Example: a clay mineral with MINFF built with the Layer Builder (layers, interlayer ions and water, GROMACS)
還沒有人認領這個 Issue。
評估
- 難度
- 4/5
- 預估耗時
- 3-5 天
- 新手友好度
- 20/100
- Issue 類型
- 文件
- 描述清晰度
- 基本清楚
- 活躍度
- 活躍
研究方向
Start with the existing Materials Chemistry examples and the Tools > Layer Builder entry in ECCE, then check how GROMACS Prepare handles MINFF typing through atomipy. The work is a worked example: build a clay layer with a substitution, stack it with interlayer ions and water, run Optimize, Equilibrate (NPT) and Dynamics, then analyse d(001), density profiles and the powder 001 reflection. It is done when the topology charges match the intended layer charge and d(001) is compared with a named published value.
由索引模型根據 Issue 內容生成。
描述
There is no example of MINFF (the min.ff mineral force field ECCE bundles with atomipy) or of building a layered material with the Layer Builder. Wanted, in the Materials Chemistry examples (and as a worked chapter of the manual):
- The layer: a clay layer from a published crystal structure (e.g. pyrophyllite or a montmorillonite model, from COD/AMCSD, source named), with its cell, in the Builder; isomorphic substitution (Al→Mg in the octahedral sheet, or Si→Al in the tetrahedral sheet) to give the layer charge, done in ECCE.
- The stack: Tools > Layer Builder: number of layers, interlayer spacing, shift; interlayer counter-ions (Na⁺) and water filled into the gaps.
- MINFF in GROMACS: GROMACS Prepare with MINFF (atomipy typing, ion parameter set HFE or IOD, minimum ion distance for a thin interlayer, #363), then Optimize, Equilibrate (NPT, so the interlayer spacing relaxes) and Dynamics.
- What it shows: the basal spacing d(001) against water content (one-layer and two-layer hydrates), the ion and water density profiles across the interlayer (MD Analysis > Density profile along c), and the powder pattern's 001 reflection from the equilibrated cell (Diffraction), which is what an XRD measurement of a clay reports.
Checks: the topology charges sum to the intended layer charge; the equilibrated d(001) compared with a published value for the same hydration state (source named). Force-field choices (MINFF version, ion set, water model) stated in the annotation; anything not checked against a published MINFF study is labelled as such. Notes in the short example style.
- 主要語言
- C
- 星號
- 10
- 分支
- 8
- PR 合併指標
- 30 天內沒有已合併 PR
環境準備
這個專案沒有提供開發容器、Dockerfile 或貢獻指南，環境需要你自己搭建：先看它的 README，通用步驟見我們的新手貢獻指南。
從這裡開始
- 先讀完整個 Issue，再讀專案的貢獻指南。
- 在 Issue 下留言說明你要接手 —— 這能避免兩個人做同樣的事。
- Fork 儲存庫，在一個分支上完成修改。
- 送出 Pull Request，並在描述裡引用這個 Issue 編號。
FriendsofECCE/ECCE 的其他 Issue
-
bug
難度 2/5 1-3 小時 新手友好度 72/100
FriendsofECCE/ECCE#1018 ·
-
難度 2/5 1-3 小時 新手友好度 70/100
FriendsofECCE/ECCE#336 · 1 則留言 ·
-
enhancement
難度 5/5 一週以上 新手友好度 20/100
FriendsofECCE/ECCE#1021 ·
-
enhancement
難度 5/5 一週以上 新手友好度 15/100
FriendsofECCE/ECCE#1019 ·
-
enhancement
難度 5/5 一週以上 新手友好度 15/100
FriendsofECCE/ECCE#1016 · 1 則留言 ·
查看 FriendsofECCE/ECCE 的全部 Issue
相似的 Issue
-
Status: Opened
難度 2/5 1-3 小時 新手友好度 64/100
維護者通常 1 天內回覆
-
難度 2/5 1-3 小時 新手友好度 62/100
immortalwrt/immortalwrt#2522 ·
-
難度 2/5 1-3 小時 新手友好度 72/100
維護者通常 1 天內回覆
-
severity: low
難度 2/5 1-3 小時 新手友好度 64/100
luainkernel/lunatik#2530 ·
維護者通常 1 天內回覆
-
難度 2/5 1-3 小時 新手友好度 82/100
conan-io/conan#20500 · 1 則留言 ·
維護者通常 1 天內回覆