Avogadro

Molecular editor and visualizer

Avogadro is a molecular editor and visualizer for building structures, running force-field optimizations, and inspecting computational chemistry output, streamed here in a remote desktop session and backed by remote compute. It builds on the Ubuntu Desktop image — Avogadro launches maximized with the window decorations and taskbar hidden, so the viewport fills the screen.

Usage

1. Deploy

dxflow workflow create --identity avogadro hub://avogadro

# Start with defaults, or tune per run with --override
dxflow workflow start avogadro
dxflow workflow start avogadro \
    --override env.app.VNC_PASSWORD=my-strong-pass \
    --override env.app.TASKBAR=show

# Publish the web port on an HTTPS link
dxflow workflow start avogadro --link

2. Open the app

Open your browser at http://localhost:6082/vnc.html and enter the password you set in VNC_PASSWORD. Avogadro is already running and maximized. Port 5901 is also exposed for connecting a native VNC client. A start given --link publishes port 6082 at an HTTPS URL printed on the start line — open it at /vnc.html to reach Avogadro from anywhere.

3. Persist data

Anything under /volume persists across restarts — save your work there to keep it.

Configuration

name: avogadro
tags:
    - molecular
steps:
    - name: app
      runtime: docker
      mode: parallel
      image: ghcr.io/dxflow-ai/avogadro:latest
      volumes:
          - name: volume
            host: ./volume
            container: /volume
      ports:
          - name: web
            host: "6082"
            container: "6082"
          - name: vnc
            host: "5901"
            container: "5901"
          - name: audio
            host: "6100"
            container: "6100"
      env:
          - VNC_PASSWORD=dxflow
          - WALLPAPER=show
          - PANEL=hide
          - TASKBAR=hide
          - AUDIO=off
          - AUDIO_PORT=6100
          - AUDIO_CHANNELS=1
          - AUDIO_RATE=22050
      resources:
          cpu: "2"
          memory: 4G
      link: web

[volume]
app.volume = ./volume

[port]
app.web = 6082
app.vnc = 5901
app.audio = 6100

[env]
app.VNC_PASSWORD = dxflow
app.WALLPAPER = show
app.PANEL = hide
app.TASKBAR = hide
app.AUDIO = off
app.AUDIO_PORT = 6100
app.AUDIO_CHANNELS = 1
app.AUDIO_RATE = 22050

[resource]
app.cpu = 2
app.memory = 4G

{
    "arch": ["amd64", "arm64"],
    "image": "ghcr.io/dxflow-ai/avogadro:latest",
    "version": "1.101.0",
    "size": {
        "amd64": "521M",
        "arm64": "509M"
    },
    "minimum": {
        "cpu": 2,
        "memory": "2G",
        "storage": "20G"
    }
}

Notes

Set a strong VNC_PASSWORD; it defaults to dxflow, which every reader of this page knows.
The panel and taskbar are hidden by default so the viewport fills the screen. Set PANEL=show or TASKBAR=show to bring back the window decorations and taskbar.
Audio: off by default. Set AUDIO=on to stream desktop sound; tune with AUDIO_CHANNELS (1 or 2) and AUDIO_RATE (8000/16000/22050/32000/44100). The audio port is AUDIO_PORT (default 6100) — the client follows it, so to run two sessions on one host give each its own port by setting AUDIO_PORT and the matching audio port mapping together.
The Ubuntu avogadro package ships Avogadro 2, whose binary is avogadro2 — that is what this entry launches.
Void has no Avogadro package, so this entry builds on the Ubuntu desktop instead.

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