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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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|
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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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|
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info_->prepareTopology(); |
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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|
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< |
// Force fields can set options on how to scale van der Waals and |
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< |
// electrostatic interactions for atoms connected via bonds, bends |
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< |
// and torsions in this case the topological distance between |
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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 |
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> |
//! electrostatic interactions for atoms connected via bonds, bends |
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> |
//! and torsions in this case the topological distance between |
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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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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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< |
if (info_->getSimParams()->haveElectricField()) { |
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< |
ElectricField* eField = new ElectricField(info_); |
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> |
if (info_->getSimParams()->haveUniformField()) { |
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> |
UniformField* eField = new UniformField(info_); |
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perturbations_.push_back(eField); |
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} |
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