Add provider-neutral Agent evaluation guide

EVALUATION_GUIDE.md

@@ -0,0 +1,219 @@
+# Running an Agent on MATTER-604
+
+This guide defines the provider-neutral solve protocol for MATTER-604. It
+explains what an evaluated Agent receives, how task files are prepared, and how
+to retain an answer, artifacts, and a native execution trace for later scoring.
+
+The evaluated Agent must have access only to this public task repository and
+the software or compute services declared for the run. Do not expose the
+private evaluator, reference answers, rubrics, Gold files, evaluator access
+tokens, or previous answers to the Agent.
+
+## 1. Record the run configuration
+
+Before solving any task, record:
+
+- Agent name and version;
+- model name and exact model version when available;
+- system prompt, enabled skills, tools, and permission policy;
+- container image or operating-system environment;
+- scientific-software and command-line tool versions;
+- start time and any task-level timeout;
+- whether the Agent or model may previously have seen MATTER questions or
+  answers.
+
+Keep the Agent's native system prompt, reasoning loop, and tool interface. To
+compare Agents, use the same task preparation and the same public task content;
+do not rewrite a question for one Agent but not the others.
+
+## 2. Select one task
+
+Each line of `data/test.jsonl` is one independent task:
+
+```json
+{
+  "task_id": "...",
+  "capability": "...",
+  "domain": "...",
+  "prompt": "...",
+  "tags": [],
+  "data_files": []
+}
+```
+
+Use `task_id` as the stable identity. `prompt` is the task statement delivered
+to the Agent. `data_files` declares every task input; do not add undeclared
+benchmark files to the workspace.
+
+## 3. Create an isolated workspace
+
+Create a fresh directory for each task. A recommended layout is:
+
+```text
+runs/<agent>/<task_id>/
+├── workspace/          # the Agent's working directory
+├── prompt.txt         # exact effective user prompt
+├── final_answer.txt  # final response returned by the Agent
+├── trace/             # native conversation and tool events
+├── submission.json   # one schema-valid submission record
+└── run_metadata.json # full reproducibility metadata
+```
+
+Do not reuse a workspace between tasks. Do not let parallel tasks share mutable
+files, conversation state, shell history, or result directories.
+
+## 4. Stage the declared input files
+
+For each entry in `data_files`:
+
+1. Verify its `size_bytes` and `sha256` before the Agent starts.
+2. For `distribution=bundled`, copy the file from its repository-relative
+   `path` into the task workspace root using the source basename.
+3. Replace occurrences of the repository path in the task prompt with that
+   basename.
+4. Append one neutral line listing the staged filenames:
+
+   `[The following data files are already in your working directory: \`file1\`, \`file2\`]`
+
+For `distribution=restricted`, obtain the file through the stated lawful
+`acquisition` route, place it at the declared path outside version control,
+verify the declared size and SHA-256, and then stage it in the same way. Do not
+substitute a different pseudopotential, paper, or file merely because it has a
+similar name.
+
+The file staging above matches the canonical MATTER runner. If an adapter uses
+a different workspace layout, it must preserve the filenames visible to the
+Agent and the effective prompt text.
+
+## 5. Construct the effective prompt
+
+Start from the record's `prompt`, apply only the path rewriting and staged-file
+listing described above, and then add any run-wide safety or compute guidance
+identically for every applicable Agent. Save the exact UTF-8 text as
+`prompt.txt`.
+
+Compute `metadata.prompt_sha256` from the exact bytes delivered as the user
+prompt, after all additions and path rewriting:
+
+```bash
+shasum -a 256 prompt.txt
+```
+
+Do not add answer hints, scoring criteria, expected values, tolerances, or
+information obtained from the evaluator.
+
+## 6. Run the Agent
+
+Launch the Agent with `workspace/` as its working directory and provide the
+contents of `prompt.txt` as the task input. Allow the Agent to use only the
+tools, software, network access, and remote-compute routes declared in the run
+configuration.
+
+Capture the Agent's native conversation and tool events from start to finish.
+The trace should retain commands, software calls, job identifiers, failures,
+retries, and result extraction. Redact credentials, authorization headers, and
+authentication caches; do not remove ordinary scientific failures or failed
+attempts.
+
+Save the Agent's final response verbatim in `final_answer.txt`. Preserve files
+created by the Agent before running the evaluator. Evaluation must not modify
+the recorded solve trace or make post-hoc checks appear to be part of the
+Agent's original work.
+
+## 7. Bohr CLI tasks
+
+Fifty-three tasks carry the `bohr-cli` tag. A complete comparable run must make
+a real, authenticated `bohr` executable available while those tasks are being
+solved. The evaluation adapter must audit the CLI process and retain
+`bohr_cli_receipts.jsonl` as execution evidence; the gated evaluator package
+contains the canonical audit implementation.
+The published three-Agent environment used Node.js 22 and Bohr CLI 2.5.17:
+
+```bash
+npm install -g @dptech-corp/bohr-cli@2.5.17
+bohr version -o json
+```
+
+Keep Bohrium credentials and authentication caches outside the workspace and
+outside all submitted artifacts. Record the CLI version and the project used
+for the run in protected operator metadata; never place access keys in the
+prompt, trace, or submission. Installing Bohr CLI after solving cannot recreate
+missing execution receipts.
+
+The remaining 551 tasks do not have a benchmark-wide mandatory Bohr CLI
+dependency. They may still use remote compute when the individual task and the
+declared run environment permit it.
+
+## 8. Build one submission record
+
+Create one JSON object conforming to `submission.schema.json`:
+
+```json
+{
+  "task_id": "TASK_ID",
+  "final_answer": "verbatim final response",
+  "artifacts": [
+    {
+      "path": "workspace/result.ext",
+      "sha256": "64-lowercase-hex-digits"
+    }
+  ],
+  "trace_path": "trace/trace.jsonl",
+  "metadata": {
+    "agent": "agent name and version",
+    "model": "model name and version",
+    "prompt_sha256": "64-lowercase-hex-digits",
+    "runtime": "container or host environment",
+    "started_at": "ISO-8601 timestamp",
+    "finished_at": "ISO-8601 timestamp"
+  }
+}
+```
+
+Artifact paths must be relative to the task result directory. Hash the exact
+submitted bytes. List only files produced or deliberately retained as evidence
+for this task; exclude credentials, caches, unrelated downloads, and evaluator
+files.
+
+Validate the record locally before submission:
+
+```bash
+python -m pip install jsonschema
+python - submission.schema.json runs/AGENT/TASK_ID/submission.json <<'PY'
+import json
+import sys
+from pathlib import Path
+from jsonschema import Draft202012Validator
+
+schema = json.loads(Path(sys.argv[1]).read_text(encoding="utf-8"))
+record = json.loads(Path(sys.argv[2]).read_text(encoding="utf-8"))
+Draft202012Validator(schema).validate(record)
+print("submission schema: PASS")
+PY
+```
+
+## 9. Score only after the solve is frozen
+
+Freeze the answer, artifacts, trace, and metadata before scoring. Send the
+submission bundle to the evaluator operator or service designated for the run.
+The evaluated Agent must not receive evaluator output and then revise its
+answer within the same attempt.
+
+Scores produced by the canonical MatMaster-DP private evaluator may be reported
+as official MATTER scores. Scores produced with the separately gated evaluator
+must be labeled `self-hosted MATTER-604`, together with the public dataset
+revision, evaluator commitment, Agent/model configuration, and runtime.
+
+## 10. Batch-run checklist
+
+For every one of the 604 task IDs, verify that:
+
+- a fresh workspace was used;
+- the effective prompt and its SHA-256 were retained;
+- all declared inputs were staged and hash-checked;
+- the final answer was saved verbatim;
+- artifact hashes match the submitted files;
+- a native trace and reproducibility metadata were retained;
+- no private evaluator content or credentials entered the Agent environment;
+- Bohr receipts exist for applicable `bohr-cli` executions;
+- the submission record passes `submission.schema.json`.

README.md

@@ -31,6 +31,7 @@ artifacts through the benchmark evaluation service.
 ```text
 MATTER-604/
 ├── README.md
+├── EVALUATION_GUIDE.md
 ├── LICENSE
 ├── data/
 │   └── test.jsonl
@@ -44,6 +45,7 @@ MATTER-604/
 | Path | Description |
 |---|---|
 | `README.md` | Dataset Card: scientific scope, task distribution, runtime requirements, scoring summary, and release boundaries. |
+| `EVALUATION_GUIDE.md` | Provider-neutral instructions for preparing one-task workspaces, invoking an Agent, recording traces and artifacts, and producing schema-valid submissions. |
 | `LICENSE` | Apache-2.0 license for MATTER-owned content. It does not license excluded VASP POTCAR files or third-party PDFs. |
 | `data/test.jsonl` | The 604 evaluation tasks, one JSON object per line. Each record contains only `task_id`, `capability`, `domain`, `prompt`, `tags`, and `data_files`. |
 | `fixtures/` | 238 redistributable task inputs declared by 147 tasks, including crystal structures, simulation inputs, spectra, electrochemical data, tabular data, and small model/test files. |
@@ -57,6 +59,8 @@ logical paths. Of these, 238 files are bundled under `fixtures/`; six restricted
 inputs are represented only by their identity, SHA-256, size, restriction reason,
 source, and lawful acquisition instructions.
 
+To run an Agent on the benchmark, follow [`EVALUATION_GUIDE.md`](EVALUATION_GUIDE.md).
+
 ## Capability distribution
 
 The capability label describes the main research action being evaluated. A task