From f5b6281d395f45b68216f7a3cbee46f6a79b8907 Mon Sep 17 00:00:00 2001 From: Bryan Rumsey Date: Wed, 2 Feb 2022 15:40:53 -0500 Subject: [PATCH] Updated copyright to 'Copyright (C) 2019 - 2022'. --- COPYRIGHT | 2 +- setup.py | 2 +- spatialpy/__init__.py | 2 +- spatialpy/__version__.py | 2 +- spatialpy/core/BoundaryCondition.py | 40 ++++++++++++++----- spatialpy/core/DataFunction.py | 2 +- spatialpy/core/Domain.py | 2 +- spatialpy/core/Geometry.py | 2 +- spatialpy/core/InitialCondition.py | 2 +- spatialpy/core/Model.py | 2 +- spatialpy/core/Parameter.py | 2 +- spatialpy/core/Reaction.py | 2 +- spatialpy/core/Result.py | 2 +- spatialpy/core/Species.py | 2 +- spatialpy/core/VTKReader.py | 2 +- spatialpy/core/__init__.py | 2 +- spatialpy/core/cleanup.py | 2 +- spatialpy/core/spatialpyError.py | 2 +- spatialpy/solvers/Solver.py | 2 +- spatialpy/solvers/__init__.py | 2 +- spatialpy/solvers/build/__init__.py | 2 +- spatialpy/solvers/build/expression.py | 2 +- .../include/NRMConstant_v5.hpp | 2 +- .../include/count_cores.h | 2 +- .../include/model.h | 2 +- .../include/output.h | 2 +- .../include/particle.hpp | 2 +- .../include/particle_system.hpp | 2 +- .../include/propensities.hpp | 2 +- .../include/pthread_barrier.h | 2 +- .../include/read_lammps_input_file.h | 2 +- .../include/simulate.hpp | 2 +- .../include/simulate_rdme.hpp | 2 +- .../propensity_file_template.cpp | 2 +- .../src/NRMConstant_v5.cpp | 2 +- .../src/count_cores.c | 2 +- .../ssa_sdpd-c-simulation-engine/src/model.c | 2 +- .../ssa_sdpd-c-simulation-engine/src/output.c | 2 +- .../src/particle.cpp | 2 +- .../src/pthread_barrier.c | 2 +- .../src/read_lammps_input_file.c | 2 +- .../src/simulate.cpp | 2 +- .../src/simulate_rdme.cpp | 2 +- .../src/simulate_threads.c | 2 +- spatialpy/stochss/StochSSexport.py | 2 +- spatialpy/stochss/__init__.py | 2 +- test/ioperformance.py | 2 +- test/models/__init__.py | 2 +- test/models/cylinder_demo3D.py | 2 +- test/models/mincde.py | 2 +- test/models/mincde_5r.py | 2 +- test/run_tests.py | 2 +- test/test_mincde.py | 2 +- test/test_model.py | 2 +- test/test_parameter.py | 2 +- test/test_reaction.py | 2 +- test/test_solver.py | 2 +- test/test_species.py | 2 +- test/test_threads.py | 2 +- 59 files changed, 87 insertions(+), 69 deletions(-) diff --git a/COPYRIGHT b/COPYRIGHT index 4bd90fb7..116227b0 100644 --- a/COPYRIGHT +++ b/COPYRIGHT @@ -1,6 +1,6 @@ SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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/setup.py b/setup.py index 05fd25a9..b802fe9f 100644 --- a/setup.py +++ b/setup.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 d62ab566..5fe61474 100644 --- a/spatialpy/__init__.py +++ b/spatialpy/__init__.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 4af08306..6386b853 100644 --- a/spatialpy/__version__.py +++ b/spatialpy/__version__.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 0077c3fc..1c3cdc2c 100644 --- a/spatialpy/core/BoundaryCondition.py +++ b/spatialpy/core/BoundaryCondition.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 @@ -18,6 +18,8 @@ import numpy +from spatialpy.core.Model import Model +from spatialpy.core.Species import Species from spatialpy.core.spatialpyError import BoundaryConditionError @@ -72,16 +74,32 @@ class BoundaryCondition(): :param model: Target model of boundary condition :type model: spatialpy.Model.Model """ - def __init__(self, - xmin=None, xmax=None, - ymin=None, ymax=None, - zmin=None, zmax=None, - type_id=None, - species=None, - deterministic=True, - property=None, - value=None, - model=None): + def __init__(self, xmin=None, xmax=None, ymin=None, ymax=None, zmin=None, zmax=None, type_id=None, + species=None, deterministic=True, property=None, value=None, model=None): + + if xmin is not None and not isinstance(xmin, (int, float)): + raise BoundaryConditionError("X-min must be of type int or float.") + if xmax is not None and not isinstance(xmax, (int, float)): + raise BoundaryConditionError("X-max must be of type int or float.") + if ymin is not None and not isinstance(ymin, (int, float)): + raise BoundaryConditionError("Y-min must be of type int or float.") + if ymax is not None and not isinstance(ymax, (int, float)): + raise BoundaryConditionError("Y-max must be of type int or float.") + if zmin is not None and not isinstance(zmin, (int, float)): + raise BoundaryConditionError("Z-min must be of type int or float.") + if zmax is not None and not isinstance(zmax, (int, float)): + raise BoundaryConditionError("Z-max must be of type int or float.") + if type_id is not None and not isinstance(type_id, int): + raise BoundaryConditionError("Type-ID must be of type int.") + if not (species is None or isinstance(species, (str, Species)) or type(species).__name__ == 'Species'): + raise BoundaryConditionError("Species must be of type string or SpatialPy.Species") + if property is not None and not (isinstance(property, str) and property in ('nu', 'rho', 'v')): + raise BoundaryConditionError("Property must be 'nu' 'rho' or 'v'") + if not (value is None or isinstance(value, float) or (isinstance(value, list) and len(value) == 3)): + raise BoundaryConditionError("Value must be of type float or float[3].") + if not (model is None or isinstance(model, Model) or type(model).__name__ == 'Model'): + raise BoundaryConditionError("Model must be of type SpatialPy.Model.") + self.xmin = xmin self.xmax = xmax diff --git a/spatialpy/core/DataFunction.py b/spatialpy/core/DataFunction.py index e6b12d39..d16fd988 100644 --- a/spatialpy/core/DataFunction.py +++ b/spatialpy/core/DataFunction.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 40155ac2..db9d4ce0 100644 --- a/spatialpy/core/Domain.py +++ b/spatialpy/core/Domain.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 3e086bc3..6af57766 100644 --- a/spatialpy/core/Geometry.py +++ b/spatialpy/core/Geometry.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 5469e171..243dde2e 100644 --- a/spatialpy/core/InitialCondition.py +++ b/spatialpy/core/InitialCondition.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 ec5c6498..4c4f05b5 100644 --- a/spatialpy/core/Model.py +++ b/spatialpy/core/Model.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 40099c0b..868b727c 100644 --- a/spatialpy/core/Parameter.py +++ b/spatialpy/core/Parameter.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 8da46eee..e10d3d0a 100644 --- a/spatialpy/core/Reaction.py +++ b/spatialpy/core/Reaction.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 5885221c..21436db7 100644 --- a/spatialpy/core/Result.py +++ b/spatialpy/core/Result.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 bcbfe9d0..eaad14c3 100644 --- a/spatialpy/core/Species.py +++ b/spatialpy/core/Species.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 c24bad1d..99b87313 100644 --- a/spatialpy/core/VTKReader.py +++ b/spatialpy/core/VTKReader.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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/__init__.py b/spatialpy/core/__init__.py index e12ccfd5..8a505c25 100644 --- a/spatialpy/core/__init__.py +++ b/spatialpy/core/__init__.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 1b966b9d..30ecac4e 100644 --- a/spatialpy/core/cleanup.py +++ b/spatialpy/core/cleanup.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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/spatialpyError.py b/spatialpy/core/spatialpyError.py index 2139d212..9c47682e 100644 --- a/spatialpy/core/spatialpyError.py +++ b/spatialpy/core/spatialpyError.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 59612e8f..defe4896 100644 --- a/spatialpy/solvers/Solver.py +++ b/spatialpy/solvers/Solver.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 030a087b..54e2aa86 100644 --- a/spatialpy/solvers/__init__.py +++ b/spatialpy/solvers/__init__.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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/__init__.py b/spatialpy/solvers/build/__init__.py index f0969dae..4cb912d4 100644 --- a/spatialpy/solvers/build/__init__.py +++ b/spatialpy/solvers/build/__init__.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 4b464273..92b1907d 100644 --- a/spatialpy/solvers/build/expression.py +++ b/spatialpy/solvers/build/expression.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 51b329c6..be4b090e 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) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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.h b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.h index af4f7c5e..4d410ab7 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.h +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.h @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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.h b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.h index 1898b2f4..5109c107 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.h +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.h @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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.h b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.h index 96d216ad..356137c7 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.h +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.h @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 0de4690a..ed237085 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) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 6331c290..50de5b4a 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) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 0cdedcd6..c9135e60 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) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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.h b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.h index 39abea82..4c029d99 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.h +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.h @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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.h b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.h index 423f4850..18581750 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.h +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.h @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 bd80368c..d6811f05 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) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 cad35097..8481863e 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) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 240f0ec5..d523f72d 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) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 dfdc9fe2..3ba38a5a 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) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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.c b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.c index ea0986c3..03123125 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.c +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.c @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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.c b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.c index 34200390..af3232e2 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.c +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.c @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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.c b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.c index 3193a3ab..023f64ae 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.c +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.c @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 bb3160eb..c2825347 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) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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.c b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.c index 9179990a..b3573437 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.c +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.c @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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.c b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.c index 260590d8..638e77c1 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.c +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.c @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 4362982a..00ac7db0 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) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 f4370162..1f88ae1d 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) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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.c b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.c index 7894234a..de60e34b 100644 --- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.c +++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.c @@ -1,7 +1,7 @@ /** SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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/StochSSexport.py b/spatialpy/stochss/StochSSexport.py index 77a55f62..ecc725ab 100644 --- a/spatialpy/stochss/StochSSexport.py +++ b/spatialpy/stochss/StochSSexport.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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/__init__.py b/spatialpy/stochss/__init__.py index ce7ccfa4..ed0af9eb 100644 --- a/spatialpy/stochss/__init__.py +++ b/spatialpy/stochss/__init__.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 26f95364..9603f788 100644 --- a/test/ioperformance.py +++ b/test/ioperformance.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 4b747b83..f7ca2dba 100644 --- a/test/models/__init__.py +++ b/test/models/__init__.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 73a91e39..0a15eefc 100644 --- a/test/models/cylinder_demo3D.py +++ b/test/models/cylinder_demo3D.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 00388f4d..57f9f954 100644 --- a/test/models/mincde.py +++ b/test/models/mincde.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 eb44f4c3..3a73e092 100644 --- a/test/models/mincde_5r.py +++ b/test/models/mincde_5r.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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_tests.py b/test/run_tests.py index 15c8c2b3..8f9b5d21 100755 --- a/test/run_tests.py +++ b/test/run_tests.py @@ -2,7 +2,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 99b0f15a..f089df1a 100644 --- a/test/test_mincde.py +++ b/test/test_mincde.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 3aa74f11..d5a4dbc0 100644 --- a/test/test_model.py +++ b/test/test_model.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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_parameter.py b/test/test_parameter.py index a26de6cc..d080f8a9 100644 --- a/test/test_parameter.py +++ b/test/test_parameter.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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_reaction.py b/test/test_reaction.py index 970504d2..65acf0b3 100644 --- a/test/test_reaction.py +++ b/test/test_reaction.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 53817a09..1a9b87ce 100644 --- a/test/test_solver.py +++ b/test/test_solver.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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_species.py b/test/test_species.py index 73d357da..6b183b1f 100644 --- a/test/test_species.py +++ b/test/test_species.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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 7fd8972a..feeba6f0 100644 --- a/test/test_threads.py +++ b/test/test_threads.py @@ -1,7 +1,7 @@ ''' SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems -Copyright (C) 2021 SpatialPy developers. +Copyright (C) 2019 - 2022 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