XMDVIEW

This program runs under X Windows on Linux, and displays COR files in three dimensions. You must start the program with the command

xmdview inputfile
where inputfile is the name of the desired input file. Valid types of input files are cor, rcv, and xyz files.

XMDVIEW can be used from Marigold (that is, when you are sitting in front of Marigold), if you run it on a Linux machine. In other words, if you sit at Marigold and log into a Linux computer, you can run XMDVIEW on the Linux computer and view the output on Marigold.
The way to do this is to run XMDVIEW with the following command:

xmdview -display Marigold:0.0 output.cor
This tells the Linux computer to run XMDVIEW but to display the output on Marigold. The program displays a menubar and toolbar across the top of the screen, from which commands will be activated. The 4 menus (in blue) and their submenus are:
Menus
File
Open Open a new file.
Print Print the current selection to a PostScript file.
Quit Quit the program.
Options
Reset Increments Reset all increments to the default values:
  • Rotations: 5 degree increments
  • Moves: 1 Angstroms (1e-8 cm) increments
  • Zoom: Magnification of 1.0
  • Atom Size: 0.1 Angstroms (0.1e-8 cm) radius
  • Atom Center Size: 0.0 percent of atom radius
  • Atom Center Position: center of atom
Set Rotation Increment Set (in degrees) by how much the atoms will be rotated each time a rotation command is activated.
Set Move Increment Set (in centimeters) by how much the atoms will move each time a move command is activated.
Set Zoom Increment Set by how much the magnification will change each time a zoom command is activated.
Set Atom Increment Set (in centimeters) by how much the atom radius will change each time a "change atom size" command is activated.
Set Atom Center Size Set (as a percentage of actual atom radius) how large to draw a white circle inside the atoms on the screen.
Set Atom Center Position Set (as a percentage of actual atom radius) where to draw the white circle inside the atom. For example "0 0" means to in the actual center of each atom, while "33 33" means to draw circles with centers about 1/3 of the atom radius to the right and above the actual atom center.
Atom Numbers Display the actual atom numbers on top of the points or circles drawn for the atoms.
Stereo Vision Display the atoms in Stereo Vision format for 3D viewing.
Hide Atoms When selected, any atoms that are clicked on will be removed from the screen (hidden) until a "Show All Atoms" command is recieved.
Show All Atoms Show all atoms, including any that were previously hidden from viewing by the Hide Atoms command.
Goto Step Go to a certain step (or the nearest) in the INPUT file.
Filters
Filtngh Not yet operational.
Help
Topics Lists all of the quick key combinations for using the keyboard to activate commands in XMDVIEW.
About Provides the version information and name of the program authors.

The toolbar contains buttons which activate commands when clicked on. Some of the buttons can be held to repeatedly activate their commands.    The available buttons are:
Buttons
[|<<] Goto the First Step in the INPUT file.
[<] Goto the Previous Step in the INPUT file.
[>] Goto the Next Step in the INPUT file.
[>>|] Goto the Last Step in the INPUT file.
[RES] Restore all rotations, moves, zooms, and size changes to the default values. Also resets the atom type to Points.
[Rt<] Rotate Left.
[Rt>] Rotate Right.
[Rt+] Rotate Up.
[Rt-] Rotate Down.
[Mv<] Move Left.
[Mv>] Move Right.
[Mv+] Move Up.
[Mv-] Move Down.
[Zm+] Zoom In.
[Zm-] Zoom Out.
[At+] Make the Atoms appear Larger.
[At-] Make the Atoms appear Smaller.
[Points/Circles] This button toggles between drawing the atoms as points or as circles. When the button reads Points clicking on it will redraw the atoms as points; when the button reads Circles clicking on it will draw atoms as circles.

In addition to the buttons, there is an information window which displays:
On-Screen Information
[FILE:] The name of the INPUT file.
[STEP:] The current step in the INPUT file.
[RUN:] The run number of the INPUT file.
[BOUND COND:] The free surface/repeating boundary conditions for the current file. Note that 1 stands for a repeating boundary, while 0 stands for a free surface. So, 0,1,0 would mean free surfaces in the X and Z directions, and a repeating boundary in the Y direction.
[BOX SIZE:] The size, in Angstroms, of the box.
[PARTICLES:] The total number of particles.
[ORIENTATION:] The current orientation axes of the partile array.
[XCEN:] The current horizontal center (in centimeters) of the screen. A value of 0 is the actual center of the screen.
[YCEN:] The current vertical center (in centimeters) of the screen. A value of 0 is the actual center of the screen.
[ZOOM:] The current magnification of the atoms. The initial (default) magnification is 1, but in order to clearly see atom numbers a zoom of around 4 is usually preferable.
[ATOM:] The drawing radius of the atoms. The initial (default) radius is 1.
[PNUM:] The atom number of the Selected Particle, which can be chosen by left-clicking on any atom on the screen.
[TYPE:] The atom type of the Selected Particle.
[POS:] The position, in angstroms, of the Selected Particle.
[NNUM:] The atom number of the Neighbor Particle, which can be chosen by right-clicking on any atom on the screen.
[TYPE:] The atom type of the Neighbor Particle.
[POS:] The position, in angstroms, of the Neighbor Particle.
[SEP:] The distance, in angstroms, between the Selected Particle and the Neighbor Particle.