Come back to the Adun User’s Manual
Overview
As well as running a simulation from the Adun GUI you can also run it from the command line. This useful for a number of reasons – for example if you want to run a long-time, computationally demanding, simulation on a remote cluster. To do this you first create the simulation as normal in the GUI and then export it.
To run a simulation from the command line:
- Create the simulation as normal (see ‘Creating a Simulation’)
- Select the simulation entry in the process table and choose Object->Export
- Choose where to save it. This creates a directory containing all the files necessary
for running from the command line. - Copy the directory to where you want to run the simulation.
- The machine can be a Mac or Linux machine but must have Adun installed
- From a terminal cd to the directory and run - AdunCore -Template [templateName].
This will create a directory called “SimulationOutput” containing your simulation
Template Files
Coming Soon
Linking
Linking allows the starting state (coordinates & velocities) of systems in a simulation to be initialised using their (checkpointed) state from another simulation. Note: Systems must have the same name in the new simulation and old to be linked.
Linking is done by adding a link section to a template. This has the following general format (in ASCII format)
links = (
{
simulation=/home/user/sims/somesim.simulation;
trajectory=Trajectory0;
checkpoint=100;
systems= (system1, system2);
},
.....(next link)
);
The links section can have any number of links (deonoted by the curly-brackets {}). This allows you to link different systems to checkpoints in different simulations.
There are four link keywords, only one of which is required
- simulation – The path to the simulation to link
- REQUIRED
- trajectory – The trajectory to link to
- OPTIONAL: defaults to the first trajectory
- checkpoint – The trajectory checkpoint to use
- OPTIONAL: defaults to the last recorded frame.
- Note: This is the value of the checkpoint to use NOT the value of the time the checkpoint was taken. e.g. if there are 100 checkpoints this is a value between 1 and 100.
- systems – The systems to link
- OPTIONAL: defaults to all systems in the current template that are also in the linked simulation
By default all trajectory checkpoints contain a configuration of a system, so this can always be linked. In addition the last frame of a trajectory always corresponds to the last configuration produced by a simulation (since Adun 0.83) and includes velocity checkpoints. Hence linking to the last frame always sets a systems coordinates and velocities.
