Example: a clay mineral with MINFF built with the Layer Builder (layers, interlayer ions and water, GROMACS)

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4/5
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3-5 天
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20/100
Issue 类型
文档
描述清晰度
基本清楚
活跃度
活跃
技术栈
c, python
领域
documentation

调研方向

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.

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描述

enhancement

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):

  1. 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.
  2. The stack: Tools > Layer Builder: number of layers, interlayer spacing, shift; interlayer counter-ions (Na⁺) and water filled into the gaps.
  3. 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.
  4. 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.

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