使用量子化学程序基于簇模型计算金属表面吸附问题

djjj148

sobereva 发表于 2020-3-11 12:12
1 我说的测试指的就是stable检测。是否稳定和自旋多重度怎么设不是一码事。即便就是设的真实基态的自旋多 ...

明白了，谢谢老师！

comboy2008

从金属团簇的建模，复合物的优化，到基组和泛函的选择，单点能的计算都讲到了，非常详细的教程！

rabbitkiller

sob老师，我注意到Ag团簇构建好之后没有在orca里做几何优化，请问需要对Ag团簇做几何优化么？还是构建好之后就可以直接计算单点能？

我是量化初学者，按照我的理解，构建Ag团簇后是不是要先做一下几何优化，再算单点能？

谢谢！

sobereva

rabbitkiller 发表于 2020-4-6 12:20
sob老师，我注意到Ag团簇构建好之后没有在orca里做几何优化，请问需要对Ag团簇做几何优化么？还是构建好之 ...

只需要对那些与被吸附的分子接触的Ag优化，外围的Ag用于表现晶体中的体相环境，显然不能优化

djjj148

sob老师，请问下，您提到了“有机体系（如石墨烯），边界往往用氢饱和”，而我看了您提到的“ACS Catal., 8, 3825 (2018)研究石墨烯上催化二氧化硫与氧气反应形成硫酸盐”用vasp优化完结构好像直接就用来算单点了，并没有饱和边界。我可以这样理解吗：
1. 对于有机体系，涉及结构优化的计算(opt/ts)才需要饱和边界。
2. 对于任何体系，用第一性原理软件优化完后，可以直接把晶格去掉用量化软件算单点。

sobereva

djjj148 发表于 2020-5-1 13:03
sob老师，请问下，您提到了“有机体系（如石墨烯），边界往往用氢饱和”，而我看了您提到的“ACS Catal., 8 ...

1 我不知道作者具体怎么做的，可能饱和了但是没明确在文中提及，你可以问作者。原理上是必须饱和的，否则电子结构会很诡异。

2 没那么简单，对边界的处理是非常重要的。要说不做任何处理就能直接算的，一般也就是金属单质、有机晶体这种情况了，或者簇取得相当大，或者取得比较有技巧

rpestana94

Professor Sob I have a question, to obtain a graph like the first graph in section 2.1, you need to do a single point calculation per each 0.5 angstrom or just with one single point we can get that results

sobereva

rpestana94 发表于 2021-6-26 06:19
Professor Sob I have a question, to obtain a graph like the first graph in section 2.1, you need to  ...

If you need potential energy curve, you must perform single point calculation for every evenly distributed point on the curve. If you only need binding energy, only one single point evaluation is needed for complex and each fragment.

rpestana94

sobereva 发表于 2021-6-25 18:26
If you need potential energy curve, you must perform single point calculation for every evenly dis ...

Thanks

rpestana94

applying constraint to the Cartesian position is the same as frozen the coordinates? Because I saw orca differentiate the two, for constrains use {C atom C} and for frozen coordinates is: "atom X Y Z $", I'm trying to freeze some coordinates while doing an opt of a nanoparticle but I can't do it, if I freeze using "$" I got an error for using redundant coordinates and if I apply constrains the nanoparticle still move some atoms and lost it shape.

sobereva

rpestana94 发表于 2022-2-12 01:17
applying constraint to the Cartesian position is the same as frozen the coordinates? Because I saw o ...

It depends on the specific context. Often "constraint" refers to maintaining distance or angle between specific atoms exactly unchanged during calculation. While "frozen" often refers to keeping Cartesian or internal coordinates exactly unchanged.

However, in ORCA, to freeze atomic Cartesian coordinates you should use contraint setting. For example, the attached file freeze all aromatic carbons during geometry optimization

dopamine.inp (1.25 KB, 下载次数 Times of downloads: 4)

2022-2-12 03:21 上传 Uploaded

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Click to download

rpestana94

sobereva 发表于 2022-2-11 14:21
It depends on the specific context. Often "constraint" refers to maintaining distance or angle bet ...

Thanks professor Sob

rpestana94

To get a graph like the first one you move the benzene each 0.5 A or shorter? In each step is necessary to do an optimization and then the single point calculation or just an initial optimization of the whole system and then just a single point calculation in each step?  

sobereva

rpestana94 发表于 2022-2-15 23:41
To get a graph like the first one you move the benzene each 0.5 A or shorter? In each step is necess ...

The first graph comes from original paper DFT-D3, I think the author simply gradually moved benzene and conducted single point calculation for each geometry. No optimization is needed.

rpestana94

sobereva 发表于 2022-2-15 20:07
The first graph comes from original paper DFT-D3, I think the author simply gradually moved benzen ...

thanks professor