• transiesta

  • Referenced in 6 articles [sw33754]
  • initio method for calculating the electronic structure, electronic transport, and forces acting on the atoms ... states . We fully deal with the atomistic structure of the whole system, treating both...
  • WulffPack

  • Referenced in 2 articles [sw31375]
  • WulffPack constructs both continuum models and atomistic structures for further modeling with, e.g., molecular dynamics...
  • REACH

  • Referenced in 6 articles [sw00788]
  • covariance matrix obtained from atomistic molecular dynamics simulation. Secondary-structure dependence of the force constants ... method involves self-consistent, direct mapping of atomistic simulation results onto a coarse-grained force...
  • RandSpg

  • Referenced in 1 article [sw25040]
  • open-source program for generating atomistic crystal structures with specific spacegroups . A new algorithm, RandSpg...
  • NanoSCULPT

  • Referenced in 1 article [sw39415]
  • generating complex realistic configurations for atomistic simulations. Atomistic simulations have now become commonplace ... well-defined structures are often required to obtain quantitative information from atomistic simulations, for qualitative ... reconstruction of experimentally observed structures. To this end, we propose a new method and software ... geometries and structures obtained from simulation methods other than atomistic simulations. The tool enables...
  • ASE

  • Referenced in 13 articles [sw30602]
  • setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python ... performed through interfaces to many external electronic structure codes or force fields using a uniform...
  • RLSCODE

  • Referenced in 3 articles [sw12468]
  • Recognition and analysis of local structure in polycrystalline configurations. A method is described for obtaining ... solids or real materials based on their atomistic configurations. An efficient algorithmic implementation is provided ... type of the (usually non-ideal) crystal structure to which atoms surrounded by their relevant...
  • pyscal

  • Referenced in 1 article [sw30907]
  • structural environments including Steinhardt’s bond orientational order parameters [1] during post-processing of atomistic...
  • DL-FIND

  • Referenced in 1 article [sw06333]
  • FIND: A Geometry Optimizer for Atomistic Simulation Codes A geometry optimization library for quantum chemical ... QM/MM calculations to be included into electronic structure codes. DL-FIND can be used...
  • Fidimag

  • Referenced in 2 articles [sw27243]
  • nano- or micro-scale using either atomistic or finite difference micromagnetic simulations, which are based ... creating a simple code structure that can be readily installed, tested, and extended. An agile...
  • MSMBuilder

  • Referenced in 2 articles [sw23802]
  • particular focus on the analysis of atomistic simulations of biomolecular dynamics such as protein folding ... such as hidden Markov models and time-structure based independent component analysis. MSMBuilder boasts...
  • DL_ANALYSER

  • Referenced in 1 article [sw37768]
  • This notation can annotate precisely the detailed atomistic interactions without having to resolve to diagrammatic ... hydrogen, resulting in a series of linear structures that intertwined with pockets of methyl clusters...
  • OptiMic

  • Referenced in 1 article [sw39414]
  • Polycrystal microstructures, with their distinct physical, chemical, structural and topological entities, play an important role ... both finite element as well as atomistic simulations. OptiMic allows for both monodispersive grains...
  • ASR

  • Referenced in 1 article [sw38328]
  • open source Python framework for working with atomistic materials simulations in an efficient and sustainable ... schemes. These Recipes utilize the GPAW electronic structure code, but may be adapted to other...
  • ProtPOS

  • Referenced in 0 articles [sw18972]
  • protein preferred orientation on a surface. Summary: Atomistic molecular dynamics simulation is a promising technique ... system at hand and provide structural output readily available for further simulation studies. Availability...
  • ANSYS

  • Referenced in 666 articles [sw00044]
  • ANSYS offers a comprehensive software suite that spans...
  • Gmsh

  • Referenced in 635 articles [sw00366]
  • Gmsh is a 3D finite element grid generator...
  • LAPACK

  • Referenced in 1649 articles [sw00503]
  • LAPACK is written in Fortran 90 and provides...
  • Matlab

  • Referenced in 12640 articles [sw00558]
  • MATLAB® is a high-level language and interactive...