Last modified September, 1996 - Armel Le Bail

- Generalities
- Typical example file
- Instructions list
- Heading comment : TITL
- Output control : MODI
- Plot specification : PARA
- Cell constants : CELL
- Space group symbol : SPGR
- Symmetry operators : SYMM
- Format for atom parameters : FORM
- View direction : VIEW
- Rotation : ROTA
- Filecodes : FILE
- Range in X, Y, and Z directions : XYZR
- Circle specifications : CIRC
- Tetrahedra specifications : TETR
- Octahedra specifications : OCTA
- Exclusion of atoms : OMIT
- Hatching polyhedra : SHAD
- Color specifications for HPGL output : COLO
- Perspective distance : PERS
- Bizarre polyhedra : BZRR
- End of instruction list : END
- Atom parameters

The input of all data is in free format. Numbers or symbols are separated by blanks, typed in any arbitrary column between columns 5 and 80. The first four columns of the instruction data are reserved for options specifying the type of instruction. Any text in the first four columns, other than the options listed here, will be ignored. Numbers can be given as integer, floating point, or floating comma numbers; all three types will be transformed to floating point numbers. Atom parameters may be given in free format or fixed format as described below.

WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING :

ALL CHARACTERS IN UPPERCASE (ex: TITL, CELL, SPGR, SYMM, PARA ...) INCLUDING ATOM NAMES (ex: H, LI, BE, AL, CO... not h, Li, Be, Al, Co). INCLUDING SPACEGROUPS (ex: P M M M, C 2/C, F D 3 M...)

The sequence of instructions is arbitrary except that TITL and END must be the first and last options, respectively, followed by the atom parameters.

TITL COSO4 H2O C2/C CELL 6.963 7.580 7.470 90. 116.30 90. SPGR C 2/C FORM 4 VIEW 0 1 0 XYZR -0.25 2.25 -0.25 2.25 -0.25 2.25 OCTA 90 20 2.05 0.25 TETR 109. 20. 1.5 0.2 PARA 1 1 1 1 1 1 1 2.6 END CO 1 0.25 0.25 0.0 S 1 0.0 0.093 0.25 O 1 0.203 -.017 0.362 O 2 0.021 0.196 0.104 O 3 0.0 0.615 0.25

1. Heading comment : TITL

Option : TITL text

Default : TITL (blank)

Up to 40 characters can be plotted as a heading. TITL must be the first option, even if the text is left blank. Subsequent lines, starting with TITL, are without action and can be used as comments.

2. Output control : MODI

some are obsolete in STRUVIR : take the default options, do not put any MODI line

Option : MODI D PA1 PA2 AR1 AR2 OR1 OR2

Default : MODI 1 0 0 28.8 21.6 0 0

D - selects the plotting device. D is not used in the STRUPLO version of June 86. This can be modified by the user in subroutine DRAW where D has the variable name ID.

PA1 PA2 - are length and width of the paper; these parameters are only needed for the PAGE call in the DISSPLA software.

AR1 AR2 - are length and width defining the plotting area. The plot will be scaled with regard to these parameters.

OR1 OR2 - are coordinates in cm (or inches) to translate the plot. This usually will cut off the plot, but might be desired in special cases.

In most cases this option can be omitted; default values can be changed in BLOCK DATA if necessary. Only if the plot output will be sent to different devices (plotter, laser printer, etc.) will parameter D need to be given.

3. Plot specification : PARA

Option : PARA A B C D E F G H I J

Default : PARA 1 1 1 1 1 1 1 3.2 0 0.01

A - Scale factor

The plot is scaled to the full width of the paper, leaving a margin for
the heading. The width of the paper is defined in AR1 and AR2 in BLOCK
DATA, or as specified with option MODI. Scale factors > 1 will cut off
the drawing, but might be desired in special cases.

B - Index for center in origin

= 0 no center in the origin = 1 centrosymmetric with center in the origin

C - Index for outlines of unit cell

= 0 no outlines = 1 outlines are drawn

The present version of the program does not check overlaps of the outlines with polyhedra or spheres. It might be necessary to draw the outlines of the parallelepiped by hand if the view direction is not parallel to one of the crystallographic unit vectors.

D - Index for type of representation

= 0 skeleton model

This representation, often used for framework structures, shows only the connections between the centers of neighboring polyhedra.

= 1 polyhedral representation

Tetrahedra and octahedra are sought by the program within the limits given in options TETR and OCTA. All polyhedra are hatched with equidistant lines parallel to that edge of the triangle which is opposite the vertex with the highest Z-coordinate. In this way the density of hatching illustrates the inclination of a polyhedral face.

E - Index for tetrahedra

= 0 no tetrahedra = 1 tetrahedra are sought and drawn within the values
given in option TETR. The default values correspond
to average Si-O distances.

F - Index for octahedra

= 0 no octahedra = 1 octahedra are sought and drawn within the values given
in option OCTA. The default values correspond to average
(Na,Ca)-O distances

If lines are drawn belonging neither to tetrahedra nor octahedra, the default parameters have to be changed in option TETR or OCTA.

G - Index for program execution

= 0 only tables with atomic coordinates and distances and angles are printed,
no plot is produced. = 1 tables with atomic coordinates and distances and
angles are printed and a projection of the crystal structure is drawn.

H - Maximum value for interatomic distances to be calculated

If more than 100 distances up to the value H are calculated, the execution
of the program will be terminated. In this case the maximum distance should
be given a lower value.

I - Retrace parameter NRES

Outlines of polyhedra and circles are plotted 2*NRES+1 times with a distance
given by RES (see J).

J - Retrace displacement RES

This value is multiplied by the scale factor.

4. Cell constants : CELL

Option : CELL a b c alpha beta gamma

Default : CELL 10 10 10 90 90 90

The cell constants are expected in Angstroms and degrees.

5. Space group symbol : SPGR

Option : SPGR space group symbol

Default : SPGR P1-

This is interpreted by Burzlaff's (Erlangen) symmetry interpretation routine. The centricity parameter B of PARA is overridden. The generated symmetry operations and Bravais translations can be found in the output file.

WARNING: Any SYMM input, that is input after this, is added to the generated symmetry operations.

6. Symmetry operators : SYMM

Option : SYMM symmetry operators

Default : SYMM X,Y,Z

To be used only if the choice of origin is different from the one generated by the Burzlaff routine.

Each line begining with SYMM contains several operators separated from each other by a semicolon. The last symbol in a line must not be a semicolon. Translations are given as fractions (1/2, 2/3 ...). The identity operator x,y,z and centrosymmetric counterparts are not required. The syntax is consistent with the syntax in International Tables for Crystallography.

7. Format for atom parameters : FORM

Option : FORM A

Default : FORM 4

A format index; note that in all cases the atom name is read in A2,I2.

= 1 reads a SHELX parameter file (not instructions) including FVAR and interprets constraints. This part of the program has been taken from the 1983 version of STRUPLO and could not be tested in the current form. Check carefully for possible errors! = 2 Format (2A1,I2,26X,3F10.6) corresponding to the input format of the atomic parameters in the least-squares program ORFLS. = 3 Format (2A1,I2,3F10.6) = 4 Free format An atom name consisting of two letters is expected in the first two columns, followed by a sequence number and the X,Y,Z-coordinates.

8. View direction : VIEW

Option : VIEW X1 X2 X3 Y1 Y2 Y3

Default : VIEW 0 0 1 0 0 0

VIEW can be used to specify a view direction. X and Y are coordinate triples, where the vector defining the view direction is given by the difference X-Y: it points from Y to X. If Y is not given, the zero vector 0,0,0 is assumed. The space diagonal of a unit cell, for instance, would be defined by VIEW 1 1 1 .

VIEW automatically performs a rotation around the view direction (Z-axis, see ROTA), that brings the longest projection of the edges of the view range (given by CELL and XYZR) parallel to the X-axis, thus resulting in a landscape format picture.

9. Rotation : ROTA

Option : ROTA A B C

Default : ROTA 0 0 0

A - are rotation angles around the orthogonal axes X,Y,Z, B - with the origin in the lower left corner, X pointing C - right, Y pointing up, and Z sticking out. The sense of rotation is righthanded for X and Z and lefthanded for Y as shown in the following graph.

y | | <<<<< | | | <<<< V z ^______V_____x ^ V V

initially Z is parallel to the crystallographic c-axis Y is the trace of the crystallographic b-axis in the plane perpendicular to Z X is parallel to Y x Z but this is changed by VIEW and ROTA

Multiple ROTA commands are accumulated. This means each ROTA command is applied to the view of the structure, as it exists at this stage.

If a VIEW instruction is given, rotations start from the directions given by that instruction. VIEW always takes precedence over ROTA.

WARNING: This is true, even if ROTA commands physically precede the VIEW command.

10. Filecodes : FILE

Option : FILE A B C

Default : FILE 3 4 6

A - input file for all instructions B - output file for coordinates, distance table C - screen unit for some informational output

Default values can be changed in BLOCK DATA for IO1, IO2, IO3. Note that a change in parameter A only affects those instruction lines which follow after FILE.

11. Range in X, Y, and Z directions : XYZR

Option : XYZR A1 A2 B1 B2 C1 C2 D1 D2 E1 E2 F1 F2

Default : XYZR calculated by program

All data given here refer to the unit vectors of the unit cell. A1 A2, B1 B2, C1 C2 are minimum and maximum range (X,Y,Z) for polyhedra, D1 D2, E1 E2, F1 F2 are the X,Y,Z components for the range in which circles are to be drawn defined in CIRC. The range for the circles must lie within the range for the polyhedra. If only the range for the polyhedra is given, this range will be taken also for the circles.

12. Circle specifications : CIRC

Option : CIRC R N1 N2 N3 ...

Default : no circles

R - Radius [A] N1 - Atom names consisting of two letters corresponding to ... the names of the atomic parameters.

'CIRC 0.8 NA CA' draws sodium and calcium atoms as circles with radius 0.8 A. The symbols listed in one line refer only to one radius which is always the first number in option CIRC. Up to 10 different radii (= 10 options CIRC) are accepted. If circles appear not to be drawn completely, change RES and NRES in PARA.

13. Tetrahedra specifications : TETR

Option : TETR A B C D

Default : TETR 109 20 1.62 0.2

A - tetrahedral angle B - angle tolerance C - mean distance from central atom to coordinated atoms D - tolerance for C

Tetrahedra are sought and drawn with distances between central atom and vertices of C+-D [A] and angles between central atom and two vertices of A+-B [deg].

14. Octahedra specifications : OCTA

Option : OCTA A B C D

Default : OCTA 90 20 1.97 0.4

A - octahedral angle B - angle tolerance C - mean distance from central atom to coordinated atoms D - tolerance for C

Octahedra are sought and drawn with distances between central atom and vertices of C+-D [A] and angles between central atom and two vertices of A+-B [deg].

15. Exclusion of atoms : OMIT

Option : OMIT A B C D ...

Default : OMIT no atoms are excluded

A B C D ... refer to the numbers in parentheses in the output list on unit 6. If the numbers follow each other in direct sequence they may be given as A -B, where A and B are the first and last numbers in this sequence. With instruction 'OMIT 9 15 -18 23 26' atoms with sequence numbers 9, 15, 16, 17, 18, 23 and 26 are are excluded from the parameter list and will not be drawn. If an excluded atom belongs to a polyhedron the whole polyhedron will be omitted.

16. Hatching polyhedra : SHAD

Option : SHAD NL N1 N2 N3 ...

Default : SHAD 9 1 -H(8)

With this option the number of lines NL for the hatching of a polyhedral face can be chosen. If NL is negative, all polyhedra are left blank. NL from 0 to 20 gives the number of lines per face of the polyhedra N1 N2 N3 ... These numbers refer to the numbers of the central atoms. For explanation of the syntax, see 15.

17. Color specifications : COLO

Applicable to HPGL output.

WARNING : Not applicable to VRML and STRUPOV
outputs (see the VRML chapter).

Option : COLO N1 C1 N2 C2 N3 C3 ...

Default : COLO pen 1 (normally black)

N1 - Atom name consisting of two letters corresponding to the name of the atomic parameters C1 - Pen number corresponding to atom name N1 ...

WARNING : For POSTSCRIPT output, "Pen" colors used by PSPLOT are: 1=black, 2=grey, 3=red, 4=green, 5=blue, 6=magenta, 7=yellow, and 8=orange.

18. Perspective distance : PERS

Option : PERS D

Default : PERS infinite distance (parallel projection)

D - distance from the origin to the observer's eye [A]

19. Bizarre polyhedra : BZRR, i.e., not tetrahedra nor octahedra

Option : BZRR R N

Default : BZRR no such polyhedra

R - radius of sphere within which neighboring atoms are searched N - Atom name consisting of two letters corresponding to the names of the atomic parameters

A maximum of 5 BZRR instructions is allowed

20. End of instruction list : END

Option : END

no default option

STRUPLO expects 5 values per atom

a) atom name (one or two letters in UPPERCASE : CO for Cobalt, not Co) b) atom label (any number < 100) c) fractional coordinates (X, Y, Z)

Only the atoms in the asymmetric unit are required.

The format for the atom parameters is specified by the FORM option (see page 5). The default is "free format".