Index

A | C | D | E | G | I | M | N | P | R | S | T | U | V

A

add_data_function() (pyurdme.pyurdme.URDMEModel method)
add_parameter() (pyurdme.model.Model method)
add_periodic_boundary_condition() (pyurdme.pyurdme.URDMEMesh method)
add_product() (pyurdme.model.Reaction method)
add_reactant() (pyurdme.model.Reaction method)
add_reaction() (pyurdme.model.Model method)
add_species() (pyurdme.model.Model method)
add_subdomain() (pyurdme.pyurdme.URDMEModel method)
annotate() (pyurdme.model.Reaction method)
assemble() (pyurdme.pyurdme.URDMEModel method)

C

closest_vertex() (pyurdme.pyurdme.URDMEMesh method)
compile() (pyurdme.pyurdme.URDMESolver method)
create_connectivity_matrix() (pyurdme.pyurdme.URDMEModel method)
create_dependency_graph() (pyurdme.pyurdme.URDMEModel method)
create_extended_mesh() (pyurdme.pyurdme.URDMEModel method)
create_mass_action() (pyurdme.model.Reaction method)
create_propensity_file() (pyurdme.pyurdme.URDMESolver method)
create_stoichiometric_matrix() (pyurdme.pyurdme.URDMEModel method)
create_system_matrix() (pyurdme.pyurdme.URDMEModel method)
CubeMeshPeriodicBoundary (class in pyurdme.pyurdme)

D

delete_all_parameters() (pyurdme.model.Model method)
delete_all_reactions() (pyurdme.model.Model method)
delete_all_species() (pyurdme.model.Model method)
delete_parameter() (pyurdme.model.Model method)
delete_reaction() (pyurdme.model.Model method)
delete_species() (pyurdme.model.Model method)
dim() (pyurdme.model.Species method)
display() (pyurdme.pyurdme.URDMEResult method)

E

evaluate() (pyurdme.model.Parameter method)
export_to_particle_js() (pyurdme.pyurdme.URDMEResult method)
export_to_three_js() (pyurdme.pyurdme.URDMEMesh method)
(pyurdme.pyurdme.URDMEResult method)
export_to_vtk() (pyurdme.pyurdme.URDMEResult method)
export_to_xyx() (pyurdme.pyurdme.URDMEResult method)

G

generate_cube_mesh() (pyurdme.pyurdme.URDMEMesh class method)
generate_interval_mesh() (pyurdme.pyurdme.URDMEMesh class method)
generate_square_mesh() (pyurdme.pyurdme.URDMEMesh class method)
generate_unit_cube_mesh() (pyurdme.pyurdme.URDMEMesh class method)
generate_unit_interval_mesh() (pyurdme.pyurdme.URDMEMesh class method)
generate_unit_square_mesh() (pyurdme.pyurdme.URDMEMesh class method)
get_all_parameters() (pyurdme.model.Model method)
get_all_reactions() (pyurdme.model.Model method)
get_all_species() (pyurdme.model.Model method)
get_d2v() (pyurdme.pyurdme.URDMEResult method)
get_endtime_model() (pyurdme.pyurdme.URDMEResult method)
get_function_space() (pyurdme.pyurdme.URDMEMesh method)
get_mesh_size() (pyurdme.pyurdme.URDMEMesh method)
get_normalized_coordinates() (pyurdme.pyurdme.URDMEMesh method)
get_num_dof_voxels() (pyurdme.pyurdme.URDMEMesh method)
get_num_reactions() (pyurdme.model.Model method)
get_num_species() (pyurdme.model.Model method)
get_num_voxels() (pyurdme.pyurdme.URDMEMesh method)
get_parameter() (pyurdme.model.Model method)
get_reaction() (pyurdme.model.Model method)
get_scaled_coordinates() (pyurdme.pyurdme.URDMEMesh method)
get_scaled_normalized_coordinates() (pyurdme.pyurdme.URDMEMesh method)
get_solver_datastructure() (pyurdme.pyurdme.URDMEModel method)
get_species() (pyurdme.model.Model method)
(pyurdme.pyurdme.URDMEResult method)
get_species_map() (pyurdme.pyurdme.URDMEModel method)
get_subdomain_vector() (pyurdme.pyurdme.URDMEModel method)
get_timespan() (pyurdme.pyurdme.URDMEResult method)
get_v2d() (pyurdme.pyurdme.URDMEResult method)
get_voxels() (pyurdme.pyurdme.URDMEMesh method)

I

initialize_initial_condition() (pyurdme.pyurdme.URDMEModel method)
inside() (pyurdme.pyurdme.CubeMeshPeriodicBoundary method)
(pyurdme.pyurdme.IntervalMeshPeriodicBoundary method)
(pyurdme.pyurdme.SquareMeshPeriodicBoundary method)
IntervalMeshPeriodicBoundary (class in pyurdme.pyurdme)
InvalidSystemMatrixException

M

map() (pyurdme.pyurdme.CubeMeshPeriodicBoundary method)
(pyurdme.pyurdme.IntervalMeshPeriodicBoundary method)
(pyurdme.pyurdme.SquareMeshPeriodicBoundary method)
(pyurdme.pyurdme.URDMEDataFunction method)
MeshImportError
Model (class in pyurdme.model)
ModelError
ModelException

N

NAME (pyurdme.nsmsolver.NSMSolver attribute)
name (pyurdme.pyurdme.URDMEDataFunction attribute)
NSMSolver (class in pyurdme.nsmsolver)

P

Parameter (class in pyurdme.model)
ParameterError
pyurdme.model (module)
pyurdme.nsmsolver (module)
pyurdme.pyurdme (module)

R

Reaction (class in pyurdme.model)
ReactionError
read_dolfin_mesh() (pyurdme.pyurdme.URDMEMesh class method)
read_solution() (pyurdme.pyurdme.URDMEResult method)
resolve_parameters() (pyurdme.model.Model method)
restrict() (pyurdme.pyurdme.URDMEModel method)
run() (pyurdme.pyurdme.URDMEModel method)
(pyurdme.pyurdme.URDMESolver method)

S

serialize() (pyurdme.pyurdme.URDMESolver method)
set_expression() (pyurdme.model.Parameter method)
set_initial_condition_distribute_uniformly() (pyurdme.pyurdme.URDMEModel method)
set_initial_condition_place_near() (pyurdme.pyurdme.URDMEModel method)
set_initial_condition_scatter() (pyurdme.pyurdme.URDMEModel method)
set_num_dof_voxels() (pyurdme.pyurdme.URDMEMesh method)
set_parameter() (pyurdme.model.Model method)
set_subdomain_vector() (pyurdme.pyurdme.URDMEModel method)
set_type() (pyurdme.model.Reaction method)
Species (class in pyurdme.model)
SpeciesError
SquareMeshPeriodicBoundary (class in pyurdme.pyurdme)

T

timespan() (pyurdme.pyurdme.URDMEModel method)

U

update_namespace() (pyurdme.model.Model method)
urdme() (in module pyurdme.pyurdme)
URDMEDataFunction (class in pyurdme.pyurdme)
URDMEError
URDMEMesh (class in pyurdme.pyurdme)
URDMEModel (class in pyurdme.pyurdme)
URDMEResult (class in pyurdme.pyurdme)
URDMESolver (class in pyurdme.pyurdme)
URDMEXmesh (class in pyurdme.pyurdme)

V

validate() (pyurdme.pyurdme.URDMEModel method)