Most .toml examples in the examples/ directory won't run

[ddmcode]

Description
The examples/ directory contains a few .py examples along with a number of .toml examples. I can run the python examples, but the only .toml example I can run is layered_geometry.toml.

As an example, if I try to run the layered_geometry_1d.toml example as follows:

simulation_boundary_points = [ [ 0.6, -0.6,], [ -0.1, -0.6,], [ -0.1, 0.6,], [ 0.6, 0.6,], [ 0.6, -0.6,],]

I get the following error message:

Running "/home/derek/src/rust/rustBCA/target/release/RustBCA layered_geometry_1D.toml" thread 'main' panicked at src/input.rs:35:11:
called "Result::unwrap()" on an "Err" value: Could not parse TOML file. Be sure you are using the correct input file mode (e.g.,
          ./RustBCA SPHERE sphere.toml or RustBCA.exe 0D mesh_0d.toml).

Caused by:
    TOML parse error at line 50, column 1
       |
    50 | [geometry_input]
       | ^^^^^^^^^^^^^^^^
    missing field "energy_barrier_thickness"

If I add a value for it complains I need a value for "triangles". Using layered_geometry.toml as a template I need to add input for:

• points
• triangles
• boundary
• simulation_boundary_points
• energy_barrier_thickness

in order to get the simulation to run. However, it then complains about other issues, presumably because I have not chosen suitable default values for these inputs. I have been unable to find suitable values.

To Reproduce
Checkout commit 1312dd3

Build and run any of the .toml examples (except layered_geometry.toml) following the instructions in the readme / wiki.

Expected behavior
Not applicable.

Error messages, output files, or figures
See above for typical error message.

System (please complete the following information):
OS: Ubuntu linux 22.04.03 LTS

Additional context
I failed to get some of the additional features to build, and I'm unfamiliar with building / running rust programs so there may be some learning / user issue here. I am however, as noted above, able to run the layered_geometry.toml.

[drobnyjt]

Hi @ddmcode - when you are running the 1D example, are you running it in the 1D input mode?

e.g.:

cargo run 1D layered_geometry_1D.toml

[ddmcode]

Hi @drobnyjt,

First, thanks for this clever code and your excellent thesis!

Your suggestion worked, thank you. I missed this detail in the docs I guess. I can now run most examples after a little trial and error. I have:

As shown, I was unable to figure out the option to run "multiple_interaction_potentials.toml" and "tungsten_twist_trimesh.toml".

Is there a rule / guide as to what option to used for a given .toml file?

Thanks,

Derek

[drobnyjt]

Great! While technically you can work backwards from the input file to determine which input mode to use (e.g., by comparing the listed options to each subsection on the input files page), you are correct that there's no obvious way.

While each example has its own wiki page that says which mode to use (e.g., tungsten_twist_trimesh requires RustBCA be built with the parry3d feature enabled and run in the TRIMESH input mode), it might be a good idea for me to add a comment to the top of each input file that says how to run it. Automatic detection is possible but would be difficult the way toml files are currently parsed, so that is unlikely to be added in the near future.

[ddmcode]

Sorry, I hadn't noticed the run instructions on the wiki, thanks.

I have most cases running now, I just have two issues:

• Running 'cargo run --release --features cpr_rootfinder_netlib multiple_interaction_potentials.toml' still fails for me with error message:

    error: none of the selected packages contains these features: cpr_rootfinder_netlib
  

I suspect this reflects some build issues I had, I will revisit.

• Running 'cargo run --release boron_nitride_sphere.toml', as suggested in the tutorial, failed for me, however, if I change this to 'cargo run SPHERE --release boron_nitride_sphere.toml' it ran fine, so I guess this is just an omission on the wiki.

I will close the issue now. Thanks for you very prompt assistance, I really apricate it :)

[drobnyjt]

@ddmcode you're very welcome.

To answer your two remaining questions, both of those reflect erroneous or out of date wiki entries; thanks for pointing them out so they can be fixed! I just fixed the former, where, as you note, the input mode keyword was simply omitted.

The second is out of date due to a change I made in version 2.8.4 where a netlib/Intel MKL/OpenBLAS linear algebra backend was replaced with a pure Rust linear algebra backend. You can run that input file with --features cpr_rootfinder; that page on the wiki has also been fixed.