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#include "primitives/Torsion.hpp" |
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#include "primitives/Inversion.hpp" |
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#include "nonbonded/NonBondedInteraction.hpp" |
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#include "perturbations/ElectricField.hpp" |
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> |
#include "perturbations/UniformField.hpp" |
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#include "parallel/ForceMatrixDecomposition.hpp" |
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#include <cstdio> |
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interactionMan_->setSimInfo(info_); |
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interactionMan_->initialize(); |
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// We want to delay the cutoffs until after the interaction |
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// manager has set up the atom-atom interactions so that we can |
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// query them for suggested cutoff values |
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> |
//! We want to delay the cutoffs until after the interaction |
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> |
//! manager has set up the atom-atom interactions so that we can |
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//! query them for suggested cutoff values |
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setupCutoffs(); |
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info_->prepareTopology(); |
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if (doHeatFlux_) doParticlePot_ = true; |
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doElectricField_ = info_->getSimParams()->getOutputElectricField(); |
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doSitePotential_ = info_->getSimParams()->getOutputSitePotential(); |
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} |
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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| 426 |
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// Force fields can set options on how to scale van der Waals and |
| 427 |
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// electrostatic interactions for atoms connected via bonds, bends |
| 428 |
< |
// and torsions in this case the topological distance between |
| 429 |
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// atoms is: |
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// 0 = topologically unconnected |
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// 1 = bonded together |
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// 2 = connected via a bend |
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// 3 = connected via a torsion |
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> |
//! Force fields can set options on how to scale van der Waals and |
| 427 |
> |
//! electrostatic interactions for atoms connected via bonds, bends |
| 428 |
> |
//! and torsions in this case the topological distance between |
| 429 |
> |
//! atoms is: |
| 430 |
> |
//! 0 = topologically unconnected |
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//! 1 = bonded together |
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//! 2 = connected via a bend |
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> |
//! 3 = connected via a torsion |
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vdwScale_.reserve(4); |
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fill(vdwScale_.begin(), vdwScale_.end(), 0.0); |
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electrostaticScale_[2] = fopts.getelectrostatic13scale(); |
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electrostaticScale_[3] = fopts.getelectrostatic14scale(); |
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| 451 |
< |
if (info_->getSimParams()->haveElectricField()) { |
| 452 |
< |
ElectricField* eField = new ElectricField(info_); |
| 451 |
> |
if (info_->getSimParams()->haveUniformField()) { |
| 452 |
> |
UniformField* eField = new UniformField(info_); |
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perturbations_.push_back(eField); |
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} |
| 455 |
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potVec exPot(0.0); |
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Vector3d eField1(0.0); |
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Vector3d eField2(0.0); |
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RealType sPot1(0.0); |
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RealType sPot2(0.0); |
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|
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vector<int>::iterator ia, jb; |
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int loopStart, loopEnd; |
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idat.dVdFQ1 = &dVdFQ1; |
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idat.dVdFQ2 = &dVdFQ2; |
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idat.eField1 = &eField1; |
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idat.eField2 = &eField2; |
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> |
idat.eField2 = &eField2; |
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idat.sPot1 = &sPot1; |
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idat.sPot2 = &sPot2; |
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idat.f1 = &f1; |
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idat.sw = &sw; |
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idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false; |
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idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false; |
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idat.doParticlePot = doParticlePot_; |
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idat.doElectricField = doElectricField_; |
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idat.doSitePotential = doSitePotential_; |
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sdat.doParticlePot = doParticlePot_; |
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loopEnd = PAIR_LOOP; |
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fij.zero(); |
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eField1.zero(); |
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eField2.zero(); |
| 787 |
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sPot1 = 0.0; |
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sPot2 = 0.0; |
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} |
| 790 |
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in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
