NEWLAUE - LAUE SIMULATIONS AND INDEXING

INTRODUCTION

When the program starts the option menu is displayed on the left of the screen. Options may be selected by typing the first four characters of the displayed name. A prompt is output at the bottom of the screen requesting the selection of an option with the current default option being displayed in square brackets. Options are of two types, those which set parameter values and those which are program commands. When a parameter value is to be input, this may be done, in general, in a number of ways.

If the default option is the required option then a carriage return, <CR>, may be input in which case the program will prompt for the required value. Alternatively the value itself may be given directly (or the parameter name followed by the value).

If the default option is not the required option then the required parameter name is given. If this is not followed by a value then the program will prompt for the required value. If it is followed by a value then this value will become the new value for the parameter.

CTRL/Z reprints the option menu. This may be necessary on some terminals if the alpha screen is erased after a plot has been displayed. CTRL/Z may also be used to cancel any other prompts throughout the program (but not cancel cursor options).

Calculation of the pattern commences when the START option is selected. START has to be reused every time a pattern parameter is altered.

List of sections:

Parameters
Commands
Files

PARAMETERS

Introduction

CELL
WMIN
WMAX
DMIN
DISTANCE
RADIUS
ORIENT
PX
PY
PZ
SYSTEM
SPINDLE
ABSENCES

CELL

Each parameter is individually selected by name and the program prompts for input value (cell length in Angstroms, angles in degrees).

For some crystal systems only some of the parameters need be defined, e.g., for Cubic systems only A is sufficient, B=A, C=A , ALPHA=90, BETA=ALPHA, GAMMA=ALPHA are implied. If the user insists in supplying values to surplus parameters, correct or incorrect ones, the program will ignore them, in fact it resets them when the calculation starts. In such cases the list in the Menu and the hard copy will leave the value field blank.

WMIN

WMAX

DMIN

DISTANCE

For transmission (forward reflection) Laue enter a positive number.

For back reflection Laue enter a negative number.

RADIUS

Topographers Note: The cassette used in topography stations is square with half-diagonal (equivalent to radius here) of 50mm.

Notice that if the SCALE option is set to FULL all spots within this radius will be plotted. If SCALE is set for another device and if the value of radius is large compared with the physical dimensions of the plotting area for that device (defined by the square border) will not be plotted.

ORIENT

A = Mis-setting angles:

This the orientation method used by protein crystallographers.

Prompts are given for:

• Reciprocal axis along rotation axis

• Reciprocal axis nearest x-ray beam axis in plane defined by beam axis and rotation axis.

• Camera type or fiducial positions. The prompt is:

  >>> Camera type (C1=Arndt-Wonacott, C2=Huber) or fiducial values
  [current values]:
  

  For the camera type question the reply may be either C1, C2 or six numerical values. The fiducial values for the camera types C1 and C2 are as follows:

  C1 (Arndt-Wonacott): -5000 -4000   -5000  4000    5000  4000
  C2 (Huber):          -4000  5000   -4000 -5000    4000 -5000
  

  These fiducial positions are used by NEWLAUE for plotting on predicted patterns as well as being made available for output to a .gen file via the DATSAV command.

V = Vector (Poles or Direction):

This option, for topographers, invokes code taken from program FSLP.

There is little information at present on the options and method of calculation used as well as conventions assumed. One useful reference is the report "Stereographic Projections by Computer", R.A.Ploc and P.C.Barnett, Atomic Energy of Canada Ltd, AECL-3741 and papers by the same authors in Journal of Materials Science (1983), pp.1083-1088 and in Journal of Applied Crystallography 5 (1972) 135 and 11 (1978) 713.

It prompts for Poles or Directions defined in the form

PQ=xx,xx,xx     or      Dq=xx,xx,xx
where           Q is  A,B,C,1 or 2
and        xx is a value

For example: DA=1,1,1, DB=0,-1,0 is valid input

DA corresponds to a vector parallel to the X-ray beam

DB is a vector which is horizontal

DC is a vector which is vertical and perpendicular to both DA and DB

Note that only two directions are needed, the third is implied. The program gives the option to define the third direction as well but it is not clear why.

Thus for <111>  (body diagonal)
enter DA=1,1,1
and   DB=any vector perpendicular to [111], for example 1,-1,0.

The effect of this method of orienting the crystal is to set the mis-setting angles Phi(x), Phi(y), Phi(z) by the amount needed to correspond to Orientation +c*,+a*. It is not clear at present whether this means that a* is along DA and a* along the projection of DB.

The values of the vectors are listed before returning to the command menu. Notice that subsequent change of the mis-setting angles using the PX,PY,PZ commands directly does not update the vector values.

PX

PY

PZ

SYSTEM

The value of `crystal system' determines the cell parameters required as shown below.

System           Required params      Implied relationship

Triclinic        a,b,c                No relationships
                 alpha,beta,gamma

Monoclinic       a,b,c beta           a NE b NE c
(NB Unique axis b only)               alpha=gamma=90

Orthorhombic     a,b,c                a NE b NE c
                                      alpha=beta=gamma=90

Tetragonal       a,c                  a = b NE c

Hexagonal        a,c                  a=b NE c
                                      alpha=beta=90
                                      gamma=120

Rhombohedral     a alpha              a = b = c
                                      alpha=beta=gamma not 90

Cubic            a                    a=b=c
                                      alpha=beta=gamma=90

P   Primitive

R   Rhombohedral centring

A   Face centering in which there is a translation vector b/2  c/2  in
    the A faces of the basic unit of the space lattice

B   Face centering in which there is a translation vector a/2  c/2  in
    the B faces of the basic unit of the space lattice

C   Face centering in which there is a translation vector a/2  b/2  in
    the C faces of the basic unit of the space lattice

F   Face centering equivalent to simultaneous ABC face centering

I   Centering -  translation  vector  a/2  b/2  c/2  giving  point  of
    intersection of body diagonal of  the  basic  unit  of  the  space
    lattice

SPINDLE

ABSENCES

You can either ADD to the rules for the crystal which you have, or START again and enter the rules completely.

Consult a crystallography text for the rules of systematic absences.

COMMANDS

Introduction

VECTOR
DATGET
DATSAV
START
PLOT
HARD
SCALE
EXPAND
INDEX
AUTO
PICSAV
OVERLAY
HELP
STOP

VECTOR

DATGET

Directories may be given as part of the file name. The filename indicated on the screen will have the directory and file extension removed. If no extension is specified then .gen will be added.

DATSAV

Directories may be given as part of the file name. The filename indicated on the screen will have the directory and file extension removed. If no extension is specified then .gen will be added.

When a .gen file is written, then the user has the option of writing the current values of these items (default values or values read in as indicated above) or changing some or all of these values.

The initial prompts are:

>>> Enter name of .gen file in which to save control data [default]:

>>> Use default .gen file specific parameter values [y]:

or

>>> Use current .gen file specific parameter values [y]:

If a reply is no to the latter questions, the following questions are then asked. A carriage return on its own confirms the current values in each case.

>>> Film (f) or image plate (i) [f]:     (The default will be 'i' if
                                         an image-plate .gen file was
                                         read in)
>>> xc, yc, wc [current values]:
>>> twist, tilt, bulge [current values]:
>>> yscale [current value]:
>>> xrej, yrej [current values]:
>>> Camera type (C1=Arndt-Wonacott, C2=Huber) or fiducial values
[current values]:                        (Omitted for image-plate)
>>> wfilm, fidbox [current values]:
>>> n1od [current value]:
>>> Film type (CEA or DEF) or baseod, g1od, curve
[current values]:                        (Omitted for image-plate)
>>> nxrast, nyrast, dscal [current values]:
>>> xcen_in, ycen_in, rastsiz [current values]:
>>> xlow, xhigh, ylow, yhigh [current values]:

C1 (Arndt-Wonacott): -5000 -4000   -5000  4000    5000  4000
C2 (Huber):          -4000  5000   -4000 -5000    4000 -5000

CEA:   baseod = 0.04, g1od = 2.3, curve = 0.07
DEF:   baseod = 0.05, g1od = 2.4, curve = 0.06

START

NOTE: At present only up to 50000 reflections can be calculated and displayed. More development work is required before the program can operate correctly for more reflections.

Projections

Currently LAUE supports three projections: a "Laue projection" in which the positions of reflections are generated as in an actual Laue diffraction experiment; and inverted Stereographic and Gnomonic projections of the poles of lattice planes. The projections are inverted through the centre of the plot so that a pole in the projection is plotted on the same side of the centre as the corresponding Laue reflection. This is done for ease of comparison. But note that spots on the OUTSIDE of the Laue plot correspond to spots on the INSIDE of the projected plots.

Stereographic projection

In this option, the crystal-to-film distance is interpreted as the radius of the sphere of projection, and the radius of the plot is the "Primitive circle" (90 deg circle).

Gnomonic projection

In this option, the crystal-to-film distance is interpreted as the radius of the sphere of projection, and the radius of the plot corresponds to a "Minimum circle" whose radius in Laue plot space is supplied by the user. (ie. spots just outside the minimum circle are mapped to spots just inside the boundary circle of the plot.) The mimimum radius specified must be greater than or equal to 5.0.

PLOT

When plots are drawn, the user has the option of selecting points to be drawn for each reflection as an alternative to a variety of symbols indicating the reflection types. The following new prompt is output:

>>> Plot reflection symbols (S) or points (P) [S]:

When symbols are requested, crosses (+) are used for singlet spots, and stars (*) for multiplets.

To produce plots scaled for a given plotting device see SCALE.

HARD

SCALE

Plotters :  HP7550  HP7475  HP7470  BENSON  VERSATEC

Terminals:  SELANAR PERICOM VT100   VC3100

Other    :  FULL    USERSET

If USERSET is selected you may define your own scaling factor.

Note: Not all the devices specified are still available at Daresbury.

EXPAND

INDEX

You may optionally select to have indexed spots annotated on the graph. Four options are offered:

NONE     : No spots are annotated on graph. Indices and wavelength
           multiplicities are displayed on VDU screen only.
SINGLE   : Every spot identified using the cursor is annotated.
LOW INDEX: All spots with indices above given value are annotated.
           This  includes high order spots which after dividing their
           Miller indices by the higest common denominator have
           absolute values => index value supplied by user.
ALL      : All spots are annotated (up to highest index 99).

           In all last three cases only the low order index hkl sets
           are displayed if the spot ha wavelength multiplicity.

YOU SHOULD NOT ATTEMPT TO ABORT THE OPTION BY TYPING CTRL/Z WHEN THE CURSOR IS DISPLAYED, THIS WILL CRASH THE PROGRAM SINCE THE CURSOR ROUTINE DOES NOT TRAP CTRL/Z (end-of-file mark).

The presence of a graph is assumed. INDEX may also be used on an expanded graph but not on an expansion of an expanded one.

Note: When the indices are found, the terminal is switched to its ANSI (text) mode and the found indices are output. The terminal isthen switched immediately back to the graphics mode. If the terminal is incorrectly set then the text screen may be cleared when the graphics mode is re-entered. This has the effect that the displayed indices on the text screen are lost.

On a SELANAR the terminal can be correctly set by toggling the appropriate bit in SETUP C (this is the 4'th flag from the left. This can be achieved by the following keystrokes:

SET-UP up_arrow up_arrow right_arrow right_arrow right_arrow right_arrow right_arrow right_arrow SHIFT/T SET-UP.

AUTO

The program calculates reciprocal lattice vectors for low index spots (a maximum of 280 can be stored) and the angles between them. These angles are then compared with those based on the entered spot positions in order to index these spots and hence derive the crystal orientation. The user is asked to supply a maximum value for h**2 + k**2 + l**2 to determine how many reciprocal lattice vectors are calculated. A low value speeds up the calculation but may miss some spots. A relatively high value should usually be used for non-primitive cells to make up for the systematically absent spots. The user is also prompted to supply an estimate of the error in spot positions, 1 to 1.5 mms is usually sensible for this.

If the setting is known very approximately, for example the crystal may be approximately set along axes, then the user can greatly enhance the chance of AUTO succeeding (and speed up the operation) by providing the indices of the spots input, as well as their (x,y) positions. The indices can be obtained by generating the approximate Laue pattern, then using the INDEX option to identify the Miller indices of the specific spots which are chosen for AUTO.

When refining angles during the auto-indexing option the program will issue a prompt after every 50 iterations even if its current refinement cycle is not complete. This allows the user to decide whether or not to continue the refinement which might possibly take a long time to complete.

The program saves up to 12 solutions which have the lowest rms values. The rms values in question are either the unrefined values, if no refinement has been requested by the user, or the latest values when the user stops making further attempts at refinement. After all solutions have been processed, these values are displayed in a table on the terminal sorted in order of increasing rms values. The follwing prompt is then output:

>>> Enter w=write a data file, r=reset spindle and phis or c=continue:

The replies are as follows:

w (write)

Save the solution in a .gen file. This is useful if more than one solution is to be examined further. The position, in the table, is used to identify the required solution and the name of an output .gen file is requested as in the DATSAV option. The above prompt is then repeated.

r (reset)

Replace the current orientation parameters with the parameters obtained for one of the solutions given in the table. The position, in the table, is used to identify the required solution. The above prompt is then repeated.

c (continue)

Return to the main program menu without any further alteration to the orientation parameters.

PICSAV

The extension ".pic" is always added to the filename. Only files in current directory are accepted.

OVERLAY

This mode may for instance be used to produce patterns from twins or mixed crystal systems. If the HARD option is used after two or more patterns have been superimposed the parameter values of the last pattern are printed only. The overlay mode is set to OFF after HARD is used.

HELP

STOP

FILES

NEWLAUE can read and writes .gen files. Thus NEWLAUE may be used as a means of preparing a .gen file for GENLAUE if required. There are a number of items in the .gen file which are not required by NEWLAUE. These items have default values written into the program and are as follows:

Compound name: TEST SAMPLE
Crystal identifier: CRYS
xc, yc, wc: 0.0, 0.0, 0.0
twist, tilt, bulge: 0.0, 0.0, 0.0
yscale: 0.998
xrej, yrej: 0.0, 0.0
nfid fidx1 fidy1 fidx2 fidy2 fidx3 fidy3:
3 -5000 -4000 -5000 4000 5000 4000
wfilm fidbox n1od baseod g1od curve: 120 5 128 0.04 2.3 0.07
nrec ylen dscal: 2400 2400 2.0