.gitignore
CMakeLists.txt
LICENSE.txt
PYCYTOSIM.md
README.md
WARRANTY.txt
makefile
makefile.inc
setup.py
cytoplay.egg-info/PKG-INFO
cytoplay.egg-info/SOURCES.txt
cytoplay.egg-info/dependency_links.txt
cytoplay.egg-info/not-zip-safe
cytoplay.egg-info/top_level.txt
pycytoplay/CMakeLists.txt
pycytoplay/package/__init__.py
pycytoplay/package/play
pycytoplay/package/sim
pycytoplay/package/sim_wrapper.py
pycytosim/CMakeLists.txt
python/index.md
python/look/collect.py
python/look/compare_config.py
python/look/get_data.py
python/look/make_image.py
python/look/make_movie.py
python/look/make_page.py
python/look/make_plots.py
python/look/read_config.py
python/look/scan.py
python/look/tell.py
python/misc/battery_test.py
python/misc/cleanup.py
python/misc/compare.py
python/misc/plot.py
python/misc/pyned.py
python/misc/reduce.py
python/run/go_sim.py
python/run/go_sim_lib.py
python/run/preconfig.py
python/run/submit_one.py
python/run/submit_slurm.py
src/CMakeLists.txt
src/index.md
src/base/CMakeLists.txt
src/base/array.h
src/base/assert_macro.h
src/base/backtrace.cc
src/base/backtrace.h
src/base/buddy.h
src/base/exceptions.cc
src/base/exceptions.h
src/base/filepath.cc
src/base/filepath.h
src/base/filewrapper.cc
src/base/filewrapper.h
src/base/glossary.cc
src/base/glossary.h
src/base/inventoried.h
src/base/inventory.cc
src/base/inventory.h
src/base/iowrapper.cc
src/base/iowrapper.h
src/base/makefile.inc
src/base/messages.cc
src/base/messages.h
src/base/node_list.cc
src/base/node_list.h
src/base/noder.h
src/base/operator_new.cc
src/base/print_color.cc
src/base/print_color.h
src/base/property.cc
src/base/property.h
src/base/property_list.cc
src/base/property_list.h
src/base/stream_func.cc
src/base/stream_func.h
src/base/tictoc.cc
src/base/tictoc.h
src/base/timer.h
src/base/tokenizer.cc
src/base/tokenizer.h
src/cpython/couple_modules.h
src/cpython/fiber_modules.h
src/cpython/glossary_modules.h
src/cpython/hand_modules.h
src/cpython/interface_modules.h
src/cpython/lattice_modules.h
src/cpython/meca_modules.h
src/cpython/object_modules.h
src/cpython/organizer_modules.h
src/cpython/point_modules.h
src/cpython/python_frame.h
src/cpython/python_utilities.h
src/cpython/simul_modules.h
src/cpython/single_modules.h
src/cpython/solid_modules.h
src/cpython/space_modules.h
src/cpython/thread_modules.h
src/disp/CMakeLists.txt
src/disp/display.cc
src/disp/display.h
src/disp/display1.cc
src/disp/display1.h
src/disp/display2.cc
src/disp/display2.h
src/disp/display3.cc
src/disp/display3.h
src/disp/display_prop.cc
src/disp/display_prop.h
src/disp/fiber_disp.cc
src/disp/fiber_disp.h
src/disp/glapp.cc
src/disp/glapp.h
src/disp/gle.cc
src/disp/gle.h
src/disp/gle_color.cc
src/disp/gle_color.h
src/disp/gle_color_list.cc
src/disp/gle_color_list.h
src/disp/glu_unproject.cc
src/disp/glut.h
src/disp/grid_display.cc
src/disp/grid_display.h
src/disp/line_disp.cc
src/disp/line_disp.h
src/disp/makefile.inc
src/disp/miniz.c
src/disp/miniz.h
src/disp/offscreen.cc
src/disp/offscreen.h
src/disp/offscreen_fbo.cc
src/disp/offscreen_glx.cc
src/disp/opengl.h
src/disp/point_disp.cc
src/disp/point_disp.h
src/disp/save_image.cc
src/disp/save_image.h
src/disp/spng.c
src/disp/spng.h
src/disp/view.cc
src/disp/view.h
src/disp/view_prop.cc
src/disp/view_prop.h
src/math/CMakeLists.txt
src/math/SFMT-avx2.h
src/math/SFMT-common.h
src/math/SFMT-params.h
src/math/SFMT-params19937.h
src/math/SFMT-sse2.h
src/math/SFMT.c
src/math/SFMT.h
src/math/accumulator.h
src/math/allocator.h
src/math/bicgstab.h
src/math/cblas.h
src/math/clapack.h
src/math/dgtsv.c
src/math/dim.h
src/math/evaluator.h
src/math/gmres.h
src/math/grid.h
src/math/grid_base.h
src/math/isometry.h
src/math/linear_operator.h
src/math/makefile.inc
src/math/matrix.cc
src/math/matrix.h
src/math/matrix11.cc
src/math/matrix11.h
src/math/matrix22.cc
src/math/matrix22.h
src/math/matrix33.cc
src/math/matrix33.h
src/math/matrix44.h
src/math/matrixbase.h
src/math/matsparse.cc
src/math/matsparse.h
src/math/matsparsesym.cc
src/math/matsparsesym.h
src/math/matsparsesym1.cc
src/math/matsparsesym1.h
src/math/matsparsesym2.cc
src/math/matsparsesym2.h
src/math/matsparsesymblk.cc
src/math/matsparsesymblk.h
src/math/monitor.h
src/math/platonic.cc
src/math/platonic.h
src/math/pointsonsphere.cc
src/math/pointsonsphere.h
src/math/polygon.cc
src/math/polygon.h
src/math/project_ellipse.cc
src/math/project_ellipse.h
src/math/quaternion.h
src/math/random.cc
src/math/random.h
src/math/random_vector.cc
src/math/random_vector.h
src/math/rasterizer.cc
src/math/rasterizer.h
src/math/real.h
src/math/simd.h
src/math/simd_print.h
src/math/smath.h
src/math/vecprint.h
src/math/vector.h
src/math/vector1.cc
src/math/vector1.h
src/math/vector2.cc
src/math/vector2.h
src/math/vector3.cc
src/math/vector3.h
src/math/vector4.cc
src/math/vector4.h
src/misc/check_dump.m
src/misc/installation/RtMidi.cpp
src/misc/installation/RtMidi.h
src/misc/installation/cytobuilder.cpp
src/misc/installation/cytomaster.cpp
src/misc/installation/makefile
src/misc/installation/rtmidi_c.cpp
src/misc/installation/rtmidi_c.h
src/misc/installation/builder/0-live.command
src/misc/installation/builder/config.cym
src/misc/installation/builder/config0.cym
src/misc/installation/builder/config1.cym
src/misc/installation/builder/config2.cym
src/misc/installation/builder/config3.cym
src/misc/installation/builder/config4.cym
src/misc/installation/builder/config5.cym
src/misc/installation/builder/config6.cym
src/misc/installation/builder/config7.cym
src/misc/installation/builder/config8.cym
src/misc/installation/builder/france.txt
src/misc/installation/cytomaster.xcodeproj/project.pbxproj
src/misc/installation/master/0-live.command
src/misc/installation/master/config0.cym
src/misc/installation/master/config1.cym
src/misc/installation/master/config2.cym
src/misc/installation/master/config4.cym
src/misc/installation/master/config6.cym
src/misc/installation/master/config7.cym
src/misc/installation/master/config8.cym
src/misc/installation/master/config9.cym
src/misc/installation/master/france.txt
src/play/CMakeLists.txt
src/play/makefile.inc
src/play/play.cc
src/play/play.h
src/play/play_keys.cc
src/play/play_menus.cc
src/play/play_mouse.cc
src/play/player.cc
src/play/player.h
src/play/player_disp.cc
src/play/player_prop.cc
src/play/player_prop.h
src/sim/CMakeLists.txt
src/sim/bead.cc
src/sim/bead.h
src/sim/bead_prop.cc
src/sim/bead_prop.h
src/sim/bead_set.cc
src/sim/bead_set.h
src/sim/chain.cc
src/sim/chain.h
src/sim/common.cc
src/sim/common.h
src/sim/couple.cc
src/sim/couple.h
src/sim/couple_prop.cc
src/sim/couple_prop.h
src/sim/couple_set.cc
src/sim/couple_set.h
src/sim/event.cc
src/sim/event.h
src/sim/event_set.cc
src/sim/event_set.h
src/sim/fiber.cc
src/sim/fiber.h
src/sim/fiber_grid.cc
src/sim/fiber_grid.h
src/sim/fiber_grid2.cc
src/sim/fiber_prop.cc
src/sim/fiber_prop.h
src/sim/fiber_segment.cc
src/sim/fiber_segment.h
src/sim/fiber_set.cc
src/sim/fiber_set.h
src/sim/fiber_site.cc
src/sim/fiber_site.h
src/sim/field.cc
src/sim/field.h
src/sim/field_prop.cc
src/sim/field_prop.h
src/sim/field_set.cc
src/sim/field_set.h
src/sim/field_values.h
src/sim/frame_reader.cc
src/sim/frame_reader.h
src/sim/hand.cc
src/sim/hand.h
src/sim/hand_monitor.cc
src/sim/hand_monitor.h
src/sim/hand_prop.cc
src/sim/hand_prop.h
src/sim/interface.cc
src/sim/interface.h
src/sim/interpolation.cc
src/sim/interpolation.h
src/sim/interpolation4.cc
src/sim/interpolation4.h
src/sim/lattice.cc
src/sim/lattice.h
src/sim/makefile.inc
src/sim/meca.cc
src/sim/meca.h
src/sim/meca1d.h
src/sim/meca_inter.cc
src/sim/mecable.cc
src/sim/mecable.h
src/sim/mecafil.cc
src/sim/mecafil.h
src/sim/mecafil_project.cc
src/sim/mecafil_projectmat.cc
src/sim/mecapoint.cc
src/sim/mecapoint.h
src/sim/modulo.cc
src/sim/modulo.h
src/sim/movable.cc
src/sim/movable.h
src/sim/object.cc
src/sim/object.h
src/sim/object_set.cc
src/sim/object_set.h
src/sim/organizer.cc
src/sim/organizer.h
src/sim/organizer_set.cc
src/sim/organizer_set.h
src/sim/parser.cc
src/sim/parser.h
src/sim/point_grid.cc
src/sim/point_grid.h
src/sim/sim.cc
src/sim/sim.h
src/sim/sim_thread.cc
src/sim/sim_thread.h
src/sim/simul.cc
src/sim/simul.h
src/sim/simul_custom.cc
src/sim/simul_file.cc
src/sim/simul_prop.cc
src/sim/simul_prop.h
src/sim/simul_report.cc
src/sim/simul_solve.cc
src/sim/simul_step.cc
src/sim/single.cc
src/sim/single.h
src/sim/single_prop.cc
src/sim/single_prop.h
src/sim/single_set.cc
src/sim/single_set.h
src/sim/solid.cc
src/sim/solid.h
src/sim/solid_prop.cc
src/sim/solid_prop.h
src/sim/solid_set.cc
src/sim/solid_set.h
src/sim/space.cc
src/sim/space.h
src/sim/space_prop.cc
src/sim/space_prop.h
src/sim/space_set.cc
src/sim/space_set.h
src/sim/sphere.cc
src/sim/sphere.h
src/sim/sphere_prop.cc
src/sim/sphere_prop.h
src/sim/sphere_set.cc
src/sim/sphere_set.h
src/sim/splash.cc
src/sim/splash.h
src/sim/couples/bridge.cc
src/sim/couples/bridge.h
src/sim/couples/bridge_prop.cc
src/sim/couples/bridge_prop.h
src/sim/couples/couple_long.cc
src/sim/couples/couple_long.h
src/sim/couples/crosslink.cc
src/sim/couples/crosslink.h
src/sim/couples/crosslink_long.cc
src/sim/couples/crosslink_long.h
src/sim/couples/crosslink_prop.cc
src/sim/couples/crosslink_prop.h
src/sim/couples/duo.cc
src/sim/couples/duo.h
src/sim/couples/duo_long.cc
src/sim/couples/duo_long.h
src/sim/couples/duo_prop.cc
src/sim/couples/duo_prop.h
src/sim/couples/fork.cc
src/sim/couples/fork.h
src/sim/couples/fork_prop.cc
src/sim/couples/fork_prop.h
src/sim/couples/shackle.cc
src/sim/couples/shackle.h
src/sim/couples/shackle_long.cc
src/sim/couples/shackle_long.h
src/sim/couples/shackle_prop.cc
src/sim/couples/shackle_prop.h
src/sim/fibers/classic_fiber.cc
src/sim/fibers/classic_fiber.h
src/sim/fibers/classic_fiber_prop.cc
src/sim/fibers/classic_fiber_prop.h
src/sim/fibers/dynamic_fiber.cc
src/sim/fibers/dynamic_fiber.h
src/sim/fibers/dynamic_fiber_prop.cc
src/sim/fibers/dynamic_fiber_prop.h
src/sim/fibers/growing_fiber.cc
src/sim/fibers/growing_fiber.h
src/sim/fibers/growing_fiber_prop.cc
src/sim/fibers/growing_fiber_prop.h
src/sim/fibers/treadmilling_fiber.cc
src/sim/fibers/treadmilling_fiber.h
src/sim/fibers/treadmilling_fiber_prop.cc
src/sim/fibers/treadmilling_fiber_prop.h
src/sim/hands/actor.cc
src/sim/hands/actor.h
src/sim/hands/actor_prop.cc
src/sim/hands/actor_prop.h
src/sim/hands/chewer.cc
src/sim/hands/chewer.h
src/sim/hands/chewer_prop.cc
src/sim/hands/chewer_prop.h
src/sim/hands/cutter.cc
src/sim/hands/cutter.h
src/sim/hands/cutter_prop.cc
src/sim/hands/cutter_prop.h
src/sim/hands/digit.cc
src/sim/hands/digit.h
src/sim/hands/digit_prop.cc
src/sim/hands/digit_prop.h
src/sim/hands/dynein.cc
src/sim/hands/dynein.h
src/sim/hands/dynein_prop.cc
src/sim/hands/dynein_prop.h
src/sim/hands/kinesin.cc
src/sim/hands/kinesin.h
src/sim/hands/kinesin_prop.cc
src/sim/hands/kinesin_prop.h
src/sim/hands/mighty.cc
src/sim/hands/mighty.h
src/sim/hands/mighty_prop.cc
src/sim/hands/mighty_prop.h
src/sim/hands/motor.cc
src/sim/hands/motor.h
src/sim/hands/motor_prop.cc
src/sim/hands/motor_prop.h
src/sim/hands/myosin.cc
src/sim/hands/myosin.h
src/sim/hands/myosin_prop.cc
src/sim/hands/myosin_prop.h
src/sim/hands/nucleator.cc
src/sim/hands/nucleator.h
src/sim/hands/nucleator_prop.cc
src/sim/hands/nucleator_prop.h
src/sim/hands/regulator.cc
src/sim/hands/regulator.h
src/sim/hands/regulator_prop.cc
src/sim/hands/regulator_prop.h
src/sim/hands/rescuer.cc
src/sim/hands/rescuer.h
src/sim/hands/rescuer_prop.cc
src/sim/hands/rescuer_prop.h
src/sim/hands/slider.cc
src/sim/hands/slider.h
src/sim/hands/slider_prop.cc
src/sim/hands/slider_prop.h
src/sim/hands/tracker.cc
src/sim/hands/tracker.h
src/sim/hands/tracker_prop.cc
src/sim/hands/tracker_prop.h
src/sim/hands/walker.cc
src/sim/hands/walker.h
src/sim/hands/walker_prop.cc
src/sim/hands/walker_prop.h
src/sim/organizers/aster.cc
src/sim/organizers/aster.h
src/sim/organizers/aster_prop.cc
src/sim/organizers/aster_prop.h
src/sim/organizers/bundle.cc
src/sim/organizers/bundle.h
src/sim/organizers/bundle_prop.cc
src/sim/organizers/bundle_prop.h
src/sim/organizers/fake.cc
src/sim/organizers/fake.h
src/sim/organizers/fake_prop.cc
src/sim/organizers/fake_prop.h
src/sim/organizers/nucleus.cc
src/sim/organizers/nucleus.h
src/sim/organizers/nucleus_prop.cc
src/sim/organizers/nucleus_prop.h
src/sim/singles/picket.cc
src/sim/singles/picket.h
src/sim/singles/picket_long.cc
src/sim/singles/picket_long.h
src/sim/singles/wrist.cc
src/sim/singles/wrist.h
src/sim/singles/wrist_long.cc
src/sim/singles/wrist_long.h
src/sim/spaces/space_banana.cc
src/sim/spaces/space_banana.h
src/sim/spaces/space_capsule.cc
src/sim/spaces/space_capsule.h
src/sim/spaces/space_cylinder.cc
src/sim/spaces/space_cylinder.h
src/sim/spaces/space_cylinderP.cc
src/sim/spaces/space_cylinderP.h
src/sim/spaces/space_cylinderZ.cc
src/sim/spaces/space_cylinderZ.h
src/sim/spaces/space_dice.cc
src/sim/spaces/space_dice.h
src/sim/spaces/space_ellipse.cc
src/sim/spaces/space_ellipse.h
src/sim/spaces/space_periodic.cc
src/sim/spaces/space_periodic.h
src/sim/spaces/space_polygon.cc
src/sim/spaces/space_polygon.h
src/sim/spaces/space_polygonZ.cc
src/sim/spaces/space_polygonZ.h
src/sim/spaces/space_ring.cc
src/sim/spaces/space_ring.h
src/sim/spaces/space_sphere.cc
src/sim/spaces/space_sphere.h
src/sim/spaces/space_square.cc
src/sim/spaces/space_square.h
src/sim/spaces/space_strip.cc
src/sim/spaces/space_strip.h
src/sim/spaces/space_torus.cc
src/sim/spaces/space_torus.h
src/test/CMakeLists.txt
src/test/makefile.inc
src/test/test.cc
src/test/test_blas.cc
src/test/test_code.cc
src/test/test_cxx.cc
src/test/test_dispatch.cc
src/test/test_gillespie.cc
src/test/test_glapp.cc
src/test/test_glos.cc
src/test/test_glut.cc
src/test/test_glut3D.cc
src/test/test_grid.cc
src/test/test_math.cc
src/test/test_matrix.cc
src/test/test_omp.cc
src/test/test_opengl.cc
src/test/test_pipe.cc
src/test/test_platonic.cc
src/test/test_quaternion.cc
src/test/test_random.cc
src/test/test_rasterizer.cc
src/test/test_signal.cc
src/test/test_simd.cc
src/test/test_sizeof.cc
src/test/test_solve.cc
src/test/test_space.cc
src/test/test_sphere.cc
src/test/test_string.cc
src/test/test_thread.cc
src/test/test_vbo.cc
src/tools/CMakeLists.txt
src/tools/cymart.cc
src/tools/frametool.cc
src/tools/makefile.inc
src/tools/pycytoplay.cc
src/tools/pycytosim.cc
src/tools/pycytosim.h
src/tools/reader.cc
src/tools/report.cc
src/tools/reportF.cc
src/tools/sieve.cc