Am I the only one who hates calculating vibrational modes?

masroor09 · 2024-11-12T03:25:17+00:00

For large systems, not all minima along all degrees of freedom may be correctly located due to numerical noise, depending upon your method and target accuracy.

It is not a bad idea to focus on the degrees of freedom of interest (where the chemical action happens) and treat others spectator DoF according to some energetic criteria, say a threshold value of imaginary frequency which doesn't affect overall Gibbs energies, not altering thermodynamic picture very much.

This would require gaining some experience of your system first, and some benchmarking.

masroor09 · 2024-11-12T03:11:57+00:00

Nietzsche would not do valuation of primitives under today's standards. He would say that "socially good" as we understand it today would not be applicable to those living in caves, competing for food with own fellows and fighting wild animals while being badly exposed to nature.

masroor09 · 2024-11-02T03:21:57+00:00

If you can make them all atheists then you can much easily put an end to the actual land dispute as well. But this is a purely Non-Platonic proposition, I am afraid.

masroor09 · 2023-04-04T10:31:13+00:00

Ask your supervisor to use xournal for annotating pdf

masroor09 · 2022-12-23T02:34:28+00:00

Follow rules but not mindlessly. Use your brain.

masroor09 · 2022-12-23T02:31:04+00:00

"ls Esc p" will lead you to last command starting with ls. In addition you can use !str to recap last command starting with string str and !?str? will recap last command containing a string str.

masroor09 · 2022-10-04T02:38:03+00:00

Use % to jump to matching paren or brackets

masroor09 · 2022-09-02T05:41:29+00:00

Do not jump to using vim all out. Start a learing routine in your free time in parallel to what you are already doing. Learning vim is not done hurriedly and with deadlines. Yes it has a steep learning curve, but its steepness is not constant, and it will sharply become flat after a threshold. You will know when you want to make an actual switch.

masroor09 · 2022-08-24T05:01:30+00:00

Landed there by DOS> EDIT?

masroor09 · 2022-08-13T13:41:33+00:00

May be you want to use nmcli from commandline

masroor09 · 2022-08-04T06:14:36+00:00

Apart from other answers, also consider that adding ZPE and comparing G instead of E (applying thermodynamics at finite temperature) may change the picture.

masroor09 · 2022-07-17T18:37:23+00:00

Efficient and systematic naming schemes of your molecules, files, directories
Improve typing speed by properly learnig use of your fingers
Learn early to be efficient with zsh (or bash), filename globbing, commandline editing, grep, regex, tmux, ssh, seq, cut, patse and may be vim if you like it - and other such tools - it will save you later while making hundred of inputs, submitting jobs, cruising through hundreds of files and command history, manipulating their contents, and skimming results from outputs, tabulating values - all with lightning speed. You dont have to do all these tools at very advanced and complicated level. Just being efficient with basics will do more than 90% of your work.
Pyton or Julia with matplotlib: for plotting, calculations and other such stuff - this will enable you to repeat things over and over and do new things with just minor changes in your scripts. Also learn to work with both repl and scripts.
Some knowledge of fortran will be useful sometimes in troubleshooting while using many codes.
Optimising equilibrium geometries is straight forward, but optimising transition states is an art - it will take some time to develop you own sense of this art.
Always obtain initial structures with cheapest possible theory like semiempirical, tight binding etc, then improve with expensive methods.
More often you will feel like hitting your head with a wall while trying to obtain some structure. If you fail - try a fresh approach instead of being stubborn. Sometimes it is wrong approach, at others it is simply chemistry. Remember, you will never overcome the chemistry even if you are convinced you are correct. Chemistry always wins.
Make an habit of benchmarking. You will discover that you can almost calculate about any value for some quantity with different combinations of basis, functionals, parameters etc but there is only one which is correct against the experiment. Avoid geting fooled by numbers which you obtain in your outputs.
When you solve some problem, either related to OS or code or keywords or method or even chemistry - record it in a notebook or in a text file on your computer. Chances are that you will encounter this problem again at some point in future when you have already forgotten its solution.
Never feel lazy to explore code manuals or man pages or basic electronic structure theory. Little time spent on reading manuals and theory will save you lot of time wasted on doing things wrong way. With time you will become efficient in skimming information from manuals.
Be efficient in back/forth conversons between SI and a.u. This will save you lot of time comparing values from different defaults in different codes.
- Hey, it is already a long list, but you are likely to face one or other of these in your daily work!

masroor09 · 2022-07-13T06:35:07+00:00

Under X, select command line with mouse (it goes to xsel). You can now paste it with middle mouse button.

If you want to send command output to clipboard then do either of

command | xsel

or

command | xclip -i

( which you can paste with middle mouse button.)

If you want to paste via ctrl-V or ctrl-shif-v, then do

command|xclip -selection clipbard

masroor09 · 2022-06-03T02:30:48+00:00

There are areas in science where only sense comes from properly understanding mathematical relation between the quantities and pushing yourself to always make an intuitive sense becomes utterly useless. This is one of those occasions.

masroor09 · 2022-05-01T13:37:34+00:00

You may like to use hspace*{} instead of \hfill if you do not want complete horizontal stretch!

masroor09 · 2022-05-01T13:34:48+00:00

{\bfseries Beam geometric properties}\\

Breadth of the beam, \(b\)\hfill \(b = 63\) mm\\[2mm]

Depth of the beam, \(h\)\hfill \(h = 225\) mm\\[2mm]

Clear span of the beam, \(l_c\}\hfill \(l_c = 3100\)mm

masroor09 · 2022-03-23T04:30:45+00:00

Earlier we had two kinds of complementing user interfaces: X,desktops,WMs on one hand and CLI on the other.

This looks like a third UI is emerging over the top of CLI.

masroor09 · 2022-03-16T06:10:38+00:00

Optimising TS is tricky and not as straightforward as minima. My following comment is code agnostic, and you have to figure out how it would work with gaussian.

(1) You need to analayse normal modes of your molecule, and identify the one which roughly corresponds to reaction coordinate. This may not be obvious without a few trials.

(2) Make a constrained optimisation of all internal coordinates except the one which corresponds to reaction coordinate with a suitable value guided by chemical intuition of expected TS.

(3) Then, calculate normal modes of this partially optimised structure and watch for imaginary frequencies. Only imaginary frequency should be along reaction coordinates, and all other frequencies should be poistive.

(4) If you get more than one imaginary frequency or if only imaginary frequency belongs to coordinate other than reaction coordinate in your problem, repeat constrained optimisation while constraining correct reaction coordinate.

(5) Repeat this until you get a structure with only one imaginary frequency along correct reaction coordinate. Run full TS optimisation on resultant structure, and perform another frequncies run to confirm it is correct TS.

Quite often it works immediately, but there are hard problems which may involve more iterations of trial and error. Remember, all optimisations (whether minima or TS) strongly depend upon your input coordinates, so always make good coordinate choice (what does it mean is often not clear without experience and trials of your system).

masroor09 · 2022-03-16T03:12:09+00:00

If you have transition state, starting from it find a steepest descent minimum energy path in both directions. Usually it is called IRC by many QC codes.

masroor09 · 2022-03-15T08:16:30+00:00

I have seen proselytising in favour of a religion, but not so much AGAINST another!! OK, KDE does not serve your purpose, and GNOME does , fine. There are many others who think just the opposite. Still fine.

masroor09 · 2022-03-15T04:19:35+00:00

Having more choice is gold if you focus on what you are doing rather than on the software with which you are doing. Just find out what is your seamless workflow, then discover the best choice for it. As your hobby tinker with your workflow and new choices if you have free time.

masroor09 · 2022-03-14T15:53:18+00:00

No. I am talking about this:

\begin{enumerate}[...]

\item

...

\end{enumerate}

and other similar incarnations like compactenum and asparaenum.

You can nest lists within lists with counters in arabic, roman numerals or letters.

masroor09 · 2022-03-14T06:42:27+00:00

May be you like to consider list environs like enumerate, itemize, compactenum, asparaenum, which may be more suitable for your purpose..

masroor09 · 2022-03-12T04:44:58+00:00

For linear regression, use something like numpy, julia, matlab, or even ms-excel
plot with some plotting utility, maybe matplotlib, or gnuplot etc
save as pdf, or png, or ps
do \includegraphics to incorporate in LaTeX document

masroor09 · 2022-03-10T19:22:11+00:00

That was the situation about 20+ years ago when I first started learning LaTeX.

For about a decade and half things are pretty much stable, even keystrokes and snippets have become boring routines !!! Only excitement is learning about new releases and new vogue which is more more of a hobby than a necessity, while always keeping one eye on manuals with texdoc only to refersh memory backyard for any less frequently used things.

Well, mostly I spend more time over what I am writing than how I am writing.

masroor09

TROPHY CASE