sme.SimulationResult.species_dcdt

property SimulationResult.species_dcdt

the species concentration rate of change at this timepoint

for each species, the rate of change of concentration is provided as a 3d array, where species_dcdt['A'][z][y][x] is the rate of change of the concentration of species “A” at the point (x,y,z)

Note

The rate of change of species concentrations is only provided for the last timepoint of a simulation, and only when using the Pixel simulator. Otherwise species_dcdt is an empty dict.

Examples

do a short Pixel simulation and get the rate of change of species concentrations from the last timepoint:

>>> import sme
>>> model = sme.open_example_model()
>>> results = model.simulate(10, 1)
>>> species_dcdt = results[-1].species_dcdt

this is a dict with an entry for each species:

>>> type(species_dcdt)
<class 'dict'>
>>> species_dcdt.keys()
dict_keys(['B_out', 'A_cell', 'B_cell', 'A_nucl', 'B_nucl'])

the rate of change of concentration is a 2d ndarray of doubles, one for each pixel in the geometry image:

>>> b_cell = species_dcdt['B_cell']
>>> type(b_cell)
<class 'numpy.ndarray'>
>>> b_cell.dtype
dtype('float64')
>>> b_cell.shape
(1, 100, 100)

the rate of change of concentration can be displayed using matplotlib:

>>> import matplotlib.pyplot as plt
>>> imgplot = plt.imshow(b_cell[0])

Type:

Dict[str, numpy.ndarray]