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Viewer

ICC 1

Conservation Principles:

Conservation Laws and
Accounting

Conservation of Mass

Conservation of Energy

Conservation of Linear
Momentum

Conservation of Angular
Momentum

ICC 2

Materials:

Equations of State

Energy Properties

Entropy

Transport
Properties

ICC 3

Microchemical Systems:

Fluid Mechanics

Heat and Mass Transfer

Microfluidics

ICC 4

Molecular Modeling:

Models and Interactions

Molecular Simulation

Property
Prediction

ICC 5

Environment and
Sustainability:

Life Cycle
Analysis

ICC 6

Process
Dynamics

ICC 7

System Synthesis and Process
Integration

ICC 8

Conservation Principles for
Continua:

Conservation Laws and
Accounting

Conservation of Mass

Conservation of Energy

Conservation of Linear
Momentum

Conservation of Angular
Momentum

Crystal Viewer

I. Pre-Test

II. Topic Notes

Introduction

Motivation and Process

Heat Transfer

Mass

Momentum and Fluid
Transport

Industrial Process

Models

Van der Waals

Electrostatic
Interactions

Stretching Interactions

Bending Interactions

Torsion Interactions

Inversion
Interactions

III. Examples

Lennard-Jones
Potential

Lennard-Jones Force

Crystal Viewer

Reaction Equilibrium

Piston
Cylinder

IV. Exercises

V. Post-Test

When the Crystal Viewer application is started, it should look something like
this.

The left side of the display, referred to as the
"Control Panel", contains controls that allow the user to interact with the
simulation.

The "Crystal " tab (crystal tab) has a drop-down menu
(crystal selection) that allwos the user to select different
crystal structures.

Below the crystal selection are text boxes where the lengths
of the three primitive vectors, a vector, b
vector, and c vector can be changed. Not all vectors
can be adjusted independently for all crystal structures. That is to say,
changing the length of the a vector may also (automatically)
change the length of the b vector. Vectors which have values
that are tied together are denoted by the color of the surrounding box. Changing
the length of a vector with a red surrounding box will automatically change all
other vector lengths with a red surrounding box. The lengths are given in units
such that each sphere is of unit diameter.

Next are text boxes where the angles between vectors can be adjusted
(alpha, beta and gamma). Some
crystal structures require that some or all of these angles remain constant, and
in those cases, the angles cannot be changed by the user. The angles are
measured in degrees.

The last item on the crystal tab is a slider (cells
per side slider) that allows the user to change the size of the
crystal. The values on the slider indicate the number of planes repeated in each
primitive-vector direction.

In the image shown below, the values are :

crystal selection is Monoclinic

a vector is 1.0

b vector is 1.25

c vector is 1.5

beta is 91

cells per side slider is 7

All vector lengths can be adjusted independently as the boxes surrounding
them are different colors. The beta angle is the only angle that the user can
adjust.

The second tab on the "Control Panel" is the plane tab. The
plane tab primary purpose it to allow the user to select the
crystal's plane to view. Additionaly, several graphic options can be toggled.
The plane tab is shown below.

The "Display Features" section contains buttons to turn on/off various
graphic related features. The clip button clips the right side
of the crystal to the currently select plane as shown below :

The highlight button colors the molecules that are in the
currently selected plane yellow so they are easy to identify. Molecules not in
the currenly selected plane remain red.

The show plane button displays a "thin transparant sheet"
through the currently selected plane position as shown below :

The show boundary button toggles the display of the white
frame surrounding the crystal.

The Miller indices can be controlled by the user with the h miller
indices, k miller indices and l miller
indices values. Negative indices are entered using a minus sign (no
overbar is used).

The slider (plane selection slider) below the Miller index
allows the user to move the plane to different positions at fixed orientation.
If clipping is turned on, planes of atoms will appear or disappear as the plane
is moved. The slider moves the plane continuously. The text box next to the
plane selection slider displays the distance from the origin in
unit vector increments.

On the right is the "Graphics Panel" which contains an image of the crystal.
Although the image appears two dimensional, the crystal is actually three
dimensional.

The following table outlines the features available for manipulating the
three dimensional figure.

Key/Mouse Combination

Function

h

Move figure to home (original) position.

x or X

Rotate figure around the X axis. Case of letter determines direction
of rotation.

y or Y

Rotate figure around the Y axis. Case of letter determines direction
of rotation.

z or Z

Rotate figure around the Z axis. Case of letter determines direction
of rotation.

=

Zoom in on center of graphic.

-

Zoom out on center of graphic.

p

Toggle "perspective" on/off.

1 - 9

Set the number of "shells" to display.

i

Toggle "shell" display on/off.

a

Toggle molecule display on/off.

Left Mouse Button + Mouse Drag

Rotate the figure in the direction of the mouse drag (only applicable
to X and Y axis.

Right Mouse Button + Mouse Drag

Move the figure in the direction of the mouse drag.

Ctrl + Left Mouse Button + Mouse Drag

Set depth percentage.

Ctrl + Right Mouse Button + Mouse Drag

Set slab percentage.

Ctrl + Left Mouse Button + Mouse Drag Up

Zoom in on center of graphic.

Ctrl + Left Mouse Button + Mouse Drag Down

Zoom out on center of graphic.

Ctrl + Right Mouse Button + Mouse Drag

Inertially rotate in direction of mouse drag.

Ctrl + Right Mouse Button Click

Stop Inertial rotation.

Ctrl + Shift + Left Mouse Button Drag

Rotate around the Z axis.

Example:

NOTE : THE CRYSTAL VIEWER APPLICATION DOES NOT CURRENTLY SUPPORT
PLANE SELECTION FOR CRYSTALS THAT CONTAIN MOLECULES WITH MORE THAN ONE
ATOM.

Select the fcc structure, and in the Plane tab set clipping 'on' and
have the plane show the (111) face. Then rotate the image so that you are
looking straight on at this face, as shown here.

Note the atom that is at the center of the face, at or near the point where
the three lines of the reference box intersect (or hold a pencil at this point
on your screen so you can keep reference to it). Now click the cursor in the
Position text box on the left, and use the arrow keys on your keyboard to move
the plane toward or away from you. As the plane travels from one layer to the
next, note what happens on and directly around the point of reference. You
should see three distinct structures that repeat ABCABC as you move the plane
back and forth. All planes have a 2-D hexagonal structure, but each is
positioned differently from one layer to the next.

Now do the same with the hcp structure. Set the Miller index to show
the (0001) plane, and rotate the image so you are looking down at it. The
hcp uses a two-atom basis, and as you increment the plane from one
layer to the next, two layers of atoms will appear or disappear at a
time, and you won't be able to see the alteration of the layers (each layer that
appears will be positioned as the previous one). So instead of using the text
box to position the plane, move the slider in small increments. It is also
better to turn off the "Show plane" toggle. Note that the 2-D structure within
each layer is again hexagonal---the same as that for the fcc
system---but the layers now alternate ABABAB.

Crystal Viewer

The development of this page is sponsored by the National Science Foundation through an Engineering
Departmental Level Reform grant.
Copyright 2006-2009, Texas A&M
Chemical Engineering Department, All Rights Reserved.

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