# | Line 63 | Line 63 | |
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63 | #include "utils/MemoryUtils.hpp" | |
64 | #include "utils/simError.h" | |
65 | #include "selection/SelectionManager.hpp" | |
66 | + | #include "io/ForceFieldOptions.hpp" |
67 | + | #include "UseTheForce/ForceField.hpp" |
68 | ||
69 | #ifdef IS_MPI | |
70 | #include "UseTheForce/mpiComponentPlan.h" | |
# | Line 80 | Line 82 | namespace oopse { | |
82 | return result; | |
83 | } | |
84 | ||
85 | < | SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
86 | < | ForceField* ff, Globals* simParams) : |
85 | < | stamps_(stamps), forceField_(ff), simParams_(simParams), |
85 | > | SimInfo::SimInfo(ForceField* ff, Globals* simParams) : |
86 | > | forceField_(ff), simParams_(simParams), |
87 | ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), | |
88 | nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), | |
89 | nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), | |
# | Line 90 | Line 91 | namespace oopse { | |
91 | nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), | |
92 | sman_(NULL), fortranInitialized_(false) { | |
93 | ||
93 | – | |
94 | – | std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
94 | MoleculeStamp* molStamp; | |
95 | int nMolWithSameStamp; | |
96 | int nCutoffAtoms = 0; // number of atoms belong to cutoff groups | |
# | Line 99 | Line 98 | namespace oopse { | |
98 | CutoffGroupStamp* cgStamp; | |
99 | RigidBodyStamp* rbStamp; | |
100 | int nRigidAtoms = 0; | |
101 | < | |
102 | < | for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
103 | < | molStamp = i->first; |
104 | < | nMolWithSameStamp = i->second; |
101 | > | std::vector<Component*> components = simParams->getComponents(); |
102 | > | |
103 | > | for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) { |
104 | > | molStamp = (*i)->getMoleculeStamp(); |
105 | > | nMolWithSameStamp = (*i)->getNMol(); |
106 | ||
107 | addMoleculeStamp(molStamp, nMolWithSameStamp); | |
108 | ||
109 | //calculate atoms in molecules | |
110 | nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; | |
111 | ||
112 | – | |
112 | //calculate atoms in cutoff groups | |
113 | int nAtomsInGroups = 0; | |
114 | int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); | |
115 | ||
116 | for (int j=0; j < nCutoffGroupsInStamp; j++) { | |
117 | < | cgStamp = molStamp->getCutoffGroup(j); |
117 | > | cgStamp = molStamp->getCutoffGroupStamp(j); |
118 | nAtomsInGroups += cgStamp->getNMembers(); | |
119 | } | |
120 | ||
# | Line 128 | Line 127 | namespace oopse { | |
127 | int nRigidBodiesInStamp = molStamp->getNRigidBodies(); | |
128 | ||
129 | for (int j=0; j < nRigidBodiesInStamp; j++) { | |
130 | < | rbStamp = molStamp->getRigidBody(j); |
130 | > | rbStamp = molStamp->getRigidBodyStamp(j); |
131 | nAtomsInRigidBodies += rbStamp->getNMembers(); | |
132 | } | |
133 | ||
# | Line 167 | Line 166 | namespace oopse { | |
166 | } | |
167 | molecules_.clear(); | |
168 | ||
170 | – | delete stamps_; |
169 | delete sman_; | |
170 | delete simParams_; | |
171 | delete forceField_; | |
# | Line 274 | Line 272 | namespace oopse { | |
272 | } | |
273 | } | |
274 | ||
275 | < | }//end for (integrableObject) |
276 | < | }// end for (mol) |
275 | > | } |
276 | > | } |
277 | ||
278 | // n_constraints is local, so subtract them on each processor | |
279 | ndf_local -= nConstraints_; | |
# | Line 924 | Line 922 | namespace oopse { | |
922 | ||
923 | void SimInfo::setupCutoff() { | |
924 | ||
925 | + | ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); |
926 | + | |
927 | // Check the cutoff policy | |
928 | < | int cp = TRADITIONAL_CUTOFF_POLICY; |
929 | < | if (simParams_->haveCutoffPolicy()) { |
930 | < | std::string myPolicy = simParams_->getCutoffPolicy(); |
928 | > | int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default |
929 | > | |
930 | > | std::string myPolicy; |
931 | > | if (forceFieldOptions_.haveCutoffPolicy()){ |
932 | > | myPolicy = forceFieldOptions_.getCutoffPolicy(); |
933 | > | }else if (simParams_->haveCutoffPolicy()) { |
934 | > | myPolicy = simParams_->getCutoffPolicy(); |
935 | > | } |
936 | > | |
937 | > | if (!myPolicy.empty()){ |
938 | toUpper(myPolicy); | |
939 | if (myPolicy == "MIX") { | |
940 | cp = MIX_CUTOFF_POLICY; | |
# | Line 962 | Line 969 | namespace oopse { | |
969 | if (simParams_->haveSwitchingRadius()) { | |
970 | rsw_ = simParams_->getSwitchingRadius(); | |
971 | } else { | |
972 | < | rsw_ = rcut_; |
973 | < | } |
972 | > | if (fInfo_.SIM_uses_Charges | |
973 | > | fInfo_.SIM_uses_Dipoles | |
974 | > | fInfo_.SIM_uses_RF) { |
975 | > | |
976 | > | rsw_ = 0.85 * rcut_; |
977 | > | sprintf(painCave.errMsg, |
978 | > | "SimCreator Warning: No value was set for the switchingRadius.\n" |
979 | > | "\tOOPSE will use a default value of 85\% of the cutoffRadius" |
980 | > | "\tswitchingRadius = %f. for this simulation\n", rsw_); |
981 | > | painCave.isFatal = 0; |
982 | > | simError(); |
983 | > | } else { |
984 | > | rsw_ = rcut_; |
985 | > | sprintf(painCave.errMsg, |
986 | > | "SimCreator Warning: No value was set for the switchingRadius.\n" |
987 | > | "\tOOPSE will use the same value as the cutoffRadius.\n" |
988 | > | "\tswitchingRadius = %f. for this simulation\n", rsw_); |
989 | > | painCave.isFatal = 0; |
990 | > | simError(); |
991 | > | } |
992 | > | |
993 | notifyFortranCutoffs(&rcut_, &rsw_); | |
994 | ||
995 | } else { | |
# | Line 1092 | Line 1118 | namespace oopse { | |
1118 | ||
1119 | // let's pass some summation method variables to fortran | |
1120 | setElectrostaticSummationMethod( &esm ); | |
1121 | < | notifyFortranElectrostaticMethod( &esm ); |
1121 | > | setFortranElectrostaticMethod( &esm ); |
1122 | setScreeningMethod( &sm ); | |
1123 | setDampingAlpha( &alphaVal ); | |
1124 | setReactionFieldDielectric( &dielectric ); |
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