10.1.1. pyopencl_scripts.network_visualization

This module provides examples and functions for visualizing simulations of networks or particles using PyOpenCL or python.

10.1.1.1. Overview

10.1.1.2. Classes and Functions

ilpm.pyopencl_scripts.network_visualization.get_points_per_unit(ax=None)

Use the size of the matplotlib axis to measure the number of points per unit

ilpm.pyopencl_scripts.network_visualization.absolute_sizer(ax=None)

Use the size of the matplotlib axis to create a function for sizing objects

ilpm.pyopencl_scripts.network_visualization.ensure_dir(f)

Check if directory exists, and make it if not.

Parameters:

f : string

directory path to ensure

ilpm.pyopencl_scripts.network_visualization.get_fname_and_index_size(hostdir)

Obtain the name of the first nontrivial file in a directory and the length of its numerical index. For example, if “hostdir/xyz00001.txt” exist, get_fname_and_index_size(hostdir) returns (‘xyz’, 5). This function is robust to having ‘.’s in the filename.

Parameters:

hostdir : string

Directory in which the files you want to grab exist.

Returns:

fname : string

First file name in that directory

index_size : int

Length of the index (how many numbers make up its index)

ilpm.pyopencl_scripts.network_visualization.data2stills_2D(datadir, params={}, framedir_name='stills', vsaved=True, init_skip=10, climv=0.1, numbering='adopt', rough=False, roughmov=True, exaggerate=1.0, rm_stills=False)

Converts a list of data into a stack of png images of mass-spring lattice using movie_plot_2D for each timestep. If roughmov is True, make a movie of every init_skip frames before going back and making detailed movie

Parameters:

datadir : string

The output directory for the data (contains subdirs for xyv, KL if KL is changing, also contains xy0.txt)

params : dict (optional)

the parameters for the simulation

framedir_name : string

Subdirectory of datadir in which to save movie images

init_skip : int

One out of every init_skip frames will be written first, then the intermittent frames will be written, to see briefly what happens

climv : float or tuple

Color limit for coloring bonds by bond strain

numbering : ‘natural’ or ‘adopt’ (default = ‘adopt’)

Use indexing ‘0’,‘1’,‘2’,‘3’,... or adopt the index of the input file.

rough : boolean

Plot every init_skip files ONLY

roughmov : bool

Make a movie of every init_skip files before plotting every frame

exaggerate : float (default 1.0 –> in which case it is ignored)

Exaggerate the displacements of each particle from its initial position by this factor. Ignored if == 1.0

ilpm.pyopencl_scripts.network_visualization.stills2mov_util(todo, datadir, NL, xy0, xyfiles, KLfiles, params, h, numbering, index_sz, framedir_name, name, update_KL_each_timestep, exaggerate, xlimv, ylimv, climv, framerate=10, mov_exten='')

Make a sequence of images and save it as a movie. This funciton is a utility function called by data2stills_2D()

Parameters:

todo : int array or list

The indices of the stills to plot and save in a movie

xyfiles : list of strings

paths of xy data to load

KLfiles : list of strings

paths of connectivity files to load, if connectivity changes during sequence

params : dict

parameters for the simulation

h : float

timestep

numbering : string specifier (‘natural’ or other)

Whether to place the index of the frame as the index of the output timestep or of the frame index

index_sz : int

How many digits in the index (with leading zeros)

framedir_name : str

path for the frames

name : str

non-index part of the frame names

update_KL_each_timestep : bool

Whether connectivity is changing during simulation

exaggerate : float

Exaggeration of the displacement

xlimv : tuple of floats

limits for x axis

ylimv : tuple of floats

limits for y axis

climv : tuple of floats

limits for color axis

mov_exten : str (optional, default is ‘’)

an extension to the movie name describing the movie

ilpm.pyopencl_scripts.network_visualization.movie_plot_2D(xy, BL, bs=None, fname='none', title='', NL=[], KL=[], BLNNN=[], NLNNN=[], KLNNN=[], PVx=[], PVy=[], PVxydict={}, ax=None, fig=None, axcb='auto', xlimv='auto', ylimv='auto', climv=0.1, colorz=True, ptcolor=None, figsize='auto', colorpoly=False, bondcolor=None, colormap='seismic', bgcolor='#E8E8E8', axis_off=False, axis_equal=True, text_topleft=None, lw=-1.0, ptsize=10, negative_NNN_arrows=False, show=False, arrow_alpha=1.0, fontsize=8)

Plots (and saves if fname is not ‘none’) a 2D image of the lattice with colored bonds and particles colored by coordination (both optional).

Parameters:

xy : array of dimension nx2

2D lattice of points (positions x,y)

BL : array of dimension #bonds x 2

Each row is a bond and contains indices of connected points

bs : array of dimension #bonds x 1

Strain in each bond

fname : string

Full path including name of the file (.png, etc), if None, will not save figure

title : string

The title of the frame

NL : NP x NN int array (optional, for speed)

Specify to speed up computation, if colorz or colorpoly or if periodic boundary conditions

KL : NP x NN int array (optional, for speed)

Specify to speed up computation, if colorz or colorpoly or if periodic boundary conditions

PVx : NP x NN float array (optional, for periodic lattices and speed)

ijth element of PVx is the x-component of the vector taking NL[i,j] to its image as seen by particle i If PVx and PVy are specified, PVxydict need not be specified.

PVy : NP x NN float array (optional, for periodic lattices and speed)

ijth element of PVy is the y-component of the vector taking NL[i,j] to its image as seen by particle i If PVx and PVy are specified, PVxydict need not be specified.

PVxydict : dict (optional, for periodic lattices)

dictionary of periodic bonds (keys) to periodic vectors (values)

ax: matplotlib figure axis instance

Axis on which to draw the network

fig: matplotlib figure instance

Figure on which to draw the network

axcb: matplotlib colorbar instance

Colorbar to use for strains in bonds

xlimv: float or tuple of floats

ylimv: float or tuple of floats

climv : float or tuple

Color limit for coloring bonds by bs

colorz: bool

whether to color the particles by their coordination number

ptcolor: string color spec or tuple color spec or None

color specification for coloring the points, if colorz is False. Default is None (no coloring of points)

figsize : tuple

w,h tuple in inches

colorpoly : bool

Whether to color in polygons formed by bonds according to the number of sides

bondcolor : color specification (hexadecimal or RGB)

colormap : if bondcolor is None, uses bs array to color bonds

bgcolor : hex format string, rgb color spec, or None

If not None, sets the bgcolor. Often used is ‘#d9d9d9’

axis_off

axis_equal

text_topleft

lw: float

line width for plotting bonds. If lw == -1, then uses automatic line width to adjust for bond density..

ptsize: float

size of points passed to absolute_sizer

Returns:

[ax,axcb] : stuff to clear after plotting