EqtypeSpecifies the PDE system to solve. The following values are supported:
Monodomain: solve the monodomain equation.
BidomainRoth: solve the bidomain equations using the Roth formulation.
CellModelSpecifies the cell model to use. Available cell models are
ProjectionSpecifies the Galerkin projection type to use. Only
Continuoushas been extensively tested.
TimeIntegrationMethodSpecifies the time integration scheme to use for advancing the PDE system. This must be an IMEX scheme. Suitable choices are:
IMEXdirk_3_4_3. The cell model state variables are time advanced using Forward Euler for the ion concentrations, and Rush-Larsen for the cell model gating variables.
DiffusionAdvancementSpecifies whether the diffusion is handled implicitly or explicitly in the time integration scheme. The current code only supports
Implicitintegration of the diffusion term. The cell model is always integrated explicitly.
The following parameters can be specified in the
PARAMETERS section of the session file.
Example values are taken from .
Chisets the surface-to-volume ratio (Units: mm-1).
Cmsets the specific membrane capacitance (Units: μFmm-2).
Substepssets the number of substeps taken in time integrating the cell model for each PDE timestep.
o_maxspecifies a bijective map to assign conductivity values σ to intensity values μ when using the
IsotropicConductivityfunction. The intensity map is first thresholded to the range [dmin,dmax] and then the conductivity is calculated as
|σ = (1 - μ) + omin|
The following functions can be specified inside the
CONDITIONS section of the session file. If
both are specified, the effect is multiplicative. Example values are taken from .
IsotropicConductivityspecifies the conductivity σ of the tissue.
The variable name to use is
intensity since the conductivity may be derived
from late-Gadolinium enhanced MRA imaging. Example specifications are
scarmap.con is a Nektar++ field file containing a variable
the conductivity across the domain.
AnisotropicConductivityspecifies the conductivity σ of the tissue.
CellHistoryPointswrites all cell model states over time at fixed points. Can be used along with the
HistoryPointsfilter to record all variables at specific points during a simulation.
OutputFilespecifies the filename to write history data to.
OutputFrequencyspecifies the number of steps between successive outputs.
Pointslists coordinates at which history data is to be recorded.
CheckpointCellModelcheckpoints the cell model. Can be used along with the
Checkpointfilter to record complete simulation state and regular intervals.
OutputFile(optional) specifies the base filename to use. If not specified, the session name is used. Checkpoint files are suffixed with the process ID and the extension ‘.chk‘.
OutputFrequencyspecifies the number of timesteps between checkpoints.
ElectrogramComputes virtual unipolar electrograms at a prescribed set of points.
OutputFile(optional) specifies the base filename to use. If not specified, the session name is used. The extension ‘.ecg‘ is appended if not already specified.
OutputFrequencyspecifies the number of resolution of the electrogram data.
Pointsspecifies a list of coordinates at which electrograms are desired. They must not lie within the domain.
BenchmarkRecords spatially distributed event times for activation and repolarisation (recovert) during a simulation, for undertaking benchmark test problems.
ThresholdValuespecifies the value above which tissue is considered to be depolarised and below which is considered repolarised.
InitialValuespecifies the initial value of the activation or repolarisation time map.
OutputFilespecifies the base filename of activation and repolarisation maps output from the filter. This name is appended with the index of the event and the suffix ‘.fld‘.
StartTime(optional) specifies the simulation time at which to start detecting events.
Electrophysiological propagaion is initiated through the stimulus current Iion. The
section describes one or more regions of stimulus and the time-dependent protocol with which
they are applied.
A number of stimulus types are available
StimulusRectstimulates a cuboid-shaped region of the domain, specified by two coordinates (x1,y1,z1) and (x2,y2,z2). An additional parameter specifies the "smoothness" of the boundaries of the region; higher values produce a sharper boundary. Finally, the maximum strength of the stimulus current is specified in μA∕mm3
StimulusCircstimulates a spherical region of the domain, as specified by a centre and radius. The smoothness and strength parameters are also specified as for ‘StimulusRect‘.
A protocol specifies the time-dependent function indicating the strength of the stimulus and
PROTOCOL section should be included within each
STIMULUS. This can be expressed as
ProtocolSinglea single stimulus is applied at a given start time and for a given duration
ProtocolS1a train of pulses of fixed duration applied at a given start time and with a given cycle length.
ProtocolS1S2same as ‘ProtocolS1‘ except with an additional single pulse applied at a different cycle length at the end of the train of S1 pulses.