From fc995b105709410aa365521c128f2c9ed873d77c Mon Sep 17 00:00:00 2001 From: Alexey Serenko Date: Thu, 9 Nov 2017 14:51:08 +0300 Subject: [PATCH 1/3] Correct a few typos in documentation comments post-syapic -> postsynaptic, neruons -> neurons, is achieve -> is achieved. --- models/hh_psc_alpha.h | 2 +- models/hh_psc_alpha_gap.h | 2 +- models/iaf_neuron.h | 2 +- models/iaf_psc_alpha.h | 2 +- models/iaf_psc_exp.h | 2 +- models/iaf_tum_2000.h | 2 +- nestkernel/nestmodule.cpp | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/models/hh_psc_alpha.h b/models/hh_psc_alpha.h index a57dd03ca6..9a5024bf6d 100644 --- a/models/hh_psc_alpha.h +++ b/models/hh_psc_alpha.h @@ -65,7 +65,7 @@ Name: hh_psc_alpha - Hodgkin Huxley neuron model. hh_psc_alpha is an implementation of a spiking neuron using the Hodkin-Huxley formalism. - (1) Post-syaptic currents + (1) Post-synaptic currents Incoming spike events induce a post-synaptic change of current modelled by an alpha function. The alpha function is normalised such that an event of weight 1.0 results in a peak current of 1 pA. diff --git a/models/hh_psc_alpha_gap.h b/models/hh_psc_alpha_gap.h index 5a1ea539d9..afd4ce35c3 100644 --- a/models/hh_psc_alpha_gap.h +++ b/models/hh_psc_alpha_gap.h @@ -69,7 +69,7 @@ Name: hh_psc_alpha_gap - Hodgkin Huxley neuron model with gap-junction support. additionally supports gap junctions. - (1) Post-syaptic currents + (1) Post-synaptic currents Incoming spike events induce a post-synaptic change of current modelled by an alpha function. The alpha function is normalised such that an event of weight 1.0 results in a peak current of 1 pA. diff --git a/models/iaf_neuron.h b/models/iaf_neuron.h index c9f29b3828..eb0ece8cac 100644 --- a/models/iaf_neuron.h +++ b/models/iaf_neuron.h @@ -98,7 +98,7 @@ I_e double - Constant external input current in pA. Remarks: If tau_m is very close to tau_syn, the model will numerically behave as if tau_m is equal to tau_syn to avoid numerical instabilities. -For details, please see IAF_Neruons_Singularity.ipynb in +For details, please see IAF_Neurons_Singularity.ipynb in the NEST source code (docs/model_details). References: diff --git a/models/iaf_psc_alpha.h b/models/iaf_psc_alpha.h index adea2b7a3f..f7df1e9b7e 100644 --- a/models/iaf_psc_alpha.h +++ b/models/iaf_psc_alpha.h @@ -102,7 +102,7 @@ Name: iaf_psc_alpha - Leaky integrate-and-fire neuron model. If tau_m is very close to tau_syn_ex or tau_syn_in, the model will numerically behave as if tau_m is equal to tau_syn_ex or tau_syn_in, respectively, to avoid numerical instabilities. - For details, please see IAF_Neruons_Singularity.ipynb in + For details, please see IAF_Neurons_Singularity.ipynb in the NEST source code (docs/model_details). References: diff --git a/models/iaf_psc_exp.h b/models/iaf_psc_exp.h index e0c0a80c46..5cc60abdc8 100644 --- a/models/iaf_psc_exp.h +++ b/models/iaf_psc_exp.h @@ -93,7 +93,7 @@ namespace nest If tau_m is very close to tau_syn_ex or tau_syn_in, the model will numerically behave as if tau_m is equal to tau_syn_ex or tau_syn_in, respectively, to avoid numerical instabilities. - For details, please see IAF_Neruons_Singularity.ipynb in the + For details, please see IAF_Neurons_Singularity.ipynb in the NEST source code (docs/model_details). iaf_psc_exp can handle current input in two ways: Current input diff --git a/models/iaf_tum_2000.h b/models/iaf_tum_2000.h index a501e49648..50b23922d7 100644 --- a/models/iaf_tum_2000.h +++ b/models/iaf_tum_2000.h @@ -104,7 +104,7 @@ namespace nest If tau_m is very close to tau_syn_ex or tau_syn_in, the model will numerically behave as if tau_m is equal to tau_syn_ex or tau_syn_in, respectively, to avoid numerical instabilities. - For details, please see IAF_Neruons_Singularity.ipynb in + For details, please see IAF_Neurons_Singularity.ipynb in the NEST source code (docs/model_details). References: diff --git a/nestkernel/nestmodule.cpp b/nestkernel/nestmodule.cpp index 49f2c5b82b..43f904cfef 100644 --- a/nestkernel/nestmodule.cpp +++ b/nestkernel/nestmodule.cpp @@ -726,7 +726,7 @@ NestModule::ResetKernelFunction::execute( SLIInterpreter* i ) const at T=0. The dynamic state comprises typically the membrane potential, synaptic currents, buffers holding input that has been delivered, but not yet become effective, and all events pending delivery. Technically, this - is achieve by calling init_state() on all nodes and forcing a call to + is achieved by calling init_state() on all nodes and forcing a call to init_buffers() upon the next call to Simulate. Node parameters, such as time constants and threshold potentials, are not affected. From d845c825be9eed2634ec7a385d43fbf73f8038aa Mon Sep 17 00:00:00 2001 From: Alexey Serenko Date: Wed, 29 Nov 2017 11:22:51 +0300 Subject: [PATCH 2/3] Correct the reference to IPython notebook in docs IAF_Neurons_Singularity.ipynb -> IAF_neurons_singularity.ipynb, because this is how it is named there in doc/model_details. --- models/iaf_psc_alpha.h | 2 +- models/iaf_psc_exp.h | 2 +- models/iaf_tum_2000.h | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/models/iaf_psc_alpha.h b/models/iaf_psc_alpha.h index f7df1e9b7e..4152866244 100644 --- a/models/iaf_psc_alpha.h +++ b/models/iaf_psc_alpha.h @@ -102,7 +102,7 @@ Name: iaf_psc_alpha - Leaky integrate-and-fire neuron model. If tau_m is very close to tau_syn_ex or tau_syn_in, the model will numerically behave as if tau_m is equal to tau_syn_ex or tau_syn_in, respectively, to avoid numerical instabilities. - For details, please see IAF_Neurons_Singularity.ipynb in + For details, please see IAF_neurons_singularity.ipynb in the NEST source code (docs/model_details). References: diff --git a/models/iaf_psc_exp.h b/models/iaf_psc_exp.h index 5cc60abdc8..6776fb2bf1 100644 --- a/models/iaf_psc_exp.h +++ b/models/iaf_psc_exp.h @@ -93,7 +93,7 @@ namespace nest If tau_m is very close to tau_syn_ex or tau_syn_in, the model will numerically behave as if tau_m is equal to tau_syn_ex or tau_syn_in, respectively, to avoid numerical instabilities. - For details, please see IAF_Neurons_Singularity.ipynb in the + For details, please see IAF_neurons_singularity.ipynb in the NEST source code (docs/model_details). iaf_psc_exp can handle current input in two ways: Current input diff --git a/models/iaf_tum_2000.h b/models/iaf_tum_2000.h index 50b23922d7..26c264c9fd 100644 --- a/models/iaf_tum_2000.h +++ b/models/iaf_tum_2000.h @@ -104,7 +104,7 @@ namespace nest If tau_m is very close to tau_syn_ex or tau_syn_in, the model will numerically behave as if tau_m is equal to tau_syn_ex or tau_syn_in, respectively, to avoid numerical instabilities. - For details, please see IAF_Neurons_Singularity.ipynb in + For details, please see IAF_neurons_singularity.ipynb in the NEST source code (docs/model_details). References: From ffe6c1cbca665d685e27de375b9d84ae50ea4292 Mon Sep 17 00:00:00 2001 From: Alexey Serenko Date: Wed, 29 Nov 2017 12:28:16 +0300 Subject: [PATCH 3/3] Correct a few more minor typos The variable TauR in comments about refractory period is changed to how the corresponding refractory variables are named in the code. Also, leed -> lead, and a comma added before "defining" in "A time object r is constructed defining representation", because it is r what is defining, not the construction. --- models/iaf_chs_2007.h | 2 +- models/iaf_psc_delta.cpp | 10 +++++----- models/iaf_psc_exp.cpp | 10 +++++----- models/iaf_tum_2000.cpp | 29 +++++++++++++++-------------- models/iaf_tum_2000.h | 14 +++++++------- models/mat2_psc_exp.cpp | 4 ++-- 6 files changed, 35 insertions(+), 34 deletions(-) diff --git a/models/iaf_chs_2007.h b/models/iaf_chs_2007.h index 3b385f2284..a999478d73 100644 --- a/models/iaf_chs_2007.h +++ b/models/iaf_chs_2007.h @@ -45,7 +45,7 @@ namespace nest potentials (V_syn), waveforms that include a spike and the subsequent after-hyperpolarization (V_spike) and Gaussian-distributed white noise. - The postsynaptic potential is described by alpha function where where + The postsynaptic potential is described by alpha function where U_epsp is the maximal amplitude of the EPSP and tau_epsp is the time to peak of the EPSP. diff --git a/models/iaf_psc_delta.cpp b/models/iaf_psc_delta.cpp index eb51eea2d3..89cc7ad7df 100644 --- a/models/iaf_psc_delta.cpp +++ b/models/iaf_psc_delta.cpp @@ -250,20 +250,20 @@ nest::iaf_psc_delta::calibrate() V_.P30_ = 1 / P_.c_m_ * ( 1 - V_.P33_ ) * P_.tau_m_; - // TauR specifies the length of the absolute refractory period as + // t_ref_ specifies the length of the absolute refractory period as // a double in ms. The grid based iaf_psp_delta can only handle refractory // periods that are integer multiples of the computation step size (h). // To ensure consistency with the overall simulation scheme such conversion // should be carried out via objects of class nest::Time. The conversion // requires 2 steps: - // 1. A time object r is constructed defining representation of - // TauR in tics. This representation is then converted to computation + // 1. A time object r is constructed, defining representation of + // t_ref_ in tics. This representation is then converted to computation // time steps again by a strategy defined by class nest::Time. // 2. The refractory time in units of steps is read out get_steps(), a // member function of class nest::Time. // - // Choosing a TauR that is not an integer multiple of the computation time - // step h will leed to accurate (up to the resolution h) and self-consistent + // Choosing a t_ref_ that is not an integer multiple of the computation time + // step h will lead to accurate (up to the resolution h) and self-consistent // results. However, a neuron model capable of operating with real valued // spike time may exhibit a different effective refractory time. diff --git a/models/iaf_psc_exp.cpp b/models/iaf_psc_exp.cpp index 0b9b1e3366..06531cb592 100644 --- a/models/iaf_psc_exp.cpp +++ b/models/iaf_psc_exp.cpp @@ -269,20 +269,20 @@ nest::iaf_psc_exp::calibrate() V_.P20_ = P_.Tau_ / P_.C_ * ( 1.0 - V_.P22_ ); // P20_ = h/C_; - // TauR specifies the length of the absolute refractory period as + // t_ref_ specifies the length of the absolute refractory period as // a double in ms. The grid based iaf_psc_exp can only handle refractory // periods that are integer multiples of the computation step size (h). // To ensure consistency with the overall simulation scheme such conversion // should be carried out via objects of class nest::Time. The conversion // requires 2 steps: - // 1. A time object r is constructed defining representation of - // TauR in tics. This representation is then converted to computation + // 1. A time object r is constructed, defining representation of + // t_ref_ in tics. This representation is then converted to computation // time steps again by a strategy defined by class nest::Time. // 2. The refractory time in units of steps is read out get_steps(), a // member function of class nest::Time. // - // Choosing a TauR that is not an integer multiple of the computation time - // step h will leed to accurate (up to the resolution h) and self-consistent + // Choosing a t_ref_ that is not an integer multiple of the computation time + // step h will lead to accurate (up to the resolution h) and self-consistent // results. However, a neuron model capable of operating with real valued // spike time may exhibit a different effective refractory time. diff --git a/models/iaf_tum_2000.cpp b/models/iaf_tum_2000.cpp index 856c1c6f97..0e24a69c31 100644 --- a/models/iaf_tum_2000.cpp +++ b/models/iaf_tum_2000.cpp @@ -271,23 +271,24 @@ nest::iaf_tum_2000::calibrate() V_.P20_ = P_.Tau_ / P_.C_ * ( 1.0 - V_.P22_ ); // P20_ = h/C_; - // TauR specifies the length of the absolute refractory period as - // a double in ms. The grid based iaf_tum_2000 can only handle refractory - // periods that are integer multiples of the computation step size (h). - // To ensure consistency with the overall simulation scheme such conversion - // should be carried out via objects of class nest::Time. The conversion - // requires 2 steps: - // 1. A time object r is constructed defining representation of - // TauR in tics. This representation is then converted to computation - // time steps again by a strategy defined by class nest::Time. + // tau_ref_abs_ and tau_ref_tot_ specify the length of the corresponding + // refractory periods as doubles in ms. The grid based iaf_tum_2000 can + // only handle refractory periods that are integer multiples of the + // computation step size (h). To ensure consistency with the overall + // simulation scheme such conversion should be carried out via objects of + // class nest::Time. The conversion requires 2 steps: + // 1. A time object r is constructed, defining representation of + // tau_ref_{abs,tot} in tics. This representation is then converted + // to computation time steps again by a strategy defined by class + // nest::Time. // 2. The refractory time in units of steps is read out get_steps(), a // member function of class nest::Time. // - // Choosing a TauR that is not an integer multiple of the computation time - // step h will leed to accurate (up to the resolution h) and self-consistent - // results. However, a neuron model capable of operating with real valued - // spike time may exhibit a different effective refractory time. - // + // Choosing a tau_ref_{abs,tot} that is not an integer multiple of the + // computation time step h will lead to accurate (up to the resolution h) + // and self- consistent results. However, a neuron model capable of + // operating with real valued spike time may exhibit a different + // effective refractory time. V_.RefractoryCountsAbs_ = Time( Time::ms( P_.tau_ref_abs_ ) ).get_steps(); diff --git a/models/iaf_tum_2000.h b/models/iaf_tum_2000.h index 26c264c9fd..b171670b12 100644 --- a/models/iaf_tum_2000.h +++ b/models/iaf_tum_2000.h @@ -46,13 +46,13 @@ namespace nest In particular, this model allows setting an absolute and relative refractory time separately, as required by [1]. - The threshold crossing is followed by an absolute refractory period (tau_abs) - during which the membrane potential is clamped to the resting potential. - During the total refractory period, the membrane potential evolves, - but the neuron will not emit a spike, even if the membrane potential - reaches threshold. The total refractory time must be larger or equal to - the absolute refractory time. If equal, the refractoriness of the model - if equivalent to the other models of NEST. + The threshold crossing is followed by an absolute refractory period + (t_ref_abs) during which the membrane potential is clamped to the resting + potential. During the total refractory period (t_ref_tot), the membrane + potential evolves, but the neuron will not emit a spike, even if the + membrane potential reaches threshold. The total refractory time must be + larger or equal to the absolute refractory time. If equal, the + refractoriness of the model if equivalent to the other models of NEST. The linear subthreshold dynamics is integrated by the Exact Integration scheme [2]. The neuron dynamics is solved on the time diff --git a/models/mat2_psc_exp.cpp b/models/mat2_psc_exp.cpp index f6a69a19e2..7c23e78199 100644 --- a/models/mat2_psc_exp.cpp +++ b/models/mat2_psc_exp.cpp @@ -292,7 +292,7 @@ nest::mat2_psc_exp::calibrate() // To ensure consistency with the overall simulation scheme such conversion // should be carried out via objects of class nest::Time. The conversion // requires 2 steps: - // 1. A time object r is constructed defining representation of + // 1. A time object r is constructed, defining representation of // tau_ref_ in tics. This representation is then converted to // computation time steps again by a strategy defined by class // nest::Time. @@ -300,7 +300,7 @@ nest::mat2_psc_exp::calibrate() // member function of class nest::Time. // // Choosing a tau_ref_ that is not an integer multiple of the computation time - // step h will leed to accurate (up to the resolution h) and self-consistent + // step h will lead to accurate (up to the resolution h) and self-consistent // results. However, a neuron model capable of operating with real valued // spike time may exhibit a different effective refractory time.