Documentation for specific functionality

At present we do not have a detailed full manual for the code. However, we do have documents explaining the use of certain elements of functionality.

Conduction NGWF Optimisation Δ
Pseudoatomic Solver Δ
Implicit Solvation Δ
Realspace Local Pseudopotentials Δ
DFT+U Calculations (also called LDA+U) Δ
Phonon Calculations Δ
Local Density of States Calculations Δ
Natural Bond Orbital Calculations Δ
Van der Waals Density Functional Calculations Δ
Born-Oppenheimer Molecular Dynamics Δ
Finite-temperature Ensemble-DFT calculations Δ
Density kernel and Hamiltonian mixing (kernel_diis) Δ
Linear-Response Time-Dependent DFT calculations (lr_tddft) Δ
Empirical dispersion corrections (dispersion) Δ
Constrained DFT keyword list Δ (work in progress)
Constrained DFT input file checklist Δ (work in progress)

For general help on standard total energy and force calculations, see the tutorials and the input file documentation below.

Documentation for input files

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
BS_KPOINT_PATH Block K-point path for bandstructure calculation
CHARGE Integer Total charge of system
CLASSICAL_INFO Block Include classical point charges in the system
COND_PLOT_JOINT_ORBITALS Logical Plot orbitals in joint val-cond basis following COND task
COND_PLOT_VC_ORBITALS Logical Plot orbitals in separate val cond bases following COND task
COND_READ_DENSKERN Logical Read in the conduction density kernel from disk
COND_READ_TIGHTBOX_NGWFS Logical Read in the conduction NGWFs from disk
COND_KERNEL_CUTOFF Real Conduction state density kernel cutoff radius in bohr.
COND_NUM_STATES Logical The number of conduction states to be optimised.
COND_INIT_SHIFT Real Initial shifting factor for projected cond Hamiltonian.
COND_SHIFT_BUFFER Real Buffer added to highest calculated eigenvalue when updating cond shift
COND_FIXED_SHIFT Logical Keep shift for projected conduction Hamiltonian constant in COND task
COND_CALC_MAX_EIGEN Logical Calc maximum cond Hamiltonian eigenvalue at each NGWF CG opt step
COND_CALC_OPTICAL_SPECTRA Logical Calculate matrix elements for use in optical absorption spectra
COND_SPEC_CALC_MOM_MAT_ELS Logical Calculate optical matrix elements in momentum representation
COND_SPEC_CALC_NONLOC_COMM Logical Calculate commutator between nonloc pot and position operator
COND_SPEC_CONT_DERIV Logical Calculate commutator between the nonloc pot and pos operator using continuous derivative in k-space
COND_SPEC_NONLOC_COMM_SHIFT Real Finite difference shift for calculating commutator between nonloc pot and the pos operator
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
DISPERSION Integer Activate dispersion corrections
DO_PROPERTIES Logical Permit calculation of properties
DX_FORMAT Logical Use OpenDX format for plot files
EDFT Logical Enable finite-temperature DFT calculations with the Ensemble-DFT method
EDFT_MAXIT Integer Maximum number of inner loop iterations with the EDFT method.
EDFT_SMEARING_WIDTH Physical Occupation smearing width for EDFT calculations.
FINE_GRID_SCALE Real Spacing of fine grid as multiple of standard grid
GEOM_MAX_ITER Integer Maximum number of geometry optimisation iterations
GEOM_METHOD Text Geometry optimisation method
GRD_FORMAT Logical Use.grdformat for plot files
HOMO_DENS_PLOT Integer Number of canonical orbital densities to plot below HOMO
HOMO_PLOT Integer Number of canonical orbitals to plot below HOMO
IS_BULK_PERMITTIVITY Real Defines the relative dielectric permittivity of the solvent
IS_IMPLICIT_SOLVENT Logical Makes the calculation use implicit solvent
IS_INCLUDE_CAVITATION Logical Turns on the cavitation term in an implicit solvent calculation
IS_SOLVENT_SURFACE_TENSION Physical Defines the surface tension of the solvent
KERNEL_CUTOFF Real Density kernel cutoff radius in bohr
LATTICE_CART Block Simulation cell lattice vectors in Cartesian coordinates
LUMO_PLOT Integer Number of canonical orbitals to plot above LUMO
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_RESET_DKN_NGWFS Integer Full reset of the NGWFs and density kernel SCF cycle every Nth time steps
MD_RESTART Logical Restart MD from previous backup files
NNHO Logical Convert NGWFs into non-orthogonal natural hybrid orbitals
OUTPUT_DETAIL Text Specify level of output detail
PAW Logical Activate PAW calculation.
POLARISATION_CALCULATE Logical Activate Polarisation Calculation
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_SW_NGWFS Logical Read NGWFS in spherical waves format to restart
READ_TIGHTBOX_NGWFS Logical Read NGWFs to restart
SPECIES Block Atomic species information
SPECIES_COND Block Atomic species information for conduction NGWFs
SPECIES_LDOS_GROUPS Block Local Density of States species group definitions
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
SPREAD_CALCULATE Logical Activate Calculation of NGWF Spreads
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_SW_NGWFS Logical Write NGWFs in spherical waves format for future restart
WRITE_TIGHTBOX_NGWFS Logical Write NGWFs for future restart
WRITE_XYZ Logical Write .xyz file of atom coordinates for visualisation
XC_FUNCTIONAL Text Exchange-correlation functional

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Intermediate keywords

Keyword Type Description
BS_KPOINT_PATH_SPACING Physical K-point spacing along the bandstructure path
BS_METHOD Text Which method to use for the calculation of bandstructures
BS_NUM_EIGENVALUES Integer Number of energy eigenvalues to print in a bandstructure calculation
COND_NUM_EXTRA_STATES Integer Num additional conduction states optimised during pre-optimisation stage
COND_NUM_EXTRA_ITS Integer Number of iterations of pre-optimisation stage during COND task
COULOMB_CUTOFF_LENGTH Physical Length of cylinder or width of slab for cutoff coulomb interaction
COULOMB_CUTOFF_RADIUS Physical Radius of sphere or cylinder for cutoff coulomb interaction
COULOMB_CUTOFF_TYPE Text Type of cutoff coulomb interaction: NONE, SPHERE, CYLINDER, SLAB, WIRE
COULOMB_CUTOFF_WRITE_INT Logical Write real-space cutoff Coulomb interaction scalarfield
DENSE_THRESHOLD Real Threshold for matrix segments to be treated as dense
DOS_SMEAR Physical Half-width for Gaussian smearing of density of states
DX_FORMAT_COARSE Logical Makes the .dx files (see DX_FORMAT) smaller by outputting only odd points along every axis, discarding even points.
DX_FORMAT_DIGITS Integer Selects the number of significant digits in .dx file (see DX_FORMAT) output.
EDFT_COMMUTATOR_THRES Physical Tolerance on the total Hamiltonian-density matrix commutator during EDFT inner loop.
EDFT_ENERGY_THRES Physical Tolerance on total energy change during EDFT inner loop.
EDFT_ENTROPY_THRES Physical Tolerance on total entropy change during EDFT inner loop.
EDFT_FERMI_THRES Physical Tolerance on total Fermi energy change during EDFT inner loop.
EDFT_FREE_ENERGY_THRES Physical Tolerance on total free energy change during EDFT inner loop.
EDFT_RMS_GRADIENT_THRES Real Tolerance on the total occupancies RMS gradient during EDFT inner loop.
ELEC_ENERGY_TOL Physical Tolerance on total energy change during NGWF optimisation.
ELEC_FORCE_TOL Physical Tolerance on maximum force change per electronic optimisation step during NGWF optimisation
ETRANS_CALCULATE Logical Compute electronic transmission coefficients as a function of energy
ETRANS_ECMPLX Physical Imaginary energy accounting for the boundary conditions of the retarded Green's function
ETRANS_EMAX Physical Highest energy for the calculation of the transmission coefficients
ETRANS_EMIN Physical Lowest energy for the calculation of the transmission coefficients
ETRANS_ENUM Integer Number of energy steps for the calculation of the transmission coefficients
ETRANS_SAME_LEADS Logical Use the same self-energy for all the leads
ETRANS_SETUP Block Transport setup description
EXACT_LNV Logical Use Li-Nunes-Vanderbilt algorithm (not Millam-Scuseria variant)
EXTRA_N_SW Integer Generate extra spherical waves for NGWF representation (the extra SW will suffer of aliasing)
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
HUBBARD Block Activate DFT+U, or LDA+U, functionality
IS_AUTO_SOLVATION Logical Automatically runs a calculation in vacuum before any calculation that requires implicit solvation.
IS_BC_COARSENESS Integer Block size for bulk charge coarse-graining in open boundary conditions
IS_BC_SURFACE_COARSENESS Integer Block size for surface charge coarse-graining in open boundary conditions
IS_CHECK_SOLV_ENERGY_GRAD Logical Checks the gradient of solvation energy by finite differences
IS_DENSITY_THRESHOLD Real The parameter rho_0 in the definition of the cavity (atomic units)
IS_DIELECTRIC_FUNCTION Text Determines how the dielectric cavity is generated
IS_DIELECTRIC_MODEL Text Determines how the dielectric cavity is generated
IS_DISCRETIZATION_ORDER Integer The discretization order used for the defect correction in the multigrid calculation
IS_MULTIGRID_DEFECT_ERROR_TOL Real Stop criterion for the defect correction in the multigrid calculation
IS_MULTIGRID_ERROR_TOL Real Stop criterion for the multigrid calculation
IS_SEPARATE_RESTART_FILES Logical Uses a different set of files (.vacuum_dkn and .vacuum_tightbox_ngwfs) to construct the solute cavity for implicit solvation.
IS_SMEARED_ION_REP Logical Turns on the smeared ion representation for electrostatics calculation.
IS_SMEARED_ION_WIDTH Real Characteristic width for the Gaussian smearing of ions (atomic units)
IS_SOLVATION_BETA Real The parameter beta in the definition of the cavity (unitless)
IS_SOLVATION_METHOD Text Chooses between the direct and corrective solvation approach.
IS_SOLVATION_OUTPUT_DETAIL Text Controls details of additional implicit solvent output
KERNEL_DIIS_SCHEME Text Enable self-consistent density kernel mixing or Hamiltonian mixing in the inner loop
KERNEL_DIIS_SIZE Integer Maximum number of density kernels or Hamiltonians to be mixed during inner loop DIIS
KERNEL_DIIS_MAXIT Integer Maximum number of inner loop DIIS iterations
LDOS_SMEAR Physical Half-width for Gaussian smearing of local density of states
LIBXC_X_FUNC_ID Integer Functional ID for exchange functional in a LIBXC calculation.
LIBXC_C_FUNC_ID Integer Functional ID for correlation functional in a LIBXC calculation.
LNV_THRESHOLD_ORIG Real Convergence threshold for density kernel RMS gradient
LNV_CHECK_TRIAL_STEPS Logical Check stability of kernel at each trial step during LNV
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
MINIT_LNV Integer Minimum number of density kernel iterations
NGWF_MAX_GRAD Real Convergence threshold for maximum NGWF gradient at any psinc grid point.
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
OPENBC_HARTREE Logical Switches from periodic to open boundary conditions in the calculation of Hartree energy
OPENBC_ION_ION Logical Switches from periodic to open boundary conditions in the calculation of ion-ion energy
OPENBC_PSPOT Logical Switches from periodic to open boundary conditions in the calculation of local pseudopotential energy
PADDED_LATTICE_CART Block The simulation cell lattice vectors for the padded cell for Cutoff Coulomb
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
READ_HAMILTONIAN Logical Read the Hamiltonian matrix from a file (EDFT only)
READ_MAX_L Integer Set maximum SW angular momentum (l number) when reading from file
SPECIES_ATOMIC_SET Block Atomic species initial NGWFs
THERMOSTAT Block Molecular dynamics thermostat
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
WRITE_CONVERGED_DKNGWFS Logical Only write Density Kernel and NGWFs to disk upon convergence of NGWF optimisation.
WRITE_HAMILTONIAN Logical Write the Hamiltonian matrix on a file (EDFT only)
WRITE_MAX_L Integer Set maximum SW angular momentum (l number) when writing to file

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Expert keywords

Keyword Type Description
CHECK_ATOMS Logical Check atoms are a reasonable distance apart
COMMS_GROUP_SIZE Integer Size of a comms group
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
EDFT_EXTRA_BANDS Integer Number of extra energy bands in EDFT calculations.
EDFT_MAX_STEP Real Maximum step length for the line-search update in the inner loop of EDFT calculations.
EDFT_ROUND_EVALS Integer Round up the energy eigenvalues in EDFT calculations.
EDFT_WRITE_OCC Logical Write occupancies in a file.
EIGENSOLVER_ABSTOL Real Precision to which ScaLapack PDSYGVX eigensolver will resolve the eigenvalues.
EIGENSOLVER_ORFAC Real Precision to which ScaLapack PDSYGVX eigensolver will orthonormalise the eigenvectors.
ELEC_CG_MAX Integer Reset frequency for NGWF conjugate gradients
GEOM_PRINT_INV_HESSIAN Logical Print inverse Hessian
GEOM_REUSE_DK_NGWFS Logical Re-use density kernel and NGWFs during geometry optimisation steps
GEOM_RESET_DK_NGWFS_ITER Logical Number of geom iterations between resets of kernel and NGWFs
IS_BC_THRESHOLD Real Charge density threshold for bulk charge coarse-graining in open boundary conditions
INITIAL_DENS_REALSPACE Real Construct initial density in real space from atomsolver density
IS_MULTIGRID_MAX_ITERS Integer Maximum number of iterations for the multigrid solver
IS_MULTIGRID_NLEVELS Integer Number of multigrid levels for the multigrid solver
IS_SURFACE_THICKNESS Real Surface film thickness (in atomic units of charge density) used for the determination of cavity surface area
K_ZERO Real Parameter for kinetic energy preconditioning in inverse bohr
KERNEL_DIIS_THRESHOLD Real Convergence threshold for inner loop DIIS
KERNEL_DIIS_LINEAR_ITER Integer Number of linear-mixing iterations preceeding Pulay or LiST mixing in the inner loop DIIS method
KERNEL_DIIS_COEFF Real Fraction of the output density kernel or Hamiltonian matrix for linear-mixing inner loop DIIS
KERNEL_DIIS_CONV_CRITERIA Text Convergence criteria for inner loop DIIS
KERNEL_DIIS_LSHIFT Physical Level-shifting energy during inner loop DIIS.
KERNEL_DIIS_LS_ITER Integer Number of inner loop DIIS iterations with level-shifting enabled.
KERNEL_UPDATE Logical Update density kernel during NGWF line search
KINETIC_INT_BATCH_SIZE Integer Batch size for NGWF communications during kinetic energy integrals
LNV_CG_MAX_STEP Real Maximum length of trial step for kernel optimisation line search
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
LOCPOT_SCHEME Text Scheme for symmetrising local potential matrix
MAX_RESID_HOTELLING Real Maximum residual value allowed when inverting overlap matrix
MIX_DENSKERN_NUM Integer Number of independent coefficients used to build new guesses for the density kernel
MIX_DENSKERN_TYPE Integer Type of mixing used to build new guesses for the density kernel
MIX_LOCAL_LENGTH Physical Characteristic length of the mixing scheme
MIX_LOCAL_SMEAR Physical Smearing length of the mixing scheme
MIX_NGWFS_NUM Integer Number of independent coefficients used to build new guesses for the NGWFs
MIX_NGWFS_TYPE Integer Type of mixing used to build new guesses for the NGWFs
NGWF_CG_MAX_STEP Real Maximum length of trial step for NGWF optimisation line search
NGWF_CG_ROTATE Logical Rotate density kernel to the new NGWF representation after CG update. In EDFT calculations, it also rotates the eigenvectors.
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
NONSC_FORCES Logical Calculate residual non self-consistent forces
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
OPENBC_PSPOT_FINETUNE_ALPHA Real Controls the alpha parameter used in the calculation of open-BC local pseudopotential
OPENBC_PSPOT_FINETUNE_F Integer Controls the f parameter used in the calculation of open-BC local pseudopotential
OPENBC_PSPOT_FINETUNE_NPTSX Integer Controls the npts_x parameter used in the calculation of open-BC local pseudopotential
OVLP_FOR_NONLOCAL Logical Use overlap sparsity pattern for nonlocal pseudopotential matrix
PBC_CORRECTION_CUTOFF Real Turn on Martyna-Tuckerman correction to the effects of periodic boundary conditions, with a specified dimensionless cutoff.
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
PROJECTORS_PRECALCULATE Logical Whether to pre-evaluate projectors in FFTboxes
R_PRECOND Real Radial cutoff for real-space preconditioning in bohr
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
ZERO_TOTAL_FORCE Logical Subtract average ionic force from all forces to make the total ionic force zero

BS_KPOINT_PATH

Syntax: BS_KPOINT_PATH [Block]
Syntax:

%BLOCK BS_KPOINT_PATH
k1x k1y k1z
k2x k2y k2z
. . .
kNx kNy kNz
%ENDBLOCK BS_KPOINT_PATH

Description: K-point path for bandstructure calculation.
Example:

%block bs_kpoint_path
0.0 0.0 0.0
0.0 0.0 0.5
%endblock bs_kpoint_path

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BS_KPOINT_PATH_SPACING

Syntax: BS_KPOINT_PATH_SPACING [Physical]
Description: K-point spacing along the bandstructure path.
Default: 0.1889727 "1/bohr"
Example: bs_kpoint_path_spacing 0.004 "1/bohr"

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BS_METHOD

Syntax: BS_METHOD [Integer]
Description: The method to use for the calculation of band structures - either the tight-binding style method or the k.p perturbation theory style method.
Default: TB
Example: bs_method kp

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BS_NUM_EIGENVALUES

Syntax: BS_NUM_EIGENVALUES [Integer]
Description: Number of energy and occupancy eigenvalues to print below and above the Fermi level from a bandstructure calculation. If left as default all eigenvalues (2 x number of occupied states) will be printed.
Default: all eigenvalues
Example: bs_num_eigenvalues 10

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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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CLASSICAL_INFO

Syntax: CLASSICAL_INFO [Block]
Syntax:

%BLOCK CLASSICAL_INFO
S1 R1x R1y R1z Ch1
S2 R2x R2y R2z Ch2
. . . . .
. . . . .
SN RNx RNy RNz ChN
%ENDBLOCK CLASSICAL_INFO

Description: Introduce classical point charges in the system (no NGWFs are associated to them). The classical point charges interact via classical Coulomb interactions with the atoms and the rest of point charges. Specifies the atomic positions as Cartesian coordinates in atomic units (a0). In the above syntax, Si denotes the species of the charge (max 4 characters),Ri its position vector and Chi the charge in atomic units.
Example:

%block classical_info
O 19.7 21.8 22.6 -0.3
H 17.6 22.1 22.6 0.12
H 20.7 23.6 22.6 0.17
%endblock classical_info

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COMMS_GROUP_SIZE

Syntax: COMMS_GROUP_SIZE [Text]
Description: To reduce comms bandwidth in an MPI job, groups of MPI processes are specified which pre-share matrix and cell-grid data between themselves before communications-heavy routines, such as sparse matrix algebra and cell extract/deposit routines. This integer specifies the size of these groups. This might often be most advantageously be set to the size of a physical "node" of a the parallel computer (ie the number of processes which share each chunk of physical memory).
Default: 4
Example: comms_group_size 16

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COND_PLOT_JOINT_ORBITALS

Syntax: COND_PLOT_JOINT_ORBITALS [Logical]
Description: Plot orbitals in the joint valence-conduction NGWF basis following a conduction calculation. Applies to HOMO_PLOT and LUMO_PLOT. See also COND_PLOT_VC_ORBITALS.
Default: True
Example: cond_plot_joint_orbitals F

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COND_PLOT_VC_ORBITALS

Syntax: COND_PLOT_VC_ORBITALS [Logical]
Description: Plot orbitals in the separate valence and conduction NGWF basis sets following a conduction calculation. Applies to HOMO_PLOT and LUMO_PLOT. See also COND_PLOT_VC_ORBITALS.
Default: True
Example: cond_plot_vc_orbitals F

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COND_READ_DENSKERN

Syntax: COND_READ_DENSKERN [Logical]
Description: Read in the conduction density kernel from disk. If the input filename is rootname.dat then the conduction density kernel filename is rootname.dkn_cond.
Default: False
Example: cond_read_denskern T

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COND_READ_TIGHTBOX_NGWFS

Syntax: COND_READ_TIGHTBOX_NGWFS [Logical]
Description: Read in the conduction NGWFs from disk. If the input filename is rootname.dat then the conduction NGWFs filename is rootname.tightbox_ngwfs_cond.
Default: False
Example: cond_read_tightbox_ngwfs T

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COND_KERNEL_CUTOFF

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

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COND_NUM_STATES

Syntax: COND_NUM_STATES [Integer]
Description: The number of conduction states to be optimised (spin up + down). For non-spin-polarised calculations, this should be an even number.
Default: Equal to the number of valence electrons
Example: cond_num_states 20

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COND_INIT_SHIFT

Syntax: COND_INIT_SHIFT [Real]
Description: Initial shifting factor for projected conduction Hamiltonian, added to each eigenvalue.
Default: 0.0
Example: cond_init_shift 1.0

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COND_SHIFT_BUFFER

Syntax: COND_SHIFT_BUFFER [Real]
Description: Additional buffer to add to the highest calculated eigenvalue when updating the shift for the projected conduction Hamiltonian.
Default: 0.1
Example: cond_shift_buffer 0.5

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COND_FIXED_SHIFT

Syntax: COND_FIXED_SHIFT [Logical]
Description: Keep the shift for the projected conduction Hamiltonian constant throughout the calculation.
Default: False
Example: cond_fixed_shift T

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COND_CALC_MAX_EIGEN

Syntax: COND_CALC_MAX_EIGEN [Logical]
Description: Calculate maximum conduction Hamiltonian eigenvalue at the start of each NGWF CG optimisation step, for use in updating the shift for the projected conduction Hamiltonian.
Default: True
Example: cond_calc_max_eigen

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COND_CALC_OPTICAL_SPECTRA

Syntax: COND_CALC_OPTICAL_SPECTRA [Logical]
Description: Calculate the optical matrix elements in the momentum representation, required for extended systems and molecules with large NGWF radii. If false the position representation is instead used.
Default: False
Example: cond_calc_optical_spectra T

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COND_SPEC_CALC_MOM_MAT_ELS

Syntax: COND_SPEC_CALC_MOM_MAT_ELS [Logical]
Description: Calculate the optical matrix elements in the momentum representation, required for extended systems and molecules with large NGWF radii. If false the position representation is instead used.
Default: True
Example: cond_spec_calc_mom_mat_els F

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COND_SPEC_CALC_NONLOC_COMM

Syntax: COND_SPEC_CALC_NONLOC_COMM [Logical]
Description: Calculate the commutator between the nonlocal potential and the position operator, required for accurate calculation of optical absorption spectra when COND_SPEC_CALC_MOM_MAT_ELS = true.
Default: True
Example: cond_spec_calc_nonloc_comm F

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COND_SPEC_CONT_DERIV

Syntax: COND_SPEC_CONT_DERIV [Logical]
Description: Calculate the commutator between the nonlocal potential and the position operator (when COND_SPEC_CALC_NONLOC_COMM : true) using a continuous derivative in k-space. If false a finite difference is instead used in k-space.
Default: True
Example: cond_spec_cont_deriv F

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COND_SPEC_NONLOC_COMM_SHIFT

Syntax: COND_SPEC_NONLOC_COMM_SHIFT [Real]
Description: Finite difference shift used for calculating the commutator between the nonlocal potential and the position operator if calculating using finite differences (i.e. when COND_SPEC_CONT_DERIV : false).
Default: 0.0001
Example: cond_spec_nonloc_comm_shift 0.00001

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COND_NUM_EXTRA_STATES

Syntax: COND_NUM_EXTRA_STATES [Integer]
Description: The number of additional conduction states to be optimised during an initial pre-optimisation stage to help avoid becoming trapped in local minima. This follows the same guidelines as COND_NUM_STATES . See also COND_NUM_EXTRA_ITS.
Default: 0
Example: cond_num_extra_states 10

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COND_NUM_EXTRA_ITS

Syntax: COND_NUM_EXTRA_ITS [Integer]
Description: The number of iterations for which the conduction NGWFs are optimised for COND_NUM_STATES + COND_NUM_EXTRA_STATES during an initial pre-optimisation stage to help avoid becoming trapped in local minima. If COND_NUM_EXTRA_STATES = 0 this is ignored.
Default: 0
Example: cond_num_extra_its 5

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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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COULOMB_CUTOFF_LENGTH

Syntax: COULOMB_CUTOFF_LENGTH [Value] [Unit]
Description: Cutoff Coulomb only. Chooses the length of either (a) the cylinder on which the Coulomb interaction is truncated, in the case of a cylindrical cutoff, or (b) the slab on which the Coulomb interaction is truncated, in the case of a slab cutoff.
Default: 0
Example: coulomb_cutoff_length 100 bohr

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COULOMB_CUTOFF_RADIUS

Syntax: COULOMB_CUTOFF_RADIUS [Value] [Unit]
Description: Cutoff Coulomb only. Chooses the radius of the sphere, cylinder or wire on which the Coulomb interaction is truncated.
Default: 0
Example: coulomb_cutoff_radius 100 bohr

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COULOMB_CUTOFF_TYPE

Syntax: COULOMB_CUTOFF_RADIUS [Value]
Description: Activates Cutoff Coulomb interactions, and chooses which type of cutoff to apply. Allowed values are: NONE, SPHERE, CYLINDER, SLAB, WIRE.
Default: NONE
Example: coulomb_cutoff_type SPHERE

COULOMB_CUTOFF_WRITE_INT

Syntax: COULOMB_CUTOFF_WRITE_INT [Value]
Description: Writes a scalarfield plot of the Cutoff Coulomb interaction for the chosen geometry and cutoff type. Plots .grd or .cube according to the options chosen for GRD_FORMAT and CUBE_FORMAT
Default: F
Example: coulomb_cutoff_write_int 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 Skylariset al.,J. Phys.: Condens. Matter17, 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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DENSE_THRESHOLD

Syntax: DENSE_THRESHOLD [Value]
Description: Sets the filling fraction threshold above which a section of a sparse matrix will be set to dense. Dense matrix algebra is computationally faster above filling fractions of ~10%, but higher communications bandwidth is required so higher values may degrade performance on low-bandwidth parallel architectures. Most users will not need to change this, but in some cases, a higher value than the default can reduce communications bottlenecks during sparse matrix multiplication.
Default: 0.35
Example: dense_threshold 0.80

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DISPERSION

Syntax: DISPERSION [Integer]
Description: Specifies the damping function to be used in the calculation of dispersion corrections:
  • 0 - No dispersion correction
  • 1 - Damping function from Elstner [J. Chem. Phys. 114(12), 5149-5155]
  • 2 - First damping function from Wu and Yang (I) [J. Chem. Phys. 116(2), 515-524]
  • 3 - Second damping function from Wu and Yang (II) [J. Chem. Phys. 116(2), 515\u2013524]

See Proceedings of the Royal Society A 465(2103), 669\u2013683 for more details.

Default: 0
Example: dispersion 1

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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 calculatedif 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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DX_FORMAT

Syntax: DX_FORMAT [Logical]
Description: Output volumetric data (e.g. charge density, potential, NGWFs, canonical orbitals) in Open DX format. This can be visualized using free software such as OpenDX or VMD.
Default: False
Example: dx_format T
New in: 2.4.12

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DX_FORMAT_COARSE

Syntax: DX_FORMAT_COARSE [Logical]
Description: Makes the .dx files (see DX_FORMAT) smaller by outputting only odd points along every axis, discarding even points. This allows for smaller output files, eliminates Gibbs ringing.
Default: False
Example: dx_format_coarse T
New in: 2.4.12

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DX_FORMAT_DIGITS

Syntax: DX_FORMAT_DIGITS [Integer]
Description: Selects the number of significant digits in .dx file (see DX_FORMAT) output. This allows for smaller files if some precision can be sacrificed, or to increase output precision of need arises.
Default: 7 (that is, 1 before and 6 after the decimal point)
Example: dx_format_digits 12
New in: 2.4.12

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EDFT

Syntax: EDFT [Logical]
Description: Enable finite-temperature DFT calculations with the Ensemble-DFT method. Recommended for calculations on metallic systems.
Default: F
Example: edft T
New in: 3.4

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EDFT_MAXIT

Syntax: EDFT_MAXIT [Integer]
Description: Maximum number of inner loop iterations in calculations with the EDFT method.
Default: 10
Example: edft_maxit 5
New in: 3.4

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EDFT_SMEARING_WIDTH

Syntax: EDFT_SMEARING_WIDTH [Value] [Unit]
Description: Occupation smearing width in EDFT calculations, based on the Fermi-Dirac distribution.
Default: 0.1 eV
Example: edft_smearing_width 0.2 eV
Example: edft_smearing_width 800 K (sets the electronic temperature to 800 degree Kelvin)
New in: 3.4

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EDFT_COMMUTATOR_THRES

Syntax: EDFT_COMMUTATOR_THRES [Value] [Unit]
Description: Tolerance threshold for the Hamiltonian-density matrix commutator during the EDFT inner loop.
Default: 1.0e-5 Hartree
Example: edft_commutator_thres 1.0e-6
New in: 3.4

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EDFT_ENERGY_THRES

Syntax: EDFT_ENERGY_THRES [Value] [Unit]
Description: Tolerance threshold for the maximum change of the total energy during two consecutive EDFT inner loop iteratrions.
Default: 1.0e-6 Hartree
Example: edft_energy_thres 1.0e-4 eV
New in: 3.4

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EDFT_ENTROPY_THRES

Syntax: EDFT_ENTROPY_THRES [Value] [Unit]
Description: Tolerance threshold for the maximum change of the total entropy during two consecutive EDFT inner loop iteratrions.
Default: 1.0e-6 Hartree
Example: edft_entropy_thres 1.0e-5 eV
New in: 3.4

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EDFT_FERMI_THRES

Syntax: EDFT_FERMI_THRES [Value] [Unit]
Description: Tolerance threshold for the maximum change of the Fermi energy during two consecutive EDFT inner loop
Default: 1.0e-3 Hartree
Example: edft_fermi_thres 1.0e-4 eV
New in: 3.4

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EDFT_FREE_ENERGY_THRES

Syntax: EDFT_FREE_ENERGY_THRES [Value] [Unit]
Description: Tolerance threshold for the maximum change of the Helmholtz free energy during two consecutive EDFT inner loop iteratrions.
Default: 1.0e-6 Hartree
Example: edft_free_energy_thres 1.0e-4 eV
New in: 3.4

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EDFT_RMS_GRADIENT_THRES

Syntax: EDFT_RMS_GRADIENT_THRES [Value]
Description: Tolerance threshold for the maximum occupancies RMS gradient during the EDFT inner loop.
Default: 1.0e-4
Example: edft_rms_gradient_thres 1.0e-5
New in: 3.4

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EDFT_EXTRA_BANDS

Syntax: EDFT_EXTRA_BANDS [Integer]
Description: Extra energy bands in EDFT calculations. If set to 0 or a negative number, the total number of bands is equal to the total number of NGWFs. Set to a positive integer to add more energy bands.
Default: -1
Example: edft_extra_bands 16
New in: 3.4

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EDFT_MAX_STEP

Syntax: EDFT_MAX_STEP [Value]
Description: Maximum step during the EDFT inner loop line search.
Default: 1.0
Example: edft_max_step 0.8
New in: 3.4

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EDFT_ROUND_EVALS

Syntax: EDFT_ROUND_EVALS [Integer]
Description: Round up the energy eigenvalues to n decimal positions. It helps in calculations where there is a numerical error arising from the grid representation of the NGWFs. If set to a negative number, this directive is ignored.
Default: -1
Example: edft_round_evals 5
New in: 3.4

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EDFT_WRITE_OCC

Syntax: EDFT_WRITE_OCC [Logical]
Description: Write the occupancies and the energy levels on disk. If set to true, this directive will generate a .occ file.
Default: False
Example: edft_write_occ T
New in: 3.4

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EIGENSOLVER_ABSTOL

Syntax: EIGENSOLVER_ABSTOL [Value]
Description: Indicates the precision to which the ScaLapack PDSYGVX eigensolver will resolve the eigenvalues of a matrix. Active only if ONETEP is compiled against ScaLapack. Set to a negative number to use ScaLAPACK default.
Default: 1.0e-9
Example: eigensolver_abstol 1.0e-5
New in: 3.4

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EIGENSOLVER_ORFAC

Syntax: EIGENSOLVER_ORFAC [Value]
Description: Indicates the precision to which the ScaLapack PDSYGVX eigensolver will reorthonormalise the eigenvectors of a matrix. Active only if ONETEP is compiled against ScaLapack. Set to a negative number to tell ScaLAPACK to not to perform any kind of orthonormalisation.
Default: 1.0e-4
Example: eigensolver_abstol 1.0e-3
New in: 3.4

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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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ELEC_ENERGY_TOL

Syntax: ELEC_ENERGY_TOL [Value] [Unit]
Description: Convergence criterion for minimisation of electronic energy: Energy change per NGWF optimisation iteration must be less than this amount PER ATOM before the calculation is regarded as converged. Ignored if negative.
Default: -0.001 eV
Example: elec_energy_tol 0.00001 eV

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ELEC_FORCE_TOL

Syntax: ELEC_FORCE_TOL [Value] [Unit]
Description: Convergence criterion for minimisation of electronic energy: Maximum change in any component of the forces from NGWF optimisation iteration to the next must be less than this amount before the calculation is regarded as converged. Ignored if negative.
Default: -0.001 "ha/bohr"
Example: elec_force_tol 0.01 "eV/ang"

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ETRANS_CALCULATE

Syntax: ETRANS_CALCULATE [Logical]
Description: Computes the electronic transmission coefficients as a function of the energy. See ETRANS_SETUP for the description of the transport setup.
Default: False
Example: etrans_calculate T

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ETRANS_ECMPLX

Syntax: ETRANS_ECMPLX [Value] [Unit]
Description: Small imaginary part added to the energy in order to impose the appropriate boundary condition to the computed retarded Green's function. This parameter should theoretically tends toward zero. However, too small values of etrans_cmplx could lead to instabilities in the calculation of the leads self-energies.
Default: 0.001 "hartree"
Example: etrans_ecmplx 0.00001 "hartree"

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ETRANS_EMAX

Syntax: ETRANS_EMAX [Value] [Unit]
Description: Highest energy for the calculation of the transmission coefficients (defined with respect to the computed Fermi level).
Default: 0.2 "hartree"
Example: etrans_emax 0.2 "hartree"

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ETRANS_EMIN

Syntax: ETRANS_EMIN [Value] [Unit]
Description: Lowest energy for the calculation of the transmission coefficients (defined with respect to the computed Fermi level).
Default: -0.2 "hartree"
Example: etrans_emin -0.2 "hartree"

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ETRANS_ENUM

Syntax: ETRANS_ENUM [Integer]
Description: Number of energy points equally spaced between ETRANS_EMIN and ETRANS_EMAX for the calculation of the electronic transmission coefficients as a function of the energy.
Default: 50
Example: etrans_enum 100

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ETRANS_SAME_LEADS

Syntax: ETRANS_SAME_LEADS [Logical]
Description: Defines whether the source and drain leads are equivalent (i.e. identical sets of ordered atoms directly related by means of a rigid body translation) or not. When this flag is set to true, the code only computes the self-energy associated with the source lead, saving some computational time.
Default: False
Example: etrans_same_leads T

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ETRANS_SETUP

Syntax:

%BLOCK ETRANS_SETUP
source_start source_stop
drain_start drain_stop
%ENDBLOCK ETRANS_SETUP

Description: Defines the transport setup used for the calculation of the transport coefficients. The block should contain two lines referring respectively to the "source" and "drain" leads. Each line should contain two entries corresponding respectively to the first and last atoms to be included in the lead. This block is mandatory when ETRANS_CALCULATE is set to true.
Example:

In this example, the leads are made up from the atoms [61,120] and [361,420]. Note that the code assumes that those leads respectively couple with the central region via the atoms [121,180] and [301,360]. Eventually, the retarded Green's function associated will be computed for the atoms [61,420] (i.e. all other atoms are considered as "buffer atoms").

%block etrans_setup
061 120
361 420
%endblock etrans_setup

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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. B47, 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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EXTRA_N_SW

Syntax: EXTRA_N_SW [Integer]
Description: Generates extra spherical waves for the NGWFs representation. The extra SW will suffer of aliasing as their frequency is higher than the maximum plane waves basis set given by the kinetic cut-off.
Default: 0
Example: extra_n_sw 10
Example: extra_n_sw -5

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FINE_GRID_SCALE

Syntax: FINE_GRID_SCALE [Real]
Description: Specifies the spacing of the fine grid as a multiple of the spacing of the standard grid (which is determined by psinc_spacing or by cutoff_energy).
Default: 2.0 ;
Example: fine_grid_scale 4.0

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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 thea1,a2anda3directions 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: 10-3a0
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: 10-6Ha 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: 0.002 Ha/Bohr
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: 0.0073 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. Pfrommeret 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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GEOM_REUSE_DK_NGWFS

Syntax: GEOM_REUSE_DK_NGWFS [Logical]
Description: Re-use density kernel and NGWFs during geometry optimisation steps
Default: T
Example: geom_reuse_dk_ngwfs F

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GEOM_RESET_DK_NGWFS_ITER

Syntax: GEOM_RESET_DK_NGWFS_ITER [Integer]
Description: Number of geom iterations between resets of kernel and NGWFs
Default: 6
Example: geom_reset_dk_ngwfs_iter 20

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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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HOMO_PLOT

Syntax: HOMO_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_plot 0

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HUBBARD

Syntax: HUBBARD [Block]
Syntax:

%BLOCK HUBBARD
S1 L1 U1 Z1 a1 s1
S2 L2 U2 Z2 a2 s1
. . . . .
. . . . .
SN LN UN ZN aN sN
%ENDBLOCK HUBBARD

Description: Applies the DFT+U, also known as LDA+U, correction for strongly correlated materials. For species S and correlated subspace of angular momentum channel L (with principal quantum number n=L+1) we apply a DFT+U correction with Hubbard parameter U (eV). An effective nuclear charge Z defines the hydrogenic orbitals spanning this subspace unless a negative value is given, e.g., Z=-10, in which case the NGWF initial guess orbitals (numerical atomic orbitals) are used. The a and s parameters (eV) are a rigid potential shift and a spin-splitting, respectively, applied to the subspaces.
Example:

%block hubbard
O 1 0.0 4.5 0.0 0.0
Fe 2 3.0 9.5 0.0 0.0
%endblock hubbard

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INITIAL_DENS_REALSPACE

Syntax: INITIAL_DENS_REALSPACE [Logical]
Description: Specifies whether to construct the initial density passed to Palser-Manolopoulos (or diagonalisation) in real-space, from the sum of the atom-solver densities (if true), or the default of a superposition of gaussians (if false).
Default: F
Example: initial_dens_realspace T
New in: 3.0.0

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IS_AUTO_SOLVATION

Syntax: IS_AUTO_SOLVATION [Logical]
Description: Specifies that a calculation in vacuum should be automatically performed before any calculation that employs implicit solvent.
Default: F
Example: is_auto_solvation T
New in: 3.5.7.3

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IS_BC_COARSENESS

Syntax: IS_BC_COARSENESS [Integer]
Description: Specifies the edge length of the cubic block, in units of fine grid delta, over which charge will be coarse-grained in the calculation of open boundary conditions. This is only relevant in implicit solvent calculations and in calculations with open boundary conditions (such as calculations with smeared ions).
Default: 5
Example: is_bc_coarseness 7 ; Use blocks 7x7x7
New in: 3.0.0

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IS_BC_SURFACE_COARSENESS

Syntax: IS_BC_SURFACE_COARSENESS [Integer]
Description: Specifies the edge length of the square block, in units of fine grid delta, over which the potential will be bilinearly interpolated in the calculation of open boundary conditions. This is only relevant in implicit solvent calculations and in calculations with open boundary conditions (such as calculations with smeared ions). Values larger than 1 will speed up the calculation but can impact accuracy for charged systems -- use with care.
Default: 1
Example: is_bc_surface_coarseness 3 ; Use surface blocks of 3x3
New in: 3.0.0

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IS_BC_THRESHOLD

Syntax: IS_BC_THRESHOLD [Real]
Description: Specifies the charge density threshold used for coarse-graining in the calculation of open boundary conditions. Fine grid points with charge magnitudes below this threshold will be ignored during the coarse-graining procedure. This serves to eliminate the unnecessary integration of noise and ringing. Decreasing this threshold (to, say, 1E-10) might be necessary in rare situations, such as in runs using simulation cells with inadequate padding and fine_grid_scale > 2.0, which may lead to more severe ringing. Increasing this threshold mainly serves to increase performance, however, accuracy will be impacted if this threshold is set too high (higher than, say, 5E-8).

This is only relevant in implicit solvent calculations and in calculations with open boundary conditions (such as calculations with smeared ions).

Default: 1E-9
Example: is_bc_threshold 1E-10 ; Be extra accurate
New in: 3.0.0

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IS_BULK_PERMITTIVITY

Syntax: IS_BULK_PERMITTIVITY [Value]
Description: Sets the relative dielectric permittivity of the solvent.
Default: 80.0 if IS_IMPLICIT_SOLVENT T, 1.0 if IS_IMPLICIT_SOLVENT F
Example: IS_BULK_PERMITTIVITY 14.2 ; ethanediamine as solvent
New in: 3.0.0

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IS_CHECK_SOLV_ENERGY_GRAD

Syntax: IS_CHECK_SOLV_ENERGY_GRAD [Logical]
Description: Checks the gradient of solvation energy with finite differences. This is only relevant in implicit solvent calculations.
Default: F
Example: IS_CHECK_SOLV_ENERGY_GRAD T
New in: 3.0.0

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IS_DENSITY_THRESHOLD

Syntax: IS_DENSITY_THRESHOLD [Value]
Description: Sets the value of the rho_0 parameter (in atomic units) in the definition of the dielectric cavity as described in DA Scherlis, J-L Fattebert, F Gygi, M Cococcioni, and N Marzari, Journal of Chemical Physics 124, 074103 (2006). This is only relevant in implicit solvent calculations.
Default: 0.00078
Example: IS_DENSITY_THRESHOLD 0.00035
New in: 3.0.0

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IS_DIELECTRIC_FUNCTION

Syntax: IS_DIELECTRIC_FUNCTION [FGF | GAUSSIAN]
Description: Chooses the function used to generate the dielectric cavity from the electronic density. FGF uses the one described in DA Scherlis, J-L Fattebert, F Gygi, M Cococcioni, and N Marzari, Journal of Chemical Physics 124, 074103 (2006). GAUSSIAN uses the core density to generate the cavity, this is not currently supported. This is only relevant in implicit solvent calculations.
Default: FGF
Example: IS_DIELECTRIC_FUNCTION FGF
New in: 3.0.0

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IS_DIELECTRIC_MODEL

Syntax: IS_DIELECTRIC_MODEL [FIX_INITIAL | SELF_CONSISTENT | GAUSSIAN_IONS]
Description: Chooses how the dielectric cavity responds to changes in the electronic density. With FIX_INITIAL the cavity remains fixed (and the calculation is still self-consistent). With SELF_CONSISTENT, the cavity self-consistently reacts to changes in the density. With GAUSSIAN_IONS the core density is used to generate the cavity, so it remains fixed as well. GAUSSIAN_IONS is not currently supported. FIX_INITIAL is strongly recommended. SELF_CONSISTENT offers slightly improved accuracy, but requires very fine grids to converge (such as FINE_GRID_SCALE 4.0), which translates into extremely high memory requirements -- thus it is not recommended, unless for very small molecules. This keyword is only relevant in implicit solvent calculations.
Default: FIX_INITIAL
Example: IS_DIELECTRIC_MODEL SELF_CONSISTENT
New in: 3.0.0

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IS_DISCRETIZATION_ORDER

Syntax: IS_DISCRETIZATION_ORDER [Integer]
Description: Sets the discretization order used for finite-differences. The available orders are: 2, 4, 6, 8, 10 and 12. Recommended is 8 or 10. Currently this keyword is only relevant in multigrid calculations (which are those using implicit solvent or open boundary conditions), where it controls the discretization order used for defect-correcting the multigrid solution and for calculating gradients and laplacians.
Default: 8
Example: IS_DISCRETIZATION_ORDER 10
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IS_IMPLICIT_SOLVENT

Syntax: IS_IMPLICIT_SOLVENT [Logical]
Description: Turns the implicit solvent on or off. As the implicit solvent requires the smeared ion representation, it also sets IS_SMEARED_ION_REP to T. When on, open boundary conditions are used for the calculation of ion-ion, Hartree and local pseudopotential terms.
Default: F
Example: IS_IMPLICIT_SOLVENT T
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IS_INCLUDE_CAVITATION

Syntax: IS_INCLUDE_CAVITATION [Logical]
Description: When T, includes the cavitation term in an implicit solvent calculation. Can only be used with IS_IMPLICIT_SOLVENT T.
Default: F
Example: IS_INCLUDE_CAVITATION T
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IS_MULTIGRID_DEFECT_ERROR_TOL

Syntax: IS_MULTIGRID_DEFECT_ERROR_TOL [Value]
Description: Sets the error tolerance for the defect-correction algorithm in a multigrid calculation. This controls the maximum error when solving the defect equation in every defect-correction iteration and is *not* directly related to the magnitude of the error in the final solution. This keyword is only relevant in multigrid calculations (which are those using implicit solvent or open boundary conditions).
Default: 0.01
Example: IS_MULTIGRID_DEFECT_ERROR_TOL 1E-4 ; Try a stricter tolerance in case defect-correction diverges
New in: 3.0.0

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IS_MULTIGRID_ERROR_TOL

Syntax: IS_MULTIGRID_ERROR_TOL [Value]
Description: Sets the error tolerance for the solution obtained through multigrid. If IS_DISCRETIZATION_ORDER is larger than 2, this is the final error obtained after defect correction, otherwise this is the error of the uncorrected multigrid solution. This keyword is only relevant in multigrid calculations (which are those using implicit solvent or open boundary conditions).
Default: 1E-5
Example: IS_MULTIGRID_ERROR_TOL 1E-4 ; Try a relaxed tolerance to speed calculation up
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IS_MULTIGRID_MAX_ITERS

Syntax: IS_MULTIGRID_MAX_ITERS [Integer]
Description: Sets the maximum number of iterations for the multigrid calculation. This controls both the maximum number of defect-correction steps and the maximum number of iterations of the multigrid process in each defect-correction step (and in the first solution with 2nd order, prior to defect correction). This value is best left at its default. This keyword is only relevant in multigrid calculations (which are those using implicit solvent or open boundary conditions).
Default: 100
Example: IS_MULTIGRID_MAX_ITERS 200 ; purposefully waste time
New in: 3.0.0

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IS_MULTIGRID_NLEVELS

Syntax: IS_MULTIGRID_NLEVELS [Integer]
Description: Sets the number of multigrid levels for a multigrid calculation. This keyword is only relevant in multigrid calculations (which are those using implicit solvent or open boundary conditions).
Default: 4
Example: IS_MULTIGRID_NLEVELS 3
New in: 3.0.0

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IS_SEPARATE_RESTART_FILES

Syntax: IS_SEPARATE_RESTART_FILES [Logical]
Description: Causes the solute cavity used in implicit solvation calculations to be constructed from a separate set of restart files (.vacuum_dkn, .vacuum_tightbox_ngwfs) from those that are used to restart the calculation itself (.dkn, .tightbox_ngwfs).
Default: F
Example: IS_SEPARATE_RESTART FILES T
New in: 3.5.3.2

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IS_SMEARED_ION_REP

Syntax: IS_SMEARED_ION_REP [Logical]
Description: Turns the smeared ion representation on or off. All smeared ion calculations are performed in open boundary conditions. Turning on the smeared ion representation is a necessary condition for performing implicit solvent calculations. Calculations in vacuum that will serve as reference calculations for calculations in solvent should also used smeared ions. Smeared ions are not compatible with cutoff Coulomb (COULOMB_CUTOFF_TYPE) or Martyna-Tuckerman (PBC_CORRECTION_CUTOFF), which are other ways of realizing open boundary conditions.
Default: F
Example: IS_SMEARED_ION_REP T
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IS_SMEARED_ION_WIDTH

Syntax: IS_SMEARED_ION_WIDTH [Value]
Description: Sets the smearing width for smeared ions (in atomic units). This is only relevant when IS_SMEARED_ION_REP is @T@. Values larger than default, especially larger than 1.0, are likely to lead to non-physical results in implicit solvent calculations. Values smaller than default, especially smaller than 0.6 will negatively impact the convergence of the multigrid.
Default: 0.8
Example: IS_SMEARED_ION_WIDTH 0.6
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IS_SOLVATION_BETA

Syntax: IS_SOLVATION_BETA [Value]
Description: Sets the value of the beta parameter (unitless) in the definition of the dielectric cavity as described in DA Scherlis, J-L Fattebert, F Gygi, M Cococcioni, and N Marzari, Journal of Chemical Physics 124, 074103 (2006). This is only relevant in implicit solvent calculations.
Default: 1.3
Example: IS_SOLVATION_BETA 1.6
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IS_SOLVATION_METHOD

Syntax: IS_SOLVATION_METHOD [DIRECT | CORRECTIVE]
Description: Chooses either the direct approach or a corrective approach to solving the Poisson equation in solvent. This keyword is reserved for future development, CORRECTIVE is not currently implemented. This is only relevant in implicit solvent calculations.
Default: DIRECT
Example: IS_SOLVATION_METHOD DIRECT
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IS_SOLVATION_OUTPUT_DETAIL

Syntax: IS_SOLVATION_OUTPUT_DETAIL [Text]
Description: With the sensible default of NONE no additional information is produced. With any other value, regardless of what it is, relevant solvation data, such as densities, potentials, dielectric permittivities, gradient terms are produced in 3D grid formats (cube, dx, grd -- depending on CUBE_FORMAT, DX_FORMAT and GRD_FORMAT) in every step. These consume a lot of disk space and should only be used for debugging.
Default: NONE
Example: IS_SOLVATION_OUTPUT_DETAIL SOME
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IS_SOLVENT_SURFACE_TENSION

Syntax: IS_SOLVENT_SURFACE_TENSION [Value] [Unit]
Description: Sets the surface tension of the solvent. This is only relevant in implicit solvent calculations.
Default: 4.7624E-5 Ha/bohr**2 (corresponding to H2O)
Example: IS_SOLVENT_SURFACE_TENSION 1.33859E-5 ha/bohr**2 ; corresponds to H2O with approximate inclusion of dispersion-repulsion
New in: 3.0.0

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IS_SURFACE_THICKNESS

Syntax: IS_SURFACE_THICKNESS [Value]
Description: Sets the electronic iso-surface thickness (in atomic units of charge density) used to calculate the surface area of the dielectric cavity. This is only relevant in implicit solvent calculations.
Default: 0.0002
Example: IS_SURFACE_THICKNESS 0.0003
New in: 3.0.0

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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_DIIS_SCHEME

Syntax: KERNEL_DIIS_SCHEME [Text]
Description: Enable self-consistent density kernel or Hamiltonian mixing during the inner loop. Possible options:
  • NONE - no mixing - use LNV optimisation method instead.
  • DKN_LINEAR - linear mixing of density kernels.
  • HAM_LINEAR - linear mixing of Hamiltonians.
  • DKN_PULAY - Pulay mixing of density kernels.
  • HAM_PULAY - Pulay mixing of Hamiltonians.
  • DKN_LISTI - LiSTi mixing of density kernels.
  • HAM_LISTI - LiSTi mixing of Hamiltonians.
  • DKN_LISTB - LiSTb mixing of density kernels.
  • HAM_LISTB - LiSTb mixing of Hamiltonians.
  • DIAG - no mixing, only Hamiltonian diagonalisation. Not recommended.

References:

P. Pulay, Chem. Phys. Lett. 73(2):393, 1980.

Y. A. Wang, C. Y. Yam, Y. K. Chen, and G. Chen, J. Chem. Phys. 134(24):241103, 2011

Y. K. Chen, and Y. A. Wang, J. Chem. Theory Comput. 7(10):3045, 2011.

Default: NONE
Example: kernel_diis_scheme DKN_PULAY
New in: 3.5.2.9

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KERNEL_DIIS_COEFF

Syntax: KERNEL_DIIS_COEFF [Real]
Description: Fraction of the output density kernel or Hamiltonian matrix in the inner loop DIIS. Its value must be in the range [0,1]. Set to a negative number to enable the ODA method for calculating the optimum mixing parameter. References:

E. Cancès, and C. Le Bris, Int. J. Quantum Chem. 79(2):82, 2000.

E. Cancès, J. Chem. Phys. 114(24):10616, 2001.

Default: 0.1000
Example: kernel_diis_coeff 0.2500
New in: 3.5.2.9

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KERNEL_DIIS_CONV_CRITERIA

Syntax: KERNEL_DIIS_CRITERIA [Text]
Description: Set convergence criteria for inner loop diis. This input flag acts as a logical switch whose terms can only have the values 0 for false and 1 for true. Written as kernel_diis_criteria = wxyz, each component refers to:
 w : residual: sqrt[sum(K_{out} - K_{in})^2]
 x : [HKS,SKH] commutator
 y : delta energy gap (in Hartree)
 z : delta energy: E(n+1)-E(n) (in Hartree)

Two or more elements activated means that the two criteria have to be true at the same time to achieve convergence (i.e. they have to be lower than kernel_diis_threshold).

Default: 1000
Example: kernel_diis_conv_criteria 0110 (activates x and y but not w or z)
New in: 3.5.2.9

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KERNEL_DIIS_LINEAR_ITER

Syntax: KERNEL_DIIS_LINEAR_ITER [Integer]
Description: Set the number of linear mixing iterations before activating Pulay, LiSTi or LiSTb mixing. The aim of these iterations is to generate a history of accurate density kernels to be used with the Pulay, LiSTi or LiSTb methods.
Default: 5
Example: kernel_diis_linear_iter 10
New in: 3.5.2.9

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KERNEL_DIIS_SIZE

Syntax: KERNEL_DIIS_SIZE [Integer]
Description: Maximum number of density kernel or Hamiltonian matrices that will be stored in memory. These kernels are then used with the Pulay, LiSTi or LiSTb schemes to generate the next input matrix. Warning: the more matrices are stored, the better the convergence will be, but also the more memory resources will be needed.
Default: 10
Example: kernel_diis_size 25
New in: 3.5.2.9

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KERNEL_DIIS_MAXIT

Syntax: KERNEL_DIIS_MAXIT [Integer]
Description: Maximum number of inner loop DIIS iterations
Default: 25
Example: kernel_diis_maxit 40
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KERNEL_DIIS_THRESHOLD

Syntax: KERNEL_DIIS_THRESHOLD [Real]
Description: Convergence threshold for the inner loop self-consistent optimisation. It acts for all active values of kernel_diis_conv_criteria.
Default: 1.0e-9
Example: kernel_diis_thres 1.0e-7
New in: 3.0.0

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KERNEL_DIIS_LSHIFT

Syntax: KERNEL_DIIS_LSHIFT [Value] [Units]
Description: Value of the shift in energy of the conduction bands with the level-shifting technique during the inner loop DIIS. Reference:

V. R. Saunders, and I. H. Hillier, Int. J. Quantum Chem. 7(4):699, 1973.

Default: 1.0 Hartree
Example: kernel_diis_lshift: 1 eV
New in: 3.5.2.9

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KERNEL_DIIS_LS_ITER

Syntax: KERNEL_DIIS_LS_ITER [Integer]
Description: Number of iterations of the inner loop DIIS method with level-shifting enabled.
Default: 0
Example: kernel_diis_ls_iter: 5
New in: 3.5.2.9

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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
a1x a1y a1z
a2x a2y a2z
a3x a3y a3z
%ENDBLOCK LATTICE_CART

Description: Specifies the lattice vectors a1, a2 and a3 for the simulation cell as Cartesian coordinates. By default, these will be interpreted as being in atomic units (a0), but they will be interpreted as being Angstroms if "ang" is on the first line of the block.
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

or
%block lattice_cart
ang
50.000000 0.000000 0.000000 ; large cubic cell
0.000000 50.000000 0.000000 ;
0.000000 0.000000 50.000000 ;
%endblock lattice_cart

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LDOS_SMEAR

Syntax: LDOS_SMEAR [Value] [Unit]
Description: Specifies the Gaussian smearing for the local density of states calculated if properties are requested and species_ldos_groups has defined at least one LDOS group. If the smearing width is negative, the local density of states is not calculated.
Default: 0.1 eV
Example: ldos_smear 7 mRy

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LIBXC_X_FUNC_ID

Syntax: LIBXC_X_FUNC_ID [Integer]
Description: Functional ID for the exchange functional (used in calculations employing the LIBXC library). The value of FUNCTIONAL must be set to LIBXC for this value to be accessed
Default: 0
Example: libxc_x_func_id 13

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LIBXC_C_FUNC_ID

Syntax: LIBXC_C_FUNC_ID [Integer]
Description: Functional ID for the correlation functional (used in calculations employing the LIBXC library). The value of FUNCTIONAL must be set to LIBXC for this value to be accessed
Default: 0
Example: libxc_c_func_id 13

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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-Ribiere.
Default: LNV_FLETCHER
Example: lnv_cg_type LNV_POLAK

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LNV_CG_MAX_STEP

Syntax: LNV_CG_MAX_STEP [Value]
Description: Maximum length of trial step for kernel optimisation line search
Default: 2.0
Example: lnv_cg_max_step 10.0

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LNV_CHECK_TRIAL_STEPS

Syntax: LNV_CHECK_TRIAL_STEPS [Logical]
Description: Activate checks on the stability of kernel at each trial step during LNV line search. Checks occupancy bounds and RMS occupancy error
Default: F
Example: lnv_check_trial_steps T

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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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LOCPOT_SCHEME

Syntax: LOCPOT_SCHEME [Text]
Description: Scheme for evaluating local potential matrix elements. Possible values: FULL = Calculate matrix and symmetrize explicitly; LOWER = Calculate lower triangle elements only and infer upper triangle; ALTERNATE = Calculate alternating elements from both triangles and expand (fastest).
Default: FULL
Example: locpot_scheme ALTERNATE

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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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LUMO_PLOT

Syntax: LUMO_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_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(N^3) 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 traditionalO(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 [ Hayneset 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_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_RESET_DKN_NGWFS

Syntax: MD_RESET_DKN_NGWFS [Integer]
Description: By default, in a molecular dynamics calculation, the initial guess for the electronic degrees of freedom is provided by the optimized NGWFs and density kernel from the previous time step. MD_RESET_DKN_NGWFS specifies the number of MD steps to be performed before the generation of new initial guesses for the NGWFs and density kernel. See MIX_DKN_TYPE and MIX_NGWFS_TYPE for more advanced mixing options.
Default: 100
Example: md_reset_dkn_ngwfs 1000

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MD_RESTART

Syntax: MD_RESTART [Logical]
Description: Restart the molecular dynamics calculation from previously generated backup files (i.e. *.md.restart and *.thermo.restart files).
Default: False
Example: md_restart T

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MIX_DENSKERN_NUM

Syntax: MIX_DENSKERN_NUM [Integer]
Description: Number of density kernels required by the density kernel mixing scheme in order to generate the new initial guesses for the density kernel SCF process. See MIX_DENSKERN_TYPE for a description of the available mixing schemes.
Default: 1
Example: mix_denskern_num 2

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MIX_DENSKERN_TYPE

Syntax: MIX_DENSKERN_TYPE [Integer]
Description: Specifies the mixing scheme used to generate new initial guesses for the density kernel from the density kernels optimized at previous MD steps.
  • 0 : no mixing, rely on COREHAM_DENSKERN_GUESS to initialize the density kernel at each MD step;
  • 1 : use the density kernel optimized at the previous step as initial guess for the current SCF process;
  • 2 : linear mixing of the MIX_DENSKERN_NUM former density kernels (see PRB 45, 1538 (1992) for further description of the algorithm);
  • 3 : apply Christoffel corrections to the density kernel optimized at the previous step in order to account for the update of the NGWFs mixing;
  • 4 : project the density kernel optimized at the previous step onto the current set of NGWFs;
  • 5 : apply correction to the density kernel optimized at the previous step in order to preserve the KS product;
  • 6 : time reversible propagation of an auxiliary density kernel (algorithm based on J. Chem. Phys. 130, 214109);
  • 7 : (under development) dissipative propagation of an auxiliary density kernel (algorithm based on J. Chem. Phys. 130, 214109)).
Default: 1
Example: mix_denskern_type 2

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MIX_LOCAL_LENGTH

Syntax: MIX_LOCAL_LENGTH [Value] [Unit]
Description: Specifies the localization length required by MIX_NGWFS_TYPE=3.
Default: 10.0 bohr ;
Example: mix_local_length 15.0 bohr

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MIX_LOCAL_SMEAR

Syntax: MIX_LOCAL_SMEAR [Value] [Unit]
Description: Allows to smear out the localization sphere used when MIX_NGWFS_TYPE=3.
Default: 0.0 bohr ;
Example: mix_local_length 3.0 bohr

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MIX_NGWFS_NUM

Syntax: MIX_NGWFS_NUM [Integer]
Description: Number of NGWFs sets required by the NGWFs mixing scheme in order to generate the new initial guesses for the NGWFs optimization process. See MIX_NGWFS_TYPE for a description of the available mixing schemes.
Default: 1
Example: mix_ngwfs_num 2

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MIX_NGWFS_TYPE

Syntax: MIX_NGWFS_TYPE [Integer]
Description: Specifies the mixing scheme used to generate new initial guesses for the NGWFs from the NGWFs optimized at previous MD steps.
  • 0 : no mixing, rely on SPECIES_ATOMIC_SET to initialize the NGWFs at each MD step;
  • 1 : use the NGWFs optimized at the previous step as initial guess for the current SCF process;
  • 2 : linear mixing of the MIX_NGWFS_NUM former sets of NGWFs (see PRB 45, 1538 (1992) for further description of the algorithm);
  • 3 : same algorithm as in 2, but using a different set of coefficients for each atom as a function of its local environment (relies on MIX_LOCAL_LENGTH and MIX_LOCAL_SMEAR in order to define the localization radius);
  • 4 : polynomial extrapolation of the MIX_NGWFS_NUM former sets of NGWFs in real space;
  • 6 : time reversible propagation of a set of auxiliary NGWFs (algorithm based on J. Chem. Phys. 130, 214109);
  • 7 : (under development) dissipative propagation of a set of auxiliary NGWFs (algorithm based on J. Chem. Phys. 130, 214109)).
Default: 1
Example: mix_ngwfs_type 2

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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-Ribiere.
Default: NGWF_FLETCHER
Example: ngwf_cg_type NGWF_POLAK

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NGWF_CG_ROTATE

Syntax: NGWF_CG_ROTATE [Logical]
Description: Rotate the density kernel to the new NGWF representation after CG update. In EDFT calculations, it also rotates the eigenvectors.
Default: False
Example: ngwf_cg_rotate T

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NGWF_CG_MAX_STEP

Syntax: NGWF_CG_MAX_STEP [Value]
Description: Maximum length of trial step for NGWF optimisation line search
Default: 2.0
Example: ngwf_cg_max_step 10.0

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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_MAX_GRAD

Syntax: NGWF_MAX_GRAD [Real]
Description: Specifies the convergence threshold for the maximum value of the NGWF gradient at any psinc grid point. Ignored if negative.
Default: -2 times 10-5
Example: ngwf_max_grad 1.0e-4

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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 times 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 Fosteret al.,J. Am. Chem. Soc.102, 7211 (1980) for more details.
Default: False
Example: nnho T

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NONSC_FORCES

Syntax: NONSC_FORCES [Logical]
Description: Calculates the residual non self-consistent forces due to the NGWF gradient.
Default: false
Example: nonsc_forces true
New in: 3.0.0

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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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OPENBC_HARTREE

Syntax: OPENBC_HARTREE [Logical]
Description: Forces open boundary conditions in the calculation of the Hartree energy. These are automatically used whenever smeared ions (IS_SMEARED_ION_REP) are in use. This keyword can be used to force them in other (extremely rare) situations. It cannot be used to force them off.
Default: F
Example: OPENBC_HARTREE T
New in: 3.0.0

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OPENBC_ION_ION

Syntax: OPENBC_ION ION [Logical]
Description: Forces open boundary conditions in the calculation of the ion-ion energy. These are automatically used whenever Martyna-Tuckerman (PBC_CORRECTION_CUTOFF), cutoff Coulomb (COULOMB_CUTOFF_TYPE) or smeared ions (IS_SMEARED_ION_REP) are in use. This keyword can be used to force them in other (extremely rare) situations. It cannot be used to force them off.
Default: F
Example: OPENBC_ION_ION T
New in: 3.0.0

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OPENBC_PSPOT

Syntax: OPENBC_PSPOT [Logical]
Description: Forces open boundary conditions in the calculation of the local pseudopotential energy. These are automatically used whenever smeared ions (IS_SMEARED_ION_REP) are in use. This keyword can be used to force them in other (extremely rare) situations. It cannot be used to force them off.
Default: F
Example: OPENBC_PSPOT T
New in: 3.0.0

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OPENBC_PSPOT_FINETUNE_ALPHA

Syntax: OPENBC_PSPOT_FINETUNE_ALPHA [Value]
Description: Sets the value of a numerical parameter (alpha) used in the calculation of the local pseudopotential in open boundary conditions. This parameter controls the transition between the short-range and long-range parts of the pseudopotential. Its impact on the total energy is negligible, provided it stays within reasonable bounds. Units of 1/bohr are implicitly assumed. This keyword is only relevant for calculations with open boundary conditions.
Default: 0.3
Example: OPENBC_PSPOT_FINETUNE_ALPHA 0.5
New in: 3.0.0

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OPENBC_PSPOT_FINETUNE_F

Syntax: OPENBC_PSPOT_FINETUNE_F [INTEGER]
Description: Sets the value of a unitless numerical parameter (grid fineness factor, f) used in the calculation of the local pseudopotential in open boundary conditions. This parameter controls the fineness of the reciprocal space radial grid used in the calculation. Its impact on the total energy is negligible, provided it stays within reasonable bounds. The default value of -1 causes f to be determined automatically -- this will generate a 'safe' value, making the grid as fine as necessary to have at least 50 sample g-points in any period of sin(gx) for the largest x in use in the calculation (the diagonal of the simulation cell). Thus, the automatically generated value depends on the cell size. Increasing this value makes little sense. Decreasing this value allows calculations to start faster, but decreases accuracy. This keyword is only relevant for calculations with open boundary conditions.
Default: -1
Example: OPENBC_PSPOT_FINETUNE_F 6
New in: 3.0.0

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OPENBC_PSPOT_FINETUNE_NPTSX

Syntax: OPENBC_PSPOT_FINETUNE_NPTS_X [INTEGER]
Description: Sets the value of a unitless numerical parameter npts_x used in the calculation of the local pseudopotential in open boundary conditions. This parameter controls the number of points in the radial real-space grid on which the local pseudopotential is evaluated before interpolation to the 3D grid takes place. Increasing this value will offer marginal increase in accuracy at the expense of calculation wall time. This keyword is only relevant for calculations with open boundary conditions.
Default: 100000
Example: OPENBC_PSPOT_FINETUNE_NPTS_X 500000
New in: 3.0.0

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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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PADDED_LATTICE_CART

Syntax:

%BLOCK PADDED_LATTICE_CART
a1x a1y a1z
a2x a2y a2z
a3x a3y a3z
%ENDBLOCK PADDED_LATTICE_CART

Description: Cutoff Coulomb only. Specifies the padded lattice vectors a1, a2 and a3 for the 'padded' simulation cell as Cartesian coordinates. By default, these will be interpreted as being in atomic units (a0), but they will be interpreted as being Angstroms if "ang" is on the first line of the block.
Example:

%block padded_lattice_cart
100.00000 0.00000 0.00000 ; cubic unit cell
0.00000 100.00000 0.00000 ; side length 100 bohr
0.00000 0.000000 100.00000 ;
%endblock padded_lattice_cart

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PAW

Syntax: PAW [Logical]
Description: Activates the Projector Augmented Wave Formalism: PAW potentials must then be supplied in the species_pot block.
Default: False
Example: PAW : T

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PBC_CORRECTION_CUTOFF

Syntax: PBC_CORRECTION_CUTOFF [Real]
Description: Turns on the Martyna-Tuckerman correction to the effects of periodic boundary conditions (PBCs), specifies the dimensionless cutoff parameter. A value of 7.0 is recommended by the authors in Martyna GJ and Tuckerman ME, J. Chem. Phys. 110, 2810 (1999), DOI:10.1063/1.477923.
Default: 0.0 ; turned off
Example: pbc_correction_cutoff 7.0
New in: 2.4.9

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PEN_PARAM

Syntax: PEN_PARAM [Real]
Description: Specifies the energy parameter in hartrees for the penalty-functional algorithm [ Hayneset 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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POLARISATION_CALCULATE

Syntax: POLARISATION_CALCULATE [Logical]
Description: Activates the calculation of polarisation
Default: False
Example: polarisation_calculate T

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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 Angstroms
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 R1x R1y R1z
S2 R2x R2y R2z
. . . .
. . . .
SN RNx RNy RNz
%ENDBLOCK POSITIONS_ABS

Description: Specifies the atomic positions as Cartesian coordinates). In the above syntax, Si denotes the species of atomi(max 4 characters) and Ri its position vector. Note that all atoms are currently required to be positioned within the simulation cell. By default, these will be interpreted as being in atomic units (a0), but they will be interpreted as being Angstroms if "ang" is on the first line of the block.
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 Mostofiet 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 Mostofiet 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. B40, 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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PROJECTORS_PRECALCULATE

Syntax: PROJECTORS_PRECALCULATE [Text]
Description: Controls whether the projectors are all evaluated in FFTboxes simultaneously, whenever the projector-NGWF overlap or projector gradient is required. If true, all projectors are evaluated at once (requiring many FFTboxes and significant memory usage if many projectors are present). If false, only one projector is evaluated at a time (which is slower, as new projectors must be re-evaluated many times over, but uses minimal memory).
Default: True
Example: projectors_precalculate F

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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 a3directions respectively. These spacings must all be factors of the simulation cell lengths in the relevant directions. By default, these will be interpreted as being in atomic units (a0), but any recognised unit symbol can be used after the third value to override to a specific choice of units.
Default: 0.0 0.0 0.0 ; select automatically
Example: psinc_spacing 0.4 0.5 0.5

or

 psinc_spacing 0.25 0.25 0.25 ang 

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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_HAMILTONIAN

Syntax: READ_HAMILTONIAN [Logical]
Description: Read the Hamiltonian matrix from a .ham file. Currently, only used for restarting EDFT calculations.
Default: F
Example: read_hamiltonian F

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READ_MAX_L

Syntax: READ_MAX_L [Integer]
Description: Specifies the maximum angular momentum of the spherical waves (l number) when reading from file.
Default: 3
Example: read_max_l 5

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READ_SW_NGWFS

Syntax: READ_SW_NGWFS [Logical]
Description: Read in the NGWFs from disk in spherical waves format and generates a linear combination of SW to restart the NGWFs. If the input filename is rootname.dat then the NGWFs filename is rootname.sw_ngwfs .
Default: False
Example: read_sw_ngwfs 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
. . . . .
. . . . .
SN XN ZN nN RN
%ENDBLOCK SPECIES

Description: Defines the atomic species. In the above syntax, Si denotes the species of atom i(max 4 characters), corresponding to the element with symbol Xi and atomic number ZN , and with which are associated ni NGWFs of radius RN. More than one atomic species may refer to the same element, e.g. so that different ionic constraints may be applied to them. By default, the radii will be interpreted as being in atomic units (a0), but they will be interpreted as being Angstroms if "ang" is on the first line of the block.
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 | SOLVE
S2 <Fireball filename 2> | AUTO | SOLVE
. .. .
%ENDBLOCK SPECIES_ATOMIC_SET

Description: Specifies the set of initial atomic or pseudoatomic orbitals which will be used to initialise the NGWFs. One can either specify "fireball" (truncated pseudoatomic orbital) files,or use AUTO to generate STO-3G and 6-31G* basis functions, or one can use the built-in pseudoatomic solver, using "SOLVE". With "SOLVE", a configuration for the neutral pseudoatom is guessed on the basis of the ion charge and the atomic number, but this can be overridden. See the help file "pseudoatomic_solver.pdf" in the documentation folder (/doc in the distribution) for more information on how to use the pseudoatomic solver
In the above syntax, Si denotes atomic species i(max 4 characters).

automatically as required.

Default: SOLVE for all species when this block is absent
Example:

%block species_atomic_set
C1 C_01.fbl
H SOLVE
%endblock species_atomic_set

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SPECIES_COND

Syntax:

%BLOCK SPECIES_COND
S1 X1 Z1 n1 R1
S2 X2 Z2 n2 R2
. . . . .
. . . . .
SN XN ZN nN RN
%ENDBLOCK SPECIES

Description: Defines the atomic species used for conduction optimisation. The atomic species details must match those given in the SPECIES block, and the same guidelines apply. By default, the radii will be interpreted as being in atomic units (a0), but they will be interpreted as being Angstroms if "ang" is on the first line of the block.
Example:

%block species
C1 C 6 9 12.0 ; species C1 is carbon with 9 NGWFs of radius 12.0 a0
C2 C 6 9 12.0 ; species C2 is also carbon but has 12.0 a0 NGWF radii
H H 1 4 10.0 ; species H is hydrogen with 4 NGWFs of radius 10.0 a0
%endblock species

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SPECIES_CONSTRAINTS

Syntax:

%BLOCK SPECIES_CONSTRAINTS
S1 NONE | FIXED | LINE | PLANE [C1x C1y C1z]
. . . . .
%ENDBLOCK SPECIES_CONSTRAINTS

Description: Defines the constraints for the atomic species for use during geometry optimization. In the above syntax, Si denotes atomic speciesi(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 thex-axis
H PLANE 0.0 0.0 1.0 ; atoms of species H can only move in thexy-plane
%endblock species_constraints

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SPECIES_LDOS_GROUPS

Syntax:

%BLOCK SPECIES_LDOS_GROUPS
S1 S2 S3
. . .
%ENDBLOCK SPECIES_LDOS_GROUPS

Description: Defines the groups of species identifiers for which the groups of an LDOS plot are defined. Each line defines a group with any number of entries allowed on the line. Species identifier labels must correspond to those defined in %block species.
Example:

%block species_ldos_groups
C1 H1 ; atoms of species C1 and H1 are in first group
C2 H2 ; atoms of species C1 and H1 are in second group
%endblock species_ldos_groups

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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, Si 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 a norm-conserving pseudopotential calculation, or the PAW potentials in a PAW Calculation. In the above syntax, Si denotes atomic species i (max 4 characters). Pseudopotential files can be in the CASTEP .recpot format or .usp format and must define norm-conserving pseudopotentials. PAW Potentials can be in the ABINIT .paw format.
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 1/2;h/(2pi). 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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SPREAD_CALCULATE

Syntax: SPREAD_CALCULATE [Text]
Description: Activates the Calculation of NGWF spreads
Default: F
Example: spread_calculate 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
COND - Conduction NGWF optimisation calculation
PROPERTIES - properties using results from a previous calculation of the ground state.
PROPERTIES_COND - properties using results from a previous calculation of the conduction NGWFs.
GEOMETRYOPTIMIZATION - geometry optimization using Cartesian or delocalized internal coordinates.
MOLECULARDYNAMICS - molecular dynamics simulation.
TRANSITIONSTATESEARCH - transition state search
PHONON - a phonon frequencies and thermodynamics calculation.
HUBBARDSCF - a projector-self-consistent DFT+U calculation.
Default: SINGLEPOINT
Example: task GEOMETRYOPTIMIZATION

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THERMOSTAT

Syntax:

%BLOCK THERMOSTAT
time_start time_stop thermo_type thermo_temp
option1 = value1 (optional)
option2 = value2 (optional)
%ENDBLOCK THERMOSTAT

Description: Defines the molecular dynamics thermostat. For each thermostat, the first line should contain the following mandatory parameters,
  • time_start (integer): the time step at which the thermostat is initialized;
  • time_stop (integer): the time step at which the thermostat is closed;
  • thermo_type (text): the kind of thermostat to be used, currently NONE, ANDERSEN, LANGEVIN, or NOSEHOOVER;
  • thermo_temp (physical): the thermostat temperature in physical units.

Each thermostat may also be tuned using the options,

  • tgrad (physical): incremental temperature, in physical units, to be added at each time step;
  • group (integer): specifies the group of atoms subjected to the thermostat (this option requires groups of atoms to be defined in POSITION_ABS);
  • freq (real): characteristic thermostat's frequency,
    • if ANDERSEN : defines the collision probability via P_collision = 1-exp(-freq),
    • if NOSEHOOVER : specifies the thermostat coupling frequency in units of 1/MD_DELTA_T);
  • damp (real): Langevin damping parameter;
  • mix (real): mixing coefficient for a "softer" ANDERSEN thermostat (i.e. partial incorporation of the old momentum into the new momentum drawn from the Boltzmann distribution);
  • nchain (integer): number of thermostats in the Nose-Hoover chain;
  • nstep (integer): number of steps used to integrate the Nose-Hoover chain dynamics at each MD step;
  • update (logical): if tgrad .ne. zero, then force new initialization of the Nose-Hoover thermostats masses at every MD steps.
Example:

In this example, the system is quenched from 3000 K using an ANDERSEN thermostat and then equilibrated by means of a Nose-Hoover chain. Here the value of the asymmetric stretching mode in water (0.053213/fs) has been used as the coupling frequency.

%block thermostat 
0001 1350  ANDERSEN  3000 K 
   tgrad = -2 K 
1351 5000 NOSEHOOVER 300 K 
   nchain = 4
   nstep = 8 
   freq = 0.053213 
%endblock thermostat

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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 reported1 - timings for routines averaged across all processors2 - 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: 10-2a0
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/Bohr
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_CONVERGED_DKNGWFS

Syntax: WRITE_CONVERGED_DKNGWFS [Logical]
Description: Specifies that the density kernel and NGWF output files should only be written at the end of a converged calculation, rather than after every iteration.
Default: F
Example: write_converged_dkngwfs 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 plottingif 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_HAMILTONIAN

Syntax: WRITE_HAMILTONIAN [Logical]
Description: Write the Hamiltonian matrix on a .ham file. Currently, only used in EDFT calculations. Set to true if a calculation is intended to be restarted at some point in the future.
Default: False
Example: write_hamiltonian T

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WRITE_MAX_L

Syntax: WRITE_MAX_L [Integer]
Description: Specifies the maximum angular momentum of the spherical waves (l number) when writing to file.
Default: 3
Example: write_max_l 2

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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_SW_NGWFS

Syntax: WRITE_SW_NGWFS [Logical]
Description: Write the NGWFs to disk in spherical waves decomposition. If the input filename is rootname.dat then the NGWFs filename is rootname.sw_ngwfs .
Default: False
Example: write_sw_ngwfs 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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WRITE_XYZ

Syntax: WRITE_XYZ [Logical]
Description: Write the atom coordinates to disk as an .xyz file
Default: F
Example: write_xyz T

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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)]
  • PW92 - Perdew and Wang 1992 LDA [Phys. Rev. B 45, 13244 (1992)]
  • 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)]
  • PBESOL - revised PBE for solids by Perdew et al. [Phys. Rev. Lett. 100, 136406 (2008)]
  • BLYP -Becke 88 + LYP (Lee, Yang, Parr) GGA [Phys. Rev. A 38, 3098 (1988); Phys. Rev. B 37, 785 (1988)]
  • XLYP - Xu and Goddard GGA [PNAS 101, 2673 (2004)]
Default: LDA
Example: xc_functional PBE

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ZERO_TOTAL_FORCE

Syntax: ZERO_TOTAL_FORCE [Logical]
Description: Forces the total ionic force to be zero by subtracting the average ionic force from all ionic forces.
Default: True
Example: zero_total_force F
New in: 3.5.2.16

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Page last modified on March 04, 2014, at 07:12 PM