-

Documentation for SpatialPy 1.2.0

+

Documentation for SpatialPy 1.2.1

SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems embedded in Lagrangian reference frame particle based fluid dynamics domain

This package is intended to replace the PyURDME software https://github.com/pyurdme/pyurdme and will feature both a NSM solver for RDME simulation on static domains and a sSSA-SDPD particle based fluid dynamics solver as described in the publication “A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection–diffusion–reaction problems” by Drawert, Jacob, Li, Yi, Petzold https://www.sciencedirect.com/science/article/pii/S0021999118307101

diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv index 269d44cd..b4acc45d 100644 Binary files a/docs/build/html/objects.inv and b/docs/build/html/objects.inv differ diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html index 084aae2c..35205203 100644 --- a/docs/build/html/py-modindex.html +++ b/docs/build/html/py-modindex.html @@ -5,7 +5,7 @@ - Python Module Index — SpatialPy 1.2.0 documentation + Python Module Index — SpatialPy 1.2.1 documentation diff --git a/docs/build/html/search.html b/docs/build/html/search.html index 9e7c6664..8a281b08 100644 --- a/docs/build/html/search.html +++ b/docs/build/html/search.html @@ -5,7 +5,7 @@ - Search — SpatialPy 1.2.0 documentation + Search — SpatialPy 1.2.1 documentation diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js index 1fbae23b..a94d8000 100644 --- a/docs/build/html/searchindex.js +++ b/docs/build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["classes/spatialpy", "classes/spatialpy.core", "classes/spatialpy.solvers", "classes/spatialpy.stochss", "index"], "filenames": ["classes/spatialpy.rst", "classes/spatialpy.core.rst", "classes/spatialpy.solvers.rst", "classes/spatialpy.stochss.rst", "index.rst"], "titles": ["spatialpy package", "spatialpy.core package", "spatialpy.solvers package", "spatialpy.stochss package", "Documentation for SpatialPy 1.2.0"], "terms": {"core": [0, 2, 3, 4], "submodul": 0, "boundarycondit": 0, "express": [0, 1, 2], "cleanup": 0, "cleanup_build_fil": [0, 1], "cleanup_core_fil": [0, 1], "cleanup_result_fil": [0, 1], "cleanup_tempfil": [0, 1], "datafunct": 0, "map": [0, 1, 2], "domain": [0, 4], "add_fill_act": [0, 1], "add_point": [0, 1], "add_remove_act": [0, 1], "add_set_act": [0, 1], "apply_act": [0, 1], "apply_fill_act": [0, 1], "apply_remove_act": [0, 1], "apply_set_act": [0, 1], "calculate_vol": [0, 1], "closest_vertex": [0, 1], "compile_prep": [0, 1], "coordin": [0, 1], "create_2d_domain": [0, 1], "create_3d_domain": [0, 1], "distance_between_2_vertic": [0, 1], "fill_with_particl": [0, 1], "find_boundary_point": [0, 1], "find_h": [0, 1], "get_bounding_box": [0, 1], "get_domain_s": [0, 1], "get_num_voxel": [0, 1], "get_type_def": [0, 1], "get_vol": [0, 1], "import_meshio_object": [0, 1], "plot_typ": [0, 1], "preview_act": [0, 1], "read_msh_fil": [0, 1], "read_stochss_domain": [0, 1], "read_stochss_subdomain_fil": [0, 1], "read_xml_mesh": [0, 1], "set_properti": [0, 1], "validate_act": [0, 1], "geometri": 0, "combinatorygeometri": [0, 1], "insid": [0, 1], "valid": [0, 1, 2], "geometryal": [0, 1], "geometryexterior": [0, 1], "geometryinterior": [0, 1], "initialcondit": 0, "appli": [0, 1], "placeinitialcondit": [0, 1], "scatterinitialcondit": [0, 1], "uniforminitialcondit": [0, 1], "lattic": 0, "cartesianlattic": [0, 1], "cylindricallattic": [0, 1], "meshiolattic": [0, 1], "sphericallattic": [0, 1], "stochsslattic": [0, 1], "xmlmeshlattic": [0, 1], "model": [0, 2, 3, 4], "add": [0, 1, 2], "add_boundary_condit": [0, 1], "add_data_funct": [0, 1], "add_domain": [0, 1], "add_initial_condit": [0, 1], "add_paramet": [0, 1], "add_react": [0, 1], "add_speci": [0, 1], "delete_all_boundary_condit": [0, 1], "delete_all_data_funct": [0, 1], "delete_all_initial_condit": [0, 1], "delete_all_paramet": [0, 1], "delete_all_react": [0, 1], "delete_all_speci": [0, 1], "delete_boundary_condit": [0, 1], "delete_data_funct": [0, 1], "delete_initial_condit": [0, 1], "delete_paramet": [0, 1], "delete_react": [0, 1], "delete_speci": [0, 1], "get_all_boundary_condit": [0, 1], "get_all_data_funct": [0, 1], "get_all_initial_condit": [0, 1], "get_all_paramet": [0, 1], "get_all_react": [0, 1], "get_all_speci": [0, 1], "get_data_funct": [0, 1], "get_el": [0, 1], "get_num_react": [0, 1], "get_num_speci": [0, 1], "get_paramet": [0, 1], "get_react": [0, 1], "get_speci": [0, 1], "reserved_nam": [0, 1], "run": [0, 1, 2], "sanitized_data_function_nam": [0, 1], "sanitized_parameter_nam": [0, 1], "sanitized_species_nam": [0, 1], "set_timestep": [0, 1], "special_charact": [0, 1], "timespan": 0, "update_namespac": [0, 1], "export_stochss": [0, 1], "paramet": [0, 2, 3], "reaction": [0, 4], "add_product": [0, 1], "annot": [0, 1], "from_json": [0, 1], "initi": [0, 1], "sanitized_propensity_funct": [0, 1], "set_annot": [0, 1], "set_propens": [0, 1], "set_rat": [0, 1], "to_dict": [0, 1], "result": [0, 2], "export_to_csv": [0, 1], "get_properti": [0, 1], "get_timespan": [0, 1], "plot_properti": [0, 1], "plot_speci": [0, 1], "read_step": [0, 1], "spatialpyerror": 0, "boundaryconditionerror": [0, 1], "datafunctionerror": [0, 1], "domainerror": [0, 1], "geometryerror": [0, 1], "initialconditionerror": [0, 1], "latticeerror": [0, 1], "modelerror": [0, 1], "parametererror": [0, 1], "reactionerror": [0, 1], "resulterror": [0, 1], "simulationerror": [0, 1, 2], "simulationtimeout": [0, 1, 2], "specieserror": [0, 1], "timespanerror": [0, 1], "transformationerror": [0, 1], "vtkreadererror": [0, 1], "vtkreaderioerror": [0, 1], "visualizationerror": [0, 1], "speci": 0, "set_diffusion_coeffici": [0, 1], "arang": [0, 1], "linspac": [0, 1], "transform": 0, "reflectiontransform": [0, 1], "reverse_transform": [0, 1], "rotationtransform": [0, 1], "scalingtransform": [0, 1], "translationtransform": [0, 1], "visual": 0, "mpl_height": [0, 1], "mpl_size": [0, 1], "mpl_width": [0, 1], "plot_scatt": [0, 1], "vtkreader": 0, "get_array_nam": [0, 1], "get_arrai": [0, 1], "get_num_point": [0, 1], "get_point": [0, 1], "read_fil": [0, 1], "set_filenam": [0, 1], "solver": [0, 1, 4], "build_express": 0, "buildexpress": [0, 2], "validationvisitor": [0, 2], "getexpr_cpp": [0, 2], "getexpr_python": [0, 2], "map_oper": [0, 2], "operator_map": [0, 2], "with_blacklist": [0, 2], "with_namespac": [0, 2], "cppconvert": [0, 2], "cppexpressiontransform": [0, 2], "get_str": [0, 2], "visit_and": [0, 2], "visit_or": [0, 2], "expressionconvert": [0, 2], "convert_str": [0, 2], "parse_comparison": [0, 2], "parse_log": [0, 2], "parse_oper": [0, 2], "visit_add": [0, 2], "visit_binop": [0, 2], "visit_boolop": [0, 2], "visit_byt": [0, 2], "visit_cal": [0, 2], "visit_compar": [0, 2], "visit_const": [0, 2], "visit_div": [0, 2], "visit_ellipsi": [0, 2], "visit_eq": [0, 2], "visit_gt": [0, 2], "visit_lt": [0, 2], "visit_mult": [0, 2], "visit_nam": [0, 2], "visit_nameconst": [0, 2], "visit_noteq": [0, 2], "visit_num": [0, 2], "visit_pow": [0, 2], "visit_str": [0, 2], "visit_sub": [0, 2], "visit_usub": [0, 2], "visit_unaryop": [0, 2], "expressionresult": [0, 2], "pythonconvert": [0, 2], "compil": [0, 1, 2], "stochss": [0, 1, 4], "stochss_export": 0, "export": [0, 1, 3], "class": [1, 2], "xmin": 1, "none": [1, 2, 3], "xmax": 1, "ymin": 1, "ymax": 1, "zmin": 1, "zmax": 1, "type_id": 1, "determinist": [1, 4], "true": [1, 2, 3], "target": [1, 2], "valu": [1, 2], "sourc": [1, 2, 3, 4], "base": [1, 2, 4], "object": [1, 2], "set": [1, 2], "spatial": [1, 2, 4], "region": 1, "where": 1, "properti": [1, 2], "particl": [1, 4], "ar": [1, 2], "held": 1, "constant": [1, 2], "updat": 1, "each": 1, "simul": [1, 2, 4], "step": 1, "condit": [1, 2], "one": [1, 2], "more": [1, 2, 4], "follow": [1, 2], "must": 1, "float": 1, "min": 1, "max": 1, "x": 1, "dimens": 1, "y": 1, "z": 1, "type": [1, 2, 3], "subdomain": 1, "partcil": 1, "str": [1, 2, 3], "nu": 1, "rho": 1, "v": 1, "name": [1, 2], "chemic": 1, "also": [1, 2, 4], "fals": [1, 2, 3], "flag": [1, 2], "axi": 1, "lower": 1, "bound": 1, "upper": 1, "int": [1, 2], "id": 1, "bool": [1, 2, 3], "i": [1, 2, 3, 4], "boundari": 1, "yet": 1, "implemenet": 1, "stochast": [1, 4], "can": [1, 2, 4], "If": [1, 2, 4], "determinst": 1, "3": [1, 4], "take": 1, "defin": [1, 2], "creat": [1, 2], "evalu": 1, "string": [1, 2], "return": [1, 2, 3], "A": [1, 2, 4], "represent": [1, 2], "build_dir": 1, "all": [1, 2], "spatialpy_build": 1, "directori": 1, "path": [1, 3], "build": [1, 2, 4], "remov": 1, "option": 1, "tempfil": 1, "result_dir": 1, "spatialpy_result": 1, "abstract": [1, 2], "us": [1, 2, 4], "constuct": 1, "data": [1, 2], "function": [1, 2], "rais": [1, 2], "provid": [1, 2, 4], "point": 1, "thi": [1, 2, 4], "method": [1, 2], "overridden": 1, "subclass": [1, 2], "note": [1, 2], "The": [1, 2, 4], "locat": 1, "evaul": 1, "t": [1, 2], "0": [1, 2], "re": 1, "fluid": [1, 4], "move": 1, "over": 1, "time": [1, 2], "posit": 1, "numpoint": 1, "xlim": 1, "ylim": 1, "zlim": 1, "rho0": 1, "1": [1, 2], "c0": 1, "10": 1, "p0": 1, "graviti": [1, 4], "action": 1, "attribut": 1, "space": 1, "total": 1, "number": [1, 2], "2": 1, "rang": 1, "along": 1, "background": 1, "densiti": 1, "system": [1, 4], "speed": 1, "sound": 1, "pressur": 1, "acceler": 1, "cartesian": 1, "spheric": 1, "cylindr": 1, "enabl": 1, "prop": 1, "an": [1, 2, 4], "when": [1, 2], "fill": [1, 4], "default": 1, "dict": [1, 2, 3], "argument": 1, "ignor": 1, "indic": [1, 2], "els": [1, 3], "addit": [1, 2], "pass": [1, 2], "ad": [1, 2], "wasn": 1, "could": [1, 2], "construct": 1, "vol": 1, "mass": 1, "unassign": 1, "fix": 1, "c": [1, 2], "singl": [1, 2], "vertic": 1, "volum": 1, "cradded": 1, "viscos": 1, "artifici": 1, "contain": [1, 2], "invalid": [1, 2], "charact": 1, "from": [1, 2], "start": [1, 2, 4], "end": 1, "preserve_act": 1, "order": 1, "index": [1, 4], "inclus": 1, "exclus": 1, "after": 1, "its": 1, "support": [1, 4], "within": 1, "have": 1, "exampl": 1, "lattice_obj": 1, "geometry_obj": 1, "miss": 1, "calcul": 1, "find": [1, 4], "nearest": 1, "vertex": 1, "given": [1, 2], "gener": [1, 4], "list": [1, 2], "check": [1, 2], "preper": 1, "file": [1, 3], "get": [1, 2], "numpi": 1, "arrai": 1, "classmethod": [1, 2], "numx": 1, "numi": 1, "kwarg": 1, "2d": 1, "highest": 1, "lowest": 1, "keyword": 1, "uniform": 1, "numz": 1, "3d": [1, 4], "distanc": 1, "between": [1, 2], "measur": 1, "geometry_ivar": 1, "deltax": 1, "deltai": 1, "deltaz": 1, "geometr": 1, "shape": 1, "instanc": [1, 2], "minimum": 1, "box": 1, "maximum": [1, 2], "were": [1, 2], "exist": 1, "np": 1, "ndarrai": 1, "dtype": 1, "h": 1, "off": 1, "which": [1, 2], "ha": [1, 4], "greatest": 1, "neighbor": 1, "entir": 1, "limit": 1, "tupl": 1, "estim": 1, "size": 1, "averag": 1, "diamet": 1, "circumradiu": 1, "tetrahedron": 1, "part": 1, "mean": 1, "incid": 1, "cell": 1, "voxel": 1, "definit": 1, "mesh_obj": 1, "subdomain_fil": 1, "import": 1, "python": [1, 2, 4], "meshio": 1, "mesh": 1, "v1": 1, "descript": 1, "filenam": [1, 3], "indeci": 1, "width": 1, "height": 1, "colormap": 1, "titl": 1, "included_types_list": 1, "use_matplotlib": 1, "return_plotly_figur": 1, "plot": 1, "plotli": 1, "onli": [1, 2], "view": 1, "jupyt": 1, "notebook": [1, 4], "pixel": 1, "output": [1, 2], "matplotlib": 1, "inch": 1, "500": 1, "specif": 1, "plotly3": 1, "jet": 1, "blue": 1, "ylorrd": 1, "purd": 1, "bugn": 1, "ylorbr": 1, "pubugn": 1, "bupu": 1, "ylgnbu": 1, "pubu": 1, "gnbu": 1, "ylgn": 1, "green": 1, "red": 1, "grei": 1, "rdpu": 1, "orrd": 1, "purpl": 1, "orang": 1, "graph": 1, "describ": [1, 4], "includ": 1, "By": [1, 2], "displai": 1, "whether": [1, 2, 3], "figur": 1, "dictionari": [1, 2], "trace": 1, "layout": 1, "mai": 1, "edit": 1, "user": [1, 4], "proprti": 1, "preview": 1, "effect": 1, "read": 1, "gmsh": 1, "style": 1, "msh": 1, "domn": 1, "pull": 1, "smdl": 1, "txt": 1, "conain": 1, "fenic": 1, "dolfin": 1, "xml": 1, "assign": [1, 2], "identifi": [1, 2], "immobil": 1, "coverag": 1, "scope": 1, "accept": [1, 2], "doaminerror": 1, "met": 1, "": [1, 4], "formula": 1, "geo_namespac": 1, "combinatori": 1, "multipl": [1, 2], "boolean": 1, "logic": [1, 2], "geo1": 1, "geo2": 1, "geo3": 1, "namespac": [1, 2], "geometry1": 1, "geometry2": 1, "geometry3": 1, "found": [1, 2, 4], "on_boundari": 1, "coodin": 1, "edg": 1, "satisfi": 1, "geometi": 1, "ani": [1, 2, 4], "doe": 1, "tag": 1, "separ": 1, "mark": 1, "work": 1, "triangl": 1, "implement": [1, 2], "direct": 1, "modifi": 1, "u0": 1, "matrix": 1, "count": 1, "contian": 1, "place": 1, "scatter": 1, "randomli": 1, "center": 1, "two": [1, 2], "doesn": 1, "restrict": 1, "depend": 1, "radiu": 1, "length": 1, "delta": 1, "deltar": 1, "surfac": 1, "radial": 1, "skip_valid": 1, "arg": 1, "io": 1, "un": 1, "biochem": 1, "compon": 1, "befor": 1, "other": [1, 2], "combin": 1, "than": 1, "do": 1, "need": [1, 4], "particular": 1, "bound_cond": 1, "conidit": 1, "data_funct": 1, "scalar": 1, "you": [1, 4], "vari": 1, "input": 1, "your": [1, 4], "It": 1, "positon": 1, "toth": 1, "init_cond": 1, "fail": [1, 2], "make": 1, "sure": 1, "paramt": 1, "diffus": [1, 4], "util": 1, "stoichiometr": 1, "dependency_graph": 1, "timestep": 1, "exce": 1, "frequenc": 1, "ordereddict": 1, "form": [1, 4], "kei": [1, 2], "specifi": 1, "element": 1, "differ": [1, 2], "rname": [], "number_of_trajectori": [1, 2], "seed": [1, 2], "timeout": [1, 2], "number_of_thread": [1, 2], "debug_level": [1, 2], "debug": [1, 2], "profil": [1, 2], "how": [1, 2, 4], "mani": [1, 2], "trajectori": [1, 2], "should": [1, 2], "random": [1, 2], "second": [1, 2], "kill": 1, "upon": 1, "reach": 1, "thread": [1, 2], "level": [1, 2], "print": [1, 2], "out": [1, 4], "info": 1, "dure": [1, 2], "addtion": [1, 2], "perform": 1, "chosen": 1, "simplifi": 1, "format": 1, "later": [1, 2], "spatialpysolv": 1, "propens": 1, "intern": 1, "notat": 1, "output_interv": 1, "num_step": 1, "timestep_s": 1, "simlat": 1, "span": 1, "first": [1, 2], "zero": 1, "time_span": 1, "ssa": 1, "sdpd": [1, 4], "engin": 1, "non": 1, "tspan": 1, "evenli": 1, "sampl": 1, "popul": 1, "flatten": 1, "spatialpy_model": 1, "return_stochss_model": [1, 3], "convert": [1, 2, 3], "json": 1, "platform": 1, "directli": [1, 4], "understood": 1, "parent": 1, "call": [1, 2], "referenc": 1, "requir": 1, "outsid": 1, "reactant": 1, "product": 1, "propensity_funct": 1, "ode_propensity_funct": 1, "rate": 1, "restrict_to": 1, "conatain": 1, "neg": 1, "union": 1, "For": [1, 4], "zeroth": 1, "attempt": 1, "higher": 1, "error": 1, "consum": 1, "stoichiometri": 1, "would": 1, "r1": 1, "r2": 1, "event": 1, "same": 1, "custom": 1, "oper": [1, 2], "od": 1, "care": 1, "unit": 1, "about": 1, "execut": [1, 2], "NOT": 1, "both": [1, 4], "term": 1, "repres": 1, "independ": 1, "wa": 1, "impact": 1, "preserv": 1, "produc": 1, "particip": 1, "deprec": 1, "param": 1, "json_object": 1, "defer": 1, "species_map": 1, "parameter_map": 1, "chang": 1, "marat": 1, "urdm": 1, "folder_nam": 1, "write": 1, "csv": 1, "modelname_mesh": 1, "modelname_species_": 1, "column": 1, "n": 1, "vtk": 1, "written": 1, "current": [1, 2], "property_nam": 1, "timepoint": 1, "integ": 1, "1d": 1, "veloc": 1, "bvf_phi": 1, "fraction": 1, "across": 1, "concentr": 1, "retreiv": 1, "inform": [1, 2, 4], "raw": 1, "copy_numb": 1, "unabl": 1, "retriev": 1, "t_ndx": 1, "t_val": 1, "p_ndx": 1, "anim": 1, "t_ndx_list": 1, "f_durat": 1, "t_durat": 1, "300": 1, "6": 1, "4": 1, "8": 1, "indec": 1, "interv": 1, "durat": 1, "frame": [1, 4], "transit": 1, "5": 1, "show": 1, "instead": 1, "step_num": 1, "except": 1, "initailcondit": 1, "bass": 1, "messag": 1, "o": 1, "diffusion_coeffici": 1, "coeffic": 1, "coeffici": 1, "listoftyp": 1, "movement": 1, "setter": 1, "item": [1, 2], "iter": 1, "best": 1, "increment": [1, 2], "20": 1, "num_point": 1, "empti": [1, 2], "repeat": 1, "point1": 1, "normal": 1, "point2": 1, "point3": 1, "reflect": 1, "revers": 1, "around": 1, "arbitrari": 1, "plane": 1, "serv": 1, "vector": 1, "onc": 1, "wrap": 1, "prior": 1, "angl": 1, "rotat": 1, "basic": 1, "factor": 1, "scale": 1, "wrapper": 1, "translat": 1, "40": 1, "plot_arg": 1, "scatter_arg": 1, "multiple_graph": 1, "maplotlib": 1, "pyplot": 1, "subplot": 1, "dist": 1, "group": 1, "nrow": 1, "ncol": 1, "entri": 1, "plote": 1, "py": 1, "minim": 1, "legaci": 1, "reader": 1, "refer": 1, "http": [1, 4], "org": 1, "wp": 1, "upload": 1, "2015": 1, "04": 1, "pdf": 1, "arraid": 1, "ascii": 1, "blacklist": 2, "sanit": 2, "allow": 2, "pre": 2, "flight": 2, "syntax": 2, "well": 2, "manag": 2, "context": 2, "statement": 2, "expect": 2, "forward": 2, "ideal": 2, "univers": 2, "constructor": 2, "granular": 2, "bare": 2, "equival": 2, "trigger": 2, "substitut": 2, "convers": 2, "automat": 2, "correspond": 2, "getexpr_": 2, "nodetransform": 2, "ast": 2, "expres": 2, "spactialpi": 2, "node": 2, "visit_assign": 2, "visitor": 2, "origin": 2, "binop": 2, "boolop": 2, "binboolopop": 2, "otherwis": 2, "compar": 2, "unaryop": 2, "syntaxerror": 2, "imposs": 2, "convet": 2, "built": 2, "_ast": 2, "Not": 2, "noteq": 2, "mod": 2, "bitand": 2, "mult": 2, "pow": 2, "sub": 2, "div": 2, "floordiv": 2, "lt": 2, "lshift": 2, "lte": 2, "eq": 2, "gt": 2, "gte": 2, "rshift": 2, "matmult": 2, "bitxor": 2, "And": 2, "Or": 2, "bitor": 2, "so": 2, "far": 2, "ensur": 2, "pars": 2, "against": 2, "addition": 2, "reject": 2, "rvalu": 2, "new": 2, "duplic": 2, "overrid": 2, "handl": 2, "behavior": 2, "copi": 2, "rtype": 2, "present": 2, "caus": 2, "what": 2, "tree": 2, "super": 2, "nodevisitor": 2, "self": 2, "comparison": 2, "last": 2, "mathemat": 2, "right": 2, "visit": 2, "left": 2, "most": 2, "recent": 2, "append": 2, "token": 2, "alwai": 2, "hand": 2, "u": 2, "pop": 2, "process": 2, "assum": 2, "inherit": 2, "byte": 2, "ellipsi": 2, "nameconst": 2, "num": 2, "usub": 2, "invalid_nam": 2, "invalid_oper": 2, "is_valid": 2, "struct": 2, "infer": 2, "invalid_": 2, "verbos": 2, "gdbgui": 2, "debugg": 2, "symbol": 2, "hasn": 2, "happen": 2, "gprof": 2, "avail": [2, 4], "consol": 2, "seri": 2, "exceed": 2, "packag": 4, "advect": 4, "problem": 4, "embed": 4, "lagrangian": 4, "dynam": 4, "intend": 4, "replac": 4, "pyurdm": 4, "softwar": 4, "github": 4, "com": 4, "featur": 4, "nsm": 4, "rdme": 4, "static": 4, "sssa": 4, "public": 4, "hybrid": 4, "smooth": 4, "dissip": 4, "algorithm": 4, "drawert": 4, "jacob": 4, "li": 4, "yi": 4, "petzold": 4, "www": 4, "sciencedirect": 4, "scienc": 4, "articl": 4, "pii": 4, "s0021999118307101": 4, "latest": 4, "version": 4, "pypi": 4, "code": 4, "licens": 4, "under": 4, "gnu": 4, "pleas": 4, "regist": 4, "develop": 4, "fund": 4, "nih": 4, "grant": 4, "2r01eb014877": 4, "continu": 4, "we": 4, "prove": 4, "our": 4, "short": 4, "registr": 4, "see": 4, "here": 4, "cylind": 4, "demo": 4, "physic": 4, "flow": 4, "weir": 4, "tracker": 4, "project": 4, "contact": 4, "main": 4, "author": 4, "dr": 4, "brian": 4, "question": 4, "suggest": 4, "subpackag": 4, "modul": 4, "content": 4, "search": 4, "page": 4, "allow_all_typ": 1}, "objects": {"": [[0, 0, 0, "-", "spatialpy"]], "spatialpy": [[1, 0, 0, "-", "core"], [2, 0, 0, "-", "solvers"], [3, 0, 0, "-", "stochss"]], "spatialpy.core": [[1, 1, 1, "", "BoundaryCondition"], [1, 3, 1, "", "BoundaryConditionError"], [1, 1, 1, "", "CartesianLattice"], [1, 1, 1, "", "CombinatoryGeometry"], [1, 1, 1, "", "CylindricalLattice"], [1, 1, 1, "", "DataFunction"], [1, 3, 1, "", "DataFunctionError"], [1, 1, 1, "", "Domain"], [1, 3, 1, "", "DomainError"], [1, 1, 1, "", "Geometry"], [1, 1, 1, "", "GeometryAll"], [1, 3, 1, "", "GeometryError"], [1, 1, 1, "", "GeometryExterior"], [1, 1, 1, "", "GeometryInterior"], [1, 1, 1, "", "InitialCondition"], [1, 3, 1, "", "InitialConditionError"], [1, 3, 1, "", "LatticeError"], [1, 1, 1, "", "MeshIOLattice"], [1, 1, 1, "", "Model"], [1, 3, 1, "", "ModelError"], [1, 1, 1, "", "Parameter"], [1, 3, 1, "", "ParameterError"], [1, 1, 1, "", "PlaceInitialCondition"], [1, 1, 1, "", "Reaction"], [1, 3, 1, "", "ReactionError"], [1, 1, 1, "", "ReflectionTransformation"], [1, 1, 1, "", "Result"], [1, 3, 1, "", "ResultError"], [1, 1, 1, "", "RotationTransformation"], [1, 1, 1, "", "ScalingTransformation"], [1, 1, 1, "", "ScatterInitialCondition"], [1, 3, 1, "", "SimulationError"], [1, 3, 1, "", "SimulationTimeout"], [1, 1, 1, "", "Species"], [1, 3, 1, "", "SpeciesError"], [1, 1, 1, "", "SphericalLattice"], [1, 1, 1, "", "StochSSLattice"], [1, 1, 1, "", "TimeSpan"], [1, 3, 1, "", "TimespanError"], [1, 1, 1, "", "Transformation"], [1, 3, 1, "", "TransformationError"], [1, 1, 1, "", "TranslationTransformation"], [1, 1, 1, "", "UniformInitialCondition"], [1, 1, 1, "", "VTKReader"], [1, 3, 1, "", "VTKReaderError"], [1, 3, 1, "", "VTKReaderIOError"], [1, 1, 1, "", "Visualization"], [1, 3, 1, "", "VisualizationError"], [1, 1, 1, "", "XMLMeshLattice"], [1, 0, 0, "-", "boundarycondition"], [1, 0, 0, "-", "cleanup"], [1, 5, 1, "", "cleanup_build_files"], [1, 5, 1, "", "cleanup_core_files"], [1, 5, 1, "", "cleanup_result_files"], [1, 5, 1, "", "cleanup_tempfiles"], [1, 0, 0, "-", "datafunction"], [1, 0, 0, "-", "domain"], [1, 5, 1, "", "export_StochSS"], [1, 0, 0, "-", "geometry"], [1, 0, 0, "-", "initialcondition"], [1, 0, 0, "-", "lattice"], [1, 0, 0, "-", "model"], [1, 0, 0, "-", "parameter"], [1, 0, 0, "-", "reaction"], [1, 0, 0, "-", "result"], [1, 0, 0, "-", "spatialpyerror"], [1, 0, 0, "-", "species"], [1, 0, 0, "-", "timespan"], [1, 0, 0, "-", "transformation"], [1, 0, 0, "-", "visualization"], [1, 0, 0, "-", "vtkreader"]], "spatialpy.core.BoundaryCondition": [[1, 2, 1, "", "expression"]], "spatialpy.core.CartesianLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.CombinatoryGeometry": [[1, 2, 1, "", "inside"], [1, 2, 1, "", "validate"]], "spatialpy.core.CylindricalLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.DataFunction": [[1, 2, 1, "", "map"]], "spatialpy.core.Domain": [[1, 2, 1, "", "add_fill_action"], [1, 2, 1, "", "add_point"], [1, 2, 1, "", "add_remove_action"], [1, 2, 1, "", "add_set_action"], [1, 2, 1, "", "apply_actions"], [1, 2, 1, "", "apply_fill_action"], [1, 2, 1, "", "apply_remove_action"], [1, 2, 1, "", "apply_set_action"], [1, 2, 1, "", "calculate_vol"], [1, 2, 1, "", "closest_vertex"], [1, 2, 1, "", "compile_prep"], [1, 2, 1, "", "coordinates"], [1, 2, 1, "", "create_2D_domain"], [1, 2, 1, "", "create_3D_domain"], [1, 2, 1, "", "distance_between_2_vertices"], [1, 2, 1, "", "fill_with_particles"], [1, 2, 1, "", "find_boundary_points"], [1, 2, 1, "", "find_h"], [1, 2, 1, "", "get_bounding_box"], [1, 2, 1, "", "get_domain_size"], [1, 2, 1, "", "get_num_voxels"], [1, 2, 1, "", "get_type_def"], [1, 2, 1, "", "get_vol"], [1, 2, 1, "", "import_meshio_object"], [1, 2, 1, "", "plot_types"], [1, 2, 1, "", "preview_actions"], [1, 2, 1, "", "read_msh_file"], [1, 2, 1, "", "read_stochss_domain"], [1, 2, 1, "", "read_stochss_subdomain_file"], [1, 2, 1, "", "read_xml_mesh"], [1, 2, 1, "", "set_properties"], [1, 2, 1, "", "validate_action"]], "spatialpy.core.Geometry": [[1, 2, 1, "", "inside"]], "spatialpy.core.GeometryAll": [[1, 2, 1, "", "inside"]], "spatialpy.core.GeometryExterior": [[1, 2, 1, "", "inside"]], "spatialpy.core.GeometryInterior": [[1, 2, 1, "", "inside"]], "spatialpy.core.InitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.MeshIOLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.Model": [[1, 2, 1, "", "add"], [1, 2, 1, "", "add_boundary_condition"], [1, 2, 1, "", "add_data_function"], [1, 2, 1, "", "add_domain"], [1, 2, 1, "", "add_initial_condition"], [1, 2, 1, "", "add_parameter"], [1, 2, 1, "", "add_reaction"], [1, 2, 1, "", "add_species"], [1, 2, 1, "", "compile_prep"], [1, 2, 1, "", "delete_all_boundary_conditions"], [1, 2, 1, "", "delete_all_data_functions"], [1, 2, 1, "", "delete_all_initial_conditions"], [1, 2, 1, "", "delete_all_parameters"], [1, 2, 1, "", "delete_all_reactions"], [1, 2, 1, "", "delete_all_species"], [1, 2, 1, "", "delete_boundary_condition"], [1, 2, 1, "", "delete_data_function"], [1, 2, 1, "", "delete_initial_condition"], [1, 2, 1, "", "delete_parameter"], [1, 2, 1, "", "delete_reaction"], [1, 2, 1, "", "delete_species"], [1, 2, 1, "", "get_all_boundary_conditions"], [1, 2, 1, "", "get_all_data_functions"], [1, 2, 1, "", "get_all_initial_conditions"], [1, 2, 1, "", "get_all_parameters"], [1, 2, 1, "", "get_all_reactions"], [1, 2, 1, "", "get_all_species"], [1, 2, 1, "", "get_data_function"], [1, 2, 1, "", "get_element"], [1, 2, 1, "", "get_num_reactions"], [1, 2, 1, "", "get_num_species"], [1, 2, 1, "", "get_parameter"], [1, 2, 1, "", "get_reaction"], [1, 2, 1, "", "get_species"], [1, 4, 1, "", "reserved_names"], [1, 2, 1, "", "run"], [1, 2, 1, "", "sanitized_data_function_names"], [1, 2, 1, "", "sanitized_parameter_names"], [1, 2, 1, "", "sanitized_species_names"], [1, 2, 1, "", "set_timesteps"], [1, 4, 1, "", "special_characters"], [1, 2, 1, "", "timespan"], [1, 2, 1, "", "update_namespace"]], "spatialpy.core.Parameter": [[1, 2, 1, "", "validate"]], "spatialpy.core.PlaceInitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.Reaction": [[1, 2, 1, "", "add_product"], [1, 2, 1, "", "add_reactant"], [1, 2, 1, "", "annotate"], [1, 2, 1, "", "from_json"], [1, 2, 1, "", "initialize"], [1, 2, 1, "", "sanitized_propensity_function"], [1, 2, 1, "", "set_annotation"], [1, 2, 1, "", "set_propensities"], [1, 2, 1, "", "set_rate"], [1, 2, 1, "", "to_dict"], [1, 2, 1, "", "validate"]], "spatialpy.core.ReflectionTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"]], "spatialpy.core.Result": [[1, 2, 1, "", "export_to_csv"], [1, 2, 1, "", "get_property"], [1, 2, 1, "", "get_species"], [1, 2, 1, "", "get_timespan"], [1, 2, 1, "", "plot_property"], [1, 2, 1, "", "plot_species"], [1, 2, 1, "", "read_step"]], "spatialpy.core.RotationTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.ScalingTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.ScatterInitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.Species": [[1, 2, 1, "", "set_diffusion_coefficient"], [1, 2, 1, "", "validate"]], "spatialpy.core.SphericalLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.StochSSLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.TimeSpan": [[1, 2, 1, "", "arange"], [1, 2, 1, "", "linspace"], [1, 2, 1, "", "validate"]], "spatialpy.core.Transformation": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "inside"], [1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.TranslationTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.UniformInitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.VTKReader": [[1, 2, 1, "", "get_array_name"], [1, 2, 1, "", "get_arrays"], [1, 2, 1, "", "get_num_points"], [1, 2, 1, "", "get_points"], [1, 2, 1, "", "read_file"], [1, 2, 1, "", "set_filename"]], "spatialpy.core.Visualization": [[1, 4, 1, "", "MPL_HEIGHT"], [1, 4, 1, "", "MPL_SIZE"], [1, 4, 1, "", "MPL_WIDTH"], [1, 2, 1, "", "plot_scatter"]], "spatialpy.core.XMLMeshLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.boundarycondition": [[1, 1, 1, "", "BoundaryCondition"]], "spatialpy.core.boundarycondition.BoundaryCondition": [[1, 2, 1, "", "expression"]], "spatialpy.core.cleanup": [[1, 5, 1, "", "cleanup_build_files"], [1, 5, 1, "", "cleanup_core_files"], [1, 5, 1, "", "cleanup_result_files"], [1, 5, 1, "", "cleanup_tempfiles"]], "spatialpy.core.datafunction": [[1, 1, 1, "", "DataFunction"]], "spatialpy.core.datafunction.DataFunction": [[1, 2, 1, "", "map"]], "spatialpy.core.domain": [[1, 1, 1, "", "Domain"]], "spatialpy.core.domain.Domain": [[1, 2, 1, "", "add_fill_action"], [1, 2, 1, "", "add_point"], [1, 2, 1, "", "add_remove_action"], [1, 2, 1, "", "add_set_action"], [1, 2, 1, "", "apply_actions"], [1, 2, 1, "", "apply_fill_action"], [1, 2, 1, "", "apply_remove_action"], [1, 2, 1, "", "apply_set_action"], [1, 2, 1, "", "calculate_vol"], [1, 2, 1, "", "closest_vertex"], [1, 2, 1, "", "compile_prep"], [1, 2, 1, "", "coordinates"], [1, 2, 1, "", "create_2D_domain"], [1, 2, 1, "", "create_3D_domain"], [1, 2, 1, "", "distance_between_2_vertices"], [1, 2, 1, "", "fill_with_particles"], [1, 2, 1, "", "find_boundary_points"], [1, 2, 1, "", "find_h"], [1, 2, 1, "", "get_bounding_box"], [1, 2, 1, "", "get_domain_size"], [1, 2, 1, "", "get_num_voxels"], [1, 2, 1, "", "get_type_def"], [1, 2, 1, "", "get_vol"], [1, 2, 1, "", "import_meshio_object"], [1, 2, 1, "", "plot_types"], [1, 2, 1, "", "preview_actions"], [1, 2, 1, "", "read_msh_file"], [1, 2, 1, "", "read_stochss_domain"], [1, 2, 1, "", "read_stochss_subdomain_file"], [1, 2, 1, "", "read_xml_mesh"], [1, 2, 1, "", "set_properties"], [1, 2, 1, "", "validate_action"]], "spatialpy.core.geometry": [[1, 1, 1, "", "CombinatoryGeometry"], [1, 1, 1, "", "Geometry"], [1, 1, 1, "", "GeometryAll"], [1, 1, 1, "", "GeometryExterior"], [1, 1, 1, "", "GeometryInterior"]], "spatialpy.core.geometry.CombinatoryGeometry": [[1, 2, 1, "", "inside"], [1, 2, 1, "", "validate"]], "spatialpy.core.geometry.Geometry": [[1, 2, 1, "", "inside"]], "spatialpy.core.geometry.GeometryAll": [[1, 2, 1, "", "inside"]], "spatialpy.core.geometry.GeometryExterior": [[1, 2, 1, "", "inside"]], "spatialpy.core.geometry.GeometryInterior": [[1, 2, 1, "", "inside"]], "spatialpy.core.initialcondition": [[1, 1, 1, "", "InitialCondition"], [1, 1, 1, "", "PlaceInitialCondition"], [1, 1, 1, "", "ScatterInitialCondition"], [1, 1, 1, "", "UniformInitialCondition"]], "spatialpy.core.initialcondition.InitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.initialcondition.PlaceInitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.initialcondition.ScatterInitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.initialcondition.UniformInitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.lattice": [[1, 1, 1, "", "CartesianLattice"], [1, 1, 1, "", "CylindricalLattice"], [1, 1, 1, "", "Lattice"], [1, 1, 1, "", "MeshIOLattice"], [1, 1, 1, "", "SphericalLattice"], [1, 1, 1, "", "StochSSLattice"], [1, 1, 1, "", "XMLMeshLattice"]], "spatialpy.core.lattice.CartesianLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.lattice.CylindricalLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.lattice.Lattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.lattice.MeshIOLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.lattice.SphericalLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.lattice.StochSSLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.lattice.XMLMeshLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.model": [[1, 1, 1, "", "Model"], [1, 5, 1, "", "export_StochSS"]], "spatialpy.core.model.Model": [[1, 2, 1, "", "add"], [1, 2, 1, "", "add_boundary_condition"], [1, 2, 1, "", "add_data_function"], [1, 2, 1, "", "add_domain"], [1, 2, 1, "", "add_initial_condition"], [1, 2, 1, "", "add_parameter"], [1, 2, 1, "", "add_reaction"], [1, 2, 1, "", "add_species"], [1, 2, 1, "", "compile_prep"], [1, 2, 1, "", "delete_all_boundary_conditions"], [1, 2, 1, "", "delete_all_data_functions"], [1, 2, 1, "", "delete_all_initial_conditions"], [1, 2, 1, "", "delete_all_parameters"], [1, 2, 1, "", "delete_all_reactions"], [1, 2, 1, "", "delete_all_species"], [1, 2, 1, "", "delete_boundary_condition"], [1, 2, 1, "", "delete_data_function"], [1, 2, 1, "", "delete_initial_condition"], [1, 2, 1, "", "delete_parameter"], [1, 2, 1, "", "delete_reaction"], [1, 2, 1, "", "delete_species"], [1, 2, 1, "", "get_all_boundary_conditions"], [1, 2, 1, "", "get_all_data_functions"], [1, 2, 1, "", "get_all_initial_conditions"], [1, 2, 1, "", "get_all_parameters"], [1, 2, 1, "", "get_all_reactions"], [1, 2, 1, "", "get_all_species"], [1, 2, 1, "", "get_data_function"], [1, 2, 1, "", "get_element"], [1, 2, 1, "", "get_num_reactions"], [1, 2, 1, "", "get_num_species"], [1, 2, 1, "", "get_parameter"], [1, 2, 1, "", "get_reaction"], [1, 2, 1, "", "get_species"], [1, 4, 1, "", "reserved_names"], [1, 2, 1, "", "run"], [1, 2, 1, "", "sanitized_data_function_names"], [1, 2, 1, "", "sanitized_parameter_names"], [1, 2, 1, "", "sanitized_species_names"], [1, 2, 1, "", "set_timesteps"], [1, 4, 1, "", "special_characters"], [1, 2, 1, "", "timespan"], [1, 2, 1, "", "update_namespace"]], "spatialpy.core.parameter": [[1, 1, 1, "", "Parameter"]], "spatialpy.core.parameter.Parameter": [[1, 2, 1, "", "validate"]], "spatialpy.core.reaction": [[1, 1, 1, "", "Reaction"]], "spatialpy.core.reaction.Reaction": [[1, 2, 1, "", "add_product"], [1, 2, 1, "", "add_reactant"], [1, 2, 1, "", "annotate"], [1, 2, 1, "", "from_json"], [1, 2, 1, "", "initialize"], [1, 2, 1, "", "sanitized_propensity_function"], [1, 2, 1, "", "set_annotation"], [1, 2, 1, "", "set_propensities"], [1, 2, 1, "", "set_rate"], [1, 2, 1, "", "to_dict"], [1, 2, 1, "", "validate"]], "spatialpy.core.result": [[1, 1, 1, "", "Result"]], "spatialpy.core.result.Result": [[1, 2, 1, "", "export_to_csv"], [1, 2, 1, "", "get_property"], [1, 2, 1, "", "get_species"], [1, 2, 1, "", "get_timespan"], [1, 2, 1, "", "plot_property"], [1, 2, 1, "", "plot_species"], [1, 2, 1, "", "read_step"]], "spatialpy.core.spatialpyerror": [[1, 3, 1, "", "BoundaryConditionError"], [1, 3, 1, "", "DataFunctionError"], [1, 3, 1, "", "DomainError"], [1, 3, 1, "", "GeometryError"], [1, 3, 1, "", "InitialConditionError"], [1, 3, 1, "", "LatticeError"], [1, 3, 1, "", "ModelError"], [1, 3, 1, "", "ParameterError"], [1, 3, 1, "", "ReactionError"], [1, 3, 1, "", "ResultError"], [1, 3, 1, "", "SimulationError"], [1, 3, 1, "", "SimulationTimeout"], [1, 3, 1, "", "SpeciesError"], [1, 3, 1, "", "TimespanError"], [1, 3, 1, "", "TransformationError"], [1, 3, 1, "", "VTKReaderError"], [1, 3, 1, "", "VTKReaderIOError"], [1, 3, 1, "", "VisualizationError"]], "spatialpy.core.species": [[1, 1, 1, "", "Species"]], "spatialpy.core.species.Species": [[1, 2, 1, "", "set_diffusion_coefficient"], [1, 2, 1, "", "validate"]], "spatialpy.core.timespan": [[1, 1, 1, "", "TimeSpan"]], "spatialpy.core.timespan.TimeSpan": [[1, 2, 1, "", "arange"], [1, 2, 1, "", "linspace"], [1, 2, 1, "", "validate"]], "spatialpy.core.transformation": [[1, 1, 1, "", "ReflectionTransformation"], [1, 1, 1, "", "RotationTransformation"], [1, 1, 1, "", "ScalingTransformation"], [1, 1, 1, "", "Transformation"], [1, 1, 1, "", "TranslationTransformation"]], "spatialpy.core.transformation.ReflectionTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"]], "spatialpy.core.transformation.RotationTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.transformation.ScalingTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.transformation.Transformation": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "inside"], [1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.transformation.TranslationTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.visualization": [[1, 1, 1, "", "Visualization"]], "spatialpy.core.visualization.Visualization": [[1, 4, 1, "", "MPL_HEIGHT"], [1, 4, 1, "", "MPL_SIZE"], [1, 4, 1, "", "MPL_WIDTH"], [1, 2, 1, "", "plot_scatter"]], "spatialpy.core.vtkreader": [[1, 1, 1, "", "VTKReader"]], "spatialpy.core.vtkreader.VTKReader": [[1, 2, 1, "", "get_array_name"], [1, 2, 1, "", "get_arrays"], [1, 2, 1, "", "get_num_points"], [1, 2, 1, "", "get_points"], [1, 2, 1, "", "read_file"], [1, 2, 1, "", "set_filename"]], "spatialpy.solvers": [[2, 0, 0, "-", "build_expression"], [2, 0, 0, "-", "solver"]], "spatialpy.solvers.build_expression": [[2, 1, 1, "", "BuildExpression"], [2, 1, 1, "", "CppConverter"], [2, 1, 1, "", "ExpressionConverter"], [2, 1, 1, "", "ExpressionResults"], [2, 1, 1, "", "PythonConverter"]], "spatialpy.solvers.build_expression.BuildExpression": [[2, 1, 1, "", "ValidationVisitor"], [2, 2, 1, "", "getexpr_cpp"], [2, 2, 1, "", "getexpr_python"], [2, 2, 1, "", "map_operator"], [2, 4, 1, "", "operator_map"], [2, 2, 1, "", "validate"], [2, 2, 1, "", "with_blacklist"], [2, 2, 1, "", "with_namespace"]], "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor": [[2, 2, 1, "", "visit_Assign"], [2, 2, 1, "", "visit_BinOp"], [2, 2, 1, "", "visit_BoolOp"], [2, 2, 1, "", "visit_Call"], [2, 2, 1, "", "visit_Compare"], [2, 2, 1, "", "visit_Name"], [2, 2, 1, "", "visit_UnaryOp"]], "spatialpy.solvers.build_expression.CppConverter": [[2, 1, 1, "", "CppExpressionTransformer"], [2, 2, 1, "", "get_str"], [2, 2, 1, "", "visit_And"], [2, 2, 1, "", "visit_Or"]], "spatialpy.solvers.build_expression.CppConverter.CppExpressionTransformer": [[2, 2, 1, "", "visit_BinOp"]], "spatialpy.solvers.build_expression.ExpressionConverter": [[2, 2, 1, "", "convert_str"], [2, 2, 1, "", "get_str"], [2, 2, 1, "", "parse_comparison"], [2, 2, 1, "", "parse_logical"], [2, 2, 1, "", "parse_operator"], [2, 2, 1, "", "visit_Add"], [2, 2, 1, "", "visit_BinOp"], [2, 2, 1, "", "visit_BoolOp"], [2, 2, 1, "", "visit_Bytes"], [2, 2, 1, "", "visit_Call"], [2, 2, 1, "", "visit_Compare"], [2, 2, 1, "", "visit_Constant"], [2, 2, 1, "", "visit_Div"], [2, 2, 1, "", "visit_Ellipsis"], [2, 2, 1, "", "visit_Eq"], [2, 2, 1, "", "visit_Gt"], [2, 2, 1, "", "visit_GtE"], [2, 2, 1, "", "visit_Lt"], [2, 2, 1, "", "visit_LtE"], [2, 2, 1, "", "visit_Mult"], [2, 2, 1, "", "visit_Name"], [2, 2, 1, "", "visit_NameConstant"], [2, 2, 1, "", "visit_NotEq"], [2, 2, 1, "", "visit_Num"], [2, 2, 1, "", "visit_Pow"], [2, 2, 1, "", "visit_Str"], [2, 2, 1, "", "visit_Sub"], [2, 2, 1, "", "visit_USub"], [2, 2, 1, "", "visit_UnaryOp"]], "spatialpy.solvers.build_expression.PythonConverter": [[2, 2, 1, "", "visit_And"], [2, 2, 1, "", "visit_Or"]], "spatialpy.solvers.solver": [[2, 1, 1, "", "Solver"]], "spatialpy.solvers.solver.Solver": [[2, 2, 1, "", "compile"], [2, 2, 1, "", "run"]], "spatialpy.stochss": [[3, 0, 0, "-", "stochss_export"]], "spatialpy.stochss.stochss_export": [[3, 5, 1, "", "export"]]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:exception", "4": "py:attribute", "5": "py:function"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "exception", "Python exception"], "4": ["py", "attribute", "Python attribute"], "5": ["py", "function", "Python function"]}, "titleterms": {"spatialpi": [0, 1, 2, 3, 4], "packag": [0, 1, 2, 3], "subpackag": 0, "modul": [0, 1, 2, 3], "content": [0, 1, 2, 3], "core": 1, "submodul": [1, 2, 3], "boundarycondit": 1, "cleanup": 1, "datafunct": 1, "domain": 1, "geometri": 1, "initialcondit": 1, "lattic": 1, "model": 1, "paramet": 1, "reaction": 1, "result": 1, "spatialpyerror": 1, "speci": 1, "timespan": 1, "transform": 1, "visual": 1, "vtkreader": 1, "solver": 2, "build_express": 2, "stochss": 3, "stochss_export": 3, "document": 4, "1": 4, "2": 4, "get": 4, "copi": 4, "exampl": 4, "report": 4, "issu": 4, "api": 4, "refer": 4, "indic": 4, "tabl": 4, "3": [], "0": 4}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx.ext.todo": 2, "sphinx": 57}, "alltitles": {"spatialpy package": [[0, "spatialpy-package"]], "Subpackages": [[0, "subpackages"]], "Module contents": [[0, "module-spatialpy"], [1, "module-spatialpy.core"], [2, "module-spatialpy.solvers"], [3, "module-spatialpy.stochss"]], "spatialpy.core package": [[1, "spatialpy-core-package"]], "Submodules": [[1, "submodules"], [2, "submodules"], [3, "submodules"]], "spatialpy.core.boundarycondition module": [[1, "module-spatialpy.core.boundarycondition"]], "spatialpy.core.cleanup module": [[1, "module-spatialpy.core.cleanup"]], "spatialpy.core.datafunction module": [[1, "module-spatialpy.core.datafunction"]], "spatialpy.core.domain module": [[1, "module-spatialpy.core.domain"]], "spatialpy.core.geometry module": [[1, "module-spatialpy.core.geometry"]], "spatialpy.core.initialcondition module": [[1, "module-spatialpy.core.initialcondition"]], "spatialpy.core.lattice module": [[1, "module-spatialpy.core.lattice"]], "spatialpy.core.model module": [[1, "module-spatialpy.core.model"]], "spatialpy.core.parameter module": [[1, "module-spatialpy.core.parameter"]], "spatialpy.core.reaction module": [[1, "module-spatialpy.core.reaction"]], "spatialpy.core.result module": [[1, "module-spatialpy.core.result"]], "spatialpy.core.spatialpyerror module": [[1, "module-spatialpy.core.spatialpyerror"]], "spatialpy.core.species module": [[1, "module-spatialpy.core.species"]], "spatialpy.core.timespan module": [[1, "module-spatialpy.core.timespan"]], "spatialpy.core.transformation module": [[1, "module-spatialpy.core.transformation"]], "spatialpy.core.visualization module": [[1, "module-spatialpy.core.visualization"]], "spatialpy.core.vtkreader module": [[1, "module-spatialpy.core.vtkreader"]], "spatialpy.solvers package": [[2, "spatialpy-solvers-package"]], "spatialpy.solvers.build_expression module": [[2, "module-spatialpy.solvers.build_expression"]], "spatialpy.solvers.solver module": [[2, "module-spatialpy.solvers.solver"]], "spatialpy.stochss package": [[3, "spatialpy-stochss-package"]], "spatialpy.stochss.stochss_export module": [[3, "module-spatialpy.stochss.stochss_export"]], "Documentation for SpatialPy 1.2.0": [[4, "documentation-for-spatialpy-release"]], "Getting a copy of SpatialPy": [[4, "getting-a-copy-of-spatialpy"]], "Examples": [[4, "examples"]], "Reporting Issues": [[4, "reporting-issues"]], "Documentation": [[4, "documentation"]], "API reference": [[4, null]], "Indices and tables": [[4, "indices-and-tables"]]}, "indexentries": {"module": [[0, "module-spatialpy"], [1, "module-spatialpy.core"], [1, "module-spatialpy.core.boundarycondition"], [1, "module-spatialpy.core.cleanup"], [1, "module-spatialpy.core.datafunction"], [1, "module-spatialpy.core.domain"], [1, "module-spatialpy.core.geometry"], [1, "module-spatialpy.core.initialcondition"], [1, "module-spatialpy.core.lattice"], [1, "module-spatialpy.core.model"], [1, "module-spatialpy.core.parameter"], [1, "module-spatialpy.core.reaction"], [1, "module-spatialpy.core.result"], [1, "module-spatialpy.core.spatialpyerror"], [1, "module-spatialpy.core.species"], [1, "module-spatialpy.core.timespan"], [1, "module-spatialpy.core.transformation"], [1, "module-spatialpy.core.visualization"], [1, "module-spatialpy.core.vtkreader"], [2, "module-spatialpy.solvers"], [2, "module-spatialpy.solvers.build_expression"], [2, "module-spatialpy.solvers.solver"], [3, "module-spatialpy.stochss"], [3, "module-spatialpy.stochss.stochss_export"]], "spatialpy": [[0, "module-spatialpy"]], "boundarycondition (class in spatialpy.core)": [[1, "spatialpy.core.BoundaryCondition"]], "boundarycondition (class in spatialpy.core.boundarycondition)": [[1, "spatialpy.core.boundarycondition.BoundaryCondition"]], "boundaryconditionerror": [[1, "spatialpy.core.BoundaryConditionError"], [1, "spatialpy.core.spatialpyerror.BoundaryConditionError"]], "cartesianlattice (class in spatialpy.core)": [[1, "spatialpy.core.CartesianLattice"]], "cartesianlattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.CartesianLattice"]], "combinatorygeometry (class in spatialpy.core)": [[1, "spatialpy.core.CombinatoryGeometry"]], "combinatorygeometry (class in spatialpy.core.geometry)": [[1, "spatialpy.core.geometry.CombinatoryGeometry"]], "cylindricallattice (class in spatialpy.core)": [[1, "spatialpy.core.CylindricalLattice"]], "cylindricallattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.CylindricalLattice"]], "datafunction (class in spatialpy.core)": [[1, "spatialpy.core.DataFunction"]], "datafunction (class in spatialpy.core.datafunction)": [[1, "spatialpy.core.datafunction.DataFunction"]], "datafunctionerror": [[1, "spatialpy.core.DataFunctionError"], [1, "spatialpy.core.spatialpyerror.DataFunctionError"]], "domain (class in spatialpy.core)": [[1, "spatialpy.core.Domain"]], "domain (class in spatialpy.core.domain)": [[1, "spatialpy.core.domain.Domain"]], "domainerror": [[1, "spatialpy.core.DomainError"], [1, "spatialpy.core.spatialpyerror.DomainError"]], "geometry (class in spatialpy.core)": [[1, "spatialpy.core.Geometry"]], "geometry (class in spatialpy.core.geometry)": [[1, "spatialpy.core.geometry.Geometry"]], "geometryall (class in spatialpy.core)": [[1, "spatialpy.core.GeometryAll"]], "geometryall (class in spatialpy.core.geometry)": [[1, "spatialpy.core.geometry.GeometryAll"]], "geometryerror": [[1, "spatialpy.core.GeometryError"], [1, "spatialpy.core.spatialpyerror.GeometryError"]], "geometryexterior (class in spatialpy.core)": [[1, "spatialpy.core.GeometryExterior"]], "geometryexterior (class in spatialpy.core.geometry)": [[1, "spatialpy.core.geometry.GeometryExterior"]], "geometryinterior (class in spatialpy.core)": [[1, "spatialpy.core.GeometryInterior"]], "geometryinterior (class in spatialpy.core.geometry)": [[1, "spatialpy.core.geometry.GeometryInterior"]], "initialcondition (class in spatialpy.core)": [[1, "spatialpy.core.InitialCondition"]], "initialcondition (class in spatialpy.core.initialcondition)": [[1, "spatialpy.core.initialcondition.InitialCondition"]], "initialconditionerror": [[1, "spatialpy.core.InitialConditionError"], [1, "spatialpy.core.spatialpyerror.InitialConditionError"]], "lattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.Lattice"]], "latticeerror": [[1, "spatialpy.core.LatticeError"], [1, "spatialpy.core.spatialpyerror.LatticeError"]], "mpl_height (spatialpy.core.visualization attribute)": [[1, "spatialpy.core.Visualization.MPL_HEIGHT"]], "mpl_height (spatialpy.core.visualization.visualization attribute)": [[1, "spatialpy.core.visualization.Visualization.MPL_HEIGHT"]], "mpl_size (spatialpy.core.visualization attribute)": [[1, "spatialpy.core.Visualization.MPL_SIZE"]], "mpl_size (spatialpy.core.visualization.visualization attribute)": [[1, "spatialpy.core.visualization.Visualization.MPL_SIZE"]], "mpl_width (spatialpy.core.visualization attribute)": [[1, "spatialpy.core.Visualization.MPL_WIDTH"]], "mpl_width (spatialpy.core.visualization.visualization attribute)": [[1, "spatialpy.core.visualization.Visualization.MPL_WIDTH"]], "meshiolattice (class in spatialpy.core)": [[1, "spatialpy.core.MeshIOLattice"]], "meshiolattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.MeshIOLattice"]], "model (class in spatialpy.core)": [[1, "spatialpy.core.Model"]], "model (class in spatialpy.core.model)": [[1, "spatialpy.core.model.Model"]], "modelerror": [[1, "spatialpy.core.ModelError"], [1, "spatialpy.core.spatialpyerror.ModelError"]], "parameter (class in spatialpy.core)": [[1, "spatialpy.core.Parameter"]], "parameter (class in spatialpy.core.parameter)": [[1, "spatialpy.core.parameter.Parameter"]], "parametererror": [[1, "spatialpy.core.ParameterError"], [1, "spatialpy.core.spatialpyerror.ParameterError"]], "placeinitialcondition (class in spatialpy.core)": [[1, "spatialpy.core.PlaceInitialCondition"]], "placeinitialcondition (class in spatialpy.core.initialcondition)": [[1, "spatialpy.core.initialcondition.PlaceInitialCondition"]], "reaction (class in spatialpy.core)": [[1, "spatialpy.core.Reaction"]], "reaction (class in spatialpy.core.reaction)": [[1, "spatialpy.core.reaction.Reaction"]], "reactionerror": [[1, "spatialpy.core.ReactionError"], [1, "spatialpy.core.spatialpyerror.ReactionError"]], "reflectiontransformation (class in spatialpy.core)": [[1, "spatialpy.core.ReflectionTransformation"]], "reflectiontransformation (class in spatialpy.core.transformation)": [[1, "spatialpy.core.transformation.ReflectionTransformation"]], "result (class in spatialpy.core)": [[1, "spatialpy.core.Result"]], "result (class in spatialpy.core.result)": [[1, "spatialpy.core.result.Result"]], "resulterror": [[1, "spatialpy.core.ResultError"], [1, "spatialpy.core.spatialpyerror.ResultError"]], "rotationtransformation (class in spatialpy.core)": [[1, "spatialpy.core.RotationTransformation"]], "rotationtransformation (class in spatialpy.core.transformation)": [[1, "spatialpy.core.transformation.RotationTransformation"]], "scalingtransformation (class in spatialpy.core)": [[1, "spatialpy.core.ScalingTransformation"]], "scalingtransformation (class in spatialpy.core.transformation)": [[1, "spatialpy.core.transformation.ScalingTransformation"]], "scatterinitialcondition (class in spatialpy.core)": [[1, "spatialpy.core.ScatterInitialCondition"]], "scatterinitialcondition (class in spatialpy.core.initialcondition)": [[1, "spatialpy.core.initialcondition.ScatterInitialCondition"]], "simulationerror": [[1, "spatialpy.core.SimulationError"], [1, "spatialpy.core.spatialpyerror.SimulationError"]], "simulationtimeout": [[1, "spatialpy.core.SimulationTimeout"], [1, "spatialpy.core.spatialpyerror.SimulationTimeout"]], "species (class in spatialpy.core)": [[1, "spatialpy.core.Species"]], "species (class in spatialpy.core.species)": [[1, "spatialpy.core.species.Species"]], "specieserror": [[1, "spatialpy.core.SpeciesError"], [1, "spatialpy.core.spatialpyerror.SpeciesError"]], "sphericallattice (class in spatialpy.core)": [[1, "spatialpy.core.SphericalLattice"]], "sphericallattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.SphericalLattice"]], "stochsslattice (class in spatialpy.core)": [[1, "spatialpy.core.StochSSLattice"]], "stochsslattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.StochSSLattice"]], "timespan (class in spatialpy.core)": [[1, "spatialpy.core.TimeSpan"]], "timespan (class in spatialpy.core.timespan)": [[1, "spatialpy.core.timespan.TimeSpan"]], "timespanerror": [[1, "spatialpy.core.TimespanError"], [1, "spatialpy.core.spatialpyerror.TimespanError"]], "transformation (class in spatialpy.core)": [[1, "spatialpy.core.Transformation"]], "transformation (class in spatialpy.core.transformation)": [[1, "spatialpy.core.transformation.Transformation"]], "transformationerror": [[1, "spatialpy.core.TransformationError"], [1, "spatialpy.core.spatialpyerror.TransformationError"]], "translationtransformation (class in spatialpy.core)": [[1, "spatialpy.core.TranslationTransformation"]], "translationtransformation (class in spatialpy.core.transformation)": [[1, "spatialpy.core.transformation.TranslationTransformation"]], "uniforminitialcondition (class in spatialpy.core)": [[1, "spatialpy.core.UniformInitialCondition"]], "uniforminitialcondition (class in spatialpy.core.initialcondition)": [[1, "spatialpy.core.initialcondition.UniformInitialCondition"]], "vtkreader (class in spatialpy.core)": [[1, "spatialpy.core.VTKReader"]], "vtkreader (class in spatialpy.core.vtkreader)": [[1, "spatialpy.core.vtkreader.VTKReader"]], "vtkreadererror": [[1, "spatialpy.core.VTKReaderError"], [1, "spatialpy.core.spatialpyerror.VTKReaderError"]], "vtkreaderioerror": [[1, "spatialpy.core.VTKReaderIOError"], [1, "spatialpy.core.spatialpyerror.VTKReaderIOError"]], "visualization (class in spatialpy.core)": [[1, "spatialpy.core.Visualization"]], "visualization (class in spatialpy.core.visualization)": [[1, "spatialpy.core.visualization.Visualization"]], "visualizationerror": [[1, "spatialpy.core.VisualizationError"], [1, "spatialpy.core.spatialpyerror.VisualizationError"]], "xmlmeshlattice (class in spatialpy.core)": [[1, "spatialpy.core.XMLMeshLattice"]], "xmlmeshlattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.XMLMeshLattice"]], "add() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add"]], "add() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add"]], "add_boundary_condition() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_boundary_condition"]], "add_boundary_condition() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_boundary_condition"]], "add_data_function() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_data_function"]], "add_data_function() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_data_function"]], "add_domain() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_domain"]], "add_domain() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_domain"]], "add_fill_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.add_fill_action"]], "add_fill_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.add_fill_action"]], "add_initial_condition() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_initial_condition"]], "add_initial_condition() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_initial_condition"]], "add_parameter() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_parameter"]], "add_parameter() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_parameter"]], "add_point() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.add_point"]], "add_point() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.add_point"]], "add_product() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.add_product"]], "add_product() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.add_product"]], "add_reactant() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.add_reactant"]], "add_reactant() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.add_reactant"]], "add_reaction() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_reaction"]], "add_reaction() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_reaction"]], "add_remove_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.add_remove_action"]], "add_remove_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.add_remove_action"]], "add_set_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.add_set_action"]], "add_set_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.add_set_action"]], "add_species() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_species"]], "add_species() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_species"]], "annotate() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.annotate"]], "annotate() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.annotate"]], "apply() (spatialpy.core.cartesianlattice method)": [[1, "spatialpy.core.CartesianLattice.apply"]], "apply() (spatialpy.core.cylindricallattice method)": [[1, "spatialpy.core.CylindricalLattice.apply"]], "apply() (spatialpy.core.initialcondition method)": [[1, "spatialpy.core.InitialCondition.apply"]], "apply() (spatialpy.core.meshiolattice method)": [[1, "spatialpy.core.MeshIOLattice.apply"]], "apply() (spatialpy.core.placeinitialcondition method)": [[1, "spatialpy.core.PlaceInitialCondition.apply"]], "apply() (spatialpy.core.scatterinitialcondition method)": [[1, "spatialpy.core.ScatterInitialCondition.apply"]], "apply() (spatialpy.core.sphericallattice method)": [[1, "spatialpy.core.SphericalLattice.apply"]], "apply() (spatialpy.core.stochsslattice method)": [[1, "spatialpy.core.StochSSLattice.apply"]], "apply() (spatialpy.core.transformation method)": [[1, "spatialpy.core.Transformation.apply"]], "apply() (spatialpy.core.uniforminitialcondition method)": [[1, "spatialpy.core.UniformInitialCondition.apply"]], "apply() (spatialpy.core.xmlmeshlattice method)": [[1, "spatialpy.core.XMLMeshLattice.apply"]], "apply() (spatialpy.core.initialcondition.initialcondition method)": [[1, "spatialpy.core.initialcondition.InitialCondition.apply"]], "apply() (spatialpy.core.initialcondition.placeinitialcondition method)": [[1, "spatialpy.core.initialcondition.PlaceInitialCondition.apply"]], "apply() (spatialpy.core.initialcondition.scatterinitialcondition method)": [[1, "spatialpy.core.initialcondition.ScatterInitialCondition.apply"]], "apply() (spatialpy.core.initialcondition.uniforminitialcondition method)": [[1, "spatialpy.core.initialcondition.UniformInitialCondition.apply"]], "apply() (spatialpy.core.lattice.cartesianlattice method)": [[1, "spatialpy.core.lattice.CartesianLattice.apply"]], "apply() (spatialpy.core.lattice.cylindricallattice method)": [[1, "spatialpy.core.lattice.CylindricalLattice.apply"]], "apply() (spatialpy.core.lattice.lattice method)": [[1, "spatialpy.core.lattice.Lattice.apply"]], "apply() (spatialpy.core.lattice.meshiolattice method)": [[1, "spatialpy.core.lattice.MeshIOLattice.apply"]], "apply() (spatialpy.core.lattice.sphericallattice method)": [[1, "spatialpy.core.lattice.SphericalLattice.apply"]], "apply() (spatialpy.core.lattice.stochsslattice method)": [[1, "spatialpy.core.lattice.StochSSLattice.apply"]], "apply() (spatialpy.core.lattice.xmlmeshlattice method)": [[1, "spatialpy.core.lattice.XMLMeshLattice.apply"]], "apply() (spatialpy.core.transformation.transformation method)": [[1, "spatialpy.core.transformation.Transformation.apply"]], "apply_actions() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.apply_actions"]], "apply_actions() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.apply_actions"]], "apply_fill_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.apply_fill_action"]], "apply_fill_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.apply_fill_action"]], "apply_remove_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.apply_remove_action"]], "apply_remove_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.apply_remove_action"]], "apply_set_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.apply_set_action"]], "apply_set_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.apply_set_action"]], "arange() (spatialpy.core.timespan class method)": [[1, "spatialpy.core.TimeSpan.arange"]], "arange() (spatialpy.core.timespan.timespan class method)": [[1, "spatialpy.core.timespan.TimeSpan.arange"]], "calculate_vol() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.calculate_vol"]], "calculate_vol() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.calculate_vol"]], "cleanup_build_files() (in module spatialpy.core)": [[1, "spatialpy.core.cleanup_build_files"]], "cleanup_build_files() (in module spatialpy.core.cleanup)": [[1, "spatialpy.core.cleanup.cleanup_build_files"]], "cleanup_core_files() (in module spatialpy.core)": [[1, "spatialpy.core.cleanup_core_files"]], "cleanup_core_files() (in module spatialpy.core.cleanup)": [[1, "spatialpy.core.cleanup.cleanup_core_files"]], "cleanup_result_files() (in module spatialpy.core)": [[1, "spatialpy.core.cleanup_result_files"]], "cleanup_result_files() (in module spatialpy.core.cleanup)": [[1, "spatialpy.core.cleanup.cleanup_result_files"]], "cleanup_tempfiles() (in module spatialpy.core)": [[1, "spatialpy.core.cleanup_tempfiles"]], "cleanup_tempfiles() (in module spatialpy.core.cleanup)": [[1, "spatialpy.core.cleanup.cleanup_tempfiles"]], "closest_vertex() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.closest_vertex"]], "closest_vertex() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.closest_vertex"]], "compile_prep() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.compile_prep"]], "compile_prep() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.compile_prep"]], "compile_prep() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.compile_prep"]], "compile_prep() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.compile_prep"]], "coordinates() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.coordinates"]], "coordinates() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.coordinates"]], "create_2d_domain() (spatialpy.core.domain class method)": [[1, "spatialpy.core.Domain.create_2D_domain"]], "create_2d_domain() (spatialpy.core.domain.domain class method)": [[1, "spatialpy.core.domain.Domain.create_2D_domain"]], "create_3d_domain() (spatialpy.core.domain class method)": [[1, "spatialpy.core.Domain.create_3D_domain"]], "create_3d_domain() (spatialpy.core.domain.domain class method)": [[1, "spatialpy.core.domain.Domain.create_3D_domain"]], "delete_all_boundary_conditions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_all_boundary_conditions"]], "delete_all_boundary_conditions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_all_boundary_conditions"]], "delete_all_data_functions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_all_data_functions"]], "delete_all_data_functions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_all_data_functions"]], "delete_all_initial_conditions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_all_initial_conditions"]], "delete_all_initial_conditions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_all_initial_conditions"]], "delete_all_parameters() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_all_parameters"]], "delete_all_parameters() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_all_parameters"]], "delete_all_reactions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_all_reactions"]], "delete_all_reactions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_all_reactions"]], "delete_all_species() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_all_species"]], "delete_all_species() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_all_species"]], "delete_boundary_condition() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_boundary_condition"]], "delete_boundary_condition() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_boundary_condition"]], "delete_data_function() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_data_function"]], "delete_data_function() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_data_function"]], "delete_initial_condition() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_initial_condition"]], "delete_initial_condition() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_initial_condition"]], "delete_parameter() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_parameter"]], "delete_parameter() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_parameter"]], "delete_reaction() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_reaction"]], "delete_reaction() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_reaction"]], "delete_species() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_species"]], "delete_species() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_species"]], "distance_between_2_vertices() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.distance_between_2_vertices"]], "distance_between_2_vertices() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.distance_between_2_vertices"]], "export_stochss() (in module spatialpy.core)": [[1, "spatialpy.core.export_StochSS"]], "export_stochss() (in module spatialpy.core.model)": [[1, "spatialpy.core.model.export_StochSS"]], "export_to_csv() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.export_to_csv"]], "export_to_csv() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.export_to_csv"]], "expression() (spatialpy.core.boundarycondition method)": [[1, "spatialpy.core.BoundaryCondition.expression"]], "expression() (spatialpy.core.boundarycondition.boundarycondition method)": [[1, "spatialpy.core.boundarycondition.BoundaryCondition.expression"]], "fill_with_particles() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.fill_with_particles"]], "fill_with_particles() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.fill_with_particles"]], "find_boundary_points() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.find_boundary_points"]], "find_boundary_points() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.find_boundary_points"]], "find_h() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.find_h"]], "find_h() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.find_h"]], "from_json() (spatialpy.core.reaction class method)": [[1, "spatialpy.core.Reaction.from_json"]], "from_json() (spatialpy.core.reaction.reaction class method)": [[1, "spatialpy.core.reaction.Reaction.from_json"]], "get_all_boundary_conditions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_all_boundary_conditions"]], "get_all_boundary_conditions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_all_boundary_conditions"]], "get_all_data_functions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_all_data_functions"]], "get_all_data_functions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_all_data_functions"]], "get_all_initial_conditions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_all_initial_conditions"]], "get_all_initial_conditions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_all_initial_conditions"]], "get_all_parameters() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_all_parameters"]], "get_all_parameters() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_all_parameters"]], "get_all_reactions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_all_reactions"]], "get_all_reactions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_all_reactions"]], "get_all_species() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_all_species"]], "get_all_species() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_all_species"]], "get_array_name() (spatialpy.core.vtkreader method)": [[1, "spatialpy.core.VTKReader.get_array_name"]], "get_array_name() (spatialpy.core.vtkreader.vtkreader method)": [[1, "spatialpy.core.vtkreader.VTKReader.get_array_name"]], "get_arrays() (spatialpy.core.vtkreader method)": [[1, "spatialpy.core.VTKReader.get_arrays"]], "get_arrays() (spatialpy.core.vtkreader.vtkreader method)": [[1, "spatialpy.core.vtkreader.VTKReader.get_arrays"]], "get_bounding_box() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.get_bounding_box"]], "get_bounding_box() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.get_bounding_box"]], "get_data_function() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_data_function"]], "get_data_function() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_data_function"]], "get_domain_size() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.get_domain_size"]], "get_domain_size() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.get_domain_size"]], "get_element() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_element"]], "get_element() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_element"]], "get_num_points() (spatialpy.core.vtkreader method)": [[1, "spatialpy.core.VTKReader.get_num_points"]], "get_num_points() (spatialpy.core.vtkreader.vtkreader method)": [[1, "spatialpy.core.vtkreader.VTKReader.get_num_points"]], "get_num_reactions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_num_reactions"]], "get_num_reactions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_num_reactions"]], "get_num_species() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_num_species"]], "get_num_species() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_num_species"]], "get_num_voxels() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.get_num_voxels"]], "get_num_voxels() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.get_num_voxels"]], "get_parameter() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_parameter"]], "get_parameter() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_parameter"]], "get_points() (spatialpy.core.vtkreader method)": [[1, "spatialpy.core.VTKReader.get_points"]], "get_points() (spatialpy.core.vtkreader.vtkreader method)": [[1, "spatialpy.core.vtkreader.VTKReader.get_points"]], "get_property() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.get_property"]], "get_property() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.get_property"]], "get_reaction() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_reaction"]], "get_reaction() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_reaction"]], "get_species() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_species"]], "get_species() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.get_species"]], "get_species() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_species"]], "get_species() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.get_species"]], "get_timespan() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.get_timespan"]], "get_timespan() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.get_timespan"]], "get_type_def() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.get_type_def"]], "get_type_def() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.get_type_def"]], "get_vol() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.get_vol"]], "get_vol() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.get_vol"]], "import_meshio_object() (spatialpy.core.domain class method)": [[1, "spatialpy.core.Domain.import_meshio_object"]], "import_meshio_object() (spatialpy.core.domain.domain class method)": [[1, "spatialpy.core.domain.Domain.import_meshio_object"]], "initialize() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.initialize"]], "initialize() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.initialize"]], "inside() (spatialpy.core.combinatorygeometry method)": [[1, "spatialpy.core.CombinatoryGeometry.inside"]], "inside() (spatialpy.core.geometry method)": [[1, "spatialpy.core.Geometry.inside"]], "inside() (spatialpy.core.geometryall method)": [[1, "spatialpy.core.GeometryAll.inside"]], "inside() (spatialpy.core.geometryexterior method)": [[1, "spatialpy.core.GeometryExterior.inside"]], "inside() (spatialpy.core.geometryinterior method)": [[1, "spatialpy.core.GeometryInterior.inside"]], "inside() (spatialpy.core.transformation method)": [[1, "spatialpy.core.Transformation.inside"]], "inside() (spatialpy.core.geometry.combinatorygeometry method)": [[1, "spatialpy.core.geometry.CombinatoryGeometry.inside"]], "inside() (spatialpy.core.geometry.geometry method)": [[1, "spatialpy.core.geometry.Geometry.inside"]], "inside() (spatialpy.core.geometry.geometryall method)": [[1, "spatialpy.core.geometry.GeometryAll.inside"]], "inside() (spatialpy.core.geometry.geometryexterior method)": [[1, "spatialpy.core.geometry.GeometryExterior.inside"]], "inside() (spatialpy.core.geometry.geometryinterior method)": [[1, "spatialpy.core.geometry.GeometryInterior.inside"]], "inside() (spatialpy.core.transformation.transformation method)": [[1, "spatialpy.core.transformation.Transformation.inside"]], "linspace() (spatialpy.core.timespan class method)": [[1, "spatialpy.core.TimeSpan.linspace"]], "linspace() (spatialpy.core.timespan.timespan class method)": [[1, "spatialpy.core.timespan.TimeSpan.linspace"]], "map() (spatialpy.core.datafunction method)": [[1, "spatialpy.core.DataFunction.map"]], "map() (spatialpy.core.datafunction.datafunction method)": [[1, "spatialpy.core.datafunction.DataFunction.map"]], "plot_property() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.plot_property"]], "plot_property() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.plot_property"]], "plot_scatter() (spatialpy.core.visualization method)": [[1, "spatialpy.core.Visualization.plot_scatter"]], "plot_scatter() (spatialpy.core.visualization.visualization method)": [[1, "spatialpy.core.visualization.Visualization.plot_scatter"]], "plot_species() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.plot_species"]], "plot_species() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.plot_species"]], "plot_types() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.plot_types"]], "plot_types() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.plot_types"]], "preview_actions() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.preview_actions"]], "preview_actions() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.preview_actions"]], "read_file() (spatialpy.core.vtkreader method)": [[1, "spatialpy.core.VTKReader.read_file"]], "read_file() (spatialpy.core.vtkreader.vtkreader method)": [[1, "spatialpy.core.vtkreader.VTKReader.read_file"]], "read_msh_file() (spatialpy.core.domain class method)": [[1, "spatialpy.core.Domain.read_msh_file"]], "read_msh_file() (spatialpy.core.domain.domain class method)": [[1, "spatialpy.core.domain.Domain.read_msh_file"]], "read_step() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.read_step"]], "read_step() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.read_step"]], "read_stochss_domain() (spatialpy.core.domain class method)": [[1, "spatialpy.core.Domain.read_stochss_domain"]], "read_stochss_domain() (spatialpy.core.domain.domain class method)": [[1, "spatialpy.core.domain.Domain.read_stochss_domain"]], "read_stochss_subdomain_file() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.read_stochss_subdomain_file"]], "read_stochss_subdomain_file() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.read_stochss_subdomain_file"]], "read_xml_mesh() (spatialpy.core.domain class method)": [[1, "spatialpy.core.Domain.read_xml_mesh"]], "read_xml_mesh() (spatialpy.core.domain.domain class method)": [[1, "spatialpy.core.domain.Domain.read_xml_mesh"]], "reserved_names (spatialpy.core.model attribute)": [[1, "spatialpy.core.Model.reserved_names"]], "reserved_names (spatialpy.core.model.model attribute)": [[1, "spatialpy.core.model.Model.reserved_names"]], "reverse_transform() (spatialpy.core.reflectiontransformation method)": [[1, "spatialpy.core.ReflectionTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.rotationtransformation method)": [[1, "spatialpy.core.RotationTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.scalingtransformation method)": [[1, "spatialpy.core.ScalingTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.transformation method)": [[1, "spatialpy.core.Transformation.reverse_transform"]], "reverse_transform() (spatialpy.core.translationtransformation method)": [[1, "spatialpy.core.TranslationTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.transformation.reflectiontransformation method)": [[1, "spatialpy.core.transformation.ReflectionTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.transformation.rotationtransformation method)": [[1, "spatialpy.core.transformation.RotationTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.transformation.scalingtransformation method)": [[1, "spatialpy.core.transformation.ScalingTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.transformation.transformation method)": [[1, "spatialpy.core.transformation.Transformation.reverse_transform"]], "reverse_transform() (spatialpy.core.transformation.translationtransformation method)": [[1, "spatialpy.core.transformation.TranslationTransformation.reverse_transform"]], "run() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.run"]], "run() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.run"]], "sanitized_data_function_names() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.sanitized_data_function_names"]], "sanitized_data_function_names() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.sanitized_data_function_names"]], "sanitized_parameter_names() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.sanitized_parameter_names"]], "sanitized_parameter_names() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.sanitized_parameter_names"]], "sanitized_propensity_function() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.sanitized_propensity_function"]], "sanitized_propensity_function() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.sanitized_propensity_function"]], "sanitized_species_names() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.sanitized_species_names"]], "sanitized_species_names() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.sanitized_species_names"]], "set_annotation() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.set_annotation"]], "set_annotation() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.set_annotation"]], "set_diffusion_coefficient() (spatialpy.core.species method)": [[1, "spatialpy.core.Species.set_diffusion_coefficient"]], "set_diffusion_coefficient() (spatialpy.core.species.species method)": [[1, "spatialpy.core.species.Species.set_diffusion_coefficient"]], "set_filename() (spatialpy.core.vtkreader method)": [[1, "spatialpy.core.VTKReader.set_filename"]], "set_filename() (spatialpy.core.vtkreader.vtkreader method)": [[1, "spatialpy.core.vtkreader.VTKReader.set_filename"]], "set_propensities() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.set_propensities"]], "set_propensities() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.set_propensities"]], "set_properties() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.set_properties"]], "set_properties() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.set_properties"]], "set_rate() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.set_rate"]], "set_rate() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.set_rate"]], "set_timesteps() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.set_timesteps"]], "set_timesteps() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.set_timesteps"]], "spatialpy.core": [[1, "module-spatialpy.core"]], "spatialpy.core.boundarycondition": [[1, "module-spatialpy.core.boundarycondition"]], "spatialpy.core.cleanup": [[1, "module-spatialpy.core.cleanup"]], "spatialpy.core.datafunction": [[1, "module-spatialpy.core.datafunction"]], "spatialpy.core.domain": [[1, "module-spatialpy.core.domain"]], "spatialpy.core.geometry": [[1, "module-spatialpy.core.geometry"]], "spatialpy.core.initialcondition": [[1, "module-spatialpy.core.initialcondition"]], "spatialpy.core.lattice": [[1, "module-spatialpy.core.lattice"]], "spatialpy.core.model": [[1, "module-spatialpy.core.model"]], "spatialpy.core.parameter": [[1, "module-spatialpy.core.parameter"]], "spatialpy.core.reaction": [[1, "module-spatialpy.core.reaction"]], "spatialpy.core.result": [[1, "module-spatialpy.core.result"]], "spatialpy.core.spatialpyerror": [[1, "module-spatialpy.core.spatialpyerror"]], "spatialpy.core.species": [[1, "module-spatialpy.core.species"]], "spatialpy.core.timespan": [[1, "module-spatialpy.core.timespan"]], "spatialpy.core.transformation": [[1, "module-spatialpy.core.transformation"]], "spatialpy.core.visualization": [[1, "module-spatialpy.core.visualization"]], "spatialpy.core.vtkreader": [[1, "module-spatialpy.core.vtkreader"]], "special_characters (spatialpy.core.model attribute)": [[1, "spatialpy.core.Model.special_characters"]], "special_characters (spatialpy.core.model.model attribute)": [[1, "spatialpy.core.model.Model.special_characters"]], "timespan() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.timespan"]], "timespan() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.timespan"]], "to_dict() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.to_dict"]], "to_dict() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.to_dict"]], "transform() (spatialpy.core.reflectiontransformation method)": [[1, "spatialpy.core.ReflectionTransformation.transform"]], "transform() (spatialpy.core.rotationtransformation method)": [[1, "spatialpy.core.RotationTransformation.transform"]], "transform() (spatialpy.core.scalingtransformation method)": [[1, "spatialpy.core.ScalingTransformation.transform"]], "transform() (spatialpy.core.transformation method)": [[1, "spatialpy.core.Transformation.transform"]], "transform() (spatialpy.core.translationtransformation method)": [[1, "spatialpy.core.TranslationTransformation.transform"]], "transform() (spatialpy.core.transformation.reflectiontransformation method)": [[1, "spatialpy.core.transformation.ReflectionTransformation.transform"]], "transform() (spatialpy.core.transformation.rotationtransformation method)": [[1, "spatialpy.core.transformation.RotationTransformation.transform"]], "transform() (spatialpy.core.transformation.scalingtransformation method)": [[1, "spatialpy.core.transformation.ScalingTransformation.transform"]], "transform() (spatialpy.core.transformation.transformation method)": [[1, "spatialpy.core.transformation.Transformation.transform"]], "transform() (spatialpy.core.transformation.translationtransformation method)": [[1, "spatialpy.core.transformation.TranslationTransformation.transform"]], "update_namespace() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.update_namespace"]], "update_namespace() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.update_namespace"]], "validate() (spatialpy.core.cartesianlattice method)": [[1, "spatialpy.core.CartesianLattice.validate"]], "validate() (spatialpy.core.combinatorygeometry method)": [[1, "spatialpy.core.CombinatoryGeometry.validate"]], "validate() (spatialpy.core.cylindricallattice method)": [[1, "spatialpy.core.CylindricalLattice.validate"]], "validate() (spatialpy.core.meshiolattice method)": [[1, "spatialpy.core.MeshIOLattice.validate"]], "validate() (spatialpy.core.parameter method)": [[1, "spatialpy.core.Parameter.validate"]], "validate() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.validate"]], "validate() (spatialpy.core.rotationtransformation method)": [[1, "spatialpy.core.RotationTransformation.validate"]], "validate() (spatialpy.core.scalingtransformation method)": [[1, "spatialpy.core.ScalingTransformation.validate"]], "validate() (spatialpy.core.species method)": [[1, "spatialpy.core.Species.validate"]], "validate() (spatialpy.core.sphericallattice method)": [[1, "spatialpy.core.SphericalLattice.validate"]], "validate() (spatialpy.core.stochsslattice method)": [[1, "spatialpy.core.StochSSLattice.validate"]], "validate() (spatialpy.core.timespan method)": [[1, "spatialpy.core.TimeSpan.validate"]], "validate() (spatialpy.core.transformation method)": [[1, "spatialpy.core.Transformation.validate"]], "validate() (spatialpy.core.translationtransformation method)": [[1, "spatialpy.core.TranslationTransformation.validate"]], "validate() (spatialpy.core.xmlmeshlattice method)": [[1, "spatialpy.core.XMLMeshLattice.validate"]], "validate() (spatialpy.core.geometry.combinatorygeometry method)": [[1, "spatialpy.core.geometry.CombinatoryGeometry.validate"]], "validate() (spatialpy.core.lattice.cartesianlattice method)": [[1, "spatialpy.core.lattice.CartesianLattice.validate"]], "validate() (spatialpy.core.lattice.cylindricallattice method)": [[1, "spatialpy.core.lattice.CylindricalLattice.validate"]], "validate() (spatialpy.core.lattice.lattice method)": [[1, "spatialpy.core.lattice.Lattice.validate"]], "validate() (spatialpy.core.lattice.meshiolattice method)": [[1, "spatialpy.core.lattice.MeshIOLattice.validate"]], "validate() (spatialpy.core.lattice.sphericallattice method)": [[1, "spatialpy.core.lattice.SphericalLattice.validate"]], "validate() (spatialpy.core.lattice.stochsslattice method)": [[1, "spatialpy.core.lattice.StochSSLattice.validate"]], "validate() (spatialpy.core.lattice.xmlmeshlattice method)": [[1, "spatialpy.core.lattice.XMLMeshLattice.validate"]], "validate() (spatialpy.core.parameter.parameter method)": [[1, "spatialpy.core.parameter.Parameter.validate"]], "validate() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.validate"]], "validate() (spatialpy.core.species.species method)": [[1, "spatialpy.core.species.Species.validate"]], "validate() (spatialpy.core.timespan.timespan method)": [[1, "spatialpy.core.timespan.TimeSpan.validate"]], "validate() (spatialpy.core.transformation.rotationtransformation method)": [[1, "spatialpy.core.transformation.RotationTransformation.validate"]], "validate() (spatialpy.core.transformation.scalingtransformation method)": [[1, "spatialpy.core.transformation.ScalingTransformation.validate"]], "validate() (spatialpy.core.transformation.transformation method)": [[1, "spatialpy.core.transformation.Transformation.validate"]], "validate() (spatialpy.core.transformation.translationtransformation method)": [[1, "spatialpy.core.transformation.TranslationTransformation.validate"]], "validate_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.validate_action"]], "validate_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.validate_action"]], "buildexpression (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.BuildExpression"]], "buildexpression.validationvisitor (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor"]], "cppconverter (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.CppConverter"]], "cppconverter.cppexpressiontransformer (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.CppConverter.CppExpressionTransformer"]], "expressionconverter (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter"]], "expressionresults (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.ExpressionResults"]], "pythonconverter (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.PythonConverter"]], "solver (class in spatialpy.solvers.solver)": [[2, "spatialpy.solvers.solver.Solver"]], "compile() (spatialpy.solvers.solver.solver method)": [[2, "spatialpy.solvers.solver.Solver.compile"]], "convert_str() (spatialpy.solvers.build_expression.expressionconverter class method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.convert_str"]], "get_str() (spatialpy.solvers.build_expression.cppconverter method)": [[2, "spatialpy.solvers.build_expression.CppConverter.get_str"]], "get_str() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.get_str"]], "getexpr_cpp() (spatialpy.solvers.build_expression.buildexpression method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.getexpr_cpp"]], "getexpr_python() (spatialpy.solvers.build_expression.buildexpression method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.getexpr_python"]], "map_operator() (spatialpy.solvers.build_expression.buildexpression class method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.map_operator"]], "operator_map (spatialpy.solvers.build_expression.buildexpression attribute)": [[2, "spatialpy.solvers.build_expression.BuildExpression.operator_map"]], "parse_comparison() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.parse_comparison"]], "parse_logical() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.parse_logical"]], "parse_operator() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.parse_operator"]], "run() (spatialpy.solvers.solver.solver method)": [[2, "spatialpy.solvers.solver.Solver.run"]], "spatialpy.solvers": [[2, "module-spatialpy.solvers"]], "spatialpy.solvers.build_expression": [[2, "module-spatialpy.solvers.build_expression"]], "spatialpy.solvers.solver": [[2, "module-spatialpy.solvers.solver"]], "validate() (spatialpy.solvers.build_expression.buildexpression method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.validate"]], "visit_add() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Add"]], "visit_and() (spatialpy.solvers.build_expression.cppconverter method)": [[2, "spatialpy.solvers.build_expression.CppConverter.visit_And"]], "visit_and() (spatialpy.solvers.build_expression.pythonconverter method)": [[2, "spatialpy.solvers.build_expression.PythonConverter.visit_And"]], "visit_assign() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_Assign"]], "visit_binop() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_BinOp"]], "visit_binop() (spatialpy.solvers.build_expression.cppconverter.cppexpressiontransformer method)": [[2, "spatialpy.solvers.build_expression.CppConverter.CppExpressionTransformer.visit_BinOp"]], "visit_binop() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_BinOp"]], "visit_boolop() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_BoolOp"]], "visit_boolop() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_BoolOp"]], "visit_bytes() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Bytes"]], "visit_call() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_Call"]], "visit_call() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Call"]], "visit_compare() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_Compare"]], "visit_compare() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Compare"]], "visit_constant() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Constant"]], "visit_div() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Div"]], "visit_ellipsis() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Ellipsis"]], "visit_eq() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Eq"]], "visit_gt() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Gt"]], "visit_gte() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_GtE"]], "visit_lt() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Lt"]], "visit_lte() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_LtE"]], "visit_mult() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Mult"]], "visit_name() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_Name"]], "visit_name() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Name"]], "visit_nameconstant() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_NameConstant"]], "visit_noteq() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_NotEq"]], "visit_num() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Num"]], "visit_or() (spatialpy.solvers.build_expression.cppconverter method)": [[2, "spatialpy.solvers.build_expression.CppConverter.visit_Or"]], "visit_or() (spatialpy.solvers.build_expression.pythonconverter method)": [[2, "spatialpy.solvers.build_expression.PythonConverter.visit_Or"]], "visit_pow() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Pow"]], "visit_str() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Str"]], "visit_sub() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Sub"]], "visit_usub() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_USub"]], "visit_unaryop() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_UnaryOp"]], "visit_unaryop() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_UnaryOp"]], "with_blacklist() (spatialpy.solvers.build_expression.buildexpression method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.with_blacklist"]], "with_namespace() (spatialpy.solvers.build_expression.buildexpression method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.with_namespace"]], "export() (in module spatialpy.stochss.stochss_export)": [[3, "spatialpy.stochss.stochss_export.export"]], "spatialpy.stochss": [[3, "module-spatialpy.stochss"]], "spatialpy.stochss.stochss_export": [[3, "module-spatialpy.stochss.stochss_export"]]}}) \ No newline at end of file +Search.setIndex({"docnames": ["classes/spatialpy", "classes/spatialpy.core", "classes/spatialpy.solvers", "classes/spatialpy.stochss", "index"], "filenames": ["classes/spatialpy.rst", "classes/spatialpy.core.rst", "classes/spatialpy.solvers.rst", "classes/spatialpy.stochss.rst", "index.rst"], "titles": ["spatialpy package", "spatialpy.core package", "spatialpy.solvers package", "spatialpy.stochss package", "Documentation for SpatialPy 1.2.1"], "terms": {"core": [0, 2, 3, 4], "submodul": 0, "boundarycondit": 0, "express": [0, 1, 2], "cleanup": 0, "cleanup_build_fil": [0, 1], "cleanup_core_fil": [0, 1], "cleanup_result_fil": [0, 1], "cleanup_tempfil": [0, 1], "datafunct": 0, "map": [0, 1, 2], "domain": [0, 4], "add_fill_act": [0, 1], "add_point": [0, 1], "add_remove_act": [0, 1], "add_set_act": [0, 1], "apply_act": [0, 1], "apply_fill_act": [0, 1], "apply_remove_act": [0, 1], "apply_set_act": [0, 1], "calculate_vol": [0, 1], "closest_vertex": [0, 1], "compile_prep": [0, 1], "coordin": [0, 1], "create_2d_domain": [0, 1], "create_3d_domain": [0, 1], "distance_between_2_vertic": [0, 1], "fill_with_particl": [0, 1], "find_boundary_point": [0, 1], "find_h": [0, 1], "get_bounding_box": [0, 1], "get_domain_s": [0, 1], "get_num_voxel": [0, 1], "get_type_def": [0, 1], "get_vol": [0, 1], "import_meshio_object": [0, 1], "plot_typ": [0, 1], "preview_act": [0, 1], "read_msh_fil": [0, 1], "read_stochss_domain": [0, 1], "read_stochss_subdomain_fil": [0, 1], "read_xml_mesh": [0, 1], "set_properti": [0, 1], "validate_act": [0, 1], "geometri": 0, "combinatorygeometri": [0, 1], "insid": [0, 1], "valid": [0, 1, 2], "geometryal": [0, 1], "geometryexterior": [0, 1], "geometryinterior": [0, 1], "initialcondit": 0, "appli": [0, 1], "placeinitialcondit": [0, 1], "scatterinitialcondit": [0, 1], "uniforminitialcondit": [0, 1], "lattic": 0, "cartesianlattic": [0, 1], "cylindricallattic": [0, 1], "meshiolattic": [0, 1], "sphericallattic": [0, 1], "stochsslattic": [0, 1], "xmlmeshlattic": [0, 1], "model": [0, 2, 3, 4], "add": [0, 1, 2], "add_boundary_condit": [0, 1], "add_data_funct": [0, 1], "add_domain": [0, 1], "add_initial_condit": [0, 1], "add_paramet": [0, 1], "add_react": [0, 1], "add_speci": [0, 1], "delete_all_boundary_condit": [0, 1], "delete_all_data_funct": [0, 1], "delete_all_initial_condit": [0, 1], "delete_all_paramet": [0, 1], "delete_all_react": [0, 1], "delete_all_speci": [0, 1], "delete_boundary_condit": [0, 1], "delete_data_funct": [0, 1], "delete_initial_condit": [0, 1], "delete_paramet": [0, 1], "delete_react": [0, 1], "delete_speci": [0, 1], "get_all_boundary_condit": [0, 1], "get_all_data_funct": [0, 1], "get_all_initial_condit": [0, 1], "get_all_paramet": [0, 1], "get_all_react": [0, 1], "get_all_speci": [0, 1], "get_data_funct": [0, 1], "get_el": [0, 1], "get_num_react": [0, 1], "get_num_speci": [0, 1], "get_paramet": [0, 1], "get_react": [0, 1], "get_speci": [0, 1], "reserved_nam": [0, 1], "run": [0, 1, 2], "sanitized_data_function_nam": [0, 1], "sanitized_parameter_nam": [0, 1], "sanitized_species_nam": [0, 1], "set_timestep": [0, 1], "special_charact": [0, 1], "timespan": 0, "update_namespac": [0, 1], "export_stochss": [0, 1], "paramet": [0, 2, 3], "reaction": [0, 4], "add_product": [0, 1], "annot": [0, 1], "from_json": [0, 1], "initi": [0, 1], "sanitized_propensity_funct": [0, 1], "set_annot": [0, 1], "set_propens": [0, 1], "set_rat": [0, 1], "to_dict": [0, 1], "result": [0, 2], "export_to_csv": [0, 1], "get_properti": [0, 1], "get_timespan": [0, 1], "plot_properti": [0, 1], "plot_speci": [0, 1], "read_step": [0, 1], "spatialpyerror": 0, "boundaryconditionerror": [0, 1], "datafunctionerror": [0, 1], "domainerror": [0, 1], "geometryerror": [0, 1], "initialconditionerror": [0, 1], "latticeerror": [0, 1], "modelerror": [0, 1], "parametererror": [0, 1], "reactionerror": [0, 1], "resulterror": [0, 1], "simulationerror": [0, 1, 2], "simulationtimeout": [0, 1, 2], "specieserror": [0, 1], "timespanerror": [0, 1], "transformationerror": [0, 1], "vtkreadererror": [0, 1], "vtkreaderioerror": [0, 1], "visualizationerror": [0, 1], "speci": 0, "set_diffusion_coeffici": [0, 1], "arang": [0, 1], "linspac": [0, 1], "transform": 0, "reflectiontransform": [0, 1], "reverse_transform": [0, 1], "rotationtransform": [0, 1], "scalingtransform": [0, 1], "translationtransform": [0, 1], "visual": 0, "mpl_height": [0, 1], "mpl_size": [0, 1], "mpl_width": [0, 1], "plot_scatt": [0, 1], "vtkreader": 0, "get_array_nam": [0, 1], "get_arrai": [0, 1], "get_num_point": [0, 1], "get_point": [0, 1], "read_fil": [0, 1], "set_filenam": [0, 1], "solver": [0, 1, 4], "build_express": 0, "buildexpress": [0, 2], "validationvisitor": [0, 2], "getexpr_cpp": [0, 2], "getexpr_python": [0, 2], "map_oper": [0, 2], "operator_map": [0, 2], "with_blacklist": [0, 2], "with_namespac": [0, 2], "cppconvert": [0, 2], "cppexpressiontransform": [0, 2], "get_str": [0, 2], "visit_and": [0, 2], "visit_or": [0, 2], "expressionconvert": [0, 2], "convert_str": [0, 2], "parse_comparison": [0, 2], "parse_log": [0, 2], "parse_oper": [0, 2], "visit_add": [0, 2], "visit_binop": [0, 2], "visit_boolop": [0, 2], "visit_byt": [0, 2], "visit_cal": [0, 2], "visit_compar": [0, 2], "visit_const": [0, 2], "visit_div": [0, 2], "visit_ellipsi": [0, 2], "visit_eq": [0, 2], "visit_gt": [0, 2], "visit_lt": [0, 2], "visit_mult": [0, 2], "visit_nam": [0, 2], "visit_nameconst": [0, 2], "visit_noteq": [0, 2], "visit_num": [0, 2], "visit_pow": [0, 2], "visit_str": [0, 2], "visit_sub": [0, 2], "visit_usub": [0, 2], "visit_unaryop": [0, 2], "expressionresult": [0, 2], "pythonconvert": [0, 2], "compil": [0, 1, 2], "stochss": [0, 1, 4], "stochss_export": 0, "export": [0, 1, 3], "class": [1, 2], "xmin": 1, "none": [1, 2, 3], "xmax": 1, "ymin": 1, "ymax": 1, "zmin": 1, "zmax": 1, "type_id": 1, "determinist": [1, 4], "true": [1, 2, 3], "target": [1, 2], "valu": [1, 2], "sourc": [1, 2, 3, 4], "base": [1, 2, 4], "object": [1, 2], "set": [1, 2], "spatial": [1, 2, 4], "region": 1, "where": 1, "properti": [1, 2], "particl": [1, 4], "ar": [1, 2], "held": 1, "constant": [1, 2], "updat": 1, "each": 1, "simul": [1, 2, 4], "step": 1, "condit": [1, 2], "one": [1, 2], "more": [1, 2, 4], "follow": [1, 2], "must": 1, "float": 1, "min": 1, "max": 1, "x": 1, "dimens": 1, "y": 1, "z": 1, "type": [1, 2, 3], "subdomain": 1, "partcil": 1, "str": [1, 2, 3], "nu": 1, "rho": 1, "v": 1, "name": [1, 2], "chemic": 1, "also": [1, 2, 4], "fals": [1, 2, 3], "flag": [1, 2], "axi": 1, "lower": 1, "bound": 1, "upper": 1, "int": [1, 2], "id": 1, "bool": [1, 2, 3], "i": [1, 2, 3, 4], "boundari": 1, "yet": 1, "implemenet": 1, "stochast": [1, 4], "can": [1, 2, 4], "If": [1, 2, 4], "determinst": 1, "3": [1, 4], "take": 1, "defin": [1, 2], "creat": [1, 2], "evalu": 1, "string": [1, 2], "return": [1, 2, 3], "A": [1, 2, 4], "represent": [1, 2], "build_dir": 1, "all": [1, 2], "spatialpy_build": 1, "directori": 1, "path": [1, 3], "build": [1, 2, 4], "remov": 1, "option": 1, "tempfil": 1, "result_dir": 1, "spatialpy_result": 1, "abstract": [1, 2], "us": [1, 2, 4], "constuct": 1, "data": [1, 2], "function": [1, 2], "rais": [1, 2], "provid": [1, 2, 4], "point": 1, "thi": [1, 2, 4], "method": [1, 2], "overridden": 1, "subclass": [1, 2], "note": [1, 2], "The": [1, 2, 4], "locat": 1, "evaul": 1, "t": [1, 2], "0": [1, 2], "re": 1, "fluid": [1, 4], "move": 1, "over": 1, "time": [1, 2], "posit": 1, "numpoint": 1, "xlim": 1, "ylim": 1, "zlim": 1, "rho0": 1, "1": [1, 2], "c0": 1, "10": 1, "p0": 1, "graviti": [1, 4], "action": 1, "attribut": 1, "space": 1, "total": 1, "number": [1, 2], "2": 1, "rang": 1, "along": 1, "background": 1, "densiti": 1, "system": [1, 4], "speed": 1, "sound": 1, "pressur": 1, "acceler": 1, "cartesian": 1, "spheric": 1, "cylindr": 1, "enabl": 1, "prop": 1, "an": [1, 2, 4], "when": [1, 2], "fill": [1, 4], "default": 1, "dict": [1, 2, 3], "argument": 1, "ignor": 1, "indic": [1, 2], "els": [1, 3], "addit": [1, 2], "pass": [1, 2], "ad": [1, 2], "wasn": 1, "could": [1, 2], "construct": 1, "vol": 1, "mass": 1, "unassign": 1, "fix": 1, "c": [1, 2], "singl": [1, 2], "vertic": 1, "volum": 1, "cradded": 1, "viscos": 1, "artifici": 1, "contain": [1, 2], "invalid": [1, 2], "charact": 1, "from": [1, 2], "start": [1, 2, 4], "end": 1, "preserve_act": 1, "order": 1, "index": [1, 4], "inclus": 1, "exclus": 1, "after": 1, "its": 1, "support": [1, 4], "within": 1, "have": 1, "exampl": 1, "lattice_obj": 1, "geometry_obj": 1, "miss": 1, "calcul": 1, "find": [1, 4], "nearest": 1, "vertex": 1, "given": [1, 2], "gener": [1, 4], "list": [1, 2], "check": [1, 2], "preper": 1, "file": [1, 3], "get": [1, 2], "numpi": 1, "arrai": 1, "classmethod": [1, 2], "numx": 1, "numi": 1, "kwarg": 1, "2d": 1, "highest": 1, "lowest": 1, "keyword": 1, "uniform": 1, "numz": 1, "3d": [1, 4], "distanc": 1, "between": [1, 2], "measur": 1, "geometry_ivar": 1, "deltax": 1, "deltai": 1, "deltaz": 1, "geometr": 1, "shape": 1, "instanc": [1, 2], "minimum": 1, "box": 1, "maximum": [1, 2], "were": [1, 2], "exist": 1, "np": 1, "ndarrai": 1, "dtype": 1, "h": 1, "off": 1, "which": [1, 2], "ha": [1, 4], "greatest": 1, "neighbor": 1, "entir": 1, "limit": 1, "tupl": 1, "estim": 1, "size": 1, "averag": 1, "diamet": 1, "circumradiu": 1, "tetrahedron": 1, "part": 1, "mean": 1, "incid": 1, "cell": 1, "voxel": 1, "definit": 1, "mesh_obj": 1, "subdomain_fil": 1, "import": 1, "python": [1, 2, 4], "meshio": 1, "mesh": 1, "v1": 1, "descript": 1, "filenam": [1, 3], "indeci": 1, "width": 1, "height": 1, "colormap": 1, "titl": 1, "included_types_list": 1, "use_matplotlib": 1, "return_plotly_figur": 1, "plot": 1, "plotli": 1, "onli": [1, 2], "view": 1, "jupyt": 1, "notebook": [1, 4], "pixel": 1, "output": [1, 2], "matplotlib": 1, "inch": 1, "500": 1, "specif": 1, "plotly3": 1, "jet": 1, "blue": 1, "ylorrd": 1, "purd": 1, "bugn": 1, "ylorbr": 1, "pubugn": 1, "bupu": 1, "ylgnbu": 1, "pubu": 1, "gnbu": 1, "ylgn": 1, "green": 1, "red": 1, "grei": 1, "rdpu": 1, "orrd": 1, "purpl": 1, "orang": 1, "graph": 1, "describ": [1, 4], "includ": 1, "By": [1, 2], "displai": 1, "whether": [1, 2, 3], "figur": 1, "dictionari": [1, 2], "trace": 1, "layout": 1, "mai": 1, "edit": 1, "user": [1, 4], "proprti": 1, "preview": 1, "effect": 1, "read": 1, "gmsh": 1, "style": 1, "msh": 1, "domn": 1, "pull": 1, "smdl": 1, "txt": 1, "conain": 1, "fenic": 1, "dolfin": 1, "xml": 1, "assign": [1, 2], "identifi": [1, 2], "immobil": 1, "coverag": 1, "scope": 1, "accept": [1, 2], "doaminerror": 1, "met": 1, "": [1, 4], "formula": 1, "geo_namespac": 1, "combinatori": 1, "multipl": [1, 2], "boolean": 1, "logic": [1, 2], "geo1": 1, "geo2": 1, "geo3": 1, "namespac": [1, 2], "geometry1": 1, "geometry2": 1, "geometry3": 1, "found": [1, 2, 4], "on_boundari": 1, "coodin": 1, "edg": 1, "satisfi": 1, "geometi": 1, "ani": [1, 2, 4], "doe": 1, "tag": 1, "separ": 1, "mark": 1, "work": 1, "triangl": 1, "implement": [1, 2], "direct": 1, "modifi": 1, "u0": 1, "matrix": 1, "count": 1, "contian": 1, "place": 1, "scatter": 1, "randomli": 1, "center": 1, "two": [1, 2], "doesn": 1, "restrict": 1, "depend": 1, "radiu": 1, "length": 1, "delta": 1, "deltar": 1, "surfac": 1, "radial": 1, "skip_valid": 1, "arg": 1, "io": 1, "un": 1, "biochem": 1, "compon": 1, "befor": 1, "other": [1, 2], "combin": 1, "than": 1, "do": 1, "need": [1, 4], "particular": 1, "bound_cond": 1, "conidit": 1, "data_funct": 1, "scalar": 1, "you": [1, 4], "vari": 1, "input": 1, "your": [1, 4], "It": 1, "positon": 1, "toth": 1, "init_cond": 1, "fail": [1, 2], "make": 1, "sure": 1, "paramt": 1, "diffus": [1, 4], "util": 1, "stoichiometr": 1, "dependency_graph": 1, "timestep": 1, "exce": 1, "frequenc": 1, "ordereddict": 1, "form": [1, 4], "kei": [1, 2], "specifi": 1, "element": 1, "differ": [1, 2], "rname": [], "number_of_trajectori": [1, 2], "seed": [1, 2], "timeout": [1, 2], "number_of_thread": [1, 2], "debug_level": [1, 2], "debug": [1, 2], "profil": [1, 2], "how": [1, 2, 4], "mani": [1, 2], "trajectori": [1, 2], "should": [1, 2], "random": [1, 2], "second": [1, 2], "kill": 1, "upon": 1, "reach": 1, "thread": [1, 2], "level": [1, 2], "print": [1, 2], "out": [1, 4], "info": 1, "dure": [1, 2], "addtion": [1, 2], "perform": 1, "chosen": 1, "simplifi": 1, "format": 1, "later": [1, 2], "spatialpysolv": 1, "propens": 1, "intern": 1, "notat": 1, "output_interv": 1, "num_step": 1, "timestep_s": 1, "simlat": 1, "span": 1, "first": [1, 2], "zero": 1, "time_span": 1, "ssa": 1, "sdpd": [1, 4], "engin": 1, "non": 1, "tspan": 1, "evenli": 1, "sampl": 1, "popul": 1, "flatten": 1, "spatialpy_model": 1, "return_stochss_model": [1, 3], "convert": [1, 2, 3], "json": 1, "platform": 1, "directli": [1, 4], "understood": 1, "parent": 1, "call": [1, 2], "referenc": 1, "requir": 1, "outsid": 1, "reactant": 1, "product": 1, "propensity_funct": 1, "ode_propensity_funct": 1, "rate": 1, "restrict_to": 1, "conatain": 1, "neg": 1, "union": 1, "For": [1, 4], "zeroth": 1, "attempt": 1, "higher": 1, "error": 1, "consum": 1, "stoichiometri": 1, "would": 1, "r1": 1, "r2": 1, "event": 1, "same": 1, "custom": 1, "oper": [1, 2], "od": 1, "care": 1, "unit": 1, "about": 1, "execut": [1, 2], "NOT": 1, "both": [1, 4], "term": 1, "repres": 1, "independ": 1, "wa": 1, "impact": 1, "preserv": 1, "produc": 1, "particip": 1, "deprec": 1, "param": 1, "json_object": 1, "defer": 1, "species_map": 1, "parameter_map": 1, "chang": 1, "marat": 1, "urdm": 1, "folder_nam": 1, "write": 1, "csv": 1, "modelname_mesh": 1, "modelname_species_": 1, "column": 1, "n": 1, "vtk": 1, "written": 1, "current": [1, 2], "property_nam": 1, "timepoint": 1, "integ": 1, "1d": 1, "veloc": 1, "bvf_phi": 1, "fraction": 1, "across": 1, "concentr": 1, "retreiv": 1, "inform": [1, 2, 4], "raw": 1, "copy_numb": 1, "unabl": 1, "retriev": 1, "t_ndx": 1, "t_val": 1, "p_ndx": 1, "anim": 1, "t_ndx_list": 1, "f_durat": 1, "t_durat": 1, "300": 1, "6": 1, "4": 1, "8": 1, "indec": 1, "interv": 1, "durat": 1, "frame": [1, 4], "transit": 1, "5": 1, "show": 1, "instead": 1, "step_num": 1, "except": 1, "initailcondit": 1, "bass": 1, "messag": 1, "o": 1, "diffusion_coeffici": 1, "coeffic": 1, "coeffici": 1, "listoftyp": 1, "movement": 1, "setter": 1, "item": [1, 2], "iter": 1, "best": 1, "increment": [1, 2], "20": 1, "num_point": 1, "empti": [1, 2], "repeat": 1, "point1": 1, "normal": 1, "point2": 1, "point3": 1, "reflect": 1, "revers": 1, "around": 1, "arbitrari": 1, "plane": 1, "serv": 1, "vector": 1, "onc": 1, "wrap": 1, "prior": 1, "angl": 1, "rotat": 1, "basic": 1, "factor": 1, "scale": 1, "wrapper": 1, "translat": 1, "40": 1, "plot_arg": 1, "scatter_arg": 1, "multiple_graph": 1, "maplotlib": 1, "pyplot": 1, "subplot": 1, "dist": 1, "group": 1, "nrow": 1, "ncol": 1, "entri": 1, "plote": 1, "py": 1, "minim": 1, "legaci": 1, "reader": 1, "refer": 1, "http": [1, 4], "org": 1, "wp": 1, "upload": 1, "2015": 1, "04": 1, "pdf": 1, "arraid": 1, "ascii": 1, "blacklist": 2, "sanit": 2, "allow": 2, "pre": 2, "flight": 2, "syntax": 2, "well": 2, "manag": 2, "context": 2, "statement": 2, "expect": 2, "forward": 2, "ideal": 2, "univers": 2, "constructor": 2, "granular": 2, "bare": 2, "equival": 2, "trigger": 2, "substitut": 2, "convers": 2, "automat": 2, "correspond": 2, "getexpr_": 2, "nodetransform": 2, "ast": 2, "expres": 2, "spactialpi": 2, "node": 2, "visit_assign": 2, "visitor": 2, "origin": 2, "binop": 2, "boolop": 2, "binboolopop": 2, "otherwis": 2, "compar": 2, "unaryop": 2, "syntaxerror": 2, "imposs": 2, "convet": 2, "built": 2, "_ast": 2, "Not": 2, "noteq": 2, "mod": 2, "bitand": 2, "mult": 2, "pow": 2, "sub": 2, "div": 2, "floordiv": 2, "lt": 2, "lshift": 2, "lte": 2, "eq": 2, "gt": 2, "gte": 2, "rshift": 2, "matmult": 2, "bitxor": 2, "And": 2, "Or": 2, "bitor": 2, "so": 2, "far": 2, "ensur": 2, "pars": 2, "against": 2, "addition": 2, "reject": 2, "rvalu": 2, "new": 2, "duplic": 2, "overrid": 2, "handl": 2, "behavior": 2, "copi": 2, "rtype": 2, "present": 2, "caus": 2, "what": 2, "tree": 2, "super": 2, "nodevisitor": 2, "self": 2, "comparison": 2, "last": 2, "mathemat": 2, "right": 2, "visit": 2, "left": 2, "most": 2, "recent": 2, "append": 2, "token": 2, "alwai": 2, "hand": 2, "u": 2, "pop": 2, "process": 2, "assum": 2, "inherit": 2, "byte": 2, "ellipsi": 2, "nameconst": 2, "num": 2, "usub": 2, "invalid_nam": 2, "invalid_oper": 2, "is_valid": 2, "struct": 2, "infer": 2, "invalid_": 2, "verbos": 2, "gdbgui": 2, "debugg": 2, "symbol": 2, "hasn": 2, "happen": 2, "gprof": 2, "avail": [2, 4], "consol": 2, "seri": 2, "exceed": 2, "packag": 4, "advect": 4, "problem": 4, "embed": 4, "lagrangian": 4, "dynam": 4, "intend": 4, "replac": 4, "pyurdm": 4, "softwar": 4, "github": 4, "com": 4, "featur": 4, "nsm": 4, "rdme": 4, "static": 4, "sssa": 4, "public": 4, "hybrid": 4, "smooth": 4, "dissip": 4, "algorithm": 4, "drawert": 4, "jacob": 4, "li": 4, "yi": 4, "petzold": 4, "www": 4, "sciencedirect": 4, "scienc": 4, "articl": 4, "pii": 4, "s0021999118307101": 4, "latest": 4, "version": 4, "pypi": 4, "code": 4, "licens": 4, "under": 4, "gnu": 4, "pleas": 4, "regist": 4, "develop": 4, "fund": 4, "nih": 4, "grant": 4, "2r01eb014877": 4, "continu": 4, "we": 4, "prove": 4, "our": 4, "short": 4, "registr": 4, "see": 4, "here": 4, "cylind": 4, "demo": 4, "physic": 4, "flow": 4, "weir": 4, "tracker": 4, "project": 4, "contact": 4, "main": 4, "author": 4, "dr": 4, "brian": 4, "question": 4, "suggest": 4, "subpackag": 4, "modul": 4, "content": 4, "search": 4, "page": 4, "allow_all_typ": 1}, "objects": {"": [[0, 0, 0, "-", "spatialpy"]], "spatialpy": [[1, 0, 0, "-", "core"], [2, 0, 0, "-", "solvers"], [3, 0, 0, "-", "stochss"]], "spatialpy.core": [[1, 1, 1, "", "BoundaryCondition"], [1, 3, 1, "", "BoundaryConditionError"], [1, 1, 1, "", "CartesianLattice"], [1, 1, 1, "", "CombinatoryGeometry"], [1, 1, 1, "", "CylindricalLattice"], [1, 1, 1, "", "DataFunction"], [1, 3, 1, "", "DataFunctionError"], [1, 1, 1, "", "Domain"], [1, 3, 1, "", "DomainError"], [1, 1, 1, "", "Geometry"], [1, 1, 1, "", "GeometryAll"], [1, 3, 1, "", "GeometryError"], [1, 1, 1, "", "GeometryExterior"], [1, 1, 1, "", "GeometryInterior"], [1, 1, 1, "", "InitialCondition"], [1, 3, 1, "", "InitialConditionError"], [1, 3, 1, "", "LatticeError"], [1, 1, 1, "", "MeshIOLattice"], [1, 1, 1, "", "Model"], [1, 3, 1, "", "ModelError"], [1, 1, 1, "", "Parameter"], [1, 3, 1, "", "ParameterError"], [1, 1, 1, "", "PlaceInitialCondition"], [1, 1, 1, "", "Reaction"], [1, 3, 1, "", "ReactionError"], [1, 1, 1, "", "ReflectionTransformation"], [1, 1, 1, "", "Result"], [1, 3, 1, "", "ResultError"], [1, 1, 1, "", "RotationTransformation"], [1, 1, 1, "", "ScalingTransformation"], [1, 1, 1, "", "ScatterInitialCondition"], [1, 3, 1, "", "SimulationError"], [1, 3, 1, "", "SimulationTimeout"], [1, 1, 1, "", "Species"], [1, 3, 1, "", "SpeciesError"], [1, 1, 1, "", "SphericalLattice"], [1, 1, 1, "", "StochSSLattice"], [1, 1, 1, "", "TimeSpan"], [1, 3, 1, "", "TimespanError"], [1, 1, 1, "", "Transformation"], [1, 3, 1, "", "TransformationError"], [1, 1, 1, "", "TranslationTransformation"], [1, 1, 1, "", "UniformInitialCondition"], [1, 1, 1, "", "VTKReader"], [1, 3, 1, "", "VTKReaderError"], [1, 3, 1, "", "VTKReaderIOError"], [1, 1, 1, "", "Visualization"], [1, 3, 1, "", "VisualizationError"], [1, 1, 1, "", "XMLMeshLattice"], [1, 0, 0, "-", "boundarycondition"], [1, 0, 0, "-", "cleanup"], [1, 5, 1, "", "cleanup_build_files"], [1, 5, 1, "", "cleanup_core_files"], [1, 5, 1, "", "cleanup_result_files"], [1, 5, 1, "", "cleanup_tempfiles"], [1, 0, 0, "-", "datafunction"], [1, 0, 0, "-", "domain"], [1, 5, 1, "", "export_StochSS"], [1, 0, 0, "-", "geometry"], [1, 0, 0, "-", "initialcondition"], [1, 0, 0, "-", "lattice"], [1, 0, 0, "-", "model"], [1, 0, 0, "-", "parameter"], [1, 0, 0, "-", "reaction"], [1, 0, 0, "-", "result"], [1, 0, 0, "-", "spatialpyerror"], [1, 0, 0, "-", "species"], [1, 0, 0, "-", "timespan"], [1, 0, 0, "-", "transformation"], [1, 0, 0, "-", "visualization"], [1, 0, 0, "-", "vtkreader"]], "spatialpy.core.BoundaryCondition": [[1, 2, 1, "", "expression"]], "spatialpy.core.CartesianLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.CombinatoryGeometry": [[1, 2, 1, "", "inside"], [1, 2, 1, "", "validate"]], "spatialpy.core.CylindricalLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.DataFunction": [[1, 2, 1, "", "map"]], "spatialpy.core.Domain": [[1, 2, 1, "", "add_fill_action"], [1, 2, 1, "", "add_point"], [1, 2, 1, "", "add_remove_action"], [1, 2, 1, "", "add_set_action"], [1, 2, 1, "", "apply_actions"], [1, 2, 1, "", "apply_fill_action"], [1, 2, 1, "", "apply_remove_action"], [1, 2, 1, "", "apply_set_action"], [1, 2, 1, "", "calculate_vol"], [1, 2, 1, "", "closest_vertex"], [1, 2, 1, "", "compile_prep"], [1, 2, 1, "", "coordinates"], [1, 2, 1, "", "create_2D_domain"], [1, 2, 1, "", "create_3D_domain"], [1, 2, 1, "", "distance_between_2_vertices"], [1, 2, 1, "", "fill_with_particles"], [1, 2, 1, "", "find_boundary_points"], [1, 2, 1, "", "find_h"], [1, 2, 1, "", "get_bounding_box"], [1, 2, 1, "", "get_domain_size"], [1, 2, 1, "", "get_num_voxels"], [1, 2, 1, "", "get_type_def"], [1, 2, 1, "", "get_vol"], [1, 2, 1, "", "import_meshio_object"], [1, 2, 1, "", "plot_types"], [1, 2, 1, "", "preview_actions"], [1, 2, 1, "", "read_msh_file"], [1, 2, 1, "", "read_stochss_domain"], [1, 2, 1, "", "read_stochss_subdomain_file"], [1, 2, 1, "", "read_xml_mesh"], [1, 2, 1, "", "set_properties"], [1, 2, 1, "", "validate_action"]], "spatialpy.core.Geometry": [[1, 2, 1, "", "inside"]], "spatialpy.core.GeometryAll": [[1, 2, 1, "", "inside"]], "spatialpy.core.GeometryExterior": [[1, 2, 1, "", "inside"]], "spatialpy.core.GeometryInterior": [[1, 2, 1, "", "inside"]], "spatialpy.core.InitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.MeshIOLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.Model": [[1, 2, 1, "", "add"], [1, 2, 1, "", "add_boundary_condition"], [1, 2, 1, "", "add_data_function"], [1, 2, 1, "", "add_domain"], [1, 2, 1, "", "add_initial_condition"], [1, 2, 1, "", "add_parameter"], [1, 2, 1, "", "add_reaction"], [1, 2, 1, "", "add_species"], [1, 2, 1, "", "compile_prep"], [1, 2, 1, "", "delete_all_boundary_conditions"], [1, 2, 1, "", "delete_all_data_functions"], [1, 2, 1, "", "delete_all_initial_conditions"], [1, 2, 1, "", "delete_all_parameters"], [1, 2, 1, "", "delete_all_reactions"], [1, 2, 1, "", "delete_all_species"], [1, 2, 1, "", "delete_boundary_condition"], [1, 2, 1, "", "delete_data_function"], [1, 2, 1, "", "delete_initial_condition"], [1, 2, 1, "", "delete_parameter"], [1, 2, 1, "", "delete_reaction"], [1, 2, 1, "", "delete_species"], [1, 2, 1, "", "get_all_boundary_conditions"], [1, 2, 1, "", "get_all_data_functions"], [1, 2, 1, "", "get_all_initial_conditions"], [1, 2, 1, "", "get_all_parameters"], [1, 2, 1, "", "get_all_reactions"], [1, 2, 1, "", "get_all_species"], [1, 2, 1, "", "get_data_function"], [1, 2, 1, "", "get_element"], [1, 2, 1, "", "get_num_reactions"], [1, 2, 1, "", "get_num_species"], [1, 2, 1, "", "get_parameter"], [1, 2, 1, "", "get_reaction"], [1, 2, 1, "", "get_species"], [1, 4, 1, "", "reserved_names"], [1, 2, 1, "", "run"], [1, 2, 1, "", "sanitized_data_function_names"], [1, 2, 1, "", "sanitized_parameter_names"], [1, 2, 1, "", "sanitized_species_names"], [1, 2, 1, "", "set_timesteps"], [1, 4, 1, "", "special_characters"], [1, 2, 1, "", "timespan"], [1, 2, 1, "", "update_namespace"]], "spatialpy.core.Parameter": [[1, 2, 1, "", "validate"]], "spatialpy.core.PlaceInitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.Reaction": [[1, 2, 1, "", "add_product"], [1, 2, 1, "", "add_reactant"], [1, 2, 1, "", "annotate"], [1, 2, 1, "", "from_json"], [1, 2, 1, "", "initialize"], [1, 2, 1, "", "sanitized_propensity_function"], [1, 2, 1, "", "set_annotation"], [1, 2, 1, "", "set_propensities"], [1, 2, 1, "", "set_rate"], [1, 2, 1, "", "to_dict"], [1, 2, 1, "", "validate"]], "spatialpy.core.ReflectionTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"]], "spatialpy.core.Result": [[1, 2, 1, "", "export_to_csv"], [1, 2, 1, "", "get_property"], [1, 2, 1, "", "get_species"], [1, 2, 1, "", "get_timespan"], [1, 2, 1, "", "plot_property"], [1, 2, 1, "", "plot_species"], [1, 2, 1, "", "read_step"]], "spatialpy.core.RotationTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.ScalingTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.ScatterInitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.Species": [[1, 2, 1, "", "set_diffusion_coefficient"], [1, 2, 1, "", "validate"]], "spatialpy.core.SphericalLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.StochSSLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.TimeSpan": [[1, 2, 1, "", "arange"], [1, 2, 1, "", "linspace"], [1, 2, 1, "", "validate"]], "spatialpy.core.Transformation": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "inside"], [1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.TranslationTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.UniformInitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.VTKReader": [[1, 2, 1, "", "get_array_name"], [1, 2, 1, "", "get_arrays"], [1, 2, 1, "", "get_num_points"], [1, 2, 1, "", "get_points"], [1, 2, 1, "", "read_file"], [1, 2, 1, "", "set_filename"]], "spatialpy.core.Visualization": [[1, 4, 1, "", "MPL_HEIGHT"], [1, 4, 1, "", "MPL_SIZE"], [1, 4, 1, "", "MPL_WIDTH"], [1, 2, 1, "", "plot_scatter"]], "spatialpy.core.XMLMeshLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.boundarycondition": [[1, 1, 1, "", "BoundaryCondition"]], "spatialpy.core.boundarycondition.BoundaryCondition": [[1, 2, 1, "", "expression"]], "spatialpy.core.cleanup": [[1, 5, 1, "", "cleanup_build_files"], [1, 5, 1, "", "cleanup_core_files"], [1, 5, 1, "", "cleanup_result_files"], [1, 5, 1, "", "cleanup_tempfiles"]], "spatialpy.core.datafunction": [[1, 1, 1, "", "DataFunction"]], "spatialpy.core.datafunction.DataFunction": [[1, 2, 1, "", "map"]], "spatialpy.core.domain": [[1, 1, 1, "", "Domain"]], "spatialpy.core.domain.Domain": [[1, 2, 1, "", "add_fill_action"], [1, 2, 1, "", "add_point"], [1, 2, 1, "", "add_remove_action"], [1, 2, 1, "", "add_set_action"], [1, 2, 1, "", "apply_actions"], [1, 2, 1, "", "apply_fill_action"], [1, 2, 1, "", "apply_remove_action"], [1, 2, 1, "", "apply_set_action"], [1, 2, 1, "", "calculate_vol"], [1, 2, 1, "", "closest_vertex"], [1, 2, 1, "", "compile_prep"], [1, 2, 1, "", "coordinates"], [1, 2, 1, "", "create_2D_domain"], [1, 2, 1, "", "create_3D_domain"], [1, 2, 1, "", "distance_between_2_vertices"], [1, 2, 1, "", "fill_with_particles"], [1, 2, 1, "", "find_boundary_points"], [1, 2, 1, "", "find_h"], [1, 2, 1, "", "get_bounding_box"], [1, 2, 1, "", "get_domain_size"], [1, 2, 1, "", "get_num_voxels"], [1, 2, 1, "", "get_type_def"], [1, 2, 1, "", "get_vol"], [1, 2, 1, "", "import_meshio_object"], [1, 2, 1, "", "plot_types"], [1, 2, 1, "", "preview_actions"], [1, 2, 1, "", "read_msh_file"], [1, 2, 1, "", "read_stochss_domain"], [1, 2, 1, "", "read_stochss_subdomain_file"], [1, 2, 1, "", "read_xml_mesh"], [1, 2, 1, "", "set_properties"], [1, 2, 1, "", "validate_action"]], "spatialpy.core.geometry": [[1, 1, 1, "", "CombinatoryGeometry"], [1, 1, 1, "", "Geometry"], [1, 1, 1, "", "GeometryAll"], [1, 1, 1, "", "GeometryExterior"], [1, 1, 1, "", "GeometryInterior"]], "spatialpy.core.geometry.CombinatoryGeometry": [[1, 2, 1, "", "inside"], [1, 2, 1, "", "validate"]], "spatialpy.core.geometry.Geometry": [[1, 2, 1, "", "inside"]], "spatialpy.core.geometry.GeometryAll": [[1, 2, 1, "", "inside"]], "spatialpy.core.geometry.GeometryExterior": [[1, 2, 1, "", "inside"]], "spatialpy.core.geometry.GeometryInterior": [[1, 2, 1, "", "inside"]], "spatialpy.core.initialcondition": [[1, 1, 1, "", "InitialCondition"], [1, 1, 1, "", "PlaceInitialCondition"], [1, 1, 1, "", "ScatterInitialCondition"], [1, 1, 1, "", "UniformInitialCondition"]], "spatialpy.core.initialcondition.InitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.initialcondition.PlaceInitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.initialcondition.ScatterInitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.initialcondition.UniformInitialCondition": [[1, 2, 1, "", "apply"]], "spatialpy.core.lattice": [[1, 1, 1, "", "CartesianLattice"], [1, 1, 1, "", "CylindricalLattice"], [1, 1, 1, "", "Lattice"], [1, 1, 1, "", "MeshIOLattice"], [1, 1, 1, "", "SphericalLattice"], [1, 1, 1, "", "StochSSLattice"], [1, 1, 1, "", "XMLMeshLattice"]], "spatialpy.core.lattice.CartesianLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.lattice.CylindricalLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.lattice.Lattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.lattice.MeshIOLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.lattice.SphericalLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.lattice.StochSSLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.lattice.XMLMeshLattice": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "validate"]], "spatialpy.core.model": [[1, 1, 1, "", "Model"], [1, 5, 1, "", "export_StochSS"]], "spatialpy.core.model.Model": [[1, 2, 1, "", "add"], [1, 2, 1, "", "add_boundary_condition"], [1, 2, 1, "", "add_data_function"], [1, 2, 1, "", "add_domain"], [1, 2, 1, "", "add_initial_condition"], [1, 2, 1, "", "add_parameter"], [1, 2, 1, "", "add_reaction"], [1, 2, 1, "", "add_species"], [1, 2, 1, "", "compile_prep"], [1, 2, 1, "", "delete_all_boundary_conditions"], [1, 2, 1, "", "delete_all_data_functions"], [1, 2, 1, "", "delete_all_initial_conditions"], [1, 2, 1, "", "delete_all_parameters"], [1, 2, 1, "", "delete_all_reactions"], [1, 2, 1, "", "delete_all_species"], [1, 2, 1, "", "delete_boundary_condition"], [1, 2, 1, "", "delete_data_function"], [1, 2, 1, "", "delete_initial_condition"], [1, 2, 1, "", "delete_parameter"], [1, 2, 1, "", "delete_reaction"], [1, 2, 1, "", "delete_species"], [1, 2, 1, "", "get_all_boundary_conditions"], [1, 2, 1, "", "get_all_data_functions"], [1, 2, 1, "", "get_all_initial_conditions"], [1, 2, 1, "", "get_all_parameters"], [1, 2, 1, "", "get_all_reactions"], [1, 2, 1, "", "get_all_species"], [1, 2, 1, "", "get_data_function"], [1, 2, 1, "", "get_element"], [1, 2, 1, "", "get_num_reactions"], [1, 2, 1, "", "get_num_species"], [1, 2, 1, "", "get_parameter"], [1, 2, 1, "", "get_reaction"], [1, 2, 1, "", "get_species"], [1, 4, 1, "", "reserved_names"], [1, 2, 1, "", "run"], [1, 2, 1, "", "sanitized_data_function_names"], [1, 2, 1, "", "sanitized_parameter_names"], [1, 2, 1, "", "sanitized_species_names"], [1, 2, 1, "", "set_timesteps"], [1, 4, 1, "", "special_characters"], [1, 2, 1, "", "timespan"], [1, 2, 1, "", "update_namespace"]], "spatialpy.core.parameter": [[1, 1, 1, "", "Parameter"]], "spatialpy.core.parameter.Parameter": [[1, 2, 1, "", "validate"]], "spatialpy.core.reaction": [[1, 1, 1, "", "Reaction"]], "spatialpy.core.reaction.Reaction": [[1, 2, 1, "", "add_product"], [1, 2, 1, "", "add_reactant"], [1, 2, 1, "", "annotate"], [1, 2, 1, "", "from_json"], [1, 2, 1, "", "initialize"], [1, 2, 1, "", "sanitized_propensity_function"], [1, 2, 1, "", "set_annotation"], [1, 2, 1, "", "set_propensities"], [1, 2, 1, "", "set_rate"], [1, 2, 1, "", "to_dict"], [1, 2, 1, "", "validate"]], "spatialpy.core.result": [[1, 1, 1, "", "Result"]], "spatialpy.core.result.Result": [[1, 2, 1, "", "export_to_csv"], [1, 2, 1, "", "get_property"], [1, 2, 1, "", "get_species"], [1, 2, 1, "", "get_timespan"], [1, 2, 1, "", "plot_property"], [1, 2, 1, "", "plot_species"], [1, 2, 1, "", "read_step"]], "spatialpy.core.spatialpyerror": [[1, 3, 1, "", "BoundaryConditionError"], [1, 3, 1, "", "DataFunctionError"], [1, 3, 1, "", "DomainError"], [1, 3, 1, "", "GeometryError"], [1, 3, 1, "", "InitialConditionError"], [1, 3, 1, "", "LatticeError"], [1, 3, 1, "", "ModelError"], [1, 3, 1, "", "ParameterError"], [1, 3, 1, "", "ReactionError"], [1, 3, 1, "", "ResultError"], [1, 3, 1, "", "SimulationError"], [1, 3, 1, "", "SimulationTimeout"], [1, 3, 1, "", "SpeciesError"], [1, 3, 1, "", "TimespanError"], [1, 3, 1, "", "TransformationError"], [1, 3, 1, "", "VTKReaderError"], [1, 3, 1, "", "VTKReaderIOError"], [1, 3, 1, "", "VisualizationError"]], "spatialpy.core.species": [[1, 1, 1, "", "Species"]], "spatialpy.core.species.Species": [[1, 2, 1, "", "set_diffusion_coefficient"], [1, 2, 1, "", "validate"]], "spatialpy.core.timespan": [[1, 1, 1, "", "TimeSpan"]], "spatialpy.core.timespan.TimeSpan": [[1, 2, 1, "", "arange"], [1, 2, 1, "", "linspace"], [1, 2, 1, "", "validate"]], "spatialpy.core.transformation": [[1, 1, 1, "", "ReflectionTransformation"], [1, 1, 1, "", "RotationTransformation"], [1, 1, 1, "", "ScalingTransformation"], [1, 1, 1, "", "Transformation"], [1, 1, 1, "", "TranslationTransformation"]], "spatialpy.core.transformation.ReflectionTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"]], "spatialpy.core.transformation.RotationTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.transformation.ScalingTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.transformation.Transformation": [[1, 2, 1, "", "apply"], [1, 2, 1, "", "inside"], [1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.transformation.TranslationTransformation": [[1, 2, 1, "", "reverse_transform"], [1, 2, 1, "", "transform"], [1, 2, 1, "", "validate"]], "spatialpy.core.visualization": [[1, 1, 1, "", "Visualization"]], "spatialpy.core.visualization.Visualization": [[1, 4, 1, "", "MPL_HEIGHT"], [1, 4, 1, "", "MPL_SIZE"], [1, 4, 1, "", "MPL_WIDTH"], [1, 2, 1, "", "plot_scatter"]], "spatialpy.core.vtkreader": [[1, 1, 1, "", "VTKReader"]], "spatialpy.core.vtkreader.VTKReader": [[1, 2, 1, "", "get_array_name"], [1, 2, 1, "", "get_arrays"], [1, 2, 1, "", "get_num_points"], [1, 2, 1, "", "get_points"], [1, 2, 1, "", "read_file"], [1, 2, 1, "", "set_filename"]], "spatialpy.solvers": [[2, 0, 0, "-", "build_expression"], [2, 0, 0, "-", "solver"]], "spatialpy.solvers.build_expression": [[2, 1, 1, "", "BuildExpression"], [2, 1, 1, "", "CppConverter"], [2, 1, 1, "", "ExpressionConverter"], [2, 1, 1, "", "ExpressionResults"], [2, 1, 1, "", "PythonConverter"]], "spatialpy.solvers.build_expression.BuildExpression": [[2, 1, 1, "", "ValidationVisitor"], [2, 2, 1, "", "getexpr_cpp"], [2, 2, 1, "", "getexpr_python"], [2, 2, 1, "", "map_operator"], [2, 4, 1, "", "operator_map"], [2, 2, 1, "", "validate"], [2, 2, 1, "", "with_blacklist"], [2, 2, 1, "", "with_namespace"]], "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor": [[2, 2, 1, "", "visit_Assign"], [2, 2, 1, "", "visit_BinOp"], [2, 2, 1, "", "visit_BoolOp"], [2, 2, 1, "", "visit_Call"], [2, 2, 1, "", "visit_Compare"], [2, 2, 1, "", "visit_Name"], [2, 2, 1, "", "visit_UnaryOp"]], "spatialpy.solvers.build_expression.CppConverter": [[2, 1, 1, "", "CppExpressionTransformer"], [2, 2, 1, "", "get_str"], [2, 2, 1, "", "visit_And"], [2, 2, 1, "", "visit_Or"]], "spatialpy.solvers.build_expression.CppConverter.CppExpressionTransformer": [[2, 2, 1, "", "visit_BinOp"]], "spatialpy.solvers.build_expression.ExpressionConverter": [[2, 2, 1, "", "convert_str"], [2, 2, 1, "", "get_str"], [2, 2, 1, "", "parse_comparison"], [2, 2, 1, "", "parse_logical"], [2, 2, 1, "", "parse_operator"], [2, 2, 1, "", "visit_Add"], [2, 2, 1, "", "visit_BinOp"], [2, 2, 1, "", "visit_BoolOp"], [2, 2, 1, "", "visit_Bytes"], [2, 2, 1, "", "visit_Call"], [2, 2, 1, "", "visit_Compare"], [2, 2, 1, "", "visit_Constant"], [2, 2, 1, "", "visit_Div"], [2, 2, 1, "", "visit_Ellipsis"], [2, 2, 1, "", "visit_Eq"], [2, 2, 1, "", "visit_Gt"], [2, 2, 1, "", "visit_GtE"], [2, 2, 1, "", "visit_Lt"], [2, 2, 1, "", "visit_LtE"], [2, 2, 1, "", "visit_Mult"], [2, 2, 1, "", "visit_Name"], [2, 2, 1, "", "visit_NameConstant"], [2, 2, 1, "", "visit_NotEq"], [2, 2, 1, "", "visit_Num"], [2, 2, 1, "", "visit_Pow"], [2, 2, 1, "", "visit_Str"], [2, 2, 1, "", "visit_Sub"], [2, 2, 1, "", "visit_USub"], [2, 2, 1, "", "visit_UnaryOp"]], "spatialpy.solvers.build_expression.PythonConverter": [[2, 2, 1, "", "visit_And"], [2, 2, 1, "", "visit_Or"]], "spatialpy.solvers.solver": [[2, 1, 1, "", "Solver"]], "spatialpy.solvers.solver.Solver": [[2, 2, 1, "", "compile"], [2, 2, 1, "", "run"]], "spatialpy.stochss": [[3, 0, 0, "-", "stochss_export"]], "spatialpy.stochss.stochss_export": [[3, 5, 1, "", "export"]]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:exception", "4": "py:attribute", "5": "py:function"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "exception", "Python exception"], "4": ["py", "attribute", "Python attribute"], "5": ["py", "function", "Python function"]}, "titleterms": {"spatialpi": [0, 1, 2, 3, 4], "packag": [0, 1, 2, 3], "subpackag": 0, "modul": [0, 1, 2, 3], "content": [0, 1, 2, 3], "core": 1, "submodul": [1, 2, 3], "boundarycondit": 1, "cleanup": 1, "datafunct": 1, "domain": 1, "geometri": 1, "initialcondit": 1, "lattic": 1, "model": 1, "paramet": 1, "reaction": 1, "result": 1, "spatialpyerror": 1, "speci": 1, "timespan": 1, "transform": 1, "visual": 1, "vtkreader": 1, "solver": 2, "build_express": 2, "stochss": 3, "stochss_export": 3, "document": 4, "1": 4, "2": 4, "get": 4, "copi": 4, "exampl": 4, "report": 4, "issu": 4, "api": 4, "refer": 4, "indic": 4, "tabl": 4, "3": [], "0": []}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx.ext.todo": 2, "sphinx": 57}, "alltitles": {"spatialpy package": [[0, "spatialpy-package"]], "Subpackages": [[0, "subpackages"]], "Module contents": [[0, "module-spatialpy"], [1, "module-spatialpy.core"], [2, "module-spatialpy.solvers"], [3, "module-spatialpy.stochss"]], "spatialpy.core package": [[1, "spatialpy-core-package"]], "Submodules": [[1, "submodules"], [2, "submodules"], [3, "submodules"]], "spatialpy.core.boundarycondition module": [[1, "module-spatialpy.core.boundarycondition"]], "spatialpy.core.cleanup module": [[1, "module-spatialpy.core.cleanup"]], "spatialpy.core.datafunction module": [[1, "module-spatialpy.core.datafunction"]], "spatialpy.core.domain module": [[1, "module-spatialpy.core.domain"]], "spatialpy.core.geometry module": [[1, "module-spatialpy.core.geometry"]], "spatialpy.core.initialcondition module": [[1, "module-spatialpy.core.initialcondition"]], "spatialpy.core.lattice module": [[1, "module-spatialpy.core.lattice"]], "spatialpy.core.model module": [[1, "module-spatialpy.core.model"]], "spatialpy.core.parameter module": [[1, "module-spatialpy.core.parameter"]], "spatialpy.core.reaction module": [[1, "module-spatialpy.core.reaction"]], "spatialpy.core.result module": [[1, "module-spatialpy.core.result"]], "spatialpy.core.spatialpyerror module": [[1, "module-spatialpy.core.spatialpyerror"]], "spatialpy.core.species module": [[1, "module-spatialpy.core.species"]], "spatialpy.core.timespan module": [[1, "module-spatialpy.core.timespan"]], "spatialpy.core.transformation module": [[1, "module-spatialpy.core.transformation"]], "spatialpy.core.visualization module": [[1, "module-spatialpy.core.visualization"]], "spatialpy.core.vtkreader module": [[1, "module-spatialpy.core.vtkreader"]], "spatialpy.solvers package": [[2, "spatialpy-solvers-package"]], "spatialpy.solvers.build_expression module": [[2, "module-spatialpy.solvers.build_expression"]], "spatialpy.solvers.solver module": [[2, "module-spatialpy.solvers.solver"]], "spatialpy.stochss package": [[3, "spatialpy-stochss-package"]], "spatialpy.stochss.stochss_export module": [[3, "module-spatialpy.stochss.stochss_export"]], "Documentation for SpatialPy 1.2.1": [[4, "documentation-for-spatialpy-release"]], "Getting a copy of SpatialPy": [[4, "getting-a-copy-of-spatialpy"]], "Examples": [[4, "examples"]], "Reporting Issues": [[4, "reporting-issues"]], "Documentation": [[4, "documentation"]], "API reference": [[4, null]], "Indices and tables": [[4, "indices-and-tables"]]}, "indexentries": {"module": [[0, "module-spatialpy"], [1, "module-spatialpy.core"], [1, "module-spatialpy.core.boundarycondition"], [1, "module-spatialpy.core.cleanup"], [1, "module-spatialpy.core.datafunction"], [1, "module-spatialpy.core.domain"], [1, "module-spatialpy.core.geometry"], [1, "module-spatialpy.core.initialcondition"], [1, "module-spatialpy.core.lattice"], [1, "module-spatialpy.core.model"], [1, "module-spatialpy.core.parameter"], [1, "module-spatialpy.core.reaction"], [1, "module-spatialpy.core.result"], [1, "module-spatialpy.core.spatialpyerror"], [1, "module-spatialpy.core.species"], [1, "module-spatialpy.core.timespan"], [1, "module-spatialpy.core.transformation"], [1, "module-spatialpy.core.visualization"], [1, "module-spatialpy.core.vtkreader"], [2, "module-spatialpy.solvers"], [2, "module-spatialpy.solvers.build_expression"], [2, "module-spatialpy.solvers.solver"], [3, "module-spatialpy.stochss"], [3, "module-spatialpy.stochss.stochss_export"]], "spatialpy": [[0, "module-spatialpy"]], "boundarycondition (class in spatialpy.core)": [[1, "spatialpy.core.BoundaryCondition"]], "boundarycondition (class in spatialpy.core.boundarycondition)": [[1, "spatialpy.core.boundarycondition.BoundaryCondition"]], "boundaryconditionerror": [[1, "spatialpy.core.BoundaryConditionError"], [1, "spatialpy.core.spatialpyerror.BoundaryConditionError"]], "cartesianlattice (class in spatialpy.core)": [[1, "spatialpy.core.CartesianLattice"]], "cartesianlattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.CartesianLattice"]], "combinatorygeometry (class in spatialpy.core)": [[1, "spatialpy.core.CombinatoryGeometry"]], "combinatorygeometry (class in spatialpy.core.geometry)": [[1, "spatialpy.core.geometry.CombinatoryGeometry"]], "cylindricallattice (class in spatialpy.core)": [[1, "spatialpy.core.CylindricalLattice"]], "cylindricallattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.CylindricalLattice"]], "datafunction (class in spatialpy.core)": [[1, "spatialpy.core.DataFunction"]], "datafunction (class in spatialpy.core.datafunction)": [[1, "spatialpy.core.datafunction.DataFunction"]], "datafunctionerror": [[1, "spatialpy.core.DataFunctionError"], [1, "spatialpy.core.spatialpyerror.DataFunctionError"]], "domain (class in spatialpy.core)": [[1, "spatialpy.core.Domain"]], "domain (class in spatialpy.core.domain)": [[1, "spatialpy.core.domain.Domain"]], "domainerror": [[1, "spatialpy.core.DomainError"], [1, "spatialpy.core.spatialpyerror.DomainError"]], "geometry (class in spatialpy.core)": [[1, "spatialpy.core.Geometry"]], "geometry (class in spatialpy.core.geometry)": [[1, "spatialpy.core.geometry.Geometry"]], "geometryall (class in spatialpy.core)": [[1, "spatialpy.core.GeometryAll"]], "geometryall (class in spatialpy.core.geometry)": [[1, "spatialpy.core.geometry.GeometryAll"]], "geometryerror": [[1, "spatialpy.core.GeometryError"], [1, "spatialpy.core.spatialpyerror.GeometryError"]], "geometryexterior (class in spatialpy.core)": [[1, "spatialpy.core.GeometryExterior"]], "geometryexterior (class in spatialpy.core.geometry)": [[1, "spatialpy.core.geometry.GeometryExterior"]], "geometryinterior (class in spatialpy.core)": [[1, "spatialpy.core.GeometryInterior"]], "geometryinterior (class in spatialpy.core.geometry)": [[1, "spatialpy.core.geometry.GeometryInterior"]], "initialcondition (class in spatialpy.core)": [[1, "spatialpy.core.InitialCondition"]], "initialcondition (class in spatialpy.core.initialcondition)": [[1, "spatialpy.core.initialcondition.InitialCondition"]], "initialconditionerror": [[1, "spatialpy.core.InitialConditionError"], [1, "spatialpy.core.spatialpyerror.InitialConditionError"]], "lattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.Lattice"]], "latticeerror": [[1, "spatialpy.core.LatticeError"], [1, "spatialpy.core.spatialpyerror.LatticeError"]], "mpl_height (spatialpy.core.visualization attribute)": [[1, "spatialpy.core.Visualization.MPL_HEIGHT"]], "mpl_height (spatialpy.core.visualization.visualization attribute)": [[1, "spatialpy.core.visualization.Visualization.MPL_HEIGHT"]], "mpl_size (spatialpy.core.visualization attribute)": [[1, "spatialpy.core.Visualization.MPL_SIZE"]], "mpl_size (spatialpy.core.visualization.visualization attribute)": [[1, "spatialpy.core.visualization.Visualization.MPL_SIZE"]], "mpl_width (spatialpy.core.visualization attribute)": [[1, "spatialpy.core.Visualization.MPL_WIDTH"]], "mpl_width (spatialpy.core.visualization.visualization attribute)": [[1, "spatialpy.core.visualization.Visualization.MPL_WIDTH"]], "meshiolattice (class in spatialpy.core)": [[1, "spatialpy.core.MeshIOLattice"]], "meshiolattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.MeshIOLattice"]], "model (class in spatialpy.core)": [[1, "spatialpy.core.Model"]], "model (class in spatialpy.core.model)": [[1, "spatialpy.core.model.Model"]], "modelerror": [[1, "spatialpy.core.ModelError"], [1, "spatialpy.core.spatialpyerror.ModelError"]], "parameter (class in spatialpy.core)": [[1, "spatialpy.core.Parameter"]], "parameter (class in spatialpy.core.parameter)": [[1, "spatialpy.core.parameter.Parameter"]], "parametererror": [[1, "spatialpy.core.ParameterError"], [1, "spatialpy.core.spatialpyerror.ParameterError"]], "placeinitialcondition (class in spatialpy.core)": [[1, "spatialpy.core.PlaceInitialCondition"]], "placeinitialcondition (class in spatialpy.core.initialcondition)": [[1, "spatialpy.core.initialcondition.PlaceInitialCondition"]], "reaction (class in spatialpy.core)": [[1, "spatialpy.core.Reaction"]], "reaction (class in spatialpy.core.reaction)": [[1, "spatialpy.core.reaction.Reaction"]], "reactionerror": [[1, "spatialpy.core.ReactionError"], [1, "spatialpy.core.spatialpyerror.ReactionError"]], "reflectiontransformation (class in spatialpy.core)": [[1, "spatialpy.core.ReflectionTransformation"]], "reflectiontransformation (class in spatialpy.core.transformation)": [[1, "spatialpy.core.transformation.ReflectionTransformation"]], "result (class in spatialpy.core)": [[1, "spatialpy.core.Result"]], "result (class in spatialpy.core.result)": [[1, "spatialpy.core.result.Result"]], "resulterror": [[1, "spatialpy.core.ResultError"], [1, "spatialpy.core.spatialpyerror.ResultError"]], "rotationtransformation (class in spatialpy.core)": [[1, "spatialpy.core.RotationTransformation"]], "rotationtransformation (class in spatialpy.core.transformation)": [[1, "spatialpy.core.transformation.RotationTransformation"]], "scalingtransformation (class in spatialpy.core)": [[1, "spatialpy.core.ScalingTransformation"]], "scalingtransformation (class in spatialpy.core.transformation)": [[1, "spatialpy.core.transformation.ScalingTransformation"]], "scatterinitialcondition (class in spatialpy.core)": [[1, "spatialpy.core.ScatterInitialCondition"]], "scatterinitialcondition (class in spatialpy.core.initialcondition)": [[1, "spatialpy.core.initialcondition.ScatterInitialCondition"]], "simulationerror": [[1, "spatialpy.core.SimulationError"], [1, "spatialpy.core.spatialpyerror.SimulationError"]], "simulationtimeout": [[1, "spatialpy.core.SimulationTimeout"], [1, "spatialpy.core.spatialpyerror.SimulationTimeout"]], "species (class in spatialpy.core)": [[1, "spatialpy.core.Species"]], "species (class in spatialpy.core.species)": [[1, "spatialpy.core.species.Species"]], "specieserror": [[1, "spatialpy.core.SpeciesError"], [1, "spatialpy.core.spatialpyerror.SpeciesError"]], "sphericallattice (class in spatialpy.core)": [[1, "spatialpy.core.SphericalLattice"]], "sphericallattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.SphericalLattice"]], "stochsslattice (class in spatialpy.core)": [[1, "spatialpy.core.StochSSLattice"]], "stochsslattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.StochSSLattice"]], "timespan (class in spatialpy.core)": [[1, "spatialpy.core.TimeSpan"]], "timespan (class in spatialpy.core.timespan)": [[1, "spatialpy.core.timespan.TimeSpan"]], "timespanerror": [[1, "spatialpy.core.TimespanError"], [1, "spatialpy.core.spatialpyerror.TimespanError"]], "transformation (class in spatialpy.core)": [[1, "spatialpy.core.Transformation"]], "transformation (class in spatialpy.core.transformation)": [[1, "spatialpy.core.transformation.Transformation"]], "transformationerror": [[1, "spatialpy.core.TransformationError"], [1, "spatialpy.core.spatialpyerror.TransformationError"]], "translationtransformation (class in spatialpy.core)": [[1, "spatialpy.core.TranslationTransformation"]], "translationtransformation (class in spatialpy.core.transformation)": [[1, "spatialpy.core.transformation.TranslationTransformation"]], "uniforminitialcondition (class in spatialpy.core)": [[1, "spatialpy.core.UniformInitialCondition"]], "uniforminitialcondition (class in spatialpy.core.initialcondition)": [[1, "spatialpy.core.initialcondition.UniformInitialCondition"]], "vtkreader (class in spatialpy.core)": [[1, "spatialpy.core.VTKReader"]], "vtkreader (class in spatialpy.core.vtkreader)": [[1, "spatialpy.core.vtkreader.VTKReader"]], "vtkreadererror": [[1, "spatialpy.core.VTKReaderError"], [1, "spatialpy.core.spatialpyerror.VTKReaderError"]], "vtkreaderioerror": [[1, "spatialpy.core.VTKReaderIOError"], [1, "spatialpy.core.spatialpyerror.VTKReaderIOError"]], "visualization (class in spatialpy.core)": [[1, "spatialpy.core.Visualization"]], "visualization (class in spatialpy.core.visualization)": [[1, "spatialpy.core.visualization.Visualization"]], "visualizationerror": [[1, "spatialpy.core.VisualizationError"], [1, "spatialpy.core.spatialpyerror.VisualizationError"]], "xmlmeshlattice (class in spatialpy.core)": [[1, "spatialpy.core.XMLMeshLattice"]], "xmlmeshlattice (class in spatialpy.core.lattice)": [[1, "spatialpy.core.lattice.XMLMeshLattice"]], "add() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add"]], "add() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add"]], "add_boundary_condition() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_boundary_condition"]], "add_boundary_condition() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_boundary_condition"]], "add_data_function() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_data_function"]], "add_data_function() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_data_function"]], "add_domain() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_domain"]], "add_domain() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_domain"]], "add_fill_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.add_fill_action"]], "add_fill_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.add_fill_action"]], "add_initial_condition() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_initial_condition"]], "add_initial_condition() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_initial_condition"]], "add_parameter() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_parameter"]], "add_parameter() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_parameter"]], "add_point() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.add_point"]], "add_point() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.add_point"]], "add_product() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.add_product"]], "add_product() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.add_product"]], "add_reactant() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.add_reactant"]], "add_reactant() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.add_reactant"]], "add_reaction() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_reaction"]], "add_reaction() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_reaction"]], "add_remove_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.add_remove_action"]], "add_remove_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.add_remove_action"]], "add_set_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.add_set_action"]], "add_set_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.add_set_action"]], "add_species() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.add_species"]], "add_species() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.add_species"]], "annotate() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.annotate"]], "annotate() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.annotate"]], "apply() (spatialpy.core.cartesianlattice method)": [[1, "spatialpy.core.CartesianLattice.apply"]], "apply() (spatialpy.core.cylindricallattice method)": [[1, "spatialpy.core.CylindricalLattice.apply"]], "apply() (spatialpy.core.initialcondition method)": [[1, "spatialpy.core.InitialCondition.apply"]], "apply() (spatialpy.core.meshiolattice method)": [[1, "spatialpy.core.MeshIOLattice.apply"]], "apply() (spatialpy.core.placeinitialcondition method)": [[1, "spatialpy.core.PlaceInitialCondition.apply"]], "apply() (spatialpy.core.scatterinitialcondition method)": [[1, "spatialpy.core.ScatterInitialCondition.apply"]], "apply() (spatialpy.core.sphericallattice method)": [[1, "spatialpy.core.SphericalLattice.apply"]], "apply() (spatialpy.core.stochsslattice method)": [[1, "spatialpy.core.StochSSLattice.apply"]], "apply() (spatialpy.core.transformation method)": [[1, "spatialpy.core.Transformation.apply"]], "apply() (spatialpy.core.uniforminitialcondition method)": [[1, "spatialpy.core.UniformInitialCondition.apply"]], "apply() (spatialpy.core.xmlmeshlattice method)": [[1, "spatialpy.core.XMLMeshLattice.apply"]], "apply() (spatialpy.core.initialcondition.initialcondition method)": [[1, "spatialpy.core.initialcondition.InitialCondition.apply"]], "apply() (spatialpy.core.initialcondition.placeinitialcondition method)": [[1, "spatialpy.core.initialcondition.PlaceInitialCondition.apply"]], "apply() (spatialpy.core.initialcondition.scatterinitialcondition method)": [[1, "spatialpy.core.initialcondition.ScatterInitialCondition.apply"]], "apply() (spatialpy.core.initialcondition.uniforminitialcondition method)": [[1, "spatialpy.core.initialcondition.UniformInitialCondition.apply"]], "apply() (spatialpy.core.lattice.cartesianlattice method)": [[1, "spatialpy.core.lattice.CartesianLattice.apply"]], "apply() (spatialpy.core.lattice.cylindricallattice method)": [[1, "spatialpy.core.lattice.CylindricalLattice.apply"]], "apply() (spatialpy.core.lattice.lattice method)": [[1, "spatialpy.core.lattice.Lattice.apply"]], "apply() (spatialpy.core.lattice.meshiolattice method)": [[1, "spatialpy.core.lattice.MeshIOLattice.apply"]], "apply() (spatialpy.core.lattice.sphericallattice method)": [[1, "spatialpy.core.lattice.SphericalLattice.apply"]], "apply() (spatialpy.core.lattice.stochsslattice method)": [[1, "spatialpy.core.lattice.StochSSLattice.apply"]], "apply() (spatialpy.core.lattice.xmlmeshlattice method)": [[1, "spatialpy.core.lattice.XMLMeshLattice.apply"]], "apply() (spatialpy.core.transformation.transformation method)": [[1, "spatialpy.core.transformation.Transformation.apply"]], "apply_actions() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.apply_actions"]], "apply_actions() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.apply_actions"]], "apply_fill_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.apply_fill_action"]], "apply_fill_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.apply_fill_action"]], "apply_remove_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.apply_remove_action"]], "apply_remove_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.apply_remove_action"]], "apply_set_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.apply_set_action"]], "apply_set_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.apply_set_action"]], "arange() (spatialpy.core.timespan class method)": [[1, "spatialpy.core.TimeSpan.arange"]], "arange() (spatialpy.core.timespan.timespan class method)": [[1, "spatialpy.core.timespan.TimeSpan.arange"]], "calculate_vol() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.calculate_vol"]], "calculate_vol() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.calculate_vol"]], "cleanup_build_files() (in module spatialpy.core)": [[1, "spatialpy.core.cleanup_build_files"]], "cleanup_build_files() (in module spatialpy.core.cleanup)": [[1, "spatialpy.core.cleanup.cleanup_build_files"]], "cleanup_core_files() (in module spatialpy.core)": [[1, "spatialpy.core.cleanup_core_files"]], "cleanup_core_files() (in module spatialpy.core.cleanup)": [[1, "spatialpy.core.cleanup.cleanup_core_files"]], "cleanup_result_files() (in module spatialpy.core)": [[1, "spatialpy.core.cleanup_result_files"]], "cleanup_result_files() (in module spatialpy.core.cleanup)": [[1, "spatialpy.core.cleanup.cleanup_result_files"]], "cleanup_tempfiles() (in module spatialpy.core)": [[1, "spatialpy.core.cleanup_tempfiles"]], "cleanup_tempfiles() (in module spatialpy.core.cleanup)": [[1, "spatialpy.core.cleanup.cleanup_tempfiles"]], "closest_vertex() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.closest_vertex"]], "closest_vertex() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.closest_vertex"]], "compile_prep() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.compile_prep"]], "compile_prep() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.compile_prep"]], "compile_prep() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.compile_prep"]], "compile_prep() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.compile_prep"]], "coordinates() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.coordinates"]], "coordinates() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.coordinates"]], "create_2d_domain() (spatialpy.core.domain class method)": [[1, "spatialpy.core.Domain.create_2D_domain"]], "create_2d_domain() (spatialpy.core.domain.domain class method)": [[1, "spatialpy.core.domain.Domain.create_2D_domain"]], "create_3d_domain() (spatialpy.core.domain class method)": [[1, "spatialpy.core.Domain.create_3D_domain"]], "create_3d_domain() (spatialpy.core.domain.domain class method)": [[1, "spatialpy.core.domain.Domain.create_3D_domain"]], "delete_all_boundary_conditions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_all_boundary_conditions"]], "delete_all_boundary_conditions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_all_boundary_conditions"]], "delete_all_data_functions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_all_data_functions"]], "delete_all_data_functions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_all_data_functions"]], "delete_all_initial_conditions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_all_initial_conditions"]], "delete_all_initial_conditions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_all_initial_conditions"]], "delete_all_parameters() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_all_parameters"]], "delete_all_parameters() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_all_parameters"]], "delete_all_reactions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_all_reactions"]], "delete_all_reactions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_all_reactions"]], "delete_all_species() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_all_species"]], "delete_all_species() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_all_species"]], "delete_boundary_condition() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_boundary_condition"]], "delete_boundary_condition() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_boundary_condition"]], "delete_data_function() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_data_function"]], "delete_data_function() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_data_function"]], "delete_initial_condition() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_initial_condition"]], "delete_initial_condition() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_initial_condition"]], "delete_parameter() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_parameter"]], "delete_parameter() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_parameter"]], "delete_reaction() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_reaction"]], "delete_reaction() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_reaction"]], "delete_species() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.delete_species"]], "delete_species() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.delete_species"]], "distance_between_2_vertices() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.distance_between_2_vertices"]], "distance_between_2_vertices() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.distance_between_2_vertices"]], "export_stochss() (in module spatialpy.core)": [[1, "spatialpy.core.export_StochSS"]], "export_stochss() (in module spatialpy.core.model)": [[1, "spatialpy.core.model.export_StochSS"]], "export_to_csv() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.export_to_csv"]], "export_to_csv() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.export_to_csv"]], "expression() (spatialpy.core.boundarycondition method)": [[1, "spatialpy.core.BoundaryCondition.expression"]], "expression() (spatialpy.core.boundarycondition.boundarycondition method)": [[1, "spatialpy.core.boundarycondition.BoundaryCondition.expression"]], "fill_with_particles() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.fill_with_particles"]], "fill_with_particles() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.fill_with_particles"]], "find_boundary_points() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.find_boundary_points"]], "find_boundary_points() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.find_boundary_points"]], "find_h() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.find_h"]], "find_h() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.find_h"]], "from_json() (spatialpy.core.reaction class method)": [[1, "spatialpy.core.Reaction.from_json"]], "from_json() (spatialpy.core.reaction.reaction class method)": [[1, "spatialpy.core.reaction.Reaction.from_json"]], "get_all_boundary_conditions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_all_boundary_conditions"]], "get_all_boundary_conditions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_all_boundary_conditions"]], "get_all_data_functions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_all_data_functions"]], "get_all_data_functions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_all_data_functions"]], "get_all_initial_conditions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_all_initial_conditions"]], "get_all_initial_conditions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_all_initial_conditions"]], "get_all_parameters() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_all_parameters"]], "get_all_parameters() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_all_parameters"]], "get_all_reactions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_all_reactions"]], "get_all_reactions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_all_reactions"]], "get_all_species() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_all_species"]], "get_all_species() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_all_species"]], "get_array_name() (spatialpy.core.vtkreader method)": [[1, "spatialpy.core.VTKReader.get_array_name"]], "get_array_name() (spatialpy.core.vtkreader.vtkreader method)": [[1, "spatialpy.core.vtkreader.VTKReader.get_array_name"]], "get_arrays() (spatialpy.core.vtkreader method)": [[1, "spatialpy.core.VTKReader.get_arrays"]], "get_arrays() (spatialpy.core.vtkreader.vtkreader method)": [[1, "spatialpy.core.vtkreader.VTKReader.get_arrays"]], "get_bounding_box() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.get_bounding_box"]], "get_bounding_box() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.get_bounding_box"]], "get_data_function() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_data_function"]], "get_data_function() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_data_function"]], "get_domain_size() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.get_domain_size"]], "get_domain_size() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.get_domain_size"]], "get_element() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_element"]], "get_element() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_element"]], "get_num_points() (spatialpy.core.vtkreader method)": [[1, "spatialpy.core.VTKReader.get_num_points"]], "get_num_points() (spatialpy.core.vtkreader.vtkreader method)": [[1, "spatialpy.core.vtkreader.VTKReader.get_num_points"]], "get_num_reactions() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_num_reactions"]], "get_num_reactions() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_num_reactions"]], "get_num_species() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_num_species"]], "get_num_species() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_num_species"]], "get_num_voxels() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.get_num_voxels"]], "get_num_voxels() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.get_num_voxels"]], "get_parameter() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_parameter"]], "get_parameter() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_parameter"]], "get_points() (spatialpy.core.vtkreader method)": [[1, "spatialpy.core.VTKReader.get_points"]], "get_points() (spatialpy.core.vtkreader.vtkreader method)": [[1, "spatialpy.core.vtkreader.VTKReader.get_points"]], "get_property() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.get_property"]], "get_property() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.get_property"]], "get_reaction() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_reaction"]], "get_reaction() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_reaction"]], "get_species() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.get_species"]], "get_species() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.get_species"]], "get_species() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.get_species"]], "get_species() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.get_species"]], "get_timespan() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.get_timespan"]], "get_timespan() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.get_timespan"]], "get_type_def() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.get_type_def"]], "get_type_def() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.get_type_def"]], "get_vol() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.get_vol"]], "get_vol() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.get_vol"]], "import_meshio_object() (spatialpy.core.domain class method)": [[1, "spatialpy.core.Domain.import_meshio_object"]], "import_meshio_object() (spatialpy.core.domain.domain class method)": [[1, "spatialpy.core.domain.Domain.import_meshio_object"]], "initialize() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.initialize"]], "initialize() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.initialize"]], "inside() (spatialpy.core.combinatorygeometry method)": [[1, "spatialpy.core.CombinatoryGeometry.inside"]], "inside() (spatialpy.core.geometry method)": [[1, "spatialpy.core.Geometry.inside"]], "inside() (spatialpy.core.geometryall method)": [[1, "spatialpy.core.GeometryAll.inside"]], "inside() (spatialpy.core.geometryexterior method)": [[1, "spatialpy.core.GeometryExterior.inside"]], "inside() (spatialpy.core.geometryinterior method)": [[1, "spatialpy.core.GeometryInterior.inside"]], "inside() (spatialpy.core.transformation method)": [[1, "spatialpy.core.Transformation.inside"]], "inside() (spatialpy.core.geometry.combinatorygeometry method)": [[1, "spatialpy.core.geometry.CombinatoryGeometry.inside"]], "inside() (spatialpy.core.geometry.geometry method)": [[1, "spatialpy.core.geometry.Geometry.inside"]], "inside() (spatialpy.core.geometry.geometryall method)": [[1, "spatialpy.core.geometry.GeometryAll.inside"]], "inside() (spatialpy.core.geometry.geometryexterior method)": [[1, "spatialpy.core.geometry.GeometryExterior.inside"]], "inside() (spatialpy.core.geometry.geometryinterior method)": [[1, "spatialpy.core.geometry.GeometryInterior.inside"]], "inside() (spatialpy.core.transformation.transformation method)": [[1, "spatialpy.core.transformation.Transformation.inside"]], "linspace() (spatialpy.core.timespan class method)": [[1, "spatialpy.core.TimeSpan.linspace"]], "linspace() (spatialpy.core.timespan.timespan class method)": [[1, "spatialpy.core.timespan.TimeSpan.linspace"]], "map() (spatialpy.core.datafunction method)": [[1, "spatialpy.core.DataFunction.map"]], "map() (spatialpy.core.datafunction.datafunction method)": [[1, "spatialpy.core.datafunction.DataFunction.map"]], "plot_property() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.plot_property"]], "plot_property() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.plot_property"]], "plot_scatter() (spatialpy.core.visualization method)": [[1, "spatialpy.core.Visualization.plot_scatter"]], "plot_scatter() (spatialpy.core.visualization.visualization method)": [[1, "spatialpy.core.visualization.Visualization.plot_scatter"]], "plot_species() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.plot_species"]], "plot_species() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.plot_species"]], "plot_types() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.plot_types"]], "plot_types() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.plot_types"]], "preview_actions() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.preview_actions"]], "preview_actions() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.preview_actions"]], "read_file() (spatialpy.core.vtkreader method)": [[1, "spatialpy.core.VTKReader.read_file"]], "read_file() (spatialpy.core.vtkreader.vtkreader method)": [[1, "spatialpy.core.vtkreader.VTKReader.read_file"]], "read_msh_file() (spatialpy.core.domain class method)": [[1, "spatialpy.core.Domain.read_msh_file"]], "read_msh_file() (spatialpy.core.domain.domain class method)": [[1, "spatialpy.core.domain.Domain.read_msh_file"]], "read_step() (spatialpy.core.result method)": [[1, "spatialpy.core.Result.read_step"]], "read_step() (spatialpy.core.result.result method)": [[1, "spatialpy.core.result.Result.read_step"]], "read_stochss_domain() (spatialpy.core.domain class method)": [[1, "spatialpy.core.Domain.read_stochss_domain"]], "read_stochss_domain() (spatialpy.core.domain.domain class method)": [[1, "spatialpy.core.domain.Domain.read_stochss_domain"]], "read_stochss_subdomain_file() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.read_stochss_subdomain_file"]], "read_stochss_subdomain_file() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.read_stochss_subdomain_file"]], "read_xml_mesh() (spatialpy.core.domain class method)": [[1, "spatialpy.core.Domain.read_xml_mesh"]], "read_xml_mesh() (spatialpy.core.domain.domain class method)": [[1, "spatialpy.core.domain.Domain.read_xml_mesh"]], "reserved_names (spatialpy.core.model attribute)": [[1, "spatialpy.core.Model.reserved_names"]], "reserved_names (spatialpy.core.model.model attribute)": [[1, "spatialpy.core.model.Model.reserved_names"]], "reverse_transform() (spatialpy.core.reflectiontransformation method)": [[1, "spatialpy.core.ReflectionTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.rotationtransformation method)": [[1, "spatialpy.core.RotationTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.scalingtransformation method)": [[1, "spatialpy.core.ScalingTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.transformation method)": [[1, "spatialpy.core.Transformation.reverse_transform"]], "reverse_transform() (spatialpy.core.translationtransformation method)": [[1, "spatialpy.core.TranslationTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.transformation.reflectiontransformation method)": [[1, "spatialpy.core.transformation.ReflectionTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.transformation.rotationtransformation method)": [[1, "spatialpy.core.transformation.RotationTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.transformation.scalingtransformation method)": [[1, "spatialpy.core.transformation.ScalingTransformation.reverse_transform"]], "reverse_transform() (spatialpy.core.transformation.transformation method)": [[1, "spatialpy.core.transformation.Transformation.reverse_transform"]], "reverse_transform() (spatialpy.core.transformation.translationtransformation method)": [[1, "spatialpy.core.transformation.TranslationTransformation.reverse_transform"]], "run() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.run"]], "run() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.run"]], "sanitized_data_function_names() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.sanitized_data_function_names"]], "sanitized_data_function_names() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.sanitized_data_function_names"]], "sanitized_parameter_names() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.sanitized_parameter_names"]], "sanitized_parameter_names() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.sanitized_parameter_names"]], "sanitized_propensity_function() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.sanitized_propensity_function"]], "sanitized_propensity_function() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.sanitized_propensity_function"]], "sanitized_species_names() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.sanitized_species_names"]], "sanitized_species_names() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.sanitized_species_names"]], "set_annotation() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.set_annotation"]], "set_annotation() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.set_annotation"]], "set_diffusion_coefficient() (spatialpy.core.species method)": [[1, "spatialpy.core.Species.set_diffusion_coefficient"]], "set_diffusion_coefficient() (spatialpy.core.species.species method)": [[1, "spatialpy.core.species.Species.set_diffusion_coefficient"]], "set_filename() (spatialpy.core.vtkreader method)": [[1, "spatialpy.core.VTKReader.set_filename"]], "set_filename() (spatialpy.core.vtkreader.vtkreader method)": [[1, "spatialpy.core.vtkreader.VTKReader.set_filename"]], "set_propensities() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.set_propensities"]], "set_propensities() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.set_propensities"]], "set_properties() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.set_properties"]], "set_properties() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.set_properties"]], "set_rate() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.set_rate"]], "set_rate() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.set_rate"]], "set_timesteps() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.set_timesteps"]], "set_timesteps() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.set_timesteps"]], "spatialpy.core": [[1, "module-spatialpy.core"]], "spatialpy.core.boundarycondition": [[1, "module-spatialpy.core.boundarycondition"]], "spatialpy.core.cleanup": [[1, "module-spatialpy.core.cleanup"]], "spatialpy.core.datafunction": [[1, "module-spatialpy.core.datafunction"]], "spatialpy.core.domain": [[1, "module-spatialpy.core.domain"]], "spatialpy.core.geometry": [[1, "module-spatialpy.core.geometry"]], "spatialpy.core.initialcondition": [[1, "module-spatialpy.core.initialcondition"]], "spatialpy.core.lattice": [[1, "module-spatialpy.core.lattice"]], "spatialpy.core.model": [[1, "module-spatialpy.core.model"]], "spatialpy.core.parameter": [[1, "module-spatialpy.core.parameter"]], "spatialpy.core.reaction": [[1, "module-spatialpy.core.reaction"]], "spatialpy.core.result": [[1, "module-spatialpy.core.result"]], "spatialpy.core.spatialpyerror": [[1, "module-spatialpy.core.spatialpyerror"]], "spatialpy.core.species": [[1, "module-spatialpy.core.species"]], "spatialpy.core.timespan": [[1, "module-spatialpy.core.timespan"]], "spatialpy.core.transformation": [[1, "module-spatialpy.core.transformation"]], "spatialpy.core.visualization": [[1, "module-spatialpy.core.visualization"]], "spatialpy.core.vtkreader": [[1, "module-spatialpy.core.vtkreader"]], "special_characters (spatialpy.core.model attribute)": [[1, "spatialpy.core.Model.special_characters"]], "special_characters (spatialpy.core.model.model attribute)": [[1, "spatialpy.core.model.Model.special_characters"]], "timespan() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.timespan"]], "timespan() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.timespan"]], "to_dict() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.to_dict"]], "to_dict() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.to_dict"]], "transform() (spatialpy.core.reflectiontransformation method)": [[1, "spatialpy.core.ReflectionTransformation.transform"]], "transform() (spatialpy.core.rotationtransformation method)": [[1, "spatialpy.core.RotationTransformation.transform"]], "transform() (spatialpy.core.scalingtransformation method)": [[1, "spatialpy.core.ScalingTransformation.transform"]], "transform() (spatialpy.core.transformation method)": [[1, "spatialpy.core.Transformation.transform"]], "transform() (spatialpy.core.translationtransformation method)": [[1, "spatialpy.core.TranslationTransformation.transform"]], "transform() (spatialpy.core.transformation.reflectiontransformation method)": [[1, "spatialpy.core.transformation.ReflectionTransformation.transform"]], "transform() (spatialpy.core.transformation.rotationtransformation method)": [[1, "spatialpy.core.transformation.RotationTransformation.transform"]], "transform() (spatialpy.core.transformation.scalingtransformation method)": [[1, "spatialpy.core.transformation.ScalingTransformation.transform"]], "transform() (spatialpy.core.transformation.transformation method)": [[1, "spatialpy.core.transformation.Transformation.transform"]], "transform() (spatialpy.core.transformation.translationtransformation method)": [[1, "spatialpy.core.transformation.TranslationTransformation.transform"]], "update_namespace() (spatialpy.core.model method)": [[1, "spatialpy.core.Model.update_namespace"]], "update_namespace() (spatialpy.core.model.model method)": [[1, "spatialpy.core.model.Model.update_namespace"]], "validate() (spatialpy.core.cartesianlattice method)": [[1, "spatialpy.core.CartesianLattice.validate"]], "validate() (spatialpy.core.combinatorygeometry method)": [[1, "spatialpy.core.CombinatoryGeometry.validate"]], "validate() (spatialpy.core.cylindricallattice method)": [[1, "spatialpy.core.CylindricalLattice.validate"]], "validate() (spatialpy.core.meshiolattice method)": [[1, "spatialpy.core.MeshIOLattice.validate"]], "validate() (spatialpy.core.parameter method)": [[1, "spatialpy.core.Parameter.validate"]], "validate() (spatialpy.core.reaction method)": [[1, "spatialpy.core.Reaction.validate"]], "validate() (spatialpy.core.rotationtransformation method)": [[1, "spatialpy.core.RotationTransformation.validate"]], "validate() (spatialpy.core.scalingtransformation method)": [[1, "spatialpy.core.ScalingTransformation.validate"]], "validate() (spatialpy.core.species method)": [[1, "spatialpy.core.Species.validate"]], "validate() (spatialpy.core.sphericallattice method)": [[1, "spatialpy.core.SphericalLattice.validate"]], "validate() (spatialpy.core.stochsslattice method)": [[1, "spatialpy.core.StochSSLattice.validate"]], "validate() (spatialpy.core.timespan method)": [[1, "spatialpy.core.TimeSpan.validate"]], "validate() (spatialpy.core.transformation method)": [[1, "spatialpy.core.Transformation.validate"]], "validate() (spatialpy.core.translationtransformation method)": [[1, "spatialpy.core.TranslationTransformation.validate"]], "validate() (spatialpy.core.xmlmeshlattice method)": [[1, "spatialpy.core.XMLMeshLattice.validate"]], "validate() (spatialpy.core.geometry.combinatorygeometry method)": [[1, "spatialpy.core.geometry.CombinatoryGeometry.validate"]], "validate() (spatialpy.core.lattice.cartesianlattice method)": [[1, "spatialpy.core.lattice.CartesianLattice.validate"]], "validate() (spatialpy.core.lattice.cylindricallattice method)": [[1, "spatialpy.core.lattice.CylindricalLattice.validate"]], "validate() (spatialpy.core.lattice.lattice method)": [[1, "spatialpy.core.lattice.Lattice.validate"]], "validate() (spatialpy.core.lattice.meshiolattice method)": [[1, "spatialpy.core.lattice.MeshIOLattice.validate"]], "validate() (spatialpy.core.lattice.sphericallattice method)": [[1, "spatialpy.core.lattice.SphericalLattice.validate"]], "validate() (spatialpy.core.lattice.stochsslattice method)": [[1, "spatialpy.core.lattice.StochSSLattice.validate"]], "validate() (spatialpy.core.lattice.xmlmeshlattice method)": [[1, "spatialpy.core.lattice.XMLMeshLattice.validate"]], "validate() (spatialpy.core.parameter.parameter method)": [[1, "spatialpy.core.parameter.Parameter.validate"]], "validate() (spatialpy.core.reaction.reaction method)": [[1, "spatialpy.core.reaction.Reaction.validate"]], "validate() (spatialpy.core.species.species method)": [[1, "spatialpy.core.species.Species.validate"]], "validate() (spatialpy.core.timespan.timespan method)": [[1, "spatialpy.core.timespan.TimeSpan.validate"]], "validate() (spatialpy.core.transformation.rotationtransformation method)": [[1, "spatialpy.core.transformation.RotationTransformation.validate"]], "validate() (spatialpy.core.transformation.scalingtransformation method)": [[1, "spatialpy.core.transformation.ScalingTransformation.validate"]], "validate() (spatialpy.core.transformation.transformation method)": [[1, "spatialpy.core.transformation.Transformation.validate"]], "validate() (spatialpy.core.transformation.translationtransformation method)": [[1, "spatialpy.core.transformation.TranslationTransformation.validate"]], "validate_action() (spatialpy.core.domain method)": [[1, "spatialpy.core.Domain.validate_action"]], "validate_action() (spatialpy.core.domain.domain method)": [[1, "spatialpy.core.domain.Domain.validate_action"]], "buildexpression (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.BuildExpression"]], "buildexpression.validationvisitor (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor"]], "cppconverter (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.CppConverter"]], "cppconverter.cppexpressiontransformer (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.CppConverter.CppExpressionTransformer"]], "expressionconverter (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter"]], "expressionresults (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.ExpressionResults"]], "pythonconverter (class in spatialpy.solvers.build_expression)": [[2, "spatialpy.solvers.build_expression.PythonConverter"]], "solver (class in spatialpy.solvers.solver)": [[2, "spatialpy.solvers.solver.Solver"]], "compile() (spatialpy.solvers.solver.solver method)": [[2, "spatialpy.solvers.solver.Solver.compile"]], "convert_str() (spatialpy.solvers.build_expression.expressionconverter class method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.convert_str"]], "get_str() (spatialpy.solvers.build_expression.cppconverter method)": [[2, "spatialpy.solvers.build_expression.CppConverter.get_str"]], "get_str() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.get_str"]], "getexpr_cpp() (spatialpy.solvers.build_expression.buildexpression method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.getexpr_cpp"]], "getexpr_python() (spatialpy.solvers.build_expression.buildexpression method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.getexpr_python"]], "map_operator() (spatialpy.solvers.build_expression.buildexpression class method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.map_operator"]], "operator_map (spatialpy.solvers.build_expression.buildexpression attribute)": [[2, "spatialpy.solvers.build_expression.BuildExpression.operator_map"]], "parse_comparison() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.parse_comparison"]], "parse_logical() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.parse_logical"]], "parse_operator() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.parse_operator"]], "run() (spatialpy.solvers.solver.solver method)": [[2, "spatialpy.solvers.solver.Solver.run"]], "spatialpy.solvers": [[2, "module-spatialpy.solvers"]], "spatialpy.solvers.build_expression": [[2, "module-spatialpy.solvers.build_expression"]], "spatialpy.solvers.solver": [[2, "module-spatialpy.solvers.solver"]], "validate() (spatialpy.solvers.build_expression.buildexpression method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.validate"]], "visit_add() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Add"]], "visit_and() (spatialpy.solvers.build_expression.cppconverter method)": [[2, "spatialpy.solvers.build_expression.CppConverter.visit_And"]], "visit_and() (spatialpy.solvers.build_expression.pythonconverter method)": [[2, "spatialpy.solvers.build_expression.PythonConverter.visit_And"]], "visit_assign() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_Assign"]], "visit_binop() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_BinOp"]], "visit_binop() (spatialpy.solvers.build_expression.cppconverter.cppexpressiontransformer method)": [[2, "spatialpy.solvers.build_expression.CppConverter.CppExpressionTransformer.visit_BinOp"]], "visit_binop() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_BinOp"]], "visit_boolop() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_BoolOp"]], "visit_boolop() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_BoolOp"]], "visit_bytes() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Bytes"]], "visit_call() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_Call"]], "visit_call() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Call"]], "visit_compare() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_Compare"]], "visit_compare() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Compare"]], "visit_constant() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Constant"]], "visit_div() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Div"]], "visit_ellipsis() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Ellipsis"]], "visit_eq() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Eq"]], "visit_gt() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Gt"]], "visit_gte() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_GtE"]], "visit_lt() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Lt"]], "visit_lte() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_LtE"]], "visit_mult() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Mult"]], "visit_name() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_Name"]], "visit_name() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Name"]], "visit_nameconstant() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_NameConstant"]], "visit_noteq() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_NotEq"]], "visit_num() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Num"]], "visit_or() (spatialpy.solvers.build_expression.cppconverter method)": [[2, "spatialpy.solvers.build_expression.CppConverter.visit_Or"]], "visit_or() (spatialpy.solvers.build_expression.pythonconverter method)": [[2, "spatialpy.solvers.build_expression.PythonConverter.visit_Or"]], "visit_pow() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Pow"]], "visit_str() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Str"]], "visit_sub() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_Sub"]], "visit_usub() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_USub"]], "visit_unaryop() (spatialpy.solvers.build_expression.buildexpression.validationvisitor method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.ValidationVisitor.visit_UnaryOp"]], "visit_unaryop() (spatialpy.solvers.build_expression.expressionconverter method)": [[2, "spatialpy.solvers.build_expression.ExpressionConverter.visit_UnaryOp"]], "with_blacklist() (spatialpy.solvers.build_expression.buildexpression method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.with_blacklist"]], "with_namespace() (spatialpy.solvers.build_expression.buildexpression method)": [[2, "spatialpy.solvers.build_expression.BuildExpression.with_namespace"]], "export() (in module spatialpy.stochss.stochss_export)": [[3, "spatialpy.stochss.stochss_export.export"]], "spatialpy.stochss": [[3, "module-spatialpy.stochss"]], "spatialpy.stochss.stochss_export": [[3, "module-spatialpy.stochss.stochss_export"]]}}) \ No newline at end of file diff --git a/setup.py b/setup.py index 32d8db35..b9676937 100644 --- a/setup.py +++ b/setup.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/__init__.py b/spatialpy/__init__.py index 8e541f81..0ff58136 100644 --- a/spatialpy/__init__.py +++ b/spatialpy/__init__.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/__version__.py b/spatialpy/__version__.py index 9d043308..31bd194c 100644 --- a/spatialpy/__version__.py +++ b/spatialpy/__version__.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as @@ -21,7 +21,7 @@ # @website https://github.com/StochSS/SpatialPy # ============================================================================= -__version__ = '1.2.0' +__version__ = '1.2.1' __title__ = 'SpatialPy' __description__ = 'Python Interface for Spatial Stochastic Biochemical Simulations' __url__ = 'https://spatialpy.github.io/SpatialPy/' @@ -29,4 +29,4 @@ __author__ = 'See AUTHORS' __email__ = 'bdrawert@unca.edu' __license__ = 'GPL-3.0-only' -__copyright__ = 'Copyright (C) 2019-2022' +__copyright__ = 'Copyright (C) 2019-2023' diff --git a/spatialpy/core/__init__.py b/spatialpy/core/__init__.py index af5e9d71..a9cff809 100644 --- a/spatialpy/core/__init__.py +++ b/spatialpy/core/__init__.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/boundarycondition.py b/spatialpy/core/boundarycondition.py index 8c833c2a..98204859 100644 --- a/spatialpy/core/boundarycondition.py +++ b/spatialpy/core/boundarycondition.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/cleanup.py b/spatialpy/core/cleanup.py index 6da34ccf..502b89ee 100644 --- a/spatialpy/core/cleanup.py +++ b/spatialpy/core/cleanup.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/datafunction.py b/spatialpy/core/datafunction.py index 5cfaff1b..a61bd7c6 100644 --- a/spatialpy/core/datafunction.py +++ b/spatialpy/core/datafunction.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/domain.py b/spatialpy/core/domain.py index 870022ee..0db0c0d3 100644 --- a/spatialpy/core/domain.py +++ b/spatialpy/core/domain.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/geometry.py b/spatialpy/core/geometry.py index 055418a2..4a0b482d 100644 --- a/spatialpy/core/geometry.py +++ b/spatialpy/core/geometry.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/initialcondition.py b/spatialpy/core/initialcondition.py index 94e35f32..4ebe5bdb 100644 --- a/spatialpy/core/initialcondition.py +++ b/spatialpy/core/initialcondition.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/lattice.py b/spatialpy/core/lattice.py index b9c5f5f6..0b1fa890 100644 --- a/spatialpy/core/lattice.py +++ b/spatialpy/core/lattice.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/model.py b/spatialpy/core/model.py index f5fe3687..6bf033c8 100644 --- a/spatialpy/core/model.py +++ b/spatialpy/core/model.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/parameter.py b/spatialpy/core/parameter.py index d3e9904f..0a588314 100644 --- a/spatialpy/core/parameter.py +++ b/spatialpy/core/parameter.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/reaction.py b/spatialpy/core/reaction.py index 7d5f5dff..678d98c1 100644 --- a/spatialpy/core/reaction.py +++ b/spatialpy/core/reaction.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/result.py b/spatialpy/core/result.py index 1753a1d9..46703636 100644 --- a/spatialpy/core/result.py +++ b/spatialpy/core/result.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as @@ -156,6 +156,19 @@ def __init__(self, model=None, result_dir=None): self.timeout = False self.official_vtk = False self.result_dir = result_dir + self.listOfResultObjects = [self] + + def __len__(self): + return len(self.listOfResultObjects) + + def __getitem__(self, index): + return self.listOfResultObjects[index] + + def __setitem__(self, index, item): + self.listOfResultObjects[index] = item + + def append(self, item): + self.listOfResultObjects.append(item) def __eq__(self, other): if isinstance(other, Result) and self.result_dir and other.result_dir: diff --git a/spatialpy/core/spatialpyerror.py b/spatialpy/core/spatialpyerror.py index 51f89815..a0cccb69 100644 --- a/spatialpy/core/spatialpyerror.py +++ b/spatialpy/core/spatialpyerror.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/species.py b/spatialpy/core/species.py index e7533750..c85255d4 100644 --- a/spatialpy/core/species.py +++ b/spatialpy/core/species.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/timespan.py b/spatialpy/core/timespan.py index f8b7cfed..d32ea1ee 100644 --- a/spatialpy/core/timespan.py +++ b/spatialpy/core/timespan.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/transformation.py b/spatialpy/core/transformation.py index ebd86579..e2a90af0 100644 --- a/spatialpy/core/transformation.py +++ b/spatialpy/core/transformation.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/visualization.py b/spatialpy/core/visualization.py index b69abc9b..523a058c 100644 --- a/spatialpy/core/visualization.py +++ b/spatialpy/core/visualization.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/core/vtkreader.py b/spatialpy/core/vtkreader.py index 99e5f1a7..fe402091 100644 --- a/spatialpy/core/vtkreader.py +++ b/spatialpy/core/vtkreader.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/__init__.py b/spatialpy/solvers/__init__.py index fd7a442b..a6a2bb10 100644 --- a/spatialpy/solvers/__init__.py +++ b/spatialpy/solvers/__init__.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/build_expression.py b/spatialpy/solvers/build_expression.py index 573a1ea8..8e27a735 100644 --- a/spatialpy/solvers/build_expression.py +++ b/spatialpy/solvers/build_expression.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/NRMConstant_v5.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/NRMConstant_v5.hpp index be4b090e..89de6dce 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/NRMConstant_v5.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/NRMConstant_v5.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.hpp index 4d410ab7..758bc14b 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.hpp index 5109c107..facefba5 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.hpp index 356137c7..ed652abf 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle.hpp index ed237085..7066333c 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle_system.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle_system.hpp index 50de5b4a..54a3d141 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle_system.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/particle_system.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/propensities.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/propensities.hpp index c9135e60..7543dcd5 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/propensities.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/propensities.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.hpp index 4c029d99..64c0868d 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.hpp index cfd9001e..9865d0b4 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate.hpp index d6811f05..ba4cf09b 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate_rdme.hpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate_rdme.hpp index 8481863e..556cbb55 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate_rdme.hpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/simulate_rdme.hpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/propensity_file_template.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/propensity_file_template.cpp index 8b1e80e7..a1cddb1e 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/propensity_file_template.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/propensity_file_template.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/NRMConstant_v5.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/NRMConstant_v5.cpp index 3ba38a5a..f38015bb 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/NRMConstant_v5.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/NRMConstant_v5.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.cpp index 03123125..430c01b8 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.cpp index 346b505e..5d745007 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp index a37b75e1..4ebaef43 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/particle.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/particle.cpp index 4efd1b28..c2555ea0 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/particle.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/particle.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp index 254ee855..2f7d9be3 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp index 6a4ed8ee..4fcb7b8f 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp index f8bc80ee..7597f80d 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp index 351b97b3..6c704144 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.cpp index 0c6227ca..3645f16d 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.cpp +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.cpp @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2019 - 2022 SpatialPy developers. +Copyright (C) 2019 - 2023 SpatialPy developers. This program is free software: you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/solvers/solver.py b/spatialpy/solvers/solver.py index c884a6f8..5332b2a4 100644 --- a/spatialpy/solvers/solver.py +++ b/spatialpy/solvers/solver.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as @@ -27,7 +27,7 @@ import numpy -from spatialpy.core.spatialpyerror import ModelError, SimulationError, SimulationTimeout +from spatialpy.core.spatialpyerror import ModelError, SimulationError def _read_from_stdout(stdout ,verbose=True): try: @@ -534,14 +534,11 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None, :type verbose: bool :returns: A SpatialPy Result object containing spatial and time series data from simulation. - :rtype: spatialpy.Result.Result | list(spatialpy.Result.Result) + :rtype: spatialpy.Result.Result - :raises SimulationTimeout: Simulation exceeded timeout. :raises SimulationError: Simulation execution failed. """ from spatialpy.core.result import Result # pylint: disable=import-outside-toplevel - if number_of_trajectories > 1: - result_list = [] # Check if compiled, call compile() if not. if not self.is_compiled: self.compile(debug=debug, profile=profile) @@ -587,7 +584,7 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None, result.timeout = True # send signal to the process group os.killpg(process.pid, signal.SIGINT) - raise SimulationTimeout("SpatialPy solver timeout exceded.") from err + except OSError as err: print(f"Error, execution of solver raised an exception: {err}") print(f"cmd = {solver_cmd}") @@ -602,9 +599,9 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None, result.success = True if profile: self.__read_profile_info(result) - if number_of_trajectories > 1: - result_list.append(result) - else: - return result + if run_ndx == 0: + first_result = result + elif number_of_trajectories > 1: + first_result.append(result) - return result_list + return first_result diff --git a/spatialpy/stochss/__init__.py b/spatialpy/stochss/__init__.py index 5449def2..be5b9eea 100644 --- a/spatialpy/stochss/__init__.py +++ b/spatialpy/stochss/__init__.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/spatialpy/stochss/stochss_export.py b/spatialpy/stochss/stochss_export.py index 5d7d586d..eaff6be4 100644 --- a/spatialpy/stochss/stochss_export.py +++ b/spatialpy/stochss/stochss_export.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/ioperformance.py b/test/ioperformance.py index bef0b459..9cf8cf9b 100644 --- a/test/ioperformance.py +++ b/test/ioperformance.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/models/__init__.py b/test/models/__init__.py index 5449def2..be5b9eea 100644 --- a/test/models/__init__.py +++ b/test/models/__init__.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/models/cylinder_demo3D.py b/test/models/cylinder_demo3D.py index 2e5835b4..e358649a 100644 --- a/test/models/cylinder_demo3D.py +++ b/test/models/cylinder_demo3D.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/models/mincde.py b/test/models/mincde.py index c11f66a5..ca17e866 100644 --- a/test/models/mincde.py +++ b/test/models/mincde.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/models/mincde_5r.py b/test/models/mincde_5r.py index 6f945ed3..8525b213 100644 --- a/test/models/mincde_5r.py +++ b/test/models/mincde_5r.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/run_integration_tests.py b/test/run_integration_tests.py index b84d845f..ed430f1f 100644 --- a/test/run_integration_tests.py +++ b/test/run_integration_tests.py @@ -1,7 +1,7 @@ #!/usr/bin/env python3 # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/run_unit_tests.py b/test/run_unit_tests.py index d54c1fff..f1eb8932 100755 --- a/test/run_unit_tests.py +++ b/test/run_unit_tests.py @@ -1,7 +1,7 @@ #!/usr/bin/env python3 # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/test_mincde.py b/test/test_mincde.py index 13ad6641..13d2482f 100644 --- a/test/test_mincde.py +++ b/test/test_mincde.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/test_model.py b/test/test_model.py index d0ab2afd..7b11cc09 100644 --- a/test/test_model.py +++ b/test/test_model.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/test_solver.py b/test/test_solver.py index 38e76c02..01a72455 100644 --- a/test/test_solver.py +++ b/test/test_solver.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/test_threads.py b/test/test_threads.py index 81224e6a..79f06bf3 100644 --- a/test/test_threads.py +++ b/test/test_threads.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/unit_tests/test_parameter.py b/test/unit_tests/test_parameter.py index 04ebcee6..f4d57786 100644 --- a/test/unit_tests/test_parameter.py +++ b/test/unit_tests/test_parameter.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/unit_tests/test_reaction.py b/test/unit_tests/test_reaction.py index 3220fb22..2e7cbe8a 100644 --- a/test/unit_tests/test_reaction.py +++ b/test/unit_tests/test_reaction.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/unit_tests/test_species.py b/test/unit_tests/test_species.py index af62456e..5af1c7e2 100644 --- a/test/unit_tests/test_species.py +++ b/test/unit_tests/test_species.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as diff --git a/test/unit_tests/test_timespan.py b/test/unit_tests/test_timespan.py index 87e3bc5d..35283672 100644 --- a/test/unit_tests/test_timespan.py +++ b/test/unit_tests/test_timespan.py @@ -1,6 +1,6 @@ # SpatialPy is a Python 3 package for simulation of # spatial deterministic/stochastic reaction-diffusion-advection problems -# Copyright (C) 2019 - 2022 SpatialPy developers. +# Copyright (C) 2019 - 2023 SpatialPy developers. # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as