From 32cf64b6f1610e3857b097a104963e9297d12789 Mon Sep 17 00:00:00 2001 From: nrnhines Date: Sat, 9 Nov 2024 11:35:59 -0500 Subject: [PATCH] fix mispelling of Crank-Nicolson (#3186) --- docs/courses/state_and_parameter_discontinuities.rst | 2 +- docs/guide/what_is_neuron.rst | 2 +- docs/hoc/modelspec/programmatic/topology/geometry.rst | 2 +- docs/hoc/simctrl/programmatic.rst | 4 ++-- docs/python/modelspec/programmatic/topology/geometry.rst | 2 +- docs/python/simctrl/programmatic.rst | 4 ++-- docs/videos/neuron-course-2021.rst | 2 +- share/examples/nrniv/nrnoc/implic.hoc | 2 +- 8 files changed, 10 insertions(+), 10 deletions(-) mode change 100755 => 100644 docs/python/modelspec/programmatic/topology/geometry.rst mode change 100755 => 100644 docs/python/simctrl/programmatic.rst mode change 100755 => 100644 share/examples/nrniv/nrnoc/implic.hoc diff --git a/docs/courses/state_and_parameter_discontinuities.rst b/docs/courses/state_and_parameter_discontinuities.rst index 29f169c86d..07bff67f6a 100644 --- a/docs/courses/state_and_parameter_discontinuities.rst +++ b/docs/courses/state_and_parameter_discontinuities.rst @@ -75,4 +75,4 @@ To work properly with variable time step methods, models that change states and/ fih = h.FInitializeHandler(setup_discontinuities) - It will be helpful to use the Crank-Nicholson fixed step method and compare the variable step method with and without the ``cvode.re_init()``. Zoom in around the discontinuity at 2 ms. \ No newline at end of file + It will be helpful to use the Crank-Nicolson fixed step method and compare the variable step method with and without the ``cvode.re_init()``. Zoom in around the discontinuity at 2 ms. \ No newline at end of file diff --git a/docs/guide/what_is_neuron.rst b/docs/guide/what_is_neuron.rst index bda8f24084..5aea93157d 100644 --- a/docs/guide/what_is_neuron.rst +++ b/docs/guide/what_is_neuron.rst @@ -41,7 +41,7 @@ Integrator-independent model specification NEURON offers several different, user-selectable numerical integration methods. * The default integration method is implicit Euler, which provides robust stability and first order accuracy in time (sufficient for most applications). -* There is also a Crank-Nicholson method that provides second order accuracy at little additional computational cost. However, this is prone to numerical oscillations if dt is too long, voltage clamps are present, or system states are described by algebraic equations. +* There is also a Crank-Nicolson method that provides second order accuracy at little additional computational cost. However, this is prone to numerical oscillations if dt is too long, voltage clamps are present, or system states are described by algebraic equations. * Increased accuracy, faster run times, and sometimes both, may be achieved by choosing adaptive integration, which adjusts integration order and time step as necessary to satisfy a local error criterion. For historical reasons, the adaptive integrators are genericallly called "CVODE" in NEURON; the actual method is either IDA (Hindmarsh and Taylor, 1999) or CVODES (Hindmarsh and Serban, 2002), a decision that is made automatically (i.e. without requiring user judgement) depending on whether or not a model involves states that are described by algebraic equations. Users can switch between these integration methods without having to rewrite the model specification because NEURON avoids computation-specific representations of biological properties. This convenience is essential because deciding which method is best in any particular situation is often an empirical question. Further details about numeric integration in NEURON are provided in chapter 4 of The NEURON Book (Carnevale and Hines, 2006). diff --git a/docs/hoc/modelspec/programmatic/topology/geometry.rst b/docs/hoc/modelspec/programmatic/topology/geometry.rst index dc144af124..1f51b064de 100644 --- a/docs/hoc/modelspec/programmatic/topology/geometry.rst +++ b/docs/hoc/modelspec/programmatic/topology/geometry.rst @@ -13,7 +13,7 @@ any tree-shaped structure but loops are not permitted. (You may, however, develop membrane mechanisms, such as electrical gap junctions which do not have the loop restriction. But be aware that the electrical current flows through such connections are calculated by a modified euler -method instead of the more numerically robust fully implicit/crank-nicholson +method instead of the more numerically robust fully implicit/crank-nicolson methods) Do not confuse sections with segments. Sections are divided into segments diff --git a/docs/hoc/simctrl/programmatic.rst b/docs/hoc/simctrl/programmatic.rst index 4f3d46e59e..ea51915914 100644 --- a/docs/hoc/simctrl/programmatic.rst +++ b/docs/hoc/simctrl/programmatic.rst @@ -230,14 +230,14 @@ Functions are proportional to :hoc:data:`dt`. =1 - crank-nicholson Can give large (but damped) numerical error + crank-nicolson Can give large (but damped) numerical error oscillations. For small :hoc:data:`dt` the numerical errors are proportional to ``dt^2``. Cannot be used with voltage clamps. Ionic currents are first order correct. Channel conductances are second order correct when plotted at ``t+dt/2`` =2 - crank-nicholson like 1 but in addition Ion currents (*ina*, *ik*, + crank-nicolson like 1 but in addition Ion currents (*ina*, *ik*, etc) are fixed up so that they are second order correct when plotted at ``t-dt/2`` diff --git a/docs/python/modelspec/programmatic/topology/geometry.rst b/docs/python/modelspec/programmatic/topology/geometry.rst old mode 100755 new mode 100644 index edc855739d..66041336c4 --- a/docs/python/modelspec/programmatic/topology/geometry.rst +++ b/docs/python/modelspec/programmatic/topology/geometry.rst @@ -11,7 +11,7 @@ any tree-shaped structure but loops are not permitted. (You may, however, develop membrane mechanisms, such as electrical gap junctions which do not have the loop restriction. But be aware that the electrical current flows through such connections are calculated by a modified euler -method instead of the more numerically robust fully implicit/crank-nicholson +method instead of the more numerically robust fully implicit/crank-nicolson methods) Do not confuse sections with segments. Sections are divided into segments diff --git a/docs/python/simctrl/programmatic.rst b/docs/python/simctrl/programmatic.rst old mode 100755 new mode 100644 index 1f4646da54..153648367b --- a/docs/python/simctrl/programmatic.rst +++ b/docs/python/simctrl/programmatic.rst @@ -231,14 +231,14 @@ Functions are proportional to :data:`dt`. =1 - crank-nicholson Can give large (but damped) numerical error + crank-nicolson Can give large (but damped) numerical error oscillations. For small :data:`dt` the numerical errors are proportional to ``dt^2``. Cannot be used with voltage clamps. Ionic currents are first order correct. Channel conductances are second order correct when plotted at ``t+dt/2`` =2 - crank-nicholson like 1 but in addition Ion currents (*ina*, *ik*, + crank-nicolson like 1 but in addition Ion currents (*ina*, *ik*, etc) are fixed up so that they are second order correct when plotted at ``t-dt/2`` diff --git a/docs/videos/neuron-course-2021.rst b/docs/videos/neuron-course-2021.rst index 49c22ff54c..eb2dafe06f 100644 --- a/docs/videos/neuron-course-2021.rst +++ b/docs/videos/neuron-course-2021.rst @@ -149,7 +149,7 @@ Topics: - synapses, spike-triggered transmission, :class:`NetCon` - artificial spiking cells (:class:`IntFire1`, :class:`IntFire2`, :class:`IntFire4`) -- Forward Euler vs Backward Euler vs Crank-Nicholson; fixed step vs variable step +- Forward Euler vs Backward Euler vs Crank-Nicolson; fixed step vs variable step .. raw:: html diff --git a/share/examples/nrniv/nrnoc/implic.hoc b/share/examples/nrniv/nrnoc/implic.hoc old mode 100755 new mode 100644 index 722b6c6e44..9cc7547d70 --- a/share/examples/nrniv/nrnoc/implic.hoc +++ b/share/examples/nrniv/nrnoc/implic.hoc @@ -1,4 +1,4 @@ -/* Comparison of implicit and crank-nicholson */ +/* Comparison of implicit and crank-nicolson */ /* showing that C-N can have error oscillations */ /* lambda = sqrt(1e4/4 * diam / (Ra * gl)) microns */