| 57 |
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#include "primitives/Torsion.hpp" |
| 58 |
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#include "primitives/Inversion.hpp" |
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#include "nonbonded/NonBondedInteraction.hpp" |
| 60 |
< |
#include "perturbations/ElectricField.hpp" |
| 60 |
> |
#include "perturbations/UniformField.hpp" |
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#include "parallel/ForceMatrixDecomposition.hpp" |
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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 |
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setupCutoffs(); |
| 412 |
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|
| 413 |
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info_->prepareTopology(); |
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if (doHeatFlux_) doParticlePot_ = true; |
| 418 |
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|
| 419 |
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doElectricField_ = info_->getSimParams()->getOutputElectricField(); |
| 420 |
+ |
doSitePotential_ = info_->getSimParams()->getOutputSitePotential(); |
| 421 |
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|
| 422 |
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} |
| 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); |
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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 |
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} |
| 455 |
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|
| 638 |
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// Collect from all nodes. This should eventually be moved into a |
| 639 |
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// SystemDecomposition, but this is a better place than in |
| 640 |
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// Thermo to do the collection. |
| 641 |
< |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE, |
| 642 |
< |
MPI::SUM); |
| 643 |
< |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE, |
| 644 |
< |
MPI::SUM); |
| 645 |
< |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1, |
| 646 |
< |
MPI::REALTYPE, MPI::SUM); |
| 647 |
< |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1, |
| 648 |
< |
MPI::REALTYPE, MPI::SUM); |
| 641 |
> |
|
| 642 |
> |
MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE, |
| 643 |
> |
MPI_SUM, MPI_COMM_WORLD); |
| 644 |
> |
MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE, |
| 645 |
> |
MPI_SUM, MPI_COMM_WORLD); |
| 646 |
> |
MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1, |
| 647 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 648 |
> |
MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1, |
| 649 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 650 |
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#endif |
| 651 |
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|
| 652 |
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Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 712 |
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RealType dVdFQ1(0.0); |
| 713 |
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RealType dVdFQ2(0.0); |
| 714 |
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potVec longRangePotential(0.0); |
| 715 |
< |
potVec reciprocalPotential(0.0); |
| 715 |
> |
RealType reciprocalPotential(0.0); |
| 716 |
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potVec workPot(0.0); |
| 717 |
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potVec exPot(0.0); |
| 718 |
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Vector3d eField1(0.0); |
| 719 |
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Vector3d eField2(0.0); |
| 720 |
+ |
RealType sPot1(0.0); |
| 721 |
+ |
RealType sPot2(0.0); |
| 722 |
+ |
|
| 723 |
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vector<int>::iterator ia, jb; |
| 724 |
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|
| 725 |
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int loopStart, loopEnd; |
| 735 |
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idat.dVdFQ1 = &dVdFQ1; |
| 736 |
|
idat.dVdFQ2 = &dVdFQ2; |
| 737 |
|
idat.eField1 = &eField1; |
| 738 |
< |
idat.eField2 = &eField2; |
| 738 |
> |
idat.eField2 = &eField2; |
| 739 |
> |
idat.sPot1 = &sPot1; |
| 740 |
> |
idat.sPot2 = &sPot2; |
| 741 |
|
idat.f1 = &f1; |
| 742 |
|
idat.sw = &sw; |
| 743 |
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idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false; |
| 744 |
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idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false; |
| 745 |
|
idat.doParticlePot = doParticlePot_; |
| 746 |
|
idat.doElectricField = doElectricField_; |
| 747 |
+ |
idat.doSitePotential = doSitePotential_; |
| 748 |
|
sdat.doParticlePot = doParticlePot_; |
| 749 |
|
|
| 750 |
|
loopEnd = PAIR_LOOP; |
| 784 |
|
fij.zero(); |
| 785 |
|
eField1.zero(); |
| 786 |
|
eField2.zero(); |
| 787 |
+ |
sPot1 = 0.0; |
| 788 |
+ |
sPot2 = 0.0; |
| 789 |
|
} |
| 790 |
|
|
| 791 |
|
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 938 |
|
fDecomp_->collectData(); |
| 939 |
|
if (cutoffMethod_ == EWALD_FULL) { |
| 940 |
|
interactionMan_->doReciprocalSpaceSum(reciprocalPotential); |
| 941 |
+ |
|
| 942 |
+ |
curSnapshot->setReciprocalPotential(reciprocalPotential); |
| 943 |
|
} |
| 944 |
|
|
| 945 |
|
if (info_->requiresSelfCorrection()) { |
| 953 |
|
fDecomp_->collectSelfData(); |
| 954 |
|
|
| 955 |
|
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 956 |
< |
*(fDecomp_->getPairwisePotential()) + reciprocalPotential; |
| 956 |
> |
*(fDecomp_->getPairwisePotential()); |
| 957 |
|
|
| 958 |
|
curSnapshot->setLongRangePotential(longRangePotential); |
| 959 |
|
|
| 987 |
|
} |
| 988 |
|
|
| 989 |
|
#ifdef IS_MPI |
| 990 |
< |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9, |
| 991 |
< |
MPI::REALTYPE, MPI::SUM); |
| 990 |
> |
MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9, |
| 991 |
> |
MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 992 |
|
#endif |
| 993 |
|
curSnapshot->setStressTensor(stressTensor); |
| 994 |
|
|
