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Inputing Structures
A new structure can be entered into Amass with a few simple steps.
First, ensure that you have a structure datafile in the correct format.
Here is an example of the current format:
2
0.0 0.0 0.0 0.5
1.0 0.0 0.0 0.5
3
0.5 0.0 0.0 0.1 1.0 0.0 0.0 0.1
0.0 0.5 0.0 0.0 0.0 1.0 0.0 0.1
0.0 0.0 0.5 0.2 0.0 0.0 1.0 0.1
The first line is the number of spheres in the dataset,
followed by the correct number of lines of sphere information,
followed by the number of cylinders/cones in the dataset, followed
by the correct number of lines of cylinder information.
Sphere
information consists of the X, Y, and Z coordinates of the center,
followed by the radius. Cylinder/cone information consists of
X, Y, and Z coordinates and radii of each base. To make a conventional
cylinder, set R_1 = R_2. To make a true cone, set one of radii = 0.
Here's what it all means:
## of Spheres (integer)
X Y Z R (may have decimals, any number of spaces separating, no commas)
.
.
.
## of Cylinders (integer)
X_1 Y_1 Z_1 R_1 X_2 Y_2 Z_2 R_2
.
.
.
In order to enter a file, you must select Read File in the drag menu
in the main Amass display window. Hold down the right mouse button
to do drag down to Read File.
Once selected, Amass will query you for a structure number. You
may enter 1-6. If you will be entering multiple structures, it is
a good idea to keep track of what goes where. Enter the structure
number in the xterm in which you opened Amass, and press return.
Now Amass will query you for the filename of your structure file.
Enter it in the xterm. If Amass cannot find or read the file, you
will have to repeat the process.
Once the file is opened, Amass will automatically switch the display
to that structure number, and compute the added mass matrix of each
component of the structure, summing to get the entire structure.
At this point, you may choose to enter a
motion file,
and carry out runs using this structure.
Additionally, you can alter the
current dataset, creating a new one based on a translation
in X, Y, and Z.
Continue
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