Assimulo: A unified framework for ODE solvers

Andersson, Christian; Führer, Claus; Åkesson, Johan

doi:10.1016/j.matcom.2015.04.007

Cited by 80 publications

(64 citation statements)

References 15 publications

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“…By parsing a chemical equation file, obtained from the MCM project, PyBox creates files that account for the gas phase chemistry as well as automatically calculating properties that dictate gas-to-particle partitioning through connection with the UManSysProp informatics suite (Topping et al, 2016). Written in Python, PyBox uses Numba (Lam, Pitrou, & Seibert, 2015) or the Fortran-toPython-Generator f2py (Peterson, 2009) to perform calculations currently within a library of ODE solvers provided by the Assimulo package (Andersson, Führer, & Åkesson, 2015).…”

Section: Discussionmentioning

confidence: 99%

PyBox: An automated box-model generator for atmospheric chemistry and aerosol simulations.

Topping¹,

Connolly²,

Reid³

2018

JOSS

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SummaryAir pollution and climate change are two of the biggest multidisciplinary challenges in society today. The need to understand the chemical and physical processes in the atmosphere that dictate the impacts of both has created a wide range of research platforms. These include numerical models. Volatile organic compounds (VOCs), emitted from both natural and anthropogenic sources, are oxidised in the atmosphere to form lower-volatility species that form organic particulate matter in the atmosphere through gas-to-particle partitioning. Chemical mechanisms, such as the Master Chemical Mechanism (MCM) (Jenkin, Saunders, Wagner, & Pilling, 2003), have been built to hold information of all relevant species and reactions in the atmosphere.However, it is becoming extremely hard to develop models that can respond to our growing body of knowledge since these mechanisms now treat thousands of species and tens of thousands of reactions. Researchers need to simulate the evolution of each individual species over a range of time-scales and ambient conditions. Manually setting up the relevant ordinary differential equations definitions [ODEs] and associated solvers would present a huge challenge given the number of compounds and equations involved. In addition, it is important to test sensitivity to rate coefficients or evaluate the impact of emerging laboratory data that might identify new reaction pathways or new, improved rate coefficients. Added to this complexity is the need to account for gas-to-particle partitioning of each compound. The atmosphere has varying concentrations of particulate matter that might act as a condensational sink for each compound. Predicting that partitioning requires calculations of molecular properties including saturation vapour pressures. Automation is essential, not least to ensure the gas phase chemistry is accounted for alongside the gas-to-particle partitioning and reproducibility is ensured. This is the driver behind PyBox.

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Section: Discussionmentioning

confidence: 99%

PyBox: An automated box-model generator for atmospheric chemistry and aerosol simulations.

Topping¹,

Connolly²,

Reid³

2018

JOSS

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“…The DAE solver in Assimulo (Andersson et al, 2014) was used to integrate the extraction curves. Given the nonlinear, multi-parameter nature of the optimisation, it was important to use a global minimisation algorithm in conjunction with a local minimiser.…”

Section: Optimisation Methodsmentioning

confidence: 99%

“…For each combination of parameter values, Equation (7) was integrated over βt * using the Assimulo differential algebraic solver (Andersson et al, 2014). n ′ was then tuned so that Equation (21) gave the smallest least squares error in X compared to the standard model's curve.…”

Section: Separation Of the Shrinking Core Model Equationmentioning

confidence: 99%

Models for apparent reaction kinetics in heap leaching: A new semi-empirical approach and its comparison to shrinking core and other particle-scale models

et al. 2016

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Particle-scale effects are critically important to the performance of heap leaching operations. In a heap-scale simulation, the transport of fluid phases and reactive species external to the ore particles might be modelled with thousands of grid elements by the finite volume or finite element method. The inter-and intra-particle diffusions and reactions are usually parametrised by a deterministic model, such as the shrinking core model (SCM), that translates the external conditions into an effective product extraction rate. However, the rate equation takes the form of an implicit or partial differential equation for all but the simplest models and kinetic regimes, becoming expensive to solve on large grids. We instead propose an economical, easily calibrated semi-empirical approach in which the dependencies on external conditions and the current state of the ore are considered to be mathematically separable. We show that the standard SCM does not suffer greatly from this approximation even when there is a mixed control regime with nonlinear kinetics. The dependency on the state of the ore is derived empirically, inherently capturing heterogeneous features and cluster-scale effects. We demonstrate that this method scales correctly when fitted to data from physical column leaching experiments.

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“…Assimulo [54]. Finally, the model was fitted to the transient permeation data using the Nelder-Mead method and subsequently refined by the least-squares method, both from lmfit package [55].…”

Section: Permeation Experimentsmentioning

confidence: 99%

Aging of polymers of intrinsic microporosity tracked by methanol vapour permeation

Pilnáček

Vopička

Lanč

et al. 2016

Journal of Membrane Science

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The initially very promising transport properties of glassy high free volume polymers deteriorate rapidly over time. In this work, we focused on this aging phenomenon in two polymers of intrinsic microporosity (PIMs), namely PIM-1 and PIM-EA-TB. To identify the main mechanisms involved, we studied the time-declines of permeability and diffusivity of methanol vapours in flat membranes with approximately equal thicknesses. The permeation measurements were carried out using a continuous flow permeation method with carrier gas, where the methanol vapours were held at constant activity 0.2 at 25°C. Two different experimental modes were used: (i) continuous experiments that consisted of one long experiment with a duration of over 650 hours for each polymer and (ii) momentary experiments that consisted of a vast number of short (ca. 6 hours) consecutive measurements of transient permeation. The observed decreases of methanol permeability due to aging were more intense in the case of continuous mode for both polymers. In other words, the aging was ca.

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Assimulo: A unified framework for ODE solvers

Cited by 80 publications

References 15 publications

PyBox: An automated box-model generator for atmospheric chemistry and aerosol simulations.

PyBox: An automated box-model generator for atmospheric chemistry and aerosol simulations.

Models for apparent reaction kinetics in heap leaching: A new semi-empirical approach and its comparison to shrinking core and other particle-scale models

Aging of polymers of intrinsic microporosity tracked by methanol vapour permeation

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