154. Vim -- weird pasting behaviour

The problem:
Get this

 when you want this?

The solution:

This is perhaps a bit superfluous as it comes from the vim wiki, but it might help someone: 

Edit your ~/.vimrc and add

set pastetoggle=<F3>

Now, before you paste, hit F3 and you can paste as usual (notice the little 'paste' after the 'insert' in the screenshot below).

My full ~/.vimrc is now

set number
set pastetoggle=
set spell
set wrap
nnoremap  :set nonumber!<

Other cool stuff:

* Line number toggle -- nnoremap <F4> :set nonumber!<CR> will map line numbering on /off to F4.

* Substituting only within selection. Go to visual mode and select the text.
Then hit  : which brings up '<,'>.  Anyway, the key is \%V which confines the substitution to the visually selected area.

:'<,'>s/\%Voldphrase/newphrase/g

* Commenting out lines -- the key is ^

: %s/^/#/g 

or

 :'<,'>s/\%V^/#/g

---

I previously had a bigger ~/.vimrc posted here, but now, a year later, I've reduced it to what I've posted above.
Anyway, the old one is here:

set number
filetype plugin on
filetype indent on
set expandtab
set shiftwidth=4
set tabstop=4
set smarttab
set spell
set lbr
set ai "Auto indent
set si "Smart indent
set wrap "Wrap lines
set grepprg=grep\ -nH\ $*
let g:tex_flavor='latex'
highlight Cursor guifg=white guibg=black
highlight iCursor guifg=white guibg=steelblue
set guicursor=n-v-c:block-Cursor
set guicursor+=i:ver100-iCursor
set guicursor+=n-v-c:blinkon0
set guicursor+=i:blinkwait10
set pastetoggle=<F3>
nnoremap <F4> :set nonumber!<CR>

153. dft gridsize: ecce defaults to medium for nwchem and fine for g09

I set out to reproduce Malagoli and Brédas in Chemical Physics Letter, 2000, 327, 13-17 (Link). Essentially it's a paper on calculating reorganisational energies in a few simple organic species, such as biphenyl.

I'm a computational noob -- I'm stronger in the computer department than the computational one. The following will most likely only be useful to other newcomers like myself. Anyway...

The authors used ub3lyp/g-31g** and g03. While it may have taken a substantial amount of time in 2000, today the entire paper can be reproduced in a few hours on a simple beowulf cluster. So I set out to do just that -- partly to make sure that I understood the approach, partly to make sure that g09 and g03 gave the same results, and also importantly to make sure i can use nwchem for these calculations if I so desire. I'm getting to the point where nwchem is almost as fast as gaussian for some calculations (cosmo excepted...) and I much prefer the nwchem syntax and python support.

For biphenyl, g09 gave (in Hartree)

Neutral, ground state:     -463.3219416650 (geometry opt)
Cation, neutral geometry:-463.0352702000 (single point calc)
Cation, cation geometry:  -463.0422747850 (geometry opt)
Neutral, cation geometry: -463.3157130000 (single point calc)

That works out to a total energy of ca 0.36 eV -- same as in the paper

while nwchem gave

Neutral, ground state:      -463.3219454524 (geometry opt)
Cation, neutral geometry: -459.0525026266 (single point calc)
Cation, cation geometry:  -463.0422952505 (geometry opt)
Neutral, cation geometry: -459.0556262940 (single point calc)

The order of the stabilities don't even match!

Recalculating the energies by adding

dft
    grid fine
    .....
end

gave the 'correct' results:

Cation, neutral geometry: -463.0353366421
Neutral, cation geometry: -463.3157251871

which gives about 0.36 eV

Here's what puzzles me a bit: you definitely need to add 'fine' in nwchem, and that's what g09 defaults to. But the energies reported for the optimised structures (cation, cation geometry and neutral, ground state) must have been calculated using a fine grid too or one would presume that they'd be off too. Repeating this with the other structures in the paper gives the same result.

Anyway, if you get weird and wacky energies from you single point calcs maybe you should make sure you've specified the dft grid size consistently.

152. Hiking maps using google maps

This is only vaguely computer related.

http://www.mappedometer.com/ is a neat way to create your own hiking routes. It's not a replacement for a proper topological map if you're going to do long-distance hiking, but it's certainly enough to plot out a day hike.