dice_visualise.py File Reference

Go to the source code of this file.

Namespaces
	repo.DicePy.dice_visualise
	DicePy.dice_visualise
	Contains functions for burning/thinning and visualization for Dice.

Functions
def	repo.DicePy.dice_visualise.QHOProbPlot (chain_file)
	Wrapper function for QHO_prob_plot() More...
def	repo.DicePy.dice_visualise.QHO_prob_plot (positions, energies)
	Fancy Plotly plotter for QHO Markov chains. More...
def	repo.DicePy.dice_visualise.HydProbPlot (chain_file, opacity=0.2)
	Wrapper function for H2_prob_plot() More...
def	repo.DicePy.dice_visualise.H2_prob_plot (positions, energies, R1, R2, opacity)
	Plots the sampled wavefunction for H2plus/H2. More...
def	repo.DicePy.dice_visualise.QHOEnergyPlot (results_file, sliceby=(None, None))
	Energy against \( \alpha \) plotter for the QHO problem. More...
def	repo.DicePy.dice_visualise.QHOWfnPlot (chain_file, show_analytic=False)
	Scatter plotter of the sampled QHO wavefunction. More...
def	repo.DicePy.dice_visualise.H2plusEnergyPlot (results_file, sliceby=(None, None))
	\( H_{2}^{+} \) H-H bond energy and parameter plotter. More...
def	repo.DicePy.dice_visualise.H2EnergyPlot (results_file, sliceby=(None, None))
	\( H_{2} \) H-H bond energy and parameter plotter. More...
def	repo.DicePy.dice_visualise.view_original_trace (equil_file)
	Plots the original trace(s) of an MCMC run. More...
def	repo.DicePy.dice_visualise.BurnThinUI (equil_file)
	Wrapper function for interacting with get_autocorrelation_time() More...
def	repo.DicePy.dice_visualise.get_autocorrelation_time (filename, burn, tuning, plotting=True)
	Function which suggests a thinning parameter for a MCMC chain. More...
def	repo.DicePy.dice_visualise.load_results (filename='results.nc')
	Loads the results as a dataset NetCDF object to be passed to other functions. More...
def	repo.DicePy.dice_visualise.load_global_attr (rootgrp, verbose=True)
	Loads the global metadata in the results file into a dictionary. More...
def	repo.DicePy.dice_visualise.load_variables (rootgrp, verbose=True)
	Loads the variables in the results file into a dictionary. More...
def	repo.DicePy.dice_visualise.H2_eng_plot (variables)
	Plots the energies against the parameters checked during the grid search Parameters: variables: Dictionary which contains data about the variables in the netcdf4 object. More...
def	repo.DicePy.dice_visualise.QHO_eng_plot (rootgrp, equil=False)
	energy_plot() Plots the energy at each step as the MC converges More...
def	repo.DicePy.dice_visualise.plot_3D (X, Y, Z, wfn)
def	repo.DicePy.dice_visualise.process_main_results (filename='results.nc', verbose=True)
	Processes the results output as a result of the parameter search from the NetCDF4 file. More...
def	repo.DicePy.dice_visualise.plot_markov_chain (filename)
def	repo.DicePy.dice_visualise.orb_1s (X, Y, Z, R_a)
	functions plotting the wavefunction ab initio ####### More...
def	repo.DicePy.dice_visualise.orb_2s (r, R_a)
def	repo.DicePy.dice_visualise.polar_to_cart (r, theta, phi)
def	repo.DicePy.dice_visualise.lcao_wfn (X, Y, Z, R1, R2, pqn=1)
def	repo.DicePy.dice_visualise.plot_3D (X, Y, Z, wfn, R1, R2)
	Function for plotting the wavefunction analytically. More...
def	repo.DicePy.dice_visualise.example_H1s_wfn (bond_length=2.0)