
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 userspecified 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 gyrokinetic 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 postprocessing 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 nonequilibrium 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 stateoftheart optimization solvers...

CHNOSZ
 Referenced in 0 articles
[sw15144]
 KirkhamFlowers 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 ... timedependent system is integrated to steady state. A limitation that is identified for UEDGE...

BCYCLIC
 Referenced in 4 articles
[sw00070]
 processor numbers. Comparison with a stateofthe art parallel sparse solver is presented ... solver in magnetohydrodynamic (MHD), threedimensional equilibrium solvers for hightemperature 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...

DRAIN2D
 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 ... manybody systems in and out of equilibrium. In particular, the onedimensional matrixproduct...

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 steadystate 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 stateoftheart 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 opensource software distributed...

VENUSLEVIS
 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 timedependent or statedependent switching, and in particular provide...