znvis

A visualisation engine for particle simulations

https://github.com/zincware/znvis

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
✓
Committers with academic emails
1 of 4 committers (25.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.9%) to scientific vocabulary

Keywords

3d open3d particles visualization

Last synced: 4 months ago · JSON representation ·

Repository

A visualisation engine for particle simulations

Basic Info

Host: GitHub
Owner: zincware
License: epl-2.0
Language: Python
Default Branch: main
Homepage: https://znvis.readthedocs.io/en/latest/
Size: 12 MB

Statistics

Stars: 10
Watchers: 0
Forks: 3
Open Issues: 11
Releases: 4

Topics

3d open3d particles visualization

Created about 4 years ago · Last pushed over 1 year ago

Metadata Files

Readme License Citation

ZnVis

ZnVis is a visualisation engine for particle simulation data. Simply define the particles in the simulation with details including their positions, colour, direction, and shape, and the visualization engine will display the system using the Open3D engine. ZnVis works both from a Python script and in Jupyter!

ZnVis can currently perform the following tasks:

Visualize simulations and trajectories
Create spherical and cylindrical mesh's for visualization
Handle custom mesh objects
Export png stills from the visualizer
Export scences as .obj files.

Installation

ZnVis is a purely Python package hosted on PyPi. It can therefore be installed using pip with:

sh pip install znvis

If you prefer to access the source code, run the following from a terminal:

sh git clone https://github.com/zincware/ZnVis.git cd ZnVis pip install .

Once complete, you will be able to start using the visualizer by importing it as:

python import znvis

How does it work?

ZnVis is essentially a convenience wrapper of the Open3D project with a focus on mesh visualization. The idea came out of wanting a simple way of visualizing particle trajectories from numpy arrays directly from a simulation script.

Below we show an example script from a reinforcement learning experiment built using Shameless plug alert SwarmRL

```python import numpy as np import h5py as hf

import znvis as vis

Load data from the database

with hf.File("training/trajectory.hdf5", 'r') as db: positions = db["colloids"]["Unwrapped_Positions"][:]

Split data for convenience

colloidpositions = positions[:, 0:10, :] rodpositions = positions[:, 10:, :]

Create free colloid mesh

colloidmesh = vis.Sphere(radius=2.14, colour=np.array([30, 144, 255]) / 255, resolution=10) colloidparticle = vis.Particle(name="Colloid", mesh=mesh, position=colloid_positions)

Create rod colloid mesh

rodmesh = vis.Sphere(radius=2.14, colour=np.array([255, 140, 0]) / 255, resolution=10) rodparticle = vis.Particle(name="Rod", mesh=mesh, position=rod_positions)

Run the visualizer

visualizer = vis.Visualizer(particles=[colloidparticle, rodparticle], framerate=80) visualizer.runvisualization() ```

Just like that, a visualization window (shown below) will pop up from which you can play the trajectory and watch your RL agents rotate a rod.

Visualizer Example

Owner

Name: Zincware
Login: zincware
Kind: organization
Email: zincwarecode@gmail.com
Location: Germany

Website: zincwarecode.com
Twitter: zincwarecode
Repositories: 33
Profile: https://github.com/zincware

Open source software organisation hosting software built for computational physics and chemistry.

Citation (CITATION.cff)

cff-version: 1.2.0
title: >-
  ZnVis: A Visualisation Package for Particle
  Simulations
message: >-
  If you use this package, please include the
  following citation:
type: software
authors:
  - given-names: Samuel
    family-names: Tovey
    email: tovey.samuel@gmail.com
    affiliation: University of Stuttgart
    orcid: 'https://orcid.org/0000-0001-9537-8361'
version: 2.0.4

GitHub Events

Total

Issues event: 2
Watch event: 1
Issue comment event: 3
Pull request review event: 12
Pull request review comment event: 13

Last Year

Issues event: 2
Watch event: 1
Issue comment event: 3
Pull request review event: 12
Pull request review comment event: 13

Committers

Last synced: 5 months ago

All Time

Total Commits: 150
Total Committers: 4
Avg Commits per committer: 37.5
Development Distribution Score (DDS): 0.26

Past Year

Commits: 8
Committers: 1
Avg Commits per committer: 8.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
SamTov	t**l@g**m	111
Paul Hohenberger	4****r	31
jdrotleff	1****e	7
Christoph Lohrmann	c**n@i**e	1

Committer Domains (Top 20 + Academic)

icp.uni-stuttgart.de: 1

Issues and Pull Requests

Last synced: 5 months ago

All Time

Total issues: 16
Total pull requests: 33
Average time to close issues: 11 months
Average time to close pull requests: 28 days
Total issue authors: 2
Total pull request authors: 4
Average comments per issue: 0.13
Average comments per pull request: 0.21
Merged pull requests: 30
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 12
Average time to close issues: 5 days
Average time to close pull requests: about 1 month
Issue authors: 1
Pull request authors: 3
Average comments per issue: 0.0
Average comments per pull request: 0.58
Merged pull requests: 10
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

SamTov (15)
PythonFZ (1)
jpd-de (1)

Pull Request Authors

SamTov (35)
phohenberger (4)
jpd-de (3)
christophlohrmann (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 154 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 2
Total maintainers: 1

pypi.org: znvis

Visualization of particle trajectories.

Homepage: https://github.com/zincware/ZnVis
Documentation: https://znvis.readthedocs.io/
License: Eclipse Public License 2.0 (EPL-2.0)
Latest release: 0.1.0
published almost 3 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 154 Last month

Rankings

Dependent packages count: 10.1%

Downloads: 14.7%

Average: 17.5%

Stargazers count: 18.5%

Dependent repos count: 21.6%

Forks count: 22.6%

Maintainers (1)

zincware

Last synced: 5 months ago

Dependencies

dev-requirements.txt pypi

IPython * development
Sphinx ==4.3.0 development
black * development
coverage * development
coveralls * development
isort * development
mdanalysis * development
nbsphinx * development
nbsphinx-link * development
numpydoc * development
pandoc * development
pybtex * development
pytest * development
sphinx-copybutton * development
sphinx_rtd_theme * development
sphinxcontrib.bibtex * development

requirements.txt pypi

numpy *
open3d *
pytest *

.github/workflows/lint.yaml actions

actions/checkout v3 composite
actions/setup-python v3 composite
psf/black stable composite

.github/workflows/publish-to-pypi.yaml actions

actions/checkout master composite
actions/setup-python v1 composite
pypa/gh-action-pypi-publish master composite

.github/workflows/pytest.yaml actions

actions/checkout v4 composite
actions/setup-python v4 composite

setup.py pypi

znvis

Science Score: 54.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

ZnVis

Installation

How does it work?

Load data from the database

Split data for convenience

Create free colloid mesh

Create rod colloid mesh

Run the visualizer

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: znvis

Rankings

Maintainers (1)

Dependencies