| 40 |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
| 42 |
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|
| 43 |
– |
#include "FluctuatingChargeConstraints.hpp" |
| 44 |
– |
#include "primitives/Molecule.hpp" |
| 45 |
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|
| 43 |
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#ifdef IS_MPI |
| 44 |
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#include <mpi.h> |
| 45 |
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#endif |
| 46 |
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|
| 47 |
+ |
#include "FluctuatingChargeConstraints.hpp" |
| 48 |
+ |
#include "primitives/Molecule.hpp" |
| 49 |
+ |
|
| 50 |
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namespace OpenMD { |
| 51 |
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|
| 52 |
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FluctuatingChargeConstraints::FluctuatingChargeConstraints(SimInfo* info) : |
| 53 |
< |
info_(info), constrainRegions_(false), hasFlucQ_(false) { |
| 54 |
< |
|
| 55 |
< |
if (info_->usesFluctuatingCharges()) { |
| 56 |
< |
if (info_->getNFluctuatingCharges() > 0) { |
| 57 |
< |
hasFlucQ_ = true; |
| 53 |
> |
info_(info), constrainRegions_(false), hasFlucQ_(false), initialized_(false) { |
| 54 |
> |
} |
| 55 |
> |
|
| 56 |
> |
void FluctuatingChargeConstraints::initialize(){ |
| 57 |
> |
if(info_->usesFluctuatingCharges()){ |
| 58 |
> |
if(info_->getNFluctuatingCharges() > 0){ |
| 59 |
> |
hasFlucQ_ = true; |
| 60 |
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} |
| 61 |
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} |
| 62 |
+ |
initialized_ = true; |
| 63 |
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} |
| 64 |
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| 65 |
+ |
|
| 66 |
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void FluctuatingChargeConstraints::setConstrainRegions(bool cr) { |
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constrainRegions_ = cr; |
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+ |
|
| 69 |
+ |
if (!initialized_) initialize(); |
| 70 |
+ |
|
| 71 |
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regionKeys_.clear(); |
| 72 |
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regionForce_.clear(); |
| 73 |
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regionCharges_.clear(); |
| 82 |
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mol = info_->nextMolecule(i)) { |
| 83 |
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reg = mol->getRegion(); |
| 84 |
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if (reg >= 0) regions.insert(reg); |
| 78 |
– |
|
| 85 |
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} |
| 86 |
+ |
// resize the keys vector to the largest found value for regions. |
| 87 |
+ |
regionKeys_.resize( *(regions.end()) ); |
| 88 |
+ |
int which = 0; |
| 89 |
|
for (std::set<int>::iterator r=regions.begin(); r!=regions.end(); ++r) { |
| 90 |
< |
regionKeys_.push_back( (*r) ); |
| 90 |
> |
regionKeys_[ (*r) ] = which; |
| 91 |
> |
which++; |
| 92 |
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} |
| 93 |
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regionForce_.resize( regionKeys_.size() ); |
| 94 |
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regionCharges_.resize( regionKeys_.size() ); |
| 97 |
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|
| 98 |
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|
| 99 |
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void FluctuatingChargeConstraints::applyConstraints() { |
| 100 |
+ |
if (!initialized_) initialize(); |
| 101 |
|
if (!hasFlucQ_) return; |
| 102 |
< |
|
| 102 |
> |
|
| 103 |
|
SimInfo::MoleculeIterator i; |
| 104 |
|
Molecule::FluctuatingChargeIterator j; |
| 105 |
|
Molecule* mol; |
| 106 |
|
Atom* atom; |
| 107 |
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|
| 108 |
|
RealType totalFrc, totalMolFrc, regionFrc, constrainedFrc; |
| 98 |
– |
|
| 109 |
|
// accumulate the total system fluctuating charge forces |
| 110 |
|
totalFrc = 0.0; |
| 111 |
|
if (constrainRegions_) { |
| 124 |
|
RealType frc = atom->getFlucQFrc(); |
| 125 |
|
totalFrc += frc; |
| 126 |
|
if (constrainRegions_) { |
| 127 |
< |
regionForce_[regionKeys_[region]] += frc; |
| 128 |
< |
regionCharges_[regionKeys_[region]] += 1; |
| 127 |
> |
if (region >= 0) { |
| 128 |
> |
regionForce_[regionKeys_[region]] += frc; |
| 129 |
> |
regionCharges_[regionKeys_[region]] += 1; |
| 130 |
> |
} |
| 131 |
|
} |
| 132 |
|
} |
| 133 |
|
} |
| 152 |
|
|
| 153 |
|
// do the same in the regions: |
| 154 |
|
if (constrainRegions_) { |
| 155 |
< |
for (int i = 0; i < regionForce_.size(); ++i) { |
| 155 |
> |
for (unsigned int i = 0; i < regionForce_.size(); ++i) { |
| 156 |
|
regionForce_[ i ] /= regionCharges_[ i ]; |
| 157 |
|
} |
| 158 |
|
} |
| 162 |
|
|
| 163 |
|
if (constrainRegions_) { |
| 164 |
|
int region = mol->getRegion(); |
| 165 |
< |
regionFrc = regionForce_[regionKeys_[region]]; |
| 165 |
> |
if (region >= 0) |
| 166 |
> |
regionFrc = regionForce_[regionKeys_[region]]; |
| 167 |
> |
else |
| 168 |
> |
regionFrc = 0.0; |
| 169 |
|
} else { |
| 170 |
|
regionFrc = 0.0; |
| 171 |
|
} |
