| 417 |
|
if (doHeatFlux_) doParticlePot_ = true; |
| 418 |
|
|
| 419 |
|
doElectricField_ = info_->getSimParams()->getOutputElectricField(); |
| 420 |
+ |
doSitePotential_ = info_->getSimParams()->getOutputSitePotential(); |
| 421 |
|
|
| 422 |
|
} |
| 423 |
|
|
| 638 |
|
// Collect from all nodes. This should eventually be moved into a |
| 639 |
|
// SystemDecomposition, but this is a better place than in |
| 640 |
|
// 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 |
|
#endif |
| 651 |
|
|
| 652 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 668 |
|
DataStorage* config = &(curSnapshot->atomData); |
| 669 |
|
DataStorage* cgConfig = &(curSnapshot->cgData); |
| 670 |
|
|
| 671 |
+ |
|
| 672 |
|
//calculate the center of mass of cutoff group |
| 673 |
|
|
| 674 |
|
SimInfo::MoleculeIterator mi; |
| 712 |
|
RealType dVdFQ1(0.0); |
| 713 |
|
RealType dVdFQ2(0.0); |
| 714 |
|
potVec longRangePotential(0.0); |
| 715 |
< |
potVec reciprocalPotential(0.0); |
| 715 |
> |
RealType reciprocalPotential(0.0); |
| 716 |
|
potVec workPot(0.0); |
| 717 |
|
potVec exPot(0.0); |
| 718 |
|
Vector3d eField1(0.0); |
| 719 |
|
Vector3d eField2(0.0); |
| 720 |
+ |
RealType sPot1(0.0); |
| 721 |
+ |
RealType sPot2(0.0); |
| 722 |
+ |
|
| 723 |
|
vector<int>::iterator ia, jb; |
| 724 |
|
|
| 725 |
|
int loopStart, loopEnd; |
| 735 |
|
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 |
|
idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false; |
| 744 |
|
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; |
| 779 |
|
rgrpsq = d_grp.lengthSquare(); |
| 780 |
|
|
| 781 |
|
if (rgrpsq < rCutSq) { |
| 773 |
– |
|
| 782 |
|
if (iLoop == PAIR_LOOP) { |
| 783 |
|
vij = 0.0; |
| 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, |
| 837 |
|
|
| 838 |
|
r = sqrt( *(idat.r2) ); |
| 839 |
|
idat.rij = &r; |
| 840 |
< |
|
| 840 |
> |
|
| 841 |
|
if (iLoop == PREPAIR_LOOP) { |
| 842 |
|
interactionMan_->doPrePair(idat); |
| 843 |
|
} else { |
| 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 |
|
|
