myMols = entry_plug->molecules; |
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numMol = entry_plug->n_mol; |
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for(int i = 0; i < numMol; i++){ |
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|
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numCutoffGroups = myMols[i].getNCutoffGroups(); |
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for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; |
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myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
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//get center of mass of the cutoff group |
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myCutoffGroup->getCOM(com); |
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|
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rcGroup.push_back(com[0]); |
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rcGroup.push_back(com[1]); |
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rcGroup.push_back(com[2]); |
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|
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}// end for(myCutoffGroup) |
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}//end for(int i = 0) |
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rc = &rcGroup[0]; |
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} |
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else{ |
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// center of mass of the group is the same as position of the atom if cutoff group does not exist |
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rc = pos; |
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} |
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isError = 0; |
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entry_plug->lrPot = 0.0; |
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|
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for (i=0; i<9; i++) { |
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entry_plug->tau[i] = 0.0; |
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} |
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|
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#ifdef PROFILE |
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startProfile(pro8); |
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#endif |
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|
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fortranForceLoop( pos, |
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rc, |
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A, |
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u_l, |
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frc, |
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trq, |
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entry_plug->tau, |
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&(entry_plug->lrPot), |
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&passedCalcPot, |
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&passedCalcStress, |
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&isError ); |
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#ifdef PROFILE |
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endProfile(pro8); |
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#endif |
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|
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|
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if( isError ){ |
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sprintf( painCave.errMsg, |
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"Error returned from the fortran force calculation.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (entry_plug->useSolidThermInt && !entry_plug->useLiquidThermInt) { |
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factor = pow(entry_plug->thermIntLambda, entry_plug->thermIntK); |
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for (i=0; i < entry_plug->n_atoms; i++) { |
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for (j=0; j< 3; j++) |
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frc[3*i + j] *= factor; |
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if (entry_plug->atoms[i]->isDirectional()) { |
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for (j=0; j< 3; j++) |
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trq[3*i + j] *= factor; |
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} |
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} |
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entry_plug->vRaw = entry_plug->lrPot; |
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entry_plug->lrPot *= factor; |
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entry_plug->lrPot += entry_plug->restraint->Calc_Restraint_Forces(entry_plug->integrableObjects); |
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entry_plug->vHarm = entry_plug->restraint->getVharm(); |
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} |
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|
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if (entry_plug->useLiquidThermInt) { |
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factor = pow(entry_plug->thermIntLambda, entry_plug->thermIntK); |
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for (i=0; i < entry_plug->n_atoms; i++) { |
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for (j=0; j< 3; j++) |
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frc[3*i + j] *= factor; |
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if (entry_plug->atoms[i]->isDirectional()) { |
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for (j=0; j< 3; j++) |
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trq[3*i + j] *= factor; |
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} |
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} |
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entry_plug->vRaw = entry_plug->lrPot; |
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entry_plug->lrPot *= factor; |
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} |
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|
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for(i=0; i<entry_plug->n_mol; i++ ){ |
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entry_plug->molecules[i].atoms2rigidBodies(); |
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} |
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|
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|
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#ifdef IS_MPI |
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sprintf( checkPointMsg, |
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"returned from the force calculation.\n" ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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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 ForceFields::initFortran(int ljMixPolicy, int useReactionField ){ |
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int isError; |
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isError = 0; |
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initFortranFF( &ljMixPolicy, &useReactionField, &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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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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|
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#ifdef IS_MPI |
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sprintf( checkPointMsg, "ForceField successfully initialized the fortran component list.\n" ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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|
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} |
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|
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|
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void ForceFields::initRestraints(){ |
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int i; |
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// store the initial info. |
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// set the omega values to zero |
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for (i=0; i<entry_plug->integrableObjects.size(); i++) |
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entry_plug->integrableObjects[i]->setZangle( 0.0 ); |
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entry_plug->restraint->Store_Init_Info(entry_plug->integrableObjects); |
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|
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} |
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void ForceFields::dumpzAngle(){ |
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// store the initial info. |
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entry_plug->restraint->Write_zAngle_File(entry_plug->integrableObjects); |
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|
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} |
