%0 Journal Article
%A Chen, Qile P.
%A Xue, Bai
%A Siepmann, J. Ilja
%D 2017
%T Using the k‑d Tree Data Structure
to Accelerate Monte Carlo Simulations
%U https://acs.figshare.com/articles/journal_contribution/Using_the_i_k_i_d_Tree_Data_Structure_to_Accelerate_Monte_Carlo_Simulations/4728526
%R 10.1021/acs.jctc.6b01222.s001
%2 https://ndownloader.figshare.com/files/7719403
%K configurational-bias MC moves
%K MC simulation efficiency
%K Gibbs ensemble gain
%K interaction sites
%K TIP 4P water
%K NVT
%K Accelerate Monte Carlo Simulations
%K NpT ensemble
%K Tree Data Structure
%K TIP 4P water model
%K tree data structure
%K range search
%K efficiency gain
%X The k-d tree data structure is implemented in
a Monte Carlo (MC) molecular simulation program to accelerate the
range search for particles or interaction sites within the cutoff
distance when Lennard-Jones and Coulomb interactions are computed.
MC simulations are performed for different molecules in various ensembles
to assess the efficiency enhancements due to the k-d tree data structure. It is found that the use of k-d trees accelerates significantly simulations for Lennard-Jones
particles in the NVT and NVT-Gibbs
ensembles and for n-butane and 2,4,6,8,10,12,14,16,18,20,22-undecamethylpentacosane
represented by the TraPPE–UA force field in the NpT ensemble. Simulations for TraPPE–UA ethanol in the NpT ensemble and for the rigid TIP4P water model in the
Gibbs ensemble gain slightly in efficiency with the k-d tree, whereas simulations for TIP4P water in the NpT ensemble do not benefit from the use of the k-d
tree. The speed-up can be attributed to the reduction in the number
of distance calculations in the range search from scaling as O(N) to O(log2N). In addition, these tests suggest that
the efficiency gain from the use of the k-d tree
data structure depends on the flexibility of the molecular model (requiring
configurational-bias MC moves to sample changes in conformation),
on the ensemble (with open ensembles requiring special MC moves to
aid particle transfers), and on the number of interaction sites per
molecule (with compact multisite models not seeing an efficiency gain).
Overall, the use of the k-d tree data structure can
substantially enhance MC simulation efficiency for a variety of systems,
and it will enable simulations for larger system sizes in the future.
%I ACS Publications