| 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" |
| 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), |
| 91 |
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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 |
| 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 |
|
|
| 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 |
|
|
| 166 |
|
} |
| 167 |
|
molecules_.clear(); |
| 168 |
|
|
| 170 |
– |
delete stamps_; |
| 169 |
|
delete sman_; |
| 170 |
|
delete simParams_; |
| 171 |
|
delete forceField_; |
| 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_; |
| 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; |
| 1099 |
|
|
| 1100 |
|
// let's pass some summation method variables to fortran |
| 1101 |
|
setElectrostaticSummationMethod( &esm ); |
| 1102 |
< |
notifyFortranElectrostaticMethod( &esm ); |
| 1102 |
> |
setFortranElectrostaticMethod( &esm ); |
| 1103 |
|
setScreeningMethod( &sm ); |
| 1104 |
|
setDampingAlpha( &alphaVal ); |
| 1105 |
|
setReactionFieldDielectric( &dielectric ); |
