diff --git a/doc/concepts/decor.rst b/doc/concepts/decor.rst
index f1696e7a6e01d86e0151281ffc28a92d577dea56..f06b1be9b77976afb93f104fd1adf091322cd66f 100644
--- a/doc/concepts/decor.rst
+++ b/doc/concepts/decor.rst
@@ -137,25 +137,25 @@ Because a global parameter is fixed over the entire spatial extent
of a density mechanism, a new mechanism has to be created for every
combination of global parameter values.
-Take for example a mechanism passive leaky dynamics:
+Take for example the built-in mechanism for passive leaky dynamics:
-* Name: ``"passive"``.
-* Global variable: reversal potential ``"el"``.
+* Name: ``"pas"``
+* Global variable: reversal potential ``"e"``.
* Range variable: conductance ``"g"``.
.. code-block:: Python
- # Create pas mechanism with default parameter values (set in NMODL file).
- m1 = arbor.mechanism('passive')
+ # Create passive mechanism with default parameter values (set in NMODL file).
+ m1 = arbor.mechanism('pas')
- # Create default mechanism with custom conductance (range)
- m2 = arbor.mechanism('passive', {'g': 0.1})
+ # Create mechanism with custom conductance (range)
+ m2 = arbor.mechanism('pas', {'g': 0.1})
- # Create a new pas mechanism with that changes reversal potential (global)
- m3 = arbor.mechanism('passive/el=-45')
+ # Create a new passive mechanism with that changes reversal potential (global)
+ m3 = arbor.mechanism('pas/e=-45')
# Create an instance of the same mechanism, that also sets conductance (range)
- m4 = arbor.mechanism('passive/el=-45', {'g': 0.1})
+ m4 = arbor.mechanism('pas/e=-45', {'g': 0.1})
decor = arbor.decor()
decor.paint('"soma"', m1)
diff --git a/doc/concepts/mechanisms.rst b/doc/concepts/mechanisms.rst
index b67ea243d9bf6d5464ecb6c7ebe0e0a746a96ce4..8bc847ccaabe42bbc2522e07a942cb8bba0b0967 100644
--- a/doc/concepts/mechanisms.rst
+++ b/doc/concepts/mechanisms.rst
@@ -97,17 +97,17 @@ that specifies values for range parameters.
For example, consider a mechanism that models passive leaky dynamics with
the following parameters:
-* *Name*: ``"passive"``.
-* *Global parameter*: reversal potential ``el``, default -65 mV.
+* *Name*: ``"pas"``.
+* *Global parameter*: reversal potential ``e``, default -70 mV.
* *Range parameter*: conductance ``g``, default 0.001 Sâ‹…cmâ»Â².
The following example mechanism descriptions for our passive mechanism show that parameters and
ion species dependencies only need to be specified when they differ from their defaults:
-* ``("passive")``: the passive mechanism with default parameters.
-* ``("passive/el=-80")``: derive a new passive mechanism with a non-default value for global parameter.
-* ``("passive", {"gl": 0.005})``: passive mechanism with a new a non-default range parameter value.
-* ``("passive/el=-80", {"gl": 0.005})``: derive a new passive mechanism that overrides both
+* ``("pas")``: the passive mechanism with default parameters.
+* ``("pas/e=-80")``: derive a new passive mechanism with a non-default value for global parameter.
+* ``("pas", {"g": 0.005})``: passive mechanism with a new a non-default range parameter value.
+* ``("pas/e=-80", {"g": 0.005})``: derive a new passive mechanism that overrides both
Similarly to global parameters, ion species can be renamed in the mechanism name.
This allows the use of generic mechanisms that can be adapted to a specific species
diff --git a/doc/python/mechanisms.rst b/doc/python/mechanisms.rst
index f1825e85136c3e3ced419345a5312ab0d3b2b39c..abab8e535477aad1adf6ec3ef154a7bcc3ce6b25 100644
--- a/doc/python/mechanisms.rst
+++ b/doc/python/mechanisms.rst
@@ -41,7 +41,7 @@ mechanism that is to be painted or placed on the cable cell.
hh = arbor.mechanism('hh')
# A passive leaky channel with custom parameters
- pas = arbor.mechanism('pas', {'e': -55, 'gl': 0.02})
+ pas = arbor.mechanism('pas/e=-55.0', {'g': 0.02})
# Reversal potential using Nernst equation with GLOBAL parameter values
# for Faraday's constant and the target ion species, set with a '/' followed
@@ -96,13 +96,13 @@ mechanism that is to be painted or placed on the cable cell.
m2 = arbor.mechanism('pas', {'g', 0.1})
# Create a new pas mechanism with that changes reversal potential (global).
- m3 = arbor.mechanism('pas/el=-45')
+ m3 = arbor.mechanism('pas/e=-45')
# Create an instance of the same mechanism, that also sets conductance (range).
- m4 = arbor.mechanism('pas/el=-45', {'g', 0.1})
+ m4 = arbor.mechanism('pas/e=-45', {'g', 0.1})
# This is an equivalent to m4, using set method to specify range parameters.
- m5 = arbor.mechanism('pas/el=-45')
+ m5 = arbor.mechanism('pas/e=-45')
m5.set('g', 0.1)
# Decorate the 'soma' on a cable_cell.
@@ -110,7 +110,7 @@ mechanism that is to be painted or placed on the cable cell.
cell.paint('"soma"', m1)
cell.paint('"soma"', m2) # Error: can't place the same mechanism on overlapping regions
cell.paint('"soma"', m3) # This would be ok: m3 is a new, derived mechanism by virtue of
- # having a different name, i.e. 'pas/el=-45' vs. 'pas'.
+ # having a different name, i.e. 'pas/e=-45' vs. 'pas'.
.. py:class:: mechanism_info
diff --git a/example/gap_junctions/gap_junctions.cpp b/example/gap_junctions/gap_junctions.cpp
index 316efbcd227190bf24236cd9b0b5e020659553e4..323d7667bac3b96d864d63e4ed21375bb1e2f0ec 100644
--- a/example/gap_junctions/gap_junctions.cpp
+++ b/example/gap_junctions/gap_junctions.cpp
@@ -302,9 +302,8 @@ arb::cable_cell gj_cell(cell_gid_type gid, unsigned ncell, double stim_duration)
arb::mechanism_desc kamt("kamt");
kamt["gbar"] = 0.004;
- arb::mechanism_desc pas("pas");
+ arb::mechanism_desc pas("pas/e=-65.0");
pas["g"] = 1.0/12000.0;
- pas["e"] = -65;
// Paint density channels on all parts of the cell
decor.paint("(all)", nax);
diff --git a/example/lfp/lfp.cpp b/example/lfp/lfp.cpp
index dabba6de26be039baaf56f1e840027a966032a85..29a557d822b52cfe14e4947fc11aa72e55683ba5 100644
--- a/example/lfp/lfp.cpp
+++ b/example/lfp/lfp.cpp
@@ -91,7 +91,7 @@ private:
// Add pas and hh mechanisms:
dec.paint(reg::tagged(1), "hh"); // (default parameters)
- dec.paint(reg::tagged(4), mechanism_desc("pas").set("e", -70));
+ dec.paint(reg::tagged(4), mechanism_desc("pas/e=-70.0"));
// Add exponential synapse at centre of soma.
synapse_location_ = ls::on_components(0.5, reg::tagged(1));
diff --git a/mechanisms/default/pas.mod b/mechanisms/default/pas.mod
index 6653f34e1bf3a0b53f367c826f2d424ca7f86927..d7ffb028db72ab3be03e532042b9723f58968b5d 100644
--- a/mechanisms/default/pas.mod
+++ b/mechanisms/default/pas.mod
@@ -1,23 +1,21 @@
+NEURON {
+ SUFFIX pas
+ NONSPECIFIC_CURRENT i
+ RANGE g
+ GLOBAL e
+}
+
UNITS {
(mV) = (millivolt)
(S) = (siemens)
}
-NEURON {
- SUFFIX pas
- NONSPECIFIC_CURRENT i
- RANGE g, e
-}
INITIAL {}
PARAMETER {
g = .001 (S/cm2)
- e = -65 (mV) : we use -65 for the ball and stick model, instead of Neuron default of -70
-}
-
-ASSIGNED {
- v (mV)
+ e = -70 (mV) : Taken from nrn
}
BREAKPOINT {