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Register a new userPCMSolver: an Open-Source Library for Solvation Modeling
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PCMSolver is an open-source library for continuum electrostatic solvation. It can be combined with any quantum chemistry code and requires a minimal interface with the host program, greatly reducing programming effort. As input, PCMSolver needs only the molecular geometry to generate the cavity and the expectation value of the molecular electrostatic potential on the cavity surface. It then returns the solvent polarization back to the host program. The design is powerful and versatile: minimal loss of performance is expected, and a standard single point self-consistent field implementation requires no more than 2 days of work. We provide a brief theoretical overview, followed by two tutorials: one aimed at quantum chemistry program developers wanting to interface their code with PCMSolver, the other aimed at contributors to the library. We finally illustrate past and ongoing work, showing the librarys features, combined with several quantum chemistry programs.
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AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922-1930). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin
Polynomial multiplication is a bottleneck in most of the public-key cryptography protocols, including Elliptic-curve cryptography and several of the post-quantum cryptography algorithms presently being studied. In this paper, we present a library of various large integer polynomial multipliers to be used in hardware cryptocores. Our library contains both digitized and non-digitized multiplier flavours for circuit designers to choose from. The library is supported by a C++ generator that automatically produces the multipliers logic in Verilog HDL that is amenable for FPGA and ASIC designs. Moreover, for ASICs, it also generates configurable and parameterizable synthesis scripts. The features of the generator allow for a quick generation and assessment of several architectures at the same time, thus allowing a designer to easily explore the (complex) optimization search space of polynomial multiplication.
Familia is an open-source toolkit for pragmatic topic modeling in industry. Familia abstracts the utilities of topic modeling in industry as two paradigms: semantic representation and semantic matching. Efficient implementations of the two paradigms are made publicly available for the first time. Furthermore, we provide off-the-shelf topic models trained on large-scale industrial corpora, including Latent Dirichlet Allocation (LDA), SentenceLDA and Topical Word Embedding (TWE). We further describe typical applications which are successfully powered by topic modeling, in order to ease the confusions and difficulties of software engineers during topic model selection and utilization.
Advances in imaging methods such as electron microscopy, tomography and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this study, we outline the steps for a naive user to approach GAMer 2, a mesh generation code written in C++ designed to convert structural datasets to realistic geometric meshes, while preserving the underlying shapes. We present two example cases, 1) mesh generation at the subcellular scale as informed by electron tomography, and 2) meshing a protein with structure from x-ray crystallography. We further demonstrate that the meshes generated by GAMer are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric meshes from structural biology data.
In this paper, we present an open-source multi-resolution and multi-physics library: SPHinXsys (pronunciation: sfinksis) which is an acronym for underline{S}moothed underline{P}article underline{H}ydrodynamics (SPH) for underline{in}dustrial compleunderline{X} underline{sys}tems. As an open-source library, SPHinXsys is developed and released under the terms of Apache License (2.0). Along with the source code, a complete documentation is also distributed to make the compilation and execution easy. SPHinXsys aims at modeling coupled multi-physics industrial dynamic systems including fluids, solids, multi-body dynamics and beyond, in a multi-resolution unified SPH framework. As an SPH solver, SPHinXsys has many advantages namely, (1) the generic design provides a C++ API showing a very good flexibility when building domain-specific applications, (2) numerous industrial or scientific applications can be coupled within the same framework and (3) with the open-source philosophy, the community of users can collaborate and improve the library. SPHinXsys presently (v0.2.0) includes validations and applications in the fields of fluid dynamics, solid dynamics, thermal and mass diffusion, reaction-diffusion, electromechanics and fluid-structure interactions (FSI).
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