Castep

CASTEP
Training Manual
Version 2008
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CASTEP
About …
CASTEP is a state-of-the-art quantum mechanics-

based program designed specifically for solid-
state materials science (i.e. crystals and
surfaces in materials such as semiconductors,
ceramics, metals, minerals, and zeolites
CASTEP employs the density functional theory

plane-wave pseudopotential method, which
allows you to perform first-principles quantum
mechanics calculations
CASTEP 1
Theoretical Foundation
HΨ = EΨ
Hamilton operator operates on wavefunction
of all electronic degrees of freedom
⎧ h 2 ⎫ Erwin Schrödinger
⎨− ∇ + V ({ri }) ⎬Ψ ({ri }) = EΨ ({ri })
⎩ 2m ⎭
In practice, wave functions are expressed in

terms of one particle functions
Ψ ({ri }) = F [{Φ i }]
Density Functional Theory

Hohenberg-Kohn E[Ψ (r1 ,...rN )] = E[ ρ (r )]
theorem
E[ρ]= To[ρ]+ U[ρ]+ Exc [ρ]
Kohn-Sham ∂ E [ρ ]
=0
Walter Kohn
theorem ρ ρ =0
Kohn-Sham
equations
[∇ 2
]
+ veff [ ρ (r )] ϕ i ,k (r ) = ε i ,kϕi ,k (r )
• Exact only for ground state

• Needs approximation to Exc
CASTEP 2
Theoretical and Computational Choices

all-electron full potential
pseudopotential
LDA
GGA
⎧ 1 ⎫
⎨− ∇
2
+ V ( r ) + μ xc ( r ) ⎬ Ψ i k = ε ik Ψ i k
⎩ 2 ⎭
non-periodic plane waves

numerical
periodic Slater type orbitals
LCAO
symmetry Gaussians
non-spin-polarized Fully numerical

spin-polarized
CASTEP & DMol3 provide fundamentally different basis sets to implement DFT
Basic Concepts for Solid State
• Periodic Systems
• Slabs and Gaps
• Band Structure
CASTEP 3
Periodic Boundary Conditions
The system is considered

to be surrounded on all
sides by replicas of
itself, forming an
infinite macro-lattice.
Geometric Models - Slabs and Gaps
Surfaces
Slab
Vacuum
Periodic Cell
CASTEP 4
Band Structure
• The electrons of a single free-standing atom occupy atomic

orbitals, which form a discrete set of energy levels
• According to molecular orbital theory, if several atoms are brought

together into a molecule, their atomic orbitals split, producing a
number of molecular orbitals proportional to the number of atoms
• When a large number of atoms (of order 1020 or more) are brought
together to form a solid, the number of orbitals becomes
exceedingly large, and the difference in energy between them
becomes very small. However, some intervals of energy contain no
orbitals, no matter how many atoms are aggregated
Conductors, insulators, semiconductors, and special bands
Solids can be divided in three classes based upon their

band structure
Metal Semiconductor Insulator
Conduction
band
Conduction
Energy
band
Conduction Energy gap
band
kT Energy gap kT
Valence Valence Valence

band band band
CASTEP 5
Band Structure - Example
Periodic boundary conditions

r r r
r = rUC + ∑ ni Ri
i
r
r
r
R1 r
rUC
r
R2
Any point r can be represented by a point in
the unit cell UC + sum of lattice vectors Ri
CASTEP 6
Implications…
r
H = −∇ 2 + U (r )
r r r
Bloch theorem U (r ) = U ( R + r )
r r r r r
Ψnkr (r + R ) = e ik ⋅R Ψnkr (r )
r r r r r
Reciprocal lattice eiK ⋅( r + R ) = eiK ⋅r
r r
(with unit cell)
e iK ⋅ R = 1
Sampling in real & reciprocal space

• In real space (unit-cell)
– Find a representation of basis function that is
“dense”, i.e. accurate, defined everywhere
• In reciprocal space
– Need to sample the irreducible unit cell in k-space.
This is the Brillouin-zone (BZ)
r r
i K ⋅R
• Because of e = 1 the number of k-points needed to sample
the BZ is cut by half if the size of the unit-cell is doubled
Comparison of systems with varying size is only

meaningful if sampling density is constant
CASTEP 7
CASTEP – Setup
• Task: Energy, Geometry
Optimization, Dynamics,
Elastic Constants, TS
Search, Properties
• Quality: coarse, medium,

fine, fine, ultra-fine
• Functional: GGA and LDA
• Spin polarized
• Charge
Exc = exchange correlation potential!
• Exchange : electrons do not have an identity –

and are exchange-able
• Correlation: electrons are fermions and have a

negative charge – Pauli principle and coloumb
interaction Æ they can move only in correlation
to each other
CASTEP 8
Local Density Approximation (LDA)

“Nearsightedness of electrons“
Exc ≈ ∫ ρ(r) ε xc [ρ(r)]dr
o
dr2
ρ2
dr1
ρ1
LDA is good: (1) slowly varying density (e.g. in a metal)

(2) high density (e.g. transition metals)
(3) for most geometries
LDA is not sufficient:
1. for very few electrons (e.g. for transition

states in chemical reaction)
2. for absolute values of binding energies
3. Underestimates the bandgap
4. NiO is described metallic and not as insulator
5. Defect levels are wrong
6. Gives wrong pattern of the spectra
CASTEP 9
Local Density Approximation (LDA)

CA-PZ
Ceperley, D. M.; Alder, B. J. Phys. Rev. Lett., 45, 566-569 (1980).
Perdew, J. P.; Zunger, A. Phys. Rev. B, 23, 5048-5079 (1981).
LDA+U or Hubbard model

• generalization of LDA faces a certain challenge: there are no
exactly solvable problems which can be used to parametrize
the generalized exchange-correlation energy, we need a model
• the LDA+U approach subdivides charge density into delocalized

and localized. The former remains described by its charge-
density, while for the latter a site diagonal charge density
matrix is introduced:
effective LDA+U energy functional:
ELDA … standard LDA energy functional

EHF Hartree-Fock like functional
Edc double counting term, already taken into account in ELDA
U1324 renormalized Coulomb integrals
CASTEP 10
LDA + U
• The Hubbard U is a parameter which allows correlation

effects to be included in DFT calculations
• U is defined as a floating point quantity defined per
valence orbital (of s, p, d or f type) that is passed to
the computational server
• Note: This option is only enabled if the Spin polarized
checkbox is checked.
• Note. can only be used with the Energy task. It is not
compatible with stress, NMR, phonon or polarizability
calculations. The formalism cannot be used with
mixture atoms or real-space pseudopotentials.
How to change U?
• Menu: Modify | Electronic Configuration | Hubbard U
s: Specify a Hubbard U value in eV for

the valence s shell.
p: Specify a Hubbard U value in eV for
the valence p shell.
d: Specify a Hubbard U value in eV for
the valence d shell.
f: Specify a Hubbard U value in eV for
the valence p shell.
CASTEP 11
Generalized Gradient Approximation

(GGA)
Better binding (cohesive) energies
EGGA=ELSD+EGx +EGc
Becke (1988) ρσ x2σ

Gradient-corrected E Gx = b∑ ∫ dr
σ 1+ 6bx σ sinh−1 x σ
exchange
∇ρ
xσ = 4
σ = ↑ or ↓
ρσ 3
Perdew (1986)
∫( ) −g(ρ ) ∇ρ
E c = f ρ↑, ρ↓ e ∇ρ dr
G 2
Gradient-corrected
correlation
Generalized Gradient Approximation

(GGA)
• PW91 - Perdew, J. P.; Wang, Y. Phys. Rev. B, 45,
13244 (1992)
• PBE - Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys.

Rev. Lett., 77, 3865 (1996)
• RPBE - Hammer, B.; Hansen, L. B.; Norskov, J. K. Phys.

Rev. B, 59, 7413 (1999)
• WC - Wu, Z.; Cohen, R. E., Phys. Rev. B, 73, 235116

(2006)
CASTEP 12
Nonlocal exchange-correlation functionals

• LDA and GGA underestimate the band gap substantially!
• Possible correction: use of an empirical scissors correction (i.e. a rigid

shift of the conduction band with respect to the valence band)
• Another solution: screened exchange, or sX-LDA scheme, developed in

the context of the generalized Kohn-Sham procedure (Seidl et al., 1996):
splits exchange contribution to the total energy into a screened, nonlocal
and a local density component.
• Implemented Kohn-Sham schemes:

– HF: exact exchange, no correlation
– HF-LDA: exact exchange, LDA correlation
– sX: screened exchange, no correlation
– sX-LDA: screened exchange, LDA correlation
– PBE0: combination of PBE functional with a predefined amount of
exact exchange (Adamo and Barony, 1998)
Nonlocal exchange-correlation functionals

• certain limitations compared with LDA and GGA functionals:
– no known analytical expression for the stress tensor components
– cannot be used to optimize the unit cell of a crystal or to perform
NPT/NPH dynamics
– optical properties can be inaccurate
• currently only for norm-conserving potentials, not for ultrasoft ones.
• Currently only non self-consistent band structure calculations fully support

nonlocal potentials Æ use either the LDA or the GGA approach to produce
self-consistent charge density (and possibly optimize the structure) Æ then
apply nonlocal functional to request electronic properties
• Important difference:
– Non-local: potential used in the latter scenario depends on the SCF k-
points
– Local: potential depends only on electron density
– Watch the number of k-points, especially in small unit cells; otherwise
the calculation will be very expensive!
CASTEP 13
Spin-Polarization/Spin unrestricted
r r r
Define up and down electron densities such that: n ( r ) = n↓ ( r ) + n↑ ( r )
r r r
Define a spin density: μ ( r )
= n↓ ( r ) − n↑ ( r )
r r 3
The total magnetic moment is : M = ∫ n↓ ( r ) − n↑ ( r )d r
For a spin imbalance we need a spin polarized xc-potential:

r r
v xc = v xc [n↓ ( r ), n↑ ( r )]
This gives raise to a spin polarized Hamiltonian
Note that:
• In practice, the spin polarized problem is treated for up and down spin
separately. This doubles the CPU time cost per SCF cycle
• Spin polarized calculation need more SCF cycles to converge, since ρ and μ
have to converge (separate mixing parameter for μ!)
Electronic Tab
• Energy cutoff
• SCF tolerlance
• K-point set
• Pseudopotentials
CASTEP 14
Pseudopotentials
Pseudopotentials are crucial for plane wave total energy
methods since the alternative full Coulomb potential of
the electron-ion interaction decays too slowly to be
accurately represented by a small number of Fourier
components
CASTEP replaces the true atomic Effectively reduces number of
potential by a pseudopotential plane waves
pseudo wave function
pseudopotential
Pseudopotentials Options
• Ultrasoft - the preferred option.
Allows lower energy cutoff
• Norm-conserving - more CPU

expensive
– Advisable for optical
properties calculations
– Required for: linear
response-based calculations
of phonon properties and of
polarizabilities
• On the fly - required for CASTEP

NMR calculations Pseudo-Potentials can be
chosen for each element
CASTEP 15
The Cutoff Energy

• The coefficients Ck+G for the
plane waves with small kinetic
energies are more important
that the large ones
• We truncate the plane wave

basis set to include only those
that have kinetic energies
smaller than some particular Ecut
• Energy monotonically decreases

k+G
2
to ground states energy as Ecut
increases ≤ Ecut
Kinetic 2
Energy
You should remember

• The plane wave basis is only applicable to periodic
systems
• It is necessary to check for plane wave convergence
Yttrium Plane-Wave Convergence
1.0
0.8
E'(eV/atom)
0.6
0.4
0.2
0.0
200 250 300 350 400
Ecut
Epw
CASTEP 16
SCF and k-point set
SCF
Density mixing: used for mixing
the input densities and output
densities from the current
iteration to obtain the input
density for the next iteration
Empty bands: should be

sufficiently large to cater for
nearly degenerate bands close
to the Fermi level (relevant for
transition or rare earth metal
compounds)
CASTEP 17
Empty bands – warning!
increase the percentage of empty bands in gui electron ->SCF

and check nextra-bands parameter in the .param file
Filling of bands
Not all of these states are occupied by electrons ("filled") at any

time. The likelihood of any particular state being filled at any
temperature is given by the Fermi-Dirac statistics
f (ε )
1
f (ε ) =
ε −μ
+1
e
k BT ε
μ
CASTEP 18
Smearing - Effects of thermal occupancy mode
Initial configuration Final configuration

red states not occupied
red states occupied
“Made visible” by smearing
k-points
Use either a Monkhorst-Pack set
of the selected quality
(Coarse, Medium, or Fine) or
instructs CASTEP to use only
one Γ-point (the origin in
reciprocal space).
Explicit selection of Γ -point

sampling is not
recommended. CASTEP will
automatically use this option
if the cell is very large in real
space, so that the Brillouin
zone is small and no sampling
is required. In all other cases,
the Γ-point is the least
representative of all Brillouin
zone points and using it as
the only sampling point can
distort the results severely.
CASTEP 19
CASTEP - Tasks
Several tasks can be carried out in CASTEP
• Energy
• Geometry Optimization
• Dynamics
• Elastic Constants
• TS search
• Properties
CASTEP Energy task
The CASTEP Energy task allows you to calculate the total

energy of the specified system, as well its physical
properties.
The "total energy" of a molecule or crystal refers to the

energy of a specific arrangement of atoms as
calculated using
The zero of energy is taken to be the infinite separation

of all electrons and nuclei, so the total energy is
generally negative (bound state)
The default unit of energy in CASTEP is eV (1eV

equivalent to 0.036749308 Ha = 23.0605 kcal/mole =
96.4853 kJ/mole
CASTEP 20
Energy Optimization: Self Consistent Field (SCF) cycle
ρstart(r)
r r
Generate Potential ΔV (r ) = −4 π ρ in (r )
Solve KS equation H Ψ i ,kr = ε S Ψ i ,kr
r r
ρ out (r ) = ∑r Ψi ,kr (r )
2
New nout(r)
i ,k
Update n(r) ρupdate = α ⋅ ρ out + (1 − α ) ⋅ ρ in
Converged ?
Minimiser
Damped MD
Move ions using velocities and forces, adds
damping term to forces set by algorithm to
find the optimal one
BFGS (Broyden-Fletcher-Goldfarb-Shanno)
Go via an approximation to the Hessian matrix
(matrix of second derivatives)
CASTEP 21
Geometric Models - Slabs and Gaps
• Problems
– The surface slab must be thick enough to

represent a real materials - both bulk and
surface atoms
– The vacuum must be large enough to prevent

the slabs from interacting with each other
– Dangling bonds & Charge neutrality
Geometric Models - Slab Thickness
• Sometimes, for numerically Free

intensive calculations, the slabs
become too thick
– e.g. systems with strong
electrostatic forces
• Solution
– Fix lower layers at bulk
Fixed
positions and use smaller
slab
CASTEP 22
Geometric Models - Slab thickness
Do a series of single point

energies calculations 1.0
E'(eV/atom)
0.8
– Start with a small 0.6
slab (e.g. 3 layers) 0.4
0.2
– Gradually increase 0.0

3 4 5 6 7
slab thickness until N°of layers

Epw
energy per atom or

molecule stops
changing
Transition State Search

Z1
Without
Without
catalyst
catalyst
Ea,0 Z2
Energy
Ea,1 Ea,2
RG ΔHR
A* PG
With
With
catalyst P*
catalyst
Reaction Coordinate
• Examples of direct simulation of reaction mechanisms are appearing
rapidly (e.g. HDS, ODH, hydrogenation, epoxidation, MTG, Fischer
Tropsch….)
• Computation provides a highly attractive laboratory for performing what if
experiments (poisons, dopants, promoters, bimetallic surfaces…)
CASTEP 23
A schematic view of the LST (Linear Synchronous

Transit) and QST (Quadratic Synchronous Transit)
approach
LST line search

maximum QST line search
maximum
Transition State Calculation

• LST Maximum - single LST maximization, bracketing the
maximum between the reactants and product
• Halgren-Lipscomb - LST maximization + single-line search

minimization
• LST/Optimization - LST maximization + conjugate gradient

minimization
•
• Complete LST/QST – LST maximisation + repeated conjugate
gradient minimizations + QST maximizations
•
• QST/Optimization - starting from a QST, performs repeated
maximizations and conjugate gradient minimizations
CASTEP 24
Geometry Optimization
CASTEP presents some additional
options when compared to DMol3
• Optimization under constant

pressure
• Stress tensor can be calculated
NOTE: In DMol3 delocalized internal

coordinates are the default option
during the optimization, in CASTEP
is Cartesian coordinates
r
Elastic constants: Mechanical Deformation displace ions
from equilibrium positions R
σ i : stress
σ i = Cijε j Cij: elastic constant
Crystal system Elastic constants
ε j : strain
Triclinic 21
Monoclinic 13
Orthorhombic 9
The total number of elastic
Tetragonal (C4, C4h, S4: 7)
(other: 6) constants depends from
symmetry (space groups and
Rhombohedral (C3, S6: 7) (other: 6)
point groups)
Hexagonal 5
Cubic 3
CASTEP 25
Elastic constants: Setup
The orthorhombic
space group has 9 The minimum
elastic constants number of
independent
calculations
needed is
determined
automatically
Elastic constants : Results
CASTEP 26
Elastic constants: Validation

• Several materials tested Elastic Constants (GPa)
BeO 1200
TiB2 1000
BN cubic 800
Experiment
Ge
600
Si
400
MgSiO3
200
Diamond
0
Graphite…
0 200 400 600 800 1000 1200
• DFT provides elastic CASTEP
constants typically within
5-10% of experiment
Workflow
Spin
Setup Task Functional
unrestricted
Electronic Energy cutoff SCF tolerance Pseudopotentials
More Basis SCF k-points Potentials
FFT
Properties Improve convergence

density mixing, smearing
CASTEP 27
CASTEP Properties
Properties requested through the CASTEP Calculation | Properties tab
• Band structure • Phonon density of

• Density of states states
• Electron density • Electric field
difference response
• NMR • Population analysis
• Optical properties • Stress
• Phonon dispersion • Thermodynamic
Properties
Density of States (DOS)

DOS of AlAs
DOS for a given band n, Nn(E):
δ [E − En (k)]
dk
Nn (E) = ∫
4π 3
En(k) : dispersion of the given band
Total density of states, N(E)

N(E) = ∑Nn (E)
n
Total number of electrons, N

EF
∫ N (E) = N
−∞
EF: Energy of the Fermi level
CASTEP 28
Example : PDOS of AlAs
Application : LDOS of AlAs
LDOS of Al in AlAs LDOS of As in AlAs
CASTEP 29
Optical properties
•Dielectric function
•Reflectivity/Absorption
•Refractive Index α-Quartz (bulk)
•Conductivity/Loss Function
Phonons
• Phonons are the quantum units of a crystal vibration, i.e. the ionic
displacement field that describe classical sound; compare:
photons- the quanta of the radiation field that describe classical
light
• Large number of properties can be understood in terms of phonons
- Infrared, Raman, and neutron scattering spectra
- Specific heat, thermal expansion, and heat

conduction
- Electron-phonon interaction (and thus resistivity

and superconductivity)
CASTEP 30
Phonons and Thermodynamic Properties
• Phonon calculations in CASTEP can be used to evaluate the

temperature dependence of
– Enthalpy
– Entropy
– Free energy
– Lattice heat capacity of a crystal
• These results can be used to compare with experimental data

(e.g., on heat capacity measurements)
– To predict phase stability of different structural
modifications, etc.
– To perform studies of phase transitions
Phonons : Example
Phonon Dispersion : Experimental
Germanium Frequency (cm-1)

400
Phonon Dispersion : CASTEP
CASTEP Phonon Dispersion
300
200
100
0
W L G X W K
W L Γ X W
K
CASTEP 31
Practical schemes for phonon calculations
find the equilibrium structure of a material; build up the matrix

of force constants by calculating forces acting due to small
displacements of the atoms
Analytical: direct evaluation of the second derivatives of the

energy with respect to atomic displacements - Linear Response
Numerical: perturbing the positions of the atoms slightly and

calculating the reaction forces (necessary to use supercells of the
original cell when there are long ranged interatomic interaction
in the system) – Finite Displacement
You select the

method in the
Properties
section when
you set up a
CASTEP
calculation
CASTEP 32
Thermodynamic Properties : Examples
Scanning Tunnelling Microscope Profile
• Scanning probe microscopy become a powerful measuring and imaging

technology
• STM probes the electronic properties of the surface
– Enables the user to obtain images high resolution
– Perform electrical spectroscopy at different sites
• CASTEP models STM profile by representing it as an electron density
generated only by specific orbitals
– Specify distance above or below the Fermi level
– Corresponds to the bias used in experimental STM
• Limitations
– Most appropriate for slabs
– Less reliable the farther you get from the surface
CASTEP 33
Generating STM images

• STM is always “on”
– No need to select from Setup option
• Select STM Profile from Analysis
• STM bias: Specify the value of the bias

for STM modeling
– Positive bias corresponds to the
imaging of occupied states
– Negative bias to the imaging of
empty states
• View isosurface on import: When

checked, an isosurface will be created
Example STM Images
Simulated STM image of Xe on Ni (110) surface
CASTEP 34
Limitations of DFT
• DFT is a ground state theory
• Strongly correlated systems
• Underestimation of van der Waals bonding
• Underestimation of transition state energies

(especially LDA)
• Underestimation of band gaps
CASTEP 35
Appendix A
Hubbard U
Typically, the default values of Hubbard U are set when a structure is being
prepared as input for a calculation, using for example CASTEP, according to
the table below.
Note. Elements and angular momenta not mentioned here are getting by
default zero Hubbard U values.
Element Name Atomic number Angular Momentum Hubbard U

Sc 21 d 2.5 eV
Ti 22 d 2.5 eV
V 23 d 2.5 eV
Cr 24 d 2.5 eV
Mn 25 d 2.5 eV
Fe 26 d 2.5 eV
Co 27 d 2.5 eV
Ni 28 d 2.5 eV
Cu 29 d 2.5 eV
Y 39 d 2.0 eV
Zr 40 d 2.0 eV
Nb 41 d 2.0 eV
Mo 42 d 2.0 eV
Tc 43 d 2.0 eV
Ru 44 d 2.0 eV
Rh 45 d 2.0 eV
Pd 46 d 2.0 eV
Ag 47 d 2.0 eV
Cd 48 d 2.0 eV
La 57 f 6.0 eV
Ce 58 f 6.0 eV
Pr 59 f 6.0 eV
Nd 60 f 6.0 eV
Pm 61 f 6.0 eV
Sm 62 f 6.0 eV
Eu 63 f 6.0 eV
Gd 64 f 6.0 eV
Tb 65 f 6.0 eV
Dy 66 f 6.0 eV
Ho 67 f 6.0 eV
Er 68 f 6.0 eV
Tm 69 f 6.0 eV
Yb 70 f 6.0 eV
Fr 87 f 2.0 eV
Ra 88 f 2.0 eV
Ac 89 f 2.0 eV
Th 90 f 2.0 eV
Pa 91 f 2.0 eV
U 92 f 2.0 eV
Np 93 f 2.0 eV
Pu 94 f 2.0 eV
Am 95 f 2.0 eV
Cm 96 f 2.0 eV
Bk 97 f 2.0 eV
Cf 98 f 2.0 eV
Es 99 f 2.0 eV
Fm 100 f 2.0 eV
Md 101 f 2.0 eV
No 102 f 2.0 eV
Hands-on exercise: Convergence test for plane waves
Purpose: How to choose the right cut-off?
Modules: Materials Visualizer, CASTEP
Time:
Prerequisites: None
Background:
Bloch's theorem states that the electronic wavefunctions at each k-point can be
expanded in terms of a discrete plane-wave basis set. In principle, an infinite number of
plane waves is required for such an expansion. However, the coefficients, Ck+G, for the
plane waves with small kinetic energies, |k+G|2, are more important than those with
large kinetic energies. Thus, the plane wave basis set can be truncated to include only
plane waves that have kinetic energies that are smaller than some particular cutoff
energy:
k+G
2
≤ Ecut
2
The truncation of the basis set at a finite cutoff energy will lead to an error in the
computed total energy and its derivatives. It is possible to reduce the magnitude of the
error in a systematic way by increasing the value of the cutoff energy. In principle, the
cutoff energy should be increased until the calculated total energy converges within the
required tolerance.
Introduction:
We want to investigate the plane wave cutoff energy dependency of Yttrium. We

increase the cutoff energy until the calculated total energy is converged within the
required tolerance.
This tutorial covers:
• Setting up the structure for the calculation

• Setting up the CASTEP calculation
• Analyze the results
HO CASTEP 1
LESSON1: Setting up the structure for the calculations
We have chosen Yttrium (Y) as an example. Your first task is to import the structure.
Select File | Import... from the menu bar or click on the Import button on the
toolbar. On the Import Document dialog, navigate to Structures|metals|pure-
metals|Y.msi. Press Import.
The bulk Y structure is displayed. You can change the display style to ball and stick.
Right-click in the Y 3D Model document and select Display Style. On the Atom tab,
select Ball and stick. Close the dialog.
Bulk structure of Yttrium
Transform the structure to a primitive cell for improved calculation speed without
compromising the accuracy level.
Choose Build|Symmetry|MakeP1 from the menu bar.
The model document displays the primitive cell.
LESSON2: Setting up the CASTEP calculation
Choose the CASTEP tool from the toolbar then select Calculation or select
Modules|CASTEP|Calculation from the menu bar.
The CASTEP dialog is displayed.
HO CASTEP 2
CASTEP Calculation dialog, Setup tab
Change the Task on Geometry Optimisation and the Quality to Medium. You will use
the GGA functional PW91, so change PBE to PW91.
In the Electronic tab you have to change the energy cut-off values:
In the Electronic tab click the More button, which leads you to CASTEP electronic
options dialog. Tick Use custom energy cut-off and type 200 in the field. Then close
the dialog again.
HO CASTEP 3
In the CASTEP Calculation dialog go to the Job Control tab and uncheck Automatic. In
the Job description field type Y_200eV. Then press Run.
The calculation starts in a Folder Y-200eV CASTEP GeomOpt. You can move on to
prepare calculations using energy cut-offs of 230, 260, 290 and 400 eV.
Tip. If you are running on a (remote) machine with a lot of space you can
submit on job after the other.
Now do four more calculations:
Make sure that Y.xsd is the active document whenever you start a CASTEP calculation
- double-click it in the Project Explorer.
Change the value in Use custom energy cut-off to 230, and change the Job
description to Y_230eV. Run the calculation.
Repeat the procedure for 260, 290 and 400 eV and name the jobs Y_260eV,
Y_290eV and Y_400eV, respectively.
HO CASTEP 4
LESSON 3. Analyze the results
After all calculations are done you have five new folders called Y_200eV GeomOpt,
Y_230eV CASTEP GeomOpt, Y_260eV CASTEP GeomOpt, Y_290eV CASTEP
GeomOpt and Y_400eV CASTEP GeomOpt.
When the results documents are transferred, you should have several documents,
among them:
• Y_[value]eV.xsd - the final optimized structure

• Y_[value]eV.castep - an output text document containing the optimization
information
• Y_[value]eV.param - input information for the simulation
CASTEP thus attempts to minimize the total energy and stress of the system. Therefore,
to ensure that the calculation has completed properly, it is important to check that the
stresses have converged as well.
In the Project Explorer, click on Y.castep to make it active. Choose Edit | Find... from
the menu bar and type completed successfully in the text box. Press the Find
Next button. Scroll a few lines up.
dE/ion is the change of energy, |F|max is the maximum allowed force on any atom and
|dR|max is the tolerance for the change in any atomic position between iterations. The
last column in each row should say Yes. This indicates that the calculation has
succeeded.
Open the output file Y_200eV.castep and in the output file search for (with CRTL-F)
Final Energy.
HO CASTEP 5
Repeat for all output files.
You can collect all the values in a study table.
Thus, click the New button and open a new study table document. Type in the
values.
It is common to look at the energies with respect to the lowest energy, which is in this
case the energy of the structure where the cutoff is 400 eV.
The Define Function dialog allows you to specify a mathematical expression used to
create a function model.
Select column C and click the Define Function button and type B-(-
387.4902337005) in the Expression section and press Apply.
Then plot the results by using the Quick Plot button on the Study Table Viewer toolbar.
Select the column heading cell for column A. Hold down the CTRL key and select the
column heading cell for column C. Right-click in any of the selected column heading
cells (A or C) and select Quick Plot from the context menu. You also can click the
Quick Plot button in the Study Table Viewer tool bar.
HO CASTEP 6
Or you can use a program such as Excel:
Ec(eV) Etotal(eV) ΔE(eV)(*)

200 -387.37247697 0.12069329
230 -387.41944374 0.07372652
260 -387.43583610 0.05733416
290 -387.44596829 0.04720197
400 -387.49023370 0.00293656
450 -387.49317023 0
(*)ΔE = Etotal (Ec) - Etotal(Ec =400eV)
HO CASTEP 7
0.14
0.12
0.1
Ec [eV]
0.08
0.06
0.04
0.02
0
200 250 300 350 400 450
ΔE [eV]
Thus, with an increase of the cutoff energy value, Ec, there is a change in the total
energy, which reaches a plateau after certain cutoff. A cutoff of 400-450 eV is sufficient
for modeling Y.
It may be desirable to perform convergence tests with respect to other

parameters such as k point sampling, FFT (fast Fourier transform) mesh or SCF
tolerance. You usually do that when you have only little information (from literature) on
the structure you are modeling.
This is the end of the tutorial.
HO CASTEP 8
Hands-On Exercise: Adsorption of CO onto a Pd(110) Surface

Purpose: Introduces the use of CASTEP for calculating the adsorption energy of a gas
onto a metal surface.
Time:
Prerequisites: None
Background
In this tutorial you will examine the adsorption of CO on Pd(110). The Pd surface plays a
crucial role in a variety of catalytic reactions. Understanding how molecules interact with
such surfaces is one of the first steps to understanding catalytic reactions. In this context,
DFT simulation can contribute to this understanding by addressing the following questions:
Where does the molecule want to adsorb? How many molecules will stick to the surface?
What is the adsorption energy? What does the structure look like? What are the
mechanisms of adsorption?
You will focus on one adsorption site, the short bridge site, as it is known to be
energetically preferred.
Tip. When you deal with an unknown surface, you had to find preferred adsorption
sites by probing them – i.e. you take the molecule of interest and put it on different
places on the surface of interest and calculate a set of interaction energies. The highest
interaction energies indicate the preferred adsorption sites
Also, the coverage will be fixed (1 ML). At 1 ML coverage the CO molecules repel each
other preventing the CO molecules from aligning exactly perpendicular to the surface. You
will calculate the energy contribution of this tilting to the chemisorption energy by
considering a (1 x 1) and (2 x 1) surface unit cell.
HO CASTEP 9
Figure 1. Pd bulk and a top view on the Pd(110) surface. The (110) cleave plane is
highlighted in blue. a0 is the bulk lattice constant, also known as the lattice parameter.
Note: You will need the dimensions described in Figure 1 at a later stage in this
example when you put the CO molecule in the position required.
Introduction
In this tutorial, you will use CASTEP to optimize and calculate the total energies of several
different systems. Once you have determined these energies, you will be able to calculate
the chemisorption energy for CO on Pd(110).

• Preparing the project
• Optimizing bulk Pd
• Building and optimizing CO
• Building the Pd(110) surface
• Relaxing the Pd(110) surface
• Adding CO to the 1 x 1 Pd(110) surface and optimizing the structure
• Setting up and optimizing the 2 x 1 Pd(110) surface
• Analyzing the energies
• Analyzing the density of states (DOS)
Tip. This tutorial is best carried out with the file extensions for each document
displayed. If the file extensions are not displayed in your Project Explorer,
refer to the Project Explorer topic for instructions on how to reconfigure.
HO CASTEP 10
LESSON 1: Preparing the project
This tutorial consists of five distinct calculations. To make it easier to manage your project,
you should begin by preparing five subfolders in your project.
Right-click on the root icon in the Project Explorer and select New | Folder. Repeat this
four more times. Right-click on New Folder and select Rename and type Pd bulk. Repeat
this procedure for the other folders, naming them Pd(110), CO molecule, (1x1) CO on
Pd(110) and (2x1) CO on Pd(110).
LESSON 2: Optimizing bulk Pd
The crystal structure of Pd is included in the structure library provided with MS Modeling.
In the Project Explorer, right-click on the Pd bulk folder and select Import.... Navigate to
Structures/metals/pure-metals and import Pd.msi.
The bulk Pd structure is displayed. You can change the display style to ball and stick.
Right-click in the Pd 3D Model document and select Display Style. On the Atom tab,
select Ball and stick. Close the dialog.
Now optimize the geometry of the bulk Pd using CASTEP.
Choose the CASTEP tool from the toolbar then select Calculation or select Modules
|CASTEP | Calculation from the menu bar.
HO CASTEP 11
The default values for geometry optimization do not include optimization of the cell.
Change the Task from Energy to Geometry Optimization. Press the More... button and,
in the CASTEP Geometry Optimization dialog, check Optimize Cell. Press Run. A
message dialog about conversion to the primitive cell is displayed. Press Yes.
The job is submitted and starts to run. You should proceed to the next section and build the
CO molecule but return here when the calculation is complete to display the Lattice
Parameters.
NOTE. When the job has finished, you must convert the primitive cell result back to
a conventional cell representation in order to proceed with building the
Pd(110) surface in step 4.
In the Project Explorer, open Pd.xsd located in the Pd CASTEP GeomOpt folder. Select
Build |Symmetry | Conventional Cell from the menu bar.
You should now save your project files.
Select the file File | Save Project, then Window | Close All from the menu bar. In the
Project Explorer, open Pd.xsd located in the Pd CASTEP GeomOpt folder.
This is the optimized structure of Pd.
Right-click in the 3D Model document and select Lattice Parameters.
HO CASTEP 12
The value of a should be approximately 3.92 Å compared with the experimental value of
3.89 Å.
LESSON 3: Building and optimizing CO
CASTEP will only work with periodic systems. Therefore, to optimize the geometry of the
CO molecule, you must put it into a crystal lattice.
In the Project Explorer, right-click on CO molecule and select New | 3D Atomistic

Document. Right-click on 3D Atomistic.xsd and select Rename. Type CO and press the
RETURN key.
An empty 3D model document is displayed. You will use the Build Crystal tool to create an
empty cell and then add the CO molecules to it.
Select Build | Crystals | Build Crystal from the menu bar. Choose the Lattice
Parameters tab and change each cell Length a, b, and c to 8.00. Press the Build button.
An empty cell is displayed in the 3D model document.
Select Build | Add Atoms from the menu bar.
The C-O bond length in the CO molecule has been determined experimentally as 1.1283
Å. By adding the atoms using cartesian coordinates you can create your CO molecule with
exactly this bond length.
On the Add Atoms dialog, select to the Options tab. Ensure that the Coordinate system is
set to Cartesian. Select the Atoms tab. Press the Add button.
A carbon atom is added at the origin of the cell.
On the Add Atoms dialog, change the Element to O. Leave the x and y values as 0.000.
Change the z value to 1.1283. Press the Add button. Close the Add Atoms dialog.
You are now ready to optimize your CO molecule.
Choose the CASTEP tool from the toolbar then select Calculation.
The settings from the previous calculation have been retained. However, you do not need
to optimize the cell for this calculation.
HO CASTEP 13
On the Setup tab, press the More... button. Uncheck Optimize Cell and close the dialog.
Select the Electronic tab and change the k-point set from Medium to Gamma.
Choose the Properties tab and select Density of states. Change the k-point set to
Gamma and check Calculate PDOS. Press the Run button.
The calculation starts. You can move onto building the Pd surface as you will analyze the
energy at the end of the tutorial.
LESSON 4: Building the Pd(110) surface

This section of the tutorial uses the optimized Pd structure from the Pd bulk part of the
tutorial.
Select File | Save Project then Window | Close All from the menu bar. Open Pd.xsd in
the Pd bulk/Pd CASTEP GeomOpt folder.
Creating the surface is a two step process. The first step is to cleave the surface and the
second is to create a vacuum slab containing the surface.
Select Build | Surfaces | Cleave Surface from the menu bar. Change the Cleave plane
(h k l) from -1 0 0 to 1 1 0 and press the TAB key. Increase the Fractional Depth to 1.5.
Press the Cleave button and close the dialog.
A new 3D model document is opened containing the 2D periodic surface. However,

CASTEP requires a 3D periodic system as input. This is obtained using the Vacuum Slab
tool.
Select Build | Crystals | Vacuum Slab from the menu bar. Change the Vacuum
thickness from 10.00 to 8.00 and press the Build button.
The structure changes from 2D to 3D periodic and a vacuum is added above the atoms.
NOTE: Before continuing, you must reorient the lattice.
Right-click in the 3D model document and select Lattice Parameters from the context
menu. Select the Advanced tab and press the Reorient to standard button. Close the
dialog.
You should also change the lattice display style and rotate the structure so that the z-axis
is vertical on the screen.
HO CASTEP 14
Right-click in the 3D model document and select Display Style from the context menu.
Select the Lattice tab. In the Display style section, change the Style from Default to
Original. Close the dialog. Press the Up cursor key twice.
The 3D model document shown below is displayed:
The Pd atom with the largest z-coordinate will be called "the uppermost Pd layer".
NOTE. Later in this tutorial, you will need to know the bulk interlayer spacing d0. You
can calculate this using the atom coordinates.
Select View | Explorers | Properties Explorer from the menu bar. Select the Pd atom
with FractionalXYZ x = 0.5 and y = 0.5. Note the z value of this atom from the XYZ
property.
The z value should be 1.386 Å and this is the interlayer spacing. This z value refers to the
Z coordinate from the (Cartesian) XYZ property and not Fractional XYZ.
a0
Note. For a fcc(110) system, d0 can be calculated as d 0 = .
8
Before you relax the surface, you must constrain the Pd atoms in the bulk as you only need
to relax the surface.
Hold down the SHIFT key and select all the Pd atoms except the uppermost Pd layer.
Select Modify| Constraints from the menu bar. Check Fix fractional position and close
the dialog.
The bulk atoms have been constrained. You can see the constrained atoms by changing
their display color.
HO CASTEP 15
In the 3D model document, click to deselect the atoms. Right-click and select Display Style
from the context menu. In the Coloring section of the Atom tab, change the Color by option
to Constraint.
The 3D model document is now displayed like this:
RED
RED
Change the Color by option back to Element and close the dialog.
This structure is needed for the Pd(110) surface relaxation and also as a starting model for
(1x1) CO on Pd(110) optimization.
Select File | Save As... from the menu bar. Navigate to the Pd(110) folder and press the
Save button. Repeat this for the (1x1) CO on Pd(110) folder but this time, change the
name of the document to (1x1) CO on Pd(110). Select File | Save Project then Window |
Close All from the menu bar.
LESSON 5: Relaxing the Pd(110) surface
Now you are ready to optimize the Pd (110) surface.
From the Project Explorer, open Pd(110).xsd in the Pd(110) folder. Choose the CASTEP
tool from the toolbar then select Calculation. Press the More... button and ensure
that Optimize Cell is unchecked. Close the dialog.
To maintain consistency across the calculations that you are going to perform, you should
make some changes on the Electronic tab.
HO CASTEP 16
Select the Electronic tab and press the More... button. Choose the Basis tab from the
CASTEP Electronic Options dialog. Check Use custom energy cutoff and change the
field value from 260.0 to 300.0.
Select the k-points tab and check Custom grid parameters. In the Mesh parameters
field,
change a to 3, b to 4 and c to 1. Close the dialog.
You should also calculate the Density of States for the system.
Select the Properties tab on the CASTEP Calculation dialog. Check Density of states.
Check Calculate PDOS and change the k-point set to Medium.
The properties tab
You are ready to run the calculation.
Press the Run button. Close the dialog.
The calculation will take some time to run and so you will perform the analysis at the end.
You should move on and construct the next set of surfaces.
Select File | Save Project then Window | Close All from the menu bar.
HO CASTEP 17
LESSON 6: Adding CO to the 1 x 1 Pd(110) surface and optimizing the

structure
Now you are going to work with the structure in the (1x1) Co on Pd(110) folder.
In the Project Explorer, open (1x1) CO on Pd(110).xsd in the (1x1) CO on Pd(110) folder.
Now add the CO molecule above the short bridge position. You will make use of the fact
that for CO on Pd(110), bond lengths have been experimentally determined.
Geometry of CO on Pd(110) in the yz-

plane.
NOTE: Hatched atoms are not displayed in Lattice: Original display mode.
The following section demonstrates how to find the coordinates for the C and the O atom of
the CO molecule:
The first step is to add the carbon atom. The Pd-C bond length (denoted above as dPd-C)
should be 1.93 Å. When you use the Add Atom tool you can enter either cartesian or
fractional coordinates but in this case you will use fractional coordinates, xC, yC, and zC. xC
and yC are simple as yC = 0.5 and xC = 0. However, zC is a more difficult. You will construct
it from the two distances zPd-C and zPd-Pd. (look also at Figure 1)
zPd-Pd is simply the lattice parameter a0 divided by √2 (it should be 2.77 Å).
zPd-C is obtained from the formula (it should be 1.35 Å).
HO CASTEP 18
Add zPd-C and zPd-Pd to obtain zC (it should be 4.12 Å).
Now convert this distance into a fractional length. You do this using the Lattice parameters.
Right-click on the 3D model document and select Lattice Parameters from the context
menu. Note the value of c.
To calculate the fractional z coordinate, you simply divide zC by the c lattice parameter (you
should obtain 0.382 Å).
Select Build | Add Atoms from the menu bar and choose the Options tab. Check that the
Coordinate system is Fractional. Choose the Atoms tab and change the Element to C.
Change a to 0.0, b to 0.5, and c to 0.382. Press the Add button.
If you want to confirm that you have set up the model correctly, use the Measure/Change
tool.
Click on the options arrow associated with the Measure/Change tool on the toolbar
and select Distance. Click on the Pd-C bond.
The next step is to add the oxygen atom.
On the Add Atoms dialog, change the Element to O.
Experimentally, the C-O bond length has been determined as 1.15 Å. In fractional
coordinates this is 0.107. Adding this value to the fractional z-coordinate of carbon (0.382),
the z-coordinate of oxygen is 0.489.
Change the value in the c field to 0.489 and press the Add button. Close the dialog.
NOTE: The original symmetry of the Pd model was P1 but this has changed with the
addition of the CO.
You can find and impose symmetry using the Find Symmetry tool.
Choose the Find Symmetry tool on the toolbar. Press the Find Symmetry button
followed by the Impose Symmetry button.
The symmetry is PMM2.
Right-click in the 3D model document and select Display Style from the context menu.
Select the Lattice tab and change the Style to Default.
HO CASTEP 19
The structure should look similar to this:
NOTE: Before you optimize the geometry of the structure, you should save it in the
(2x1) CO on Pd(110) folder.
Select File | Save As... from the menu bar. Navigate to the (2x1) CO on Pd(110) folder.
Save the document as (2x1) CO on Pd(110).xsd.
You are now ready to optimize the structure.
Select File | Save Project then Window | Close All from the menu bar. In the Project
Explorer, open (1x1)CO on Pd(110).xsd in the (1x1)CO on Pd(110) folder.
The parameters from the previous calculation should have been retained.
Press the Run button.
Once again, you can move onto building the final structure whilst the calculation
progresses.
HO CASTEP 20
LESSON 7: Setting up and optimizing the 2 x 1 Pd(110) surface
The first step is to open the 3D Atomistic document in the (2x1) CO on Pd(110) folder.
In the Project Explorer, open (2x1) CO on Pd(110).xsd in the (2x1) CO on Pd(110) folder.
This is currently a 1 x 1 cell so you need to use the Supercell tool to change it to a 2 x 1
cell.
Select Build | Symmetry | Supercell from the menu bar. Increase b to 2 and press the
CreateSupercell button. Close the dialog.
The structure should look like this:
A B
(2 x 1) Cell of CO on Pd(110)
Now tilt the CO molecules with respect to each other. To simplify this operation, identify the
CO molecule at y = 0.5 as molecule A and the one at y = 0.0 as molecule B.
Select the carbon atom of molecule B.

In the Properties Explorer, open the XYZ property and subtract 0.6 from the X field. Repeat
this for the oxygen atom of molecule B but subtract 1.2 from the X field.
Now repeat this for molecule A.
Select the carbon atom of molecule A. In the Properties Explorer, open the XYZ property
and add 0.6 to the X field. Repeat this for the oxygen atom of molecule A but add 1.2 to
the X field.
NOTE: You have to change XYZ (at the bottom of the list in the Properties Explorer)
NOT the FractionalXYZ!!!
HO CASTEP 21
The view down the z-axis of the molecule should look like this:
However, you will notice that the Pd-C and C-O bond lengths have changed from their
original values.
Select the carbon atom in molecule A and use the Properties Explorer to change the Z
field of the FractionalXYZ property to 0.369. Repeat this for molecule B.
This corrects the Pd-C bond length. You can use the Measure/Change tool to correct the
C-O bond length.
Click on the options arrow associated with the Measure/Change tool on the toolbar
and select Distance. Click on the C-O bond for molecule A, choose the 3D Viewer
Selection Mode tool on the toolbar and select the monitor. In the Properties Explorer,
change the Filter to Distance. Change the Distance property to 1.15 Å. Repeat this for
molecule B.
Now recalculate the symmetry of the system.
Choose the Find Symmetry tool on the toolbar. Press the Find Symmetry button
followed by the Impose Symmetry button.
NOTE: The symmetry is PMA2. The view of the unit cell changes from 3 CO
molecules on the Pd surface to only 2.
You are now ready to optimize the geometry of your system.
For this calculation, you need to change the k-points grid parameters so that you can
compare the energies from this and the previous calculation.
HO CASTEP 22
Select the Electronic tab on the CASTEP Calculation dialog. Press the More... button.
Select the k-points tab and change the Custom grid parameters so that a is 2, b is 3,
and c is 1. Close the dialog. Press the Run button.
The calculation starts. When the calculation finishes, you will need to extract the total
energy of the system as detailed in the next section. You can move onto the next section to
extract the energies from the previous calculations.
LESSON 8. Analyzing the energies
In this section you are going to calculate the chemisorption ΔEchem. This is defined as:
ΔEchem = 0.5* E(2x1)CO on Pd (110) – EPd(110) – ECO molecule
Allowing the CO atoms to tilt against each other, hence reducing the self repulsion of the
CO molecules, should result in a gain in energy. The repulsion energy can be calculated
from:
ΔErep = 0.5* E(2x1)CO on Pd (110) – E(1x1)CO on Pd (110)
To calculate these properties, you need to extract the total energies from CASTEP text
output documents for each simulation.
In the Project Explorer, open CO.castep in the CO molecule/CO CASTEP GeomOpt

folder. Press CTRL-F and search for Final Enthalpy. Note down the value that appears in
that line.
Repeat the procedure to find the total energies of the other systems and so complete the
table.
HO CASTEP 23
Once you have the energies, simply use the above equations to calculate Echem and
Erep. These should have values of approximately 1.96 eV and ~ 0.1 eV, respectively.
LESSON 9. Analyzing the density of states (DOS)

Next, you will examine the changes in the density of states (DOS). This will allow you to
obtain an insight into the bonding mechanism of CO on Pd(110). To do this, you need to
display the density of states of the isolated CO molecule and of (2x1) CO on Pd(110).
In the Project Explorer, open CO.xsd in the CO molecule/CO CASTEP GeomOpt folder.
Choose the CASTEP tool from the toolbar then select Analysis. Select Density of states.
Check Partial and uncheck f and sum but leave everything else as it is. Press the View
button.
A chart document is displayed showing the PDOS for the CO molecule.
HO CASTEP 24
PDOS of CO molecule
Repeat the above for (2x1) CO on Pd(110).xsd.
PDOS of (2x1) CO on Pd(110)
HO CASTEP 25
It is clear that the electronic states of the isolated CO molecule at approximately -20, -5,
and -2.5 eV are considerably lowered in energy as the CO binds to the surface.
HO CASTEP 26
Hands-On Exercise: Simulating the STM profile of CO on Pd(110)

Purpose: Demonstrates the use of CASTEP for simulating the transmission microscope
(STM) profile of a system.
Time:
Prerequisites: Adsorption of CO onto a Pd(110) surface
Background
The scanning transmission microscope (STM) provides an image of a material, but it

can also be used to provide quantitative information at the atomic scale. The ability to
simulate the STM image therefore provides a way to compare computed results with
experiment.
CASTEP models the STM profile by representing it as an isosurface of the electron

density generated only by states at a certain energy away from the Fermi level. The
distance from the Fermi level corresponds to the applied bias in STM experiments:
positive bias corresponds to occupied (valence) states and negative bias to empty
(conduction) states. This approach neglects the actual geometry of the STM tip.
STM profile visualization makes sense only for models that represent surfaces in the
slab supercell geometry. In addition, information about charge density at a distance
from the surface is likely to be inaccurate as a result of DFT failing to reproduce the
asymptotics of the wavefunction decay into a vacuum.
Introduction
In this tutorial, you will use CASTEP to simulate the STM profile of a CO molecule
adsorbed onto a Pd (110) surface. You will make use of results obtained previously for
this system.
• Creating an STM isosurface

• Adding extra information to the STM isosurface
LESSON 1: Creating an STM isosurface
There is no need to select special options to set up an STM profile calculation. The STM
analysis uses data that are saved every time you run a CASTEP calculation. Therefore,
you do not need to run an extra calculation to perform this tutorial. Instead, you simply
open the results of the calculation you ran previously.
So, begin by opening the MS Modeling project that you created for the tutorial
Adsorption of CO onto a Pd(110) surface. If you have not performed this tutorial or if
HO CASTEP 27
you did not save the project files, you run through it before proceeding.
Open the file (1x1) CO on Pd(110).xsd in the folder (1x1) CO on Pd(110)\(1x1) CO on

Pd (1 1 0) CASTEP GeomOpt.
Right-click in the 3D Atomistic document and choose Display Style from the context
menu. On the Display Style dialog, choose the Lattice tab. Set the maximum value of
the range in the B direction to 2.00.
The model should look similar to the image below.
1 x 2 Supercell of CO on Pd(110)
Press the CASTEP button from the toolbar, then select Analysis from the
dropdown list.
Select STM profile from the list at the top of the CASTEP Analysis dialog. Use the
Results file selector to choose (1x1) CO on Pd (1 1 0).castep as the input results file.
Check View isosurface on import. Set the value of STM bias to 1.0.Press Import.
An isosurface is created, but it is very small and does not convey a lot of information.
You will now use the Display Style dialog to set more appropriate values for the
isosurface.
Right-click in the 3D Atomistic document and select Display Style from the context
menu. Select the Isosurface tab on the Display Style dialog. Set the Iso-value to 0.002
and press the TAB key.
You should now be able to see an isosurface which looks something like the one shown
below.
HO CASTEP 28
1 x 2 Supercell of CO on Pd(110) with simulated STM profile
LESSON 2: Adding extra information to the STM isosurface
You can get additional detail from the image by adding extra information to it. You will
use the total charge density as the source of this extra information.
Choose Modules | CASTEP | Analysis from the menu bar. Select Electron density
from the list at the top of the CASTEP Analysis dialog. Make sure that the View
isosurface on import checkbox is not checked. Press the Import button.
On the Display Style dialog, select the Isosurface tab. Select CASTEP total electron
density of Pd from the Mapped field dropdown list. Set the Iso-value to 0.0015 and
press the TAB key.
Press the Color Maps button on the Volume Visualization toolbar. On the Color
Maps dialog, set the To value to 2.0.
The structure should now resemble the one shown below.
HO CASTEP 29
Simulated STM profile colored by total charge density
The isosurface is constructed from the density due only to orbitals corresponding to the
bias, i.e., those about 1 eV above the Fermi level. The color corresponds to the total
charge density, with the red regions corresponding to the highest density, which
surrounds the Pd atoms. However, these would, of course, be invisible in an
experiment. The majority of the STM profile is in regions of the surface with a very low
charge density, colored blue. Notice that the polarized p-orbital on the oxygen atom
corresponds to mid-range charge density.
An experimental STM would be viewed along the c-axis of the cell.
Rotate the cell until you are looking down the c-axis.
You cannot see much because the isosurface generated by the Pd atoms at the top of
the cell blocks the view of the inside of the cell. You will use the Display Style dialog to
hide this part of the isosurface.
On the Display Style dialog, select the Field tab. In the Display range section, set the
value of C to 0.80 and press the TAB key.
HO CASTEP 30
Examine the structure. What parts of the CO molecule and the Pd surface are you
looking at? Does the size and shape of the STM image of the oxygen atom seem
reasonable?
Set the value of C on the Field tab to 0.50 and press the TAB key.
This shows another view of the STM isosurface cutting through the oxygen atom.
HO CASTEP 31
Hands-On Exercise: Charge density difference of CO on Pd(110)

Purpose: Demonstrates the use of CASTEP for calculating the charge density
difference that occurs when a molecule adsorbs on a surface.
Time:
Prerequisites: Adsorption of CO onto a Pd(110) surface
Background
In this tutorial you will investigate how the bonding of the CO molecule affects the
electron distribution relative to the isolated CO molecule and the unperturbed Pd(110)
surface. The charge density difference can be computed in two different ways.
The first option is to compute the charge density with respect to fragments. This is
useful for describing the formation of large systems in terms of smaller ones. This
method illustrates how the charge density changes during a chemical reaction or on
binding of a molecule to a surface.
In the case of CO on Pd(110) the electron density difference can be expressed as:
Δρ = ρCO@Pd(110) - (ρCO + ρPd(110))
where ρCO@Pd(110) is the electron density of the total CO + Pd(110) system, and ρCO and
ρPd(110) are the unperturbed electron densities of the sorbate and substrate, respectively.
The other option is to compute the density difference with respect to atoms:
Δρ = ρCO@Pd(110) - ∑(ρi)
where the subscript i runs over all atoms. This option shows the changes in the electron
distribution due to the formation of all the bonds. It is useful for illustrating how chemical
bonds are formed across the whole system by delocalization of atomic charge density.
The display of the density difference can contribute to an understanding of adsorption

processes. Where does the molecule want to adsorb? Why does the molecule adsorb
there? What bonding mechanisms contribute to the stabilization of the molecule at this
site?
You will focus on one adsorption site: the short bridge site you studied in the tutorial
Adsorption of CO onto a Pd(110) surface.
Introduction
In this tutorial, you will use CASTEP to compute the charge density difference of CO on
Pd(110) in two different ways. You will use the optimized geometry of CO on Pd, as
determined previously. Once you have completed the calculations you will use the
Materials Visualizer to display the density differences as 3D fields and 2D slices.
HO CASTEP 32
• Defining fragments
• Running the calculation
• Displaying the fragment density difference
LESSON 1. Defining fragments
Begin by opening the MS Modeling project that you created for the tutorial Adsorption of
CO onto a Pd (110) surface. If you have not performed this tutorial or if you did not save
the project files, you must do so before proceeding.
Open file (1x1) CO on Pd(110).xsd in the folder (1x1) CO on Pd(110)\(1x1) CO on Pd

(1 1 0) CASTEP GeomOpt. To compute the fragment density difference you must first
define the fragments. You will do this using the Edit Sets option. Begin by creating a set
containing the carbon and oxygen atoms.
Select Edit | Edit sets from the menu bar.

Click on the carbon atom to select it. Hold down the SHIFT key and click on the
oxygen atom. In the Edit Sets dialog, click on New. In the Define New Set dialog enter
the name CO DensityDifference. Press OK.
NOTE. In order for CASTEP to recognize the set as a fragment for charge density
difference calculations, the name must contain the text string
DensityDifference.
Notice that in the model (1x1) CO on Pd (1 1 0).xsd the CO molecule is now highlighted
and labelled using the name you gave the set.
You do not have to define the Pd surface as set since CASTEP automatically assumes
that the remaining atoms are to be subtracted when computing the electron density
difference.
Close the Edit Sets dialog.
Atoms belonging to a set are displayed with a mesh around them. You can hide the
mesh as follows.
Click on the mesh to select the set.

Select View | Explorers | Properties Explorer from the menu bar. In the Properties
Explorer, set the value of the Filter to Set. In the list of properties for Set there is one
called IsVisible. Double-click on IsVisible. In the Edit IsVisible dialog select No /
False.
Press OK.
The set is no longer highlighted with the mesh.
HO CASTEP 33
Tip. In order to remove the label CO DensityDifference, select it with the mouse
and press the DELETE key.
Finally, before you can start the calculation, you must reset the symmetry of the
structure to P1.
Select Build | Symmetry | Make P1 from the menu bar.
LESSON 2: Running the calculation
Choose the CASTEP tool from the toolbar then select Calculation or choose
Modules | CASTEP | Calculation from the menu bar.
Since you have already run a geometry optimization on the system, you only need to
perform a single point energy calculation in order to obtain the density differences.
Change the Task to Energy.

Choose the Properties tab and select Electron density difference. Check Both
atomic densities and sets of atoms. Ensure that you deselect any other properties.
Press Run then OK.
The job is submitted and begins to run. You should wait for it to complete before
proceeding to the next section.
When the job has finished, you should save the project.
HO CASTEP 34
Select File | Save Project from the menu bar.
LESSON 3: Displaying the fragment density difference
When the calculation finishes, you can display the charge density difference. Begin by
closing all the open windows.
Select Window | Close All from the menu bar.
Now open the output structure for the job you just ran.
Open the document (1x1) CO on Pd (1 1 0).xsd in the folder (1x1) CO on Pd (1 1 0)

CASTEP Energy.
Choose the CASTEP tool from the toolbar then select Analysis. Select Electron
density difference. Check View isosurface on import and uncheck Use atomic
densities. Press the
Import button.
Tip. When you select Use atomic densities the density difference is computed
with respect to atoms. When it is unchecked, the difference is computed
with respect to fragments.
This displays an isosurface of the difference density at a value of about 0.1 electrons /
Å3.
Now you should create a more chemically useful isosurface.
HO CASTEP 35
Right-click on the document and select Display Style from the context menu.
In the Display Style dialog select the Isosurface tab. Set the Iso-value to 0.05 and
check +/-.
This procedure displays two isosurfaces together. One is at a value of 0.05 and is
colored blue, the other is at -0.05 and is colored yellow. The blue areas show where the
electron density has been enriched with respect to the fragments. Conversely, the
yellow areas show where the density has been depleted.
Charge density difference for CO Pd (110)
You can gain further insight into the changes in bonding by displaying the density
difference as a 2D slice. You can do this using the Volume Visualization toolbar.
Select the isosurface (click either blue or yellow) by clicking on it with the mouse, and
press the DELETE key.
Tip. The visibility of isosurfaces and slices can also be controlled, without
deleting, using the Volumetric Selection dialog.
Select View | Toolbars | Volume Visualization from the menu bar.
Now use the Create Slices tool to create a 2D slice from the data.
HO CASTEP 36
Select the dropdown arrow associated with the Create Slices tool and choose a
slice Parallel to B & C Axis. Click on the 2D slice to select it.
Hold down the SHIFT and ALT keys and the right mouse button to move the slice so
that it cuts through the CO molecule.
You now have a 2D slice showing the density difference through the CO molecule. Next
you will adjust the data range of the slice and change the color scheme to differentiate
more easily between regions of electron depletion and electron enrichment.
Click on the slice to select it. Choose the Color Maps tool from the Volume
Visualization toolbar. In the Color Maps dialog change the Spectrum to Blue-White-
Red. Set From to - 0.2 and To to 0.2. Finally, set the value of Bands to 16.
HO CASTEP 37
Each of the 16 colors represents a specific range of the charge density. In this plot a
loss of electrons is indicated in blue, while electron enrichment is indicated in red. White
indicates regions with very little change in the electron density. You can see the red and
blue areas more clearly if you hide the white areas.
Click on the two colors in the center of the selector on the Color Maps dialog.
The selector should now look like this:
HO CASTEP 38
The final image should resemble the one shown here:
2D charge density difference for CO Pd (110)
Based on this, which atoms have lost electron density? Can you tell which orbitals lost
electrons? Which orbitals on which atoms gained electrons? Does this match your
expectations for carbon-metal bonding?
If you are interested you could repeat this section of the tutorial using the atomic density
difference rather than the fragment density difference. Simply make sure that you check
Use atomic densities when you import the density difference.
HO CASTEP 39
Hands-on Exercise: Calculating elastic constants for BN

Purpose: Illustrates the use of CASTEP to calculate elastic constants
Modules: MS Visualizer, CASTEP
Time:
Prerequisites: None
Background:
Recent developments in density functional theory (DFT) methods applicable to

studies of large periodic systems have become essential in addressing problems in
materials design and processing. The theory allows one to interpret experimental
data and to determine the underlying properties of a material from the structural
properties of an unknown crystal to the binding energy and reactivity of a molecule
on a surface. These tools can be used to guide and lead in the design of new
materials, allowing researchers to understand the underlying chemistry and physics
of a process.
Introduction:
In this tutorial, you will learn how to use CASTEP to calculate Elastic Constants and
other mechanical properties. In the first part you will optimize the structure of BN
cubic structure and then you will calculate its elastic constants.
This Tutorial covers:
• Optimizing the structure of BN cubic

• Calculating the elastic constants of BN
• Description of the elastic constants file
Lesson 1: Optimizing the structure of BN cubic

It is not necessary to perform geometry optimization before calculating elastic
constants, so you can generate Cij data for experimentally observed structures.
However, more consistent results are obtained if you perform full geometry
optimization, including cell optimization, and then calculate the elastic constants for
the structure corresponding to the theoretical ground state.
The accuracy of the elastic constants, especially of the shear constants, depends
strongly on the quality of the SCF calculation and, in particular, on the quality of the
Brillouin zone sampling and the degree of convergence of wavefunctions. Therefore,
HO CASTEP 40
you should use the Fine setting for SCF tolerance and k-point sampling and a Fine
derived FFT grid.
Begin by importing the BN structure.
Select File | Import from the menu bar to display the Import Document dialog.
Navigate to the folder Structures/semiconductors/ and select BN.msi. Press
Import.
The structure of BN is displayed:
This is the conventional representation of the BN structure. In order to reduce the

computation time, you should convert to the primitive representation.
Select Build | Symmetry | Primitive Cell from the menu bar.
Now set up the geometry optimization.
Press the CASTEP button on the toolbar and select Calculation from the
dropdown menu or choose Modules | CASTEP | Calculation from the menu bar.
The CASTEP Calculation dialog is displayed:
HO CASTEP 41
On the Setup tab, set the Task to Geometry Optimization, the Quality to Fine, and
the Functional to GGA and PW91.
Press the More... button. On the CASTEP Geometry Optimization dialog, check the
Optimize cell checkbox. Close the CASTEP Geometry Optimization dialog.
Select the Electronic tab on the CASTEP Calculation dialog. Press the More...
button to display the CASTEP Electronic Options dialog. Change the Derived grid
setting from Standard to Fine. Close the CASTEP Electronic Options dialog.
Choose the Job Control tab on the CASTEP Calculation dialog and select the
Gateway on which you wish to run the CASTEP job.
Press Run.
After optimization, the structure should have cell parameters of about

a = b = c = 2.5488 Å.
Right-click in the 3D Atomistic document and select Lattice Parameters from the
context menu.
The lattice parameters are shown. Now you can go on to calculate the elastic
constants of the optimized structure.
HO CASTEP 42
LESSON 2: Calculating the elastic constants of BN
Choose the Setup tab on the CASTEP Calculation dialog. Select Elastic Constants
from the Task dropdown list. Press the More... button.
The CASTEP Elastic Constants dialog is displayed:
Increase the Number of steps for each strain from 4 to 6. Close the CASTEP
Elastic Constants dialog and press Run on the CASTEP Calculation dialog. The BN
CASTEP GeomOpt/BN.xsd document must be active.
Note: If BN CASTEP GeomOpt/BN.xsd is made active before the CASTEP

Elastic constants dialog is opened, the Strain pattern grid on this dialog
will contain values.
CASTEP results for the Elastic Constants task are returned as a set of .castep output
files. Each of them represents a geometry optimization run with a fixed cell, for a
given strain pattern and strain amplitude. The naming convention for these files is:
seedname_cij__m__n
where m is the current strain pattern and n is the current strain amplitude for the
given pattern.
CASTEP can use these results to analyze the calculated stress tensors for each of
these runs and generate a file with information about elastic properties.
HO CASTEP 43
Press the CASTEP button on the toolbar and select Analysis from the
dropdown menu or choose Modules | CASTEP | Analysis from the menu bar.
Select Elastic constants from the list of properties at the top of the CASTEP
Analysis dialog. The results file from the Elastic Constants job for BN should be
displayed automatically in the Results file selector. Press the Calculate button.
A new text document, BN Elastic Constants.txt, is created in the results folder.
The information in this document includes a summary of the input strains and
calculated stresses, results of linear fitting for each strain pattern (including quality of
the fit), the correspondence between calculated stresses and elastic constants for a
given symmetry, a table of elastic constants (Cij) and elastic compliances (Sij). The
derived properties, such as bulk modulus and its inverse, compressibility, Young
modulus, and Poisson ratios for three directions, and the Lame constants that are
needed for modeling the material as an isotropic medium, are also reported in this
document.
LESSON 3: Description of the elastic constants file
Two strain patterns are required for this lattice type. For each strain pattern, there is a
summary of calculated stresses as extracted from the respective .castep files:
HO CASTEP 44
HO CASTEP 45
Any information about the connection between components of the stress, strain, and
elastic constants tensors is provided. At this stage, each elastic constant is
represented by a single compact index rather than by a pair of ij indices. The
correspondence between the compact notation and the conventional indexing is
provided later in the file:
A linear fit of the stress-strain relationship for each component of the stress is given in the
following:
HO CASTEP 46
HO CASTEP 47
HO CASTEP 48
The gradient provides the value of the elastic constant (or a linear combination of
elastic constants); the quality of the fit, indicated by the correlation coefficient,
provides the statistical uncertainty of that value. The stress intercept value is not
used in further analysis, it is simply an indication of how far the converged ground
state was from the initial structure.
The results for all the strain patterns are then summarized:
The errors are only provided when more than two values for the strain amplitude are
used, since there is no statistical uncertainty associated with fitting a straight line to
only two points.
Elastic constants are then presented in a conventional 6 x 6 tensor form, followed by

a similar 6 x 6 representation of the compliances:
HO CASTEP 49
The final part of the file contains the derived properties:
HO CASTEP 50
Hands-on Exercise: Calculation of the optical properties of

diamond
Purpose: Introduces the use of CASTEP to calculate optical properties.
Modules: Material Visualizer, CASTEP
Time:
Prerequisites: None
Background
Graphite and diamond differ from each other only in the way in which the
carbon atoms are arranged to create the solid material. Graphite and diamond, both
are polymorphs of the element carbon; graphite is a black material (coal is an impure
form of graphite) while diamond is transparent and has the optical properties that
make it so desired as a jewel. Diamond has a three dimensional structure with each
carbon atom joined to form other identical carbon atoms. This three dimensional
structure is very rigid and this helps to explain on an atomic scale the observed
properties of diamond as a very hard material. Graphite is different: its carbon atoms
are arranged in flat sheets. There is relatively little attraction between neighboring
sheets, and the slippage of the sheets past each other allows solid graphite to be
used as a lubricant. Diamond has long held a special place in the hearts and minds
both of scientists and the public at large. For some, the word diamond conjures up
images of brilliant gem stones, wealth and special occasions. To the scientist,
diamond is impressive because of its wide range of extreme properties. It is the
hardest known material, has the lowest coefficient of thermal expansion, is
chemically inert and wear resistant, offers low friction, has high thermal conductivity,
is electrically insulating and optically transparent from the ultra-violet (UV) to the far
infrared (IR). Given these many notable properties, it should come as no surprise to
learn that diamond already finds use in many diverse applications including, of
course, its use as a precious gem, but also as a heat sink, as an abrasive, and as
inserts and/or wear-resistant coatings for cutting tools. We will use CASTEP to
calculate the optical properties of diamond and graphite to figure out why they show
different behavior.
Introduction
This tutorial introduces you to the optical properties calculation tool in

CASTEP. You will learn how to use the optical property tool to calculate them for
diamond and graphite, respectively.
HO CASTEP 51
The tutorial covers:
• Setting up the structures

• Setting up and running the CASTEP calculations
• Analyzing the results
LESSON 1. Setting up the structures

Begin by importing the crystal structure of diamond and graphite.
toolbar. On the Import Document dialog, navigate to
Structures/ceramics/diamond.msi and then press import. Repeat for the same for
graphite, i.e. Structures/ceramics/graphite.msi.
Structure of diamond
HO CASTEP 52
Structure of graphite
The crystal structure of diamond in the 3D Viewer is the conventional unit cell, which
shows the cubic symmetry of the lattice. Diamond belongs to the Fd3m space-group.
CASTEP uses the full symmetry of the lattice if any exists. Thus, the primitive lattice,
containing 2 atoms per unit cell, can be used, as opposed to the conventional cell,
which contains 8 atoms. The charge density, bond distances, and total energy per
atom will all be the same no matter how the unit cell is defined, and thus, by using
fewer atoms in the unit cell, the computation time will be decreased.
Note. The only time one needs to be careful in these situations is when a
spin - polarized calculation is performed on a magnetic system, where
the charge density spin wave has a period, which is a multiple of the
primitive unit cell.
Make diamond.msi the active document and choose Build | Symmetry | Primitive
Cell from the menu bar.
HO CASTEP 53
Primitive Cell of diamond
Graphite is already a primitive cell as it belongs to the P63/mmc space group.
LESSON 2: Setting up and running the CASTEP calculation
Make diamond.xsd the active document. Select the CASTEP tool from the
toolbar then select Calculation or choose Modules | CASTEP | Calculation from the
menu bar.
The CASTEP Calculation dialog is displayed.
CASTEP, Calculation Dialog
In the setup tab, set Task to Energy, the Quality to Fine and the Functional to LDA
and CA-PZ, respectively.
HO CASTEP 54
You have to specify the number of additional bands (empty bands) to be included in
an electronic minimization as a percentage of the number of occupied bands.
The number of empty bands is important too. When calculating a metallic system,
empty bands are needed as part of the minimization procedure, so that the Fermi
level can be found. In spin polarized calculations, quite often quite a few more empty
bands are needed than in the non-spin polarized case because the up and down
electrons are not equally populated.
If not enough empty bands are included in the calculation, you might not be able to
get to the required spin state; also if the SCF convergence is slow look for insufficient
empty bands – look for occupancies of the highest energy electronic states. They
should be close to 0 for all k-points in a calculation, which is setup correctly.
Go to the Electronic tab in the Calculation dialog and press the More button. Go to
the SCF tab and set Empty bands to 12.
CASTEP Electronic Options Tab
One more comment about Density Mixing: this is the mixing of input and output
densities from the current iteration to obtain the input density for the next iteration in
the interactive solution of SCF.
Go back to the Calculation dialog and select the Properties Tab. Check Optical
properties.
HO CASTEP 55
CASTEP, Properties tab
Finally, press Run. Repeat for graphite.msi.
LESSON 3: Analyzing the results
You obtain two new folders: diamond CASTEP energy and graphite CASTEP
Energy, respectively.
Open diamond.xsd in the folder diamond CASTEP energy. Click the CASTEP
tool and select Analysis. In the scroll-down menu click Optical properties. Set
Function to Adsorption and Units to nm.
HO CASTEP 56
CASTEP Analysis Dialog
A few points to this dialog:
• Polarized - optical properties are calculated for plane polarized with the
specified polarization direction.
• Unpolarized - optical properties are averaged over polarization directions
perpendicular to the specified incident direction.
• Polycrystalline - optical properties are averaged over all polarization
directions, thereby imitating an experiment on a polycrystalline sample.
• Scissors - Specify the scissors operator to be used for calculating the
dielectric function.
Note: The scissors operator is only applied for insulating systems, which have
a clear separation between valence band and conduction band states. It
is ignored for metallic systems.
Press Calculate and then View. Repeat for graphite.xsd in the folder graphite
CASTEP Energy.
You obtain two absorption spectra:
HO CASTEP 57
Make the diamond adsorption spectrum the active document and click File|Export.
Set Export as type to Comma-separated Files (for 2d Charts)(*.csv). Repeat for
the spectrum of graphite.
You can load the .csv files into Excel and manipulate them.
HO CASTEP 58
700000
600000
Diamond
500000
Graphite
400000
300000
200000
100000
0
0 100 200 300 400 500 600 700 800 900 1000
You see that graphite is absorbing within the visible light range (wave length
approximately 350 nm to 800nm) whereas diamond is not. Thus, graphite is black
and diamond is transparent.
Comments
The direction of the polarization may have a great influence here. Especially
for stratified substances like graphite; if the polarization light direction is changed
from 1,0,0 to 0,0,1 the spectrum will change as graphite is a layered structure.
HO CASTEP 59
Hands-on Exercise: Computing band structures and density of

states with CASTEP
Purpose: To introduce the electronic properties of band structures and density of
states.
Time:
Prerequisites: None
Background
Extended periodic systems may be characterized by their energy bands. These are
analagous to orbital eigenvalues in molecular systems. Unlike the orbital
eigenvalues, the energy of each band will vary at different points in the cell. The
bands are plotted in the so-called reciprocal space of the cell. In fact, there are a
limited number of symmetry-unique directions in reciprocal space, so only a finite
number of points are needed to characterize the bands. By observing the energy
gaps between bands at various points, it is possible to draw conclusions about the
nature of a material, i.e., whether it is an insulator, a conductor, or a semiconductor.
Another way of characterizing the electronic structure of a material is by the density

of states (DOS). The DOS counts the relative number of energy levels in each
energy range. In a molecule, there are distinct energy eigenvalues, so, strictly
speaking, the DOS has a value of 1 at each of these values and a value of 0
elsewhere. For a crystal, by contrast, the energy levels are a continuum, with more or
less energy values squeezed into an energy range. Examining the DOS also allows
you to see whether a system is conducting or insulating. In addition, the partial
density of states (PDOS) allows you to characterize the DOS in terms of particular
atomic orbitals, s, p, d, or f.
Introduction
In this tutorial, you will use CASTEP to compute and analyze the band structure,
DOS, and PDOS of a semiconductor.

• Setting up the CASTEP calculation
• Controlling the job settings and running the job
• Analyzing the band structure
• Analyzing the DOS and PDOS
HO CASTEP 60
LESSON 1: Setting up the CASTEP calculation

The first step is to import the structure that you will analyze. MS Modeling includes a
wide range of prebuilt structures. In this tutorial, you will perform calculations on AlAs
(a semiconductor).
Select File | Import... from the menu bar or click on the Import button on the toolbar.
On the Import Document dialog, navigate to and select
Structures\semiconductors\AlAs.msi, then press Import.
The structure of AlAs is displayed.
The crystal structure in the 3D Viewer is the conventional unit cell, which shows the
cubic symmetry of the lattice. CASTEP uses the full symmetry of the lattice, if any
exists. Thus, the primitive lattice, containing 2 atoms per unit cell, can be used, as
opposed to the conventional cell, which contains 8 atoms. The charge density, bond
distances, and total energy per atom will all be the same no matter how the unit cell
is defined, but, by using fewer atoms in the unit cell, the computation time will be
decreased.
Choose Build | Symmetry | Primitive Cell from the menu bar.
HO CASTEP 61
The primitive cell of AlAs
CASTEP is one of several modules available for MS Modeling and is accessed

through the Modules toolbar or the Modules menu.
Press the CASTEP button on the toolbar and choose Calculation or select
Ensure that Geometry Optimization is selected from the Task dropdown list. Set the
Functional settings to GGA and PBE, and the Quality to Medium.
You will use all the default options associated with the Medium quality setting, so
there is no need to change any of the other calculation parameters.
HO CASTEP 62
Select the Properties tab.
This tab allows you to calculate certain properties after the structure is optimized.
CASTEP Calculation dialog, Properties tab
Check the Band structure checkbox.
Notice that the default number of Empty bands to be included is 12 and the default
value of k-point set is Medium. These values are suitable for most applications.
However, you should examine the k-point set in more detail.
Click the More... button to display the CASTEP Band Structure Options dialog.
HO CASTEP 63
CASTEP Band Structure Options dialog
Each row of the table indicates a path through reciprocal space. The paths traverse
all the symmetry-unique points in the Brillouin zone. The coordinates are indicated
with respect to the relative position in the zone. In row 1, for example, a path will be
traced from [0.5, 0.25, 0.75] to [0.5, 0.5, 0.5], and a total of five k-points will be used
on the path. The energy will be computed at each one of the points, and the results
will be displayed as a plot of k-point vs. energy. By convention, each of the points is
assigned a letter corresponding to its position in the Brillouin zone. As you can see,
for example, W corresponds to [0.5, 0.25, 0.75]. The gamma point, Γ, represented
here by a G, corresponds to [0, 0, 0].
Using the controls at the bottom of the panel, you can add or delete rows or you can
change the value of the coordinates. You could also change the number of divisions,
Div, by changing the value of kpoint set on the Properties tab. However, you do not
need to change any of these values for this tutorial.
Click OK to close the CASTEP Band Structure Options dialog.

Check the Density of states checkbox on the Properties tab. Check the Calculate
PDOS checkbox to compute the partial density of states.
HO CASTEP 64
LESSON 2. Controlling the job settings and running the job

You will use the commands on the Job Control tab to control the CASTEP
calculation.
Select the Job Control tab.
CASTEP Calculation dialog, Job Control tab
Here, you can choose the gateway location where you will run your calculation and
set various options, such as the job description, whether the job will be launched
using multiple processors, and the number of processors to employ. You can access
further job options via the More... button, including live update settings and controls
that determine what happens when the job completes.
You are now ready to run your CASTEP calculation.
Press the Run button.
The Job Explorer opens, containing information about status of the calculation.
A text document called status.txt, containing the CASTEP run status opens. This
document is updated regularly until the calculation is complete.
HO CASTEP 65
LESSON3: Analyzing the band structure
When the calculation is complete, the results are returned to the AlAs CASTEP
GeomOpt folder in the Project Explorer.
In the AlAs CASTEP GeomOpt folder, double-click on AlAs.xsd.
The AlAs structure is displayed. The crystal structure is the same as that of the
original, but this structure has results associated with it from running a CASTEP
calculation. In the remainder of this tutorial, you will analyze the band structure and
DOS results.
Press the CASTEP button on the toolbar and choose Analysis or select
Modules | CASTEP |Analysis from the menu bar.
The CASTEP Analysis dialog is displayed.
CASTEP Analysis Dialog
HO CASTEP 66
Ensure that Band structure is highlighted in the dialog and that AlAs.xsd is the
active document.
Click on View.
A band structure plot is displayed.
CASTEP band structure for AlAs
The energies of the bands are plotted with respect to the Fermi level, which is
assigned a value of zero.
Notice that the band gap at the gamma point, Γ, is only about 1.6 eV, indicating that
this is a semiconductor. You can use the zoom controls to expand this area of the
chart and measure the band gap more precisely.
HO CASTEP 67
LESSON 4: Analyzing the DOS and PDOS
Highlight Density of states in the CASTEP Analysis dialog. Select the radio button
labeled Partial and check the checkboxes for s, p, d, f and Sum. Click on View.
A PDOS plot is displayed.
CASTEP PDOS for AlAs
Examine the number of energy states at the Fermi level, i.e., the point where
Energy = 0. An insulator will have a distinct gap, while a conductor will have many
states.
The plot here is typical of a semiconductor.
Notice that you can see how many of the states arise from each type of orbital.
HO CASTEP 68
It also is possible to see how many of the states are associated with a particular atom
in the structure.
The AlAs structure is displayed.
Select one of the Al atoms by clicking on it (the Al atoms are at the corners of the
cell).
Recreate the PDOS chart using the same procedure as above.
CASTEP PDOS for Al
The AlAs structure is displayed.
Now, select the As atom in AlAs and create another PDOS plot for this atom.
HO CASTEP 69
CASTEP PDOS for As
Compare the results for Al, As, and for the entire unit cell. Which atom contributes
more states to the DOS at the Fermi level?
HO CASTEP 70
Hands-on Exercise: Transition state searching using LST/QST

tools
Purpose: Introduces the use of CASTEP and the Reaction Preview tool to perform a
transition state calculation.
Time:
Prerequisites: None
Background:
Exploring the potential energy surface of any reaction requires both structural and
energetic (or kinetic and thermodynamic) snapshots of each step in the reaction
process. Of particular importance is the rate-determining step, which usually involves
finding the elusive transition-state structure. A number of techniques have been used to
find transition-state structures and among the better known and validated of these are
the Linear Synchronous Transit (LST) and Quadratic Synchronous Transit (QST)
methods.
Introduction:
This tutorial introduces you to the LST/QST tool in CASTEP. You will learn how to use
the LST/QST tool to find a transition-state structure for a hydrogen dissociation reaction
on a Pd (1 1 1) surface.
• Setting up the structure for the calculations

• Optimizing the geometry
• Defining the atom pairing
• Calculating the transition-state structure using the LST/QST/CG method
Lesson 1: Setting up the structure for the calculations
Your first task is to build the Pd (1 1 1) surface.
Begin by importing the crystal structure of palladium metal.
toolbar. On the Import Document dialog, navigate to Structures/metals/pure-metals
and select Pd.msi, then press Import.
HO CASTEP 71
Now modify the way in which the structure is displayed.

Right-click in Pd.xsd and select Display Style from the context menu. On the Atom
tab of the Display Style dialog, choose Ball and stick from the Display style section.
Close the Display Style dialog.
You obtain:
Crystal structure of Pd
The Cleave Surface tool in Materials Visualizer allows you to cleave any surface from a
bulk crystal.
Select Build | Surfaces | Cleave Surface from the menu bar.
The Cleave Surface dialog is displayed:
HO CASTEP 72
Cleave Surface Dialog
Change the Miller indices of the Cleave plane to 1 1 1 and set the Fractional
Thickness to 2.0. Press the Cleave button.
Pd, after being cleaved
Select the Surface Mesh tab and set the surface vector U to 0.5 -1 0.5, then press
TAB. Set the surface vector V to 0.5 0.5 -1 and press TAB. Close the Cleave Surface
dialog.
HO CASTEP 73
Pd, after changing the mesh
A new 3D Atomistic document Pd (1 1 1).xsd containing the 2D periodic surface is

created. However, CASTEP requires a 3D periodic system as input. This is obtained
using the Vacuum Slab tool.
Select Build | Crystals | Build Vacuum Slab... from the menu bar. On the Vacuum
Slab tab of the Build Vacuum Slab Crystal dialog, change the Vacuum thickness to
7.00 Å and press the Build button.
The structure changes from 2D to 3D periodic and a vacuum is added above the atoms.
3D with Vacuum
You can remove the symmetry images of atoms at the bottom of the unit cell that
appear at the top of the cell.
Select Build | Bonds from the menu bar to open the Bond Calculation dialog and check
the Monitor bonding checkbox. Close the Bond Calculation dialog.
HO CASTEP 74
Click in Pd (1 1 1).xsd and press the Display Style button on the toolbar to
open the Display Style dialog. Choose the Lattice tab and set the Style to In-Cell.
Finally, reset the Style to Default. Close the Display Style dialog.
3D, without symmetry images
Now, you are going to use the Pd (1 1 1) surface you have built to construct the
structure corresponding to the reactants.
Select File | New... from the menu bar and choose 3D Atomistic. Make
Pd (1 1 1).xsd the active document. Choose Edit | Select All from the menu bar,
followed by Edit | Copy.
In Project Explorer, double-click on 3D Atomistic.xsd to make it the active document.

Choose Edit | Paste from the menu bar. Click in the document to deselect everything.
Right-click on 3D Atomistic.xsd in the Project Explorer and select Rename from the
context menu. Name the document reactants.
Now you need to add a hydrogen molecule to the Pd surface.
Select Build | Add Atoms from the menu bar.
The Add Atoms dialog is displayed:
HO CASTEP 75
Add Atoms Dialog
Using this dialog, you can add atoms at specific positions within the unit cell.
On the Atoms tab, select H from the Element dropdown list and enter H1 as the Name.
Select the Options tab and set the Coordinate system to Fractional.
Return to the Atoms tab and set a to 0.56, b to 0.47, and c to 0.70. Press the Add
button.
A hydrogen atom appears in the cell.
HO CASTEP 76
Using the same procedure, add a second hydrogen atom named H2 at a = 0.47, b =
0.56, c =0.70. Close the Add Atoms dialog.
Tip. When you attempt to add the second hydrogen atom, MS Modeling may
generate a warning message. This warning appears because the hydrogen
atom you are trying to add is within a defined tolerance (1.0 Å) of the first
hydrogen. In this case, there is no problem because you are trying to build
a hydrogen molecule with an H-H bond length of less than 1.0 Å. Press the
Yes button to continue and add the second hydrogen atom.
An H2 molecule is formed with an H-H bond length of 0.743 Å. The molecule is located
parallel to the Pd-Pd bond in the center of the cell at a distance of about 4.00 Å from the
surface.
Reactants structure
HO CASTEP 77
For simplicity, you will make the assumption that the surface is fixed during the reaction.
To do this, you must constrain the surface atoms to remain at their actual positions.
Select one of the Pd atoms in reactants.xsd, then hold down the ALT key and double-
click on it to select all of the Pd atoms.
Choose Modify | Constraints from the menu bar to open the Edit Constraints dialog.
Fix the fractional and Cartesian coordinates of the Pd atoms by checking both the Fix
Cartesian position and Fix fractional position checkboxes on the Atom tab. Close
the Edit Constraints dialog.
Now, you are going to build the structure of the products. This time, you will use the
structure in reactants.xsd as the starting point.
Click on the options arrow associated with the New button on the toolbar and
select 3D Atomistic Document from the dropdown menu.
Click in reactants.xsd to make it the active document. Choose Edit | Select All from
the menu bar, then press the Copy button on the toolbar. In the Project Explorer,
double-click on 3D Atomistic.xsd to make it the active document Press the Paste
button on the toolbar. Click in the document to deselect everything.
Right-click 3D Atomistic.xsd in the Project Explorer and select Rename from the
context menu. Enter the name products.
Next, you will use the Properties Explorer to change the positions of the hydrogen
atoms in the structure.
Click on one of the hydrogen atoms in products.xsd. Its FractionalXYZ coordinates

are displayed in the Properties Explorer.
Locate the hydrogen atom named H2 at 0.47, 0.56, 0.70. Double-click in the
FractionalXYZ text box and change the fractional coordinates for this atom to
0.333333, 0.666667, 0.414103. Use the same procedure to move the hydrogen atom
H1 to 0.666667, 0.333333, 0.414103.
Select Build | Bonds from the menu bar to open the Bond Calculation dialog and check
the Monitor bonding checkbox. Close the Bond Calculation dialog.
The new structure has one hydrogen atom bonded to each of the two central Pd atoms
in the cell at a distance of 1.583 Å.
HO CASTEP 78
Products structure
Note. Both the reactants and the products have the same cell parameters. This is
necessary, since the version of LST/QST implemented in CASTEP cannot
take into account variation in the cell parameters. However, the limitation is
not significant, as long as you are interested in processes where cell
variation is unimportant, such as reactions on surfaces, diffusion of atoms,
and vacancies in the bulk
Lesson 2: Optimizing the Geometry

As has already been discussed, the cell parameters must be the same for both
reactants and products. For this reason, any optimization will involve only the positions
of the atoms within the cell. Moreover, you can consider the structure of the reactants
'as is', so there is no need to optimize their structures.
Ensure that products.xsd is the active document. Press the CASTEP button on
the toolbar and select Calculation.
HO CASTEP 79
You are going to optimize the geometry of the structure.
On the Setup tab, change the Task to Geometry Optimization and ensure that the
Quality is set to Medium. The Functional settings should be GGA and PBE.
Press More… and make sure Optimize cell is not checked.
Select the Electronic tab and set the k-point set to Gamma. Ensure that the
Pseudopotentials are set to Ultrasoft.
Press the More... button to open the CASTEP Electronic Options dialog and then select
the SCF tab.
Under Density mixing, set the value of the Charge to 0.4. Press the More... button
associated with this option to open the CASTEP Density Mixing Options dialog. Change
the DIIS history list to 5. Close the CASTEP Density Mixing Options dialog.
On the SCF tab of the CASTEP Electronic Options dialog, ensure that the Fix
occupancy checkbox is not checked.
Close the CASTEP Electronic Options dialog.
You can also specify the job control options, such as live updates.
Select the Job Control tab of the CASTEP Calculation dialog and press the More...
button to open the CASTEP Job Control Options dialog. Change the Update interval to
30.0 seconds. Close the CASTEP Job Control Options dialog.
If you want to run the job on a remote server, you can select it from the Job Control tab.
HO CASTEP 80
Press the Run button. Close the CASTEP Calculation dialog.
After a few seconds, a new folder is displayed in the Project Explorer. This will contain
all the results from the calculation.
The Job Explorer displays the status of any currently active jobs that are associated
with this project. It shows useful information such as the server and job identification
number. You can also use the Job Explorer to stop the job.
As the job progresses, four documents that relay information on the job status are
opened. These documents include the crystal structure, showing updates of the
structure during optimization, a status document relaying information about the job's
setup parameters and run information, and charts of the total energy and convergence
in energy, forces, stress, and displacement as a function of the iteration number.
When the job finishes, the files are transferred back to the client. This process may take
some time due to the size of certain files.
Repeat the geometry optimization for reactants.xsd. Be sure to use all the same
input settings as detailed above.
LESSON 3: Defining the atom pairing
For CASTEP to perform a transition-state search, all the atoms in the reactants and
products documents need to be paired. This task is performed using the Reaction
Preview functionality available on the Tools menu.
First, you should display the optimized structures of the reactants and products side-by-
side. Begin by closing all the windows.
Select File | Save Project from the menu bar, then Window | Close All.
In the Project Explorer, locate and open the files containing the optimized structures,
products CASTEP GeomOpt\products.xsd and reactants CASTEP
GeomOpt\reactants.xsd. Select Window | Tile Vertically from the menu bar.
Now you are ready to start pairing atoms in the reactants and products structures.
Select Tools | Reaction Preview from the menu bar.
The Reaction Preview dialog is displayed:
HO CASTEP 81
Reaction Preview dialog
Choose reactants CASTEP GeomOpt\reactants.xsd and products CASTEP

GeomOpt\products.xsd as the Reactant and Product, respectively. Click on the
Match... button.
The Find Equivalent Atoms dialog is displayed. You should see that, initially, 0 atoms
are matched and 8 are unmatched.
Press the Auto Find button.
HO CASTEP 82
Now the atoms are separated into two groups. There are 6 matched Pd atoms and 2
unmatched H atoms.
Double-click on the 2xH folder in the reactants column.
The corresponding folder in the products column also opens. The reactants column
should contain 7:H1 and 8:H2. These should map directly onto their counterparts in the
products window, but take the following steps to make sure.
With both the reactants and products 3D Atomistic documents open, click on 7:H1 in the
reactants column of the Find Equivalent Atoms dialog. Then click on 7:H1 in the
products column. The hydrogen atoms in both panes should be selected and these
should be identical in the two 3D Viewers. Confirm that these two atoms correspond to
one another in the reactants and products and click on Set Match.
Once you specify the match between 7:H1 in the reactants and the products, MS
Modeling automatically assigns 8:H2 between the reactants and products. The 6xPd
folder is automatically opened for you to confirm the matches for the remaining
palladium atoms.
Click on 1:PD1 in the reactants column and then 1:PD1 in the products column of the
Find Equivalent Atoms dialog. The palladium atoms in both panes should be selected
and the atoms highlighted in the reactants and products 3D Viewers should correspond
to one another.
Continue reviewing the atom matches between reactants and products in this manner
until you are satisfied.
Close the Find Equivalent Atoms dialog when you are satisfied that all the matches
have been made correctly.
To perform a transition-state search with the CASTEP LST/QST functionality, you need
to create a pathway between the reactants and products, as this is required as input to
the CASTEP calculation.
On the Reaction Preview dialog, ensure that the Number of frames is 10. Press the
Preview button. Close the Reaction Preview dialog.
Within a few seconds, a new 3D Atomistic Trajectory document, entitled reactants-

products.xtd, is displayed. You will run the CASTEP calculation on this file. You can
animate the trajectory document using the tools on the Animation toolbar.
Use the View menu to display the Animation toolbar, if it is not already visible. Use the
Play button to animate the trajectory.
Tip. The animation looks best when viewed in Bounce mode.
HO CASTEP 83
You can set the animation mode by clicking on the options arrow associated with the
Animation Mode button and selecting a setting from the dropdown list.
You can switch on bond monitoring so that bonds are recalculated after each step
Select Build | Bonds from the menu bar to open the Bond Calculation dialog. On the
Bonding Scheme tab, check the Monitor bonding checkbox. Close the Bond
Calculation dialog Reanimate the trajectory. When you have finished watching the
animation, press the Stop button on the toolbar.
LESSON 4: Calculating the transition-state structure using the

LST/QST/CG method
You are now ready to set up the CASTEP calculation to determine the transition-state
structure.
Select Modules | CASTEP | Calculation from the menu bar to open the CASTEP
Calculation dialog. On the Setup tab, change the Task from Geometry Optimization to
TS Search.
Click on the More... button. On the CASTEP Transition State Search dialog, make sure
that the Search protocol is set to Complete LST/QST and the Quality is set to
Medium. Close the CASTEP Transition State Search dialog.
Ensure that the remaining input options are the same as those used for the geometry
optimization calculations.
Finally, you should update the Job description.
Select the Job Control tab and make sure that the Automatic checkbox is unchecked.
Enter TS as the Job description.
You are now ready to run the calculation.
Press the Run button. Close the CASTEP Calculation dialog.
During the calculation, several different documents and an LST/QST graph are
displayed in the Visualizer. These report the status of the calculation. In particular, the
LST/QST graph monitors the progress of the TS search by showing a plot of energy vs.
path coordinate via LST, QST, and CG (conjugate gradient).
When the LST/QST calculation is complete, the transition state structure is written to the
document TS.xsd.
HO CASTEP 84
If the document is not displayed automatically, double-click on TS.xsd in the Project

Explorer.
Transition-state structure
The textual results of the calculation are contained in the TS.castep file.
If the document is not displayed automatically, double-click on TS.castep in the
Project Explorer.
Press CTRL + F and search for Transition State Found.
The energy of reaction is about -0.96 eV. The energy barrier from the reactants should
be about 0.08 eV and the barrier from the products should be about 1.04 eV.
Now you can explore the reaction pathway.
Make TS.xsd the active document. Press the CASTEP button on the toolbar, then
select Analysis or choose Modules | CASTEP | Analysis from the menu bar. Select
Energy evolution from the list at the top of the CASTEP Analysis dialog.
Click on View. A chart document, TS CASTEP TSSearch\TS TSSearch.xcd,
containing the history of the TS search is displayed. Select the Chart Viewer Selection
Mode tool from the toolbar. Double-click on TS Trajectory.xtd. Click on
various points on the chart to see the corresponding structure in the trajectory file.
Note. The calculation presented in this tutorial aims merely to demonstrate the
LST/QST functionality. In order to run reliable calculations on slabs, you
should consider more layers of Pd atoms, a larger vacuum layer, and more
accurate electronic structure settings (in particular, more k-points to
describe the metallic substrate properly - only the Gamma point was used
in this tutorial). Finally, more strict convergence criteria would be needed
for the TS search.
HO CASTEP 85
Assigning the 17O NMR spectrum of L-alanine

Purpose: Introduces the capabilities of NMR CASTEP and the use of the
visualization tools for displaying isotropic shielding values.
Modules: Materials Visualizer, CASTEP, NMR CASTEP
Time:
Prerequisites: None
Background
NMR CASTEP predicts the NMR chemical shielding of molecules and solid-state
materials from first principles. Based on density functional theory (DFT), NMR
CASTEP provides a way to predict key magnetic resonance properties, NMR
chemical shielding and electric field gradient (EFG) tensors, with unprecedented
accuracy. The method can be applied to compute the NMR shifts of molecules,
solids, interfaces, and surfaces for a wide range of materials classes including
organic molecules, ceramics and semiconductors. First-principles calculations allow
researchers to investigate the nature and origin of the magnetic resonance properties
of a system without the need for any empirical parameters.
NMR is often used as an analytical tool to aid in structure prediction. The relative
complexity of solid state structures makes this a challenging task. Often, even though
the general features of the crystal structure are understood, a detailed analysis of the
geometry proves elusive. Using NMR CASTEP it is possible to simulate the NMR
spectrum for a series of related structures until a match is discovered between the
computed and experimental results. In this way, theory complements experiment,
with both contributing to the determination of the structure.
Note. NMR in CASTEP is part of the separately licensed module NMR CASTEP.
NMR calculations can only be performed if you have purchased this
module.
Introduction
In this tutorial, you will use NMR CASTEP to assign the observed 17O chemical shifts
to the two unique atoms in crystalline L-alanine. You will learn how to run an NMR
CASTEP calculation, display the results in the Materials Visualizer, and to interpret
the results.
L-Alanine is one of the smaller amino acids. The unit cell contains 4 molecules for a
total of 48 atoms.
HO CASTEP 86
There are 2 distinct oxygen sites. This tutorial will use the computed NMR chemical
isotropic shielding values to tell them apart. Experiment can also distinguish between
the two oxygens, but only with a very sophisticated solid-state NMR apparatus.

• Running an NMR CASTEP calculation
• Analyzing the results
• Comparing the results with experimental data
Note. This tutorial entails running an NMR CASTEP calculation, which may take
a considerable amount of time if your server machine does not have a
fast CPU.
LESSON 1: Running an NMR CASTEP calculation
Begin by opening the crystal structure for L-alanine. This is a neutron diffraction
crystal structure (Lehmann et al., 1972). You could also build this crystal structure
from scratch and optimize it with CASTEP. Using experimental crystal structures,
however, yields results comparable with the DFToptimized geometry and saves
computation time.
Select File | Import from the menu bar. Use the file import dialog to navigate to
\Examples\Documents\3D Model\. Locate the file l_alanine.xsd and double-
click on it.
The l_alanine document is displayed.
Crystal structure of L-alanine
HO CASTEP 87
Select the CASTEP tool from the toolbar then choose Calculation or select
CASTEP Calculation dialog
You are going to run an energy calculation on the structure and request a calculation
of the NMR chemical shielding tensor.
Change the Task to Energy, Quality to Ultra-fine, and set Functional to GGA PBE.
Note. As a rule, the computed NMR results are sensitive to the Quality of the
calculation. In order to obtain results that are comparable with
experiment, you should use the Ultra-fine Quality setting.
These calculations will take longer than Fine or Medium calculations, but the results
are considerably more reliable.
Select the Electronic tab. Set the value of Pseudopotentials to On the fly.
On the fly (OTFG) pseudopotentials are required to compute the magnetic shielding
properties. If you choose a different type of pseudopotential, the NMR calculation
cannot be performed.
Currently, OTFG pseudopotentials are not available for all elements. Magnetic
resonance properties will be computed only for the elements in your crystal with
OTFG pseudopotentials. Any others will be ignored. To determine which elements in
your system have OTFG pseudopotentials, examine the CASTEP electronic options
as follows:
HO CASTEP 88
On the Electronic tab, click the More... button, and select the Potentials tab.
CASTEP Electronic Options dialog
All elements in the crystal will appear in this list. Elements that have an OTFG
pseudopotential will have the extension .otgf. When an OTFG potential is not
available, an ultrasoft potential (USP) will be used instead. These have the file
extension .usp.
After you have examined the list, close the CASTEP Electronic Options dialog.
Now specify the properties you want to calculate from the Properties tab.
Select the Properties tab.
Check the NMR box and set the value of Calculate to Shielding and EFG.
This will compute both the NMR chemical shielding and the value of the electric field
gradient at the nuclei. If you are running the calculation on a remote server, you can
specify this using the Job Control tab.
Select the Job Control tab. Select an appropriate server from the Gateway
dropdown list. Press the Run button. Close the dialog.
HO CASTEP 89
Depending on the speed of the computer you are using the NMR calculation will take
quite some time to complete. As a point of reference, using the Ultra-fine quality
settings the NMR shielding calculation on L-alanine required about 18 hours on a
1.70 GHz laptop computer. You can complete the calculation using the Medium
Quality setting in about 20% of that time. This will give you an understanding of how
to run an NMR calculation; however, the results will not be the same as those
discussed in the subsequent sections of the tutorial. Alternatively, rather than running
the calculation yourself, you can open the pre-computed results in the Examples
folder as described below.
While the calculation is running several things will happen in the MS Modeling
interface. After a few seconds, a new folder is displayed in the Project Explorer and
this will contain all the results from the calculation. The Job Explorer is displayed,
which contains information about the status of the job. The Job Explorer displays the
status of any currently active jobs that are associated with this project. It shows
useful information such as the server and job identification number. You can also use
this explorer to stop the job if you need to.
As the job progresses, four documents open which relay information on the job
status. These documents include the crystal structure, a status document to relay
information about the job setup parameters and run information, and charts of the
total energy, and convergence in Energy as a function of the iteration number.
When the job finishes, the files are transferred back to the client and this can take
some time due to the size of certain files.
LESSON 2: Analyzing the results

When the results are transferred, you should have several documents, among them:
• l_alanine.xsd - the crystal structure
• l_alanine.castep - an output file from the CASTEP energy calculation
• l_alanine_NMR.castep - an output file from the NMR CASTEP calculation
• l_alanine.param - input information
• l_alanine.check and
• l_alanine_NMR.check - binary files containing a summary of the results.
Although not visible in the Explorer, these hidden files are required for the analysis. If
you chose to run the NMR calculation, you should find these files in folder called
l_alanine CASTEP Energy once the calculation completes.
If you decide not wait for the job to finish, you can access pre-computed version of
these files as follows.
Use Windows Explorer to navigate to the \Data\Examples\Projects\CASTEP

directory, from the top level of your MS Modeling installation. Double-click on the file
l_alanine.stp.
HO CASTEP 90
Whether you choose to wait for the long calculation to finish or you decide to open
the pre-computed results, the tutorial is the same from this point. If you ran the
l_alanine calculations using the Medium Quality setting to save time, the steps are
still the same, but your numerical results will differ from the ones discussed here.
In the Project Explorer, open the l_alanine CASTEP Energy folder.
First, examine the data in the NMR output file.
Locate the file named l_alanine_NMR.castep and double-click on it. Locate the
line that reads Chemical Shielding and Electric Field Gradient Tensors.
This is located about 100 lines up from the end of the file. The output data will look
something like this (for clarity, the results for H, C, and N have been removed):
The magnetic shielding data are displayed for each element that used an OTGF
pseudopotential. In the case of L-alanine, this includes the elements, H, C, N, and O.
In this tutorial, we will focus on the 17O results.
The first column of the results simply indicates the element symbol. The second
column, called Ion, is the relative order of a particular atom in the input file. The
subsequent columns are defined as follows:
• Iso (ppm) - the isotropic chemical shielding in ppm. This is defined as σiso =
(σxx + σyy + σzz)/3, where σ refers to the chemical shielding tensor in the
principal axis frame, i.e., after diagonalization. This is an absolute value of the
isotropic chemical shielding, not relative to a standard.
• Aniso (ppm) - the anisotropy defined as Δ = σzz - σiso.
• Asym - the asymmetry parameter defined as η = (σxx - σyy)/Δ.
HO CASTEP 91
• Cq (MHz) - the quadrupolar coupling constant, CQ = eQVzz/h, where Vzz is

the largest component of the diagonalized EFG tensor, Q is the nuclear
quadrupole moment, and h is Plank's constant.
• Eta - the quadrupolar asymmetry parameter, ηQ = (Vxx - Vyy)/Vzz.
Scroll down to the results for oxygen. Notice that although there are 8 individual
oxygen atoms in the unit cell, there are only 2 distinct results. This is because there
are only 2 symmetry-unique oxygen atoms in the cell.
Now you will use the Materials Visualizer and the experimental data to determine
which NMR signal corresponds to which atom.
Open l_alanine.xsd. Be sure you open the file that is in the results folder
l_alanine CASTEP Energy, not the structure you originally imported.
Select the CASTEP tool from the toolbar, then choose Analysis or select
Modules | CASTEP | Analysis from the menu bar. Choose the NMR option. Click on
the button labeled Assign isotropic chemical shielding to structure.
CASTEP NMR analysis dialog
The isotropic chemical shielding values have been loaded into the structure. Now you
will display the shielding values for the oxygen atoms.
Hold down the ALT key and double-click on any of the oxygen atoms.
HO CASTEP 92
This selects all the oxygen atoms in the system.
Right-click in l_alanine.xsd and select Label from the context menu. Scroll
down the Properties list until you reach NMRShielding. Select it and press Apply.
The NMR isotropic shielding values are displayed for the oxygen atoms.
L-Alanine with 17O isotropic chemical shielding displayed
You can use a similar process to import the electric field gradient data. Atoms can be
labeled using either the quadrupolar coupling or the asymmetry parameter.
LESSON 3: Comparing the structure with experimental data

The experimental results for the 17O magnetic resonance data may be found in Pike
et al., (2004). In general, the EFG values and asymmetry parameters can be
compared directly with experiment. The isotropic chemical shifts require some
analysis because the program reports absolute chemical shielding whereas most
experimentalists are concerned with shifts relative to a known standard. We can deal
with this difference in 2 ways:
HO CASTEP 93
1. In most cases, such as in this example, the primary interest is in comparative

shifts, i.e., which is shift lowest and which is highest, so there is no need to convert
the shielding to the same relative standard used by the experiment. The relative
positions are all that is needed in order to assign the shifts to atoms unambiguously.
This is easy to do because the relative positions of the peaks do not change when
shifted with respect to a standard.
2. When dealing with several related systems, it is necessary to determine a value

empirically such that you can convert the shielding to a relative shift. Rather than
calculate the chemical shielding of the reference compound explicitly, the reference
is obtained by comparing it to a system that is experimentally well-characterized and
is similar to the systems being investigated. For example, Yates et al. (2004)
investigated 17O shifts for glutamic acid polymorphs. The reference that was chosen
was the one which provided the best match between computed and observed values
for D-glutamic acid-HCl. The same value was applied to all of the polymorphs.
So, why not compute the value of the standard? Typical standards are liquids like
water and tetramethylsilane (TMS). A simple calculation on an isolated molecule is
quite easy to do, but yields a result very different from the experimental value. On the
other hand, computing a value for the liquid state is a complex task, involving the
creation of an accurate model of the liquid and subsequent evaluation of the NMR
chemical shielding averaged over time and molecular orientation. The results
obtained by comparing to one known experimental system provides a more rapid
approach, and in addition, provides an immediate sanity check on the results.
The table below summarizes the computed and observed results.
HO CASTEP 94
Notice that the values of CQ and ηQ are in close enough agreement to experiment to
provide an unambiguous assignment of the spectrum. Notice also that the spacing
between the 17O peaks is comparable: 17.26 ppm versus 23.5 ppm. The larger
experimentally observed shift corresponds to the smaller (i.e., more negative)
computed value of the shielding. This is because of the way the experimentally
observed shifts are computed with respect to the standard:
δiso = σreference - σobserved
Assume a reference value of 267.3 ppm and convert each computed σiso into a δiso.
How well do the computed and observed shifts match?
You can see how hydrogen bonding in the crystal affects the chemical shifts.
Label the oxygen atoms by the NMR chemical shifts as you did at the end of
LESSON 2.
Select Build | Hydrogen bonds from the menu bar and click on the Calculate
button.
Hydrogen bonds are displayed as dashed lines.
HO CASTEP 95
L-Alanine with hydrogen bonds displayed
Notice that one oxygen is hydrogen bonded to 2 hydrogen atoms associated with the
amine group, whereas the other is bonded only to one. The oxygen bonded to 2
hydrogen atoms is nominally the hydroxyl oxygen while the other is the carbonyl
oxygen. Based on the computed results and the visualization you can see that the
carbonyl oxygen is the one with the observed shift of 284 ppm and the hydroxyl
oxygen has the observed shift of 260.5 ppm.
References
Lehmann, M. S.; Koetzle, T. F.; Hamilton, W. C. J. Am. Chem. Soc., 94, 2657 (1972).
Pike, K. J., et al. J. Phys. Chem. B, 108, 9256 (2004).
Yates, J. R., et al. J. Phys. Chem A, 108, 6032 (2004).
HO CASTEP 96
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CASTEP is a state-of-the-art quantum mechanics-

CASTEP employs the density functional theory

In practice, wave functions are expressed in

Density Functional Theory

• Exact only for ground state

Theoretical and Computational Choices

non-periodic plane waves

non-spin-polarized Fully numerical

Basic Concepts for Solid State

• Slabs and Gaps

Periodic Boundary Conditions

The system is considered

Geometric Models - Slabs and Gaps

• The electrons of a single free-standing atom occupy atomic

• According to molecular orbital theory, if several atoms are brought

Conductors, insulators, semiconductors, and special bands

Solids can be divided in three classes based upon their

Valence Valence Valence

Band Structure - Example

Periodic boundary conditions

Sampling in real & reciprocal space

Comparison of systems with varying size is only

• Quality: coarse, medium,

• Functional: GGA and LDA

Exc = exchange correlation potential!

• Exchange : electrons do not have an identity –

• Correlation: electrons are fermions and have a

Local Density Approximation (LDA)

LDA is good: (1) slowly varying density (e.g. in a metal)

LDA is not sufficient:

1. for very few electrons (e.g. for transition

Local Density Approximation (LDA)

Ceperley, D. M.; Alder, B. J. Phys. Rev. Lett., 45, 566-569 (1980).

Perdew, J. P.; Zunger, A. Phys. Rev. B, 23, 5048-5079 (1981).

LDA+U or Hubbard model

• the LDA+U approach subdivides charge density into delocalized

effective LDA+U energy functional:

ELDA … standard LDA energy functional

• The Hubbard U is a parameter which allows correlation

s: Specify a Hubbard U value in eV for

Generalized Gradient Approximation

Becke (1988) ρσ x2σ

Generalized Gradient Approximation

• PBE - Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys.

• RPBE - Hammer, B.; Hansen, L. B.; Norskov, J. K. Phys.

• WC - Wu, Z.; Cohen, R. E., Phys. Rev. B, 73, 235116

Nonlocal exchange-correlation functionals

• Possible correction: use of an empirical scissors correction (i.e. a rigid

• Another solution: screened exchange, or sX-LDA scheme, developed in

• Implemented Kohn-Sham schemes:

Nonlocal exchange-correlation functionals

• currently only for norm-conserving potentials, not for ultrasoft ones.

• Currently only non self-consistent band structure calculations fully support

For a spin imbalance we need a spin polarized xc-potential:

pseudo wave function