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This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

My email : jonas.frantz@helsinki.fi

GDPC Documentation

Contents

Background
Usage
Input file formats
Source files and compiling
Reporting bugs, suggesting features and known bugs
Disclaimer
About the author
Background

gdpc was written as a replacement for dpc, a visualising tool for molecular dynamics. dpc was written in the beginning of the nineties by Kai Nordlund and had various problems with event handling. Kai asked me to take a look at it, and fix it if I could. After writing the original sourcecode, Kai had added many different features, leaving the code as a total mess. I had no chance of making out what was wrong with it, so I decided to try to write it from scratch using GTK+.

After some weeks of coding I had a usable version of it, which I asked some of my co-workers to try out. They gave me suggestions for new features and reported bugs, after some more weeks of coding I implemented the graphical setupwindow so new users could learn to use it more easily. After major code cleanup in version 1.20, I decided that gdpc was stable and bugfree enough that it could be released to the public.

2. Usage

gdpc is mainly and most easily used from the graphical initialization window but for faster usage I recommend the command prompt. Using gdpc:s setupwindow is almost selfexplanatory, if you cant figure out what an option does test it. From the command prompt the only necessary options to run gdpc are the column representations and the input file. The column representations describe from what column gdpc tries to read certain data, the first column respresents x, the second y, the third z and the fourth t. If the input file s in xyz format the t column will be skipt and the time will be read from the input datas headers.

The usage of the program is pretty easy to learn and by doing some testing with it you should learn to master it. To demonstrate gdpc I have included som example input files liquid.out and md.movie, the first being in general file format and the other in xyz file format.

They can best be tested with the commands: gdpc m 2 d 20 erase 1 2 3 4 liquid.test gdpc m 2 d 10 erase xyz 2 3 4 5 md.test gdpc m 2 d 10 erase usetypes xyz 2 3 4 5 manytypes.test

3. Input file formats

The general file format consists of at least four coulmns of data, x,y,z and t. gdpc will read data to each frame as long as the t column data stays the same, after that it will plot the frame and start reading the next frames data.

The xyz file format consists of several frames with their own headers. The header consists of two lines, the first consists of only one number the number of atoms. The second line is a comment line and it is from this line that gdpc searches for the time, actually it searches for the string "fs" and when found it, takes the number before this string. Then follows as many lines of atom data as was declared on the first row of the header. After reading the data it expects another header directly after the atomdata has ended.

4. Source files and compiling

  main.c        The programs main code can be found in this file. The confi-
                guration of the window and calling other important functions
                is handled here.
  drawatoms.c   This file contains functions relevant to the drawing of the
                atoms to the pixmap and the rotating of the coordinates.
  rotate.c      This files contain functions that handle the buttons of the
                rotations.
  sort.c        This file contains a function for sorting the coordinates.
  colors.c      In this file the settings of the colorschemes are made.
  setup.c       This file contains the functions for the graphical initialization 
                and setup window and everything related to it.
  parameters.h  This file contains default parameters for most options, the
                version number and some basic structures.

To compile gdpc you have to have gtk+ 1.2 and Imlib installed on your system. You can get gtk+ from http://www.gtk.org and you'll find Imlib on http://www.labs.redhat.com/imlib. gdpc has to this moment only been compiled in a Redhat 6.0 both i386 and alpha environments, but I can't see why it wouldn't be compilable in another environment as long as you have gtk+ and Imlib installed.

5. Repoting bugs, suggesting features and known bugs

Bugs can be reported to jons.frantz@helsinki.fi or to knordlun@beam.helsinki.fi. Please include the input files you were running, the exact parameters used when the bug occured and a reproducable description of what you're doing when the bug occures.

New features can be reported to jonas.frantz@helsinki.fi, dont expect them to get implemented at the moment of the arrival of the mail, because I got other things to do as well.

No known bugs at this moment (V 1.24)

6. Disclaimer

I can not be held responsible if this program fucks up your computer. gdpc comes with no warranty.

7. About the author

My name is Jonas Frantz, when I'm not working as a research associate at the Helsinki University accelerator lab I'm studying physics. I'm beginning my third year of studies this fall and I expect to finish them in about 1-2 years.

My summerjob at the acceleratorlab contains of simulating SiGe interface recoils, if you don't know anything about materialphysics, I can tell you that it practically about giving a kinetic energy to one atom in the SiGe interface and to watch what happends (mostly atomic movement over the interface(mixing)).

Update Summer 2000 : This summer I'm simulation bond breaking in Si, primarily electronic sputtering of Si surfaces and reconstruction of amorphous areas in c-Si.

gdpc is a very useful tool in visualising what happends in the simulation and creating demonstrative pictures from them and I have had lots of help from it.