Merging updates to LAMMPS agent into Main#152
Merging updates to LAMMPS agent into Main#152Somasundaram-Rahul wants to merge 37 commits intomainfrom
Conversation
…ose potentials only, i.e. without actually running LAMMPS
…d back to generic lmp_mpi
…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
left a comment
luiarthur
left a comment
There was a problem hiding this comment.
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.
docs/lammps_agent.md
Outdated
|
|
||
| ## 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. |
There was a problem hiding this comment.
| 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. |
docs/lammps_agent.md
Outdated
|
|
||
| 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`. |
There was a problem hiding this comment.
| 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`. |
There was a problem hiding this comment.
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.
There was a problem hiding this comment.
I think the html parsing utility uses trafilatura as well, so it's required more broadly. This error should really only mention atomman
There was a problem hiding this comment.
Updated the doc to only indicate that atomman was optional.
| summarize_results=True, | ||
| ) | ||
|
|
||
| with open("eos_template.txt", "r") as file: |
There was a problem hiding this comment.
What does this file look like?
| ) | ||
|
|
||
| if final_lammps_state.get("run_returncode") == 0: | ||
| print("\nLAMMPS Workflow completed successfully. Exiting.....") |
There was a problem hiding this comment.
Consider using console.print for consistency.
|
|
||
| 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." |
There was a problem hiding this comment.
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."
)3 participants
This PR merges several updates to the LAMMPS agent into the Main branch. In summary, they are: