帮助处理量子化学计算数据的一些脚本

sobereva

CCL上很久没什么动静了，最近有个人问了个问题

I would like to start a discussion as to some of the tools/scripts some of you use to build input files and analyze results.

I find myself using bash, awk/sed, Python, and the fantastic egrep utility for the bulk of the work (finding frequencies, enthalpies, termination instances) for the bulk of the work. However, as of late I want to start streamlining an input file generation script and here is where I can't quite figure out the best approach.

Suppose I have 1 geometry, and want to generate several input files with varying basis sets. My approach has been to create a database file with names such as atom_basis_set and another template file with the starting geometry. I then call the database file, read the template, and write the appropriate atom_basis_set and save as a new file. This so far gets the job done, but still requires some manual changes. Ideally I want something where I can use the terminal for user input of the template file, and atom/basis set descriptors. This seems doable, but I cant quite figure out a Pythonic way of doing this.

引来很多回复。提问者把回复做了个汇总，有点意义，转载过来（个别完全没价值的我给去了）：

Some interesting links/scripts:

Vladislav Vasilyev Homepage (several tools; CBS exptrapolation calculator)
http://sf.anu.edu.au/~vvv900/

Look4bas (basis set builder)
https://github.com/mfherbst/lo

Gaussian Tools (Some Gaussian post processing scripts)

https://github.com/chauncey-ga

ESIgen (create supporting information):

https://github.com/insilichem/

Meant to create automated "Supporting Information" reports ready for publication attachment, but it also works in the command-line for more day-to-day tasks. It can be used in two ways: with a webserver (public demo here: http://esi.insilichem.com/), or from the command-line with the `esigen` executable.

Cauchian (Chimera GUI extension to create Gaussian input files):

https://github.com/insilichem/

UCSF Chimera extension that provides a GUI to create Gaussian input files. Created to deal with QM/MM, it also supports standard QM jobs. The dialog includes a fast Basis Set explorer like the one in BSE thanks to the included ebsel fork.

Pnictogen (input file builder based on Jinja)

https://github.com/dudektria/pnictogen

ExcelAutomat (Excel/LibreOffice VBA input/output processing)

ExcelAutomat: a tool for systematic processing of files as applied to quantum chemical calculations.

https://sites.google.com/view/excelautomat/home

Launchanew (tools for managing Gaussian calculations; might be outdated)

https://github.com/esmuigors/

Shine剪水

谢谢社长的转载和整理，有个小疑问想求解答：CCL是哪个论坛？能不能放一个链接或者全称上来，闲时也可以去淘淘宝。另外，ExcelAutomat的下载链接 http://tinyurl.com/gq4qkd2打开速度很慢，能否私下分享一下，将不胜感激。

sobereva

Shine剪水 发表于 2018-3-16 19:53
谢谢社长的转载和整理，有个小疑问想求解答：CCL是哪个论坛？能不能放一个链接或者全称上来，闲时也可以去 ...

http://www.ccl.net/chemistry/

用不着专门去，里面的讨论Google都搜得到

Shine剪水

sobereva 发表于 2018-3-17 02:44
http://www.ccl.net/chemistry/

用不着专门去，里面的讨论Google都搜得到

谢谢社长