ecell/ecell4_base-v2.1.0b1.zip
ecell-ecell4_base-d35a4a9
.circleci
config.yml
1.8 kB
.github
workflows
ccpp.yml
1.8 kB
release.yml
1.4 kB
.gitignore
135 Bytes
.gitmodules
191 Bytes
.travis.yml
1.0 kB
.zenodo.json
1.2 kB
AUTHORS
339 Bytes
CMakeLists.txt
1.6 kB
LICENSE
39.9 kB
MANIFEST.in
122 Bytes
README.md
3.6 kB
appveyor.yml
800 Bytes
azure-pipelines.yml
1.6 kB
conda.recipe
bld.bat
79 Bytes
build.sh
96 Bytes
meta.yaml
906 Bytes
ecell4
CMakeLists.txt
223 Bytes
bd
BDFactory.hpp
2.1 kB
BDPropagator.cpp
10.8 kB
BDPropagator.hpp
3.2 kB
BDSimulator.cpp
2.5 kB
BDSimulator.hpp
3.5 kB
BDWorld.hpp
11.3 kB
CMakeLists.txt
177 Bytes
functions3d.cpp
4.2 kB
functions3d.hpp
1.7 kB
samples
CMakeLists.txt
80 Bytes
hardbody.cpp
1.9 kB
tests
BDSimulator_test.cpp
1.8 kB
BDWorld_test.cpp
1.1 kB
CMakeLists.txt
536 Bytes
core
AABB.cpp
1.0 kB
AABB.hpp
2.0 kB
AABBSurface.cpp
4.0 kB
AABBSurface.hpp
2.2 kB
Attribute.cpp
2.9 kB
Attribute.hpp
2.4 kB
BDMLWriter.hpp
12.1 kB
Barycentric.cpp
5.2 kB
Barycentric.hpp
3.0 kB
BoundaryCondition.hpp
3.5 kB
CMakeLists.txt
673 Bytes
Circle.hpp
5.2 kB
CompartmentSpace.cpp
3.8 kB
CompartmentSpace.hpp
6.2 kB
CompartmentSpaceHDF5Writer.hpp
9.0 kB
Cone.hpp
5.3 kB
Context.cpp
42.3 kB
Context.hpp
13.6 kB
Cylinder.cpp
2.8 kB
Cylinder.hpp
2.5 kB
Doxyfile
77.7 kB
DynamicPriorityQueue.hpp
14.5 kB
EventScheduler.hpp
3.2 kB
HCPLatticeSpace.cpp
1.5 kB
HCPLatticeSpace.hpp
6.0 kB
Identifier.hpp
5.7 kB
Integer3.cpp
1.0 kB
Integer3.hpp
4.0 kB
Journal.cpp
1.3 kB
Journal.hpp
1.8 kB
LatticeSpaceCellListImpl.cpp
6.0 kB
LatticeSpaceCellListImpl.hpp
11.3 kB
LatticeSpaceHDF5Writer.hpp
12.7 kB
LatticeSpaceVectorImpl.cpp
14.1 kB
LatticeSpaceVectorImpl.hpp
3.7 kB
Mesh.cpp
5.5 kB
Mesh.hpp
1.7 kB
Model.cpp
54 Bytes
Model.hpp
7.5 kB
ModelWrapper.hpp
3.7 kB
MoleculePool.hpp
5.5 kB
NetfreeModel.cpp
13.9 kB
NetfreeModel.hpp
3.8 kB
NetworkModel.cpp
9.2 kB
NetworkModel.hpp
3.5 kB
ObjectIDContainer.hpp
6.0 kB
OffLatticeSpace.cpp
7.2 kB
OffLatticeSpace.hpp
3.6 kB
Particle.hpp
3.7 kB
ParticleSpace.cpp
6.4 kB
ParticleSpace.hpp
12.2 kB
ParticleSpaceCellListImpl.cpp
10.6 kB
ParticleSpaceCellListImpl.hpp
15.6 kB
ParticleSpaceHDF5Writer.hpp
11.1 kB
ParticleSpaceRTreeImpl.cpp
4.3 kB
ParticleSpaceRTreeImpl.hpp
11.7 kB
PeriodicRTree.hpp
53.8 kB
PlanarSurface.cpp
2.1 kB
PlanarSurface.hpp
1.0 kB
Polygon.cpp
47.4 kB
Polygon.hpp
28.7 kB
PolygonHDF5Writer.hpp
5.3 kB
Quantity.hpp
1.1 kB
RandomNumberGenerator.cpp
3.1 kB
RandomNumberGenerator.hpp
3.2 kB
ReactionRule.cpp
8.8 kB
ReactionRule.hpp
4.8 kB
ReactionRuleDescriptor.hpp
7.1 kB
Real3.hpp
5.1 kB
Rod.cpp
5.1 kB
Rod.hpp
2.0 kB
STLFileIO.cpp
9.3 kB
STLFileIO.hpp
799 Bytes
Segment.hpp
1.5 kB
SerialIDGenerator.hpp
8.3 kB
Shape.hpp
917 Bytes
Simulator.hpp
1.4 kB
SimulatorBase.hpp
6.6 kB
SimulatorFactory.hpp
1.9 kB
Space.hpp
262 Bytes
Species.cpp
4.3 kB
Species.hpp
3.4 kB
Sphere.cpp
2.5 kB
Sphere.hpp
1.8 kB
StructureType.hpp
1.1 kB
SubvolumeSpace.cpp
10.5 kB
SubvolumeSpace.hpp
16.9 kB
SubvolumeSpaceHDF5Writer.hpp
12.7 kB
Triangle.cpp
4.5 kB
Triangle.hpp
3.4 kB
TriangleView.hpp
6.1 kB
UnitSpecies.cpp
4.3 kB
UnitSpecies.hpp
3.9 kB
VacantType.hpp
647 Bytes
VoxelPool.hpp
3.3 kB
VoxelSpaceBase.cpp
8.0 kB
VoxelSpaceBase.hpp
9.0 kB
VoxelView.hpp
488 Bytes
WorldInterface.hpp
5.4 kB
collision.cpp
14.3 kB
collision.hpp
5.9 kB
comparators.hpp
2.1 kB
config.h.in
439 Bytes
converter.hpp
782 Bytes
exceptions.hpp
3.1 kB
extras.cpp
8.7 kB
extras.hpp
3.6 kB
functions.hpp
2.0 kB
geometry.cpp
648 Bytes
geometry.hpp
570 Bytes
observers.cpp
17.4 kB
observers.hpp
29.9 kB
shape_operators.hpp
10.7 kB
tests
Barycentric_test.cpp
2.8 kB
CMakeLists.txt
844 Bytes
CompartmentSpace_test.cpp
2.0 kB
EventScheduler_test.cpp
428 Bytes
Halfedge_test.cpp
64.2 kB
LatticeSpace_test.cpp
22.2 kB
NetfreeModel_test.cpp
12.4 kB
NetworkModel_test.cpp
6.0 kB
OffLatticeSpace_test.cpp
5.8 kB
ParticleSpaceRTreeImpl_test.cpp
9.2 kB
ParticleSpace_test.cpp
5.6 kB
PeriodicRTree_test.cpp
11.2 kB
RandomNumberGenerator_test.cpp
888 Bytes
ReactionRule_test.cpp
19.3 kB
Real3_test.cpp
646 Bytes
STLIO_test.cpp
4.6 kB
Shape_test.cpp
2.2 kB
Species_test.cpp
5.4 kB
SubvolumeSpace_test.cpp
2.5 kB
extras_test.cpp
4.8 kB
geometry_test.cpp
1.5 kB
triangle_geometry.cpp
4.8 kB
triangle_geometry.hpp
2.5 kB
type_name_of.hpp
458 Bytes
types.hpp
261 Bytes
egfrd
.gitignore
916 Bytes
.hgignore
854 Bytes
AUTHORS
66 Bytes
AnalyticalPair.hpp
6.3 kB
AnalyticalSingle.hpp
3.2 kB
BDPropagator.hpp
17.5 kB
BDSimulator.hpp
9.7 kB
CMakeLists.txt
286 Bytes
COPYING
18.0 kB
ChangeLog
0 Bytes
ConsoleAppender.cpp
551 Bytes
ConsoleAppender.hpp
441 Bytes
Defs.hpp
493 Bytes
Domain.hpp
2.7 kB
DomainFactory.hpp
1.5 kB
DomainID.hpp
938 Bytes
DomainUtils.hpp
3.5 kB
EGFRDSimulator.hpp
159.6 kB
FaceTriangle.hpp
5.4 kB
INSTALL
1.8 kB
Logger.cpp
7.0 kB
Logger.hpp
3.9 kB
MatrixSpace.hpp
19.3 kB
Multi.hpp
17.2 kB
NEWS
0 Bytes
NetworkRulesAdapter.hpp
6.9 kB
Pair.hpp
1.5 kB
ParticleContainer.hpp
4.5 kB
ParticleContainerBase.hpp
11.6 kB
ParticleSimulator.hpp
6.5 kB
ParticleTraits.hpp
3.9 kB
Polygon.hpp
7.9 kB
PotentialField.hpp
3.5 kB
README
3.2 kB
ReactionRecord.hpp
4.0 kB
ReactionRecorder.hpp
367 Bytes
ReactionRecorderWrapper.hpp
3.2 kB
ReactionRuleInfo.hpp
3.2 kB
Real3Type.hpp
1.3 kB
ShapedDomain.hpp
852 Bytes
Shell.hpp
2.6 kB
ShellID.hpp
928 Bytes
Single.hpp
1.2 kB
StlFileReader.hpp
7.5 kB
Transaction.hpp
9.4 kB
TriangleOperation.hpp
6.0 kB
VolumeClearer.hpp
571 Bytes
World.hpp
40.4 kB
abstract_set.hpp
2.5 kB
egfrd.hpp
6.9 kB
exceptions.hpp
3.8 kB
factorial.hpp
17.4 kB
filters.hpp
2.4 kB
generator.hpp
14.6 kB
geometry.hpp
6.8 kB
linear_algebra.hpp
13.5 kB
pyport.patch
801 Bytes
samples
CMakeLists.txt
158 Bytes
mymapk.cpp
8.8 kB
polygon.cpp
7.4 kB
wscript
774 Bytes
sorted_list.hpp
6.0 kB
structures.hpp
3.6 kB
tests
GreensFunction3DRadInf_test.cpp
947 Bytes
twofold_container.hpp
6.3 kB
utils
array_helper.hpp
1.0 kB
array_traits.hpp
757 Bytes
assoc_container_traits.hpp
520 Bytes
fun_composition.hpp
5.5 kB
fun_wrappers.hpp
3.2 kB
map_adapter.hpp
4.3 kB
math.hpp
844 Bytes
memberwise_compare.hpp
1.3 kB
pair.hpp
3.8 kB
pointer_as_ref.hpp
1.1 kB
random.hpp
565 Bytes
range.hpp
10.3 kB
range_support.hpp
2.4 kB
reference_or_instance.hpp
1.2 kB
reset.hpp
308 Bytes
stringizer.hpp
867 Bytes
unassignable_adapter.hpp
9.7 kB
gillespie
CMakeLists.txt
191 Bytes
GillespieFactory.hpp
1.5 kB
GillespieSimulator.cpp
8.5 kB
GillespieSimulator.hpp
17.5 kB
GillespieWorld.cpp
3.8 kB
GillespieWorld.hpp
5.5 kB
samples
CMakeLists.txt
81 Bytes
simple.cpp
1.6 kB
tests
CMakeLists.txt
557 Bytes
GillespieSimulator_test.cpp
1.3 kB
GillespieWorld_test.cpp
1.1 kB
meso
CMakeLists.txt
181 Bytes
MesoscopicFactory.hpp
2.6 kB
MesoscopicSimulator.cpp
9.6 kB
MesoscopicSimulator.hpp
36.2 kB
MesoscopicWorld.cpp
9.9 kB
MesoscopicWorld.hpp
12.3 kB
samples
CMakeLists.txt
91 Bytes
simple-meso.cpp
1.3 kB
tests
CMakeLists.txt
533 Bytes
MesoscopicSimulator_test.cpp
1.5 kB
ode
CMakeLists.txt
179 Bytes
ODEFactory.hpp
2.3 kB
ODESimulator.cpp
5.7 kB
ODESimulator.hpp
29.7 kB
ODEWorld.cpp
2.2 kB
ODEWorld.hpp
9.4 kB
samples
CMakeLists.txt
564 Bytes
dissociation.cpp
1.6 kB
equilibrium.cpp
1.8 kB
equilibrium2.cpp
2.0 kB
equilibrium_new.cpp
4.5 kB
odesimulator2.cpp
2.7 kB
run_test.cpp
6.6 kB
tests
CMakeLists.txt
526 Bytes
ODESimulator_new_test.cpp
2.5 kB
ODESimulator_test.cpp
2.0 kB
python_api
CMakeLists.txt
620 Bytes
bd.cpp
5.0 kB
core.cpp
59.8 kB
egfrd.cpp
9.1 kB
gillespie.cpp
3.9 kB
main.cpp
1.2 kB
meso.cpp
7.7 kB
model.hpp
5.4 kB
observers.hpp
1.3 kB
ode.cpp
4.5 kB
python_api.hpp
635 Bytes
random_number_generator.hpp
3.9 kB
reaction_rule_descriptor.hpp
2.4 kB
sgfrd.cpp
8.6 kB
shape.hpp
2.4 kB
simulator.hpp
2.7 kB
simulator_factory.hpp
1.9 kB
spatiocyte.cpp
9.3 kB
type_caster.hpp
939 Bytes
world_interface.hpp
4.0 kB
sgfrd
BDPropagator.hpp
27.5 kB
BDSimulator.hpp
8.2 kB
Birth.hpp
971 Bytes
CMakeLists.txt
248 Bytes
Multi.hpp
6.7 kB
MultiContainer.hpp
8.8 kB
Pair.hpp
4.3 kB
ReactionInfo.hpp
3.6 kB
SGFRDEvent.hpp
1.4 kB
SGFRDFactory.hpp
4.6 kB
SGFRDSimulator.cpp
73.0 kB
SGFRDSimulator.hpp
91.2 kB
SGFRDWorld.cpp
15.4 kB
SGFRDWorld.hpp
28.9 kB
Shell.hpp
1.9 kB
ShellContainer.hpp
17.9 kB
ShellID.hpp
1.1 kB
ShellVisitorApplier.hpp
2.6 kB
ShellVisitors.hpp
2.2 kB
Single.hpp
1.9 kB
StructureRegistrator.hpp
8.3 kB
distance.hpp
5.8 kB
distance_calculator.hpp
1.9 kB
expected.hpp
5.0 kB
samples
CMakeLists.txt
109 Bytes
bdonly.cpp
8.8 kB
diffusion.cpp
3.7 kB
plane10x10.stl
22.1 kB
reaction.cpp
10.2 kB
reaction.inp
362 Bytes
rebinding_bd.cpp
12.1 kB
sphere.stl
151.7 kB
statistics.hpp
1.9 kB
tracer.hpp
7.0 kB
spatiocyte
CMakeLists.txt
193 Bytes
OffLattice.hpp
1.9 kB
OneToManyMap.hpp
1.6 kB
ReactionEvent.cpp
3.6 kB
SpatiocyteEvent.hpp
7.2 kB
SpatiocyteFactory.hpp
1.8 kB
SpatiocyteReactions.cpp
15.2 kB
SpatiocyteReactions.hpp
3.2 kB
SpatiocyteSimulator.cpp
6.4 kB
SpatiocyteSimulator.hpp
2.5 kB
SpatiocyteWorld.cpp
11.7 kB
SpatiocyteWorld.hpp
31.2 kB
StepEvent.cpp
311 Bytes
Voxel.hpp
1.4 kB
samples
CMakeLists.txt
198 Bytes
diffusion.cpp
1.6 kB
simple_lattice.cpp
2.2 kB
tests
CMakeLists.txt
586 Bytes
OneToManyMap_test.cpp
1.2 kB
SpatiocyteSimulator_test.cpp
11.7 kB
SpatiocyteWorld_test.cpp
7.5 kB
utils.cpp
3.5 kB
utils.hpp
570 Bytes
exclude_files
84 Bytes
greens_functions
misc
benchmark.png
147.9 kB
benchmark.py
8.6 kB
ecell4paraview.py
3.7 kB
tests
spatiocyte
birth_death.py
870 Bytes
msd.py
1.6 kB
reversible.py
1.3 kB
reversible_diffusion_limited.py
1.3 kB
pybind11
setup.py
4.5 kB
tests
__init__.py
0 Bytes
core
__init__.py
398 Bytes
network_model.py
2.6 kB
particle.py
862 Bytes
reaction_rule.py
4.7 kB
rr_descriptor_pyfunc.py
522 Bytes
species.py
5.6 kB
types.py
3.4 kB
spatiocyte
__init__.py
68 Bytes
offlattice.py
1.2 kB