• DINAMelt

  • Referenced in 12 articles [sw36131]
  • hybridized pair of nucleic acids, but entire equilibrium melting profiles as a function of temperature ... factors over every possible hybridized or folded state. For temperatures within a user-specified range...
  • ChemSage

  • Referenced in 2 articles [sw19061]
  • energy with respect to a chosen reference state for a given phase and, if this ... partial properties of its components. Chemical equilibrium calculations can be made for a system which...
  • GKW

  • Referenced in 3 articles [sw10271]
  • effects that can be expected from a state of the art gyro-kinetic simulation code ... geometry with a coupling to a MHD equilibrium code, and E×B shearing. In addition...
  • RADIS

  • Referenced in 1 article [sw34321]
  • high resolution infrared molecular spectra (emission / absorption, equilibrium / nonequilibrium). It also includes post-processing tools ... databases for molecules in their electronic ground state. Energy levels are read from tabulated databases ... calculated from Dunham developments. Boltzmann, Treanor, and state specific vibrational distributions can be generated. Thus ... featured for non-equilibrium calculations, and all species present in the HITRAN database are featured...
  • pyomo.dae

  • Referenced in 2 articles [sw26557]
  • integer programming models and mathematical programs with equilibrium constraint formulations. Collectively, these features enable ... concepts, discretization schemes, and the benchmarking of state-of-the-art optimization solvers...
  • CHNOSZ

  • Referenced in 0 articles [sw15144]
  • Kirkham-Flowers equations of state for aqueous species; construction of equilibrium activity diagrams...
  • BOUT

  • Referenced in 8 articles [sw06564]
  • plasma and neutral gas profiles over long equilibrium time scales, and BOUT, which calculates three ... time-dependent system is integrated to steady state. A limitation that is identified for UEDGE...
  • BCYCLIC

  • Referenced in 4 articles [sw00070]
  • processor numbers. Comparison with a state-of-the art parallel sparse solver is presented ... solver in magneto-hydrodynamic (MHD), three-dimensional equilibrium solvers for high-temperature fusion plasmas...
  • ProDy

  • Referenced in 4 articles [sw24072]
  • these variations with the theoretically predicted equilibrium dynamics. Datasets include structural ensembles for a given ... conformations that are accessible in different functional states. ProDy application programming interface (API) has been...
  • DRAIN-2D

  • Referenced in 1 article [sw30111]
  • performed, and detailed logs of energy and equilibrium errors can be obtained. Static and dynamic ... applied in any sequence. The structure state can be saved permanently...
  • TeNPy

  • Referenced in 1 article [sw27023]
  • Networks: Tensor Network Python (TeNPy). Tensor product state (TPS) based methods are powerful tools ... many-body systems in and out of equilibrium. In particular, the one-dimensional matrix-product...
  • HAGIS

  • Referenced in 4 articles [sw08581]
  • coordinate system related to an equilibrium magnetic field whose surfaces are perturbed by a magnetohydrodynamic ... linear growth regime to a nonlinear saturated state...
  • Plasimo

  • Referenced in 2 articles [sw10736]
  • plasma sources of various degrees of equilibrium. It comes with a number of electromagnetic modules ... coordinate systems. Plasimo supports transient and steady-state simulations of plasma sources...
  • RactIP

  • Referenced in 2 articles [sw17120]
  • integrate approximate information on an ensemble of equilibrium joint structures into the objective function ... least comparable to that of several state-of-the-art methods for RNA–RNA interaction...
  • TSolMod

  • Referenced in 2 articles [sw19062]
  • TSolMod C++ class library for equation of state and activity models, which ensures broad applicability ... efficient data exchange with the GEM IPM equilibrium solver; open conceptual design that allows straightforward...
  • bsmKinetic

  • Referenced in 0 articles [sw22296]
  • molecular systems with many electronic states involved in photochemical transformations. It also allows simulating ... charge transfer occurring in both equilibrium and nonequilibrium regimes. bsmKinetic is open-source software distributed...
  • VENUS-LEVIS

  • Referenced in 1 article [sw19957]
  • structures such as helical saturated tokamak plasma states, stellarator geometry and resonant magnetic perturbations ... vacuum field is added to the 2D equilibrium, creating islands and stochastic regions, the other...
  • Lightweaver

  • Referenced in 1 article [sw39364]
  • spectral line profiles out of local thermodynamic equilibrium have always been focused on speed ... Python, without sacrificing speed against the current state of the art. The goal of providing...
  • PyBerny

  • Referenced in 1 article [sw33442]
  • input, and returns a new equilibrium structure estimate. The package implements a single optimization algorithm ... crystal geometries, coordinate constraints, coordinate weighting, transition state search. PyBerny is available in PySCF...
  • HyRG

  • Referenced in 0 articles [sw20152]
  • those that yield stable, unstable, etc. equilibrium points. We partition the components describing discrete behavior ... invariants) to allow either time-dependent or state-dependent switching, and in particular provide...