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gdpc - a program for visualising molecular dynamic simulations
Copyright (C) 1999 Jonas Frantz
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
1. Background
2. Usage
3. Input file formats
4. Source files and compiling
5. Reporting bugs, suggesting features and known bugs
6. Disclaimer
7. About the author
1. 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 cube 30 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.
readinput.c This file contains the functions which handles reading the
data from the inputfile.
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 been compiled on
Redhat 6.0 both i386 and alpha architectures, but I can't see why it
wouldn't be compilable in another environment as long as you have gtk+ and
Imlib properly installed.
5. Repoting bugs, suggesting features and known bugs
Bugs can be reported to jonas.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 1.28)
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 recristallisation of amorphous areas in
a-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.
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