Chapter 3: Computational chemistry
3.10 General computational methodology
Over the course of this thesis a number of computing resources were used to run planewave DFT calculations. These resources included Wardlaw and Kennedy, local clusters at the EaStCHEM computing facility at the University of St Andrews, the UK national tier-2 high performance computing hub in materials and molecular modelling (Thomas) hosted at
Table 3.4: Summary of the hardware specifics for the computing resources used for this work presented in this thesis.
Cluster Number of nodes
Cores per node
CPU type Memory per core / GB
Interconnect
Wardlaw 290 12 Intel Westmere 2 InfiniBand Kennedy 90 32 Intel Broadwell 4 FDR InfiniBand
Thomas 720 24 Intel Broadwell 4 InfiniBand ARCHER 4290 24 Ivy Bridge 4 Cray Aries
UCL, and the national ARCHER facility, based in Edinburgh. A brief summary of the cluster specifics is given in Table 3.4.
Unless explicitly stated otherwise, all DFT calculations carried out for this thesis were performed using CASTEP version 7.01, 8.0 or 16.11. For CASTEP calculations, two input files, a .cell and a .param file, are required. The
.cell file contains all the structural information on the system, including the unit cell size and shape, and fractional coordinates for all atoms, in addition to the k-point spacing to be implemented and the pseudopotentials used. In all geometry optimisations and all calculations of NMR parameters the recommended ultrasoft pseudopotentials were used, with CASTEP on-the- fly pseudopotentials used for calculations performed in versions 8.0 or 16.11 of the code, and generated from a stated pseudopotential string in calculations with version 7.01. The calculation type (geometry optimisation,
single-point energy, NMR parameter, phonon etc.), exchange-correlation
functional, Ecut, and all other parameters were specified in the .param file.
Within this thesis the predicted solid-state NMR parameters for 1
H, 2 H, 17 O, 29 Si, 89 Y and 119
Sn were investigated in detail. In all calculations the electric quadrupole moment, Q, for 2H and 17O were 0.00286 and –0.02558 Barn,
respectively. Typically parameters used for geometry optimisation and the
calculation of NMR parameters were Ecut of 50-60 Ry and k-point spacing of
0.04-0.05 2π Å–1
. For all calculations performed using CASTEP versions 8.0 or 16.11, ZORA was employed. The TS SEDC scheme was used during the geometry optimisation of hydrous minerals (see Chapter 6) when CASTEP
version 8.0 was used. Over the course of this thesis, the importance of the electronic energy tolerance (defined as elec_energy_tol in the .param file), the parameter that determines the tolerance to be used when determining the convergence of the total energy of a system during an electronic energy minimisation, was investigated and will be discussed in Chapter 5. Table 3.5 contains a summary of the typical parameters used in typical CASTEP geometry optimisation and the calculation of NMR parameter using CASTEP during this thesis. Depending on the computational resource being used, the type of calculation, size, atomic species and complexity of the system, calculation times varied significantly, with geometry optimisation and calculation of NMR parameter typically taking between 8 and 48 hours on two nodes of Kennedy, i.e., using 64 cores.
Table 3.5: Selected input options (from .cell and .param files) used during a typical geometry optimisation or calculation of NMR parameters using CASTEP.
CASTEP option Description Typical value(s)
task defines the type of calculation to be performed
geometryoptimisation, magres
xc_functional
controls which functional is used to calculate the exchange-correlation
potential
PBE
opt_strategy determines the optimisation
strategy speed
opt_method determines the optimiser used LBFGS, BFGS
calculate_stress determines whether or not a stress
calculation will be performed true
max_SCF_cycles
determines the maximum number of SCF cycles performed during an
electronic minimisation
50
geom_max_iter determines the maximum number
of steps in a geometry optimisation 200
geom_energy_tol
controls the tolerance for accepting convergence of the free energy per
atom during a geometry optimisation
1 × 10–4, 1 × 10–5 eV / atom
kpoints_mp_spacing specifies the maximum distance
between k-points 0.04, 0.05 2π Å –1
cut_off_energy specifies the cut-off energy for the
planewave basis set 50, 60 Ry
SEDC_scheme specifies the semi-empirical
dispersion correction scheme TS
relativistic_treatment specifies the relativistic treatment
scheme ZORA
elec_energy_tol
controls the tolerance for accepting convergence of the total energy in
an electronic minimisation
1 × 10–5, 1 × 10–9 eV /atom
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