Merge branch 'master' of https://github.com/PrabhuUdurg/nest-simulator

Updates

doc/htmldoc/connect_nest/nest_server.rst

@@ -79,9 +79,9 @@ consideration, each of the restrictions can be disabled by setting a correspondi
 * ``NEST_SERVER_DISABLE_AUTH``: By default, the NEST Server requires a NESTServerAuth tokens. Setting this variable to
   ``1`` disables this restriction. A token is automatically created and printed to the console by NEST Server upon
   start-up. If needed, a custom token can be set using the environment variable  ``NEST_SERVER_ACCESS_TOKEN``
-* ``NEST_SERVER_CORS_ORIGINS``: By default, the NEST Server only allows requests from localhost (see `CORS
-  <https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS>`_). Other hosts can be explicitly allowed by supplying them
-  in the form `http://host_or_ip:*`` to this variable (By default: http://localhost:*).
+* ``NEST_SERVER_CORS_ORIGINS``: By default, the NEST Server only allows requests from localhost (see
+  `CORS <https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS>`_). Other hosts can be explicitly allowed by supplying them
+  in the form http://host_or_ip:\* to this variable (By default: http://localhost:\*).
 * ``NEST_SERVER_ENABLE_EXEC_CALL``: By default, NEST Server only allows calls to its PyNEST-like API. If the use-case
   requires the execution of scripts via the ``/exec`` route, this variable can be set to ``1``. PLEASE BE AWARE THAT
   THIS OPENS YOUR COMPUTER TO REMOTE CODE EXECUTION.

doc/htmldoc/devices/index.rst

@@ -8,7 +8,7 @@ All about devices in NEST
 
     .. grid-item-card::  Stimulate the network
        :class-title: sd-d-flex-row sd-align-minor-center
-       :link: stimuate_network
+       :link: stimulate_network
        :link-type: ref
 
     .. grid-item-card:: Get data from simulation

doc/htmldoc/get-started_index.rst

@@ -232,8 +232,6 @@ More topics
 .. toctree::
    :hidden:
 
-   understand_index
-
 .. |nav| image:: static/img/GPS-Settings-256_nest.svg
 .. |script| image:: static/img/script_white.svg
       :scale: 20%

doc/htmldoc/index.rst

@@ -1,29 +1,35 @@
-Welcome to the NEST Simulator documentation
-===========================================
-
-
+Welcome to the NEST Simulator documentation!
+============================================
 
 
 .. grid::
+  :gutter: 2
 
   .. grid-item::
 
-    NEST is used in computational neuroscience to model and study behavior of large networks of neurons.
+     .. grid:: 1 1 1 1
+       :gutter: 2
 
-    The models describe single neuron and synapse behavior and their connections.
-    Different mechanisms of plasticity can be used to investigate artificial learning
-    and help to shed light on the fundamental principles of how the brain works.
+       .. grid-item::
+
+          NEST is used in computational neuroscience to model and study behavior of large networks of neurons.
 
-    NEST offers convenient and efficient commands to define and connect large networks,
-    ranging from algorithmically determined connections to data-driven connectivity.
-    Create connections between neurons using numerous synapse models from STDP to gap junctions.
+          The models describe single neuron and synapse behavior and their connections.
+          Different mechanisms of plasticity can be used to investigate learning
+          and help to shed light on the fundamental principles of how the brain works.
 
-    .. button-ref:: tutorials_guides
-       :ref-type: ref
-       :shadow:
-       :color: primary
+          NEST offers convenient and efficient commands to define and connect large networks,
+          ranging from algorithmically determined connections to data-driven connectivity.
+          Create connections between neurons using numerous synapse models from STDP to gap junctions.
 
-       Start exploring NEST
+       .. grid-item::
+
+          .. button-ref:: tutorials_guides
+             :ref-type: ref
+             :shadow:
+             :color: primary
+
+             Start exploring NEST
 
   .. grid-item::
 
@@ -47,7 +53,7 @@ Welcome to the NEST Simulator documentation
                 .. figure:: static/img/astrocyte_interaction.png
 
 
-                  Investigate neuron and astrocyte interactions
+                  Inspect neuron and astrocyte interactions
 
 
                 .. figure:: static/img/hpc_benchmark_connectivity.svg
@@ -58,7 +64,7 @@ Welcome to the NEST Simulator documentation
                 .. figure:: static/img/pong_sim.gif
 
 
-                  Play PONG with NEST
+                  Simulate a game of PONG with NEST
 
                 .. figure:: static/img/gapjunctions.png
 
@@ -76,6 +82,36 @@ Welcome to the NEST Simulator documentation
              Discover all our examples!
 
 
+How NEST works --- The Big Picture
+----------------------------------
+
+.. grid::
+
+    .. grid-item::
+
+        .. raw:: html
+
+           <object data="_static/img/excalidraw_nestconcept_horiz.svg" type="image/svg+xml"></object>
+
+
+.. grid::
+
+    .. grid-item::
+
+
+        A NEST simulation is created with input from :doc:`stimulation devices </models/index_generator>`,
+        :doc:`neuron models </models/index_neuron>`, and :doc:`synapse models </models/index_synapse>`,
+        along with  :ref:`connection rules <connectivity_concepts>`.
+        You can choose what data to record with :doc:`recording devices </models/index_recorder>`.
+        After simulation, the output is ready for analysis with NEST's built in :py:mod:`.raster_plot` and :py:mod:`.voltage_trace`
+        modules or external tools such as :doc:`Elephant <elephant:index>`.
+
+
+        You can find these components in NEST or you can implement your own custom
+        models and extend NEST's functionalities using :doc:`NESTML <nestml:index>` and the :doc:`NEST extension module <extmod:index>`, respectively.
+        Check out our wide-ranging list of :doc:`network model <examples/index>` examples.
+
+
 .. toctree::
    :caption: USAGE
    :hidden:

doc/htmldoc/neurons/parametrization.rst

@@ -19,6 +19,16 @@ The following parameters and functionalities are provided:
 -  :ref:`Combination of parameters <combine_ex>`
 
 
+.. admonition:: Create parameters after setting number of threads!
+
+   For correct results, it is essential to create parameter objects
+   only *after* the number of threads (virtual processes) has been
+   set. If parameter objects are created first and the number of
+   threads changed afterwards, this will result incorrect behavior and
+   possibly a segmentation fault. Unfortunately, NEST cannot currently
+   detect existing parameter objects when the number of threads change.
+
+
 .. _random_ex:
 
 Random parameters

doc/htmldoc/related_projects.rst

@@ -90,10 +90,10 @@ real-time operation.
 TheVirtualBrain (TVB)
 ---------------------
 
-:ref:`TVB <tvb:top_basic>` is a framework for the simulation of the dynamics of large-scale brain networks with
+:ref:`TVB <tvb:index>` is a framework for the simulation of the dynamics of large-scale brain networks with
 biologically realistic connectivity.
 
-* :ref:`Get started with TVB <tvb:tutorial_0_gettingstarted>`
+* :ref:`Get started with TVB <tvb:tutorial_0_GettingStarted>`
 
 ConnPlotter
 -----------

doc/htmldoc/static/css/custom.css

@@ -115,6 +115,20 @@ section#kernel-attributes-nest-nestmodule dd {
 	padding-bottom: 20px !important;
   box-shadow: 3px 3px var(--nest-orange) !important;
 }
+
+
+.center {
+
+  text-align: center;
+  font-style: italic;
+}
+/* Provide a specific height to the svg object on index page
+ * Reason: Safari does not interpret percentages or max-content
+ * correctly
+ * there is an additional @media setting for <768px screens*/
+section#welcome-to-the-nest-simulator-documentation  object {
+  height: 400px;
+}
 /*************************************************************
  * Rules for  mermaid diagrams
  *************************************************************/
@@ -141,12 +155,6 @@ figure.align-default {
 	outline-style: groove;
 }
 
-.center {
-
-  text-align: center;
-  font-style: italic;
-}
-
 /**************************************************************************************
  * Rules for carousel
  * ***********************************************************************************/
@@ -212,10 +220,11 @@ div[role="main"] .md-source {
 	border-radius: 5px;
 }
 /* Add padding around buttons on index page */
-#welcome-to-the-nest-simulator-documentation [data-md-color-primary="orange"] .md-typeset a {
+#welcome-to-the-nest-simulator-documentation [data-md-color-primary="orange"] .sd-button {
    padding: 6px;
 }
 
+
 .md-typeset details {
    background-color: white;
 }
@@ -347,6 +356,11 @@ nav.md-nav.md-nav--secondary label.md-nav__title:after{
   font-weight: bold;
   display: flex;
   align-items: center;
+
+}
+
+#welcome-to-the-nest-simulator-documentation .sd-row-cols-lg-1 > *{
+width: 85%;
 }
 
 #pynest-examples img.sd-card-img-top {
@@ -975,7 +989,11 @@ This is for the larger monitors and possibly full screen viewers.
 @media only screen and (min-width: 1240px) {
 #hero h1{ font-size:2em;}
 }
-
+@media only screen and (max-width: 768px) {
+ section#welcome-to-the-nest-simulator-documentation  object {
+  height: 200px;
+ }
+}
 /*
 RETINA (2x RESOLUTION DEVICES)
 This applies to the retina iPhone (4s) and iPad (2,3) along with

doc/htmldoc/synapses/synapse_specification.rst

@@ -65,7 +65,7 @@ Array parameters
 
 Array parameters can be used with the rules ``one_to_one``, ``all_to_all``,
 ``fixed_total_number``, ``fixed_indegree``, and ``fixed_outdegree``.
-For details on connection rules, see :ref:`connectivity_concept`.
+For details on connection rules, see :ref:`connectivity_concepts`.
 The arrays can be specified as NumPy arrays or Python
 lists. As with the scalar parameters, all parameters have to be
 specified as arrays of the correct type.

models/amat2_psc_exp.h

@@ -128,6 +128,9 @@ The following parameters can be set in the status dictionary:
      implementation to avoid a degenerate case of the ODE describing the
      model [1]_.  For very similar values, numerics will be unstable.
 
+   - Some parameter values given in Table 1 of [4]_ are incorrect. For
+     correct values, see Table 4 of [5]_.
+
 References
 ++++++++++
 
@@ -147,6 +150,10 @@ References
        for reproducing diverse firing patterns and predicting precise
        firing times. Frontiers in Computational Neuroscience, 5:42.
        DOI: https://doi.org/10.3389/fncom.2011.00042
+.. [5] Heiberg T, Kriener B, Tetzlaff T, Einevoll GT, Plesser HE (2018).
+       Firing-rate model for neurons with a broad repertoire of spiking behaviors.
+       J Comput Neurosci, 45:103.
+       DOI: https://doi.org/10.1007/s10827-018-0693-9
 
 Sends
 +++++

models/hh_cond_beta_gap_traub.h

@@ -94,7 +94,7 @@ Postsynaptic currents
 
 Incoming spike events induce a postsynaptic change of conductance modelled by a
 beta function as outlined in [4]_ [5]_. The beta function is normalized such that an
-event of weight 1.0 results in a peak current of 1 nS at :math:`t = \tau_{rise,xx}`
+event of weight 1.0 results in a peak conductance of 1 nS at :math:`t = \tau_{rise,xx}`
 where xx is `ex` or `in`.
 
 Spike Detection

models/iaf_cond_alpha.h

@@ -69,7 +69,7 @@ Description
 ``iaf_cond_alpha`` is an implementation of a spiking neuron using IAF dynamics with
 conductance-based synapses. Incoming spike events induce a postsynaptic change
 of conductance modelled by an alpha function. The alpha function
-is normalized such that an event of weight 1.0 results in a peak current of 1 nS
+is normalized such that an event of weight 1.0 results in a peak conductance of 1 nS
 at :math:`t = \tau_{syn}`.
 
 See also [1]_, [2]_, [3]_.

models/iaf_cond_exp_sfa_rr.h

@@ -74,7 +74,7 @@ spike-frequency adaptation and relative refractory mechanisms as described in
 
 Incoming spike events induce a postsynaptic change of conductance modelled by
 an exponential function. The exponential function is normalized such that an
-event of weight 1.0 results in a peak current of 1 nS.
+event of weight 1.0 results in a peak conductance of 1 nS.
 
 Outgoing spike events induce a change of the adaptation and relative refractory
 conductances by ``q_sfa`` and ``q_rr``, respectively. Otherwise these conductances

models/iaf_psc_delta.h

@@ -121,6 +121,10 @@ hyperpolarization to biophysically plausible values, set parameter
 
 
 .. note::
+
+   NEST uses exact integration [1]_, [2]_ to integrate subthreshold membrane
+   dynamics.
+
    Spikes arriving while the neuron is refractory, are discarded by
    default. If the property ``refractory_input`` is set to True, such
    spikes are added to the membrane potential at the end of the

nestkernel/recording_backend_ascii.h

@@ -46,7 +46,7 @@ each MPI process. This can cause a high load on the file system in
 large simulations. This backend can become prohibitively inefficient,
 particularly on machines with distributed filesystems. In case you
 experience such scaling problems, the :doc:`recording backend for
-SIONlib <recording_backend_sionlib>` may be a possible alternative.
+SIONlib </models/recording_backend_sionlib>` may be a possible alternative.
 
 Filenames of data files are determined according to the following
 pattern:

nestkernel/recording_backend_sionlib.h

@@ -47,7 +47,7 @@ a binary container file (or to a rather small set of such files). This
 is especially useful for large-scale simulations running in a
 distributed way on many MPI processes/OpenMP threads. In such usage
 scenarios, writing to plain text files (see :doc:`recording backend
-for ASCII files <recording_backend_ascii>`) would cause a large
+for ASCII files </models/recording_backend_ascii>`) would cause a large
 overhead because of the huge number of generated files and thus be
 very inefficient.
 

pynest/examples/EI_clustered_network/README.rst

@@ -16,24 +16,24 @@ If you use this code, we ask you to cite the paper by Rostami et al. [1]_ and th
 File structure
 --------------
 
-* :doc:`run_simulation.py <run_simulation>`: an example script to try out the EI-clustered circuit model
-* :doc:`network.py <network>`: the main ``Network`` class with functions to build and simulate the network
-* :doc:`helper.py <helper>`: helper functions for calculation of synaptic weights and currents and plot function for raster plots
-* :doc:`network_params.py <network_params>`: network and neuron parameters
-* :doc:`stimulus_params.py <stimulus_params>`: parameters for optional external stimulation
-* :doc:`sim_params.py <sim_params>`: simulation parameters
+* :doc:`run_simulation_EI.py <run_simulation_EI>`: an example script to try out the EI-clustered circuit model
+* :doc:`network_EI.py <network_EI>`: the main ``Network`` class with functions to build and simulate the network
+* :doc:`helper_EI.py <helper_EI>`: helper functions for calculation of synaptic weights and currents and plot function for raster plots
+* :doc:`network_params_EI.py <network_params_EI>`: network and neuron parameters
+* :doc:`stimulus_params_EI.py <stimulus_params_EI>`: parameters for optional external stimulation
+* :doc:`sim_params_EI.py <sim_params_EI>`: simulation parameters
 
 Running the simulation
 ----------------------
 
 .. code-block:: bash
 
-   python run_simulation.py
+   python run_simulation_EI.py
 
 A raster plot of the network activity is saved as ``clustered_ei_raster.png``.
 
 The code can be parallelized by using multiple threads during the NEST simulation.
-This can be done by setting the parameter ``n_vp`` in the ``run_simulation.py`` script.
+This can be done by setting the parameter ``n_vp`` in the ``run_simulation_EI.py`` script.
 
 Contributions to this PyNEST model implementation
 -------------------------------------------------

pynest/examples/EI_clustered_network/helper.py → pynest/examples/EI_clustered_network/helper_EI.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# helper.py
+# helper_EI.py
 #
 # This file is part of NEST.
 #

pynest/examples/EI_clustered_network/network.py → pynest/examples/EI_clustered_network/network_EI.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# network.py
+# network_EI.py
 #
 # This file is part of NEST.
 #
@@ -58,8 +58,8 @@ class ClusteredNetwork:
     def __init__(self, sim_dict, net_dict, stim_dict):
         """Initialize the ClusteredNetwork object.
 
-        Parameters are given and explained in the files network_params.py,
-        sim_params.py and stimulus_params.py.
+        Parameters are given and explained in the files network_params_EI.py,
+        sim_params_EI.py and stimulus_params_EI.py.
 
         Parameters
         ----------