--- trunk/src/brains/SimInfo.cpp 2005/11/21 22:59:21 764 +++ trunk/src/brains/SimInfo.cpp 2006/04/25 02:09:01 945 @@ -63,6 +63,8 @@ #include "utils/MemoryUtils.hpp" #include "utils/simError.h" #include "selection/SelectionManager.hpp" +#include "io/ForceFieldOptions.hpp" +#include "UseTheForce/ForceField.hpp" #ifdef IS_MPI #include "UseTheForce/mpiComponentPlan.h" @@ -80,18 +82,15 @@ namespace oopse { return result; } - SimInfo::SimInfo(MakeStamps* stamps, std::vector >& molStampPairs, - ForceField* ff, Globals* simParams) : - stamps_(stamps), forceField_(ff), simParams_(simParams), - ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), + SimInfo::SimInfo(ForceField* ff, Globals* simParams) : + forceField_(ff), simParams_(simParams), + ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), sman_(NULL), fortranInitialized_(false) { - - std::vector >::iterator i; MoleculeStamp* molStamp; int nMolWithSameStamp; int nCutoffAtoms = 0; // number of atoms belong to cutoff groups @@ -99,23 +98,23 @@ namespace oopse { CutoffGroupStamp* cgStamp; RigidBodyStamp* rbStamp; int nRigidAtoms = 0; - - for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { - molStamp = i->first; - nMolWithSameStamp = i->second; + std::vector components = simParams->getComponents(); + + for (std::vector::iterator i = components.begin(); i !=components.end(); ++i) { + molStamp = (*i)->getMoleculeStamp(); + nMolWithSameStamp = (*i)->getNMol(); addMoleculeStamp(molStamp, nMolWithSameStamp); //calculate atoms in molecules nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; - //calculate atoms in cutoff groups int nAtomsInGroups = 0; int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); for (int j=0; j < nCutoffGroupsInStamp; j++) { - cgStamp = molStamp->getCutoffGroup(j); + cgStamp = molStamp->getCutoffGroupStamp(j); nAtomsInGroups += cgStamp->getNMembers(); } @@ -128,7 +127,7 @@ namespace oopse { int nRigidBodiesInStamp = molStamp->getNRigidBodies(); for (int j=0; j < nRigidBodiesInStamp; j++) { - rbStamp = molStamp->getRigidBody(j); + rbStamp = molStamp->getRigidBodyStamp(j); nAtomsInRigidBodies += rbStamp->getNMembers(); } @@ -167,7 +166,6 @@ namespace oopse { } molecules_.clear(); - delete stamps_; delete sman_; delete simParams_; delete forceField_; @@ -274,8 +272,8 @@ namespace oopse { } } - }//end for (integrableObject) - }// end for (mol) + } + } // n_constraints is local, so subtract them on each processor ndf_local -= nConstraints_; @@ -292,6 +290,15 @@ namespace oopse { } + int SimInfo::getFdf() { +#ifdef IS_MPI + MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); +#else + fdf_ = fdf_local; +#endif + return fdf_; + } + void SimInfo::calcNdfRaw() { int ndfRaw_local; @@ -924,10 +931,19 @@ namespace oopse { void SimInfo::setupCutoff() { + ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); + // Check the cutoff policy - int cp = TRADITIONAL_CUTOFF_POLICY; - if (simParams_->haveCutoffPolicy()) { - std::string myPolicy = simParams_->getCutoffPolicy(); + int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default + + std::string myPolicy; + if (forceFieldOptions_.haveCutoffPolicy()){ + myPolicy = forceFieldOptions_.getCutoffPolicy(); + }else if (simParams_->haveCutoffPolicy()) { + myPolicy = simParams_->getCutoffPolicy(); + } + + if (!myPolicy.empty()){ toUpper(myPolicy); if (myPolicy == "MIX") { cp = MIX_CUTOFF_POLICY; @@ -962,8 +978,28 @@ namespace oopse { if (simParams_->haveSwitchingRadius()) { rsw_ = simParams_->getSwitchingRadius(); } else { - rsw_ = rcut_; + if (fInfo_.SIM_uses_Charges | + fInfo_.SIM_uses_Dipoles | + fInfo_.SIM_uses_RF) { + + rsw_ = 0.85 * rcut_; + sprintf(painCave.errMsg, + "SimCreator Warning: No value was set for the switchingRadius.\n" + "\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n" + "\tswitchingRadius = %f. for this simulation\n", rsw_); + painCave.isFatal = 0; + simError(); + } else { + rsw_ = rcut_; + sprintf(painCave.errMsg, + "SimCreator Warning: No value was set for the switchingRadius.\n" + "\tOOPSE will use the same value as the cutoffRadius.\n" + "\tswitchingRadius = %f. for this simulation\n", rsw_); + painCave.isFatal = 0; + simError(); + } } + notifyFortranCutoffs(&rcut_, &rsw_); } else { @@ -1092,7 +1128,7 @@ namespace oopse { // let's pass some summation method variables to fortran setElectrostaticSummationMethod( &esm ); - notifyFortranElectrostaticMethod( &esm ); + setFortranElectrostaticMethod( &esm ); setScreeningMethod( &sm ); setDampingAlpha( &alphaVal ); setReactionFieldDielectric( &dielectric );