Molecular

Build the molecule,then look at it

Avogadro's editor and viewer, on an Ubuntu desktop of your own.Draw a structure, relax it, and read what a calculation returned.

Avogadro 1.101.02 cores · 4 GBOpens in a browser tab

hub://avogadro

$ dxflow workflow create --identity avogadro hub://avogadro --start --link

01Pick a machinecores, memory and a rate per hour

02Create the workflowpulled from the hub, once

03Run it, then stopstopped when the work is done

The application

Draw it,then settle it

Sketch a structure by hand and let a force field find the geometry.

Sketch and optimize

Place atoms and bonds, then run a force field until the geometry stops moving.

Read the output back

Open what Gaussian, ORCA or NWChem wrote and see the orbitals drawn over it.

Scriptable underneath

The Python console does the same build and optimize over a folder on the volume.

How you run it

Every defaultis one override away

The session reads its settings from the environment, so you set them on the start line.

VNC_PASSWORDWhat the tab asks for. It ships as dxflow, and everyone reading this knows that.

PANEL and TASKBARBoth hidden, so the viewport has the whole screen. Show either one to get the desktop back.

AUDIOOff here. Turn it on and the desktop sound is streamed beside the picture.

start it your way

$ dxflow workflow start avogadro --override env.app.VNC_PASSWORD=something-long

$ dxflow workflow start avogadro --override env.app.PANEL=show --link

The session

The viewportfills the screen

Streamed to your browser, with Avogadro already maximized.

6082Browserin the tab, at /vnc.html

5901VNCin a native client

/volumeStorageyour files, kept between runs

Open it from anywhereStart with --link and the session comes back on an HTTPS address.

Set a password firstVNC_PASSWORD defaults to dxflow, and everyone can read this page.

Good to know

It is Avogadro 2,under the old name

The package is called avogadro and the binary is avogadro2. This entry launches the second one.

Two names, one program

Ubuntu ships Avogadro 2 under the avogadro package. If you go looking on the command line, it answers to avogadro2.

Built on Ubuntu

Void has no Avogadro package at all, so this entry sits on the Ubuntu desktop instead of the usual base.

Structures belong on the volume

Keep what you build and what you import under /volume, and it survives the stop.

The image

Pulled once,then it stays

Avogadro arrives as one image. This is what comes down the first time, and what the disk should have free for it.

521Mamd64compressed, the way the registry counts it

509Marm64compressed, the way the registry counts it

20GOn diskunpacked, with room to work beside it

ghcr.io/dxflow-ai/avogadro:latestPublished from the hub, pulled on the first start and kept for the ones after it.

Either architectureamd64 and arm64 are both published, and the machine pulls the one it runs.

What it asks for

What it wants,and what it needs

The definition asks for 2 cores and 4 GB. The image comes up on less than that, and a start given --fit trims the ask to whatever the machine actually has.

2 cores · 4 GBAsks forwhat the definition writes down

2 cores · 2 GBRuns onthe least the image comes up on

Not neededGPUit works on the cores alone

The ask is not the floorThe definition writes down what suits the work. The image itself starts on less, which is what the second figure is.

--fit caps it to the hostA start given --fit trims each step to what the machine actually has, for that start alone. The definition is never rewritten.

Machines that fit it

Avogadro asks for 2 cores and 4 GB. Cheapest first.

E2 Medium

$0.042/ hour2 cores · 4 GBStart this machine

T3 Medium

$0.052/ hour2 cores · 4 GBStart this machine

B2s

$0.052/ hour2 cores · 4 GBStart this machine

Run Avogadro on your own machinePick a machine that meets it, and it opens about a minute after you ask.

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