Problems with pronounced differences in intensity, such as those that appear in contact mechanics, where locally concentrated high stresses are present, are usually attacked with a spatially variable ...nodal distribution. In a meshless context, such distribution has to be quasi-smooth with minimal spacing requirements to produce satisfactory results. To that end, development of fast discretization procedures, which distribute the nodes according to given (non-constant) spacing function, has become of interest. We improve a recently published algorithm for fast 2D meshless discretizations, by lowering its time complexity from O(NS) to O(N log S) resulting in an algorithm that generates a million nodes per second. The proposed algorithm is independent of the dimensionality of the space, does not rely on a coordinate system and has provable minimal node spacing requirements. The original and new algorithms are compared in terms of node quality and execution time. The usability and robustness of the new algorithm is presented by solving PDE examples on irregular 3D domains with the RBF-FD method and by using it as a node generation algorithm in fully the automatic adaptive solver for linear elasticity.
Background
Analyzing files containing chemical information is at the core of cheminformatics. Each analysis may require a unique workflow. This paper describes the chemalot and chemalot_knime open ...source packages. Chemalot is a set of command line programs with a wide range of functionalities for cheminformatics. The chemalot_knime package allows command line programs that read and write SD files from stdin and to stdout to be wrapped into KNIME nodes. The combination of chemalot and chemalot_knime not only facilitates the compilation and maintenance of sequences of command line programs but also allows KNIME workflows to take advantage of the compute power of a LINUX cluster.
Results
Use of the command line programs is demonstrated in three different workflow examples: (1) A workflow to create a data file with project-relevant data for structure–activity or property analysis and other type of investigations, (2) The creation of a quantitative structure–property-relationship model using the command line programs via KNIME nodes, and (3) The analysis of strain energy in small molecule ligand conformations from the Protein Data Bank database.
Conclusions
The chemalot and chemalot_knime packages provide lightweight and powerful tools for many tasks in cheminformatics. They are easily integrated with other open source and commercial command line tools and can be combined to build new and even more powerful tools. The chemalot_knime package facilitates the generation and maintenance of user-defined command line workflows, taking advantage of the graphical design capabilities in KNIME.
Graphical abstract
Example KNIME workflow with chemalot nodes and the corresponding command line pipe
Element-free Galerkin method (EFGM) is one of the numerical methods which is used for solving partial differential equations with moving least squares interpolations. This method is based on ...finite-element method (FEM) on an integral formulation requires only a set of nodes distributed on the analysis domain for weight function construction. No element connectivity is needed. The objective of this study is to present a modified weight function including automatic node generation for improvement of the EFGM calculation accuracy. Numerical examples show that the effect of the proposed weight function on results accuracy. Verification of improved EFGM simulation results is done by FEM.
This paper describes a meshless of element-free method based on fuzzy knowledge processing. Node is generated if its distance from existing node points is similar to the node spacing function at the ...point. The node spacing function is well controlled by the fuzzy knowledge processing. Practical performance of the present system is demonstrated through ladle apparatus of casting solutions.
This article describes a biologically inspired node generator for the path planning of serially connected hyper-redundant manipulators using probabilistic roadmap planners. The generator searches the ...configuration space surrounding existing nodes in the roadmap and uses a combination of random and deterministic search methods that emulate the behaviour of octopus limbs. The strategy consists of randomly mutating the states of the links near the end-effector, and mutating the states of the links near the base of the robot toward the states of the goal configuration. When combined with the small tree probabilistic roadmap planner, the method was successfully used to solve the narrow passage motion planning problem of a 17 degree-of-freedom manipulator.
In this paper, the defect of traditional fast-expanding random tree (RRT) is optimized for the path planning in three-dimensional environment. Due to the randomness generated by its own nodes, the ...traditional RRT algorithm has the defects of the planned path twist and easy to cross the target point, and greatly differs from the ideal path, so that the time required for the robot to implement path tracking is greatly increased. In this paper, an RRT algorithm based on cylindrical sampling space is proposed. The algorithm uses the line connecting the starting point and the ending point of the path as the central axis. The maximum distance from all nodes on the path to the cylinder axis is taken as the radius value of the first cylinder. The cylinder space is used as the new node sampling space in the next path planning. Then, a new cylinder is generated by reducing the radius of the previous cylinder as the current sample sampling space. Repeat the above steps until find the last optimized path. The path generated by the traditional RRT algorithm and the path generated by the RRT optimization algorithm based on cylindrical sampling space are compared and analyzed under the given obstacle and obstacle-free environment. The simulation results show that the path generated by the RRT optimization algorithm based on the cylindrical sampling space is smoother and shorter, almost no redundant path. The path meets the actual motion requirements of the robot.
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