Merging updates to LAMMPS agent into Main #152

Somasundaram-Rahul · 2026-01-16T20:39:47Z

This PR merges several updates to the LAMMPS agent into the Main branch. In summary, they are:

Added detailed documentation for the LAMMPS agent. This is in the form of an MD file here: ursa/docs/lammps_agent.md
Updated the progression of the agent's terminal output using Rich
Updated how the agent attempts to fix the input script: it now uses the full run history instead of looking at the latest run
The agent can now take in a user-provided potential file
The user can now provide data files for the agent to use in its simulations
The agent can now use GPUs for the LAMMPS runs

…ose potentials only, i.e. without actually running LAMMPS

…d back to generic lmp_mpi

…t error

…zation/visualization of results

Updating and handling conflicts. Co-authored-by: Somasundaram-Rahul

I forgot to merge changes that had been pushed to the repo since my last push. This should be resolved and up to date with current version.

luiarthur

Thanks, @Somasundaram-Rahul! This is great.

I have a few suggestions.

Would adding a test to tests/ be possible? I think your examples might be sufficient. The test should ideally be fast and can be crude. Just want to make we know if/when future changes will break this code.

luiarthur · 2026-01-31T05:44:56Z

docs/lammps_agent.md

+
+## Dependencies
+
+The main dependency is the [LAMMPS](https://www.lammps.org) code that needs to be installed separately. LAMMPS is a classical molecular dynamics code developed by Sandia National Laboratories. Installation instructions can be found [here](https://docs.lammps.org/Install.html). On macOS and linux systems, the simplest way to install LAMMPS is often via [Conda](https://anaconda.org/channels/conda-forge/packages/lammps/overview), in the same conda environment where `ursa` is installed.  


Suggested change

The main dependency is the [LAMMPS](https://www.lammps.org) code that needs to be installed separately. LAMMPS is a classical molecular dynamics code developed by Sandia National Laboratories. Installation instructions can be found [here](https://docs.lammps.org/Install.html). On macOS and linux systems, the simplest way to install LAMMPS is often via [Conda](https://anaconda.org/channels/conda-forge/packages/lammps/overview), in the same conda environment where `ursa` is installed.

The main dependency is the [LAMMPS](https://www.lammps.org) code that needs to be separately installed. LAMMPS is a classical molecular dynamics code developed by Sandia National Laboratories. Installation instructions can be found [here](https://docs.lammps.org/Install.html). On MacOS and Linux systems, the simplest way to install LAMMPS is often via [Conda](https://anaconda.org/channels/conda-forge/packages/lammps/overview), in the same conda environment where `ursa` is installed.

luiarthur · 2026-01-31T05:45:42Z

docs/lammps_agent.md

+
+The main dependency is the [LAMMPS](https://www.lammps.org) code that needs to be installed separately. LAMMPS is a classical molecular dynamics code developed by Sandia National Laboratories. Installation instructions can be found [here](https://docs.lammps.org/Install.html). On macOS and linux systems, the simplest way to install LAMMPS is often via [Conda](https://anaconda.org/channels/conda-forge/packages/lammps/overview), in the same conda environment where `ursa` is installed.  
+
+Two additional dependencies, that are not installed along with `ursa`, are `atomman` and `trafilatura`. These can be installed via `pip install atomman` and `pip install trafilatura`.  


Suggested change

Two additional dependencies, that are not installed along with `ursa`, are `atomman` and `trafilatura`. These can be installed via `pip install atomman` and `pip install trafilatura`.

Two additional dependencies, that are not installed along with `ursa`, are `atomman` and `trafilatura`. These can be installed via `pip install atomman trafilatura`.

Actually, it looks like trafilatura is in the dependencies. So the only other dependency is atomman. @mikegros does it make sense to remove trafilatura from dependencies and remove the lammps group; and then add trafilatura and atomman as optional dependencies? I can make the change if wanted.

I think the html parsing utility uses trafilatura as well, so it's required more broadly. This error should really only mention atomman

luiarthur · 2026-01-31T05:51:49Z

examples/two_agent_examples/lammps_execute/EOS_of_Cu.py

+    summarize_results=True,
+)
+
+with open("eos_template.txt", "r") as file:


What does this file look like?

luiarthur · 2026-01-31T05:52:12Z

examples/two_agent_examples/lammps_execute/EOS_of_Cu.py

+)
+
+if final_lammps_state.get("run_returncode") == 0:
+    print("\nLAMMPS Workflow completed successfully. Exiting.....")


Consider using console.print for consistency.

luiarthur · 2026-01-31T05:53:28Z

examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py


-        Summarize the contents of this file in a markdown document. Include a plot, if relevent.
-        """
+simulation_task = "Carry out a LAMMPS simulation of the high entropy alloy Co-Cr-Fe-Mn-Ni to determine its stiffness tensor."


I didn't count, but if this is longer than 80 lines, split into two lines. e.g.,

simulation_task = ( "Carry out a LAMMPS ..." "its stiffness tensor." )

Somasundaram-Rahul and others added 29 commits September 5, 2025 14:06

Adding a LAMMPS agent

89dcc45

Added .ipynb_checkpoints/ to .gitignore

36ea0ad

Added another example for the LAMMPS agent

686e8a2

Improved prompts in Lammps Agent

cad9b7c

Added workspace directory for lammps agent

3013e80

Minor edits to lammps agent

61f305c

Merge branch 'main' into lammps_agent

611ef46

Updated lammps_agent prompts

3752ad1

Added atomman and trafilatura to the environment

50b69fe

Linted and formatted code using ruff

576f1eb

Merged main into lammps_agent

b0ec232

Fixed minor bugs created from merging main-->lammps_agent

c7cedef

Added option of providing input file templates to lammps_agent

7e6e277

Cleaned up unrequired variables in LammpsState

f8f1f06

Added option for the user to provide the potential to the lammps_agent

7f8dfb8

Added option of using the lammps_agent as a tool to summarize and cho…

6d68b0c

…ose potentials only, i.e. without actually running LAMMPS

Merge branch 'main' into lammps_agent

a51ba65

Linted and Formatted Code using ruff

16da862

Updated by merging main --> lammps_agent

cca5538

Added gpu run commands to the lammps agent

e5edf1b

Added structure data file given as an input into the agent.

67f54d1

Added the capability to take user defined potential files

363ff50

Minor changes to the example files, reverted lammps executable comman…

0879820

…d back to generic lmp_mpi

Minor update to lammps agent prompt

4819fd4

Full error history passed to the _fix node, instead of just the lates…

a0dfbb8

…t error

Used Rich to improve terminal outputs

b14c050

Added documentation for LAMMPS Agent

1ca41bf

Merged main --> lammps_agent

e998562

Linted and Formatted code with Ruff

12b7a9c

Somasundaram-Rahul requested a review from luiarthur January 16, 2026 20:39

Somasundaram-Rahul requested a review from mikegros January 16, 2026 20:39

Somasundaram-Rahul assigned luiarthur and mikegros Jan 16, 2026

Somasundaram-Rahul requested a review from adela-habib January 16, 2026 22:31

Somasundaram-Rahul and others added 5 commits January 20, 2026 16:48

Minor bug fixed

a03f3da

Added ability to call Execution agent within Lammps agent for summari…

0cef0cd

…zation/visualization of results

Merge branch 'main' into lammps_agent

d1457cb

Updating and handling conflicts. Co-authored-by: Somasundaram-Rahul

Merge branch 'lammps_agent' of github.com:lanl/ursa into lammps_agent

2136e97

I forgot to merge changes that had been pushed to the repo since my last push. This should be resolved and up to date with current version.

Also ruff formatting

293f712

luiarthur requested changes Jan 31, 2026

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Merging updates to LAMMPS agent into Main #152

Merging updates to LAMMPS agent into Main #152

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		## Dependencies

		The main dependency is the [LAMMPS](https://www.lammps.org) code that needs to be installed separately. LAMMPS is a classical molecular dynamics code developed by Sandia National Laboratories. Installation instructions can be found [here](https://docs.lammps.org/Install.html). On macOS and linux systems, the simplest way to install LAMMPS is often via [Conda](https://anaconda.org/channels/conda-forge/packages/lammps/overview), in the same conda environment where `ursa` is installed.


		The main dependency is the [LAMMPS](https://www.lammps.org) code that needs to be installed separately. LAMMPS is a classical molecular dynamics code developed by Sandia National Laboratories. Installation instructions can be found [here](https://docs.lammps.org/Install.html). On macOS and linux systems, the simplest way to install LAMMPS is often via [Conda](https://anaconda.org/channels/conda-forge/packages/lammps/overview), in the same conda environment where `ursa` is installed.

		Two additional dependencies, that are not installed along with `ursa`, are `atomman` and `trafilatura`. These can be installed via `pip install atomman` and `pip install trafilatura`.

Merging updates to LAMMPS agent into Main #152

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