├── .bbp-project.yaml ├── .clang-format.changes ├── .cmake-format.changes.yaml ├── .flake8 ├── .git-blame-ignore-revs ├── .githooks └── pre-commit ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── ci.md │ ├── config.yml │ ├── feature_request.md │ ├── release-patch.md │ └── release.md ├── problem-matchers │ ├── address.json │ ├── gcc.json │ ├── thread.json │ └── undefined.json └── workflows │ ├── coverage.yml │ ├── external.yml │ ├── formatting.yml │ ├── neuron-ci.yml │ ├── nvhpc.yml │ ├── release.yml │ ├── wheels-ci.yml │ ├── wheels-nightly.yml │ ├── wheels-template.yml │ ├── windows.yml │ └── yaml_validator.yml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── .sanitizers ├── thread.supp └── undefined.supp ├── CMakeLists.txt ├── CONTRIBUTING.md ├── Copyright ├── README.md ├── azure-pipelines.yml ├── bin ├── CMakeLists.txt ├── mkthreadsafe ├── mos2nrn2.sh.in ├── neurondemo.in ├── nrn-enable-sanitizer.in ├── nrndiagnose.sh.in ├── nrngui.in ├── nrnivmodl-core.in ├── nrnivmodl.in ├── nrnivmodl_core_makefile.in ├── nrnivmodl_makefile_cmake.in ├── nrnpyenv.sh.in ├── set_nrnpyenv.sh └── sortspike ├── bldnrnmacpkg.sh ├── ci ├── association.hoc ├── azure-wheel-test-upload.yml ├── requirements.txt ├── uv_requirements.txt ├── validate_yaml.sh ├── win_build_cmake.sh ├── win_download_deps.cmd ├── win_install_deps.cmd ├── win_install_neuron.cmd └── win_test_installer.cmd ├── ci_requirements.txt ├── cmake ├── BuildOptionDefaults.cmake ├── CMakeListsNrnMech.cmake ├── CheckGitDescribeCompatibility.cmake ├── CompilerFlagsHelpers.cmake ├── CompilerHelper.cmake ├── ConfigFileSetting.cmake ├── Coverage.cmake ├── ExecuteFindPython │ └── CMakeLists.txt ├── ExternalProjectHelper.cmake ├── FetchLatestRelease.cmake ├── GetLIKWID.cmake ├── MPIDynamicHelper.cmake ├── MacroHelper.cmake ├── NanoBindMinimal.cmake ├── NeuronFileLists.cmake ├── NeuronTestHelper.cmake ├── PlatformHelper.cmake ├── PythonCompileHelper.cmake ├── PythonHelper.cmake ├── PythonNotebookHelper.cmake ├── ReleaseDebugAutoFlags.cmake ├── RpathHelper.cmake ├── RunHOCTest.cmake ├── SanitizerHelper.cmake ├── check_pep440_version.py ├── coreneuron │ ├── CrayPortability.cmake │ ├── GitRevision.cmake │ ├── MakefileBuildOptions.cmake │ ├── OpenAccHelper.cmake │ ├── SetRpath.cmake │ ├── TestHelpers.cmake │ └── packages │ │ └── Findlikwid.cmake ├── modules │ ├── FindCython.cmake │ ├── FindMUSIC.cmake │ ├── FindPythonModule.cmake │ ├── FindReadline.cmake │ ├── FindSphinx.cmake │ └── FindTermcap.cmake └── nmodl │ ├── ClangTidyHelper.cmake │ ├── CompilerHelper.cmake │ ├── Config.cmake.in │ ├── ExternalProjectHelper.cmake │ ├── FlexHelper.cmake │ ├── GitRevision.cmake │ ├── PythonLinkHelper.cmake │ └── RpathHelper.cmake ├── cmake_nrnconf.h.in ├── codecov.yml ├── codemeta.json ├── docs ├── Doxyfile.in ├── DoxygenLayout.xml ├── README.md ├── _generated │ └── .gitignore ├── _static │ ├── custom.css │ └── osx_installer_warning_solution.png ├── _templates │ └── breadcrumbs.html ├── capi.rst ├── changelog.md ├── cmake_doc │ └── options.rst ├── conf.py ├── coreneuron │ ├── _static │ │ └── bluebrain_coreneuron.jpg │ ├── compatibility.rst │ ├── examples.rst │ ├── index.rst │ ├── inputs.rst │ ├── installation.rst │ └── running-a-simulation.rst ├── courses │ ├── artificial_cells_neuron.rst │ ├── batch_runs_bulletin_board_parallelization.rst │ ├── batch_runs_with_bulletin_board.rst │ ├── building_and_labeling_a_two_electrod.rst │ ├── bulletin_board_walkthrough.rst │ ├── cellbuilder_overview_and_hints.rst │ ├── code │ │ ├── 111200A.asc │ │ ├── axon.hoc │ │ ├── bilayer.hoc │ │ ├── cell.ho.txt │ │ ├── cell.py │ │ ├── hh_patch.py │ │ ├── hhkchan.mod │ │ ├── initbatpar.ho.txt │ │ ├── initbatpar.py │ │ ├── initbatser.ho.txt │ │ ├── initbatser.py │ │ ├── initonerun.ho.txt │ │ ├── initonerun.py │ │ ├── initplotfi.ho.txt │ │ ├── initplotfi.py │ │ ├── lincir1.hoc │ │ ├── net1run.hoc.txt │ │ ├── net1spec.ho.txt │ │ ├── net2run.hoc │ │ ├── net2spec.ho.txt │ │ └── test0.hoc.txt │ ├── custom-initialization.rst │ ├── electrotonic_analysis.rst │ ├── exercises2018.rst │ ├── hints_for_inhomogeneous_channel_dist.rst │ ├── hoc_exercises.rst │ ├── hopfield_brody_network_in_python.rst │ ├── img │ │ ├── 15arrange.gif │ │ ├── 1invoke.gif │ │ ├── 2arrange.gif │ │ ├── 3mlabel.gif │ │ ├── 4chlabel.gif │ │ ├── ballstk.gif │ │ ├── bilayer.gif │ │ ├── cb_stickfigs.gif │ │ ├── cbbio.gif │ │ ├── cbc1.gif │ │ ├── cbgeom.gif │ │ ├── cellbuilder.png │ │ ├── cellbuilderpic.gif │ │ ├── choose_file.gif │ │ ├── continuouscreate.png │ │ ├── currentaxis.png │ │ ├── export_cellbuilder.gif │ │ ├── freq.gif │ │ ├── geometry.gif │ │ ├── hh.gif │ │ ├── iclampamptryagain.png │ │ ├── label.gif │ │ ├── logAvsx.gif │ │ ├── net1.gif │ │ ├── net1cre.gif │ │ ├── net1edge.gif │ │ ├── net1run.gif │ │ ├── net1type.gif │ │ ├── net2cbld.gif │ │ ├── net2con1.gif │ │ ├── net2con2.gif │ │ ├── net2con3.gif │ │ ├── net2cre.gif │ │ ├── net2edge.gif │ │ ├── net2mod.gif │ │ ├── net2nrc1.gif │ │ ├── net2nrc2.gif │ │ ├── net2plt1.gif │ │ ├── net2plt2.gif │ │ ├── net2stim.gif │ │ ├── net2wgrp.gif │ │ ├── net2wt.gif │ │ ├── parm.gif │ │ ├── passiveconductancechannel.png │ │ ├── path.gif │ │ ├── pcell.gif │ │ ├── pointmanager.png │ │ ├── pyramid.gif │ │ ├── rig_and_pfwm.gif │ │ ├── runcontrol.png │ │ ├── save_ballstkses.gif │ │ ├── shape.gif │ │ ├── shapetool.gif │ │ ├── showing_points_and_diam.gif │ │ ├── showpoints_off.gif │ │ ├── sim.gif │ │ ├── two_cellbuilders.gif │ │ ├── v0.gif │ │ ├── v5.gif │ │ ├── variablestepcontrol.png │ │ ├── vc.gif │ │ ├── voltageaxis.png │ │ ├── zoomo.gif │ │ └── zoomp.gif │ ├── interactive_modeling.rst │ ├── intro_to_gui.rst │ ├── intro_to_the_network_builder.rst │ ├── introduction_to_the_linear_circuit.rst │ ├── managing_models_on_the_fly.rst │ ├── mpi_parallelization.rst │ ├── multithread_parallelization.rst │ ├── network_ready_cells_from_the_cellb.rst │ ├── neuron_scripting_exercises.rst │ ├── numerical-methods-exercises.rst │ ├── quality_issues_with_morphometric.rst │ ├── rxd_exercises.rst │ ├── saving_windows.rst │ ├── specifying_inhomogeneous_channel_dis.rst │ ├── state_and_parameter_discontinuities.rst │ ├── the_cellbuilder.rst │ ├── using_modeldb_and_modelview.rst │ ├── using_morphometric_data.rst │ ├── using_nmodl_files.rst │ ├── using_nsg_portal.rst │ └── working_with_shape_plots.rst ├── dealing_simulations_generate_lot.rst ├── dev │ ├── HOCInterpreter │ │ ├── HOCInterpreter.md │ │ └── images │ │ │ ├── 51567124.png │ │ │ ├── 51567142.png │ │ │ ├── 51567143.png │ │ │ ├── 51567144.png │ │ │ ├── 58786474.png │ │ │ ├── 58788080.png │ │ │ ├── 58788141.png │ │ │ ├── 58788144.png │ │ │ ├── 58788147.png │ │ │ ├── 58791210.png │ │ │ └── 58791244.png │ ├── circuit_creation.svg │ ├── data-structures.rst │ ├── execution_flow.svg │ ├── gpu-testing.rst │ ├── hocdomain-sphinx.md │ ├── how-do-i │ │ └── how-do-i.rst │ ├── index.rst │ ├── initialization.svg │ ├── insert_mechanism.svg │ ├── mechanism_registration.svg │ ├── memory_allocation.svg │ ├── morphology │ │ ├── Import3D-hoc-morphio-backward.png │ │ ├── Import3D-hoc.png │ │ └── morphology.rst │ ├── python │ │ └── wheels.md │ ├── soa-advanced-tag-types.svg │ ├── soa-architecture.svg │ ├── soa-array-var-layout.svg │ └── workflow-code-paths.rst ├── docs_requirements.txt ├── domains │ └── hocdomain.py ├── doxygen.rst ├── example_of_generating_movie.rst ├── footer.html ├── generate_hocdomain.py ├── guide │ ├── bio_faq.rst │ ├── cellbuilder.rst │ ├── cellbuilder1.rst │ ├── cellbuilder2.rst │ ├── cellbuilder3.rst │ ├── data │ │ ├── finithnd1.hoc.txt │ │ ├── gsyn.dat │ │ ├── iclamp.dat │ │ ├── idraw-more.pdf │ │ ├── idraw-readme.txt │ │ ├── ipulse1.mod │ │ ├── ipulse2.mod │ │ ├── ipulse3.mod │ │ ├── ipulse3rig.ses │ │ ├── nets.zip │ │ ├── neurontoolforneuroscientists.pdf │ │ ├── ocfig1.ps │ │ ├── parameterizedcode.zip │ │ ├── printing.pdf │ │ ├── rawmodel.ses │ │ ├── readme.txt │ │ ├── solution.ses.txt │ │ ├── synchronize.hoc │ │ ├── test_1_and_2.hoc │ │ ├── test_3.hoc │ │ ├── units.dat.txt │ │ └── vecplay.hoc │ ├── differences_between_idraw_and_core.rst │ ├── example_hybrid_network.rst │ ├── example_of_simple_network.rst │ ├── faq.rst │ ├── fig │ │ ├── addff.gif │ │ ├── addparam0.gif │ │ ├── addparam1.gif │ │ ├── addparam2.gif │ │ ├── addparam3.gif │ │ ├── all3.gif │ │ ├── alldiffers.gif │ │ ├── alldl.gif │ │ ├── allpasx.gif │ │ ├── allracm.gif │ │ ├── allravalue0.gif │ │ ├── allravalue1.gif │ │ ├── allrax.gif │ │ ├── aphhx.gif │ │ ├── apicalhx.gif │ │ ├── apicalshh.gif │ │ ├── apicalshhvalues0.gif │ │ ├── apicalshhvalues1.gif │ │ ├── attachedx.gif │ │ ├── attachx.gif │ │ ├── axonfixx.gif │ │ ├── axonhh.gif │ │ ├── axonpasx.gif │ │ ├── badfit.gif │ │ ├── badfitearly.gif │ │ ├── basnam0.gif │ │ ├── basnam1.gif │ │ ├── basnam2.gif │ │ ├── baspasvalue1.gif │ │ ├── biophys0.gif │ │ ├── build_from_cb.gif │ │ ├── build_net.gif │ │ ├── build_net1.gif │ │ ├── cb0.gif │ │ ├── cbstickfigs.gif │ │ ├── ccoff.gif │ │ ├── ccon.gif │ │ ├── cellmap.gif │ │ ├── cellname0.gif │ │ ├── cellname1.gif │ │ ├── cellname2.gif │ │ ├── cellp.gif │ │ ├── celltype.gif │ │ ├── changename0.gif │ │ ├── changename1.gif │ │ ├── changename2.gif │ │ ├── changename3.gif │ │ ├── changename4.gif │ │ ├── changename5.gif │ │ ├── charging2.gif │ │ ├── color0.gif │ │ ├── color1.gif │ │ ├── color2.gif │ │ ├── color3.gif │ │ ├── create.gif │ │ ├── create1.gif │ │ ├── create_c_2x.gif │ │ ├── create_new.gif │ │ ├── create_s_0x.gif │ │ ├── create_s_1x.gif │ │ ├── create_s_2x.gif │ │ ├── currents.gif │ │ ├── datafromclip.gif │ │ ├── datafromclip0.gif │ │ ├── datafromclip1.gif │ │ ├── dbltrbl.gif │ │ ├── del0.gif │ │ ├── del1.gif │ │ ├── del2.gif │ │ ├── del20.gif │ │ ├── directentry.gif │ │ ├── display0.gif │ │ ├── display1.gif │ │ ├── display2.gif │ │ ├── dlambda.gif │ │ ├── dlambda2.gif │ │ ├── domain0.gif │ │ ├── domain1.gif │ │ ├── domain2.gif │ │ ├── donex.gif │ │ ├── enablericm.gif │ │ ├── enablerm.gif │ │ ├── errorval0.gif │ │ ├── errorval1.gif │ │ ├── export.gif │ │ ├── export_cellbuilder.gif │ │ ├── expsyn0.gif │ │ ├── expsyn1.gif │ │ ├── expsyn2.gif │ │ ├── exptldata.gif │ │ ├── fig1.gif │ │ ├── fig2L.gif │ │ ├── fig2R.gif │ │ ├── fig3.gif │ │ ├── fig4L.gif │ │ ├── fig4R.gif │ │ ├── fig5L.gif │ │ ├── fig5R.gif │ │ ├── fig6L.gif │ │ ├── fig6R.gif │ │ ├── fig7L.gif │ │ ├── fig7R.gif │ │ ├── fig9L.gif │ │ ├── fig9M.gif │ │ ├── fig9R.gif │ │ ├── finfig3.gif │ │ ├── firstrnopt.gif │ │ ├── geom0.gif │ │ ├── geom1.gif │ │ ├── geomstratfin.gif │ │ ├── getplotwhat.gif │ │ ├── gotit0.gif │ │ ├── gotit1.gif │ │ ├── graph.gif │ │ ├── graph1.gif │ │ ├── graph2.gif │ │ ├── iclampgen1.gif │ │ ├── iclampname.gif │ │ ├── iclamprig.gif │ │ ├── import.gif │ │ ├── import3d_0.gif │ │ ├── import3d_1.gif │ │ ├── import3d_2.gif │ │ ├── import3d_3.gif │ │ ├── import3d_4.gif │ │ ├── inhib.gif │ │ ├── inhsyn.gif │ │ ├── listnam1.gif │ │ ├── listnam2.gif │ │ ├── locatesyn0.gif │ │ ├── locatesyn1.gif │ │ ├── locatesyn2.gif │ │ ├── locatesyn3.gif │ │ ├── locatesyn4.gif │ │ ├── locatesyn5.gif │ │ ├── lucky13.gif │ │ ├── lucky13first5.gif │ │ ├── m1r2_3c.gif │ │ ├── make1.gif │ │ ├── make2.gif │ │ ├── make3.gif │ │ ├── make4.gif │ │ ├── menusquare.gif │ │ ├── micronetc.gif │ │ ├── mknrndll1.gif │ │ ├── mknrndll2.gif │ │ ├── mknrndll3.gif │ │ ├── mknrndll4.gif │ │ ├── mknrndll5.gif │ │ ├── mknrndll6.gif │ │ ├── mn.gif │ │ ├── modlunit1.gif │ │ ├── modlunit2.gif │ │ ├── modlunit3.gif │ │ ├── modlunit4.gif │ │ ├── modlunit5.gif │ │ ├── move0.gif │ │ ├── move1.gif │ │ ├── move2.gif │ │ ├── move3.gif │ │ ├── move4.gif │ │ ├── movedandrescaled.gif │ │ ├── mrf0.gif │ │ ├── mygui.gif │ │ ├── namesoff.gif │ │ ├── netbuilder_0.gif │ │ ├── netbuilder_01.gif │ │ ├── netbuilder_1.gif │ │ ├── netcel_artcel.gif │ │ ├── netstim_independence.png │ │ ├── newL.gif │ │ ├── new_ifx.gif │ │ ├── new_ns.gif │ │ ├── newdiam0.gif │ │ ├── newdiam1.gif │ │ ├── newlist.gif │ │ ├── noinhib.gif │ │ ├── nrcgui0.gif │ │ ├── nrcguiz.gif │ │ ├── ocfig.gif │ │ ├── ocfig2.ps │ │ ├── optimization-addparams.gif │ │ ├── optimization-addregion1.gif │ │ ├── optimization-addregion2.gif │ │ ├── optimization-adj1.gif │ │ ├── optimization-adj2.gif │ │ ├── optimization2-usegen.gif │ │ ├── optimization_charging.png │ │ ├── optimizationcell.gif │ │ ├── optimize0.gif │ │ ├── optimize1-1.gif │ │ ├── optimize1.gif │ │ ├── optimize2.gif │ │ ├── optimize3.gif │ │ ├── optimize4.gif │ │ ├── parampanel0-1.gif │ │ ├── parampanel0-2.gif │ │ ├── parampanel0.gif │ │ ├── parampanel1-1.gif │ │ ├── parampanel1.gif │ │ ├── parampanel2-1.gif │ │ ├── parampanel2.gif │ │ ├── parampanel3.gif │ │ ├── pardompg0.gif │ │ ├── paths1.gif │ │ ├── pd1.gif │ │ ├── pd10.gif │ │ ├── pd11.gif │ │ ├── pd12.gif │ │ ├── pd13.gif │ │ ├── pd2.gif │ │ ├── pd3.gif │ │ ├── pd4.gif │ │ ├── pd5.gif │ │ ├── pd6.gif │ │ ├── pd7.gif │ │ ├── pd8.gif │ │ ├── pd9.gif │ │ ├── pfwm.gif │ │ ├── primenu.gif │ │ ├── print1.gif │ │ ├── print10.gif │ │ ├── print11.gif │ │ ├── print13.gif │ │ ├── print14.gif │ │ ├── print15.gif │ │ ├── print16.gif │ │ ├── print17.gif │ │ ├── print18.gif │ │ ├── print19.gif │ │ ├── print2.gif │ │ ├── print3.gif │ │ ├── print4.gif │ │ ├── print5.gif │ │ ├── print6.gif │ │ ├── print7.gif │ │ ├── print8.gif │ │ ├── print9.gif │ │ ├── pw0.gif │ │ ├── pw1.gif │ │ ├── pw10.gif │ │ ├── pw11.gif │ │ ├── pw12.gif │ │ ├── pw2.gif │ │ ├── pw3.gif │ │ ├── pw4.gif │ │ ├── pw5.gif │ │ ├── pw6.gif │ │ ├── pw7.gif │ │ ├── pw8.gif │ │ ├── pw9.gif │ │ ├── pyr.gif │ │ ├── pyrtest_with_movierun.gif │ │ ├── r2m1_1c.gif │ │ ├── r2m1_2c.gif │ │ ├── r2m1_3c.gif │ │ ├── r_gui.gif │ │ ├── rawmodelcharging.gif │ │ ├── refresh_nrc0.gif │ │ ├── refresh_nrc1.gif │ │ ├── refresh_nrc2.gif │ │ ├── refresh_nrca.gif │ │ ├── rename_0x.gif │ │ ├── rename_1.gif │ │ ├── renamed_iclamp.gif │ │ ├── renamed_ifx.gif │ │ ├── rensyn0.gif │ │ ├── rensyn1.gif │ │ ├── rensyn2.gif │ │ ├── s0m1_1.gif │ │ ├── s0m1_2c.gif │ │ ├── s0m1_3c.gif │ │ ├── secmenu.gif │ │ ├── select0.gif │ │ ├── selectfunc0.gif │ │ ├── selectfunc1.gif │ │ ├── selectfunc2.gif │ │ ├── selectfunc3.gif │ │ ├── selectgsyn.gif │ │ ├── selecti.gif │ │ ├── selecticlamp_.gif │ │ ├── selectpraxis0.gif │ │ ├── selsrcx.gif │ │ ├── selsubtr.gif │ │ ├── seltree.gif │ │ ├── showgraph.gif │ │ ├── showobjects.gif │ │ ├── showpoints_off.gif │ │ ├── simplec.gif │ │ ├── somafixx.gif │ │ ├── somapasx.gif │ │ ├── sos0.gif │ │ ├── sos1.gif │ │ ├── spawncellbld.gif │ │ ├── spawnmrf.gif │ │ ├── spikeplot_1.gif │ │ ├── srctar_0x.gif │ │ ├── startafter2.gif │ │ ├── subset0.gif │ │ ├── subset2.gif │ │ ├── subsetx.gif │ │ ├── syntypegui0.gif │ │ ├── tapersim.gif │ │ ├── testdatafromclip.gif │ │ ├── tinyiclamp.gif │ │ ├── top0.gif │ │ ├── two_cellbuilders.gif │ │ ├── unnamedff.gif │ │ ├── unnamedsrp.gif │ │ ├── usegen0.gif │ │ ├── usegen1.gif │ │ ├── usegen2.gif │ │ ├── usegen3.gif │ │ ├── variablenamebrowser.gif │ │ ├── variablenamesomavx.gif │ │ ├── vartofit.gif │ │ ├── vecretrieve.gif │ │ ├── veqp.gif │ │ ├── viewplot.gif │ │ ├── warn.gif │ │ ├── weights_0x.gif │ │ ├── weights_1.gif │ │ ├── weights_2.gif │ │ ├── weights_3.gif │ │ ├── xhair.gif │ │ ├── xlat0.gif │ │ ├── xlat1.gif │ │ ├── xlat2.gif │ │ ├── zoom0.gif │ │ └── zoom1.gif │ ├── finitialize_handler.rst │ ├── fixing_funny_axes.rst │ ├── heres_how_delete_v5.rst │ ├── heres_how_page.rst │ ├── hoc_chapter_11_old_reference.rst │ ├── how_to_get_started.rst │ ├── how_to_get_started_with_neuron.rst │ ├── how_to_move_labels.rst │ ├── how_to_translate_view.rst │ ├── import3d.rst │ ├── index.rst │ ├── introduction_to_network_construction.rst │ ├── modelview_compact_display.rst │ ├── network_builder_tutorials.rst │ ├── nmodls_built_in_functions.rst │ ├── nrn_defaults.rst │ ├── optimization.rst │ ├── optimization1.rst │ ├── optimization1a.rst │ ├── optimization2.rst │ ├── plot_what.rst │ ├── porting_mechanisms_to_cpp.rst │ ├── print_file_manager.rst │ ├── randomness.rst │ ├── run_simulation_plot_input_output.rst │ ├── run_simulation_plot_input_output2.rst │ ├── saveses.rst │ ├── set_up_a_subsetdomainiterator.rst │ ├── specify_and_verify_the_functions.rst │ ├── specify_the_model_parameters_varied.rst │ ├── step_1_define_type_cell.rst │ ├── step_1_define_type_of_cell.rst │ ├── step_1_define_type_of_cell2.rst │ ├── step_1_define_type_of_cell3.rst │ ├── step_2_create_each_cell.rst │ ├── step_2_create_network_cell.rst │ ├── step_3_connect_cells.rst │ ├── step_3_connect_cells_continued.rst │ ├── step_3_connect_the_cells.rst │ ├── step_3_connect_the_cells_continued.rst │ ├── tutorial_2_hybrid_nets.rst │ ├── tutorial_artificial_neurons.rst │ ├── units.rst │ ├── units_tutorial.rst │ ├── use_the_model_specification.rst │ ├── using_neuron_on_the_mac.rst │ ├── using_plotwhat_to_specify_a_variable.rst │ ├── using_session_files_for_saving.rst │ ├── using_the_d_lambda_rule.rst │ ├── what_is_neuron.rst │ └── working_with_postscript_and_idraw.rst ├── how_to_develop_and_debug_code.rst ├── index.rst.in ├── install │ ├── code_coverage.md │ ├── debug.md │ ├── developer.rst │ ├── formatting.md │ ├── images │ │ ├── azure-release-no-upload.png │ │ ├── docker-workflow.png │ │ ├── nrn_likwid_presoa_master_comparison.png │ │ ├── nrn_vtune_memacs_caliper_step12_acs_lat.png │ │ ├── nrn_vtune_memacs_caliper_step13_acs_lat_code.png │ │ ├── nrn_vtune_uarch_caliper_step10_bottom_up_expand.png │ │ ├── nrn_vtune_uarch_caliper_step11_grouping_expand.png │ │ ├── nrn_vtune_uarch_caliper_step1_bottom_up.png │ │ ├── nrn_vtune_uarch_caliper_step3_bottom_up.png │ │ ├── nrn_vtune_uarch_caliper_step8_summary_compare.png │ │ ├── nrn_vtune_uarch_caliper_step9_bottom_up_compare.png │ │ └── nrn_vtune_uarch_default_bottom_up.png │ ├── install.rst │ ├── install_instructions.md │ ├── mac_pkg.md │ ├── python_wheels.md │ └── windows.md ├── julia_ap.png ├── logo.png ├── neuron-overview.jpg ├── nmodl │ ├── NMODL_language.ipynb │ ├── language.rst │ ├── language │ │ ├── nmodl.rst │ │ └── nmodl_neuron_extension.rst │ ├── mod │ │ ├── cadif.mod │ │ ├── fornetcon.mod │ │ ├── hhwatch.mod │ │ ├── k3st.mod │ │ ├── table.mod │ │ └── variabletypes.mod │ ├── python_scripts │ │ ├── __init__.py │ │ ├── function_table.py │ │ ├── iclamp.py │ │ ├── kinetic.py │ │ ├── table.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ └── cell.py │ └── transpiler │ │ ├── Doxyfile.in │ │ ├── DoxygenLayout.xml │ │ ├── background.png │ │ ├── conf.py │ │ ├── contents │ │ ├── cable_equations.rst │ │ ├── currents.rst │ │ ├── cvode.rst │ │ ├── globals.rst │ │ ├── ions.rst │ │ ├── longitudinal_diffusion.rst │ │ ├── pointers.rst │ │ └── visitors.rst │ │ ├── contributing.rst │ │ ├── doxygen_nmodl.css │ │ ├── footer.html │ │ ├── generate_docs.sh │ │ ├── images │ │ ├── cable-eqn_circuit.svg │ │ ├── cable-eqn_nodes.svg │ │ ├── currents_circuit.svg │ │ ├── currents_types.svg │ │ ├── ion_storage-opt.svg │ │ ├── ion_storage.svg │ │ ├── nmodl-perf-stats.png │ │ └── nmodl.ast.png │ │ ├── index.rst │ │ ├── language.rst │ │ ├── logo.graffle │ │ ├── logo.png │ │ ├── modules.rst │ │ ├── nmodl.rst │ │ ├── notebooks.rst │ │ ├── notebooks │ │ ├── README.rst │ │ ├── nmodl-kinetic-schemes.ipynb │ │ ├── nmodl-linear-solver.ipynb │ │ ├── nmodl-nonlinear-solver.ipynb │ │ ├── nmodl-odes-overview.ipynb │ │ ├── nmodl-python-tutorial.ipynb │ │ ├── nmodl-sympy-conductance.ipynb │ │ ├── nmodl-sympy-solver-cnexp.ipynb │ │ ├── nmodl-sympy-solver-derivimplicit.ipynb │ │ ├── nmodl-sympy-solver-sparse.ipynb │ │ └── tree.js │ │ ├── readme.rst │ │ └── test_status.txt ├── otherscripting.rst ├── parse_rst.py ├── progref │ ├── analysis │ │ ├── guitools.rst │ │ ├── guitools │ │ │ ├── funfit.rst │ │ │ ├── impedancetools.rst │ │ │ ├── impedanx.rst │ │ │ ├── impratio.rst │ │ │ ├── mulfit.rst │ │ │ └── runfit.rst │ │ ├── programmatic.rst │ │ └── programmatic │ │ │ ├── impedance.rst │ │ │ ├── misc.rst │ │ │ └── optimization.rst │ ├── compilationoptions.rst │ ├── envvariables.rst │ ├── images │ │ ├── ExecCommand.png │ │ ├── GatherVec.png │ │ ├── VecWrap.png │ │ ├── VectorPlay.png │ │ ├── boolean_dialog.png │ │ ├── continue_dialog.png │ │ ├── deck-constructor.png │ │ ├── fft1.png │ │ ├── fft2.png │ │ ├── filechooser.png │ │ ├── function_table_vT.png │ │ ├── function_table_vkT.png │ │ ├── geometry1.png │ │ ├── geometry2.png │ │ ├── geometry3.png │ │ ├── geometry4.png │ │ ├── geometry5.png │ │ ├── glyphcircle.png │ │ ├── graph-addexpr.png │ │ ├── graph-align.png │ │ ├── graph-constructor.png │ │ ├── graph-fastflush.png │ │ ├── graph-menuaction.png │ │ ├── graph-vector.png │ │ ├── graph-xexpr.png │ │ ├── guiwidgets-example.png │ │ ├── hh_sim_cpp.png │ │ ├── impedanx-logavsx.png │ │ ├── linmod.png │ │ ├── list-browser1.png │ │ ├── list-browser2.png │ │ ├── list-browser2b.png │ │ ├── makeFamily.png │ │ ├── mcran4-graph1.png │ │ ├── mcran4-graph2.png │ │ ├── mcran4-xvalue.png │ │ ├── mechanismstandard.png │ │ ├── oldgrph.png │ │ ├── panel.png │ │ ├── parameterizedfunctionfitter.png │ │ ├── plotsin.png │ │ ├── plotsin2.png │ │ ├── random-binomial.png │ │ ├── random-geometric.png │ │ ├── random-lognormal.png │ │ ├── random-mcellran4.png │ │ ├── random-negexp.png │ │ ├── random-normal.png │ │ ├── random-poisson.png │ │ ├── rangevarplot1.png │ │ ├── rangevarplot2.png │ │ ├── rangevarplotrxd.png │ │ ├── secbrows-sectionList.png │ │ ├── secbrows-select.png │ │ ├── section-connection.png │ │ ├── string_dialog.png │ │ ├── svclmp.png │ │ ├── svclmp.svg │ │ ├── symchooser.png │ │ ├── texteditor-map.png │ │ ├── value_panel.png │ │ ├── vbox-intercept.png │ │ ├── vector-histogram.png │ │ ├── vector-line.png │ │ ├── vector-plot.png │ │ ├── vector-ploterr.png │ │ ├── vector-psth.png │ │ ├── vector-setrand.png │ │ ├── xbutton.png │ │ ├── xbutton2.png │ │ ├── xmenu1.png │ │ ├── xmenu2.png │ │ ├── xpvalue.png │ │ ├── xradiobutton.png │ │ ├── xslider.png │ │ ├── xstatebutton.png │ │ ├── xvalue.png │ │ └── xvarlabel.png │ ├── index.rst │ ├── modelspec │ │ ├── guitools.rst │ │ ├── guitools │ │ │ ├── cellbuilder.rst │ │ │ ├── inserter.rst │ │ │ ├── pointman.rst │ │ │ └── showmech.rst │ │ ├── programmatic.rst │ │ └── programmatic │ │ │ ├── electrod.rst │ │ │ ├── hocmech.rst │ │ │ ├── ions.rst │ │ │ ├── kschan.rst │ │ │ ├── linmod.rst │ │ │ ├── mechanisms.rst │ │ │ ├── mechanisms │ │ │ └── mech.rst │ │ │ ├── mechtype.rst │ │ │ ├── network.rst │ │ │ ├── network │ │ │ ├── lyttonmpi.rst │ │ │ ├── netcon.rst │ │ │ ├── parcon.rst │ │ │ └── parnet.rst │ │ │ ├── obsoletestimuli.rst │ │ │ ├── rxd.rst │ │ │ ├── rxdmath.rst │ │ │ ├── ste.rst │ │ │ ├── topology.rst │ │ │ └── topology │ │ │ ├── geometry.rst │ │ │ ├── seclist.rst │ │ │ ├── secref.rst │ │ │ └── secspec.rst │ ├── programming │ │ ├── dynamiccode.rst │ │ ├── errors.rst │ │ ├── gui │ │ │ ├── dialog.rst │ │ │ ├── layout.rst │ │ │ ├── list.rst │ │ │ ├── misc.rst │ │ │ ├── nfunc.rst │ │ │ ├── pwman.rst │ │ │ ├── secbrows.rst │ │ │ ├── symchooser.rst │ │ │ ├── texteditor.rst │ │ │ ├── vfe.rst │ │ │ └── widgets.rst │ │ ├── guidesign.rst │ │ ├── hoc-from-python.rst │ │ ├── internals.rst │ │ ├── io │ │ │ ├── file.rst │ │ │ ├── printf.rst │ │ │ ├── read.rst │ │ │ └── ropen.rst │ │ ├── math │ │ │ ├── constants.rst │ │ │ ├── eqnsolve.rst │ │ │ ├── functions.rst │ │ │ ├── guimath.rst │ │ │ ├── matrix.rst │ │ │ ├── mcran4.rst │ │ │ ├── misc.rst │ │ │ ├── random.rst │ │ │ └── vector.rst │ │ ├── mathematics.rst │ │ ├── mechstan.rst │ │ ├── pointers │ │ │ ├── misc.rst │ │ │ ├── pointer.rst │ │ │ └── ptrvector.rst │ │ ├── projectmanagement.rst │ │ ├── python-from-hoc.rst │ │ ├── references.rst │ │ ├── sscanf.rst │ │ ├── strfun.rst │ │ ├── strings.rst │ │ └── system.rst │ ├── simctrl │ │ ├── batch.rst │ │ ├── bbsavestate.rst │ │ ├── cvode.rst │ │ ├── family.rst │ │ ├── interpretermanagement.rst │ │ ├── programmatic.rst │ │ ├── runctrl.rst │ │ ├── savstate.rst │ │ ├── sessionsave.rst │ │ └── stdrun.rst │ └── visualization │ │ ├── glyph.rst │ │ ├── graph.rst │ │ ├── grapher.rst │ │ ├── gui.rst │ │ ├── notify.rst │ │ ├── oldgrph.rst │ │ ├── plotshape.rst │ │ ├── plotshapeclass.rst │ │ ├── rvarplt.rst │ │ ├── shape.rst │ │ └── shapebox.rst ├── publications-using-neuron.rst ├── publications.rst ├── removed_features.rst ├── rst_substitutions.txt ├── rxd-tutorials │ ├── Changing initial conditions and parameters.ipynb │ ├── Reaction-Diffusion tutorial.ipynb │ ├── Restricting reactions to certain sections.ipynb │ ├── basic-initialization.ipynb │ ├── calcium waves.ipynb │ ├── circadian.ipynb │ ├── combining currents from mod files with rxd.ipynb │ ├── degradable_buffer.ipynb │ ├── extracellular.ipynb │ ├── index.rst │ ├── ip3-demo.ipynb │ ├── radial_diffusion.ipynb │ └── thresholds.ipynb ├── scm │ ├── guide │ │ └── SCMGuide.md │ ├── guidelines │ │ ├── SCMGuidelines.md │ │ ├── release_workflow.rst │ │ └── workflow.mmd │ ├── images │ │ ├── image1.png │ │ ├── image2.png │ │ ├── image3.png │ │ ├── image4.png │ │ ├── image5.png │ │ ├── image6.png │ │ ├── image7.png │ │ └── image8.png │ ├── index.rst │ └── policies │ │ └── policies.md ├── scripting.rst ├── translators │ └── html2.py ├── tutorials │ ├── ball-and-stick-1.ipynb │ ├── ball-and-stick-2.ipynb │ ├── ball-and-stick-3.ipynb │ ├── ball-and-stick-4.ipynb │ ├── ballandstick.py │ ├── index.rst │ ├── pythontutorial.ipynb │ ├── scripting-neuron-basics.ipynb │ ├── test_ring1_ref.svgz │ └── test_ring2_ref.svgz └── videos │ ├── cns-tutorial-2021.rst │ ├── incfcns-tutorial-2022.rst │ ├── index.rst │ ├── netpyne-course-2021.rst │ └── neuron-course-2021.rst ├── mingw_files └── nrnmingwenv.sh ├── nmodl_requirements.txt ├── nrn_requirements.txt ├── packaging └── python │ ├── Dockerfile │ ├── README.md │ ├── build_requirements.txt │ ├── build_static_readline_osx.bash │ ├── build_wheels.bash │ ├── change_name.py │ ├── oldest_numpy_requirements.txt │ ├── test_requirements.txt │ └── test_wheels.sh ├── pyproject.toml ├── share ├── demo │ ├── CMakeLists.txt │ ├── cycle.hoc │ ├── d3init.hoc │ ├── demo.hoc │ ├── demo.ses │ ├── dend3.ses │ ├── dend3 │ │ ├── control.hoc │ │ ├── dend3.nrn │ │ └── syn3.hoc │ ├── dynchan.ses │ ├── dynclamp.hoc │ ├── dynclamp.ses │ ├── hh.hoc │ ├── hh.ses │ ├── nomodel.hoc │ ├── pyramid.nrn │ ├── pyramid.ses │ ├── reconst.hoc │ ├── release.hoc │ ├── release.ses │ ├── release │ │ ├── CMakeLists.txt │ │ ├── cabpump.mod │ │ ├── cachan1.mod │ │ ├── camchan.mod │ │ ├── capmpr.mod │ │ ├── capump.mod │ │ ├── invlfire.mod │ │ ├── khhchan.mod │ │ ├── nacaex.mod │ │ ├── nachan.mod │ │ └── release.mod │ ├── singhh.hoc │ ├── singhh.ses │ ├── singhhchan.hoc │ ├── sync │ │ ├── cell.hoc │ │ ├── demosync.hoc │ │ ├── init.hoc │ │ ├── spkplot.hoc │ │ ├── start.ses │ │ └── synchronize.hoc │ └── testca.hoc ├── examples │ └── nrniv │ │ ├── netcon │ │ ├── ampa.hoc │ │ ├── ampa.mod │ │ ├── ampa.ses │ │ ├── expsyn.hoc │ │ ├── expsyn.ses │ │ ├── gsyn.hoc │ │ ├── gsyn.mod │ │ ├── gsyn.ses │ │ ├── k2syn.hoc │ │ ├── k2syn.mod │ │ ├── k2syn.ses │ │ ├── line.hoc │ │ ├── line.ses │ │ ├── netcon.inc │ │ ├── pregen.mod │ │ ├── sns.hoc │ │ ├── sns.ses │ │ ├── test.hoc │ │ ├── vecevent.hoc │ │ ├── vecevent.mod │ │ └── vecevent.ses │ │ ├── nmodl │ │ ├── argpass.mod │ │ ├── ca_ap.hoc │ │ ├── cabpump.hoc │ │ ├── cabpump.mod │ │ ├── cachan.hoc │ │ ├── cachan.mod │ │ ├── cacum.mod │ │ ├── cacur.mod │ │ ├── cadif.hoc │ │ ├── cadif.mod │ │ ├── cadif.ses │ │ ├── cadifusl.hoc │ │ ├── cadifusl.mod │ │ ├── cadifusl1.hoc │ │ ├── cadifusl2.hoc │ │ ├── cagk.hoc │ │ ├── cagk.mod │ │ ├── cagkftab.mod │ │ ├── capmp.hoc │ │ ├── capmp.mod │ │ ├── cv.hoc │ │ ├── expsynspine.mod │ │ ├── expsynspine.ses │ │ ├── fh.hoc │ │ ├── fh.mod │ │ ├── fit1.hoc │ │ ├── fit1.mod │ │ ├── gap.hoc │ │ ├── gap.mod │ │ ├── hh1.hoc │ │ ├── hh1.mod │ │ ├── hhvect.hoc │ │ ├── hhvect.mod │ │ ├── inatest.mod │ │ ├── ionleak.mod │ │ ├── nacum.hoc │ │ ├── nacum.mod │ │ ├── nacur.mod │ │ ├── nadifl.mod │ │ ├── nadifl1.hoc │ │ ├── nadifl1.ses │ │ ├── nadifl2.hoc │ │ ├── nadifl2.ses │ │ ├── nadifl3.hoc │ │ ├── nadifl3.ses │ │ ├── nadifl4.hoc │ │ ├── nadifl4.ses │ │ ├── nonlin.mod │ │ ├── obj_ex.hoc │ │ ├── obj_ex.mod │ │ ├── order.hoc │ │ ├── order.mod │ │ ├── passiv.hoc │ │ ├── passiv.mod │ │ ├── rchan.mod │ │ ├── standard.inc │ │ ├── stim1.hoc │ │ ├── stim1.mod │ │ ├── str.mod │ │ ├── syn1.hoc │ │ ├── syn1.mod │ │ ├── synpre.hoc │ │ ├── synpre.mod │ │ ├── test_cagkftab.py │ │ ├── test_expsynspine.py │ │ ├── test_nonlin.py │ │ ├── test_pnt1.py │ │ ├── test_pnt2.py │ │ ├── test_vlag.py │ │ ├── trivial.mod │ │ ├── tstdarray.mod │ │ ├── tstextrn.hoc │ │ ├── tstextrn.mod │ │ ├── tstpnt1.hoc │ │ ├── tstpnt1.mod │ │ ├── tstpnt2.hoc │ │ ├── tstpnt2.mod │ │ ├── tstvec.hoc │ │ ├── tstvec.mod │ │ ├── vclmp1.mod │ │ └── vlag.mod │ │ └── nrnoc │ │ ├── ancab.hoc │ │ ├── batch.hoc │ │ ├── clamp.hoc │ │ ├── craytest.hoc │ │ ├── diamtst.hoc │ │ ├── distance.hoc │ │ ├── extcab1.hoc │ │ ├── extcab11.hoc │ │ ├── extcab2.hoc │ │ ├── extcab4.hoc │ │ ├── extcab41.hoc │ │ ├── extvc.hoc │ │ ├── fit1.hoc │ │ ├── hhmemb.hoc │ │ ├── hhpap.hoc │ │ ├── hhrate.hoc │ │ ├── implic.hoc │ │ ├── motor.hoc │ │ ├── pascab1.hoc │ │ ├── pascab2.hoc │ │ ├── pascab3.hoc │ │ ├── pascab4.hoc │ │ ├── pascab5.hoc │ │ ├── pascab6.hoc │ │ ├── ppatch.hoc │ │ ├── recon.hoc │ │ ├── secrefte.hoc │ │ ├── soma.hoc │ │ ├── syn1.hoc │ │ ├── test1.hoc │ │ ├── test2.hoc │ │ ├── test3.hoc │ │ ├── test4.hoc │ │ └── test6.hoc ├── lib │ ├── auditscripts │ │ ├── gettarname │ │ ├── hocaudit.sh │ │ ├── notes │ │ ├── retrieve.sh │ │ └── saveaudit │ ├── helpdict │ ├── hoc │ │ ├── CMakeLists.txt │ │ ├── atoltool.hoc │ │ ├── attshape.hoc │ │ ├── binfo.hoc │ │ ├── celbild.hoc │ │ ├── celbild │ │ │ ├── celbild1.hoc │ │ │ ├── celgeom.hoc │ │ │ ├── celmang.hoc │ │ │ ├── celmemb.hoc │ │ │ ├── celset.hoc │ │ │ ├── celtopol.hoc │ │ │ ├── inhomofn.hoc │ │ │ └── psubset.hoc │ │ ├── chanbild.hoc │ │ ├── chanbild │ │ │ ├── chanbild1.hoc │ │ │ ├── const.hoc │ │ │ ├── exp.hoc │ │ │ ├── gategui.hoc │ │ │ ├── kschanbg.hoc │ │ │ ├── ksgate.hoc │ │ │ ├── ksstate.hoc │ │ │ ├── kstgui.hoc │ │ │ ├── kstrans.hoc │ │ │ ├── linoid.hoc │ │ │ ├── properties.hoc │ │ │ ├── sigmoid.hoc │ │ │ └── table.hoc │ │ ├── corenrn.hoc │ │ ├── electrod.hoc │ │ ├── family.hoc │ │ ├── funfit.hoc │ │ ├── gatherv.hoc │ │ ├── grapher.hoc │ │ ├── impedanc.hoc │ │ ├── impedanx.hoc │ │ ├── import3d.hoc │ │ ├── import3d │ │ │ ├── import3d_gui.hoc │ │ │ ├── import3d_sec.hoc │ │ │ ├── read_morphml.hoc │ │ │ ├── read_nlcda.hoc │ │ │ ├── read_nlcda3.hoc │ │ │ ├── read_nts.hoc │ │ │ └── read_swc.hoc │ │ ├── impratio.hoc │ │ ├── inserter.hoc │ │ ├── lincir.hoc │ │ ├── lincir │ │ │ ├── elmbase.hoc │ │ │ ├── lincir1.hoc │ │ │ ├── lingraph.hoc │ │ │ └── linmech.hoc │ │ ├── loadbal.hoc │ │ ├── logax.hoc │ │ ├── macload.hoc │ │ ├── mkcurve.hoc │ │ ├── mknrndll.hoc │ │ ├── modlunit.hoc │ │ ├── movierun.hoc │ │ ├── mulfit.hoc │ │ ├── mulfit │ │ │ ├── clampfit.hoc │ │ │ ├── e_actpot.hoc │ │ │ ├── e_norm.hoc │ │ │ ├── e_xy.hoc │ │ │ ├── e_y.hoc │ │ │ ├── eonefunc.hoc │ │ │ ├── eoneprim.hoc │ │ │ ├── eonerun.hoc │ │ │ ├── eparmlst.hoc │ │ │ ├── fitparm.hoc │ │ │ ├── mulfit1.hoc │ │ │ ├── optwrap.hoc │ │ │ └── protorun.hoc │ │ ├── mview.hoc │ │ ├── mview │ │ │ ├── allcell.hoc │ │ │ ├── allpp.hoc │ │ │ ├── artview.hoc │ │ │ ├── distinct.hoc │ │ │ ├── distinctparm.hoc │ │ │ ├── mview1.hoc │ │ │ ├── mviewgui.hoc │ │ │ ├── mviewxml.hoc │ │ │ ├── ncview.hoc │ │ │ ├── parmsets.hoc │ │ │ ├── parmvals.hoc │ │ │ ├── ppanal.hoc │ │ │ ├── rcclasses.hoc │ │ │ ├── realcell.hoc │ │ │ ├── secanal.hoc │ │ │ └── treeview.hoc │ │ ├── netbild.hoc │ │ ├── netbild │ │ │ ├── artcel.hoc │ │ │ ├── edgegui.hoc │ │ │ ├── grstrlst.hoc │ │ │ ├── netdata.hoc │ │ │ ├── netgui.hoc │ │ │ ├── netready.hoc │ │ │ ├── spkplot.hoc │ │ │ └── syntypes.hoc │ │ ├── netparmpi.hoc │ │ ├── noload.hoc │ │ ├── nrngui.hoc │ │ ├── nrngui1.hoc │ │ ├── parcom.hoc │ │ ├── pcchdir.hoc │ │ ├── pointbsr.hoc │ │ ├── pointgrp.hoc │ │ ├── pointman.hoc │ │ ├── prcellstate.hoc │ │ ├── runfit.hoc │ │ ├── shapebox.hoc │ │ ├── showmech.hoc │ │ ├── single.hoc │ │ ├── single1.hoc │ │ ├── stdgui.hoc │ │ ├── stdlib.hoc │ │ ├── stdrun.hoc │ │ ├── subiter.hoc │ │ ├── thresh.hoc │ │ ├── varmeth1.hoc │ │ ├── vecwrap.hoc │ │ ├── vplay.hoc │ │ └── wingroup.hoc │ ├── nrn.defaults.in │ ├── nrnunits.lib.in │ ├── prologue.id │ ├── python │ │ ├── neuron │ │ │ ├── CMakeLists.txt │ │ │ ├── __init__.py │ │ │ ├── config.py │ │ │ ├── coreneuron.py │ │ │ ├── crxd │ │ │ │ └── __init__.py │ │ │ ├── doc.py │ │ │ ├── expect_hocerr.py │ │ │ ├── gui.py │ │ │ ├── gui2 │ │ │ │ ├── __init__.py │ │ │ │ ├── config.py │ │ │ │ ├── plotshape.py │ │ │ │ ├── rangevar.py │ │ │ │ ├── setup_threejs.py │ │ │ │ └── utilities.py │ │ │ ├── hclass3.py │ │ │ ├── neuroml │ │ │ │ ├── __init__.py │ │ │ │ ├── biophysics.py │ │ │ │ ├── metadata.py │ │ │ │ ├── morphml.py │ │ │ │ ├── neuroml.py │ │ │ │ ├── rdxml.py │ │ │ │ └── xml2nrn.py │ │ │ ├── nmodl │ │ │ │ ├── __init__.py │ │ │ │ ├── ast.py │ │ │ │ ├── dsl.py │ │ │ │ ├── ext │ │ │ │ │ ├── example │ │ │ │ │ │ ├── exp2syn.mod │ │ │ │ │ │ ├── expsyn.mod │ │ │ │ │ │ ├── hh.mod │ │ │ │ │ │ └── passive.mod │ │ │ │ │ └── viz │ │ │ │ │ │ ├── css │ │ │ │ │ │ └── tree.css │ │ │ │ │ │ ├── index.html │ │ │ │ │ │ └── js │ │ │ │ │ │ ├── d3.min.js │ │ │ │ │ │ └── tree.js │ │ │ │ ├── ode.py │ │ │ │ ├── symtab.py │ │ │ │ └── visitor.py │ │ │ ├── nonvint_block_supervisor.py │ │ │ ├── psection.py │ │ │ ├── rxd │ │ │ │ ├── __init__.py │ │ │ │ ├── constants.py │ │ │ │ ├── dimension3.py │ │ │ │ ├── export.py │ │ │ │ ├── generalizedReaction.py │ │ │ │ ├── geometry.py │ │ │ │ ├── geometry3d │ │ │ │ │ ├── CMakeLists.txt │ │ │ │ │ ├── FullJoinMorph.py │ │ │ │ │ ├── GeneralizedVoxelization.py │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── ctng.pyx │ │ │ │ │ ├── graphicsPrimitives.pyx │ │ │ │ │ ├── scalarField.py │ │ │ │ │ ├── simplevolume_helper.py │ │ │ │ │ ├── surface.py │ │ │ │ │ ├── surface_a.py │ │ │ │ │ ├── surfaces.pyx │ │ │ │ │ ├── triangularMesh.py │ │ │ │ │ ├── voxelize.py │ │ │ │ │ └── voxelize2.py │ │ │ │ ├── gui.py │ │ │ │ ├── initializer.py │ │ │ │ ├── multiCompartmentReaction.py │ │ │ │ ├── node.py │ │ │ │ ├── nodelist.py │ │ │ │ ├── options.py │ │ │ │ ├── plugins.py │ │ │ │ ├── rangevar.py │ │ │ │ ├── rate.py │ │ │ │ ├── reaction.py │ │ │ │ ├── region.py │ │ │ │ ├── rxd.py │ │ │ │ ├── rxdException.py │ │ │ │ ├── rxdmath.py │ │ │ │ ├── rxdsection.py │ │ │ │ ├── section1d.py │ │ │ │ └── species.py │ │ │ ├── rxdtests │ │ │ │ ├── do_test.py │ │ │ │ ├── readme.txt │ │ │ │ ├── run_all.py │ │ │ │ └── tests │ │ │ │ │ ├── 3d │ │ │ │ │ ├── circadian_rhythm.py │ │ │ │ │ ├── include_flux3d.py │ │ │ │ │ ├── include_flux3d_cvode.py │ │ │ │ │ ├── multicompartment_reactions.py │ │ │ │ │ ├── pure_diffusion_3d.py │ │ │ │ │ ├── pure_diffusion_3d_cvode.py │ │ │ │ │ └── torun.txt │ │ │ │ │ ├── IraHH.py │ │ │ │ │ ├── c91662.swc │ │ │ │ │ ├── ca_pump.py │ │ │ │ │ ├── cabuf.py │ │ │ │ │ ├── cabuf_fixed_step.py │ │ │ │ │ ├── ecs │ │ │ │ │ ├── ecs_before_sections.py │ │ │ │ │ ├── ecs_example.py │ │ │ │ │ ├── ecs_example_cvode.py │ │ │ │ │ ├── ecs_include_flux.py │ │ │ │ │ ├── ecs_include_flux_cvode.py │ │ │ │ │ ├── ecs_multi_example.py │ │ │ │ │ ├── ecs_multi_example_cvode.py │ │ │ │ │ ├── pump.mod │ │ │ │ │ └── torun.txt │ │ │ │ │ ├── hh.py │ │ │ │ │ ├── hh_cvode.py │ │ │ │ │ ├── hh_morph.py │ │ │ │ │ ├── hh_param.py │ │ │ │ │ ├── hh_param_cvode.py │ │ │ │ │ ├── hybrid │ │ │ │ │ ├── bistable_hybrid.py │ │ │ │ │ ├── bistable_hybrid_change_nthread.py │ │ │ │ │ ├── bistable_hybrid_cvode.py │ │ │ │ │ ├── bistable_hybrid_cvode_change_nthread.py │ │ │ │ │ ├── pure_diffusion_hybrid.py │ │ │ │ │ ├── pure_diffusion_hybrid_cvode.py │ │ │ │ │ └── torun.txt │ │ │ │ │ ├── include_flux.py │ │ │ │ │ ├── include_flux_cvode.py │ │ │ │ │ ├── multicompartment_mebrane_mismatch.py │ │ │ │ │ ├── multicompartment_reactions.py │ │ │ │ │ ├── multicompartment_reactions_del.py │ │ │ │ │ ├── multicompartment_reactions_with_v.py │ │ │ │ │ ├── nodes_update.py │ │ │ │ │ ├── pure_diffusion.py │ │ │ │ │ ├── pure_diffusion_cvode.py │ │ │ │ │ ├── react_region_specified.py │ │ │ │ │ ├── reaction_null_dest.py │ │ │ │ │ ├── reaction_param_test.py │ │ │ │ │ ├── reaction_test.py │ │ │ │ │ ├── torun.txt │ │ │ │ │ ├── verify_no_initialization_order_issue.py │ │ │ │ │ └── wave1d │ │ │ │ │ ├── cal2.mod │ │ │ │ │ ├── caleak.mod │ │ │ │ │ ├── readme.txt │ │ │ │ │ ├── torun.txt │ │ │ │ │ ├── wave1d_125_1.py │ │ │ │ │ ├── wave1d_25_5.py │ │ │ │ │ ├── wave1d_taper_125_1.py │ │ │ │ │ ├── wave1d_taper_25_5.py │ │ │ │ │ ├── wave1d_tree2_125_1.py │ │ │ │ │ ├── wave1d_tree2_25_5.py │ │ │ │ │ ├── wave1d_tree_125_1.py │ │ │ │ │ └── wave1d_tree_25_5.py │ │ │ ├── sections.py │ │ │ ├── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── _subclass.py │ │ │ │ ├── test_all.py │ │ │ │ ├── test_neuron.py │ │ │ │ ├── test_nmodl.py │ │ │ │ ├── test_rxd.json │ │ │ │ ├── test_rxd.py │ │ │ │ ├── test_vector.py │ │ │ │ └── utils │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── capture_stdout.py │ │ │ │ │ ├── checkresult.py │ │ │ │ │ ├── coreneuron_available.py │ │ │ │ │ └── strtobool.py │ │ │ └── units.py │ │ └── scripts │ │ │ ├── CMakeLists.txt │ │ │ ├── README.txt │ │ │ └── binwrapper.py │ ├── shape.cm1 │ └── shape.cm2 └── nmodl │ └── nrnunits.lib.in ├── sonar-project.properties ├── src ├── coreneuron │ ├── CMakeLists.txt │ ├── README.md │ ├── apps │ │ ├── coreneuron.cpp │ │ ├── corenrn_parameters.cpp │ │ ├── corenrn_parameters.hpp │ │ └── main1.cpp │ ├── config │ │ ├── config.cpp.in │ │ ├── config.h │ │ ├── neuron_version.hpp.in │ │ └── version_macros.hpp │ ├── coreneuron.hpp │ ├── engine.h.in │ ├── gpu │ │ ├── nrn_acc_manager.cpp │ │ └── nrn_acc_manager.hpp │ ├── io │ │ ├── core2nrn_data_return.cpp │ │ ├── core2nrn_data_return.hpp │ │ ├── global_vars.cpp │ │ ├── lfp.cpp │ │ ├── lfp.hpp │ │ ├── mech_report.cpp │ │ ├── mech_report.h │ │ ├── mem_layout_util.cpp │ │ ├── mem_layout_util.hpp │ │ ├── mk_mech.cpp │ │ ├── nrn2core_data_init.cpp │ │ ├── nrn2core_direct.h │ │ ├── nrn_checkpoint.cpp │ │ ├── nrn_checkpoint.hpp │ │ ├── nrn_filehandler.cpp │ │ ├── nrn_filehandler.hpp │ │ ├── nrn_setup.cpp │ │ ├── nrn_setup.hpp │ │ ├── nrnsection_mapping.hpp │ │ ├── output_spikes.cpp │ │ ├── output_spikes.hpp │ │ ├── phase1.cpp │ │ ├── phase1.hpp │ │ ├── phase2.cpp │ │ ├── phase2.hpp │ │ ├── phase3.cpp │ │ ├── phase3.hpp │ │ ├── prcellstate.cpp │ │ ├── prcellstate.hpp │ │ ├── reports │ │ │ ├── nrnreport.cpp │ │ │ ├── nrnreport.hpp │ │ │ ├── report_configuration_parser.cpp │ │ │ ├── report_event.cpp │ │ │ ├── report_event.hpp │ │ │ ├── report_handler.cpp │ │ │ ├── report_handler.hpp │ │ │ ├── sonata_report_handler.cpp │ │ │ └── sonata_report_handler.hpp │ │ ├── setup_fornetcon.cpp │ │ ├── setup_fornetcon.hpp │ │ └── user_params.hpp │ ├── mechanism │ │ ├── capac.cpp │ │ ├── eion.cpp │ │ ├── eion.hpp │ │ ├── mech │ │ │ ├── cfile │ │ │ │ └── cabvars.h │ │ │ ├── enginemech.cpp │ │ │ ├── mod2c_core_thread.hpp │ │ │ ├── mod_func.c.sh │ │ │ └── modfile │ │ │ │ ├── exp2syn.mod │ │ │ │ ├── expsyn.mod │ │ │ │ ├── hh.mod │ │ │ │ ├── netstim.mod │ │ │ │ ├── passive.mod │ │ │ │ ├── pattern.mod │ │ │ │ ├── stim.mod │ │ │ │ └── svclmp.mod │ │ ├── mech_mapping.cpp │ │ ├── mech_mapping.hpp │ │ ├── mechanism.hpp │ │ ├── membfunc.hpp │ │ ├── patternstim.cpp │ │ ├── register_mech.cpp │ │ └── register_mech.hpp │ ├── membrane_definitions.h │ ├── mpi │ │ ├── core │ │ │ ├── nrnmpi.hpp │ │ │ ├── nrnmpi_def_cinc.cpp │ │ │ └── resolve.cpp │ │ ├── lib │ │ │ ├── mpispike.cpp │ │ │ ├── nrnmpi.cpp │ │ │ └── nrnmpi.hpp │ │ ├── nrnmpi.h │ │ ├── nrnmpidec.h │ │ └── nrnmpiuse.h │ ├── network │ │ ├── cvodestb.cpp │ │ ├── have2want.h │ │ ├── multisend.cpp │ │ ├── multisend.hpp │ │ ├── multisend_setup.cpp │ │ ├── netcon.hpp │ │ ├── netcvode.cpp │ │ ├── netcvode.hpp │ │ ├── netpar.cpp │ │ ├── netpar.hpp │ │ ├── partrans.cpp │ │ ├── partrans.hpp │ │ ├── partrans_setup.cpp │ │ ├── tnode.hpp │ │ ├── tqueue.cpp │ │ ├── tqueue.hpp │ │ └── tqueue.ipp │ ├── nrnconf.h │ ├── nrniv │ │ └── nrniv_decl.h │ ├── nrnoc │ │ ├── md1redef.h │ │ └── md2redef.h │ ├── permute │ │ ├── balance.cpp │ │ ├── cellorder.cpp │ │ ├── cellorder.cu │ │ ├── cellorder.hpp │ │ ├── cellorder1.cpp │ │ ├── cellorder2.cpp │ │ ├── data_layout.hpp │ │ ├── node_permute.cpp │ │ └── node_permute.h │ ├── sim │ │ ├── fadvance_core.cpp │ │ ├── fast_imem.cpp │ │ ├── fast_imem.hpp │ │ ├── finitialize.cpp │ │ ├── multicore.cpp │ │ ├── multicore.hpp │ │ ├── scopmath │ │ │ ├── abort.cpp │ │ │ ├── crout_thread.hpp │ │ │ ├── errcodes.h │ │ │ ├── newton_struct.h │ │ │ ├── newton_thread.cpp │ │ │ ├── newton_thread.hpp │ │ │ ├── sparse_thread.hpp │ │ │ └── ssimplic_thread.hpp │ │ ├── solve_core.cpp │ │ └── treeset_core.cpp │ └── utils │ │ ├── ivocvect.cpp │ │ ├── ivocvect.hpp │ │ ├── lpt.cpp │ │ ├── lpt.hpp │ │ ├── memory.cpp │ │ ├── memory.h │ │ ├── memory_utils.cpp │ │ ├── memory_utils.h │ │ ├── nrn_assert.h │ │ ├── nrn_stats.cpp │ │ ├── nrn_stats.h │ │ ├── nrnmutdec.hpp │ │ ├── nrnoc_aux.cpp │ │ ├── nrnoc_aux.hpp │ │ ├── nrntimeout.cpp │ │ ├── offload.hpp │ │ ├── profile │ │ └── profiler_interface.h │ │ ├── progressbar │ │ ├── progressbar.cpp │ │ └── progressbar.hpp │ │ ├── randoms │ │ ├── nrnran123.cpp │ │ └── nrnran123.h │ │ ├── string_utils.cpp │ │ ├── string_utils.h │ │ ├── units.hpp │ │ ├── utils.cpp │ │ ├── utils.hpp │ │ ├── utils_cuda.h │ │ ├── vrecitem.h │ │ └── vrecord.cpp ├── gnu │ ├── .clang-format │ ├── Binomial.cpp │ ├── Binomial.h │ ├── CMakeLists.txt │ ├── DiscUnif.cpp │ ├── DiscUnif.h │ ├── Erlang.cpp │ ├── Erlang.h │ ├── Geom.cpp │ ├── Geom.h │ ├── HypGeom.cpp │ ├── HypGeom.h │ ├── LogNorm.cpp │ ├── LogNorm.h │ ├── MCellRan4RNG.cpp │ ├── MCellRan4RNG.hpp │ ├── NegExp.cpp │ ├── NegExp.h │ ├── Normal.cpp │ ├── Normal.h │ ├── NrnRandom123RNG.cpp │ ├── NrnRandom123RNG.hpp │ ├── Poisson.cpp │ ├── Poisson.h │ ├── RNG.h │ ├── Rand.cpp │ ├── Rand.hpp │ ├── Random.cpp │ ├── Random.h │ ├── Uniform.cpp │ ├── Uniform.h │ ├── Weibull.cpp │ ├── Weibull.h │ ├── mcran4.cpp │ ├── mcran4.h │ ├── nrnran123.cpp │ └── nrnran123.h ├── ivoc │ ├── apwindow.cpp │ ├── apwindow.h │ ├── axis.cpp │ ├── axis.h │ ├── bimap.hpp │ ├── bndedval.cpp │ ├── bndedval.h │ ├── cbwidget.cpp │ ├── cbwidget.h │ ├── epsprint.cpp │ ├── epsprint.h │ ├── field.cpp │ ├── field.h │ ├── fourier.cpp │ ├── fourier.h │ ├── gifimage.cpp │ ├── graph.cpp │ ├── graph.h │ ├── graphvec.cpp │ ├── grglyph.cpp │ ├── grglyph.h │ ├── grmanip.cpp │ ├── hocmark.cpp │ ├── hocmark.h │ ├── idraw.cpp │ ├── idraw.h │ ├── ivoc.cpp │ ├── ivoc.h │ ├── ivocconf.h │ ├── ivocmain.cpp │ ├── ivocrand.cpp │ ├── ivocvect.cpp │ ├── ivocvect.h │ ├── ivocwin.cpp │ ├── matrix.cpp │ ├── mlinedit.cpp │ ├── mymath.cpp │ ├── mymath.h │ ├── nrngsl.h │ ├── nrngsl_hc_radix2.cpp │ ├── nrngsl_real_radix2.cpp │ ├── nrnmain.cpp │ ├── nrnmutdec.h │ ├── nrnsymdiritem.h │ ├── objcmd.cpp │ ├── objcmd.h │ ├── oc2iv.cpp │ ├── oc2iv.h │ ├── ocbox.cpp │ ├── ocbox.h │ ├── ocbrowsr.cpp │ ├── ocbrowsr.h │ ├── ocdeck.cpp │ ├── ocdeck.h │ ├── ocfile.cpp │ ├── ocfile.h │ ├── ocglyph.h │ ├── ochelp.cpp │ ├── oclist.cpp │ ├── oclist.h │ ├── ocmatrix.cpp │ ├── ocmatrix.h │ ├── ocnoiv1.cpp │ ├── ocnotify.h │ ├── ocobserv.cpp │ ├── ocobserv.h │ ├── ocpicker.cpp │ ├── ocpicker.h │ ├── ocpointer.cpp │ ├── ocpointer.h │ ├── ocptrvector.cpp │ ├── ocptrvector.h │ ├── octimer.cpp │ ├── pwman.cpp │ ├── rect.cpp │ ├── rect.h │ ├── rubband.cpp │ ├── rubband.h │ ├── scene.cpp │ ├── scenepic.cpp │ ├── scenepic.h │ ├── scenevie.h │ ├── strfun.cpp │ ├── symchoos.cpp │ ├── symchoos.h │ ├── utility.cpp │ ├── utility.h │ ├── xdep.cpp │ ├── xmenu.cpp │ ├── xmenu.h │ └── xyview.cpp ├── ivos │ ├── .clang-format │ ├── InterViews │ │ ├── _defines.h │ │ ├── _enter.h │ │ ├── _leave.h │ │ ├── _names.h │ │ ├── _undefs.h │ │ ├── boolean.h │ │ ├── coord.h │ │ ├── enter-scope.h │ │ ├── geometry.h │ │ ├── iv.h │ │ ├── observe.h │ │ └── resource.h │ ├── OS │ │ ├── _defines.h │ │ ├── _undefs.h │ │ ├── enter-scope.h │ │ ├── leave-scope.h │ │ └── os.h │ ├── observe.cpp │ └── resource.cpp ├── mac │ ├── CMakeLists.txt │ ├── activate-apps-cmake.sh │ ├── clean-for-pkg-cmake.sh │ ├── idraw.icns │ ├── idraw.sh │ ├── launch_inst.sh │ ├── launch_inst_cmake.sh │ ├── macdist.pkgproj.in │ ├── macnrn.term │ ├── mkdmg.sh │ ├── mknrndll.icns │ ├── mknrndll.sh │ ├── modlunit.icns │ ├── modlunit.sh │ ├── mos2nrn.icns │ ├── mos2nrn.sh │ ├── neurondemo.icns │ ├── neurondemo.sh │ ├── nrn_codesign.sh.in │ ├── nrn_entitlements.plist │ ├── nrn_notarize.sh │ ├── nrn_productsign.sh │ ├── nrn_x11_opt2usr.sh │ ├── nrngui.icns │ ├── nrngui.sh │ ├── nrniv.icns │ ├── postinstall.sh.in │ ├── prototype_applescript.txt │ └── prototype_applescript_cmake.txt ├── modlunit │ ├── consist.cpp │ ├── declare.cpp │ ├── extargs.h │ ├── extdef.h │ ├── init.cpp │ ├── io.cpp │ ├── kinunit.cpp │ ├── lex.lpp │ ├── list.cpp │ ├── model.cpp │ ├── model.h │ ├── modlunit.h │ ├── nrnunit.cpp │ ├── parse1.ypp │ ├── passn.cpp │ ├── symbol.cpp │ ├── symbol.h │ ├── units.cpp │ ├── units.h │ └── units1.cpp ├── mswin │ ├── CMakeLists.txt │ ├── bin │ │ ├── mknrndll │ │ ├── neurondemo │ │ ├── nrngui │ │ └── nrnivmodl.bat │ ├── dlfcn.c │ ├── dlfcn.h │ ├── extra │ │ ├── d2upath.cpp │ │ ├── d2upath.h │ │ ├── mos2nrn.cpp │ │ ├── neuron.cpp │ │ └── nrnbinstr.cpp │ ├── lib │ │ ├── bshstart.sh │ │ ├── minttyrc │ │ ├── mknrndl2.sh │ │ ├── mknrndl2a.sh │ │ ├── mknrndll.mak.in │ │ ├── mknrndll.sh │ │ ├── modlunit.sh │ │ ├── mos2nrn.sh │ │ ├── mos2nrn1.sh │ │ ├── mos2nrn3.sh │ │ ├── neuron.sh │ │ ├── neuron2.sh │ │ ├── neuron3.sh │ │ ├── nrnstart.bsh │ │ ├── nrnsys.sh │ │ ├── nrnsys1.sh │ │ └── psfilt.sed │ ├── nmodl2a.ico │ ├── notes.txt │ ├── nrniv.ico │ ├── nrniv10.ico │ ├── nrnsetupmingw.nsi.in │ ├── pre_setup_exe.sh.in │ └── readme.txt ├── neuron │ ├── cache │ │ ├── mechanism_range.hpp │ │ └── model_data.hpp │ ├── container │ │ ├── data_handle.hpp │ │ ├── generic_data_handle.hpp │ │ ├── mechanism.hpp │ │ ├── mechanism_data.hpp │ │ ├── memory_usage.hpp │ │ ├── node.hpp │ │ ├── node_data.hpp │ │ ├── non_owning_soa_identifier.hpp │ │ ├── soa_container.hpp │ │ ├── soa_identifier.hpp │ │ └── view_utils.hpp │ ├── model_data.hpp │ ├── model_data_fwd.hpp │ └── unique_cstr.hpp ├── neuronmusic │ ├── CMakeLists.txt │ ├── neuronmusic.pxd │ ├── neuronmusic.pyx │ ├── nrnmusic.cpp │ ├── nrnmusic.h │ ├── nrnmusic_dynam.cpp │ └── nrnmusicapi.h ├── nmodl │ ├── CMakeLists.txt │ ├── ast │ │ └── ast_common.hpp │ ├── codegen │ │ ├── CMakeLists.txt │ │ ├── codegen_acc_visitor.cpp │ │ ├── codegen_acc_visitor.hpp │ │ ├── codegen_compatibility_visitor.cpp │ │ ├── codegen_compatibility_visitor.hpp │ │ ├── codegen_coreneuron_cpp_visitor.cpp │ │ ├── codegen_coreneuron_cpp_visitor.hpp │ │ ├── codegen_cpp_visitor.cpp │ │ ├── codegen_cpp_visitor.hpp │ │ ├── codegen_helper_visitor.cpp │ │ ├── codegen_helper_visitor.hpp │ │ ├── codegen_info.cpp │ │ ├── codegen_info.hpp │ │ ├── codegen_naming.hpp │ │ ├── codegen_neuron_cpp_visitor.cpp │ │ ├── codegen_neuron_cpp_visitor.hpp │ │ ├── codegen_transform_visitor.cpp │ │ ├── codegen_transform_visitor.hpp │ │ ├── codegen_utils.cpp │ │ └── codegen_utils.hpp │ ├── config │ │ ├── config.cpp.in │ │ └── config.h │ ├── language │ │ ├── CMakeLists.txt │ │ ├── argument.py │ │ ├── code_generator.py │ │ ├── code_generator_opts.in │ │ ├── codegen.yaml │ │ ├── language_parser.py │ │ ├── nmodl.yaml │ │ ├── node_info.py │ │ ├── nodes.py │ │ ├── templates │ │ │ ├── ast │ │ │ │ ├── all.hpp │ │ │ │ ├── ast.cpp │ │ │ │ ├── ast.hpp │ │ │ │ ├── ast_decl.hpp │ │ │ │ ├── node.hpp │ │ │ │ └── node_class.template │ │ │ ├── code_generator.cmake │ │ │ ├── pybind │ │ │ │ ├── pyast.cpp │ │ │ │ ├── pyast.hpp │ │ │ │ ├── pynode.cpp │ │ │ │ ├── pysymtab.cpp │ │ │ │ ├── pyvisitor.cpp │ │ │ │ └── pyvisitor.hpp │ │ │ └── visitors │ │ │ │ ├── ast_visitor.cpp │ │ │ │ ├── ast_visitor.hpp │ │ │ │ ├── checkparent_visitor.cpp │ │ │ │ ├── checkparent_visitor.hpp │ │ │ │ ├── json_visitor.cpp │ │ │ │ ├── json_visitor.hpp │ │ │ │ ├── lookup_visitor.cpp │ │ │ │ ├── lookup_visitor.hpp │ │ │ │ ├── nmodl_visitor.cpp │ │ │ │ ├── nmodl_visitor.hpp │ │ │ │ ├── symtab_visitor.cpp │ │ │ │ ├── symtab_visitor.hpp │ │ │ │ └── visitor.hpp │ │ └── utils.py │ ├── lexer │ │ ├── CMakeLists.txt │ │ ├── c11.ll │ │ ├── c11_lexer.hpp │ │ ├── diffeq.ll │ │ ├── diffeq_lexer.hpp │ │ ├── main_c.cpp │ │ ├── main_nmodl.cpp │ │ ├── main_units.cpp │ │ ├── modl.h │ │ ├── modtoken.cpp │ │ ├── modtoken.hpp │ │ ├── nmodl.ll │ │ ├── nmodl_lexer.hpp │ │ ├── nmodl_utils.cpp │ │ ├── nmodl_utils.hpp │ │ ├── token_mapping.cpp │ │ ├── token_mapping.hpp │ │ ├── unit.ll │ │ ├── unit_lexer.hpp │ │ └── verbatim.l │ ├── main.cpp │ ├── parser │ │ ├── CMakeLists.txt │ │ ├── c11.yy │ │ ├── c11_driver.cpp │ │ ├── c11_driver.hpp │ │ ├── diffeq.yy │ │ ├── diffeq_context.cpp │ │ ├── diffeq_context.hpp │ │ ├── diffeq_driver.cpp │ │ ├── diffeq_driver.hpp │ │ ├── diffeq_helper.hpp │ │ ├── main_c.cpp │ │ ├── main_nmodl.cpp │ │ ├── main_units.cpp │ │ ├── nmodl.yy │ │ ├── nmodl_driver.cpp │ │ ├── nmodl_driver.hpp │ │ ├── unit.yy │ │ ├── unit_driver.cpp │ │ ├── unit_driver.hpp │ │ ├── verbatim.yy │ │ └── verbatim_driver.hpp │ ├── printer │ │ ├── CMakeLists.txt │ │ ├── code_printer.cpp │ │ ├── code_printer.hpp │ │ ├── decl.hpp │ │ ├── json_printer.cpp │ │ ├── json_printer.hpp │ │ ├── nmodl_printer.cpp │ │ └── nmodl_printer.hpp │ ├── pybind │ │ ├── CMakeLists.txt │ │ ├── docstrings.hpp │ │ ├── ode_py.hpp.inc │ │ ├── pybind_utils.hpp │ │ ├── pyembed.cpp │ │ ├── pyembed.hpp │ │ ├── pynmodl.cpp │ │ ├── wrapper.cpp │ │ └── wrapper.hpp │ ├── solver │ │ ├── CMakeLists.txt │ │ ├── crout │ │ │ └── crout.hpp │ │ ├── newton │ │ │ └── newton.hpp │ │ └── solver.hpp.inc │ ├── symtab │ │ ├── CMakeLists.txt │ │ ├── decl.hpp │ │ ├── symbol.cpp │ │ ├── symbol.hpp │ │ ├── symbol_properties.cpp │ │ ├── symbol_properties.hpp │ │ ├── symbol_table.cpp │ │ └── symbol_table.hpp │ ├── units │ │ ├── units.cpp │ │ └── units.hpp │ ├── utils │ │ ├── CMakeLists.txt │ │ ├── blame.cpp │ │ ├── blame.hpp │ │ ├── common_utils.cpp │ │ ├── common_utils.hpp │ │ ├── file_library.cpp │ │ ├── file_library.hpp │ │ ├── fmt.h │ │ ├── logger.cpp │ │ ├── logger.hpp │ │ ├── perf_stat.cpp │ │ ├── perf_stat.hpp │ │ ├── string_utils.cpp │ │ ├── string_utils.hpp │ │ ├── table_data.cpp │ │ └── table_data.hpp │ └── visitors │ │ ├── CMakeLists.txt │ │ ├── after_cvode_to_cnexp_visitor.cpp │ │ ├── after_cvode_to_cnexp_visitor.hpp │ │ ├── constant_folder_visitor.cpp │ │ ├── constant_folder_visitor.hpp │ │ ├── cvode_visitor.cpp │ │ ├── cvode_visitor.hpp │ │ ├── defuse_analyze_visitor.cpp │ │ ├── defuse_analyze_visitor.hpp │ │ ├── function_callpath_visitor.cpp │ │ ├── function_callpath_visitor.hpp │ │ ├── global_var_visitor.cpp │ │ ├── global_var_visitor.hpp │ │ ├── implicit_argument_visitor.cpp │ │ ├── implicit_argument_visitor.hpp │ │ ├── index_remover.cpp │ │ ├── index_remover.hpp │ │ ├── indexedname_visitor.cpp │ │ ├── indexedname_visitor.hpp │ │ ├── initial_block_visitor.cpp │ │ ├── initial_block_visitor.hpp │ │ ├── inline_visitor.cpp │ │ ├── inline_visitor.hpp │ │ ├── kinetic_block_visitor.cpp │ │ ├── kinetic_block_visitor.hpp │ │ ├── local_to_assigned_visitor.cpp │ │ ├── local_to_assigned_visitor.hpp │ │ ├── local_var_rename_visitor.cpp │ │ ├── local_var_rename_visitor.hpp │ │ ├── localize_visitor.cpp │ │ ├── localize_visitor.hpp │ │ ├── longitudinal_diffusion_visitor.cpp │ │ ├── longitudinal_diffusion_visitor.hpp │ │ ├── loop_unroll_visitor.cpp │ │ ├── loop_unroll_visitor.hpp │ │ ├── main.cpp │ │ ├── neuron_solve_visitor.cpp │ │ ├── neuron_solve_visitor.hpp │ │ ├── nmodl_visitor_helper.ipp │ │ ├── perf_visitor.cpp │ │ ├── perf_visitor.hpp │ │ ├── rename_function_arguments.cpp │ │ ├── rename_function_arguments.hpp │ │ ├── rename_visitor.cpp │ │ ├── rename_visitor.hpp │ │ ├── semantic_analysis_visitor.cpp │ │ ├── semantic_analysis_visitor.hpp │ │ ├── solve_block_visitor.cpp │ │ ├── solve_block_visitor.hpp │ │ ├── steadystate_visitor.cpp │ │ ├── steadystate_visitor.hpp │ │ ├── sympy_conductance_visitor.cpp │ │ ├── sympy_conductance_visitor.hpp │ │ ├── sympy_replace_solutions_visitor.cpp │ │ ├── sympy_replace_solutions_visitor.hpp │ │ ├── sympy_solver_visitor.cpp │ │ ├── sympy_solver_visitor.hpp │ │ ├── symtab_visitor_helper.hpp │ │ ├── units_visitor.cpp │ │ ├── units_visitor.hpp │ │ ├── var_usage_visitor.cpp │ │ ├── var_usage_visitor.hpp │ │ ├── verbatim_var_rename_visitor.cpp │ │ ├── verbatim_var_rename_visitor.hpp │ │ ├── verbatim_visitor.cpp │ │ ├── verbatim_visitor.hpp │ │ ├── visitor_utils.cpp │ │ └── visitor_utils.hpp ├── nocmodl │ ├── consist.cpp │ ├── deriv.cpp │ ├── difeqdef.h │ ├── diffeq.ypp │ ├── discrete.cpp │ ├── extdef.h │ ├── extdef2.h │ ├── extdef5.h │ ├── init.cpp │ ├── io.cpp │ ├── kinetic.cpp │ ├── lex.lpp │ ├── list.cpp │ ├── modl.cpp │ ├── modl.h │ ├── netrec_discon.cpp │ ├── nmodlfunc.h │ ├── noccout.cpp │ ├── nocpout.cpp │ ├── parsact.cpp │ ├── parse1.ypp │ ├── simultan.cpp │ ├── solve.cpp │ ├── symbol.cpp │ └── symbol.h ├── node_order_optim │ ├── README │ ├── node_order_optim.h │ └── permute_utils.hpp ├── nrncvode │ ├── cvodeobj.cpp │ ├── cvodeobj.h │ ├── cvodestb.cpp │ ├── cvtrset.cpp │ ├── htlist.cpp │ ├── htlist.h │ ├── netcon.h │ ├── netcvode.cpp │ ├── netcvode.h │ ├── nrndaspk.cpp │ ├── nrndaspk.h │ ├── nrnneosm.h.in │ ├── occvode.cpp │ ├── pool.hpp │ ├── sptree.hpp │ ├── tqitem.hpp │ ├── tqueue.cpp │ ├── tqueue.hpp │ └── vrecitem.h ├── nrniv │ ├── CMakeLists.txt │ ├── arraypool.h │ ├── backtrace_utils.cpp │ ├── backtrace_utils.h │ ├── bbsavestate.cpp │ ├── bbsavestate.h │ ├── classreg.cpp │ ├── cxprop.cpp │ ├── datapath.cpp │ ├── datapath.h │ ├── finithnd.cpp │ ├── glinerec.cpp │ ├── glinerec.h │ ├── have2want.hpp │ ├── hocmech.cpp │ ├── impedanc.cpp │ ├── kschan.cpp │ ├── kschan.h │ ├── kssingle.cpp │ ├── kssingle.h │ ├── linmod.cpp │ ├── linmod.h │ ├── linmod1.cpp │ ├── matrixmap.cpp │ ├── matrixmap.h │ ├── memory_usage.cpp │ ├── multisend.cpp │ ├── multisend_setup.cpp │ ├── multisplit.cpp │ ├── multisplitcontrol.h │ ├── ndatclas.cpp │ ├── ndatclas.h │ ├── netpar.cpp │ ├── netpar.h │ ├── neuronapi.cpp │ ├── neuronapi.h │ ├── nmodlrandom.cpp │ ├── nonlinz.cpp │ ├── nonlinz.h │ ├── nrncore_write.cpp │ ├── nrncore_write.h │ ├── nrncore_write │ │ ├── callbacks │ │ │ ├── nrncore_callbacks.cpp │ │ │ └── nrncore_callbacks.h │ │ ├── data │ │ │ ├── cell_group.cpp │ │ │ ├── cell_group.h │ │ │ ├── datum_indices.cpp │ │ │ └── datum_indices.h │ │ ├── io │ │ │ ├── nrncore_io.cpp │ │ │ └── nrncore_io.h │ │ └── utils │ │ │ ├── nrncore_utils.cpp │ │ │ └── nrncore_utils.h │ ├── nrndae.cpp │ ├── nrndae.h │ ├── nrnmenu.cpp │ ├── nrnmenu.h │ ├── nrnoc2iv.h │ ├── nrnpy.cpp │ ├── nrnpy.h │ ├── nrnsection_mapping.h │ ├── nrnste.cpp │ ├── nrnste.h │ ├── nvector_nrnparallel_ld.cpp │ ├── nvector_nrnparallel_ld.h │ ├── nvector_nrnserial_ld.cpp │ ├── nvector_nrnserial_ld.h │ ├── nvector_nrnthread.cpp │ ├── nvector_nrnthread.h │ ├── nvector_nrnthread_ld.cpp │ ├── nvector_nrnthread_ld.h │ ├── ocjump.cpp │ ├── ocjump.h │ ├── partrans.cpp │ ├── partrans.h │ ├── ppshape.cpp │ ├── ppshape.h │ ├── prcellstate.cpp │ ├── pysecname2sec.cpp │ ├── rot3band.h │ ├── rotate3d.cpp │ ├── rotate3d.h │ ├── savstate.cpp │ ├── secbrows.cpp │ ├── secbrows.h │ ├── shape.cpp │ ├── shape.h │ ├── shapeplt.cpp │ ├── shapeplt.h │ ├── spaceplt.cpp │ ├── splitcell.cpp │ ├── structpool.h │ ├── symdir.cpp │ ├── symdir.h │ └── vrecord.cpp ├── nrnmpi │ ├── bbsmpipack.cpp │ ├── memory_usage.cpp │ ├── mkdynam.sh │ ├── mpispike.cpp │ ├── mpispike.h │ ├── notes_nrnrt │ ├── nrnmpi.cpp │ ├── nrnmpi_def_cinc │ ├── nrnmpi_dynam.cpp │ ├── nrnmpi_dynam_stubs.cpp │ ├── nrnmpi_impl.h │ └── nrnmpidec.h ├── nrnoc │ ├── apcount.mod │ ├── cabcode.cpp │ ├── cabcode.h │ ├── cabvars.h │ ├── capac.cpp │ ├── clamp.cpp │ ├── container.cpp │ ├── eion.cpp │ ├── exp2syn.mod │ ├── expsyn.mod │ ├── extcelln.cpp │ ├── fadvance.cpp │ ├── feature.mod │ ├── fstim.cpp │ ├── gui-redirect.h │ ├── hh.mod │ ├── hocprax.cpp │ ├── init.cpp │ ├── intfire1.mod │ ├── intfire2.mod │ ├── intfire4.mod │ ├── ion_semantics.h │ ├── ldifus.cpp │ ├── md1redef.h │ ├── md2redef.h │ ├── membdef.h │ ├── membfunc.cpp │ ├── membfunc.h │ ├── memblist.cpp │ ├── multicore.cpp │ ├── multicore.h │ ├── multisplit.h │ ├── netstim.mod │ ├── neuron.h │ ├── nmodlmutex.h │ ├── nonvintblock.h │ ├── nrn_ansi.h │ ├── nrnconfigargs.h.in │ ├── nrncvode.h │ ├── nrndae_c.h │ ├── nrniv_mf.h │ ├── nrnoc_ml.h │ ├── nrnredef.h │ ├── nrnsemanticversion.h.in │ ├── nrntimeout.cpp │ ├── nrnversion.cpp │ ├── nrnversionmacros.h │ ├── oclmp.mod │ ├── options.h │ ├── passive.mod │ ├── passive0.cpp │ ├── pattern.mod │ ├── point.cpp │ ├── ppmark.mod │ ├── psection.cpp │ ├── seclist.cpp │ ├── seclist.h │ ├── secref.cpp │ ├── section.h │ ├── section_fwd.hpp │ ├── solve.cpp │ ├── stim.mod │ ├── svclmp.mod │ ├── syn.mod │ ├── synapse.cpp │ ├── treeset.cpp │ ├── treeset.h │ ├── vclmp.mod │ └── xmech.mod ├── nrnpython │ ├── CMakeLists.txt │ ├── _config_params.py.in │ ├── convert_cxx_exceptions.hpp │ ├── examples │ │ ├── test0.py │ │ └── test1.py │ ├── grids.cpp │ ├── grids.h │ ├── hoccontext.h │ ├── inithoc.cpp │ ├── nrn_export.hpp │ ├── nrn_metaclass.cpp │ ├── nrn_pyhocobject.h │ ├── nrnpy_hoc.cpp │ ├── nrnpy_hoc.h │ ├── nrnpy_nrn.cpp │ ├── nrnpy_nrn.h │ ├── nrnpy_p2h.cpp │ ├── nrnpy_utils.cpp │ ├── nrnpy_utils.h │ ├── nrnpython.cpp │ ├── nrnpython.h │ ├── nrnwrap_Python.h │ ├── rxd.cpp │ ├── rxd.h │ ├── rxd_extracellular.cpp │ ├── rxd_intracellular.cpp │ ├── rxd_llgramarea.cpp │ ├── rxd_marching_cubes.cpp │ ├── rxd_vol.cpp │ └── rxdmath.cpp ├── oc │ ├── audit.cpp │ ├── axis.cpp │ ├── classreg.h │ ├── code.cpp │ ├── code.h │ ├── code2.cpp │ ├── debug.cpp │ ├── equation.h │ ├── fileio.cpp │ ├── ftime.cpp │ ├── functabl.cpp │ ├── getsym.cpp │ ├── hoc.cpp │ ├── hoc.h │ ├── hoc_init.cpp │ ├── hoc_oop.cpp │ ├── hocassrt.h │ ├── hocdec.h │ ├── hocgetsym.h │ ├── hoclist.h │ ├── hocmodl.h │ ├── hocparse.h │ ├── hocstr.h │ ├── hocusr.cpp │ ├── list.cpp │ ├── math.cpp │ ├── mech_api.h │ ├── memory.cpp │ ├── memory.hpp │ ├── mk_hocusr_h.py │ ├── modlreg.cpp │ ├── mswinprt.cpp │ ├── nonlin.cpp │ ├── nrnapi.h │ ├── nrnassrt.h │ ├── nrndigest.h │ ├── nrnfilewrap.h │ ├── nrnmpi.h │ ├── nrnmpi_dynam.cpp │ ├── nrnmpi_dynam_stubs.cpp │ ├── nrnmpiuse.h.in │ ├── nrnrandom.h │ ├── nrnunits.h │ ├── nrnwrap_dlfcn.h │ ├── oc_ansi.h │ ├── oc_mcran4.cpp │ ├── oc_mcran4.hpp │ ├── ocfunc.h │ ├── ockludge.cpp │ ├── ocmain.cpp │ ├── ocmisc.h │ ├── parse.ypp │ ├── parse_with_deps.hpp │ ├── plot.cpp │ ├── plt.cpp │ ├── profile.h │ ├── scoprand.cpp │ ├── spinit1.cpp │ ├── spinit2.cpp │ ├── symbol.cpp │ ├── wrap_sprintf.h │ ├── x.cpp │ └── xred.cpp ├── parallel │ ├── bbs.cpp │ ├── bbs.h │ ├── bbsclimpi.cpp │ ├── bbsdirect.h │ ├── bbsdirectmpi.cpp │ ├── bbsimpl.h │ ├── bbslocal.cpp │ ├── bbslocal.h │ ├── bbslsrv.cpp │ ├── bbslsrv.hpp │ ├── bbslsrv2.h │ ├── bbsrcli.h │ ├── bbssrv.h │ ├── bbssrv2mpi.cpp │ ├── bbssrv2mpi.h │ ├── bbssrvmpi.cpp │ ├── ocbbs.cpp │ ├── test0.hoc │ ├── test0.py │ ├── test1.hoc │ ├── test2.hoc │ ├── test3.hoc │ ├── test4.hoc │ ├── test5.hoc │ ├── test6.hoc │ ├── test7.hoc │ └── testsw1.hoc ├── scopmath │ ├── abort.cpp │ ├── advance.cpp │ ├── boundary.cpp │ ├── crank.cpp │ ├── crout.hpp │ ├── crout_thread.hpp │ ├── deflate.hpp │ ├── dimplic.hpp │ ├── errcodes.hpp │ ├── euler.hpp │ ├── euler_thread.hpp │ ├── expfit.cpp │ ├── exprand.cpp │ ├── f2c.h │ ├── f2cmisc.cpp │ ├── factoria.cpp │ ├── force.cpp │ ├── gauss.cpp │ ├── getmem.cpp │ ├── harmonic.cpp │ ├── hyperbol.cpp │ ├── invert.cpp │ ├── lag.cpp │ ├── legendre.cpp │ ├── newton.hpp │ ├── newton_struct.h │ ├── newton_thread.hpp │ ├── normrand.cpp │ ├── perpulse.cpp │ ├── perstep.cpp │ ├── poisrand.cpp │ ├── poisson.cpp │ ├── praxis.cpp │ ├── pulse.cpp │ ├── ramp.cpp │ ├── revhyper.cpp │ ├── revsawto.cpp │ ├── revsigmo.cpp │ ├── romberg.cpp │ ├── row_view.hpp │ ├── runge.hpp │ ├── sawtooth.cpp │ ├── scoperf.cpp │ ├── scoplib.h │ ├── sigmoid.cpp │ ├── simeq.hpp │ ├── sparse.hpp │ ├── sparse_thread.hpp │ ├── spline.cpp │ ├── squarewa.cpp │ ├── ssimplic.hpp │ ├── ssimplic_thread.hpp │ ├── step.cpp │ ├── threshol.cpp │ └── tridiag.cpp ├── sparse │ ├── .clang-format │ ├── bksub.cpp │ ├── getelm.cpp │ ├── lineq.cpp │ ├── lineq.h │ ├── prmat.cpp │ └── subrows.cpp ├── sparse13 │ ├── .clang-format │ ├── CMakeLists.txt │ ├── spalloc.cpp │ ├── spbuild.cpp │ ├── spconfig.h │ ├── spdefs.h │ ├── spfactor.cpp │ ├── spmatrix.h │ ├── spoutput.cpp │ ├── spsolve.cpp │ └── sputils.cpp ├── sundials │ ├── .clang-format │ ├── LICENSE │ ├── README │ ├── cvodes │ │ ├── cvband.c │ │ ├── cvband.h │ │ ├── cvband_impl.h │ │ ├── cvbandpre.c │ │ ├── cvbandpre.h │ │ ├── cvbandpre_impl.h │ │ ├── cvbbdpre.c │ │ ├── cvbbdpre.h │ │ ├── cvbbdpre_impl.h │ │ ├── cvdense.c │ │ ├── cvdense.h │ │ ├── cvdense_impl.h │ │ ├── cvdiag.c │ │ ├── cvdiag.h │ │ ├── cvdiag_impl.h │ │ ├── cvodea.c │ │ ├── cvodea.h │ │ ├── cvodea_impl.h │ │ ├── cvodes.c │ │ ├── cvodes.h │ │ ├── cvodes_impl.h │ │ ├── cvodesio.c │ │ ├── cvspgmr.c │ │ ├── cvspgmr.h │ │ └── cvspgmr_impl.h │ ├── ida │ │ ├── ida.c │ │ ├── ida.h │ │ ├── ida_impl.h │ │ ├── idaband.c │ │ ├── idaband.h │ │ ├── idaband_impl.h │ │ ├── idabbdpre.c │ │ ├── idabbdpre.h │ │ ├── idabbdpre_impl.h │ │ ├── idadense.c │ │ ├── idadense.h │ │ ├── idadense_impl.h │ │ ├── idaic.c │ │ ├── idaio.c │ │ ├── idaspgmr.c │ │ ├── idaspgmr.h │ │ └── idaspgmr_impl.h │ ├── shared │ │ ├── band.c │ │ ├── band.h │ │ ├── dense.c │ │ ├── dense.h │ │ ├── fnvector_parallel.c │ │ ├── fnvector_parallel.h │ │ ├── fnvector_serial.c │ │ ├── fnvector_serial.h │ │ ├── iterative.c │ │ ├── iterative.h │ │ ├── nvector.c │ │ ├── nvector.h │ │ ├── nvector_parallel.c │ │ ├── nvector_parallel.h │ │ ├── nvector_serial.c │ │ ├── nvector_serial.h │ │ ├── smalldense.c │ │ ├── smalldense.h │ │ ├── spgmr.c │ │ ├── spgmr.h │ │ ├── sundialsmath.c │ │ ├── sundialsmath.h │ │ └── sundialstypes.h │ └── sundials_config.h.in └── utils │ ├── enumerate.h │ ├── formatting.hpp │ ├── logger.hpp │ ├── profile │ └── profiler_interface.h │ └── signal.hpp └── test ├── CMakeLists.txt ├── api ├── CMakeLists.txt ├── hh_sim.cpp ├── netcon.cpp ├── sections.cpp ├── test_common.h └── vclamp.cpp ├── benchmarks └── threads │ ├── test_multicore.cpp │ └── test_multicore.h ├── common └── catch2_main.cpp ├── coreneuron ├── mod files │ ├── axial.inc │ ├── axial.mod │ ├── axial_pp.mod │ ├── bacur.mod │ ├── banocur.mod │ ├── fornetcon.mod │ ├── green.mod │ ├── invlfire.mod │ ├── netmove.mod │ ├── noisychan.mod │ ├── red.mod │ ├── sample.mod │ ├── watchrange.mod │ └── watchrange2.mod ├── test_array_variables_transfer.py ├── test_ba.py ├── test_datareturn.py ├── test_direct.hoc ├── test_direct.py ├── test_fornetcon.py ├── test_inputpresyn.py ├── test_netmove.py ├── test_nmodlrandom.py ├── test_nmodlrandom_syntax.py ├── test_pointer.py ├── test_psolve.py ├── test_spikes.py ├── test_subworlds.py ├── test_units.py ├── test_watchrange.py └── unit │ ├── CMakeLists.txt │ ├── alignment │ ├── CMakeLists.txt │ └── alignment.cpp │ ├── cmdline_interface │ ├── CMakeLists.txt │ └── test_cmdline_interface.cpp │ ├── interleave_info │ ├── CMakeLists.txt │ └── check_constructors.cpp │ ├── lfp │ ├── CMakeLists.txt │ └── lfp.cpp │ ├── mech_mapping │ ├── CMakeLists.txt │ └── test_mech_mapping.cpp │ ├── queueing │ ├── CMakeLists.txt │ └── test_queueing.cpp │ ├── random │ ├── CMakeLists.txt │ └── test_random.cpp │ └── solver │ ├── CMakeLists.txt │ └── test_solver.cpp ├── cover ├── mod │ └── ppxsrc.mod ├── test_netcvode.json ├── test_netcvode.py └── unit_tests │ └── cover.cpp ├── datahandle ├── opaque_ptr_mod.mod ├── opaque_token.mod ├── psection_regression.mod ├── ptr.mod ├── ptr_mod.mod ├── random.mod ├── test_1.py ├── test_opaque_ptr.py ├── test_psection.py └── test_token.py ├── external ├── CMakeLists.txt ├── channel-benchmark │ └── CMakeLists.txt ├── nrntest │ └── CMakeLists.txt ├── olfactory-bulb-3d │ └── CMakeLists.txt ├── reduced_dentate │ └── CMakeLists.txt ├── ringtest │ └── CMakeLists.txt ├── testcorenrn │ └── CMakeLists.txt └── tqperf │ └── CMakeLists.txt ├── gjtests ├── ggap.mod ├── natrans.mod ├── test_natrans.py └── test_par_gj.py ├── hoc_tests └── connect_dend │ ├── cell3soma.dat.ref │ └── connect_dend.hoc ├── hoctests ├── atest.mod ├── expect_err.hoc ├── netrec_init.mod ├── rand.mod ├── rand_art.mod ├── rand_pp.mod ├── sdata.inc ├── sdata.mod ├── sdata_pp.mod ├── sdata_ppts.mod ├── sdata_ts.mod ├── tests │ ├── test_bbss.py │ ├── test_cvinterp.py │ ├── test_eion_cover.py │ ├── test_hocGUI2.py │ ├── test_hoc_class_instance.py │ ├── test_hocmech.py │ ├── test_kschan.json │ ├── test_kschan.py │ ├── test_legacy_setpointer.py │ ├── test_loadbal.hoc │ ├── test_mechfunc.py │ ├── test_mechstd.py │ ├── test_mode.py │ ├── test_mview.py │ ├── test_netrec_init.py │ ├── test_neurondemo.json │ ├── test_neurondemo.py │ ├── test_nrniv-launch.py │ ├── test_optim_node_order.json │ ├── test_optim_node_order.py │ ├── test_pyret.py │ ├── test_random.hoc │ ├── test_random.json │ ├── test_random.py │ ├── test_seclist.py │ ├── test_secref.py │ ├── test_setdata.py │ ├── test_shape.py │ ├── test_thread_partition.py │ └── test_vector.py └── vardimtests │ ├── perf1.hoc │ ├── test1.hoc │ ├── test1.py │ ├── test2.hoc │ ├── test2.py │ ├── test3.hoc │ ├── test4.hoc │ ├── test5.hoc │ ├── test6.hoc │ ├── test7.hoc │ ├── test8.hoc │ ├── test9.hoc │ └── test9.py ├── music_tests ├── README ├── runtests.py ├── test2.music ├── test2.py ├── test3.music └── test3.py ├── nmodl ├── Project Path Space │ ├── test.mod │ └── test.py ├── test_function_table.py ├── test_kinetic.py ├── test_random.py ├── test_table.py └── transpiler │ ├── integration │ ├── CMakeLists.txt │ └── mod │ │ ├── cabpump.mod │ │ ├── glia_sparse.mod │ │ ├── ican.mod │ │ ├── test_functor.mod │ │ ├── var_init.inc │ │ ├── variable_names.mod │ │ └── watch_test.mod │ ├── unit │ ├── CMakeLists.txt │ ├── codegen │ │ ├── codegen_compatibility_visitor.cpp │ │ ├── codegen_coreneuron_cpp_visitor.cpp │ │ ├── codegen_helper.cpp │ │ ├── codegen_info.cpp │ │ ├── codegen_neuron_cpp_visitor.cpp │ │ ├── codegen_utils.cpp │ │ ├── main.cpp │ │ └── transform.cpp │ ├── crout │ │ └── crout.cpp │ ├── lexer │ │ └── tokens.cpp │ ├── modtoken │ │ └── modtoken.cpp │ ├── newton │ │ └── newton.cpp │ ├── ode │ │ ├── __init__.py │ │ └── test_ode.py │ ├── parser │ │ └── parser.cpp │ ├── printer │ │ └── printer.cpp │ ├── pybind │ │ ├── __init__.py │ │ ├── conftest.py │ │ ├── test_ast.py │ │ ├── test_examples.py │ │ ├── test_parser.py │ │ ├── test_symtab.py │ │ └── test_visitor.py │ ├── symtab │ │ └── symbol_table.cpp │ ├── units │ │ ├── lexer.cpp │ │ └── parser.cpp │ ├── utils │ │ ├── nmodl_constructs.cpp │ │ ├── nmodl_constructs.hpp │ │ ├── string_utils.cpp │ │ ├── test_utils.cpp │ │ └── test_utils.hpp │ └── visitor │ │ ├── after_cvode_to_cnexp.cpp │ │ ├── constant_folder.cpp │ │ ├── cvode.cpp │ │ ├── defuse_analyze.cpp │ │ ├── external.cpp │ │ ├── global_to_range.cpp │ │ ├── implicit_argument.cpp │ │ ├── initial_block.cpp │ │ ├── inline.cpp │ │ ├── json.cpp │ │ ├── kinetic_block.cpp │ │ ├── local_to_assigned.cpp │ │ ├── localize.cpp │ │ ├── localrename.cpp │ │ ├── lookup.cpp │ │ ├── loop_unroll.cpp │ │ ├── main.cpp │ │ ├── misc.cpp │ │ ├── neuron_solve.cpp │ │ ├── nmodl.cpp │ │ ├── node_index.cpp │ │ ├── perf.cpp │ │ ├── rename.cpp │ │ ├── rename_function_arguments.cpp │ │ ├── semantic_analysis.cpp │ │ ├── solve_block.cpp │ │ ├── steadystate.cpp │ │ ├── sympy_conductance.cpp │ │ ├── sympy_solver.cpp │ │ ├── units.cpp │ │ ├── var_usage.cpp │ │ └── verbatim.cpp │ └── usecases │ ├── .gitignore │ ├── CMakeLists.txt │ ├── at_time │ ├── example.mod │ └── simulate.py │ ├── builtin_functions │ └── compile_only.mod │ ├── check_references.sh │ ├── constant │ ├── constant.mod │ └── test_constant.py │ ├── constructor │ ├── cvode │ ├── derivative.mod │ └── test_cvode.py │ ├── electrode_current │ ├── leonhard.mod │ └── simulate.py │ ├── external │ ├── dst.mod │ ├── src.mod │ └── test_external.py │ ├── function │ ├── artificial_functions.mod │ ├── compile_only.mod │ ├── functions.mod │ ├── localize_arguments.mod │ ├── point_functions.mod │ ├── recursion.mod │ ├── test_functions.py │ ├── test_localize_arguments.py │ └── test_recursion.py │ ├── function_table │ ├── art_function_table.mod │ ├── function_table.inc │ ├── function_table.mod │ ├── point_function_table.mod │ └── test_function_table.py │ ├── generate_references.py │ ├── global │ ├── global.mod │ ├── parameter.mod │ ├── read_only.mod │ ├── references.json │ ├── simulate.py │ ├── test_callables.py │ ├── test_read_only.py │ ├── test_thread_newton.py │ ├── test_top_local.py │ ├── test_without_instance.py │ ├── thread_newton.mod │ ├── threading_effects.mod │ └── top_local.mod │ ├── hodgkin_huxley │ ├── hodhux.mod │ └── simulate.py │ ├── kinetic │ ├── X2Y.mod │ ├── side_effects.mod │ ├── simulate.py │ └── test_side_effects.py │ ├── linear │ ├── lin.mod │ └── test_lin.py │ ├── longitudinal_diffusion │ ├── heat_eqn_array.mod │ ├── heat_eqn_function.mod │ ├── heat_eqn_global.mod │ ├── heat_eqn_scalar.mod │ ├── heat_eqn_thread_vars.mod │ └── test_heat_eqn.py │ ├── morphology │ ├── test_morphology.py │ └── two_radii.mod │ ├── net_event │ ├── receiver.mod │ ├── simulate.py │ └── spiker.mod │ ├── net_move │ ├── art_spiker.mod │ ├── simulate.py │ └── spiker.mod │ ├── net_receive │ ├── NetReceiveCalls.mod │ ├── for_netcons_syn.mod │ ├── initsyn.mod │ ├── simulate.py │ ├── snapsyn.mod │ ├── test_calls.py │ ├── test_for_netcons.py │ └── test_initial.py │ ├── net_send │ ├── art_toggle.mod │ ├── simulate.py │ └── toggle.mod │ ├── neuron_variables │ ├── neuron_variables.mod │ └── simulate.py │ ├── nonlinear │ ├── art_nonlin.mod │ ├── nonlin.mod │ └── test_nonlin.py │ ├── nonspecific_current │ ├── leonhard.mod │ └── simulate.py │ ├── parameter │ ├── default_parameter.mod │ ├── limits.mod │ ├── range_parameter.mod │ ├── test_default.py │ └── test_range_parameter.py │ ├── point_process │ ├── pp.mod │ └── test_point_process.py │ ├── pointer │ ├── basic_pointer.mod │ ├── point_basic.mod │ ├── pointing.mod │ ├── test_basic_pointer.py │ └── test_pointing.py │ ├── procedure │ ├── point_procedures.mod │ ├── procedures.mod │ └── test_procedures.py │ ├── protect │ ├── shared_counter.mod │ └── test_shared_counter.py │ ├── random │ ├── random_variable.mod │ └── test_random_variable.py │ ├── run_test.sh │ ├── solve │ ├── cnexp_array.mod │ ├── cnexp_scalar.mod │ ├── cnexp_to_derivimplicit.mod │ ├── derivimplicit_array.mod │ ├── derivimplicit_scalar.mod │ ├── finite_difference.mod │ ├── test_array.py │ ├── test_cnexp_to_derivimplicit.py │ ├── test_finite_difference.py │ └── test_scalar.py │ ├── spike_travel │ ├── expsyn2.mod │ ├── hodhux.mod │ └── simulate.py │ ├── state │ ├── default_values.mod │ └── test_default_values.py │ ├── steady_state │ ├── minipump.mod │ └── test_minipump.py │ ├── suffix │ ├── no_suffix.mod │ ├── point_suffix.mod │ ├── suffix_nothing.mod │ ├── suffix_nothing_again.mod │ ├── test_suffix.py │ └── test_suffix_nothing.py │ ├── table │ ├── simulate.py │ ├── table.mod │ └── table_point_process.mod │ ├── useion │ ├── ionic.mod │ ├── read_cai.mod │ ├── read_cao.mod │ ├── read_eca.mod │ ├── simulate.py │ ├── style_ion.mod │ ├── style_ion.py │ ├── test_read_cai.py │ ├── test_read_cao.py │ ├── test_valence.py │ ├── test_write_cai.py │ ├── test_write_cao.py │ ├── test_write_eca.py │ ├── valence.mod │ ├── write_cai.mod │ ├── write_cao.mod │ └── write_eca.mod │ ├── verbatim │ ├── globals.mod │ ├── internal_function.mod │ ├── locals.mod │ ├── nothing.mod │ ├── pointer_in_double.mod │ ├── test_globals.py │ ├── test_internal_function.py │ ├── test_locals.py │ ├── test_nothing.py │ └── test_pointer_in_double.py │ └── voltage │ ├── accessors.mod │ ├── ode.mod │ ├── state_ode.mod │ └── test_voltage.py ├── parallel_tests ├── test_bas.py └── test_subworld.py ├── pyinit ├── CMakeLists.txt ├── assert_false.py ├── assert_last_args_are_foo_and_bar.py ├── check_sys_attr.hoc ├── check_sys_attr.py ├── do_nothing.py └── dump_sys_attr.py ├── pytest ├── mcna.mod ├── test_nrntest_thread.json └── test_nrntest_thread.py ├── pytest_coreneuron ├── follower.mod ├── gap.mod ├── gui_pycallobject.py ├── name_clashes.mod ├── run_pytest.py ├── test_a_neuronoptions.py ├── test_basic.py ├── test_bbss.py ├── test_coreneuron_configuration.py ├── test_fast_imem.py ├── test_hoc_po.py ├── test_imem.py ├── test_inheritance.py ├── test_loadbal.py ├── test_memory_usage.py ├── test_multigid.py ├── test_netpar.py ├── test_nlayer.py ├── test_nrnste.py ├── test_nrntest_fast.json ├── test_nrntest_fast.py ├── test_partrans.py ├── test_py2nrnstring.py ├── test_pycallobject.py ├── test_pyobj.py ├── test_swc.py ├── test_template_err.py ├── test_vector_api.py ├── test_version_macros.py ├── test_zptrlist.py ├── unitstest.mod └── version_macros.mod ├── ringtest ├── cell.hoc ├── out.dat.ref └── ring.hoc ├── rxd ├── 3d │ ├── simple.asc │ ├── test_ics_currents.py │ ├── test_include_flux3d.py │ ├── test_multi_gridding_mix.py │ ├── test_multigeometry.py │ ├── test_multigridding_allowed.py │ ├── test_node_selection.py │ ├── test_pure_diffusion_3d.py │ ├── test_pure_diffusion_3d_anisotropic.py │ ├── test_region_sections.py │ ├── test_soma_outlines.py │ ├── test_surface_area.py │ └── test_volumes_areas.py ├── __init__.py ├── beforestep_py.mod ├── conftest.py ├── ecs │ ├── test_ecs_example.py │ ├── test_ecs_include_flux.py │ ├── test_ecs_init.py │ ├── test_ecs_multicompartment_alignment.py │ ├── test_ecs_pure_diffusion.py │ └── test_ecs_reinit.py ├── hybrid │ └── test_pure_diffusion_hybrid.py ├── pump.mod ├── test_arith_include_flux.py ├── test_contains.py ├── test_currents.py ├── test_distance.py ├── test_empty_regions.py ├── test_include_flux.py ├── test_multicompartment_reactions.py ├── test_multicompartment_reactions_aligment.py ├── test_nodelist.py ├── test_nodelist_include_flux.py ├── test_parameter_reaction.py ├── test_pltvar.py ├── test_pure_diffusion.py ├── test_rangevarplot.py ├── test_region_sections.py ├── test_region_volume.py ├── test_reinit.py ├── test_savestate.py ├── test_savestate_basic.py ├── test_species_del.py ├── test_species_exception.py ├── test_state_reaction.py ├── test_unicode_names.py └── testutils.py ├── 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