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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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| 408 |
< |
// We want to delay the cutoffs until after the interaction |
| 409 |
< |
// manager has set up the atom-atom interactions so that we can |
| 410 |
< |
// query them for suggested cutoff values |
| 408 |
> |
//! 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 |
< |
// 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 |
| 431 |
< |
// 1 = bonded together |
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< |
// 2 = connected via a bend |
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< |
// 3 = connected via a torsion |
| 426 |
> |
//! 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 |
| 431 |
> |
//! 1 = bonded together |
| 432 |
> |
//! 2 = connected via a bend |
| 433 |
> |
//! 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(); |
| 450 |
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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; |
| 738 |
< |
idat.eField2 = &eField2; |
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> |
idat.eField2 = &eField2; |
| 739 |
> |
idat.sPot1 = &sPot1; |
| 740 |
> |
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(); |
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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, |
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} else { |
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interactionMan_->doPair(idat); |
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fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 846 |
+ |
/* |
| 847 |
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if(atom1 == 971){ |
| 848 |
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cerr << "972: " << *(idat.dVdFQ1) << "\n"; |
| 849 |
+ |
} |
| 850 |
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if(atom2 == 971){ |
| 851 |
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cerr << "972: " << *(idat.dVdFQ2) << "\n"; |
| 852 |
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} |
| 853 |
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if(atom1 == 766){ |
| 854 |
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cerr << "767: " << *(idat.dVdFQ1) << "\n"; |
| 855 |
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} |
| 856 |
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if(atom2 == 766){ |
| 857 |
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cerr << "767: " << *(idat.dVdFQ2) << "\n"; |
| 858 |
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} |
| 859 |
+ |
*/ |
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vij += vpair; |
| 861 |
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fij += f1; |
| 862 |
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stressTensor -= outProduct( *(idat.d), f1); |
| 959 |
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if (info_->requiresSelfCorrection()) { |
| 960 |
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for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 961 |
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fDecomp_->fillSelfData(sdat, atom1); |
| 962 |
+ |
/* |
| 963 |
+ |
if(atom1 == 971 || atom1 == 766 || atom1 == 898){ |
| 964 |
+ |
cout << "atom id: " << atom1 << "\tsdat.dVdFQ: " << *(sdat.dVdFQ) << "\n"; |
| 965 |
+ |
} |
| 966 |
+ |
*/ |
| 967 |
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interactionMan_->doSelfCorrection(sdat); |
| 968 |
+ |
/* |
| 969 |
+ |
if(atom1 == 971 || atom1 == 766 || atom1 == 898){ |
| 970 |
+ |
cout << "\tsdat.dVdFQ: " << *(sdat.dVdFQ) << "\n"; |
| 971 |
+ |
} |
| 972 |
+ |
*/ |
| 973 |
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} |
| 974 |
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} |
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