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Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. [1] LAMMPS makes use of Message Passing Interface (MPI) for parallel communication and is free and open-source software , distributed under the terms of the GNU General Public License .
PLUMED is an open-source library implementing enhanced-sampling algorithms, various free-energy methods, and analysis tools for molecular dynamics simulations. It is designed to be used together with ACEMD, AMBER, DL_POLY, GROMACS, LAMMPS, NAMD, OpenMM, ABIN, CP2K, i-PI, PINY-MD, and Quantum ESPRESSO, but it can also be used together with analysis and visualization tools VMD, HTMD, and ...
A related, and more commonly used algorithm is the velocity Verlet algorithm, [5] similar to the leapfrog method, except that the velocity and position are calculated at the same value of the time variable (leapfrog does not, as the name suggests). This uses a similar approach, but explicitly incorporates velocity, solving the problem of the ...
When a statement in one iteration of a loop depends in some way on a statement in a different iteration of the same loop, a loop-carried dependence exists. [1] [2] [3] However, if a statement in one iteration of a loop depends only on a statement in the same iteration of the loop, this creates a loop independent dependence. [1] [2] [3]
Metadynamics (MTD; also abbreviated as METAD or MetaD) is a computer simulation method in computational physics, chemistry and biology.It is used to estimate the free energy and other state functions of a system, where ergodicity is hindered by the form of the system's energy landscape.
The effectiveness of loop interchange depends on and must be considered in light of the cache model used by the underlying hardware and the array model used by the compiler. In C programming language , array elements in the same row are stored consecutively in memory (a[1,1], a[1,2], a[1,3]) ‒ in row-major order .
The programming control structures on which autoparallelization places the most focus are loops, because, in general, most of the execution time of a program takes place inside some form of loop. There are two main approaches to parallelization of loops: pipelined multi-threading and cyclic multi-threading. [ 3 ]
Here is the one-body term, the two-body term, the three body term, the number of atoms in the system, the position of atom , etc. , and are indices that loop over atom positions. Note that in case the pair potential is given per atom pair, in the two-body term the potential should be multiplied by 1/2 as otherwise each bond is counted twice ...