scholarly journals Symplectic All-at-Once Method for Hamiltonian Systems

Symmetry ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1930
Author(s):  
Bei-Bei Zhu ◽  
Yong-Liang Zhao
Keyword(s):  
Hamiltonian Systems ◽  
Fast Algorithm ◽  
Numerical Experiments ◽  
Degrees Of Freedom ◽  
Computational Cost ◽  
Symplectic Method ◽  
System A ◽  
Symmetric Method

The all-at-once technique has attracted many researchers’ interest in recent years. In this paper, we combine this technique with a classical symplectic and symmetric method for solving Hamiltonian systems. The solutions at all time steps are obtained at one-shot. In order to reduce the computational cost of solving the all-at-once system, a fast algorithm is designed. Numerical experiments of Hamiltonian systems with degrees of freedom n≤3 are provided to show that our method is more efficient than the classical symplectic method.

Driving Torsion Scans with Wavefront Propagation

2020 ◽  
Author(s):  
Yudong Qiu ◽  
Daniel Smith ◽  
Chaya Stern ◽  
mudong feng ◽  
Lee-Ping Wang
Keyword(s):  
Potential Energy ◽  
Force Field ◽  
Degrees Of Freedom ◽  
Computational Cost ◽  
Initial Guess ◽  
Field Development ◽  
Force Field Development ◽  
Wavefront Propagation ◽  
Open Source Software Package

<div>The parameterization of torsional / dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields.</div><div>Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms.</div><div>To ensure that the sampled molecular configurations are thermodynamically feasible, constrained QM geometry optimizations are typically carried out, which relax the orthogonal degrees of freedom while fixing the target torsion angle(s) on a grid of values.</div><div>However, the quality of results and computational cost are affected by various factors on a non-trivial PES, such as dependence on the chosen scan direction and the lack of efficient approaches to integrate results started from multiple initial guesses.</div><div>In this paper we propose a systematic and versatile workflow called \textit{TorsionDrive} to generate energy-minimized structures on a grid of torsion constraints by means of a recursive wavefront propagation algorithm, which resolves the deficiencies of conventional scanning approaches and generates higher quality QM data for force field development.</div><div>The capabilities of our method are presented for multi-dimensional scans and multiple initial guess structures, and an integration with the MolSSI QCArchive distributed computing ecosystem is described.</div><div>The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes.</div>

Reversibly Sampling Conformations and Binding Modes Using Molecular Darting

2020 ◽  
Author(s):  
Samuel C. Gill ◽  
David Mobley
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Sites ◽  
Degrees Of Freedom ◽  
Dynamics Simulation ◽  
Hiv Integrase ◽  
Binding Modes ◽  
System A ◽  
Multiple Binding ◽  
Internal Degrees Of Freedom

<div>Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We have developed a novel Monte Carlo move called Molecular Darting (MolDarting) to reversibly sample between predefined binding modes of a ligand. Here, we couple this with nonequilibrium candidate Monte Carlo (NCMC) to improve acceptance of moves.</div><div>We apply this technique to a simple dipeptide system, a ligand binding to T4 Lysozyme L99A, and ligand binding to HIV integrase in order to test this new method. We observe significant increases in acceptance compared to uniformly sampling the internal, and rotational/translational degrees of freedom in these systems.</div>

An accurate method to include lubrication forces in numerical simulations of dense Stokesian suspensions

2015 ◽  
Vol 769 ◽  
pp. 369-386 ◽  
Author(s):  
A. Lefebvre-Lepot ◽  
B. Merlet ◽  
T. N. Nguyen
Keyword(s):  
Short Range ◽  
Degrees Of Freedom ◽  
Computational Cost ◽  
Parameter Tuning ◽  
Accurate Method ◽  
Spherical Particles ◽  
Particle Model ◽  
Stokesian Dynamics ◽  
New Feature ◽  
The Many

We address the problem of computing the hydrodynamic forces and torques among $N$ solid spherical particles moving with given rotational and translational velocities in Stokes flow. We consider the original fluid–particle model without introducing new hypotheses or models. Our method includes the singular lubrication interactions which may occur when some particles come close to one another. The main new feature is that short-range interactions are propagated to the whole flow, including accurately the many-body lubrication interactions. The method builds on a pre-existing fluid solver and is flexible with respect to the choice of this solver. The error is the error generated by the fluid solver when computing non-singular flows (i.e. with negligible short-range interactions). Therefore, only a small number of degrees of freedom are required and we obtain very accurate simulations within a reasonable computational cost. Our method is closely related to a method proposed by Sangani & Mo (Phys. Fluids, vol. 6, 1994, pp. 1653–1662) but, in contrast with the latter, it does not require parameter tuning. We compare our method with the Stokesian dynamics of Durlofsky et al. (J. Fluid Mech., vol. 180, 1987, pp. 21–49) and show the higher accuracy of the former (both by analysis and by numerical experiments).

scholarly journals Diagonal scaling of stiffness matrices in the Galerkin boundary element method

2000 ◽  
Vol 42 (1) ◽  
pp. 141-150 ◽  
Author(s):  
Mark Ainsworth ◽  
Bill McLean ◽  
Thanh Tran
Keyword(s):  
Integral Equation ◽  
Stiffness Matrix ◽  
Numerical Experiments ◽  
Degrees Of Freedom ◽  
Boundary Integral ◽  
Piecewise Constant ◽  
Stiffness Matrices ◽  
Diagonal Scaling ◽  
Mesh Ratio ◽  
Galerkin Boundary Element Method

AbstractA boundary integral equation of the first kind is discretised using Galerkin's method with piecewise-constant trial functions. We show how the condition number of the stiffness matrix depends on the number of degrees of freedom and on the global mesh ratio. We also show that diagonal scaling eliminates the latter dependence. Numerical experiments confirm the theory, and demonstrate that in practical computations involving strong local mesh refinement, diagonal scaling dramatically improves the conditioning of the Galerkin equations.

Numerical Solution of a Wave Propagation Problem Along Plate Structures Based on the Isogeometric Approach

2018 ◽  
Vol 26 (01) ◽  
pp. 1750030 ◽  
Author(s):  
V. Hernández ◽  
J. Estrada ◽  
E. Moreno ◽  
S. Rodríguez ◽  
A. Mansur
Keyword(s):  
Degrees Of Freedom ◽  
Eigenvalue Problems ◽  
Computational Cost ◽  
Dispersion Curves ◽  
Wave Number ◽  
Spline Functions ◽  
Shape Functions ◽  
B Spline ◽  
Generalized Eigenvalue ◽  
Generalized Eigenvalue Problems

Ultrasonic guided waves propagating along large structures have great potential as a nondestructive evaluation method. In this context, it is very important to obtain the dispersion curves, which depend on the cross-section of the structure. In this paper, we compute dispersion curves along infinite isotropic plate-like structures using the semi-analytical method (SAFEM) with an isogeometric approach based on B-spline functions. The SAFEM method leads to a family of generalized eigenvalue problems depending on the wave number. For a prescribed wave number, the solution of this problem consists of the nodal displacement vector and the frequency of the guided wave. In this work, the results obtained with B-splines shape functions are compared to the numerical SAFEM solution with quadratic Lagrange shape functions. Advantages of the isogeometric approach are highlighted and include the smoothness of the displacement field components and the computational cost of solving the corresponding generalized eigenvalue problems. Finally, we investigate the convergence of Lagrange and B-spline approaches when the number of degrees of freedom grows. The study shows that cubic B-spline functions provide the best solution with the smallest relative errors for a given number of degrees of freedom.

Toward a Minimal Dynamic Model of a 6-DOF Parallel Robot

1997 ◽  
Author(s):  
L. Beji ◽  
M. Pascal ◽  
P. Joli
Keyword(s):  
Dynamic Model ◽  
Degrees Of Freedom ◽  
Equations Of Motion ◽  
Computational Cost ◽  
Closed Form Solution ◽  
Parallel Robot ◽  
Form Solution ◽  
Lagrangian Formalism ◽  
Inverse Kinematic Problem ◽  
Geometrical Properties

Abstract In this paper, an architecture of a six degrees of freedom (dof) parallel robot and three limbs is described. The robot is called Space Manipulator (SM). In a first step, the inverse kinematic problem for the robot is solved in closed form solution. Further, we need to inverse only a 3 × 3 passive jacobian matrix to solve the direct kinematic problem. In a second step, the dynamic equations are derived by using the Lagrangian formalism where the coordinates are the passive and active joint coordinates. Based on geometrical properties of the robot, the equations of motion are derived in terms of only 9 coordinates related by 3 kinematic constraints. The computational cost of the obtained dynamic model is reduced by using a minimum set of base inertial parameters.

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