Kenneth Geisshirt

Blogging about science and technology - mostly

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Open Source Days 2012

I'm going to the Open Source Days 2012 conference this weekend. This year's program is really interesting, and I'm looking forward to spend two days listening to geeky talks. The organizers have ask me to take the role as chairman. Saturday I will chair the session of web programming, but I'm not sure about Sunday.

Actually, for me the conference began yesterday. I gave a full day course on JavaScript programming. It was really great to explains the language in details for a group of experience software developers. You can find my slides at slide share.

Morse codes and Arduino

My son Svante came home Friday and told me that he had been working on Morse codes in science class. We talked a bit on how to translate sentences to Morse code. Yesterday evening I had to construct a translator using my Arduino board, a LED and a LCD display. The program is pretty simple. It processes the message - letter by letter - and shows the current letter in capital and the Morse code on the second line. Moreover, it blinks the Morse code using the LED. You find my program below.


#include <stdio.h>
#include <stdlib.h>
#include <LiquidCrystal.h>

int LED  = 9;
LiquidCrystal lcd(10, 11, 12, 13, 14, 15, 16);
char msg[] = "super seje mig";
char m[16];
char *morse[] = {
  "*-",       // A
  "-***",     // B
  "-*-*",     // C
  "*--",      // D
  "*",        // E
  "**-*",     // F
  "--*",      // G
  "****",     // H
  "**",       // I
  "*---",     // J
  "-*-",      // K
  "*-**",     // L
  "--",       // M
  "-*",       // N
  "---",      // O
  "*--*",     // P
  "--*-",     // Q
  "*-*",      // R
  "***",      // S
  "-",        // T
  "**-",      // U
  "***-",     // V
  "*--",      // W
  "-**-",     // X
  "-*--",     // Y
  "--**"      // Z
};
void setup() {
  lcd.begin(16, 2);
  lcd.clear();
  lcd.setCursor(0, 0);
  lcd.print("Booting");
  for(int i=0; i<16; i++) {
    lcd.setCursor(i, 1);
    lcd.write('.');
    delay(100);
  }
  lcd.clear();
  lcd.setCursor(0, 0);
  lcd.print("K. Geisshirt");
  lcd.setCursor(0, 1);
  lcd.print("Copyright 2012");
  delay(1000);
  pinMode(LED, OUTPUT);
}
void loop() {
  for(int i=0; i<strlen(msg); i++) {
    for(int j=0; j<strlen(msg); j++) m[j] = msg[j];
    m[strlen(msg)] ='\0';
    if (m[i] != ' ') m[i] = m[i]+('A'-'a');
    lcd.clear();
    lcd.setCursor(0, 0);
    lcd.print(m);
    lcd.setCursor(0, 1);
    if (m[i] != ' ') {
      lcd.print(morse[m[i]-'A']);
      for(int j=0; j<strlen(morse[m[i]-'A']); j++) {
        digitalWrite(LED, HIGH);
        if (morse[m[i]-'A'][j] == '*') {
          delay(500);
        } else {
          delay(1000);
        }
        digitalWrite(LED, LOW);
        delay(250);
      }
    }
    if (m[i] != ' ') {  
      delay(1000);
    } else {
      delay(100);
    }
  }
}

If you haven't tried an Arduino board, it is highly recommended. With an electronic brick and a few components, it is much like LEGO for adults.

Edit: I have added a video.


GNOME 3

GNOME 3 - a review

After the arrivel of GNOME 3 and Unity, we have seen months of discussion on the future of the free desktops. Both GNOME 3 and Unity have been considered as a step backward. Many old-school Linux users believe that these new offerings are worse than the good well-documented desktops like GNOME 2 and XFCE.

Over the years I have used many different desktop environments and window managers. GNOME 2 (both for Debian GNU/Linux and Ubuntu Linux) has served me well. A couple of weeks ago, I decided to try out GNOME 3. And to jump to the conclusion - GNOME 3 is different!

In my test of GNOME 3, I use my four years old Dell XPS 1330M laptop. With an Intel Core2 Duo (2 GHz), 4 GB memory and Intel graphics, it is not a speed devil. But it is a small laptop, and I can carry it around (I'm usually on bike) easily. I have upgraded the battery to a 9-cell battery, and that gives me enough power to work for long period without plugging it to the wall. The operating system is Arch Linux (64 bit).

Is the difference between GNOME 2 (old-school desktop) and GNOME 3 a good thing? Yes, I like it. I like that the panel is so small - yeah, I know it's not a panel. And I the activity concept. I use the same 5 applications (browser, editor, terminal, word processor, and photo manager) so adding them to the activity panel is pretty nice. It took a couple of days to get use to the virtual desktops. In many years I have visualized my virtual desktops horisontal (and used Ctrl-Alt-Left/Right to move between them). Now, they are vertically organized (Ctrl-Alt-Down/Up). One thing I like is that the number of virtual desktops are changed dynamically as I move between them and starting and stopping applications.

The idea that you must use the Alt key together with the top-right menu is new to me. Luckily, a friend showed me after a week that I can power down my laptop as the menu changes when I press Alt. For one week I logged out and powered down. Knowing that the meta keys (Alt, Windows, etc.) is used throughout the GNOME Shell, makes me a bit more productive - or probably closer to my GNOME 2 productivity. I can only recommend that you read the user's manual to GNOME 3 and the GNOME Shell when you start using GNOME 3 for the first time.

One of the most critized parts of GNOME 3 has been that it is not possible to customize the desktop. Strangely, I have not encountered many problems with this. Maybe the default values are just right for me. Of course I have changed a few things, but I have not wished to customized an item and haven't been able to find it.

The network manager has been upgraded, and this is the place where I think it is a downgrade. The VPN dialogs do not allow to import configuration files. Typically your network administrator will send you the configuration in some sort of file (each VPN implementation has it own format). I can manually type in the information, but it was much nicer in previous versions where I could import it.

The default applications in GNOME 3 are fine with me. I have only changed two applications: Firefox as browser, and Emacs as editor. The GNOME Editor (gedit) is not powerful enough for a full time software developer like me (working in 3-4 programming languages at the same time).

GNOME 3 introduces a concept of online accounts. The idea is that you register your accounts on place and all application can use the information. Currently, only Google accounts are supported, but it is really nice that Evolution, Empathy and GNOME Shell calendar take advantage of it. I hope that Twitter, Facebook, LinkedIn and other web services soon will be supported.

For almost three weeks I have been using GNOME 3, and I must say I am impressed. The GNOME developers have really tried to rethink the free software desktop - and they have produced a cool desktop!

Free chemistry software - quantum chemistry

Free chemistry software - quantum chemistry
In the previous part of the journey into free chemistry software I wrote about molecular mechanics. The molecular mechanics view of a molecular system is a classical mechanical view i.e., the atoms move according to Newton's law.

Quantum mechanics revolutionized the view of the atomic world. The Schrödinger equation is a general model and number of parameters is limited. Solving a Schrödinger equation for an atomic or molecular system is often referred to an ab initio calculation. The word ab initio is latin and can be translated to from the beginning or  from first principles.

The Schrödinger equaiton - in particular the time-independent equation - can be used to calculate many different properties of chemical substances. Properties like enthalpy and entropy, and heat capacity can calculated as the partition function can be calculated from the solution. Moreover, it is possible to predict data for various spectra (IR, Raman, UV-VIS, etc.). The problem is that it is not possible to find an analytical solution for any non-trivial cases. The solutions to the equation are called wave functions. The Copenhagen interpretation of quantum mechanics is that the wave function represents the probably distribution (in space) of the electron.

In order to solve the (time independent) Schrödinger equation you must make two important approximations. The first approximation is that the nucleus of the atom is fixed in space, and the Schrödinger equation is reduced to only model the electrons. This approximation is called the Born-Oppenheimer approximation. The rationale behind the approximation is that the nucleus of an atom is much heavier that the electrons, and the nucleus moves much slower (this is probably a classical mechanical picture). The second approximation is that the wave function is a sum - or linear combination - of other functions. These functions form a basis set. The basis set is often atom orbitals (solution to the Schrödinger equation for a single atom), and they are often selected in much a manner that they require so few CPU cycles to process as possible. A popular family of basis set is the Slater-type orbitals.

There are many quantum chemistry packages in the world. From a license perspective, they fall in three groups. The first group is completely proprietary software. You buy the package (maybe the source code is included so you can compile it yourself) and can use it for the set of computers, you have bought a license for. It is not rare to find special pricing schemes for users in the academic world. Gaussian is a leading software vendor in this field, and a site licence (with UNIX source code) for commercial use is listed as roughly 40,000 USD. This might sound like a high price tag but you must remember that the development of a new drug can easily run in billions. Compared to that, the software is quite cheap - if you are in big pharma. Gaussian does provided must more that just a quantum chemistry calculation engine - it includes various supporting utilities. The group of free software packages is another group with a completely different licensing model. A typical example is MPQC (Massive Parallel Quantum Chemistry). Released under GNU General Public License it is a truly free software package. The motivation of the developers is to test new algorithm - in particular for the parallellization for using either compute clusters or multicore computers. Somewhere in between you find the third group. Software packages in this group are free to download (if you are in academia or using it for personal purposes) but you are allowed to redistribute the source code or binary. And often you must include a citation to a particular scientific paper if you publish any results based on the software. In this group you find packages like GAMESS (both US and UK versions). 


Gabedit
The program gabedit provides a uniform interface to many quantum chemistry packages including GAMESS-US, GAMESS-UK, Gaussian and MPQC. The program exists as a binary package for most Linux distributions including Ubuntu Linux and Debian GNU/Linux which makes the installation quite simple.

1,3,7-trimethylxanthine is a known (legal) psycho-active chemical. It is found naturally in coffee, tea, and soft drinks. The trivial (non systematic) name is cafferine. It is a small molecule with an aromatic ring structure.

Setting up a calculation in Gabedit
You can either draw your molecule or load a file. The structure of many molecules can be found at PubChem or similar services. A 3-dimensional structure of Cafferine can be found at PubChem. A 3-dimensional structure is nothing more that the coordinates of the nuclei of the atoms in the molecule. Using OpenBabel (discussed in previous blog entries), you can convert the PubChem files format to something that Gabedit can understand.

Setting up a calculation is simple but you are required to know and understand all the parameters and methods. For a causal user of quantum chemistry software, Gabedit might help you to allow to write configuration files manually, but the program is a thin wrapper only.

Monitoring a calculation
Once you have edited the calculation paramters, you are ready to go. It is possible to monitor the progress of your simulation but beware that quantum chemistry calculation might take hours. Gabedit will use the good old UNIX trick called nohup so you can come back later. Moreover, Gabedit let you perform the calculation on remote machines. This is useful for long calculations.

When the calculation has finished, Gabedit can assist you in analyzing the result. It is only a limited number of analyses offered, and if you need more advanced analysis, you will probably write small scripts and programs to help you.

Analyzing the result of a geometry optimization using Gabedit
The really good thing about Gabedit is that it provides a uniform interface to the most common quantum chemistry packages.

Other software packages exists e.g., Ghemical. Ghemical is fairly tight bound to GNOME, and tries to solve all needs for computational chemistry in one packages. The latest version of Ghemical is recent (October 2011).


MPQC
MPQC is a pure free software project which provides an ab initio package. It is designed to run in multicore or cluster environments i.e., in massive parallel environment. Ubuntu and Debian packages exists. Currently, two packages exist: the core program and supporting utilities. Even an Emacs mode can be found for editing the configuration files. The main mode of operation is that the user writes a configuration or input file and run the program from the command-line or through a batch system. The OpenBabel conversion utility supports MPQC and can write raw input files from structure file formats. This simplifies the usage a lot in the learning period.

In order to test MPQC, I have prepared an input file using Caffeine. As MPQC supports the calculation of thermodynamics properties (non-electronic enthalpy and entropy), my test input file will perform this analysis after the geometry optimization using the STO-6G basis set and a Hartree-Fock method. The Hartree-Fock method is only calculating the ground level state, and the thermodynamics will be somewhat inaccurate.

MPQC/Linux Speed-up
As MPQC is a parallel calculation program, it is worth analyzing the speed-up i.e., how well does scale as the number of core/CPUs increases. MPQC is parallellized using either MPI, SysV shared memory and Posix threads.

Running on multiple cores is simple with MPQC. You can specify the number of threads on the command-line. For a 4-thread calculation, the command-line is: mpqc -threadgrp "<PthreadThreadGrp>:(num_threads = 4) -o caffeine.out caffeine.in where caffeine.in is the input file and the output is found in caffeine.out.
As I have access to a hyperthreaded quad-core computer, I have tested the Posix thread parallellization (please remember that Linux has a highly optimized Posix thread implementation).

The result of my simple benchmark shows that hyperthreading is not a good idea in heavy computing environment - notice that the speed-up levels off at four cores. The reason is probably that the threads are competing for a limited resource: the floating-point units. A calculation of the Caffeine molecule took about 8 hours using 4 Posix threads, and this only calculated the ground state using the STO-6G basis set.

Summary
In general it is possible to carry out quantum chemistry calculation using free software if you can live without a fancy user interface. If you do many calculations, you might be happy to know that you can modify and extend the source code. For a causal computational chemist (maybe an organic chemist predicting spectras), free chemistry software might not be the solution yet.

Saved by Dropbox

Saved by Dropbox


I have installed Dropbox on my laptops and my phone. On my laptops I use it for two purposes: synchronization and backup. Initially, I used it for synchronization of my private and my work laptop (both computers are running Linux).

The laptop at work is a bit unstable. It crashes probably 3-4 times a week, and I believe it has something to do with the temperature of the processor. It happened to me the other way, and an OpenOffice document was left in a state where the file did not contain anything else that zeroes.

Luckily, Dropbox keeps track on my revisions of the files. That means that I was able to go one revision back and recover much of my file (probably lost half a page). Needless to say, I'm pretty happy with the Dropbox service now!