From 89dcc456a912c1d07d831692698e839355d46a2c Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Fri, 5 Sep 2025 14:06:32 -0600
Subject: [PATCH 01/31] Adding a LAMMPS agent

---
 .../lammps_execute/EOS_of_Cu.py               |  48 +++
 src/ursa/agents/__init__.py                   |   2 +
 src/ursa/agents/lammps_agent.py               | 359 ++++++++++++++++++
 3 files changed, 409 insertions(+)
 create mode 100644 examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
 create mode 100644 src/ursa/agents/lammps_agent.py

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
new file mode 100644
index 00000000..bdebe74a
--- /dev/null
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -0,0 +1,48 @@
+from ursa.agents import LammpsAgent
+from ursa.agents import ExecutionAgent
+
+from langchain_core.messages import HumanMessage
+from langchain_openai import ChatOpenAI
+
+model = "gpt-5"
+
+llm = ChatOpenAI(model      = model,
+                timeout     = None,
+                max_retries =  2
+                )
+
+
+wf = LammpsAgent(
+    llm = llm,
+    max_potentials=2,
+    max_fix_attempts=5,      
+    mpi_procs=8,
+    lammps_cmd="lmp_mpi",
+    mpirun_cmd="mpirun",
+)
+
+high_level="Carry out a LAMMPS simulation of Cu to determine its equation of state."
+elements=["Cu"]
+
+final_lammps_state = wf.run(high_level,elements)
+
+if final_lammps_state.get("run_returncode") == 0:
+
+    print ("\nNow handing things off to execution agent.....")
+
+    executor = ExecutionAgent(llm=llm)
+    exe_plan = f"""
+    You are part of a larger scientific workflow whose purpose is to accomplish this task: {high_level}
+    
+    A LAMMPS simulation has been done and the output is located here: ../log.lammps
+    
+    Summarize the contents of this file in a markdown document. Include a plot, if relevent.
+    """
+    
+    init = {"messages": [HumanMessage(content=exe_plan)]}
+    
+    final_results = executor.action.invoke(init, {"recursion_limit": 10000})
+    
+    for x in final_results["messages"]:
+        print(x.content)
+
diff --git a/src/ursa/agents/__init__.py b/src/ursa/agents/__init__.py
index 6f4b90d2..982ea75f 100644
--- a/src/ursa/agents/__init__.py
+++ b/src/ursa/agents/__init__.py
@@ -15,3 +15,5 @@
 from .recall_agent import RecallAgent as RecallAgent
 from .websearch_agent import WebSearchAgent as WebSearchAgent
 from .websearch_agent import WebSearchState as WebSearchState
+from .lammps_agent import LammpsAgent as LammpsAgent
+from .lammps_agent import LammpsState as LammpsState
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
new file mode 100644
index 00000000..8cb44813
--- /dev/null
+++ b/src/ursa/agents/lammps_agent.py
@@ -0,0 +1,359 @@
+from typing import TypedDict, List, Optional, Any, Dict
+import json
+import subprocess
+
+import atomman as am
+import trafilatura
+import tiktoken
+
+from langchain_core.prompts import ChatPromptTemplate
+from langchain_core.output_parsers import StrOutputParser
+
+from langgraph.graph import StateGraph, END
+
+from .base import BaseAgent
+
+
+class LammpsState(TypedDict, total=False):
+    high_level: str
+    elements: List[str]
+    
+    matches: List[Any]
+    db_message: str
+
+    idx: int
+    summaries: List[str]
+    full_texts: List[str]
+
+    summaries_combined: str
+    choice_json: str
+    chosen_index: int
+
+    input_script: str
+    run_returncode: Optional[int]
+    run_stdout: str
+    run_stderr: str
+
+    fix_attempts: int 
+
+
+
+class LammpsAgent(BaseAgent):
+    def __init__(
+        self,
+        llm,
+        max_potentials: int = 5,
+        max_fix_attempts: int = 10,       
+        mpi_procs: int = 8,
+        lammps_cmd: str = "lmp_mpi",     
+        mpirun_cmd: str = "mpirun",
+        tiktoken_model: str = "o3",
+        max_tokens: int = 200000,
+        **kwargs,
+    ):
+
+        self.max_potentials = max_potentials
+        self.max_fix_attempts = max_fix_attempts
+        self.mpi_procs = mpi_procs
+        self.lammps_cmd = lammps_cmd
+        self.mpirun_cmd = mpirun_cmd
+        self.tiktoken_model = tiktoken_model
+        self.max_tokens = max_tokens
+
+        self.pair_styles = ["eam", "eam/alloy", "eam/fs",
+                            "meam", "adp",            # classical, HEA-relevant
+                            "kim",                    # OpenKIM models
+                            "snap", "quip", "mlip", "pace", "nep"  # ML/ACE families (if available)
+                            ]
+
+        
+        super().__init__(llm, **kwargs)
+        
+        self.str_parser = StrOutputParser()
+
+        self.summ_chain = (ChatPromptTemplate.from_template(
+            "Here is some data about an interatomic potential: {metadata}\n\n"
+            "Briefly summarize why it could be useful for this task: {high_level}."
+        ) | self.llm | self.str_parser)
+
+        
+        self.choose_chain = (
+            ChatPromptTemplate.from_template(
+                "Here are the summaries of a certain number of interatomic potentials: {summaries_combined}\n\n"
+                "Pick one potential which would be most useful for this task: {high_level}.\n\n"
+                "Return your answer **only** as valid JSON, with no extra text or formatting.\n\n"
+                "Use this exact schema:\n"
+                "{{\n"
+                '  "Chosen index": <int>,\n'
+                '  "rationale": "<string>",\n'
+                '  "Potential name": "<string>"\n'
+                "}}\n"
+            )
+            | self.llm
+            | self.str_parser
+        )
+        
+        self.author_chain = (
+            ChatPromptTemplate.from_template(
+                "Your task is to write a LAMMPS input file for this purpose: {high_level}.\n"
+                "Here is metadata about the interatomic potential that will be used: {metadata}.\n"
+                "Note that all potential files are in the ./ directory.\n"
+                "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
+                "Return your answer **only** as valid JSON, with no extra text or formatting.\n"
+                "Use this exact schema:\n"
+                "{{\n"
+                '  "input_script": "<string>"\n'
+                "}}\n"
+            )
+            | self.llm
+            | self.str_parser
+        )
+        
+        self.fix_chain = (
+            ChatPromptTemplate.from_template(
+                "You are part of a larger scientific workflow whose purpose is to accomplish this task: {high_level}\n"
+                "For this purpose, this input file for LAMMPS was written: {input_script}\n"
+                "However, when running the simulation, an error was raised.\n"
+                "Here is the full stdout message that includes the error message: {err_message}\n"
+                "Your task is to write a new input file that resolves the error.\n"
+                "Here is metadata about the interatomic potential that will be used: {metadata}.\n"
+                "Note that all potential files are in the ./ directory.\n"
+                "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
+                "Return your answer **only** as valid JSON, with no extra text or formatting.\n"
+                "Use this exact schema:\n"
+                "{{\n"
+                '  "input_script": "<string>"\n'
+                "}}\n"
+            )
+            | self.llm
+            | self.str_parser
+        )
+
+        
+        self.graph = self._build_graph().compile()
+
+
+
+    @staticmethod
+    def _safe_json_loads(s: str) -> Dict[str, Any]:
+        s = s.strip()
+        if s.startswith("```"):
+            s = s.strip("`")
+            i = s.find("\n")
+            if i != -1:
+                s = s[i + 1 :].strip()
+        return json.loads(s)
+
+    def _fetch_and_trim_text(self, url: str) -> str:
+        downloaded = trafilatura.fetch_url(url)
+        if not downloaded:
+            return "No metadata available"
+        text = trafilatura.extract(
+            downloaded,
+            include_comments=False,
+            include_tables=True,
+            include_links=False,
+            favor_recall=True,
+        )
+        if not text:
+            return "No metadata available"
+        text = text.strip()
+        try:
+            enc = tiktoken.encoding_for_model(self.tiktoken_model)
+            toks = enc.encode(text)
+            if len(toks) > self.max_tokens:
+                toks = toks[: self.max_tokens]
+                text = enc.decode(toks)
+        except Exception:
+            pass
+        return text
+
+
+    def _find_potentials(self, state: LammpsState) -> LammpsState:
+        db = am.library.Database(remote=True)
+        matches = db.get_lammps_potentials(pair_style=self.pair_styles, elements=state["elements"])
+        msg_lines = []
+        if not list(matches):
+            msg_lines.append("No potentials found for this task in NIST.")
+        else:
+            msg_lines.append("Found these potentials in NIST:")
+            for rec in matches:
+                msg_lines.append(f"{rec.id}  {rec.pair_style}  {rec.symbols}")
+        return {
+            **state,
+            "matches": list(matches),
+            "db_message": "\n".join(msg_lines),
+            "idx": 0,
+            "summaries": [],
+            "full_texts": [],
+            "fix_attempts": 0,
+        }
+
+    def _should_summarize(self, state: LammpsState) -> str:
+        matches = state.get("matches", [])
+        i = state.get("idx", 0)
+        if not matches:
+            print ("No potentials found in NIST for this task. Exiting....")
+            return "done_no_matches"
+        if i < min(self.max_potentials, len(matches)):
+            return "summarize_one"
+        return "summarize_done"
+
+    def _summarize_one(self, state: LammpsState) -> LammpsState:
+        i = state["idx"]
+        print (f"Summarizing potential #{i}")
+        match = state["matches"][i]
+        md = match.metadata()
+
+        if md.get("comments") is None:
+            text = "No metadata available"
+            summary = "No summary available"
+        else:
+            lines = md["comments"].split("\n")
+            url = lines[1] if len(lines) > 1 else ""
+            text = self._fetch_and_trim_text(url) if url else "No metadata available"
+            summary = self.summ_chain.invoke({"metadata": text, "high_level": state["high_level"]})
+
+        return {
+            **state,
+            "idx": i + 1,
+            "summaries": [*state["summaries"], summary],
+            "full_texts": [*state["full_texts"], text],
+        }
+
+    def _build_summaries(self, state: LammpsState) -> LammpsState:
+        parts = []
+        for i, s in enumerate(state["summaries"]):
+            rec = state["matches"][i]
+            parts.append(f"\nSummary of potential #{i}: {rec.id}\n{s}\n")
+        return {**state, "summaries_combined": "".join(parts)}
+
+    def _choose(self, state: LammpsState) -> LammpsState:
+        print ("Choosing one potential for this task...")
+        choice = self.choose_chain.invoke({
+            "summaries_combined": state["summaries_combined"],
+            "high_level": state["high_level"]
+        })
+        choice_dict = self._safe_json_loads(choice)
+        chosen_index = int(choice_dict["Chosen index"])
+        print (f"Chosen potential #{chosen_index}")
+        return {**state, "choice_json": choice, "chosen_index": chosen_index}
+
+    def _author(self, state: LammpsState) -> LammpsState:
+        print("First attempt at writing LAMMPS input file....")
+        match = state["matches"][state["chosen_index"]]
+        match.download_files("./")
+        text = state["full_texts"][state["chosen_index"]]
+        pair_info = match.pair_info()
+        authored_json = self.author_chain.invoke({
+            "high_level": state["high_level"],
+            "metadata": text,
+            "pair_info": pair_info
+        })
+        script_dict = self._safe_json_loads(authored_json)
+        input_script = script_dict["input_script"]
+        with open("in.lammps", "w") as f:
+            f.write(input_script)
+        return {**state, "input_script": input_script}
+
+    def _run_lammps(self, state: LammpsState) -> LammpsState:
+        print ("Running LAMMPS....")
+        result = subprocess.run(
+            [self.mpirun_cmd, "-np", str(self.mpi_procs), self.lammps_cmd, "-in", "in.lammps"],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            text=True,
+            check=False
+        )
+        return {
+            **state,
+            "run_returncode": result.returncode,
+            "run_stdout": result.stdout,
+            "run_stderr": result.stderr,
+        }
+
+    def _route_run(self, state: LammpsState) -> str:
+        rc = state.get("run_returncode", 0)
+        attempts = state.get("fix_attempts", 0)
+        if rc == 0:
+            print ("LAMMPS run successful! Exiting...")
+            return "done_success"
+        if attempts < self.max_fix_attempts:
+            print ("LAMMPS run Failed. Attempting to rewrite input file...")
+            return "need_fix"
+        print ("LAMMPS run Failed and maximum fix attempts reached. Exiting...")
+        return "done_failed"
+
+    def _fix(self, state: LammpsState) -> LammpsState:
+        match = state["matches"][state["chosen_index"]]
+        text = state["full_texts"][state["chosen_index"]]
+        pair_info = match.pair_info()
+        err_blob = state.get("run_stdout") 
+        
+        fixed_json = self.fix_chain.invoke({
+            "high_level": state["high_level"],
+            "input_script": state["input_script"],
+            "err_message": err_blob,
+            "metadata": text,
+            "pair_info": pair_info
+        })
+        script_dict = self._safe_json_loads(fixed_json)
+        new_input = script_dict["input_script"]
+        with open("in.lammps", "w") as f:
+            f.write(new_input)
+        return {**state, "input_script": new_input, "fix_attempts": state.get("fix_attempts", 0) + 1}
+
+
+    
+    def _build_graph(self):
+        g = StateGraph(LammpsState)
+
+        g.add_node("find_potentials", self._find_potentials)
+        g.add_node("summarize_one", self._summarize_one)
+        g.add_node("build_summaries", self._build_summaries)
+        g.add_node("choose", self._choose)
+        g.add_node("author", self._author)
+        g.add_node("run_lammps", self._run_lammps)
+        g.add_node("fix", self._fix)
+
+        g.set_entry_point("find_potentials")
+
+        g.add_conditional_edges(
+            "find_potentials",
+            self._should_summarize,
+            {
+                "summarize_one": "summarize_one",
+                "summarize_done": "build_summaries",
+                "done_no_matches": END,
+            },
+        )
+
+        g.add_conditional_edges(
+            "summarize_one",
+            self._should_summarize,
+            {
+                "summarize_one": "summarize_one",
+                "summarize_done": "build_summaries",
+            },
+        )
+
+        g.add_edge("build_summaries", "choose")
+        g.add_edge("choose", "author")
+        g.add_edge("author", "run_lammps")
+
+        g.add_conditional_edges(
+            "run_lammps",
+            self._route_run,
+            {
+                "need_fix": "fix",
+                "done_success": END,
+                "done_failed": END,
+            },
+        )
+        g.add_edge("fix", "run_lammps")
+        return g
+
+    
+    def run(self,high_level,elements):
+        return self.graph.invoke({"high_level": high_level,"elements": elements})
+        
\ No newline at end of file

From 36ea0ad36756374c44c1c1eb5870a890d3f842d8 Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Fri, 5 Sep 2025 14:43:51 -0600
Subject: [PATCH 02/31] Added .ipynb_checkpoints/ to .gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 90205761..fb1a0c08 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,6 +12,7 @@ dist/
 wheels/
 *.egg-info
 *.sql
+.ipynb_checkpoints/
 
 # Virtual environments
 .venv/

From 686e8a29377cf662dc07b380211f82d8ed320c1e Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Fri, 5 Sep 2025 15:34:05 -0600
Subject: [PATCH 03/31] Added another example for the LAMMPS agent

---
 .../lammps_execute/stiffness_tensor_of_hea.py | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py

diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
new file mode 100644
index 00000000..39409afd
--- /dev/null
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -0,0 +1,48 @@
+from ursa.agents import LammpsAgent
+from ursa.agents import ExecutionAgent
+
+from langchain_core.messages import HumanMessage
+from langchain_openai import ChatOpenAI
+
+model = "gpt-5"
+
+llm = ChatOpenAI(model      = model,
+                timeout     = None,
+                max_retries =  2
+                )
+
+
+wf = LammpsAgent(
+    llm = llm,
+    max_potentials=5,
+    max_fix_attempts=10,      
+    mpi_procs=8,
+    lammps_cmd="lmp_mpi",
+    mpirun_cmd="mpirun",
+)
+
+high_level="Carry out a LAMMPS simulation of the high entropy alloy Co-Cr-Fe-Mn-Ni to determine its stiffness tensor."
+elements=["Co","Cr","Fe","Mn","Ni"]
+
+final_lammps_state = wf.run(high_level,elements)
+
+if final_lammps_state.get("run_returncode") == 0:
+
+    print ("\nNow handing things off to execution agent.....")
+
+    executor = ExecutionAgent(llm=llm)
+    exe_plan = f"""
+    You are part of a larger scientific workflow whose purpose is to accomplish this task: {high_level}
+    
+    A LAMMPS simulation has been done and the output is located here: ../log.lammps
+    
+    Summarize the contents of this file in a markdown document. Include a plot, if relevent.
+    """
+    
+    init = {"messages": [HumanMessage(content=exe_plan)]}
+    
+    final_results = executor.action.invoke(init, {"recursion_limit": 10000})
+    
+    for x in final_results["messages"]:
+        print(x.content)
+

From cad9b7c1e3bf6f2e215382ccad322ae40d44cd5c Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Fri, 5 Sep 2025 16:24:14 -0600
Subject: [PATCH 04/31] Improved prompts in Lammps Agent

---
 .../lammps_execute/stiffness_tensor_of_hea.py                   | 2 +-
 src/ursa/agents/lammps_agent.py                                 | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index 39409afd..fc13ceb3 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -15,7 +15,7 @@
 wf = LammpsAgent(
     llm = llm,
     max_potentials=5,
-    max_fix_attempts=10,      
+    max_fix_attempts=15,      
     mpi_procs=8,
     lammps_cmd="lmp_mpi",
     mpirun_cmd="mpirun",
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 8cb44813..0c940741 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -99,6 +99,7 @@ def __init__(
                 "Here is metadata about the interatomic potential that will be used: {metadata}.\n"
                 "Note that all potential files are in the ./ directory.\n"
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
+                "Ensure that all output data is written only to the ./log.lammps file. Do not create any other output file.\n"
                 "Return your answer **only** as valid JSON, with no extra text or formatting.\n"
                 "Use this exact schema:\n"
                 "{{\n"
@@ -119,6 +120,7 @@ def __init__(
                 "Here is metadata about the interatomic potential that will be used: {metadata}.\n"
                 "Note that all potential files are in the ./ directory.\n"
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
+                "Ensure that all output data is written only to the ./log.lammps file. Do not create any other output file.\n"
                 "Return your answer **only** as valid JSON, with no extra text or formatting.\n"
                 "Use this exact schema:\n"
                 "{{\n"

From 3013e8083e382569398fc379baebc3c1d6cd9661 Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Mon, 15 Sep 2025 15:24:35 -0600
Subject: [PATCH 05/31] Added workspace directory for lammps agent

---
 .../two_agent_examples/lammps_execute/EOS_of_Cu.py  | 13 ++++++++-----
 .../lammps_execute/stiffness_tensor_of_hea.py       | 12 ++++++++----
 src/ursa/agents/lammps_agent.py                     | 12 +++++++++---
 3 files changed, 25 insertions(+), 12 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index bdebe74a..74bc0a2b 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -11,12 +11,14 @@
                 max_retries =  2
                 )
 
+workspace = "./workspace_eos_cu"
 
 wf = LammpsAgent(
     llm = llm,
     max_potentials=2,
     max_fix_attempts=5,      
     mpi_procs=8,
+    workspace = workspace,
     lammps_cmd="lmp_mpi",
     mpirun_cmd="mpirun",
 )
@@ -34,14 +36,15 @@
     exe_plan = f"""
     You are part of a larger scientific workflow whose purpose is to accomplish this task: {high_level}
     
-    A LAMMPS simulation has been done and the output is located here: ../log.lammps
+    A LAMMPS simulation has been done and the output is located here in the file log.lammps.
     
     Summarize the contents of this file in a markdown document. Include a plot, if relevent.
     """
-    
-    init = {"messages": [HumanMessage(content=exe_plan)]}
-    
-    final_results = executor.action.invoke(init, {"recursion_limit": 10000})
+
+    executor_config = {"recursion_limit": 999_999}
+        
+    final_results = executor.action.invoke({"messages": [HumanMessage(content=exe_plan)],
+                                            "workspace": workspace,},executor_config,)
     
     for x in final_results["messages"]:
         print(x.content)
diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index fc13ceb3..8e597e94 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -12,11 +12,14 @@
                 )
 
 
+workspace = "./workspace_stiffness_tensor"
+
 wf = LammpsAgent(
     llm = llm,
     max_potentials=5,
     max_fix_attempts=15,      
     mpi_procs=8,
+    workspace = workspace,
     lammps_cmd="lmp_mpi",
     mpirun_cmd="mpirun",
 )
@@ -34,14 +37,15 @@
     exe_plan = f"""
     You are part of a larger scientific workflow whose purpose is to accomplish this task: {high_level}
     
-    A LAMMPS simulation has been done and the output is located here: ../log.lammps
+    A LAMMPS simulation has been done and the output is located here in the file log.lammps.
     
     Summarize the contents of this file in a markdown document. Include a plot, if relevent.
     """
     
-    init = {"messages": [HumanMessage(content=exe_plan)]}
-    
-    final_results = executor.action.invoke(init, {"recursion_limit": 10000})
+    executor_config = {"recursion_limit": 999_999}
+        
+    final_results = executor.action.invoke({"messages": [HumanMessage(content=exe_plan)],
+                                            "workspace": workspace,},executor_config,)
     
     for x in final_results["messages"]:
         print(x.content)
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 0c940741..161c5bde 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -1,6 +1,7 @@
 from typing import TypedDict, List, Optional, Any, Dict
 import json
 import subprocess
+import os 
 
 import atomman as am
 import trafilatura
@@ -45,6 +46,7 @@ def __init__(
         max_potentials: int = 5,
         max_fix_attempts: int = 10,       
         mpi_procs: int = 8,
+        workspace: str = "./workspace",
         lammps_cmd: str = "lmp_mpi",     
         mpirun_cmd: str = "mpirun",
         tiktoken_model: str = "o3",
@@ -66,6 +68,9 @@ def __init__(
                             "snap", "quip", "mlip", "pace", "nep"  # ML/ACE families (if available)
                             ]
 
+        self.workspace = workspace
+        os.makedirs(self.workspace, exist_ok=True)
+
         
         super().__init__(llm, **kwargs)
         
@@ -244,7 +249,7 @@ def _choose(self, state: LammpsState) -> LammpsState:
     def _author(self, state: LammpsState) -> LammpsState:
         print("First attempt at writing LAMMPS input file....")
         match = state["matches"][state["chosen_index"]]
-        match.download_files("./")
+        match.download_files(self.workspace)
         text = state["full_texts"][state["chosen_index"]]
         pair_info = match.pair_info()
         authored_json = self.author_chain.invoke({
@@ -254,7 +259,7 @@ def _author(self, state: LammpsState) -> LammpsState:
         })
         script_dict = self._safe_json_loads(authored_json)
         input_script = script_dict["input_script"]
-        with open("in.lammps", "w") as f:
+        with open(os.path.join(self.workspace, "in.lammps"), "w") as f:
             f.write(input_script)
         return {**state, "input_script": input_script}
 
@@ -262,6 +267,7 @@ def _run_lammps(self, state: LammpsState) -> LammpsState:
         print ("Running LAMMPS....")
         result = subprocess.run(
             [self.mpirun_cmd, "-np", str(self.mpi_procs), self.lammps_cmd, "-in", "in.lammps"],
+            cwd=self.workspace,
             stdout=subprocess.PIPE,
             stderr=subprocess.PIPE,
             text=True,
@@ -301,7 +307,7 @@ def _fix(self, state: LammpsState) -> LammpsState:
         })
         script_dict = self._safe_json_loads(fixed_json)
         new_input = script_dict["input_script"]
-        with open("in.lammps", "w") as f:
+        with open(os.path.join(self.workspace, "in.lammps"), "w") as f:
             f.write(new_input)
         return {**state, "input_script": new_input, "fix_attempts": state.get("fix_attempts", 0) + 1}
 

From 61f305ced44bc40ee479f7bd696129515b53fcf9 Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Mon, 15 Sep 2025 17:32:24 -0600
Subject: [PATCH 06/31] Minor edits to lammps agent

---
 .../lammps_execute/EOS_of_Cu.py               |  6 ++---
 .../lammps_execute/stiffness_tensor_of_hea.py |  7 +++---
 src/ursa/agents/lammps_agent.py               | 22 +++++++++----------
 3 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index 74bc0a2b..e1d1fad1 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -23,10 +23,10 @@
     mpirun_cmd="mpirun",
 )
 
-high_level="Carry out a LAMMPS simulation of Cu to determine its equation of state."
+simulation_task="Carry out a LAMMPS simulation of Cu to determine its equation of state."
 elements=["Cu"]
 
-final_lammps_state = wf.run(high_level,elements)
+final_lammps_state = wf.run(simulation_task,elements)
 
 if final_lammps_state.get("run_returncode") == 0:
 
@@ -34,7 +34,7 @@
 
     executor = ExecutionAgent(llm=llm)
     exe_plan = f"""
-    You are part of a larger scientific workflow whose purpose is to accomplish this task: {high_level}
+    You are part of a larger scientific workflow whose purpose is to accomplish this task: {simulation_task}
     
     A LAMMPS simulation has been done and the output is located here in the file log.lammps.
     
diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index 8e597e94..6dc67e78 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -24,10 +24,11 @@
     mpirun_cmd="mpirun",
 )
 
-high_level="Carry out a LAMMPS simulation of the high entropy alloy Co-Cr-Fe-Mn-Ni to determine its stiffness tensor."
+simulation_task="Carry out a LAMMPS simulation of the high entropy alloy Co-Cr-Fe-Mn-Ni to determine its stiffness tensor."
+
 elements=["Co","Cr","Fe","Mn","Ni"]
 
-final_lammps_state = wf.run(high_level,elements)
+final_lammps_state = wf.run(simulation_task,elements)
 
 if final_lammps_state.get("run_returncode") == 0:
 
@@ -35,7 +36,7 @@
 
     executor = ExecutionAgent(llm=llm)
     exe_plan = f"""
-    You are part of a larger scientific workflow whose purpose is to accomplish this task: {high_level}
+    You are part of a larger scientific workflow whose purpose is to accomplish this task: {simulation_task}
     
     A LAMMPS simulation has been done and the output is located here in the file log.lammps.
     
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 161c5bde..9e6f4666 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -16,7 +16,7 @@
 
 
 class LammpsState(TypedDict, total=False):
-    high_level: str
+    simulation_task: str
     elements: List[str]
     
     matches: List[Any]
@@ -78,14 +78,14 @@ def __init__(
 
         self.summ_chain = (ChatPromptTemplate.from_template(
             "Here is some data about an interatomic potential: {metadata}\n\n"
-            "Briefly summarize why it could be useful for this task: {high_level}."
+            "Briefly summarize why it could be useful for this task: {simulation_task}."
         ) | self.llm | self.str_parser)
 
         
         self.choose_chain = (
             ChatPromptTemplate.from_template(
                 "Here are the summaries of a certain number of interatomic potentials: {summaries_combined}\n\n"
-                "Pick one potential which would be most useful for this task: {high_level}.\n\n"
+                "Pick one potential which would be most useful for this task: {simulation_task}.\n\n"
                 "Return your answer **only** as valid JSON, with no extra text or formatting.\n\n"
                 "Use this exact schema:\n"
                 "{{\n"
@@ -100,7 +100,7 @@ def __init__(
         
         self.author_chain = (
             ChatPromptTemplate.from_template(
-                "Your task is to write a LAMMPS input file for this purpose: {high_level}.\n"
+                "Your task is to write a LAMMPS input file for this purpose: {simulation_task}.\n"
                 "Here is metadata about the interatomic potential that will be used: {metadata}.\n"
                 "Note that all potential files are in the ./ directory.\n"
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
@@ -117,7 +117,7 @@ def __init__(
         
         self.fix_chain = (
             ChatPromptTemplate.from_template(
-                "You are part of a larger scientific workflow whose purpose is to accomplish this task: {high_level}\n"
+                "You are part of a larger scientific workflow whose purpose is to accomplish this task: {simulation_task}\n"
                 "For this purpose, this input file for LAMMPS was written: {input_script}\n"
                 "However, when running the simulation, an error was raised.\n"
                 "Here is the full stdout message that includes the error message: {err_message}\n"
@@ -219,7 +219,7 @@ def _summarize_one(self, state: LammpsState) -> LammpsState:
             lines = md["comments"].split("\n")
             url = lines[1] if len(lines) > 1 else ""
             text = self._fetch_and_trim_text(url) if url else "No metadata available"
-            summary = self.summ_chain.invoke({"metadata": text, "high_level": state["high_level"]})
+            summary = self.summ_chain.invoke({"metadata": text, "simulation_task": state["simulation_task"]})
 
         return {
             **state,
@@ -239,7 +239,7 @@ def _choose(self, state: LammpsState) -> LammpsState:
         print ("Choosing one potential for this task...")
         choice = self.choose_chain.invoke({
             "summaries_combined": state["summaries_combined"],
-            "high_level": state["high_level"]
+            "simulation_task": state["simulation_task"]
         })
         choice_dict = self._safe_json_loads(choice)
         chosen_index = int(choice_dict["Chosen index"])
@@ -253,7 +253,7 @@ def _author(self, state: LammpsState) -> LammpsState:
         text = state["full_texts"][state["chosen_index"]]
         pair_info = match.pair_info()
         authored_json = self.author_chain.invoke({
-            "high_level": state["high_level"],
+            "simulation_task": state["simulation_task"],
             "metadata": text,
             "pair_info": pair_info
         })
@@ -299,7 +299,7 @@ def _fix(self, state: LammpsState) -> LammpsState:
         err_blob = state.get("run_stdout") 
         
         fixed_json = self.fix_chain.invoke({
-            "high_level": state["high_level"],
+            "simulation_task": state["simulation_task"],
             "input_script": state["input_script"],
             "err_message": err_blob,
             "metadata": text,
@@ -362,6 +362,6 @@ def _build_graph(self):
         return g
 
     
-    def run(self,high_level,elements):
-        return self.graph.invoke({"high_level": high_level,"elements": elements})
+    def run(self,simulation_task,elements):
+        return self.graph.invoke({"simulation_task": simulation_task,"elements": elements},{"recursion_limit": 999_999})
         
\ No newline at end of file

From 3752ad1c71a325344950fc558af82fcb48610b5f Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Wed, 17 Sep 2025 22:49:31 -0600
Subject: [PATCH 07/31] Updated lammps_agent prompts

---
 .../two_agent_examples/lammps_execute/EOS_of_Cu.py   |  2 +-
 .../lammps_execute/stiffness_tensor_of_hea.py        |  2 +-
 src/ursa/agents/lammps_agent.py                      | 12 ++++++++----
 3 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index e1d1fad1..b82a4cc2 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -36,7 +36,7 @@
     exe_plan = f"""
     You are part of a larger scientific workflow whose purpose is to accomplish this task: {simulation_task}
     
-    A LAMMPS simulation has been done and the output is located here in the file log.lammps.
+    A LAMMPS simulation has been done and the output is located in the file 'log.lammps'.
     
     Summarize the contents of this file in a markdown document. Include a plot, if relevent.
     """
diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index 6dc67e78..4e4bd498 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -38,7 +38,7 @@
     exe_plan = f"""
     You are part of a larger scientific workflow whose purpose is to accomplish this task: {simulation_task}
     
-    A LAMMPS simulation has been done and the output is located here in the file log.lammps.
+    A LAMMPS simulation has been done and the output is located in the file 'log.lammps'.
     
     Summarize the contents of this file in a markdown document. Include a plot, if relevent.
     """
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 9e6f4666..4549a17b 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -102,9 +102,10 @@ def __init__(
             ChatPromptTemplate.from_template(
                 "Your task is to write a LAMMPS input file for this purpose: {simulation_task}.\n"
                 "Here is metadata about the interatomic potential that will be used: {metadata}.\n"
-                "Note that all potential files are in the ./ directory.\n"
+                "Note that all potential files are in the './' directory.\n"
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
-                "Ensure that all output data is written only to the ./log.lammps file. Do not create any other output file.\n"
+                "Ensure that all output data is written only to the './log.lammps' file. Do not create any other output file.\n"
+                "To create the log, use only the 'log ./log.lammps' command. Do not use any other command like 'echo' or 'screen'.\n"
                 "Return your answer **only** as valid JSON, with no extra text or formatting.\n"
                 "Use this exact schema:\n"
                 "{{\n"
@@ -123,9 +124,10 @@ def __init__(
                 "Here is the full stdout message that includes the error message: {err_message}\n"
                 "Your task is to write a new input file that resolves the error.\n"
                 "Here is metadata about the interatomic potential that will be used: {metadata}.\n"
-                "Note that all potential files are in the ./ directory.\n"
+                "Note that all potential files are in the './' directory.\n"
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
-                "Ensure that all output data is written only to the ./log.lammps file. Do not create any other output file.\n"
+                "Ensure that all output data is written only to the './log.lammps' file. Do not create any other output file.\n"
+                "To create the log, use only the 'log ./log.lammps' command. Do not use any other command like 'echo' or 'screen'.\n"
                 "Return your answer **only** as valid JSON, with no extra text or formatting.\n"
                 "Use this exact schema:\n"
                 "{{\n"
@@ -244,6 +246,8 @@ def _choose(self, state: LammpsState) -> LammpsState:
         choice_dict = self._safe_json_loads(choice)
         chosen_index = int(choice_dict["Chosen index"])
         print (f"Chosen potential #{chosen_index}")
+        print ("Rationale for choosing this potential:")
+        print(choice_dict["rationale"])
         return {**state, "choice_json": choice, "chosen_index": chosen_index}
 
     def _author(self, state: LammpsState) -> LammpsState:

From 50b69fe294c0d385bc9ed8b24851d0f037f72e7a Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Thu, 18 Sep 2025 17:01:09 -0600
Subject: [PATCH 08/31] Added atomman and trafilatura to the environment

---
 pyproject.toml |   2 +
 uv.lock        | 545 +++++++++++++++++++++++++++++++++++++++++++++----
 2 files changed, 508 insertions(+), 39 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 505c7812..01e6451b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,6 +38,8 @@ dependencies = [
     "langgraph-checkpoint-sqlite>=2.0.10,<3.0",
     "langchain-ollama>=0.3.6,<0.4",
     "ddgs>=9.5.5",
+    "atomman>=1.5.2",
+    "trafilatura>=1.6.1",
 ]
 classifiers = [
     "Operating System :: OS Independent",
diff --git a/uv.lock b/uv.lock
index 5dc30bed..cccaf32a 100644
--- a/uv.lock
+++ b/uv.lock
@@ -4,14 +4,19 @@ requires-python = ">=3.10"
 resolution-markers = [
     "python_full_version >= '3.14' and sys_platform == 'win32'",
     "python_full_version == '3.13.*' and sys_platform == 'win32'",
-    "python_full_version >= '3.14' and sys_platform != 'win32'",
-    "python_full_version == '3.13.*' and sys_platform != 'win32'",
+    "python_full_version >= '3.14' and sys_platform == 'darwin'",
+    "python_full_version >= '3.14' and sys_platform != 'darwin' and sys_platform != 'win32'",
+    "python_full_version == '3.13.*' and sys_platform == 'darwin'",
+    "python_full_version == '3.13.*' and sys_platform != 'darwin' and sys_platform != 'win32'",
     "python_full_version == '3.12.*' and sys_platform == 'win32'",
-    "python_full_version == '3.12.*' and sys_platform != 'win32'",
+    "python_full_version == '3.12.*' and sys_platform == 'darwin'",
+    "python_full_version == '3.12.*' and sys_platform != 'darwin' and sys_platform != 'win32'",
     "python_full_version == '3.11.*' and sys_platform == 'win32'",
-    "python_full_version == '3.11.*' and sys_platform != 'win32'",
+    "python_full_version == '3.11.*' and sys_platform == 'darwin'",
+    "python_full_version == '3.11.*' and sys_platform != 'darwin' and sys_platform != 'win32'",
     "python_full_version < '3.11' and sys_platform == 'win32'",
-    "python_full_version < '3.11' and sys_platform != 'win32'",
+    "python_full_version < '3.11' and sys_platform == 'darwin'",
+    "python_full_version < '3.11' and sys_platform != 'darwin' and sys_platform != 'win32'",
 ]
 
 [[package]]
@@ -213,7 +218,8 @@ version = "21.2.0"
 source = { registry = "https://pypi.org/simple" }
 resolution-markers = [
     "python_full_version >= '3.14' and sys_platform == 'win32'",
-    "python_full_version >= '3.14' and sys_platform != 'win32'",
+    "python_full_version >= '3.14' and sys_platform == 'darwin'",
+    "python_full_version >= '3.14' and sys_platform != 'darwin' and sys_platform != 'win32'",
 ]
 dependencies = [
     { name = "cffi", marker = "python_full_version >= '3.14'" },
@@ -238,13 +244,17 @@ version = "25.1.0"
 source = { registry = "https://pypi.org/simple" }
 resolution-markers = [
     "python_full_version == '3.13.*' and sys_platform == 'win32'",
-    "python_full_version == '3.13.*' and sys_platform != 'win32'",
+    "python_full_version == '3.13.*' and sys_platform == 'darwin'",
+    "python_full_version == '3.13.*' and sys_platform != 'darwin' and sys_platform != 'win32'",
     "python_full_version == '3.12.*' and sys_platform == 'win32'",
-    "python_full_version == '3.12.*' and sys_platform != 'win32'",
+    "python_full_version == '3.12.*' and sys_platform == 'darwin'",
+    "python_full_version == '3.12.*' and sys_platform != 'darwin' and sys_platform != 'win32'",
     "python_full_version == '3.11.*' and sys_platform == 'win32'",
-    "python_full_version == '3.11.*' and sys_platform != 'win32'",
+    "python_full_version == '3.11.*' and sys_platform == 'darwin'",
+    "python_full_version == '3.11.*' and sys_platform != 'darwin' and sys_platform != 'win32'",
     "python_full_version < '3.11' and sys_platform == 'win32'",
-    "python_full_version < '3.11' and sys_platform != 'win32'",
+    "python_full_version < '3.11' and sys_platform == 'darwin'",
+    "python_full_version < '3.11' and sys_platform != 'darwin' and sys_platform != 'win32'",
 ]
 dependencies = [
     { name = "cffi", marker = "python_full_version < '3.14'" },
@@ -334,6 +344,28 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/a7/fa/e01228c2938de91d47b307831c62ab9e4001e747789d0b05baf779a6488c/async_timeout-4.0.3-py3-none-any.whl", hash = "sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028", size = 5721, upload-time = "2023-08-10T16:35:55.203Z" },
 ]
 
+[[package]]
+name = "atomman"
+version = "1.5.2"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "cython" },
+    { name = "datamodeldict" },
+    { name = "matplotlib" },
+    { name = "numericalunits" },
+    { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
+    { name = "numpy", version = "2.3.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+    { name = "pandas" },
+    { name = "potentials" },
+    { name = "requests" },
+    { name = "scipy", version = "1.15.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
+    { name = "scipy", version = "1.16.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+    { name = "toolz" },
+    { name = "xmltodict" },
+    { name = "yabadaba" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/b8/ce/d7bc59594756b28eaba406b00faa1efb0ca37063dd167034e149006a2a8d/atomman-1.5.2.tar.gz", hash = "sha256:0d301454e7a253c025529b50d043feb4d923f1f22210a5422606fe0f60508d5c", size = 1080536, upload-time = "2025-08-04T19:43:06.388Z" }
+
 [[package]]
 name = "attrs"
 version = "25.3.0"
@@ -491,7 +523,7 @@ name = "build"
 version = "1.3.0"
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+    "python_full_version < '3.11' and sys_platform == 'darwin'",
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+    "python_full_version >= '3.14' and sys_platform == 'darwin'",
+    "python_full_version >= '3.14' and sys_platform != 'darwin' and sys_platform != 'win32'",
+    "python_full_version == '3.13.*' and sys_platform == 'darwin'",
+    "python_full_version == '3.13.*' and sys_platform != 'darwin' and sys_platform != 'win32'",
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-    "python_full_version == '3.12.*' and sys_platform != 'win32'",
+    "python_full_version == '3.12.*' and sys_platform == 'darwin'",
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-    "python_full_version == '3.11.*' and sys_platform != 'win32'",
+    "python_full_version == '3.11.*' and sys_platform == 'darwin'",
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+    "python_full_version == '3.12.*' and sys_platform == 'darwin'",
+    "python_full_version == '3.11.*' and sys_platform == 'darwin'",
+    "python_full_version < '3.11' and sys_platform == 'darwin'",
+]
+dependencies = [
+    { name = "certifi", marker = "sys_platform == 'darwin'" },
+    { name = "charset-normalizer", marker = "sys_platform == 'darwin'" },
+    { name = "courlan", marker = "sys_platform == 'darwin'" },
+    { name = "htmldate", version = "1.4.3", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'darwin'" },
+    { name = "justext", marker = "sys_platform == 'darwin'" },
+    { name = "lxml", marker = "sys_platform == 'darwin'" },
+    { name = "urllib3", marker = "sys_platform == 'darwin'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/44/d8/e9f20c95d2e1189258a84467956a00d85a68563cbaec19920302b8a414f6/trafilatura-1.6.1.tar.gz", hash = "sha256:a7792b037d624d04ab05fcce556cfe08b771dfc8c1db1494c750879530c9a30c", size = 3853959, upload-time = "2023-06-15T12:59:19.284Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/96/47/d3523bdbf4e49233a17c2af6964b3dc9d8707c862847c49b324fbd7f9ba4/trafilatura-1.6.1-py3-none-any.whl", hash = "sha256:fe94ed68fb50ec80ae698095010e1a0a7827bee0542ecd33c2cb55ca3e985aa7", size = 1031276, upload-time = "2023-06-15T12:59:12.869Z" },
+]
+
+[[package]]
+name = "trafilatura"
+version = "1.6.3"
+source = { registry = "https://pypi.org/simple" }
+resolution-markers = [
+    "python_full_version >= '3.14' and sys_platform == 'win32'",
+    "python_full_version == '3.13.*' and sys_platform == 'win32'",
+    "python_full_version >= '3.14' and sys_platform != 'darwin' and sys_platform != 'win32'",
+    "python_full_version == '3.13.*' and sys_platform != 'darwin' and sys_platform != 'win32'",
+    "python_full_version == '3.12.*' and sys_platform == 'win32'",
+    "python_full_version == '3.12.*' and sys_platform != 'darwin' and sys_platform != 'win32'",
+    "python_full_version == '3.11.*' and sys_platform == 'win32'",
+    "python_full_version == '3.11.*' and sys_platform != 'darwin' and sys_platform != 'win32'",
+    "python_full_version < '3.11' and sys_platform == 'win32'",
+    "python_full_version < '3.11' and sys_platform != 'darwin' and sys_platform != 'win32'",
+]
+dependencies = [
+    { name = "certifi", marker = "sys_platform != 'darwin'" },
+    { name = "charset-normalizer", marker = "sys_platform != 'darwin'" },
+    { name = "courlan", marker = "sys_platform != 'darwin'" },
+    { name = "htmldate", version = "1.6.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'darwin'" },
+    { name = "justext", marker = "sys_platform != 'darwin'" },
+    { name = "lxml", marker = "sys_platform != 'darwin'" },
+    { name = "urllib3", marker = "sys_platform != 'darwin'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/aa/2d/e91ca57ca6ead5bf72e2c651fc81d47052c4c794a27d729598fba90404b4/trafilatura-1.6.3.tar.gz", hash = "sha256:671dd6e0000e101c4bce8d70f4408bcb79fcbf2275ee25591efe33e2c8a1600d", size = 3865064, upload-time = "2023-11-29T13:42:25.814Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/2c/c3/4c3dc70948b8727dd4dd9634634bf5f985d14201b23cb3eb453a0d98d075/trafilatura-1.6.3-py3-none-any.whl", hash = "sha256:4f879045c6854d71e488cc669c42ee83b97fe584684bd288c752b7e5ae7402cf", size = 1033241, upload-time = "2023-11-29T13:42:16.879Z" },
+]
+
 [[package]]
 name = "traitlets"
 version = "5.14.3"
@@ -6027,6 +6428,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/5c/23/c7abc0ca0a1526a0774eca151daeb8de62ec457e77262b66b359c3c7679e/tzdata-2025.2-py2.py3-none-any.whl", hash = "sha256:1a403fada01ff9221ca8044d701868fa132215d84beb92242d9acd2147f667a8", size = 347839, upload-time = "2025-03-23T13:54:41.845Z" },
 ]
 
+[[package]]
+name = "tzlocal"
+version = "5.3.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "tzdata", marker = "sys_platform == 'win32'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/8b/2e/c14812d3d4d9cd1773c6be938f89e5735a1f11a9f184ac3639b93cef35d5/tzlocal-5.3.1.tar.gz", hash = "sha256:cceffc7edecefea1f595541dbd6e990cb1ea3d19bf01b2809f362a03dd7921fd", size = 30761, upload-time = "2025-03-05T21:17:41.549Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/c2/14/e2a54fabd4f08cd7af1c07030603c3356b74da07f7cc056e600436edfa17/tzlocal-5.3.1-py3-none-any.whl", hash = "sha256:eb1a66c3ef5847adf7a834f1be0800581b683b5608e74f86ecbcef8ab91bb85d", size = 18026, upload-time = "2025-03-05T21:17:39.857Z" },
+]
+
 [[package]]
 name = "uncertainties"
 version = "3.2.3"
@@ -6036,6 +6449,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/8f/5e/f1e1dd319e35e962a4e00b33150a8868b6329cc1d19fd533436ba5488f09/uncertainties-3.2.3-py3-none-any.whl", hash = "sha256:313353900d8f88b283c9bad81e7d2b2d3d4bcc330cbace35403faaed7e78890a", size = 60118, upload-time = "2025-04-21T19:58:26.864Z" },
 ]
 
+[[package]]
+name = "unidecode"
+version = "1.4.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/94/7d/a8a765761bbc0c836e397a2e48d498305a865b70a8600fd7a942e85dcf63/Unidecode-1.4.0.tar.gz", hash = "sha256:ce35985008338b676573023acc382d62c264f307c8f7963733405add37ea2b23", size = 200149, upload-time = "2025-04-24T08:45:03.798Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/8f/b7/559f59d57d18b44c6d1250d2eeaa676e028b9c527431f5d0736478a73ba1/Unidecode-1.4.0-py3-none-any.whl", hash = "sha256:c3c7606c27503ad8d501270406e345ddb480a7b5f38827eafe4fa82a137f0021", size = 235837, upload-time = "2025-04-24T08:45:01.609Z" },
+]
+
 [[package]]
 name = "uri-template"
 version = "1.3.0"
@@ -6059,6 +6481,7 @@ name = "ursa-ai"
 source = { editable = "." }
 dependencies = [
     { name = "arxiv" },
+    { name = "atomman" },
     { name = "beautifulsoup4" },
     { name = "chromadb" },
     { name = "coolname" },
@@ -6079,6 +6502,8 @@ dependencies = [
     { name = "pymupdf" },
     { name = "pypdf" },
     { name = "rich" },
+    { name = "trafilatura", version = "1.6.1", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'darwin'" },
+    { name = "trafilatura", version = "1.6.3", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'darwin'" },
 ]
 
 [package.dev-dependencies]
@@ -6092,6 +6517,7 @@ dev = [
 [package.metadata]
 requires-dist = [
     { name = "arxiv", specifier = ">=2.2.0,<3.0" },
+    { name = "atomman", specifier = ">=1.5.2" },
     { name = "beautifulsoup4", specifier = ">=4.13.4,<5.0" },
     { name = "chromadb", specifier = ">=1.0.20,<1.1" },
     { name = "coolname", specifier = ">=2.2.0,<3.0" },
@@ -6112,6 +6538,7 @@ requires-dist = [
     { name = "pymupdf", specifier = ">=1.26.0,<2.0" },
     { name = "pypdf", specifier = ">=5.9.0,<6.0" },
     { name = "rich", specifier = ">=13.9.4,<14.0" },
+    { name = "trafilatura", specifier = ">=1.6.1" },
 ]
 
 [package.metadata.requires-dev]
@@ -6389,6 +6816,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/fa/a8/5b41e0da817d64113292ab1f8247140aac61cbf6cfd085d6a0fa77f4984f/websockets-15.0.1-py3-none-any.whl", hash = "sha256:f7a866fbc1e97b5c617ee4116daaa09b722101d4a3c170c787450ba409f9736f", size = 169743, upload-time = "2025-03-05T20:03:39.41Z" },
 ]
 
+[[package]]
+name = "widgetsnbextension"
+version = "4.0.14"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/41/53/2e0253c5efd69c9656b1843892052a31c36d37ad42812b5da45c62191f7e/widgetsnbextension-4.0.14.tar.gz", hash = "sha256:a3629b04e3edb893212df862038c7232f62973373869db5084aed739b437b5af", size = 1097428, upload-time = "2025-04-10T13:01:25.628Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/ca/51/5447876806d1088a0f8f71e16542bf350918128d0a69437df26047c8e46f/widgetsnbextension-4.0.14-py3-none-any.whl", hash = "sha256:4875a9eaf72fbf5079dc372a51a9f268fc38d46f767cbf85c43a36da5cb9b575", size = 2196503, upload-time = "2025-04-10T13:01:23.086Z" },
+]
+
 [[package]]
 name = "wrapt"
 version = "1.17.3"
@@ -6458,6 +6894,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/1f/f6/a933bd70f98e9cf3e08167fc5cd7aaaca49147e48411c0bd5ae701bb2194/wrapt-1.17.3-py3-none-any.whl", hash = "sha256:7171ae35d2c33d326ac19dd8facb1e82e5fd04ef8c6c0e394d7af55a55051c22", size = 23591, upload-time = "2025-08-12T05:53:20.674Z" },
 ]
 
+[[package]]
+name = "xmltodict"
+version = "1.0.2"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/6a/aa/917ceeed4dbb80d2f04dbd0c784b7ee7bba8ae5a54837ef0e5e062cd3cfb/xmltodict-1.0.2.tar.gz", hash = "sha256:54306780b7c2175a3967cad1db92f218207e5bc1aba697d887807c0fb68b7649", size = 25725, upload-time = "2025-09-17T21:59:26.459Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/c0/20/69a0e6058bc5ea74892d089d64dfc3a62ba78917ec5e2cfa70f7c92ba3a5/xmltodict-1.0.2-py3-none-any.whl", hash = "sha256:62d0fddb0dcbc9f642745d8bbf4d81fd17d6dfaec5a15b5c1876300aad92af0d", size = 13893, upload-time = "2025-09-17T21:59:24.859Z" },
+]
+
 [[package]]
 name = "xxhash"
 version = "3.5.0"
@@ -6531,6 +6976,28 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/62/e3/bef7b82c1997579c94de9ac5ea7626d01ae5858aa22bf4fcb38bf220cb3e/xxhash-3.5.0-pp310-pypy310_pp73-win_amd64.whl", hash = "sha256:5a74f23335b9689b66eb6dbe2a931a88fcd7a4c2cc4b1cb0edba8ce381c7a1da", size = 30064, upload-time = "2024-08-17T09:20:15.925Z" },
 ]
 
+[[package]]
+name = "yabadaba"
+version = "0.3.2"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "cdcs" },
+    { name = "datamodeldict" },
+    { name = "ipython", version = "8.37.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
+    { name = "ipython", version = "9.4.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+    { name = "lxml" },
+    { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
+    { name = "numpy", version = "2.3.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+    { name = "pandas" },
+    { name = "pillow" },
+    { name = "pymongo" },
+    { name = "tqdm" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/ce/c5/0fa03ab364f8d66335802046e5ca38f241f0b7e82c790456c2cb77ff32d6/yabadaba-0.3.2.tar.gz", hash = "sha256:fd4bc16914c463df83f146d909709761aa158b842808e71c89f3462de08cea26", size = 59136, upload-time = "2025-07-07T20:03:51.548Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/d9/98/196ac9775756c0788b4f660c0e3153e9a1e355df075ac086a2238a97ee33/yabadaba-0.3.2-py3-none-any.whl", hash = "sha256:82c9b28616ae7e955452f0a49ef48e1a97b3b5cf0e141b908b70dbc5128e2065", size = 89959, upload-time = "2025-07-07T20:03:50.349Z" },
+]
+
 [[package]]
 name = "yarl"
 version = "1.20.1"

From 576f1ebd9c8107f4a7a62685123db382bf175c98 Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Thu, 18 Sep 2025 17:11:05 -0600
Subject: [PATCH 09/31] Linted and formatted code using ruff

---
 .../lammps_execute/EOS_of_Cu.py               |  41 +++---
 .../lammps_execute/stiffness_tensor_of_hea.py |  41 +++---
 src/ursa/agents/__init__.py                   |   4 +-
 src/ursa/agents/lammps_agent.py               | 135 ++++++++++--------
 4 files changed, 121 insertions(+), 100 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index b82a4cc2..48b5787e 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -1,36 +1,33 @@
-from ursa.agents import LammpsAgent
-from ursa.agents import ExecutionAgent
-
 from langchain_core.messages import HumanMessage
 from langchain_openai import ChatOpenAI
 
+from ursa.agents import ExecutionAgent, LammpsAgent
+
 model = "gpt-5"
 
-llm = ChatOpenAI(model      = model,
-                timeout     = None,
-                max_retries =  2
-                )
+llm = ChatOpenAI(model=model, timeout=None, max_retries=2)
 
 workspace = "./workspace_eos_cu"
 
 wf = LammpsAgent(
-    llm = llm,
+    llm=llm,
     max_potentials=2,
-    max_fix_attempts=5,      
+    max_fix_attempts=5,
     mpi_procs=8,
-    workspace = workspace,
+    workspace=workspace,
     lammps_cmd="lmp_mpi",
     mpirun_cmd="mpirun",
 )
 
-simulation_task="Carry out a LAMMPS simulation of Cu to determine its equation of state."
-elements=["Cu"]
+simulation_task = (
+    "Carry out a LAMMPS simulation of Cu to determine its equation of state."
+)
+elements = ["Cu"]
 
-final_lammps_state = wf.run(simulation_task,elements)
+final_lammps_state = wf.run(simulation_task, elements)
 
 if final_lammps_state.get("run_returncode") == 0:
-
-    print ("\nNow handing things off to execution agent.....")
+    print("\nNow handing things off to execution agent.....")
 
     executor = ExecutionAgent(llm=llm)
     exe_plan = f"""
@@ -42,10 +39,14 @@
     """
 
     executor_config = {"recursion_limit": 999_999}
-        
-    final_results = executor.action.invoke({"messages": [HumanMessage(content=exe_plan)],
-                                            "workspace": workspace,},executor_config,)
-    
+
+    final_results = executor.action.invoke(
+        {
+            "messages": [HumanMessage(content=exe_plan)],
+            "workspace": workspace,
+        },
+        executor_config,
+    )
+
     for x in final_results["messages"]:
         print(x.content)
-
diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index 4e4bd498..c6a66c47 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -1,38 +1,33 @@
-from ursa.agents import LammpsAgent
-from ursa.agents import ExecutionAgent
-
 from langchain_core.messages import HumanMessage
 from langchain_openai import ChatOpenAI
 
+from ursa.agents import ExecutionAgent, LammpsAgent
+
 model = "gpt-5"
 
-llm = ChatOpenAI(model      = model,
-                timeout     = None,
-                max_retries =  2
-                )
+llm = ChatOpenAI(model=model, timeout=None, max_retries=2)
 
 
 workspace = "./workspace_stiffness_tensor"
 
 wf = LammpsAgent(
-    llm = llm,
+    llm=llm,
     max_potentials=5,
-    max_fix_attempts=15,      
+    max_fix_attempts=15,
     mpi_procs=8,
-    workspace = workspace,
+    workspace=workspace,
     lammps_cmd="lmp_mpi",
     mpirun_cmd="mpirun",
 )
 
-simulation_task="Carry out a LAMMPS simulation of the high entropy alloy Co-Cr-Fe-Mn-Ni to determine its stiffness tensor."
+simulation_task = "Carry out a LAMMPS simulation of the high entropy alloy Co-Cr-Fe-Mn-Ni to determine its stiffness tensor."
 
-elements=["Co","Cr","Fe","Mn","Ni"]
+elements = ["Co", "Cr", "Fe", "Mn", "Ni"]
 
-final_lammps_state = wf.run(simulation_task,elements)
+final_lammps_state = wf.run(simulation_task, elements)
 
 if final_lammps_state.get("run_returncode") == 0:
-
-    print ("\nNow handing things off to execution agent.....")
+    print("\nNow handing things off to execution agent.....")
 
     executor = ExecutionAgent(llm=llm)
     exe_plan = f"""
@@ -42,12 +37,16 @@
     
     Summarize the contents of this file in a markdown document. Include a plot, if relevent.
     """
-    
+
     executor_config = {"recursion_limit": 999_999}
-        
-    final_results = executor.action.invoke({"messages": [HumanMessage(content=exe_plan)],
-                                            "workspace": workspace,},executor_config,)
-    
+
+    final_results = executor.action.invoke(
+        {
+            "messages": [HumanMessage(content=exe_plan)],
+            "workspace": workspace,
+        },
+        executor_config,
+    )
+
     for x in final_results["messages"]:
         print(x.content)
-
diff --git a/src/ursa/agents/__init__.py b/src/ursa/agents/__init__.py
index 982ea75f..831c7972 100644
--- a/src/ursa/agents/__init__.py
+++ b/src/ursa/agents/__init__.py
@@ -9,11 +9,11 @@
 from .execution_agent import ExecutionState as ExecutionState
 from .hypothesizer_agent import HypothesizerAgent as HypothesizerAgent
 from .hypothesizer_agent import HypothesizerState as HypothesizerState
+from .lammps_agent import LammpsAgent as LammpsAgent
+from .lammps_agent import LammpsState as LammpsState
 from .mp_agent import MaterialsProjectAgent as MaterialsProjectAgent
 from .planning_agent import PlanningAgent as PlanningAgent
 from .planning_agent import PlanningState as PlanningState
 from .recall_agent import RecallAgent as RecallAgent
 from .websearch_agent import WebSearchAgent as WebSearchAgent
 from .websearch_agent import WebSearchState as WebSearchState
-from .lammps_agent import LammpsAgent as LammpsAgent
-from .lammps_agent import LammpsState as LammpsState
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 4549a17b..4c503ab4 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -1,16 +1,14 @@
-from typing import TypedDict, List, Optional, Any, Dict
 import json
+import os
 import subprocess
-import os 
+from typing import Any, Dict, List, Optional, TypedDict
 
 import atomman as am
-import trafilatura
 import tiktoken
-
-from langchain_core.prompts import ChatPromptTemplate
+import trafilatura
 from langchain_core.output_parsers import StrOutputParser
-
-from langgraph.graph import StateGraph, END
+from langchain_core.prompts import ChatPromptTemplate
+from langgraph.graph import END, StateGraph
 
 from .base import BaseAgent
 
@@ -18,7 +16,7 @@
 class LammpsState(TypedDict, total=False):
     simulation_task: str
     elements: List[str]
-    
+
     matches: List[Any]
     db_message: str
 
@@ -35,8 +33,7 @@ class LammpsState(TypedDict, total=False):
     run_stdout: str
     run_stderr: str
 
-    fix_attempts: int 
-
+    fix_attempts: int
 
 
 class LammpsAgent(BaseAgent):
@@ -44,16 +41,15 @@ def __init__(
         self,
         llm,
         max_potentials: int = 5,
-        max_fix_attempts: int = 10,       
+        max_fix_attempts: int = 10,
         mpi_procs: int = 8,
         workspace: str = "./workspace",
-        lammps_cmd: str = "lmp_mpi",     
+        lammps_cmd: str = "lmp_mpi",
         mpirun_cmd: str = "mpirun",
         tiktoken_model: str = "o3",
         max_tokens: int = 200000,
         **kwargs,
     ):
-
         self.max_potentials = max_potentials
         self.max_fix_attempts = max_fix_attempts
         self.mpi_procs = mpi_procs
@@ -62,26 +58,36 @@ def __init__(
         self.tiktoken_model = tiktoken_model
         self.max_tokens = max_tokens
 
-        self.pair_styles = ["eam", "eam/alloy", "eam/fs",
-                            "meam", "adp",            # classical, HEA-relevant
-                            "kim",                    # OpenKIM models
-                            "snap", "quip", "mlip", "pace", "nep"  # ML/ACE families (if available)
-                            ]
+        self.pair_styles = [
+            "eam",
+            "eam/alloy",
+            "eam/fs",
+            "meam",
+            "adp",  # classical, HEA-relevant
+            "kim",  # OpenKIM models
+            "snap",
+            "quip",
+            "mlip",
+            "pace",
+            "nep",  # ML/ACE families (if available)
+        ]
 
         self.workspace = workspace
         os.makedirs(self.workspace, exist_ok=True)
 
-        
         super().__init__(llm, **kwargs)
-        
+
         self.str_parser = StrOutputParser()
 
-        self.summ_chain = (ChatPromptTemplate.from_template(
-            "Here is some data about an interatomic potential: {metadata}\n\n"
-            "Briefly summarize why it could be useful for this task: {simulation_task}."
-        ) | self.llm | self.str_parser)
+        self.summ_chain = (
+            ChatPromptTemplate.from_template(
+                "Here is some data about an interatomic potential: {metadata}\n\n"
+                "Briefly summarize why it could be useful for this task: {simulation_task}."
+            )
+            | self.llm
+            | self.str_parser
+        )
 
-        
         self.choose_chain = (
             ChatPromptTemplate.from_template(
                 "Here are the summaries of a certain number of interatomic potentials: {summaries_combined}\n\n"
@@ -97,7 +103,7 @@ def __init__(
             | self.llm
             | self.str_parser
         )
-        
+
         self.author_chain = (
             ChatPromptTemplate.from_template(
                 "Your task is to write a LAMMPS input file for this purpose: {simulation_task}.\n"
@@ -115,7 +121,7 @@ def __init__(
             | self.llm
             | self.str_parser
         )
-        
+
         self.fix_chain = (
             ChatPromptTemplate.from_template(
                 "You are part of a larger scientific workflow whose purpose is to accomplish this task: {simulation_task}\n"
@@ -138,11 +144,8 @@ def __init__(
             | self.str_parser
         )
 
-        
         self.graph = self._build_graph().compile()
 
-
-
     @staticmethod
     def _safe_json_loads(s: str) -> Dict[str, Any]:
         s = s.strip()
@@ -177,10 +180,11 @@ def _fetch_and_trim_text(self, url: str) -> str:
             pass
         return text
 
-
     def _find_potentials(self, state: LammpsState) -> LammpsState:
         db = am.library.Database(remote=True)
-        matches = db.get_lammps_potentials(pair_style=self.pair_styles, elements=state["elements"])
+        matches = db.get_lammps_potentials(
+            pair_style=self.pair_styles, elements=state["elements"]
+        )
         msg_lines = []
         if not list(matches):
             msg_lines.append("No potentials found for this task in NIST.")
@@ -202,7 +206,7 @@ def _should_summarize(self, state: LammpsState) -> str:
         matches = state.get("matches", [])
         i = state.get("idx", 0)
         if not matches:
-            print ("No potentials found in NIST for this task. Exiting....")
+            print("No potentials found in NIST for this task. Exiting....")
             return "done_no_matches"
         if i < min(self.max_potentials, len(matches)):
             return "summarize_one"
@@ -210,7 +214,7 @@ def _should_summarize(self, state: LammpsState) -> str:
 
     def _summarize_one(self, state: LammpsState) -> LammpsState:
         i = state["idx"]
-        print (f"Summarizing potential #{i}")
+        print(f"Summarizing potential #{i}")
         match = state["matches"][i]
         md = match.metadata()
 
@@ -220,8 +224,15 @@ def _summarize_one(self, state: LammpsState) -> LammpsState:
         else:
             lines = md["comments"].split("\n")
             url = lines[1] if len(lines) > 1 else ""
-            text = self._fetch_and_trim_text(url) if url else "No metadata available"
-            summary = self.summ_chain.invoke({"metadata": text, "simulation_task": state["simulation_task"]})
+            text = (
+                self._fetch_and_trim_text(url)
+                if url
+                else "No metadata available"
+            )
+            summary = self.summ_chain.invoke({
+                "metadata": text,
+                "simulation_task": state["simulation_task"],
+            })
 
         return {
             **state,
@@ -238,15 +249,15 @@ def _build_summaries(self, state: LammpsState) -> LammpsState:
         return {**state, "summaries_combined": "".join(parts)}
 
     def _choose(self, state: LammpsState) -> LammpsState:
-        print ("Choosing one potential for this task...")
+        print("Choosing one potential for this task...")
         choice = self.choose_chain.invoke({
             "summaries_combined": state["summaries_combined"],
-            "simulation_task": state["simulation_task"]
+            "simulation_task": state["simulation_task"],
         })
         choice_dict = self._safe_json_loads(choice)
         chosen_index = int(choice_dict["Chosen index"])
-        print (f"Chosen potential #{chosen_index}")
-        print ("Rationale for choosing this potential:")
+        print(f"Chosen potential #{chosen_index}")
+        print("Rationale for choosing this potential:")
         print(choice_dict["rationale"])
         return {**state, "choice_json": choice, "chosen_index": chosen_index}
 
@@ -259,7 +270,7 @@ def _author(self, state: LammpsState) -> LammpsState:
         authored_json = self.author_chain.invoke({
             "simulation_task": state["simulation_task"],
             "metadata": text,
-            "pair_info": pair_info
+            "pair_info": pair_info,
         })
         script_dict = self._safe_json_loads(authored_json)
         input_script = script_dict["input_script"]
@@ -268,14 +279,21 @@ def _author(self, state: LammpsState) -> LammpsState:
         return {**state, "input_script": input_script}
 
     def _run_lammps(self, state: LammpsState) -> LammpsState:
-        print ("Running LAMMPS....")
+        print("Running LAMMPS....")
         result = subprocess.run(
-            [self.mpirun_cmd, "-np", str(self.mpi_procs), self.lammps_cmd, "-in", "in.lammps"],
+            [
+                self.mpirun_cmd,
+                "-np",
+                str(self.mpi_procs),
+                self.lammps_cmd,
+                "-in",
+                "in.lammps",
+            ],
             cwd=self.workspace,
             stdout=subprocess.PIPE,
             stderr=subprocess.PIPE,
             text=True,
-            check=False
+            check=False,
         )
         return {
             **state,
@@ -288,35 +306,37 @@ def _route_run(self, state: LammpsState) -> str:
         rc = state.get("run_returncode", 0)
         attempts = state.get("fix_attempts", 0)
         if rc == 0:
-            print ("LAMMPS run successful! Exiting...")
+            print("LAMMPS run successful! Exiting...")
             return "done_success"
         if attempts < self.max_fix_attempts:
-            print ("LAMMPS run Failed. Attempting to rewrite input file...")
+            print("LAMMPS run Failed. Attempting to rewrite input file...")
             return "need_fix"
-        print ("LAMMPS run Failed and maximum fix attempts reached. Exiting...")
+        print("LAMMPS run Failed and maximum fix attempts reached. Exiting...")
         return "done_failed"
 
     def _fix(self, state: LammpsState) -> LammpsState:
         match = state["matches"][state["chosen_index"]]
         text = state["full_texts"][state["chosen_index"]]
         pair_info = match.pair_info()
-        err_blob = state.get("run_stdout") 
-        
+        err_blob = state.get("run_stdout")
+
         fixed_json = self.fix_chain.invoke({
             "simulation_task": state["simulation_task"],
             "input_script": state["input_script"],
             "err_message": err_blob,
             "metadata": text,
-            "pair_info": pair_info
+            "pair_info": pair_info,
         })
         script_dict = self._safe_json_loads(fixed_json)
         new_input = script_dict["input_script"]
         with open(os.path.join(self.workspace, "in.lammps"), "w") as f:
             f.write(new_input)
-        return {**state, "input_script": new_input, "fix_attempts": state.get("fix_attempts", 0) + 1}
-
+        return {
+            **state,
+            "input_script": new_input,
+            "fix_attempts": state.get("fix_attempts", 0) + 1,
+        }
 
-    
     def _build_graph(self):
         g = StateGraph(LammpsState)
 
@@ -365,7 +385,8 @@ def _build_graph(self):
         g.add_edge("fix", "run_lammps")
         return g
 
-    
-    def run(self,simulation_task,elements):
-        return self.graph.invoke({"simulation_task": simulation_task,"elements": elements},{"recursion_limit": 999_999})
-        
\ No newline at end of file
+    def run(self, simulation_task, elements):
+        return self.graph.invoke(
+            {"simulation_task": simulation_task, "elements": elements},
+            {"recursion_limit": 999_999},
+        )

From c7cedef70fd0e4b697eecc2ec5ac3abc53867670 Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Wed, 15 Oct 2025 10:29:12 -0600
Subject: [PATCH 10/31] Fixed minor bugs created from merging
 main-->lammps_agent

---
 examples/two_agent_examples/lammps_execute/EOS_of_Cu.py    | 5 +----
 .../lammps_execute/stiffness_tensor_of_hea.py              | 7 ++-----
 src/ursa/agents/lammps_agent.py                            | 2 +-
 3 files changed, 4 insertions(+), 10 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index e8dc11b2..01826932 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -40,14 +40,11 @@
     Summarize the contents of this file in a markdown document. Include a plot, if relevent.
     """
 
-    executor_config = {"recursion_limit": 999_999}
-
     final_results = executor.invoke(
         {
             "messages": [HumanMessage(content=exe_plan)],
             "workspace": workspace,
-        },
-        executor_config,
+        }
     )
 
     for x in final_results["messages"]:
diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index c15f231c..e7f01645 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -39,15 +39,12 @@
     
     Summarize the contents of this file in a markdown document. Include a plot, if relevent.
     """
-
-    executor_config = {"recursion_limit": 999_999}
-
+    
     final_results = executor.invoke(
         {
             "messages": [HumanMessage(content=exe_plan)],
             "workspace": workspace,
-        },
-        executor_config,
+        }
     )
 
     for x in final_results["messages"]:
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 685b9c9d..804242d9 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -399,7 +399,7 @@ def _invoke(
         inputs: Mapping[str, Any],
         *,
         summarize: bool | None = None,
-        recursion_limit: int = 1000,
+        recursion_limit: int = 999_999,
         **_,
     ) -> str:
         config = self.build_config(

From 7e6e277c8e00cdafc5f79028421b29e3e535dfda Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Fri, 17 Oct 2025 16:22:24 -0600
Subject: [PATCH 11/31] Added option of providing input file templates to
 lammps_agent

---
 .../lammps_execute/EOS_of_Cu.py               |   5 +-
 .../lammps_execute/elastic_template.txt       | 390 ++++++++++++++++++
 .../lammps_execute/eos_template.txt           |  74 ++++
 .../lammps_execute/stiffness_tensor_of_hea.py |   6 +-
 src/ursa/agents/lammps_agent.py               |  14 +-
 5 files changed, 485 insertions(+), 4 deletions(-)
 create mode 100644 examples/two_agent_examples/lammps_execute/elastic_template.txt
 create mode 100644 examples/two_agent_examples/lammps_execute/eos_template.txt

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index 01826932..ef9dbb7b 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -19,13 +19,16 @@
     mpirun_cmd="mpirun",
 )
 
+with open("eos_template.txt", "r") as file:
+    template = file.read()
+
 simulation_task = (
     "Carry out a LAMMPS simulation of Cu to determine its equation of state."
 )
 elements = ["Cu"]
 
 final_lammps_state = wf.invoke(
-    simulation_task=simulation_task, elements=elements
+    simulation_task=simulation_task, elements=elements, template=template
 )
 
 if final_lammps_state.get("run_returncode") == 0:
diff --git a/examples/two_agent_examples/lammps_execute/elastic_template.txt b/examples/two_agent_examples/lammps_execute/elastic_template.txt
new file mode 100644
index 00000000..926a6652
--- /dev/null
+++ b/examples/two_agent_examples/lammps_execute/elastic_template.txt
@@ -0,0 +1,390 @@
+log ./log.lammps
+
+units           metal
+atom_style      atomic
+boundary        p p p
+newton          on
+
+variable        a0           equal xxx
+variable        nrep         equal xxx
+variable        seed         equal xxx
+variable        delta        equal xxx
+variable        etol         equal xxx
+variable        ftol         equal xxx
+variable        maxiter      equal xxx
+variable        maxeval      equal xxx
+
+# ------------ SYSTEM / STRUCTURE ------------
+lattice        xxx (fcc,bcc,etc....) ${a0}
+region         box block 0 ${nrep} 0 ${nrep} 0 ${nrep}
+create_box     xx box
+create_atoms   xx box
+
+# Example random equiatomic assignment across 5 types (1..5)
+# Adjust according to your needs
+set type 1 type/fraction 2 0.20 ${seed}
+set type 1 type/fraction 3 0.25 ${seed}
+set type 1 type/fraction 4 0.3333 ${seed}
+set type 1 type/fraction 5 0.5 ${seed}
+
+# Masses 
+mass 1 xxxx
+mass 2 xxxx
+mass 3 xxxx
+mass 4 xxxx
+mass 5 xxxx
+
+# pair_style and pair_coeff details should be entered here
+
+neighbor        2.0 bin   
+neigh_modify    delay 0 every 1 check yes
+
+# ------------ MINIMIZATION TO 0 K ------------
+reset_timestep  0
+thermo          xxxxx
+thermo_style    custom step pe lx ly lz pxx pyy pzz pxy pxz pyz
+
+min_style       cg
+min_modify      dmax 0.1 line quadratic
+minimize        ${etol} ${ftol} ${maxiter} ${maxeval}
+
+# Store reference cell (for shear normalization)
+variable Lx0 equal lx
+variable Ly0 equal ly
+variable Lz0 equal lz
+
+# ------------ HELPER VARIABLES ------------
+# Precompute scale factors for normal strains
+variable facP   equal 1.0+v_delta          # 1 + delta
+variable facM   equal 1.0-v_delta          # 1 - delta
+variable facPi  equal 1.0/${facP}          # 1/(1+delta)
+variable facMi  equal 1.0/${facM}          # 1/(1-delta)
+
+# A macro to relax atoms after each strain change
+variable relax string "minimize ${etol} ${ftol} ${maxiter} ${maxeval}"
+
+# ------------ STRESS (GPa, tension-positive) ------------
+# LAMMPS 'metal' pressure is bar (compression positive). Convert and flip sign.
+variable S1 equal -pxx*1.0e-4
+variable S2 equal -pyy*1.0e-4
+variable S3 equal -pzz*1.0e-4
+variable S4 equal -pyz*1.0e-4
+variable S5 equal -pxz*1.0e-4
+variable S6 equal -pxy*1.0e-4
+
+# Initialize holders for +/- stress states
+variable Sp1 equal 0.0
+variable Sp2 equal 0.0
+variable Sp3 equal 0.0
+variable Sp4 equal 0.0
+variable Sp5 equal 0.0
+variable Sp6 equal 0.0
+
+variable Sm1 equal 0.0
+variable Sm2 equal 0.0
+variable Sm3 equal 0.0
+variable Sm4 equal 0.0
+variable Sm5 equal 0.0
+variable Sm6 equal 0.0
+
+variable Tp1 equal 0.0
+variable Tp2 equal 0.0
+variable Tp3 equal 0.0
+variable Tp4 equal 0.0
+variable Tp5 equal 0.0
+variable Tp6 equal 0.0
+
+variable Tm1 equal 0.0
+variable Tm2 equal 0.0
+variable Tm3 equal 0.0
+variable Tm4 equal 0.0
+variable Tm5 equal 0.0
+variable Tm6 equal 0.0
+
+variable Up1 equal 0.0
+variable Up2 equal 0.0
+variable Up3 equal 0.0
+variable Up4 equal 0.0
+variable Up5 equal 0.0
+variable Up6 equal 0.0
+
+variable Um1 equal 0.0
+variable Um2 equal 0.0
+variable Um3 equal 0.0
+variable Um4 equal 0.0
+variable Um5 equal 0.0
+variable Um6 equal 0.0
+
+
+# ------------ NORMAL STRAINS ------------
+# X: +delta then -delta
+label strain_x_plus
+change_box all x scale ${facP} remap units box
+${relax}
+variable Sp1 equal ${S1}
+variable Sp2 equal ${S2}
+variable Sp3 equal ${S3}
+variable Sp4 equal ${S4}
+variable Sp5 equal ${S5}
+variable Sp6 equal ${S6}
+change_box all x scale ${facPi} remap units box
+${relax}
+
+label strain_x_minus
+change_box all x scale ${facM} remap units box
+${relax}
+variable Sm1 equal ${S1}
+variable Sm2 equal ${S2}
+variable Sm3 equal ${S3}
+variable Sm4 equal ${S4}
+variable Sm5 equal ${S5}
+variable Sm6 equal ${S6}
+change_box all x scale ${facMi} remap units box
+${relax}
+
+# Y
+label strain_y_plus
+change_box all y scale ${facP} remap units box
+${relax}
+variable Tp1 equal ${S1}
+variable Tp2 equal ${S2}
+variable Tp3 equal ${S3}
+variable Tp4 equal ${S4}
+variable Tp5 equal ${S5}
+variable Tp6 equal ${S6}
+change_box all y scale ${facPi} remap units box
+${relax}
+
+label strain_y_minus
+change_box all y scale ${facM} remap units box
+${relax}
+variable Tm1 equal ${S1}
+variable Tm2 equal ${S2}
+variable Tm3 equal ${S3}
+variable Tm4 equal ${S4}
+variable Tm5 equal ${S5}
+variable Tm6 equal ${S6}
+change_box all y scale ${facMi} remap units box
+${relax}
+
+# Z
+label strain_z_plus
+change_box all z scale ${facP} remap units box
+${relax}
+variable Up1 equal ${S1}
+variable Up2 equal ${S2}
+variable Up3 equal ${S3}
+variable Up4 equal ${S4}
+variable Up5 equal ${S5}
+variable Up6 equal ${S6}
+change_box all z scale ${facPi} remap units box
+${relax}
+
+label strain_z_minus
+change_box all z scale ${facM} remap units box
+${relax}
+variable Um1 equal ${S1}
+variable Um2 equal ${S2}
+variable Um3 equal ${S3}
+variable Um4 equal ${S4}
+variable Um5 equal ${S5}
+variable Um6 equal ${S6}
+change_box all z scale ${facMi} remap units box
+${relax}
+
+# ------------ SHEAR STRAINS (triclinic + proper gamma) ------------
+# Convert to triclinic once so we can tilt
+change_box all triclinic remap units box
+
+# Define tilt distances so that engineering shear gamma == delta
+# divisors: xy->Ly, xz->Lz, yz->Lz
+variable dxy equal v_delta*v_Ly0
+variable dxz equal v_delta*v_Lz0
+variable dyz equal v_delta*v_Lz0
+
+# XY
+label shear_xy_plus
+change_box all xy delta ${dxy} remap units box
+${relax}
+variable Xp1 equal ${S1}
+variable Xp2 equal ${S2}
+variable Xp3 equal ${S3}
+variable Xp4 equal ${S4}
+variable Xp5 equal ${S5}
+variable Xp6 equal ${S6}
+change_box all xy delta -${dxy} remap units box
+${relax}
+
+label shear_xy_minus
+change_box all xy delta -${dxy} remap units box
+${relax}
+variable Xm1 equal ${S1}
+variable Xm2 equal ${S2}
+variable Xm3 equal ${S3}
+variable Xm4 equal ${S4}
+variable Xm5 equal ${S5}
+variable Xm6 equal ${S6}
+change_box all xy delta ${dxy} remap units box
+${relax}
+
+# XZ
+label shear_xz_plus
+change_box all xz delta ${dxz} remap units box
+${relax}
+variable Yp1 equal ${S1}
+variable Yp2 equal ${S2}
+variable Yp3 equal ${S3}
+variable Yp4 equal ${S4}
+variable Yp5 equal ${S5}
+variable Yp6 equal ${S6}
+change_box all xz delta -${dxz} remap units box
+${relax}
+
+label shear_xz_minus
+change_box all xz delta -${dxz} remap units box
+${relax}
+variable Ym1 equal ${S1}
+variable Ym2 equal ${S2}
+variable Ym3 equal ${S3}
+variable Ym4 equal ${S4}
+variable Ym5 equal ${S5}
+variable Ym6 equal ${S6}
+change_box all xz delta ${dxz} remap units box
+${relax}
+
+# YZ
+label shear_yz_plus
+change_box all yz delta ${dyz} remap units box
+${relax}
+variable Zp1 equal ${S1}
+variable Zp2 equal ${S2}
+variable Zp3 equal ${S3}
+variable Zp4 equal ${S4}
+variable Zp5 equal ${S5}
+variable Zp6 equal ${S6}
+change_box all yz delta -${dyz} remap units box
+${relax}
+
+label shear_yz_minus
+change_box all yz delta -${dyz} remap units box
+${relax}
+variable Zm1 equal ${S1}
+variable Zm2 equal ${S2}
+variable Zm3 equal ${S3}
+variable Zm4 equal ${S4}
+variable Zm5 equal ${S5}
+variable Zm6 equal ${S6}
+change_box all yz delta ${dyz} remap units box
+${relax}
+
+# (Optional tidy-up: zero tilts and return to orthogonal)
+change_box all xy final 0.0 xz final 0.0 yz final 0.0 remap units box
+change_box all ortho remap units box
+
+# ------------ BUILD THE 6x6 C MATRIX (GPa) ------------
+# Voigt: 1=xx,2=yy,3=zz,4=yz,5=xz,6=xy
+# Normal: epsilon = +/- delta
+# Shear:  epsilon4..6 = gamma/2 = +/- delta/2  -> divide by delta below
+
+# j=1 (exx)
+variable C11 equal ( ${Sp1}-${Sm1} )/( 2*${delta} )
+variable C21 equal ( ${Sp2}-${Sm2} )/( 2*${delta} )
+variable C31 equal ( ${Sp3}-${Sm3} )/( 2*${delta} )
+variable C41 equal ( ${Sp4}-${Sm4} )/( 2*${delta} )
+variable C51 equal ( ${Sp5}-${Sm5} )/( 2*${delta} )
+variable C61 equal ( ${Sp6}-${Sm6} )/( 2*${delta} )
+
+# j=2 (eyy)
+variable C12 equal ( ${Tp1}-${Tm1} )/( 2*${delta} )
+variable C22 equal ( ${Tp2}-${Tm2} )/( 2*${delta} )
+variable C32 equal ( ${Tp3}-${Tm3} )/( 2*${delta} )
+variable C42 equal ( ${Tp4}-${Tm4} )/( 2*${delta} )
+variable C52 equal ( ${Tp5}-${Tm5} )/( 2*${delta} )
+variable C62 equal ( ${Tp6}-${Tm6} )/( 2*${delta} )
+
+# j=3 (ezz)
+variable C13 equal ( ${Up1}-${Um1} )/( 2*${delta} )
+variable C23 equal ( ${Up2}-${Um2} )/( 2*${delta} )
+variable C33 equal ( ${Up3}-${Um3} )/( 2*${delta} )
+variable C43 equal ( ${Up4}-${Um4} )/( 2*${delta} )
+variable C53 equal ( ${Up5}-${Um5} )/( 2*${delta} )
+variable C63 equal ( ${Up6}-${Um6} )/( 2*${delta} )
+
+# j=6 (exy = gamma/2): divide by delta
+variable C16 equal ( ${Xp1}-${Xm1} )/( ${delta} )
+variable C26 equal ( ${Xp2}-${Xm2} )/( ${delta} )
+variable C36 equal ( ${Xp3}-${Xm3} )/( ${delta} )
+variable C46 equal ( ${Xp4}-${Xm4} )/( ${delta} )
+variable C56 equal ( ${Xp5}-${Xm5} )/( ${delta} )
+variable C66 equal ( ${Xp6}-${Xm6} )/( ${delta} )
+
+# j=5 (exz = gamma/2): divide by delta
+variable C15 equal ( ${Yp1}-${Ym1} )/( ${delta} )
+variable C25 equal ( ${Yp2}-${Ym2} )/( ${delta} )
+variable C35 equal ( ${Yp3}-${Ym3} )/( ${delta} )
+variable C45 equal ( ${Yp4}-${Ym4} )/( ${delta} )
+variable C55 equal ( ${Yp5}-${Ym5} )/( ${delta} )
+variable C65 equal ( ${Yp6}-${Ym6} )/( ${delta} )
+
+# j=4 (eyz = gamma/2): divide by delta
+variable C14 equal ( ${Zp1}-${Zm1} )/( ${delta} )
+variable C24 equal ( ${Zp2}-${Zm2} )/( ${delta} )
+variable C34 equal ( ${Zp3}-${Zm3} )/( ${delta} )
+variable C44 equal ( ${Zp4}-${Zm4} )/( ${delta} )
+variable C54 equal ( ${Zp5}-${Zm5} )/( ${delta} )
+variable C64 equal ( ${Zp6}-${Zm6} )/( ${delta} )
+
+# ------------ REPORT: raw, symmetrized, cubic averages, stability ------------
+print "Elastic stiffness matrix C_ij (GPa):"
+print "  ${C11} ${C12} ${C13} ${C14} ${C15} ${C16}"
+print "  ${C21} ${C22} ${C23} ${C24} ${C25} ${C26}"
+print "  ${C31} ${C32} ${C33} ${C34} ${C35} ${C36}"
+print "  ${C41} ${C42} ${C43} ${C44} ${C45} ${C46}"
+print "  ${C51} ${C52} ${C53} ${C54} ${C55} ${C56}"
+print "  ${C61} ${C62} ${C63} ${C64} ${C65} ${C66}"
+
+
+
+# ---- Symmetrize C (recommended for reporting) ----
+variable Cs12 equal 0.5*(${C12}+${C21})
+variable Cs13 equal 0.5*(${C13}+${C31})
+variable Cs23 equal 0.5*(${C23}+${C32})
+variable Cs14 equal 0.5*(${C14}+${C41})
+variable Cs15 equal 0.5*(${C15}+${C51})
+variable Cs16 equal 0.5*(${C16}+${C61})
+variable Cs24 equal 0.5*(${C24}+${C42})
+variable Cs25 equal 0.5*(${C25}+${C52})
+variable Cs26 equal 0.5*(${C26}+${C62})
+variable Cs34 equal 0.5*(${C34}+${C43})
+variable Cs35 equal 0.5*(${C35}+${C53})
+variable Cs36 equal 0.5*(${C36}+${C63})
+variable Cs44 equal ${C44}
+variable Cs55 equal ${C55}
+variable Cs66 equal ${C66}
+variable Cs11 equal ${C11}
+variable Cs22 equal ${C22}
+variable Cs33 equal ${C33}
+
+print "Symmetrized C_ij (GPa) key entries:"
+print "C11=${Cs11} C22=${Cs22} C33=${Cs33}"
+print "C12=${Cs12} C13=${Cs13} C23=${Cs23}"
+print "C44=${Cs44} C55=${Cs55} C66=${Cs66}"
+
+# ---- Cubic-averaged moduli (for near-cubic HEAs) ----
+variable C11_c equal ( ${Cs11}+${Cs22}+${Cs33} )/3.0
+variable C12_c equal ( ${Cs12}+${Cs13}+${Cs23} )/3.0
+variable C44_c equal ( ${Cs44}+${Cs55}+${Cs66} )/3.0
+print "Cubic-averaged: C11bar=${C11_c} GPa, C12bar=${C12_c} GPa, C44bar=${C44_c} GPa"
+
+# ---- Born stability (cubic) using cubic-averaged values ----
+variable born1 equal ${C11_c}-${C12_c}
+variable born2 equal ${C11_c}+2.0*${C12_c}
+variable born3 equal ${C44_c}
+print "Born (cubic) checks: C11-C12=${born1} (>0), C11+2C12=${born2} (>0), C44=${born3} (>0)"
+
+# ------------ DERIVED MODULI (Voigt estimates from raw C) ------------
+variable K_V equal ( ( ${C11}+${C22}+${C33} ) + 2*( ${Cs12}+${Cs13}+${Cs23} ) )/9.0
+variable G_V equal ( ( ${C11}+${C22}+${C33} ) - ( ${Cs12}+${Cs13}+${Cs23} ) + 3*( ${C44}+${C55}+${C66} ) )/15.0
+variable E_V equal 9.0*${K_V}*${G_V}/(3.0*${K_V}+${G_V})
+variable nu_V equal (3.0*${K_V}-2.0*${G_V})/(2.0*(3.0*${K_V}+${G_V}))
+print "Voigt estimates (polycrystal): K=${K_V} GPa, G=${G_V} GPa, E=${E_V} GPa, nu=${nu_V}"
diff --git a/examples/two_agent_examples/lammps_execute/eos_template.txt b/examples/two_agent_examples/lammps_execute/eos_template.txt
new file mode 100644
index 00000000..1cf5a4fd
--- /dev/null
+++ b/examples/two_agent_examples/lammps_execute/eos_template.txt
@@ -0,0 +1,74 @@
+log ./log.lammps
+
+units           metal
+atom_style      atomic
+boundary        p p p
+
+# Lattice and supercell
+variable        a0    equal xxx
+variable        nx    equal xxx
+variable        ny    equal xxx
+variable        nz    equal xxx
+variable        Lx0   equal ${a0}*${nx}
+variable        Ly0   equal ${a0}*${ny}
+variable        Lz0   equal ${a0}*${nz}
+
+lattice         xxx (fcc,bcc,etc....) ${a0}
+region          box block 0 ${Lx0} 0 ${Ly0} 0 ${Lz0} units box
+create_box     xx box
+create_atoms   xx box
+
+# Example random equiatomic assignment across 5 types (1..5)
+# Adjust according to your needs
+set type 1 type/fraction 2 0.20 ${seed}
+set type 1 type/fraction 3 0.25 ${seed}
+set type 1 type/fraction 4 0.3333 ${seed}
+set type 1 type/fraction 5 0.5 ${seed}
+
+# Masses 
+mass 1 xxxx
+mass 2 xxxx
+mass 3 xxxx
+mass 4 xxxx
+mass 5 xxxx
+
+# pair_style and pair_coeff details should be entered here
+
+neighbor        2.0 bin
+neigh_modify    delay 0 every 1 check yes
+
+thermo          1
+thermo_style    custom step pe press vol lx ly lz
+
+# Energy minimization settings
+min_style       cg
+min_modify      dmax 0.1 line quadratic
+
+# Variables for reporting
+variable        e    equal pe
+variable        p    equal press
+variable        vvol equal vol
+
+# Loop over scale factors (volume scan)
+variable        i loop 11
+label           loop
+  variable      scale equal 0.94 + (v_i-1)*0.01
+  variable      newa  equal ${a0}*${scale}
+  variable      newLx equal ${newa}*${nx}
+  variable      newLy equal ${newa}*${ny}
+  variable      newLz equal ${newa}*${nz}
+
+  # Rescale box and atoms to target volume
+  change_box    all x final 0 ${newLx} y final 0 ${newLy} z final 0 ${newLz} remap units box
+
+  reset_timestep 0
+  minimize      1.0e-12 1.0e-12 10000 10000
+  run           0
+
+  # Report one line per state: scale, a(Ang), Vol(Ang^3), Pressure(bar), Energy(eV)
+  print         "scale ${scale} a ${newa} vol ${vvol} press ${p} pe ${e}"
+
+  next          i
+jump            SELF loop
+
+print           "# EOS scan complete."
diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index e7f01645..2b63568c 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -7,7 +7,6 @@
 
 llm = ChatOpenAI(model=model, timeout=None, max_retries=2)
 
-
 workspace = "./workspace_stiffness_tensor"
 
 wf = LammpsAgent(
@@ -20,12 +19,15 @@
     mpirun_cmd="mpirun",
 )
 
+with open("elastic_template.txt", "r") as file:
+    template = file.read()
+
 simulation_task = "Carry out a LAMMPS simulation of the high entropy alloy Co-Cr-Fe-Mn-Ni to determine its stiffness tensor."
 
 elements = ["Co", "Cr", "Fe", "Mn", "Ni"]
 
 final_lammps_state = wf.invoke(
-    simulation_task=simulation_task, elements=elements
+    simulation_task=simulation_task, elements=elements, template=template
 )
 
 if final_lammps_state.get("run_returncode") == 0:
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 804242d9..1a95ce26 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -21,6 +21,7 @@
 class LammpsState(TypedDict, total=False):
     simulation_task: str
     elements: List[str]
+    template: Optional[str]
 
     matches: List[Any]
     db_message: str
@@ -119,6 +120,8 @@ def __init__(
                 "Here is metadata about the interatomic potential that will be used: {metadata}.\n"
                 "Note that all potential files are in the './' directory.\n"
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
+                "If a template for the input file is provided, you should adapt it appropriately to meet the task requirements.\n"
+                "Template provided (if any): {template}\n"
                 "Ensure that all output data is written only to the './log.lammps' file. Do not create any other output file.\n"
                 "To create the log, use only the 'log ./log.lammps' command. Do not use any other command like 'echo' or 'screen'.\n"
                 "Return your answer **only** as valid JSON, with no extra text or formatting.\n"
@@ -141,6 +144,8 @@ def __init__(
                 "Here is metadata about the interatomic potential that will be used: {metadata}.\n"
                 "Note that all potential files are in the './' directory.\n"
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
+                "If a template for the input file is provided, you should adapt it appropriately to meet the task requirements.\n"
+                "Template provided (if any): {template}\n"
                 "Ensure that all output data is written only to the './log.lammps' file. Do not create any other output file.\n"
                 "To create the log, use only the 'log ./log.lammps' command. Do not use any other command like 'echo' or 'screen'.\n"
                 "Return your answer **only** as valid JSON, with no extra text or formatting.\n"
@@ -280,6 +285,7 @@ def _author(self, state: LammpsState) -> LammpsState:
             "simulation_task": state["simulation_task"],
             "metadata": text,
             "pair_info": pair_info,
+            "template": state["template"],
         })
         script_dict = self._safe_json_loads(authored_json)
         input_script = script_dict["input_script"]
@@ -335,6 +341,7 @@ def _fix(self, state: LammpsState) -> LammpsState:
             "err_message": err_blob,
             "metadata": text,
             "pair_info": pair_info,
+            "template": state["template"],
         })
         script_dict = self._safe_json_loads(fixed_json)
         new_input = script_dict["input_script"]
@@ -411,4 +418,9 @@ def _invoke(
                 "'simulation_task' and 'elements' are required arguments"
             )
 
-        return self._action.invoke(inputs, config)
\ No newline at end of file
+        if "template" not in inputs:
+            inputs = {**inputs, "template": "No template provided."}
+
+        return self._action.invoke(inputs, config)
+
+        
\ No newline at end of file

From f8f1f067bd533f750e4ee2a80c6d7118310dc9fc Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Mon, 20 Oct 2025 11:47:50 -0600
Subject: [PATCH 12/31] Cleaned up unrequired variables in LammpsState

---
 src/ursa/agents/lammps_agent.py | 35 ++++++++++++++++-----------------
 1 file changed, 17 insertions(+), 18 deletions(-)

diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 1a95ce26..ea3ae127 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -24,15 +24,12 @@ class LammpsState(TypedDict, total=False):
     template: Optional[str]
 
     matches: List[Any]
-    db_message: str
-
     idx: int
     summaries: List[str]
     full_texts: List[str]
-
     summaries_combined: str
-    choice_json: str
-    chosen_index: int
+    
+    chosen_potential: Any
 
     input_script: str
     run_returncode: Optional[int]
@@ -117,7 +114,7 @@ def __init__(
         self.author_chain = (
             ChatPromptTemplate.from_template(
                 "Your task is to write a LAMMPS input file for this purpose: {simulation_task}.\n"
-                "Here is metadata about the interatomic potential that will be used: {metadata}.\n"
+                #"Here is metadata about the interatomic potential that will be used: {metadata}.\n"
                 "Note that all potential files are in the './' directory.\n"
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
                 "If a template for the input file is provided, you should adapt it appropriately to meet the task requirements.\n"
@@ -141,7 +138,7 @@ def __init__(
                 "However, when running the simulation, an error was raised.\n"
                 "Here is the full stdout message that includes the error message: {err_message}\n"
                 "Your task is to write a new input file that resolves the error.\n"
-                "Here is metadata about the interatomic potential that will be used: {metadata}.\n"
+                #"Here is metadata about the interatomic potential that will be used: {metadata}.\n"
                 "Note that all potential files are in the './' directory.\n"
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
                 "If a template for the input file is provided, you should adapt it appropriately to meet the task requirements.\n"
@@ -209,7 +206,6 @@ def _find_potentials(self, state: LammpsState) -> LammpsState:
         return {
             **state,
             "matches": list(matches),
-            "db_message": "\n".join(msg_lines),
             "idx": 0,
             "summaries": [],
             "full_texts": [],
@@ -273,17 +269,20 @@ def _choose(self, state: LammpsState) -> LammpsState:
         print(f"Chosen potential #{chosen_index}")
         print("Rationale for choosing this potential:")
         print(choice_dict["rationale"])
-        return {**state, "choice_json": choice, "chosen_index": chosen_index}
+
+        chosen_potential = state["matches"][chosen_index]
+        
+        return {**state, "chosen_potential": chosen_potential}
 
     def _author(self, state: LammpsState) -> LammpsState:
         print("First attempt at writing LAMMPS input file....")
-        match = state["matches"][state["chosen_index"]]
-        match.download_files(self.workspace)
-        text = state["full_texts"][state["chosen_index"]]
-        pair_info = match.pair_info()
+        #match = state["matches"][state["chosen_index"]]
+        state["chosen_potential"].download_files(self.workspace)
+        #text = state["full_texts"][state["chosen_index"]]
+        pair_info = state["chosen_potential"].pair_info()
         authored_json = self.author_chain.invoke({
             "simulation_task": state["simulation_task"],
-            "metadata": text,
+            #"metadata": text,
             "pair_info": pair_info,
             "template": state["template"],
         })
@@ -330,16 +329,16 @@ def _route_run(self, state: LammpsState) -> str:
         return "done_failed"
 
     def _fix(self, state: LammpsState) -> LammpsState:
-        match = state["matches"][state["chosen_index"]]
-        text = state["full_texts"][state["chosen_index"]]
-        pair_info = match.pair_info()
+        #match = state["matches"][state["chosen_index"]]
+        #text = state["full_texts"][state["chosen_index"]]
+        pair_info = state["chosen_potential"].pair_info().pair_info()
         err_blob = state.get("run_stdout")
 
         fixed_json = self.fix_chain.invoke({
             "simulation_task": state["simulation_task"],
             "input_script": state["input_script"],
             "err_message": err_blob,
-            "metadata": text,
+            #"metadata": text,
             "pair_info": pair_info,
             "template": state["template"],
         })

From 7f8dfb8cff468d42f2a271ad0f6a072ec7ed5df2 Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Mon, 20 Oct 2025 12:34:57 -0600
Subject: [PATCH 13/31] Added option for the user to provide the potential to
 the lammps_agent

---
 .../lammps_execute/EOS_of_Cu.py               | 26 +++++++++---
 src/ursa/agents/lammps_agent.py               | 40 +++++++++----------
 2 files changed, 39 insertions(+), 27 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index ef9dbb7b..450853b6 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -3,6 +3,15 @@
 
 from ursa.agents import ExecutionAgent, LammpsAgent
 
+try:
+    import atomman as am
+except Exception:
+    raise ImportError(
+        "This example requires the atomman dependency. "
+        "This can be installed using 'pip install ursa-ai[lammps]' or, "
+        "if working from a local installation, 'pip install -e .[lammps]' ."
+    )
+    
 model = "gpt-5"
 
 llm = ChatOpenAI(model=model, timeout=None, max_retries=2)
@@ -22,14 +31,19 @@
 with open("eos_template.txt", "r") as file:
     template = file.read()
 
-simulation_task = (
-    "Carry out a LAMMPS simulation of Cu to determine its equation of state."
-)
+simulation_task = ("Carry out a LAMMPS simulation of Cu to determine its equation of state.")
+
 elements = ["Cu"]
 
-final_lammps_state = wf.invoke(
-    simulation_task=simulation_task, elements=elements, template=template
-)
+db = am.library.Database(remote=True)
+matches = db.get_lammps_potentials(pair_style=["eam"], elements=elements)
+chosen_potential = matches[-1]
+
+final_lammps_state = wf.invoke(simulation_task=simulation_task, 
+                               elements=elements, 
+                               template=template, 
+                               chosen_potential=chosen_potential,
+                              )
 
 if final_lammps_state.get("run_returncode") == 0:
     print("\nNow handing things off to execution agent.....")
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index ea3ae127..5f28dbcf 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -22,6 +22,7 @@ class LammpsState(TypedDict, total=False):
     simulation_task: str
     elements: List[str]
     template: Optional[str]
+    chosen_potential: Optional[Any]
 
     matches: List[Any]
     idx: int
@@ -29,8 +30,6 @@ class LammpsState(TypedDict, total=False):
     full_texts: List[str]
     summaries_combined: str
     
-    chosen_potential: Any
-
     input_script: str
     run_returncode: Optional[int]
     run_stdout: str
@@ -114,7 +113,6 @@ def __init__(
         self.author_chain = (
             ChatPromptTemplate.from_template(
                 "Your task is to write a LAMMPS input file for this purpose: {simulation_task}.\n"
-                #"Here is metadata about the interatomic potential that will be used: {metadata}.\n"
                 "Note that all potential files are in the './' directory.\n"
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
                 "If a template for the input file is provided, you should adapt it appropriately to meet the task requirements.\n"
@@ -138,7 +136,6 @@ def __init__(
                 "However, when running the simulation, an error was raised.\n"
                 "Here is the full stdout message that includes the error message: {err_message}\n"
                 "Your task is to write a new input file that resolves the error.\n"
-                #"Here is metadata about the interatomic potential that will be used: {metadata}.\n"
                 "Note that all potential files are in the './' directory.\n"
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
                 "If a template for the input file is provided, you should adapt it appropriately to meet the task requirements.\n"
@@ -191,18 +188,17 @@ def _fetch_and_trim_text(self, url: str) -> str:
             pass
         return text
 
+
+    def _entry_router(self, state: LammpsState) -> dict:
+        return {}
+            
+            
     def _find_potentials(self, state: LammpsState) -> LammpsState:
         db = am.library.Database(remote=True)
         matches = db.get_lammps_potentials(
             pair_style=self.pair_styles, elements=state["elements"]
         )
-        msg_lines = []
-        if not list(matches):
-            msg_lines.append("No potentials found for this task in NIST.")
-        else:
-            msg_lines.append("Found these potentials in NIST:")
-            for rec in matches:
-                msg_lines.append(f"{rec.id}  {rec.pair_style}  {rec.symbols}")
+        
         return {
             **state,
             "matches": list(matches),
@@ -269,20 +265,15 @@ def _choose(self, state: LammpsState) -> LammpsState:
         print(f"Chosen potential #{chosen_index}")
         print("Rationale for choosing this potential:")
         print(choice_dict["rationale"])
-
         chosen_potential = state["matches"][chosen_index]
-        
         return {**state, "chosen_potential": chosen_potential}
 
     def _author(self, state: LammpsState) -> LammpsState:
         print("First attempt at writing LAMMPS input file....")
-        #match = state["matches"][state["chosen_index"]]
         state["chosen_potential"].download_files(self.workspace)
-        #text = state["full_texts"][state["chosen_index"]]
         pair_info = state["chosen_potential"].pair_info()
         authored_json = self.author_chain.invoke({
             "simulation_task": state["simulation_task"],
-            #"metadata": text,
             "pair_info": pair_info,
             "template": state["template"],
         })
@@ -329,8 +320,6 @@ def _route_run(self, state: LammpsState) -> str:
         return "done_failed"
 
     def _fix(self, state: LammpsState) -> LammpsState:
-        #match = state["matches"][state["chosen_index"]]
-        #text = state["full_texts"][state["chosen_index"]]
         pair_info = state["chosen_potential"].pair_info().pair_info()
         err_blob = state.get("run_stdout")
 
@@ -338,7 +327,6 @@ def _fix(self, state: LammpsState) -> LammpsState:
             "simulation_task": state["simulation_task"],
             "input_script": state["input_script"],
             "err_message": err_blob,
-            #"metadata": text,
             "pair_info": pair_info,
             "template": state["template"],
         })
@@ -354,7 +342,8 @@ def _fix(self, state: LammpsState) -> LammpsState:
 
     def _build_graph(self):
         g = StateGraph(LammpsState)
-
+        
+        self.add_node(g, self._entry_router)
         self.add_node(g, self._find_potentials)
         self.add_node(g, self._summarize_one)
         self.add_node(g, self._build_summaries)
@@ -363,8 +352,17 @@ def _build_graph(self):
         self.add_node(g, self._run_lammps)
         self.add_node(g, self._fix)
 
-        g.set_entry_point("_find_potentials")
+        g.set_entry_point("_entry_router")
 
+        g.add_conditional_edges(
+            "_entry_router",
+            lambda state: "user_choice" if state.get("chosen_potential") else "agent_choice",
+            {
+                "user_choice": "_author",
+                "agent_choice": "_find_potentials",
+            },
+        )
+        
         g.add_conditional_edges(
             "_find_potentials",
             self._should_summarize,

From 6d68b0c3903d9cd2a1f2fbd8f89f2d09aec98b86 Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Mon, 20 Oct 2025 16:53:42 -0600
Subject: [PATCH 14/31] Added option of using the lammps_agent as a tool to
 summarize and choose potentials only, i.e. without actually running LAMMPS

---
 .../lammps_execute/EOS_of_Cu.py               |  1 +
 .../lammps_execute/stiffness_tensor_of_hea.py |  1 +
 src/ursa/agents/lammps_agent.py               | 47 +++++++++++++++++--
 3 files changed, 44 insertions(+), 5 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index 450853b6..acd2d5aa 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -22,6 +22,7 @@
     llm=llm,
     max_potentials=2,
     max_fix_attempts=5,
+    find_potential_only=False,
     mpi_procs=8,
     workspace=workspace,
     lammps_cmd="lmp_mpi",
diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index 2b63568c..7b42c7e5 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -13,6 +13,7 @@
     llm=llm,
     max_potentials=5,
     max_fix_attempts=15,
+    find_potential_only=False,
     mpi_procs=8,
     workspace=workspace,
     lammps_cmd="lmp_mpi",
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 5f28dbcf..3d5597d0 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -44,6 +44,7 @@ def __init__(
         llm,
         max_potentials: int = 5,
         max_fix_attempts: int = 10,
+        find_potential_only: bool = False,
         mpi_procs: int = 8,
         workspace: str = "./workspace",
         lammps_cmd: str = "lmp_mpi",
@@ -58,6 +59,7 @@ def __init__(
             )
         self.max_potentials = max_potentials
         self.max_fix_attempts = max_fix_attempts
+        self.find_potential_only = find_potential_only
         self.mpi_procs = mpi_procs
         self.lammps_cmd = lammps_cmd
         self.mpirun_cmd = mpirun_cmd
@@ -69,13 +71,13 @@ def __init__(
             "eam/alloy",
             "eam/fs",
             "meam",
-            "adp",  # classical, HEA-relevant
-            "kim",  # OpenKIM models
+            "adp",  
+            "kim",  
             "snap",
             "quip",
             "mlip",
             "pace",
-            "nep",  # ML/ACE families (if available)
+            "nep",  
         ]
 
         self.workspace = workspace
@@ -190,6 +192,12 @@ def _fetch_and_trim_text(self, url: str) -> str:
 
 
     def _entry_router(self, state: LammpsState) -> dict:
+        if self.find_potential_only and state.get("chosen_potential"):
+            raise Exception("You cannot set find_potential_only=True and also specify your own potential!") 
+            
+        if not state.get("chosen_potential"):
+            self.potential_summaries_dir = os.path.join(self.workspace, "potential_summaries")
+            os.makedirs(self.potential_summaries_dir, exist_ok=True)
         return {}
             
             
@@ -240,6 +248,10 @@ def _summarize_one(self, state: LammpsState) -> LammpsState:
                 "simulation_task": state["simulation_task"],
             })
 
+        summary_file = os.path.join(self.potential_summaries_dir,"potential_"+str(i)+".txt")
+        with open(summary_file, "w") as f:
+            f.write(summary)
+            
         return {
             **state,
             "idx": i + 1,
@@ -262,12 +274,28 @@ def _choose(self, state: LammpsState) -> LammpsState:
         })
         choice_dict = self._safe_json_loads(choice)
         chosen_index = int(choice_dict["Chosen index"])
+        
         print(f"Chosen potential #{chosen_index}")
         print("Rationale for choosing this potential:")
         print(choice_dict["rationale"])
+        
         chosen_potential = state["matches"][chosen_index]
+
+        out_file = os.path.join(self.potential_summaries_dir,"Rationale.txt")
+        with open(out_file, "w") as f:
+            f.write(f"Chosen potential #{chosen_index}")
+            f.write("\n")
+            f.write("Rationale for choosing this potential:")
+            f.write("\n")
+            f.write(choice_dict["rationale"])
+            
         return {**state, "chosen_potential": chosen_potential}
 
+    def _route_after_summarization(self, state: LammpsState) -> str:
+        if self.find_potential_only:
+            return "Exit"
+        return "continue_author"
+
     def _author(self, state: LammpsState) -> LammpsState:
         print("First attempt at writing LAMMPS input file....")
         state["chosen_potential"].download_files(self.workspace)
@@ -320,7 +348,7 @@ def _route_run(self, state: LammpsState) -> str:
         return "done_failed"
 
     def _fix(self, state: LammpsState) -> LammpsState:
-        pair_info = state["chosen_potential"].pair_info().pair_info()
+        pair_info = state["chosen_potential"].pair_info()
         err_blob = state.get("run_stdout")
 
         fixed_json = self.fix_chain.invoke({
@@ -383,7 +411,16 @@ def _build_graph(self):
         )
 
         g.add_edge("_build_summaries", "_choose")
-        g.add_edge("_choose", "_author")
+        
+        g.add_conditional_edges(
+            "_choose",
+            self._route_after_summarization,
+            {
+                "continue_author": "_author",
+                "Exit": END,
+            },
+        )
+        
         g.add_edge("_author", "_run_lammps")
 
         g.add_conditional_edges(

From 16da86297a20563bacac2fc610a8a2d0e9ebc5a0 Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Mon, 27 Oct 2025 11:15:03 -0600
Subject: [PATCH 15/31] Linted and Formatted Code using ruff

---
 .../lammps_execute/EOS_of_Cu.py               | 27 +++++-----
 .../lammps_execute/stiffness_tensor_of_hea.py | 12 ++---
 src/ursa/agents/lammps_agent.py               | 52 ++++++++++---------
 3 files changed, 47 insertions(+), 44 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index acd2d5aa..228a38c6 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -11,7 +11,7 @@
         "This can be installed using 'pip install ursa-ai[lammps]' or, "
         "if working from a local installation, 'pip install -e .[lammps]' ."
     )
-    
+
 model = "gpt-5"
 
 llm = ChatOpenAI(model=model, timeout=None, max_retries=2)
@@ -32,7 +32,9 @@
 with open("eos_template.txt", "r") as file:
     template = file.read()
 
-simulation_task = ("Carry out a LAMMPS simulation of Cu to determine its equation of state.")
+simulation_task = (
+    "Carry out a LAMMPS simulation of Cu to determine its equation of state."
+)
 
 elements = ["Cu"]
 
@@ -40,11 +42,12 @@
 matches = db.get_lammps_potentials(pair_style=["eam"], elements=elements)
 chosen_potential = matches[-1]
 
-final_lammps_state = wf.invoke(simulation_task=simulation_task, 
-                               elements=elements, 
-                               template=template, 
-                               chosen_potential=chosen_potential,
-                              )
+final_lammps_state = wf.invoke(
+    simulation_task=simulation_task,
+    elements=elements,
+    template=template,
+    chosen_potential=chosen_potential,
+)
 
 if final_lammps_state.get("run_returncode") == 0:
     print("\nNow handing things off to execution agent.....")
@@ -58,12 +61,10 @@
     Summarize the contents of this file in a markdown document. Include a plot, if relevent.
     """
 
-    final_results = executor.invoke(
-        {
-            "messages": [HumanMessage(content=exe_plan)],
-            "workspace": workspace,
-        }
-    )
+    final_results = executor.invoke({
+        "messages": [HumanMessage(content=exe_plan)],
+        "workspace": workspace,
+    })
 
     for x in final_results["messages"]:
         print(x.content)
diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index 7b42c7e5..4f6739f6 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -42,13 +42,11 @@
     
     Summarize the contents of this file in a markdown document. Include a plot, if relevent.
     """
-    
-    final_results = executor.invoke(
-        {
-            "messages": [HumanMessage(content=exe_plan)],
-            "workspace": workspace,
-        }
-    )
+
+    final_results = executor.invoke({
+        "messages": [HumanMessage(content=exe_plan)],
+        "workspace": workspace,
+    })
 
     for x in final_results["messages"]:
         print(x.content)
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 3d5597d0..e4cbbade 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -29,7 +29,7 @@ class LammpsState(TypedDict, total=False):
     summaries: List[str]
     full_texts: List[str]
     summaries_combined: str
-    
+
     input_script: str
     run_returncode: Optional[int]
     run_stdout: str
@@ -71,13 +71,13 @@ def __init__(
             "eam/alloy",
             "eam/fs",
             "meam",
-            "adp",  
-            "kim",  
+            "adp",
+            "kim",
             "snap",
             "quip",
             "mlip",
             "pace",
-            "nep",  
+            "nep",
         ]
 
         self.workspace = workspace
@@ -190,23 +190,25 @@ def _fetch_and_trim_text(self, url: str) -> str:
             pass
         return text
 
-
     def _entry_router(self, state: LammpsState) -> dict:
         if self.find_potential_only and state.get("chosen_potential"):
-            raise Exception("You cannot set find_potential_only=True and also specify your own potential!") 
-            
+            raise Exception(
+                "You cannot set find_potential_only=True and also specify your own potential!"
+            )
+
         if not state.get("chosen_potential"):
-            self.potential_summaries_dir = os.path.join(self.workspace, "potential_summaries")
+            self.potential_summaries_dir = os.path.join(
+                self.workspace, "potential_summaries"
+            )
             os.makedirs(self.potential_summaries_dir, exist_ok=True)
         return {}
-            
-            
+
     def _find_potentials(self, state: LammpsState) -> LammpsState:
         db = am.library.Database(remote=True)
         matches = db.get_lammps_potentials(
             pair_style=self.pair_styles, elements=state["elements"]
         )
-        
+
         return {
             **state,
             "matches": list(matches),
@@ -248,10 +250,12 @@ def _summarize_one(self, state: LammpsState) -> LammpsState:
                 "simulation_task": state["simulation_task"],
             })
 
-        summary_file = os.path.join(self.potential_summaries_dir,"potential_"+str(i)+".txt")
+        summary_file = os.path.join(
+            self.potential_summaries_dir, "potential_" + str(i) + ".txt"
+        )
         with open(summary_file, "w") as f:
             f.write(summary)
-            
+
         return {
             **state,
             "idx": i + 1,
@@ -274,21 +278,21 @@ def _choose(self, state: LammpsState) -> LammpsState:
         })
         choice_dict = self._safe_json_loads(choice)
         chosen_index = int(choice_dict["Chosen index"])
-        
+
         print(f"Chosen potential #{chosen_index}")
         print("Rationale for choosing this potential:")
         print(choice_dict["rationale"])
-        
+
         chosen_potential = state["matches"][chosen_index]
 
-        out_file = os.path.join(self.potential_summaries_dir,"Rationale.txt")
+        out_file = os.path.join(self.potential_summaries_dir, "Rationale.txt")
         with open(out_file, "w") as f:
             f.write(f"Chosen potential #{chosen_index}")
             f.write("\n")
             f.write("Rationale for choosing this potential:")
             f.write("\n")
             f.write(choice_dict["rationale"])
-            
+
         return {**state, "chosen_potential": chosen_potential}
 
     def _route_after_summarization(self, state: LammpsState) -> str:
@@ -370,7 +374,7 @@ def _fix(self, state: LammpsState) -> LammpsState:
 
     def _build_graph(self):
         g = StateGraph(LammpsState)
-        
+
         self.add_node(g, self._entry_router)
         self.add_node(g, self._find_potentials)
         self.add_node(g, self._summarize_one)
@@ -384,13 +388,15 @@ def _build_graph(self):
 
         g.add_conditional_edges(
             "_entry_router",
-            lambda state: "user_choice" if state.get("chosen_potential") else "agent_choice",
+            lambda state: "user_choice"
+            if state.get("chosen_potential")
+            else "agent_choice",
             {
                 "user_choice": "_author",
                 "agent_choice": "_find_potentials",
             },
         )
-        
+
         g.add_conditional_edges(
             "_find_potentials",
             self._should_summarize,
@@ -411,7 +417,7 @@ def _build_graph(self):
         )
 
         g.add_edge("_build_summaries", "_choose")
-        
+
         g.add_conditional_edges(
             "_choose",
             self._route_after_summarization,
@@ -420,7 +426,7 @@ def _build_graph(self):
                 "Exit": END,
             },
         )
-        
+
         g.add_edge("_author", "_run_lammps")
 
         g.add_conditional_edges(
@@ -456,5 +462,3 @@ def _invoke(
             inputs = {**inputs, "template": "No template provided."}
 
         return self._action.invoke(inputs, config)
-
-        
\ No newline at end of file

From e5edf1b3ee293c6b5e219f6b64884305d3c9a899 Mon Sep 17 00:00:00 2001
From: Adela Habib <ahabib@lanl.gov>
Date: Mon, 1 Dec 2025 12:41:34 -0700
Subject: [PATCH 16/31] Added gpu run commands to the lammps agent

---
 .../lammps_execute/EOS_of_Cu.py               |  1 +
 src/ursa/agents/lammps_agent.py               | 60 ++++++++++++++-----
 2 files changed, 46 insertions(+), 15 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index 228a38c6..7c2d1ec8 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -23,6 +23,7 @@
     max_potentials=2,
     max_fix_attempts=5,
     find_potential_only=False,
+    ngpus= -1, # if -1  will not use gpus. Lammps executable must be installed with kokkos package for gpu usage 
     mpi_procs=8,
     workspace=workspace,
     lammps_cmd="lmp_mpi",
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 76366d66..0256c65d 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -46,6 +46,7 @@ def __init__(
         max_potentials: int = 5,
         max_fix_attempts: int = 10,
         find_potential_only: bool = False,
+        ngpus: int = -1,
         mpi_procs: int = 8,
         workspace: str = "./workspace",
         lammps_cmd: str = "lmp_mpi",
@@ -61,6 +62,7 @@ def __init__(
         self.max_potentials = max_potentials
         self.max_fix_attempts = max_fix_attempts
         self.find_potential_only = find_potential_only
+        self.ngpus = ngpus
         self.mpi_procs = mpi_procs
         self.lammps_cmd = lammps_cmd
         self.mpirun_cmd = mpirun_cmd
@@ -318,21 +320,49 @@ def _author(self, state: LammpsState) -> LammpsState:
 
     def _run_lammps(self, state: LammpsState) -> LammpsState:
         print("Running LAMMPS....")
-        result = subprocess.run(
-            [
-                self.mpirun_cmd,
-                "-np",
-                str(self.mpi_procs),
-                self.lammps_cmd,
-                "-in",
-                "in.lammps",
-            ],
-            cwd=self.workspace,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.PIPE,
-            text=True,
-            check=False,
-        )
+        if self.ngpus >= 0:
+            result = subprocess.run(
+                [
+                    self.mpirun_cmd,
+                    self.lammps_cmd,
+                    "-in",
+                    "in.lammps",
+                    "-k",
+                    "on",
+                    "g",
+                    str(self.ngpus),
+                    "-sf",
+                    "kk",
+                    "-pk",
+                    "kokkos",
+                    "neigh",
+                    "full",
+                    "newton",
+                    "on"
+                ],
+                cwd=self.workspace,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE,
+                text=True,
+                check=False,
+            )
+            print(result)
+        else:
+            result = subprocess.run(
+                [
+                    self.mpirun_cmd,
+                    "-np",
+                    str(self.mpi_procs),
+                    self.lammps_cmd,
+                    "-in",
+                    "in.lammps",
+                ],
+                cwd=self.workspace,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE,
+                text=True,
+                check=False,
+            )
         return {
             **state,
             "run_returncode": result.returncode,

From 67f54d1e1a6edc5fe7e8daa594d52014ce46e265 Mon Sep 17 00:00:00 2001
From: Adela Habib <ahabib@lanl.gov>
Date: Tue, 2 Dec 2025 16:26:46 -0700
Subject: [PATCH 17/31] Added structure data file given as an input into the
 agent.

---
 src/ursa/agents/lammps_agent.py | 60 +++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 0256c65d..771fbe14 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -46,6 +46,8 @@ def __init__(
         max_potentials: int = 5,
         max_fix_attempts: int = 10,
         find_potential_only: bool = False,
+        data_file: str = None,
+        data_max_lines: int = 50,
         ngpus: int = -1,
         mpi_procs: int = 8,
         workspace: str = "./workspace",
@@ -62,6 +64,8 @@ def __init__(
         self.max_potentials = max_potentials
         self.max_fix_attempts = max_fix_attempts
         self.find_potential_only = find_potential_only
+        self.data_file = data_file
+        self.data_max_lines = data_max_lines
         self.ngpus = ngpus
         self.mpi_procs = mpi_procs
         self.lammps_cmd = lammps_cmd
@@ -115,6 +119,7 @@ def __init__(
             | self.str_parser
         )
 
+        
         self.author_chain = (
             ChatPromptTemplate.from_template(
                 "Your task is to write a LAMMPS input file for this purpose: {simulation_task}.\n"
@@ -122,9 +127,13 @@ def __init__(
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
                 "If a template for the input file is provided, you should adapt it appropriately to meet the task requirements.\n"
                 "Template provided (if any): {template}\n"
+                "If a data file is provided, use it in the input script via the 'read_data' command.\n"
+                "Name of data file (if any): {data_file}\n"
+                "First few lines of data file (if any):\n{data_content}\n"
                 "Ensure that all output data is written only to the './log.lammps' file. Do not create any other output file.\n"
                 "To create the log, use only the 'log ./log.lammps' command. Do not use any other command like 'echo' or 'screen'.\n"
                 "Return your answer **only** as valid JSON, with no extra text or formatting.\n"
+                "IMPORTANT: Properly escape all special characters in the input_script string (use \\n for newlines, \\\\ for backslashes, etc.).\n"
                 "Use this exact schema:\n"
                 "{{\n"
                 '  "input_script": "<string>"\n'
@@ -145,9 +154,13 @@ def __init__(
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
                 "If a template for the input file is provided, you should adapt it appropriately to meet the task requirements.\n"
                 "Template provided (if any): {template}\n"
+                "If a data file is provided, use it in the input script via the 'read_data' command.\n"
+                "Name of data file (if any): {data_file}\n"
+                "First few lines of data file (if any):\n{data_content}\n"
                 "Ensure that all output data is written only to the './log.lammps' file. Do not create any other output file.\n"
                 "To create the log, use only the 'log ./log.lammps' command. Do not use any other command like 'echo' or 'screen'.\n"
                 "Return your answer **only** as valid JSON, with no extra text or formatting.\n"
+                "IMPORTANT: Properly escape all special characters in the input_script string (use \\n for newlines, \\\\ for backslashes, etc.).\n"
                 "Use this exact schema:\n"
                 "{{\n"
                 '  "input_script": "<string>"\n'
@@ -169,6 +182,33 @@ def _safe_json_loads(s: str) -> dict[str, Any]:
                 s = s[i + 1 :].strip()
         return json.loads(s)
 
+    def _read_and_trim_data_file(self, data_file_path: str) -> str:
+        """Read LAMMPS data file and trim to token limit for LLM context."""
+        if os.path.exists(data_file_path):
+            with open(data_file_path, 'r') as f:
+                content = f.read()
+            lines = content.splitlines()
+            if len(lines) > self.data_max_lines:
+                content = "\n".join(lines[:self.data_max_lines])
+                print(f"Data file trimmed from {len(lines)} to {self.data_max_lines} lines")
+            return content
+        else:       
+            return (f"Could not read data file.")
+        
+    def _copy_data_file(self, data_file_path: str) -> str:
+        """Copy data file to workspace and return new path."""
+        if not os.path.exists(data_file_path):
+            raise FileNotFoundError(f"Data file not found: {data_file_path}")
+    
+        filename = os.path.basename(data_file_path)
+        dest_path = os.path.join(self.workspace, filename)
+        with open(data_file_path, 'r') as src:
+            with open(dest_path, 'w') as dst:
+                dst.write(src.read())
+    
+        print(f"Data file copied to workspace: {dest_path}")
+        return dest_path
+
     def _fetch_and_trim_text(self, url: str) -> str:
         downloaded = trafilatura.fetch_url(url)
         if not downloaded:
@@ -198,6 +238,13 @@ def _entry_router(self, state: LammpsState) -> dict:
             raise Exception(
                 "You cannot set find_potential_only=True and also specify your own potential!"
             )
+        
+        if self.data_file:
+            try:
+                self._copy_data_file(self.data_file)
+                print(f"Data file copied to workspace.")
+            except Exception as e:
+                print(f"Warning: Could not process data file: {e}")
 
         if not state.get("chosen_potential"):
             self.potential_summaries_dir = os.path.join(
@@ -307,10 +354,17 @@ def _author(self, state: LammpsState) -> LammpsState:
         print("First attempt at writing LAMMPS input file....")
         state["chosen_potential"].download_files(self.workspace)
         pair_info = state["chosen_potential"].pair_info()
+        
+        data_content = ""
+        if self.data_file:
+            data_content = self._read_and_trim_data_file(self.data_file)
+
         authored_json = self.author_chain.invoke({
             "simulation_task": state["simulation_task"],
             "pair_info": pair_info,
             "template": state["template"],
+            "data_file": self.data_file,
+            "data_content": data_content,
         })
         script_dict = self._safe_json_loads(authored_json)
         input_script = script_dict["input_script"]
@@ -386,12 +440,18 @@ def _fix(self, state: LammpsState) -> LammpsState:
         pair_info = state["chosen_potential"].pair_info()
         err_blob = state.get("run_stdout")
 
+        data_content = ""
+        if self.data_file:
+            data_content = self._read_and_trim_data_file(self.data_file)
+
         fixed_json = self.fix_chain.invoke({
             "simulation_task": state["simulation_task"],
             "input_script": state["input_script"],
             "err_message": err_blob,
             "pair_info": pair_info,
             "template": state["template"],
+            "data_file": self.data_file,
+            "data_content": data_content,
         })
         script_dict = self._safe_json_loads(fixed_json)
         new_input = script_dict["input_script"]

From 363ff50a58ca6897cfbdb80bc1866dbcc2ce9bb5 Mon Sep 17 00:00:00 2001
From: Adela Habib <ahabib@lanl.gov>
Date: Fri, 12 Dec 2025 11:37:30 -0700
Subject: [PATCH 18/31] Added the capability to take user defined potential
 files

---
 .../lammps_execute/EOS_of_Cu.py               |  2 +-
 .../lammps_execute/stiffness_tensor_of_hea.py |  2 +-
 src/ursa/agents/lammps_agent.py               | 78 ++++++++++++++++---
 3 files changed, 68 insertions(+), 14 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index 7c2d1ec8..cc76c859 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -26,7 +26,7 @@
     ngpus= -1, # if -1  will not use gpus. Lammps executable must be installed with kokkos package for gpu usage 
     mpi_procs=8,
     workspace=workspace,
-    lammps_cmd="lmp_mpi",
+    lammps_cmd="/usr/projects/artimis/ahabib/envs/p311g-alf-packages/lammps/build-ml4chem/lmp",
     mpirun_cmd="mpirun",
 )
 
diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index 4f6739f6..970ccf40 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -16,7 +16,7 @@
     find_potential_only=False,
     mpi_procs=8,
     workspace=workspace,
-    lammps_cmd="lmp_mpi",
+    lammps_cmd="/usr/projects/artimis/ahabib/envs/p311g-alf-packages/lammps/build-ml4chem/lmp",
     mpirun_cmd="mpirun",
 )
 
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 771fbe14..369efdd0 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -43,6 +43,9 @@ class LammpsAgent(BaseAgent):
     def __init__(
         self,
         llm: BaseChatModel,
+        potential_files: Optional[list[str]] = None,
+        pair_style: Optional[str] = None,
+        pair_coeff: Optional[str] = None,
         max_potentials: int = 5,
         max_fix_attempts: int = 10,
         find_potential_only: bool = False,
@@ -61,6 +64,12 @@ def __init__(
             raise ImportError(
                 "LAMMPS agent requires the atomman and trafilatura dependencies. These can be installed using 'pip install ursa-ai[lammps]' or, if working from a local installation, 'pip install -e .[lammps]' ."
             )
+        
+        self.user_potential_files = potential_files
+        self.user_pair_style = pair_style
+        self.user_pair_coeff = pair_coeff
+        self.use_user_potential = (potential_files is not None and pair_style is not None and pair_coeff is not None)
+        
         self.max_potentials = max_potentials
         self.max_fix_attempts = max_fix_attempts
         self.find_potential_only = find_potential_only
@@ -202,13 +211,44 @@ def _copy_data_file(self, data_file_path: str) -> str:
     
         filename = os.path.basename(data_file_path)
         dest_path = os.path.join(self.workspace, filename)
-        with open(data_file_path, 'r') as src:
-            with open(dest_path, 'w') as dst:
-                dst.write(src.read())
-    
+        os.system(f"cp {data_file_path} {dest_path}")
         print(f"Data file copied to workspace: {dest_path}")
         return dest_path
 
+    def _copy_user_potential_files(self):
+        """Copy user-provided potential files to workspace."""
+        print("Copying user-provided potential files to workspace...")
+        for pot_file in self.user_potential_files:
+            if not os.path.exists(pot_file):
+                raise FileNotFoundError(f"Potential file not found: {pot_file}")
+            
+            filename = os.path.basename(pot_file)
+            dest_path = os.path.join(self.workspace, filename)
+            
+            try:
+                os.system(f"cp {pot_file} {dest_path}")
+                print(f"Potential files copied to workspace: {dest_path}")
+            except Exception as e:
+                print(f"Error copying {filename}: {e}")
+                raise
+
+    def _create_user_potential_wrapper(self, state: LammpsState) -> LammpsState:
+        """Create a wrapper object for user-provided potential to match atomman interface."""
+        self._copy_user_potential_files()
+        
+        # Create a simple object that mimics the atomman potential interface
+        class UserPotential:
+            def __init__(self, pair_style, pair_coeff):
+                self._pair_style = pair_style
+                self._pair_coeff = pair_coeff
+            
+            def pair_info(self):
+                return f"pair_style {self._pair_style}\npair_coeff {self._pair_coeff}"
+        
+        user_potential = UserPotential(self.user_pair_style, self.user_pair_coeff)
+        
+        return {**state, "chosen_potential": user_potential, "fix_attempts": 0}
+    
     def _fetch_and_trim_text(self, url: str) -> str:
         downloaded = trafilatura.fetch_url(url)
         if not downloaded:
@@ -234,6 +274,14 @@ def _fetch_and_trim_text(self, url: str) -> str:
         return text
 
     def _entry_router(self, state: LammpsState) -> dict:
+        # Check if using user-provided potential
+        if self.use_user_potential:
+            if self.find_potential_only:
+                raise Exception(
+                    "Cannot set find_potential_only=True when providing your own potential!"
+                )
+            print("Using user-provided potential files")
+
         if self.find_potential_only and state.get("chosen_potential"):
             raise Exception(
                 "You cannot set find_potential_only=True and also specify your own potential!"
@@ -242,7 +290,6 @@ def _entry_router(self, state: LammpsState) -> dict:
         if self.data_file:
             try:
                 self._copy_data_file(self.data_file)
-                print(f"Data file copied to workspace.")
             except Exception as e:
                 print(f"Warning: Could not process data file: {e}")
 
@@ -352,7 +399,9 @@ def _route_after_summarization(self, state: LammpsState) -> str:
 
     def _author(self, state: LammpsState) -> LammpsState:
         print("First attempt at writing LAMMPS input file....")
-        state["chosen_potential"].download_files(self.workspace)
+
+        if not self.use_user_potential:
+            state["chosen_potential"].download_files(self.workspace)
         pair_info = state["chosen_potential"].pair_info()
         
         data_content = ""
@@ -378,6 +427,8 @@ def _run_lammps(self, state: LammpsState) -> LammpsState:
             result = subprocess.run(
                 [
                     self.mpirun_cmd,
+                    "-np",
+                    str(self.mpi_procs),
                     self.lammps_cmd,
                     "-in",
                     "in.lammps",
@@ -390,9 +441,9 @@ def _run_lammps(self, state: LammpsState) -> LammpsState:
                     "-pk",
                     "kokkos",
                     "neigh",
-                    "full",
+                    "half",
                     "newton",
-                    "on"
+                    "on",
                 ],
                 cwd=self.workspace,
                 stdout=subprocess.PIPE,
@@ -471,6 +522,7 @@ def _build_graph(self):
         self.add_node(g, self._summarize_one)
         self.add_node(g, self._build_summaries)
         self.add_node(g, self._choose)
+        self.add_node(g, self._create_user_potential_wrapper)
         self.add_node(g, self._author)
         self.add_node(g, self._run_lammps)
         self.add_node(g, self._fix)
@@ -479,10 +531,11 @@ def _build_graph(self):
 
         g.add_conditional_edges(
             "_entry_router",
-            lambda state: "user_choice"
-            if state.get("chosen_potential")
-            else "agent_choice",
-            {
+            lambda state: "user_potential" if self.use_user_potential else ( 
+                "user_choice" if state.get("chosen_potential") else "agent_choice"
+            ),
+            {   
+                "user_potential": "_create_user_potential_wrapper",
                 "user_choice": "_author",
                 "agent_choice": "_find_potentials",
             },
@@ -518,6 +571,7 @@ def _build_graph(self):
             },
         )
 
+        g.add_edge("_create_user_potential_wrapper", "_author")
         g.add_edge("_author", "_run_lammps")
 
         g.add_conditional_edges(

From 0879820c7a05e9ac8657bc593c61efb86be20d75 Mon Sep 17 00:00:00 2001
From: Adela Habib <ahabib@lanl.gov>
Date: Fri, 12 Dec 2025 11:39:24 -0700
Subject: [PATCH 19/31] Minor changes to the example files, reverted lammps
 executable command back to generic lmp_mpi

---
 examples/two_agent_examples/lammps_execute/EOS_of_Cu.py         | 2 +-
 .../lammps_execute/stiffness_tensor_of_hea.py                   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index cc76c859..7c2d1ec8 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -26,7 +26,7 @@
     ngpus= -1, # if -1  will not use gpus. Lammps executable must be installed with kokkos package for gpu usage 
     mpi_procs=8,
     workspace=workspace,
-    lammps_cmd="/usr/projects/artimis/ahabib/envs/p311g-alf-packages/lammps/build-ml4chem/lmp",
+    lammps_cmd="lmp_mpi",
     mpirun_cmd="mpirun",
 )
 
diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index 970ccf40..4f6739f6 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -16,7 +16,7 @@
     find_potential_only=False,
     mpi_procs=8,
     workspace=workspace,
-    lammps_cmd="/usr/projects/artimis/ahabib/envs/p311g-alf-packages/lammps/build-ml4chem/lmp",
+    lammps_cmd="lmp_mpi",
     mpirun_cmd="mpirun",
 )
 

From 4819fd4a715cd55886a96396c4efb469bacbbb13 Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram - 365493 <rsomasundaram@darwin-fe2.lanl.gov>
Date: Tue, 13 Jan 2026 12:41:12 -0700
Subject: [PATCH 20/31] Minor update to lammps agent prompt

---
 src/ursa/agents/lammps_agent.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 369efdd0..6806e96b 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -139,8 +139,8 @@ def __init__(
                 "If a data file is provided, use it in the input script via the 'read_data' command.\n"
                 "Name of data file (if any): {data_file}\n"
                 "First few lines of data file (if any):\n{data_content}\n"
-                "Ensure that all output data is written only to the './log.lammps' file. Do not create any other output file.\n"
-                "To create the log, use only the 'log ./log.lammps' command. Do not use any other command like 'echo' or 'screen'.\n"
+                "Ensure that all logs are recorded in a './log.lammps' file.\n"
+                "To create the log file, use may use the 'log ./log.lammps' command. \n"
                 "Return your answer **only** as valid JSON, with no extra text or formatting.\n"
                 "IMPORTANT: Properly escape all special characters in the input_script string (use \\n for newlines, \\\\ for backslashes, etc.).\n"
                 "Use this exact schema:\n"
@@ -166,8 +166,8 @@ def __init__(
                 "If a data file is provided, use it in the input script via the 'read_data' command.\n"
                 "Name of data file (if any): {data_file}\n"
                 "First few lines of data file (if any):\n{data_content}\n"
-                "Ensure that all output data is written only to the './log.lammps' file. Do not create any other output file.\n"
-                "To create the log, use only the 'log ./log.lammps' command. Do not use any other command like 'echo' or 'screen'.\n"
+                "Ensure that all logs are recorded in a './log.lammps' file.\n"
+                "To create the log file, use may use the 'log ./log.lammps' command. \n"
                 "Return your answer **only** as valid JSON, with no extra text or formatting.\n"
                 "IMPORTANT: Properly escape all special characters in the input_script string (use \\n for newlines, \\\\ for backslashes, etc.).\n"
                 "Use this exact schema:\n"

From a0dfbb8d6aea64671a02246f1f10ff1a97880f9d Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram - 365493 <rsomasundaram@darwin-fe1.lanl.gov>
Date: Thu, 15 Jan 2026 14:51:02 -0700
Subject: [PATCH 21/31] Full error history passed to the _fix node, instead of
 just the latest error

---
 src/ursa/agents/lammps_agent.py | 44 ++++++++++++++++++++++++++++++---
 1 file changed, 40 insertions(+), 4 deletions(-)

diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 6806e96b..62f495d0 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -35,7 +35,8 @@ class LammpsState(TypedDict, total=False):
     run_returncode: Optional[int]
     run_stdout: str
     run_stderr: str
-
+    run_history: list[dict[str, Any]]  
+    
     fix_attempts: int
 
 
@@ -157,7 +158,8 @@ def __init__(
                 "You are part of a larger scientific workflow whose purpose is to accomplish this task: {simulation_task}\n"
                 "For this purpose, this input file for LAMMPS was written: {input_script}\n"
                 "However, when running the simulation, an error was raised.\n"
-                "Here is the full stdout message that includes the error message: {err_message}\n"
+                "Here is the run history across attempts (each includes the input script and its stdout/stderr):\n{err_message}\n"
+                "Use the history to identify what changed between attempts and avoid repeating failed approaches.\n"
                 "Your task is to write a new input file that resolves the error.\n"
                 "Note that all potential files are in the './' directory.\n"
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
@@ -247,7 +249,7 @@ def pair_info(self):
         
         user_potential = UserPotential(self.user_pair_style, self.user_pair_coeff)
         
-        return {**state, "chosen_potential": user_potential, "fix_attempts": 0}
+        return {**state, "chosen_potential": user_potential, "fix_attempts": 0,"run_history": []}
     
     def _fetch_and_trim_text(self, url: str) -> str:
         downloaded = trafilatura.fetch_url(url)
@@ -313,6 +315,7 @@ def _find_potentials(self, state: LammpsState) -> LammpsState:
             "summaries": [],
             "full_texts": [],
             "fix_attempts": 0,
+            "run_history": [],
         }
 
     def _should_summarize(self, state: LammpsState) -> str:
@@ -468,13 +471,26 @@ def _run_lammps(self, state: LammpsState) -> LammpsState:
                 text=True,
                 check=False,
             )
+
+
+        hist = list(state.get("run_history", []))
+        hist.append({
+            "attempt": state.get("fix_attempts", 0),
+            "input_script": state.get("input_script", ""),
+            "returncode": result.returncode,
+            "stdout": result.stdout,
+            "stderr": result.stderr,
+        })
+
         return {
             **state,
             "run_returncode": result.returncode,
             "run_stdout": result.stdout,
             "run_stderr": result.stderr,
+            "run_history": hist,
         }
 
+
     def _route_run(self, state: LammpsState) -> str:
         rc = state.get("run_returncode", 0)
         attempts = state.get("fix_attempts", 0)
@@ -489,8 +505,28 @@ def _route_run(self, state: LammpsState) -> str:
 
     def _fix(self, state: LammpsState) -> LammpsState:
         pair_info = state["chosen_potential"].pair_info()
-        err_blob = state.get("run_stdout")
 
+        hist = state.get("run_history", [])
+        if not hist:
+            hist = [{
+                "attempt": state.get("fix_attempts", 0),
+                "input_script": state.get("input_script", ""),
+                "returncode": state.get("run_returncode"),
+                "stdout": state.get("run_stdout", ""),
+                "stderr": state.get("run_stderr", ""),
+            }]
+        
+        parts = []
+        for h in hist:
+            parts.append(
+                "=== Attempt {attempt} | returncode={returncode} ===\n"
+                "--- input_script ---\n{input_script}\n"
+                "--- stdout ---\n{stdout}\n"
+                "--- stderr ---\n{stderr}\n"
+            .format(**h)
+            )
+        err_blob = "\n".join(parts)
+        
         data_content = ""
         if self.data_file:
             data_content = self._read_and_trim_data_file(self.data_file)

From b14c05099550268e1be54277d1e2d0ee076f311b Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram - 365493 <rsomasundaram@darwin-fe3.lanl.gov>
Date: Thu, 15 Jan 2026 16:30:35 -0700
Subject: [PATCH 22/31] Used Rich to improve terminal outputs

---
 src/ursa/agents/lammps_agent.py | 88 ++++++++++++++++++++++++++-------
 1 file changed, 71 insertions(+), 17 deletions(-)

diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 62f495d0..97ce740f 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -9,6 +9,16 @@
 from langchain_core.prompts import ChatPromptTemplate
 from langgraph.graph import END, StateGraph
 
+from rich.console import Console
+from rich.panel import Panel
+from rich.text import Text
+from rich.syntax import Syntax
+from rich.rule import Rule
+from rich.table import Table
+from rich import box
+from rich.console import Group
+import difflib
+
 from .base import BaseAgent
 
 working = True
@@ -83,6 +93,8 @@ def __init__(
         self.tiktoken_model = tiktoken_model
         self.max_tokens = max_tokens
 
+        self.console = Console()
+        
         self.pair_styles = [
             "eam",
             "eam/alloy",
@@ -156,11 +168,10 @@ def __init__(
         self.fix_chain = (
             ChatPromptTemplate.from_template(
                 "You are part of a larger scientific workflow whose purpose is to accomplish this task: {simulation_task}\n"
-                "For this purpose, this input file for LAMMPS was written: {input_script}\n"
-                "However, when running the simulation, an error was raised.\n"
-                "Here is the run history across attempts (each includes the input script and its stdout/stderr):\n{err_message}\n"
+                "Multiple attempts at writing and running a LAMMPS input file have been made.\n"
+                "Here is the run history across attempts (each includes the input script and its stdout/stderr):{err_message}\n"
                 "Use the history to identify what changed between attempts and avoid repeating failed approaches.\n"
-                "Your task is to write a new input file that resolves the error.\n"
+                "Your task is to write a new input file that resolves the latest error.\n"
                 "Note that all potential files are in the './' directory.\n"
                 "Here is some information about the pair_style and pair_coeff that might be useful in writing the input file: {pair_info}.\n"
                 "If a template for the input file is provided, you should adapt it appropriately to meet the task requirements.\n"
@@ -183,6 +194,32 @@ def __init__(
 
         self._action = self._build_graph()
 
+    def _section(self, title: str):
+        self.console.print(Rule(f"[bold cyan]{title}[/bold cyan]"))
+    
+    def _panel(self, title: str, body: str, style: str = "cyan"):
+        self.console.print(Panel(body, title=f"[bold]{title}[/bold]", border_style=style))
+    
+    def _code_panel(self, title: str, code: str, language: str = "bash", style: str = "magenta"):
+        syn = Syntax(code, language, theme="monokai", line_numbers=True, word_wrap=True)
+        self.console.print(Panel(syn, title=f"[bold]{title}[/bold]", border_style=style))
+
+    def _diff_panel(self, old: str, new: str, title: str = "LAMMPS input diff"):
+        diff = "\n".join(
+            difflib.unified_diff(
+                old.splitlines(),
+                new.splitlines(),
+                fromfile="in.lammps (before)",
+                tofile="in.lammps (after)",
+                lineterm="",
+            )
+        )
+        if not diff.strip():
+            diff = "(no changes)"
+        syn = Syntax(diff, "diff", theme="monokai", line_numbers=False, word_wrap=True)
+        self.console.print(Panel(syn, title=f"[bold]{title}[/bold]", border_style="cyan"))
+
+
     @staticmethod
     def _safe_json_loads(s: str) -> dict[str, Any]:
         s = s.strip()
@@ -330,7 +367,7 @@ def _should_summarize(self, state: LammpsState) -> str:
 
     def _summarize_one(self, state: LammpsState) -> LammpsState:
         i = state["idx"]
-        print(f"Summarizing potential #{i}")
+        self._section(f"Summarizing potential #{i}")
         match = state["matches"][i]
         md = match.metadata()
 
@@ -371,20 +408,22 @@ def _build_summaries(self, state: LammpsState) -> LammpsState:
         return {**state, "summaries_combined": "".join(parts)}
 
     def _choose(self, state: LammpsState) -> LammpsState:
-        print("Choosing one potential for this task...")
+        self._section("Choosing potential")
         choice = self.choose_chain.invoke({
             "summaries_combined": state["summaries_combined"],
             "simulation_task": state["simulation_task"],
         })
         choice_dict = self._safe_json_loads(choice)
         chosen_index = int(choice_dict["Chosen index"])
-
-        print(f"Chosen potential #{chosen_index}")
-        print("Rationale for choosing this potential:")
-        print(choice_dict["rationale"])
-
+        
         chosen_potential = state["matches"][chosen_index]
 
+        self._panel(
+            "Chosen Potential",
+            f"[bold]Index:[/bold] {chosen_index}\n[bold]ID:[/bold] {chosen_potential.id}\n\n[bold]Rationale:[/bold]\n{choice_dict['rationale']}",
+            style="green",
+        )
+        
         out_file = os.path.join(self.potential_summaries_dir, "Rationale.txt")
         with open(out_file, "w") as f:
             f.write(f"Chosen potential #{chosen_index}")
@@ -401,7 +440,7 @@ def _route_after_summarization(self, state: LammpsState) -> str:
         return "continue_author"
 
     def _author(self, state: LammpsState) -> LammpsState:
-        print("First attempt at writing LAMMPS input file....")
+        self._section("First attempt at writing LAMMPS input file")
 
         if not self.use_user_potential:
             state["chosen_potential"].download_files(self.workspace)
@@ -422,10 +461,15 @@ def _author(self, state: LammpsState) -> LammpsState:
         input_script = script_dict["input_script"]
         with open(os.path.join(self.workspace, "in.lammps"), "w") as f:
             f.write(input_script)
+
+        self._section("Authored LAMMPS input")
+        self._code_panel("in.lammps", input_script, language="bash", style="magenta")
+                    
         return {**state, "input_script": input_script}
 
     def _run_lammps(self, state: LammpsState) -> LammpsState:
-        print("Running LAMMPS....")
+        self._section("Running LAMMPS")
+        
         if self.ngpus >= 0:
             result = subprocess.run(
                 [
@@ -472,7 +516,13 @@ def _run_lammps(self, state: LammpsState) -> LammpsState:
                 check=False,
             )
 
+        status_style = "green" if result.returncode == 0 else "red"
+        self._panel("Run Result", f"returncode = {result.returncode}", style=status_style)
 
+        if result.returncode != 0:
+            err_view = (result.stderr.strip() + "\n" + result.stdout.strip()).strip() or "(no output captured)"
+            self._panel("Run error/output", err_view[-6000:], style="red") 
+        
         hist = list(state.get("run_history", []))
         hist.append({
             "attempt": state.get("fix_attempts", 0),
@@ -495,12 +545,12 @@ def _route_run(self, state: LammpsState) -> str:
         rc = state.get("run_returncode", 0)
         attempts = state.get("fix_attempts", 0)
         if rc == 0:
-            print("LAMMPS run successful! Exiting...")
+            self._section("LAMMPS run successful! Exiting...")
             return "done_success"
         if attempts < self.max_fix_attempts:
-            print("LAMMPS run Failed. Attempting to rewrite input file...")
+            self._section("LAMMPS run Failed. Attempting to rewrite input file...")
             return "need_fix"
-        print("LAMMPS run Failed and maximum fix attempts reached. Exiting...")
+        self._section("LAMMPS run Failed and maximum fix attempts reached. Exiting..")
         return "done_failed"
 
     def _fix(self, state: LammpsState) -> LammpsState:
@@ -533,7 +583,6 @@ def _fix(self, state: LammpsState) -> LammpsState:
 
         fixed_json = self.fix_chain.invoke({
             "simulation_task": state["simulation_task"],
-            "input_script": state["input_script"],
             "err_message": err_blob,
             "pair_info": pair_info,
             "template": state["template"],
@@ -541,9 +590,14 @@ def _fix(self, state: LammpsState) -> LammpsState:
             "data_content": data_content,
         })
         script_dict = self._safe_json_loads(fixed_json)
+        
         new_input = script_dict["input_script"]
+        old_input = state["input_script"]
+        self._diff_panel(old_input, new_input)
+                
         with open(os.path.join(self.workspace, "in.lammps"), "w") as f:
             f.write(new_input)
+            
         return {
             **state,
             "input_script": new_input,

From 1ca41bf25883443bc82bb2f85bd5f4ac962241d5 Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Fri, 16 Jan 2026 12:50:18 -0700
Subject: [PATCH 23/31] Added documentation for LAMMPS Agent

---
 docs/lammps_agent.md | 191 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 191 insertions(+)
 create mode 100644 docs/lammps_agent.md

diff --git a/docs/lammps_agent.md b/docs/lammps_agent.md
new file mode 100644
index 00000000..f9138731
--- /dev/null
+++ b/docs/lammps_agent.md
@@ -0,0 +1,191 @@
+# LammpsAgent Documentation
+
+`LammpsAgent` is a class that helps set up and run a LAMMPS simulation workflow. At the highest level, it can:
+
+- discover candidate interatomic potentials from the NIST database for a set of elements,
+- summarize and choose a potential for the simulation task at hand,
+- author a LAMMPS input script using the chosen potential (and an optional template / data file),
+- execute LAMMPS via MPI (CPU or Kokkos GPU),
+- iteratively “fix” the input script on failures by using run history until success or a max attempt limit.
+
+The agent writes the outputs into a local `workspace` directory and uses rich console panels to display progress, choices, diffs, and errors.
+
+---
+
+## 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.  
+
+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`.  
+
+---
+
+## Basic Usage
+
+```python
+from ursa.agents import LammpsAgent
+from langchain_openai import ChatOpenAI
+
+agent = LammpsAgent(llm = ChatOpenAI(model='gpt-5'))
+
+result = agent.invoke({
+    "simulation_task": "Carry out a LAMMPS simulation of Cu to determine its equation of state.",
+    "elements": ["Cu"],
+    "template": "No template provided."  #Template for the input file
+})
+```
+
+For more advanced usage see examples here: `ursa/examples/two_agent_examples/lammps_execute/`.
+
+---
+
+## High-level flow
+
+The agent compiles a `StateGraph(LammpsState)` with this logic:
+
+### Entry routing
+Chooses one of three paths:
+
+1. **User-provided potential**:
+   - This path is chosen when the user provides a specific potential file, along with the `pair_style`/`pair_coeff` information required to generate the input script
+   - In this case the autonomous potential search/selection by the agent is skipped
+   - The provided potential file is copied to `workspace`
+
+2. **User-chosen potential already in state** (`state["chosen_potential"]` exists):
+   - This is similar to the above path, but the user selects a potential from the `atomman` database and initializes the state with this entry before invoking the agent
+   - This path also skips the potential search/selection and goes straight to authoring a LAMMPS input script for the user-chosen potential
+
+3. **Agent-selected potential**:
+   - Agent queries NIST (via atomman) for potentials matching the requested elements
+   - Summarizes NIST's data on each potential (up to `max_potentials`) with regards to the applicability of the potential for the given `simulation task`
+   - Ultimately picks one potential 
+
+If a `data_file` is provided to the agent, the entry router attempts to copy it into the workspace.
+
+### Potential search & selection (agent-selected path)
+- `_find_potentials`: queries `atomman.library.Database(remote=True)` for potentials matching:
+  - `elements` from state
+  - supported `pair_styles` list (see `self.pair_styles`)
+- `_summarize_one`: for each candidate potential:
+  - extracts data on potential from  NIST
+  - trims extracted text to a token budget using `tiktoken`
+  - summarizes usefulness for the requested `simulation_task`
+  - writes summary to `workspace/potential_summaries/potential_<i>.txt`
+- `_build_summaries`: builds a combined string of summaries for selection
+- `_choose`: the agent selects the final potential to be used and the rationale for choosing it
+  - writes rationale to `workspace/potential_summaries/Rationale.txt`
+  - stores `chosen_potential` in state
+
+If `find_potential_only=True`, the graph exits after choosing the potential (or finding no matches).
+
+### Author input
+- Downloads potential files into `workspace` (only if not user-provided)
+- Gets `pair_info` via `chosen_potential.pair_info()`
+- Optionally includes:
+  - `template` from state for the LAMMPS input script
+  - `data_file` (usually for the atomic structure that can be included in the input script) 
+- The agent authors the input script: `{ "input_script": "<string>" }`
+- Writes `workspace/in.lammps`
+- Enforces that logs should go to `./log.lammps` 
+
+### Run LAMMPS 
+
+Runs `<mpirun_cmd>` with `-np <mpi_procs>` in `workspace`:
+
+Allowed options for `<mpirun_cmd>` are `mpirun` and `mpiexec` (see also Parameters section below).
+
+For example, LAMMPS run commands executed by the agent look like: 
+
+- **CPU mode** (default, when `ngpus < 0`):
+  - `mpirun -np <mpi_procs> <lammps_cmd> -in in.lammps`
+
+- **GPU/Kokkos mode** (when `ngpus >= 0`):
+  - `mpirun -np <mpi_procs> <lammps_cmd> -in in.lammps -k on g <ngpus> -sf kk -pk kokkos neigh half newton on`
+
+Note that the running under GPU mode is preliminary.
+
+The agent captures `stdout`, `stderr`, and `returncode`, and appends an entry to `run_history`.
+
+### Fix loop 
+If the run fails:
+- formats the entire `run_history` (scripts + stdout/stderr) into an error blob
+- the agent produces a new `input_script` 
+- prints a unified diff between old and new scripts
+- overwrites `workspace/in.lammps`
+- increments `fix_attempts`
+- reruns LAMMPS
+
+Stops when:
+- run succeeds (`returncode == 0`), or
+- `fix_attempts >= max_fix_attempts`
+
+---
+
+## State model (`LammpsState`)
+
+The graph state is a `TypedDict` containing (key fields):
+
+- **Inputs / problem definition**
+  - `simulation_task: str` — natural language description of what to simulate
+  - `elements: list[str]` — chemical symbols used to identify candidate potentials
+  - `template: Optional[str]` — optional LAMMPS input template to adapt
+  - `chosen_potential: Optional[Any]` — selected potential object (user-chosen)
+
+- **Potential selection internals**
+  - `matches: list[Any]` — candidate potentials from atomman
+  - `idx: int` — index used for summarization loop
+  - `summaries: list[str]` — a brief summary of each potential
+  - `full_texts: list[str]` — the data/metadata on the potential from NIST (capped at `max_tokens`)
+  - `summaries_combined: str` - a single string with the summaries of all the considered potentials
+
+- **Run artifacts**
+  - `input_script: str` — current LAMMPS input text written to `in.lammps`
+  - `run_returncode: Optional[int]` - generally, `returncode = 0` indicates a successful simulation run
+  - `run_stdout: str` - the stdout from the LAMMPS execution
+  - `run_stderr: str` - the stderr from the LAMMPS execution 
+  - `run_history: list[dict[str, Any]]` — attempt-by-attempt record
+  - `fix_attempts: int` - the number of times the agent has attempted to fix the LAMMPS input script
+
+---
+
+## Parameters
+
+Key parameters you can tune:
+
+### Potential selection
+- `potential_files`, `pair_style`, `pair_coeff`: if all provided, the agent uses the user's potential files and skips search
+- `max_potentials` (default `5`): max number of candidate potentials to summarize before choosing one
+- `find_potential_only` (default `False`): exit after selecting a potential (no input LAMMPS input writing/running)
+
+### Fix loop
+- `max_fix_attempts` (default `10`): maximum number of input rewrite attempts after failures
+
+### Data file support
+- `data_file` (default `None`): path to a LAMMPS data file; the agent copies it to `workspace`
+- `data_max_lines` (default `50`): number of lines from data included in the agent's prompt
+
+### Execution
+- `workspace` (default `./workspace`): where `in.lammps`, potentials, and summaries are written
+- `mpi_procs` (default `8`): number of mpi processes for LAMMPS run
+- `ngpus` (default `-1`): set `>= 0` to enable Kokkos GPU flags
+- `lammps_cmd` (default `lmp_mpi`): the name of the LAMMPS executable to launch
+- `mpirun_cmd` (default `mpirun`): currently available options are `mpirun` and `mpiexec`. Other options such as `srun` will be added soon
+
+### LLM / context trimming
+- `tiktoken_model` (default `gpt-5-mini`): tokenizer model name used to trim fetched potential metadata text
+- `max_tokens` (default `200000`): token cap for extracted metadata text
+
+---
+
+## Files and directories created
+
+Inside `workspace/`:
+
+- `in.lammps` — generated/updated input script
+- `log.lammps` — expected LAMMPS log output (the LLM is instructed to create it)
+- `potential_summaries/`
+  - `potential_<i>.txt` — per-potential LLM summaries
+  - `Rationale.txt` — rationale for the selected potential
+- downloaded potential files (from atomman or copied from user paths)
+- copied `data_file` (if provided)
+

From 12b7a9c76ae04b9534f040e6503dd36626f87820 Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Fri, 16 Jan 2026 13:31:35 -0700
Subject: [PATCH 24/31] Linted and Formatted code with Ruff

---
 .../lammps_execute/EOS_of_Cu.py               |   2 +-
 src/ursa/agents/lammps_agent.py               | 187 +++++++++++-------
 2 files changed, 114 insertions(+), 75 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index 7c2d1ec8..95aadb5e 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -23,7 +23,7 @@
     max_potentials=2,
     max_fix_attempts=5,
     find_potential_only=False,
-    ngpus= -1, # if -1  will not use gpus. Lammps executable must be installed with kokkos package for gpu usage 
+    ngpus=-1,  # if -1  will not use gpus. Lammps executable must be installed with kokkos package for gpu usage
     mpi_procs=8,
     workspace=workspace,
     lammps_cmd="lmp_mpi",
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index ce32349c..d9bb52b6 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -1,3 +1,4 @@
+import difflib
 import json
 import os
 import subprocess
@@ -8,16 +9,10 @@
 from langchain_core.output_parsers import StrOutputParser
 from langchain_core.prompts import ChatPromptTemplate
 from langgraph.graph import END
-
 from rich.console import Console
 from rich.panel import Panel
-from rich.text import Text
-from rich.syntax import Syntax
 from rich.rule import Rule
-from rich.table import Table
-from rich import box
-from rich.console import Group
-import difflib
+from rich.syntax import Syntax
 
 from .base import BaseAgent
 
@@ -45,8 +40,8 @@ class LammpsState(TypedDict, total=False):
     run_returncode: Optional[int]
     run_stdout: str
     run_stderr: str
-    run_history: list[dict[str, Any]]  
-    
+    run_history: list[dict[str, Any]]
+
     fix_attempts: int
 
 
@@ -79,12 +74,16 @@ def __init__(
             )
 
         super().__init__(llm, **kwargs)
-        
+
         self.user_potential_files = potential_files
         self.user_pair_style = pair_style
         self.user_pair_coeff = pair_coeff
-        self.use_user_potential = (potential_files is not None and pair_style is not None and pair_coeff is not None)
-        
+        self.use_user_potential = (
+            potential_files is not None
+            and pair_style is not None
+            and pair_coeff is not None
+        )
+
         self.max_potentials = max_potentials
         self.max_fix_attempts = max_fix_attempts
         self.find_potential_only = find_potential_only
@@ -98,7 +97,7 @@ def __init__(
         self.max_tokens = max_tokens
 
         self.console = Console()
-        
+
         self.pair_styles = [
             "eam",
             "eam/alloy",
@@ -143,7 +142,6 @@ def __init__(
             | self.str_parser
         )
 
-        
         self.author_chain = (
             ChatPromptTemplate.from_template(
                 "Your task is to write a LAMMPS input file for this purpose: {simulation_task}.\n"
@@ -193,18 +191,30 @@ def __init__(
             | self.llm
             | self.str_parser
         )
-        
+
         self._action = self._build_graph()
 
     def _section(self, title: str):
         self.console.print(Rule(f"[bold cyan]{title}[/bold cyan]"))
-    
+
     def _panel(self, title: str, body: str, style: str = "cyan"):
-        self.console.print(Panel(body, title=f"[bold]{title}[/bold]", border_style=style))
-    
-    def _code_panel(self, title: str, code: str, language: str = "bash", style: str = "magenta"):
-        syn = Syntax(code, language, theme="monokai", line_numbers=True, word_wrap=True)
-        self.console.print(Panel(syn, title=f"[bold]{title}[/bold]", border_style=style))
+        self.console.print(
+            Panel(body, title=f"[bold]{title}[/bold]", border_style=style)
+        )
+
+    def _code_panel(
+        self,
+        title: str,
+        code: str,
+        language: str = "bash",
+        style: str = "magenta",
+    ):
+        syn = Syntax(
+            code, language, theme="monokai", line_numbers=True, word_wrap=True
+        )
+        self.console.print(
+            Panel(syn, title=f"[bold]{title}[/bold]", border_style=style)
+        )
 
     def _diff_panel(self, old: str, new: str, title: str = "LAMMPS input diff"):
         diff = "\n".join(
@@ -218,9 +228,13 @@ def _diff_panel(self, old: str, new: str, title: str = "LAMMPS input diff"):
         )
         if not diff.strip():
             diff = "(no changes)"
-        syn = Syntax(diff, "diff", theme="monokai", line_numbers=False, word_wrap=True)
-        self.console.print(Panel(syn, title=f"[bold]{title}[/bold]", border_style="cyan"))
-        
+        syn = Syntax(
+            diff, "diff", theme="monokai", line_numbers=False, word_wrap=True
+        )
+        self.console.print(
+            Panel(syn, title=f"[bold]{title}[/bold]", border_style="cyan")
+        )
+
     @staticmethod
     def _safe_json_loads(s: str) -> dict[str, Any]:
         s = s.strip()
@@ -234,21 +248,23 @@ def _safe_json_loads(s: str) -> dict[str, Any]:
     def _read_and_trim_data_file(self, data_file_path: str) -> str:
         """Read LAMMPS data file and trim to token limit for LLM context."""
         if os.path.exists(data_file_path):
-            with open(data_file_path, 'r') as f:
+            with open(data_file_path, "r") as f:
                 content = f.read()
             lines = content.splitlines()
             if len(lines) > self.data_max_lines:
-                content = "\n".join(lines[:self.data_max_lines])
-                print(f"Data file trimmed from {len(lines)} to {self.data_max_lines} lines")
+                content = "\n".join(lines[: self.data_max_lines])
+                print(
+                    f"Data file trimmed from {len(lines)} to {self.data_max_lines} lines"
+                )
             return content
-        else:       
-            return (f"Could not read data file.")
-        
+        else:
+            return "Could not read data file."
+
     def _copy_data_file(self, data_file_path: str) -> str:
         """Copy data file to workspace and return new path."""
         if not os.path.exists(data_file_path):
             raise FileNotFoundError(f"Data file not found: {data_file_path}")
-    
+
         filename = os.path.basename(data_file_path)
         dest_path = os.path.join(self.workspace, filename)
         os.system(f"cp {data_file_path} {dest_path}")
@@ -261,10 +277,10 @@ def _copy_user_potential_files(self):
         for pot_file in self.user_potential_files:
             if not os.path.exists(pot_file):
                 raise FileNotFoundError(f"Potential file not found: {pot_file}")
-            
+
             filename = os.path.basename(pot_file)
             dest_path = os.path.join(self.workspace, filename)
-            
+
             try:
                 os.system(f"cp {pot_file} {dest_path}")
                 print(f"Potential files copied to workspace: {dest_path}")
@@ -275,20 +291,27 @@ def _copy_user_potential_files(self):
     def _create_user_potential_wrapper(self, state: LammpsState) -> LammpsState:
         """Create a wrapper object for user-provided potential to match atomman interface."""
         self._copy_user_potential_files()
-        
+
         # Create a simple object that mimics the atomman potential interface
         class UserPotential:
             def __init__(self, pair_style, pair_coeff):
                 self._pair_style = pair_style
                 self._pair_coeff = pair_coeff
-            
+
             def pair_info(self):
                 return f"pair_style {self._pair_style}\npair_coeff {self._pair_coeff}"
-        
-        user_potential = UserPotential(self.user_pair_style, self.user_pair_coeff)
-        
-        return {**state, "chosen_potential": user_potential, "fix_attempts": 0,"run_history": []}
-    
+
+        user_potential = UserPotential(
+            self.user_pair_style, self.user_pair_coeff
+        )
+
+        return {
+            **state,
+            "chosen_potential": user_potential,
+            "fix_attempts": 0,
+            "run_history": [],
+        }
+
     def _fetch_and_trim_text(self, url: str) -> str:
         downloaded = trafilatura.fetch_url(url)
         if not downloaded:
@@ -326,7 +349,7 @@ def _entry_router(self, state: LammpsState) -> dict:
             raise Exception(
                 "You cannot set find_potential_only=True and also specify your own potential!"
             )
-        
+
         if self.data_file:
             try:
                 self._copy_data_file(self.data_file)
@@ -416,7 +439,7 @@ def _choose(self, state: LammpsState) -> LammpsState:
         })
         choice_dict = self._safe_json_loads(choice)
         chosen_index = int(choice_dict["Chosen index"])
-        
+
         chosen_potential = state["matches"][chosen_index]
 
         self._panel(
@@ -424,7 +447,7 @@ def _choose(self, state: LammpsState) -> LammpsState:
             f"[bold]Index:[/bold] {chosen_index}\n[bold]ID:[/bold] {chosen_potential.id}\n\n[bold]Rationale:[/bold]\n{choice_dict['rationale']}",
             style="green",
         )
-        
+
         out_file = os.path.join(self.potential_summaries_dir, "Rationale.txt")
         with open(out_file, "w") as f:
             f.write(f"Chosen potential #{chosen_index}")
@@ -446,7 +469,7 @@ def _author(self, state: LammpsState) -> LammpsState:
         if not self.use_user_potential:
             state["chosen_potential"].download_files(self.workspace)
         pair_info = state["chosen_potential"].pair_info()
-        
+
         data_content = ""
         if self.data_file:
             data_content = self._read_and_trim_data_file(self.data_file)
@@ -464,13 +487,15 @@ def _author(self, state: LammpsState) -> LammpsState:
             f.write(input_script)
 
         self._section("Authored LAMMPS input")
-        self._code_panel("in.lammps", input_script, language="bash", style="magenta")
-                    
+        self._code_panel(
+            "in.lammps", input_script, language="bash", style="magenta"
+        )
+
         return {**state, "input_script": input_script}
 
     def _run_lammps(self, state: LammpsState) -> LammpsState:
         self._section("Running LAMMPS")
-        
+
         if self.ngpus >= 0:
             result = subprocess.run(
                 [
@@ -518,12 +543,18 @@ def _run_lammps(self, state: LammpsState) -> LammpsState:
             )
 
         status_style = "green" if result.returncode == 0 else "red"
-        self._panel("Run Result", f"returncode = {result.returncode}", style=status_style)
+        self._panel(
+            "Run Result",
+            f"returncode = {result.returncode}",
+            style=status_style,
+        )
 
         if result.returncode != 0:
-            err_view = (result.stderr.strip() + "\n" + result.stdout.strip()).strip() or "(no output captured)"
-            self._panel("Run error/output", err_view[-6000:], style="red") 
-        
+            err_view = (
+                result.stderr.strip() + "\n" + result.stdout.strip()
+            ).strip() or "(no output captured)"
+            self._panel("Run error/output", err_view[-6000:], style="red")
+
         hist = list(state.get("run_history", []))
         hist.append({
             "attempt": state.get("fix_attempts", 0),
@@ -541,7 +572,6 @@ def _run_lammps(self, state: LammpsState) -> LammpsState:
             "run_history": hist,
         }
 
-
     def _route_run(self, state: LammpsState) -> str:
         rc = state.get("run_returncode", 0)
         attempts = state.get("fix_attempts", 0)
@@ -549,9 +579,13 @@ def _route_run(self, state: LammpsState) -> str:
             self._section("LAMMPS run successful! Exiting...")
             return "done_success"
         if attempts < self.max_fix_attempts:
-            self._section("LAMMPS run Failed. Attempting to rewrite input file...")
+            self._section(
+                "LAMMPS run Failed. Attempting to rewrite input file..."
+            )
             return "need_fix"
-        self._section("LAMMPS run Failed and maximum fix attempts reached. Exiting..")
+        self._section(
+            "LAMMPS run Failed and maximum fix attempts reached. Exiting.."
+        )
         return "done_failed"
 
     def _fix(self, state: LammpsState) -> LammpsState:
@@ -559,25 +593,26 @@ def _fix(self, state: LammpsState) -> LammpsState:
 
         hist = state.get("run_history", [])
         if not hist:
-            hist = [{
-                "attempt": state.get("fix_attempts", 0),
-                "input_script": state.get("input_script", ""),
-                "returncode": state.get("run_returncode"),
-                "stdout": state.get("run_stdout", ""),
-                "stderr": state.get("run_stderr", ""),
-            }]
-        
+            hist = [
+                {
+                    "attempt": state.get("fix_attempts", 0),
+                    "input_script": state.get("input_script", ""),
+                    "returncode": state.get("run_returncode"),
+                    "stdout": state.get("run_stdout", ""),
+                    "stderr": state.get("run_stderr", ""),
+                }
+            ]
+
         parts = []
         for h in hist:
             parts.append(
                 "=== Attempt {attempt} | returncode={returncode} ===\n"
                 "--- input_script ---\n{input_script}\n"
                 "--- stdout ---\n{stdout}\n"
-                "--- stderr ---\n{stderr}\n"
-            .format(**h)
+                "--- stderr ---\n{stderr}\n".format(**h)
             )
         err_blob = "\n".join(parts)
-        
+
         data_content = ""
         if self.data_file:
             data_content = self._read_and_trim_data_file(self.data_file)
@@ -591,14 +626,14 @@ def _fix(self, state: LammpsState) -> LammpsState:
             "data_content": data_content,
         })
         script_dict = self._safe_json_loads(fixed_json)
-        
+
         new_input = script_dict["input_script"]
         old_input = state["input_script"]
         self._diff_panel(old_input, new_input)
-                
+
         with open(os.path.join(self.workspace, "in.lammps"), "w") as f:
             f.write(new_input)
-            
+
         return {
             **state,
             "input_script": new_input,
@@ -615,15 +650,19 @@ def _build_graph(self):
         self.add_node(self._author)
         self.add_node(self._run_lammps)
         self.add_node(self._fix)
-        
+
         self.graph.set_entry_point("_entry_router")
-        
+
         self.graph.add_conditional_edges(
             "_entry_router",
-            lambda state: "user_potential" if self.use_user_potential else ( 
-                "user_choice" if state.get("chosen_potential") else "agent_choice"
+            lambda state: "user_potential"
+            if self.use_user_potential
+            else (
+                "user_choice"
+                if state.get("chosen_potential")
+                else "agent_choice"
             ),
-            {   
+            {
                 "user_potential": "_create_user_potential_wrapper",
                 "user_choice": "_author",
                 "agent_choice": "_find_potentials",
@@ -659,7 +698,7 @@ def _build_graph(self):
                 "Exit": END,
             },
         )
-        
+
         self.graph.add_edge("_create_user_potential_wrapper", "_author")
         self.graph.add_edge("_author", "_run_lammps")
 

From a03f3da471d98fb70d5f56cd53674b1285f78015 Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram <rsomasundaram@lanl.gov>
Date: Tue, 20 Jan 2026 16:48:37 -0700
Subject: [PATCH 25/31] Minor bug fixed

---
 src/ursa/agents/lammps_agent.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index d9bb52b6..af2cad51 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -192,8 +192,6 @@ def __init__(
             | self.str_parser
         )
 
-        self._action = self._build_graph()
-
     def _section(self, title: str):
         self.console.print(Rule(f"[bold cyan]{title}[/bold cyan]"))
 

From 0cef0cddc881872a972a8a87fa99d5af86e26436 Mon Sep 17 00:00:00 2001
From: Rahul Somasundaram - 365493 <rsomasundaram@darwin-fe2.lanl.gov>
Date: Tue, 20 Jan 2026 17:30:21 -0700
Subject: [PATCH 26/31] Added ability to call Execution agent within Lammps
 agent for summarization/visualization of results

---
 .../lammps_execute/EOS_of_Cu.py               | 24 ++---------
 .../lammps_execute/stiffness_tensor_of_hea.py | 24 ++---------
 src/ursa/agents/lammps_agent.py               | 43 ++++++++++++++++++-
 3 files changed, 48 insertions(+), 43 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index 95aadb5e..35d66d84 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -1,7 +1,5 @@
-from langchain_core.messages import HumanMessage
 from langchain_openai import ChatOpenAI
-
-from ursa.agents import ExecutionAgent, LammpsAgent
+from ursa.agents import LammpsAgent
 
 try:
     import atomman as am
@@ -28,6 +26,7 @@
     workspace=workspace,
     lammps_cmd="lmp_mpi",
     mpirun_cmd="mpirun",
+    summarize_results=True,
 )
 
 with open("eos_template.txt", "r") as file:
@@ -51,21 +50,4 @@
 )
 
 if final_lammps_state.get("run_returncode") == 0:
-    print("\nNow handing things off to execution agent.....")
-
-    executor = ExecutionAgent(llm=llm)
-    exe_plan = f"""
-    You are part of a larger scientific workflow whose purpose is to accomplish this task: {simulation_task}
-    
-    A LAMMPS simulation has been done and the output is located in the file 'log.lammps'.
-    
-    Summarize the contents of this file in a markdown document. Include a plot, if relevent.
-    """
-
-    final_results = executor.invoke({
-        "messages": [HumanMessage(content=exe_plan)],
-        "workspace": workspace,
-    })
-
-    for x in final_results["messages"]:
-        print(x.content)
+    print("\nLAMMPS Workflow completed successfully. Exiting.....")
diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index 4f6739f6..dd4e1c60 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -1,7 +1,5 @@
-from langchain_core.messages import HumanMessage
 from langchain_openai import ChatOpenAI
-
-from ursa.agents import ExecutionAgent, LammpsAgent
+from ursa.agents import LammpsAgent
 
 model = "gpt-5"
 
@@ -18,6 +16,7 @@
     workspace=workspace,
     lammps_cmd="lmp_mpi",
     mpirun_cmd="mpirun",
+    summarize_results=True,
 )
 
 with open("elastic_template.txt", "r") as file:
@@ -32,21 +31,4 @@
 )
 
 if final_lammps_state.get("run_returncode") == 0:
-    print("\nNow handing things off to execution agent.....")
-
-    executor = ExecutionAgent(llm=llm)
-    exe_plan = f"""
-    You are part of a larger scientific workflow whose purpose is to accomplish this task: {simulation_task}
-    
-    A LAMMPS simulation has been done and the output is located in the file 'log.lammps'.
-    
-    Summarize the contents of this file in a markdown document. Include a plot, if relevent.
-    """
-
-    final_results = executor.invoke({
-        "messages": [HumanMessage(content=exe_plan)],
-        "workspace": workspace,
-    })
-
-    for x in final_results["messages"]:
-        print(x.content)
+    print("\nLAMMPS Workflow completed successfully. Exiting.....")
diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index af2cad51..98a31fe9 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -8,6 +8,7 @@
 from langchain.chat_models import BaseChatModel
 from langchain_core.output_parsers import StrOutputParser
 from langchain_core.prompts import ChatPromptTemplate
+from langchain_core.messages import HumanMessage
 from langgraph.graph import END
 from rich.console import Console
 from rich.panel import Panel
@@ -15,6 +16,7 @@
 from rich.syntax import Syntax
 
 from .base import BaseAgent
+from ursa.agents.execution_agent import ExecutionAgent
 
 working = True
 try:
@@ -66,6 +68,7 @@ def __init__(
         mpirun_cmd: str = "mpirun",
         tiktoken_model: str = "gpt-5-mini",
         max_tokens: int = 200000,
+        summarize_results: bool = True,
         **kwargs,
     ):
         if not working:
@@ -95,6 +98,7 @@ def __init__(
         self.mpirun_cmd = mpirun_cmd
         self.tiktoken_model = tiktoken_model
         self.max_tokens = max_tokens
+        self.summarize_results = summarize_results
 
         self.console = Console()
 
@@ -637,6 +641,28 @@ def _fix(self, state: LammpsState) -> LammpsState:
             "input_script": new_input,
             "fix_attempts": state.get("fix_attempts", 0) + 1,
         }
+        
+
+    def _summarize(self, state: LammpsState) -> LammpsState:
+        self._section("Now handing things off to execution agent for summarization/visualization")
+        
+        executor = ExecutionAgent(llm=self.llm)
+        
+        exe_plan = f"""
+        You are part of a larger scientific workflow whose purpose is to accomplish this task: {state["simulation_task"]}
+        A LAMMPS simulation has been done and the output is located in the file 'log.lammps'.
+        Summarize the contents of this file in a markdown document. Include a plot, if relevent.
+        """
+
+        exe_results = executor.invoke({"messages": [HumanMessage(content=exe_plan)],"workspace": self.workspace})
+
+        for x in exe_results["messages"]:
+            print(x.content)
+            
+        return state
+
+    def _post_run(self, state: LammpsState) -> LammpsState:
+        return state
 
     def _build_graph(self):
         self.add_node(self._entry_router)
@@ -648,6 +674,8 @@ def _build_graph(self):
         self.add_node(self._author)
         self.add_node(self._run_lammps)
         self.add_node(self._fix)
+        self.add_node(self._post_run)
+        self.add_node(self._summarize)
 
         self.graph.set_entry_point("_entry_router")
 
@@ -705,8 +733,21 @@ def _build_graph(self):
             self._route_run,
             {
                 "need_fix": "_fix",
-                "done_success": END,
+                "done_success": "_post_run",
                 "done_failed": END,
             },
         )
+        
         self.graph.add_edge("_fix", "_run_lammps")
+
+        self.graph.add_conditional_edges(
+            "_post_run",
+            lambda _: "summarize" if self.summarize_results else "skip",
+            {
+                "summarize": "_summarize",
+                "skip": END,
+            },
+        )
+
+        self.graph.add_edge("_summarize", END)
+        

From 293f7127eae8dbc70972cd36d1bfaa24ab376e8f Mon Sep 17 00:00:00 2001
From: Mike Grosskopf <mikegros@lanl.gov>
Date: Thu, 29 Jan 2026 13:44:02 -0700
Subject: [PATCH 27/31] Also ruff formatting

---
 src/ursa/agents/lammps_agent.py | 24 ++++++++++++++----------
 1 file changed, 14 insertions(+), 10 deletions(-)

diff --git a/src/ursa/agents/lammps_agent.py b/src/ursa/agents/lammps_agent.py
index 98a31fe9..7ad4ba9d 100644
--- a/src/ursa/agents/lammps_agent.py
+++ b/src/ursa/agents/lammps_agent.py
@@ -6,18 +6,19 @@
 
 import tiktoken
 from langchain.chat_models import BaseChatModel
+from langchain_core.messages import HumanMessage
 from langchain_core.output_parsers import StrOutputParser
 from langchain_core.prompts import ChatPromptTemplate
-from langchain_core.messages import HumanMessage
 from langgraph.graph import END
 from rich.console import Console
 from rich.panel import Panel
 from rich.rule import Rule
 from rich.syntax import Syntax
 
-from .base import BaseAgent
 from ursa.agents.execution_agent import ExecutionAgent
 
+from .base import BaseAgent
+
 working = True
 try:
     import atomman as am
@@ -641,24 +642,28 @@ def _fix(self, state: LammpsState) -> LammpsState:
             "input_script": new_input,
             "fix_attempts": state.get("fix_attempts", 0) + 1,
         }
-        
 
     def _summarize(self, state: LammpsState) -> LammpsState:
-        self._section("Now handing things off to execution agent for summarization/visualization")
-        
+        self._section(
+            "Now handing things off to execution agent for summarization/visualization"
+        )
+
         executor = ExecutionAgent(llm=self.llm)
-        
+
         exe_plan = f"""
         You are part of a larger scientific workflow whose purpose is to accomplish this task: {state["simulation_task"]}
         A LAMMPS simulation has been done and the output is located in the file 'log.lammps'.
         Summarize the contents of this file in a markdown document. Include a plot, if relevent.
         """
 
-        exe_results = executor.invoke({"messages": [HumanMessage(content=exe_plan)],"workspace": self.workspace})
+        exe_results = executor.invoke({
+            "messages": [HumanMessage(content=exe_plan)],
+            "workspace": self.workspace,
+        })
 
         for x in exe_results["messages"]:
             print(x.content)
-            
+
         return state
 
     def _post_run(self, state: LammpsState) -> LammpsState:
@@ -737,7 +742,7 @@ def _build_graph(self):
                 "done_failed": END,
             },
         )
-        
+
         self.graph.add_edge("_fix", "_run_lammps")
 
         self.graph.add_conditional_edges(
@@ -750,4 +755,3 @@ def _build_graph(self):
         )
 
         self.graph.add_edge("_summarize", END)
-        

From a3ac5d178ae9e912a7eca8643faec073be6a8558 Mon Sep 17 00:00:00 2001
From: Mike Grosskopf <mikegros@lanl.gov>
Date: Wed, 4 Feb 2026 16:27:09 -0700
Subject: [PATCH 28/31] Addresses Arthurs review comments and merged updates to
 main.

---
 docs/lammps_agent.md                                         | 4 ++--
 .../lammps_execute/stiffness_tensor_of_hea.py                | 5 ++++-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/docs/lammps_agent.md b/docs/lammps_agent.md
index f9138731..538303b1 100644
--- a/docs/lammps_agent.md
+++ b/docs/lammps_agent.md
@@ -14,9 +14,9 @@ The agent writes the outputs into a local `workspace` directory and uses rich co
 
 ## 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 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.  
 
-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`.  
+One additional dependency, that are not installed along with `ursa`, is `atomman`. This can be installed via `pip install atomman`.  
 
 ---
 
diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index b63a5861..7d7d5f77 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -23,7 +23,10 @@
 with open("elastic_template.txt", "r") as file:
     template = file.read()
 
-simulation_task = "Carry out a LAMMPS simulation of the high entropy alloy Co-Cr-Fe-Mn-Ni to determine its stiffness tensor."
+simulation_task = (
+    "Carry out a LAMMPS simulation of the high entropy alloy Co-Cr-Fe-Mn-Ni "
+    "to determine its stiffness tensor."
+)
 
 elements = ["Co", "Cr", "Fe", "Mn", "Ni"]
 

From a9416fb143f570b7c0d603603cce69c8930f00bb Mon Sep 17 00:00:00 2001
From: Mike Grosskopf <mikegros@lanl.gov>
Date: Wed, 4 Feb 2026 16:33:54 -0700
Subject: [PATCH 29/31] Adding the console printing as recommended as well

---
 examples/two_agent_examples/lammps_execute/EOS_of_Cu.py    | 7 ++++++-
 .../lammps_execute/stiffness_tensor_of_hea.py              | 7 ++++++-
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
index a793e754..dd20577f 100644
--- a/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
+++ b/examples/two_agent_examples/lammps_execute/EOS_of_Cu.py
@@ -1,7 +1,10 @@
 from langchain_openai import ChatOpenAI
+from rich import get_console
 
 from ursa.agents import LammpsAgent
 
+console = get_console()
+
 try:
     import atomman as am
 except Exception:
@@ -51,4 +54,6 @@
 )
 
 if final_lammps_state.get("run_returncode") == 0:
-    print("\nLAMMPS Workflow completed successfully. Exiting.....")
+    console.print(
+        "\n[green]LAMMPS Workflow completed successfully.[/green] Exiting....."
+    )
diff --git a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
index 7d7d5f77..1cb70eac 100644
--- a/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
+++ b/examples/two_agent_examples/lammps_execute/stiffness_tensor_of_hea.py
@@ -1,7 +1,10 @@
 from langchain_openai import ChatOpenAI
+from rich import get_console
 
 from ursa.agents import LammpsAgent
 
+console = get_console()
+
 model = "gpt-5"
 
 llm = ChatOpenAI(model=model, timeout=None, max_retries=2)
@@ -35,4 +38,6 @@
 )
 
 if final_lammps_state.get("run_returncode") == 0:
-    print("\nLAMMPS Workflow completed successfully. Exiting.....")
+    console.print(
+        "\n[green]LAMMPS Workflow completed successfully.[/green] Exiting....."
+    )

From 48c51099c664231ac95231dbe4242c73322d4490 Mon Sep 17 00:00:00 2001
From: Arthur Lui <alui@lanl.gov>
Date: Fri, 6 Feb 2026 11:11:01 -0700
Subject: [PATCH 30/31] move lammps to optional-dependencies

---
 pyproject.toml |  6 +++---
 uv.lock        | 12 ++++++------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2b00537c..81699cdd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -66,6 +66,9 @@ Issues = "https://github.com/lanl/ursa/issues"
 
 [project.optional-dependencies]
 fm = ["torch>=2.9.0"] # Ursa's MCP FM interface
+lammps = [
+    "atomman>=1.5.2",
+]
 
 [build-system]
 requires = ["setuptools>=74.1,<80", "setuptools-git-versioning>=2.0,<3"]
@@ -113,9 +116,6 @@ docs = [
     "mkdocs-material>=9.6.21",
     "mkdocstrings-python>=1.18.2",
 ]
-lammps = [
-    "atomman>=1.5.2",
-]
 opt = [
     "ortools>=9.14,<9.15",
 ]
diff --git a/uv.lock b/uv.lock
index 2bcab590..e8118307 100644
--- a/uv.lock
+++ b/uv.lock
@@ -7954,6 +7954,9 @@ dependencies = [
 fm = [
     { name = "torch" },
 ]
+lammps = [
+    { name = "atomman" },
+]
 
 [package.dev-dependencies]
 dev = [
@@ -7971,9 +7974,6 @@ docs = [
     { name = "mkdocs-material" },
     { name = "mkdocstrings-python" },
 ]
-lammps = [
-    { name = "atomman" },
-]
 opt = [
     { name = "ortools" },
 ]
@@ -7985,6 +7985,7 @@ otel = [
 [package.metadata]
 requires-dist = [
     { name = "arxiv", specifier = ">=2.2.0,<3.0" },
+    { name = "atomman", marker = "extra == 'lammps'", specifier = ">=1.5.2" },
     { name = "beautifulsoup4", specifier = ">=4.13.4,<5.0" },
     { name = "ddgs", specifier = ">=9.5.5" },
     { name = "fastmcp", specifier = ">=2.13.3" },
@@ -8012,7 +8013,7 @@ requires-dist = [
     { name = "trafilatura", specifier = ">=1.6.1,<1.7" },
     { name = "typer", specifier = ">=0.16.1" },
 ]
-provides-extras = ["fm"]
+provides-extras = ["fm", "lammps"]
 
 [package.metadata.requires-dev]
 dev = [
@@ -8030,7 +8031,6 @@ docs = [
     { name = "mkdocs-material", specifier = ">=9.6.21" },
     { name = "mkdocstrings-python", specifier = ">=1.18.2" },
 ]
-lammps = [{ name = "atomman", specifier = ">=1.5.2" }]
 opt = [{ name = "ortools", specifier = ">=9.14,<9.15" }]
 otel = [
     { name = "opentelemetry-exporter-otlp", specifier = ">=1.39.0" },
@@ -8801,4 +8801,4 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/c2/38/f249a2050ad1eea0bb364046153942e34abba95dd5520af199aed86fbb49/zstandard-0.25.0-cp314-cp314-win32.whl", hash = "sha256:da469dc041701583e34de852d8634703550348d5822e66a0c827d39b05365b12", size = 444513, upload-time = "2025-09-14T22:18:20.61Z" },
     { url = "https://files.pythonhosted.org/packages/3a/43/241f9615bcf8ba8903b3f0432da069e857fc4fd1783bd26183db53c4804b/zstandard-0.25.0-cp314-cp314-win_amd64.whl", hash = "sha256:c19bcdd826e95671065f8692b5a4aa95c52dc7a02a4c5a0cac46deb879a017a2", size = 516118, upload-time = "2025-09-14T22:18:17.849Z" },
     { url = "https://files.pythonhosted.org/packages/f0/ef/da163ce2450ed4febf6467d77ccb4cd52c4c30ab45624bad26ca0a27260c/zstandard-0.25.0-cp314-cp314-win_arm64.whl", hash = "sha256:d7541afd73985c630bafcd6338d2518ae96060075f9463d7dc14cfb33514383d", size = 476940, upload-time = "2025-09-14T22:18:19.088Z" },
-]
\ No newline at end of file
+]

From b7fed3fd286c545518b50db93f277347d18a15e9 Mon Sep 17 00:00:00 2001
From: Arthur Lui <alui@lanl.gov>
Date: Fri, 6 Feb 2026 11:23:05 -0700
Subject: [PATCH 31/31] added note on installing lammps

---
 docs/lammps_agent.md | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/docs/lammps_agent.md b/docs/lammps_agent.md
index 538303b1..2a4518c4 100644
--- a/docs/lammps_agent.md
+++ b/docs/lammps_agent.md
@@ -14,9 +14,17 @@ The agent writes the outputs into a local `workspace` directory and uses rich co
 
 ## Dependencies
 
-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.  
-
-One additional dependency, that are not installed along with `ursa`, is `atomman`. This can be installed via `pip install atomman`.  
+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.
+
+The dependencies for `LammpsAgent` are not included with the basic `ursa`
+installation, but can be installed via `pip install 'ursa[lammps]'` or `uv add
+'ursa[lammps]'`.
 
 ---