Visualization
Plot DNA Base Frequency
- qDNA.visualization.plot_dna_base_frequency(lifetime_dict, cutoff_num=10)
Plots the frequency of A-T and G-C base pairs against the exciton lifetime.
- Parameters:
- lifetime_dictDict[str, float]
Dictionary where keys are DNA sequences and values are lifetimes in femtoseconds.
- cutoff_numint, optional
The number of initial sequences to exclude from the plot, by default 10.
Plot Eigenspectrum
- qDNA.visualization.plot_eigv(ax, tb_ham, energy_unit='100meV')
Plots the eigenenergies.
- Parameters:
- axmatplotlib.axes.Axes
The axes to plot on.
- tb_hamTB_Ham
The tight-binding Hamiltonian.
- energy_unitstr, optional
The unit of energy to plot, by default ‘100meV’.
- qDNA.visualization.plot_eigs(ax, tb_ham, eigenstate_idx)
Plots the distribution of eigenstates over tight-binding sites.
- Parameters:
- axmatplotlib.axes.Axes
The axes to plot on.
- tb_hamTB_Ham
The tight-binding Hamiltonian.
- eigenstate_idxint
The index of the eigenstate to plot.
Plot Fourier Analysis
- qDNA.visualization.plot_fourier(ax, tb_ham, init_state, end_state, x_axis)
Plots the Fourier transform of the transition amplitudes.
- Parameters:
- axmatplotlib.axes.Axes
The axes to plot on.
- tb_hamTB_Ham
The tight-binding Hamiltonian.
- init_stateAny
The initial state.
- end_stateAny
The end state.
- x_axisstr
The x-axis type (‘frequency’ or ‘period’).
- qDNA.visualization.plot_average_pop(ax, tb_ham, J_list, J_unit)
Plots the average population for each interaction parameter.
- Parameters:
- axlist of matplotlib.axes.Axes
The axes to plot on.
- tb_hamTB_Ham
The tight-binding Hamiltonian.
- J_listlist
List of interaction parameters.
- J_unitstr
The unit of the interaction parameters.
Plot Populations and Coherences
- qDNA.visualization.plot_pop_fourier(ax, tb_ham, init_state, end_state, times, t_unit)
Plots population using the Fourier decomposition.
- Parameters:
- axmatplotlib.axes.Axes
The axes to plot on.
- tb_hamTB_Ham
The tight-binding Hamiltonian.
- init_statestr
The initial state.
- end_statestr
The end state.
- timeslist of float
The time points for plotting.
- t_unitstr
The unit of time.
- qDNA.visualization.plot_pop(ax, tb_site, me_solver, add_legend=True)
Plots population of one base.
- Parameters:
- axmatplotlib.axes.Axes
The axes to plot on.
- tb_sitestr
The tight-binding site.
- me_solverME_Solver
The master equation solver instance.
- add_legendbool, optional
Whether to add a legend, by default True.
- qDNA.visualization.plot_pops(me_solver)
Plots populations of all bases.
- Parameters:
- me_solverME_Solver
The master equation solver instance.
- Returns:
- tuple
A tuple containing the figure and axes.
- qDNA.visualization.plot_pops_heatmap(me_solver, vmax_list=[1, 1, 1], heatmap_type='seaborn')
Plots a heatmap of populations for each particle in the system.
- Parameters:
- me_solverobject
An instance of a solver that contains the time evolution data and Hamiltonian information.
- vmax_listlist of float, optional
A list of maximum values for the color scale of each particle’s heatmap. Default is [1, 1, 1].
- heatmap_typestr, optional
The type of heatmap to plot. Options are “seaborn” or “matplotlib”. Default is “seaborn”.
- Returns:
- figmatplotlib.figure.Figure
The figure object containing the heatmaps.
- axnumpy.ndarray of matplotlib.axes._subplots.AxesSubplot
An array of axes objects for each particle’s heatmap.
Notes
Note
The function uses seaborn or matplotlib to generate heatmaps.
The color maps used are “Blues”, “Reds”, and “Greens” for different particles.
- qDNA.visualization.plot_coh(ax, me_solver)
Plots a measure of coherence as the sum of absolute values of the off- diagonal elements.
- Parameters:
- axmatplotlib.axes.Axes
The axes to plot on.
- me_solverME_Solver
The master equation solver instance.
- qDNA.visualization.plot_test_fourier(ax, tb_site, me_solver)
Plots a comparison of the result obtained by Fourier decomposition and the result obtained solving the Schrödinger equation with the qutip mesolver.
- Parameters:
- axmatplotlib.axes.Axes
The axes to plot on.
- tb_sitestr
The tight-binding site.
- me_solverME_Solver
The master equation solver instance.