題:
如何計算水分子的電荷分佈?
uhoh
2015-05-06 15:15:43 UTC
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I would like to obtain the 3D charge density of a water molecule for plotting purposes (i.e. not necessarily super-accurate). I know this is a tough problem, but I'd like to give it a try. Since I'm currently using python, I've identified PyQuante and PySCF, and gather that I should learn how to run density functional theory (DFT) calculations. Before I do that, I'd like to find out if there is something else out there I should use instead. Multiple suggestions are welcome.

I've installed PyQuante, which according to it's README.txt may be more accessible to understanding.

For example, the color plots in this answer give a hint of what I'm talking about, though I'll ultimately plot the field strength contours and some electric field lines.

I'd like to obtain a large table of values (or expressions/expansions?), so I can create and work with surfaces and field line plots myself.

Additionally is it possible that there exist supplementary data in published articles. Where I might find that? Although this is about existing data, I actually do plan on putting in the time to have at least a minimal understanding of the calculation itself. If DFT is it, then I will be spending time studying that.

我莫名其妙地看不到您實際上試圖實現的目標。如果您想要一張大桌子,那張桌子應該是什麼?請具體說明您需要的情節。您對場強輪廓和電場線是什麼意思?也許您可以添加一個草圖來說明您的目標。那裡有許多[量子化學軟件包](http://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid-state_physics_software),其中一些甚至附帶了文檔。基本上,您只需要電子密度或波函數的映射即可。
五 答案:
Jan Jensen
2015-05-06 16:03:40 UTC
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Two suggestions: MolCalc: Calculate Properties > Polarity and Solvation gives you a 3D surface plot with the electrostatic potential superimposed.

Another suggestion is Avogadro/GAMESS/MacMolPlt. See for example here

謝謝!我已經對問題添加了一些修改。看起來這些無濟於事。
Qiming Sun
2015-07-03 11:40:37 UTC
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pyscf中,我們通常運行moden.py來生成moulden文件並使用Jmol繪製軌道表面。編寫較小的腳本以生成密度或其他電荷表面,然後用Jmol繪製表面應該不太困難。您可能需要的基本功能應該與dft模塊使用的功能非常接近,例如eval_ao,eval_rho。

在最新的Pyscf alpha 2版本中,腳本pyscf / tools / cubegen.py已被使用。添加以生成高斯立方體文件格式。在我的linux框中,密度在Jmol中看起來不錯。您可以以它為例來生成其他 Jmol格式

好的,我來看看@qiming-sun。它當前是否可以進行DFT(以及HF?)?這可能讓我感到頭疼-當我在文檔中看到`mol.light_speed = 137.035989`(1 /精細結構)時,我認為它可能適合已經有經驗的人。
我應該指出,我想要的是電荷分佈(或場),以便我自己進行繪圖。 @qiming-sun,我需要物理部分-我想自己做圖形/顯示部分。謝謝!
DFT可用。該軟件包假定用戶具有計算化學的基本知識。它提供了許多基本功能來實現基本操作,例如積分,現實空間中的基礎評估等。默認設置對於大多數情況應該足夠了,並且您無需修改任何內容即可進行常規計算,例如DFT。腳本cubegen.py是有關如何使用兩行dft函數在立方網狀網格上計算電荷密度的示例。您仍然需要考慮自己的數據格式來記錄其餘信息,例如分子的幾何形狀。
Burak Ulgut
2015-05-06 15:35:25 UTC
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如果您不想真正學習這些計算,而只需要等高線圖,則可以使用 Arguslab

這將為您提供示例性的軌道圖以及總電子密度。它們不會非常精確,但是會很快。

謝謝!我已經對問題添加了一些修改。看起來這無濟於事。
Klaus-Dieter Warzecha
2015-05-07 11:08:38 UTC
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您需要(一些)背景知識和工具

  • 使用分子的坐標和要執行的計算命令來生成輸入文件

  • 運行計算

  • 後處理結果

所有工具都在那裡!除非您可以通過您的機構使用市售套件,否則我建議使用那些免費的套件(例如免費啤酒免費語音)。實際上,在任何情況下,其中一些免費工具都是一個不錯的選擇!

要引用一家鞋類公司的口號:

只要這樣做!

哇!那正是我所需要的!這會讓我現在很忙。感謝您抽出寶貴的時間為我提供可用的“大圖”。
Pu Zhang
2015-05-06 19:34:39 UTC
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If you only need the electron density distribution of a water molecule, it doesn't make much sense for you to leanr DFT method. Although I don't think there will be such data out there, it's pretty easy to run such a calculation for people who do DFT calculation regularly. It will take several minutes. My suggestion is that you find someone to help you with the calculation. The calculation could give you the data describing electron density in the 3D space. Then you can play with the data by yourself.

歡迎來到Chem.SE!我認為您的答案會縮小為“我的建議是您找到可以幫助您進行計算的人”。我不參與DFT,因此我將其留給其他人來決定是否應該發表評論。
您好@Pu Zhang,謝謝您的評論。我認為學習新事物總是有意義的。儘管我很感謝您的觀點,並且毫無疑問地*真正*學習DFT需要花費大量時間,但是我使用輸出時會感到很有趣,而至少沒有粗略的理解。


該問答將自動從英語翻譯而來。原始內容可在stackexchange上找到,我們感謝它分發的cc by-sa 3.0許可。
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