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- Method resolution order:
- ReactionDiffusionSystem
- artchem.ReactionVessel.ODESystem
- artchem.ReactionVessel.ReactionVessel
Methods defined here:
- __init__(self, x, y, dx=1.0, periodic=True, nneighs=4)
- add_patch(self, mol, conc)
- add a patch of chemical at a random location
- add_patch_at(self, mol, conc, x, y)
- add some concentration to a patch of chemical at a given
location
- add_patches(self, npatches, mol, initconc)
- add some random patches of chemicals
- animate(self, sleeptime=1.0, transparent=True, blur=False)
- display the reaction-diffusion grid using vpytyon
transparent: use transparent background instead of black
blur: produce fuzzy borders between cells on the grid
- close(self)
- closes the PDE system such that it can be integrated
- computeTextureMatrix(self, transparent)
- produce a texture matrix to be used by animate()
- conc2img(self, cellsizex, cellsizey, transparent)
- convert the concentration matrix to the ARGB format
accepted by png.saveAsPNG()
if the transparent flag is set, the resulting png image
will have a transparent background in the spots where
there are no chemicals;
else the image will have a black background in those spots
TODO: implement hexagonal grid
- conc2img_DISABLED(self, cellsizex, cellsizey, transparent)
- convert the concentration matrix to the ARGB format
accepted by png.saveAsPNG()
tried to use matrix ops for speedup, but it turned out
slower than the element-by-element implementation above
- deposit(self, mol, conc, x, y)
- deposit a given amount of a molecule at a precise location
- diffusion_term(self, n)
- calculate diffusion term for molecule with index n, for
whole grid at once using matrix operations; leave result
on self.diff
- diffusion_term_NOTUSED(self, n)
- calculate diffusion term for molecule with index n, leave
result on self.diff (calculate one by one, far too slow,
but I leave the code here to illustrate conceptually how
it works, it's more readable than the matrix form below)
- disrupt(self, mol, val, x0, y0, x1, y1)
- disrupt the concentration of a chemical within a given
rectangle: clamp the concentr to at most val
- get_color(self, mol)
- returns the color that has been assigned to molecule mol
- get_conc(self, mol, x, y)
- get concentration of molecule by name, respecting boundaries
- get_conc_by_index(self, idx, x, y)
- get concentration of molecule by index, respecting boundaries
- get_diffcoef(self, mol)
- returns the diffusion coefficient of molecule mol
- get_neighbors(self)
- returns the current neighborhood configuration
- get_periodic(self)
- True if the current setup is periodic boundary
- get_pos(self, x, y)
- make sure coordinates always fall within boundaries
- integrate(self, dt=1.0)
- PDE integration of reaction-diffusion system with timestep dt
- perturb(self, mol, prob, ampl, x, y)
- perturb concentration at the given point
- perturbAll(self, mol, prob, ampl)
- perturb the given chemical with a given probability and
amplitude: a random concentration value in the range
[-amp/2 ; ampl/2] will be deposited at each node with
probability prob (if the chemical is not in the node,
nothing happens)
- perturb_region(self, mol, prob, ampl, x0, y0, x1, y1)
- perturb concentrations in the given region
- reaction_term(self, n)
- calculate reaction term for molecule with index n, leaving
the result on self.dcdt
- reset(self, mol, x, y)
- reset the concentration of a given molecule to zero
- resetAll(self, mol='', conc=0.0)
- reset the concentration of a given molecule to a given
value, overall on the grid; if no molecule is specified,
reset the concentrations of all molecules
- reset_region(self, mol, val, x0, y0, x1, y1)
- set the concentration of substances in this region to the
given value
- rnd_deposit(self, npoints, mol, conc, ampl=0.0)
- deposit a random amount of a molecule at random locations
- set_color(self, mol, color)
- set color of molecule to color=(red, green, blue)
- set_conc(self, mol, conc, x, y)
- set the concentration of a molecule at position x,y to a
given value, respecting boundary conditions
- set_diffcoef(self, mol, value)
- set the diffusion coefficient of molecule mol
- set_neighbors(self, nn)
- set neighborhood configuration: nn =
2: simple (north and right neighbors)
4: Von Neumann
6: hexagonal lattice
8: Moore
- set_patch(self, mol, conc)
- create a patch of chemical at a random location
- set_patch_at(self, mol, conc, x, y)
- create a patch of chemical at a given location
- set_patches(self, npatches, mol, initconc)
- create some initial random patches of chemicals
- set_periodic(self, flag)
- periodic (toroidal) vs. non-periodic boundary conditions
- trace(self)
- print internal variables, for debug purposes
- trace_conc(self)
- print the full grid of concentrations for each chemical,
producing a tab-separated matrix for each chemical
- trace_conc_xy(self, x, y)
- print the concentations of all chemicals at position (x,y)
- trace_title(self)
- output tab-separated title line for plotting
- writepng(self, fname, pngsizex=256, pngsizey=256, transparent=True)
- write molecule concentrations to a png image; each grid
position will have a size of cellsize per cellsize pixels
Methods inherited from artchem.ReactionVessel.ODESystem:
- get_coefficient(self, i)
- get kinetic coefficient for reaction (overrides default
ReactionVessel method in order to use vector kv directly;
the result of both methods should be the same though)
- set_coefficient(self, i, k)
- update kinetic coefficient for reaction
Methods inherited from artchem.ReactionVessel.ReactionVessel:
- add(self, reaction)
- add a new chemical reaction to the vessel's set of reactions;
'reaction' must be an object of the Reaction class
- get_names(self)
- list of all possible molecular species (set S of S,R,A)
- nreactions(self)
- total number of reactions: |R| in S,R,A
- nspecies(self)
- total number of molecular species: |S| in S,R,A
- parse(self, reactlist)
- invoke the ReactionParser to parse a list of reactions
- parse_file(self, fname)
- invoke the ReactionParser to parse the file named 'fname'
- parse_input(self, infile)
- invoke the ReactionParser to parse an already open input file
- parse_stdin(self)
- invoke the ReactionParser to parse the standard input (stdin)
- vtime(self)
- current simulation time
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