├── .github └── workflows │ ├── pylint_on_pull_request.yml │ ├── pypi_publish.yaml │ ├── run-integration-tests.yml │ ├── run-unit-tests.yml │ ├── run_system_tests.yaml │ └── update-docs.yml ├── .gitignore ├── .graphics ├── SpatialPy_logo.png ├── SpatialPy_logo.svg ├── UNCASEAL_blue.png ├── US-NIH-NIGMS-Logo.png ├── US-NIH-NIGMS-Logo.svg ├── birth-death-example-plot.png ├── caltech-round.png ├── caltech-round.svg ├── stochss-logo.png ├── stochss-logo.svg ├── ucsb-seal-navy.jpg ├── uppsala-universitet-logo-svg-vector.png └── uppsala-universitet-logo-svg-vector.svg ├── .nojekyll ├── .pylintrc ├── AUTHORS ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── COPYRIGHT ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── _static │ ├── css │ │ └── spatialpy_alabaster_customizations.css │ ├── fonts │ │ ├── FiraCode-Retina.ttf │ │ └── Roboto-Regular.ttf │ └── img │ │ └── SpatialPy_logo.png ├── build │ └── html │ │ ├── .buildinfo │ │ ├── .doctrees │ │ ├── classes │ │ │ ├── spatialpy.core.doctree │ │ │ ├── spatialpy.doctree │ │ │ ├── spatialpy.solvers.doctree │ │ │ └── spatialpy.stochss.doctree │ │ ├── environment.pickle │ │ └── index.doctree │ │ ├── _modules │ │ ├── collections.html │ │ ├── index.html │ │ ├── plotly │ │ │ └── offline │ │ │ │ └── offline.html │ │ ├── scipy │ │ │ └── spatial │ │ │ │ └── kdtree.html │ │ └── spatialpy │ │ │ ├── core │ │ │ ├── boundarycondition.html │ │ │ ├── cleanup.html │ │ │ ├── datafunction.html │ │ │ ├── domain.html │ │ │ ├── geometry.html │ │ │ ├── initialcondition.html │ │ │ ├── lattice.html │ │ │ ├── model.html │ │ │ ├── parameter.html │ │ │ ├── reaction.html │ │ │ ├── result.html │ │ │ ├── spatialpyerror.html │ │ │ ├── species.html │ │ │ ├── timespan.html │ │ │ ├── transformation.html │ │ │ ├── visualization.html │ │ │ └── vtkreader.html │ │ │ ├── solvers │ │ │ ├── build_expression.html │ │ │ └── solver.html │ │ │ └── stochss │ │ │ └── stochss_export.html │ │ ├── _sources │ │ ├── classes │ │ │ ├── spatialpy.core.rst.txt │ │ │ ├── spatialpy.rst.txt │ │ │ ├── spatialpy.solvers.rst.txt │ │ │ └── spatialpy.stochss.rst.txt │ │ └── index.rst.txt │ │ ├── _static │ │ ├── _sphinx_javascript_frameworks_compat.js │ │ ├── alabaster.css │ │ ├── basic.css │ │ ├── css │ │ │ └── spatialpy_alabaster_customizations.css │ │ ├── custom.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── fonts │ │ │ ├── FiraCode-Retina.ttf │ │ │ └── Roboto-Regular.ttf │ │ ├── img │ │ │ └── SpatialPy_logo.png │ │ ├── jquery-3.5.1.js │ │ ├── jquery-3.6.0.js │ │ ├── jquery.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── sphinx_highlight.js │ │ ├── underscore-1.13.1.js │ │ └── underscore.js │ │ ├── classes │ │ ├── spatialpy.core.html │ │ ├── spatialpy.html │ │ ├── spatialpy.solvers.html │ │ └── spatialpy.stochss.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ └── searchindex.js ├── classes │ ├── spatialpy.core.rst │ ├── spatialpy.rst │ ├── spatialpy.solvers.rst │ └── spatialpy.stochss.rst ├── conf.py ├── index.rst └── make.bat ├── examples ├── 3D_Cylinder_Demo-lattice.ipynb ├── 3D_Cylinder_Demo.ipynb ├── Coral_Reef.ipynb ├── Domain_Files │ ├── GRN_Spatial.mesh.xml │ ├── GRN_Spatial.subdomains.txt │ ├── Gravity.webm │ ├── SpatialPy_Image.pkl │ ├── cylinder.xml │ └── hes1_mesh │ │ ├── cell.geo │ │ ├── cell.msh │ │ ├── cell_facet_region.xml │ │ └── cell_physical_region.xml ├── Gravity.ipynb ├── Hes1.ipynb ├── README.md ├── Start_Here.ipynb ├── Tests │ ├── 3D_Cylinder_Demo_Results_Check.ipynb │ ├── Boundary_Condition.ipynb │ ├── Compile_Time_Comparison.ipynb │ ├── Diffusion_Validation.ipynb │ ├── Mesh_Files │ │ ├── cube.geo │ │ └── cube.msh │ └── Read_Domain_Files.ipynb ├── Under_Construction │ ├── Bistable_Biochem_Elf_Ehrenberg.ipynb │ ├── Domain_Files │ │ ├── coli.msh │ │ └── mesh │ │ │ ├── coli.geo │ │ │ ├── coli.xml │ │ │ ├── coli_facet_region.xml │ │ │ └── coli_physical_region.xml │ ├── Lid driven cavity.ipynb │ ├── Natural_Convection.ipynb │ ├── Sploosh.ipynb │ ├── mincde.ipynb │ └── turing_pattern │ │ ├── new_turing_pattern.ipynb │ │ └── turing_pattern.ipynb ├── Weir.ipynb └── Yeast_Polarization │ ├── Cdc42.ipynb │ ├── G-Protein_1D.ipynb │ └── Polarisome_1D.ipynb ├── index.html ├── requirements.txt ├── run_coverage.sh ├── setup.cfg ├── setup.py ├── spatialpy ├── __init__.py ├── __version__.py ├── core │ ├── __init__.py │ ├── boundarycondition.py │ ├── cleanup.py │ ├── datafunction.py │ ├── domain.py │ ├── geometry.py │ ├── initialcondition.py │ ├── lattice.py │ ├── model.py │ ├── parameter.py │ ├── reaction.py │ ├── result.py │ ├── spatialpyerror.py │ ├── species.py │ ├── timespan.py │ ├── transformation.py │ ├── visualization.py │ └── vtkreader.py ├── solvers │ ├── __init__.py │ ├── build_expression.py │ ├── c_base │ │ └── ssa_sdpd-c-simulation-engine │ │ │ ├── build │ │ │ └── SConstruct │ │ │ ├── external │ │ │ └── ANN │ │ │ │ ├── Copyright.txt │ │ │ │ ├── License.txt │ │ │ │ ├── MS_Win32 │ │ │ │ ├── Ann.sln │ │ │ │ ├── Makefile │ │ │ │ ├── ann2fig │ │ │ │ │ └── ann2fig.vcproj │ │ │ │ ├── dll │ │ │ │ │ └── dll.vcproj │ │ │ │ ├── sample │ │ │ │ │ └── sample.vcproj │ │ │ │ └── test │ │ │ │ │ └── test.vcproj │ │ │ │ ├── Make-config │ │ │ │ ├── Makefile │ │ │ │ ├── ReadMe.txt │ │ │ │ ├── ann2fig │ │ │ │ ├── Makefile │ │ │ │ └── ann2fig.cpp │ │ │ │ ├── doc │ │ │ │ └── ANNmanual.pdf │ │ │ │ ├── include │ │ │ │ └── ANN │ │ │ │ │ ├── ANN.h │ │ │ │ │ ├── ANNperf.h │ │ │ │ │ └── ANNx.h │ │ │ │ ├── sample │ │ │ │ ├── Makefile │ │ │ │ ├── ann_sample.cpp │ │ │ │ ├── data.pts │ │ │ │ ├── query.pts │ │ │ │ └── sample.save │ │ │ │ ├── src │ │ │ │ ├── ANN.cpp │ │ │ │ ├── Makefile │ │ │ │ ├── SConscript │ │ │ │ ├── bd_fix_rad_search.cpp │ │ │ │ ├── bd_pr_search.cpp │ │ │ │ ├── bd_search.cpp │ │ │ │ ├── bd_tree.cpp │ │ │ │ ├── bd_tree.h │ │ │ │ ├── brute.cpp │ │ │ │ ├── kd_dump.cpp │ │ │ │ ├── kd_fix_rad_search.cpp │ │ │ │ ├── kd_fix_rad_search.h │ │ │ │ ├── kd_pr_search.cpp │ │ │ │ ├── kd_pr_search.h │ │ │ │ ├── kd_search.cpp │ │ │ │ ├── kd_search.h │ │ │ │ ├── kd_split.cpp │ │ │ │ ├── kd_split.h │ │ │ │ ├── kd_tree.cpp │ │ │ │ ├── kd_tree.h │ │ │ │ ├── kd_util.cpp │ │ │ │ ├── kd_util.h │ │ │ │ ├── perf.cpp │ │ │ │ ├── pr_queue.h │ │ │ │ └── pr_queue_k.h │ │ │ │ └── test │ │ │ │ ├── Makefile │ │ │ │ ├── ann_test.cpp │ │ │ │ ├── rand.cpp │ │ │ │ ├── rand.h │ │ │ │ ├── test1-data.pts │ │ │ │ ├── test1-query.pts │ │ │ │ ├── test1.in │ │ │ │ ├── test1.save │ │ │ │ ├── test2-data.pts │ │ │ │ ├── test2-query.pts │ │ │ │ ├── test2.in │ │ │ │ └── test2.save │ │ │ ├── include │ │ │ ├── NRMConstant_v5.hpp │ │ │ ├── count_cores.hpp │ │ │ ├── model.hpp │ │ │ ├── output.hpp │ │ │ ├── particle.hpp │ │ │ ├── particle_system.hpp │ │ │ ├── propensities.hpp │ │ │ ├── pthread_barrier.hpp │ │ │ ├── read_lammps_input_file.hpp │ │ │ ├── simulate.hpp │ │ │ └── simulate_rdme.hpp │ │ │ ├── propensity_file_template.cpp │ │ │ └── src │ │ │ ├── NRMConstant_v5.cpp │ │ │ ├── SConscript │ │ │ ├── count_cores.cpp │ │ │ ├── model.cpp │ │ │ ├── output.cpp │ │ │ ├── particle.cpp │ │ │ ├── pthread_barrier.cpp │ │ │ ├── read_lammps_input_file.cpp │ │ │ ├── simulate.cpp │ │ │ ├── simulate_rdme.cpp │ │ │ └── simulate_threads.cpp │ └── solver.py └── stochss │ ├── __init__.py │ └── stochss_export.py └── test ├── MinCDE test.ipynb ├── __init__.py ├── assets └── evaluate.c ├── integration_tests ├── __init__.py ├── test_mincde.py ├── test_model.py ├── test_solver.py └── test_threads.py ├── ioperformance.py ├── models ├── __init__.py ├── birth_death.py ├── cylinder_demo3D.py ├── data │ ├── coli.xml │ └── cylinder.xml ├── mincde.py └── mincde_5r.py ├── run_integration_tests.py ├── run_system_tests.py ├── run_unit_tests.py ├── system_tests ├── __init__.py └── test_compiler.py └── unit_tests ├── __init__.py ├── test_parameter.py ├── test_reaction.py ├── test_species.py └── test_timespan.py 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