WWW-CrystPic

WWW-CrystPic (Java 3D-applet) is program for visual analysis of Crystal Structure Model (CSM) with possibility of calculation of interatomic distances and angles

PART I

Crystal Structure Model: REPRESENTATION and MANIPULATIONS

You find a required crystal phase in WWW-MinCryst DataBase, for instance, PHLOGOPITE [1], Card No: 3658, and start program by button “WWW-CrystPic” (Upper Menu).
Please wait... and on the screen you will see CSM of phlogopite [1].

CSM is presented by color spheres (balls) with the radii proportional to ionic radii.

Unit Cell is oriented (default): a-axes is directed on the spectator, b – to the right, c - upward the screen. XYZ-axis of View Camera are in the left bottom corner.

Click and hold the corresponding mouse button pressed to execute the following operations:

ROTATE CSM in any direction - Left Button Mouse (LBM);

ROTATE CSM around Z-axes - Shift + Left Button Mouse (Shift + LBM)

SHIFT CSM on the screen plane (Right Button Mouse - RBM);

ZOOMING CSM (Middle Button Mouse - MBM).

Note: The manual manipulations are effective for CSM of small and middle complexity.
For more complex CSM (and slow PC) it is necessary to use procedure of automatic rotation (see below).
The rotation speed visible increase in polyhedron-representation of CSM and decrease in balls-representation. In mixed (balls and polyhedrons) representation the indicators for balls can be temporarily switched off , if it is necessary to rotate a complex CSM. It concerns as continuous rotation by a mouse, and quasi-continuous rotation in an automatic mode.

You see also the control panel tools (CPT) for a visual analysis .

All indicators and commands (buttons) requires Left Button Mouse-click, further, LBM-click.

“Basic Positions”-mode presents CSM by list of basic atomic positions with their attributes (see bottom part of CPT):

  1. color rectangles with chemical symbols of the ions represent the occupancies of the positions and enable to change a color of ions in positions (LBM-click); compound rectangles represent isomorphism of ions in position.
  2. indicator on/off to represent CSM by spheres (balls);
  3. indicator on/off to represent CSM by polyhedrons;
  4. indicator on/off to highlight isomorphic positions;
  5. indicator on/off to highlight defective positions.

“Atomic Sorts”-mode presents CSM by list of atomic sorts with their attributes (see also bottom part of CPT):

  1. color rectangles with chemical symbols of the ions represent the sorts of the atoms (ions) and enable to change a color of ions on sorts (LBM-click); compound rectangles represent “isomorphism” of sorts of ions.
  2. indicators on/off to represent CSM by spheres (balls), by polyhedrons, to highlight “isomorphic” sorts and highlight “defective” sorts.

Indicators on/off for command “All” to represent all basic atomic positions and all atomic sorts in balls or in polyhedrons, to highlight all isomorphic positions or “isomorphic” atomic sorts and all defective positions or “defective” atomic sorts.

INFOFIELD – the information field for recording of calculated interatomic distances and angles.

Note: CSM representation by balls (spheres) requires to switch off polyhedrons indication and, accordingly, CSM representation by polyhedrons requires to switch off balls indication. Mixed representation of CSM (balls and polyhedrons) requires to switch on indication of balls and polyhedrons.
Isomorphic ions, if the indication is switched on, highlight by their color on 0.5 sec. and defective positions (sorts) highlight by their color 0.5 sec. with in interval 0.5 sec.

Also in upper part of CPT the following control instruments are represented.

Full Screen screen size will be increase to right;
Unit Cell indicator on/off for Unit Cell;
Camera View Position (CVP) indicator on/off for CVP
Only Selected indicator on/off to isolate the chosen CATION (one is on the screen !) coordinated by anions (selecting-operation)
Link Camera to Selection indicator on/off to shift the isolated CATION coordinated by anions in the screen centre (linking-operation)
Reset Camera to return of CSM to initial position after switch off indicators Only Selected and Link Camera to Selection
Radius dynamic decreasing/increasing of the balls radii (1 – 100); 100% - full radius; default radius is - 50%)
Ñentral Projection indicator on/off for Central Projection
Edges indicator on/off for polyhedron edges
Backgr Color to change a background color
a b c, (hkl), n, ADCn, RMCn, Orient Command Block for propagating of Unit Cells in the given direction. Accordingly, a choice of direction-hkl-indexes on a,b,c-axis, number of the added Unit Cells, addition of Unit Cells, removal of the added Unit Cells, and also hkl-orientation of CSM (the chosen direction on the spectator)
ADC a9/RMC a9, ADC b9/RMC b9, ADC c9/RMC c9, ADC v27/RMC v27 Command Block for automatic propagation of the given number of Unit Cells
Accordingly, addition/removal of 9 Unit cells in a plane, perpendicular to axes (a, b, c), addition of 27 Unit Cells
Fragment, Set HKL, n, (+, ─ ) Command Block for hkl-fragmentation of CSM. Accordingly (The sequence of commands is numbered),
  • indicator on/off for the procedure hkl-fragmentation of CSM, (4)
  • inputing hkl-indexes, deciding the orientation and thickness of hkl-fragment (1)
  • preliminary orientation of CSM (the plane of a hkl-fragment is parallel to the screen plane, (2)
  • preliminary choice of number of hkl-fragment [use (+,-), but to set not necessarily], (3)
  • consecutive viewing of fragments, (5)
Continue, X(Z) Y, Rotation Command Block, accordingly, (the sequence of commands is numbered):
  • indicator on/off for quasi-continuous rotation of CSM around of the chosen X(Z),Y-axes, (2)
  • choice of rotation-axes(is) and rotation-speed in grad/sec. (0 or from 1 up to MAX - it is equal also to turning on the given angle, if indicator “Continue” is off), (1)
  • switch on “Rotation of CSM, (3)
Max Distance (angst.) max-number for rejection of the interatomic distances calculated in an automatic mode

It is possible to use command Orient for preliminary orientation of CSM on the given hkl-indexes.
It is especially important, as automatic rotation is specified only around of two axes located in a plane of the screen. If automatic rotation around of an axis directed on the spectator is necessary, axis, preliminary, must be placed in a plane of the screen by command Orient.


PART II

Crystal Structure Model: MEASUREMENT of INTERATOMIC DISTANCES and ANGLES

For CSM presented by balls it is possible to:

a) measure the interatomic distances and angles in automatic mode for any chosen CATION coordinated by anions.

b) measure the distances and angles between any ions in manual mode.

ñ) measure the distances and angles for isolated and shifted CATION coordinated by anions in manual mode.
Isolated and shifted CATION coordinated by anions (switch on the indication of anions !) can be zoomed in and out on the screen (by MBM) and can be rotated in any direction continuously by LBM or quasi-continuously in automatic mode; CATION can be enclosed in POLYHEDRON and balls-cation will be visible through translucent polyhedron.

aa) LBM double click on chosen CATION encloses it in a cube-frame and in INFOFIELD there is the result of automatic calculation.
It is necessary to make LBM double click in “pure field” to remove cube-frame and then to choose following CATION. At that chosen CATION can be isolated (selecting-operation), shifted in the centre of the screen (linking-operation), zoomed in or out, and enclosed in translucent polyhedron.
This procedure is good for CATIONS with small C.N. (triangle or tetrahedron).
For large C.N. is applied a rejection of the superfluous distances on the given number (default > 4 angstr., see Max Distance).

bb1) Shift + double click LBM on any two chosen ions, in rapid sequence, makes their “horned” and connects their by line, and in INFOFIELD there is the results of the distance measurement (calculation).
Make RBM double click to remove “horns” and line and then to choose following two ions for measurement of the following distance.

bb2) Shift + double click LBM on any three chosen ions, in rapid sequence (second ion is vertex of angle), makes their “horned” and connects their by lines, and in INFOFIELD there is the results of the angle measurement (calculation).
Make RBM double click to remove “horns” and lines and then to choose following three ions for measurement of the following angle.

ññ) Shift + double click LBM on any chosen CATION encloses it in a cube-frame and in INFOFIELD there is the results of automatic calculation of distances and angles.

NOTE: Practically all commands (and modes) can be used in a combination with each other.
For instance, rotation of CSM
in automatic mode can carry out in any situations.
By command
Orient on the given hkl-indexes, at first, CSM is oriented and then, by commands ADCn(RMCn) or by commands ADC a9, ADC b9, ADC c9, ADC v27 are propagated Unit Cells.
In
Fragment mode, at first, can choose the required fragment [SiO(4)-chain, band or layer] and then, propagate Unit Cells in the required directions to grow, in fact, fragment.


Please direct your questions of practical using the WWW-CrystPic program to Chichagov A.V.