Open this only when you need the exact published case record, hashes, historical commands, or replay boundary.
Inspect stored evidence or run a fresh calculation
Inspect stored evidence
This track reads the published, hash-bound case records and does not launch a new DFT calculation.
Reconstruct the stored public evidence
case_root=examples/cases/aluminium-metallic-electronic-structure
(cd "$case_root" && python3 parse.py)
(cd "$case_root" && bash extract.sh)
(cd "$case_root" && bash check.sh)
Output policy: Rebuild case-local tables, figures, summaries, and isolated-copy checks from the committed route-scoped outputs.
Audit
- Retain the NSCF and bands c_bands warnings.
- Keep the Gaussian raw-NSCF representation distinct from native dos.x output.
- Preserve the exploratory convergence FAIL separately from program completion.
- Preserve the bounded E(V) fit as mathematical evidence only.
Parse and plot boundary: These commands parse and plot the stored public routes; they do not prove that a new DFT calculation ran.
Boundary: Stored reconstruction supports route-scoped parser and artifact lineage only, not case-wide historical continuity, target-observable convergence, or scientific acceptance.
Run a fresh calculation
This track launches software in a caller-controlled runtime directory. Its new outputs do not rewrite the historical records published in the case bundle.
Run the isolated Aluminium electronic route
set -euo pipefail
case_root=examples/cases/aluminium-metallic-electronic-structure
QE_PW=${QE_PW:?Set QE_PW to the absolute path to pw.x}
QE_DOS=${QE_DOS:?Set QE_DOS to the absolute path to dos.x}
QE_PSEUDO_DIR=/absolute/path/to/pseudos
RUN_OUTPUT_ROOT=/absolute/new/path/aluminium-electronic-route
test -x "$QE_PW"; test -x "$QE_DOS"; test -d "$QE_PSEUDO_DIR"; test ! -e "$RUN_OUTPUT_ROOT"
QE_PW="$QE_PW" QE_DOS="$QE_DOS" QE_PSEUDO_DIR="$QE_PSEUDO_DIR" RUN_OUTPUT_ROOT="$RUN_OUTPUT_ROOT" bash "$case_root/run.sh"
for output in scf.out nscf-full.out dos.out bands.out; do test -s "$RUN_OUTPUT_ROOT/$output"; grep -nE 'JOB DONE|convergence has been achieved|c_bands|Error in routine' "$RUN_OUTPUT_ROOT/$output" || true; done
test -s "$RUN_OUTPUT_ROOT/al.dos"; sed -n '1,12p' "$RUN_OUTPUT_ROOT/al.dos"
Output policy: Use a new caller-selected external runtime directory; never overwrite or relabel committed output/, derived/, or figures/ as the new run.
Audit
- Record the shell exit and inspect every stdout and stderr independently.
- Check program termination separately from SCF convergence and retained NSCF/bands warnings.
- Confirm the SCF, full-zone NSCF, native dos.x table, and path outputs before parsing.
- Do not infer ionic convergence because this bounded case contains no relaxation.
- Test DOS, band, or Fermi-surface observables with their own numerical convergence protocol.
- State the scientific claim only after the evidence supports it.
Parse and plot boundary: The fresh route leaves the native al.dos table and solver outputs for direct inspection; no fresh plotting route is supplied. It does not add a relaxation, a bands.x data product, observable convergence, or a material-level claim.
Boundary: This present-day route creates new external SCF, full-zone NSCF, dos.x, and path-bands process records under the exact QE_PW, QE_DOS, QE_PSEUDO_DIR, and RUN_OUTPUT_ROOT contract. No relaxation is part of the case, and no private replay or case-wide historical continuity is claimed.
Reproduce the exact published evidence
Use this section after understanding the scientific route. It retrieves the exact reviewed checkout and keeps new runtime evidence separate from the published case.
Repository: https://github.com/Maxwell3919/DFT-Research-Workflow.git
Source revision: 2ba561ac0937a938764bc283b25edb3a4700ece0
Working directory: repository-root
Case root: examples/cases/aluminium-metallic-electronic-structure
git clone https://github.com/Maxwell3919/DFT-Research-Workflow.git
cd DFT-Research-Workflow
git checkout --detach 2ba561ac0937a938764bc283b25edb3a4700ece0
test "$(git rev-parse HEAD)" = "2ba561ac0937a938764bc283b25edb3a4700ece0"
case_root=examples/cases/aluminium-metallic-electronic-structure
Inspect the explicit Aluminium model and exact pseudopotential receipt
Run from: repository-root
case_root=examples/cases/aluminium-metallic-electronic-structure
cat "$case_root/source/fixture-metadata.json"
cat "$case_root/source/pseudopotential-metadata.json"
Boundary: The structure is an explicit teaching input rather than a database identity, and the receipt establishes pseudopotential bytes rather than transferability or numerical suitability.
Recorded commands and outputs
These records distinguish captured output, replay instructions, and unavailable historical shell details. Records may belong to different declared routes; adjacency on this page does not establish one continuous run. An exit is shown only when the manifest scopes where that value came from, and a QE terminal marker is not silently converted into a shell exit code.
Case-wide timing boundary: No case-wide start, completion, or exit is claimed. The 04:21:54-04:22:02 timestamps belong only to the isolated DOS route.
Initial captured SCF/NSCF/bands outputs
Route ID: initial-captured-electronic-output-set
Route timing: 2026-08-05T00:45:36+08:00 to 2026-08-05T00:47:36+08:00. Earliest and latest QE-printed timestamps across three captured stdout files; gaps and continuous save-tree ancestry are not established.
Exact historical command: Not captured. output/recorded-commands.txt labels the listed shell lines as replay-equivalent only.
Exact historical exit: Not captured; each stdout retains a JOB DONE marker, which is not a shell exit transcript.
- input/scf.in -> output/scf.out
- input/nscf.in -> output/nscf-full.out
- input/bands.in -> output/bands.out
- No public launcher, scheduler record, or save-tree payload binds these three outputs into one continuous historical invocation.
Boundary: This initial set is real output evidence but its exact historical command/exit/continuity is unknown.
Isolated SCF/NSCF/dos.x/bands rerun
Route ID: isolated-dos-route
Route timing: 2026-08-05T04:21:54+08:00 to 2026-08-05T04:22:02+08:00. QE-printed timestamps for output/dos-route only; not a case-wide completion window.
Exact historical command: The four stage invocations and ordering are preserved in run.sh and output/recorded-commands.txt.
Exact historical exit: The existing route record reports exit 0 for each stage; JOB DONE and empty stderr are independently inspectable, but no separate shell transcript is published.
- input/scf.in -> output/dos-route/scf.out
- input/nscf.in with the same runtime prefix/outdir -> output/dos-route/nscf-full.out
- input/dos.in consumes the NSCF save state -> output/dos-route/dos.out -> output/dos-route/al.dos
- input/bands.in runs after dos.x -> output/dos-route/bands.out; retained c_bands warnings remain visible.
Boundary: The runtime save tree is not published; route ordering is declared by run.sh and does not establish observable convergence.
Later k/smearing and E(V) screens
Route ID: later-exploratory-screens
Route timing: start not recorded to completion not recorded. Not folded into the isolated DOS-route window; per-output QE timestamps remain in the committed raw stdout.
Exact historical command: Current committed runners are input/run-convergence-matrix.sh and input/run-eos.sh.
Exact historical exit: The existing route record reports runner exit 0; the convergence assessment itself is FAIL and remains distinct from program exit.
- Generated committed screen inputs -> one SCF stdout/stderr pair per input
- input/parse_convergence.py -> derived/aluminium-convergence-matrix.csv and aluminium-convergence-assessment.json
- input/parse_eos.py -> derived/aluminium-eos-samples.csv and aluminium-eos-fit.json
Boundary: A reported earlier blocked parser attempt has no standalone shell transcript; the corrected fit is mathematical evidence only.
isolated DOS-route SCF · exit 0
Route: isolated-dos-route
Record kind: existing-route-execution-record
pw.x -in scf.in > scf.out 2> scf.err
Evidence scope: output/dos-route/scf.out prints JOB DONE; stderr is hash-bound and empty.
Exit scope: Route-scoped existing record; no standalone shell transcript is published.
Inputs: input/scf.in
Outputs: output/dos-route/scf.out -> output/dos-route/scf.err
isolated DOS-route full-zone NSCF · exit 0
Route: isolated-dos-route
Record kind: existing-route-execution-record
pw.x -in nscf.in > nscf-full.out 2> nscf-full.err
Evidence scope: The NSCF stdout prints JOB DONE and retains five c_bands warnings.
Exit scope: Route-scoped existing record; no standalone shell transcript is published.
Inputs: input/nscf.in
Declared parents: output/dos-route/scf.out -> same runtime prefix/outdir; save tree not published
Outputs: output/dos-route/nscf-full.out -> output/dos-route/nscf-full.err
isolated DOS-route dos.x · exit 0
Route: isolated-dos-route
Record kind: existing-route-execution-record
dos.x -in dos.in > dos.out 2> dos.err
Evidence scope: dos.out prints JOB DONE and al.dos is a hash-bound 2,801-row native QE table.
Exit scope: Route-scoped existing record; no standalone shell transcript is published.
Inputs: input/dos.in
Declared parents: output/dos-route/nscf-full.out -> same runtime NSCF save state; payload not published
Outputs: output/dos-route/dos.out -> output/dos-route/dos.err -> output/dos-route/al.dos
isolated DOS-route bands · exit 0
Route: isolated-dos-route
Record kind: existing-route-execution-record
pw.x -in bands.in > bands.out 2> bands.err
Evidence scope: bands.out prints JOB DONE and retains five c_bands warnings.
Exit scope: Route-scoped existing record; no standalone shell transcript is published.
Inputs: input/bands.in
Declared parents: output/dos-route/scf.out -> same runtime prefix/outdir; save tree not published
Outputs: output/dos-route/bands.out -> output/dos-route/bands.err
later exploratory k/smearing screen · exit 0
Route: later-exploratory-screens
Record kind: existing-route-execution-record
bash input/run-convergence-matrix.sh
Evidence scope: Five SCF programs completed; the predeclared numerical screen result is FAIL.
Exit scope: Runner exit and numerical screen status are distinct.
Outputs: output/convergence-screen/ -> derived/aluminium-convergence-matrix.csv -> derived/aluminium-convergence-assessment.json
later bounded E(V) screen · exit 0
Route: later-exploratory-screens
Record kind: existing-route-execution-record
bash input/run-eos.sh
Evidence scope: Five SCF programs completed; the quadratic fit status is mathematical PASS only.
Exit scope: Runner exit does not establish EOS or elastic acceptance.
Outputs: output/eos-screen/ -> derived/aluminium-eos-samples.csv -> derived/aluminium-eos-fit.json
Source-bound excerpt: output/compact-source-excerpt.txt
SCF/NSCF/bands: Quantum ESPRESSO 7.5; 8x8x8 full-zone NSCF; Fermi energy 7.8018 eV; each recorded program reached JOB DONE.
Native DOS: dos.x 7.5 reached JOB DONE; al.dos has 2801 rows and prints E_F=7.802 eV.
Native DOS lineage: dos.out SHA-256 c930a07ec54184fe102d308668a5895b629087fdd977ce36b9a602e705616f6e; al.dos SHA-256 95c3342cb9229b0ff2fbc8cb17d48aa13ebd6f3ddea7a5a1c4797de9e64be5f8.
Exploratory k/smearing screen: FAIL; k10-to-k12 delta E=0.00164525 Ry/cell and delta E_F=0.2449 eV.
Five-point E(V) entry: mathematical fit PASS; c2=2.33027885266e-05 Ry/bohr^6; residual RMS=5.34111987806e-05 Ry.
The k/smearing screen FAIL is retained; the E(V) fit is not a converged EOS, bulk modulus, or elastic tensor. Observable convergence is not established; no scientific conclusion is claimed.
Evidence boundary
Evidence class: real-execution.
- Quantum ESPRESSO PWSCF and DOS 7.5 (single-process CLI)
- case-local raw-output parser 2.3 (Python CLI)
Execution host: Talos.
- Inputs and identity
- Recorded as passed within the stated scope. Declared inputs, route-scoped outputs, screen artifacts, and derived files retain strict hashes and parsing relationships; this edit records no fresh replay.
- Program completion
- Recorded as passed within the stated scope. The isolated Talos rerun outputs have terminal markers and empty captured stderr; initial historical shell exits remain unrecorded.
- Electronic solver and ionic or structural checks
- Recorded as passed within the stated scope. The isolated rerun SCF reports electronic convergence in five iterations. NSCF/bands c_bands warnings remain retained.
- Artifacts and stage ancestry
- Recorded as passed within the stated scope. Real al.dos, real screen outputs, hash-bound stdout/stderr, parser tables, figures, and route ancestry records are present.
- Observable convergence
- Not established by this case. One 8x8x8 dos.x sample plus exploratory k/smearing and E(V) screens do not establish observable-specific convergence; the convergence screen is explicitly FAIL.
- Claim boundary
- No material-level claim is made. No physical or material-level scientific conclusion is claimed.
What this case supports
- Route-scoped real QE 7.5 outputs: an initial captured SCF/NSCF/bands set, an isolated SCF/NSCF/dos.x/bands rerun, and later exploratory screens with raw-output-derived tables and figures.
What this case does not support
- One continuous historical launcher, case-wide execution interval, or unpublished save-tree ancestry.
- A converged DOS, Fermi surface, EOS, elastic property, carrier density, transport result, universal parameter prescription, or material-level conclusion.
Program completion, solver convergence, observable convergence, and physical interpretation are separate gates. The case check and parser report their tested scope; an absent gate is not implied by a passing earlier one.
Research-workflow context
Use this case together with Research Workflow for the A–E scientific map. The case illustrates one bounded case and its declared routes; it does not prescribe parameters or establish a general material conclusion.
