| 57 |
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#include "primitives/Torsion.hpp" |
| 58 |
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#include "primitives/Inversion.hpp" |
| 59 |
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#include "nonbonded/NonBondedInteraction.hpp" |
| 60 |
< |
#include "perturbations/ElectricField.hpp" |
| 60 |
> |
#include "perturbations/UniformField.hpp" |
| 61 |
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#include "parallel/ForceMatrixDecomposition.hpp" |
| 62 |
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| 63 |
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#include <cstdio> |
| 405 |
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interactionMan_->setSimInfo(info_); |
| 406 |
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interactionMan_->initialize(); |
| 407 |
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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 |
| 409 |
> |
//! manager has set up the atom-atom interactions so that we can |
| 410 |
> |
//! query them for suggested cutoff values |
| 411 |
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setupCutoffs(); |
| 412 |
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|
| 413 |
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info_->prepareTopology(); |
| 423 |
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|
| 424 |
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 425 |
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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 |
| 432 |
< |
// 2 = connected via a bend |
| 433 |
< |
// 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 |
| 434 |
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|
| 435 |
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vdwScale_.reserve(4); |
| 436 |
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fill(vdwScale_.begin(), vdwScale_.end(), 0.0); |
| 448 |
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electrostaticScale_[2] = fopts.getelectrostatic13scale(); |
| 449 |
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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_); |
| 453 |
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perturbations_.push_back(eField); |
| 454 |
|
} |
| 455 |
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|
| 843 |
|
} else { |
| 844 |
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interactionMan_->doPair(idat); |
| 845 |
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fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 846 |
+ |
/* |
| 847 |
+ |
if(atom1 == 971){ |
| 848 |
+ |
cerr << "972: " << *(idat.dVdFQ1) << "\n"; |
| 849 |
+ |
} |
| 850 |
+ |
if(atom2 == 971){ |
| 851 |
+ |
cerr << "972: " << *(idat.dVdFQ2) << "\n"; |
| 852 |
+ |
} |
| 853 |
+ |
if(atom1 == 766){ |
| 854 |
+ |
cerr << "767: " << *(idat.dVdFQ1) << "\n"; |
| 855 |
+ |
} |
| 856 |
+ |
if(atom2 == 766){ |
| 857 |
+ |
cerr << "767: " << *(idat.dVdFQ2) << "\n"; |
| 858 |
+ |
} |
| 859 |
+ |
*/ |
| 860 |
|
vij += vpair; |
| 861 |
|
fij += f1; |
| 862 |
|
stressTensor -= outProduct( *(idat.d), f1); |
| 959 |
|
if (info_->requiresSelfCorrection()) { |
| 960 |
|
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 961 |
|
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 |
|
interactionMan_->doSelfCorrection(sdat); |
| 968 |
+ |
/* |
| 969 |
+ |
if(atom1 == 971 || atom1 == 766 || atom1 == 898){ |
| 970 |
+ |
cout << "\tsdat.dVdFQ: " << *(sdat.dVdFQ) << "\n"; |
| 971 |
+ |
} |
| 972 |
+ |
*/ |
| 973 |
|
} |
| 974 |
|
} |
| 975 |
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|
