Buildcell Manual

The construction of reasonable, or sensible, random structures is central to AIRSS. The Fortran buildcell tool is provided in the AIRSS package for this purpose. It can build structures from scratch, or modify structures specified using the Castep .cell format. The random structures generated are output in the Castep .cell format. buildcell reads from standard input (stdin), and writes to standard output (stdout). The output can be passed to the supplied Fortran cabal structure conversion tool. Additional information is reported to standard error (stderr).

$ cat Al.cell

%BLOCK LATTICE_CART
2 0 0
0 2 0
0 0 2
%ENDBLOCK LATTICE_CART

%BLOCK POSITIONS_FRAC
Al 0.0 0.0 0.0 # Al1 % NUM=8
%ENDBLOCK POSITIONS_FRAC

#MINSEP=1.5

$ buildcell < Al.cell

Symm: P1         Nops:   1
Compacting the unit cell using a Niggli reduction
:----~
#              Generated by Buildcell
#
# at 12:00:00 (GMT+1.0) 1st June 2018
# in /Users/user/Al
# on
# by user
#
#      Author: C. J. Pickard (cjp20@cam.ac.uk)
#                Space group: P1
#

%BLOCK LATTICE_ABC
      3.24631      3.29003      6.29400
     92.47862    102.61547    110.29770
%ENDBLOCK LATTICE_ABC

%BLOCK POSITIONS_FRAC
  Al        0.9801918        0.2287102        0.0656909
  Al        0.7802843        0.4917482        0.8797641
  Al        0.2606859        0.2945663        0.8997372
  Al        0.4531337        0.7917730        0.6072080
  Al        0.5479149        0.1049917        0.1511797
  Al        0.6110164        0.7229138        0.0359822
  Al        0.4599122        0.2232240        0.3707223
  Al        0.6281024        0.9946698        0.8485314
%ENDBLOCK POSITIONS_FRAC

Timed:        0.00000
Total:        0.00610
Perc:         0.0%

$ buildcell < Al.cell | cabal cell res > Al.res

Symm: P1         Nops:   1
Compacting the unit cell using a Niggli reduction
:---~
Timed:        0.00000
Total:        0.01191
Perc:         0.0%

$ cat Al.res

TITL cabal-cell2res 0.0 64.004559 0.0 0 8 (n/a) n - 1
CELL 1.54180  3.35495  4.61258  4.86690 67.29051 70.27393 72.02060
LATT -1
SFAC Al
Al     1  0.7588650000000  0.6630602000000  0.4570794000000 1.0
Al     1  0.1109306000000  0.2909464000000  0.6328852000000 1.0
Al     1  0.8626585000000  0.6047508000000  0.9951972000000 1.0
Al     1  0.4688670000000  0.2785197000000  0.3177728000000 1.0
Al     1  0.3208300000000  0.8247542000000  0.7611079000000 1.0
Al     1  0.1007394000000  0.2634639000000  0.0993661000000 1.0
Al     1  0.0686251000000  0.7423036000000  0.1393760000000 1.0
Al     1  0.5536280000000  0.3415304000000  0.9743010000000 1.0
END

Cell size and shape

Show bond angles, length distributions.

Cell content

Cell symmetry

Units

Glossary

The following table lists all of the current directives that will be interpreted by buildcell, and provides a description of their intended usage.

Directive	Description	Default
ABFIX	Fix the a- and b-axis. Should be placed in the LATTICE_CART/LATTICE_ABC block.	false
ACONS	Rejects unit cells that are too flat. It takes a value of less than 1.0, and larger values favour more three dimensional cells. The volume of the unit cell is given below. The quantity in the square root must be greater than ACONS for the unit cell to be accepted.
ADJGEN	A value of 0 enforces the maximum possible use of symmetry related general positions. Larger values permit greater use of special positions. It is increased dynamically if it proves difficult to generate stuctures with smaller values.	0
ANGAMP	Amplitude of rotation for units (or molecules). It is to be supplied in degrees, and a negative value implies full rotation. It can be specified on a unit by unit basis.	−1
BREAKAMP	Amplitude of random displacement of atoms to break symmetry.	0
CELLADAPT	Permit a change in shape of the unit cell when applying distance constraints through the hard sphere potentials.	false
CELLAMP	Amplitude for the random variation of a supplied unit cell. A negative value implies no relation to original cell.	−1
CELLCON	Apply cell contraints. Specified as a vector (a, b, c, α, β, γ). For example #CELLCON = -1 -1 -1 90 90 90 specifies a cubic unit cell, and #CELLCON = -1 -1 -1 -1 -1 -1 a rhombohedral cell. #CELLCON conflicts with #SYSTEM.
CFIX	Fix the c-axis. Should be placed in the LATTICE_CART/LATTICE_ABC block.	false
CLUSTER	Selects internal settings for cluster geometries.	false
COMPACT	Force a Niggli reduction of the unit cell. False by default if #CLUSTER is false, and the unit cell is not fixed using #FIX, #ABFIX, #CFIX or #CELLAMP=0.	true
CONS
COORD
CYLINDER
FIX	Fix the unit cell.	false
FLIP	Randomly mirror the structural units.	false
FOCUS	Focus the compositional search on elements (#FOCUS=1), binaries (#FOCUS=2), ternaries (#FOCUS=3), etc.	0
MAXBANGLE	Maximum bond angle in coordination constraint application	?
MAXTIME	Determines how long, in seconds, should be spent attempting to build structures with given settings.	1
MINAMP
MINBANGLE	Minimum bond angle in coordination constraint application	?
MINSEP
NATOM
NFORM
NOCOMPACT	Force no Niggli reduction of the unit cell.	false
NOPUSH
OCTET	Checks if number of valence electrons is a multiple of eight.	false
OVERLAP
PERMFRAC
PERMUTE
POSAMP
RAD
REMOVE
SGRANK
SHIFT
SLAB
SLACK
SPECIES
SPHERE
SPIN
SUPERCELL
SURFACE
SYMM
SYMMNO
SYMMOPS
SYMMORPHIC
SYSTEM	Enforce a crystal system. Allowed values are {Rhom,Tric,Mono,Cubi,Hexa,Orth,Tetra}	none
TARGVOL
THREE
VACANCIES
VACUUM
VARVOL
WIDTH
XAMP
YAMP
ZAMP