A very useful how-to for quantum chemistry

OK, finally I found the original of Dave Young’s hints and tips:

Dave Young’s Chemical Topics

I read his posts pretty long time ago, and appreciated very much his book collecting those posts, so I am sure that others will find this usefull, too.

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How (and why) to install Cygwin on your PC?

Cygwin (link) is a UNIX-like environment that can run in Windows (any 32 and 64 verision), so it allows running GNU codes and X . If you don’t understand what this exactly means, then just believe me, that is it USEFUL and FREE, which is generally pretty good from a software nowadays. The point to  remember: you can somehow run Linux-ish programs on your Windows PC with it.

The advantages:

  • You can have a (free) X-terminal. If you are running Unix/Linux programs with graphical interface then you generally need this. A good example is Molden, which needs X for the graphical interface. You also can run Molden on a Linux machine, and have the graphical output on your PC. It means, you can directly read your output files on the Linux machine, and dont need to FTP to your PC for a short look.
  • You can have (free) c,c++,fortran etc. compilers. There are several legacy codes in computational chemistry which was written in FORTRAN, and never were translated to other language. Even new codes, like DFTB+ or Quantum Espresso, are written only for Linux / UNIX environment, and no complied version available for Windows PCs. If oyu want to compile and use this programs in a Unix/Linux like environment, then Cygwin is a good choice offering the standard development toolds like make, and free compilers like cpp, g77, gfortran, g95. Though running calculations in Cygwin is  slow, still at least you can get failiar yourself with these programs. For smaller calculation, learning or testing software functions, it can help a lot.
  • You may actually want to learn or practice some basic UNIX. Installing Cygwin on your machine is a relative easy way to have a system, which you can use for programing, editing files etc.
  • Beyond basic learning, you may need some GNU programs, other than compilers and software development related tools. Who knows..

How to install Cygwin?

First you should download a fresh “setup.exe” from the Cygwin site. You can find the download link in the upper right corner.

Once you have it on your machine, start the setup program, and answer some basic questions in the following steps:

  1. Choose A Download Source. You can install Cygwin from the internet (i.e. downloading all the necessarily files you use and immediate set it up), can download the files and not installing anything, or can choose installation from local directory, if you have already downloaded the necessarily files previously. If you dont know, then choose the “install from the Internet”.
  2. Select Root Install Directory. C:\cygwin is a pretty standard choice.
  3. Select Local Package Directory. It can be a good idea to keep the packages on your machine, but not necessary, so you can use a simple Temp directory wherever you want.
  4. Select Your Internet Connection. “Direct Connection” is the likely choice for most people.
  5. Choose A Download Site. Anything is OK, you most probably prefer something in your country and sounds fast.
  6. Select Packages. Some advice: 1) Don’t install everything! It is huge, and there are a lot of obsolete thing. Do you really need 22 text editor? 2) “Search” is slow, but useful. Same information about the packages is available in http://cygwin.com/packages/. For any programming or compiling, you should have at least make, gcc, gcc-g77 from Devel. For the X enviromnent, you should have at least xorg-server and xinit from X11. 3) Don’t worry! If you miss something, later you just re-run the setup, and choose the necessary packages! Such a”re-installation” keeps everything intact, just install the new programs, so it is fast.
  7. Hit next, and let is install everything.

Some others description of the same process with more visual help:

A note: for upgrading your Cygwin system, you can just re-run the setup from time to time, and it automatically find you the updates for the packages.

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An interesting Quantum Chemistry Blog

I just found a blog from Joaquin Barroso-Flores, PhD, about theoretical chemistry:
http://joaquinbarroso.wordpress.com/
He has a few useful summary: especially the reviews on basis sets and NBOs are good introductions.

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Tools you need for calculations: text editor

So your have your quantum chemistry software installed? Still, you are not really ready to work. These software often do not have  a GUI to create input for calculations or see the results, instead of that they communicate through formatted files. With Windows users in my mind, I have collected some utilities that can be handy.

Text editors

Input files for most programs are text files. Even if you manage to generate such files with a GUI program, generally you do not have all the options and freedom, that you can with direct editing of the input file. Also, you may want to performs similar calculations, or need only minor changes: text editors are the most convenient way.

(from http://tnerual.eriogerg.free.fr/0xBABAF000L/10_en.html)

NotePad++

License: GPL

Available systems: Windows (it runs on Linux and MacOS using wine)

Free editor, easy, intuitive interface. Small, fast, what else you need? Tabbed editing, so easily can be used for editing multiply files.

UltraEdit

License: Commercial software

Available OS: Windows, Linux, (Mac coming soon)

OK, it is not free, but i like it very much, so anyway I recomend it. Intuitive, easy to use.

So this program was created for programmers, and have many extra features for syntax highlighting and stuff like that.

Vim

License: free, similar to GPL

Available OS: Windows, Linux, Unix, Mac and many more

It is free, it is powerful, it is far from intuitive, but it looks very professional if you learn to use it. Seriously. If it reminds you to vi, it is not an accident.

SciTE

License: sort of free (check the licence)

Availabe OS: Windows, Linux

It is a nice, fast, free software. Screenshot

Continue reading

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Setting up a free Quantum Chemistry software: FireFly (PC GAMESS)

Well, there are plenty free calculation software to do quantum chemistry. Free in a sense that “gratis, if you are student or in academia”. I would like to show now the ones:
1) I use and like,
2) have relative universal capabilities,
3) relatively easy to install and use on a Windows machine, so you can play with it in your free time.

Disclaimer or whatnot:
I am sure that there are plenty of handy, good quality free software out there for similar purposes. Do you know one? Maybe wrote one? Tell us about it.

So let’s introduce the Firefly!

In science there is such thing as free lunch. And this lunch sometime can be very tasty, as the work of researchers in MSU coordinated by Alex A. Granovsky. The result is Firefly, a program package originally built on the code of US-GAMESS project. As the pieces of the were code replaced, the Firefly aka PC-GAMESS became gradually an independent quantum chemistry software with superior speed and almost complete compatibility with the original GAMESS input and output structure. It is fast. And I mean it.

The Firefly can be downloaded from the project website at MSU, just go to the “Download” section. The licence agreement allows to download and use the program to anyone, including for-profit and business related calculations! After agreed with the Terms of Use, you can download a pre-compiled version latest version of Firefly for Windows or Linux operating systems. The downloaded file can be unzipped after a registration, after extracted in a directory, and it runs. OK, I lied. You may want to set the PATH variable, but that’s it.

The website of Firefly has some introductions to the first steps of use on Windows and Linux machines. You can also download a small package of example input files: examples. There are some manuals available here and here, but they are not 100% complete.

Some program to process input/output:

  • WinCraft
  • Molekel
  • MacMolPro

Good luck!

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Quamtum Chemistry in the Backyard: Hardware

So what do you need to start your own calculations and have a little hand-on experience with such kind of calculations? Do you need a supercomputer center? No, definitely you do not need. Though if you have one it can be handy.

Hardware:
As a minimum, you can make basic calculations and have a feel for this whole business on an average laptop or desktop computer, running Windows or some Linux operating system. If the computer is enough fast to run a word processor or browse internet, then it is enough fast to start basic computations with it.

If you want a little more, then i recommend to get a decent desktop computer. You don’t need nice video cards or sounds cards inside, and it doesn’t need to be the hottest brand with design panels all around. You do not need a monitor constantly hooked up on it, so if you have a computer for everyday work with a monitor, and you want a second box just next to it, then it can be pretty cheap.

FAQ:
Can I use my iPhone/iPod?

  • Not yet.

Can I use my Macintosh?

  • Maybe, but you will be limited by the lack of software.

Can I use my (PC) laptop?

  • Yes, you can. There is only one thing: calculation generally takes time. It means, the calculation may run for hours or even days. So if you can to use your laptop or just switch off your laptop, then you have to kill the calculation.

Do I necessary need o set up a Linux machine, or Windows is OK?

  • Linux is recommended (practical things like speed), but most of the software is readily available on Windows, and can be installed without much knowledge in dark sciences.
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Musing and such

Why?

The question is why?

We live in an age when even my dog has a Facebook account and a blog to share his views on the World, and I cannot walk my dog without letting him check all the comments he got in the last hour. This very fact would stop any decent person to start any blog.

Well, maybe I have no such high moral standards as I assume about myself, but the reason I started this blog is the pain I have when I see quantum chemists and other folks closed to a conference room. This pain has two roots:

  • QChemists generally like to talk sh*t about their white coated colleagues (and they mean it), and their skills (yeah, they mean, that too).
  • Other chemists, generally wearing white coat, like to talk sh*t about QChemists (and they mean it), and their skills (yeah, they mean, that too).

I am not particularly keen on deciding who is right. Naively assuming that knowledge may help, I decided to share some practical knowledge about quantum chemistry to improve a little the situation. It doesn’t mean however the QChemists cannot learn more about Chemistry, it means only that white coat doesn’t really fit me. So if you have something to say or have a blog, please let me know.

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