Add APEX Skill and Update Gamma Surface with New Features#122
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Bundle the apex-flow agent skill (docs, helper scripts, templates, and default DPA2 model) under .cursor/skills so agents can drive APEX jobs. Co-authored-by: Cursor <cursoragent@cursor.com>
Move the agent skill into apex/skills/apex-skill, add apex skill CLI, require BOHRIUM_PROJECT_ID for global.json, and block known-bad image/scass pairs. Co-authored-by: Cursor <cursoragent@cursor.com>
Make generated jobs safer by centralizing ticket creation, preserving user structures, auto-inferring type maps, and bundling ready-to-use DPA models. Co-authored-by: Cursor <cursoragent@cursor.com>
Add periodic closed-loop scans, safer validation and reporting, while preserving property-specific LAMMPS dispatch and bundled skill packaging.
Sort generated displacement files before assigning task IDs so phonopy 4.1 can match FORCE_SETS inputs to phonopy_disp.yaml. Co-authored-by: Cursor <cursoragent@cursor.com>
…er image is deepmd-kit-phonolammps:3.1.3
Resolve phonopy 4.1 command conflicts while retaining fallback compatibility. Co-authored-by: Cursor <cursoragent@cursor.com>
Prepare the next post-release build for PyPI publication. Co-authored-by: Cursor <cursoragent@cursor.com>
Zikkying
changed the title
Default outer jobs to c1_m2_cpu and allow APEX to retrieve results automatically. Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## devel-1.3.0 #122 +/- ##
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+ Coverage 71.94% 73.29% +1.34%
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Files 103 111 +8
Lines 21279 23496 +2217
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+ Hits 15310 17221 +1911
- Misses 5969 6275 +306 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Co-authored-by: Cursor <cursoragent@cursor.com>
Cover config generation, input validation, and image-machine recommendations so agent-created jobs are checked before submission. Co-authored-by: Cursor <cursoragent@cursor.com>
Prevent agents from serializing project IDs as strings by clarifying generated config usage and rejecting malformed Bohrium settings during input validation. Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
- Updated RSS structure generation documentation to reflect new JSON configuration format and usage of `apex rss <rss.json>`. - Improved clarity in the properties documentation regarding RSS structure generation and its applications for multi-component alloys. - Refined the RSS workflow documentation to include detailed steps for generating structures, verifying outputs, and visualizing results. - Enhanced submission process by clarifying the steps for generating and refreshing configuration files, ensuring proper handling of Bohrium project IDs and access keys. - Implemented rigorous validation checks for project IDs in global configuration files to prevent mismatches and ensure integrity. - Added unit tests to validate the new configuration management features, ensuring robustness in handling project ID types and refreshing global configurations.
Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
Swap a↔b when det([a,b,c]) ≤ 0 after slab construction so left-handed cells from odd axis permutations do not fail dpdata/LAMMPS conversion. Co-authored-by: Cursor <cursoragent@cursor.com>
Add multi-structure config generation, disable non-TTY RSS tqdm by default, stage VASP POTCARs into job-relative paths, and tighten agent guidance for structure size and crystallographic planes. Co-authored-by: Cursor <cursoragent@cursor.com>
….0.post. Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
Enforce KSPACING/kspacing validation, Bohrium-safe VASP run commands, and private list_images resolution before setting vasp_image_name. Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
kevinwenminion
approved these changes
Jul 20, 2026
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Update Gammasurface with some new feature and better visulization
Update default DeepMD-kit image from Deepmd-kit 3.1.1 to Deepmd-kit 3.1.3-phonolammps
Add apex-flow skill
Add apex skill for generate prompt for Agent to install skill
Add apex skill --zip for generate zip file to upload in Matmaster