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Sam Yates authored
Address inconsistencies in unit conversions between current updates, initialization, ionic currents etc.

Fixes issues #793 and #798.

* Correct units in comments for ion state iX_ to a current density.
* Remove conversion factor for NMODL current densities [mA/cm²] to Arbor current densities [A/m²] from layout weight: from the point of view of Arbor, mechanisms now write in units that Arbor uses natively.
* Remove weight_ as a magic modcc variable; applying weight_ is now performed directly by code generated by printers.
* Change IndexedVariable interface: remove redundant index_name; remove 'op'. Whether external data is accumulated or assigned is now a property of the corresponding sourceKind.
* Conversion factors for NMODL <-> Arbor are collated in printerutils.cpp, determined by the external data sourceKind.
* Permit direct assignment of external data, as opposed to a weighted sum. This behaviour will be required for reversal potential handling.
* `current_` and `conducitivity_` get a different sourceKind in point mechanisms, allowing us to distinguish current contributions from current density contributions (and applying correct unit scaling accordingly.)
* Add unit test for correct initialization and scaling of ionic currents, together with two corresponding unit test mechanisms.
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Arbor Library

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Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models.

An installation guide and library documentation are available online at Read the Docs.

Submit a ticket if you have any questions or want help.

Citing Arbor

It is possible to cite specific versions of Arbor used to run a simulation via Zenodo:

  • Version 0.2: DOI
  • Version 0.1: DOI

The following BibTeX can be used to cite Arbor:

@INPROCEEDINGS{
    paper:arbor2019,
    author={N. A. {Akar} and B. {Cumming} and V. {Karakasis} and A. {Küsters} and W. {Klijn} and A. {Peyser} and S. {Yates}},
    booktitle={2019 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP)},
    title={{Arbor --- A Morphologically-Detailed Neural Network Simulation Library for Contemporary High-Performance Computing Architectures}},
    year={2019}, month={feb}, volume={}, number={},
    pages={274--282},
    doi={10.1109/EMPDP.2019.8671560},
    ISSN={2377-5750}}

Alternative citation formats for the paper can be downloaded here, and a preprint is available at arXiv.