ONETEP Documentation

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ONETEP calculations are defined by a single free-format input file with a .dat extension. Comments are introduced by the characters #, ; or !. The keywords are divided into three levels: basic, intermediate and expert, and may be of several types.

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Basic keywords

Keyword	Type	Description
`CHARGE`	Integer	Total charge of system
`CONSTANT_EFIELD`	Text	Constant electric field to be applied
`CUBE_FORMAT`	Logical	Use cube format for plot files
`CUTOFF_ENERGY`	Physical	Equivalent plane wave kinetic energy cutoff
`DO_PROPERTIES`	Logical	Permit calculation of properties
`GEOM_MAX_ITER`	Integer	Maximum number of geometry optimisation iterations
`GEOM_METHOD`	Text	Geometry optimisation method
`GRD_FORMAT`	Logical	Use `.grd` format for plot files
`HOMO_DENS_PLOT`	Integer	Number of canonical orbital densities to plot below HOMO
`KERNEL_CUTOFF`	Real	Density kernel cutoff radius in bohr
`LATTICE_CART`	Block	Simulation cell lattice vectors in Cartesian coordinates
`LUMO_DENS_PLOT`	Integer	Number of canonical orbital densities to plot above LUMO
`MD_DELTA_T`	Physical	Molecular dynamics time step
`MD_NUM_ITER`	Integer	Number of molecular dynamics iterations
`MD_TEMPERATURE`	Physical	Molecular dynamics temperature
`NNHO`	Logical	Convert NGWFs into non-orthogonal natural hybrid orbitals
`OUTPUT_DETAIL`	Text	Specify level of output detail
`POPN_BOND_CUTOFF`	Physical	Mulliken population analysis bond length cutoff
`POPN_CALCULATE`	Logical	Perform Mulliken population analysis
`POSITIONS_ABS`	Block	Atomic positions in Cartesian coordinates
`READ_DENSKERN`	Logical	Read density kernel to restart
`READ_TIGHTBOX_NGWFS`	Logical	Read NGWFs to restart
`SPECIES`	Block	Atomic species information
`SPECIES_CONSTRAINTS`	Block	Atomic species geometry optimisation constraints
`SPECIES_NGWF_PLOT`	Block	Atomic species for plotting NGWFs
`SPECIES_POT`	Block	Pseudopotentials for atomic species
`SPIN`	Integer	Total spin of system
`SPIN_POLARIZED`	Logical	Perform spin polarized calculation
`TASK`	Text	Specify task
`WRITE_DENSITY_PLOT`	Logical	Write out charge density and electrostatic potential for plotting
`WRITE_DENSKERN`	Logical	Write density kernel for future restart
`WRITE_FORCES`	Logical	Include ionic forces in output
`WRITE_NGWF_PLOT`	Logical	Write out NGWFs for plotting
`WRITE_TIGHTBOX_NGWFS`	Logical	Write NGWFs for future restart
`XC_FUNCTIONAL`	Text	Exchange-correlation functional

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Intermediate keywords

Keyword	Type	Description
`DOS_SMEAR`	Physical	Half-width for Gaussian smearing of density of states
`EXACT_LNV`	Logical	Use Li-Nunes-Vanderbilt algorithm (not Millam-Scuseria variant)
`FFTBOX_PREF`	Text	Preferred FFT box size
`GEOM_BACKUP_ITER`	Integer	Backup frequency for geometry optimisation
`GEOM_CONTINUATION`	Logical	Continue a previous geometry optimisation
`GEOM_CONVERGENCE_WIN`	Integer	Number of geometry optimisation iterations for convergence criteria to be met
`GEOM_DISP_TOL`	Physical	Displacement convergence tolerance for geometry optimisation
`GEOM_ENERGY_TOL`	Physical	Energy convergence tolerance for geometry optimisation
`GEOM_FORCE_TOL`	Physical	Force convergence tolerance for geometry optimisation
`GEOM_FREQUENCY_EST`	Physical	Estimated average phonon frequency for geometry optimisation
`GEOM_MODULUS_EST`	Physical	Estimated bulk modulus for geometry optimisation
`LNV_THRESHOLD_ORIG`	Real	Convergence threshold for density kernel RMS gradient
`MAXIT_HOTELLING`	Integer	Maximum number of iterations for inverting the overlap matrix
`MAXIT_LNV`	Integer	Maximum number of density kernel iterations
`MAXIT_NGWF_CG`	Integer	Maximum number of NGWF conjugate gradient iterations
`MAXIT_PALSER_MANO`	Integer	Maximum number of Palser-Manolopoulos iterations
`MAXIT_PEN`	Integer	Maximum number of penalty functional iterations
`MD_ALGORITHM`	Text	Molecular dynamics integration algorithm
`MD_THERMOSTAT`	Text	Molecular dynamics thermostat
`MINIT_LNV`	Integer	Minimum number of density kernel iterations
`NGWF_THRESHOLD_ORIG`	Real	Convergence threshold for NGWF RMS gradient
`NUM_EIGENVALUES`	Integer	Number of Kohn-Sham states above and below Fermi level to calculate
`PEN_PARAM`	Real	Penalty functional parameter in hartree
`POSITIONS_ABS_INTERMEDIATE`	Block	Intermediate atomic positions in Cartesian coordinates for transition state search
`POSITIONS_ABS_PRODUCT`	Block	Product atomic positions in Cartesian coordinates for transition state search
`SPECIES_ATOMIC_SET`	Block	Atomic species initial NGWFs
`TIMINGS_LEVEL`	Integer	Set level of detail in timings
`TSSEARCH_DISP_TOL`	Physical	Transition state search displacement tolerance
`TSSEARCH_FORCE_TOL`	Physical	Transition state search force tolerance
`TSSEARCH_METHOD`	Text	Transition state search method
`TSSEARCH_LSTQST_PROTOCOL`	Text	Transition state search LSTQST protocol

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Expert keywords

Keyword	Type	Description
`CHECK_ATOMS`	Logical	Check atoms are a reasonable distance apart
`COREHAM_DENSKERN_GUESS`	Logical	Initialize density kernel by simple diagonalisation
`DELTA_E_CONV`	Logical	Use consecutive energy gains as NGWF convergence criterion
`DENSITY_BATCH_SIZE`	Integer	Batch size for NGWF communications during density evaluation
`ELEC_CG_MAX`	Integer	Reset frequency for NGWF conjugate gradients
`GEOM_PRINT_INV_HESSIAN`	Logical	Print inverse Hessian
`KERNEL_UPDATE`	Logical	Update density kernel during NGWF line search
`KINETIC_INT_BATCH_SIZE`	Integer	Batch size for NGWF communications during kinetic energy integrals
`K_ZERO`	Real	Parameter for kinetic energy preconditioning in inverse bohr
`LNV_CG_TYPE`	Text	Variant of conjugate gradient algorithm to use for density kernel optimisation
`LOCPOT_INT_BATCH_SIZE`	Integer	Batch size for NGWF communications during local potential integrals
`MAX_RESID_HOTELLING`	Real	Maximum residual value allowed when inverting overlap matrix
`MD_COLLISION_FREQUENCY`	Physical	Molecular dynamics: collision frequency for Andersen thermostat
`NGWF_CG_TYPE`	Text	Variant of conjugate gradient algorithm to use for NGWF optimisation
`NGWF_GRAD_BATCH_SIZE`	Integer	Batch size for NGWF communications during NGWF gradient evaluation
`NGWF_HALO`	Real	Halo width for NGWF radii in bohr
`OCC_MIX`	Real	Mixing fraction of occupancy preconditioned NGWF gradient
`ODD_PSINC_GRID`	Logical	Force and odd number of points in the simulation cell psinc grid
`OLD_LNV`	Logical	Use legacy algorithm for backwards compatibility
`OVLP_FOR_NONLOCAL`	Logical	Use overlap sparsity pattern for nonlocal pseudopotential matrix
`PPD_NPOINTS`	Text	PPD size in grid points
`PRECOND_REAL`	Logical	Apply kinetic energy preconditioning in real space
`PRECOND_RECIP`	Logical	Apply kinetic energy preconditioning in reciprocal space
`PRECOND_SCHEME`	Text	Specify scheme for kinetic energy preconditioning
`PRINT_QC`	Logical	Print calculation summary for quality control testing
`PSINC_SPACING`	Text	Psinc grid spacing in bohr
`R_PRECOND`	Real	Radial cutoff for real-space preconditioning in bohr
`SMOOTH_PROJECTORS`	Real	Halfwidth of Gaussian filter for smoothing non-local projectors in bohr
`TSSEARCH_CG_MAX_ITER`	Integer	Maximum number of transition state search conjugate gradients iterations
`TSSEARCH_QST_MAX_ITER`	Integer	Maximum number of transition state search QST iterations
`USE_SPACE_FILLING_CURVE`	Logical	Distribute atoms according to a space-filling curve
`VERBOSE_EWALD_FORCES`	Logical	Print full details of Ewald forces

CHARGE

Syntax:	`CHARGE [Integer]`
Description:	Specifies the total charge of the system in units of the proton charge i.e. a positive charge corresponds to a system deficient of electrons.
Default:	0 ; charge neutral
Example:	`charge +1`

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CHECK_ATOMS

Syntax:	`CHECK_ATOMS [Logical]`
Description:	Perform a check on the atomic positions to ensure that no two atoms are unphysically close.
Default:	True
Example:	`check_atoms F`

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CONSTANT_EFIELD

Syntax:	`CONSTANT_EFIELD [Text]`
Description:	Specifies a constant electric field to apply to the system in terms of Cartesian vector components in atomic units Ha/(e a₀).
Default:	0.0 0.0 0.0 ; zero field
Example:	`constant_efield 1.0e-3 0.0 0.0`

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COREHAM_DENSKERN_GUESS

Syntax:	`COREHAM_DENSKERN_GUESS [Logical]`
Description:	Generate an initial guess for the density kernel using a Hamiltonian generated by simple atomic screening of the pseudopotential. The density kernel may be obtained by the Palser-Manolopoulos algorithm or direct diagonalization. If false, a simple diagonal approximation is used for the density kernel.
Default:	True
Example:	`coreham_denskern_guess F`

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CUBE_FORMAT

Syntax:	`CUBE_FORMAT [Logical]`
Description:	Output volumetric data (e.g. charge density, potential, NGWFs, canonical orbitals) in cube format. This can be visualized using free software such as gOpenMol, MOLEKEL and XCrySDen.
Default:	False
Example:	`cube_format T`

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CUTOFF_ENERGY

Syntax:	`CUTOFF_ENERGY [Value] [Unit]`
Description:	Chooses the psinc basis set to correspond as closely as possible to a plane-wave basis with this cutoff energy. See section 3 of Skylaris et al., J. Phys.: Condens. Matter 17, 5757 (2005) for more details.
Default:	20 Ha
Example:	`cutoff_energy 500 eV`

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DELTA_E_CONV

Syntax:	`DELTA_E_CONV [Logical]`
Description:	When aggressive density kernel truncation is applied, the energy is not guaranteed to decrease monotonically. When `DELTA_E_CONV` is true, consecutive energy gains are used as an additional convergence criterion.
Default:	True
Example:	`delta_e_conv F`

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DENSITY_BATCH_SIZE

Syntax:	`DENSITY_BATCH_SIZE [Integer]`
Description:	Specifies the number of NGWFs to communicate in a single batch during the evaluation of the electronic density. May be used for tuning parallel performance, especially if "stack full" warnings are reported.
Default:	10
Example:	`density_batch_size 5`

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DO_PROPERTIES

Syntax:	`DO_PROPERTIES [Logical]`
Description:	Enables the calculation of properties including: charge and spin densities, electrostatic potential, Mulliken population analysis, canonical orbitals and energies and density of states.
Default:	False
Example:	`do_properties T`

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DOS_SMEAR

Syntax:	`DOS_SMEAR [Value] [Unit]`
Description:	Specifies the Gaussian smearing for the density of states calculated if properties are requested. If the smearing width is negative, the density of states is not calculated.
Default:	0.1 eV
Example:	`dos_smear 7 mRy`

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ELEC_CG_MAX

Syntax:	`ELEC_CG_MAX [Integer]`
Description:	Specifies the maximum number of NGWF conjugate gradients iterations between resets.
Default:	5
Example:	`elec_cg_max 1 ; steepest descents`

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EXACT_LNV

Syntax:	`EXACT_LNV [Logical]`
Description:	Specifies that the normalization constraint on the density matrix should be imposed exactly, using the purified density kernel (as in the original Li-Nunes-Vanderbilt algorithm [Phys. Rev. B 47, 10891 (1993)]) rather than the auxiliary kernel (as in the Millam-Scuseria variant [J. Chem. Phys. 106, 5569 (1997)]).
Default:	True
Example:	`exact_lnv F`

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FFTBOX_PREF

Syntax:	`FFTBOX_PREF [Text]`
Description:	Specifies a size for the FFT-box that is preferable to the smallest possible size that would normally be chosen (e.g. if the FFT library on a particular machine favours certain sizes). The FFT-box is specified by three integers (which must all be odd) that give the number of coarse grid points in the a₁, a₂ and a₃ directions respectively.
Default:	0 0 0 ; use smallest possible
Example:	`fftbox_pref 65 65 65`

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GEOM_BACKUP_ITER

Syntax:	`GEOM_BACKUP_ITER [Integer]`
Description:	Specifies the backup frequency for geometry optimisation. If the input filename is `rootname.dat` then the backup filename is `rootname.continuation`.
Default:	1 ; every iteration
Example:	`geom_backup_iter 5`

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GEOM_CONTINUATION

Syntax:	`GEOM_CONTINUATION [Logical]`
Description:	Continue a geometry optimization from a previous run using the `.continuation` backup file.
Default:	False
Example:	`geom_continuation T`

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GEOM_CONVERGENCE_WIN

Syntax:	`GEOM_CONVERGENCE_WIN [Integer]`
Description:	Specifies the number of consecutive iterations during which the convergence criteria must be met.
Default:	2
Example:	`geom_convergence_win 3`

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GEOM_DISP_TOL

Syntax:	`GEOM_DISP_TOL [Value] [Unit]`
Description:	Specifies atomic displacement tolerance used as one of the criteria for convergence of geometry optimization. The positions of all atoms must change by less than this tolerance to satisfy this criterion.
Default:	10^-3 a₀
Example:	`geom_disp_tol 1.0e-4 nm`

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GEOM_ENERGY_TOL

Syntax:	`GEOM_ENERGY_TOL [Value] [Unit]`
Description:	Specifies the tolerance for enthalpy per atom over the convergence window as a criterion for geometry optimization convergence.
Default:	10^-6 Ha per atom
Example:	`geom_energy_tol 0.2 meV`

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GEOM_FORCE_TOL

Syntax:	`GEOM_FORCE_TOL [Value] [Unit]`
Description:	Specifies the tolerance for maximum atomic force as a criterion for geometry optimization convergence. Note that units involving a forward slash (/) must be quoted as in the example below.
Default:	0.02 Ha/a₀
Example:	`geom_force_tol 0.1 "ev/ang"`

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GEOM_FREQUENCY_EST

Syntax:	`GEOM_FREQUENCY_EST [Value] [Unit]`
Description:	Specifies the estimated average phonon frequency (as an energy) used to initialize the inverse Hessian matrix for geometry optimization.
Default:	50 Ha
Example:	`geom_frequency_est 0.2 eV`

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GEOM_MAX_ITER

Syntax:	`GEOM_MAX_ITER [Integer]`
Description:	Specifies the maximum number of iterations for geometry optimisation.
Default:	10
Example:	`geom_max_iter 30`

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GEOM_METHOD

Syntax:	`GEOM_METHOD [Text]`
Description:	Specifies the method for geometry optimisation, currently either `CARTESIAN` for the BFGS algorithm based on Cartesian atomic coordinates [e.g. Pfrommer et al., J. Comp. Phys. 131, 233 (1997)] or `DELOCALIZED` for delocalized internal coordinates [Andzelm et al., Chem. Phys. Lett. 335 321 (2001)].
Default:	CARTESIAN
Example:	`geom_method DELOCALIZED`

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GEOM_MODULUS_EST

Syntax:	`GEOM_MODULUS_EST [Value] [Unit]`
Description:	Specifies the estimated bulk modulus used to initialize the inverse Hessian matrix for geometry optimization.
Default:	500 Ha/a₀³
Example:	`geom_modulus_est 100 GPa`

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GEOM_PRINT_INV_HESSIAN

Syntax:	`GEOM_PRINT_INV_HESSIAN [Logical]`
Description:	Include information about the inverse Hessian matrix in the ouput of a geometry optimization.
Default:	False
Example:	`geom_print_inv_hessian T`

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GRD_FORMAT

Syntax:	`GRD_FORMAT [Logical]`
Description:	Output volumetric data (e.g. charge density, potential, NGWFs, canonical orbitals) in `.grd` format used by Accelrys Materials Studio.
Default:	True
Example:	`grd_format F`

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HOMO_DENS_PLOT

Syntax:	`HOMO_DENS_PLOT [Integer]`
Description:	Specifies the number of canonical orbitals below the HOMO to plot, if `DO_PROPERTIES` is set to true. Thus a value of zero plots only the HOMO, a negative value disables plotting and a positive value of N plots the N+1 highest occupied canonical orbitals.
Default:	5 ; plot the HOMO and the five canonical orbitals below
Example:	`homo_dens_plot 0`

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KERNEL_CUTOFF

Syntax:	`KERNEL_CUTOFF [Real]`
Description:	Specifies the density kernel spatial cutoff in atomic units (a₀). Matrix elements are only included if the corresponding NGWF centres are closer than this distance.
Default:	1000.0 ; i.e. effectively infinite
Example:	`kernel_cutoff 25.0`

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KERNEL_UPDATE

Syntax:	`KERNEL_UPDATE [Logical]`
Description:	Update the density kernel when taking a trial step for NGWF optimization.
Default:	False
Example:	`kernel_update T`

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KINETIC_INT_BATCH_SIZE

Syntax:	`KINETIC_INT_BATCH_SIZE [Integer]`
Description:	Specifies the number of NGWFs to communicate in a single batch during the evaluation of the kinetic energy integrals. May be used for tuning parallel performance, especially if "stack full" warnings are reported.
Default:	10
Example:	`kinetic_int_batch_size 5`

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K_ZERO

Syntax:	`K_ZERO [Real]`
Description:	Specifies the kinetic energy preconditioning parameter as an inverse length in atomic units (a₀^-1). See Mostofi et al., J. Chem. Phys. 119, 8842 (2003) for further details.
Default:	3.0
Example:	`k_zero 4.0`

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LATTICE_CART

Syntax:	`%BLOCK LATTICE_CART a_1x a_1y a_1z a_2x a_2y a_2z a_3x a_3y a_3z %ENDBLOCK LATTICE_CART`
Description:	Specifies the lattice vectors a₁, a₂ and a₃ for the simulation cell as Cartesian coordinates in atomic units (a₀).
Example:	`%block lattice_cart 7.500000 0.000000 0.000000 ; hexagonal unit cell with -3.750000 6.495191 0.000000 ; a = 7.5 a0 0.000000 0.000000 9.000000 ; c = 9.0 a0 %endblock lattice_cart`

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LNV_CG_TYPE

Syntax:	`LNV_CG_TYPE [Text]`
Description:	Specifies the variant of the conjugate gradients algorithm used for the optimization of the density kernel, currently either `LNV_FLETCHER` for Fletcher-Reeves or `LNV_POLAK` for Polak-Ribière.
Default:	LNV_FLETCHER
Example:	`lnv_cg_type LNV_POLAK`

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LNV_THRESHOLD_ORIG

Syntax:	`LNV_THRESHOLD_ORIG [Real]`
Description:	Specifies the convergence threshold for the RMS gradient of the density kernel.
Default:	10^-9
Example:	`lnv_threshold_orig 1.0e-8`

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LOCPOT_INT_BATCH_SIZE

Syntax:	`LOCPOT_INT_BATCH_SIZE [Integer]`
Description:	Specifies the number of NGWFs to communicate in a single batch during the evaluation of the local potential integrals. May be used for tuning parallel performance, especially if "stack full" warnings are reported.
Default:	10
Example:	`locpot_int_batch_size 5`

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LUMO_DENS_PLOT

Syntax:	`LUMO_DENS_PLOT [Integer]`
Description:	Specifies the number of canonical orbitals above the LUMO to plot, if `DO_PROPERTIES` is set to true. Thus a value of zero plots only the LUMO, a negative value disables plotting and a positive value of N plots the N+1 lowest unoccupied canonical orbitals.
Default:	5 ; plot the LUMO and the five canonical orbitals above
Example:	`lumo_dens_plot 0`

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MAXIT_HOTELLING

Syntax:	`MAXIT_HOTELLING [Integer]`
Description:	Specifies the maximum number of iterations in the Hotelling algorithm used to invert the overlap matrix. See Ozaki, Phys. Rev. B. 64, 195110 (2001) for more details. If `MAXIT_HOTELLING` is zero, then the inverse is computed using a traditional O(N³) method.
Default:	50
Example:	`maxit_hotelling 100`

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MAXIT_LNV

Syntax:	`MAXIT_LNV [Integer]`
Description:	Specifies the maximum number of iterations for the density kernel optimization.
Default:	8
Example:	`maxit_lnv 3`

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MAXIT_NGWF_CG

Syntax:	`MAXIT_NGWF_CG [Integer]`
Description:	Specifies the maximum number of iterations for the NGWF conjugate gradients optimization.
Default:	100
Example:	`maxit_ngwf_cg 25`

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MAXIT_PALSER_MANO

Syntax:	`MAXIT_PALSER_MANO [Integer]`
Description:	Specifies the maximum number of iterations for the Palser-Manolopoulos algorithm [Phys. Rev. B. 58, 12704 (1998)] used to initialize the density kernel before the main optimization begins (when `COREHAM_DENSKERN_GUESS` is true, the default). If `MAXIT_PALSER_MANO` is negative then a traditional O(N³) diagonalization is used.
Default:	50
Example:	`maxit_palser_mano 30`

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MAXIT_PEN

Syntax:	`MAXIT_PEN [Integer]`
Description:	Specifies the maximum number of iterations for the penalty-functional algorithm [Haynes et al., Phys. Rev. B. 59, 12173 (1999)] used to refine the density kernel intialization before the main optimization begins. When reading the density kernel from disk this should normally be set to zero.
Default:	3
Example:	`maxit_pen 5`

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MAX_RESID_HOTELLING

Syntax:	`MAX_RESID_HOTELLING [Real]`
Description:	Specifies the maximum residual allowed when inverting the overlap matrix by the Hotelling method. See Ozaki, Phys. Rev. B. 64, 195110 (2001) for more details.
Default:	10^-12
Example:	`max_resid_hotelling 1.0e-10`

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MD_ALGORITHM

Syntax:	`MD_ALGORITHM [Text]`
Description:	Specifies the integration algorithm for molecular dynamics, currently either `LEAPFROGVERLET` or `VELOCITYVERLET`.
Default:	LEAPFROGVERLET
Example:	`md_algorithm VELOCITYVERLET`

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MD_COLLISION_FREQUENCY

Syntax:	`MD_COLLISION_FREQUENCY [Value] [Unit]`
Description:	Specifies the collision frequency for the Andersen thermostat as an energy.
Default:	0.152 Ha ; about 10¹⁵ Hz
Example:	`md_collision_frequency 4.0 eV`

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MD_DELTA_T

Syntax:	`MD_DELTA_T [Value] [Unit]`
Description:	Specifies the time step for molecular dynamics.
Default:	40 aut ; 40 atomic units of time
Example:	`md_delta_t 1.0 fs`

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MD_NUM_ITER

Syntax:	`MD_NUM_ITER [Integer]`
Description:	Specifies the number of molecular dynamics steps.
Default:	100
Example:	`md_num_iter 1000`

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MD_TEMPERATURE

Syntax:	`MD_TEMPERATURE [Value] [Unit]`
Description:	Specifies the temperature for molecular dynamics as an energy.
Default:	9.5 × 10^-4 Ha ; approximately 300 K
Example:	`md_temperature 25.85 meV`

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MD_THERMOSTAT

Syntax:	`MD_THERMOSTAT [Text]`
Description:	Specifies the thermostat for molecular dynamics, currently either `NONE` or `ANDERSEN`.
Default:	NONE
Example:	`md_thermostat ANDERSEN`

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MINIT_LNV

Syntax:	`MINIT_LNV [Integer]`
Description:	Specifies the minimum number of iterations for the density kernel optimization.
Default:	3
Example:	`minit_lnv 1`

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NGWF_CG_TYPE

Syntax:	`NGWF_CG_TYPE [Text]`
Description:	Specifies the variant of the conjugate gradients algorithm used for the optimization of the NGWFs, currently either `NGWF_FLETCHER` for Fletcher-Reeves or `NGWF_POLAK` for Polak-Ribière.
Default:	NGWF_FLETCHER
Example:	`ngwf_cg_type NGWF_POLAK`

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NGWF_GRAD_BATCH_SIZE

Syntax:	`NGWF_GRAD_BATCH_SIZE [Integer]`
Description:	Specifies the number of NGWFs to communicate in a single batch during the evaluation of the NGWF gradient. May be used for tuning parallel performance, especially if "stack full" warnings are reported.
Default:	10
Example:	`ngwf_grad_batch_size 5`

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NGWF_HALO

Syntax:	`NGWF_HALO [Real]`
Description:	Specifies a halo size for the NGWFs to include matrix elements between NGWFs which do not directly overlap. In atomic units (a₀). A negative value indicates that no halo should be used.
Default:	-1.0 ; no halo
Example:	`ngwf_halo 1.0`

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NGWF_THRESHOLD_ORIG

Syntax:	`NGWF_THRESHOLD_ORIG [Real]`
Description:	Specifies the convergence threshold for the RMS gradient of the NGWFs.
Default:	2 × 10^-6
Example:	`ngwf_threshold_orig 1.0e-5`

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NNHO

Syntax:	`NNHO [Logical]`
Description:	Generate non-orthogonal natural hybrid orbitals from the NGWFs. See Foster et al., J. Am. Chem. Soc. 102, 7211 (1980) for more details.
Default:	False
Example:	`nnho T`

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NUM_EIGENVALUES

Syntax:	`NUM_EIGENVALUES [Integer]`
Description:	Specifies the number of canonical orbital eigenvalues above and below the Fermi level to print when properties are required.
Default:	10
Example:	`num_eigenvalues 5`

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OCC_MIX

Syntax:	`OCC_MIX [Real]`
Description:	Specifies the fraction of the NGWF gradient to which occupancy preconditioning is applied.
Default:	0.25
Example:	`occ_mix 1.0 ; fully preconditioned gradient`

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ODD_PSINC_GRID

Syntax:	`ODD_PSINC_GRID [Logical]`
Description:	Forces the simulation cell psinc grid to contain an odd number of points in each direction.
Default:	False
Example:	`odd_osinc_grid T`

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OLD_LNV

Syntax:	`OLD_LNV [Logical]`
Description:	Enables backwards compatibility with legacy code.
Default:	False
Example:	`old_lnv T`

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OUTPUT_DETAIL

Syntax:	`OUTPUT_DETAIL [Text]`
Description:	Specifies the level of detail in ONETEP's output: either `BRIEF`, `NORMAL` or `VERBOSE`.
Default:	NORMAL
Example:	`output_detail VERBOSE`

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OVLP_FOR_NONLOCAL

Syntax:	`OVLP_FOR_NONLOCAL [Logical]`
Description:	Forces the nonlocal pseudopotential matrix and hence the Hamiltonian to have the sparsity pattern of the overlap matrix.
Default:	False
Example:	`ovlp_for_nonlocal T`

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PEN_PARAM

Syntax:	`PEN_PARAM [Real]`
Description:	Specifies the energy parameter in hartrees for the penalty-functional algorithm [Haynes et al., Phys. Rev. B. 59, 12173 (1999)] used to refine the density kernel intialization before the main optimization begins.
Default:	4.0
Example:	`pen_param 5.0`

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POPN_BOND_CUTOFF

Syntax:	`POPN_BOND_CUTOFF [Value] [Unit]`
Description:	Specifies the bond length cutoff to use when performing Mulliken population analysis.
Default:	3 Å
Example:	`popn_bond_cutoff 5.0 ang`

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POPN_CALCULATE

Syntax:	`POPN_CALCULATE [Logical]`
Description:	Perform Mulliken population analysis.
Default:	True if `DO_PROPERTIES` is true, otherwise false.
Example:	`popn_calculate F`

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POSITIONS_ABS

Syntax:	`%BLOCK POSITIONS_ABS S₁ R_1x R_1y R_1z S₂ R_2x R_2y R_2z . . . . . . . . S_N R_Nx R_Ny R_Nz %ENDBLOCK POSITIONS_ABS`
Description:	Specifies the atomic positions as Cartesian coordinates in atomic units (a₀). In the above syntax, `S_i` denotes the species of atom i (max 4 characters) and `R_i` its position vector. Note that all atoms are currently required to be positioned within the simulation cell.
Example:	`%block positions_abs C 5.0 5.0 5.0 ; CO2 molecule O 2.7 5.0 5.0 ; centred in a cubic simulation cell O 7.3 5.0 5.0 ; with sides of 10 a0 %endblock positions_abs`

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POSITIONS_ABS_INTERMEDIATE

Syntax:	See `POSITIONS_ABS` above.
Description:	Specifies the atomic positions as Cartesian coordinates in atomic units (a₀) for the intermediate in a transition state search.
Example:	See `POSITIONS_ABS` above.

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POSITIONS_ABS_PRODUCT

Syntax:	See `POSITIONS_ABS` above.
Description:	Specifies the atomic positions as Cartesian coordinates in atomic units (a₀) for the product in a transition state search.
Example:	See `POSITIONS_ABS` above.

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PPD_NPOINTS

Syntax:	`PPD_NPOINTS [Text]`
Description:	Specifies the size of the parallelepipeds (PPDs) used to group the simulation cell psinc grid points for efficiency. The size of the PPD is given by three integers corresponding to the number of grid points in the a₁, a₂ and a₃ directions respectively. These integers must all be factors of the simulation cell psinc grid size in the relevant direction.
Default:	0 0 0 ; select automatically
Example:	`ppd_npoints 5 7 6`

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PRECOND_REAL

Syntax:	`PRECOND_REAL [Logical]`
Description:	Apply kinetic energy preconditioning by a convolution in real-space. See Mostofi et al., J. Chem. Phys. 119, 8842 (2003) for further details.
Default:	False
Example:	`precond_real T`

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PRECOND_RECIP

Syntax:	`PRECOND_RECIP [Logical]`
Description:	Apply kinetic energy preconditioning by a multiplication in reciprocal-space. See Mostofi et al., J. Chem. Phys. 119, 8842 (2003) for further details.
Default:	True
Example:	`precond_recip F`

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PRECOND_SCHEME

Syntax:	`PRECOND_SCHEME [Text]`
Description:	Specifies the form of the kinetic energy preconditioner used, currently one of: `BG` - Bowler-Gillan scheme: Comput. Phys. Commun. 112, 103 (1998) `MAURI` - Mauri scheme `TETER` - Teter-Payne-Allan scheme: Phys. Rev. B 40, 12255 (1989) `NONE` - no kinetic energy preconditioning
Default:	TETER
Example:	`precond_scheme MAURI`

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PRINT_QC

Syntax:	`PRINT_QC [Text]`
Description:	Include a summary of the calculation in the output for the purposes of "quality control" on code modifications.
Default:	False
Example:	`print_qc T`

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PSINC_SPACING

Syntax:	`PSINC_SPACING [Text]`
Description:	Specifies the spacing between psinc grid points in the simulation cell by three real values (in atomic units a₀) in the a₁, a₂ and a₃ directions respectively. These spacings must all be factors of the simulation cell lengths in the relevant directions.
Default:	0.0 0.0 0.0 ; select automatically
Example:	`psinc_spacing 0.4 0.5 0.5`

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READ_DENSKERN

Syntax:	`READ_DENSKERN [Logical]`
Description:	Read in the density kernel from disk. If the input filename is `rootname.dat` then the density kernel filename is `rootname.denskern`.
Default:	False
Example:	`read_denskern T`

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READ_TIGHTBOX_NGWFS

Syntax:	`READ_TIGHTBOX_NGWFS [Logical]`
Description:	Read in the NGWFs from disk. If the input filename is `rootname.dat` then the NGWFs filename is `rootname.tightbox_ngwfs`.
Default:	False
Example:	`read_tightbox_ngwfs T`

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R_PRECOND

Syntax:	`R_PRECOND [Real]`
Description:	Specifies the radius in atomic units (a₀) of the real-space kinetic energy preconditioner (used to accelerate the convolution).
Default:	2.0
Example:	`r_precond 1.5`

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SMOOTH_PROJECTORS

Syntax:	`SMOOTH_PROJECTORS [Real]`
Description:	Specifies the half-width in atomic units (a₀) of a Gaussian filter used to smooth the nonlocal projectors. A negative value indicates that no smoothing should be applied.
Default:	-0.4 ; no smoothing
Example:	`smooth_projectors 0.5`

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SPECIES

Syntax:	`%BLOCK SPECIES S₁ X₁ Z₁ n₁ R₁ S₂ X₂ Z₂ n₂ R₂ . . . . . . . . . . S_N X_N Z_N n_N R_N %ENDBLOCK SPECIES`
Description:	Defines the atomic species. In the above syntax, `S_i` denotes the species of atom i (max 4 characters), corresponding to the element with symbol `X_i` and atomic number `Z_N`, and with which are associated `n_i` NGWFs of radius `R_N` in atomic units (a₀). More than one atomic species may refer to the same element, e.g. so that different ionic constraints may be applied to them.
Example:	`%block species C1 C 6 4 6.0 ; species C1 is carbon with 4 NGWFs of radius 6.0 a0 C2 C 6 4 7.0 ; species C2 is also carbon but has 7.0 a0 NGWF radii H H 1 1 5.0 ; species H is hydrogen with 1 NGWF of radius 5.0 a0 %endblock species`

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SPECIES_ATOMIC_SET

Syntax:	`%BLOCK SPECIES_ATOMIC_SET S₁ <Fireball filename 1> \| AUTO S₂ <Fireball filename 2> \| AUTO . . . . %ENDBLOCK SPECIES_ATOMIC_SET`
Description:	Specifies the fireball (truncated pseudoatomic orbital) files for the atomic species which provide initial guesses for the NGWFs. In the above syntax, `S_i` denotes atomic species i (max 4 characters). If `AUTO` is specified, then STO-3G and 6-31G* basis functions are generated automatically as required.
Default:	`AUTO` for all species when this block is absent
Example:	`%block species_atomic_set C1 C_01.fbl H AUTO %endblock species_atomic_set`

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SPECIES_CONSTRAINTS

Syntax:	`%BLOCK SPECIES_CONSTRAINTS S₁ NONE\|FIXED\|LINE\|PLANE [C_1x C_1y C_1z] . . . . . . . . . . %ENDBLOCK SPECIES_CONSTRAINTS`
Description:	Defines the constraints for the atomic species for use during geometry optimization. In the above syntax, `S_i` denotes atomic species i (max 4 characters). The constraint type is one of `NONE` (no constraint), `FIXED` (atom is constrained to remain fixed), `LINE` (atom is constrained to a line) or `PLANE` (atom is constrained to a plane). In the case of `LINE` and `PLANE`, three further real values are required, to specify the direction vector of the line or the normal vector to the plane (in Cartesian coordinates) respectively.
Example:	`%block species_constraints C1 FIXED ; atoms of species C1 are fixed C2 LINE 1.0 0.0 0.0 ; atoms of species C2 can only move parallel to the x-axis H PLANE 0.0 0.0 1.0 ; atoms of species H can only move in the xy-plane %endblock species_constraints`

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SPECIES_NGWF_PLOT

Syntax:	`%BLOCK SPECIES_NGWF_PLOT S₁ S₂ . %ENDBLOCK SPECIES_NGWF_PLOT`
Description:	Defines the atomic species whose NGWFs are to be plotted during the calculation. In the above syntax, `S_i` denotes atomic species i to plot.
Example:	`%block species_ngwf_plot C1 C2 H %endblock species_ngwf_plot`

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SPECIES_POT

Syntax:	`%BLOCK SPECIES_POT S₁ <Pseudopotential filename 1> S₂ <Pseudopotential filename 2> . . . . %ENDBLOCK SPECIES_POT`
Description:	Specifies the pseudopotential files for the atomic species. In the above syntax, `S_i` denotes atomic species i (max 4 characters). The files are currently required to be in the CASTEP `.recpot` format and to define norm-conserving pseudopotentials.
Example:	`%block species_pot C1 C_01.recpot C2 C_00.recpot H H_01.recpot %endblock species_pot`

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SPIN

Syntax:	`SPIN [Integer]`
Description:	Specifies the total spin of the system in units of ½h/(2π). If the total spin is non-zero, a spin-polarized calculation will automatically be selected.
Default:	0
Example:	`spin 1`

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SPIN_POLARIZED

Syntax:	`SPIN_POLARIZED [Logical]`
Description:	Specifies that a spin-polarized calculation should be performed.
Default:	False, unless `SPIN` is non-zero, in which case true.
Example:	`spin_polarized T`

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TASK

Syntax:	`TASK [Text]`
Description:	Specifies the task to be carried out, currently one of: `SINGLEPOINT` - single point energy calculation `PROPERTIES` - properties using results from a previous calculation `GEOMETRYOPTIMIZATION` - geometry optimization using Cartesian or delocalized internal coordinates `MOLECULARDYNAMICS` - molecular dynamics simulation `TRANSITIONSTATESEARCH` - transition state search
Default:	SINGLEPOINT
Example:	`task GEOMETRYOPTIMIZATION`

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TIMINGS_LEVEL

Syntax:	`TIMINGS_LEVEL [Integer]`
Description:	Specifies the amount of detail in the timing information collected: 0 - total time only reported 1 - timings for routines averaged across all processors 2 - timings for routines on all processors individually
Default:	1
Example:	`timings_level 0`

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TSSEARCH_CG_MAX_ITER

Syntax:	`TSSEARCH_CG_MAX_ITER [Integer]`
Description:	Specifies the maximum number of conjugate gradients iterations for the transition state search.
Default:	20
Example:	`tssearch_cg_max_iter 30`

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TSSEARCH_DISP_TOL

Syntax:	`TSSEARCH_DISP_TOL [Value] [Unit]`
Description:	Specifies atomic displacement tolerance used as one of the criteria for convergence of a transition state search. The positions of all atoms must change by less than this tolerance to satisfy this criterion.
Default:	10^-2 a₀
Example:	`tssearch_disp_tol 1.0e-3 nm`

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TSSEARCH_FORCE_TOL

Syntax:	`TSSEARCH_FORCE_TOL [Value] [Unit]`
Description:	Specifies the tolerance for maximum atomic force as a criterion for transition state search convergence. Note that units involving a forward slash (/) must be quoted as in the example below.
Default:	0.005 Ha/a₀
Example:	`tssearch_force_tol 0.05 'ev/ang'`

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TSSEARCH_METHOD

Syntax:	`TSSEARCH_METHOD [Text]`
Description:	Specifies the method for transition state search, currently only `LSTQST`.
Default:	LSTQST
Example:	`tssearch_method LSTQST`

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TSSEARCH_LSTQST_PROTOCOL

Syntax:	`TSSEARCH_LSTQST_PROTOCOL [Text]`
Description:	Specifies the protocol for transition state search with the LSTQST method, currently one of `LSTMAXIMUM`, `HALGREN-LIPSCOMB`, `LST/OPTIMIZATION`, `COMPLETELSTQST` or `QST/OPTIMIZATION`.
Default:	LSTMAXIMUM
Example:	`tssearch_lstqst_protocol LST/OPTIMIZATION`

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TSSEARCH_QST_MAX_ITER

Syntax:	`TSSEARCH_QST_MAX_ITER [Integer]`
Description:	Specifies the maximum number of QST iterations for the transition state search.
Default:	5
Example:	`tssearch_qst_max_iter 10`

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USE_SPACE_FILLING_CURVE

Syntax:	`USE_SPACE_FILLING_CURVE [Logical]`
Description:	Use a Hilbert space-filling curve to distribute the atoms among processors in a parallel calculation.
Default:	True
Example:	`use_space_filling_curve F`

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VERBOSE_EWALD_FORCES

Syntax:	`VERBOSE_EWALD_FORCES [Logical]`
Description:	Include details of the Ewald forces in the output.
Default:	False
Example:	`verbose_ewald_forces T`

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WRITE_DENSITY_PLOT

Syntax:	`WRITE_DENSITY_PLOT [Logical]`
Description:	Specifies that the charge density, electrostatic potential and spin density (if appropriate) be written out for plotting if properties are requested.
Default:	True
Example:	`write_density_plot F`

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WRITE_DENSKERN

Syntax:	`WRITE_DENSKERN [Logical]`
Description:	Write the density kernel to disk. If the input filename is `rootname.dat` then the density kernel filename is `rootname.denskern`.
Default:	True
Example:	`write_denskern F`

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WRITE_FORCES

Syntax:	`WRITE_FORCES [Logical]`
Description:	Include the forces in the output of a single point energy calculation.
Default:	False
Example:	`write_forces T`

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WRITE_NGWF_PLOT

Syntax:	`WRITE_NGWF_PLOT [Logical]`
Description:	Write out NGWFs for species listed in the `SPECIES_NGWF_PLOT` to disk for plotting during a single point energy calculation, in the cube and/or `.grd` formats as requested.
Default:	False
Example:	`write_ngwf_plot T`

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WRITE_TIGHTBOX_NGWFS

Syntax:	`WRITE_TIGHTBOX_NGWFS [Logical]`
Description:	Write the NGWFs to disk. If the input filename is `rootname.dat` then the NGWFs filename is `rootname.tightbox_ngwfs`.
Default:	True
Example:	`write_tightbox_ngwfs F`

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XC_FUNCTIONAL

Syntax:	`XC_FUNCTIONAL [Text]`
Description:	Specifies the exchange-correlation functional to use, currently one of: `LDA` - default local (spin) density approximation, currently `CAPZ` `GGA` - default generalized gradient approximation, currently `RPBE` `CAPZ` - Perdew-Zunger parameterization [Phys. Rev. B 23, 5048 (1981)] of the Ceperley-Alder Monte Carlo data [Phys. Rev. Lett. 45, 566 (1980)] and Gell-Mann-Brueckner expansion [Phys. Rev. 106, 364 (1957)] `VWN` - Vosko, Wilk and Nusair parameterization [Phys. Rev. B 22, 3812 (1980)] of the LDA `PW91` - Perdew and Wang GGA [Phys. Rev. B 45, 13244 (1992)] `PBE` - Perdew, Burke and Ernzerhof GGA [Phys. Rev. Lett. 77, 3865 (1996) and Erratum] `REVPBE` - revised PBE by Zhang and Yang [Phys. Rev. Lett. 80, 890 (1998)] `RPBE` - revised PBE by Hammer, Hansen and Norskov [Phys. Rev. B 59, 7413 (1999)]
Default:	LDA
Example:	`xc_functional PBE`

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