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log to TS

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还没有人认领这个 Issue。

评估

难度
5/5
预计耗时
一周以上
新手友好度
25/100
Issue 类型
功能
描述清晰度
基本清楚
活跃度
停滞
技术栈
python
领域
backend, tooling

调研方向

Start by locating the log-to-TS method and the ASE Gaussian calculator code that writes the input title block. Review how TS metadata is currently recovered from atom sorting labels. Done means Gaussian inputs preserve ts.reaction_label, ts.reaction_family, ts.direction, and labeled atoms so log-to-TS generation remains reliable across ASE versions.

由索引模型根据 Issue 内容生成。

描述

To update the TS database, we need to work backwards: generate a TS from a log file. We currently rely on the atom sorting labels to identify the atoms in the reaction center. However, sometimes the sorting labels in the log file don't match up with the TS sorting labels (if using a different version of ase for example). We could make the log to TS method more robust if we include key information in the gaussian log file needed to generate the TS, such as ts.reaction_label, ts.reaction_family, ts.direction, and ts.rmg_molecule.get_all_labeled_atoms(). We could do this by adding these attributes to the title block of the gaussian input file (unfortunately Gaussian doesn't print comments in output). However, ase's gaussian calculator does not have a title parameter (it just writes Gaussian input prepared by ASE), so we would need to change ase Gaussian code

主要语言
Python
星标
51
派生
19
30 天内没有已合并 PR

环境准备

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从这里开始

  1. 先读完整个 Issue，再读项目的贡献指南。
  2. 在 Issue 下留言说明你要接手 —— 这能避免两个人做同样的事。
  3. Fork 仓库，在一个分支上完成修改。
  4. 提交 Pull Request，并在描述里引用这个 Issue 编号。

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