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Unverified Commit 2e035026 authored by Han Lu's avatar Han Lu Committed by GitHub
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quick fix of typo, grammar, etc (#2362)

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...@@ -14,14 +14,14 @@ is turned into an executable object. ...@@ -14,14 +14,14 @@ is turned into an executable object.
Terminology Terminology
----------- -----------
In Arbor's codebase some prefixes are used as a low-key namespacing In Arbor's codebase, some prefixes are used as a low-key namespacing.
- ``arb_``:: Mech ABI types, in general use through out Arbor, eg - ``arb_``:: Mech ABI types, in general use throughout Arbor, eg
``arb_mechanism_type``. ``arb_mechanism_type``.
- ``fvm_``:: Concerning use by the Finite Volume Method (FVM), eg - ``fvm_``:: Concerning use by the Finite Volume Method (FVM), eg
``fvm_lowered_cell``. ``fvm_lowered_cell``.
- ``mc_``:: Related to Multi-Compartment (Cells), identical to cable cells the - ``mc_``:: Related to Multi-Compartment (Cells), identical to cable cells, the
difference is purely historical, eg ``cable_cell_group``. difference is purely historical, e.g., ``cable_cell_group``.
Setting up a Cable Cell simulation Setting up a Cable Cell simulation
---------------------------------- ----------------------------------
...@@ -37,7 +37,7 @@ Arbor constructs a runnable simulation from three ingredients: ...@@ -37,7 +37,7 @@ Arbor constructs a runnable simulation from three ingredients:
The interesting part here is the ``recipe``, which is used to lazily produce the The interesting part here is the ``recipe``, which is used to lazily produce the
data required by the ``simulation`` and ``domain_decomposition``. A simple example data required by the ``simulation`` and ``domain_decomposition``. A simple example
might be this model of a single cell might be this model of a single cell.
.. code:: c++ .. code:: c++
...@@ -69,11 +69,11 @@ ion channels are described by a structure ``(name, [(parameter, value)])``. ...@@ -69,11 +69,11 @@ ion channels are described by a structure ``(name, [(parameter, value)])``.
Lowered Cells, Shared State, and the Discretisation Lowered Cells, Shared State, and the Discretisation
--------------------------------------------------- ---------------------------------------------------
To obtain a simulation we need to turn the ``cable_cell`` description object To obtain a simulation, we need to turn the ``cable_cell`` description object
into a ``fvm_lowered_cell``. However, multiple cells are collected into a into a ``fvm_lowered_cell``. However, multiple cells are collected into a
``cable_cell_group`` and ``fvm_lowered_cell`` is the lowered representation of a ``cable_cell_group`` and ``fvm_lowered_cell`` is the lowered representation of a
full cell group. The ``fvm_lowered_cell`` is responsible for holding the full cell group. The ``fvm_lowered_cell`` is responsible for holding the
backend-specific data of a cell group, managing sampling and stimuli, facilitate backend-specific data of a cell group, managing sampling and stimuli, facilitating
event processing, and driving time integration. event processing, and driving time integration.
Discretisation splits the segments described by the morphology into *control Discretisation splits the segments described by the morphology into *control
...@@ -98,10 +98,9 @@ Now we are in a state to simulate a cell group by calling ...@@ -98,10 +98,9 @@ Now we are in a state to simulate a cell group by calling
The integration in Arbor proceeds in *epochs* with a length less than half a The integration in Arbor proceeds in *epochs* with a length less than half a
time constant :math:`T_{min}`, which is the maximum time over which cell groups time constant :math:`T_{min}`, which is the maximum time over which cell groups
can evolve independently. The length :math:`T_{min}` is derived as the minimum over all can evolve independently. The length :math:`T_{min}` is derived as the minimum overall
axonal/synaptic delays. This works since we know that an event at time :math:`t` axonal/synaptic delays. This works since we know that an event at time :math:`t`
can have an effect at time :math:`t + T_{min}` at the soonest. The factor of one can have an effect at time :math:`t + T_{min}` at the soonest. The factor of one-half stems from double-buffering to overlap communication and computation. So,
half stems from double-buffering to overlap communication and computation. So,
Arbor collects all events in an epoch and transmits them in bulk, see Arbor collects all events in an epoch and transmits them in bulk, see
:ref:`Communication <communication>` for details. :ref:`Communication <communication>` for details.
......
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