graph-tool August 2020

graph-tool@skewed.de

8 participants
14 discussions

graphviz_draw() cannot plot loops anymore
by Rolf Sander 19 Aug '20

19 Aug '20

Hello, I get a segmentation fault when trying to plot a loop with graphviz_draw(). Here is a minimal example to reproduce the error: import graph_tool.all as gt g = gt.Graph() v0 = g.add_vertex() v1 = g.add_vertex() e01 = g.add_edge(v0,v1) e11 = g.add_edge(v1,v1) # loop gt.graphviz_draw(g) I have version 2.33 of python3-graph-tool installed on my computer which runs on Linux Mint 19.2 Tina (based on Ubuntu 18.04 LTS, bionic). My graphviz version is 2.40.1-2. It works fine if I don't add the loop e11 to the graph. It works fine if I use gt.graph_draw() instead of gt.graphviz_draw() It works fine if I use graphviz directly (via a .dot file). It did work fine in earlier versions of graph_tool. Can anyone reproduce this? Best regards Rolf -- ----------------------------------------------------------------------- Rolf Sander phone: [+49] 6131/305-4610 Max-Planck Institute of Chemistry email: rolf.sander(a)mpic.de PO Box 3060, 55020 Mainz, Germany homepage: www.rolf-sander.net ----------------------------------------------------------------------- https://www.encyclopedia-of-geosciences.net https://www.geoscientific-model-development.net -----------------------------------------------------------------------

3 7

Exact diameter
by Kelly Trinh 10 Aug '20

10 Aug '20

Hi all, Using python graph_tool library. I see there is the pseudo_diameter method but I was looking so something that can give me the exact diameter but cannot seem to find. Could anyone shine some light where this is (or why not included)?

2 1

optimize a function based on iterate_sync
by BleakHeart 10 Aug '20

10 Aug '20

Hi graphtool community! In this period I am stuck in a timing problem. I need to execute this function: def *evolutionSIR*(G, ep_beta, count, v0): state = SIRState(G, beta=ep_beta, gamma=gamma, v0=v0, constant_beta=True) s = state.get_state() temp_state = np.zeros((count + 1, G.num_vertices()), dtype=int) temp_state[0, :] = s.a[:] for i in range(count): state.iterate_sync() s = state.get_state() temp_state[i + 1, :] = s.a[:] return temp_state After this, I use a fuction to determine the timestep where each community is infected. My pc runs the *evolutionSIR* function in 1.1 s ± 48 ms, and the total time to run the both functions is 1.16 s ± 48 ms. For my study I need to run O(1E6) the two functions, and it takes a long time on my personal computer. Reading the documentation, I noticed that *iterate_sync* has the *niter* parameter and I tried it like this: v0 = np.random.choice(G.get_vertices(), 1) state = SIRState(G, beta=ep_beta, gamma=gamma, v0=v0, constant_beta=True) state.iterate_sync(niter=count) Doing this, it results to be almost 2.85 times faster (385 ms ± 39.3 ms) than the *evolutionSIR* I wrote before but the problem is that I can't have the states in each evolution step. Is there a way to get the history of the diffusion using *iterate_sync*(niter=count)? Or is there a way to optimize the evolutionSIR function? Greetings -- Sent from: https://nabble.skewed.de/

2 1

Wrong formula in price networks?
by Feelx234 10 Aug '20

10 Aug '20

Hello, If I compare the implementation for the probability in the graph/generation/graph_price.hh which is (can be found in multiple places) p = pow(Deg()(w, g) + c, gamma); With what is written in the documentation https://graph-tool.skewed.de/static/doc/generation.html#graph_tool.generati… I wonder whether it should actually be (the constant outside the power) or is the documentation wrong? p = pow(Deg()(w, g), gamma) + c; Greetings Feelx234 -- Sent from: https://nabble.skewed.de/

2 1

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

graph-tool August 2020