diff --git a/docs/Makefile b/docs/Makefile
deleted file mode 100644
index a8997d1c346f7c346662c40921a5ac724e994366..0000000000000000000000000000000000000000
--- a/docs/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS =
-SPHINXBUILD = sphinx-build
-SPHINXPROJ = MOOSE
-SOURCEDIR = source
-BUILDDIR = build
-
-# Put it first so that "make" without argument is like "make help".
-help:
- @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
- @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
diff --git a/docs/make.bat b/docs/make.bat
deleted file mode 100644
index a6f889c4bcb8fbf45278fe061954d3d191649c41..0000000000000000000000000000000000000000
--- a/docs/make.bat
+++ /dev/null
@@ -1,36 +0,0 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
- set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-set SPHINXPROJ=MOOSE
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
- echo.
- echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
- echo.installed, then set the SPHINXBUILD environment variable to point
- echo.to the full path of the 'sphinx-build' executable. Alternatively you
- echo.may add the Sphinx directory to PATH.
- echo.
- echo.If you don't have Sphinx installed, grab it from
- echo.http://sphinx-doc.org/
- exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-
-:end
-popd
diff --git a/docs/source/conf.py b/docs/source/conf.py
deleted file mode 100644
index 90f32dddf02f48cca52bbeedbbae1e2f091fb5b8..0000000000000000000000000000000000000000
--- a/docs/source/conf.py
+++ /dev/null
@@ -1,173 +0,0 @@
-# -*- coding: utf-8 -*-
-#
-# MOOSE documentation build configuration file, created by
-# sphinx-quickstart on Tue Jan 31 14:57:39 2017.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-import os
-import sys
-# sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('../python'))
-sys.path.append(os.path.abspath('../../../moose-examples/snippets'))
-sys.path.append(os.path.abspath('../../../moose-examples/tutorials/ChemicalOscillators'))
-sys.path.append(os.path.abspath('../../../moose-examples/tutorials/ChemicalBistables'))
-sys.path.append(os.path.abspath('../../../moose-examples/tutorials/ExcInhNet'))
-sys.path.append(os.path.abspath('../../../moose-examples/neuroml/lobster_pyloric'))
-sys.path.append(os.path.abspath('../../../moose-examples/tutorials/ExcInhNetCaPlasticity'))
-
-
-# -- General configuration ------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = ['sphinx.ext.autodoc']
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon']
-#extensions = ['numpydoc']
-#extensions = ['sphinx.ext.autodoc', 'numpydoc']
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['ntemplates']
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = 'MOOSE'
-copyright = '(c) 2017, Malav Shah <malavs@ncbs.res.in>'
-author = 'Malav Shah <malavs@ncbs.res.in>'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '3.1.1'
-# The full version, including alpha/beta/rc tags.
-release = 'Chamcham'
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = []
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = False
-
-
-# -- Options for HTML output ----------------------------------------------
-
-# The theme to use for HTML and HTML Help pages. See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'alabaster'
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further. For a list of options available for each theme, see the
-# documentation.
-#
-# html_theme_options = {}
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['nstatic']
-
-
-# -- Options for HTMLHelp output ------------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'MOOSEdoc'
-
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
- # The paper size ('letterpaper' or 'a4paper').
- #
- # 'papersize': 'letterpaper',
-
- # The font size ('10pt', '11pt' or '12pt').
- #
- # 'pointsize': '10pt',
-
- # Additional stuff for the LaTeX preamble.
- #
- # 'preamble': '',
-
- # Latex figure (float) alignment
- #
- # 'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-# author, documentclass [howto, manual, or own class]).
-latex_documents = [
- (master_doc, 'MOOSE.tex', 'MOOSE Documentation',
- 'Malav Shah', 'manual'),
-]
-
-# -----NumpyDoc----------------
-numpydoc_show_class_members = False
-#numpydoc_use_plots: True
-#numpydoc_show_class_members: True
-#numpydoc_show_inherited_class_members: True
-#numpydoc_class_members_toctree: True
-#numpydoc_edit_link: True
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
- (master_doc, 'moose', 'MOOSE Documentation',
- [author], 1)
-]
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-# dir menu entry, description, category)
-texinfo_documents = [
- (master_doc, 'MOOSE', 'MOOSE Documentation',
- author, 'MOOSE', 'One line description of project.',
- 'Miscellaneous'),
-]
-
-
-
diff --git a/docs/source/docs/source/modules.rst b/docs/source/docs/source/modules.rst
deleted file mode 100644
index 733da1c55c012340a920a07efc1c464af5967b99..0000000000000000000000000000000000000000
--- a/docs/source/docs/source/modules.rst
+++ /dev/null
@@ -1,6 +0,0 @@
-projectdir
-==========
-
-.. toctree::
- :maxdepth: 4
-
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@@ -1,369 +0,0 @@
-#FIG 3.2 Produced by xfig version 3.2.5b
-Portrait
-Center
-Metric
-A4
-200.00
-Single
--2
-1200 2
-6 3465 3285 7155 5085
-6 3465 3285 7155 5085
-6 5805 3645 6165 4770
-6 5805 3671 6165 4770
-6 5805 4320 6165 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5805 4500 6165 4500
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5895 4590 6075 4590
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5985 4500 5985 4320
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5985 4590 5985 4770
--6
-# Resistor
-6 5880 3671 6060 4346
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 5985 3686 5985 3824 5914 3847 6057 3893 5914 3939 6057 3984
- 5914 4030 6057 4076 5914 4122 6057 4167 5985 4190 5985 4329
--6
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
- 0 0 1.00 60.00 120.00
- 5850 4230 6120 3735
--6
-6 5040 3645 5400 4770
-# Resistor
-6 5115 3671 5295 4346
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 5220 3686 5220 3824 5149 3847 5292 3893 5149 3939 5292 3984
- 5149 4030 5292 4076 5149 4122 5292 4167 5220 4190 5220 4329
--6
-6 5040 4320 5400 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5400 4590 5040 4590
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5310 4500 5130 4500
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5220 4590 5220 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 5220 4500 5220 4320
--6
--6
-# Resistor
-6 3493 3585 4168 3765
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 4153 3690 4015 3690 3992 3619 3946 3762 3900 3619 3855 3762
- 3809 3619 3763 3762 3717 3619 3672 3762 3649 3690 3510 3690
--6
-# Resistor
-6 6464 3585 7139 3765
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 7124 3690 6986 3690 6963 3619 6917 3762 6871 3619 6826 3762
- 6780 3619 6734 3762 6688 3619 6643 3762 6620 3690 6481 3690
--6
-# Non-polar capacitor
-6 4237 3782 4745 4652
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 4269 4146 4730 4146
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 4500 3800 4500 4146
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 4500 4261 4500 4605
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 4269 4261 4730 4261
--6
-# Ground
-6 5265 4725 5580 5085
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 5409 4761 5409 4903
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 5266 4903 5551 4903
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 5337 4975 5480 4975
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 5380 5046 5451 5046
--6
-6 4435 3642 4570 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 4498 3689 28 28 4498 3689 4526 3689
--6
-6 5156 3642 5291 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 5219 3689 28 28 5219 3689 5247 3689
--6
-6 5921 3642 6056 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 5984 3689 28 28 5984 3689 6012 3689
--6
-6 5344 4723 5479 4813
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 5407 4770 28 28 5407 4770 5435 4770
--6
-6 4798 3374 4933 3509
-1 3 0 1 0 7 1 0 20 0.000 1 0.0000 4858 3461 47 47 4858 3461 4906 3461
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 4140 3690 6480 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 4500 3825 4500 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 4500 4590 4500 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 4500 4770 5985 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 4860 3510 4860 3690
-4 0 0 50 -1 0 12 0.0000 4 150 300 5355 4500 Em\001
-4 0 0 50 -1 0 12 0.0000 4 150 300 5355 4050 Rm\001
-4 0 0 50 -1 0 12 0.0000 4 150 270 6165 4050 Gk\001
-4 0 0 50 -1 0 12 0.0000 4 150 240 6165 4590 Ek\001
-4 0 0 50 -1 0 12 0.0000 4 150 315 4635 4500 Cm\001
-4 0 0 50 -1 0 12 0.0000 4 150 300 4955 3452 Vm\001
-4 0 0 50 -1 0 12 0.0000 4 180 405 3664 3978 Ra/2\001
-4 0 0 50 -1 0 12 0.0000 4 180 405 6637 3987 Ra/2\001
--6
-6 5158 4724 5293 4814
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 5221 4771 28 28 5221 4771 5249 4771
--6
-6 4798 3641 4933 3731
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 4861 3688 28 28 4861 3688 4889 3688
--6
--6
-6 -360 3285 3330 5085
-6 -360 3285 3330 5085
-6 1980 3645 2340 4770
-6 1980 3671 2340 4770
-6 1980 4320 2340 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 1980 4500 2340 4500
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 2070 4590 2250 4590
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 2160 4500 2160 4320
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 2160 4590 2160 4770
--6
-# Resistor
-6 2055 3671 2235 4346
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 2160 3686 2160 3824 2089 3847 2232 3893 2089 3939 2232 3984
- 2089 4030 2232 4076 2089 4122 2232 4167 2160 4190 2160 4329
--6
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
- 0 0 1.00 60.00 120.00
- 2025 4230 2295 3735
--6
-6 1215 3645 1575 4770
-# Resistor
-6 1290 3671 1470 4346
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 1395 3686 1395 3824 1324 3847 1467 3893 1324 3939 1467 3984
- 1324 4030 1467 4076 1324 4122 1467 4167 1395 4190 1395 4329
--6
-6 1215 4320 1575 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 1575 4590 1215 4590
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 1485 4500 1305 4500
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 1395 4590 1395 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 1395 4500 1395 4320
--6
--6
-# Resistor
-6 -332 3585 343 3765
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 328 3690 190 3690 167 3619 121 3762 75 3619 30 3762
- -16 3619 -62 3762 -108 3619 -153 3762 -176 3690 -315 3690
--6
-# Resistor
-6 2639 3585 3314 3765
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 3299 3690 3161 3690 3138 3619 3092 3762 3046 3619 3001 3762
- 2955 3619 2909 3762 2863 3619 2818 3762 2795 3690 2656 3690
--6
-# Non-polar capacitor
-6 412 3782 920 4652
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 444 4146 905 4146
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 675 3800 675 4146
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 675 4261 675 4605
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 444 4261 905 4261
--6
-# Ground
-6 1440 4725 1755 5085
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 1584 4761 1584 4903
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 1441 4903 1726 4903
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 1512 4975 1655 4975
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 1555 5046 1626 5046
--6
-6 610 3642 745 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 673 3689 28 28 673 3689 701 3689
--6
-6 1331 3642 1466 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 1394 3689 28 28 1394 3689 1422 3689
--6
-6 2096 3642 2231 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 2159 3689 28 28 2159 3689 2187 3689
--6
-6 1519 4723 1654 4813
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 1582 4770 28 28 1582 4770 1610 4770
--6
-6 973 3374 1108 3509
-1 3 0 1 0 7 1 0 20 0.000 1 0.0000 1033 3461 47 47 1033 3461 1081 3461
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 315 3690 2655 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 675 3825 675 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 675 4590 675 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 675 4770 2160 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 1035 3510 1035 3690
-4 0 0 50 -1 0 12 0.0000 4 150 300 1530 4500 Em\001
-4 0 0 50 -1 0 12 0.0000 4 150 300 1530 4050 Rm\001
-4 0 0 50 -1 0 12 0.0000 4 150 270 2340 4050 Gk\001
-4 0 0 50 -1 0 12 0.0000 4 150 240 2340 4590 Ek\001
-4 0 0 50 -1 0 12 0.0000 4 150 315 810 4500 Cm\001
-4 0 0 50 -1 0 12 0.0000 4 150 300 1130 3452 Vm\001
-4 0 0 50 -1 0 12 0.0000 4 180 405 -161 3978 Ra/2\001
-4 0 0 50 -1 0 12 0.0000 4 180 405 2812 3987 Ra/2\001
--6
-6 1333 4724 1468 4814
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 1396 4771 28 28 1396 4771 1424 4771
--6
-6 973 3641 1108 3731
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 1036 3688 28 28 1036 3688 1064 3688
--6
--6
-6 7290 3285 10980 5085
-6 7290 3285 10980 5085
-6 9630 3645 9990 4770
-6 9630 3671 9990 4770
-6 9630 4320 9990 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9630 4500 9990 4500
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9720 4590 9900 4590
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9810 4500 9810 4320
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9810 4590 9810 4770
--6
-# Resistor
-6 9705 3671 9885 4346
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 9810 3686 9810 3824 9739 3847 9882 3893 9739 3939 9882 3984
- 9739 4030 9882 4076 9739 4122 9882 4167 9810 4190 9810 4329
--6
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
- 0 0 1.00 60.00 120.00
- 9675 4230 9945 3735
--6
-6 8865 3645 9225 4770
-# Resistor
-6 8940 3671 9120 4346
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 9045 3686 9045 3824 8974 3847 9117 3893 8974 3939 9117 3984
- 8974 4030 9117 4076 8974 4122 9117 4167 9045 4190 9045 4329
--6
-6 8865 4320 9225 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9225 4590 8865 4590
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9135 4500 8955 4500
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9045 4590 9045 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 9045 4500 9045 4320
--6
--6
-# Resistor
-6 7318 3585 7993 3765
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 7978 3690 7840 3690 7817 3619 7771 3762 7725 3619 7680 3762
- 7634 3619 7588 3762 7542 3619 7497 3762 7474 3690 7335 3690
--6
-# Resistor
-6 10289 3585 10964 3765
-2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 12
- 10949 3690 10811 3690 10788 3619 10742 3762 10696 3619 10651 3762
- 10605 3619 10559 3762 10513 3619 10468 3762 10445 3690 10306 3690
--6
-# Non-polar capacitor
-6 8062 3782 8570 4652
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 8094 4146 8555 4146
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 8325 3800 8325 4146
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 8325 4261 8325 4605
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 8094 4261 8555 4261
--6
-# Ground
-6 9090 4725 9405 5085
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 9234 4761 9234 4903
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 9091 4903 9376 4903
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 9162 4975 9305 4975
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 9205 5046 9276 5046
--6
-6 8260 3642 8395 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 8323 3689 28 28 8323 3689 8351 3689
--6
-6 8981 3642 9116 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 9044 3689 28 28 9044 3689 9072 3689
--6
-6 9746 3642 9881 3732
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 9809 3689 28 28 9809 3689 9837 3689
--6
-6 9169 4723 9304 4813
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 9232 4770 28 28 9232 4770 9260 4770
--6
-6 8623 3374 8758 3509
-1 3 0 1 0 7 1 0 20 0.000 1 0.0000 8683 3461 47 47 8683 3461 8731 3461
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 7965 3690 10305 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 8325 3825 8325 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 8325 4590 8325 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 8325 4770 9810 4770
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 8685 3510 8685 3690
-4 0 0 50 -1 0 12 0.0000 4 150 300 9180 4500 Em\001
-4 0 0 50 -1 0 12 0.0000 4 150 300 9180 4050 Rm\001
-4 0 0 50 -1 0 12 0.0000 4 150 270 9990 4050 Gk\001
-4 0 0 50 -1 0 12 0.0000 4 150 240 9990 4590 Ek\001
-4 0 0 50 -1 0 12 0.0000 4 150 315 8460 4500 Cm\001
-4 0 0 50 -1 0 12 0.0000 4 150 300 8780 3452 Vm\001
-4 0 0 50 -1 0 12 0.0000 4 180 405 7489 3978 Ra/2\001
-4 0 0 50 -1 0 12 0.0000 4 180 405 10462 3987 Ra/2\001
--6
-6 8983 4724 9118 4814
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 9046 4771 28 28 9046 4771 9074 4771
--6
-6 8623 3641 8758 3731
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 8686 3688 28 28 8686 3688 8714 3688
--6
--6
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 3285 3690 3510 3690
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
- 7110 3690 7335 3690
-2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
- 3420 3240 7245 3240 7245 5130 3420 5130 3420 3240
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diff --git a/docs/source/images/twoCells.png b/docs/source/images/twoCells.png
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diff --git a/docs/source/index.rst b/docs/source/index.rst
deleted file mode 100644
index e6b924a2570dce52cabc101ab9fdc81ed6dc3653..0000000000000000000000000000000000000000
--- a/docs/source/index.rst
+++ /dev/null
@@ -1,23 +0,0 @@
-.. MOOSE documentation master file, created by
- sphinx-quickstart on Tue Jan 31 14:57:39 2017.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-MOOSE
-=====
-
-.. toctree::
-
- introduction/index_intro
- install/index_install
- user/py/quickstart/index_qs
- user/py/cookbook/index_ckbk
- user/py/graphics/index_graphics
- user/py/references/index_ref
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/docs/source/install/index.rst~ b/docs/source/install/index.rst~
deleted file mode 100644
index 5eb7a17d4624f8d036386d0654ee00d92cf97e92..0000000000000000000000000000000000000000
--- a/docs/source/install/index.rst~
+++ /dev/null
@@ -1,207 +0,0 @@
-Installation
-============
-
-Use pre-built packages
-----------------------
-
-Linux
-^^^^^
-
-We recommend that you use our repositories hosted at `Open Build Service
-<http://build.opensuse.org>`_. We have packages for the following distributions
-
-- Debian 7.0, 8.0
-- Ubuntu 12.04, 14.04, 15.04, 15.10, 16.04
-- CentOS 6, 7
-- Fedora 20, 21, 22, 23
-- OpenSUSE 13.1, 13.2, Factory ARM, Leap 42.1, Tumbleweed
-- SLE 12, 12 SP1
-- RHEL 7
-- Scientific Linux 7
-
-Visit `this page
-<https://software.opensuse.org/download.html?project=home:moose&package=moose>`_
-pick you distribution and follow instructions.
-
-.. note::
- ``moogli`` (tool to visualize network activity) is not available for CentOS-6.
-
-.. raw:: html
- <iframe
- src="http://software.opensuse.org/download/package.iframe?project=moose&package=moose"></iframe>
-
-.. todo:: Packages for gentoo, Arch Linux
-
-
-Mac OSX
-^^^^^^
-
-Download the ``dmg`` file from `here <https://github.com/BhallaLab/moose/releases/download/ghevar_3.0.2/Moose_3.0.2_OSX.dmg>`_.
-
-Alternatively, you can use ``homebrew`` to install ``moose``
-::
- $ brew install homebrew/science/moose
-
-
-Windows/Cygwin
-^^^^^^^^^^^^^^
-
-Building MOOSE
---------------
-
-In case your distribution is not listed on `our repository page
-<https://software.opensuse.org/download.html?project=home:moose&package=moose>`_
-, or if you want to build the lastest development code, read on.
-
-First, you need to get the source code. You can use ``git`` (clone the
-repository) or download snapshot of github repo by clicking on `this link
-<https://github.com/BhallaLab/moose/archive/master.zip>`_.::
- $ git clone https://github.com/BhallaLab/moose
-
-Or,
-::
- $ wget https://github.com/BhallaLab/moose/archive/master.zip
- $ unzip master.zip
-
-If you don't want lasest snapshot of ``MOOSE``, you can download other released
-versions from here `https://github.com/BhallaLab/moose/releases`.
-
-Install dependencies
-~~~~~~~~~~~~~~~~~~~
-
-Next, you need to install required dependencies. Depending on your OS, names of
-following packages may vary.
-
-- cmake (version 2.8 or higher)
-- gsl-1.16 or higher `download <ftp://ftp.gnu.org/gnu/gsl/>`_.
-- libhdf5 development package e.g. `libhdf5-serial-dev` or `libhdf5-devel`
-- python development package e.g. `python-dev` or `python-devel`
-- numpy e.g. `python-numpy` or `numpy`
-
-Most of the dependencies can be installed using package manager.
-
-On ``Debian/Ubuntu``
-::
- $ sudo apt-get install libhdf5-dev cmake libgsl0-dev libpython-dev python-numpy
-
-.. note::
- Ubuntu 12.04 does not have required version of ``gsl`` (required 1.16 or
- higher, available 1.15). On Ubuntu 16.04, package name is ``libgsl-dev``.
-
-On ``CentOS/Fedora/RHEL/Scientific Linux``
-::
- $ sudo yum install hdf5-devel cmake libgsl-dev python-devel python-numpy
-
-On ``OpenSUSE``
-::
- $ sudo zypper install hdf5-devel cmake libgsl-dev python-devel python-numpy
-
-Now use `cmake` to build moose
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. codeblock:: bash
- $ cd /to/moose/source/code
- $ mkdir _build
- $ cd _build
- $ cmake ..
- $ make
- $ ctest --output-on-failure # optional
-
-This will build pyMOOSE (MOOSE's python extention), `ctest` will run few tests to
-check if build process was successful.
-
-.. note::
- To install MOOSE into non-standard directory, pass additional argument
- `-DCMAKE_INSTALL_PREFIX=path/to/install/dir` to cmake
- ::
- $ cmake -DCMAKE_INSTALL_PREFIC=$HOME/.local ..
-
- To use different version of python
- ::
- $ cmake -DPYTHON_EXECUTABLE=/opt/python3/bin/python3 ..
-
-After that installation is pretty easy
-::
- $ sudo make install
-
-If everything went fine, you should be able to import moose in python shell.
-
-.. code-block:: python
- import moose
-
-
-Graphical User Interface (GUI)
-------------------------------
-
-You can get the source of ``moose-gui`` from `here
-<https://github.com/BhallaLab/moose-gui>`_. You can download it either by
-clicking on `this link <https://github.com/BhallaLab/moose-gui/archive/master.zip>`_
-or by using ``git`` ::
- $ git clone https://github.com/BhallaLab/moose-gui
-
-To be able to launch ``moose-gui``, you need to install some more packages
-
-- matplotlib
-- python-qt4
-
-On ``Ubuntu/Debian``, these can be installed with
-::
- $ sudo apt-get install python-matplotlib python-qt4
-
-On ``CentOS/Fedora/RHEL``
-::
- $ sudo yum install python-matplotlib python-qt4
-
-Now you can fire up the GUI
-::
- $ cd /to/moose-gui
- $ python mgui.py
-
-.. note::
- If you have installed ``moose`` package, then GUI is launched by
- running following commnad::
- $ moose
-
-Building moogli
----------------
-
-``moogli`` is subproject of ``MOOSE`` for visualizing models. More details can
-be found `here <http://moose.ncbs.res.in/moogli>`_.
-
-`Moogli` is part of `moose` package. Building moogli can be tricky because of
-multiple depednecies it has.
-
-
-To get the latest source code of ``moogli``, click on `this link <https://github.com/BhallaLab/moogli/archive/master.zip>`_.
-
-Moogli depends on ``OpenSceneGraph`` (version 3.2.0 or higher) which may not
-be easily available for your operating system.
-For this reason, we distribute required ``OpenSceneGraph`` with ``moogli``
-source code.
-
-Depending on distribution of your operating system, you would need following
-packages to be installed.
-
-On ``Ubuntu/Debian``
-::
- $ sudo apt-get install python-qt4-dev python-qt4-gl python-sip-dev libqt4-dev
-
-On ``Fedora/CentOS/RHEL``
-::
- $ sudo yum install sip-devel PyQt4-devel qt4-devel libjpeg-devel PyQt4
-
-On ``openSUSE``
-::
- $ sudo zypper install python-sip python-qt4-devel libqt4-devel python-qt4
-
-After this, building and installing ``moogli`` should be as simple as
-::
- $ cd /path/to/moogli
- $ mkdir _build
- $ cd _build
- $ cmake ..
- $ make
- $ sudo make install
-
-If you run into troubles, please report it on our `github repository
-<https://github.com/BhallaLab/moose/issues>`_.
diff --git a/docs/source/install/index_install.rst b/docs/source/install/index_install.rst
deleted file mode 100644
index 75b466ccc640a9d6c60481e86dfb79c106b1aa2d..0000000000000000000000000000000000000000
--- a/docs/source/install/index_install.rst
+++ /dev/null
@@ -1,208 +0,0 @@
-Installation
-=============
-
-Use pre-built packages
------------------------
-
-Linux
-^^^^^^
-
-We recommend that you use our repositories hosted at `Open Build Service
-<http://build.opensuse.org>`_. We have packages for the following distributions
-
-- Debian 7.0, 8.0
-- Ubuntu 12.04, 14.04, 15.04, 15.10, 16.04
-- CentOS 6, 7
-- Fedora 20, 21, 22, 23
-- OpenSUSE 13.1, 13.2, Factory ARM, Leap 42.1, Tumbleweed
-- SLE 12, 12 SP1
-- RHEL 7
-- Scientific Linux 7
-
-Visit `this page
-<https://software.opensuse.org/download.html?project=home:moose&package=moose>`_
-to pick your distribution and follow instructions.
-
-.. note::
- ``moogli`` (tool to visualize network activity) is not available for CentOS-6.
-
-.. raw:: html
- <iframe
- src="http://software.opensuse.org/download/package.iframe?project=moose&package=moose"></iframe>
-
-.. todo:: Packages for gentoo, Arch Linux
-
-Mac OSX
-^^^^^^^
-
-Download the ``dmg`` file from `here <https://github.com/BhallaLab/moose/releases/download/ghevar_3.0.2/Moose_3.0.2_OSX.dmg>`_.
-
-Alternatively, you can use ``homebrew`` to install ``moose``
-::
- $ brew install homebrew/science/moose
-
-
-Windows/Cygwin
-^^^^^^^^^^^^^^
-
-Building MOOSE
---------------
-
-In case your distribution is not listed on `our repository page
-<https://software.opensuse.org/download.html?project=home:moose&package=moose>`_
-, or if you want to build the lastest development code, read on.
-
-First, you need to get the source code. You can use ``git`` (clone the
-repository) or download snapshot of github repo by clicking on `this link
-<https://github.com/BhallaLab/moose/archive/master.zip>`_.::
- $ git clone https://github.com/BhallaLab/moose
-
-Or,
-::
- $ wget https://github.com/BhallaLab/moose/archive/master.zip
- $ unzip master.zip
-
-If you don't want lasest snapshot of ``MOOSE``, you can download other released
-versions from here `https://github.com/BhallaLab/moose/releases`.
-
-Install dependencies
-^^^^^^^^^^^^^^^^^^^^
-
-Next, you need to install required dependencies. Depending on your OS, names of
-following packages may vary.
-
-- cmake (version 2.8 or higher)
-- gsl-1.16 or higher `download <ftp://ftp.gnu.org/gnu/gsl/>`_.
-- libhdf5 development package e.g. `libhdf5-serial-dev` or `libhdf5-devel`
-- python development package e.g. `python-dev` or `python-devel`
-- numpy e.g. `python-numpy` or `numpy`
-
-Most of the dependencies can be installed using package manager.
-
-On ``Debian/Ubuntu``
-::
- $ sudo apt-get install libhdf5-dev cmake libgsl0-dev libpython-dev python-numpy
-
-.. note::
- Ubuntu 12.04 does not have required version of ``gsl`` (required 1.16 or
- higher, available 1.15). On Ubuntu 16.04, package name is ``libgsl-dev``.
-
-On ``CentOS/Fedora/RHEL/Scientific Linux``
-::
- $ sudo yum install hdf5-devel cmake libgsl-dev python-devel python-numpy
-
-On ``OpenSUSE``
-::
- $ sudo zypper install hdf5-devel cmake libgsl-dev python-devel python-numpy
-
-Now use `cmake` to build moose
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. code-block:: bash
-
- $ cd /to/moose/source/code
- $ mkdir _build
- $ cd _build
- $ cmake ..
- $ make
- $ ctest --output-on-failure # optional
-
-This will build pyMOOSE (MOOSE's python extention), `ctest` will run few tests to
-check if build process was successful.
-
-.. note::
- To install MOOSE into non-standard directory, pass additional argument
- `-DCMAKE_INSTALL_PREFIX=path/to/install/dir` to cmake
- ::
- $ cmake -DCMAKE_INSTALL_PREFIC=$HOME/.local ..
-
- To use different version of python
- ::
- $ cmake -DPYTHON_EXECUTABLE=/opt/python3/bin/python3 ..
-
-After that installation is pretty easy
-::
- $ sudo make install
-
-If everything went fine, you should be able to import moose in python shell.
-
-.. code-block:: python
-
- import moose
-
-
-Graphical User Interface (GUI)
-------------------------------
-
-You can get the source of ``moose-gui`` from `here
-<https://github.com/BhallaLab/moose-gui>`_. You can download it either by
-clicking on `this link <https://github.com/BhallaLab/moose-gui/archive/master.zip>`_
-or by using ``git`` ::
- $ git clone https://github.com/BhallaLab/moose-gui
-
-To be able to launch ``moose-gui``, you need to install some more packages
-
-- matplotlib
-- python-qt4
-
-On ``Ubuntu/Debian``, these can be installed with
-::
- $ sudo apt-get install python-matplotlib python-qt4
-
-On ``CentOS/Fedora/RHEL``
-::
- $ sudo yum install python-matplotlib python-qt4
-
-Now you can fire up the GUI
-::
- $ cd /to/moose-gui
- $ python mgui.py
-
-.. note::
- If you have installed ``moose`` package, then GUI is launched by
- running following commnad::
- $ moose
-
-Building moogli
----------------
-
-``moogli`` is subproject of ``MOOSE`` for visualizing models. More details can
-be found `here <http://moose.ncbs.res.in/moogli>`_.
-
-`Moogli` is part of `moose` package. Building moogli can be tricky because of
-multiple depednecies it has.
-
-
-To get the latest source code of ``moogli``, click on `this link <https://github.com/BhallaLab/moogli/archive/master.zip>`_.
-
-Moogli depends on ``OpenSceneGraph`` (version 3.2.0 or higher) which may not
-be easily available for your operating system.
-For this reason, we distribute required ``OpenSceneGraph`` with ``moogli``
-source code.
-
-Depending on distribution of your operating system, you would need following
-packages to be installed.
-
-On ``Ubuntu/Debian``
-::
- $ sudo apt-get install python-qt4-dev python-qt4-gl python-sip-dev libqt4-dev
-
-On ``Fedora/CentOS/RHEL``
-::
- $ sudo yum install sip-devel PyQt4-devel qt4-devel libjpeg-devel PyQt4
-
-On ``openSUSE``
-::
- $ sudo zypper install python-sip python-qt4-devel libqt4-devel python-qt4
-
-After this, building and installing ``moogli`` should be as simple as
-::
- $ cd /path/to/moogli
- $ mkdir _build
- $ cd _build
- $ cmake ..
- $ make
- $ sudo make install
-
-If you run into troubles, please report it on our `github repository
-<https://github.com/BhallaLab/moose/issues>`_.
diff --git a/docs/source/install/moose_quickstart.rst~ b/docs/source/install/moose_quickstart.rst~
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/docs/source/introduction/changes/index.rst b/docs/source/introduction/changes/index.rst
deleted file mode 100644
index 9a167f14daf7633c581babd2cd82e2b452ad0900..0000000000000000000000000000000000000000
--- a/docs/source/introduction/changes/index.rst
+++ /dev/null
@@ -1,4 +0,0 @@
-Changes
-=======
-
-.. todo:: collect changes from OBS.
diff --git a/docs/source/introduction/index_intro.rst b/docs/source/introduction/index_intro.rst
deleted file mode 100644
index 424ca9a2f0a5d738871656b9710d3d8800e0a4e2..0000000000000000000000000000000000000000
--- a/docs/source/introduction/index_intro.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-Introduction
-============
-
-What is MOOSE and what is it good for?
---------------------------------------
-MOOSE is the Multiscale Object-Oriented Simulation Environment. It is designed to simulate neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, circuits, and large networks. MOOSE can operate at many levels of detail, from stochastic chemical computations, to multicompartment single-neuron models, to spiking neuron network models.
-
-.. figure:: ../../images/Gallery_Moose_Multiscale.png
- :alt: **multiple scales in moose**
- :scale: 50%
-
- *Multiple scales can be modelled and simulated in MOOSE*
-
-MOOSE is multiscale: It can do all these calculations together. One of its major uses is to make biologically detailed models that combine electrical and chemical signaling.
-
-MOOSE is object-oriented. Biological concepts are mapped into classes, and a model is built by creating instances of these classes and connecting them by messages. MOOSE also has numerical classes whose job is to take over difficult computations in a certain domain, and do them fast. There are such solver classes for stochastic and deterministic chemistry, for diffusion, and for multicompartment neuronal models.
-
-MOOSE is a simulation environment, not just a numerical engine: It provides data representations and solvers (of course!), but also a scripting interface with Python, graphical displays with Matplotlib, PyQt, and OpenGL, and support for many model formats. These include SBML, NeuroML, GENESIS kkit and cell.p formats, HDF5 and NSDF for data writing.
-
-.. toctree::
-
- release_notes/index
- changes/index
- known_issues/index
diff --git a/docs/source/introduction/known_issues/index.rst b/docs/source/introduction/known_issues/index.rst
deleted file mode 100644
index 0ad5cdd653f187c374b75e0d605f748d2e3c8ea9..0000000000000000000000000000000000000000
--- a/docs/source/introduction/known_issues/index.rst
+++ /dev/null
@@ -1,9 +0,0 @@
-Known issues
-============
-
-Full report can be found at the following places
-
-- Related to build, packages and documentation `https://github.com/BhallaLab/moose/issues`
-- Related to python interface of MOOSE `https://github.com/BhallaLab/moose-core/issues`
-- Related to MOOSE GUI `https://github.com/BhallaLab/moose-gui/issues`
-- Related to ``moogli`` `https://github.com/BhallaLab/moogli/issues`
diff --git a/docs/source/introduction/release_notes/index.rst b/docs/source/introduction/release_notes/index.rst
deleted file mode 100644
index 862216e95c1d42e9c53d4f176e75ffdfe2987165..0000000000000000000000000000000000000000
--- a/docs/source/introduction/release_notes/index.rst
+++ /dev/null
@@ -1,4 +0,0 @@
-Release Notes
-============
-
-.. todo:: Collect release notes from github.
diff --git a/docs/source/user/py/cookbook/chem.rst b/docs/source/user/py/cookbook/chem.rst
deleted file mode 100644
index fa4c9cf098b2c818e3401703e3376c26eed48b5b..0000000000000000000000000000000000000000
--- a/docs/source/user/py/cookbook/chem.rst
+++ /dev/null
@@ -1,249 +0,0 @@
-****************
-Chemical Aspects
-****************
-
-.. _ckbk-chem-load-run:
-
-Load - Run - Save models
-========================
-
-Load a Kinetic Model
---------------------
-
-.. automodule:: loadKineticModel
- :members:
-
-Load an SBML Model
--------------------
-
-.. automodule:: loadSbmlmodel
- :members:
-
-Load a CSpace Model
--------------------
-
-.. automodule:: loadCspaceModel
- :members:
-
-Save a model into SBML format
------------------------------
-
-.. automodule:: convert_Genesis2Sbml
- :members:
-
-Save a model
-------------
-
-.. automodule:: savemodel
- :members:
-
-.. _ckbk-chem-snippets:
-
-Simple Examples
-===============================
-
-Set-up a kinetic solver and model
----------------------------------
-
-with Scripting
-^^^^^^^^^^^^^^
-
-.. automodule:: scriptGssaSolver
- :members:
-
-With something else
-^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: changeFuncExpression
- :members:
-
-Building a chemical Model from Parts
-------------------------------------
-
-.. automodule:: scriptKineticSolver
- :members:
-
-Cross-Compartment Reaction Systems
-----------------------------------
-
-.. automodule:: crossComptSimpleReac
- :members:
-
-.. automodule:: crossComptOscillator
- :members:
-
-.. automodule:: crossComptNeuroMesh
- :members:
-
-.. automodule:: crossComptSimpleReacGSSA
- :members:
-
-Tweaking Parameters
--------------------
-
-.. automodule:: tweakingParameters
- :members:
-
-Models' Demonstration
----------------------
-
-Oscillation Model
-^^^^^^^^^^^^^^^^^
-
-.. automodule:: slowFbOsc
- :members:
-
-Bistability Models
-^^^^^^^^^^^^^^^^^^
-
-MAPK feedback loop model
-~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. automodule:: mapkFB
- :members:
-
-Simple minimal bistable model
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. automodule:: scaleVolumes
- :members:
-
-Strongly bistable Model
-~~~~~~~~~~~~~~~~~~~~~~~
-
-.. automodule:: strongBis
- :members:
-
-Model of bidirectional synaptic plasticity
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-[showing bistable chemical switch]
-
-.. automodule:: bidirectionalPlasticity
- :members:
-
-Reaction Diffusion Models
--------------------------
-[Reaction-diffusion + transport in a tapering cylinder]
-
-.. automodule:: cylinderDiffusion
- :members:
-
-.. automodule:: cylinderMotor
- :members:
-
-.. automodule:: gssaCylinderDiffusion
- :members:
-
-Neuronal Diffusion Reaction
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: rxdFuncDiffusion
- :members:
-
-.. automodule:: rxdReacDiffusion
- :members:
-
-.. automodule:: rxdFuncDiffusionStoch
- :members:
-
-A Turing Model
---------------
-
-.. automodule:: TuringOneDim
- :members:
-
-A Spatial Bistable Model
-------------------------
-
-.. automodule::
- :members:
-
-Reaction Diffusion in Neurons
------------------------------
-
-.. automodule:: reacDiffConcGradient
- :members:
-
-.. automodule:: reacDiffBranchingNeuron
- :members:
-
-.. automodule:: reacDiffSpinyNeuron
- :members:
-
-.. automodule:: diffSpinyNeuron
- :members:
-
-Manipulating Chemical Models
-----------------------------
-
-Running with different numerical methods
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: switchKineticSolvers
- :members:
-
-Changing volumes
-^^^^^^^^^^^^^^^^
-
-.. automodule:: scaleVolumes
- :members:
-
-Feeding tabulated input to a model
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: analogStimTable
- :members:
-
-Finding steady states
-^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: findChemSteadyState
- :members:
-
-Making a dose-response curve
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: chemDoseResponse
- :members:
-
-Transport in branching dendritic tree
--------------------------------------
-
-.. automodule:: transportBranchingNeuron
- :members:
-
-.. _ckbk-chem-rde:
-
-RDesigneur
-==========
-
-.. _ckbk-chem-tut:
-
-Tutorials
-=========
-
-Deterministic Simulation
-------------------------
-
-Stochastic Simulation
----------------------
-
-Finding Steady State (CSpace)
------------------------------
-
-.. automodule:: cspaceSteadyState
- :members:
-
-Building Simple Reaction Model
-------------------------------
-
-Define a kinetic model using the scripting
----------------------
-
-.. automodule:: scriptKineticModel
- :members:
-
-.. _ckbk-chem-adv:
-
-Advanced Examples
-=================
diff --git a/docs/source/user/py/cookbook/elec.rst b/docs/source/user/py/cookbook/elec.rst
deleted file mode 100644
index 60c3974e699e4aca04200b9f12e621d5c009fbf6..0000000000000000000000000000000000000000
--- a/docs/source/user/py/cookbook/elec.rst
+++ /dev/null
@@ -1,119 +0,0 @@
-*********************************************
-Single Neuron Electrical Aspects (BioPhysics)
-*********************************************
-
-.. _ckbk-elec-load-run:
-
-Load and Run simple models
-==========================
-
-Single Cubicle Compartmental Neuron
------------------------------------
-
-.. automodule:: cubeMeshSigNeur
- :members:
-
-Single Neuron Model
--------------------
-
-.. automodule:: testSigNeur
- :members:
-
-Load neuron model from GENESIS
-------------------------------
-
-.. automodule:: neuronFromDotp
- :members:
-
-Integrate-and-fire models
--------------------------
-
-.. automodule:: IntegrateFireZoo
- :members:
-
-.. _ckbk-elec-snippets:
-
-Simple Examples
-===============================
-
-Gap Junction
-------------
-
-.. automodule:: gapjunction
- :members:
-
-Voltage Clamping
-----------------
-
-.. automodule:: vclamp
- :members:
-
-Synapse
--------
-
-.. automodule:: synapse
- :members:
-
-Generate Pulse
-----------------
-
-.. automodule:: pulsegen
- :members:
-
-.. automodule:: pulsegen2
- :members:
-
-Create a Leaky Neuron
----------------------
-
-.. automodule:: lif
- :members:
-
-Create a Leaky Compartment
---------------------------
-
-.. automodule:: lifcomp
- :members:
-
-Message transmission via synapse
---------------------------------
-
-.. automodule:: intfire
- :members:
-
-Insert Spine heads
-------------------
-
-.. automodule:: insertSpinesWithoutRdesigneur
- :members:
-
-Multi compartmental Neuron model
---------------------------------
-
-.. automodule:: testHsolve
- :members:
-
-.. _ckbk-elec-gui:
-
-GUI
-===
-
-.. _ckbk-elec-snippets:
-
-Simple Examples
-===============================
-
-.. _ckbk-elec-rde:
-
-RDesigneur
-==========
-
-.. _ckbk-elec-tut:
-
-Tutorials
-=========
-
-.. _ckbk-elec-adv:
-
-Advanced Examples
-=================
diff --git a/docs/source/user/py/cookbook/index_ckbk.rst b/docs/source/user/py/cookbook/index_ckbk.rst
deleted file mode 100644
index af47c0892c4fb126bf14751d40c8e63bfa69ae0c..0000000000000000000000000000000000000000
--- a/docs/source/user/py/cookbook/index_ckbk.rst
+++ /dev/null
@@ -1,14 +0,0 @@
-.. MOOSE documentation master file, created by
- sphinx-quickstart on Tue Jul 1 19:05:47 2014.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-Cook Book
-===========
-
-.. toctree::
-
- elec
- chem
- network
- multiscale
diff --git a/docs/source/user/py/cookbook/multiscale.rst b/docs/source/user/py/cookbook/multiscale.rst
deleted file mode 100644
index a406742280af7856067c41a85a8c8b4b2021a6f3..0000000000000000000000000000000000000000
--- a/docs/source/user/py/cookbook/multiscale.rst
+++ /dev/null
@@ -1,78 +0,0 @@
-*******************
-MultiScale Modeling
-*******************
-
-.. _ckbk-multi-load-run:
-
-Load and Run simple models
-==========================
-
-.. _ckbk-multi-snippets:
-
-Simple Examples
-===============
-
-Single-compartment multiscale model
------------------------------------
-
-.. automodule:: multiscaleOneCompt
- :members:
-
-Multi compartment Single Neuron Model
--------------------------------------
-
-.. automodule:: multiComptSigNeur
- :members:
-
-Multi-compartment multiscale model
-----------------------------------
-
-Modeling chemical reactions in neurons
---------------------------------------
-
-.. automodule:: gssaRDspiny
- :members:
-
-.. automodule:: rxdSpineSize
- :members:
-
-.. _ckbk-multi-gui:
-
-GUI
-===
-
-.. _ckbk-multi-rdes:
-
-RDesigneur
-==========
-
-Building Chemical-Electrical Signalling Models using Rdesigneur
----------------------------------------------------------------
-
-Building a compartment
-^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: testRdesigneur
- :members:
-
-Inserting Spines and viewing
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: insertSpines
- :members:
-
-Proceeding with Spines
-^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: testWigglySpines
- :members:
-
-.. _ckbk-multi-tut:
-
-Tutorials
-=========
-
-.. _ckbk-multi-adv:
-
-Advanced Examples
-=================
diff --git a/docs/source/user/py/cookbook/network.rst b/docs/source/user/py/cookbook/network.rst
deleted file mode 100644
index 94631ed52160bba03946297de7207f9a7bc67024..0000000000000000000000000000000000000000
--- a/docs/source/user/py/cookbook/network.rst
+++ /dev/null
@@ -1,94 +0,0 @@
-**********
-Networking
-**********
-
-.. _ckbk-net-load-run:
-
-Load and Run simple models
-==========================
-
-.. _ckbk-net-snippets:
-
-Simple Examples
-===============================
-
-Connecting two cells via a synapse
-----------------------------------
-
-.. automodule:: twocells
- :members:
-
-Multi Compartmental Leaky Neurons
----------------------------------
-
-.. automodule:: multicomp_lif
- :members:
-
-Providing random input to a cell
---------------------------------
-
-.. automodule:: randomspike
- :members:
-
-Plastic synapse
----------------
-
-.. automodule:: STDP
- :members:
-
-Synapse Handler for Spikes
---------------------------
-
-.. automodule:: RandSpikeStats
- :members:
-
-Recurrent integrate-and-fire network
-------------------------------------
-
-.. automodule:: recurrentIntFire
- :members:
-
-Recurrent integrate-and-fire network with plasticity
-----------------------------------------------------
-
-.. automodule:: recurrentLIF
- :members:
-
-Demonstration Models
---------------------
-
-.. automodule:: compartment_net
- :members:
-
-.. automodule:: compartment_net_no_array
- :members:
-
-Building Models
----------------
-
-.. automodule:: synapse_tutorial
- :members:
-
-.. _ckbk-net-gui:
-
-GUI
-===
-
-.. _ckbk-net-tut:
-
-Tutorials
-=========
-
-Network with Ca-based plasticity
---------------------------------
-
-.. automodule:: GraupnerBrunel2012_STDPfromCaPlasticity
- :members:
-
-.. automodule:: HigginsGraupnerBrunel2014_LifetimeCaPlasticity
- :members:
-
-.. _ckbk-net-adv:
-
-Advanced Examples
-=================
diff --git a/docs/source/user/py/graphics/index_graphics.rst b/docs/source/user/py/graphics/index_graphics.rst
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/docs/source/user/py/quickstart/demos.rst b/docs/source/user/py/quickstart/demos.rst
deleted file mode 100644
index 7451bd68adc78e9a9df2a50f7c7101c5eedb9059..0000000000000000000000000000000000000000
--- a/docs/source/user/py/quickstart/demos.rst
+++ /dev/null
@@ -1,187 +0,0 @@
-**************************************
-Demonstration of basic functionalities
-**************************************
-
-.. _quickstart-load-run:
-
-Load and Run a Model
-====================
-
-.. automodule:: helloMoose
- :members:
-
-.. _quickstart-timing:
-
-Start, Stop, and setting clocks
-===============================
-
-.. automodule:: startstop
- :members:
-
-.. automodule:: stimtable
- :members:
-
-.. _quickstart-python_from_moose:
-
-Run Python from MOOSE
-=====================
-
-.. automodule:: pyrun
- :members:
-
-.. automodule:: pyrun1
- :members:
-
-.. _quickstart-classes:
-
-MOOSE Classes
-=====================
-
-Messages
---------
-
-One-to-one message
-^^^^^^^^^^^^^^^^^^
-
-.. automodule:: onetoonemsg
- :members:
-
-Show the message
-^^^^^^^^^^^^^^^^
-
-.. automodule:: showmsg
- :members:
-
-Single Message Cross
-^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: singlemsgcross
- :members:
-
-Time
-----
-
-Clocks
-^^^^^^
-
-.. automodule:: showclocks
- :members:
-
-Generating Time Data Table
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: timetable
- :members:
-
-Vectors
--------
-
-.. automodule:: vectors
- :members:
-
-Data Entries
-------------
-
-.. automodule:: wildcard
- :members:
-
-Interpolation
--------------
-
-1-dimentional Interpolation
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: interpol
- :members:
-
-2-dimentional interpolation
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: interpol2d
- :members:
-
-Function
---------
-
-.. automodule:: func
- :members:
-
-SymCompartment
---------------
-
-.. automodule:: symcompartment
- :members:
-
-Tables
-------
-
-.. automodule:: tabledemo
- :members:
-
-Data Types
-----------
-
-HDF DataType
-^^^^^^^^^^^^
-
-.. automodule:: hdfdemo
- :members:
-
-NSDF DataType
-^^^^^^^^^^^^^
-
-.. automodule:: nsdf
- :members:
-
-.. automodule:: nsdf_vec
- :members:
-
-Threading
----------
-
-.. automodule:: threading_demo
- :members:
-
-PyMoose
--------
-
-.. automodule:: traub_naf
- :members:
-
-.. _quickstart-maths:
-
-Mathematics with MOOSE
-======================
-
-Computing an arbitrary function
--------------------------------
-
-.. automodule:: function
- :members:
-
-Differential Equation Solving
------------------------------
-
-.. automodule:: diffEqSolution
- :members:
-
-Harmonic Oscillatory Function
------------------------------
-
-.. automodule:: funcRateHarmonicOsc
- :members:
-
-Lotka-Voltera Model
--------------------
-
-.. automodule:: funcReacLotkaVolterra
- :members:
-
-.. automodule:: stochasticLotkaVolterra
- :members:
-
-Vary Concentration with mathematical function
----------------------------------------------
-
-.. automodule:: funcInputToPools
- :members:
diff --git a/docs/source/user/py/quickstart/index_qs.rst b/docs/source/user/py/quickstart/index_qs.rst
deleted file mode 100644
index d6d0c42b0785d972871b1dbb1ee561d1875e0ee7..0000000000000000000000000000000000000000
--- a/docs/source/user/py/quickstart/index_qs.rst
+++ /dev/null
@@ -1,13 +0,0 @@
-.. MOOSE documentation master file, created by
- sphinx-quickstart on Tue Jul 1 19:05:47 2014.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-Quick Start
-===========
-
-.. toctree::
- :maxdepth: 2
-
- moose_quickstart
- demos
diff --git a/docs/source/user/py/quickstart/moose_quickstart.rst b/docs/source/user/py/quickstart/moose_quickstart.rst
deleted file mode 100644
index f552fb900164f43ea2913a63241f3d552f6c89d9..0000000000000000000000000000000000000000
--- a/docs/source/user/py/quickstart/moose_quickstart.rst
+++ /dev/null
@@ -1,683 +0,0 @@
-***********************************************
-Getting started with python scripting for MOOSE
-***********************************************
-
-.. :Author: Subhasis Ray
-.. :Date: December 12, 2012,
-.. :Last-Updated: Jan 21, 2016
-.. :By: Harsha Rani
-
-.. _quickstart-intro:
-
-Introduction
-============
-
-This document describes how to use the ``moose`` module in Python
-scripts or in an interactive Python shell. It aims to give you enough
-overview to help you start scripting using MOOSE and extract farther
-information that may be required for advanced work. Knowledge of
-Python or programming in general will be helpful. If you just want to
-simulate existing models in one of the supported formats, you can fire
-the MOOSE GUI and locate the model file using the ``File`` menu and
-load it. The GUI is described in separate document. If you
-are looking for recipes for specific tasks, take a look at
-:doc:`moose_cookbook`. The example code in the boxes can be entered in
-a Python shell.
-
-.. _quickstart-importing:
-
-Importing MOOSE and accessing built-in documentation
-====================================================
-
-In a python script you import modules to access the functionalities they
-provide. ::
-
- >>> import moose
-
-This makes the ``moose`` module available for use in Python. You can use
-Python's built-in ``help`` function to read the top-level documentation
-for the moose module ::
-
- >>> help(moose)
-
-This will give you an overview of the module. Press ``q`` to exit the
-pager and get back to the interpreter. You can also access the
-documentation for individual classes and functions this way. ::
-
- >>> help(moose.connect)
-
-To list the available functions and classes you can use ``dir``
-function [1]_. ::
-
- >>> dir(moose)
-
-MOOSE has built-in documentation in the C++-source-code independent of
-Python. The ``moose`` module has a separate ``doc`` function to extract
-this documentation. ::
-
- >>> moose.doc(moose.Compartment)
-
-The class level documentation will show whatever the author/maintainer
-of the class wrote for documentation followed by a list of various kinds
-of fields and their data types. This can be very useful in an
-interactive session.
-
-Each field can have its own detailed documentation, too. ::
-
- >>> moose.doc('Compartment.Rm')
-
-Note that you need to put the class-name followed by dot followed by
-field-name within quotes. Otherwise, ``moose.doc`` will receive the
-field value as parameter and get confused.
-
-.. _quickstart-creating:
-
-Creating objects and traversing the object hierarchy
-----------------------------------------------------
-
-Different types of biological entities like neurons, enzymes, etc are
-represented by classes and individual instances of those types are
-objects of those classes. Objects are the building-blocks of models in
-MOOSE. We call MOOSE objects ``element`` and use object and element
-interchangeably in the context of MOOSE. Elements are conceptually laid
-out in a tree-like hierarchical structure. If you are familiar with file
-system hierarchies in common operating systems, this should be simple.
-
-At the top of the object hierarchy sits the ``Shell``, equivalent to the
-root directory in UNIX-based systems and represented by the path ``/``.
-You can list the existing objects under ``/`` using the ``le`` function. ::
-
- >>> moose.le()
- Elements under /
- /Msgs
- /clock
- /classes
- /postmaster
-
-``Msgs``, ``clock`` and ``classes`` are predefined objects in MOOSE. And
-each object can contain other objects inside them. You can see them by
-passing the path of the parent object to ``le`` ::
-
- >>> moose.le('/Msgs')
- Elements under /Msgs[0]
- /Msgs[0]/singleMsg
- /Msgs[0]/oneToOneMsg
- /Msgs[0]/oneToAllMsg
- /Msgs[0]/diagonalMsg
- /Msgs[0]/sparseMsg
-
-Now let us create some objects of our own. This can be done by invoking
-MOOSE class constructors (just like regular Python classes). ::
-
- >>> model = moose.Neutral('/model')
-
-The above creates a ``Neutral`` object named ``model``. ``Neutral`` is
-the most basic class in MOOSE. A ``Neutral`` element can act as a
-container for other elements. We can create something under ``model`` ::
-
- >>> soma = moose.Compartment('/model/soma')
-
-Every element has a unique path. This is a concatenation of the names of
-all the objects one has to traverse starting with the root to reach that
-element. ::
-
- >>> print soma.path
- /model/soma
-
-The name of the element can be printed, too. ::
-
- >>> print soma.name
- soma
-
-The ``Compartment`` elements model small sections of a neuron. Some
-basic experiments can be carried out using a single compartment. Let us
-create another object to act on the ``soma``. This will be a step
-current generator to inject a current pulse into the soma. ::
-
- >>> pulse = moose.PulseGen('/model/pulse')
-
-You can use ``le`` at any point to see what is there ::
-
- >>> moose.le('/model')
- Elements under /model
- /model/soma
- /model/pulse
-
-And finally, we can create a ``Table`` to record the time series of the
-soma's membrane potential. It is good practice to organize the data
-separately from the model. So we do it as below ::
-
- >>> data = moose.Neutral('/data')
- >>> vmtab = moose.Table('/data/soma_Vm')
-
-Now that we have the essential elements for a small model, we can go on
-to set the properties of this model and the experimental protocol.
-
-.. _quickstart-properties:
-
-Setting the properties of elements: accessing fields
-====================================================
-
-Elements have several kinds of fields. The simplest ones are the
-``value fields``. These can be accessed like ordinary Python members.
-You can list the available value fields using ``getFieldNames``
-function ::
-
- >>> soma.getFieldNames('valueFinfo')
-
-Here ``valueFinfo`` is the type name for value fields. ``Finfo`` is
-short form of *field information*. For each type of field there is a
-name ending with ``-Finfo``. The above will display the following
-list ::
-
- ('this',
- 'name',
- 'me',
- 'parent',
- 'children',
- 'path',
- 'class',
- 'linearSize',
- 'objectDimensions',
- 'lastDimension',
- 'localNumField',
- 'pathIndices',
- 'msgOut',
- 'msgIn',
- 'Vm',
- 'Cm',
- 'Em',
- 'Im',
- 'inject',
- 'initVm',
- 'Rm',
- 'Ra',
- 'diameter',
- 'length',
- 'x0',
- 'y0',
- 'z0',
- 'x',
- 'y',
- 'z')
-
-Some of these fields are for internal or advanced use, some give access
-to the physical properties of the biological entity we are trying to
-model. Now we are interested in ``Cm``, ``Rm``, ``Em`` and ``initVm``.
-In the most basic form, a neuronal compartment acts like a parallel
-``RC`` circuit with a battery attached. Here ``R`` and ``C`` are
-resistor and capacitor connected in parallel, and the battery with
-voltage ``Em`` is in series with the resistor, as shown below:
-
-
-
-.. figure:: ../../../images/neuronalcompartment.jpg
- :alt: **Passive neuronal compartment**
-
- **Passive neuronal compartment**
-
-
-
-The fields are populated with some defaults. ::
-
- >>> print soma.Cm, soma.Rm, soma.Vm, soma.Em, soma.initVm
- 1.0 1.0 -0.06 -0.06 -0.06
-
-
-You can set the ``Cm`` and ``Rm`` fields to something realistic using
-simple assignment (we follow SI unit) [2]_. ::
-
- >>> soma.Cm = 1e-9
- >>> soma.Rm = 1e7
- >>> soma.initVm = -0.07
-
-Instead of writing print statements for each field, you could use the
-utility function showfield to see that the changes took effect ::
-
- >>> moose.showfield(soma)
- [ /soma[0] ]
- diameter = 0.0
- Ra = 1.0
- y0 = 0.0
- Rm = 10000000.0
- numData = 1
- inject = 0.0
- initVm = -0.07
- Em = -0.06
- y = 0.0
- numField = 1
- path = /soma[0]
- dt = 5e-05
- tick = 4
- z0 = 0.0
- name = soma
- Cm = 1e-09
- x0 = 0.0
- Vm = -0.06
- className = Compartment
- length = 0.0
- Im = 0.0
- x = 0.0
- z = 0.0
-
-Now we can setup the current pulse to be delivered to the soma ::
-
- >>> pulse.delay[0] = 50e-3
- >>> pulse.width[0] = 100e-3
- >>> pulse.level[0] = 1e-9
- >>> pulse.delay[1] = 1e9
-
-This tells the pulse generator to create a 100 ms long pulse 50 ms after
-the start of the simulation. The amplitude of the pulse is set to 1 nA.
-We set the delay for the next pulse to a very large value (larger than
-the total simulation time) so that the stimulation stops after the first
-pulse. Had we set ``pulse.delay = 0`` , it would have generated a pulse
-train at 50 ms intervals.
-
-.. _quickstart-connections:
-
-Putting them together: setting up connections
-=============================================
-
-In order for the elements to interact during simulation, we need to
-connect them via messages. Elements are connected to each other using
-special source and destination fields. These types are named
-``srcFinfo`` and ``destFinfo``. You can query the available source and
-destination fields on an element using ``getFieldNames`` as before. This
-time, let us do it another way: by the class name ::
-
- >>> moose.getFieldNames('PulseGen', 'srcFinfo')
- ('childMsg', 'output')
-
-This form has the advantage that you can get information about a class
-without creating elements of that class.
-
-Here ``childMsg`` is a source field that is used by the MOOSE internals
-to connect child elements to parent elements. The second one is of our
-interest. Check out the built-in documentation here ::
-
- >>> moose.doc('PulseGen.output')
- PulseGen.output: double - source field
- Current output level.
-
-so this is the output of the pulse generator and this must be injected
-into the ``soma`` to stimulate it. But where in the ``soma`` can we send
-it? Again, MOOSE has some introspection built in. ::
-
- >>> soma.getFieldNames('destFinfo')
- ('parentMsg',
- 'setThis',
- 'getThis',
- ...
- 'setZ',
- 'getZ',
- 'injectMsg',
- 'randInject',
- 'cable',
- 'process',
- 'reinit',
- 'initProc',
- 'initReinit',
- 'handleChannel',
- 'handleRaxial',
- 'handleAxial')
-
-Now that is a long list. But much of it are fields for internal or
-special use. Anything that starts with ``get`` or ``set`` are internal
-``destFinfo`` used for accessing value fields (we shall use one of those
-when setting up data recording). Among the rest ``injectMsg`` seems to
-be the most likely candidate. Use the ``connect`` function to connect
-the pulse generator output to the soma input ::
-
- >>> m = moose.connect(pulse, 'output', soma, 'injectMsg')
-
-``connect(source, source_field, dest, dest_field)`` creates a
-``message`` from ``source`` element's ``source_field`` field to ``dest``
-elements ``dest_field`` field and returns that message. Messages are
-also elements. You can print them to see their identity ::
-
- >>> print m
- <moose.SingleMsg: id=5, dataId=733, path=/Msgs/singleMsg[733]>
-
-You can print any element as above and the string representation will
-show you the class, two numbers(\ ``id`` and ``dataId``) uniquely
-identifying it among all elements, and its path. You can get some more
-information about a message ::
-
- >>> print m.e1.path, m.e2.path, m.srcFieldsOnE1, m.destFieldsOnE2
- /model/pulse /model/soma ('output',) ('injectMsg',)
-
-
-will confirm what you already know.
-
-
-A message element has fields ``e1`` and ``e2`` referring to the elements
-it connects. For single one-directional messages these are source and
-destination elements, which are ``pulse`` and ``soma`` respectively. The
-next two items are lists of the field names which are connected by this
-message.
-
-You could also check which elements are connected to a particular field ::
-
- >>> print soma.neighbors['injectMsg']
- [<moose.vec: class=PulseGen, id=729,path=/model/pulse>]
-
-Notice that the list contains something called vec. We discuss this
-`later <#some-more-details>`__. Also ``neighbors`` is a new kind of
-field: ``lookupFinfo`` which behaves like a dictionary. Next we connect
-the table to the soma to retrieve its membrane potential ``Vm``. This is
-where all those ``destFinfo`` starting with ``get`` or ``set`` come in
-use. For each value field ``X``, there is a ``destFinfo`` ``get{X}`` to
-retrieve the value at simulation time. This is used by the table to
-record the values ``Vm`` takes. ::
-
- >>> moose.connect(vmtab, 'requestOut', soma, 'getVm')
- <moose.SingleMsg: id=5, dataIndex=0, path=/Msgs[0]/singleMsg[0]>
-
-This finishes our model and recording setup. You might be wondering
-about the source-destination relationship above. It is natural to think
-that ``soma`` is the source of ``Vm`` values which should be sent to
-``vmtab``. But here ``requestOut`` is a ``srcFinfo`` acting like a
-reply card. This mode of obtaining data is called *pull* mode. [3]_
-
-You can skip the next section on fine control of the timing of updates
-and read :ref:`quickstart-running`.
-
-.. _quickstart-scheduling:
-
-Scheduling
-==========
-
-With the model all set up, we have to schedule the
-simulation. Different components in a model may have different rates
-of update. For example, the dynamics of electrical components require
-the update intervals to be of the order 0.01 ms whereas chemical
-components can be as slow as 1 s. Also, the results may depend on the
-sequence of the updates of different components. These issues are
-addressed in MOOSE using a clock-based update scheme. Each model
-component is scheduled on a clock tick (think of multiple hands of a
-clock ticking at different intervals and the object being updated at
-each tick of the corresponding hand). The scheduling also guarantees
-the correct sequencing of operations. For example, your Table objects
-should always be scheduled *after* the computations that they are
-recording, otherwise they will miss the outcome of the latest calculation.
-
-MOOSE has a central clock element (``/clock``) to manage
-time. Clock has a set of ``Tick`` elements under it that take care of
-advancing the state of each element with time as the simulation
-progresses. Every element to be included in a simulation must be
-assigned a tick. Each tick can have a different ticking interval
-(``dt``) that allows different elements to be updated at different
-rates.
-
-By default, every object is assigned a clock tick with reasonable default
-timesteps as soon it is created::
-
- Class type tick dt
- Electrical computations: 0-7 50 microseconds
- electrical compartments,
- V and ligand-gated ion channels,
- Calcium conc and Nernst,
- stimulus generators and tables,
- HSolve.
-
- Table (to plot elec. signals) 8 100 microseconds
-
- Diffusion solver 10 0.01 seconds
- Chemical computations: 11-17 0.1 seconds
- Pool, Reac, Enz, MMEnz,
- Func, Function,
- Gsolve, Ksolve,
- Stats (to do stats on outputs)
-
- Table2 (to plot chem. signals) 18 1 second
-
- HDF5DataWriter 30 1 second
- Postmaster (for parallel 31 0.01 seconds
- computations)
-
-There are 32 available clock ticks. Numbers 20 to 29 are
-unassigned so you can use them for whatever purpose you like.
-
-If you want fine control over the scheduling, there are three things
-you can do.
-
- * Alter the 'tick' field on the object
- * Alter the dt associated with a given tick, using the
- **moose.setClock( tick, newdt)** command
- * Go through a wildcard path of objects reassigning there clock ticks,
- using **moose.useClock( path, newtick, function)**.
-
-Here we discuss these in more detail.
-
-**Altering the 'tick' field**
-
-Every object knows which tick and dt it uses::
-
- >>> a = moose.Pool( '/a' )
- >>> print a.tick, a.dt
- 13 0.1
-
-The ``tick`` field on every object can be changed, and the object will
-adopt whatever clock dt is used for that tick. The ``dt`` field is
-readonly, because changing it would have side-effects on every object
-associated with the current tick.
-
-Ticks **-1** and **-2** are special: They both tell the object that it is
-disabled (not scheduled for any operations). An object with a
-tick of **-1** will be left alone entirely. A tick of **-2** is used in
-solvers to indicate that should the solver be removed, the object will
-revert to its default tick.
-
-**Altering the dt associated with a given tick**
-
-We initialize the ticks and set their ``dt`` values using the
-``setClock`` function. ::
-
- >>> moose.setClock(0, 0.025e-3)
- >>> moose.setClock(1, 0.025e-3)
- >>> moose.setClock(2, 0.25e-3)
-
-This will initialize tick #0 and tick #1 with ``dt = 25`` μs and tick #2
-with ``dt = 250`` μs. Thus all the elements scheduled on ticks #0 and 1
-will be updated every 25 μs and those on tick #2 every 250 μs. We use
-the faster clocks for the model components where finer timescale is
-required for numerical accuracy and the slower clock to sample the
-values of ``Vm``.
-
-Note that if you alter the dt associated with a given tick, this will
-affect the update time for *all* the objects using that clock tick. If
-you're unsure that you want to do this, use one of the vacant ticks.
-
-
-**Assigning clock ticks to all objects in a wildcard path**
-
-To assign tick #2 to the table for recording ``Vm``, we pass its
-whole path to the ``useClock`` function. ::
-
- >>> moose.useClock(2, '/data/soma_Vm', 'process')
-
-Read this as "use tick # 2 on the element at path ``/data/soma_Vm`` to
-call its ``process`` method at every step". Every class that is supposed
-to update its state or take some action during simulation implements a
-``process`` method. And in most cases that is the method we want the
-ticks to call at every time step. A less common method is ``init``,
-which is implemented in some classes to interleave actions or updates
-that must be executed in a specific order [4]_. The ``Compartment``
-class is one such case where a neuronal compartment has to know the
-``Vm`` of its neighboring compartments before it can calculate its
-``Vm`` for the next step. This is done with: ::
-
- >>> moose.useClock(0, soma.path, 'init')
-
-Here we used the ``path`` field instead of writing the path explicitly.
-
-Next we assign tick #1 to process method of everything under ``/model``. ::
-
- >>> moose.useClock(1, '/model/##', 'process')
-
-Here the second argument is an example of wild-card path. The ``##``
-matches everything under the path preceding it at any depth. Thus if we
-had some other objects under ``/model/soma``, ``process`` method of
-those would also have been scheduled on tick #1. This is very useful for
-complex models where it is tedious to scheduled each element
-individually. In this case we could have used ``/model/#`` as well for
-the path. This is a single level wild-card which matches only the
-children of ``/model`` but does not go farther down in the hierarchy.
-
-.. _quickstart-running:
-
-Running the simulation
-======================
-
-Once the model is all set up, we can put the model to its
-initial state using ::
-
- >>> moose.reinit()
-
-You may remember that we had changed initVm from ``-0.06`` to ``-0.07``.
-The reinit call we initialize ``Vm`` to that value. You can verify that ::
-
- >>> print soma.Vm
- -0.07
-
-Finally, we run the simulation for 300 ms ::
-
- >>> moose.start(300e-3)
-
-The data will be recorded by the ``soma_vm`` table, which is referenced
-by the variable ``vmtab``. The ``Table`` class provides a numpy array
-interface to its content. The field is ``vector``. So you can easily plot
-the membrane potential using the `matplotlib <http://matplotlib.org/>`__
-library. ::
-
- >>> import pylab
- >>> t = pylab.linspace(0, 300e-3, len(vmtab.vector))
- >>> pylab.plot(t, vmtab.vector)
- >>> pylab.show()
-
-The first line imports the pylab submodule from matplotlib. This useful
-for interactive plotting. The second line creates the time points to
-match our simulation time and length of the recorded data. The third
-line plots the ``Vm`` and the fourth line makes it visible. Does the
-plot match your expectation?
-
-.. _quickstart-details:
-
-Some more details
-=================
-
-``vec``, ``melement`` and ``element``
------------------------------------------
-
-MOOSE elements are instances of the class ``melement``. ``Compartment``,
-``PulseGen`` and other MOOSE classes are derived classes of
-``melement``. All ``melement`` instances are contained in array-like
-structures called ``vec``. Each ``vec`` object has a numerical
-``id_`` field uniquely identifying it. An ``vec`` can have one or
-more elements. You can create an array of elements ::
-
- >>> comp_array = moose.vec('/model/comp', n=3, dtype='Compartment')
-
-This tells MOOSE to create an ``vec`` of 3 ``Compartment`` elements
-with path ``/model/comp``. For ``vec`` objects with multiple
-elements, the index in the ``vec`` is part of the element path. ::
-
- >>> print comp_array.path, type(comp_array)
-
-shows that ``comp_array`` is an instance of ``vec`` class. You can
-loop through the elements in an ``vec`` like a Python list ::
-
- >>> for comp in comp_array:
- ... print comp.path, type(comp)
- ...
-
-shows ::
-
- /model/comp[0] <type 'moose.melement'>
- /model/comp[1] <type 'moose.melement'>
- /model/comp[2] <type 'moose.melement'>
-
-Thus elements are instances of class ``melement``. All elements in an
-``vec`` share the ``id_`` of the ``vec`` which can retrieved by
-``melement.getId()``.
-
-A frequent use case is that after loading a model from a file one knows
-the paths of various model components but does not know the appropriate
-class name for them. For this scenario there is a function called
-``element`` which converts ("casts" in programming jargon) a path or any
-moose object to its proper MOOSE class. You can create additional
-references to ``soma`` in the example this way ::
-
- x = moose.element('/model/soma')
-
-Any MOOSE class can be extended in Python. But any additional attributes
-added in Python are invisible to MOOSE. So those can be used for
-functionalities at the Python level only. You can see
-``moose-examples/squid/squid.py`` for an example.
-
-``Finfos``
-----------
-
-The following kinds of ``Finfo`` are accessible in Python
-
-- **``valueFinfo``** : simple values. For each readable ``valueFinfo``
- ``XYZ`` there is a ``destFinfo`` ``getXYZ`` that can be used for
- reading the value at run time. If ``XYZ`` is writable then there will
- also be ``destFinfo`` to set it: ``setXYZ``. Example:
- ``Compartment.Rm``
-- **``lookupFinfo``** : lookup tables. These fields act like Python
- dictionaries but iteration is not supported. Example:
- ``Neutral.neighbors``.
-- **``srcFinfo``** : source of a message. Example:
- ``PulseGen.output``.
-- **``destFinfo``** : destination of a message. Example:
- ``Compartment.injectMsg``. Apart from being used in setting up
- messages, these are accessible as functions from Python.
- ``HHGate.setupAlpha`` is an example.
-- **``sharedFinfo``** : a composition of source and destination fields.
- Example: ``Compartment.channel``.
-
-.. _quickstart-moving-on:
-
-Moving on
-=========
-
-Now you know the basics of pymoose and how to access the help
-system. You can figure out how to do specific things by looking at the
-:doc:`moose_cookbook`. In addition, the ``moose-examples/snippets`` directory
-in your MOOSE installation has small executable python scripts that
-show usage of specific classes or functionalities. Beyond that you can
-browse the code in the ``moose-examples`` directory to see some more complex
-models.
-
-MOOSE is backward compatible with GENESIS and most GENESIS classes have
-been reimplemented in MOOSE. There is slight change in naming (MOOSE
-uses CamelCase), and setting up messages are different. But `GENESIS
-documentation <http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual.html>`__
-is still a good source for documentation on classes that have been
-ported from GENESIS.
-
-If the built-in MOOSE classes do not satisfy your needs entirely, you
-are welcome to add new classes to MOOSE. The API documentation will
-help you get started.
-
-
-.. [1]
- To list the classes only, use ``moose.le('/classes')``
-
-.. [2]
- MOOSE is unit agnostic and things should work fine as long as you use
- values all converted to a consistent unit system.
-
-.. [3]
- This apparently convoluted implementation is for performance reason.
- Can you figure out why? *Hint: the table is driven by a slower clock
- than the compartment.*
-
-.. [4]
- In principle any function available in a MOOSE class can be executed
- periodically this way as long as that class exposes the function for
- scheduling following the MOOSE API. So you have to consult the class'
- documentation for any nonstandard methods that can be scheduled this
- way.
diff --git a/docs/source/user/py/references/index_ref.rst b/docs/source/user/py/references/index_ref.rst
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/neuroml/GranuleCell/Granule98_hsolve.py b/neuroml/GranuleCell/Granule98_hsolve.py
index 6070f861e8024bb5a15e61ed7c2a81fa89258c7c..6825a4a4fc4c3996d4034ce2b292ea721168fb7c 100644
--- a/neuroml/GranuleCell/Granule98_hsolve.py
+++ b/neuroml/GranuleCell/Granule98_hsolve.py
@@ -8,10 +8,7 @@ The soma name below is hard coded for gran98, else any other file can be used by
"""
import os
-os.environ['NUMPTHREADS'] = '1'
import sys
-sys.path.append('../../../python')
-
import moose
from moose.utils import *
from moose.neuroml.NeuroML import NeuroML
@@ -32,7 +29,7 @@ def loadGran98NeuroML_L123(filename):
somaCa = setupTable('somaCa',moose.CaConc(soma_path+'/Gran_CaPool_98'),'Ca')
somaIKCa = setupTable('somaIKCa',moose.element(soma_path+'/Gran_KCa_98'),'Gk')
## Am not able to plot KDr gating variable X when running under hsolve
- #KDrX = setupTable('ChanX',moose.HHChannel(soma_path+'/Gran_KDr_98'),'X')
+ #KDrX = setupTable('ChanX',moose.element(soma_path+'/Gran_KDr_98'),'X')
print("Reinit MOOSE ... ")
resetSim(['/elec',cells_path], simdt, plotdt, simmethod='hsolve')