md/coord.d
, then run it for 10 timesteps with thermostat
4, then 100 timesteps with thermostat 1 at 300 K.
Now generate the main result by running the simulation for 5000 timesteps with thermostat 4. You may want to run "top" in another window to check that the simulation is getting nearly all of the CPU time; both Fungimol and Netscape tend to take up significant amounts of CPU time and slow down the long simulation run. As described earlier, you can watch the movie as it is produced. This takes about 10 minutes on a 600 Mhz Pentium Pro.
All that remains is to convert the movie into an animated
.gif
file suitable for insertion into a web page. Start
the movie playing as alluded to in the previous paragraph, and arrange
the movie on the screen the way you want it to appear in the
.gif
file. The size of the Fungimol window will be the
same as the default size of the image on the web page, so you'll
probably want to shrink it down to much smaller than you would
normally use. You may want to mark part of the barrel invisible. To
mark half the barrel invisible without marking any of the projectile
invisible, select half of the barrel when the projectile is not in the
barrel.
To generate the .gif
file, we write a .ppm
file, then use an external utility to convert the .ppm
file to a .gif
file. The command for saving screen shots
as a .ppm
file is called "SaveMovie". It is not bound
to any key, so we run it by using the command for executing any
command, which is meta-semicolon. You'll want to start recording the
movie just after it begins a repetition, so time your meta-semicolon
carfully. Since we simulated 5000 timesteps and recorded a frame
every 50 timesteps, the movie is 100 frames long. We aren't going to
be able to press meta-colon at the first frame, so we'll write 95
frames to the .ppm
file. The dialogue in the text window
goes like this:
The movie is recorded as it is displayed on the screen. The last lineThe configuration has these read/write fields: Number Field name Field type Field value 1 Command to execute Action DoNothing Give the number of a field to edit, or press 0 to exit: 1 This slot implements the protocol Action. The currently chosen factory is DoNothing. Do you want to change the factory and reset to the new factory's default configuration? y The available factories are: Number Name ... 30 SaveMovie ... What is the number of the factory you want? 30 Editing the configuration... The configuration has these read/write fields: Number Field name Field type Field value 1 Frames to skip between saved frames Integer 0 2 Frames to write Positive Integer 1 3 PPM file name to write String Unspecified.ppm Give the number of a field to edit, or press 0 to exit: 2 The old value of the slot is 1. What do you want the new value to be? 95 The configuration has these read/write fields: Number Field name Field type Field value 1 Frames to skip between saved frames Integer 0 2 Frames to write Positive Integer 95 3 PPM file name to write String Unspecified.ppm Give the number of a field to edit, or press 0 to exit: 3 The old value of the slot is Unspecified.ppm. What do you want the new value to be? pic.ppm The configuration has these read/write fields: Number Field name Field type Field value 1 Frames to skip between saved frames Integer 0 2 Frames to write Positive Integer 95 3 PPM file name to write String /tmp/pic.ppm Give the number of a field to edit, or press 0 to exit: 0 The configuration has these read/write fields: Number Field name Field type Field value 1 Command to execute Action SaveMovie Give the number of a field to edit, or press 0 to exit: 0 Finished writing to pic.ppm
Finished writing to pic.ppm
is printed when the
writing is finished, which can happen when the 95 frames have been
written or when Fungimol is exited.
If you want to decrease the temporal resolution, you can specify a
nonzero value for the configuration slot Frames to skip between
saved frames
. For example, if you wanted to see every other
frame in the result, then you would specify Frames to skip between
saved frames
as 1, and then specify half as many frames for the
Frames to write
slot.
At this point the movie is in the Portable Pixmap file
pic.ppm
. If you have ImageMagick installed, you can then
use the convert
command to convert this to an animated
GIF:
Here$ convert -delay 10 -loop 1000000 pic.ppm bang.gif
-delay 10
means to delay 10/100 seconds between
frames, and -loop 1000000
means the animation should loop
essentially forever. Here is the result: