xmdview.txt

一个很好的分子动力学程序

                                   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 all increments to the default values:

                          * Rotations: 5 degree increments
 Reset 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          Set (in degrees) by how much the atoms will be
 Increment             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 (in centimeters) by how much the atom radius
 Set Atom Increment    will change each time a "change atom size" command
                       is activated.
                       Set (as a percentage of actual atom radius) how
 Set Atom Center Size  large to draw a white circle inside the atoms on the
                       screen.
                       Set (as a percentage of actual atom radius) where to
                       draw the white circle inside the atom. For example
 Set Atom Center       "0 0" means to in the actual center of each atom,
 Position              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.
                       When selected, any atoms that are clicked on will be
 Hide Atoms            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.
                 This button toggles between drawing the atoms as points or
 [Points/Circles]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.
               The free surface/repeating boundary conditions for the
               current file. Note that 1 stands for a repeating boundary,
 [BOUND COND:] 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.
               The current magnification of the atoms. The initial
 [ZOOM:]       (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.