Typical inputs

The buildcell program is the workhorse for generating random structures. It is often useful to generate a initial cell using the gencell utility with gencell <volume> <units> [<specie> <number>]. For example to search for SrTiO3, one can input:

gencell 60 4 Sr 1 Ti 1 O 3

This prepares a seed to search for four formula units of SrTiO3, each formula unit is expected to have a volume of 60 \(\mathrm{Å^3}\).

The cell file

The content of the generated file 4SrTiO3.cell is shown below:

Example

%BLOCK LATTICE_CART
3.914865 0 0
0 3.914865 0
0 0 3.914865
%ENDBLOCK LATTICE_CART

#VARVOL=60

%BLOCK POSITIONS_FRAC
Sr 0.0 0.0 0.0 # Sr1 % NUM=1
Sr 0.0 0.0 0.0 # Sr2 % NUM=1
Sr 0.0 0.0 0.0 # Sr3 % NUM=1
Sr 0.0 0.0 0.0 # Sr4 % NUM=1
Ti 0.0 0.0 0.0 # Ti1 % NUM=1
Ti 0.0 0.0 0.0 # Ti2 % NUM=1
Ti 0.0 0.0 0.0 # Ti3 % NUM=1
Ti 0.0 0.0 0.0 # Ti4 % NUM=1
O 0.0 0.0 0.0 # O1 % NUM=1
O 0.0 0.0 0.0 # O2 % NUM=1
O 0.0 0.0 0.0 # O3 % NUM=1
O 0.0 0.0 0.0 # O4 % NUM=1
O 0.0 0.0 0.0 # O5 % NUM=1
O 0.0 0.0 0.0 # O6 % NUM=1
O 0.0 0.0 0.0 # O7 % NUM=1
O 0.0 0.0 0.0 # O8 % NUM=1
O 0.0 0.0 0.0 # O9 % NUM=1
O 0.0 0.0 0.0 # O10 % NUM=1
O 0.0 0.0 0.0 # O11 % NUM=1
O 0.0 0.0 0.0 # O12 % NUM=1
%ENDBLOCK POSITIONS_FRAC

##SPECIES=Sr,Ti,O
##NATOM=3-9
##FOCUS=3

#SYMMOPS=2-4
##SGRANK=20
#NFORM=1
##ADJGEN=0-1
#SLACK=0.25
#OVERLAP=0.1
#MINSEP=1-3 AUTO
#COMPACT
#CELLADAPT
##SYSTEM={Rhom,Tric,Mono,Cubi,Hexa,Orth,Tetra}

KPOINTS_MP_SPACING 0.07

SYMMETRY_GENERATE
SNAP_TO_SYMMETRY

%BLOCK SPECIES_POT
QC5
%ENDBLOCK SPECIES_POT

%BLOCK EXTERNAL_PRESSURE
0 0 0
0 0
0
%ENDBLOCK EXTERNAL_PRESSURE

As you can see, the input file for buildcell is essentially an marked up cell file for CASTEP. Lines starting with # provides directives for buildcell, although those with ## will still be ignored.

Options for buildcell

Several key tags are explained below:

VARVOL

Defines the variable volume of the unit cell, the exact volume will be randomise at a harded coded range of ± 5%. The actual unit cell vectors will be randomised, and those in the LATTICE_CART block takes no effect.

POSITIONS_ABC

Defines the initial positions of the atoms in the unit cell. The syntax after the # is <set name> % [<tags>...]. Where <set name> can be used to define rigid fragments by setting the same value for all of the linked sites. Since each atom should be considered independently in this example, each line has a different value. After the % comes the site-specific settings. The NUM allows a single site to be multiplicated. For example, adding 12 oxygen atoms can achieved specified by O 0. 0. 0. # O % NUM=12 instead of doing it line by line.

SYMOPS

Defines the number of symmetry operations to be included in the randomised structure. The - defines the range and a random value will be drawn from.

SGRANK

This tags can be enabled to bias the (randomly chosen) space group towards those that are more frequently found in the ICSD. The value defines a threshold rank for accepting the space group.

NFORM

This tags defines the number of formula units to be included in the generated structure. Here, the cell has the formula \(\ce{Sr4Ti4O12}\) according to the POSITIONS_ABC block. If one changes NFORM to be 2, then the effective chemical formula would be \(\ce{Sr8Ti8O24}\). If NCORM is not defined, the composition will be affect by SYMOPS, placing all atoms in the general positions.

ADJGEN

This tags is used to modify the number of general positions when generating symmetry-containing structures. By default, the number of general positions is maximised. This tags allows more special postions to be occupied if possible. For blind search, there is no need to use this tag in most cases.

MINSEP

This tags defines the specie-wise minimum separations and is one of the few tags that need to be manually changed by hand. The default 1-3 AUTO means to randomly set minimum separations per specie-pair between 1 Å and 3 Å, but also try to extract and use that of the best structure if possible. The latter part is achieved by looking for a .minsep file in the current wroking directory, which is generated by the airss.pl script on-the-fly. This approach cannot be used by DIPS searches each calculation will be run from different directories (and probably also different machines). Initial values may be composed by the knowledge of common bond lengths. The cryan -g command can also be used to extract MINSEP from existing structures.

SLACK,OVERLAP

These two tags controls the process of modifying the structure to satisfy the minimum separations. Roughly speaking, a geometry optimisation is performed ,each species-pair having a hard shell potential. The tag SLACK defines how soft the hard shell potential constructed will be, and OVERLAP defines the threshold for acceptance. There is usually no need to vary these two tags.

COMPACT,CELLADAPT

Controls if the cell should be compacted and deformed based on the hard shell potentials. There is usually no need to change these two tags.

SYSTEM

Allows limiting the generated structure to certain crystal systems, which can be useful to bias the search based on prior knowledge.

Options for CASTEP

Lines not marked up by # are often passed through, below are descriptions of some CASTEP-related tags that goes in the cell file.

Note

The buildcell program will not always pass through the native CASTEP keys, so check the output cell carefully.

KPOINTS_MP_SPACING

Defines kpoints spacing in unit of \(\mathrm{2\pi\,Å^{-1}}\). Usually a not so well-converged setting can be used for the initial search.

SYMMETRY_GENERATE

Let CASTEP determine the symmetry for acclerating calculations. You will almost always want to have this.

SNAP_TO_SYMMETRY

Snap the atoms to the positions according to the determined symmetry. You will almost always want to have this.

EXTERNAL_PRESSURE

The upper triangle of the external stress tenser. It does not get passed through after buildcell.

HUBBARD_U

The Hubbard-U values for each specie and orbital. For example, Mn d:3 will apply an effective U of 3 eV to the d orbital of Mn.

The param file

The param file read by CASTEP only, and not used for building structure. A default param file for CASTEP from gencell looks like this:

Example

task                 : geometryoptimization
xc_functional        : PBE
spin_polarized       : false
fix_occupancy        : false
metals_method        : dm
mixing_scheme        : pulay
max_scf_cycles       : 1000
cut_off_energy       : 340 eV
opt_strategy         : speed
page_wvfns           : 0
num_dump_cycles      : 0
backup_interval      : 0
geom_method          : LBFGS
geom_max_iter        : 20
mix_history_length   : 20
finite_basis_corr    : 0
fixed_npw            : true
write_cell_structure : true
write_checkpoint     : none
write_bib            : false
write_otfg           : false
write_cst_esp        : false
write_bands          : false
write_geom           : false
bs_write_eigenvalues : false
calculate_stress     : true

Several tags that you may want to modify are:

xc_functional

Defines the exchange-correlation functional to be used. Since PBE often bias towards less bonded (larger volume) phases, one may want to use PBEsol instead.

spin_polarized

If set to true the calculation will be spin polarized. Note that CASTEP does not have default set for each site, so one have to break the symmetry manually in addition to setting this tag.

fixed_npw

aka, fix the number of plane waves. CASTEP default to constant basis-quality during variable-cell geometry geometry optmisation rather than the constant basis set in many other plane wave codes. While this allows getting a reliable final energy with restarts, the castep_relax script already handles automatically restart anyway. Having consistant basis-quality may not be optimum when large pulay stress is present, e.g. using less well-converged cut off energies. Hence, it is preferable to set it to true and use the constant basis set approach.

cut_off_energy

The cut off energy should be sufficient for the pseudopotential used. There is no need to high quality but harder pseudopotentials in the initial search in most case.

geom_method

Algorithm for geometry optmisation. LBFGS works well cases, otherwise tpsd may be used instead.

mixing_scheme

This tags controls the charge density mixer. The pulay mixer is OK for most case, otherwise one can use broyden instead if convergence struggles.

max_scf_cycles

Keep a large value to avoid CASTEP giving up the structure due to electronic convergence instability.

opt_strategy

Use speed to keep everything in the RAM and avoid any slow disk IO.

geom_max_iter

Number of geometry optimisation per run. Since castep_relax will repetively restart calculation, use a small value so the basis set is reset every so often. For fixed cell optimisation, one can use a large value in combination with apporiate castep_relax arguments and avoid restarts.

metals_method

Use dm (density mixing) for speed.